Immunity; clever RNA (Introduction)
by David Turell 
, Wednesday, June 27, 2012, 14:56 (4320 days ago)
Research in immune defense:-http://phys.org/news/2012-06-role-rnai.html
Immunity in plants
by David Turell , Saturday, February 20, 2016, 01:48 (2987 days ago) @ David Turell
Plants can detect pathogens in their cells and self-destruct the cells to stop the invasion:-https://www.sciencedaily.com/releases/2016/02/160219111212.htm-"A few of such Nucleotide-binding Leucine-Rich Repeat receptors (NLRs) with additional integrated domains that act as 'baits' for the pathogen were previously identified in rice and thale cress, and experimentally shown to be involved in disease resistance. Dr Krasileva and her TSL colleagues searched for these genes across plant species, including the key UK crops: wheat, potatoes and rapeseed.-"NLRs are found within the cells, rather than at the cell membrane or in cell walls. When activated by an invasive pathogen or foreign organism, NLRs activate cellular self-destruction -- they are sensors of attack. Once a pathogen has infected a plant cell and bound these targets, the cell is likely to self-destruct, blocking pathogen growth before it can reach other cells.-Comment: Obviously plants don't have a blood system with cells that can attack pathogens. Local cell death is a good alternative to stop the spread of pathogens.
Immunity; asymmetric cell division
by David Turell , Monday, April 11, 2016, 19:02 (2935 days ago) @ David Turell
In immunity T cells play a very important role. There are two types of T cells: those that attack immediately and others that memorize attacks for future defense:-http://medicalxpress.com/news/2016-04-reveal-immune-cells.html-"Asymmetric cell division generates two types of cells with distinct properties. This type of cell division is essential for producing various cell types and plays an important role in development. Rather than producing two identical daughter cells, the cells undergoing asymmetric division produce daughter cells that are fated for vastly different roles. In the case of activated T cells, researchers knew that one daughter cell became the rapidly dividing effector T cells that launch the immediate attack on infectious agents and other threats. The other daughter cell became the slowly dividing memory T cells that function like sentries to provide long-term protection against recurring threats. Until now, the mechanism underlying the process was unknown.-***-"'Our study shows that the way in which the regulatory protein c-Myc distributes during asymmetric cell division directly influences the fate and roles of activated T cells," said corresponding author Douglas Green, Ph.D., St. Jude Department of Immunology chair. "We also show how this asymmetry is established and sustained."-"The researchers worked with cells growing in the laboratory and in mice. Scientists showed that during asymmetric cell division of activated T cells, high levels of c-Myc accumulated in one daughter cell. There, c-Myc functioned like a shot of caffeine to launch and sustain the rapid proliferation of effector T cells, including those in mice infected with the influenza virus. In contrast, the daughter cells with low levels of c-Myc functioned like memory T cells, proliferating to mount an immune response a month later when mice were again exposed to the virus.-"Researchers also identified the metabolic and signaling pathways that serve as a positive feedback loop to sustain the high levels of c-Myc that effector T-cells require to maintain their identities and function. The scientists showed that disrupting certain components of the system disturbed c-Myc production, which altered the fate of T cells and caused effector T cells to operate like memory T cells.-***-"c-Myc is an important transcription factor that regulates expression of a variety of genes and plays a pivotal role in cell growth, differentiation and death via apoptosis (programmed cell death). Excessive or inappropriate production of c-Myc is a hallmark of a wide variety of cancers. Previous research from Green and his colleagues showed that c-Myc also drives metabolic changes following T cell activation. The metabolic reprogramming fuels proliferation of effector T cells. "Activated T cells divide every four to six hours. There is no other cell in adults that can divide that fast, not even cancer cells," Green explained."-Comment: If one looks at purposeful development, one wonders how communities of cells knew to pick out this particular regulatory protein and all of the regulatory feed-back loop proteins that control the level of c-Myc. As Prof. Tour points out, the complexity of evolutionary advancement is mind-boggling, but perhaps not for a certain mind..
Immunity; T cell controls
by David Turell , Tuesday, April 12, 2016, 19:24 (2934 days ago) @ David Turell
Lymphocyte cells (T cells) are very important in the immune processes as they are attack cells and there are molecular controls over their activity:-https://www.sciencedaily.com/releases/2016/04/160412090718.htm-"The protein MALT1 is an important switch in immune cells and affects their activity. Researchers at Helmholtz Zentrum München report in 'Nature Communications' that this activation is not always equally strong. Through alternative splicing, two variants of the protein may arise which have a stronger or weaker effect on the immune system. Understanding this process is important for the pharmacological use of MALT1.-"The protein MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1) controls the activation of lymphocytes and thus the immune response following bacterial or viral infections. For this purpose, the protease cleaves other proteins in the cell and is considered a potential target for the treatment of excessive immune responses as observed in autoimmune diseases (e.g. multiple sclerosis) or distinct malignant lymphomas.-***-"To our surprise, we showed that MALT1 is regulated by posttranscriptional splicing," said first author Isabel Meininger, a doctoral student at Helmholtz Zentrum München. "Depending on which MALT1 variant is expressed, the immune system activated is more or less," she added.-"Specifically, the scientists observed that MALT1A resulted in a stronger stimulation of T cells than MALT1B. According to the study, a molecule called hnRNP U (heterogeneous nuclear ribonucleoprotein U) regulates which of the two isoforms is preferably expressed. If it is present in only small amounts, higher levels of MALT1A are expressed, resulting in stronger activation of the T cells. However, if the quantity of hnRNP U is increased, higher levels of MALT1B are expressed and the response of the T cells is weaker."-***-" Alternative splicing refers to a process in which a copy of a gene, the pre-mRNA, is spliced differently. Thus, several alternative RNA sequences can be generated that as a consequence lead to different proteins. In the case of MALT1 the variants A and B differ only through the presence of a short sequence that encodes eleven amino acids. If this region is missing, as in the case of MALT1B, this leads to an impaired ability to stimulate T cells."-Comment: Just to show the complexity of how the immune system is modulated in the degree of its responsiveness. Note the role of the genome in this modulation.
Immunity; controls over socializing?
by David Turell , Wednesday, July 13, 2016, 20:05 (2842 days ago) @ David Turell
Immunity chemical controls may encourage social cooperation:-http://medicalxpress.com/news/2016-07-role-immune-social-interaction.html-"In a startling discovery that raises fundamental questions about human behavior, researchers at the University of Virginia School of Medicine have determined that the immune system directly affects - and even controls - creatures' social behavior, such as their desire to interact with others. -***-" The relationship between people and pathogens, the researchers suggest, could have directly affected the development of our social behavior, allowing us to engage in the social interactions necessary for the survival of the species while developing ways for our immune systems to protect us from the diseases that accompany those interactions. Social behavior is, of course, in the interest of pathogens, as it allows them to spread.-"The UVA researchers have shown that a specific immune molecule, interferon gamma, seems to be critical for social behavior and that a variety of creatures, such as flies, zebrafish, mice and rats, activate interferon gamma responses when they are social. Normally, this molecule is produced by the immune system in response to bacteria, viruses or parasites. Blocking the molecule in mice using genetic modification made regions of the brain hyperactive, causing the mice to become less social. Restoring the molecule restored the brain connectivity and behavior to normal. In a paper outlining their findings, the researchers note the immune molecule plays a "profound role in maintaining proper social function."-"It's extremely critical for an organism to be social for the survival of the species. It's important for foraging, sexual reproduction, gathering, hunting," said Anthony J. Filiano, PhD, Hartwell postdoctoral fellow in the Kipnis lab and lead author of the study. "So the hypothesis is that when organisms come together, you have a higher propensity to spread infection. So you need to be social, but [in doing so] you have a higher chance of spreading pathogens. The idea is that interferon gamma, in evolution, has been used as a more efficient way to both boost social behavior while boosting an anti-pathogen response.'"-Comment: A clever solution. If humans act in groups cooperatively they are exposed to pathogens others carry, so it is a reasonable development. It looks like a purposeful development.
Immunity; controls over socializing?
DAVID: Immunity chemical controls may encourage social cooperation:-http://medicalxpress.com/news/2016-07-role-immune-social-interaction.html-"In a startling discovery that raises fundamental questions about human behavior, researchers at the University of Virginia School of Medicine have determined that the immune system directly affects - and even controls - creatures' social behavior, such as their desire to interact with others".-Quite separately from all the medical implications of this article, what fascinates me is the way in which microcosms and macrocosms reflect one another. The “desire to interact with others” is a driving force of evolution: single cells join to form cellular communities (even bacteria do it), cellular communities join to form bodies, bodies join to form social communities (tribes), social communities join to form even bigger communities (nations). And alongside this cooperation we have competition: cells wage war on one another just as communities do. It may be said to go all the way through to the universe itself, in which matter cooperates with matter (we would not have life without the positive interaction of countless celestial “bodies”) as well as waging war on itself (the break-up of solar systems). We can also regard the universe as one gigantic “body” (which perhaps might fit in with BBella's concept of a unified All That Is), though whether it has a single mind, a zillion minds, or no mind at all (apart from earthly minds) is the big question that fuels so many of our discussions.
Immunity; controls over socializing?
by David Turell , Thursday, July 14, 2016, 19:17 (2841 days ago) @ dhw
> dhw: Quite separately from all the medical implications of this article, what fascinates me is the way in which microcosms and macrocosms reflect one another. The “desire to interact with others” is a driving force of evolution: single cells join to form cellular communities (even bacteria do it), cellular communities join to form bodies, - This is obviously all programmed into original life. - > dhw: It may be said to go all the way through to the universe itself, in which matter cooperates with matter (we would not have life without the positive interaction of countless celestial “bodies”) as well as waging war on itself (the break-up of solar systems). We can also regard the universe as one gigantic “body” (which perhaps might fit in with BBella's concept of a unified All That Is), though whether it has a single mind, a zillion minds, or no mind at all (apart from earthly minds) is the big question that fuels so many of our discussions. - I think this was programmed in the quantum mechanics of the Big Bang.
Immunity; Crispr in bacteria
by David Turell , Thursday, January 19, 2017, 01:10 (2653 days ago) @ David Turell
A mechanisms that bacteria use to fight viruses by destroying their DNA, called CRISPR is used by scientists to slice DNA and edit it in experiments:
http://www.nature.com/news/five-big-mysteries-about-crispr-s-origins-1.21294?WT.ec_id=N...
"Today, much more is known about the clustered, regularly interspaced short palindromic repeats that give CRISPR its name and help the CRISPR–Cas microbial immune system to destroy invading viruses. But although most in biomedicine have come to revere the mechanics of the system — particularly of a version called CRISPR–Cas9 — for the ways in which it can be harnessed to edit genes, Mojica and other microbiologists are still puzzling over some basic questions about the system and how it works. How did it evolve, and how did it shape microbial evolution? Why do some microbes use it, whereas others don't? And might it have other, yet-to-be-appreciated roles in their basic biology?
***
"Prokaryotes have evolved a slew of weapons to cope with these threats. Restriction enzymes, for example, are proteins that cut DNA at or near a specific sequence. But these defences are blunt. Each enzyme is programmed to recognize certain sequences, and a microbe is protected only if it has a copy of the right gene. CRISPR–Cas is more dynamic. It adapts to and remembers specific genetic invaders in a similar way to how human antibodies provide long-term immunity after an infection.
***
"How did bacteria and archaea come to possess such sophisticated immune systems? That question has yet to be answered, but the leading theory is that the systems are derived from transposons — 'jumping genes' that can hop from one position to another in the genome. Evolutionary biologist Eugene Koonin of the US National Institutes of Health in Bethesda, Maryland, and his colleagues have found1 a class of these mobile genetic elements that encodes the protein Cas1, which is involved in inserting spacers into the genome. These 'casposons', he reasons, could have been the origin of CRISPR–Cas immunity. Researchers are now working to understand how these bits of DNA hop from one place to another — and then to track how that mechanism may have led to the sophistication of CRISPR–Cas.
"Many of the molecular details of how Cas proteins add spacers have been worked out in fine detail2 in recent years. But viral DNA is chemically nearly identical to host DNA. How, in a cell packed with DNA, do the proteins know which DNA to add to the CRISPR–Cas memory?
"The stakes are high: if a bacterium adds a piece of its own DNA, it risks suicide by autoimmune attack, says Virginijus Siksnys, a biochemist at Vilnius University in Lithuania. “These enzymes are a double-edged sword.”
It may be that populations of bacteria and archaea can absorb some error, says Rodolphe Barrangou, a microbiologist at North Carolina State University in Raleigh. A few cellular suicides may not matter if other cells can thrive after a viral attack.
"In fact, when viruses infiltrate a bacterial ecosystem, often only about one bacterium in 10 million will gain a spacer that lets it defend itself. Those odds make it hard to study what drives spacer acquisition, and to learn why a cell succeeded where others failed. “It's difficult to catch that bacterium when it actually is happening,” says Luciano Marraffini, a microbiologist at the Rockefeller University in New York City.
***
"Whatever other functions CRISPR–Cas has, it is clear that some microbes use it more than others. More than 90% of archaea have CRISPR-based immunity, whereas only about one-third of sequenced bacteria bother with it, says Koonin. And no non-prokaryotic organisms, even single-celled ones, have been caught troubling with CRISPR–Cas at all"
Comment: This is a highly sophisticated immune mechanism that had to be present in the beginning of life for Archaea, the oldest branch of bacteria, to defend themselves against the attacking viruses that probably were present at the same time. It has a form of memory just as we see in humans, which allows for a rapid response to future infections after an initial encounter. Early life was tolo complex for a chance appearance.
Immunity; prokaryote viral immunity
by David Turell , Friday, August 28, 2020, 21:58 (1335 days ago) @ David Turell
A complex array of enzymes:
https://www.sciencemagazinedigital.org/sciencemagazine/28_august_2020/MobilePagedArticl...
"Bacteria and archaea are frequently attacked by viruses and other mobile genetic elements and rely on dedicated antiviral defense systems, such as restriction endonucleases and CRISPR, to survive. The enormous diversity of viruses suggests that more types of defense systems exist than are currently known. By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. These systems incorporate enzymatic activities not previously implicated in antiviral defense, including RNA editing and retron satellite DNA synthesis. In addition, we computationally predict a diverse set of other putative defense genes that remain to be characterized. These results highlight an immense array of molecular functions that microbes use against viruses."
Comment: we use bacterial CRISPR enzyme to edit DNA, a perversion of its use in life, in which it is used to chop up enemy DNA's. But the real consideration is when does this type of immunity appear in relation to the origin of the organism? And it obviously has to be designed simultaneously into the first appearance of each new species..
Immunity; T cells are many different types
by David Turell , Monday, August 28, 2017, 20:12 (2431 days ago) @ David Turell
New discoveries describe very complex ways different T cells are encoded to fight infections. The article should be viewed to appreciate how this system is designed and works:
http://www.the-scientist.com/?articles.view/articleNo/49941/title/The-Ever-Expanding-T-...
"When a pathogen enters the body and starts causing tissue damage, it triggers an inflammatory response that gets the attention of antigen-presenting cells (APCs), which monitor the environment and display bits of foreign proteins that they encounter using the major histocompatibility complex class II (MHC II) molecules located on their surfaces. Once they detect a pathogen, the APCs migrate to the spleen and lymph nodes, collectively known as secondary lymphoid organs, where naive T cells (and other T-cell types) await their call to duty.
"T-cell precursors originate from stem cells in the bone marrow, but T cells mature in the thymus—hence the name “T cells.” Every mature T cell has a cell-surface receptor (TCR) that recognizes a short, nonself peptide (those that recognize self proteins are, for the most part, eliminated), as well as one of two glycoprotein coreceptors: either CD4 or CD8. These coreceptors bind not to the peptide antigens but to MHC molecules. CD4 binds to MHC Class II receptors, found uniquely on APCs; CD8 binds to MHC Class I, found on virtually all somatic cells, including APCs.
"In the secondary lymphoid organs, APCs display their bound antigens to the CD4+ T cells via MHC Class II. These interactions, combined with signaling molecules in the cell environment, stimulate the CD4+ cells to differentiate into various T helper (Th) cells with functions specific to each pathogen type. One subset of these helper cells—T follicular helper (Tfh) cells—stimulates B cells to produce antibodies specific to the antigen in question. Naive CD8+ cells also interact with APCs, via MHC Class I receptors, triggering their differentiation into what are called cytotoxic lymphocytes (CTLs), aka killer T cells, which seek and destroy cells displaying the offending antigen.
"Once activated, both the CD8+ killer cells and the CD4+ helper cells migrate to the infected tissue. The helper cells produce cytokines and other molecules to recruit an array of immune cell types, such as neutrophils, macrophages, and mast cells, to help fight the infection, while the activated CD8+ cells bind to the pathogenic cells through the TCR and release cytotoxic enzymes into the “immunological synapse” between the T cells and their targets, inducing apoptosis in the latter.
"When the infection is under control, most of the newly activated T cells die, but some of them remain as memory cells, which stay prepared to quickly combat another infection of the same type. Whereas activation of naive T cells takes more than a week, memory T cells can respond to a secondary infection within hours.
"Memory cells, which can be either CD4+ or CD8+, come in several flavors, classified by the areas that they patrol. Effector memory cells travel throughout the tissues and the blood performing their “effector functions” in response to repeat encounters with foreign antigens: CD4+ cells act in their helper roles, while CD8+ cells carry out their cytotoxic duties. Tissue-resident memory cells act similarly, but develop at the site of an infection and stay there, rather than circulating throughout the body. Finally, central memory cells, which patrol the entire body, focus more on self-renewal (like stem cells) and less on fighting pathogens.
“'Those [functions] have been documented for CD4s as well, with the possible exception of the vascular memory,” Kedl says, referring to cells that specifically patrol the vasculature to combat returning blood infections. “But certainly all of the other ones—resident memory, effector memory, central memory, and effectors themselves—those are all part of both the CD4 and CD8 T-cell world.'”
Comment: This is a very complete system which allows cells to be coded to fight all intruders. It cannot be developed by chance or hunt and peck measures. Newborn cells are produced and taught to fight. Infectious agents appear to have been present from the start of life. Bacteria fight phages as well as each other. The survival of life depends on these defense mechanisms.
Immunity; NK roaming killer cells
by David Turell , Monday, September 04, 2017, 18:30 (2424 days ago) @ David Turell
A new immunity cell has been described. It roams looking for problems:
https://www.sciencedaily.com/releases/2017/08/170831091445.htm
"The NK cell is a "vigilante" killer -- a white blood cell that destroys invaders and cancer cells through a process of "identity card" checking. The researchers' new work shows that violent vigilante NK cells act as helper cells to start up the immune response.
"Otago Associate Professor Alex McLellan says NK cells patrol the body and destroy abnormal cells, especially infected or cancer cells. NK cells closely examine the surface of all cells and look for molecules that are present on healthy cells.
"'Certain molecules act like identity cards, and NK cell are vigilantes, ready to respond if they don't see an ID card on cells. During infections or with cancer, the absence of these molecules triggers the NK cells to destroy the cells," says Associate Professor McLellan.
***
"'A few years' ago we showed that NK cells were required for the vaccination response against cancer." The group has now recognised that NK cells enhance the ability of the immune system to recognise fragments of tumour cells released into the blood," says Associate Professor McLellan.
"These fragments induce potent immune responses against cancer, he says.
"'Our new work shows that NK cells are absolutely critical for the immune activity of these cell fragments."
"These latest findings also explain how such potent immune responses arise against cell fragments.
"'This work also reveals new ways that NK cells help the immune system, aside from in their rather violent vigilante role."
"The group is currently looking at ways to improve NK cell function through living vaccines and growth factors to enhance the immune response to cancer."
Comment: These specialized cells fight infection and cancer cells. We can presume that cancer is cell division gone awry. Since cancers must have appeared early in the origin of multicellular organisms, this system had to be in place at the same time multicellular organisms arrived. Again speaks to design to handle the number of cell division mistakes that must have occurred.
Immunity; NK roaming killer cells
David: A new immunity cell has been described. It roams looking for problems:
https://www.sciencedaily.com/releases/2017/08/170831091445.htm
QUOTE: The NK cell is a "vigilante" killer -- a white blood cell that destroys invaders and cancer cells through a process of "identity card" checking. The researchers' new work shows that violent vigilante NK cells act as helper cells to start up the immune response.
Otago Associate Professor Alex McLellan says NK cells patrol the body and destroy abnormal cells, especially infected or cancer cells. NK cells closely examine the surface of all cells and look for molecules that are present on healthy cells.
It is always very difficult for these researchers to find ways of describing cellular activity without using anthropomorphic language. That may be because cells actually do their work in much the same way as humans do – using their own particular form of intelligence.
Immunity; NK roaming killer cells
by David Turell , Tuesday, September 05, 2017, 17:36 (2423 days ago) @ dhw
David: A new immunity cell has been described. It roams looking for problems:
https://www.sciencedaily.com/releases/2017/08/170831091445.htmQUOTE: The NK cell is a "vigilante" killer -- a white blood cell that destroys invaders and cancer cells through a process of "identity card" checking. The researchers' new work shows that violent vigilante NK cells act as helper cells to start up the immune response.
Otago Associate Professor Alex McLellan says NK cells patrol the body and destroy abnormal cells, especially infected or cancer cells. NK cells closely examine the surface of all cells and look for molecules that are present on healthy cells.DHW: It is always very difficult for these researchers to find ways of describing cellular activity without using anthropomorphic language. That may be because cells actually do their work in much the same way as humans do – using their own particular form of intelligence.
Of course these cells have a full list of instructions in their DNA to tell them what to do.
Immunity; can be driven by neurons
by David Turell , Wednesday, September 06, 2017, 23:42 (2422 days ago) @ David Turell
Newly discovered neurons drive immune responses much faster than vaccinations:
https://medicalxpress.com/news/2017-09-scientists-adrenaline-immune.html
"Scientists at the Champalimaud Centre for the Unknown and the Instituto de Medicina Molecular, in Lisbon, Portugal, have discovered that neurons located at mucosal tissues can immediately detect an infection in the organism, promptly producing a substance that acts as an "adrenaline rush" for immune cells. Under the effect of this signal, immune cells rapidly become poised to fight the infection and repair the damage caused to surrounding tissues.
***
"In 2016, Henrique Veiga-Fernandes and his colleagues (then at the Institute for Molecular Medicine, in Lisbon) published, also in Nature, a study where they showed that glial cells in the gut can stimulate a type of immune cells, called ILC3, to produce substances against bacterial infections.
"These immune cells that are being studied by Veiga-Fernandes - collectively called "innate lymphoid cells", or ILC -, are also very special. We are born with them; they are not produced in response to an immunization, for instance through vaccination. "ILCs were discovered very recently, in 2010, but they are very ancient in evolutionary terms. Even lampreys have them!", says Veiga-Fernandes. Lampreys belong to a very old animal lineage.
"There are several types of these innate lymphocytes (white cells). In their 2016 study, the team had analyzed the behavior of ILC3s in the gut - and their "dialog" with their glial cell neighbours. In the new study, also led by Veiga-Fernandes, they focused on another type of innate lymphoid cells: ILC2s.
***
"The study brings "two big novelties", says Veiga-Fernandes. The first, he explains, "is that neurons define the immune cells' function. Nobody could have imagined that the nervous system coordinates, commands and controls the immune response throughout the whole organism." Second, he adds, "it's one of the fastest and most powerful immune reactions we have ever seen". Comparatively, the newly discovered neuronal stimulus induces an immune response in a few minutes, while the immune response following vaccination typically takes several weeks to mount.
"How did the scientists discover this neuro-immune "tandem"? "What happened was that we observed, in high-resolution microphotographs of the lungs and gut of mice, that ILC2s were placed along the axons of neurons residing in these mucosa, a bit like pearls on a string", replies Veiga-Fernandes. "So we asked ourselves if these two distinct tissues could productively 'talk' to each other."
"To test this hypothesis, the team started by analyzing the whole genome of a series of immune cells - ILC1s, ILC2s, ILC3s, T-cells, etc. -, "searching for genes that code molecules that may act as receivers of neuronal signals", says Veiga-Fernandes. They found that only ILC2s possessed a defined "receptor" (membrane molecules that act as antennae) for nervous signals.
"Notably, the authors discovered that ILC2s have receptors to a neuronal messenger called neuromedin U (NMU). Since neurons are the only cells that produce abundant levels of NMU, this indicated that only neurons could be sending this signal to ILC2s.
"Later, they used a rodent parasite, Nippostrongylus brasiliensis (a sort of hookworm) to infect "normal" control mice and mutant mice whose ILC2s had been stripped of their NMU receptors. In the first group of animals, the innate immune cells immediately triggered a response to neutralize the parasite and repair damaged tissue. In the second group, the mice were unable to fight the infection and the damage caused by the parasite - including the internal bleeding of the lungs due to N. brasiliensis.
"The researchers also showed that neurons are able to detect the products secreted by parasites that infect the organism - and that, when this happens, they rapidly produce NMU. In turn, NMU acts vigorously on ILC2s, thus generating a protective response in a few minutes.
"Could these results be extrapolated to humans? "Maybe. In humans, ILC2s also have NMU receptors", replies Veiga-Fernandes. "But we are still very far from understanding how we could safely use this neuro-immunological 'bomb'; for now, we are at the fundamental research level", he adds."
Comment: This complex immune mechanism allows for rapid response to infection by organisms previously not known by the host animal. Shows purposeful design of the immune system.
Immunity; stopping invading viruses
by David Turell , Tuesday, September 12, 2017, 18:42 (2416 days ago) @ David Turell
A new system has been found to recognize invading viruses and setting up a defense:
https://medicalxpress.com/news/2017-09-link-viruses-trigger-immunity.html
"A discovery by Melbourne researchers has solved a longstanding mystery of how viruses trigger protective immunity within our body.
"The research team demonstrated a protein called SIDT2 was crucial for cells to detect viral components in their environment, and initiate an immune response to reduce the virus' spread.
***
"During a viral infection, RNA - a genetic material similar to DNA - is released into the environment around the infected cells. Dr Nguyen said the team showed that SIDT2 allowed viral RNA to be shuttled between compartments within cells, allowing it to reach the proteins that trigger anti-viral immunity.
"'This RNA is in a 'double-stranded' form, called 'dsRNA', that is not normally found in our body. Human cells have evolved ways to detect dsRNA as a warning sign of an active viral infection and, in this way, dsRNA acts as an important trigger for cells to mount an anti-viral immune response.
"'Cells constantly survey their environment by 'swallowing' small samples of their environment into compartments called endosomes. The enigma was that no one knew how the dsRNA escaped the endosome to reach the cytoplasm, where it can be detected by the cell." Dr Nguyen said.
"The team showed that SIDT2 was the crucial missing link needed to transport dsRNA out of endosomes, and enable an immune response to be launched.
"Viruses have many strategies to prevent an infected cell from alerting the immune system to their presence, Dr Pang said. "Intriguingly, we showed that SIDT2 is critical for uninfected 'bystander' cells to detect viral RNA in their environment," Dr Pang said. "This means bystanders can trigger protective immunity before they even encounter the virus itself.
"'Viruses have evolved many ways to switch off the immune response, allowing them to spread, while humans have evolved counter measures to allow a rapid and protective immune response that contains the viral infection. SIDT2 is helping humans in the 'arms race' between viruses and their human hosts.'"
Comment: Finding just the right organic molecule to fight viruses cannot be left to chance. Since viruses constantly are invading, survival depends upon an immediate solution to the problem. It must be designed from the beginning.
Immunity; how B cells make antibodies
by David Turell , Thursday, September 14, 2017, 18:51 (2414 days ago) @ David Turell
By first damaging or changing their DNA to make specific antibodies against specific infections:
https://www.sciencedaily.com/releases/2017/09/170913084427.htm
"In response to infection the immune system produces unique antibodies to target each illness. To make these new antibodies, cells in the immune system must intentionally damage their own genes, meaning they run the risk of becoming cancer cells. New research reveals how a proteins called Tia1 acts as a hair-trigger for DNA repair, allowing the immune system to walk the line between health and harm.
"To fight infections cells in the immune system play a dangerous game with their own genes. Damaging genes allows B cells to make antibodies that are specifically equipped to target to specific causes of illness, but damaging genes also puts them at risk of becoming cancerous.
***
"All cells experience DNA damage but it's usually minor and can be repaired. The latest research, published in the journal Nature Communications, highlights that standard repair processes are too slow for B cells, where intentional DNA damage is more severe. The results show that B cells plan ahead, priming the DNA repair process early, so when they intentionally damage their own DNA it can be fixed before it causes lasting harm.
"As the paper's first author, Dr Manuel Díaz-Muñoz said: "B cells walk a fine line, some DNA damage is needed for them to make effective antibodies to fight infections, but too much and they become harmful. It's a tough situation to manage biochemically. Tia1 controls the production of a number of proteins that help cells respond to damaged DNA. Tia1 allows a rapid response from B cells so they can repair DNA damage at a moment's notice."
"Each illness requires a specific antibody to defeat it. By damaging and repairing the genetic instructions that make antibodies, each B cell produces a unique antibody type and the most effective ones are then used to fight disease. This causes extensive damage to the DNA inside B cells and must be rapidly repaired or genetic mistakes may weaken the immune system or even cause cancer.
"Scientists believed that B cells only turn on DNA repair genes when they are needed to repair damage. Yet, these new results completely change this view. These genes are constantly active, but cells only use the information in these genes to make proteins when there is a lot of DNA damage. B cells prepare templates for the proteins but don't go on to make the proteins themselves.
"Tia1 is the protein that enables B cells to stop making DNA repair proteins part way through. When DNA damage is low, Tia1 gathers together the protein templates, called mRNAs, for lots of different DNA repair proteins. When DNA damage increases Tia1 can quickly release all the mRNAs it collected and the cell uses them to make lots of the proteins it needs to fix its genes.
***
"'Remarkably, our data suggest that regulation of mRNAs by Tia1 rather than protein destruction controls DNA repair in activated B cells. This is an attractive and little explored mechanism that we are now starting to understand. Controlling protein production in this way is important in other healthy and diseased cells and it will be interesting to see if a similar system exists in other places.'"
Comment: Since infections can always occur without warning, this hair-trigger system must have been designed intact from the beginning. It could not be built bit by bit. Specifically out of billions of different proteins, how did evolution find Tia1 to do the job without guidance?
Immunity; how junk DNA speeds the process
by David Turell , Thursday, September 21, 2017, 20:07 (2407 days ago) @ David Turell
edited by David Turell, Thursday, September 21, 2017, 20:14
Immune cells must recognize their infectious challenges and quickly develop responsive antibodies. Junk DNA is found to have the answer:
https://medicalxpress.com/news/2017-09-forgotten-strands-dna-immune-cells.html
"Intricate human physiological features such as the immune system require exquisite formation and timing to develop properly. Genetic elements must be activated at just the right moment, across vast distances of genomic space.
"'Promoter" areas, locations where genes begin to be expressed, must be paired precisely with "enhancer" clusters, where cells mature to a targeted function. Faraway promoters must be brought in proximity with their enhancer counterparts, but how do they come together?
***
"Calling it the "big bang" of immune cell development, the researchers made their discovery within previously overlooked stretches of DNA located between genes. The results, published in the September 21 edition of the journal Cell, were led by Takeshi Isoda in Cornelis Murre's laboratory in UC San Diego's Division of Biological Sciences.
"Through genomic studies and genetic experiments in mice, the scientists found that the ignored areas, known as "non-coding" DNA, activate a change in the 3D structure of DNA that brings promoters and enhancers together with stunning accuracy. Murre describes the mechanism as somewhat like a stiff wire—with enhancers and promoters on either end—that's bended together into a loop and anchored in place. Enhancers and promoters, once distantly separated, are now repositioned in close proximity to initiate the development of immune system building blocks known as T cells.
"'Nature is so clever. We think of the genome as an unstructured strand but in fact what we are seeing is a highly structured and meaningful design," said Murre. "The process of architecture remodeling we've described allows the enhancer and promoter to find each other in 3D space at precisely the right time. The beauty is that it's all very carefully orchestrated. We have seen one example but there are likely many others all occurring at the same time when cells are moving along the developmental pathway-that's kind of amazing."
While Murre and his colleagues concentrated on T cells, they believe this mechanism may be unfolding throughout the animal and plant kingdoms.
"When the mechanism fails, T cell development falters and diseases such as lymphoma and leukemia result. Murre says the results show how the forgotten strands of DNA suppress the development of leukemia and lymphoma.
"'The implications of these results are not only how normal T cells develop, but that tumor suppression is regulated through this mechanism, at least in part," said Murre."
Comment: The immune system is obviously highly complex. It is cute that the authors call nature 'clever'. the complexity is beyond simple cleverness. It requires design. Be sure to look at the website and see the diagrams. Note more 'junk' DNA disappears, which the authors call 'overlooked'. "Junk" DNA is a cornerstone of atheistic thinking about evolution. To them the junk is the result of chance attempts at advances, that then did not work out and were discarded. The disappearance of junk is a major blow to their theories of random mutation and chance evolution.
Immunity; how junk DNA speeds the process
DAVID: Note more 'junk' DNA disappears, which the authors call 'overlooked'. "Junk" DNA is a cornerstone of atheistic thinking about evolution. To them the junk is the result of chance attempts at advances, that then did not work out and were discarded. The disappearance of junk is a major blow to their theories of random mutation and chance evolution.
Then they must be pretty dim. If junk turns out to be useful, all they have to say is that natural selection ensures that whatever is useful remains and whatever is useless is discarded. It need not make the slightest difference to their faith in chance evolution.
Immunity; how junk DNA speeds the process
by David Turell , Friday, September 22, 2017, 15:16 (2407 days ago) @ dhw
DAVID: Note more 'junk' DNA disappears, which the authors call 'overlooked'. "Junk" DNA is a cornerstone of atheistic thinking about evolution. To them the junk is the result of chance attempts at advances, that then did not work out and were discarded. The disappearance of junk is a major blow to their theories of random mutation and chance evolution.
dhw: Then they must be pretty dim. If junk turns out to be useful, all they have to say is that natural selection ensures that whatever is useful remains and whatever is useless is discarded. It need not make the slightest difference to their faith in chance evolution.
They are dim. Frantic articles prove it as they try to save the 'junk' concept.
Immunity: how antibodies are created
by David Turell , Saturday, October 28, 2017, 05:55 (2371 days ago) @ David Turell
It requires controlled mutations that appear random, but are actually limited:
https://uncommondescent.com/evolution/the-immune-system-is-really-amazing-and-designed/
"There a millions of different antibodies that you have to assist you. There are essentially two parts to an antibody – the CDR region (the “complementary-determining region”, which sticks to the antigen), and the C (Constant) region (which signals the immune system that it needs to come and take a look). We only have a few different C regions, each for different types of immune responses. However, we need millions of different CDR regions, because there are millions of things to watch out for.
"However, we don’t have millions of genes. The total number of human genes is less than 25,000. So what happens? How do we get these millions of different proteins from a handful of genes? The genes for the CDR region are broken up into three different “interchangeable parts” – a V, a D, and a J (they stand for Variable, Diversity, and Joining, but that doesn’t really matter for our discussion). Pretty much any V can be matched with any D then with any J. Each of these “pieces” is marked with a marker that allows the genetic system to cut them at the proper place for recombination, called the RSS (recombination signal sequence). Because the process is combinatorial, you can get the millions of antibody genes needed from just recombining a few hundred gene parts!
"Now, each cell recombines a different set of these gene pieces. However, how is the communication handled so that each individual cell knows which combinations have already been tried so it can be sure to do a new one? Answer – they don’t. They don’t have to! In such a process, all you need is to randomize which particular pieces you are trying out, and the net effect will be almost the same as if you communicated about which ones to do, without any communication overhead!
"So, it is random in the sense that there is a combinatorial process that includes a random variable, but it is in no way random because the specific pieces which can be recombined are specifically marked, they are recombined in the proper order, and with a C region attached to the end to communicate with the rest of the cell. It is kind of a lego-like building block system – interchangeable parts that are different but with matching attachment sites. It only works if all of the parts match the design (i.e., the right size, flanked by the correct RSS so the immune system knows where to cut, etc.). There is a random component, but it is carefully controlled.
***
"The SMH System is another wonderful system that generates new antibodies when needed. If you have an unknown antigen come into your body that your body doesn’t have a matching antibody for, then it knows it has to generate one. How does it do this?
1) It detects that it needs to generate a new antibody. 2) It takes an existing, antibody gene (one that is already recombined as above) that almost matches the antigen. 3) It mutates JUST THAT GENE. Not only that, it only mutates the CDR of the gene. That is, it skips the C region (why? because it still needs to signal to the immune system that it found something! If it mutated the CDR, the communication would break down.). 4) When it detects that it has a match, it stops mutating.
"So, where is the randomness? Well, within the CDR, as best as we can figure, the immune system generates random changes. Is that really a random mutation, though? It has excluded 99.99993% of the genome and focused on the 0.00007% that it knows needs changing. What I tell people is that I will be happy to agree with them that this process is 0.00007% random if they will agree with me that it is 99.99993% designed. That usually ends the conversation.
What’s also interesting is that the cell itself starts and stops the process as needed. That is, these aren’t just happenstance mutations – the cell actively knows it needs mutations, and activates a system to produce them, then produces them within the span of 2,000 base pairs that it knows is likely to produce benefit, and then stops once it finds a benefit (it’s actually closer to 500 base pairs that get significant mutations, but there are a few rare mutations farther into the gene)."
Comment: What is described, in short, is a highly controlled mutation system in a tiny section of the necessary DNA. Not really totally at random. And such a system, which is absolutely required for life to continue unimpeded by infection, cannot be developed bit by bit. It must be designed all at once with all of its parts and controls. And it must be present at the same time pathogens appear. Not by chance. This evidence says there must be a designer.
Immunity: detecting dangerous bacteria
by David Turell , Thursday, November 16, 2017, 19:33 (2351 days ago) @ David Turell
Cells have a complex way of detecting bad bacteria. Since bacteria came first, when multicellular forms arrived on the scene, they had to have this mechanism in place to survive:
https://medicalxpress.com/news/2017-11-immune-invading-bacteria.html
"The body's homeland security unit is more thorough than any airport checkpoint. For the first time, scientists have witnessed a mouse immune system protein frisking a snippet of an invading bacterium. The inspection is far more extensive than researchers imagined: the immune system protein, similar to those in humans, scans the bacterial protein in six different ways, ensuring correct identification.
***
"'The immune system protein uses many protein parts, including some of previously unknown function."
***
"HHMI Investigator Russell Vance had been studying the NLR superfamily of immune system proteins, which plants and animals use to detect pathogens that have slipped inside cells. He wanted to see one such protein, called NAIP5, as it inspected bits of protein shed by the disease-causing bacterium Legionella pneumophila. Earlier genetic studies had identified NAIP5 as an important player in host resistance to Legionella, and Vance's team wanted to take a closer look.
***
"The researchers discovered that NAIP5 performs an in-depth inspection of bits of the bacteria's flagella, the tail-like appendages that many disease-causing bacteria use for locomotion. "This is a very effective immune response," says Vance, a microbiologist and immunologist, also at UC Berkeley. "It helps us understand why the pathogen can't escape just by mutating."
"Bacteria can't simply hide from the immune system by making minor changes to flagella proteins, he explains. And larger changes that might let bacteria evade detection could meddle with locomotion.
"The team tested the idea by creating mutant strains of Legionella and introducing them to the immune system proteins. Sure enough, minor mutations to a bacterial flagella protein weren't enough to trick NAIP5. But more significant mutations interfered with the flagella so much that the bacterium had trouble moving around.
"Intensive frisking by the immune system suggests that it is careful to identify a threat before taking out the big guns, Vance says. After glomming onto the bacterial protein snippet, the immune system protein recruits a second protein, forming a complex called an inflammasome. The second protein then sounds an alarm that the cell has been invaded, triggering events that culminate in a dramatic form of cell death.
"'The cell literally bursts open," Vance says. This dramatic finale—called pyroptosis—is a good thing if a bacterium is trying to take up residence in a cell, he says, but the chain of events can provoke disease if it happens too often. That's why it's important that the immune system is thorough, and the response is highly specific to the bacterium's flagella, he says. "
Comment: The immune system cells learn about bacteria by experience, changing its DNA to fit its discoveries. A newborn baby relies on its Mother's IGG, etc. antibodies in colostrum to start off life protected until it can build its own protection. This complexity has to be designed. Not by chance. How much complexity has to be shown in living evolved organisms before agnostics recognize design is necessary?
Immunity: detecting dangerous bacteria
DAVID’s comment: The immune system cells learn about bacteria by experience, changing its DNA to fit its discoveries. A newborn baby relies on its Mother's IGG, etc. antibodies in colostrum to start off life protected until it can build its own protection. This complexity has to be designed. Not by chance. How much complexity has to be shown in living evolved organisms before agnostics recognize design is necessary?
Amazing how cells learn by experience and change themselves to fit their discoveries, and yet are believed by some to be automatons that can't learn or change themselves.
As for design, how many times does an agnostic have to tell a panentheist that every design does not have to be preprogrammed in the first living cells 3.8 billion years ago and then passed on, or personally dabbled by a God? How many times does an agnostic have to tell a panentheist that if God exists, it would have been far simpler for him to give living cells the ability to do their own designing? No chance involved in any of these complexities, and the option open that your God designed the designers.
Immunity: detecting dangerous bacteria
by David Turell , Friday, November 17, 2017, 15:17 (2350 days ago) @ dhw
DAVID’s comment: The immune system cells learn about bacteria by experience, changing its DNA to fit its discoveries. A newborn baby relies on its Mother's IGG, etc. antibodies in colostrum to start off life protected until it can build its own protection. This complexity has to be designed. Not by chance. How much complexity has to be shown in living evolved organisms before agnostics recognize design is necessary?
dhw: Amazing how cells learn by experience and change themselves to fit their discoveries, and yet are believed by some to be automatons that can't learn or change themselves.As for design, how many times does an agnostic have to tell a panentheist that every design does not have to be preprogrammed in the first living cells 3.8 billion years ago and then passed on, or personally dabbled by a God? How many times does an agnostic have to tell a panentheist that if God exists, it would have been far simpler for him to give living cells the ability to do their own designing? No chance involved in any of these complexities, and the option open that your God designed the designers.
And you have glossed over your own point: if cells can do their own designing, God designed them to have that ability! Or they are designed to be automatic. Either way God is at work and agnosticism disappears.
Immunity: detecting dangerous bacteria
DAVID’s comment: The immune system cells learn about bacteria by experience, changing its DNA to fit its discoveries. [….] This complexity has to be designed. Not by chance. How much complexity has to be shown in living evolved organisms before agnostics recognize design is necessary?
dhw: Amazing how cells learn by experience and change themselves to fit their discoveries, and yet are believed by some to be automatons that can't learn or change themselves.
As for design, how many times does an agnostic have to tell a panentheist that every design does not have to be preprogrammed in the first living cells 3.8 billion years ago and then passed on, or personally dabbled by a God? How many times does an agnostic have to tell a panentheist that if God exists, it would have been far simpler for him to give living cells the ability to do their own designing? No chance involved in any of these complexities, and the option open that your God designed the designers.
DAVID: And you have glossed over your own point: if cells can do their own designing, God designed them to have that ability! Or they are designed to be automatic. Either way God is at work and agnosticism disappears.
The glossing is yours. You consistently maintain that cells cannot possibly think for themselves. Now you have them learning by experience and deliberately changing themselves. I’m delighted to see your change of heart.
I have ALWAYS left open the possibility that your God designed the autonomous intelligence of cells, and have repeated it here: “the option open that your God designed the designers.”
Immunity: detecting dangerous bacteria
by David Turell , Saturday, November 18, 2017, 15:12 (2350 days ago) @ dhw
dhw: As for design, how many times does an agnostic have to tell a panentheist that every design does not have to be preprogrammed in the first living cells 3.8 billion years ago and then passed on, or personally dabbled by a God? How many times does an agnostic have to tell a panentheist that if God exists, it would have been far simpler for him to give living cells the ability to do their own designing? No chance involved in any of these complexities, and the option open that your God designed the designers.[/i]
DAVID: And you have glossed over your own point: if cells can do their own designing, God designed them to have that ability! Or they are designed to be automatic. Either way God is at work and agnosticism disappears.
dhw: The glossing is yours. You consistently maintain that cells cannot possibly think for themselves. Now you have them learning by experience and deliberately changing themselves. I’m delighted to see your change of heart.
I have ALWAYS left open the possibility that your God designed the autonomous intelligence of cells, and have repeated it here: “the option open that your God designed the designers.”
Do I have to parse what I wrote? All I have stated is if God made cells totally automatic or gave them an ability to design, it is still God at work, with no other alternative source of creation. Do you have an alternative to God?
Immunity: detecting dangerous bacteria
dhw: The glossing is yours. You consistently maintain that cells cannot possibly think for themselves. Now you have them learning by experience and deliberately changing themselves. I’m delighted to see your change of heart.
I have ALWAYS left open the possibility that your God designed the autonomous intelligence of cells, and have repeated it here: “the option open that your God designed the designers.”
DAVID: Do I have to parse what I wrote? All I have stated is if God made cells totally automatic or gave them an ability to design, it is still God at work, with no other alternative source of creation. Do you have an alternative to God?
You wrote that the “immune system cells learn about bacteria by experience, changing its DNA to fit its discoveries”. If cells learn by experience and change their structure, they cannot be automatons, but until now that is what you have insisted they are. Your acknowledgement that cells learn from experience and act according to what they learn makes for a red-letter day in the history of the AgnosticWeb!
As for alternatives to your God, you know perfectly well that one is chance and one is the panpsychist hypothesis I have described over and over again (bottom up evolution), and you know that I find these hypotheses as difficult to believe in as the universal sourceless conscious mind you call God. And that is why I am an agnostic. (See also my response to the article on panpsychism)
Immunity: detecting dangerous bacteria
by David Turell , Sunday, November 19, 2017, 15:02 (2349 days ago) @ dhw
dhw: You wrote that the “immune system cells learn about bacteria by experience, changing its DNA to fit its discoveries”. If cells learn by experience and change their structure, they cannot be automatons, but until now that is what you have insisted they are. Your acknowledgement that cells learn from experience and act according to what they learn makes for a red-letter day in the history of the AgnosticWeb!
The immune system is a very specialized protection arrangement. New organisms cannot know in advance what enemy will attack, therefore they are designed to react in the way they do and teach themselves how to identify foreign foes. it is all automatic. I've described this before as a testimony to God's design ability.
dhw: As for alternatives to your God, you know perfectly well that one is chance and one is the panpsychist hypothesis I have described over and over again (bottom up evolution), and you know that I find these hypotheses as difficult to believe in as the universal sourceless conscious mind you call God. And that is why I am an agnostic. (See also my response to the article on panpsychism)
Yes I understand your hang ups.
Immunity: detecting dangerous bacteria
dhw: You wrote that the “immune system cells learn about bacteria by experience, changing its DNA to fit its discoveries”. If cells learn by experience and change their structure, they cannot be automatons, but until now that is what you have insisted they are. Your acknowledgement that cells learn from experience and act according to what they learn makes for a red-letter day in the history of the AgnosticWeb!
DAVID: The immune system is a very specialized protection arrangement. New organisms cannot know in advance what enemy will attack, therefore they are designed to react in the way they do and teach themselves how to identify foreign foes. it is all automatic. I've described this before as a testimony to God's design ability.
If they can learn by experience, change their own structures to fit in and cope with what they have learned, and even teach themselves, it would be hard to find many more attributes required for autonomous intelligence. You might just as well say your God designed their ability to think for themselves.
Immunity: detecting dangerous bacteria
by David Turell , Monday, November 20, 2017, 15:19 (2347 days ago) @ dhw
dhw: You wrote that the “immune system cells learn about bacteria by experience, changing its DNA to fit its discoveries”. If cells learn by experience and change their structure, they cannot be automatons, but until now that is what you have insisted they are. Your acknowledgement that cells learn from experience and act according to what they learn makes for a red-letter day in the history of the AgnosticWeb!
DAVID: The immune system is a very specialized protection arrangement. New organisms cannot know in advance what enemy will attack, therefore they are designed to react in the way they do and teach themselves how to identify foreign foes. it is all automatic. I've described this before as a testimony to God's design ability.
dhw: If they can learn by experience, change their own structures to fit in and cope with what they have learned, and even teach themselves, it would be hard to find many more attributes required for autonomous intelligence. You might just as well say your God designed their ability to think for themselves.
What I do say is this mechanism is intelligently designed by God to work automatically.
Immunity: detecting dangerous bacteria
dhw: If they can learn by experience, change their own structures to fit in and cope with what they have learned, and even teach themselves, it would be hard to find many more attributes required for autonomous intelligence. You might just as well say your God designed their ability to think for themselves.
DAVID: What I do say is this mechanism is intelligently designed by God to work automatically.
You have always acknowledged that our fellow animals have a degree of autonomous conscious intelligence, though it’s nothing like as developed as ours. Bearing this in mind, please tell me what attributes an organism must have for you to acknowledge that it has a degree of autonomous conscious intelligence.
Immunity: detecting dangerous bacteria
by David Turell , Tuesday, November 21, 2017, 14:57 (2347 days ago) @ dhw
dhw: If they can learn by experience, change their own structures to fit in and cope with what they have learned, and even teach themselves, it would be hard to find many more attributes required for autonomous intelligence. You might just as well say your God designed their ability to think for themselves.
DAVID: What I do say is this mechanism is intelligently designed by God to work automatically.
dhw: You have always acknowledged that our fellow animals have a degree of autonomous conscious intelligence, though it’s nothing like as developed as ours. Bearing this in mind, please tell me what attributes an organism must have for you to acknowledge that it has a degree of autonomous conscious intelligence.
Any animal with a brain.
Immunity: detecting dangerous bacteria
dhw: If they can learn by experience, change their own structures to fit in and cope with what they have learned, and even teach themselves, it would be hard to find many more attributes required for autonomous intelligence. You might just as well say your God designed their ability to think for themselves.
DAVID: What I do say is this mechanism is intelligently designed by God to work automatically.
dhw: You have always acknowledged that our fellow animals have a degree of autonomous conscious intelligence, though it’s nothing like as developed as ours. Bearing this in mind, please tell me what attributes an organism must have for you to acknowledge that it has a degree of autonomous conscious intelligence.
DAVID: Any animal with a brain.
Ah well, in the light of your avowed beliefs, you’ll be in for a pretty dumb afterlife.
Immunity: detecting dangerous bacteria
by David Turell , Wednesday, November 22, 2017, 15:00 (2346 days ago) @ dhw
dhw: If they can learn by experience, change their own structures to fit in and cope with what they have learned, and even teach themselves, it would be hard to find many more attributes required for autonomous intelligence. You might just as well say your God designed their ability to think for themselves.
DAVID: What I do say is this mechanism is intelligently designed by God to work automatically.
dhw: You have always acknowledged that our fellow animals have a degree of autonomous conscious intelligence, though it’s nothing like as developed as ours. Bearing this in mind, please tell me what attributes an organism must have for you to acknowledge that it has a degree of autonomous conscious intelligence.
DAVID: Any animal with a brain.
dhw: Ah well, in the light of your avowed beliefs, you’ll be in for a pretty dumb afterlife.
Afterlife is pure consciousness, no brain involved, but you forgot that about my ideas.
Immunity: detecting dangerous bacteria
dhw: You have always acknowledged that our fellow animals have a degree of autonomous conscious intelligence, though it’s nothing like as developed as ours. Bearing this in mind, please tell me what attributes an organism must have for you to acknowledge that it has a degree of autonomous conscious intelligence.
DAVID: Any animal with a brain.
dhw: Ah well, in the light of your avowed beliefs, you’ll be in for a pretty dumb afterlife.
DAVID: Afterlife is pure consciousness, no brain involved, but you forgot that about my ideas.
I didn’t forget it at all – it was the whole point of my comment! One moment you believe autonomous intelligence is impossible without a brain, and the next you tell us that autonomous intelligence does not depend on the brain. Look at two of your statements in the last couple of days:
“The new brain had an advanced ability for thought...” “The smaller brain does not have the ability to have the concept…” (which means only the larger brain has the ability to have the concept). And on this thread the only way an organism can be autonomously intelligent is for it to have a brain. All these statements mean that autonomous intelligence is not possible without a brain. But this apparently is your “shorthand” because “it is understood the brain is the instrument for the soul”. So it’s the soul that does the thinking, in which case autonomous intelligence (as confirmed by your belief in an afterlife) does NOT depend on the brain! You can’t have it both ways. If autonomous intelligence does NOT depend on the brain, you cannot then argue that only an organism with a brain can have autonomous intelligence!
Immunity: detecting dangerous bacteria
by David Turell , Thursday, November 23, 2017, 15:43 (2344 days ago) @ dhw
dhw: You have always acknowledged that our fellow animals have a degree of autonomous conscious intelligence, though it’s nothing like as developed as ours. Bearing this in mind, please tell me what attributes an organism must have for you to acknowledge that it has a degree of autonomous conscious intelligence.
DAVID: Any animal with a brain.
dhw: Ah well, in the light of your avowed beliefs, you’ll be in for a pretty dumb afterlife.
DAVID: Afterlife is pure consciousness, no brain involved, but you forgot that about my ideas.
I didn’t forget it at all – it was the whole point of my comment! One moment you believe autonomous intelligence is impossible without a brain, and the next you tell us that autonomous intelligence does not depend on the brain. Look at two of your statements in the last couple of days:
“The new brain had an advanced ability for thought...” “The smaller brain does not have the ability to have the concept…” (which means only the larger brain has the ability to have the concept). And on this thread the only way an organism can be autonomously intelligent is for it to have a brain. All these statements mean that autonomous intelligence is not possible without a brain. But this apparently is your “shorthand” because “it is understood the brain is the instrument for the soul”. So it’s the soul that does the thinking, in which case autonomous intelligence (as confirmed by your belief in an afterlife) does NOT depend on the brain! You can’t have it both ways. If autonomous intelligence does NOT depend on the brain, you cannot then argue that only an organism with a brain can have autonomous intelligence!
Autonomous intelligence results from having consciousness, for which the brain is a receiver. Consciousness is not created by the brain. It exists separate from it and when received is used by the brain (soul). We've been over all of this. As for size of brain, the computer analogy will do: a bigger more complex computer will do bigger more complex tasks for you.
Immunity: detecting dangerous bacteria
Dhw: One moment you believe autonomous intelligence is impossible without a brain, and the next you tell us that autonomous intelligence does not depend on the brain. Look at two of your statements in the last couple of days:
“The new brain had an advanced ability for thought...” “The smaller brain does not have the ability to have the concept…” (which means only the larger brain has the ability to have the concept). And on this thread the only way an organism can be autonomously intelligent is for it to have a brain. All these statements mean that autonomous intelligence is not possible without a brain. But this apparently is your “shorthand” because “it is understood the brain is the instrument for the soul”. So it’s the soul that does the thinking, in which case autonomous intelligence (as confirmed by your belief in an afterlife) does NOT depend on the brain! You can’t have it both ways. If autonomous intelligence does NOT depend on the brain, you cannot then argue that only an organism with a brain can have autonomous intelligence!
DAVID: Autonomous intelligence results from having consciousness, for which the brain is a receiver. Consciousness is not created by the brain. It exists separate from it and when received is used by the brain (soul). We've been over all of this.
We have indeed, and you are still getting confused! Since when did you regard the brain as the soul? We have agreed time and again that if there is such a thing as the “soul”, that is what does the thinking and the brain provides information and then obeys the “soul’s” instructions. And so if consciousness (and hence autonomous intelligence) is not created by the brain – which is only a receiver – and according to you can survive the death of the brain, how can you claim that only an organism with a brain can have consciousness and autonomous intelligence? (NB as usual, I am not arguing for dualism against materialism. I am only challenging your reasoning. One day I will find time to develop my compromise between the two –isms!)
(The size of the brain is a different subject and is dealt with elsewhere.)
Immunity: detecting dangerous bacteria
by David Turell , Friday, November 24, 2017, 14:45 (2344 days ago) @ dhw
DAVID: Autonomous intelligence results from having consciousness, for which the brain is a receiver. Consciousness is not created by the brain. It exists separate from it and when received is used by the brain (soul). We've been over all of this.We have indeed, and you are still getting confused! Since when did you regard the brain as the soul? We have agreed time and again that if there is such a thing as the “soul”, that is what does the thinking and the brain provides information and then obeys the “soul’s” instructions. And so if consciousness (and hence autonomous intelligence) is not created by the brain – which is only a receiver – and according to you can survive the death of the brain, how can you claim that only an organism with a brain can have consciousness and autonomous intelligence?
We are still in full agreement about souls. The parenthetic 'soul' simply was a reminder that the brain was the operating point for the soul. I accept God's consciousness is everywhere, but only brains 'receive' useful consciousness with which they can functionally think.
Immunity: detecting dangerous bacteria
DAVID: Autonomous intelligence results from having consciousness, for which the brain is a receiver. Consciousness is not created by the brain. It exists separate from it and when received is used by the brain (soul). We've been over all of this.
dhw: We have indeed, and you are still getting confused! Since when did you regard the brain as the soul? We have agreed time and again that if there is such a thing as the “soul”, that is what does the thinking and the brain provides information and then obeys the “soul’s” instructions. And so if consciousness (and hence autonomous intelligence) is not created by the brain – which is only a receiver – and according to you can survive the death of the brain, how can you claim that only an organism with a brain can have consciousness and autonomous intelligence?
DAVID: We are still in full agreement about souls. The parenthetic 'soul' simply was a reminder that the brain was the operating point for the soul. I accept God's consciousness is everywhere, but only brains 'receive' useful consciousness with which they can functionally think.
I don’t know about “accept”. You believe your God’s consciousness is everywhere, except apparently in bacteria, which are automatons that have no idea what they’re doing, and in immune cells, which learn about bacteria by experience and change their DNA to fit their discoveries but are also automatons, because without a brain apparently nothing can be autonomously intelligent. I don’t know how you distinguish between consciousness and “useful” consciousness, and I don’t know how brains can “functionally think” if the thinking is done by the “soul”. And I still don’t understand how consciousness (autonomous intelligence, the soul) “exists separate” from the brain (see first quote above), can even live on when the brain is dead, but cannot exist without a brain. In brief, your response is somewhat confusing.
Immunity: detecting dangerous bacteria
by David Turell , Saturday, November 25, 2017, 15:30 (2342 days ago) @ dhw
DAVID: We are still in full agreement about souls. The parenthetic 'soul' simply was a reminder that the brain was the operating point for the soul. I accept God's consciousness is everywhere, but only brains 'receive' useful consciousness with which they can functionally think.
dhw: I don’t know about “accept”. You believe your God’s consciousness is everywhere, except apparently in bacteria, which are automatons that have no idea what they’re doing, and in immune cells, which learn about bacteria by experience and change their DNA to fit their discoveries but are also automatons, because without a brain apparently nothing can be autonomously intelligent. I don’t know how you distinguish between consciousness and “useful” consciousness, and I don’t know how brains can “functionally think” if the thinking is done by the “soul”. And I still don’t understand how consciousness (autonomous intelligence, the soul) “exists separate” from the brain (see first quote above), can even live on when the brain is dead, but cannot exist without a brain. In brief, your response is somewhat confusing.
I'm not confused. Consciousness is received by the brain which the soul/consciousness uses to think. NDE's show the ability to separate and rejoin and that a soul/consciousness can function without a functional brain. In my view consciousness can only exist in brains which are the only living matter that can receive it. And, of course, God can engineer anything to look intelligent with genome programming.
Immunity: detecting dangerous bacteria
DAVID: We are still in full agreement about souls. The parenthetic 'soul' simply was a reminder that the brain was the operating point for the soul. I accept God's consciousness is everywhere, but only brains 'receive' useful consciousness with which they can functionally think.
dhw: I don’t know about “accept”. You believe your God’s consciousness is everywhere, except apparently in bacteria, which are automatons that have no idea what they’re doing, and in immune cells, which learn about bacteria by experience and change their DNA to fit their discoveries but are also automatons, because without a brain apparently nothing can be autonomously intelligent. I don’t know how you distinguish between consciousness and “useful” consciousness, and I don’t know how brains can “functionally think” if the thinking is done by the “soul”. And I still don’t understand how consciousness (autonomous intelligence, the soul) “exists separate” from the brain (see first quote above), can even live on when the brain is dead, but cannot exist without a brain. In brief, your response is somewhat confusing.
DAVID: I'm not confused. Consciousness is received by the brain which the soul/consciousness uses to think.
“Uses to think”? Let’s clarify: the brain supplies information to the soul (so the soul uses the information), and then the soul uses the brain to make the body give physical expression to the thought, e.g. by action in the form of movement, speech etc. How does that enable the brain to “functionally THINK”?
DAVID: NDE's show the ability to separate and rejoin and that a soul/consciousness can function without a functional brain.
If the soul/consciousness can function without a brain (as in the afterlife you believe in), it means that consciousness does not need a brain, and yet you continue to insist than an organism without a brain can’t be conscious.
DAVID: In my view consciousness can only exist in brains which are the only living matter that can receive it. And, of course, God can engineer anything to look intelligent with genome programming.
“Consciousness can only exist in brains”, and yet “consciousness can function without a functional brain” (and in the afterlife, without a brain of any kind). But you are not confused. Ah well, since you so often accidentally tell us that the brain thinks (you’ve done it twice more on the “learning new tasks” thread), how about this for a hypothesis: consciousness is NOT possible without certain chemical processes (materialism). In the animal world these take place within the brain. In other organisms such as bacteria the chemical processes take place within the cell itself, in its equivalent of a brain.
And here’s another hypothesis: if something learns by experience, alters its own DNA in order to cope with changing conditions, looks intelligent, and acts intelligently, then maybe it is intelligent.
Immunity: detecting dangerous bacteria
by David Turell , Sunday, November 26, 2017, 19:09 (2341 days ago) @ dhw
DAVID: I'm not confused. Consciousness is received by the brain which the soul/consciousness uses to think.dhw: “Uses to think”? Let’s clarify: the brain supplies information to the soul (so the soul uses the information), and then the soul uses the brain to make the body give physical expression to the thought, e.g. by action in the form of movement, speech etc. How does that enable the brain to “functionally THINK”?
The brain does not supply information to the soul. The soul/consciousness uses the brain as a receiver of a mechanism that allows thought and memory. Again the comparison of computer hardware (brain) and its uses of software (soul/consciousness).
DAVID: NDE's show the ability to separate and rejoin and that a soul/consciousness can function without a functional brain.dhw: If the soul/consciousness can function without a brain (as in the afterlife you believe in), it means that consciousness does not need a brain, and yet you continue to insist than an organism without a brain can’t be conscious.
NDE's show consciousness functions without a brain, but the opposite is not true. A brain doesn't function without consciousness. Consciousness can only be received by brains for function and use.
DAVID: In my view consciousness can only exist in brains which are the only living matter that can receive it. And, of course, God can engineer anything to look intelligent with genome programming.dhw: “Consciousness can only exist in brains”, and yet “consciousness can function without a functional brain” (and in the afterlife, without a brain of any kind). But you are not confused. Ah well, since you so often accidentally tell us that the brain thinks (you’ve done it twice more on the “learning new tasks” thread), how about this for a hypothesis: consciousness is NOT possible without certain chemical processes (materialism). In the animal world these take place within the brain. In other organisms such as bacteria the chemical processes take place within the cell itself, in its equivalent of a brain.
Boy, are you confused. Show me the bacterial equivalent of a brain! There isn't one neuron in sight. I've explained your afterlife point above. And I've explained my use of 'brain thinking' is shorthand so I don't have to type so much in repeated explainations, and you know it.
dhw: And here’s another hypothesis: if something learns by experience, alters its own DNA in order to cope with changing conditions, looks intelligent, and acts intelligently, then maybe it is intelligent.
And we know it can be programmed to look intelligent.
Immunity: detecting dangerous bacteria
dhw: Let’s clarify: the brain supplies information to the soul (so the soul uses the information), and then the soul uses the brain to make the body give physical expression to the thought, e.g. by action in the form of movement, speech etc. How does that enable the brain to “functionally THINK”?
DAVID: The brain does not supply information to the soul. […]
I always thought the senses provided the brain with information, which for a dualist was then passed on to the soul. So apparently nothing we see, hear, taste, touch or smell has the slightest influence on the thoughts we think.
dhw: If the soul/consciousness can function without a brain (as in the afterlife you believe in), it means that consciousness does not need a brain, and yet you continue to insist than an organism without a brain can’t be conscious.
DAVID: NDE's show consciousness functions without a brain, but the opposite is not true. A brain doesn't function without consciousness. Consciousness can only be received by brains for function and use.
We shan’t go into the brain functions that take place without our being aware of them. The salient point here is that you keep claiming that consciousness DOES function without a brain and in the next breath you say it cannot exist without a brain, as in your next comment!
DAVID: In my view consciousness can only exist in brains which are the only living matter that can receive it.
dhw: “Consciousness can only exist in brains”, and yet “consciousness can function without a functional brain” (and in the afterlife, without a brain of any kind). But you are not confused. […] how about this for a hypothesis: consciousness is NOT possible without certain chemical processes (materialism). In the animal world these take place within the brain. In other organisms such as bacteria the chemical processes take place within the cell itself, in its equivalent of a brain.
DAVID: Boy, are you confused. Show me the bacterial equivalent of a brain! There isn't one neuron in sight. I've explained your afterlife point above. And I've explained my use of 'brain thinking' is shorthand so I don't have to type so much in repeated explainations, and you know it.
Show me the “soul”. And what neurons would you expect to find in a soul? If your dualistic hypothesis is correct, the soul/consciousness is immaterial, and therefore does not need a brain. So according to you, consciousness can exist without a brain, but it cannot exist without a brain. However, for your information Albrecht-Buehler (who does not subscribe to intelligent design, and therefore presumably does not believe in a soul), offers the following
G. Albrecht-Buehler’s Cell Intelligence Website
www.basic.northwestern.edu/g-buehler/cellint0.htm
"Cell movement is not random.. The cortex consists of autonomous domains ('microplasts') whose movement is controlled by a control center (centrosome). Microtubules mediate between the control center and the autonomous domains."
Of course you do not take his work any more seriously than that of experts like McClintock, Margulis or Shapiro. Here’s a great quote from McClintock:
“Every component of the organism is as much of an organism as every other part.”
dhw: And here's another hypothesis: if something learns by experience, alters its own DNA in order to cope with changing conditions, looks intelligent, and acts intelligently, then maybe it is intelligent.
DAVID: And we know it can be programmed to look intelligent.
Please tell us what organisms we "know" your God has programmed to look intelligent without their being intelligent.
Immunity: detecting dangerous bacteria
by David Turell , Monday, November 27, 2017, 15:24 (2340 days ago) @ dhw
DAVID: The brain does not supply information to the soul. […]dhw: I always thought the senses provided the brain with information, which for a dualist was then passed on to the soul. So apparently nothing we see, hear, taste, touch or smell has the slightest influence on the thoughts we think.
The senses do supply sensory information. I was unclear and referring to knowledge and memory within the soul.
DAVID: Boy, are you confused. Show me the bacterial equivalent of a brain! There isn't one neuron in sight. I've explained your afterlife point above. And I've explained my use of 'brain thinking' is shorthand so I don't have to type so much in repeated explainations, and you know it.dhw: Show me the “soul”. And what neurons would you expect to find in a soul? If your dualistic hypothesis is correct, the soul/consciousness is immaterial, and therefore does not need a brain. So according to you, consciousness can exist without a brain, but it cannot exist without a brain.
That is what NDE's show! See my post today on Egner and dualism.
dhw: However, for your information Albrecht-Buehler (who does not subscribe to intelligent design, and therefore presumably does not believe in a soul), offers the following
G. Albrecht-Buehler’s Cell Intelligence Website
www.basic.northwestern.edu/g-buehler/cellint0.htm"Cell movement is not random.. The cortex consists of autonomous domains ('microplasts') whose movement is controlled by a control center (centrosome). Microtubules mediate between the control center and the autonomous domains."
I accept his description and this can be seen as automatic programming.
dhw: Of course you do not take his work any more seriously than that of experts like McClintock, Margulis or Shapiro. Here’s a great quote from McClintock:
“Every component of the organism is as much of an organism as every other part.”
I take them all seriously, but reinterpret their conclusions.
dhw: And here's another hypothesis: if something learns by experience, alters its own DNA in order to cope with changing conditions, looks intelligent, and acts intelligently, then maybe it is intelligent.DAVID: And we know it can be programmed to look intelligent.
dhw: Please tell us what organisms we "know" your God has programmed to look intelligent without their being intelligent.
As part of my body my kidneys act intelligently. Why can't bacteria be seen that way?
Immunity: detecting dangerous bacteria
DAVID: Boy, are you confused. Show me the bacterial equivalent of a brain! There isn't one neuron in sight. I've explained your afterlife point above. And I've explained my use of 'brain thinking' is shorthand so I don't have to type so much in repeated explainations, and you know it.
dhw: Show me the “soul”. And what neurons would you expect to find in a soul? If your dualistic hypothesis is correct, the soul/consciousness is immaterial, and therefore does not need a brain. So according to you, consciousness can exist without a brain, but it cannot exist without a brain.
DAVID: That is what NDE's show! See my post today on Egner and dualism.
The Egnor article is extremely interesting, but you have missed the point. I am not attacking dualism. (I am not defending it either.) When you say: “Show me the bacterial equivalent of a brain. There isn’t one neuron in sight”, you are clearly referring to the material presence of brain and neuron. If you believe intelligence/the “soul” to be immaterial and independent of the brain, then it cannot be shown as a material presence, and it is therefore a contradiction to say an organism can’t be intelligent if you can't see a brain.
dhw: However, for your information Albrecht-Buehler (who does not subscribe to intelligent design, and therefore presumably does not believe in a soul), offers the following
G. Albrecht-Buehler’s Cell Intelligence Website
www.basic.northwestern.edu/g-buehler/cellint0.htm
"Cell movement is not random.. The cortex consists of autonomous domains ('microplasts') whose movement is controlled by a control center (centrosome). Microtubules mediate between the control center and the autonomous domains."
DAVID: I accept his description and this can be seen as automatic programming.
dhw: Of course you do not take his work any more seriously than that of experts like McClintock, Margulis or Shapiro. Here’s a great quote from McClintock:
“Every component of the organism is as much of an organism as every other part.”
DAVID: I take them all seriously, but reinterpret their conclusions.
Albrecht-Buehler’s book is called Cell Intelligence. He and the others, who have spent a lifetime studying the evidence, have concluded that cells are intelligent. “Reinterpret their conclusions” is a fluffy way of saying you think you know more than they do, and their conclusions are wrong. You are of course fully entitled to your opinion, but a little grain of open-mindedness would be welcome.
dhw: And here's another hypothesis: if something learns by experience, alters its own DNA in order to cope with changing conditions, looks intelligent, and acts intelligently, then maybe it is intelligent.
DAVID: And we know it can be programmed to look intelligent.
dhw: Please tell us what organisms we "know" your God has programmed to look intelligent without their being intelligent.
DAVID: As part of my body my kidneys act intelligently. Why can't bacteria be seen that way?
Here you have missed the point of the McClintock quote above. And you yourself wrote that immune cells learn by experience and change themselves to fit their discoveries. That is a hallmark of autonomous intelligence.
Immunity: detecting dangerous bacteria
by David Turell , Tuesday, November 28, 2017, 15:19 (2339 days ago) @ dhw
DAVID: That is what NDE's show! See my post today on Egner and dualism.
dhw: The Egnor article is extremely interesting, but you have missed the point. I am not attacking dualism. (I am not defending it either.) When you say: “Show me the bacterial equivalent of a brain. There isn’t one neuron in sight”, you are clearly referring to the material presence of brain and neuron. If you believe intelligence/the “soul” to be immaterial and independent of the brain, then it cannot be shown as a material presence, and it is therefore a contradiction to say an organism can’t be intelligent if you can't see a brain.
You keep skipping over the point that consciousness/soul is received by the brain to be used by the owner of that brain to create the immaterial thoughts and concepts.
dhw: However, for your information Albrecht-Buehler (who does not subscribe to intelligent design, and therefore presumably does not believe in a soul), offers the following
G. Albrecht-Buehler’s Cell Intelligence Website
www.basic.northwestern.edu/g-buehler/cellint0.htm
"Cell movement is not random.. The cortex consists of autonomous domains ('microplasts') whose movement is controlled by a control center (centrosome). Microtubules mediate between the control center and the autonomous domains."
DAVID: I accept his description and this can be seen as automatic programming.
dhw: Of course you do not take his work any more seriously than that of experts like McClintock, Margulis or Shapiro. Here’s a great quote from McClintock:
“Every component of the organism is as much of an organism as every other part.”DAVID: I take them all seriously, but reinterpret their conclusions.
dhw: Albrecht-Buehler’s book is called Cell Intelligence. He and the others, who have spent a lifetime studying the evidence, have concluded that cells are intelligent. “Reinterpret their conclusions” is a fluffy way of saying you think you know more than they do, and their conclusions are wrong. You are of course fully entitled to your opinion, but a little grain of open-mindedness would be welcome.
We have covered all of this before. From the outside no one can determine whether the cell responds automatically under intelligent instructions or is actually intelligent. Believing in God as I do, I am on the side of intelligent instructions.
DAVID: As part of my body my kidneys act intelligently. Why can't bacteria be seen that way?
dhw: Here you have missed the point of the McClintock quote above. And you yourself wrote that immune cells learn by experience and change themselves to fit their discoveries. That is a hallmark of autonomous intelligence.
Not missed at all. Immune cells can be programmed to respond in the way they do in my body, just like kidney cells.
Immunity: releasing killer proteins
by David Turell , Tuesday, November 28, 2017, 18:41 (2339 days ago) @ David Turell
We have several levels of immunity, innate, from colostrum, and learned, and aat some levels requiring injections of killer proteins:
https://medicalxpress.com/news/2017-11-cells-il-decades.html
" Researchers at Boston Children's Hospital have identified, for the first time, the molecule that enables immune cells to release interleukin-1 (IL-1), a key part of our innate immune response to infections. Findings were published online today by the journal Immunity.
"IL-1, first described in 1984, is the original, highly potent member of a large family of cellular signaling molecules called cytokines, which regulate immune responses and inflammation.
***
"Most proteins have a secretion signal that causes them to leave the cell," says Jonathan Kagan, PhD, an immunology researcher in Boston Children's Hospital's Division of Gastroenterology and senior author of the new study. "IL-1 doesn't have that signal.
***
"Recent work elsewhere at Boston Children's, for example, demonstrated that a protein called gasdermin D punches holes in the membranes of infected cells by forming pores. This releases IL-1 and other cytokines—but it also kills the cell, through an inflammatory cell-death program called pyroptosis.
"In the new study, Kagan and first author Charles Evavold showed that gasdermin D also enables the release of IL-1 from living immune cells.
***
"Last year, Kagan, Ivan Zanoni, PhD, and colleagues reported in Science that IL-1 can be released from living dendritic cells, immune cells that present antigens to T cells. They showed that dendritic cells can enter a hyperactivated state in which they secrete IL-1, boosting their ability to rally memory T cells. But the question of how IL-1 gets released remained unanswered.
"The new study involved hyperactivated macrophages, immune cells that engulf and ingest pathogens. "We found, in hyperactivated cells, that gasdermin forms enough pores to let IL-1 pass through, but not enough to kill the cell," says Kagan.
"The immune response is like a yin-yang: If it's too weak, you're susceptible to infections; if it's too strong, the system can tip toward autoimmune disease and, in the face of a serious infection, sepsis.
"Gasdermin D inhibition is under study as a way of curbing inflammation-related diseases and sepsis. But Kagan's team is looking at the flip side, exploring gasdermin D as a target for stimulating IL-1 release from living, working cells to make vaccines more potent and long-lasting."
Comment: Note that this research is looking at killer proteins which are produced by cells that are protected from its effects. Only design can produce this. Chance evolution cannot form a cell that supplies lethal poison without supplying a protection for that cell at the same time. That is two coordinated steps (mutations) simultaneously.
Immunity: detecting dangerous bacteria
dhw: When you say: “Show me the bacterial equivalent of a brain. There isn’t one neuron in sight”, you are clearly referring to the material presence of brain and neuron. If you believe intelligence/the “soul” to be immaterial and independent of the brain, then it cannot be shown as a material presence, and it is therefore a contradiction to say an organism can’t be intelligent if you can't see a brain.
DAVID: You keep skipping over the point that consciousness/soul is received by the brain to be used by the owner of that brain to create the immaterial thoughts and concepts.
Nothing skipped. According to you, the owner of the brain IS the soul, since that is what survives the death of the brain! So now you have the thoughts of the soul being received by the brain so that the soul can do its thinking! Once again: it is consciousness/the soul that creates immaterial thoughts and concepts, and consciousness is not visible! Therefore it is a non sequitur to say that if you can’t see the brain of a bacterium, the bacterium can’t be conscious.
dhw: Albrecht-Buehler’s book is called Cell Intelligence. He and the others, who have spent a lifetime studying the evidence, have concluded that cells are intelligent. “Reinterpret their conclusions” is a fluffy way of saying you think you know more than they do, and their conclusions are wrong. You are of course fully entitled to your opinion, but a little grain of open-mindedness would be welcome.
DAVID: We have covered all of this before. From the outside no one can determine whether the cell responds automatically under intelligent instructions or is actually intelligent. Believing in God as I do, I am on the side of intelligent instructions.
If one can’t tell the difference, then one should acknowledge that both versions are possible. It has nothing whatsoever to do with belief in God. It is just as possible that your God created an autonomous intelligence as it is that 3.8 billion years ago he created programmes for every single action of every single cell for the rest of time, barring his dabbles.
DAVID: As part of my body my kidneys act intelligently. Why can't bacteria be seen that way?
dhw: Here you have missed the point of the McClintock quote above. And you yourself wrote that immune cells learn by experience and change themselves to fit their discoveries. That is a hallmark of autonomous intelligence.
DAVID: Not missed at all. Immune cells can be programmed to respond in the way they do in my body, just like kidney cells.
At least “can be” is an improvement on “are”. And since when was learning by experience an automatic process?
Immunity: detecting dangerous bacteria
by David Turell , Wednesday, November 29, 2017, 19:59 (2338 days ago) @ dhw
dhw: Once again: it is consciousness/the soul that creates immaterial thoughts and concepts, and consciousness is not visible!
By using the receiver brain which is visible.
dhw: Therefore it is a non sequitur to say that if you can’t see the brain of a bacterium, the bacterium can’t be conscious.
But the brain is visable and used by the soul/consciousness to create thought through its resident consciousness.
DAVID: We have covered all of this before. From the outside no one can determine whether the cell responds automatically under intelligent instructions or is actually intelligent. Believing in God as I do, I am on the side of intelligent instructions.dhw: If one can’t tell the difference, then one should acknowledge that both versions are possible. It has nothing whatsoever to do with belief in God. It is just as possible that your God created an autonomous intelligence as it is that 3.8 billion years ago he created programmes for every single action of every single cell for the rest of time, barring his dabbles.
You forget that I believe in God and have the right to make a choice of interpretation. Both are possible. One is true.
DAVID: As part of my body my kidneys act intelligently. Why can't bacteria be seen that way?
dhw: Here you have missed the point of the McClintock quote above. And you yourself wrote that immune cells learn by experience and change themselves to fit their discoveries. That is a hallmark of autonomous intelligence.
DAVID: Not missed at all. Immune cells can be programmed to respond in the way they do in my body, just like kidney cells.
dhw: At least “can be” is an improvement on “are”. And since when was learning by experience an automatic process?
Shown in the cells of the immune system of a baby !
Immunity: detecting dangerous bacteria
I have changed the sequence here, to make for a more coherent line of argument.
dhw: […] since when was learning by experience an automatic process?
DAVID: Shown in the cells of the immune system of a baby!
The argument is that the cells are intelligent/conscious. It makes no difference whether they are in a baby or in a centenarian.
dhw: Once again: it is consciousness/the soul that creates immaterial thoughts and concepts, and consciousness is not visible!
DAVID: By using the receiver brain which is visible.
The bacterium’s microplasts, centrosome and microtubules are also visible, which Albrecht-Buehler claims make up the equivalent of the brain, and which you accepted as a correct analysis but again dismissed as automatic. You might as well say that the receiver brain is automatic, and we are automatons too. After all, according to you, one cannot tell the difference between autonomous and automatic. (I would disagree in both cases.)
DAVID: We have covered all of this before. From the outside no one can determine whether the cell responds automatically under intelligent instructions or is actually intelligent. Believing in God as I do, I am on the side of intelligent instructions.
dhw: If one can’t tell the difference, then one should acknowledge that both versions are possible. It has nothing whatsoever to do with belief in God. It is just as possible that your God created an autonomous intelligence as it is that 3.8 billion years ago he created programmes for every single action of every single cell for the rest of time, barring his dabbles.
DAVID: You forget that I believe in God and have the right to make a choice of interpretation. Both are possible. One is true.
How could I forget that you believe in God? Everybody has the right to make a choice of interpretation, whether they believe in God or not, but as I pointed out above, belief in God has nothing whatsoever to do with this particular choice. However, “both are possible” was what I was hoping to hear, and we can leave it at that until the next time you dismiss the whole idea of cellular intelligence.
Immunity: detecting dangerous bacteria
by David Turell , Thursday, November 30, 2017, 14:26 (2338 days ago) @ dhw
I have changed the sequence here, to make for a more coherent line of argument.
dhw: […] since when was learning by experience an automatic process?
DAVID: Shown in the cells of the immune system of a baby!
The argument is that the cells are intelligent/conscious. It makes no difference whether they are in a baby or in a centenarian.
dhw: Once again: it is consciousness/the soul that creates immaterial thoughts and concepts, and consciousness is not visible!
DAVID: By using the receiver brain which is visible.
The bacterium’s microplasts, centrosome and microtubules are also visible, which Albrecht-Buehler claims make up the equivalent of the brain, and which you accepted as a correct analysis but again dismissed as automatic. You might as well say that the receiver brain is automatic, and we are automatons too. After all, according to you, one cannot tell the difference between autonomous and automatic. (I would disagree in both cases.)
DAVID: We have covered all of this before. From the outside no one can determine whether the cell responds automatically under intelligent instructions or is actually intelligent. Believing in God as I do, I am on the side of intelligent instructions.
dhw: If one can’t tell the difference, then one should acknowledge that both versions are possible. It has nothing whatsoever to do with belief in God. It is just as possible that your God created an autonomous intelligence as it is that 3.8 billion years ago he created programmes for every single action of every single cell for the rest of time, barring his dabbles.
DAVID: You forget that I believe in God and have the right to make a choice of interpretation. Both are possible. One is true.
How could I forget that you believe in God? Everybody has the right to make a choice of interpretation, whether they believe in God or not, but as I pointed out above, belief in God has nothing whatsoever to do with this particular choice. However, “both are possible” was what I was hoping to hear, and we can leave it at that until the next time you dismiss the whole idea of cellular intelligence.
Of course cells act intelligently. We disagree on the primary mechanism.
Immunity: detecting dangerous bacteria
DAVID: You forget that I believe in God and have the right to make a choice of interpretation. Both are possible. One is true.
dhw: How could I forget that you believe in God? Everybody has the right to make a choice of interpretation, whether they believe in God or not, but as I pointed out above, belief in God has nothing whatsoever to do with this particular choice. However, “both are possible” was what I was hoping to hear, and we can leave it at that until the next time you dismiss the whole idea of cellular intelligence.
DAVID: Of course cells act intelligently. We disagree on the primary mechanism.
Before we sign off on this, and in anticipation of the next disagreement, let’s clarify what we mean by the primary mechanism. Mine is autonomous intelligence (possibly designed by your God). Yours is a hidden, 3.8-billion-year-old computer programme containing instructions for every eventuality for the rest of time, barring those in which your God intervenes personally. Is that correct?
Immunity: detecting dangerous bacteria
by David Turell , Friday, December 01, 2017, 14:46 (2337 days ago) @ dhw
dhw: Before we sign off on this, and in anticipation of the next disagreement, let’s clarify what we mean by the primary mechanism. Mine is autonomous intelligence (possibly designed by your God). Yours is a hidden, 3.8-billion-year-old computer programme containing instructions for every eventuality for the rest of time, barring those in which your God intervenes personally. Is that correct?
Generally correct, but in my view we will eventually find by research that God's programming will be found in deeper layers of the genome and its function. As I noted in my first book increasing discovery of increasing complexity in biology requires an acceptance of God.
Immunity: detecting dangerous bacteria
dhw: Before we sign off on this, and in anticipation of the next disagreement, let’s clarify what we mean by the primary mechanism. Mine is autonomous intelligence (possibly designed by your God). Yours is a hidden, 3.8-billion-year-old computer programme containing instructions for every eventuality for the rest of time, barring those in which your God intervenes personally. Is that correct?
DAVID: Generally correct, but in my view we will eventually find by research that God's programming will be found in deeper layers of the genome and its function. As I noted in my first book increasing discovery of increasing complexity in biology requires an acceptance of God.
Understood. If the source of cellular intelligence were found in deeper layers of the “genome and its function”, biological complexity would still be such that a theist would claim it required an acceptance of God. And he may or may not be right.
Immunity: detecting dangerous bacteria
by David Turell , Saturday, December 02, 2017, 14:24 (2336 days ago) @ dhw
dhw: Before we sign off on this, and in anticipation of the next disagreement, let’s clarify what we mean by the primary mechanism. Mine is autonomous intelligence (possibly designed by your God). Yours is a hidden, 3.8-billion-year-old computer programme containing instructions for every eventuality for the rest of time, barring those in which your God intervenes personally. Is that correct?
DAVID: Generally correct, but in my view we will eventually find by research that God's programming will be found in deeper layers of the genome and its function. As I noted in my first book increasing discovery of increasing complexity in biology requires an acceptance of God.
dhw: Understood. If the source of cellular intelligence were found in deeper layers of the “genome and its function”, biological complexity would still be such that a theist would claim it required an acceptance of God. And he may or may not be right.
Is there any level of complexity in the biology of life that would cause you to change your opinion?
Immunity: detecting dangerous bacteria
dhw: Before we sign off on this, and in anticipation of the next disagreement, let’s clarify what we mean by the primary mechanism. Mine is autonomous intelligence (possibly designed by your God). Yours is a hidden, 3.8-billion-year-old computer programme containing instructions for every eventuality for the rest of time, barring those in which your God intervenes personally. Is that correct?
DAVID: Generally correct, but in my view we will eventually find by research that God's programming will be found in deeper layers of the genome and its function. As I noted in my first book increasing discovery of increasing complexity in biology requires an acceptance of God.
dhw: Understood. If the source of cellular intelligence were found in deeper layers of the “genome and its function”, biological complexity would still be such that a theist would claim it required an acceptance of God. And he may or may not be right.
DAVID: Is there any level of complexity in the biology of life that would cause you to change your opinion?
The level of complexity is such that I doubt if anything could change my opinion that one can’t dismiss the case for design and hence for a designer. However, the idea that a seemingly infinite universe – filled with galaxies that endlessly come and go for no apparent reason – contains and is contained by a single conscious mind that has no source and of whose actual presence there is no sign, demands such a leap of imagination and blind faith that I doubt if anything could change my opinion that one can’t dismiss the case for chance or for atheistic panpsychism.
Immunity: detecting dangerous bacteria
by David Turell , Sunday, December 03, 2017, 15:35 (2334 days ago) @ dhw
dhw: Before we sign off on this, and in anticipation of the next disagreement, let’s clarify what we mean by the primary mechanism. Mine is autonomous intelligence (possibly designed by your God). Yours is a hidden, 3.8-billion-year-old computer programme containing instructions for every eventuality for the rest of time, barring those in which your God intervenes personally. Is that correct?
DAVID: Generally correct, but in my view we will eventually find by research that God's programming will be found in deeper layers of the genome and its function. As I noted in my first book increasing discovery of increasing complexity in biology requires an acceptance of God.
dhw: Understood. If the source of cellular intelligence were found in deeper layers of the “genome and its function”, biological complexity would still be such that a theist would claim it required an acceptance of God. And he may or may not be right.
DAVID: Is there any level of complexity in the biology of life that would cause you to change your opinion?
dhw: The level of complexity is such that I doubt if anything could change my opinion that one can’t dismiss the case for design and hence for a designer. However, the idea that a seemingly infinite universe – filled with galaxies that endlessly come and go for no apparent reason – contains and is contained by a single conscious mind that has no source and of whose actual presence there is no sign, demands such a leap of imagination and blind faith that I doubt if anything could change my opinion that one can’t dismiss the case for chance or for atheistic panpsychism.
A fair assessment of your position, but it doesn't explain why we exist.
Immunity: detecting dangerous bacteria
DAVID: Is there any level of complexity in the biology of life that would cause you to change your opinion?
dhw: The level of complexity is such that I doubt if anything could change my opinion that one can’t dismiss the case for design and hence for a designer. However, the idea that a seemingly infinite universe – filled with galaxies that endlessly come and go for no apparent reason – contains and is contained by a single conscious mind that has no source and of whose actual presence there is no sign, demands such a leap of imagination and blind faith that I doubt if anything could change my opinion that one can’t dismiss the case for chance or for atheistic panpsychism.
DAVID: A fair assessment of your position, but it doesn't explain why we exist.
All three hypotheses explain why we exist, but you need blind faith to believe in any of them. Or do you mean for what purpose? If God exists, you will have to try to read his mind (which both of us have done). If he does not exist, I’d say our purpose is whatever we make it.
Immunity: detecting dangerous bacteria
by David Turell , Monday, December 04, 2017, 15:05 (2334 days ago) @ dhw
DAVID: Is there any level of complexity in the biology of life that would cause you to change your opinion?
dhw: The level of complexity is such that I doubt if anything could change my opinion that one can’t dismiss the case for design and hence for a designer. However, the idea that a seemingly infinite universe – filled with galaxies that endlessly come and go for no apparent reason – contains and is contained by a single conscious mind that has no source and of whose actual presence there is no sign, demands such a leap of imagination and blind faith that I doubt if anything could change my opinion that one can’t dismiss the case for chance or for atheistic panpsychism.
DAVID: A fair assessment of your position, but it doesn't explain why we exist.
dhw: All three hypotheses explain why we exist, but you need blind faith to believe in any of them. Or do you mean for what purpose? If God exists, you will have to try to read his mind (which both of us have done). If he does not exist, I’d say our purpose is whatever we make it.
Yes, I see purpose in the fact that we exist. WE are a very improbable result of blind chance. As for panpsychism, it is an obvious nod to a universe that appears to have consciousness. And the question raised is where did that come from?
Immunity: detecting dangerous bacteria
DAVID: Is there any level of complexity in the biology of life that would cause you to change your opinion?
dhw: The level of complexity is such that I doubt if anything could change my opinion that one can’t dismiss the case for design and hence for a designer. However, the idea that a seemingly infinite universe – filled with galaxies that endlessly come and go for no apparent reason – contains and is contained by a single conscious mind that has no source and of whose actual presence there is no sign, demands such a leap of imagination and blind faith that I doubt if anything could change my opinion that one can’t dismiss the case for chance or for atheistic panpsychism.
DAVID: A fair assessment of your position, but it doesn't explain why we exist.
dhw: All three hypotheses explain why we exist, but you need blind faith to believe in any of them. Or do you mean for what purpose? If God exists, you will have to try to read his mind (which both of us have done). If he does not exist, I’d say our purpose is whatever we make it.
DAVID: Yes, I see purpose in the fact that we exist. WE are a very improbable result of blind chance. As for panpsychism, it is an obvious nod to a universe that appears to have consciousness. And the question raised is where did that come from?
And since you believe in God, you try to read his mind to find his purpose. Camels, whales, ants and eagles are also an improbable result of blind chance. Atheistic panpsychism does indeed assume consciousness in the universe, as a rudimentary bottom-up and evolving form, while the God theory assumes consciousness as a supreme top-down know-it-all-from-the beginning form. The philosophical get-out answer to your question where it came from is “first cause”, which can be applied to either form.
Immunity: detecting dangerous bacteria
by David Turell , Tuesday, December 05, 2017, 14:39 (2333 days ago) @ dhw
edited by David Turell, Tuesday, December 05, 2017, 14:45
DAVID: A fair assessment of your position, but it doesn't explain why we exist.dhw: All three hypotheses explain why we exist, but you need blind faith to believe in any of them. Or do you mean for what purpose? If God exists, you will have to try to read his mind (which both of us have done). If he does not exist, I’d say our purpose is whatever we make it.
DAVID: Yes, I see purpose in the fact that we exist. WE are a very improbable result of blind chance. As for panpsychism, it is an obvious nod to a universe that appears to have consciousness. And the question raised is where did that come from?
dhw: And since you believe in God, you try to read his mind to find his purpose. Camels, whales, ants and eagles are also an improbable result of blind chance. Atheistic panpsychism does indeed assume consciousness in the universe, as a rudimentary bottom-up and evolving form, while the God theory assumes consciousness as a supreme top-down know-it-all-from-the beginning form. The philosophical get-out answer to your question where it came from is “first cause”, which can be applied to either form.
Which is a non-answer since first cause here is a blank slate. To me the presence of consciousness is critical, and demands an explanation, which cannot be found in the inorganic origin of the universe. Consciousness must require some sort of underlying organization since it must use a brain to appear, at least as we experience it.
Immunity: detecting dangerous bacteria
DAVID: Yes, I see purpose in the fact that we exist. WE are a very improbable result of blind chance. As for panpsychism, it is an obvious nod to a universe that appears to have consciousness. And the question raised is where did that come from?
dhw: And since you believe in God, you try to read his mind to find his purpose. Camels, whales, ants and eagles are also an improbable result of blind chance. Atheistic panpsychism does indeed assume consciousness in the universe, as a rudimentary bottom-up and evolving form, while the God theory assumes consciousness as a supreme top-down know-it-all-from-the beginning form. The philosophical get-out answer to your question where it came from is “first cause”, which can be applied to either form.
DAVID: Which is a non-answer since first cause here is a blank slate. To me the presence of consciousness is critical, and demands an explanation, which cannot be found in the inorganic origin of the universe. Consciousness must require some sort of underlying organization since it must use a brain to appear, at least as we experience it.
I agree that the presence of consciousness is critical, but I don’t know what you mean by “here is a blank slate”. As I see it, the first cause is either eternal energy and matter forever forming new combinations and eventually producing one that has consciousness (chance), or energy and matter have always contained a rudimentary form of consciousness which has evolved (bottom-up atheistic panpsychism), or energy has always had total consciousness of itself and of everything needed to create a universe and life (top-down God). No "blank slates" here. NONE of these (for me equally incredible) hypothetical first causes require a brain. Consciousness as WE experience it does require a brain, unless the dualists are right, and we only require it to provide us with information and give material form to our thoughts so long as we have a body. Consciousness as bacteria may experience it does not require a brain, but if materialists are right, it does require an equivalent.
Immunity: detecting dangerous bacteria
by David Turell , Wednesday, December 06, 2017, 15:15 (2332 days ago) @ dhw
DAVID: Which is a non-answer since first cause here is a blank slate. To me the presence of consciousness is critical, and demands an explanation, which cannot be found in the inorganic origin of the universe. Consciousness must require some sort of underlying organization since it must use a brain to appear, at least as we experience it.
dhw: I agree that the presence of consciousness is critical, but I don’t know what you mean by “here is a blank slate”. As I see it, the first cause is either eternal energy and matter forever forming new combinations and eventually producing one that has consciousness (chance), or energy and matter have always contained a rudimentary form of consciousness which has evolved (bottom-up atheistic panpsychism), or energy has always had total consciousness of itself and of everything needed to create a universe and life (top-down God). No "blank slates" here. NONE of these (for me equally incredible) hypothetical first causes require a brain. Consciousness as WE experience it does require a brain, unless the dualists are right, and we only require it to provide us with information and give material form to our thoughts so long as we have a body. Consciousness as bacteria may experience it does not require a brain, but if materialists are right, it does require an equivalent.
I'll stick wwith my view that the consciousness we experience is the only one that really exists other than God's. Of course I come from a position of seeing the requirement of a designer.
Immunity: detecting dangerous bacteria
DAVID: Which is a non-answer since first cause here is a blank slate. To me the presence of consciousness is critical, and demands an explanation, which cannot be found in the inorganic origin of the universe. Consciousness must require some sort of underlying organization since it must use a brain to appear, at least as we experience it.
dhw: I agree that the presence of consciousness is critical, but I don’t know what you mean by “here is a blank slate”. As I see it, the first cause is either eternal energy and matter forever forming new combinations and eventually producing one that has consciousness (chance), or energy and matter have always contained a rudimentary form of consciousness which has evolved (bottom-up atheistic panpsychism), or energy has always had total consciousness of itself and of everything needed to create a universe and life (top-down God). No "blank slates" here. NONE of these (for me equally incredible) hypothetical first causes require a brain. Consciousness as WE experience it does require a brain, unless the dualists are right, and we only require it to provide us with information and give material form to our thoughts so long as we have a body. Consciousness as bacteria may experience it does not require a brain, but if materialists are right, it does require an equivalent.
DAVID: I'll stick wwith my view that the consciousness we experience is the only one that really exists other than God's. Of course I come from a position of seeing the requirement of a designer.
It is perfectly possible to believe in a designer and to believe that other organisms are conscious, even if not to the same degree as we are.
Immunity: detecting dangerous bacteria
by David Turell , Thursday, December 07, 2017, 15:36 (2330 days ago) @ dhw
DAVID: Which is a non-answer since first cause here is a blank slate. To me the presence of consciousness is critical, and demands an explanation, which cannot be found in the inorganic origin of the universe. Consciousness must require some sort of underlying organization since it must use a brain to appear, at least as we experience it.
dhw: I agree that the presence of consciousness is critical, but I don’t know what you mean by “here is a blank slate”. As I see it, the first cause is either eternal energy and matter forever forming new combinations and eventually producing one that has consciousness (chance), or energy and matter have always contained a rudimentary form of consciousness which has evolved (bottom-up atheistic panpsychism), or energy has always had total consciousness of itself and of everything needed to create a universe and life (top-down God). No "blank slates" here. NONE of these (for me equally incredible) hypothetical first causes require a brain. Consciousness as WE experience it does require a brain, unless the dualists are right, and we only require it to provide us with information and give material form to our thoughts so long as we have a body. Consciousness as bacteria may experience it does not require a brain, but if materialists are right, it does require an equivalent.
DAVID: I'll stick wwith my view that the consciousness we experience is the only one that really exists other than God's. Of course I come from a position of seeing the requirement of a designer.
dhw: It is perfectly possible to believe in a designer and to believe that other organisms are conscious, even if not to the same degree as we are.
And I'll stick to the requirement for a present brain to have consciousness.
Immunity: babies handle new friendly bacteria
by David Turell , Saturday, January 13, 2018, 20:35 (2293 days ago) @ David Turell
Babies enter the world from a uterus that is not entirely clean, but the vagina has lots of bugs to encounter and bacteria have to colonize the baby's colon at the start. How it is handles is better understood:
https://www.the-scientist.com/?articles.view/articleNo/51317/title/How-Do-Infant-Immune...
"How our bodies learn to peacefully coexist with cells that are not our own is still unclear. Afterall, we spend most of our lives fighting off microbial invaders. “Once you’re born, you’re assaulted by billions of bacteria, so if the babies’ [immune systems] responded in the appropriate adult manner, they would just be auto-inflammatory bundles,” says Grace Aldrovandi, a professor of pediatrics at the University of California, Los Angeles. “The [question] then is: How does the immune system learn when to relax and when to respond?”
"Over the last few years, researchers have started to uncover how the immune system dampens its response to friendly microbes. For example, one 2013 study, published in Nature, revealed that a specific population of red blood cells possessing the CD71 protein—which is only plentiful during the first week or so of life—helped suppress the immune response in baby mice. In humans, these CD71+ cells, which the team found were abundant in the blood of umbilical cords (but scarce in adult blood), also appeared to have immunosuppressive properties.
“'When I went to medical school, I learned that babies had immature, wimpy immune systems,” Aldrovandi says. “We now realize that in fact they have very sophisticated immune systems, they’re just programmed in a different way.”
"Recent rodent studies have revealed that, in the adult mouse colon, bacterial metabolites such as butyrate, a product of fermentation, can accelerate the differentiation of progenitor cells into regulatory T cells, which help keep the immune system in check.
"While these studies indicate that products of some bacterial species may help induce tolerance in the adult immune system, Rodney Newberry, a professor of gastroenterology at Washington University School of Medicine, says that “the role for these tolerance-inducing species is not straightforward,” since your ability to become tolerant is better early in life when, paradoxically, these species are less abundant than in later childhood and adulthood.
***
"Newberry and his colleagues recently examined the early interactions between the immune system and certain harmless gut bacteria, such as Lachnospiraceae, in newborn mice. Their results, which they reported last month (December 17) in Science Immunology, revealed a time window during early life when the animals developed antigen-specific regulatory T cells specific to those microbes.
"This critical phase, which occurred between 10 and 20 days of life, was initiated by a drop in levels of epidermal growth factor (EGF), a protein abundant in breast milk during the pre-weaning period, in the GI tract of mice. During the first week or so, high concentrations of gut EGF in the mouse pups blocked the formation of goblet cell-associated antigen passages (GAPs)—channels that allow antigens from the gut lumen to enter the lamina propria, where the immune cells lie—preventing the development of regulatory T cells.
"Essentially, what appears to be happening is that the reduction of EGF during this time period allows bacterial antigens to pass through pups’ guts, enabling the immune system to learn to not to initiate an inflammatory response.
***
"The most surprising result in this paper, according to Gérard Eberl, an immunologist at the Instutit Pasteur in Paris who did not take part in this work, was that EGF levels determined when the animal needed to be exposed to microbes. Although levels of this protein in mothers’ milk were not directly examined in this study, Newberry says that his team is currently performing additional experiments to confirm that this process is under maternal control. If deemed true, this finding could be relevant to people as well, given that researchers have found that human breast milk is rich in EGF and tapers over time.
***
"The idea that there may be a window of optimal bacterial colonization supports the work of those who promote “vaginal seeding,” a procedure in which a newborn born via C-section is swabbed with a sterile gauze that was incubated in the mother’s vagina shortly before birth, to restore microbial communities to levels found in vaginally born babies. Last year, a group of researchers published a small pilot trial—with four mothers who volunteered to undergo the procedure—that reported promising results.
"Studies have found that exposure to the microbes in a mother’s vagina at birth might contribute to their infants’ health later in life."
Comment: Since these immune systems to protect the newborn are also active in the mother it raises the issue of how a chance Darwin style evolution can develop such systems in two separate individuals. It is a mechanism that must be developed intact in both to go with live birth, or babies would not have developed enough immunity to survive. It had to develop in the earliest placental animals. God at work!?
Immunity: lymphocytes use mitochondrial DNA
by David Turell , Monday, March 19, 2018, 14:11 (2229 days ago) @ David Turell
Human cells were studied:
https://www.the-scientist.com/?articles.view/articleNo/51900/title/Circulating-Mitochon...
"MOLECULAR BATTLEGROUND
Beyond acting as a genetic blueprint, DNA can play a direct role in the immune system. For instance, neutrophils cast webs of DNA and antibacterial proteins into the bloodstream to trap pathogens. When a team of Swedish researchers observed that B lymphocytes also appear to eject DNA, they decided to investigate further.
"IMMUNE ARTILLERY
The researchers isolated several types of lymphocytes—B cells, T cells, and natural killer cells—from healthy blood donors and leukemia patients. They exposed them to a variety of triggering molecules, such as ionomycin from Streptomyces conglobatus, together with a fluorescent DNA-binding substance in vitro. Only when exposed to a specific type of oligonucleotide that resembled pathogenic microbial DNA did the cells rapidly eject weblike, fluorescing strands of mitochondrial DNA (mtDNA). The lymphocytes remained intact and healthy.
"DANGER SIGNAL
To see whether the lymphocyte mtDNA elicited an immune response, the researchers tested it on another type of white blood cell, peripheral blood mononuclear cells (PBMCs). An immunosorbent assay revealed that mtDNA induced the PBMCs to release interferon type 1, which can trigger an immune response. “It’s like a new warning system,” says Anders Rosén, a cell biologist at Linköping University and senior author of the paper.
"UNTANGLING THE WEB
Dana Crawford, an immunologist at Albany Medical College who was not involved in the study, is surprised and puzzled by the finding. “It almost seems to be redundant that these cells are being exposed to a type of DNA, and . . . in response they’re releasing DNA that triggers a response,” he notes. The advantage of having a system set up in this way is yet to be understood.
Comment: These findings add to the complexity of the immune response. Since bacteria and viruses constantly or on the attack, these systems must have developed early in evolution in a complete defense. They must have been designed by God.
Immunity: lymphocytes use mitochondrial DNA
DAVID's comment: These findings add to the complexity of the immune response. Since bacteria and viruses constantly or on the attack, these systems must have developed early in evolution in a complete defense. They must have been designed by God.
Your God must have had lots of fun designing these killer bacteria and viruses, and then working out ways in which some organisms might or might not be able to survive them. And apparently all for the sake of the human brain.
Immunity: lymphocytes use mitochondrial DNA
by David Turell , Tuesday, March 20, 2018, 14:31 (2228 days ago) @ dhw
DAVID's comment: These findings add to the complexity of the immune response. Since bacteria and viruses constantly or on the attack, these systems must have developed early in evolution in a complete defense. They must have been designed by God.
dhw: Your God must have had lots of fun designing these killer bacteria and viruses, and then working out ways in which some organisms might or might not be able to survive them. And apparently all for the sake of the human brain.
Another non-religious thought is God created a such a strong driving force to produce life on Earth with bacteria that viruses also appeared and in each group nasty ones popped up, that then had to be controlled. Raises the issue of whether God is under total control or just well-intended? I have no way of knowing.
Immunity:controlling gut lymphocytes
by David Turell , Saturday, June 23, 2018, 19:02 (2132 days ago) @ David Turell
The mitochondria are changed in their lipid membranes composition which keeps the mitochondria in a less active state:
https://medicalxpress.com/news/2018-06-gut-immune-cells.html
"Every day, the human gut works on a fine-tuned balance that ensures the retention of essential nutrients while preventing infection by potential armful microbes. Contributing to this surveillance system is a specialised group of immune cells that are held back due to unknown reasons, although they have many characteristics of activated cells. Now, a new study led by Marc Veldhoen, group leader at Instituto de Medicina Molecular João Lobo Antunes (iMM; Portugal) shows how these cells are kept under control. The work published now in Science Immunology reveals that the mitochondria of these cells have a different composition that reduces their energy production capacity, keeping them in a controlled activated mode.
"The skin and intestines contain a special population of white blood cells called intraepithelial lymphocytes. It has been largely unknown how the activity of these cells is controlled in a state that is neither fully activated nor at rest. Using imaging and biochemical experiments, the research group led by Marc Veldhoen has now shown this is partly due to differences in the cells' mitochondria. These energy-producing structures are present insideall cells. "We hypothesised that these gut-resident white blood cells may use energy in a different way. It was surprising to see that the detection of mitochondria gave a very different picture than seen in other white blood cells, forming the basis of a new hypothesis that the mitochondria themselves are different in these cells," explains Marc Veldhoen.
"Using high magnification electron microscopy, the researchers observed that the mitochondria were present in abundance but seem to be different upon staining for light microscopy. Next, they studied the functionality of the mitochondria. "When we analysed these structures in detail, we found changes in the lipids that form a layer separating the mitochondria from the rest of the cell," says S?pela Konjar, joint first author of the study, adding that "these changes make the "batteries" work differently, as if they are in a "low energy mode."
"When the lipid landscape was purposely altered, the researchers confirmed a change in the activation potential of the cells. "Our results showed that lipids in the mitochondria of these cells could alter their metabolic state and change their activity. When the mitochondrial lipids could not be arranged similarly to those found in other white blood cells, the cells could not be properly activated when needed," explains Marc Veldhoen."
Comment: the mechanism as to how these mitochondria are modified is not yet known. A feedback loop must be present, which is the way life maitains controls within specific limits. For that simple reason feedback loops must have been present when life began and had to be designed to exist.
Immunity: modifying T cells
by David Turell , Friday, July 06, 2018, 22:34 (2119 days ago) @ David Turell
Special protein controls are discovered:
https://medicalxpress.com/news/2018-07-scientists-protein-complex-destiny-cells.html
"Like a mentor helping medical students choose between specialties, a protein complex helps shape the destiny of developing T cells, St. Jude Children's Research Hospital scientists have reported.
"The protein complex is mTORC1, which regulates cell growth and metabolism. St. Jude immunologists found mTORC1 acts in response to cues from in and around developing T cells and intersects with metabolic activity, to influence whether the cells become conventional or unconventional T cells. To their surprise, researchers found that disrupting mTORC1 led to metabolic changes that favored development of unconventional T cells at the expense of conventional T cells.
***
"T cells play a central role in the adaptive immune system, functioning like elite commando units trained to find and eliminate specific viruses and other threats. T cell development occurs in the thymus after immature (precursor) cells in the bone marrow travel there to mature and specialize. Their specialty is signaled partly by protein receptors on the cell surface known as T cell receptors (TCRs) or antigen receptors. T cells depend on the T cell receptors to recognize targets and respond to changing conditions.
"In humans, the vast majority of T cell receptors have an alpha (α) protein chain and a beta (β) chain. These are conventional T cells that circulate widely and reside in the spleen and lymph nodes. A smaller number of T cells carry receptors made from a gamma (γ) and a delta (δ) protein chain. They belong to the family of unconventional T cells that are found in the gut, skin and other barrier tissues.
"Working with mouse models and developing T cells in the laboratory, Chi and his colleagues showed that activation of mTORC1 revs up energy production through glycolysis and oxidation to fuel anabolic metabolism and promote development of αβ T cells.
"When investigators disabled mTORC1, metabolism was disrupted, which was associated with a reduction in the αβ T cells and an increase in γδ T cells.Deleting a key component of mTORC1, a protein called RAPTOR, disabled mTORC1 and altered the metabolic balance in developing T cells. The change reduced anabolic metabolism but increased levels of toxic molecules called reactive oxygen species (ROS) and upregulated activity along a molecular pathway that promotes cell growth.
"The change enhanced development of γδ T cells in the thymus and hindered development of αβ T cells.
"Researchers also reported expression of signature genes associated with γδ T cells was enhanced in mice when RAPTOR was deleted from the mTORC1 complex.
"'This research establishes mTORC1-driven metabolic signaling as a decisive factor in determining the fate of developing T cells and suggests metabolic processes are a fundamental mechanism that connects external signals with internal processes to guide the fate of immune cells," Chi said."
Comment: The immune system is so complex and so precise it must have been designed.
Immunity: modifying T cells
by Balance_Maintained , U.S.A., Saturday, July 07, 2018, 05:54 (2119 days ago) @ David Turell
Special protein controls are discovered:
https://medicalxpress.com/news/2018-07-scientists-protein-complex-destiny-cells.html
"Like a mentor helping medical students choose between specialties, a protein complex helps shape the destiny of developing T cells, St. Jude Children's Research Hospital scientists have reported.
"The protein complex is mTORC1, which regulates cell growth and metabolism. St. Jude immunologists found mTORC1 acts in response to cues from in and around developing T cells and intersects with metabolic activity, to influence whether the cells become conventional or unconventional T cells. To their surprise, researchers found that disrupting mTORC1 led to metabolic changes that favored development of unconventional T cells at the expense of conventional T cells.
***
"T cells play a central role in the adaptive immune system, functioning like elite commando units trained to find and eliminate specific viruses and other threats. T cell development occurs in the thymus after immature (precursor) cells in the bone marrow travel there to mature and specialize. Their specialty is signaled partly by protein receptors on the cell surface known as T cell receptors (TCRs) or antigen receptors. T cells depend on the T cell receptors to recognize targets and respond to changing conditions.
"In humans, the vast majority of T cell receptors have an alpha (α) protein chain and a beta (β) chain. These are conventional T cells that circulate widely and reside in the spleen and lymph nodes. A smaller number of T cells carry receptors made from a gamma (γ) and a delta (δ) protein chain. They belong to the family of unconventional T cells that are found in the gut, skin and other barrier tissues.
"Working with mouse models and developing T cells in the laboratory, Chi and his colleagues showed that activation of mTORC1 revs up energy production through glycolysis and oxidation to fuel anabolic metabolism and promote development of αβ T cells.
"When investigators disabled mTORC1, metabolism was disrupted, which was associated with a reduction in the αβ T cells and an increase in γδ T cells.Deleting a key component of mTORC1, a protein called RAPTOR, disabled mTORC1 and altered the metabolic balance in developing T cells. The change reduced anabolic metabolism but increased levels of toxic molecules called reactive oxygen species (ROS) and upregulated activity along a molecular pathway that promotes cell growth.
"The change enhanced development of γδ T cells in the thymus and hindered development of αβ T cells.
"Researchers also reported expression of signature genes associated with γδ T cells was enhanced in mice when RAPTOR was deleted from the mTORC1 complex.
"'This research establishes mTORC1-driven metabolic signaling as a decisive factor in determining the fate of developing T cells and suggests metabolic processes are a fundamental mechanism that connects external signals with internal processes to guide the fate of immune cells," Chi said."
Comment: The immune system is so complex and so precise it must have been designed.
I wonder how the position within the body of a virus or bacteria needs to attack is transmitted to all of the T cells and white blood cells when they need to converge and attack. I also wonder how they find and identify targets. How do they differentiate between hostile and benign? How do they know how to attack a particular problem? How is that information spread throughout the system? It implies an information pathway that directly increase the information level of the system on a system wide level. Where is this information stored? Could we measure the increase in information if we knew?
--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.
Immunity: modifying T cells
by David Turell , Saturday, July 07, 2018, 19:05 (2118 days ago) @ Balance_Maintained
Special protein controls are discovered:
https://medicalxpress.com/news/2018-07-scientists-protein-complex-destiny-cells.html
"'This research establishes mTORC1-driven metabolic signaling as a decisive factor in determining the fate of developing T cells and suggests metabolic processes are a fundamental mechanism that connects external signals with internal processes to guide the fate of immune cells," Chi said."
Comment: The immune system is so complex and so precise it must have been designed.
Tony: I wonder how the position within the body of a virus or bacteria needs to attack is transmitted to all of the T cells and white blood cells when they need to converge and attack. I also wonder how they find and identify targets. How do they differentiate between hostile and benign? How do they know how to attack a particular problem? How is that information spread throughout the system? It implies an information pathway that directly increase the information level of the system on a system wide level. Where is this information stored? Could we measure the increase in information if we knew?
Signals are mediated by blood carried proteins and nerve signals. We start life with generalized antibodies like interferon, the colostrum antibodies from Mom if nursed, but must build a library of specific ones throughout life, which is a form of adding useful information. The DNA in thymus cells which provides the newly T cells is the storage point of the info.
Immunity: rapidly responding T cells
by David Turell , Monday, July 16, 2018, 21:26 (2109 days ago) @ David Turell
Surface receptors on the T cell surfaces are widely dispersed to quickly pick up signals from foreign antigens:
https://www.sciencedaily.com/releases/2018/07/180716114610.htm
"Without T cells, we could not survive. They are a key component of our immune system and have highly sensitive receptors on their surface that can detect pathogens. The exact way that these receptors are distributed over the surface of the T cells is still not completely understood, but the analyses by TU Wien show that previous ideas are no longer tenable.
"It was previously thought that the T cell would concentrate the receptors at certain points in order to achieve the highest possible sensitivity. As a current publication by the biophysics research group at TU Wien shows, T cells are actually programmed to react as quickly as possible, and therefore their receptors are arranged at random.
***
"'A T cell is a highly specific molecule detector," explains Prof. Gerhard Schütz, head of the biophysics research group at the Institute of Applied Physics at TU Wien. "Each T cell only reacts to a very specific molecule, and so we need many different T cells in our bodies." Each T cell carries many thousands of copies of the same receptor on its surface.
"To trigger an immune reaction, the T cell still needs an important partner -- the so-called antigen-presenting cell. The surfaces of these cells present many different molecules with the aid of special carrier proteins. Some of these molecules originate from endogenous structures and are harmless, but characteristic antigens of harmful intruders are also transported by the body on these antigen-presenting cells.
"If the T cell comes into contact with one of these antigen-presenting cells, the search for a needle in a haystack begins. What happens if a molecule of the exact type for which the T cell is programmed, is found amongst the many hundreds of thousands of molecules that are on the surface of the antigen-presenting cell? "Imagine that the T cell has countless versions of the same key on its surface, and now has to quickly find out whether it fits any of the hundreds of thousands of locks on the antigen-presenting cell," explains Gerhard Schütz.
***
"The receptors might well be distributed randomly over the T cell. That would also explain why the immune reaction happens so quickly. Regardless of how the antigen-presenting cell comes into contact with the T cell, the T cell always has a 'key' that fits the 'lock' at this location. If this is correct, the two cells do not lose any time getting into the right position, but instead the immune reaction can be triggered immediately.
Comment: The T cells develop a library of antigen receptors to protect us. This had to be designed early in evolution for life to survive infections. The information is developed and stored in the thymus where T cells are made.
Immunity: rapidly responding T cells
by Balance_Maintained , U.S.A., Tuesday, July 17, 2018, 05:56 (2109 days ago) @ David Turell
Surface receptors on the T cell surfaces are widely dispersed to quickly pick up signals from foreign antigens:
https://www.sciencedaily.com/releases/2018/07/180716114610.htm
"Without T cells, we could not survive. They are a key component of our immune system and have highly sensitive receptors on their surface that can detect pathogens. The exact way that these receptors are distributed over the surface of the T cells is still not completely understood, but the analyses by TU Wien show that previous ideas are no longer tenable.
"It was previously thought that the T cell would concentrate the receptors at certain points in order to achieve the highest possible sensitivity. As a current publication by the biophysics research group at TU Wien shows, T cells are actually programmed to react as quickly as possible, and therefore their receptors are arranged at random.
***
"'A T cell is a highly specific molecule detector," explains Prof. Gerhard Schütz, head of the biophysics research group at the Institute of Applied Physics at TU Wien. "Each T cell only reacts to a very specific molecule, and so we need many different T cells in our bodies." Each T cell carries many thousands of copies of the same receptor on its surface.
"To trigger an immune reaction, the T cell still needs an important partner -- the so-called antigen-presenting cell. The surfaces of these cells present many different molecules with the aid of special carrier proteins. Some of these molecules originate from endogenous structures and are harmless, but characteristic antigens of harmful intruders are also transported by the body on these antigen-presenting cells.
"If the T cell comes into contact with one of these antigen-presenting cells, the search for a needle in a haystack begins. What happens if a molecule of the exact type for which the T cell is programmed, is found amongst the many hundreds of thousands of molecules that are on the surface of the antigen-presenting cell? "Imagine that the T cell has countless versions of the same key on its surface, and now has to quickly find out whether it fits any of the hundreds of thousands of locks on the antigen-presenting cell," explains Gerhard Schütz.
***
"The receptors might well be distributed randomly over the T cell. That would also explain why the immune reaction happens so quickly. Regardless of how the antigen-presenting cell comes into contact with the T cell, the T cell always has a 'key' that fits the 'lock' at this location. If this is correct, the two cells do not lose any time getting into the right position, but instead the immune reaction can be triggered immediately.
David: Comment: The T cells develop a library of antigen receptors to protect us. This had to be designed early in evolution for life to survive infections. The information is developed and stored in the thymus where T cells are made.
If what you say is true, the thymus is where we should look to see if there is a method for adding information to a genome, and if so, what the limits are. We know that our immune system learns, so that information must be getting recorded somewhere somehow.
--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.
Immunity: rapidly responding T cells
by David Turell , Tuesday, July 17, 2018, 16:08 (2109 days ago) @ Balance_Maintained
Surface receptors on the T cell surfaces are widely dispersed to quickly pick up signals from foreign antigens:
https://www.sciencedaily.com/releases/2018/07/180716114610.htm
David: Comment: The T cells develop a library of antigen receptors to protect us. This had to be designed early in evolution for life to survive infections. The information is developed and stored in the thymus where T cells are made.
Tony: If what you say is true, the thymus is where we should look to see if there is a method for adding information to a genome, and if so, what the limits are. We know that our immune system learns, so that information must be getting recorded somewhere somehow.
The cells in the Thymus actually change their DNA to add antibodies that react against antigens that have appeared over time so the T cells have the right ammunition.
Immunity: rapidly responding B and plasma cells
by David Turell , Friday, August 24, 2018, 01:12 (2071 days ago) @ David Turell
An acute infection requires a rapid response. this is how it is done:
https://www.sciencedaily.com/releases/2018/08/180822101319.htm
"In a study published this week in Nature Communications, scientists at Australia's Garvan Institute of Medical Research have identified where the immune system 'remembers' past infections and vaccinations -- and where immune cells gather to mount a rapid response against an infection the body has seen before.
***
"We have known for millennia that people exposed to an infection are often protected from getting the same infection again -- ever since the Plague of Athens in 430 BC, where plague survivors were noted to have developed immunity against reinfection. Yet, major questions remain about how the body can fight back fast when it encounters an infection that it has been previously exposed to (through a vaccine or through an earlier infection).
"The researchers reveal the existence of thin, flattened structures extending over the surface of lymph nodes in mice. These dynamic structures are not always present: instead, they appear only when needed to fight an infection against which the animal has previously been exposed.
"Crucially, researchers also saw the structures -- which they have named SPFs (or 'subcapsular proliferative foci') -- inside sections of lymph nodes from patients, suggesting that they help fight reinfection in people as well as in mice.
"Using sophisticated 'two-photon' in vivo microscopy, the researchers could see that several classes of immune cells gathered together in SPFs. Memory B cells, which carry information about how best to attack the infection, clustered there. So did other cell types that act as helpers.
"Importantly, the researchers could also see that memory B cells were changing into infection-fighting plasma cells. This is a key step in the fight against infection, because plasma cells make antibodies to recognise and fend off the invader and protect the body from disease.
"'It was exciting to see the memory B cells being activated and clustering in this new structure that had never been seen before," says Garvan's Dr Imogen Moran, the first author on the new study. "We could see them moving around, interacting with all these other immune cells and turning into plasma cells before our eyes."
"A/Prof Tri Phan (who led the research) says the SPF structures are perfectly placed to fight infection fast -- so they can stop disease in its tracks before it takes hold.
"'When you're fighting bacteria that can double in number every 20 to 30 minutes, every moment matters. To put it bluntly, if your immune system takes too long to assemble the tools to fight the infection, you die," he says.
"'This is why vaccines are so important. Vaccination trains the immune system, so that it can make antibodies very rapidly when an infection reappears. Until now we didn't know how and where this happened.
"'Now, we've shown that memory B cells rapidly turn into large numbers of plasma cells in the SPF. The SPF is located strategically where bacteria would re-enter the body and it has all the ingredients assembled in one place to make antibodies -- so it's remarkably well engineered to fight reinfection fast.'" (my bold)
Comment: The B cells change their DNA to have this form of antibody memory. Note my bold: engineered means designed!
Immunity: new T cell controls found in lymph nodes
by David Turell , Wednesday, September 05, 2018, 23:39 (2058 days ago) @ David Turell
A surprise new finding:
https://www.sciencedaily.com/releases/2018/09/180905124743.htm
"Their research shows that the so-called Fibroblastic Reticular Cells (FRCs) that form the inner structure of human tonsils and lymph nodes exert control over T cells and their response to infection.
"These larger structural cells provide both structural support and guidance to immune cells while they spend time in lymph nodes, and the researchers' new work identifies four key mechanisms by which the FRCs act to dampen down T cell responses.
"The four mechanisms that FRCs use include pathways involving prostaglandin E2, the adenosine 2a receptor, indoleamine-2,3-dioxygenase, and transforming growth factor beta. The scientists were able to inhibit all four FRC mechanisms using existing drugs, and found that T cell responses were heightened in the process. Once T cells are no longer suppressed by FRCs they are readily able to expand and proliferate.
"Using an entirely novel approach, the researchers, in collaboration with University of Birmingham, examined the activation of T cells within live slices of human tonsil, and found that (in the presence or absence of key molecules), the T cells demonstrated a heightened response when FRCs were inhibited."
Comment: Suppression systems are part of the way the body balances reactions, just as feedback loops do. Since the T cells are designed to attack, controlling them had to be designed at the same time. No Darwin here.
Immunity: new T cell controls found in lymph nodes
by Balance_Maintained , U.S.A., Thursday, September 06, 2018, 04:11 (2058 days ago) @ David Turell
A surprise new finding:
https://www.sciencedaily.com/releases/2018/09/180905124743.htm
"Their research shows that the so-called Fibroblastic Reticular Cells (FRCs) that form the inner structure of human tonsils and lymph nodes exert control over T cells and their response to infection.
"These larger structural cells provide both structural support and guidance to immune cells while they spend time in lymph nodes, and the researchers' new work identifies four key mechanisms by which the FRCs act to dampen down T cell responses.
"The four mechanisms that FRCs use include pathways involving prostaglandin E2, the adenosine 2a receptor, indoleamine-2,3-dioxygenase, and transforming growth factor beta. The scientists were able to inhibit all four FRC mechanisms using existing drugs, and found that T cell responses were heightened in the process. Once T cells are no longer suppressed by FRCs they are readily able to expand and proliferate.
"Using an entirely novel approach, the researchers, in collaboration with University of Birmingham, examined the activation of T cells within live slices of human tonsil, and found that (in the presence or absence of key molecules), the T cells demonstrated a heightened response when FRCs were inhibited."
Comment: Suppression systems are part of the way the body balances reactions, just as feedback loops do. Since the T cells are designed to attack, controlling them had to be designed at the same time. No Darwin here.
It is particularly interesting that there are positive and negative feedback loops (enhancement/suppression). I suspect they will find that there is some form of key signature in the relative balance between those four chemicals that tune T cell responses to particular threats, or perhaps types of threats. Like a 4-characteristic targeting system.
--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.
Immunity: new T cell controls found in lymph nodes
by David Turell , Thursday, September 06, 2018, 14:05 (2058 days ago) @ Balance_Maintained
A surprise new finding:
https://www.sciencedaily.com/releases/2018/09/180905124743.htm
"Their research shows that the so-called Fibroblastic Reticular Cells (FRCs) that form the inner structure of human tonsils and lymph nodes exert control over T cells and their response to infection.
"These larger structural cells provide both structural support and guidance to immune cells while they spend time in lymph nodes, and the researchers' new work identifies four key mechanisms by which the FRCs act to dampen down T cell responses.
"The four mechanisms that FRCs use include pathways involving prostaglandin E2, the adenosine 2a receptor, indoleamine-2,3-dioxygenase, and transforming growth factor beta. The scientists were able to inhibit all four FRC mechanisms using existing drugs, and found that T cell responses were heightened in the process. Once T cells are no longer suppressed by FRCs they are readily able to expand and proliferate.
"Using an entirely novel approach, the researchers, in collaboration with University of Birmingham, examined the activation of T cells within live slices of human tonsil, and found that (in the presence or absence of key molecules), the T cells demonstrated a heightened response when FRCs were inhibited."
Comment: Suppression systems are part of the way the body balances reactions, just as feedback loops do. Since the T cells are designed to attack, controlling them had to be designed at the same time. No Darwin here.
Tony: It is particularly interesting that there are positive and negative feedback loops (enhancement/suppression). I suspect they will find that there is some form of key signature in the relative balance between those four chemicals that tune T cell responses to particular threats, or perhaps types of threats. Like a 4-characteristic targeting system.
Undoubtedly. The research of complexity just takes time.
Immunity: how macrophages check surroundings for bugs
by David Turell , Sunday, September 09, 2018, 22:53 (2054 days ago) @ David Turell
Their cell walls have a rippling effect:
https://cosmosmagazine.com/biology/watch-macrophages-on-guard-against-invaders
"Macrophages are cells critical to the immune system – and new imaging reveals how they actively monitor their surroundings, searching for invaders.
"The cells are highly specialised. They are the body’s frontline troops when it comes to detecting, combatting and destroying invading bacteria and other unwanted microbes. They also trigger another part of the system, known as T-cells, to release molecules known as cytokines which initiate inflammation at wound or infection sites.
"Now, researchers at the University of Queensland’s Institute for Molecular Bioscience, in Australia, have used a form of imaging known as lattice light sheet microscopy (LLSM) to uncover for the first time the extraordinarily active surveillance carried out by the cells.
"A team led by Adam Wall and Nicholas Condon found that the imaging revealed that the macrophages sported previously unknown structures that they dubbed “tent-pole ruffles”.
"The ruffles continuously undulate, helping the immune cells to gulp in surrounding fluid for sampling – a process known as “micropinocytosis”.
“'It's really exciting to be able to see cell behaviour at unprecedented levels of resolution,” says Wall.
“'This is discovery science at the cutting edge of microscopy and reveals how much we still have to learn about how cells function.'”
Comment: The more complex the newly developed research equipment, the more complexity we find. Certainly looks designed, as it is too complex a purposeful process for chance development.
Immunity: how macrophages check surroundings for bugs
by Balance_Maintained , U.S.A., Monday, September 10, 2018, 16:51 (2053 days ago) @ David Turell
Their cell walls have a rippling effect:
https://cosmosmagazine.com/biology/watch-macrophages-on-guard-against-invaders
"Macrophages are cells critical to the immune system – and new imaging reveals how they actively monitor their surroundings, searching for invaders.
"The cells are highly specialised. They are the body’s frontline troops when it comes to detecting, combatting and destroying invading bacteria and other unwanted microbes. They also trigger another part of the system, known as T-cells, to release molecules known as cytokines which initiate inflammation at wound or infection sites.
"Now, researchers at the University of Queensland’s Institute for Molecular Bioscience, in Australia, have used a form of imaging known as lattice light sheet microscopy (LLSM) to uncover for the first time the extraordinarily active surveillance carried out by the cells.
"A team led by Adam Wall and Nicholas Condon found that the imaging revealed that the macrophages sported previously unknown structures that they dubbed “tent-pole ruffles”.
"The ruffles continuously undulate, helping the immune cells to gulp in surrounding fluid for sampling – a process known as “micropinocytosis”.
“'It's really exciting to be able to see cell behaviour at unprecedented levels of resolution,” says Wall.
“'This is discovery science at the cutting edge of microscopy and reveals how much we still have to learn about how cells function.'”
Comment: The more complex the newly developed research equipment, the more complexity we find. Certainly looks designed, as it is too complex a purposeful process for chance development.
I'm sure they will still try to claim it evolved...with no evidence to back it up, just some fairy tale.
--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.
Immunity:mitochondria can be made to gang up on cancer
by David Turell , Wednesday, September 12, 2018, 18:10 (2051 days ago) @ Balance_Maintained
They produce reactive oxygen products to kill:
https://medicalxpress.com/news/2018-09-mitochondria-cancer-cells.html
"Targeting a pathway that controls the movement of mitochondria, the powerhouses of all cells, could reduce cancer invasiveness and resistance to radiotherapy.
"A team of Hokkaido University scientists studied the molecules involved in mitochondrial movements within highly invasive breast cancer cells. They identified a pathway that ultimately leads to the dispersion of these energy-generating organelles towards the cells' periphery, increasing cancer invasiveness.
"When this pathway was blocked, mitochondria aggregated within the cell's center, where they started overproducing and leaking reactive oxygen species (ROS)—unstable oxygen-containing molecules. ROS is known to enhance cancer invasiveness but in excessive amounts, it can lead to cancer cell death.
"Mitochondria are known to relocate within the cellular cytoplasm when different types of cells move. For example, they gather at the tail end of white blood cells moving toward a foreign invader, and at the leading edge of invading cancer cells. An adhesion protein on the cell surface, called integrin, is also known to promote cancer invasiveness. The mechanisms lying behind these movements, however, are still not fully understood.
"Some treatments, including ionizing radiation, increase the production of ROS within cancer cells, contributing to their anti-cancer effects. But some cancer cells develop a tolerance to ROS that allows them to handle more of them. The researchers wanted to investigate mitochondrial movements within cancer cells, and the relation between those movements, integrin, and ROS, all of which are involved in cancer invasion.
***
"They found that a molecular pathway which facilitates the recycling of integrin within the cell, called Arf6-AMP1-PRKD2, also facilitates the localization of mitochondria. Integrin accumulation leads to the formation of an adhesion complex at the cell membrane, which ultimately induces trafficking of mitochondria to the cell periphery. Disrupting this pathway led to the aggregation of mitochondria near the cell centre, reducing cancer cell invasiveness. During the experiment, the team also directly modified the mitochondrial distribution, finding that mitochondrial aggregation by itself leads to the production of excessive ROS, resulting in cancer cell death.
"These findings suggest that the pathway favouring mitochondrial dispersal makes cancer cells more resistant to treatments that try to kill the cell by increasing reactive oxygen species production.
"According to the researchers, their findings indicate "a novel molecular link between cell movements and mitochondrial dynamics, which appears to be crucial for both the invasive activity and tolerance to reactive oxygen species of highly invasive cancers. Our findings may also lead to novel strategies to improve the efficacy of reactive oxygen species-mediated cancer therapies, such as ionizing radiation.'"
Comment: Cancers sometimes use natural pathways for their advantage. We know that reactive oxygen proteins can kill as oxygen is really a dangerous element. What is really surprising about evolution is that oxygen was chosen to be the energy burning mechanism for breathing animals with all of its ability to damage tissue. This meant that antioxidant mechanisms had to be added at the same time for animals to survive. Only by design.
Immunity: protein signal molecule guiding cells to goal
by David Turell , Friday, September 14, 2018, 20:31 (2049 days ago) @ David Turell
Immune cells when activate have to know where to go to start the attack. A signal molecule has been found and interestingly it can affect action by the brain:
https://www.sciencedaily.com/releases/2018/09/180913082142.htm
"Doctors have long known that a high level of the protein CCL17 in the body indicates an allergic reaction. Now scientists have discovered a completely new function: CCL17 also influences signal transmission in the brain. There may even be a molecular link to autism.
"The chemotactic protein CCL17 attracts immune cells to where they are currently needed. Doctors have long known: A high level of this substance in the body indicates an allergic reaction. A team of scientists led by the University of Bonn has now discovered a completely new function: CCL17 also influences signal transmission in the brain. There may even be a molecular link to autism.
"Chemotactic cytokines, chemokines for short, are signaling proteins that act like an attractant and ensure, for example, that immune cells migrate from the bloodstream into the tissues. The chemokine CCL17 is known to increase inflammation and is associated with allergic diseases. A high level of CCL17 in the blood is regarded by doctors as a diagnostic marker of ongoing allergic reactions such as atopic eczema. The further the research on chemokines progresses, however, the more functions are discovered. Thus, an earlier joint study by the Universities of Münster and Bonn showed that animals with a defect in the expression of the receptor for CCL17 have behavioral problems: For example, they were unable to build proper nests like their normally developed mates.
"'These behavioral changes indicated that CCL17 not only affects the immune system but perhaps also the brain," explains the corresponding author of the study, Prof. Dr. Irmgard Förster from the LIMES Institute at the University of Bonn, who is also a member of the Cluster of Excellence "ImmunoSensation." If there is such a connection, which cells in the brain produce CCL17? This question was investigated by doctoral student Lorenz Fülle and Irmgard Förster, together with scientists from the Institute of Cellular Neurosciences around Prof. Dr. Christian Henneberger, Dr. Annett Halle from the German Center for Neurodegenerative Diseases (DZNE) and Dr. Judith Alferink from the University of Münster.
***
"'CCL17 is mainly produced by neurons of the hippocampus," reports lead author Lorenz Fülle. This structure, which is shaped like a seahorse, is present on the right and left side of the brain, and fulfills an important function in tasks such as orientation and memory formation.
Scientists blocked the gene for CCL17.
"As a next step, the scientists blocked the gene for CCL17 production and observed the effect. In the absence of the chemokine, the microglial cells in these "knockout" mice were significantly smaller and there were only half as many as in untreated control animals. Microglial cells have long been known as immune cells of the brain, where they take responsibility as "health guards" for the disposal of cell debris and infectious agents. Meanwhile, it has been shown that these "scavenger cells" also directly support the work of the neurons independently of their phagocytic activity.
"In order to investigate the effect of CCL17 on the function of neurons, scientists in the laboratory of Prof. Dr. Christian Henneberger at the Institute of Cellular Neurosciences (University of Bonn Medical School) examined neuronal signaling in the brain. Henneberger: "The experiments indicate that CCL17 attenuates signal transmission in the hippocampal region of the brain." Since autism in humans is also associated with elevated levels of CCL17 in the blood, CCL17 could also play a role in this developmental disorder, for example due to an infection or an allergic reaction in early childhood. "But so far these are speculations," says Förster. "The exact effects of CCL17 have yet to be demonstrated by further research.'"
Comment: Obviously the brain exert effects on all sorts of bodily functions. Obviously designed. A half-formed immune system is not much of a defense against dangerous infections.
Immunity: protein signal molecule guiding cells to goal
by Balance_Maintained , U.S.A., Friday, September 14, 2018, 23:13 (2049 days ago) @ David Turell
Immune cells when activate have to know where to go to start the attack. A signal molecule has been found and interestingly it can affect action by the brain:
https://www.sciencedaily.com/releases/2018/09/180913082142.htm
"Doctors have long known that a high level of the protein CCL17 in the body indicates an allergic reaction. Now scientists have discovered a completely new function: CCL17 also influences signal transmission in the brain. There may even be a molecular link to autism.
"The chemotactic protein CCL17 attracts immune cells to where they are currently needed. Doctors have long known: A high level of this substance in the body indicates an allergic reaction. A team of scientists led by the University of Bonn has now discovered a completely new function: CCL17 also influences signal transmission in the brain. There may even be a molecular link to autism.
"Chemotactic cytokines, chemokines for short, are signaling proteins that act like an attractant and ensure, for example, that immune cells migrate from the bloodstream into the tissues. The chemokine CCL17 is known to increase inflammation and is associated with allergic diseases. A high level of CCL17 in the blood is regarded by doctors as a diagnostic marker of ongoing allergic reactions such as atopic eczema. The further the research on chemokines progresses, however, the more functions are discovered. Thus, an earlier joint study by the Universities of Münster and Bonn showed that animals with a defect in the expression of the receptor for CCL17 have behavioral problems: For example, they were unable to build proper nests like their normally developed mates.
"'These behavioral changes indicated that CCL17 not only affects the immune system but perhaps also the brain," explains the corresponding author of the study, Prof. Dr. Irmgard Förster from the LIMES Institute at the University of Bonn, who is also a member of the Cluster of Excellence "ImmunoSensation." If there is such a connection, which cells in the brain produce CCL17? This question was investigated by doctoral student Lorenz Fülle and Irmgard Förster, together with scientists from the Institute of Cellular Neurosciences around Prof. Dr. Christian Henneberger, Dr. Annett Halle from the German Center for Neurodegenerative Diseases (DZNE) and Dr. Judith Alferink from the University of Münster.
***
"'CCL17 is mainly produced by neurons of the hippocampus," reports lead author Lorenz Fülle. This structure, which is shaped like a seahorse, is present on the right and left side of the brain, and fulfills an important function in tasks such as orientation and memory formation.
Scientists blocked the gene for CCL17."As a next step, the scientists blocked the gene for CCL17 production and observed the effect. In the absence of the chemokine, the microglial cells in these "knockout" mice were significantly smaller and there were only half as many as in untreated control animals. Microglial cells have long been known as immune cells of the brain, where they take responsibility as "health guards" for the disposal of cell debris and infectious agents. Meanwhile, it has been shown that these "scavenger cells" also directly support the work of the neurons independently of their phagocytic activity.
"In order to investigate the effect of CCL17 on the function of neurons, scientists in the laboratory of Prof. Dr. Christian Henneberger at the Institute of Cellular Neurosciences (University of Bonn Medical School) examined neuronal signaling in the brain. Henneberger: "The experiments indicate that CCL17 attenuates signal transmission in the hippocampal region of the brain." Since autism in humans is also associated with elevated levels of CCL17 in the blood, CCL17 could also play a role in this developmental disorder, for example due to an infection or an allergic reaction in early childhood. "But so far these are speculations," says Förster. "The exact effects of CCL17 have yet to be demonstrated by further research.'"
Comment: Obviously the brain exert effects on all sorts of bodily functions. Obviously designed. A half-formed immune system is not much of a defense against dangerous infections.
I'm curious as to how they 'knocked out' CCL17. That could be a bigger clue to the rise in Autism and some allergies than the role of CCL17 itself.
--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.
Immunity: protein signal molecule guiding cells to goal
by David Turell , Saturday, September 15, 2018, 00:47 (2049 days ago) @ Balance_Maintained
David: Immune cells when activate have to know where to go to start the attack. A signal molecule has been found and interestingly it can affect action by the brain:
https://www.sciencedaily.com/releases/2018/09/180913082142.htm
"Doctors have long known that a high level of the protein CCL17 in the body indicates an allergic reaction. Now scientists have discovered a completely new function: CCL17 also influences signal transmission in the brain. There may even be a molecular link to autism.
"The chemotactic protein CCL17 attracts immune cells to where they are currently needed. Doctors have long known: A high level of this substance in the body indicates an allergic reaction. A team of scientists led by the University of Bonn has now discovered a completely new function: CCL17 also influences signal transmission in the brain. There may even be a molecular link to autism.
"Chemotactic cytokines, chemokines for short, are signaling proteins that act like an attractant and ensure, for example, that immune cells migrate from the bloodstream into the tissues. The chemokine CCL17 is known to increase inflammation and is associated with allergic diseases. A high level of CCL17 in the blood is regarded by doctors as a diagnostic marker of ongoing allergic reactions such as atopic eczema. The further the research on chemokines progresses, however, the more functions are discovered. Thus, an earlier joint study by the Universities of Münster and Bonn showed that animals with a defect in the expression of the receptor for CCL17 have behavioral problems: For example, they were unable to build proper nests like their normally developed mates.
"'These behavioral changes indicated that CCL17 not only affects the immune system but perhaps also the brain," explains the corresponding author of the study, Prof. Dr. Irmgard Förster from the LIMES Institute at the University of Bonn, who is also a member of the Cluster of Excellence "ImmunoSensation." If there is such a connection, which cells in the brain produce CCL17? This question was investigated by doctoral student Lorenz Fülle and Irmgard Förster, together with scientists from the Institute of Cellular Neurosciences around Prof. Dr. Christian Henneberger, Dr. Annett Halle from the German Center for Neurodegenerative Diseases (DZNE) and Dr. Judith Alferink from the University of Münster.
***
"'CCL17 is mainly produced by neurons of the hippocampus," reports lead author Lorenz Fülle. This structure, which is shaped like a seahorse, is present on the right and left side of the brain, and fulfills an important function in tasks such as orientation and memory formation.
Scientists blocked the gene for CCL17."As a next step, the scientists blocked the gene for CCL17 production and observed the effect. In the absence of the chemokine, the microglial cells in these "knockout" mice were significantly smaller and there were only half as many as in untreated control animals. Microglial cells have long been known as immune cells of the brain, where they take responsibility as "health guards" for the disposal of cell debris and infectious agents. Meanwhile, it has been shown that these "scavenger cells" also directly support the work of the neurons independently of their phagocytic activity.
"In order to investigate the effect of CCL17 on the function of neurons, scientists in the laboratory of Prof. Dr. Christian Henneberger at the Institute of Cellular Neurosciences (University of Bonn Medical School) examined neuronal signaling in the brain. Henneberger: "The experiments indicate that CCL17 attenuates signal transmission in the hippocampal region of the brain." Since autism in humans is also associated with elevated levels of CCL17 in the blood, CCL17 could also play a role in this developmental disorder, for example due to an infection or an allergic reaction in early childhood. "But so far these are speculations," says Förster. "The exact effects of CCL17 have yet to be demonstrated by further research.'"
Comment: Obviously the brain exert effects on all sorts of bodily functions. Obviously designed. A half-formed immune system is not much of a defense against dangerous infections.
Tony: I'm curious as to how they 'knocked out' CCL17. That could be a bigger clue to the rise in Autism and some allergies than the role of CCL17 itself.
The method as described above: "As a next step, the scientists blocked the gene for CCL17 production and observed the effect. In the absence of the chemokine, the microglial cells in these "knockout" mice were significantly smaller." The 'knockout the gene' approach is used now all the time to show effects, by absense.
Immunity: protein signal molecule guiding cells to goal
by Balance_Maintained , U.S.A., Saturday, September 15, 2018, 04:12 (2049 days ago) @ David Turell
David: Immune cells when activate have to know where to go to start the attack. A signal molecule has been found and interestingly it can affect action by the brain:
https://www.sciencedaily.com/releases/2018/09/180913082142.htm
"Doctors have long known that a high level of the protein CCL17 in the body indicates an allergic reaction. Now scientists have discovered a completely new function: CCL17 also influences signal transmission in the brain. There may even be a molecular link to autism.
"The chemotactic protein CCL17 attracts immune cells to where they are currently needed. Doctors have long known: A high level of this substance in the body indicates an allergic reaction. A team of scientists led by the University of Bonn has now discovered a completely new function: CCL17 also influences signal transmission in the brain. There may even be a molecular link to autism.
"Chemotactic cytokines, chemokines for short, are signaling proteins that act like an attractant and ensure, for example, that immune cells migrate from the bloodstream into the tissues. The chemokine CCL17 is known to increase inflammation and is associated with allergic diseases. A high level of CCL17 in the blood is regarded by doctors as a diagnostic marker of ongoing allergic reactions such as atopic eczema. The further the research on chemokines progresses, however, the more functions are discovered. Thus, an earlier joint study by the Universities of Münster and Bonn showed that animals with a defect in the expression of the receptor for CCL17 have behavioral problems: For example, they were unable to build proper nests like their normally developed mates.
"'These behavioral changes indicated that CCL17 not only affects the immune system but perhaps also the brain," explains the corresponding author of the study, Prof. Dr. Irmgard Förster from the LIMES Institute at the University of Bonn, who is also a member of the Cluster of Excellence "ImmunoSensation." If there is such a connection, which cells in the brain produce CCL17? This question was investigated by doctoral student Lorenz Fülle and Irmgard Förster, together with scientists from the Institute of Cellular Neurosciences around Prof. Dr. Christian Henneberger, Dr. Annett Halle from the German Center for Neurodegenerative Diseases (DZNE) and Dr. Judith Alferink from the University of Münster.
***
"'CCL17 is mainly produced by neurons of the hippocampus," reports lead author Lorenz Fülle. This structure, which is shaped like a seahorse, is present on the right and left side of the brain, and fulfills an important function in tasks such as orientation and memory formation.
Scientists blocked the gene for CCL17."As a next step, the scientists blocked the gene for CCL17 production and observed the effect. In the absence of the chemokine, the microglial cells in these "knockout" mice were significantly smaller and there were only half as many as in untreated control animals. Microglial cells have long been known as immune cells of the brain, where they take responsibility as "health guards" for the disposal of cell debris and infectious agents. Meanwhile, it has been shown that these "scavenger cells" also directly support the work of the neurons independently of their phagocytic activity.
"In order to investigate the effect of CCL17 on the function of neurons, scientists in the laboratory of Prof. Dr. Christian Henneberger at the Institute of Cellular Neurosciences (University of Bonn Medical School) examined neuronal signaling in the brain. Henneberger: "The experiments indicate that CCL17 attenuates signal transmission in the hippocampal region of the brain." Since autism in humans is also associated with elevated levels of CCL17 in the blood, CCL17 could also play a role in this developmental disorder, for example due to an infection or an allergic reaction in early childhood. "But so far these are speculations," says Förster. "The exact effects of CCL17 have yet to be demonstrated by further research.'"
Comment: Obviously the brain exert effects on all sorts of bodily functions. Obviously designed. A half-formed immune system is not much of a defense against dangerous infections.
Tony: I'm curious as to how they 'knocked out' CCL17. That could be a bigger clue to the rise in Autism and some allergies than the role of CCL17 itself.
David: The method as described above: "As a next step, the scientists blocked the gene for CCL17 production and observed the effect. In the absence of the chemokine, the microglial cells in these "knockout" mice were significantly smaller." The 'knockout the gene' approach is used now all the time to show effects, by absense.
Yes, I am just curious as to how they suppressed it, as that might be gene therapy for autistic children or those with hyper-active allergy responses.
--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.
Immunity: protein signal molecule guiding cells to goal
by David Turell , Saturday, September 15, 2018, 16:03 (2049 days ago) @ Balance_Maintained
"In order to investigate the effect of CCL17 on the function of neurons, scientists in the laboratory of Prof. Dr. Christian Henneberger at the Institute of Cellular Neurosciences (University of Bonn Medical School) examined neuronal signaling in the brain. Henneberger: "The experiments indicate that CCL17 attenuates signal transmission in the hippocampal region of the brain." Since autism in humans is also associated with elevated levels of CCL17 in the blood, CCL17 could also play a role in this developmental disorder, for example due to an infection or an allergic reaction in early childhood. "But so far these are speculations," says Förster. "The exact effects of CCL17 have yet to be demonstrated by further research.'"
David: Comment: Obviously the brain exert effects on all sorts of bodily functions. Obviously designed. A half-formed immune system is not much of a defense against dangerous infections.
Tony: I'm curious as to how they 'knocked out' CCL17. That could be a bigger clue to the rise in Autism and some allergies than the role of CCL17 itself.
David: The method as described above: "As a next step, the scientists blocked the gene for CCL17 production and observed the effect. In the absence of the chemokine, the microglial cells in these "knockout" mice were significantly smaller." The 'knockout the gene' approach is used now all the time to show effects, by absense.
Tony: Yes, I am just curious as to how they suppressed it, as that might be gene therapy for autistic children or those with hyper-active allergy responses.
They probably used CRISPR to slice out the gene.
Immunity: selecting best egg & sperm immunity
by David Turell , Monday, October 01, 2018, 18:22 (2032 days ago) @ David Turell
Contribution to immunity of the new embryo after egg and sperm meet involves sperm selection by the egg by a currently unknown mechanism in the egg which picks a compatible immunity gene selection by a currently unknown process:
https://phys.org/news/2018-10-female-gametes-sperm-immune-genes.html
"Through clever partner selection, animals can increase the future success of their offspring. With some species, this process continues even after the sex act. Researchers at the Max Planck Institute for Evolutionary Biology in Plön have discovered that among sticklebacks, the egg cells of the fish are involved in the decision regarding fertilisation. An accumulation of genes in the genetic material of the male gamete's cells determines which sperm is allowed in to the egg cell. Since vertebrates are highly similar in terms of their immune system, including with regard to the gene complex in question, the researchers assume that egg cells of other vertebrates – perhaps even those of humans – are able to control their fertilisation.
***
"Without a powerful immune system, no animal can survive for long, let alone produce offspring. Since half of the immune genes of both parents respectively are passed on in combination to the offspring, it is worth selecting a sex partner who best supplements one's own immune genes. (my bold)
***
"Here, a decisive role is played by the genes of the "Major Histocompatibility Complex (MHC)", an accumulation of extremely variable immune genes on chromosome 6. "We already discovered some time ago how the gene complex impacts the smell of a human body, and identified our body's own perfume. This plays an important role when we select a partner," Milinski explains. "With such immune genes, which complement your own genes, the immune system of your offspring is particularly diverse, and can fend off a large number of pathogens."
***
"Every human and most animals have two – often different – varieties of every individual gene. An egg or sperm cell only receives one of the two gene variants in each case. Some of the cells therefore have immune gene variants that match each other better than others. During fertilisation, an egg cell can therefore in fact merge with a sperm that has been given an MHC variant that does not match so well – despite prior partner selection and what appeared to be the matching immune genes.
***
"The egg – not the woman – must therefore select its own partner, namely the sperm with the complementary MHC variant. According to the researcher team in Plön, this is precisely what the egg cells of sticklebacks do. The scientists presented egg cells with sperm with different MHC variants and observed which of the male gametes was successful. "Our experiments show that the sperm with the highest chance of fertilisation is the sperm whose MHC may differ from that of the egg, but which still shows certain similarities," explains Tobias Lenz, who heads the Evolutionary Immunogenomics research group at the Max Planck Institute in Plön.
***
"Researchers do not yet know how the egg selects the sperm. "Our experiments show that the selection process continues even after the sex act. Since it is impossible to tell on the basis of scent which immune gene variants will finally be successful, the selection by the egg cells is an extremely important supplement to partner selection. The offspring are more resistant to pathogens as a result, and therefore have an evolutionary advantage," Milinski explains. Additionally, egg cells can in this way avoid fertilisation by the sperm of unwanted males."
Comment: Note my bold. Immunity is vital for survival. Mammals pass generalized antibodies to newborns through colostrum in milk, to help the infant survive until its own immunity begins to build an appropriate library of antibodies. The 'MHC' complex is similar to the HLA complex which is studied by implant surgeons to find compatible donors for organ transplants, except that HLA looks for compatibility and MHC is opposite and looks to fight invaders. I think research will find that the egg has receptors which can recognize the right genes in sperm, all an automatic process that had to be designed to allow sexual reproduction to be a safe way to reproduce. Sexual reproduction allows for more manipulation of genes to develop more complex organisms beyond the groups of individual cells with slight variation in function, as in bacterial mats.
Immunity: IgM mechanism
by David Turell , Wednesday, October 10, 2018, 19:25 (2023 days ago) @ David Turell
Immune globulins are giant protein molecules which fight general infections. IgM has a unique mechanism to release another smaller fighting protein molecule:
https://phys.org/news/2018-10-pentagon-beanredrawing-immune-protein.html
"Researchers verified the structure of natural immunoglobulin M (IgM) protein, an important part of the immune system, using mouse and human versions of the protein. IgM is now understood to be shaped like an incomplete hexagon, or a pentagon with a wedge-shaped gap.
***
"IgM is the first immune system protein that develops in the human fetus and remains the first responder to pathogens throughout life. The structure of IgM was first identified in 1969 as a "five-pointed, star-shaped table" and updated in 2009 to be a five-sided dome or "mushroom cap."
***
"The 2018 discovery of the incomplete hexagon was actually a secondary interest for Miyazaki, originally a medical doctor who has built his research career studying a different protein called apoptosis inhibitor of macrophage (AIM).
"Since identifying the correct shape of IgM, researchers now understand that inactive AIM is nestled inside the gap of the IgM incomplete hexagon. The structural connection between IgM and AIM means that drugs with the ability to regulate the release of AIM could be used to create AIM-based disease therapies.
"'We can think of AIM as a fighter jet and IgM as the aircraft carrier ship. When other molecules activate the immune system, IgM releases AIM. The much smaller AIM protein goes around the body to clear away damaged cells and prevent disease," said Miyazaki.
***
"AIM is a common molecule in the bloodstream, but it is only active when the body develops a disease. AIM is known to be important for preventing obesity, fatty liver disease, hepatocellular carcinoma (liver cancer), multiple sclerosis (MS), fungus-induced peritonitis (inflammation of the abdominal wall membrane), and acute kidney injury."
Comment: Note the importance of IgM as the first forming immune globulin in the fetus. How AIM and Igm worked out their arrangement of hold and release is not a result of chance. Note my bold.
Immunity: gene controls through special proteins
by David Turell , Monday, October 15, 2018, 19:03 (2018 days ago) @ David Turell
Immunity is essential to fight infection for any living organism, since infective organisms are ubiquitous. It has complex controls:
https://medicalxpress.com/news/2018-10-immune-health-meticulously-dna.html
"The new study published today in Nature Immunology shows how Pax5 helps to efficiently organise the genetic information (DNA) required for our immune cells to maintain their form, function and help fight disease. The findings also suggest that a breakdown in this process of organisation by Pax5 could increase the risk of diseases such cancer.
***
"Dr. Johanson said the researchers had shown, for the first time, that Pax5 could sweep across the genome and fold, twist and store DNA for B cells in a fantastically ordered way—making each cell into a jam-packed but very neat suitcase.
"'This immaculate organisation is crucial because each cell contains roughly two meters of DNA—that's a huge amount of material to fit inside something smaller than a grain of sand.
"'Every second of every day, different cells require access to highly specific parts of DNA in order to perform a myriad of jobs that help keep us healthy," he said.
"Dr. Johanson said life depended on cells accessing what they needed, when they needed it.
"For instance, immune B cells must access the right information to produce potentially life-saving antibodies that are critical for vaccine and immune responses.
"'Think of how a meticulously ordered suitcase increases your chance of finding a specific item of clothing at a moment's notice, and, how a jumbled case could work against you finding what you need. In the case of our bodies, the difference between order and disorder can be a matter of life and death," he said.
"'Seemingly small errors in the process of DNA organisation can turn out to be very serious drivers for disease.
"A lack of instructions required to function can put cells at risk of morphing or devolving into something they perhaps shouldn't be—like a cancer cell. It is therefore unsurprising that Pax5 is faulty in many childhood leukaemias."
***
"Dr. Allan said the findings were particularly intriguing because for two decades Pax5 was known only as a 'transcription factor'.
"'Transcription factors help cells identify the instructions they need, but there was no evidence they could also play a part in the organisation and upkeep of this information, until now," he said."
Comment: This study shows how complex the controls are to manipulate DNA to produce the correct antibodies at the right time. The system is too complex for chance Darwinist evolution to have developed it. It also shows the intelligent automaticity built into the immune system, which requires exact information to be stored, found, and presented appropriately. Life runs on stored information. This article is an exact exposition of Shapiro's work showing how cells can manipulate DNA for necessary purposes. Cells do operate intelligently they because they follow intelligent instructions.
Immunity: gene controls through special proteins
DAVID: This article is an exact exposition of Shapiro's work showing how cells can manipulate DNA for necessary purposes. Cells do operate intelligently because they follow intelligent instructions.
Thank you for another illuminating article. What a pity you have ended it by ignoring Shapiro’s explicit statements concerning the intelligence of cells. He does not say they follow intelligent instructions, and he says that people who reject the concept do so because of “large organisms chauvinism”. Of course he can’t prove it, but this is his belief based on a lifetime of research. Here are some more quotes for you, and I hope they will suffice to stop you from insinuating that Shapiro’s work supports your beliefs. (NB: As in the Egnor discussion, my aim here is to straighten out any misconceptions arising out of these posts. In my view Egnor misrepresents materialism, and here you misleadingly link Shapiro's work with your beliefs while omitting his own beliefs.)
"The capacity of living organisms to alter their own heredity is undeniable. Our current ideas about evolution have to incorporate this basic fact of life."
(Evolution: A View from the 21st Century, p.2)
Are Cells Intelligent? - evo2.org
https://evo2.org/cells-intelligent
In a discussion with a Matthew Taylor he quotes:
From Barbara McClintock’s 1984 Nobel Prize paper
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1983/mcclintock-lecture.pdf
“Life requires cognition at all scopes and scales. The critical factor in evolution was the moment of instantiation of the self-referential cell. How that occurred is unknown, but the fact that cells are self-aware problem-solving agencies cannot be reasonably disputed."
SHAPIRO: If it walks like a duck, talks like a duck, and quacks like a duck…. well, I vote for cells being intelligent. At least in some sense. [dhw: an important rider for sceptics like yourself - nobody would claim that cellular intelligence is the same as our own.]
SHAPIRO: The last question I would ask myself is: “Which hypothesis is more likely to lead us to interesting discoveries, new hypotheses and interesting observations? A) the idea that cells are dumb machines created by a series of accidental mutations and selected for survival, or B) the idea that cells are intelligent agents that direct their own development? [dhw: It could hardly be clearer which hypothesis he supports. He does not, however, mention the hypothesis that your God preprogrammed or personally dabbled every innovation in life’s history, but he could hardly support it if he believes that cells direct their own development.]
Natural genetic engineering - Wikipedia
https://en.wikipedia.org/wiki/Natural_genetic_engineering
Within the context of the article in particular and Shapiro's work on Natural Genetic Engineering in general, the "guiding intelligence" is to be found within the cell. (For example, in a Huffington Post essay entitled Cell Cognition and Cell Decision-Making Shapiro defines cognitive actions as those that are "knowledge-based and involve decisions appropriate to acquired information," arguing that cells meet this criteria.)
Immunity: gene controls through special proteins
by David Turell , Tuesday, October 16, 2018, 18:42 (2017 days ago) @ dhw
DAVID: This article is an exact exposition of Shapiro's work showing how cells can manipulate DNA for necessary purposes. Cells do operate intelligently because they follow intelligent instructions.
dhw: Thank you for another illuminating article. What a pity you have ended it by ignoring Shapiro’s explicit statements concerning the intelligence of cells. He does not say they follow intelligent instructions, and he says that people who reject the concept do so because of “large organisms chauvinism”. Of course he can’t prove it, but this is his belief based on a lifetime of research. Here are some more quotes for you, and I hope they will suffice to stop you from insinuating that Shapiro’s work supports your beliefs. (NB: As in the Egnor discussion, my aim here is to straighten out any misconceptions arising out of these posts. In my view Egnor misrepresents materialism, and here you misleadingly link Shapiro's work with your beliefs while omitting his own beliefs.)
"The capacity of living organisms to alter their own heredity is undeniable. Our current ideas about evolution have to incorporate this basic fact of life."
(Evolution: A View from the 21st Century, p.2)
Are Cells Intelligent? - evo2.org
https://evo2.org/cells-intelligentIn a discussion with a Matthew Taylor he quotes:
From Barbara McClintock’s 1984 Nobel Prize paper
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1983/mcclintock-lecture.pdf“Life requires cognition at all scopes and scales. The critical factor in evolution was the moment of instantiation of the self-referential cell. How that occurred is unknown, but the fact that cells are self-aware problem-solving agencies cannot be reasonably disputed."
SHAPIRO: If it walks like a duck, talks like a duck, and quacks like a duck…. well, I vote for cells being intelligent. At least in some sense. [dhw: an important rider for sceptics like yourself - nobody would claim that cellular intelligence is the same as our own.]
SHAPIRO: The last question I would ask myself is: “Which hypothesis is more likely to lead us to interesting discoveries, new hypotheses and interesting observations? A) the idea that cells are dumb machines created by a series of accidental mutations and selected for survival, or B) the idea that cells are intelligent agents that direct their own development? [dhw: It could hardly be clearer which hypothesis he supports. He does not, however, mention the hypothesis that your God preprogrammed or personally dabbled every innovation in life’s history, but he could hardly support it if he believes that cells direct their own development.]
Natural genetic engineering - Wikipedia
https://en.wikipedia.org/wiki/Natural_genetic_engineeringWithin the context of the article in particular and Shapiro's work on Natural Genetic Engineering in general, the "guiding intelligence" is to be found within the cell. (For example, in a Huffington Post essay entitled Cell Cognition and Cell Decision-Making Shapiro defines cognitive actions as those that are "knowledge-based and involve decisions appropriate to acquired information," arguing that cells meet this criteria.)
I'm fully aware of Shapiro's stated views. He has stated bacteria can manipulate their DNA epigenetically and we know that is true. Lenski's 60,000 plus generations of E. coli finds they are still E. coli but have made minor adaptations to provided stresses.
https://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment
What cannot be avoided is logic about cells. Either they are intelligently designed to have intelligent responses to stress and stimuli or somehow or other they have their own form of intelligence and use it. Either Shapiro or I am correct, as only those two presumptions are operational. My choice is obvious. "Guiding intelligence" can certainly be implanted intelligent instructions for proper automatic responses to the few stimuli bacteria receive.
Immunity: automatic controls of inflammation
by David Turell , Thursday, October 18, 2018, 19:48 (2015 days ago) @ David Turell
New automatic controls over neutrophils are described:
https://medicalxpress.com/news/2018-10-mechanism-inflammation.html
"The first immune cells to arrive at the infection or inflammation site are the neutrophils, and these cells are tasked with eliminating the source of the problem. However, neutrophils are very destructive and not only act on the infecting pathogen, but also damage the infected tissue. This tissue damage caused by our own defense system is known as immunopathology. It is therefore important to understand how our immune system can control the neutrophil inflammatory response to prevent it damaging our own tissues. The current study shows that tissue infiltration by neutrophils is controlled by dendritic cells. These cells are more well known for the essential role they play in directing the specific responses of T lymphocytes. The new study shows that dendritic-cell regulation of neutrophil infiltration helps to avoid excessive tissue injury."'
"'Dendritic cells attract neutrophils to the inflammatory focus by releasing factors such as the chemokine Mip-2. At the same time, these cells also express the surface receptor DNGR-1. This cell-surface molecule detects tissue injury by identifying cell components that become accessible only when the cell is damaged or 'broken'. When DNGR-1 detects damaged tissue, it reduces the capacity of the dendritic cell to produce Mip-2, thus limiting neutrophil infiltration to the damaged organ. This mechanism prevents what could otherwise be a life-threatening expansion of tissue injury."
"Paula Saz, the other co-first author on the study, emphasized the importance of understanding immune system regulation, both as a positive response, favoring the fight against infection or cancer and promoting tissue repair, and in its negative manifestations that can cause excessive inflammatory injury during infection, as well as allergic reactions or major autoimmune diseases. "This balance always exists in the immune system, and learning how to control it is the key to the fight against many diseases with an immune component.'"
Comment: All of these reactions and controls are automatic molecular effects. one molecule acting on another in a series. It is important that the inflammatory reaction is confined to the infected area only since it is damaging to normal uninfected tissue. It is like the clotting mechanism which is controlled to the damaged vessel or tissue. It cannot be allowed to clot the entire circulatory tree. How is this kind of control developed by chance? Obviously it cannot be and requires careful design.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Monday, November 12, 2018, 19:44 (1990 days ago) @ David Turell
Are cells OK or becoming cancerous is the job these newly found cells do:
https://medicalxpress.com/news/2018-11-two-pronged-device-enables-maverick-immune.html
"Immune cells called Gamma Delta T cells can act independently to identify and kill cancer cells, defying the conventional view of the immune system, reveals new research.
***
"For the past two decades, it has been dogma that the immune system is made up of two distinct subsystems: the 'innate' immune system, which offers us broad protection by detecting when things simply aren't normal; and the specialised 'adaptive' immune system which can discriminate and respond to very specific threats. The new study challenges this view, providing the first direct evidence that a single protein on a single cell type can perform both functions, detecting when things aren't normal and then mounting a specific response.
"Equipped with these unprecedented capabilities, Gamma Delta T cells patrol for pathogens or dangerously mutated cells arising in expansive body tissues, such as the skin and the gut. The new research found that the cells use two different checks to make sure they don't kill a healthy cell: checking if the cell looks dangerous but also whether it is nonetheless functioning normally. For example, if the Gamma Delta T cells see a gut cell that appears slightly mutated, but that is still normal by many other criteria, they will likely leave it alone. Without this type of check, the immune system could unleash uncontrolled attacks on healthy tissue.
***
"The analysis showed that Gamma Delta T cells are highly adaptable and can learn to tackle specific threats such as cancer cells. It also revealed that the signs of 'normality' they look for depend on the tissue that they're in; when the cells sit in the gut, they spare cells behaving like normal gut cells, whereas they seemingly use other scores of normality to make judgement calls about cells in the skin."
Comment: These are obviously automatic reactions on the part of these designed cells, which must have been present from the beginning of multicellular organisms with a circulatory system, since it appears cancer development has always been present and this balance was necessary.
Immunity: feedback loop perfects thymocytes
by David Turell , Monday, November 12, 2018, 20:00 (1990 days ago) @ David Turell
Precise controls of thymocytes makes sure they do not attack normal tissue:
https://medicalxpress.com/news/2018-11-suicide-handshakes-precursor-cells-pose.html
"Although the mechanisms are intertwined with biochemical processes, they also work mechanically, grasping, tugging and clamping, say researchers at the Georgia Institute of Technology, who, for a new study in the journal Nature Immunology, measured responses to physical force acting upon these elimination mechanisms.
"The mechanisms' purpose is to make dangerously aggressive developing immune cells called thymocytes kill themselves to keep them from attacking the body, while sparing healthy thymocytes as they mature into T cells. Understanding these selection mechanisms, which ensure T cells aggressively pursue hordes of infectors and cancers but not damage healthy human tissue, could someday lead to new immune-regulating therapies.
***
"'Before our work, force was not considered as a factor in thymocyte selection and now it is."
"In this study, they discovered a loop of physical signals resembling a double-handed handshake that encourages cell suicide. It is described in more detail below.
***
"Like blood cells, human thymocytes are born in bone marrow, but they travel to the thymus, a small organ just below the neck, where they run a gauntlet of selection tests. Failing any one selection means death by cell suicide; passing all selections promotes thymocytes to T cells that depart the thymus to battle our bodies' foes.
"One selection checks T cell receptors (TCR), which are on the thymocyte's membrane, to ensure they are properly formed then to see if they recognize self-antigens, i.e. molecules that identify the body's own cells. Then another selection, called negative selection, tests TCRs to make sure they don't react too aggressively to self-antigens.
"Cells that pass these checks then have TCRs that tolerate self- yet react to enemy antigens.
"You don't want the cells with strongly grabbing receptor sites to turn against the body itself," said Zhu, whose study focused on negative selection.
***
"For about two weeks in the thymus, multiple T cell receptor sites engage in one- or two-handed handshakes, which send signals into the thymocyte that make it either mature into a T cell or commit suicide.
"The researchers found that the two-handedness markedly resisted the force applied to break the grip between the T cell receptor and the self-antigen, thus prolonging the duration of the handshake. A long grip sent signals for the thymocyte to die.
"That's the study's elegant finding," Zhu said. "That the force is significant for the selection to work."
"The researchers also made the novel discovery that CD8's handshake participation constitutes a signal coming from inside the thymocyte back out to the self-antigen in answer to its initial signal.
"Together, the outside-in and inside-out signals create a feedback loop that perpetuates the handshake:
1. Self-antigen touches receptor.
2. Receptor fires signal into cell and interacts with self-antigen too aggressively.
3. Inside cell membrane, signal pulls CD8 closer.
4. Outside cell membrane, CD8 strengthens handshake.
5. When the self-antigen slips a bit, the double-handed grip can coax it back into the receptor, kicking off another signal, restarting the signaling cycle again and again.
6. Many feedback loops trigger cell suicide."
Comment: Au automatic system controlled by a feedback loop. All life maintains its homeostasis by these loops. This is an excellent example. Too complex for chance, it had to be designed.
Immunity: nose control of bacteria
by David Turell , Tuesday, November 13, 2018, 17:25 (1989 days ago) @ David Turell
New research shows how bacteria are blocked in the nostrils:
https://cosmosmagazine.com/biology/being-nosey-what-happens-when-we-breathe-in-bacteria
"When we breathe in bacteria, cells along our nasal passages release “tiny fluid-filled sacs,” called exosomes, that directly fight the microbes. They also warn cells further along the route, prompting them to do the same, effectively arming the whole system, according to research led by Benjamin Bleier, a sinus surgeon at Massachusetts Eye and Ear in Boston, US.
“Similar to kicking a hornets’ nest, the nose releases billions of exosomes into the mucus at the first sign of bacteria, killing the bacteria and arming cells throughout the airway with a natural, potent defence,” Bleier explains.
“'It's almost like this swarm of exosomes vaccinates cells further down the airway against a microbe before they even have a chance to see it.”
***
"Exosomes are vesicles released by cells and are found in bodily fluid such as blood, urine, and mucous. These particular ones attack bacteria and carry antimicrobial proteins along the airway.
"The defence happens rapidly. Within five minutes of making contact with bacteria, the number of exosomes in nasal mucous doubles, and within each one the amount of nitric oxide synthase, an antimicrobial, also doubles.
***
"During the study, the researchers uncovered the mechanism by first simulating an exposure to bacteria in mucous samples,. They then confirmed their findings in live patients.
"They report that the exosomes were “as effective as antibiotics at killing the bacteria”. They also found the exosomes were “rapidly taken up” by other cells, passing on antimicrobial molecules.
"'The nose provides a unique opportunity to directly study the immune system of the entire human airway – including the lungs," Bleier says."
Comment: Another beautifully desiged system of protection
Immunity: Gamma Delta T cells hunt with precision
QUOTES: […] a single protein on a single cell type can perform both functions, detecting when things aren't normal and then mounting a specific response.
" The new research found that the cells use two different checks to make sure they don't kill a healthy cell: checking if the cell looks dangerous but also whether it is nonetheless functioning normally.
"The analysis showed that Gamma Delta T cells are highly adaptable and can learn to tackle specific threats such as cancer cells. […] when the cells sit in the gut, they spare cells behaving like normal gut cells, whereas they seemingly use other scores of normality to make judgement calls about cells in the skin."
DAVID: These are obviously automatic reactions on the part of these designed cells, which must have been present from the beginning of multicellular organisms with a circulatory system, since it appears cancer development has always been present and this balance was necessary.
Yeah, yeah, the cells detect abnormalities, mount responses, use two different checks, are highly adaptable, can learn to tackle specific threats and make judgement calls – but despite all these attributes of intelligence, the reactions are “obviously automatic”. Nothing obvious about it.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Tuesday, November 13, 2018, 17:46 (1989 days ago) @ dhw
QUOTES: […] a single protein on a single cell type can perform both functions, detecting when things aren't normal and then mounting a specific response.
" The new research found that the cells use two different checks to make sure they don't kill a healthy cell: checking if the cell looks dangerous but also whether it is nonetheless functioning normally.
"The analysis showed that Gamma Delta T cells are highly adaptable and can learn to tackle specific threats such as cancer cells. […] when the cells sit in the gut, they spare cells behaving like normal gut cells, whereas they seemingly use other scores of normality to make judgement calls about cells in the skin."
DAVID: These are obviously automatic reactions on the part of these designed cells, which must have been present from the beginning of multicellular organisms with a circulatory system, since it appears cancer development has always been present and this balance was necessary.dhw: Yeah, yeah, the cells detect abnormalities, mount responses, use two different checks, are highly adaptable, can learn to tackle specific threats and make judgement calls – but despite all these attributes of intelligence, the reactions are “obviously automatic”. Nothing obvious about it.
Note the bold in what is quoted above from the article. A molecule without a brain knows what to do. No other controls found, Obviously designed to be automatic. Just a programmed response to stimuli.
Immunity: Gamma Delta T cells hunt with precision
QUOTES: […] a single protein on a single cell type can perform both functions, detecting when things aren't normal and then mounting a specific response. (David’s bold)
"The new research found that the cells use two different checks to make sure they don't kill a healthy cell: checking if the cell looks dangerous but also whether it is nonetheless functioning normally."
"The analysis showed that Gamma Delta T cells are highly adaptable and can learn to tackle specific threats such as cancer cells. […] when the cells sit in the gut, they spare cells behaving like normal gut cells, whereas they seemingly use other scores of normality to make judgement calls about cells in the skin."
DAVID: These are obviously automatic reactions on the part of these designed cells, which must have been present from the beginning of multicellular organisms with a circulatory system, since it appears cancer development has always been present and this balance was necessary.
dhw: Yeah, yeah, the cells detect abnormalities, mount responses, use two different checks, are highly adaptable, can learn to tackle specific threats and make judgement calls – but despite all these attributes of intelligence, the reactions are “obviously automatic”. Nothing obvious about it.
DAVID: Note the bold in what is quoted above from the article. A molecule without a brain knows what to do. No other controls found, Obviously designed to be automatic. Just a programmed response to stimuli.
As usual, you switch from cells to molecules. But yes, “my” scientists believe that cells are intelligent even though they do not have brains. And why do you ignore all the attributes of intelligence that I have listed? Do you want me to bold them? Or do you not agree that the ability to learn and to make judgements denotes intelligence? Not comparable to human intelligence, of course, but not even you would limit the possession of intelligence to humans.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Wednesday, November 14, 2018, 15:12 (1989 days ago) @ dhw
QUOTES: […] a single protein on a single cell type can perform both functions, detecting when things aren't normal and then mounting a specific response. (David’s bold)
"The new research found that the cells use two different checks to make sure they don't kill a healthy cell: checking if the cell looks dangerous but also whether it is nonetheless functioning normally."
"The analysis showed that Gamma Delta T cells are highly adaptable and can learn to tackle specific threats such as cancer cells. […] when the cells sit in the gut, they spare cells behaving like normal gut cells, whereas they seemingly use other scores of normality to make judgement calls about cells in the skin."
DAVID: These are obviously automatic reactions on the part of these designed cells, which must have been present from the beginning of multicellular organisms with a circulatory system, since it appears cancer development has always been present and this balance was necessary.
dhw: Yeah, yeah, the cells detect abnormalities, mount responses, use two different checks, are highly adaptable, can learn to tackle specific threats and make judgement calls – but despite all these attributes of intelligence, the reactions are “obviously automatic”. Nothing obvious about it.
DAVID: Note the bold in what is quoted above from the article. A molecule without a brain knows what to do. No other controls found, Obviously designed to be automatic. Just a programmed response to stimuli.
dhw: As usual, you switch from cells to molecules. But yes, “my” scientists believe that cells are intelligent even though they do not have brains. And why do you ignore all the attributes of intelligence that I have listed? Do you want me to bold them? Or do you not agree that the ability to learn and to make judgements denotes intelligence? Not comparable to human intelligence, of course, but not even you would limit the possession of intelligence to humans.
Not a switch. All cellular activity is down through actions of molecules, which act purposefully, by design. The intelligence is in the design of molecular response, and not due to intelligent action by molecules.
Immunity: Gamma Delta T cells hunt with precision
DAVID: Note the bold in what is quoted above from the article. A molecule without a brain knows what to do. No other controls found, Obviously designed to be automatic. Just a programmed response to stimuli.
dhw: As usual, you switch from cells to molecules. But yes, “my” scientists believe that cells are intelligent even though they do not have brains. And why do you ignore all the attributes of intelligence that I have listed? Do you want me to bold them? Or do you not agree that the ability to learn and to make judgements denotes intelligence? Not comparable to human intelligence, of course, but not even you would limit the possession of intelligence to humans.
DAVID: Not a switch. All cellular activity is down through actions of molecules, which act purposefully, by design. The intelligence is in the design of molecular response, and not due to intelligent action by molecules.
You know as well as I do that there are tens of thousands of molecules in a single cell, and of course all cellular activity takes place through their actions. The question is what DETERMINES their actions. I do not say that my arms, legs, mouth, hands, fingers are intelligent. Their actions are determined by what I would like to think of as the intelligent “me”. Similarly I (and “my” scientists) propose that the actions of the molecules are determined by the intelligent cell or cell community. Now perhaps you will tell us why you do not regard the ability to learn and to make judgements as an attribute of intelligence.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Thursday, November 15, 2018, 18:48 (1987 days ago) @ dhw
dhw: As usual, you switch from cells to molecules. But yes, “my” scientists believe that cells are intelligent even though they do not have brains. And why do you ignore all the attributes of intelligence that I have listed? Do you want me to bold them? Or do you not agree that the ability to learn and to make judgements denotes intelligence? Not comparable to human intelligence, of course, but not even you would limit the possession of intelligence to humans.
DAVID: Not a switch. All cellular activity is down through actions of molecules, which act purposefully, by design. The intelligence is in the design of molecular response, and not due to intelligent action by molecules.
dhw: You know as well as I do that there are tens of thousands of molecules in a single cell, and of course all cellular activity takes place through their actions. The question is what DETERMINES their actions. I do not say that my arms, legs, mouth, hands, fingers are intelligent. Their actions are determined by what I would like to think of as the intelligent “me”. Similarly I (and “my” scientists) propose that the actions of the molecules are determined by the intelligent cell or cell community. Now perhaps you will tell us why you do not regard the ability to learn and to make judgements as an attribute of intelligence.
Of course your statement about intelligence is a truism for anyone with a conscious state. But we look at the molecular reactions from the outside and do not see the controls.
Dr. Tour is a famous organic biomolecular scientist, an atheist Jew who accepted Christianity. His view of the cell:
https://www.hbu.edu/news-and-events/2018/11/13/world-renowned-scientist-dr-james-tour/
“'When I look at biological systems, and the amazing functionality of a biological system, even if we just take a cell – just a single cell – and you look at the mechanisms within that cell, it is utterly amazing. How can you look at that and just say, ’Oh well, 3.8 billion years ago, under a rock, it just got started up’ – that’s idiocy. It is amazing to look at that. You don’t even have to look at a human being with all of this. You just look at a single cell – a simple cell and the mechanisms within that cell are huge in complexity,” he said.
"Part of being a good scientist is realizing what is still unknown. And the more Tour has learned and studied, the more he is in wonder of creation. “Take any chemist, any biochemist, any evolutionary biologist, and say, ’I will give you all the components of a cell. I’ll give you all the nucleic acids, all the proteins, all the lipids and all the carbohydrates. Could you hook them up in the orders that they need to be hooked up?’ The answer is ’no.’ ’But even if I gave them to you in whatever order hooked up that you wanted, could you then put them together in the cell and have the cell operate?’ And the answer is ’no.’ Anybody who would claim otherwise is a rookie. They really don’t know what they’re talking about. We have no idea how to get this thing working. And when you put it all together, what is the spark of life that gets the thing running? How do you start this thing? Nobody knows. When something dies, it’s very hard to even explain what it is you’ve lost when the cell has stopped functioning. Try to restart that thing – very hard. You don’t even know.”
All he can study is the molecules. There is nothing else to study. In the cell as in the genome we do not know how controls are exerted. We can only look in from outside. We can reduce the reactions to each step. I frankly doubt we will ever fully understand how the
controls work. I view it as possible that all of the carefully orchestrated interactions are all that is needed to have a living cell emerge. I will not ever leave behind the concept that what we see is pure design and needed before each gap in the fossil record. Of course I switched from cells to molecules! I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.
Immunity: Gamma Delta T cells hunt with precision
dhw: As usual, you switch from cells to molecules. But yes, “my” scientists believe that cells are intelligent even though they do not have brains. And why do you ignore all the attributes of intelligence that I have listed? Do you want me to bold them? Or do you not agree that the ability to learn and to make judgements denotes intelligence? Not comparable to human intelligence, of course, but not even you would limit the possession of intelligence to humans.
DAVID: Not a switch. All cellular activity is down through actions of molecules, which act purposefully, by design. The intelligence is in the design of molecular response, and not due to intelligent action by molecules.
dhw: You know as well as I do that there are tens of thousands of molecules in a single cell, and of course all cellular activity takes place through their actions. The question is what DETERMINES their actions. I do not say that my arms, legs, mouth, hands, fingers are intelligent. Their actions are determined by what I would like to think of as the intelligent “me”. Similarly I (and “my” scientists) propose that the actions of the molecules are determined by the intelligent cell or cell community. Now perhaps you will tell us why you do not regard the ability to learn and to make judgements as an attribute of intelligence.
DAVID: Of course your statement about intelligence is a truism for anyone with a conscious state. But we look at the molecular reactions from the outside and do not see the controls.
If it’s a truism that the ability to learn and make judgements is an attribute of intelligence, then why do you constantly reject the argument that the ability of cells to learn and make judgements means that they are intelligent?
DAVID: Dr. Tour is a famous organic biomolecular scientist, an atheist Jew who accepted Christianity. His view of the cell:
https://www.hbu.edu/news-and-events/2018/11/13/world-renowned-scientist-dr-james-tour/
QUOTE: “'When I look at biological systems, and the amazing functionality of a biological system, even if we just take a cell – just a single cell – and you look at the mechanisms within that cell, it is utterly amazing. How can you look at that and just say, ’Oh well, 3.8 billion years ago, under a rock, it just got started up’ – that’s idiocy. It is amazing to look at that. You don’t even have to look at a human being with all of this. You just look at a single cell – a simple cell and the mechanisms within that cell are huge in complexity,” he said.
And the rest of this brilliant article goes into more detail concerning the wondrous complexity of the cell (he doesn’t mention the molecules, which are simply component parts of the cell) and offers the same highly convincing argument for design as your own. But it has nothing whatsoever to do with intelligence versus automaticity!
DAVID: All he can study is the molecules. There is nothing else to study. In the cell as in the genome we do not know how controls are exerted.
So if we do not know, why do you categorically refuse to accept the possibility that the controls are exerted by autonomous intelligence, as championed by “my” scientists.
DAVID: We can only look in from outside. We can reduce the reactions to each step. I frankly doubt we will ever fully understand how the controls work. I view it as possible that all of the carefully orchestrated interactions are all that is needed to have a living cell emerge.
The subject under discussion is not how cells emerge but whether they are intelligent.
DAVID: I will not ever leave behind the concept that what we see is pure design and needed before each gap in the fossil record. Of course I switched from cells to molecules! I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.
Once more: we are not discussing the complexity of the cell, which I acknowledge presents the best possible case for design. We are discussing the concept of cellular intelligence! I do not claim to be a biochemist. I owe my concept of cellular intelligence to people who have spent a lifetime studying cells - sources such as Barbara McClintock, Lynn Margulis, Guenter Albrecht-Buehler, James A. Shapiro – and I do not think their conclusions are superficial or based on a flimsy understanding of what is involved.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Friday, November 16, 2018, 15:15 (1987 days ago) @ dhw
DAVID: Of course your statement about intelligence is a truism for anyone with a conscious state. But we look at the molecular reactions from the outside and do not see the controls.
dhw: If it’s a truism that the ability to learn and make judgements is an attribute of intelligence, then why do you constantly reject the argument that the ability of cells to learn and make judgements means that they are intelligent?
And as I continuously remind you, the appearance of intelligent cells can just as easily be explained as intelligently designed responses, the explanation I accept.
DAVID: Dr. Tour is a famous organic biomolecular scientist, an atheist Jew who accepted Christianity. His view of the cell:
https://www.hbu.edu/news-and-events/2018/11/13/world-renowned-scientist-dr-james-tour/QUOTE: “'When I look at biological systems, and the amazing functionality of a biological system, even if we just take a cell – just a single cell – and you look at the mechanisms within that cell, it is utterly amazing. How can you look at that and just say, ’Oh well, 3.8 billion years ago, under a rock, it just got started up’ – that’s idiocy. It is amazing to look at that. You don’t even have to look at a human being with all of this. You just look at a single cell – a simple cell and the mechanisms within that cell are huge in complexity,” he said.
dhw: And the rest of this brilliant article goes into more detail concerning the wondrous complexity of the cell (he doesn’t mention the molecules, which are simply component parts of the cell) and offers the same highly convincing argument for design as your own. But it has nothing whatsoever to do with intelligence versus automaticity!
But his entire expertese is studying in making man-made organic molecules, so his view of the cell comes from that background.
DAVID: All he can study is the molecules. There is nothing else to study. In the cell as in the genome we do not know how controls are exerted.So if we do not know, why do you categorically refuse to accept the possibility that the controls are exerted by autonomous intelligence, as championed by “my” scientists.
DAVID: We can only look in from outside. We can reduce the reactions to each step. I frankly doubt we will ever fully understand how the controls work. I view it as possible that all of the carefully orchestrated interactions are all that is needed to have a living cell emerge.
dhw: The subject under discussion is not how cells emerge but whether they are intelligent.
Or are designed to respond intelligently.
DAVID: I will not ever leave behind the concept that what we see is pure design and needed before each gap in the fossil record. Of course I switched from cells to molecules! I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.dhw: Once more: we are not discussing the complexity of the cell, which I acknowledge presents the best possible case for design. We are discussing the concept of cellular intelligence! I do not claim to be a biochemist. I owe my concept of cellular intelligence to people who have spent a lifetime studying cells - sources such as Barbara McClintock, Lynn Margulis, Guenter Albrecht-Buehler, James A. Shapiro – and I do not think their conclusions are superficial or based on a flimsy understanding of what is involved.
And I view their statements as hyperbole to make the point of cells amazing responsiveness. It is simple. From the outside cells are intelligent or they are programmed to respond intelligently. I chose the latter view, as do a herd of ID folks. Note they have heretical ideas like evolution is really devolution. You made no comment.
Immunity: Gamma Delta T cells hunt with precision
DAVID: Of course your statement about intelligence is a truism for anyone with a conscious state. But we look at the molecular reactions from the outside and do not see the controls.
dhw: If it’s a truism that the ability to learn and make judgements is an attribute of intelligence, then why do you constantly reject the argument that the ability of cells to learn and make judgements means that they are intelligent?
DAVID: And as I continuously remind you, the appearance of intelligent cells can just as easily be explained as intelligently designed responses, the explanation I accept.
And that should be the end of this discussion, because “just as easily” is an acknowledgement that “my” scientists may just as easily be right. But you refuse to leave it at that.
dhw: And the rest of this brilliant article goes into more detail concerning the wondrous complexity of the cell (he doesn’t mention the molecules, which are simply component parts of the cell) and offers the same highly convincing argument for design as your own. But it has nothing whatsoever to do with intelligence versus automaticity!
DAVID: But his entire expertese is studying in making man-made organic molecules, so his view of the cell comes from that background.
Why “but”? His article supports design, and has nothing to do with intelligence versus automaticity. The background of “my scientists” is a lifetime study of the behaviour of real cells.
DAVID: I will not ever leave behind the concept that what we see is pure design and needed before each gap in the fossil record. Of course I switched from cells to molecules! I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.
dhw: Once more: we are not discussing the complexity of the cell, which I acknowledge presents the best possible case for design. We are discussing the concept of cellular intelligence! I do not claim to be a biochemist. I owe my concept of cellular intelligence to people who have spent a lifetime studying cells - sources such as Barbara McClintock, Lynn Margulis, Guenter Albrecht-Buehler, James A. Shapiro – and I do not think their conclusions are superficial or based on a flimsy understanding of what is involved.
DAVID: And I view their statements as hyperbole to make the point of cells amazing responsiveness. It is simple. From the outside cells are intelligent or they are programmed to respond intelligently. I chose the latter view, as do a herd of ID folks.
I know you have chosen the latter view. You have also acknowledged that you have a 50/50 chance of being wrong, and I trust you will now also acknowledge that the concept of cellular intelligence (as opposed to your automaticity) is not superficial or based on a flimsy understanding of what is involved.
DAVID: Note they have heretical ideas like evolution is really devolution. You made no comment.
I really don’t know why you think the heretical ideas of your ID herd should convince me that Shapiro and Co are wrong. As for devolution:
QUOTE: "This famous evolutionary experiment proves that in deep time, even given a model population that is optimal for validating evolution , populations do not evolve – but instead devolve."
Nothing to do with cellular intelligence. I actually wrote a reply to this, and then decided it wasn’t worth bothering. My reply was and is:
So humans devolved from bacteria, did they?
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Saturday, November 17, 2018, 15:31 (1985 days ago) @ dhw
DAVID: And as I continuously remind you, the appearance of intelligent cells can just as easily be explained as intelligently designed responses, the explanation I accept.
dhw: And that should be the end of this discussion, because “just as easily” is an acknowledgement that “my” scientists may just as easily be right. But you refuse to leave it at that.
You are ignoring my point that we look in at the cell from the outside and either assumption can be accepted, and I have the right to accept mine, and you have the right to accept your guys point of view. I will never accept that view, until there is proof they are correct.
dhw: And the rest of this brilliant article goes into more detail concerning the wondrous complexity of the cell (he doesn’t mention the molecules, which are simply component parts of the cell) and offers the same highly convincing argument for design as your own. But it has nothing whatsoever to do with intelligence versus automaticity!DAVID: But his entire expertese is studying in making man-made organic molecules, so his view of the cell comes from that background.
dhw: Why “but”? His article supports design, and has nothing to do with intelligence versus automaticity. The background of “my scientists” is a lifetime study of the behaviour of real cells.
Behavior as I have pointed out has two equally possible reasons. You have decided to chose one interpretation because it fits what you want to believe.
DAVID: I will not ever leave behind the concept that what we see is pure design and needed before each gap in the fossil record. Of course I switched from cells to molecules! I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.dhw: Once more: we are not discussing the complexity of the cell, which I acknowledge presents the best possible case for design. We are discussing the concept of cellular intelligence! I do not claim to be a biochemist. I owe my concept of cellular intelligence to people who have spent a lifetime studying cells - sources such as Barbara McClintock, Lynn Margulis, Guenter Albrecht-Buehler, James A. Shapiro – and I do not think their conclusions are superficial or based on a flimsy understanding of what is involved.
DAVID: And I view their statements as hyperbole to make the point of cells amazing responsiveness. It is simple. From the outside cells are intelligent or they are programmed to respond intelligently. I chose the latter view, as do a herd of ID folks.
dhw: I know you have chosen the latter view. You have also acknowledged that you have a 50/50 chance of being wrong, and I trust you will now also acknowledge that the concept of cellular intelligence (as opposed to your automaticity) is not superficial or based on a flimsy understanding of what is involved.
I never said superficial or flimsy. That is your interpretation. All of them have done magnificent work. They are as amazed at the work of cells as I am. Their statements are only a human interpretation of what they have found. They do not have proof, nor do I. You are simply offering their opinions as fact. It isn't
DAVID: Note they have heretical ideas like evolution is really devolution. You made no comment.dhw: I really don’t know why you think the heretical ideas of your ID herd should convince me that Shapiro and Co are wrong. As for devolution:
QUOTE: "This famous evolutionary experiment proves that in deep time, even given a model population that is optimal for validating evolution , populations do not evolve – but instead devolve."
dhw: Nothing to do with cellular intelligence. I actually wrote a reply to this, and then decided it wasn’t worth bothering. My reply was and is:
So humans devolved from bacteria, did they?
Do you miss the point? The claim seems to be all the information was there from the beginning and evolution advances from subtraction.
Immunity: Gamma Delta T cells hunt with precision
DAVID: And as I continuously remind you, the appearance of intelligent cells can just as easily be explained as intelligently designed responses, the explanation I accept.
dhw: And that should be the end of this discussion, because “just as easily” is an acknowledgement that “my” scientists may just as easily be right. But you refuse to leave it at that.
DAVID: You are ignoring my point that we look in at the cell from the outside and either assumption can be accepted, and I have the right to accept mine, and you have the right to accept your guys point of view. I will never accept that view, until there is proof they are correct.
I’m afraid it is you who are missing all the points. You have fixed beliefs, whereas I simply offer HYPOTHESES. As I can find no logic in your interpretation of evolution, I offer an alternative which depends on the concept of cellular intelligence (possibly God-given). You admit that the latter has a 50/50 chance of being correct. If there is a 50/50 chance, clearly there is no proof that your view is correct either, but you rigidly stick to it and therefore completely reject the opposite view. Double standards.
DAVID: But his entire expertese is studying in making man-made organic molecules, so his view of the cell comes from that background.
dhw: Why “but”? His article supports design, and has nothing to do with intelligence versus automaticity. The background of “my scientists” is a lifetime study of the behaviour of real cells.
DAVID: Behavior as I have pointed out has two equally possible reasons. You have decided to chose one interpretation because it fits what you want to believe.
What I am proposing is a hypothesis, not a belief, because I have always accepted your objections: we do not KNOW that cells are intelligent, and if they are, we do not KNOW that they are capable of designing the major innovations that lead to speciation (broad sense). Nor do we KNOW (a) that your God exists, and (b) that his purpose was humans and yet he specially designed 50,000 spider webs etc. You have rigid beliefs in all your hypotheses, and always blame me for wanting proof before I take the plunge you have taken. I can only consider the pros and cons of all the hypotheses, theistic and atheistic, but because I find flaws in all of them, I remain without belief in any of them.
dhw: I trust you will now also acknowledge that the concept of cellular intelligence (as opposed to your automaticity) is not superficial or based on a flimsy understanding of what is involved.
DAVID: I never said superficial or flimsy. That is your interpretation. All of them have done magnificent work. They are as amazed at the work of cells as I am. Their statements are only a human interpretation of what they have found. They do not have proof, nor do I. You are simply offering their opinions as fact. It isn't.
I do NOT offer it as fact. But it is a believable basis for my hypothesis concerning how evolution works. You continue to mix up the argument for design with the argument for cellular intelligence. They are totally separate, and you use the former (which I accept) to try and discredit the latter. Here are your exact words: “I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.” My theorizing, as you know perfectly well, has nothing to do with design but is based on the concept of cellular intelligence, which in turn is based entirely on the magnificent work of “my” scientists. If my concept of cellular intelligence is superficial and flimsy, that can only mean that their concept is superficial and flimsy.
DAVID: Note they [ID-ers] have heretical ideas like evolution is really devolution. You made no comment.
dhw: I really don’t know why you think the heretical ideas of your ID herd should convince me that Shapiro and Co are wrong. As for devolution:
QUOTE: "This famous evolutionary experiment proves that in deep time, even given a model population that is optimal for validating evolution , populations do not evolve – but instead devolve."
dhw: Nothing to do with cellular intelligence. I actually wrote a reply to this, and then decided it wasn’t worth bothering. My reply was and is: So humans devolved from bacteria, did they?
DAVID: Do you miss the point? The claim seems to be all the information was there from the beginning and evolution advances from subtraction.
I would suggest that multicellularity = addition, not subtraction. Why do you think their view is considered heretical?
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Sunday, November 18, 2018, 23:24 (1984 days ago) @ dhw
DAVID: You are ignoring my point that we look in at the cell from the outside and either assumption can be accepted, and I have the right to accept mine, and you have the right to accept your guys point of view. I will never accept that view, until there is proof they are correct.
dhw: I’m afraid it is you who are missing all the points. You have fixed beliefs, whereas I simply offer HYPOTHESES. As I can find no logic in your interpretation of evolution, I offer an alternative which depends on the concept of cellular intelligence (possibly God-given). You admit that the latter has a 50/50 chance of being correct. If there is a 50/50 chance, clearly there is no proof that your view is correct either, but you rigidly stick to it and therefore completely reject the opposite view. Double standards.
Of course I have fixed beliefs. I'm on one side of the fence, and you are on both. Only you have a chance of being correct 100% of the time if the issue is ever proven.
DAVID: Behavior as I have pointed out has two equally possible reasons. You have decided to chose one interpretation because it fits what you want to believe.
dhw: What I am proposing is a hypothesis, not a belief, because I have always accepted your objections: we do not KNOW that cells are intelligent, and if they are, we do not KNOW that they are capable of designing the major innovations that lead to speciation (broad sense). Nor do we KNOW (a) that your God exists, and (b) that his purpose was humans and yet he specially designed 50,000 spider webs etc. You have rigid beliefs in all your hypotheses, and always blame me for wanting proof before I take the plunge you have taken. I can only consider the pros and cons of all the hypotheses, theistic and atheistic, but because I find flaws in all of them, I remain without belief in any of them.
A definition of a rigid agnostic.
DAVID: I never said superficial or flimsy. That is your interpretation. All of them have done magnificent work. They are as amazed at the work of cells as I am. Their statements are only a human interpretation of what they have found. They do not have proof, nor do I. You are simply offering their opinions as fact. It isn't.
I do NOT offer it as fact. But it is a believable basis for my hypothesis concerning how evolution works. You continue to mix up the argument for design with the argument for cellular intelligence. They are totally separate, and you use the former (which I accept) to try and discredit the latter. Here are your exact words: “I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.” My theorizing, as you know perfectly well, has nothing to do with design but is based on the concept of cellular intelligence, which in turn is based entirely on the magnificent work of “my” scientists. If my concept of cellular intelligence is superficial and flimsy, that can only mean that their concept is superficial and flimsy.
And I have told you they have made an interpretation of their work, which is not accepted by many current scientists. Their interpretation is not proof and only a possibility.
DAVID: Note they [ID-ers] have heretical ideas like evolution is really devolution. You made no comment.dhw: I really don’t know why you think the heretical ideas of your ID herd should convince me that Shapiro and Co are wrong. As for devolution:
QUOTE: "This famous evolutionary experiment proves that in deep time, even given a model population that is optimal for validating evolution , populations do not evolve – but instead devolve."
dhw: Nothing to do with cellular intelligence. I actually wrote a reply to this, and then decided it wasn’t worth bothering. My reply was and is: So humans devolved from bacteria, did they?
DAVID: Do you miss the point? The claim seems to be all the information was there from the beginning and evolution advances from subtraction.
dhw: I would suggest that multicellularity = addition, not subtraction. Why do you think their view is considered heretical?
You misunderstand. Behe has a new book on it which I intend to read. Multicellularity is simply a larger organism than single cells. The subtraction, if it occurs, is in DNA, not phenotypes which appear from its work..
Immunity: Gamma Delta T cells hunt with precision
dhw: You have fixed beliefs, whereas I simply offer HYPOTHESES. As I can find no logic in your interpretation of evolution, I offer an alternative which depends on the concept of cellular intelligence (possibly God-given). You admit that the latter has a 50/50 chance of being correct. If there is a 50/50 chance, clearly there is no proof that your view is correct either, but you rigidly stick to it and therefore completely reject the opposite view. Double standards.
DAVID: Of course I have fixed beliefs. I'm on one side of the fence, and you are on both. Only you have a chance of being correct 100% of the time if the issue is ever proven.
It is you who have a chance of 100%, and a chance of 0%. I am 50% right and 50% wrong. But this does not alter the fact that by demanding proof of my 50% hypothesis and clinging to your own unproven 50% hypothesis, you are applying double standards.
Under “James is back” – which I’m afraid did not have me jumping up and down with excitement! - you made a very wise remark: “Fixed religious beliefs do not help in ascertaining accurate history.” Or accurate science.
dhw: I can only consider the pros and cons of all the hypotheses, theistic and atheistic, but because I find flaws in all of them, I remain without belief in any of them.
DAVID: A definition of a rigid agnostic.
Your use of the word “rigid” does not provide any defence of the flaws I keep pointing out.
DAVID: I never said superficial or flimsy.
dhw:[…] Here are your exact words: “I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.” My theorizing, as you know perfectly well, has nothing to do with design but is based on the concept of cellular intelligence, which in turn is based entirely on the magnificent work of “my” scientists. If my concept of cellular intelligence is superficial and flimsy, that can only mean that their concept is superficial and flimsy.
DAVID: And I have told you they have made an interpretation of their work, which is not accepted by many current scientists. Their interpretation is not proof and only a possibility.
Already agreed a hundred times. I was responding to your claim (bolded) that you had never called the argument for cellular design superficial or flimsy. I trust you will now withdraw that description.
DAVID: Note they [ID-ers] have heretical ideas like evolution is really devolution. You made no comment.
QUOTE: "This famous evolutionary experiment proves that in deep time, even given a model population that is optimal for validating evolution , populations do not evolve – but instead devolve."
dhw: […] So humans devolved from bacteria, did they?
DAVID: Do you miss the point? The claim seems to be all the information was there from the beginning and evolution advances from subtraction.
dhw: I would suggest that multicellularity = addition, not subtraction. Why do you think their view is considered heretical?
DAVID: You misunderstand. Behe has a new book on it which I intend to read. Multicellularity is simply a larger organism than single cells. The subtraction, if it occurs, is in DNA, not phenotypes which appear from its work.
It is not “simply” larger. It involves cells being added to cells. You have called the “devolution” idea heretical. Why? Could it be because it goes against the conventional view that evolution is evolution and not devolution? And are you now saying that parts of bacterial DNA have been subtracted on the way to human DNA?
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Monday, November 19, 2018, 20:46 (1983 days ago) @ dhw
dhw: I can only consider the pros and cons of all the hypotheses, theistic and atheistic, but because I find flaws in all of them, I remain without belief in any of them.
DAVID: A definition of a rigid agnostic.
dhw: Your use of the word “rigid” does not provide any defence of the flaws I keep pointing out.
DAVID: I never said superficial or flimsy.
dhw:[…] Here are your exact words: “I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.” My theorizing, as you know perfectly well, has nothing to do with design but is based on the concept of cellular intelligence, which in turn is based entirely on the magnificent work of “my” scientists. If my concept of cellular intelligence is superficial and flimsy, that can only mean that their concept is superficial and flimsy.
A twisted assertion of what I said. You are not in first hand knowledge of biochemistry. You are secondhandedly accepting the opinions of well-known excellent scientists who have simply expressed an interpretation of their studies that you are willing to accept. Other excellent scientists disagree with their interpretations. Interpretations are not fact but a preferred explanation. You have picked a preference. You are, as usual, missing the difference in results and their interpretation.
DAVID: Note they [ID-ers] have heretical ideas like evolution is really devolution. You made no comment.QUOTE: "This famous evolutionary experiment proves that in deep time, even given a model population that is optimal for validating evolution , populations do not evolve – but instead devolve."
dhw: […] So humans devolved from bacteria, did they?
DAVID: Do you miss the point? The claim seems to be all the information was there from the beginning and evolution advances from subtraction.
dhw: I would suggest that multicellularity = addition, not subtraction. Why do you think their view is considered heretical?
DAVID: You misunderstand. Behe has a new book on it which I intend to read. Multicellularity is simply a larger organism than single cells. The subtraction, if it occurs, is in DNA, not phenotypes which appear from its work.
dhw: It is not “simply” larger. It involves cells being added to cells. You have called the “devolution” idea heretical. Why? Could it be because it goes against the conventional view that evolution is evolution and not devolution? And are you now saying that parts of bacterial DNA have been subtracted on the way to human DNA?
That is what they Are implying.
Immunity: Gamma Delta T cells hunt with precision
DAVID: I never said superficial or flimsy.
dhw:[…] Here are your exact words: “I think your concept of complexity of the cell is superficial since you have not studied biochemistry. This is not meant to criticize you but to indicate that your theorizing is based on a flimsy basis of understanding of what is involved. I hope the Tour quote indicates that to you.” My theorizing, as you know perfectly well, has nothing to do with design but is based on the concept of cellular intelligence, which in turn is based entirely on the magnificent work of “my” scientists. If my concept of cellular intelligence is superficial and flimsy, that can only mean that their concept is superficial and flimsy.
DAVID: A twisted assertion of what I said. You are not in first hand knowledge of biochemistry. You are secondhandedly accepting the opinions of well-known excellent scientists who have simply expressed an interpretation of their studies that you are willing to accept. Other excellent scientists disagree with their interpretations. Interpretations are not fact but a preferred explanation. You have picked a preference. You are, as usual, missing the difference in results and their interpretation.
I have quoted your exact words. Of course my knowledge is second-hand. But if I quote the conclusions of experts, it is absurd to say that because I didn’t do the research myself, the conclusion I quote is superficial and based on a flimsy understanding. At that rate, everything we learn from others is superficial and flimsy! NB: I am NOT stating cellular intelligence as fact. I am using the findings of "excellent scientists" as a basis for a hypothesis concerning the mechanisms of evolution. I offer it as an alternative to your own hypothesis that there is a God who designed every innovation, lifestyle and natural wonder extant and extinct in order to produce humans. Since you have never actually met your God, and I doubt very much whether all your knowledge about innovations, lifestyles and natural wonders extant and extinct is first-hand, would you call your hypothesis superficial and flimsy?
xxxxxx
DAVID: The claim seems to be all the information was there from the beginning and evolution advances from subtraction.
dhw: I would suggest that multicellularity = addition, not subtraction. Why do you think their view is considered heretical?
DAVID: You misunderstand. Behe has a new book on it which I intend to read. Multicellularity is simply a larger organism than single cells. The subtraction, if it occurs, is in DNA, not phenotypes which appear from its work.
dhw: It is not “simply” larger. It involves cells being added to cells. You have called the “devolution” idea heretical. Why? Could it be because it goes against the conventional view that evolution is evolution and not devolution? And are you now saying that parts of bacterial DNA have been subtracted on the way to human DNA?
DAVID: That is what they Are implying.
Perhaps we should drop this subject until you have read Behe’s book. Meanwhile, I’ll stick to the conventional idea that humans resulted from evolution and not devolution.
Under “Junk DNA”:
QUOTE:"These conditions—the accumulation of "junk" DNA, the presence of retrotransposons and their interactions with NHEJ—make the genome more complex. This is one feature that may distinguish advanced organisms, like humans, from simpler ones, like bacteria.”
DAVID’s comment: Once again junk DNA is necessary. This could well explain how advances in evolution were coded into DNA, by simply rearranging DNA, with no need for enlargement. Perhaps this is what ID scientists view as devolution.
If the genome becomes more complex, how does that equate with subtraction and devolution?
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Tuesday, November 20, 2018, 18:03 (1982 days ago) @ dhw
DAVID: A twisted assertion of what I said. You are not in first hand knowledge of biochemistry. You are secondhandedly accepting the opinions of well-known excellent scientists who have simply expressed an interpretation of their studies that you are willing to accept. Other excellent scientists disagree with their interpretations. Interpretations are not fact but a preferred explanation. You have picked a preference. You are, as usual, missing the difference in results and their interpretation.
dhw: I have quoted your exact words. Of course my knowledge is second-hand. But if I quote the conclusions of experts, it is absurd to say that because I didn’t do the research myself, the conclusion I quote is superficial and based on a flimsy understanding. At that rate, everything we learn from others is superficial and flimsy! NB: I am NOT stating cellular intelligence as fact. I am using the findings of "excellent scientists" as a basis for a hypothesis concerning the mechanisms of evolution. I offer it as an alternative to your own hypothesis that there is a God who designed every innovation, lifestyle and natural wonder extant and extinct in order to produce humans. Since you have never actually met your God, and I doubt very much whether all your knowledge about innovations, lifestyles and natural wonders extant and extinct is first-hand, would you call your hypothesis superficial and flimsy?
As usual in your debate style you are not answering my comment as to its true meaning and intent. Of course you didn't do the research and neither did I, but I am trained by several courses in biochemistry and as a physician I have read biochemical articles ever since leaving medical school. I can make judgments about their conclusions that you cannot make. Of course you can quote them, but that doesn't change the point: they can just as well be wrong about their interpretations of the results as I admit I can be. That is the meaning of the 50/50 statement I have made. We are on the outside and all we can do is study molecular reactions which show automatic molecular responses. Nothing about controls which is the crux of the discussion. We have never found out how genes control what processes they manage, and we may never. We are showing more and more how complex the various layers are. Intelligent design is just as likely as any other interpretation. All that can be positively stated is cells react intelligently to stimuli. My very logical point is that level of complex design requires a designing mind.
xxxxxxDAVID: The claim seems to be all the information was there from the beginning and evolution advances from subtraction.
dhw: I would suggest that multicellularity = addition, not subtraction. Why do you think their view is considered heretical?
DAVID: You misunderstand. Behe has a new book on it which I intend to read. Multicellularity is simply a larger organism than single cells. The subtraction, if it occurs, is in DNA, not phenotypes which appear from its work.
dhw: It is not “simply” larger. It involves cells being added to cells. You have called the “devolution” idea heretical. Why? Could it be because it goes against the conventional view that evolution is evolution and not devolution? And are you now saying that parts of bacterial DNA have been subtracted on the way to human DNA?
DAVID: That is what they Are implying.
dhw:Perhaps we should drop this subject until you have read Behe’s book. Meanwhile, I’ll stick to the conventional idea that humans resulted from evolution and not devolution.
They are simply saying devolution of DNA advances evolution. The book is outv soon. I'll get one.
Under “Junk DNA”:QUOTE:"These conditions—the accumulation of "junk" DNA, the presence of retrotransposons and their interactions with NHEJ—make the genome more complex. This is one feature that may distinguish advanced organisms, like humans, from simpler ones, like bacteria.”
DAVID’s comment: Once again junk DNA is necessary. This could well explain how advances in evolution were coded into DNA, by simply rearranging DNA, with no need for enlargement. Perhaps this is what ID scientists view as devolution.
dhw: If the genome becomes more complex, how does that equate with subtraction and devolution?
The gene is changed to an earlier form in the code.
Immunity: Gamma Delta T cells hunt with precision
dhw: Of course my knowledge is second-hand. But if I quote the conclusions of experts, it is absurd to say that because I didn’t do the research myself, the conclusion I quote is superficial and based on a flimsy understanding. At that rate, everything we learn from others is superficial and flimsy! NB: I am NOT stating cellular intelligence as fact. I am using the findings of "excellent scientists" as a basis for a hypothesis concerning the mechanisms of evolution. I offer it as an alternative to your own hypothesis that there is a God who designed every innovation, lifestyle and natural wonder extant and extinct in order to produce humans. Since you have never actually met your God, and I doubt very much whether all your knowledge about innovations, lifestyles and natural wonders extant and extinct is first-hand, would you call your hypothesis superficial and flimsy?
DAVID: As usual in your debate style you are not answering my comment as to its true meaning and intent. Of course you didn't do the research and neither did I, but I am trained by several courses in biochemistry and as a physician I have read biochemical articles ever since leaving medical school. I can make judgments about their conclusions that you cannot make. Of course you can quote them, but that doesn't change the point: they can just as well be wrong about their interpretations of the results as I admit I can be. That is the meaning of the 50/50 statement I have made.
And that IS the point. I quote their conclusion (cells are intelligent), you admit that there is a 50/50 chance of their being right, but because I quote them and did not do the research myself, you tell me that the interpretation is "superficial" and "flimsy".
DAVID: We are on the outside and all we can do is study molecular reactions which show automatic molecular responses. Nothing about controls which is the crux of the discussion. We have never found out how genes control what processes they manage, and we may never. We are showing more and more how complex the various layers are. Intelligent design is just as likely as any other interpretation. All that can be positively stated is cells react intelligently to stimuli. My very logical point is that level of complex design requires a designing mind.
And you know perfectly well that this disagreement is NOT over intelligent design, and I accept the logic of the design argument. The disagreement is whether, if your God exists, he designed cells with or without the autonomous intelligence which forms the basis of my hypothetical evolutionary alternative to your God-designed-it-all-as-stepping-stones-to-humans hypothesis.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Wednesday, November 21, 2018, 22:31 (1981 days ago) @ dhw
dhw: Of course my knowledge is second-hand. But if I quote the conclusions of experts, it is absurd to say that because I didn’t do the research myself, the conclusion I quote is superficial and based on a flimsy understanding. At that rate, everything we learn from others is superficial and flimsy! NB: I am NOT stating cellular intelligence as fact. I am using the findings of "excellent scientists" as a basis for a hypothesis concerning the mechanisms of evolution. I offer it as an alternative to your own hypothesis that there is a God who designed every innovation, lifestyle and natural wonder extant and extinct in order to produce humans. Since you have never actually met your God, and I doubt very much whether all your knowledge about innovations, lifestyles and natural wonders extant and extinct is first-hand, would you call your hypothesis superficial and flimsy?
DAVID: As usual in your debate style you are not answering my comment as to its true meaning and intent. Of course you didn't do the research and neither did I, but I am trained by several courses in biochemistry and as a physician I have read biochemical articles ever since leaving medical school. I can make judgments about their conclusions that you cannot make. Of course you can quote them, but that doesn't change the point: they can just as well be wrong about their interpretations of the results as I admit I can be. That is the meaning of the 50/50 statement I have made.
And that IS the point. I quote their conclusion (cells are intelligent), you admit that there is a 50/50 chance of their being right, but because I quote them and did not do the research myself, you tell me that the interpretation is "superficial" and "flimsy".
DAVID: We are on the outside and all we can do is study molecular reactions which show automatic molecular responses. Nothing about controls which is the crux of the discussion. We have never found out how genes control what processes they manage, and we may never. We are showing more and more how complex the various layers are. Intelligent design is just as likely as any other interpretation. All that can be positively stated is cells react intelligently to stimuli. My very logical point is that level of complex design requires a designing mind.
dhw: And you know perfectly well that this disagreement is NOT over intelligent design, and I accept the logic of the design argument. The disagreement is whether, if your God exists, he designed cells with or without the autonomous intelligence which forms the basis of my hypothetical evolutionary alternative to your God-designed-it-all-as-stepping-stones-to-humans hypothesis.
You have dragged God back into the picture with an invented hypothesis that organisms can evolve themselves, even though the definition of design requires an ability to foresee future needs to which to fit the design. For example, the mammal who enters into a watery life knows how to change the physiology and anatomy aforehand!
Immunity: Gamma Delta T cells hunt with precision
dhw: And you know perfectly well that this disagreement is NOT over intelligent design, and I accept the logic of the design argument. The disagreement is whether, if your God exists, he designed cells with or without the autonomous intelligence which forms the basis of my hypothetical evolutionary alternative to your God-designed-it-all-as-stepping-stones-to-humans hypothesis.
DAVID: You have dragged God back into the picture with an invented hypothesis that organisms can evolve themselves, even though the definition of design requires an ability to foresee future needs to which to fit the design. For example, the mammal who enters into a watery life knows how to change the physiology and anatomy aforehand!
I have not dragged God back into the picture. He has always been in this particular picture as the possible inventor of the intelligent cell. (You keep forgetting that I am an agnostic, not an atheist.) Why do you call it an “invented” hypothesis? It is no more and no less “invented” than your own view that 50,000 spider webs are “stepping stones” to humans (though at least the concept of cellular intelligence has the backing of some experts in the field). And it is you who insist that the anatomy of the whale has to be changed before it can enter the water. As repeated over and over again, my proposal is that organisms change IN RESPONSE to changing conditions, as vividly illustrated by minor adaptations. NOT “aforehand”. I use the term “design” as a counter to “chance” (I suggest that the cell communities deliberately change their structure), but I have always accepted that my hypothesis, like your own, is unproven: nobody knows the extent to which adaptation to new conditions may lead to the major, more complex changes required for speciation. That is why, like your own, my hypothesis remains a hypothesis.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Friday, November 23, 2018, 01:02 (1980 days ago) @ dhw
dhw: And you know perfectly well that this disagreement is NOT over intelligent design, and I accept the logic of the design argument. The disagreement is whether, if your God exists, he designed cells with or without the autonomous intelligence which forms the basis of my hypothetical evolutionary alternative to your God-designed-it-all-as-stepping-stones-to-humans hypothesis.
DAVID: You have dragged God back into the picture with an invented hypothesis that organisms can evolve themselves, even though the definition of design requires an ability to foresee future needs to which to fit the design. For example, the mammal who enters into a watery life knows how to change the physiology and anatomy aforehand!
dhw: I have not dragged God back into the picture. He has always been in this particular picture as the possible inventor of the intelligent cell. (You keep forgetting that I am an agnostic, not an atheist.) Why do you call it an “invented” hypothesis? It is no more and no less “invented” than your own view that 50,000 spider webs are “stepping stones” to humans (though at least the concept of cellular intelligence has the backing of some experts in the field). And it is you who insist that the anatomy of the whale has to be changed before it can enter the water. As repeated over and over again, my proposal is that organisms change IN RESPONSE to changing conditions, as vividly illustrated by minor adaptations. NOT “aforehand”. I use the term “design” as a counter to “chance” (I suggest that the cell communities deliberately change their structure), but I have always accepted that my hypothesis, like your own, is unproven: nobody knows the extent to which adaptation to new conditions may lead to the major, more complex changes required for speciation. That is why, like your own, my hypothesis remains a hypothesis.
What you blithely constantly overlook is the complexity of design required by my prime example of mammals entering a watery environment and changing both physically and physiologically to enter the new situation. Somehow your brilliant cells can figure out how to change themselves to handle the new way of living. It cannot be step by step, as you should believe by accepting design, but then you do invent the idea that since cells/ animals do minor adaptations, they can somehow create giant changes. I find your concept totally illogical. And the fossil record only shows giant jumps in form and function. The fossil record at this point only supports my view. Beware the gaps. Your idea does not cover them.
Immunity: Gamma Delta T cells hunt with precision
dhw: […] And it is you who insist that the anatomy of the whale has to be changed before it can enter the water. As repeated over and over again, my proposal is that organisms change IN RESPONSE to changing conditions, as vividly illustrated by minor adaptations. NOT “aforehand”. I use the term “design” as a counter to “chance” (I suggest that the cell communities deliberately change their structure), but I have always accepted that my hypothesis, like your own, is unproven: nobody knows the extent to which adaptation to new conditions may lead to the major, more complex changes required for speciation. That is why, like your own, my hypothesis remains a hypothesis.
DAVID: What you blithely constantly overlook is the complexity of design required by my prime example of mammals entering a watery environment and changing both physically and physiologically to enter the new situation. Somehow your brilliant cells can figure out how to change themselves to handle the new way of living. It cannot be step by step, as you should believe by accepting design, but then you do invent the idea that since cells/ animals do minor adaptations, they can somehow create giant changes. I find your concept totally illogical. And the fossil record only shows giant jumps in form and function. The fossil record at this point only supports my view. Beware the gaps. Your idea does not cover them.
"What you blithely constantly overlook" is what I have bolded at the end of the response you have quoted above. Nobody knows how the major changes take place, but I don’t know why you think the fossil record supports the view that an unknown, sourceless, immaterial mind personally dabbled with a set of prewhales to give them fins before they entered the water, and then over millions of years did more dabbles to create the other features that distinguish modern whales from the known series of ancestors – each modification somehow but inexplicably being a stepping stone to Homo sapiens. The hypothesis that organisms have a mechanism that enables them to change their own structure in response to changing conditions is not illogical, because we know that is precisely what they do when they adapt (unless you now wish to tell us that your God personally dabbles every minor adaptation). But there is no evidence that the same mechanism is capable of the major changes necessary for speciation, and so it remains a logical HYPOTHESIS. The fact that you reject it while I regard it as possible does not make it illogical. A hypothesis is an idea that is suggested as an explanation for something, but has not been proved to be true. To give another example, I would describe the idea that the complexities of life have been designed by an unknown mind we call God as a logical hypothesis.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Friday, November 23, 2018, 18:23 (1979 days ago) @ dhw
dhw: […] And it is you who insist that the anatomy of the whale has to be changed before it can enter the water. As repeated over and over again, my proposal is that organisms change IN RESPONSE to changing conditions, as vividly illustrated by minor adaptations. NOT “aforehand”. I use the term “design” as a counter to “chance” (I suggest that the cell communities deliberately change their structure), but I have always accepted that my hypothesis, like your own, is unproven: nobody knows the extent to which adaptation to new conditions may lead to the major, more complex changes required for speciation. That is why, like your own, my hypothesis remains a hypothesis.
DAVID: What you blithely constantly overlook is the complexity of design required by my prime example of mammals entering a watery environment and changing both physically and physiologically to enter the new situation. Somehow your brilliant cells can figure out how to change themselves to handle the new way of living. It cannot be step by step, as you should believe by accepting design, but then you do invent the idea that since cells/ animals do minor adaptations, they can somehow create giant changes. I find your concept totally illogical. And the fossil record only shows giant jumps in form and function. The fossil record at this point only supports my view. Beware the gaps. Your idea does not cover them.
dhw: "What you blithely constantly overlook" is what I have bolded at the end of the response you have quoted above. Nobody knows how the major changes take place, but I don’t know why you think the fossil record supports the view that an unknown, sourceless, immaterial mind personally dabbled with a set of prewhales to give them fins before they entered the water, and then over millions of years did more dabbles to create the other features that distinguish modern whales from the known series of ancestors – each modification somehow but inexplicably being a stepping stone to Homo sapiens. The hypothesis that organisms have a mechanism that enables them to change their own structure in response to changing conditions is not illogical, because we know that is precisely what they do when they adapt (unless you now wish to tell us that your God personally dabbles every minor adaptation). But there is no evidence that the same mechanism is capable of the major changes necessary for speciation, and so it remains a logical HYPOTHESIS. The fact that you reject it while I regard it as possible does not make it illogical. A hypothesis is an idea that is suggested as an explanation for something, but has not been proved to be true. To give another example, I would describe the idea that the complexities of life have been designed by an unknown mind we call God as a logical hypothesis.
What you have again ignored is the obvious requirement for complex design to make the required changes. We know organisms can initiate their own minor adaptations. The fossil gaps in the records support only punctuated equilibrium with major advances which require design. Logically only a mind can design to that required degree. Your stretched hypothesis that somehow minor adaptations can reach major adaptations has no evidence of support , by which minor changes in the fossil record show the advance to a major change. What is logical is major gaps require major design. What you describe is a hypothesis which has little likelihood of being correct , based on existing evidence.
Immunity: Gamma Delta T cells hunt with precision
If anyone is still interested in this discussion, please reread my post from yesterday, which answers all the points David has raised below. I’ll try to keep today’s answers shorter.
DAVID: What you have again ignored is the obvious requirement for complex design to make the required changes. We know organisms can initiate their own minor adaptations.
From yesterday, referring back to the day before: Again you have ignored what I bolded last time: I have always accepted that my hypothesis, like your own, is unproven: nobody knows the extent to which adaptation to new conditions may lead to the major, more complex changes required for speciation. That is why, like your own, my hypothesis remains a hypothesis.
Yes, the changes require complex design, and nobody knows how this takes place. We only have unproven hypotheses, including yours and mine.
DAVID: The fossil gaps in the records support only punctuated equilibrium with major advances which require design. Logically only a mind can design to that required degree.
You know that I accept punctuated equilibrium and the need for design. You have no evidence that “logically only a mind can do the designing” if by “a mind” you mean your God. Look at your many ant articles. “Logically” – I’ll keep my theist hat on – it is perfectly possible that your God designed the mechanisms that enable ants and all other organisms to do their own designing, whether external or internal.
DAVID: Your stretched hypothesis that somehow minor adaptations can reach major adaptations has no evidence of support…
Which is why it remains an unproven hypothesis, just like your own hypothesis that your God designed every single innovation, lifestyle and natural wonder extant and extinct in advance of changing conditions and as stepping stones to humans.
DAVID: What you describe is a hypothesis which has little likelihood of being correct, based on existing evidence.
Based on your personal judgement and your fixed belief in a hypothesis for which likewise there is no existing evidence.
Under “The newly found bacterial role”:
QUOTE: "Proponents of this hologenomic concept of evolution argue that if there is a fidelity across generations between hosts and microbes, then the holobiont embodies a coming together of numerous, disparate evolutionary lineages into a singular being, a coalition of many that contributes to the functional integrity of the whole.” (dhw’s bold)
DAVID: […] They create immediate adaptations, for example, in digestion, but it is certainly obvious they do not design giant changes.
The section I have bolded seems to emphasize the process of emergence, whereby the whole is greater than the sum of its parts. (See also my post concerning ants and corvids). This essentially is the basis of my proposal that cells pool their intelligence, but I had never thought of bacteria as members of the same team. It makes perfect sense, though. As to whether these teams are or are not capable of designing giant changes, that is the hypothesis you refuse to consider, but to my mind it is certainly not “certainly obvious” that such “coalitions” cannot design giant changes as well as minor adaptations.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Saturday, November 24, 2018, 17:51 (1978 days ago) @ dhw
If anyone is still interested in this discussion, please reread my post from yesterday, which answers all the points David has raised below. I’ll try to keep today’s answers shorter.
DAVID: What you have again ignored is the obvious requirement for complex design to make the required changes. We know organisms can initiate their own minor adaptations.
dhw: From yesterday, referring back to the day before: Again you have ignored what I bolded last time: I have always accepted that my hypothesis, like your own, is unproven: nobody knows the extent to which adaptation to new conditions may lead to the major, more complex changes required for speciation. That is why, like your own, my hypothesis remains a hypothesis.
Yes, the changes require complex design, and nobody knows how this takes place. We only have unproven hypotheses, including yours and mine.
Yes, both unproven, but I take it one logical step further: complex designs to cross the gaps in the fossil record require the mentation given by a designing mind. Adaptation produces small steps, nothing more, and these are seen, but nothing more on the way to new species
DAVID: The fossil gaps in the records support only punctuated equilibrium with major advances which require design. Logically only a mind can design to that required degree.dhw: You know that I accept punctuated equilibrium and the need for design. You have no evidence that “logically only a mind can do the designing” if by “a mind” you mean your God. Look at your many ant articles. “Logically” – I’ll keep my theist hat on – it is perfectly possible that your God designed the mechanisms that enable ants and all other organisms to do their own designing, whether external or internal.
I've agreed that is possible, but all it does is keep God in control if he mechanisms hav e guidelines.
dhw: Under “The newly found bacterial role”:
QUOTE: "Proponents of this hologenomic concept of evolution argue that if there is a fidelity across generations between hosts and microbes, then the holobiont embodies a coming together of numerous, disparate evolutionary lineages into a singular being, a coalition of many that contributes to the functional integrity of the whole.” (dhw’s bold)DAVID: […] They create immediate adaptations, for example, in digestion, but it is certainly obvious they do not design giant changes.
dhw: The section I have bolded seems to emphasize the process of emergence, whereby the whole is greater than the sum of its parts. (See also my post concerning ants and corvids). This essentially is the basis of my proposal that cells pool their intelligence, but I had never thought of bacteria as members of the same team. It makes perfect sense, though. As to whether these teams are or are not capable of designing giant changes, that is the hypothesis you refuse to consider, but to my mind it is certainly not “certainly obvious” that such “coalitions” might explain innovations (giant changes) as well as adaptations (minor changes).
My objection, as always, is that it takes mental planning to create advanced designs as required by the gaps in the fossil record.
Immunity: Gamma Delta T cells hunt with precision
dhw: I have always accepted that my hypothesis, like your own, is unproven: nobody knows the extent to which adaptation to new conditions may lead to the major, more complex changes required for speciation. That is why, like your own, my hypothesis remains a hypothesis.
Yes, the changes require complex design, and nobody knows how this takes place. We only have unproven hypotheses, including yours and mine.
DAVID: Yes, both unproven, but I take it one logical step further: complex designs to cross the gaps in the fossil record require the mentation given by a designing mind. Adaptation produces small steps, nothing more, and these are seen, but nothing more on the way to new species.
Your one step further is to say that only your God can design innovations, lifestyles and natural wonders, including such items as 50,000 different spider webs, different stages of whale, and the weaverbird’s nest. My theistic proposal is that your God may have designed the mechanism that enables organisms to do their own designing, but I keep agreeing that there is no proof that this mechanism may be responsible for major changes.
DAVID: I've agreed that is possible, but all it does is keep God in control if he mechanisms have guidelines.
Why the if clause with "guidelines"? My theistic proposal is that he did not WANT to keep control, which is why he allowed his mechanism to do its own autonomous designing. Much more interesting than watching billions of automatons do exactly what you want them to do.
QUOTE: "[…] if there is a fidelity across generations between hosts and microbes, then the holobiont embodies a coming together of numerous, disparate evolutionary lineages into a singular being, a coalition of many that contributes to the functional integrity of the whole.” (dhw’s bold)
DAVID: […] They create immediate adaptations, for example, in digestion, but it is certainly obvious they do not design giant changes.
dhw: The section I have bolded seems to emphasize the process of emergence, whereby the whole is greater than the sum of its parts. […] This essentially is the basis of my proposal that cells pool their intelligence, but I had never thought of bacteria as members of the same team. It makes perfect sense, though. As to whether these teams are or are not capable of designing giant changes, that is the hypothesis you refuse to consider, but to my mind it is certainly not “certainly obvious” that such “coalitions” cannot design giant changes as well as minor adaptations. (I have retrospectively changed my own wording here, as what I wrote originally meant the opposite of what I intended! My apologies.)
DAVID: My objection, as always, is that it takes mental planning to create advanced designs as required by the gaps in the fossil record.
Gaps in the fossil record may be the result of saltations, but in any case they do not require your God to have designed every innovation, lifestyle and natural wonder in advance of the changing conditions in which each new organism lives. My proposal is that as conditions change, organisms RESPOND to them by using their possibly God-given intelligence. Intelligence is “mental”, but it is not confined to self-awareness or the ability to plan for the future.
Under “microbiome of coral”:
DAVID: Bacteria and other organisms are everywhere and obviously play a role in evolution as microbiomes:
https://phys.org/news/2018-11-corals-microbiomes-evolved.html
The term “phylosymbiosis” sent me scurrying back to Lynn Margulis, who pioneered the whole idea that symbiosis and cooperation were every bit as crucial to evolution as competition. I found this in a Wikipedia article: https://en.wikipedia.org/wiki/Lynn_Margulis
“…her theory that cell organelles such as mitochondria and chloroplasts were once independent bacteria was largely ignored for another decade, becoming widely accepted only after it was powerfully substantiated through genetic evidence.” The pattern of symbiosis and cooperation becomes clearer and clearer with all these examples, for which many thanks. Incidentally, Margulis was one of “my” scientists who believed in cellular intelligence.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Sunday, November 25, 2018, 20:42 (1977 days ago) @ dhw
dhw: Your one step further is to say that only your God can design innovations, lifestyles and natural wonders, including such items as 50,000 different spider webs, different stages of whale, and the weaverbird’s nest. My theistic proposal is that your God may have designed the mechanism that enables organisms to do their own designing, but I keep agreeing that there is no proof that this mechanism may be responsible for major changes.
Innovations are not minor adaptations. My belief is unchanged. God is in control even if an inventive mechanism exists. I have no idea why you want God to give up full control. I realize as an agnostic, you can invent any kind of God you want. I'll stick with religion's view of Him as a Supreme Being.
DAVID: I've agreed that is possible, but all it does is keep God in control if he mechanisms have guidelines.dhw: Why the if clause with "guidelines"? My theistic proposal is that he did not WANT to keep control, which is why he allowed his mechanism to do its own autonomous designing. Much more interesting than watching billions of automatons do exactly what you want them to do.
"Much more interesting" is again humanizing Him which you can't resist doing.
DAVID: My objection, as always, is that it takes mental planning to create advanced designs as required by the gaps in the fossil record.dhw: Gaps in the fossil record may be the result of saltations, but in any case they do not require your God to have designed every innovation, lifestyle and natural wonder in advance of the changing conditions in which each new organism lives.
A non-answer, Popping in the word 'saltations' applies a label to gaps. But what makes the saltation (which by definition is a new design) happen. What is the agency that causes saltation? .
dhw: Under “microbiome of coral”:
DAVID: Bacteria and other organisms are everywhere and obviously play a role in evolution as microbiomes:
https://phys.org/news/2018-11-corals-microbiomes-evolved.htmldhw: The term “phylosymbiosis” sent me scurrying back to Lynn Margulis, who pioneered the whole idea that symbiosis and cooperation were every bit as crucial to evolution as competition. I found this in a Wikipedia article: https://en.wikipedia.org/wiki/Lynn_Margulis
“…her theory that cell organelles such as mitochondria and chloroplasts were once independent bacteria was largely ignored for another decade, becoming widely accepted only after it was powerfully substantiated through genetic evidence.” The pattern of symbiosis and cooperation becomes clearer and clearer with all these examples, for which many thanks. Incidentally, Margulis was one of “my” scientists who believed in cellular intelligence.
I know. The cells are designed to make intelligent responses to stimuli.
Immunity: Gamma Delta T cells hunt with precision
dhw: Your one step further is to say that only your God can design innovations, lifestyles and natural wonders, including such items as 50,000 different spider webs, different stages of whale, and the weaverbird’s nest. My theistic proposal is that your God may have designed the mechanism that enables organisms to do their own designing, but I keep agreeing that there is no proof that this mechanism may be responsible for major changes.
DAVID: Innovations are not minor adaptations.
I know. That is why I keep repeating that we have no proof that the mechanism for adaptation is also capable of innovation. We have no proven explanation for innovation, which is why we hypothesize.
DAVID: My belief is unchanged. God is in control even if an inventive mechanism exists. I have no idea why you want God to give up full control. I realize as an agnostic, you can invent any kind of God you want. I'll stick with religion's view of Him as a Supreme Being.
Theists like yourself can and do invent any kind of God they want. If he exists, I have no quarrel with the concept of your God as a Supreme Being. That does not mean he does not have any characteristics in common with ourselves – who according to the bible are made in his image. I do not “want” him to give up full control. My theistic hypothesis is that he deliberately gave up full control (as below), and this explains the higgledy-piggledy history of life on Earth. Your own reading of his mind – that he created 50,000 spider webs etc. etc. in order to produce humans – makes no sense even to you, which is why you keep telling us his logic is different from ours.
DAVID: I've agreed that is possible, but all it does is keep God in control if he mechanisms have guidelines.
dhw: Why the if clause with "guidelines"? My theistic proposal is that he did not WANT to keep control, which is why he allowed his mechanism to do its own autonomous designing. Much more interesting than watching billions of automatons do exactly what you want them to do.
DAVID: "Much more interesting" is again humanizing Him which you can't resist doing.
That does not make my hypothesis illogical, and in any case you have frequently told us you think your God is watching us with interest. (See also under "Neanderthal".)
DAVID: My objection, as always, is that it takes mental planning to create advanced designs as required by the gaps in the fossil record.
dhw: Gaps in the fossil record may be the result of saltations, but in any case they do not require your God to have designed every innovation, lifestyle and natural wonder in advance of the changing conditions in which each new organism lives.
DAVID: A non-answer, Popping in the word 'saltations' applies a label to gaps. But what makes the saltation (which by definition is a new design) happen. What is the agency that causes saltation?
Nobody knows. You propose a divine 3.8-billion-year computer programme or direct divine dabbling. I propose a possibly God-given, autonomous intelligence.
Immunity: Gamma Delta T cells hunt with precision
by David Turell , Monday, November 26, 2018, 19:22 (1976 days ago) @ dhw
DAVID: Innovations are not minor adaptations.
I know. That is why I keep repeating that we have no proof that the mechanism for adaptation is also capable of innovation. We have no proven explanation for innovation, which is why we hypothesize.
DAVID: My belief is unchanged. God is in control even if an inventive mechanism exists. I have no idea why you want God to give up full control. I realize as an agnostic, you can invent any kind of God you want. I'll stick with religion's view of Him as a Supreme Being.
dhw: Theists like yourself can and do invent any kind of God they want. If he exists, I have no quarrel with the concept of your God as a Supreme Being. That does not mean he does not have any characteristics in common with ourselves – who according to the bible are made in his image. I do not “want” him to give up full control. My theistic hypothesis is that he deliberately gave up full control (as below), and this explains the higgledy-piggledy history of life on Earth. Your own reading of his mind – that he created 50,000 spider webs etc. etc. in order to produce humans – makes no sense even to you, which is why you keep telling us his logic is different from ours.
Why would I keep repeating the same idea? I make sense to me. Stop denigrating my thought processes. Again slighting my view: the diversity provides econiche supplies of food so life can survive for all the time evolution took. You illogically want HIM to view spectacles. You've constantly downgraded God to a human level. Of course God is logical in His own purposeful way.
Immunity: macrophage mitochondria help to fight bacteria
by David Turell , Wednesday, January 02, 2019, 21:19 (1939 days ago) @ David Turell
They add to the armamentarium:
https://www.the-scientist.com/the-literature/mitochondria-play-an-unexpected-role-in-ki...
"One piece of evidence for mitochondria’s role surfaced in 2011, when researchers curtailed the production of reactive oxygen species (ROS)—highly destructive molecules that are byproducts of metabolism—in mouse macrophage mitochondria, and found that the immune cells became less effective at killing bacteria. Four years later, immunologist Mary O’Riordan of the University of Michigan Medical School uncovered another piece of the puzzle when she exposed mouse macrophages to the bacterium Staphylococcus aureus. This appeared to activate a particular stress pathway in the cells’ endoplasmic reticulum, which in turn revved up production of ROS.
"To find out where the ROS were coming from, O’Riordan and her colleagues recently extracted macrophages from mice and used CRISPR-Cas9 to cut out the gene encoding IRE1α, a stress-sensing protein in the endoplasmic reticulum. When the researchers exposed these cells to S. aureus, they observed markedly decreased production of ROS in the macrophages’ mitochondria, and the cells were much less effective at killing the bacteria than were unaltered macrophages. The team then used fluorescent probes to visualize the ROS hydrogen peroxide in normally functioning macrophages and observed the compound travelling from mitochondria to the phagosome. Additional experiments showed that this transport occurs through vesicles that bud off from mitochondria and are shuttled to the phagosome. Macrophages deficient in Parkin, a gene involved in generating mitochondria-derived vesicles, proved less able to kill S. aureus and two other types of microbes.“
"What I think happens is the bacteria [get] engulfed, the signal is sent to turn on ER stress, that turns on mitochondrial ROS, and they quickly send out these packages to the phagosome,” where they are lobbed into bacteria, O’Riordan explains. Researchers tend to think of mitochondria primarily as power plants, she adds, “but in fact, the cell has evolved to use these organelles and many of their constituent parts in lots of different ways,” such as in peroxisome formation and for mediating programmed cell death.
"For Greg Fairn, a cell biologist at the University of Toronto who was not involved in the study, the results represent “a new twist” on macrophage antimicrobial defenses. Phagosomes have their own toxins and ROS-producing machinery to kill bacteria, he notes, so the newly discovered mechanism may destroy the tougher, more resistant strains. Repurposing mitochondrial ROS to kill pathogens is an elegant mechanism, he adds. “It’s almost taking advantage of something that’s an unwanted byproduct,” Fairn says, adding one more tool to macrophages’ arsenal against invading bacteria."
Comment: As dangerous as oxygen molecular species can be and we are filled with antioxidant defenses, this is a clever adaptation of the defense mechanisms against oxygen to repurpose them to add to defense. Another layer of immune system complexity not an antibody, but a killer chemical byproduct.
Immunity: directing T cells to site of infection
by David Turell , Friday, January 18, 2019, 21:52 (1923 days ago) @ David Turell
Another complex protein mechanism:
https://www.nature.com/articles/d41586-019-00175-0?utm_source=Nature+Briefing&utm_c...
"A fever fights infection by helping immune cells to crawl along blood-vessel walls to attack invading microbes.
"JianFeng Chen at the Shanghai Institute of Biochemistry and Cell Biology in China and his colleagues grew immune cells called T cells from mice, and raised the temperature of these cells from the normal mouse body temperature of 37 °C to 40 °C — the equivalent of a high fever. This heat triggered the T cells to start producing heat-shock proteins (Hsps), which protect cells against stress.
"The Hsps travelled to the inner surface of cells’ outer membranes, where they bound to the tails of membrane proteins known as integrins. This process pulled integrins together, and the integrin sections jutting from the cells’ outer surfaces formed complexes that stuck to blood-vessel walls. The formation of integrin complexes also triggered the migration of T cells to infection sites.
"The researchers then engineered mice to have a mutated form of integrin that couldn’t bind to Hsps. When the team infected these animals with a diarrhoea-causing bacterium (Salmonella typhimurium), the mice died quickly from fever and infection. The findings suggest that therapies designed to raise levels of Hsps could help to fight infection."
Comment: A typical chain reaction by specified molecules. Certainly looks designed. All the process had to be integrated. The T cells responded to a signal stimulus.
Immunity: basal cell importance
by David Turell , Monday, January 21, 2019, 17:37 (1920 days ago) @ David Turell
edited by David Turell, Monday, January 21, 2019, 17:49
They are a tiny portion of immune cell types, but they act to call for an inflammatory reaction at the site of infection:
https://medicalxpress.com/news/2019-01-secret-sepsis-rare-cell.html
"'As one of the rarest cell types in the body, basophils make up less than 1% of a person's white blood cells," said Piliponsky, an associate professor of pediatrics at the University of Washington School of Medicine. "Scientists have long suspected that basophils can enhance the immune defense against a bacterial infection although there was no scientific proof of this role prior to our study."
"To examine the basophils' contribution to the immune response, the researchers used a model of bacterial infection and sepsis that closely resembles the progression and characteristics of human sepsis in genetically-modified mice.
"Their studies showed that basophils were one of the first types of immune cell to appear at the infection site. The presence of basophils not only enhanced inflammation at the early stages of an immune response to infection and improved survival in mice, but did this in part by releasing a protein known as tumor necrosis factor (TNF).
"As a major player in the immune response to an infection, TNF sends the signal to other cells causing them to switch into high gear and generate the inflammatory response that is vital to protecting and healing damaged tissue. Its presence in this research adds to mounting evidence that basophil-derived TNF plays a major role in the first stages of the immune system's defense against an infection, and indicates that a reduced basophil presence or a deficiency in factors regulated by basophils can lead to sepsis.
"'These findings show that basophils, despite their low numbers, can trigger a cascade of events that both helps them to initiate an immune response against infection and enhances the effectiveness of this response," wrote Piliponsky and his co-authors in the paper. "Together, these findings provide novel insights into how basophils, and basophil-derived TNF, might have key roles in the early stages following bacterial infections and in resisting the progression of such infections to sepsis."
Comment: The basal cells automatically release TNF to call in the rest of the cells that cause inflammation. The term inflammation comes from the red appearance of tissue caused by a delivery of more blood to the area by dilation of vessels. The basal cells act as scouts. This shows that different white cells are designed for different jobs. Since infectious organisms have existed since the beginning of life (think bacteria) an immune mechanism had to designed into some of those bacteria and also into multicellular organisms when they first appeared. Uncontrolled killing infections would have ended life.
Immunity: T cells and acetylcholine
by David Turell , Saturday, February 09, 2019, 19:22 (1901 days ago) @ David Turell
Acetylcholine as a signal for T cell immune reaction:
https://www.sciencedaily.com/releases/2019/02/190207142153.htm
"During infection, T-cells of the immune system synthesize acetylcholine, explains Dr. Mak. In the brain, acetylcholine functions as a neurotransmitter and controls learning and memory. In the immune system, T-cells making this classical brain chemical are able to jump out of the blood circulation and take action in the tissues to fight infection.
"First author Maureen Cox summarizes the study findings this way: "The neurotransmitter acetylcholine is produced by T-cells during viral infection to facilitate their entry into tissues under attack, where these cells then kill the virus-infected cells."
***
"'We now have absolute genetic proof that immune cells need this brain chemical," says Dr. Mak. "We believe it's an entirely new lens though which to look at numerous diseases including cancer, viral infections and autoimmune conditions."
"With respect to cancers, a tumour is often surrounded by immune cells that can't break through its defences, perhaps because the immune cells are not producing sufficient amounts of acetylcholine. In this case, strategies to increase immune neurotransmitter production may be beneficial. The flip side is at play in autoimmune diseases such as rheumatoid arthritis or multiple sclerosis, where the autoimmune T-cells attack self tissues. In this case, a reduction in neurotransmitter signaling may quell the hordes of immune cells invading joints or the central nervous system.
"The research builds on the findings of a 2011 study also published in Science in which Dr. Mak participated. That study demonstrated for the first time that immune cells can make acetylcholine.
"Dr. Mak says the next research goal is to identify and target the key receptors that facilitate the signalling crosstalk between immune cells and diseased organs."
Comment: Acetylcholine can be produced by more than one cell type, probably following the same instructions as in neurons, which means the T cells must have same receptors as neurons.
Immunity: automatic controls of inflammation
by David Turell , Saturday, March 23, 2019, 18:05 (1859 days ago) @ David Turell
A new study of cellular controls:
https://medicalxpress.com/news/2019-03-mechanism-inflammation.html
"UT Southwestern researchers have identified two proteins that act as gatekeepers to dampen a potentially life-threatening immune response to chronic infection.
"The proteins—the transcription factors SIX1 and SIX2—activate cellular pathways required for fetal development and later switch to a new role in which they repress these pathways in adult immune system cells.
***
"Transcription factors are proteins that bind to special regions of DNA to turn genes on (activate them) or off (repress them). "One of the surprising findings was that a transcription activator that is essential for the development of tissues and organs has been repurposed as a transcriptional repressor in the immune system. While transcription factors can be used differently in various stages of life, a switch from a transcriptional activator in the fetus to a suppressor in adult immune cells is infrequent," said Dr. Alto,
***
"The researchers found that the two proteins showed inhibitory activities when bound to genes involved in inflammation. Specifically, SIX1 and SIX2 appeared to dampen the body's immune response to prevent damage associated with a potentially life-threatening condition called a cytokine storm, which can occur in chronic inflammatory conditions. "A cytokine storm can occur when the body's immune cells and activators (cytokines) show an overresponse to a health threat such as the flu," he explained.
"An experiment with transgenic mice found that expression of SIX1 in adulthood conferred near-complete recovery following exposure to a toxin released by gram-negative bacteria that can set off a cytokine storm. The two SIX proteins seem to dampen the response of the so-called noncanonical NF-κB pathway, a signaling cascade that is instrumental in the development of the lymph organs, the maturation of the immune system's antibody-producing B cells, and the development of bone cells. The same pathway is involved in the body's immune defense in adulthood.
***
"'In summary, we have established that SIX family transcription factors function as immunological gatekeepers, regulating the activity of inflammatory genes in response to noncanonical NF-κB pathway activation," he said. "These findings indicate that disruption of this pathway could have important consequences for the pathogenesis of human disease, including cancer.'"
Comment: Once again precise controls. This system is another one that had to be designed all at once since the parts are so integrated. Note a cyto kine
Immunity: protein signal molecule guiding brain neurons
by David Turell , Monday, September 14, 2020, 20:25 (1318 days ago) @ Balance_Maintained
A new study in mice:
https://medicalxpress.com/news/2020-09-immune-affects-mind-body.html
"What we've found here is that an immune molecule—IL-17—is produced by immune cells residing in areas around the brain, and it could affect brain function through interactions with neurons to influence anxiety-like behaviors in mice. We are now looking into whether too much or too little of IL-17 could be linked to anxiety in people."
"IL-17 is a cytokine, a signaling molecule that orchestrates the immune response to infection by activating and directing immune cells. IL-17 also has been linked to autism in animal studies and depression in people.
"How an immune molecule like IL-17 might influence brain disorders, however, is something of a mystery since there isn't much of an immune system in the brain and the few immune cells that do reside there don't produce IL-17. But Kipnis, along with first author and postdoctoral researcher Kalil Alves de Lima, Ph.D., realized that the tissues that surround the brain are teeming with immune cells, among them, a small population known as gamma delta T cells that produce IL-17. They set out to determine whether gamma-delta T cells near the brain have an impact on behavior.
***
"Using mice, they discovered that the meninges are rich in gamma-delta T cells and that such cells, under normal conditions, continually produce IL-17, filling the tissues surrounding the brain with IL-17.
"To determine whether gamma-delta T cells or IL-17 affect behavior, Alves de Lima put mice through established tests of memory, social behavior, foraging and anxiety. Mice that lacked gamma-delta T cells or IL-17 were indistinguishable from mice with normal immune systems on all measures but anxiety. In the wild, open fields leave mice exposed to predators such as owls and hawks, so they've evolved a fear of open spaces. The researchers conducted two separate tests that involved giving mice the option of entering exposed areas. While the mice with normal amounts of gamma-delta T cells and levels of IL-17 kept themselves mostly to the more protective edges and enclosed areas during the tests, mice without gamma-delta T cells or IL-17 ventured into the open areas, a lapse of vigilance that the researchers interpreted as decreased anxiety.
"Moreover, the scientists discovered that neurons in the brain have receptors on their surfaces that respond to IL-17. When the scientists removed those receptors so that the neurons could not detect the presence of IL-17, the mice showed less vigilance. The researchers say the findings suggest that behavioral changes are not a byproduct but an integral part of neuro-immune communication.
***
"To determine whether gamma-delta T cells or IL-17 affect behavior, Alves de Lima put mice through established tests of memory, social behavior, foraging and anxiety. Mice that lacked gamma-delta T cells or IL-17 were indistinguishable from mice with normal immune systems on all measures but anxiety. In the wild, open fields leave mice exposed to predators such as owls and hawks, so they've evolved a fear of open spaces. The researchers conducted two separate tests that involved giving mice the option of entering exposed areas. While the mice with normal amounts of gamma-delta T cells and levels of IL-17 kept themselves mostly to the more protective edges and enclosed areas during the tests, mice without gamma-delta T cells or IL-17 ventured into the open areas, a lapse of vigilance that the researchers interpreted as decreased anxiety.
"Moreover, the scientists discovered that neurons in the brain have receptors on their surfaces that respond to IL-17. When the scientists removed those receptors so that the neurons could not detect the presence of IL-17, the mice showed less vigilance. The researchers say the findings suggest that behavioral changes are not a byproduct but an integral part of neuro-immune communication.
***
"'The immune system and the brain have most likely co-evolved," Alves de Lima said. "Selecting special molecules to protect us immunologically and behaviorally at the same time is a smart way to protect against infection. This is a good example of how cytokines, which basically evolved to fight against pathogens, also are acting on the brain and modulating behavior."
"The researchers now are studying how gamma-delta T cells in the meninges detect bacterial signals from other parts of the body. They also are investigating how IL-17 signaling in neurons translates into behavioral changes."
Comment: My comment would be God evolved this system. A specific protein is not likely a result of chance.
Immunity: glial cells guide network organization
by David Turell , Monday, September 14, 2020, 21:28 (1318 days ago) @ David Turell
Glial cells are part of the immune system and guide neuron network formation:
https://medicalxpress.com/news/2020-09-immune-cells-sculpt-circuits-brain.html
"Immune cells play an unexpected role in fine-tuning the brain's neural circuits, according to research published in September, 2020 in Neuron. The immune cells that reside there, known as microglia, not only protect the brain from infection and inflammation, they also help physically sculpt circuits in the developing brain. The new work demonstrates that microglia also direct neurons to modify their own connectivity in response to sensory cues.
***
"'To a large extent, the general architecture and wiring of the brain is accomplished by birth," he says. "But it really requires this robust feedback from the environment to continue that maturation." As an animal interacts with its surroundings, some neuronal connections are eliminated while others are strengthened, he explains. It's a process that, in humans, continues for decades after birth. Cheadle says:
"'What's really important's that during development, the right neurons connect with one another in the right way. We want to have tight control over how many connections there are and how strong the connections are. So that's actually something that sensory experience is important for."
"Cheadle and colleagues monitored the connections between neurons, or synapses, in a visual processing circuit in the brains of mice. Young mice need visual input at the right time to develop brain pathways related to vision. But if the mice lack visual input for a critical period, the circuits sprout too many synapses and the mice end up with abnormal connections. The team found that the circuits relied on microglia, which, with the right visual stimuli, signaled nearby neurons to prune some of the synapses.
"This impact on neural connectivity represents a new role for microglia in the healthy brain, and could help explain why the cells have been implicated in autism and other neurodevelopmental disorders. "I think this study will be seen as a big breakthrough in our mechanistic understanding of how sensory experience and microglia coordinate the process of synaptic pruning that is critical for brain maturation in early life," Greenberg says."
Comment: this means the complexification mechanism is actually under immune control and involves synapse pruning. How some areas thicken is related to regions of the hippocampus adding neurons as in London cabbies memorizing London. In humans adding neurons is very limited to this region.
Immunity: structure of an immunoglobulin
by David Turell , Monday, December 10, 2018, 18:40 (1962 days ago) @ Balance_Maintained
Finally revealed by research. A calcium atom is placed:
https://phys.org/news/2018-12-image-atomic-important-immune.html
"A new study by investigators from Brigham and Women's Hospital provides a biophysical and structural assessment of a critical immune regulating protein called human T-cell immunoglobulin and mucin domain containing protein-3 (hTIM-3). Understanding the atomic structure of hTIM-3 provides new insights for targeting this protein for numerous cancer and autoimmune therapeutics currently under clinical development.
***
"'The hTIM-3 protein is an important immune regulator, yet it has been difficult to target for drug development as high-resolution structure conformational details have been elusive," said senior author Richard Blumberg, MD, chief of the Division of Gastroenterology, Hepatology and Endoscopy in the Department of Medicine at the Brigham. "We resolved the structure of hTIM-3 and established a novel biochemical assay to define its functionality, which will be useful for understanding the role of hTIM-3 in the immune system."
"The team captured a high-resolution X-ray crystal structure and nuclear magnetic resonance (NMR) image of the hTIM-3 IgV domain that is involved in functional interactions with CEACAM1, which is a crucial immune escape mechanism for many cancers. Importantly, the team determined the precise location of a calcium atom, an essential co-factor, bound to the hTIM-3 IgV domain.
"This is the first NMR analysis of any immune-related TIM molecule and the first high resolution structural report of the hTIM-3 IgV domain with association of critical co-factors such as calcium," said author Amit Gandhi, Ph.D., a researcher in Blumberg's laboratory in the Department of Medicine. "No one has been able to do this before. Hopefully this will help with the targeting of human hTIM-3 and the development of useful therapeutics.'"
Comment: The point as usual is how did evolution as s process find this highly specific shape with an exact position of a calcium atom to produced an exact function?
Immunity: larvae use virus for immunity
by David Turell , Friday, July 30, 2021, 16:00 (1000 days ago) @ David Turell
Larvae using virus genes for parasite protection:
https://www.sciencemag.org/news/2021/07/deadly-viruses-help-moths-and-butterflies-fight...
"Moths and butterflies have long fallen victim to two deadly threats: parasitic wasps and viruses, which battle each other over their lepidopteran hosts. Now, a new study shows some viruses transfer their weapons to infected moths and butterflies, arming them with the genes to make parasite-killing proteins.
"Many species of wasps and flies lay their eggs inside other insects, giving their young a source of food and a safe place to develop—and killing the host in the process. But even though moths and butterflies are favored hosts, some species, including armyworms, cutworms, and cabbage butterflies, have shown a strange resistance to a plethora of wasp parasites, such as Cotesia vanessae and C. kariyai.
***
"To find out what was going on, entomologist Madoka Nakai and her team at the Tokyo University of Agriculture and Technology infected northern armyworm larvae with a common pox virus before introducing the immature insects to various parasitic wasp species. Whereas uninfected larvae succumbed to the parasites, the infected larvae—and their plasma—killed almost every parasite, aside from the basket-cocoon parasitoid Meteorus pulchricornis. Researchers then identified two proteins in the infected armyworms, which they called parasitoid killing factor (PKF), that they thought might be toxic to the parasites.
***
“'We all arrived at these genes from slightly different directions. Putting our research together created this very interesting story about the biological arms race occurring on a very large scale between multiple pathogens, wasps, and hosts, which we now know are also fighting back,” Theilmann says.
"But the researchers also found an interesting twist—at least one of the PKF-harboring viruses is transmitted to moths and butterflies by the basket-cocoon parasitoid, protecting the very wasp whose larvae can survive its assaults. That suggests that even though PKFs can help the lepidopterans, they may also give an advantage to some parasitic wasps.
"The new work should help researchers understand why moths and butterflies often resist parasitoids used as pesticides for crops and forests, Herrero says. But when it comes to fully understanding the complexity of this evolutionary arms race, many questions are unanswered, Theilmann says. For example, his team still doesn’t know why some viruses have genes for PKF and others don’t. They also don’t know whether all PKFs function in the same manner."
Comment: horizontal gene transfer can come from being infected, which then provides protection in other ways!!! Work in progress. All part of protective designs.
Immunity: DNA slicing in eukaryotes
by David Turell , Saturday, October 14, 2023, 20:26 (193 days ago) @ David Turell
Very much like CRISPR in bacteria:
https://phys.org/news/2023-10-thousands-programmable-dna-cutters-algae-snails.html
"A diverse set of species, from snails to algae to amoebas, make programmable DNA-cutting enzymes called Fanzors—and a new study from scientists at MIT's McGovern Institute for Brain Research has identified thousands of them. Fanzors are RNA-guided enzymes that can be programmed to cut DNA at specific sites, much like the bacterial enzymes that power the widely used gene-editing system known as CRISPR.
***
"Researchers have since uncovered other RNA-guide enzymes throughout the bacterial world, many with features that make them valuable in the lab. The discovery of Fanzors, whose ability to cut DNA in an RNA-guided manner was reported by Zhang's group earlier this year, opens a new frontier of RNA-guided biology. Fanzors were the first such enzymes to be found in eukaryotic organisms—a wide group of lifeforms, including plants, animals, and fungi, defined by the membrane-bound nucleus that holds each cell's genetic material. (Bacteria, which lack nuclei, belong to a group known as prokaryotes.)
***
"Among the more than 3,600 Fanzors that the team found in eukaryotes and the viruses that infect them, the researchers were able to identify five different families of the enzymes. By comparing these enzymes' precise makeup, they found evidence of a long evolutionary history.
"Fanzors likely evolved from RNA-guided DNA-cutting bacterial enzymes called TnpBs. In fact, it was Fanzors' genetic similarities to these bacterial enzymes that first caught the attention of both Zhang's group and Gootenberg and Abudayyeh's team.
"The evolutionary connections that Gootenberg and Abudayyeh traced suggest that these bacterial predecessors of Fanzors probably entered eukaryotic cells, initiating their evolution, more than once. Some were likely transmitted by viruses, while others may have been introduced by symbiotic bacteria. The research also suggests that after they were taken up by eukaryotes, the enzymes evolved features suited to their new environment, such as a signal that allows them to enter a cell nucleus, where they have access to DNA.
"Through genetic and biochemical experiments led by biological engineering graduate student Kaiyi Jiang, the team determined that Fanzors have evolved a DNA-cutting active site that is distinct from that of their bacterial predecessors. This seems to allow the enzyme to cut its target sequence more precisely the ancestors of TnpB, when targeted to a sequence of DNA in a test tube, become activated and cut other sequences in the tube; Fanzors lack this promiscuous activity. When they used an RNA guide to direct the enzymes to cut specific sites in the genome of human cells, they found that certain Fanzors were able to cut these target sequences with about 10 to 20 percent efficiency."
Comment: in all this research we must use existing living mechanisms as we still have no idea how to make life. Luckily, these mechanisms are quite efficient in what they do, which is kill an invader by slicing and dicing the enemies' DNA.
Immunity; clever RNA
by David Turell , Friday, October 12, 2018, 22:04 (2021 days ago) @ David Turell
More clever RNA. A noncoding RNA activates immune protein:
https://phys.org/news/2018-10-rna-key-innate-immunity.html
"Graeme Conn, the biochemistry professor who oversaw the work, studies how RNA is involved in the body's responses to infections. When a human cell senses a virus, it activates a signaling pathway: a protein called OAS gets turned on and produces a signaling molecule, which in turn activates another protein that both directly defends against the virus as well as activating other parts of the cell's innate immune system.
"As it turns out, human RNA might play an important role in this pathway, specifically a human RNA molecule called nc886. The "nc" stands for "noncoding," which means this RNA molecule is not carrying instructions for building a protein. It's doing something all on its own.
"What it's doing, the new paper shows, is turning on OAS, thus setting off the chain of events that destroys viruses.
"'We saw that (nc886) wasn't just an activator of this pathway, but a very potent activator," said Brenda Calderon, who carried out the research as a graduate student in Conn's lab.
"The nc886 molecule can adopt two different shapes, and one of them is much better at activating OAS than the other. This is another way in which this RNA molecule acts like a protein: its function depends strongly on its 3-D shape and structure. Although nc886 is present in all human cells, it's unknown whether the relative abundance of the immune-activating and less-active form might change in response to infection."
Comment: Another immune pathway which requires a specialized RNA and a series of specific proteins to trigger the response. Specific proteins can only occur by design: Since living organisms must fight infectious organisms, all organisms which appear must have immune abilities on board from the origin their appearance. The theory that they might develop by chance after appearing in life without them is on its face ridiculous.