https://www.sciencedaily.com/releases/2025/04/250404140532.htm

The research team, headed by Professor Pla-Martín from the Institute of Biochemistry and Molecular Biology I at HHU, has identified a specialised recycling system, which cells activate when they identify damage to the mtDNA.

According to the authors in Science Advances, this mechanism relies on a protein complex known as retromer and the lysosomes -- cell organelles containing digestive enzymes. These special cellular compartments act like recycling centres, eliminating the damaged genetic material. This process is one of the mechanisms, which prevent the accumulation of faulty mtDNA, thus maintaining cellular health and potentially preventing diseases.

***

In collaboration with the cell biologist Dr Parisa Kakanj from the University of Cologne, who is also a member of the CEPLAS Cluster of Excellence, Professor Pla-Martín was able to verify and extend the findings using fruit flies (Drosophila) as a model organism. Dr Kakanj showed that damaged mitochondrial DNA are eliminated much more quickly and that mitochondrial function improves significantly when the activity of the retromer complex -- in particular the protein VPS35 -- is increased.

Dr Kakanj: "Using Drosophila allowed us to confirm our initial findings in human cells and demonstrate clear improvements in mitochondrial health. This opens up exciting possibilities for therapeutic strategies for treating mitochondrial diseases and age-related conditions."

Comment: of course mitochondria must have repair systems. Cells recognize improper proteins and react to them just as if they are immunity cells.

https://www.cell.com/cell/fulltext/S0092-8674(24)00316-7?dgcid=raven_jbs_aip_email

Centriole biogenesis, as in most organelle assemblies, involves the sequential recruitment of sub-structural elements that will support its function. To uncover this process, we correlated the spatial location of 24 centriolar proteins with structural features using expansion microscopy. A time-series reconstruction of protein distributions throughout human procentriole assembly unveiled the molecular architecture of the centriole biogenesis steps. We found that the process initiates with the formation of a naked cartwheel devoid of microtubules. Next, the bloom phase progresses with microtubule blade assembly, concomitantly with radial separation and rapid cartwheel growth. In the subsequent elongation phase, the tubulin backbone grows linearly with the recruitment of the A-C linker, followed by proteins of the inner scaffold (IS). By following six structural modules, we modeled 4D assembly of the human centriole. Collectively, this work provides a framework to investigate the spatial and temporal assembly of large macromolecules.

Comment: I cannot reproduce any portion of this study which is filled with picture illustrations of all the steps and parts. If possible open the website and skim through. The complexity of the design will be startling.

https://www.cell.com/current-biology/fulltext/S0960-9822(22)01851-6?dgcid=raven_jbs_aip...

"Microtubule self-repair has been studied both in vitro and in vivo as an underlying mechanism of microtubule stability. The turnover of tubulin dimers along the microtubule has challenged the pre-existing dogma that only growing ends are dynamic. However, although there is clear evidence of tubulin incorporation into the shaft of polymerized microtubules in vitro, the possibility of such events occurring in living cells remains uncertain. In this study, we investigated this possibility by microinjecting purified tubulin dimers labeled with a red fluorophore into the cytoplasm of cells expressing GFP-tubulin. We observed the appearance of red dots along the pre-existing green microtubule within minutes. We found that the fluorescence intensities of these red dots were inversely correlated with the green signal, suggesting that the red dimers were incorporated into the microtubules and replaced the pre-existing green dimers. Lateral distance from the microtubule center was similar to that in incorporation sites and in growing ends. The saturation of the size and spatial frequency of incorporations as a function of injected tubulin concentration and post-injection delay suggested that the injected dimers incorporated into a finite number of damaged sites. By our low estimate, within a few minutes of the injections, free dimers incorporated into major repair sites every 70 μm of microtubules. Finally, we mapped the location of these sites in micropatterned cells and found that they were more concentrated in regions where the actin filament network was less dense and where microtubules exhibited greater lateral fluctuations."

Comment: this abstract of the study is quite clear. Microtubules are vital conduits for transfer of molecules in the active cell in constant production. Only design can produce this degree of complexity. We now study at a level of function at which Darwin just-so stories won't work.

https://phys.org/news/2022-01-probing-proteins-pair-cells.html

"Despite its minute size, a single cell contains billions of molecules that bustle around and bind to one another, carrying out vital functions. The human genome encodes about 20,000 proteins, most of which interact with partner proteins to mediate upwards of 400,000 distinct interactions. These partners don't just latch onto one another haphazardly; they only bind to very specific companions that they must recognize inside the crowded cell.

***

"The average human protein is composed of approximately 400 building blocks called amino acids, which are strung together and folded into a complex 3D structure. Within this long string of building blocks, some proteins contain stretches of 4-6 amino acids called short linear motifs (SLiMs), which mediate protein-protein interactions. Despite their simplicity and small size, SLiMs and their binding partners facilitate key cellular processes. However, it's been historically difficult to devise experiments to probe how SLiMs recognize their specific binding partners.

***

"Using the detailed information they gleaned from studying these interactions, the researchers created their own synthetic molecule capable of binding extremely tightly to a protein called ENAH, which is implicated in cancer metastasis. The team shared their findings in a pair of eLife studies, one published on January 25, 2022 and the other on December 2, 2021.

***

"To survey SLiMs with a wide range of binding affinities, Keating, Hwang, and their colleagues developed their own screen called MassTitr.

"The researchers also suspected that the amino acids on either side of the SLiM's core 4-6 amino acid sequence might play an underappreciated role in binding. To test their theory, they used MassTitr to screen the human proteome in longer chunks comprised of 36 amino acids, in order to see which "extended" SLiMs would associate with the protein ENAH.

"ENAH, sometimes referred to as Mena, helps cells to move. This ability to migrate is critical for healthy cells, but cancer cells can coopt it to spread. Scientists have found that reducing the amount of ENAH decreases the cancer cells's ability to invade other tissues—suggesting that formulating drugs to disrupt this protein and its interactions could treat cancer.

"Thanks to MassTitr, the team identified 33 SLiM-containing proteins that bound to ENAH—19 of which are potentially novel binding partners. They also discovered three distinct patterns of amino acids flanking core SLiM sequences that helped the SLiMs bind even tighter to ENAH. Of these extended SLiMs, one found in a protein called PCARE bound to ENAH with the highest known affinity of any SLiM to date.

***

"Hwang's biggest takeaway from the project is that things are not always as they seem: even short, simple protein segments can play complex roles in the cell. As she puts it: "We should really appreciate SLiMs more."

Comment: this study shows how molecules know with whom to combine or react, automatically, no thought involved because of the design. Cell intelligence is in the design, not autonomously
active.

https://phys.org/news/2020-04-renew-powerhouses-cells-workshop-mode.html

"If the energy supply of a cell is disturbed by damage, it can protect itself from functional losses and repair itself in a kind of workshop mode.

***

"The tasks of mitochondria include very basic processes such as the constant energy supply of the cell. The power machinery in mitochondria consists of five components, the so-called complexes I-V. In them, the food we eat is ultimately converted into energy for the cell. If the cellular energy supply is no longer guaranteed due to disturbances in signalling processes, this has serious consequences for the entire organism,

***

"'In our most recent work, we have discovered a rescue route that enables cells to repair damage of a particularly sensitive part of complex I," said Trifunovic. "Repairing something is a far more energy-efficient self-help mechanism compared to the effort that would be required to completely destroy and rebuild this entire complex." (my bold)

"The specific rescue route Trifunovic identified also acts as a safety valve for the cell. If the rescue route becomes active, the dysfunctional component quickly switches to a shutdown mode and 'goes to the workshop.' This way, the cells prevent harmful reactive oxygen species from being produced and released in the powerhouse engine. Trifunovic remarked: "So far, very little is known about how this machinery is maintained and regulated. Our results shed light on this process and allow us to explore further therapeutic possibilities."

"In addition to the general novelty of the entire mechanism, she was particularly surprised to see that it is often better for the organism to keep some powerhouse machine components running despite damage, and not to put all damaged components into 'workshop mode' at the same time or to dismantle them completely. It is possible that functions of individual components, which go beyond energy supply, also play a role."

Comment: Note my bold. Quick repair by a backup system is obviously needed and reeks of planned design, never a chance natural event.

https://evolutionnews.org/2019/08/design-for-atp-extends-beyond-the-rotary-engine/

"A paper in PNAS by Kwangho Nam and Martin Karplus explores “Insights into the origin of the high energy-conversion efficiency of F1-ATPase.” And do they mean efficiency!

"F1-ATPase is a small motor protein, composed of 3 α- and 3 β-subunits that surround a central γ-subunit. The β-subunits alternate cyclically between 2 major conformational states to produce the rotation of the γ-subunit. Although the rotation on the microsecond timescale is powered by the differential binding of ATP and its hydrolysis products ADP and HPO42−, there is near-100% conversion efficiency of the free energy of ATP hydrolysis, which occurs on the picosecond timescale. The free-energy profile constructed for the 360° rotation cycle shows that F1-ATPase achieves its high energy-conversion efficiency by elegantly separating fast catalytic events, which involve small local conformational changes, from the slow binding/release of ligands involved in the large conformational change.

***

"How can ATP synthase achieve near-100% efficiency, such that the energy from one process is completely converted to another, with almost zero loss? Thermal escape is too rapid to overcome, even at this scale.

"The authors found an “elegant separation” between two catalytic events that operate at timescales differing by six orders of magnitude. This apparently gives the motor time for conformational changes in the protein parts and release of products that drive rotation of the rotor. The elasticity or “stiffness” in the rotor also contributes to efficient energy conversion. So finely tuned is each part of the engine to the others, the free energy “changes linearly along the rotation coordinate.” This means that the motor “functions near the maximum possible efficiency.”

***

"A description in BioArchitecture states, “Bacterial enzymes have been clocked to run at up to 42,000 rpm under low load, though for intact enzymes under physiological conditions the number is closer to 6000 rpm.” A typical car starts redlining at that value. High-performance racing cars peak a little above 10,000 rpm. Isn’t it amazing what chance can do?

"Molecular machines, like the rotary ATPases described here, seem to have much in common with man-made machines. However, the analogies hold only to a certain point and are in large parts not fully understood. What is evident is that several billion years of evolution have resulted in biological motors that are unsurpassed in efficiency, fine-tuning to their environment and sustainability.

***

"The first paper was concerned primarily with the F1 part of ATP synthase, where ATP synthesis or hydrolysis occurs. The F0 part, where protons drive rotation of a carousel-like wheel, also contributes to the efficiency. It drives the γ-subunit that acts like a camshaft. The camshaft extends into the F1 part, in effect “snapping” ADP and phosphate together to form ATP in three stages per revolution: synthesis, ejection, and loading.

***

"They solved high-resolution cryo–electron microscopy structures of the ATP synthase complex, extracting 13 rotational substates. This collection of structures revealed that the rotation of the Fo ring and central stalk is coupled with partial rotations of the F1 head. This flexibility may enable the head to better couple continuous rotation with discrete ATP synthesis events.

"An animation in the paper shows the F1 domain undergoing a rocking motion back and forth as the F0 domain rotates around continuously. The rocking motion is achieved by means of another finely tuned protein called OSCP. The beauty of this solution allows for F1 heads to accommodate differing sizes of F0 rotors through a universal joint.

***

" Some animations of ATP synthesis show the products ejecting from the machine, as if they just fly off into the air. Actually, transport of ADP into and ATP out of the motor are also tightly regulated. The “mitochondrial ADP/ATP carrier” (AAC) is right there, like a UPS truck, to get the products where they are needed.

Inside the mitochondrion, as reported here before, there are inner and outer membranes, with TIM and TOM transporters that control what enters and exits.

***

"Translating this into a more everyday analogy, the AAC truck driver keeps an eye on how many protons are leaking out into the cytoplasm, and calls back to the engine house to have them slow down production. When the truck driver can keep up with production, proton leakage is small (negative regulation). But when more protons leak out, the driver warns that ATP synthase is outpacing demand.

***

"As more details of ATP synthase come to light, more and more fine-tuning appears. The synthesis of ATP, necessary from the very start of metabolic life, is now seen to be phenomenally efficient and masterfully regulated by multiple parts working together. Just give chance billions of years, and miracles like this can happen. Not."

Comment: Better machines than humans can create.

https://phys.org/news/2018-11-tools-illuminate-mechanisms-overlooked-cellular.html

"Creating new tools that harness light to probe the mysteries of cellular behavior, Princeton researchers have made discoveries about the formation of cellular components called membraneless organelles and the key role these organelles play in cells.

"The tools developed by the researchers allow scientists to accurately probe intracellular phase separation—the process by which the chaotic liquid matter inside cells transforms into functioning cellular compartments called membraneless organelles.

"Long overlooked, these organelles have been shown to play critical roles in human health. The loss of their fluid-like consistency, for instance, is implicated in diseases including cancer, Alzheimer's, and amyotrophic lateral sclerosis (ALS). Previous work in Brangwynne's lab has shown the membraneless organelles play an important role in cell growth. And one of the two recent Cell papers demonstrates they also influence the genes controlling cellular behavior.

***

"...the researchers examine how the formation of membraneless organelles affects the cell's nucleus. Using a second tool, named CasDrop, the researchers looked at chromatin, the mixture of DNA, RNA and protein inside the nucleus. They found that as membraneless organelles form within the nucleus, they deform the chromatin in unexpected ways. They showed that the droplets push out unwanted genes, but can simultaneous pull together specifically targeted genes. The droplets can thus function like little, mechanically-active machines to restructure the genome. (my bold)

"The CasDrop system builds on the revolutionary gene-editing technology called CRISPR, which utilizes a protein machine called Cas9, to address particular genes in the cell. Brangwynne and colleagues engineered Cas9 to function as a platform, which upon light activation causes other proteins to bind to the gene, and locally phase separate, forming little dew droplets on the field of chromatin."

Comment: Another layer of gene control involving a fascinating physical change in cells, liquid-liquid phase separation creating membraneless organelles! Amazing design requires a designing mind.

https://www.quantamagazine.org/

"Think of liquids with different properties that don’t really mix but, under specific circumstances, cluster and separate like the shifting blobs in a lava lamp. That phenomenon, also known as liquid-liquid phase separation, was once considered to be an exclusively chemical process. But less than a decade ago, Brangwynne became one of the first to observe it happening inside cells as well, and ever since then, biologists have been trying to learn its significance.

"Now scientists are beginning to understand that evolution has tuned certain proteins to act in aggregate like liquids. Through phase separation, they spontaneously self-assemble into dynamic, membrane-free, dropletlike structures that can perform needed tasks in cells.

***

"One of the latest findings is that phase separation allows certain types of cells to cheat death when they are deprived of nutrients or otherwise put under stress. Phase separation enables the cells to turn a large part of their cytoplasm from a liquid to a solid — essentially putting themselves into a hardy condition of stasis until the nutrients return.

***

"That initial work by Brangwynne, Eckmann and Hyman triggered an avalanche of papers investigating the assembly and dispersal of various cytoplasmic proteins under various conditions. The evidence was getting stronger that cells had evolved a fine-tuned mechanism for organizing some of their internal structure and processes through phase separation — that is, letting proteins self-assemble into structures that could perform distinct functions.

***

"Zaburdaev and several of his colleagues, including Alberti, decided to check what happens to proteins when cells are subjected to stresses such as falling temperatures and the sudden disappearance of nutrients. The surprising result they uncovered was that phase separation can be part of a cell’s survival mechanism.

"The cells’ behavior could be likened to hibernation for bears. The animal lays still in a dormant state for weeks, minimizing its expenditure of energy. At a cellular level, phase separation helps the gelatinous cytoplasm make a protective transition into something more solid. “In this ‘solidified’ state, a cell can survive starvation,” Zaburdaev said.

***

"Simply by varying the acidity of the [yeast] cells’ environment, the scientists could induce them to switch into this survival state, even without taking away the cells’ nutrients. The cells could rest this way for hours or even days. “We found that the cells are so rigid that they keep their shape” instead of being deformable, Alberti said. They “transition into a completely different material state.”

"When their normal pH was later restored, the cells returned to normal, “dividing and living happily,” Zaburdaev said.

***

"The team found that when a protein has a certain identifiable domain or region, the protein will form easily reversible gels. In the absence of this domain, the protein forms an irreversible type of assembly — permanently removing it from further use.

"In effect, this domain modifies the protein’s phase behavior and keeps it reusable. “The domain provides a new possibility, for that protein to assemble into a benign kind of gel and not something from which you cannot come back,” Alberti said.

***

"Such results imply that nature has designed the domain sequences to tune the proteins’ material properties.

***

"Recently, for example, the neuroscientist Pietro De Camilli at Yale University and his colleagues found evidence that phase separation might be involved in the controlled release of neurotransmitters at synapses. It had been observed that vesicles containing neurotransmitters routinely hover in clusters near the presynaptic membrane until they are needed. De Camilli’s team showed that a scaffolding protein called synapsin 1 condenses into a liquid phase, along with other proteins, to bind the vesicles into these clusters. When the synapsin is phosphorylated, the droplet rapidly dissipates and the vesicles are freed to spill the neurotransmitters into the synapse."

Comment: Other than the neurological finding directly above, this is yeast research, and how it applies to multicellular organisms is not known. But what is seen at the single cell stage is usually finally found in complex organisms. Too complex for any mechanism than design of specific proteins with this property .

Life runs on the ability of organisms to absorb, pass on, process and use information, and I suspect many of us would regard that ability as a sign of intelligence. I agree with you that belief in chance mutation as the developer of such complexity requires a great deal of faith!

https://www.sciencedaily.com/releases/2018/05/180517163337.htm

"A team of Texas A&M and Texas A&M AgriLife Research scientists now have a deeper understanding of a large switch/sucrose non-fermentable (SWI/SNF) protein complex that plays a pivotal role in plant and human gene expression that causes life-threatening diseases such as cancer.

***

"The team has been working for years on how microRNAs are produced in the model plant Arabidopsis. MicroRNAs are tiny regulatory RNA molecules widely present in multicellular organisms. In humans, microRNAs inhibit more than 60 percent of human genes and are actively exploited as potent drugs to cure human diseases, according to the scientists.

"In plants, the molecules can also control many aspects of life such as plant architecture, and responses to hostile environmental conditions. MicroRNAs are also widely engineered in agricultural crops and animals for better yield and quality.

"MicroRNAs are produced in a factory inside cells from long substrates that can be hundreds or thousands of bases and also contain a distinct hairpin-structure. The factory contains a scissor-like enzyme called Dicer, and some assistants that help to fetch the long substrates. One of the assistants is known as Serrate protein, Zhang said.

"'Also, the shape of the substrates is very critical for microRNA production," Zhang said. "If the shapes are changed, then the substrates do not fit the Dicer scissor and can not be cut, and microRNAs are not made."

***

"'Also, the shape of the substrates is very critical for microRNA production," Zhang said. "If the shapes are changed, then the substrates do not fit the Dicer scissor and can not be cut, and microRNAs are not made."

***

"Wang said CHR2 is essential for producing RNA from DNA templates because its ATPase activity breaks down ATP to generate energy.

***

"'That meant, CHR2, when brought into the factory by Serrate, changes the settings inside the factory through its motor activity."

***

"'The results are significant because they provide an additional unknown layer of microRNA level regulation. For the first time an explanation is provided for many earlier reports showing that the level of microRNA substrates in many cases does not reflect the amount of mature microRNA," according to one reviewer for the paper.

"'The study is novel and exciting. It shows that the secondary structure of microRNA substrates contains a new informational code that needs to be interpreted by CHR2 and Serrate proteins (before operation of the factory)," according to the other reviewers for the paper. (my bold)

***

"The groundbreaking work from Zhang's lab reveals the two separate functions for CHR2 in production of microRNAs.

"'The work identifies a unique gene-editing target to control microRNA amount for systematically improving agricultural traits such as plant architecture, yield, quality and response to hostile environments," Zhang said."

Comment: Note my bold. Life runs on information. Enzymes and other proteins carry information to the cells to instruct changes in production. The degree of complexity cannot be developed by chance mutation.

https://phys.org/news/2018-05-mitochondria-art-dna-maintenance.html

"However, biologists also know that most of our cells have mitochondria that do, in fact, retain the circular DNA, the chromosome 'M,' which they inherited from their prokaryotic ancestors.

"One might then ask: Do mitochondria contain linear DNA? The correct answer to this second, and somewhat sneaky question is, again, affirmative. Nucleoids in mitochondria do need to be circular in order for the machinery that copies their DNA to work. Transcription in mitochondria is directly coupled to replication, and also requires circularized nucleoids. However, linear nucleoids exist in a healthy state of equilibrium with circular nucleoids within the mitochondria network. This provides a way for the cell or tissue to control the abundance of mtDNA directly, and by implication, the state and abundance of mitochondria.

"What is the fate of linear mtDNA? Double-strand breaks (DSBs) are continually generated as a byproduct of replication stalling, or from failed DNA repair of damaged and incorrectly replicated nucleotides. Although nucleoids can normally replicate themselves in about 90 minutes, DNA polymerases are hung out to dry when nucleotide stores are insufficient or become improperly balanced. When that happens, things break down; essential factors begin to leave the replication-transcription complex, and proper proofreading becomes a frequent casualty.

***

"Until recently, it was not understood how linear mtDNA was degraded. Authors of a new paper in Nature have now shown that the same exact machinery responsible for replicating mtDNA also polices it for breaks. The three main proteins involved, the helicase TWNK, the polymerase POLG, and the exonuclease MGME1, were found to bind together into a functional unit. TWNK first acts to unwind the DNA so that the individual strands can be accessed. MGME1, which has a strong bias for operation in the 5' to 3' direction of single-stranded DNA then begins to digest one strand.

***

"Some additional insights (and warnings) into how double-strand breaks might occur and resolve have been provided by researchers Doug Turnbill and Robert Taylor from the Wellcome Center for Mitochondrial Research. In one particular paper, they proposed that mtDNA deletions are most commonly generated during repair of DNA damage as opposed to replication errors. More specifically, they offer that characteristic deletions are initiated by single-stranded segments of mtDNA that were, in turn, generated by exonucleases attacking double-strand breaks. The free single strands would be able to anneal with microhomology or repeat sequences on other single-stranded mtDNA, and undergo repair to an intact but partially deleted state."

Comment: Obviously the cell and its mitochonria must have exacting repair mechanisms, and these must have been present from the beginning of life and carried into multcellularity. Only design explains this.

DAVID: We agree they certainly act intelligently. That is because of their intelligent design. Your view and my view are possible, but it is obvious the complexity of their responses to stimuli requires a designer.

dhw: This is excellent news. Since you agree that my basic premise of autonomous cellular intelligence is possible, and you have already agreed that you can find no flaw in the logical hypothesis I have built on it, clearly you now agree that your God might possibly have built an autonomous inventive mechanism through which evolution progressed in the higgledy-piggledy manner we can all observe (though we must allow for the occasional dabble).

DAVID: Nice attempt at peace. We're back to God's IM which is possible with basic guidelines so that He remains in control of evolution to produce humans.

dhw: You wrote that your view and my view were possible. As you very well know, your view is an IM “with basic guidelines” and my view is an autonomous IM, based on cellular intelligence. You have said that my view is possible, or is this yet another case of x on a Wednesday and y on a Thursday? The theistic version of my hypothesis allows for dabbling, which could apply to humans. My major objections to your hypothesis are firstly your insistence that every single innovation, lifestyle and natural wonder had to be individually dabbled or preprogrammed by your God, and secondly that all of them were somehow geared to the production of the sapiens brain.

I'll stick to humans as the supreme goal of God's evolution.

dhw: This is excellent news. Since you agree that my basic premise of autonomous cellular intelligence is possible, and you have already agreed that you can find no flaw in the logical hypothesis I have built on it, clearly you now agree that your God might possibly have built an autonomous inventive mechanism through which evolution progressed in the higgledy-piggledy manner we can all observe (though we must allow for the occasional dabble).

DAVID: Nice attempt at peace. We're back to God's IM which is possible with basic guidelines so that He remains in control of evolution to produce humans.

You wrote that your view and my view were possible. As you very well know, your view is an IM “with basic guidelines” and my view is an autonomous IM, based on cellular intelligence. You have said that my view is possible, or is this yet another case of x on a Wednesday and y on a Thursday? The theistic version of my hypothesis allows for dabbling, which could apply to humans. My major objections to your hypothesis are firstly your insistence that every single innovation, lifestyle and natural wonder had to be individually dabbled or preprogrammed by your God, and secondly that all of them were somehow geared to the production of the sapiens brain.

DAVID: Obviously intelligence is involved. Cells are so complex they must have a designer. That is where the intelligence comes from.

dhw: Two separate issues here: 1) Do cells have their own autonomous intelligence? 2) If they do, where did it come from? Your complexity = design argument is a powerful one. I hope you are now beginning to acknowledge that the case for cellular intelligence is becoming increasingly powerful!

DAVID: We agree they certainly act intelligently. That is because of their intelligent design. Your view and my view are possible, but it is obvious the complexity of their responses to stimuli requires a designer.

dhw: This is excellent news. Since you agree that my basic premise of autonomous cellular intelligence is possible, and you have already agreed that you can find no flaw in the logical hypothesis I have built on it, clearly you now agree that your God might possibly have built an autonomous inventive mechanism through which evolution progressed in the higgledy-piggledy manner we can all observe (though we must allow for the occasional dabble).

Nice attempt at peace. We're back to God's IM which is possible with basic guidelines so that He remains in control of evolution to produce humans.

DAVID: Obviously intelligence is involved. Cells are so complex they must have a designer. That is where the intelligence comes from.

dhw: Two separate issues here: 1) Do cells have their own autonomous intelligence? 2) If they do, where did it come from? Your complexity = design argument is a powerful one. I hope you are now beginning to acknowledge that the case for cellular intelligence is becoming increasingly powerful!

DAVID: We agree they certainly act intelligently. That is because of their intelligent design. Your view and my view are possible, but it is obvious the complexity of their responses to stimuli requires a designer.

This is excellent news. Since you agree that my basic premise of autonomous cellular intelligence is possible, and you have already agreed that you can find no flaw in the logical hypothesis I have built on it, clearly you now agree that your God might possibly have built an autonomous inventive mechanism through which evolution progressed in the higgledy-piggledy manner we can all observe (though we must allow for the occasional dabble).

dhw: The evidence for cellular intelligence builds with every article David posts on the subject. Not to be equated with human intelligence of course, but if you saw an animal, bird, insect in trouble and calling for help, and you saw its neighbour providing that help, you wouldn’t hesitate to acknowledge that this was a sign of intelligence. It’s only because these organisms are so tiny and invisible to the naked eye that some folk dismiss the idea.
dhw: […] Most cellular activity will be automatic. It’s only when things change that intelligence is called on..

DAVID: Obviously intelligence is involved. Cells are so complex they must have a designer. That is where the intelligence comes from.

dhw: Two separate issues here: 1) Do cells have their own autonomous intelligence? 2) If they do, where did it come from? Your complexity = design argument is a powerful one. I hope you are now beginning to acknowledge that the case for cellular intelligence is becoming increasingly powerful!

We agree they certainly act intelligently. That is because of their intelligent design. Your view and my view are possible, but it is obvious the complexity of their responses to stimuli requires a designer.

DAVID: Obviously intelligence is involved. Cells are so complex they must have a designer. That is where the intelligence comes from.

Two separate issues here: 1) Do cells have their own autonomous intelligence? 2) If they do, where did it come from? Your complexity = design argument is a powerful one. I hope you are now beginning to acknowledge that the case for cellular intelligence is becoming increasingly powerful!

QUOTE: Healthy adult cells don’t usually make TNTs, but stressed or ailing cells appear to induce them by sending out signals to call for help. It’s unclear, though, how healthy cells sense that their neighbors need help or how they physiologically “know” what specific cargo to send.

dhw: The evidence for cellular intelligence builds with every article David posts on the subject. Not to be equated with human intelligence of course, but if you saw an animal, bird, insect in trouble and calling for help, and you saw its neighbour providing that help, you wouldn’t hesitate to acknowledge that this was a sign of intelligence. It’s only because these organisms are so tiny and invisible to the naked eye that some folk dismiss the idea.

Under “Stimulus causes protein signalling”:

DAVID’s comment: These are biomechanical molecules that control the speed of reactions in an automatic fashion. Note the tail moves. It is the coordinated dance of these molecules working automatically that produces life.

dhw: One should also note that in all forms of life there are automatic activities and non-automatic activities. If we take ourselves as the macrocosm, we depend on a mass of automatic activities that we never even think about until conditions change. Then we use conscious intelligence to make adjustments (though most of the time we have to rely on someone else’s intelligence to do that). I suggest that it is the same in the microcosmic world. Most cellular activity will be automatic. It’s only when things change that intelligence is called on, and the first article tells us that cells can also call on “someone else’s intelligence” to do the job.

Obviously intelligence is involved. Cells are so complex they must have a designer. That is where the intelligence comes from.

The evidence for cellular intelligence builds with every article David posts on the subject. Not to be equated with human intelligence of course, but if you saw an animal, bird, insect in trouble and calling for help, and you saw its neighbour providing that help, you wouldn’t hesitate to acknowledge that this was a sign of intelligence. It’s only because these organisms are so tiny and invisible to the naked eye that some folk dismiss the idea.

Under “Stimulus causes protein signalling”:

DAVID’s comment: These are biomechanical molecules that control the speed of reactions in an automatic fashion. Note the tail moves. It is the coordinated dance of these molecules working automatically that produces life.

One should also note that in all forms of life there are automatic activities and non-automatic activities. If we take ourselves as the macrocosm, we depend on a mass of automatic activities that we never even think about until conditions change. Then we use conscious intelligence to make adjustments (though most of the time we have to rely on someone else’s intelligence to do that). I suggest that it is the same in the microcosmic world. Most cellular activity will be automatic. It’s only when things change that intelligence is called on, and the first article tells us that cells can also call on “someone else’s intelligence” to do the job.

https://phys.org/news/2018-05-uncovering-hidden-protein-tail-cell.html

"..researchers have found a previously-unknown mechanism that puts the brakes on an important cell signaling process involving the G proteins found in most living organisms.

"The mechanism, dubbed a "tail," is part of a small protein known mostly for its role in attaching larger structures to the cell membrane. When researchers inactivated the tail, a signaling response that had previously taken 30 minutes to occur happened almost immediately - with an intensity four times greater than normal.

***

"We have discovered the mechanism that regulates how quickly a pathway gets turned on by an external stimulus," said Matthew Torres, an associate professor in the School of Biological Sciences at the Georgia Institute of Technology. "By genetically altering the control mechanism underlying this process, we are able to modulate how much of a signal from outside the cell gets inside the cell and how quickly it gets through. It's all the more astonishing because this mechanism has been hiding in plain sight for decades."

"G proteins, also known as guanine nucleotide-binding proteins, are a family of molecules that operate as molecular switches inside cells. They transmit signals acquired from a variety of extracellular stimuli to the interior of a cell - through the membrane, which otherwise wouldn't allow communication.

"The tail found by Torres and Doctoral Candidate Shilpa Choudhury likely escaped attention because it is flexibly attached to the G protein gamma subunit of a closely-collaborating protein team known as G beta/gamma. Protein structures have generally been identified by X-ray crystallography techniques which cannot resolve structures that are in motion.

"Prior to their work, the G gamma subunit has been known primarily as the protein that connects the larger G beta subunit to the cell membrane. Without the work of SAPH-ire - an informatics program that maps PTM activity using machine learning - the role of the tail structure might not have been identified.

"In yeast, G beta/gamma subunits activate a signaling pathway in response to pheromones, a process which normally takes about 30 minutes after stimulation of a pheromone receptor at the cell membrane. Torres and Choudhury suspected that protein modifications, PTMs, were somehow causing the delay. Their computer program SAPH-ire - developed in the Torres lab and announced in 2015 - pointed the finger straight at the G gamma subunit.

"The program analyzes existing meta-data repositories of protein sequence and PTM activity to reveal "hotspots" of protein alteration. SAPH-ire was designed to accelerate the search for important regulatory targets on protein structures and to provide a better understanding of how proteins communicate with one another inside cells.

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"Beyond identifying the control mechanism for the pathway, the researchers also learned how it controls the ability of yeast to respond to pheromones in a "switch-like" manner that is either on or off versus an analog manner that is analogous to a volume knob on a stereo.

"While Torres and Choudhury made their discovery in yeast, they believe it will have broad implications because all organisms that have G proteins, including humans, have G gamma tails that are riddled with PTMs. "

Comment: These are biomechanical molecules that control the speed of reactions in an automatic fashion. Note the tail moves. It is the coordinated dance of these molecules working automatically that produces life.