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<title>AgnosticWeb.com - The biochemistry of cell: how to picture it</title>
<link>https://agnosticweb.com/</link>
<description>An Agnostic&#039;s Brief Guide to the Universe</description>
<language>en</language>
<item>
<title>The biochemistry of cell: how to picture it (reply)</title>
<content:encoded><![CDATA[<p>New techniques in seeing the activities:</p>
<p><a href="https://www.sciencedaily.com/releases/2025/03/250304114037.htm">https://www.sciencedaily.com/releases/2025/03/250304114037.htm</a></p>
<p>&quot;A new study has unveiled a precise picture of how an ion channel found in most mammalian cells regulates its own function with a &quot;ball-and-chain&quot; channel-plugging mechanism, according to investigators at Weill Cornell Medicine.</p>
<p>***</p>
<p><br />
&quot;Ion channels are protein structures embedded in cell membranes that allow charged molecules to flow into or out of the cell. They support essential biological functions, including signaling or communication between brain cells. The study, published Feb. 19 in Nature Communications, focused on the mammalian BK (&quot;big potassium&quot;) channel, which facilitates the flow of potassium ions out of cells.</p>
<p>&quot;Using advanced structural imaging and computer modeling techniques, the researchers confirmed that BK channels can stop their ion flow via a long-theorized ball-and-chain structure that plugs the channel.</p>
<p>***</p>
<p>&quot;BK channels help govern the excitability of brain and muscle cells, control blood flow through blood vessels, process auditory signals and perform many other functions throughout the body. Accordingly, genetic and other dysfunctions of BK channels have been linked to a variety of disorders, from epilepsies and movement disorders to hypertension and hearing-loss syndromes. However, the complexity and fragility of BK channels have made studying them difficult.</p>
<p>&quot;Calcium ions can trigger a BK channel to open its central passage or &quot;pore,&quot; allowing a massive flow of potassium ions out of the cell. Research had long suggested -- but never proven with direct imaging -- that a BK channel can stop the flow through its calcium-triggered, open-pore using a ball-like plug that swings from the end of a flexible protein subunit.</p>
<p>&quot;In a widely cited study in 2020, Dr. Nimigean and colleagues revealed this ball-and-chain structure in a simpler potassium channel called MthK, an evolutionarily distant relative of BK channels found in bacterial organisms. In the new study, she and her team successfully identified this structure in Slo1, a more complex mammalian BK channel.</p>
<p>&quot;The imaging work used low-temperature electron microscopy (cryo-EM) and required finding ways to stabilize the inherently loose and flexible channel structures. Dr. Nimigean and her lab collaborated with Dr. Alessio Accardi, professor of physiology and biophysics at Weill Cornell Medicine, who used computational modeling techniques to uncover the elusive structural details of how the protein plug blocks the pore.</p>
<p>&quot;'We couldn't get a clear cryo-EM picture of this pore-binding structure because it binds in many different conformations,&quot; Dr. Nimigean said. &quot;Ultimately, with the help of the modeling, we found that the first three amino acids of the plug are very important for the binding, and the rest establishes a flexible chain length.'&quot;</p>
<p>Comment: this intricately designed system cannot be produced by chance mutations. More evidence for design which manages all cell communications.</p>
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<link>https://agnosticweb.com/index.php?id=48253</link>
<guid>https://agnosticweb.com/index.php?id=48253</guid>
<pubDate>Tue, 04 Mar 2025 20:25:36 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>The biochemistry of cell: how to picture it (reply)</title>
<content:encoded><![CDATA[<p>Invented by Jane Richardson:</p>
<p><a href="https://www.quantamagazine.org/how-colorful-ribbon-diagrams-became-the-face-of-proteins-20240823/">https://www.quantamagazine.org/how-colorful-ribbon-diagrams-became-the-face-of-proteins...</a></p>
<p>&quot;Richardson’s innovation was a reproducible method of representing the folds of a protein’s amino acid backbone without getting bogged down in the details of specific atomic arrangements. She relied on proteins’ tendency to fold into two energetically favorable shapes: coils called alpha helices and flat shapes called beta strands, which can line up into so-called beta sheets. Then there are loops, which connect alpha helices to beta strands like corner pieces in a puzzle.</p>
<p>&quot;There are other folding structures, and “people have come up with lots of names” for them, Perrakis said. “But at the end of the day, the ones that matter are the helices and the sheets.”</p>
<p>***</p>
<p>&quot;In her year of sketching, Richardson came up with simple ways to illustrate these basic shapes. Alpha helices are coils that look like the tails of decorative ribbons, curled with the edge of a pair of scissors. Beta strands are arrows that point in the direction in which the amino acid chain was built. And thin wires represent the loops and turns that connect the structures. “That allowed us to follow the chain round and to see these folds and visualize them in three dimensions,” Thornton said.</p>
<p>***</p>
<p>&quot;Richardson’s ribbon diagram has become so ubiquitous, it can be difficult to imagine proteins looking any other way. Bourne often reminds his students that proteins don’t actually look like that.</p>
<p>“'A protein is nothing like a ribbon,” he said. It’s much more dynamic, he added. Sure, proteins’ backbones fold up into structures like the coils and sheets that the ribbon diagrams represent. But researchers can’t actually see those structures when they image proteins.</p>
<p>***</p>
<p>&quot;As simplifications, ribbon diagrams have their limitations, of course. They can’t convey some structural elements, such as tunnels or pockets where other molecules might bind — information critical for understanding how proteins work and designing drugs to target them. They also don’t communicate structure well for larger proteins or complexes of multiple proteins.</p>
<p>“'It gives you a three-dimensional view of the shape, but it also hides a lot of the features that we know to be true about proteins,” Bourne said. “So that then can narrow one’s thinking.” He called this “the curse of the protein ribbon diagram” in a 2022 essay.</p>
<p>&quot;Another popular representation is the space-filling model, which shows how much room atoms take up and looks more like an actual protein. It can show proteins’ pockets and tunnels — but it can’t represent the protein architecture, such as helices and sheets. “It depends what you want to show,” Perrakis said. Many researchers look at different types together to glean all the important structural information. What a protein looks like, Richardson said, is how you choose to represent it.&quot;</p>
<p>Comment: protein structures are extremely complex which implies the 3-D shapes help form the functions. Please see the illustrations. They each represent the structures of thousands of protein parts. This shows that design is required.</p>
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<link>https://agnosticweb.com/index.php?id=47350</link>
<guid>https://agnosticweb.com/index.php?id=47350</guid>
<pubDate>Fri, 23 Aug 2024 17:40:43 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>Biochemistry of cell  communication; new findings (reply)</title>
<content:encoded><![CDATA[<p>How a molecule takes in new protein into the cell: </p>
<p> <a href="https://www.sciencenews.org/article/protein-3d-maps-toxic-substances-organs">https://www.sciencenews.org/article/protein-3d-maps-toxic-substances-organs</a></p>
<p>&quot;A close look at one protein shows how it moves molecular passengers into cells in the kidneys, brain and elsewhere.</p>
<p>&quot;The protein LRP2 is part of a delivery service, catching certain molecules outside a cell and ferrying them in. Now, 3-D maps of LRP2 reveal the protein’s structure and how it captures and releases molecules, researchers report February 6 in Cell. The protein adopts a more open shape, like a net, at the near-neutral pH outside cells. But in the acidic environment inside cells, the protein crumples to drop off any passengers.</p>
<p>***</p>
<p>&quot;The various conditions associated with LRP2 dysfunction come from the protein’s numerous responsibilities — it binds to more than 75 different molecules. That’s a huge amount for one protein, earning it the nickname “molecular flypaper,” says nephrologist Jonathan Barasch of Columbia University.</p>
<p>&quot;Typically, LRP2 sits at a cell membrane’s surface, waiting to snag a molecule passing by. After the protein binds to a molecule, the cell engulfs the part of its surface containing the protein, forming an internal bubble called an endosome. LRP2 then releases the molecule inside the cell, and the endosome carries the protein back to the surface.</p>
<p>&quot;To understand this shuttle system, Barasch and colleagues collected LRP2 from 500 mouse kidneys. The researchers put some of the protein in a solution at the extracellular pH of 7.5, and some in an endosome-mimicking solution at pH 5.2. Using a cryo-electron microscope, they captured images of the proteins and then stitched the images together in a computer, rendering 3-D maps of the protein at both open and closed formations.</p>
<p>&quot;The researchers suggest that charged calcium atoms hold the protein open at extracellular pH. But as pH drops due to hydrogen ions flowing into the endosome, the hydrogen ions displace the calcium ions, causing the protein to contract.&quot;</p>
<p>Comment: this is design in action. The molecule acts automatically. Previous famous experts could not see this and assumed cells were intelligent. dhw wake up.</p>
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<link>https://agnosticweb.com/index.php?id=43327</link>
<guid>https://agnosticweb.com/index.php?id=43327</guid>
<pubDate>Tue, 14 Feb 2023 20:05:11 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>The biochemistry of cell: efficiency in cells (reply)</title>
<content:encoded><![CDATA[<p>Energy expenditure analyzed:</p>
<p><a href="https://reasons.org/explore/blogs/impact-events/should-we-expect-efficiency-inside-the-cell">https://reasons.org/explore/blogs/impact-events/should-we-expect-efficiency-inside-the-...</a></p>
<p>&quot;Kinesin-1: The Cell’s Cargo Mover<br />
Kinesin-1 moves vesicles around cells by “walking” along rod-like protein assemblies called microtubules (see video below). Kinesin-1 uses adenosine triphosphate (ATP) as fuel to move around. However, when a team of researchers at Yamaguchi University in Japan measured the motion of Kinesis-1 along the microtubules, they found that up to 80% of the energy released from ATP generated heat instead of movement!</p>
<p>***</p>
<p>&quot;As scientists continued to research the operation of Kinesin-1, they recognized that much noisier conditions exist inside the cell than outside on a piece of glass. Given this fact, scientists wanted to know whether this noise affected the energy conversion rate.</p>
<p>&quot;The Efficiency of Kinesin-1<br />
To investigate further, they attached small (~500 nanometer) polymer beads to the Kinesis-1 molecule and then used an infrared laser like a set of “optical tweezers” to grab onto the beads.1 By varying the intensity and location of the laser, they could mimic the type of noise experienced by Kinesin-1 inside the cell. Many tests with the laser setup showed a dramatic increase in efficiency of Kinesin-1 movement—specifically, the molecule sped up—under a load. More significantly, the acceleration of Kinesin-1 increased with the size of the load. Additionally, it appears that many other proteins and enzymes in the cell will experience similar efficiency gains when tested under conditions mimicking those inside the cell (although more tests are needed to confirm this).</p>
<p>***</p>
<p>&quot;In similar fashion, Kinesin-1 acts like a poorly designed molecule in the pristine conditions of the lab. However, when it operates in the noisy environment of the cell, it performs beautifully—just like it was designed to do.&quot;</p>
<p>Comment: We need to reflect on Gilbert and Sullivan wisdom, 'things are seldom what they seem'. We need to analyze the working systems right down in their environment. Superficial objections to our backwards retina come to mind. The designer knew exactly what He was doing and why. dhw's superfical analysis of God's roundabout way of producing us is a good case in point. As we dig in, every time we find superb design. Humans are a prime endpoint example.</p>
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<link>https://agnosticweb.com/index.php?id=41397</link>
<guid>https://agnosticweb.com/index.php?id=41397</guid>
<pubDate>Fri, 27 May 2022 17:38:58 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>The biochemistry of cell: information delivery (reply)</title>
<content:encoded><![CDATA[<p>Another form of chemical communication using a glutamate channel, which transmits more than glutamate:</p>
<p><a href="https://cosmosmagazine.com/science/biology/twisty-molecular-elevator/?utm_source=Cosmos+-+Master+Mailing+List&amp;utm_campaign=9265d4096c-RSS_EMAIL_CAMPAIGN&amp;utm_medium=email&amp;utm_term=0_3f5c04479a-9265d4096c-180344213&amp;mc_cid=9265d4096c&amp;mc_eid=b072569e0b">https://cosmosmagazine.com/science/biology/twisty-molecular-elevator/?utm_source=Cosmos...</a></p>
<p>&quot;A team, led by Ichia Chen of the University of Sydney, has modelled the shape of an extremely important molecular machine – the glutamate transporter. Understanding this shape and process helps to explain how brain cells “talk” to each other.</p>
<p>&quot;Cells communicate by sending chemical signals, mostly in the form of the neurotransmitter glutamate. These glutamate signals are released from a nerve through glutamate transporters, which sits on the surface of the cell and open and close to let the signal through at the right time, pumping the glutamate out when open.</p>
<p>***</p>
<p>&quot;The team captured the shape of the transporter in incredible detail with cryogenic electron microscopy (cryo-EM), and found that it looked like a “twisting elevator” inside the cell membrane, they report in their paper, published in Nature.</p>
<p>***</p>
<p>&quot;The images showed that the glutamate transporter could multi-task. The first function was to pump glutamate through the membrane and the second is to transport other molecules.</p>
<p>“'These molecular machines use a really cool twisting, elevator-like mechanism to move their cargo across the cell membrane,” says senior author Renae Ryan, from the University of Sydney.</p>
<p>“'But they also have an additional function where they can allow water and chloride ions to move across the cell membrane.&quot;</p>
<p>Comment: We are still on the outside looking in. We do not know the text of the messages or how they are interpreted by the cells. All we know is cells do talk to each other. Be sure to look at the illustrations of a  molecule that can twist around to perform a job. Just another molecular machine that demands the recognition of design.</p>
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<link>https://agnosticweb.com/index.php?id=37643</link>
<guid>https://agnosticweb.com/index.php?id=37643</guid>
<pubDate>Wed, 17 Feb 2021 23:29:23 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>The biochemistry of cell: information delivery (reply)</title>
<content:encoded><![CDATA[<p>New findings spotting specific  molecules:</p>
<p><a href="https://www.sciencedaily.com/releases/2021/02/210212101844.htm">https://www.sciencedaily.com/releases/2021/02/210212101844.htm</a></p>
<p>&quot;The researchers chose to study yeast cells, since they are similar to human cells, and their focus is on glycolytic oscillations -- a series of chemical reactions during metabolism where the concentration of substances can pulse or oscillate. The study showed how cells that initially oscillated independent of each other shifted to being more synchronized, creating partially synchronized populations of cells.</p>
<p>&quot;'One of the unique things with this study is that we have been able to study individual cells instead of simply entire cell populations. This has allowed us to really be able to see how the cells transition from their individual behaviour to coordinating with their neighbours. We have been able to map their behaviour both temporally and spatially, that is to say, when something occurs and in which cell,&quot; says Beck Adiels.</p>
<p>***</p>
<p>&quot;This type of behaviour is also found in cells such as heart muscle cells and in pancreatic cells, which can be an important piece of the puzzle in diabetes research.&quot;</p>
<p>Comment: I do not understand how glycolytic oscillations carry messages, but no else knows either. We know DNA carries information in its code. Does the pitch of the oscillations? The advancing research raises more questions than answers.</p>
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<link>https://agnosticweb.com/index.php?id=37614</link>
<guid>https://agnosticweb.com/index.php?id=37614</guid>
<pubDate>Sun, 14 Feb 2021 19:38:01 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>The biochemistry of cell: information delivery (reply)</title>
<content:encoded><![CDATA[<p>The new information has to get through cell membranes:</p>
<p><a href="https://phys.org/news/2019-04-cell.html">https://phys.org/news/2019-04-cell.html</a></p>
<p>&quot;The interior of all living cells is separated from the outside world by membranes. These membranes keep the cells intact and protect them from negative influences. But they also act as a barrier for nutrients and information. For this reason, cell membranes contain mechanisms that enable selective access to desired substances or transmit information from external signals into the cell.</p>
<p>&quot;An important signal pathway in mammals consists of three components: The first is a receptor that recognises the signal and is activated by it. The second is a so-called G protein that binds to the activated receptor and transmits the signal to one or more effector proteins. In this case, the effector is adenylyl cyclase, the third component of the signal chain. This protein is activated by a subunit of the G protein and produces, in a biochemical reaction, a secondary messenger called cyclic AMP (cAMP).</p>
<p>&quot;cAMP triggers various reactions in the cell; for example, it increases the permeability of the membrane to calcium in cardiac cells, leading to an increase in the heart beat rate.</p>
<p>***</p>
<p>&quot;'Surprisingly, in determining the structure of the adenylyl cyclase bound to the alpha subunit of the G protein, we discovered that the protein appears to be able to inhibit itself,&quot; says Korkhov. One part of the protein is responsible for this self-inhibition. This part blocks the active site of the enzyme and prevents the overproduction of cAMP.</p>
<p>&quot;This new insight into the molecular structure of adenylyl cyclase provides a much better understanding of how external signals lead to the controlled production of the important secondary messenger cAMP. &quot;</p>
<p>Comment: In this case the stimulus to the cell is meant to initiate a specific required reaction and a series of specific molecules, one of which is especially designed to employ inhibition. The research makes it clear the cell is obviously programmed to make the proper response, no innate intelligence necessary.</p>
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<link>https://agnosticweb.com/index.php?id=31685</link>
<guid>https://agnosticweb.com/index.php?id=31685</guid>
<pubDate>Thu, 25 Apr 2019 18:45:21 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>Biochemistry of cell  communication; new findings (reply)</title>
<content:encoded><![CDATA[<p>Extracellular RNA can carry biochemical molecules outside cells around the body:</p>
<p><a href="https://www.sciencedaily.com/releases/2019/04/190404143629.htm">https://www.sciencedaily.com/releases/2019/04/190404143629.htm</a></p>
<p>&quot;Scientists have improved their understanding of a new form of cell-cell communication that is based on extracellular RNA (exRNA). RNA, a molecule that was thought to only exist inside cells, now is known to also exist outside cells and participate in a cell-cell communication system that delivers messages throughout the body. </p>
<p>***</p>
<p>&quot;'Using computational deconvolution, we discovered six major types of exRNA cargo and their carriers that can be detected in bodily fluids, including serum, plasma, cerebrospinal fluid, saliva and urine,&quot; said co-first author Oscar D. Murillo, a graduate student in Baylor's Molecular and Human Genetics Graduate Program working in the Milosavljevic lab. &quot;The carriers act like molecular vessels moving their RNA cargo throughout the body. They include lipoproteins -- one of the major carriers is High-Density Lipoprotein (HDL or the &quot;good cholesterol&quot;) -- a variety of small protein-containing particles and small vesicles, all of which can be taken up by cells.&quot;</p>
<p>&quot;The researchers found that the computational method helps reveal biological signals that could not be previously detected in individual studies due to the naturally complex variation of the biological system. For example, in an exercise challenge study their computational approach revealed differences before and after exercise in the proportions of the exRNA-cargo in HDL particles and vesicles in human plasma.</p>
<p>&quot;'Exercise increased a proportion of RNA molecules involved in regulating metabolism and muscle function, suggesting adaptive response of the organism to exercise challenge,&quot; Milosavljevic said. &quot;This finding opens the possibility that in other conditions, both in health or disease, the computational method might identify signals that could have physiological and clinical relevance.'&quot;</p>
<p>Comment: This adds a new complex signalling and delivery system using exRNA messengers. What degree of complexity is needed before it is recognize a designer is required?</p>
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<link>https://agnosticweb.com/index.php?id=31549</link>
<guid>https://agnosticweb.com/index.php?id=31549</guid>
<pubDate>Thu, 04 Apr 2019 22:03:24 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>Biochemistry of cell  gene expression (reply)</title>
<content:encoded><![CDATA[<p>Obviously cells have to control their gene expresson so it stays within proper limits:</p>
<p><a href="https://phys.org/news/2019-01-scientists-insight-gene.html">https://phys.org/news/2019-01-scientists-insight-gene.html</a></p>
<p><br />
&quot;The findings, first reported on bioRxiv, could ultimately improve our understanding of how certain antibacterial drugs work against the enzyme RNA polymerase (RNAP) in treating conditions such as Clostridium difficile infections and tuberculosis.</p>
<p>&quot;Gene expression occurs when the information contained in DNA is used to produce functional gene products such as proteins and other molecules. The process has two stages. In the first stage, called transcription, RNAP reads the information in a strand on DNA, which is then copied into a new molecule of messenger ribonucleic acid (mRNA). In the second stage, the molecule then moves on to be processed or translated.</p>
<p>&quot;However, to help control gene expression levels, transcriptional pausing by RNAP can occur between the two stages, providing a kind of 'roadblock' where transcription may be terminated or modulated.</p>
<p>&quot;'A consensus pause sequence that acts on RNAPs in all organisms, from bacteria to mammals, halts the enzyme in an elemental paused state from which longer-lived pauses can arise,&quot; explains senior author Robert Landick, </p>
<p>***</p>
<p>&quot;The team's analyses first revealed that the elemental pause process involves several biological players, which together create a barrier to prevent escape from paused states. The process also causes a modest conformational shift that makes RNAP 'stumble' in feeding DNA into its reaction centre, temporarily stopping it from making RNA.</p>
<p>&quot;'We also found that transcriptional pausing makes RNAP loosen its grip and backtrack on the DNA while paused,&quot; says Landick. &quot;Together, these results provide a framework to understand how the process is controlled by certain conditions and regulators within cells.'&quot;</p>
<p>Comment: Cells which are high speed production factories and must have tight controls over outputs that are made to stay within required limits. Cells make split-second decisions based on tight controls by 'regulators'. This is all automatic molecular activity. It must be to work at such constant high speed. Only cellular design can achieve this homeostasis, and homeostasis is what creates the phenomenon of living  matter. The universe has homeostasis in its organization, but it is equal to living matter.</p>
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<link>https://agnosticweb.com/index.php?id=30816</link>
<guid>https://agnosticweb.com/index.php?id=30816</guid>
<pubDate>Tue, 08 Jan 2019 23:58:30 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>The biochemistry of cell  communication:biofilm perculation (reply)</title>
<content:encoded><![CDATA[<p>Biofilm has communication signals across the mass of cells:</p>
<p><a href="https://www.sciencedaily.com/releases/2018/07/180726085914.htm">https://www.sciencedaily.com/releases/2018/07/180726085914.htm</a></p>
<p>&quot;A concept known as 'percolation' is helping microbiologists explain how communities of bacteria can effectively relay signals across long distances. Once regarded as a simple cluster of microorganisms, communities of bacteria have been found to employ a strategy we use to brew coffee and extract oil from the sea. Percolation helps the microscopic community thrive and survive threats, such as chemical attacks from antibiotics. </p>
<p>***</p>
<p>&quot;Cells at the edge of these communities tend to grow more robustly than their interior counterparts because they have access to more nutrients. To keep this edge growth in check and ensure the entire community is fit and balanced, the &quot;hungry&quot; members of the biofilm interior send electrochemical signals to members at the exterior. These signals halt consumption at the edge, allowing nutrients to pass through to the interior cells to avoid starvation.</p>
<p>&quot;'This keeps the interior fed well enough and if a chemical attack comes and takes out some of the exterior cells, then the protected interior is able to continue and the whole population can survive,&quot; said Larkin, a UC San Diego Biological Sciences postdoctoral scholar. &quot;It is essential that the electrochemical signal be consistently transmitted all the way to the biofilm edge because that is the place where the growth must be stopped for the community to reap the most benefit from signaling.&quot;</p>
<p>***</p>
<p>&quot;In a community of bacteria, signals pass from cell to cell in a connected path over a distance of hundreds of cells. Using fluorescence microscopes, the researchers were able to track individual cells that were &quot;firing&quot; (transmitting a signal). The scientists found that the fraction of firing cells and their distribution in space precisely matched theoretical predictions of the onset of percolation. In other words, the bacterial community had a fraction of firing cells that was precisely at the tipping point between having no connectivity and full connectivity among cells, also known as a critical phase transition point.</p>
<p>&quot;'We're all familiar with how we make coffee through percolation and it's an interesting twist that bacteria appear to use the same concept to accomplish the very complicated task of efficiently relaying an electrochemical signal over very long distances from cell to cell,&quot; said Süel.</p>
<p>&quot;'It's interesting that these bacteria, which are so-called simple, single-cell organisms, are using a fairly sophisticated strategy to solve this community-level problem,&quot; said Larkin. &quot;It's sophisticated enough that we humans are using it to extract oil, for example.'&quot;</p>
<p>Comment: Most likely an automatic electrochemical series of reactions from interior to exterior, passed from contiguous cell to contiguous cell.</p>
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<link>https://agnosticweb.com/index.php?id=29198</link>
<guid>https://agnosticweb.com/index.php?id=29198</guid>
<pubDate>Sat, 04 Aug 2018 21:03:04 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>Biochemistry of cell  communication; new findings (reply)</title>
<content:encoded><![CDATA[<blockquote><blockquote><p>David Comment: This is another example of designed molecules acting according to an intelligent design. A ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein.</p>
</blockquote></blockquote><blockquote><p><br />
Tony: What do you mean, precisely, by 'produces a signal'? Is it electrical? Chemical?</p>
</blockquote><p>A ligand is on a cell  wall  and bonds to an incoming protein molecule. It is not a separate electrical signal, but ion attracting ions can be part of it in the bond.</p>
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<link>https://agnosticweb.com/index.php?id=29069</link>
<guid>https://agnosticweb.com/index.php?id=29069</guid>
<pubDate>Tue, 24 Jul 2018 03:39:10 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>Biochemistry of cell  communication; new findings (reply)</title>
<content:encoded><![CDATA[<blockquote><p>David Comment: This is another example of designed molecules acting according to an intelligent design. A ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein.</p>
</blockquote><p>What do you mean, precisely, by 'produces a signal'? Is it electrical? Chemical?</p>
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<link>https://agnosticweb.com/index.php?id=29065</link>
<guid>https://agnosticweb.com/index.php?id=29065</guid>
<pubDate>Tue, 24 Jul 2018 01:23:04 +0000</pubDate>
<category>Introduction</category><dc:creator>Balance_Maintained</dc:creator>
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<title>Biochemistry of cell  communication; new findings (reply)</title>
<content:encoded><![CDATA[<p>Part of the WnT pathway now found:</p>
<p><a href="https://www.sciencedaily.com/releases/2018/07/180720092455.htm">https://www.sciencedaily.com/releases/2018/07/180720092455.htm</a></p>
<p>&quot;This is a nice example of a rather unexpected discovery: by studying the development of the blood vessels of the brain, researchers have just shed light on a question that was pending for 10 years! They provide a molecular mechanism conferring ligand specificity to Wnt signaling, an ancestral communication pathway present in all vertebrates. </p>
<p>&quot;Wnt is ancient pathway, whose evolutionary appearance dates back to the emergence of multicellular animals. It plays pivotal roles in cell to cell communication and governs several aspects of embryonic development and tissue homeostasis. When dysfunctional, Wnt signaling can be at the origin of many diseases, in particular several cancers. With 10 receptors and 19 ligands, recognizing each other, the complexity of the pathway seemed dizzying. How do vertebrate cells manage to interpret the many Wnt signals they encounter and trigger an adequate response? It is such an interpretation mechanism that ULB researchers have just discovered.</p>
<p>***</p>
<p>&quot;Previous findings had shown that two proteins expressed by cerebral endothelial cells, Gpr124 and Reck, are required for cerebrovascular development in response Wnt7 ligands. The team went on to study the mechanism by which the complex operates. Using genetic, biophysical and zebrafish experiments, researchers have shown that the complex Gpr124 / Reck acts as a decoding module: Reck recognizes the Wnt7 ligand, but the presence of Gpr124 is necessary to trigger Wnt7 signaling via Frizzled receptors. Their results are detailed in Science.&quot;</p>
<p>Comment: This is another example of designed molecules acting according to an intelligent design. A ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein.</p>
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<link>https://agnosticweb.com/index.php?id=29059</link>
<guid>https://agnosticweb.com/index.php?id=29059</guid>
<pubDate>Mon, 23 Jul 2018 14:18:08 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Biochemistry of cell  communication; message molecules (reply)</title>
<content:encoded><![CDATA[<blockquote><p>DAVID’s comment: <em>These are organic molecules working from their innate abilities to change shape and/or electrical attraction fields with ions charges. No brain or DNA instructions involved. The molecules are designed and chosen to fill a specific repetitive role without an mental thought involved.</em></p>
<p>dhw: <em>These molecules are part of the cell. When you move your arm, all kinds of electrical actions take place, but your arm does not have a brain and does not indulge in mental thought. The concept of cellular intelligence rests on the idea that the cell itself has some sort of brain equivalent which issues instructions to the rest of the cell (see Buehler).</em></p>
<p>DAVID: <em>The molecules respond to each other. That is how they are designed with charged ions at the appropriate spots to have them interlock. The design looks like intelligent actions.</em></p>
<p>dhw: I’m not saying the molecules are intelligent. The claim made by certain experts in the field is that the molecules are directed by intelligence. The fact that an action looks intelligent might possibly be caused by the fact that it IS intelligent.</p>
</blockquote><p>More likely intelligent design with intelligent instructions.</p>
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<link>https://agnosticweb.com/index.php?id=28876</link>
<guid>https://agnosticweb.com/index.php?id=28876</guid>
<pubDate>Wed, 11 Jul 2018 17:28:37 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>Biochemistry of cell  communication; message molecules (reply)</title>
<content:encoded><![CDATA[<p>DAVID’s comment: <em>These are organic molecules working from their innate abilities to change shape and/or electrical attraction fields with ions charges. No brain or DNA instructions involved. The molecules are designed and chosen to fill a specific repetitive role without an mental thought involved.</em></p>
<p>dhw: <em>These molecules are part of the cell. When you move your arm, all kinds of electrical actions take place, but your arm does not have a brain and does not indulge in mental thought. The concept of cellular intelligence rests on the idea that the cell itself has some sort of brain equivalent which issues instructions to the rest of the cell (see Buehler).</em></p>
<p>DAVID: <em>The molecules respond to each other. That is how they are designed with charged ions at the appropriate spots to have them interlock. The design looks like intelligent actions.</em></p>
<p>I’m not saying the molecules are intelligent. The claim made by certain experts in the field is that the molecules are directed by intelligence. The fact that an action looks intelligent might possibly be caused by the fact that it IS intelligent.</p>
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<link>https://agnosticweb.com/index.php?id=28870</link>
<guid>https://agnosticweb.com/index.php?id=28870</guid>
<pubDate>Wed, 11 Jul 2018 11:12:59 +0000</pubDate>
<category>Introduction</category><dc:creator>dhw</dc:creator>
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<title>Biochemistry of cell  communication; message molecules (reply)</title>
<content:encoded><![CDATA[<blockquote><p>DAVID’s comment: <em>These are organic molecules working from their innate abilities to change shape and/or electrical attraction fields with ions charges. No brain or DNA instructions involved. The molecules are designed and chosen to fill a specific repetitive role without an mental thought involved.</em></p>
<p>dhw: These molecules are part of the cell. When you move your arm, all kinds of electrical actions take place, but your arm does not have a brain and does not indulge in mental thought. The concept of cellular intelligence rests on the idea that the cell itself has some sort of brain equivalent which issues instructions to the rest of the cell (see Buehler).</p>
</blockquote><p>The molecules  respond to each other. That is how they are designed with charged ions at the appropriate spots to have them interlock. The design looks like intelligent actions.</p>
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<link>https://agnosticweb.com/index.php?id=28862</link>
<guid>https://agnosticweb.com/index.php?id=28862</guid>
<pubDate>Wed, 11 Jul 2018 00:26:32 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Biochemistry of cell  communication; message molecules (reply)</title>
<content:encoded><![CDATA[<p>DAVID’s comment: <em>These are organic molecules working from their innate abilities to change shape and/or electrical attraction fields with ions charges. No brain or DNA instructions involved. The molecules are designed and chosen to fill a specific repetitive role without an mental thought involved.</em></p>
<p>These molecules are part of the cell. When you move your arm, all kinds of electrical actions take place, but your arm does not have a brain and does not indulge in mental thought. The concept of cellular intelligence rests on the idea that the cell itself has some sort of brain equivalent which issues instructions to the rest of the cell (see Buehler).</p>
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<link>https://agnosticweb.com/index.php?id=28859</link>
<guid>https://agnosticweb.com/index.php?id=28859</guid>
<pubDate>Tue, 10 Jul 2018 09:58:11 +0000</pubDate>
<category>Introduction</category><dc:creator>dhw</dc:creator>
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<title>Biochemistry of cell  communication; message molecules (reply)</title>
<content:encoded><![CDATA[<p>A new study of how these molecules work to pick up signals:</p>
<p><a href="https://www.sciencedaily.com/releases/2018/07/180709152701.htm">https://www.sciencedaily.com/releases/2018/07/180709152701.htm</a></p>
<p>&quot; INRS professor Nicolas Doucet and his research team contributed to the discovery of this new molecular switch, shedding new light on the role of receptor tyrosine kinases, a well-known protein family whose function is still being explored.</p>
<p>***</p>
<p>&quot;Receptor tyrosine kinases (RTKs) are a family of proteins that carry out many tasks required for organism growth and maintenance. They are found in every cell of the human body and broadly act on processes ranging from cell organization to nutrient management. Despite their distinct roles, they conserve a high degree of structural similarity at the molecular level, suggesting that each component of their three-dimensional structure plays an important role in their biological function. However, only recently has technology become sufficiently precise to peer into key molecular interactions of RTKs at the atomic level.</p>
<p>***</p>
<p>&quot;One of the main difficulties Prof. Doucet's research team had to face was the need to clearly demonstrate that NCK and EPHA4 could recognize each other at the molecular level. If not, phosphorylation would be off the table.</p>
<p>***</p>
<p>&quot;RTK receptors embedded in the cell membrane stick their 'sensory receivers' outside the cell and extend their enzymatic machinery inside the cell. Part of their equipment is a kinase, an enzyme that activates other proteins by adding a phosphate group to specific amino acids on their surface. This process is known as phosphorylation.</p>
<p>&quot;To activate a cellular signaling pathway, RTKs pair up as soon as a receiver picks up a signal. Linking together involves reciprocal action, with each partner accepting a phosphate group from the other. All partners then line up in such a way that they can interact with a new molecule, thus initiating the required cellular function.&quot;</p>
<p>Comment: These are organic molecules working from their innate abilities to change shape and/or electrical attraction fields with ions charges. No brain or DNA instructions involved. The molecules are designed and chosen to fill a specific repetitive role without an mental thought involved</p>
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<link>https://agnosticweb.com/index.php?id=28854</link>
<guid>https://agnosticweb.com/index.php?id=28854</guid>
<pubDate>Mon, 09 Jul 2018 20:18:32 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Biochemistry of cell  communication; message molecules (reply)</title>
<content:encoded><![CDATA[<p>dhw: <em>I have merely tried to point out the flaws in the article you quoted. You claim to believe in common descent, and so you should also reject everything he says about mutations. I already know you believe mutations (and speciation) are programmed or dabbled, and you already know that my hypothesis of cellular intelligence as the organizer of the mutations allows for God as the designer. And since the author sneers at the unscientific nature of belief in chance, why don't you criticize his failure to acknowledge the unscientific nature of his own theory (which of course you do recognize)? Let's have some balance here!</em></p>
<p>DAVID: <em>But his point is God speciates, to which he and I both agree. Of course he argues against chance. So do I. He does not accept common descent. I think God used evolution as a God-controlled process, so on this one point he and I do not see eye to eye. Many of the ID folks side with him, I think mainly on theological grounds. They are primarily of Christian background. I'm not. Perhaps the reason why we differ.</em></p>
<p>As above, I asked for balance. Thank you for now rejecting his point about mutations, with its implicit support for separate creation and its complete lack of scientific evidence, of which he seems unaware as he sneers at the unscientific nature of belief in chance.</p>
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<link>https://agnosticweb.com/index.php?id=27602</link>
<guid>https://agnosticweb.com/index.php?id=27602</guid>
<pubDate>Sat, 24 Feb 2018 12:25:47 +0000</pubDate>
<category>Introduction</category><dc:creator>dhw</dc:creator>
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<title>Biochemistry of cell  communication; message molecules (reply)</title>
<content:encoded><![CDATA[<blockquote><p><br />
dhw: <em>Exactly the same argument. If you believe in common descent, those mutations did happen (though as I pointed out before, not one at a time). You say your God preprogrammed or dabbled them. I propose that cellular intelligence organized them. Your author doesn’t seem to realize that he is NOT arguing against mutations but against chance. If, however, he rejects common descent, the alternative is the individual creation of every single species and variation from scratch, and I wonder what you and “the science”* say about that.</em></p>
<p>DAVID: <em>He and I have the same theory, which I am sure you recognize, and it not scientific. God speciates. And 'cellular intelligence' appeared from what? Again God supplies the answer, because intelligence is obviously required</em>.</p>
<p>dhw: I have merely tried to point out the flaws in the article you quoted. You claim to believe in common descent, and so you should also reject everything he says about mutations. I already know you believe mutations (and speciation) are programmed or dabbled, and you already know that my hypothesis of cellular intelligence as the organizer of the mutations allows for God as the designer. And since the author sneers at the unscientific nature of belief in chance, why don't you criticize his failure to acknowledge the unscientific nature of his own theory (which of course you do recognize)? Let's have some balance here!</p>
</blockquote><p>But his point is God speciates, to which he and I both agree.  Of course he argues against chance. So do I. He does not accept common descent. I think God used evolution as a God-controlled process, so on this one point he and I do not see eye to eye. Many of the ID folks side with him, I think mainly on theological grounds. They are primarily of Christian background. I'm not. Perhaps the reason why we differ.</p>
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<link>https://agnosticweb.com/index.php?id=27598</link>
<guid>https://agnosticweb.com/index.php?id=27598</guid>
<pubDate>Fri, 23 Feb 2018 22:22:49 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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