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<title>AgnosticWeb.com - evolution:  a start of multicellularity</title>
<link>https://agnosticweb.com/</link>
<description>An Agnostic&#039;s Brief Guide to the Universe</description>
<language>en</language>
<item>
<title>evolution:  a start of multicellularity (reply)</title>
<content:encoded><![CDATA[<p>A specific bacteria forms cooperative groups:</p>
<p><a href="https://www.sciencealert.com/strange-multicellular-bacteria-team-up-in-an-entirely-unexpected-way">https://www.sciencealert.com/strange-multicellular-bacteria-team-up-in-an-entirely-unex...</a></p>
<p>&quot;All bacteria exist as single cells at some point in their lives – except for one kind, known as multicellular magnetotactic bacteria (MMB), that is.</p>
<p>&quot;Scooped from the sulfide-laden sediments of a tidal salt marsh in Massachusetts, scientists think these MMBs could provide clues to our own evolutionary history, as a kind of missing link between simple, single-celled life forms and complex multicellular organisms like ourselves.</p>
<p>&quot;Other kinds of bacteria can team up with their fellow cells when needed, sure, but MMBs do everything together, to the point where each individual cell literally cannot survive being separated from its 'consortium', the nobbly super-organism it calls home.</p>
<p>&quot;The cells in an MMB consortium form a spherical shape with a hollow at the center, not unlike a blastocyst, the stage in embryonic development that comes immediately after the egg and sperm merge.</p>
<p>&quot;The fact that this bacteria so closely resembles that transition point, from two single cells with different genetics to one inseparable cluster, is fascinating: embryo comparisons have provided many clues about our evolutionary history.</p>
<p>&quot;Unlike a blastocyst, however, each cell in an MMB is its own individual organism. Scientists already knew this, but they had assumed these individuals might be clones of each other, since all the cells sync up to replicate when the entire MMB consortium divides in two.</p>
<p>&quot;A team led by environmental microbiologist George Schaible from Montana State University has made headway by mapping the metagenomes of 22 MMB consortia.</p>
<p>&quot;This revealed that the cells within a consortium are not clones, and that the variety of genes spread throughout the cluster enables individuals to serve different functions that benefit the whole – similar to organs in a body, or a society that benefits from its members' diverse skills and interests.</p>
<p>***</p>
<p>&quot;It would probably be difficult to survive if you were solely responsible for growing, hunting, and building everything your body needs, so human communities have a division of labor. That's exactly how the scientists have described the metabolism of an MMB consortium: a 'division of labor'. The genetic and metabolic diversity they found in this study sure adds some weight to that theory.&quot;</p>
<p>Comment: a very logical beginning to true multicellularity. Bacterial mats are quite similar.</p>
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<link>https://agnosticweb.com/index.php?id=48496</link>
<guid>https://agnosticweb.com/index.php?id=48496</guid>
<pubDate>Sun, 20 Apr 2025 19:10:13 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>evolution: the  role of Asgard  Archaea (reply)</title>
<content:encoded><![CDATA[<p>A gateway to eukaryotes:</p>
<p><a href="https://phys.org/news/2025-03-life-special-group-celled-laid.html">https://phys.org/news/2025-03-life-special-group-celled-laid.html</a></p>
<p> &quot;Asgard archaea appeared almost heaven-sent for research: They turned out to be a missing link between archaea and eukaryotes—that is, between archaea and organisms whose cells contain a nucleus, such as plants and animals.</p>
<p>***</p>
<p>&quot;In that study, Pilhofer and his postdoctoral researchers Jingwei Xu and Florian Wollweber demonstrated that Lokiarchaeum ossiferum possesses certain structures also typical of eukaryotes. &quot;We found an actin protein in that species that appears very similar to the protein found in eukaryotes—and occurs in almost all Asgard archaea discovered to date,&quot; says Pilhofer.</p>
<p>&quot;In the first study, the researchers combined different microscopy techniques to demonstrate that this protein—called Lokiactin—forms filamentous structures, especially in the microbes' numerous tentacle-like protrusions. &quot;They appear to form the skeleton for the complex cell architecture of Asgard archaea,&quot; adds Florian Wollweber.</p>
<p>&quot;In addition to actin filaments, eukaryotes also possess microtubules. These tube-shaped structures are the second key component of the cytoskeleton and are comprised of numerous tubulin proteins. These tiny tubes are important for transport processes within a cell and the segregation of chromosomes during cell division</p>
<p>&quot;The origin of these microtubules has been unclear—until now. In a newly published article in the journal Cell, the ETH researchers discovered related structures in Asgard archaea and describe their structure. These experiments show that Asgard tubulins form very similar microtubules, albeit smaller than those in their eukaryotic relatives.</p>
<p>&quot;However, only a few Lokiarchaeum cells form these microtubules. And, unlike actin, these tubulin proteins only appear in very few species of Asgard archaea.</p>
<p>***</p>
<p>&quot;Was the cytoskeleton essential for the development of complex life? While some questions remain unanswered, the researchers are confident that the cytoskeleton was an important step in the evolution of eukaryotes.</p>
<p>&quot;This step could have occurred eons ago, when an Asgard archaeon entwined a bacterium with its appendages. In the course of evolution, this bacterium developed into a mitochondrion, which serves as the powerhouse of modern cells. Over time, the nucleus and other compartments evolved—and the eukaryotic cell was born.</p>
<p>&quot;'This remarkable cytoskeleton was probably at the beginning of this development. It could have enabled Asgard archaea to form appendages, thereby allowing them to interact with, and then seize and engulf a bacterium,&quot; says Pilhofer.&quot;</p>
<p>Comment: it appears these are our direct ancestors as we must have came from bacteria which represent first life.</p>
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<link>https://agnosticweb.com/index.php?id=48355</link>
<guid>https://agnosticweb.com/index.php?id=48355</guid>
<pubDate>Sat, 22 Mar 2025 21:04:18 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>evolution: the effects of a theory without natural selection (reply)</title>
<content:encoded><![CDATA[<p>From Neil Thomas:</p>
<p><a href="https://evolutionnews.org/2024/10/the-fate-of-evolution-without-natural-selection/">https://evolutionnews.org/2024/10/the-fate-of-evolution-without-natural-selection/</a></p>
<p>&quot;The last four decades have produced numerous independent studies which have all found Darwin wanting on purely scientific grounds. <strong>This, as intimated above, has clear implications for materialist philosophy since, if the only materialist theory accounting for the nature of things is discredited, this in good logic leaves only supra-natural causation on the table.</strong> (my bold)</p>
<p>***</p>
<p>&quot;...Jerry Fodor and Massimo Piattelli-Palmarini mounted an uncompromising critique of Darwin’s notion of natural selection, pointing out its fundamental misconception in devastatingly simple terms:</p>
<p>&quot;Darwin was inadequately impressed by the fact that breeders have minds — they act out of their beliefs, desires and intentions and so on — whereas of course, nothing of that sort is true in the case of natural selection.</p>
<p>&quot;Darwin’s impermissibly anthropomorphic and perhaps unwittingly vitalist comparison of stock-rearing with the purely inanimate tendencies of “natural selection” had already been pointed out to him by Alfred Russel Wallace and by Sir Charles Lyell who both objected that the analogy between resourceful nurture and dumb nature was untenable. Most gravely for Darwin, Lyell also pointed out that there could be no such thing in nature as natural selection (a process which would require cognitive abilities).<strong> What Darwin had meant to say, Lyell proposed, was natural preservation (which is wholly unpremeditated and in essence merely a statistic without creative power).</strong> (my bold)</p>
<p>&quot;It was a criticism that Darwin rather grudgingly consented to accept but, despite his nominal concession, failed to explain how mere preservation  could lead to the kind of new biological pathways which would be necessary to “evolve” different kinds of limbs, physical frames, or superior brains. <strong>As Richard Milner has commented, “Natural selection is an eliminative process that does not explain the generation, proliferation and direction of varieties.</strong><br />
 (my bold)<br />
***</p>
<p>&quot;I find equivocation about the matter of evolution without natural selection puzzling. The briefest account of the historical sequence of the ideas of, first evolution, then natural selection, will explain my sense of disquiet.</p>
<p>***</p>
<p>&quot;With reference to that brief chronological reprise, my point is: If some leading 21st-century scientists and philosophers are now picking (rather large) holes in the idea of natural selection, what price evolution itself? There is surely no logical necessity to accept the truth-status of evolution without natural selection, is there? Ideally, I would like to hear an answer to that question from a competent authority since I have a nagging feeling that I, a non-specialist, might be missing something here. At any rate it does not seem reasonable to accept the veridical status of evolution on the basis of what an increasing number of scientists are beginning to perceive as a “dodgy dossier” which nevertheless furnished the essential precondition for people’s acceptance of evolution in the first place.&quot;</p>
<p>Comment: the second and third bolds above is the position we have established here. Natural selection has no design capacity. It is a result of the struggle to survive. The first bold is my position. Why not design and its designer?</p>
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<link>https://agnosticweb.com/index.php?id=47743</link>
<guid>https://agnosticweb.com/index.php?id=47743</guid>
<pubDate>Wed, 30 Oct 2024 19:10:58 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>evolution: the effect of pressure and heat (reply)</title>
<content:encoded><![CDATA[<p>Creates unexpected events:</p>
<p><a href="https://www.newscientist.com/article/2453548-weird-microbes-could-help-rewrite-the-origin-of-multicellular-life/">https://www.newscientist.com/article/2453548-weird-microbes-could-help-rewrite-the-orig...</a></p>
<p>&quot;Compressing a type of single-celled microorganism makes it develop into a multicellular tissue-like structure with different cell types. This suggests that pressure can help drive key evolutionary leaps, such as the emergence of multicellularity.</p>
<p>&quot;he organism is a type of archaea, one of the three domains of life, along with bacteria and eukaryotes. The eukaryotes are organisms with cells containing a nucleus and include animals and plants. Archaea lack a nucleus, so were originally mistaken for bacteria, but are now thought to share a common ancestor with eukaryotes.</p>
<p>&quot;Unlike most organisms, archaea also lack a stiff cell wall, a trait they share with animal cells. Lacking a cell wall gives animal cells flexibility and allows them to develop markedly different shapes. They can also change cell type in response to mechanical forces. Archaea are also able to form complex shapes and interact with each other, but little is known about how they react to such forces.</p>
<p>&quot;To find out more, Alex Bisson at Brandeis University in Massachusetts and his team squashed a salt-loving archaea called Haloferax volcanii under jelly pads, mimicking the forces they experience in their natural habitats – and saw something completely unexpected.</p>
<p>&quot;The cells grew and started making multiple copies of their genomes. When the tension in the cells’ membranes reached a critical point, new membranes grew between these genomes to create individual cells that were genetic clones of the original cell, forming a mound-shaped multicellular tissue.</p>
<p>&quot;The team tested 52 other similar species and found that more than 60 per cent of them formed tissues. This kind of cell division is also seen in a wide range of multicellular eukaryotes, such as during chick embryo development.</p>
<p>&quot;Next, the team zapped individual cells in the tissues with a laser to test whether they were connected to each other. When a cell was killed by the laser, neighbouring cells moved towards the wound, as cells in animal tissues called epithelium do.</p>
<p>&quot;This suggests that cells in the archaeal tissues are tethered together, just as they are in animal or plant tissues. Archaea lack the genes that animal and plant cells use for these tethers, so they have probably evolved their own method of doing this, says Bisson.</p>
<p>&quot;The cells in the tissues also developed into two distinct types. Those around the edge – where less pressure was applied – were flat, while those in the middle formed an angular structure resembling a scutoid, a shape first identified in animal epithelial cells in 2018.</p>
<p>&quot;This shows the advantages of exploring the biomechanical properties of cells across domains of life – rather than just genetic information – when studying evolution, says Bisson.</p>
<p>“'The idea that gene novelty alone governs evolutionary leaps now seems insufficient,” says Omaya Dudin at the University of Geneva in Switzerland. “Physical and mechanical factors are emerging as key players in orchestrating complex biological innovations in single-celled creatures.'”</p>
<p>Comment: an exciting finding that physical forces can play such a role, which means their DNA is coded for the proper responses. Of course, this means they could have been designed.</p>
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<link>https://agnosticweb.com/index.php?id=47736</link>
<guid>https://agnosticweb.com/index.php?id=47736</guid>
<pubDate>Mon, 28 Oct 2024 19:44:23 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>evolution: another eukaryote article (reply)</title>
<content:encoded><![CDATA[<p>Today:</p>
<p><a href="https://www.quantamagazine.org/meet-the-eukaryote-the-first-cell-to-get-organized-20241028/">https://www.quantamagazine.org/meet-the-eukaryote-the-first-cell-to-get-organized-20241...</a></p>
<p>&quot;The eukaryotes invented organization, if we use the literal definition of “organize”: to be furnished with organs. Inside a eukaryotic cell are self-contained, membrane-bound bundles that perform special functions, called organelles. All eukaryotic cells — animal, plant, fungus or protist — have a nucleus that encloses and protects DNA. Nearly all of them have mitochondria, which produce energy to fuel biochemical reactions. (Any eukaryotic lineages that lack mitochondria used to have them and then lost them sometime in evolutionary history.) And across the evolutionary tree, different eukaryotes have evolved or procured additional organelles that assemble proteins, store water, turn sunlight into energy, digest biomolecules, get rid of waste, and more. If prokaryotes are a loose pile of papers on the floor, eukaryotes are a sophisticated filing system that binds pages into packets and labels them.</p>
<p>“'They’ve got the endoplasmic reticulum, Golgi apparatus, peroxisomes, lysosomes, vacuoles — all this machinery not present in bacteria or archaea cells,” said Thijs Ettema(opens a new tab), an evolutionary microbiologist at Wageningen University in the Netherlands.</p>
<p>&quot;How this all happened isn’t entirely clear, but today, most experts agree that 2 billion or 3 billion years ago, an archaean cell engulfed a bacterial cell, which somehow escaped digestion and adapted to life inside its host. That bacterium evolved to become the organelle we now know as the mitochondrion.</p>
<p>&quot;Since that original act, the eukaryote has transformed again and again. It first evolved into a smattering of unique unicellular creatures, such as the ancestors of modern diplomonads(opens a new tab), which swim with dual tail clusters, and the parasitic microsporidians(opens a new tab), which shoot out coiled tubes to infect victim cells.</p>
<p>***</p>
<p>&quot;At some point, in a sequel to mitochondrial capture, a eukaryote engulfed a cyanobacterium capable of photosynthesis — the process of using sunlight to harvest carbon from the air and spin it into energy. That branch of the eukaryotic family, freshly equipped with green organelles called chloroplasts, evolved into plants and other photosynthesizers.</p>
<p>&quot;Then, within the last billion years, some individual eukaryotes began working together. Collectives became colonies, and they further organized when entire cells began to specialize, or perform unique functions within a complex multicellular body. Multicellularity unlocked even higher levels of sophistication, resulting in mushrooms, trees, hippos and humans.</p>
<p>***</p>
<p>&quot;Ettema and his team were surprised to find genes that looked suspiciously eukaryotic among the expected traces of archaea and bacteria. Upon further investigation, they found what might very well be the missing link in our understanding of eukaryotic evolution: a prokaryote(opens a new tab) with hallmark eukaryotic complexity in its genome. They named the microbe Lokiarchaea(opens a new tab) after its home vent.</p>
<p>&quot;<strong>Ettema suspected that a cell from this family, later dubbed “Asgards,” might make a convincing candidate for that first hungry host that engulfed a bacterium that became a mitochondrion. If so, he proposed, that ancient Asgard archaean might have evolved into the eukaryotic branch while the rest of its family forged on as prokaryotes.</strong> (my bold)</p>
<p>***</p>
<p>&quot;Researchers have since dug up Asgard DNA all over the world, including in North Carolina and Yellowstone National Park. But only two labs have successfully cultured Asgard cells. Those cells reveal some eukaryote-like features(opens a new tab), such as a cytoskeleton built with the protein actin. The rest are still under investigation, and their cellular structures are unknown.</p>
<p>&quot;Today, most researchers agree(opens a new tab) that Asgards are the closest known prokaryotic relatives of eukaryotes. Modern Asgards aren’t our ancestors, but we likely share an ancestor somewhere in deep time. “You could argue that eukaryotes are Asgards in the same way that birds are dinosaurs,” said Itay Budin(opens a new tab), a biochemist at the University of California, San Diego. “They’re kind of our cousins.”</p>
<p>&quot;The process by which an archaean cell turned a free-living bacterium into its own cellular machinery — called endosymbiosis — remains largely obscured by evolutionary history. Most biologists believe that one prokaryote “swallowed” another in a process called phagocytosis. However, phagocytosis takes a lot of energy. In fact, it is so energy-expensive that some believe it would have been impossible without the first host cell already having energy-generating mitochondria — opening a tricky, microbial chicken-and-egg debate.</p>
<p>&quot;Modern Asgards offer a clue that could get us around this mind bender: Their cytoskeleton suggests that they might use tiny, armlike projections called blebs to entrap prokaryotic food, without needing mitochondria. Maybe the first eukaryotic ancestor did, too.&quot;</p>
<p>Comment: to followers of this website, this is all old news. Somehow all of this got cobbled together or evolved. Perhaps all designed. Note the bold. Asgards are the best clue we have</p>
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<link>https://agnosticweb.com/index.php?id=47735</link>
<guid>https://agnosticweb.com/index.php?id=47735</guid>
<pubDate>Mon, 28 Oct 2024 19:01:12 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>evolution: another asteroid may have helped kill dinosaurs (reply)</title>
<content:encoded><![CDATA[<p>Off West Africa:</p>
<p><a href="https://www.nature.com/articles/s43247-024-01700-4">https://www.nature.com/articles/s43247-024-01700-4</a></p>
<p>&quot;The Nadir Crater offshore West Africa is a recently proposed near K-Pg impact structure identified on 2D seismic. Here we present 3D seismic data that image this crater in exceptional detail, unique for any such structure, which demonstrates beyond reasonable doubt that the crater-forming mechanism was a hypervelocity impact. Seismic mapping reveals a near-circular crater rim of 9.2 km and an outer brim of ~23 km diameter defined by concentric normal faults. An extended damage zone is evident across the region, well beyond the perceived limit of subsurface deformation for impact craters, except in a ‘sheltered zone’ to the east. The paleo-seabed shows evidence for widespread liquefaction because of seismic shaking, and scars and gullies formed by tsunami wave propagation and resurge. Deformation within the ~425 m high stratigraphic uplift and annular moat allows us to reconstruct the evolution of the crater, with radial thrusts at the periphery of the uplift suggesting a low-angle impact from the east. Structural relationships are used to reconstruct the deformation processes during the crater modification stage, with the central uplift forming first, followed by centripetal flow of surrounding sediments into the evacuated crater floor in the seconds to minutes after impact.&quot;</p>
<p>Here is another report on the paper:</p>
<p><a href="https://mail.google.com/mail/u/0/#inbox/FMfcgzQXJkQwcBGpvjXhJPqXVSxsqrpr">https://mail.google.com/mail/u/0/#inbox/FMfcgzQXJkQwcBGpvjXhJPqXVSxsqrpr</a></p>
<p>&quot;Geologists from the University of Edinburgh, U.K., report that a second large asteroid impacted Earth at around the same time as the large one that has been held responsible for the extinction of dinosaurs. The dinosaurs are believed to have fallen victim to the aftermath of the impact of an asteroid with a diameter of about 10 kilometres that left a crater in Middle America about 66 million years ago. The new crater is just off the West Coast of Africa, stems from an asteroid with approximately half a kilometre in diameter, and has been dated to around the same time. It’s unclear how much this made things worse for dinosaurs, but it probably didn’t help.&quot;</p>
<p>Comment: looks like Chixculub had help.</p>
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<link>https://agnosticweb.com/index.php?id=47666</link>
<guid>https://agnosticweb.com/index.php?id=47666</guid>
<pubDate>Wed, 16 Oct 2024 21:07:05 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>evolution: new Archaea found (reply)</title>
<content:encoded><![CDATA[<p>In a California pool:</p>
<p><a href="https://www.nature.com/articles/s41467-024-49872-z?utm_campaign=related_content&amp;utm_source=HEALTH&amp;utm_medium=communities">https://www.nature.com/articles/s41467-024-49872-z?utm_campaign=related_content&amp;utm...</a></p>
<p>&quot;Abstract<br />
The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.</p>
<p>***</p>
<p>&quot;Atabeyarchaeia and Freyarchaeia use different enzymes to produce pyruvate. Atabeyarchaeia encodes the oxygen-sensitive reversible enzyme, pyruvate:phosphate dikinase (PpdK), whereas Freyarchaeia encodes unidirectional pyruvate water dikinase/phosphoenolpyruvate synthase (PpS) and pyruvate kinase (Pk), producing phosphoenolpyruvate and pyruvate52, respectively. Pyruvate generated via the EMP pathway can then be converted to acetyl-CoA by pyruvate:ferredoxin oxidoreductase (PorABCDG) complex using a low-potential electron acceptor such as a ferredoxin. Alternatively, acetyl-CoA can also be generated via pyruvate formate-lyase (pflD) generating formate as a byproduct. The final step involves the conversion of acetyl-CoA to acetate via acetate-CoA ligase (ADP-forming), producing ATP via substrate-level phosphorylation, in a crucial energy-conserving step during the fermentation of carbon compounds in both lineages.</p>
<p>***</p>
<p>&quot;We manually curated three complete genomes for Asgard archaea from wetland soils, uncovering bidirectional replication and an unexpected abundance of introns in tRNA genes. <strong>These features suggest another facet of the evolutionary relationship between archaea and eukaryotes.</strong> Metabolic reconstruction and metatranscriptomic measurements of in situ activity revealed a non-methanogenic, acetogenic lifestyle and a diverse array of proteins likely involved in energy conservation. The genome analysis uncovered some metabolic similarities between soil and sediment-associated Asgard archaea. In addition, the unusual genomic features, such as high intron prevalence and the presence of ESPs call for deeper investigations into their biological significance and contribution to the adaptability and evolution of Asgard archaea. Overall, the findings point to metabolic flexibility and adaptation to soil conditions of wetlands. Finally, they contribute to the cycling of carbon compounds that are relevant for methane production by coexisting methanogenic archaea. Future studies should aim to explore the functional roles of the identified genes and pathways in situ, which will further elucidate the ecological impacts and evolutionary history of these enigmatic microorganisms.&quot; (my bold)</p>
<p>Comment: it is amazing to find how chemically active are these newly found Archaea. They hold a unique position as very ancient forms yet closely related to Eukaryotes. Their chemical activities helped transform the Earth soils into useful substrates for life to use.</p>
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<link>https://agnosticweb.com/index.php?id=47229</link>
<guid>https://agnosticweb.com/index.php?id=47229</guid>
<pubDate>Tue, 06 Aug 2024 15:21:31 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>evolution:  how bacteria protect Antarctic worms (reply)</title>
<content:encoded><![CDATA[<p>By producing anti-freeze:</p>
<p><a href="https://www.sciencenews.org/article/bacteria-marine-worms-survive-cold">https://www.sciencenews.org/article/bacteria-marine-worms-survive-cold</a></p>
<p>&quot;Specialized bacteria living inside three different species of Antarctic polychaetes make proteins that help the worms not freeze to death, Corinaldesi and colleagues report June 21 in Science Advances.</p>
<p>&quot;The finding illustrates how important microbes can be for their hosts, says Amy Apprill, a microbial ecologist at Woods Hole Oceanographic Institution in Massachusetts who wasn’t involved with the study. “Our knowledge of host-microbe interactions in the ocean is still incredibly limited.”</p>
<p>***</p>
<p>&quot;The most common bacteria found in the worms were Meiothermus silvanus and two types of Anoxybacillus, which were not found in a separate analysis of the sediment itself or within DNA collected from other related worms.</p>
<p>&quot;Bacterial proteins extracted from the polychaetes are known to be involved in cold tolerance. Two enzymatic proteins, for example, produce glycerol and proline, which are thought to protect against extreme cold “due to their ability to reduce the freezing point of internal liquids,” Corinaldesi says.</p>
<p>&quot;Though missing from today’s Antarctic ocean floor, Meiothermus bacteria have previously been found in frozen sediment from underneath the nearby Ross Ice Shelf, which “suggests a long-term connection between polychaetes and these bacteria,” Corinaldesi says. She and colleagues think that the bacteria are passed down from parent worms to their offspring.</p>
<p>***</p>
<p>&quot;The bacteria benefit from their partnership with the worms too, Corinaldesi says, as they receive a safe home in exchange for making protective proteins.&quot;</p>
<p>Comment: it is a perfect arrangement. If both species migrated from warmer areas into colder climates, it could explain the relationship. But that raises the issue of why the bacteria were producing antifreeze in a warm climate, and why they would get together with mutual benefits, if not needed. Worms crawl in seabed's so picking up the bacteria poses no problem. The most likely origin is they adapted together somehow.</p>
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<link>https://agnosticweb.com/index.php?id=46879</link>
<guid>https://agnosticweb.com/index.php?id=46879</guid>
<pubDate>Fri, 21 Jun 2024 20:12:34 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>evolution:  sessile Ediacarans stirred water flow (reply)</title>
<content:encoded><![CDATA[<p>An obvious event:</p>
<p><a href="https://phys.org/news/2024-05-earth-earliest-sea-creatures-drove.html">https://phys.org/news/2024-05-earth-earliest-sea-creatures-drove.html</a></p>
<p>&quot;Using state-of-the-art computer simulations of fossils from the Ediacaran time period—approximately 565 million years ago—scientists discovered how these animals mixed the surrounding seawater. This may have affected the distribution of important resources such as food particles and could have increased local oxygen levels.</p>
<p>&quot;Through this process, the scientists think these early communities could have played a crucial role in shaping the initial emergence of large and complex organisms prior to a major evolutionary radiation of different forms of animal life, the so-called Cambrian &quot;explosion.&quot;</p>
<p>***</p>
<p>&quot;Dr. Emily Mitchell at the University of Cambridge's Department of Zoology, a co-author of the report, said, &quot;It's exciting to learn that the very first animals from 580 million years ago had a significant impact on their environment, despite not being able to move or swim. We've found they mixed up the water and enabled resources to spread more widely—potentially encouraging more evolution.&quot;</p>
<p>***</p>
<p>&quot;First author Dr. Susana Gutarra, a Scientific Associate at the Natural History Museum, said, &quot;We used ecological modeling and computer simulations to investigate how 3D virtual assemblages of Ediacaran life forms affected water flow. Our results showed that these communities were capable of ecological functions similar to those seen in present-day marine ecosystems.&quot;</p>
<p>&quot;The study showed that one of the most important Ediacaran organisms for disrupting the flow of water was the cabbage-shaped animal Bradgatia, named after Bradgate Park in England. The Bradgatia from Mistaken Point are among some of the largest fossils known from this site, reaching diameters of over 50 centimeters.</p>
<p>&quot;Through their influence on the water around them, the scientists believe these Ediacaran organisms might have been capable of enhancing local oxygen concentrations. This biological mixing might also have had repercussions for the wider environment, possibly making other areas of the sea floor more habitable and perhaps even driving evolutionary innovation.</p>
<p>&quot;Dr. Imran Rahman, lead author and Principal Researcher at the Natural History Museum, said, &quot;The approach we've developed to study Ediacaran fossil communities is entirely new in paleontology, providing us with a powerful tool for studying how past and present marine ecosystems might shape and influence their environment.'&quot;</p>
<p>Common: anyone who has seen a stream knows standing objects will stir up flow. As A grantor of study funds. I would not have funded this one with such obvious results.</p>
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<link>https://agnosticweb.com/index.php?id=46571</link>
<guid>https://agnosticweb.com/index.php?id=46571</guid>
<pubDate>Sun, 19 May 2024 18:11:39 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>evolution:  gut nerve controls (reply)</title>
<content:encoded><![CDATA[<p>Glial cells in the gut:</p>
<p><a href="https://www.quantamagazine.org/in-the-guts-second-brain-key-agents-of-health-emerge-20231121/">https://www.quantamagazine.org/in-the-guts-second-brain-key-agents-of-health-emerge-202...</a></p>
<p>&quot;Breaking down food requires coordination across dozens of cell types and many tissues — from muscle cells and immune cells to blood and lymphatic vessels. Heading this effort is the gut’s very own network of nerve cells, known as the enteric nervous system, which weaves through the intestinal walls from the esophagus down to the rectum. This network can function nearly independently from the brain; indeed, its complexity has earned it the nickname “the second brain.” And just like the brain, it’s made up of two kinds of nervous system cells: neurons and glia.</p>
<p>***</p>
<p>&quot;...Neuroscientists have increasingly discovered that glia play physiological roles in the brain and nervous system that once seemed reserved for neurons.</p>
<p>&quot;A similar glial reckoning is now happening in the gut. A number of studies have pointed to the varied active roles that enteric glia play in digestion, nutrient absorption, blood flow and immune responses. Others reveal the diversity of glial cells that exist in the gut, and how each type may fine-tune the system in previously unknown ways. One recent study, not yet peer-reviewed, has identified a new subset of glial cells that senses food as it moves through the digestive tract, signaling to the gut tissue to contract and move it along its way.</p>
<p>***</p>
<p>&quot;Thanks to some of these newer technologies, scientists now know that enteric glia are among the first responders to injury or inflammation in gut tissue. They help maintain the gut’s barrier to keep toxins out. They mediate the contractions of the gut that allow food to flow through the digestive tract. Glia regulate stem cells in the gut’s outer layer, and are critical for tissue regeneration. They chat with the microbiome, neurons and immune-system cells, managing and coordinating their functions.</p>
<p>***</p>
<p>&quot;Those methods allowed her to get the “first glimpse into the diversity of these glial cells” across all tissues of the duodenum, Scavuzzo said. In June, in a paper published on the biorxiv.org preprint server that has not yet been peer-reviewed, she reported her team’s discovery of six subtypes of glial cells, including one that they named “hub cells.”</p>
<p>&quot;Hub cells express genes for a mechanosensory channel called PIEZO2 — a membrane protein that can sense force and is typically found in tissues that respond to physical touch. Other researchers recently found PIEZO2 present in some gut neurons; the channel allows neurons to sense food in the intestines and move it along. Scavuzzo hypothesized that glial hub cells can also sense force and instruct other gut cells to contract. She found evidence that these hub cells existed not only in the duodenum, but also in the ileum and colon, which suggests they’re likely regulating motility throughout the digestive tract.</p>
<p>***</p>
<p>&quot;Glia are likely involved because of their central role in communicating between the microbiome, immune cells and other gut cells. Healthy glia strengthen the intestines’ epithelial barrier, a layer of cells that keeps out toxins and pathogens and absorbs nutrients. But in patients with Crohn’s disease, glial cells don’t function properly, resulting in a weaker barrier and inappropriate immune response.</p>
<p>“Different subtypes of glia can be functioning differently or dysfunctioning in a wide range of diseases and disorders where motility is impacted,” Scavuzzo said. They have also been linked to neural inflammation, hypersensitivity in the organs and even neuron death.</p>
<p>&quot;For instance, Gulbransen and his team recently discovered that glia contribute to gut pain by secreting molecules that sensitize neurons. This is likely an adaptive response intended to draw the gut’s attention to damaging substances to dispose of them, Gulbransen said, which as a side effect causes pain.&quot;</p>
<p>Comment: glia were ignored for a long time. It just shows everything is there for a reason.</p>
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<link>https://agnosticweb.com/index.php?id=46510</link>
<guid>https://agnosticweb.com/index.php?id=46510</guid>
<pubDate>Wed, 15 May 2024 16:53:08 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>Evolution:  convergence of eyes (reply)</title>
<content:encoded><![CDATA[<p>Adapted to lifestyle:</p>
<p><a href="https://www.sciencealert.com/the-weirdest-eyes-in-the-animal-kingdom-see-a-world-we-cant-even-imagine?utm_source=ScienceAlert+-+Daily+Email+Updates&amp;utm_campaign=b9e3d1b4e1-RSS_EMAIL_CAMPAIGN&amp;utm_medium=email&amp;utm_term=0_fe5632fb09-b9e3d1b4e1-366098385">https://www.sciencealert.com/the-weirdest-eyes-in-the-animal-kingdom-see-a-world-we-can...</a></p>
<p>&quot;... different organisms have evolved to view the world differently, with eye structures and configurations optimized for various kinds of existence.</p>
<p>&quot;...the horizontal pupils of herbivores give them a panoramic view of their surroundings, which helps both to see predators coming, and to avoid obstacles as the animals make an escape. Meanwhile, nocturnal predators have vertical pupils to maximize their night vision.</p>
<p>&quot;No other animal has a pupil quite like the cuttlefish. It's shaped like a W, a trait biologists have determined helps the animals balance a vertically uneven field of light, which is common in the watery depths they inhabit. But that's just the start.</p>
<p>&quot;Cuttlefish only have one type of photoreceptor, which should mean they can only see in monochrome. Yet those strange, wide pupils of cuttlefish and other cephalopods could facilitate an entirely different way of seeing color – by using the way light passing through a prism splits into a rainbow.</p>
<p>***</p>
<p>&quot;Unlike other cephalopods, though, cuttlefish eyes can swivel, allowing them to see the world in 3D as well; recently, scientists found these swivelly eyes result in stereoscopic vision, giving cuttlefish yet another advantage in their environment.</p>
<p>***</p>
<p>&quot;Cephalopods only have one photoreceptor type, as we have established. Humans have four, three cones and a rod, which means we have color sensitivities at three peak wavelengths, what we call trichromatic vision. (The rod is for low-light vision.)</p>
<p>&quot;Birds have six – four cones giving tetrachromatic vision, a rod, and an unusual double cone for non-colored motion perception.</p>
<p>&quot;In addition, a protein in their eyes could allow them to see magnetic fields. Migratory birds can navigate extraordinarily well; scientists narrowed it down to a class of proteins called cryptochromes, which are sensitive to blue light.</p>
<p>&quot;Birds' magnetoreception – that is, their ability to perceive magnetic fields – seems dependent on blue light, suggesting that the sense may be vision-based. There's the distinct possibility that this magnetic filter for the color blue is the result of a quantum quirk. More recent lab studies have shown how a magnetic field affects a quantum property of cryptochromes, governing their electrons.</p>
<p>&quot;Behold the largescale four-eyes (Anableps anableps), of the four-eyed fish genus.</p>
<p>&quot;This fascinating beastie doesn't actually have four eyes – but its two eyes have evolved an incredible adaptation. Their ecological niche is the surface of the water, where they spend the majority of their time, preying on insects that hover around aquatic ecosystems.</p>
<p>&quot;Their eyes are situated on top of their heads, all the better to see the flying bugs in an aerial environment. But a portion of their optic organ sits below the surface of the water, and this is where things get interesting: each pupil is divided into two halves, one of which sits above the waterline (dorsal), while the other sits below (ventral), pointing downwards into the murky depths.</p>
<p>&quot;In this way, the fish can simultaneously see above and below the water – environments through which light propagates differently – to watch for both predators and prey. The thickness of the lens varies too, to accommodate the different refractive indices of aerial and aquatic media, as does the thickness of the corneal epithelium.</p>
<p>&quot;And the proteins in the retinal photoreceptor cells are slightly different as well – more sensitive to green light in the dorsal retina, and more sensitive to yellow light in the ventral retina. Since the fish often live in muddy environments, like mangroves, this is thought to improve vision in murky waters.</p>
<p>***</p>
<p>&quot;Mantis shrimps of the order Stomatopoda, have 16 in their compound peepers. What do they do with these photoreceptors? They see. They see all of the things...They can see five different ultraviolet frequency bands.</p>
<p>&quot;In addition, mantis shrimps can see polarized light; that is, the orientation of the oscillations of the wave of propagating light. Many animals can see linearly polarized light, including cuttlefish. Mantis shrimps are the only animals that can see circularly polarized light that we know of.</p>
<p>&quot;Each eye is mounted on a stalk, and can be moved independently. And each eye has the ability to perceive depth. Humans rely on binocular vision for depth perception. Mantis shrimps only need one. </p>
<p>&quot;Chitons have eyes, but they're embedded in their armor, and made of mineral; more specifically, a type of calcium carbonate known as aragonite.</p>
<p>&quot;The simple eyes of chitons, which litter the surface of their shells alongside hundreds of sensory organs known as aesthetes, consist of an aragonite lens covered by a cornea, and some sort of retina; to the surprise of scientists, these tiny primitive organs can actually resolve images.</p>
<p>&quot;Trilobites, for example, also had mineral eyes, with lenses made of calcite. These extinct creatures had the first truly complex eyes that we know of, so understanding them can tell us a lot about how vision evolved on Earth in all its dazzling complexity.&quot;</p>
<p>Comment: see the illustrations. Adaptations with a purpose. Designed.</p>
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<link>https://agnosticweb.com/index.php?id=46169</link>
<guid>https://agnosticweb.com/index.php?id=46169</guid>
<pubDate>Mon, 01 Apr 2024 15:16:33 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>Evolution: more evidence of early life (reply)</title>
<content:encoded><![CDATA[<p>In Africa:</p>
<p><a href="https://www.newscientist.com/article/2413292-traces-of-ancient-life-reveal-a-3-4-billion-year-old-ecosystem/">https://www.newscientist.com/article/2413292-traces-of-ancient-life-reveal-a-3-4-billio...</a></p>
<p>&quot;Manuel Reinhardt at the University of Göttingen in Germany and his colleagues studied rocks from the Buck Reef Chert, part of the Barberton Greenstone Belt in South Africa. The rocks are 3.42 billion years old and are thought to be the preserved remnants of the shallow seas around a chain of volcanic islands.</p>
<p>&quot;The layers of rock contain microscopic blobs of carbon-based matter, believed to be the remains of microorganisms that lived in these seas. Reinhardt and his group subjected this matter to a battery of analyses to determine its chemical makeup, which they used to infer what sort of metabolism these microorganisms had.</p>
<p>&quot;The team focused on the carbon itself. Carbon comes in several forms called isotopes, which are identical apart from the number of neutrons in the nucleus of the atom. The main two carbon isotopes are carbon-12 and carbon-13. Living things prefer to use carbon-12, so biological matter tends to have more carbon-12 and less carbon-13 than non-biological matter.</p>
<p>&quot;However, not all living things are equally good at preferentially absorbing carbon-12. That means the ratio between the two forms can provide clues about an organism’s metabolism.</p>
<p>&quot;Much of the material has a carbon signature that matches photosynthesis: the ability to use light energy to make sugar. This suggests there were enormous quantities of photosynthetic microbes living near the surface of the sea billions of years ago.</p>
<p>&quot;However, some of the blobs had less carbon-12. Photosynthetic organisms can’t achieve this, so Reinhardt says those microbes must have been feeding on a chemical called acetyl coenzyme A.</p>
<p>&quot;Other blobs had still lower levels of carbon-12, suggesting the microbes in them were making either methane or acetate as waste products, which other microbes were then feeding on.</p>
<p>***</p>
<p>&quot;The study also adds to the evidence for an early origin of life on Earth, earlier than a crude reading of the fossil record might suggest.</p>
<p>The oldest widely accepted evidence for life is 3.5 billion years old, from Pilbara in Australia. Researchers have reported evidence of older fossils from 3.7 billion years ago or even earlier, but others say the evidence isn’t convincing in most of those cases.</p>
<p>***</p>
<p>&quot;What does seem clear is that life is significantly older than 3.5 billion years. “Personally, I think life emerged on Earth during the Hadean [eon], probably about 4.2, 4.1 billion years [ago],” says Westall.&quot;</p>
<p>Comment: with the arrival of Earth 4.5 billon years ago such a quick appearance ofc life is surprising. Fits the theory of a designer, not a chance development..</p>
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<link>https://agnosticweb.com/index.php?id=45668</link>
<guid>https://agnosticweb.com/index.php?id=45668</guid>
<pubDate>Mon, 22 Jan 2024 18:10:13 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>Evolution:  Euglenids (reply)</title>
<content:encoded><![CDATA[<p>Not plant nor animals:</p>
<p><a href="https://www.sciencealert.com/bizarre-fossils-are-neither-plant-nor-animal-but-a-weird-fusion-of-life?utm_source=ScienceAlert+-+Daily+Email+Updates&amp;utm_campaign=5d9b9e3d0a-RSS_EMAIL_CAMPAIGN&amp;utm_medium=email&amp;utm_term=0_fe5632fb09-5d9b9e3d0a-366098385">https://www.sciencealert.com/bizarre-fossils-are-neither-plant-nor-animal-but-a-weird-f...</a></p>
<p>&quot;It is neither animal, vegetable, nor mineral. It's not even a bacterium or fungi.</p>
<p>&quot;It's called a Euglenid – and it's a weird fusion of a bunch of different living things.</p>
<p>Euglenids are a group of unicellular eukaryotes that gain energy through both photosynthesis, like a plant, and through consuming other beings, like an animal.</p>
<p>&quot;These aquatic organisms split off from other eukaryotes roughly a billion years ago, and yet their fossil record for all that time on Earth is scarce.</p>
<p>***</p>
<p>&quot;Their similarities over the years have stumped experts, as these fossils span immense timelines, from almost half a billion years ago to the present.</p>
<p>***</p>
<p>Using advanced microscopic techniques, they then established the structure of these cysts.</p>
<p>&quot;'We were much surprised by the ultrastructure of the cysts,&quot; says paleontologist Wilson Taylor from the University of Wisconsin-Eau-Claire.</p>
<p>&quot;'The structure of the wall does not resemble anything that is known. The ribs are not ornaments, like in pollen and spores, but part of the wall structure. The layered structure of the walls is also clearly different from many other fresh-water green algae.&quot;</p>
<p>&quot;Researchers struggle to get living Euglenids to encyst in the lab, but a YouTube video by microscopy enthusiast Fabian Weston from Australia made for a perfect comparison.</p>
<p>&quot;&quot;Unwittingly, Fabian provided a key piece of evidence. He is probably the only person on the planet to have witnessed Euglena encyst under a microscope,&quot; says Strother.</p>
<p>&quot;Now that the researchers have established a possible deep timeline of Euglenid life, Strother hopes it will make it easier for scientists to recognize even older examples, possibly even ones that &quot;go back to the very root of the eukaryotic tree of life.&quot;</p>
<p>&quot;&quot;Perhaps related to their capabilities to encyst, these organisms have endured and survived every major extinction on the planet,&quot; suggests Van de Schootbrugge</p>
<p>&quot;'Unlike the behemoths that were done in by volcanoes and asteroids, these tiny creatures have weathered it all.'&quot;</p>
<p>Comment: a plant/animal type organism is a reasonable part of evolution.</p>
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<link>https://agnosticweb.com/index.php?id=45656</link>
<guid>https://agnosticweb.com/index.php?id=45656</guid>
<pubDate>Sun, 21 Jan 2024 16:07:46 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>Evolution:  females have bigger brains in animals (reply)</title>
<content:encoded><![CDATA[<p>New study:</p>
<p><a href="https://www.nationalgeographic.com/premium/article/female-male-animals-brain-brawn-evolution?rid=1863706AFE9E96AC3148BDF808F42C4D&amp;cmpid=org%3Dngp%3A%3Amc%3Dcrm-email%3A%3Asrc%3Dngp%3A%3Acmp%3Deditorial%3A%3Aadd%3DDaily_NL_Science_Saturday_20240120&amp;loggedin=true&amp;rnd=1705781092417">https://www.nationalgeographic.com/premium/article/female-male-animals-brain-brawn-evol...</a></p>
<p>&quot;In fact, a study published today in the journal Behavioral Ecology and Sociobiology provides the first evidence that, as male mammals evolve larger weapons for combat and to signal their fitness, the females of those species develop larger brains than expected.</p>
<p>***</p>
<p>&quot;However, while the focus has always been on what’s happening atop the heads of the males, there may be something just as remarkable taking place within the heads of the females. And it may upend what we thought about how much agency they have in choosing a mate.</p>
<p>***</p>
<p>Ummat Somjee, an evolutionary biologist at the University of Texas in Austin and the Smithsonian Tropical Research Institute in Panama, notes several limitations with the study. For instance, as the authors note, <strong>brain size does not necessarily translate to intelligence</strong>. For that conclusion, you would need behavioral data for every species involved, which is much harder to come by. (my bold)</p>
<p>&quot;Similarlybrain size does not necessarily translate to intelligence. For that conclusion, , while he applauded the authors for examining as many specimens as they did, 29 species represents only a fraction of the weaponed ungulates on Earth. Who knows if the pattern might change when other antlered, horned, or tusked species are evaluated?</p>
<p>***</p>
<p>“'It’s amazing natural phenomena. It’s really weird, and strange,” says Somjee of rapid antler growth and loss. “But I think one thing that’s been left out is that what’s happening in females is also quite amazing.”</p>
<p>&quot;For instance, females also divert vast amounts of calcium, phosphorus, and other nutrients from their own bodies to build entire offspring within their wombs. And of course, any tissues that go on to create antlers, horns, or tusks are first created by those females.</p>
<p>&quot;For Lopez’s part, she points out that much of the scientific literature has focused on the battles between males to understand the sexual selection happening within these species. After all, the prevailing story has long been that the biggest, most heavily armed males get the females.</p>
<p>“'But it might just be that we’re not testing it in the right ways to show that [females] do have some type of decision in the males that they end up mating with,” says Lopez.&quot;</p>
<p>Comment: I guess the fairer sex has more to think about. I am not aware of a human difference in brain  size, but then again we don't grow horns.</p>
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<link>https://agnosticweb.com/index.php?id=45652</link>
<guid>https://agnosticweb.com/index.php?id=45652</guid>
<pubDate>Sat, 20 Jan 2024 20:25:28 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<item>
<title>Evolution:  interaction of genes importance (reply)</title>
<content:encoded><![CDATA[<p>Some control of mutations is present:</p>
<p><a href="https://www.sciencealert.com/the-forces-that-drive-evolution-may-not-be-as-random-as-we-thought">https://www.sciencealert.com/the-forces-that-drive-evolution-may-not-be-as-random-as-we...</a></p>
<p><br />
&quot;It's known that some areas of the genome are more likely to be mutable than others, but a new study now suggests a species' evolutionary history may play a role in making mutations more predictable too.</p>
<p>***</p>
<p>&quot;University of Nottingham biologist Alan Beavan and colleagues harnessed the calculating power of AI to investigate more than 2,000 complete genomes of Escherichia coli bacteria.</p>
<p>&quot;Bacteria are particularly tricksy when it comes to changing their DNA, being rather adept at stealing genes from their environment and incorporating them into their genome. Known as horizontal gene transfer, the process gives bacteria ready access to new traits, such as neatly sidestepping antibiotics – no pesky waiting around for selection to work across generations required.</p>
<p>&quot;Curiously, horizontally transferred genes belonging to the same basic group can end up parking in different positions of the bacteria's genome. By investigating horizontal genes in different places, the researchers were able to see how the genes' immediate environment influenced them.</p>
<p>&quot;They were able to test renowned evolutionary biologist Stephen J. Gould's thought experiment: replaying a tape of evolutionary history would result in a different, unpredictable outcome each time, since evolutionary paths depend on unpredictable events.</p>
<p>&quot;If this is true, the bacteria's genome would keep evolving randomly after acquiring a new horizontal gene. But the AI found patterns of predictability across these thousands of &quot;tape replays&quot; after these gene acquisition events.</p>
<p>&quot;'We found that some gene families never turned up in a genome when a particular other gene family was already there, and on other occasions, some genes were very much dependent on a different gene family being present,&quot; explains University of Nottingham microbiologist Maria Rosa Domingo-Sananes.</p>
<p>&quot;So the history of the genome, amounting to which genes it has at the time, can determine which genes it will or won't have in the future. We've seen hints of this before through genes that are closely physically positioned on genetic molecules being lost or gained together – linked genes – but this was also happening with genes that had no close physical connection on the bacteria's genomes.</p>
<p>&quot;'Some aspects of evolution are deterministic – i.e., they are likely to happen each time we replay the tape,&quot; confirm Beavan and team in their paper. &quot;Gene presence or absence is predictable based only on other genes in the genome. For example, a hypothetical gene A may predict the presence of gene B only in the absence of gene C.&quot;</p>
<p>&quot;This doesn't break the rule of random mutation; it's more that the forces of natural selection are working at a molecular level too, something we haven't had the computing power to fully see until recently. Essentially the genomes themselves are their own microscopic ecosystems, within which genes can help or hinder each other.&quot;</p>
<p>Comment: these genetic interactions are not a surprise. Years ago, I presented evidence of HAR regions in human genomes, areas of increased genetic activity. (Friday, August 14, 2020, 22:11) This work complements Shapiro's DNA studies in bacteria.</p>
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<link>https://agnosticweb.com/index.php?id=45649</link>
<guid>https://agnosticweb.com/index.php?id=45649</guid>
<pubDate>Sat, 20 Jan 2024 18:23:36 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
</item>
<item>
<title>evolution:  the speed of evolution (reply)</title>
<content:encoded><![CDATA[<p>Seen in adaptability:</p>
<p><a href="https://www.quantamagazine.org/evolution-fast-or-slow-lizards-help-resolve-a-paradox-20240102/">https://www.quantamagazine.org/evolution-fast-or-slow-lizards-help-resolve-a-paradox-20...</a></p>
<p>&quot;These Anolis lizards had looked the same for millennia; they had apparently evolved very little in all that time. Logic told Stroud that if evolution had favored the same traits over millions of years, then he should expect to see little to no change over a single generation.</p>
<p>&quot;Except that’s not what he found. Instead of stability, Stroud saw variability. One season, shorter-legged anoles survived better than the others. The next season, those with larger heads might have an advantage.</p>
<p>***</p>
<p>&quot;His data reflected a paradox that had stymied biologists for years. In the long term, the anoles had traits that appeared to stay the same, a phenomenon called stasis — presumably caused by stabilizing selection, a process which favors moderate traits. However, over the short term, the lizards showed variation, with fluctuating traits. Stroud’s data was better explained by directional selection, which sometimes favors extreme traits that lead evolution in a new direction, and other times doesn’t appear to favor anything in particular.</p>
<p>&quot;Because he had followed four species for three generations, he was able to show that a long-term pattern of stasis could emerge from such short-term fluctuating selection.</p>
<p>“'There’s lots of noise, but overall, it leads to fairly stable patterns,” said Stroud, who now runs his own lab at the Georgia Institute of Technology. </p>
<p>***</p>
<p>&quot;Evolutionary biologists rapidly adopted the approach. Princeton University’s Rosemary and Peter Grant used the method in their celebrated studies of Darwin’s finches on the island of Daphne Major in the Galápagos. Their study, which began in 1973 and continues to this day, followed a population of the medium ground finch (Geospiza fortis) through a severe drought that began in 1977. That’s when the plants of Daphne Major stopped producing the small seeds on which the birds relied; only thick seeds remained.</p>
<p>&quot;With little food, the finch population plummeted from 1,400 individuals to a few hundred in only two years. Then the Grants watched the population recover while taking careful measurements of the birds’ traits. The birds that survived, they found, had larger beaks suited to the larger seeds: The average beak depth had increased from 9.2 mm to 9.9 mm — a change of more than 7%.</p>
<p>&quot;All told, a shift in annual rainfall had rapidly resulted in a change in the birds’ beaks. The Grants’ work became a classic example of evolution in action. They had identified marked, if often subtle, evidence of the directional push and pull of evolution acting on traits.</p>
<p>***</p>
<p>&quot;Over and over again, on island after island, the anoles evolved to fill different niches, gaining characteristic sets of traits to help their survival in their preferred habitat. One species kept long legs — ideal for sprinting — and small, sticky toe pads more often planted on terra firma. Three others scampered up tree trunks: a small-bodied species that preferred the lower half of the trunk, one that ventured into the low canopy on large toe pads, and one that favored the high canopy, evolving short limbs to expertly navigate thin branches.</p>
<p>&quot;After that initial burst of evolution, the lizards remained virtually identical over millions of years. And that’s how Losos found them when he began studying the reptiles in the 1980s.</p>
<p>***</p>
<p>&quot;However, his years of data didn’t show stability at all. Instead, he saw evolution constantly shifting the traits that were best adapted to the environment. “If we look at any one period on its own, we very rarely see stabilizing selection,” Stroud said.</p>
<p>***</p>
<p>&quot;Over time, however, that variability averaged out into stasis. Even if traits wobbled off their optimal, moderate peak from one generation to the next, there was a net effect of stabilization — ultimately leading to little change over the multiple generations.</p>
<p>***</p>
<p>&quot;recent research from other labs also helps to support Stroud’s results. A study published in Evolution in September 2023 from the lab of Andrew Hendry, an eco-evolutionary biologist at McGill University, studied evolutionary changes in a community of finches on the Galápagos island of Santa Cruz over 17 years. There, too, Hendry found evidence of natural selection’s regular tug of war on traits that was embedded within a “remarkable stability,” he said, of the finches over evolutionary time.&quot;</p>
<p>Comment: These studies of minor adaptations to changing conditions do not tell us about the speed of past evolution when new species appeared. What we see now is a stasis of the evolutionary process that has obviously ended.</p>
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<link>https://agnosticweb.com/index.php?id=45501</link>
<guid>https://agnosticweb.com/index.php?id=45501</guid>
<pubDate>Tue, 02 Jan 2024 18:16:19 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>evolution:  bird origin questionable (reply)</title>
<content:encoded><![CDATA[<p>From dinosaurs, but when?:</p>
<p><a href="https://evolutionnews.org/2023/12/fossil-friday-fossil-bird-tracks-expand-the-temporal-paradox/">https://evolutionnews.org/2023/12/fossil-friday-fossil-bird-tracks-expand-the-temporal-...</a></p>
<p>&quot;The origin of birds involves a severe problem for Darwinists, which paleo-ornithologist Alan Feduccia has called a temporal paradox (1994, 1996). The paradox lies in the fact that primitive fossil birds are contemporaneous with or even appear earlier in the fossil record than their assumed theropod dinosaur ancestors. This is the opposite of the natural expectations from a Darwinian point of view, and therefore has to be explained away with ad hoc hypotheses such as ghost lineages, which are long spans of existence of groups that leave no fossil record. </p>
<p>***</p>
<p>&quot;Now, a new discovery published in the journal PLOS ONE may have made the notorious temporal paradox of birds even worse — much worse — because it extends the existence of bird-like forms many million years further into the past, preceding any of the less bird-like theropods.</p>
<p>&quot;Earlier this month, a team of scientists from the University of Cape Town (Abrahams &amp; Bordy 2023) reported the identification of bird-like footprints from the Upper Triassic of Lesotho in southern Africa, which are at least 210 million years old. Actually, the fossil tracks were already discovered and described by paleontologist Paul Ellenberger in the mid 20th century and classified as ichnogenus Trisauropodiscus. The validity of this ichnogenus was later questioned by other scientists, and an avian affinity has been hotly debated. Abrahams and Bordy re-examined original field material, casts, historical photographs, and interpretative sketches in previous publications. Based on this revision they could identify “two distinct Trisauropodiscus morphotypes, one of which resembles footprints made by birds.” </p>
<p>***</p>
<p>&quot;Consequently, the press release of the discovery says that “unknown animals were leaving bird-like footprints in Late Triassic Southern Africa” (PLOS 2023), and Smithsonian Magazine commented that “mysterious creatures with bird-like feet made these tracks long before birds evolved” (Kuta 2023). In the same spirit, another commenter (Yazgin 2023) asked “who made the footprints if the earliest known birds didn’t emerge until at least 50 million years later?” and answered: “Until the fossil of an animal that lived at the right time, in the right place, and with the right proportions is found, the mystery of who created the Trisauropodiscus tracks remains.”</p>
<p>&quot;To be clear: nothing in these fossil footprints themselves suggests that they are anything but bird tracks, but they have to reinterpreted as something else to protect the evolutionary narrative from inconvenient conflicting evidence and unsolved mysteries. Theory trumps data in evolutionary biology.&quot;</p>
<p>Comment: hopefully the fossil gap will be explained by new discoveries. Whatever made the tracks was large enough to make the impressions.</p>
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<link>https://agnosticweb.com/index.php?id=45481</link>
<guid>https://agnosticweb.com/index.php?id=45481</guid>
<pubDate>Sun, 31 Dec 2023 16:40:25 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>evolution: symbiosis with many good bacteria (reply)</title>
<content:encoded><![CDATA[<p>Can influence animal behavior:</p>
<p><a href="https://phys.org/news/2023-11-bacteria-contribute-modulation-animal-behavior.html">https://phys.org/news/2023-11-bacteria-contribute-modulation-animal-behavior.html</a></p>
<p>In recent years, researchers have gathered growing evidence that the composition and balance of the microbiome plays a decisive role in the function and health of the organism as a whole.</p>
<p>They have identified a fundamentally important aspect of these functional relationships in the communication between nerve cells of the host and its microbiome, which was first established very early in evolution. The significance of this cooperation and how these interactions affect behavior is still largely unknown.</p>
<p>a research team from the Collaborative Research Center (CRC) 1182 &quot;Origin and Function of Metaorganisms&quot; at Kiel University has gained new insights into the cooperation between the nervous system and the microbiome. Using the freshwater polyp Hydra as an example, the Kiel researchers investigated the neuronal basis of their feeding behavior and whether and in what way the microbiome intervenes in this behavior.</p>
<p>In doing so, they were able to prove mechanistically for the first time that a microbiome with reduced diversity affects the function of certain nerve cells and thus alters the feeding behavior. They published their research results today in the journal Current Biology.</p>
<p>***</p>
<p>&quot;Underlying the feeding behavior is a neuronal control that is significantly more complex than was previously assumed from the simple nerve network of Hydra,&quot; Giez continues. Using a calcium-based visualization method, the research team was able to observe the nerve populations involved in feeding behavior in real-time in the living animal and thus identify the neuronal circuit involved.</p>
<p>***</p>
<p>In order to find out which bacteria have a particularly significant influence, the Kiel researchers first colonized germ-free animals with one defined bacterial species each in the next step. &quot;A particularly interesting effect was seen when colonizing with the bacterium Curvibacter. The feeding behavior of animals colonized only with Curvibacter is very strongly impaired: These animals can only open their mouths to a very limited extent,&quot; Giez continues.</p>
<p>In further studies, Curvibacter was found to produce the amino acid glutamate, which also plays an important role in human metabolism. When the microbiome is greatly reduced in composition and only Curvibacter is present, glutamate accumulates, binds to neurons, and leads to a blockage of the mouth opening. The inhibitory effect of the Curvibacter bacteria is reversed as soon as the remaining members of the microbiome are also reintroduced to the tissue.</p>
<p>&quot;Overall, we were able to prove that even in phylogenetically ancient animals, a diverse microbiome is necessary for normal feeding behavior. If the composition of this microbiome is severely disturbed, significant changes in behavior occur,&quot; says Professor Thomas Bosch, head of the Cell and Developmental Biology group.</p>
<p>The researchers have gathered evidence that this is due to interactions between the different members of the microbiome. If there is a species-rich, &quot;normal&quot; microbiome, the glutamate produced is taken up and utilized by other bacterial species, and the neuronal circuit responsible for feeding behavior is not disturbed.</p>
<p>***</p>
<p>&quot;Our study opens the door for further research into the effects of the interplay between the microbiome and the nervous system on the functions of the whole organism. Among other things, we want to find out in the future whether and how microorganisms are already involved in the formation of the nervous system during embryonic development and what part the microbiome plays in the production of neurotransmitters,&quot; Bosch says.</p>
<p>Comment: constant contact with bacteria is part of life on Earth. Most of the contact is important to all living functions.</p>
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<link>https://agnosticweb.com/index.php?id=45143</link>
<guid>https://agnosticweb.com/index.php?id=45143</guid>
<pubDate>Wed, 22 Nov 2023 18:59:11 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>evolution: symbiosis with Cycads (reply)</title>
<content:encoded><![CDATA[<p>New research:</p>
<p><a href="https://www.nature.com/articles/s41559-023-02251-1?et_rid=825383635&amp;et_cid=4994162">https://www.nature.com/articles/s41559-023-02251-1?et_rid=825383635&amp;et_cid=4994162</a></p>
<p>&quot;Cycads are ancient seed plants (gymnosperms) that emerged by the early Permian. Although they were common understory flora and food for dinosaurs in the Mesozoic, their abundance declined markedly in the Cenozoic. Extant cycads persist in restricted populations in tropical and subtropical habitats and, with their conserved morphology, are often called ‘living fossils.’ All surviving taxa receive nitrogen from symbiotic N2-fixing cyanobacteria living in modified roots, suggesting an ancestral origin of this symbiosis. However, such an ancient acquisition is discordant with the abundance of cycads in Mesozoic fossil assemblages, as modern N2-fixing symbioses typically occur only in nutrient-poor habitats where advantageous for survival. Here, we use foliar nitrogen isotope ratios—a proxy for N2 fixation in modern plants—to probe the antiquity of the cycad–cyanobacterial symbiosis. We find that fossilized cycad leaves from two Cenozoic representatives of extant genera have nitrogen isotopic compositions consistent with microbial N2 fixation. In contrast, all extinct cycad genera have nitrogen isotope ratios that are indistinguishable from co-existing non-cycad plants and generally inconsistent with microbial N2 fixation, pointing to nitrogen assimilation from soils and not through symbiosis. This pattern indicates that, rather than being ancestral within cycads, N2-fixing symbiosis arose independently in the lineages leading to living cycads during or after the Jurassic. The preferential survival of these lineages may therefore reflect the effects of competition with angiosperms and Cenozoic climatic change.&quot;</p>
<p>***</p>
<p><a href="https://mail.google.com/mail/u/0/#inbox/FMfcgzGwHpPGcvZrwjwFXZNBKjFQQMxG">https://mail.google.com/mail/u/0/#inbox/FMfcgzGwHpPGcvZrwjwFXZNBKjFQQMxG</a></p>
<p>&quot;Modern cycads live in partnership with bacteria: The cycads share the sugars they make, and in exchange, the microbes convert nitrogen from the air into a form that the plants can use. This means that the nitrogen in cycad tissues comes more directly from the atmosphere than it does in other plants—and, therefore, examining it can tell researchers about that air. Kipp had already demonstrated this with living cycads , so he started applying methods to examine nitrogen in ancient foliage samples to cycad fossils. But his analysis didn’t tell him about the Mesozoic air. Instead, it revealed that the ancient cycads didn’t have microbial partners.</p>
<p>“'Instead of being a story about the atmosphere, we realized this was a story about the ecology of these plants that changed through time,” Kipp says.</p>
<p>&quot;How nitrogen-fixing bacteria helped cycads survive the mass extinction isn’t clear. Maybe the nitro-boost helped them stay competitive in the face of rapidly diversifying flowering plants, Kipp suggests. The methods he helped develop should let researchers dig deeper. And hopefully, they’ll prove useful for studying ancient atmospheres, too.&quot;</p>
<p>Comment: we can't live without good bacteria. A major defense in theodicy essays.</p>
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<link>https://agnosticweb.com/index.php?id=45130</link>
<guid>https://agnosticweb.com/index.php?id=45130</guid>
<pubDate>Tue, 21 Nov 2023 15:59:12 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>evolution: starfish are all head, no trunk (reply)</title>
<content:encoded><![CDATA[<p>Most of the rest of us are bilaterians:</p>
<p><a href="https://www.newscientist.com/article/2400256-starfish-dont-have-a-body-theyre-just-a-big-squished-head/">https://www.newscientist.com/article/2400256-starfish-dont-have-a-body-theyre-just-a-bi...</a></p>
<p>&quot;Scientists trying to work out where a starfish’s head is have come to a startling conclusion: it is effectively the whole animal. As well as solving this longstanding mystery, the finding will help us understand how evolution generates the dramatic diversity of animal forms on Earth.</p>
<p>&quot;Starfish, also known as sea stars, belong to a group of animals called echinoderms, which includes sea urchins and sea cucumbers. Their strange body plans have long puzzled biologists. Most animals, including humans, have a distinct head end and tail end, with a line of symmetry running down the middle of their body dividing it into two mirror-image halves. Animals with this two-sided symmetry are called bilaterians.</p>
<p>&quot;Echinoderms, on the other hand, have five lines of symmetry radiating from a central point and no physically obvious head or tail. Yet they are closely related to animals like us and evolved from a bilaterian ancestor. Even their larvae are bilaterally symmetrical, later radically re-organising their bodies as they metamorphose into adults.</p>
<p>***</p>
<p>&quot;To the team’s surprise, the genes that determine the head end in bilaterians were expressed in a line running down the middle of each arm on the underside of the starfish. The next head-most genes were expressed on either side of this line, and so on.</p>
<p>&quot;Even more strangely, the genes normally expressed in the trunk of bilaterians were missing in the outer layer of the animal. This suggests that starfish have jettisoned their trunk regions and freed up the outer layer to evolve in new directions, says Formery.</p>
<p>&quot;The findings show that “the body of an echinoderm, at least in terms of the external body surface, is essentially a head walking about the seafloor on its lips”, says Thurston Lacalli at the University of Victoria in Canada, who wasn’t involved in the study. Animals like us may have kept their trunks to escape predation by swimming away. “Echinoderms hunkered down and armoured themselves, so they didn’t need a trunk,” says Lacalli.</p>
<p>&quot;The idea that echinoderms are “head-like” animals is “interesting and powerful”, says Andreas Heyland at the University of Guelph in Ontario, Canada. It raises some very important and fundamental questions about how ecological factors shape the evolution of anatomy, he says. “Finding underlying conserved patterns really provides critical insights into how development evolves.'”</p>
<p>Comment: perhaps the way they fit into their ecosystem dictates their shape.</p>
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<link>https://agnosticweb.com/index.php?id=44982</link>
<guid>https://agnosticweb.com/index.php?id=44982</guid>
<pubDate>Wed, 01 Nov 2023 20:25:02 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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