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<title>AgnosticWeb.com - Evolution: first land animals</title>
<link>https://agnosticweb.com/</link>
<description>An Agnostic&#039;s Brief Guide to the Universe</description>
<language>en</language>
<item>
<title>Evolution: first land animals (reply)</title>
<content:encoded><![CDATA[<p>Fill a gap:</p>
<p><a href="https://www.sciencedaily.com/releases/2025/05/250529194648.htm">https://www.sciencedaily.com/releases/2025/05/250529194648.htm</a></p>
<p>The fossils of ancient salamander-like creatures in Scotland are among the most well-&quot;preserved examples of early stem tetrapods -- some of the first animals to make the transition from water to land. Thanks to new research, scientists believe that these creatures are 14 million years older than previously thought. The new age -- dating back to 346 million years ago -- adds to the significance of the find because it places the specimens in a mysterious hole in the fossil record called Romer's Gap.</p>
<p>***</p>
<p>&quot;Garza took a risk when he embarked on his mission to date the ancient fossils using a geochemical technique called radiometric dating.</p>
<p>&quot;That's because while geoscientists can use zircon crystals to determine how long ago a rock was formed, not all rock types are amenable to this type of analysis. And the site in Scotland where the fossils were discovered was near ancient volcanoes whose lava flows had long hardened into basalt rock, where zircons do not typically form. Fellow scientists warned Garza that chemically dating the rocks might be fruitless.</p>
<p>***</p>
<p>&quot;In 1984, an amateur paleontologist in Scotland found a remarkable specimen: a nearly complete fossil of what looked to be a lizard or salamander. Rather small in size at 20 centimeters, it would turn out to be a crucial piece in the puzzle of animal evolution.</p>
<p>&quot;This creature, called Westlothiana lizziae, is one of the earliest examples of a four-legged animal that had evolved from living underwater to dwelling on earth. It, and other stem tetrapods like it, are common ancestors of the amphibians, birds, reptiles and mammals that exist today, including humans.</p>
<p>***</p>
<p>&quot;Garza X-rayed 11 of the rock samples at the Jackson School and was able to extract zircons from the rock surrounding six of the fossils. He then conducted uranium-lead laser dating on the zircons at the University of Houston to determine their oldest possible age.</p>
<p>***</p>
<p>&quot;The more accurate, older maximum age of 346 million years is significant because it places the specimens in Romer's Gap. This is a time period from 360 to 345 million years ago where, for reasons scientists are not exactly sure of, very few fossils have been discovered. It is during this crucial point in history that water-dwelling fish took an evolutionary leap, growing lungs and four legs to become land animals. This is one of the most pivotal milestones in the history of animal evolution.&quot;</p>
<p>Comment: This finding satisfies dhw's wish for more fossil discoveries by filling a recognized gap in specimens. That is what is left to find, just specimens to fill recognized gaps in the fossil record. New, dramatic, theory changing discoveries are most unlikely.</p>
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<link>https://agnosticweb.com/index.php?id=48681</link>
<guid>https://agnosticweb.com/index.php?id=48681</guid>
<pubDate>Mon, 02 Jun 2025 17:51:15 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: very early oxygen use (reply)</title>
<content:encoded><![CDATA[<p>A new study supporting the early appearance of oxygen before the Big Oxygen Event:</p>
<p><a href="https://www.sciencealert.com/oxygen-metabolism-emerged-on-earth-before-the-great-oxidation-event-study-reveals?utm_source=ScienceAlert+-+Daily+Email+Updates&amp;utm_campaign=9a4c42de4c-RSS_EMAIL_CAMPAIGN&amp;utm_medium=email&amp;utm_term=0_fe5632fb09-9a4c42de4c-366098385">https://www.sciencealert.com/oxygen-metabolism-emerged-on-earth-before-the-great-oxidat...</a></p>
<p><a href="https://www.science.org/doi/10.1126/science.adp1853">https://www.science.org/doi/10.1126/science.adp1853</a></p>
<p>&quot;The Great Oxidation Event (GOE) some 2.4 billion years ago established the oxygen-rich atmosphere that many living things depend on today.</p>
<p>&quot;Curiously, when it came to evolving ways to actively use the element for respiration, some strains of bacteria had a head start.</p>
<p>&quot;Using a combination of bacterial genome data, geological markers, and machine learning techniques designed to spot genetic patterns, an international team of researchers searched for evidence describing the earliest aerobic (oxygen-breathing) bacteria.</p>
<p>&quot;While most strains took up the ability to tolerate and use oxygen after the GOE, the researchers did spot some outliers – certain bacteria that were aerobic approximately 900 million years before oxygen levels rapidly rose in Earth's atmosphere.</p>
<p>&quot;Among 1007 species of related bacteria, the researchers identified more than 80 genetic transitions from metabolisms that couldn't use oxygen to metabolisms that could. Estimates based on the rate at which mutations accumulate suggest at least a few of these happened before oxygen levels rose to significant levels in Earth's atmosphere.</p>
<p>&quot;'At least three transitions predated [the GOE], suggesting that aerobic respiration evolved before widespread atmospheric oxygenation and may have facilitated the evolution of oxygenic photosynthesis in cyanobacteria,&quot; write the researchers in their published paper.</p>
<p>&quot;In other words, these early oxygen-breathers may have laid the foundations for their descendents to use water and carbon dioxide to capture sunlight, freeing up stored oxygen in what would become the Great Oxidation Event.</p>
<p>***</p>
<p>&quot;There are some assumptions being made here, about how genes in modern bacteria might link back to genes in ancient bacteria – and do the same oxygen processing job – but the researchers are confident that they included enough bacteria species and corroborating evidence to confirm the link.</p>
<p>&quot;'This allowed us to calibrate bacterial evolution to the record of biospheric oxygenation, greatly augmenting the limited fossil record of early life and bringing a new level of resolution to the study of evolution in deep time,&quot; write the researchers.</p>
<p>&quot;As well as validating the idea that aerobic bacteria have a history that goes way, way back, these findings also give us more evidence that cyanobacteria evolution happened relatively slowly, with its roots streching back far before the GOE.</p>
<p>Comment: as I noted before, oxygen is a dangerous substance and requires antioxidants to control it. This advance required increasing complexity and infers the need for design.  Evolution seems to know what is coming next, as if someone is planning its advance. Noted in yesterday's entry:   Thursday, April 03, 2025, 20:58</p>
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<link>https://agnosticweb.com/index.php?id=48430</link>
<guid>https://agnosticweb.com/index.php?id=48430</guid>
<pubDate>Fri, 04 Apr 2025 15:50:32 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: dinosaurs to birds; Bechly redux (reply)</title>
<content:encoded><![CDATA[<p>A new real bird finding in China:</p>
<p><a href="https://www.wsj.com/public/resources/documents/rOo8HrgVnGDego919P0Y-WSJNewsPaper-3-1-2025.pdf">https://www.wsj.com/public/resources/documents/rOo8HrgVnGDego919P0Y-WSJNewsPaper-3-1-20...</a></p>
<p>&quot;FOR MORE THAN a century,  scientists believed that a fossil  of a winged dinosaur from the<br />
 Jurassic Period discovered 160 years ago in Germany represented the earliest birds.  Now, researchers have unearthed another creature from the same period that more  closely resembled the avians  of today—indicating that birds  evolved much earlier than previously thought.</p>
<p>&quot;The newly discovered bird,  known as Baminornis zhenghensis, weighed about 3.5n  ounces and was about the size  of a common quail. It had a  short tail with some vertebrae  fused into a stubby nubbin—a  crucial aerodynamic feature of modern birds that shifts the  body’s center of mass toward  the wings, improving flight.  Creatures with bone structures resembling modern birds  weren’t believed to have appeared until nearly 20 million  years later, in the early Cretaceous Period. But the new fossil, uncovered in southeastern  China in 2023, tells a different  evolutionary story.</p>
<p>&quot;Isotope dating of the surrounding mudstone indicated that the fossils were between  148 million and 150 million  years old, roughly the same  age as Archaeopteryx,  previously believed to  be the oldest example  of a bird.  With feathers like a  bird but a long tail  and claws similar to a  reptile, the hybrid  characteristics of Archaeopteryx have led to debates about its classification. About a dozen Archaeopteryx fossils have been uncovered, all in the southern  German state of Bavaria. “Paleontologists once expected more Jurassic bird fossils to emerge, but none did— until now,” said Stephen  Brusatte, a paleontologist at<br />
the University of Edinburgh who wasn’t involved in the  research. “This is very exciting.&quot;</p>
<p>&quot;Fossils of birds are rare be cause of their fragile bones.  When Wang held the Baminornis zhenghensis fossil for  the first time, he said, his  heart raced.  “If there are still any doubts  about how birdy Archaeopteryx is,” he said, “Baminornis  is undoubtedly a real bird.”</p>
<p>Comment: this settles the argument. Dinosaurs gave us birds.</p>
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<link>https://agnosticweb.com/index.php?id=48236</link>
<guid>https://agnosticweb.com/index.php?id=48236</guid>
<pubDate>Sat, 01 Mar 2025 19:35:20 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: how dinosaurs dominated the Earth (reply)</title>
<content:encoded><![CDATA[<p>A study of dinosaur poop and vomit:</p>
<p><a href="https://www.nature.com/articles/d41586-024-03889-y">https://www.nature.com/articles/d41586-024-03889-y</a></p>
<p>&quot;Faeces and vomit fossils from dinosaurs reveal how evolved dinosaurs to rule Earth. The study, which was published in Nature on 27 November, analysed hundreds of pieces of fossilized digestive material, called bromalites, to reconstruct what dinosaurs ate and how this changed1. The fossils reveal that the rise of the dinosaurs, over millions of years during the Triassic period, was influenced by factors including climate change and other species’ extinction.</p>
<p>***</p>
<p>&quot;Analysis of the digestive materials allowed the researchers to “reconstruct these food webs, so who was eating whom in all these assemblages and see this trend over such a long period of time”, Qvarnström says.</p>
<p>***</p>
<p>&quot;The team found that the number and variety of the contents of the fossils increased over time, suggesting that larger dinosaurs with more diverse feeding habits began to gain prominence in the late Triassic period (between 237 million and 201 million years ago). By comparing the fossils with plant data from the period, the researchers found that dinosaurs’ rise was shaped by chance and by adaptations. For example, climate change led to increased humidity, which changed the vegetation available. Dinosaurs were able to better adapt to this shifting climate and change in diet than other land animals.</p>
<p>***</p>
<p>“'What we learnt was that the rise of dinosaurs, it took quite a long time, and it was really complex,” says Qvarnström.</p>
<p>&quot;This is “an impressive piece of work”, says Suresh Singh, who studies palaeoecological dynamics at the University of Bristol, UK. He adds that this is the first time he’s seen bromalite-focused research applied at such scale.</p>
<p>&quot;Singh says dinosaurs are an important source of data for understanding of how life responds to different pressures, for example climate change.&quot;</p>
<p>Comment. the dinosaurs were around for a very long period, matching the Trilobites. Our current period is very small in comparison. However we will hopefully match them.</p>
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<link>https://agnosticweb.com/index.php?id=47895</link>
<guid>https://agnosticweb.com/index.php?id=47895</guid>
<pubDate>Wed, 27 Nov 2024 19:33:12 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: earthworm DNA is weird (reply)</title>
<content:encoded><![CDATA[<p>Not like any other:</p>
<p><a href="https://www.sciencealert.com/a-profound-mystery-gave-earthworms-the-most-chaotic-genomes-ever-seen?utm_source=ScienceAlert+-+Daily+Email+Updates&amp;utm_campaign=5708674c36-RSS_EMAIL_CAMPAIGN&amp;utm_medium=email&amp;utm_term=0_fe5632fb09-5708674c36-366098385">https://www.sciencealert.com/a-profound-mystery-gave-earthworms-the-most-chaotic-genome...</a></p>
<p>&quot;Back around when worms wriggled out of saltwater and into freshwater, they experienced a cataclysmic rearrangement of their genetic material.</p>
<p>&quot;This event ripped once functioning genes asunder, including some of those involved in critical cell division processes, leaving earthworms, leeches, and their other clitellate relatives with the most scrambled genomes known.</p>
<p>&quot;'Everything broke and then rearranged completely randomly,&quot; Rosa Fernández, from Spain's Institute of Evolutionary Biology (CSIC-UPF), told Christie Wilcox at Science. &quot;I made my team repeat the analysis a thousand times.&quot;</p>
<p>&quot;Three groups of researchers have now independently reached this same conclusion, upending a long held assumption that there's a certain level of genetic stability required for animal species to avoid extinction.</p>
<p>&quot;Evolutionary biologist Carlos Vargas-Chávez, also from CSIC-UPF, and colleagues discovered gene loss is about 25 percent higher in the line of worms that became clitellata, compared to their other relatives.</p>
<p>&quot;They suspect the worm's genomes scrambled in response to shifts into new habitats, but have yet to determine which came first, the worm's ventures into freshwater and land or their genes' adventures into new positions in their genetic molecules (chromosomes).</p>
<p>&quot;'While the timing of this genomic rearrangement remains unclear, we argue that the genomic hallmarks observed in clitellates are highly unlikely to have arisen via… rearrangements over time,&quot; the researchers explain in their paper.</p>
<p>***</p>
<p>&quot;Most bilaterians, animals like us that have a mirror image left and right side, were thought to have highly conserved sections of chromosomes. This stability is vital for properly aligning the two strands of DNA that form them, when they're pulled apart and then paired off with one strand from each parent during reproduction.</p>
<p>&quot;Genomes from sponges to monkeys have these long ribbons of genes that stay together in a specific order across distantly related species, conserved for hundreds of millions of years.</p>
<p>&quot;These ribbons may move around to some extent, but their sequences within these sections remain relatively intact. But not in leeches and earthworms.</p>
<p>&quot;'Overall, the ancient bilaterian genome architecture has been completely lost within the clitellates,&quot; a second team, led by evolutionary genomicist Thomas Lewin from Taiwan's Biodiversity Research Center, found.</p>
<p>***</p>
<p>&quot;'One outstanding question is how this profound genome reshaping event did not result in extinction,&quot; write Vargas-Chávez and colleagues.</p>
<p>&quot;They found ancestral marine worm genomes do not seem to be organized in compartments, and so are &quot;much more floppy&quot; than in other animals.</p>
<p>&quot;This &quot;may have resulted in a high resilience to the deep genome reshaping occurring after chromosome scrambling,&quot; the team concludes. It also suggests such dramatic genetic rearrangements are likely to be ongoing in these species.&quot;</p>
<p>Comment: it appears descent with modification is not required in every genome (step side Darwin) and reminds us it is better to use genetic studies to discover relationships than phenotypic ones.</p>
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<link>https://agnosticweb.com/index.php?id=47480</link>
<guid>https://agnosticweb.com/index.php?id=47480</guid>
<pubDate>Sun, 15 Sep 2024 15:38:23 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: dinosaurs to birds; Bechly redux (reply)</title>
<content:encoded><![CDATA[<p>Bechly's current comment:</p>
<p><a href="https://evolutionnews.org/2024/09/fossil-friday-more-evidence-that-feathered-dinosaurs-were-secondarily-flightless-birds/">https://evolutionnews.org/2024/09/fossil-friday-more-evidence-that-feathered-dinosaurs-...</a></p>
<p>&quot;...in one of my recent Fossil Friday articles (Bechly 2024) I elaborated on the neoflightless hypothesis by paleo-ornithologist Alan Feduccia, who convincingly argues that all those feathered bipedal “dinosaurs” are in fact not related to theropod dinosaurs at all but rather represent secondarily flightless birds. I also discussed new evidence that strongly supports this view. Indeed, Agnolin et al. (2019) already commented in their study on the dinosaur-bird transition:</p>
<p>&quot;In a ground-breaking proposal, Xu et al. (2011) hypothesized that Archaeopteryx was more nearly related to deinonychosaurians than to birds and that deinonychosaurs become secondarily flightless, a hypothesis previously envisaged by Paul (2002). This hypothesis was supported by a variety of more recent analyses.</p>
<p>***</p>
<p>&quot;Just about a decade ago, Godefroit et al. (2013b) described a new supposed theropod dinosaur from the Middle-Late Jurassic Tiaojishan Formation of Liaoning in China. With an estimated age of 160 million years it is 10 million years older than the famous Archaeopteryx. They named the new species Eosinopteryx brevipenna, because of its reduced plumage. The single known specimen (an artist’s depiction of the living animal is above, or see here for the fossil) represents a very well-preserved fossil and almost complete skeleton, which allowed scientists to identify the new taxon as a close relative of the feathered dinosaur Anchiornis.</p>
<p>&quot;But this generated a problem: the new dinosaur appeared to be nested deeply in the tree of feathered dinosaurs, so that its reduced plumage cannot be a primitive state but has to be a secondary reduction from a more complete set of feathers. Furthermore, the bone structures of the shoulder articulation showed that the animal was not capable of flapping its arms or wings. This is even more perplexing, as this case of reduced flight adaptations predates the famous missing link Archaeopteryx. Consequently, the press release to the new study  announced that this fossil “challenges bird evolution theory” and suggested “that the origin of flight was much more complex than previously thought.” The lead author, Dr. Gareth Dyke from the University of Southampton, is quoted with this remarkable admission: “This discovery sheds further doubt on the theory that the famous fossil Archaeopteryx — or “first bird” as it is sometimes referred to — was pivotal in the evolution of modern birds.”</p>
<p>***</p>
<p>&quot;But these studies partly disagreed on certain crucial issues, such as the question of whether the shorter tail in Eosinopteryx is complete and diagnostic (Pei et al. 2017) or not (Hu et al. 2018, Agnolin et al. 2019). Moreover, other experts had recorded further diagnostic differences between the skeletons of two taxa, such as anteriorly convex pubic shafts that are present in Anchiornis but absent in Eosinopteryx (Foth &amp; Rauhut 2017), or the length and shape of the prefrontal and maxillary processes (Guo et al. 2018). Also the cladistic studies by Lefèvre et al. (2014), Guo et al. (2018), Hu et al. (2018), and Pei et al. (2020) did not recover Eosinopteryx as closest relative of Anchiornis, or even rejected the monophyly of Anchiornithidae. One could almost get the impression that the desire to explain away inconvenient results may have guided the interpretations of those scientists, who denied the distinctness of Eosinopteryx.</p>
<p>&quot;There are clearly open questions and it definitely looks like the common dino-to-bird narrative has been massively oversold to the public and represents a theory with numerous holes and problems.&quot;</p>
<p>Comment: this article calls into question dhw's assertion that 696 dinosaur species produced four bird types.</p>
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<link>https://agnosticweb.com/index.php?id=47470</link>
<guid>https://agnosticweb.com/index.php?id=47470</guid>
<pubDate>Fri, 13 Sep 2024 19:06:41 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: the speed of adaptations (reply)</title>
<content:encoded><![CDATA[<p>Can be very quick:</p>
<p><a href="https://www.livescience.com/planet-earth/evolution/how-fast-does-evolution-happen?utm_term=C3CFD69C-A485-4C10-9DB4-812DF4E4CC15&amp;lrh=44525984c2b11ce2f5746c650cfc94f0f733452d62b09eb2139365ed45c5c2e5&amp;utm_campaign=368B3745-DDE0-4A69-A2E8-62503D85375D&amp;utm_medium=email&amp;utm_content=549A2685-5224-40EC-9471-753219DB5802&amp;utm_source=SmartBrief">https://www.livescience.com/planet-earth/evolution/how-fast-does-evolution-happen?utm_t...</a></p>
<p>&quot;First, let's define evolution, which is the process by which a species' genes or physical appearance changes gradually over time. The driving force is natural selection, in which individuals with more beneficial traits survive and reproduce, sending those traits to the next generation. Over many generations, this is known as adaptive evolution.</p>
<p>&quot;Combined, natural selection and adaptive evolution allow a &quot;species to track changes in its environment,&quot; said Timothée Bonnet, an evolutionary biologist at the French National Center for Scientific Research and La Rochelle University.</p>
<p>&quot;In the famous example of Darwin's finches on the Galápagos Islands, different species evolved different beak shapes and sizes within a few decades to specialize in feeding on different types of nuts and insects. This finding made waves following the publication of the Pulitzer Prize-winning book, &quot;The Beak of the Finch: A Story of Evolution in Our Time&quot; (Knopf, 1994).</p>
<p><strong>&quot;Then, there's a third component: speciation. This is when one species branches off into two distinct species over time. Bonnet said this happens much more slowly than adaptive evolution.</strong> (my bold)</p>
<p>&quot;By the early to mid-20th century, scientists realized that evolution can happen much more quickly than Darwin ever thought by using the theory of natural selection to make crops more palatable in as few as seven years and domesticate dogs over a few generations. &quot;We made evolution happen,&quot; Bonnet told Live Science. &quot;We could see that the change happening at this scale of a few generations (can) be quite dramatic.&quot;</p>
<p>***</p>
<p>&quot;Bonnet and an international team of researchers analyzed decades of genetic data for 19 bird and mammal species. They found that the rate of adaptive evolution was two to four times faster than previous estimates. More specifically, each generation increased its survival and reproduction by 18.5%, on average, under completely stable conditions.</p>
<p>&quot;This means that if survival and reproduction decreased by a third, adaptive evolution would help a population recover in three to seven generations. Bighorn sheep (Ovis canadensis) evolved horns that were 0.7 inches (2 centimeters) shorter than before over 20 years, or three generations, because hunters had targeted those with larger horns. Snow voles (Chionomys nivalis) shrank by up to 0.1 ounces (3 grams) over 10 years, or eight generations, probably because of changes in snowfall.</p>
<p>***</p>
<p>&quot;'Rates of evolution can be fantastically fast because of that constant environmental change,&quot; Michael Benton, a vertebrate paleontologist at the University of Bristol, told Live Science. But &quot;the shorter the time scale, the faster the rate, and this is after you have corrected for time,&quot; he added.</p>
<p>&quot;Stroud and his colleagues at the University of Miami are now using nonnative green iguanas as a case study for rapid evolution. The warm-adapted lizards are known to freeze and fall out of trees during Miami's infrequent cold snaps.</p>
<p>&quot;'What we saw is that some die, but some survive — and the ones that survive can actually tolerate colder temperatures than the ones we measured before,&quot; Stroud said. &quot;So it suggests that evolution might be happening.&quot;</p>
<p>&quot;The fossil record holds some clues, too. In the Triassic period (251.9 million to 201.3 million years ago), after the Permian extinction, large marine reptiles called ichthyosaurs evolved to be gigantic in less than 3 million years — more quickly than whales did — because they became the ocean's top predators.</p>
<p>&quot;Factors such as adjusting to new conditions, filling new niches, evading predators and competing with other animals often increase how quickly an animal can evolve, Benton said.&quot;</p>
<p>Comment: to think clearly about evolution do not confuse adaptive evolution with speciation. Adaptations can occur very quickly as the article shows. Note my bold. Speciation takes extended time. We currently find species new to us, but we do not see speciation in action, and do not know how it works.</p>
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<link>https://agnosticweb.com/index.php?id=47451</link>
<guid>https://agnosticweb.com/index.php?id=47451</guid>
<pubDate>Tue, 10 Sep 2024 15:49:51 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: the role of dGRNs (reply)</title>
<content:encoded><![CDATA[<p>In experimental gene studies:</p>
<p><a href="https://evolutionnews.org/2024/07/on-developmental-gene-regulatory-networks-the-scientific-literature-supports-stephen-meyer/">https://evolutionnews.org/2024/07/on-developmental-gene-regulatory-networks-the-scienti...</a></p>
<p>&quot;...over 100 years of mutagenesis experiments show that mutations in genes regulating development are invariably deleterious (or in some cases have only trivial effects). Meyer summarizes: “This generates a dilemma: major changes are not viable; viable changes are not major. In neither case do the kinds of mutation that actually occur produce viable major changes of the kind necessary to build new body plans.”</p>
<p>&quot;We see these deleterious effects particularly in experiments on developmental gene regulatory networks (dGRNs), complex networks of gene-interaction which regulate the expression of genes early in development as an organism’s body plan begins to grow. After reviewing experimental work on dGRNs, Meyer finds that, “These dGRNs cannot vary without causing catastrophic effects to the organism.” </p>
<p>***</p>
<p>&quot;...if changes to dGRNs are lethal to an embryo, how can they be modified to explain how new body plans evolve? Meyer’s writes in the book: “The system of gene regulation that controls animal-body-plan development is exquisitely integrated, so that significant alterations in these gene regulatory networks inevitably damage or destroy the developing animal. But given this, how could a new animal body plan, and the new dGRNs necessary to produce it, ever evolve gradually via mutation and selection from a preexisting body plan and set of dGRNs?” </p>
<p>***</p>
<p>&quot;Meyer was justified in making these arguments. The work of the late Caltech developmental biologist Eric Davidson, an eminent expert in the field of evo-devo, shows that mutations in genes that affect body plan characteristics (which tend to be expressed early, as the body plan is being put in place) don’t lead to new body plans — they lead to dead embryos.</p>
<p>***</p>
<p>&quot; [Davidson:] Interference with expression of any [genes in the dGRN kernel] by mutation or experimental manipulation has severe effects on the phase of development that they initiate. This accentuates the selective conservation of the whole subcircuit, on pain of developmental catastrophe.</p>
<p>&quot;This intolerance of body plan-affecting dGRNs to fundamental perturbations indicates that they could not have evolved by undirected mutations. Many coordinated mutations would be needed to convert one functional dGRN that generates a particular body plan into a different dGRN that generates a different body plan.&quot;</p>
<p>Comment: careful DNA studies show no way to have major evolutionary advances in phenotype by specific mutations affecting dGRNs. There is another viewpoint from ID folks in this article:</p>
<p>&quot;What we do know from experience, however, is that large increases in functionally specified information — especially information expressed in an alphabetic or digital form — are always produced by conscious and rational agents. So the best explanation for the explosion of information necessary to produce the Cambrian animals (whether that explosion occurred during or before the Cambrian period) remains intelligent design.&quot;<br />
Darwin’s Doubt, p. 448</p>
<p>I agree.</p>
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<link>https://agnosticweb.com/index.php?id=47182</link>
<guid>https://agnosticweb.com/index.php?id=47182</guid>
<pubDate>Sat, 27 Jul 2024 17:29:02 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: multicellularity from snowball Earth (reply)</title>
<content:encoded><![CDATA[<p>A new reasonable theory:</p>
<p><a href="https://www.quantamagazine.org/the-physics-of-cold-water-may-have-jump-started-complex-life-20240724/">https://www.quantamagazine.org/the-physics-of-cold-water-may-have-jump-started-complex-...</a></p>
<p>&quot;To very small single-celled creatures, thick seawater would have posed some big problems. Bacteria feed by diffusion — the movement of nutrients through water from areas of high concentration to low concentration — and tend to wait for food to come to them. However, at low temperatures, diffusion slows down. Nutrients don’t travel as quickly or as far. For cells, living in a cold and more viscous fluid means getting less to eat. Even very small organisms that can propel themselves, such as cells with flagella, move more slowly in cold water. As a result, they encounter food less frequently.</p>
<p>&quot;A bigger organism, on the other hand, can navigate thicker waters without much trouble. A cluster of cells has the benefit of inertia: Their combined mass is large enough to allow them to build up steam and barrel through thicker fluid. “At some point, you are too big for this to matter,” Simpson said.</p>
<p>***</p>
<p>&quot;There’s no way for biologists to travel back in time to test the real conditions of Snowball Earth, but they can try to re-create aspects of them in the lab. In an enormous, custom-made petri dish, Halling and Simpson created a bull’s-eye target of agar gel — their own experimental gauntlet of viscosity. At the center, it was the standard viscosity used for growing these algae in the lab. Moving outward, each concentric ring had higher and higher viscosity, finally reaching a medium with four times the standard level. The scientists placed the algae in the middle, turned on a camera, and left them alone for 30 days — enough time for about 70 generations of algae to live, swim around for nutrients and die.</p>
<p>***</p>
<p>&quot;Simpson was particularly curious as to whether algae that made it into the highest viscosity ring would find ways to increase their swimming speed. The algae are photosynthetic, so they get energy from the sun. But they need to pick up nutrients such as phosphorus from the environment, so movement is still important to their survival. Maintaining the same level of nutrients in high-viscosity surroundings would require them to find a way to keep up their speed.</p>
<p>&quot;After 30 days, the algae in the middle were still unicellular. As the scientists put algae from thicker and thicker rings under the microscope, however, they found larger clumps of cells. The very largest were wads of hundreds. But <strong>what interested Simpson the most were mobile clusters of four to 16 cells, arranged so that their flagella were all on the outside. These clusters moved around by coordinating the movement of their flagella, the ones at the back of the cluster holding still, the ones at the front wriggling. </strong> (my bold)</p>
<p>Comparing the speed of these clusters to the single cells in the middle revealed something interesting. “They all swim at the same speed,” Simpson said. By working together as a collective, the algae could preserve their mobility.</p>
<p>***</p>
<p>Intriguingly, when the scientists took these little clusters from the high-viscosity gel and put them back at low viscosity, the cells stuck together. They remained this way, in fact, for as long as the scientists continued to watch them, about 100 more generations. Clearly, whatever changes they underwent to survive at high viscosity were hard to reverse, Simpson said — perhaps a move toward evolution rather than a short-term shift.</p>
<p>Modern-day algae are not early animals. But the fact that these physical pressures forced a unicellular creature into an alternate way of life that was hard to reverse feels quite powerful, Simpson said. He suspects that if scientists explore the idea that when organisms are very small, viscosity dominates their existence, we could learn something about conditions that might have led to the explosion of large forms of life.</p>
<p>***</p>
<p>From the time Simpson first realized that such limits on movement could be a monumental obstacle to microscopic life, he hasn’t been able to stop thinking about it. <strong>Viscosity may have mattered quite a lot in the origins of complex life, whenever that was. </strong> (my bold)</p>
<p>***</p>
<p>it’s difficult to say how much importance to assign to this era. Butterfield also remarked on this uncertainty: “There’s no evidence of anything getting large until quite a bit after [Snowball Earth].”</p>
<p>That said, Brocks found Simpson’s experiment quite clever and beautiful. The fact that organisms might respond to high viscosity by developing collective behavior deserves to be better understood, he said — whether Snowball Earth led to the evolution of complex animal life or not.</p>
<p>Comment: A revolutionary idea to explain how multicellular life arrived. God, as designer, could have directed this method.</p>
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<link>https://agnosticweb.com/index.php?id=47169</link>
<guid>https://agnosticweb.com/index.php?id=47169</guid>
<pubDate>Wed, 24 Jul 2024 17:45:00 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: Bechly revisits snake explosion (reply)</title>
<content:encoded><![CDATA[<p>Snake evolution is a big bang in evolution:</p>
<p><a href="https://evolutionnews.org/2024/06/fossil-friday-snake-origins-yet-another-biological-big-bang/">https://evolutionnews.org/2024/06/fossil-friday-snake-origins-yet-another-biological-bi...</a></p>
<p>&quot;...there was another open question concerning the origin of snakes: Did their distinct body plan evolve gradually as predicted by Darwinian evolution, or did snakes appear abruptly on the scene as predicted by intelligent design theory? Earlier this year a seminal new study was published by a team of researchers from the University of Michigan and Stony Brook University in the prestigious journal Science.</p>
<p>***</p>
<p>&quot; The study found that all the characteristic traits of the snake body plan, such as the flexible skull with articulated jaws, the loss of limbs, and the elongated body with hundreds of vertebrae, all appeared in a short window of time about 100-110 million years ago. This arguably would imply that snakes became “evolutionary winners” because they evolved “in breakneck pace” (Wilcox 2024), which the senior author of the study explained with the ad hoc hypothesis that “snakes have an evolutionary clock that ticks a lot faster than many other groups of animals, allowing them to diversify and evolve at super quick speeds” (Osborne 2024). Well, that is not an explanation at all, but just a rephrasing of the problem. How could such a super quick evolution be accommodated within the framework of Darwinian population genetics and thus overcome the waiting time problem?</p>
<p>&quot; My prediction is that this will prove to be another good example of the fatal waiting time problem for neo-Darwinism. In any case we can add the origin of snakes to the large number of abrupt appearances in the history of life (Bechly 2024), and I am happy to embrace the name coined by the authors of the new study for this remarkable event: The macroevolutionary singularity of snakes. This does not sound very Darwinian, does it? So what do the authors suggest as causal explanation? They have none and the press release from Stony Brook University (SBU 2024) therefore concludes with this remarkable admission: “The authors note that the ultimate causes, or triggers, of adaptive radiations is a major mystery in biology. In the case of snakes, it’s likely there were multiple contributing factors, and it may never be possible to fully define each factor and their role in this unique evolutionary process.” It other words, it was a biological Big Bang and they have no clue what caused it. But of course it must have been unguided evolution, no intelligence allowed!&quot;</p>
<p>Comment: dhw will ask if snakes are necessary for God's goal to produce humans. He made them so rapidly He must have thought so. I entered a more complete coverage of the actual literature here:  2024-02-23, 16:16. There are multiple sudden appearances of species throughout evolution, first admitted by Gould years ago.</p>
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<link>https://agnosticweb.com/index.php?id=46954</link>
<guid>https://agnosticweb.com/index.php?id=46954</guid>
<pubDate>Sat, 29 Jun 2024 17:50:55 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: how Archaea use hydrogen differently (reply)</title>
<content:encoded><![CDATA[<p>As the most ancient animal before oxygenation, itvis a logical finding:</p>
<p><a href="https://www.sciencealert.com/third-form-of-life-makes-energy-in-remarkable-ways-scientists-discover?utm_source=ScienceAlert+-+Daily+Email+Updates&amp;utm_campaign=a3d4a139b5-RSS_EMAIL_CAMPAIGN&amp;utm_medium=email&amp;utm_term=0_fe5632fb09-a3d4a139b5-366098385">https://www.sciencealert.com/third-form-of-life-makes-energy-in-remarkable-ways-scienti...</a></p>
<p>&quot;...scientists have discovered that archaea – the third form of life after bacteria and eukaryotes – have been making energy using hydrogen gas and 'ultraminimal' enzymes for billions of years.</p>
<p>&quot;Specifically, the international team of researchers discovered that at least nine phyla of archaea, a domain of single-celled organisms lacking internal membrane-bound structures, produce hydrogen gas using enzymes thought to only exist in the other two forms of life.</p>
<p>&quot;Archaea, they realized, not only have the smallest hydrogen-using enzymes compared to bacteria and eukaryotes, but their enzymes for consuming and producing hydrogen are also the most complex characterized so far.</p>
<p>&quot;Small and mighty, these enzymes have seemingly allowed archaea to survive and thrive in some of Earth's most hostile environments where little to no oxygen is found.</p>
<p>***</p>
<p>&quot;Microorganisms produce and release hydrogen gas (H2) for entirely different purposes, mainly to dispose of excess electrons produced during fermentation, a process whereby organisms extract energy from carbohydrates such as sugars without oxygen.</p>
<p>&quot;Enzymes used for consuming or producing H2 are called hydrogenases, and they were first comprehensively surveyed across the tree of life only eight years ago. Since then, the number of known microbial species has exploded, particularly archaea, which hide out in extreme environments, such as hot springs, volcanoes, and deep-sea vents.</p>
<p>&quot;However, most archaea are known only from chunks of their genetic code found in these environments, and many haven't been cultured in the lab because it's very difficult to do so.</p>
<p>***</p>
<p>&quot;But unlike bacteria and eukaryotes, further analyses showed that archaea assemble &quot;remarkable hybrid complexes&quot; for their hydrogen production needs, fusing two types of hydrogenases together.</p>
<p>&quot;'These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes,&quot; the team writes in their paper.</p>
<p>&quot;Many of the cataloged archaea genomes analyzed in this study are, however, incomplete, and who knows how many more species are yet to be discovered.</p>
<p>&quot;It's more than likely that archaea harbor other ingenious ways of making energy that we are yet to find.&quot;</p>
<p>Comment: as the most ancient form of life, it required these mechanisms to survive, using hydrogen as the available gas for 'respiration'.</p>
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<link>https://agnosticweb.com/index.php?id=46801</link>
<guid>https://agnosticweb.com/index.php?id=46801</guid>
<pubDate>Wed, 12 Jun 2024 14:55:28 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: monkey works for the theory (reply)</title>
<content:encoded><![CDATA[<p>Dispersal of dinosaurs just like the monkeys. Same dinosaurs in North America and Africa when separated by huge oceans:</p>
<p><a href="https://evolutionnews.org/2024/05/fossil-friday-did-giant-dinosaurs-swim-across-oceans/">https://evolutionnews.org/2024/05/fossil-friday-did-giant-dinosaurs-swim-across-oceans/</a></p>
<p>&quot;I discussed the unlikelihood of trans-oceanic dispersal for terrestrial animals, which is implied by certain evolutionary hypotheses, for example about the origin of New World monkeys. This Fossil Friday we will add another absurd case, which made headlines after the highly unexpected discovery of duckbill dinosaurs in Africa. Therefore, today’s featured fossil is the duckbill dinosaur Edmontosaurus from the Late Cretaceous of North America.</p>
<p>&quot;Duckbill dinosaurs (Hadrosauridae) originated during the Late Cretaceous in North America and later spread via a land bridge to Eurasia. Due to the breakup of the supercontinent Pangaea in the Mesozoic and high sea levels, Africa was for 75 million years (including the Late Cretaceous) an isolated island continent similar to modern Australia. The vast ancient Tethys ocean separated Africa from Eurasia and America. Consequently, duckbill dinosaurs were not expected to be found in Africa.</p>
<p>&quot;Therefore, it was a big surprise when Longrich et al. (2021) described the first duckbill dinosaur from the Late Cretaceous of Morocco in North Africa. The new species belonged to a clade of lambeosaurine hadrosaurids otherwise only known from Europe, which arguably implies that these animals had to somehow cross the Tethys ocean to reach the shores of Africa. Longrich et al. discussed the various possibilities for trans-oceanic dispersal by rafting and swimming, and even mentioned that “dispersal across marine barriers also occurs in other hadrosaurid lineages and titanosaurian sauropods, suggesting oceanic dispersal played a key role.” Really? Just imagine a giant sauropod swimming or rafting in the middle of the wild ocean, not to speak about sharks and the large diversity of voracious large marine reptile predators (e.g., mosasaurs and pliosaurs) in the Late Cretaceous that would have happily feasted on such a helpless meat ball. Even mainstream paleontologists considered such “long-distance trans-oceanic dispersal of such large-bodied and highly terrestrial animals” as highly unlikely and implausible.&quot;</p>
<p>Comment: Bechly continues with a wry look at Darwinist just-so explanations: swimming, rafting, the geology is wrong, there were archipelagoes to skip along, etc. Any excuse to explain the fossil dispersal. Bechly, as a highly trained Ph.D. in paleontology, has taken up fossil studies which dispute Darwin in any way, and his examples are numerous, presenting a different one every Friday.</p>
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<link>https://agnosticweb.com/index.php?id=46628</link>
<guid>https://agnosticweb.com/index.php?id=46628</guid>
<pubDate>Fri, 24 May 2024 15:58:52 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution:  origin of sympathetic nervous system (reply)</title>
<content:encoded><![CDATA[<p>It runs our organs:</p>
<p><a href="https://www.sciencenews.org/article/lampreys-nervous-system-evolution-cells">https://www.sciencenews.org/article/lampreys-nervous-system-evolution-cells</a></p>
<p>&quot;With terrifyingly sharp teeth arranged around a circular mouth, lampreys look about as primitive a vertebrate as you could imagine. But a new study finds that the animals have a surprising similarity to people: Lampreys have the nerve cells responsible for the “fight or flight” response. The finding challenges the idea that this part of the nervous system emerged later in evolutionary history, and it puts lampreys closer to complex vertebrates — like humans.</p>
<p>***</p>
<p>&quot;Sea lampreys (Petromyzon marinus) belong to a group of fish called jawless vertebrates, which scientists thought lacked nervous system characteristics seen in jawed vertebrates, such as the sympathetic nervous system. This system is what’s behind the “fight or flight” response, and it activates the body by releasing hormones to control body temperature and cardiovascular function.</p>
<p>***</p>
<p>&quot;The team used a technique that tags and lights up specific mRNA in individual cells of lamprey embryos. That allowed the researchers to look at three or four genetic factors associated with sympathetic neurons simultaneously. A cluster of cells lining the heart and the trunk of the embryonic lampreys had these genetic factors, indicating that the cells were the sympathetic neurons seen in other vertebrates, the team reports April 17 in Nature.</p>
<p>&quot;Next, the team tracked where these cells originated by injecting a dye to label cells of the neural crest, a patch of stem cells that migrate during development and give rise to cells of the peripheral nervous system. The lamprey’s sympathetic neurons lit up with the dye, showing that the cells came from the neural crest, just like they do in more complex vertebrates.</p>
<p>&quot;But there were also key differences. Compared with other vertebrates, the lamprey’s sympathetic nervous system formed much later in development and the clusters of cells were smaller. Previous studies may have missed these cells by looking for them at the wrong time during embryo development. So even though the sympathetic system is present, it’s rudimentary nonetheless, Bronner says. “It’s very simplified compared to what it would be in mammals.”</p>
<p><strong>&quot;The findings suggest that the sympathetic nervous system was not an innovation of jawed vertebrates, but rather that the blueprint for it has been around since even before lampreys diverged from the main vertebrate line about half a billion years ago, </strong>says Shreyas Suryanarayana, a neuroscientist at Duke University who was not involved with the study. (my bold)</p>
<p>“'As you look deeper, it becomes clear that the basic building blocks of these complex systems present in humans are, in fact, very old,” Suryanarayana says. In more complex vertebrates, this system then diversified, expanded and grew larger, he says.</p>
<p>Comment: note my bold. This article shows that what develops in evolution is not a sudden appearance of a new innovation, but a step based upon much older preparatory developments. Viewing evolution from a purposeful point of view, this makes perfect sense. Bake in steps to the future early on. This is what a designer would do. This answers dhw's complaint that God made 99.9% of unnecessary organisms just to throw them away. They were all part of a purposeful development, step-by-step to a goal, or as in evolution steps to many, many goals.</p>
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<link>https://agnosticweb.com/index.php?id=46449</link>
<guid>https://agnosticweb.com/index.php?id=46449</guid>
<pubDate>Thu, 09 May 2024 14:57:10 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution:  chance and random mutations (reply)</title>
<content:encoded><![CDATA[<p>Any chance for coherence?:</p>
<p><a href="https://www.scientificamerican.com/article/the-mathematical-case-for-monkeys-producing-shakespeare-eventually/">https://www.scientificamerican.com/article/the-mathematical-case-for-monkeys-producing-...</a></p>
<p>&quot;In one of the most bizarre research experiments in the history of mathematics, researchers at the University of Plymouth in England gave six Celebes crested macaques at the nearby Paignton Zoo a keyboard. From May 1 to June 22, 2002, the animals let off steam by banging at the keys. The letters they typed were transmitted to the Internet. The scientists’ aim was to test the “infinite monkey theorem”: the idea that a monkey typing randomly on a keyboard will, after an infinite amount of time, produce every conceivable text—including the complete works of Shakespeare.</p>
<p>&quot;But—surprise, surprise—the primates’ poetry fell short. After more than seven weeks, the macaques produced only one five-page document, consisting almost entirely of the letter “S.” The researchers nonetheless released the result as a book.</p>
<p>&quot;In defense of Elmo, Gum, Heather, Holly, Mistletoe and Rowan—the six macaques who participated in this experiment—they did not have an infinite amount of time for their work. Still, the result was sobering. It seems highly questionable that these monkeys would have produced Hamlet or the “Scottish play.”</p>
<p>&quot;Although the study in no way disproved the infinite monkey theorem, it showed that monkeys are not necessarily ideal candidates for generating random content in the way the theorem’s creator had assumed. The infinite monkey theorem owes its name to mathematician Émile Borel, who used the animals metaphorically to illustrate his theory of probability in 1913. The ideas behind the theorem are much older, however. </p>
<p>***</p>
<p>&quot;In 2024 data analyst Ergon Cugler de Moraes Silva of the University of São Paulo in Brazil wanted to find out how long it would take, on average, to actually obtain a work by Shakespeare by chance. Instead of monkeys, he programmed a character generator. As described in a preprint paper, his technique was designed to rapidly spit out several hundred pseudorandom spaces, punctuation and letters (in both upper and lower case) each second until a famous sentence from Hamlet appeared: “To be, or not to be, that is the Question” (including the spaces).</p>
<p>&quot;Cugler proceeded in several steps. First, he examined how long it takes on average to find “T” in isolation. He repeated that procedure 10 times and then recorded the average time and number of characters required to generate the desired output. Then he repeated this procedure to determine how long it would take to randomly generate “To” and then did so again for “To” followed by a space, and so forth.</p>
<p>***</p>
<p>&quot;Cugler’s calculation showed that it would take an extreme amount of patience for “To be, or not to be, that is the Question” to appear: about 2.68 x 1069 characters would have to be generated, which would take about 2.95 x 1066 seconds, or 9.35 x 1058 years.</p>
<p>&quot;Since our universe is estimated to be 13.8 billion years old, we would have to wait nearly 7 x 1048 times as long as the time that has passed between the big bang and today. And all this just to produce a single sentence from Hamlet by chance. In this respect, Cicero was right: it is very unlikely that chance will produce even a single readable verse of a poem—or any other text—after a finite amount of time.&quot;</p>
<p>Comment: Darwin's chance mutation theory is a dead end, as shown here mathematically.</p>
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<link>https://agnosticweb.com/index.php?id=46445</link>
<guid>https://agnosticweb.com/index.php?id=46445</guid>
<pubDate>Wed, 08 May 2024 21:52:16 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: transitional fish, Tiktaalik new findings (reply)</title>
<content:encoded><![CDATA[<p>New technique:</p>
<p><a href="https://www.sciencedaily.com/releases/2024/04/240405231833.htm">https://www.sciencedaily.com/releases/2024/04/240405231833.htm</a></p>
<p>&quot;Before the evolution of legs from fins, the axial skeleton -- including the bones of the head, neck, back and ribs -- was already going through changes that would eventually help our ancestors support their bodies to walk on land. A research team including a Penn State biologist completed a new reconstruction of the skeleton of Tiktaalik, the 375-million-year-old fossil fish that is one of the closest relatives to limbed vertebrates. The new reconstruction shows that the fish's ribs likely attached to its pelvis, an innovation thought to be crucial to supporting the body and for the eventual evolution of walking.</p>
<p>***</p>
<p>&quot;The pelvic fins of fish are evolutionarily related to hind limbs in tetrapods -- four-limbed vertebrates, including humans. In fish, the pelvic fins and bones of the pelvic girdle are relatively small and float freely in the body. For the evolution of walking, the researchers explained, the hind limbs and pelvis became much larger and formed a connection to the vertebral column as a way of bracing the forces related to supporting the body.</p>
<p>&quot;'Tiktaalik is remarkable because it gives us glimpses into this major evolutionary transition,&quot; Stewart said. &quot;Across its whole skeleton, we see a combination of traits that are typical of fish and life in water as well as traits that are seen in land-dwelling animals.&quot;</p>
<p>***</p>
<p>&quot;'This reconstruction shows, for the first-time, how it all fit together and gives us clues about how walking might have first evolved.&quot;</p>
<p>&quot;The researchers explained that, unlike our own hips where our bones fit tightly together, the connection between the pelvis and axial skeleton of Tiktaalik was likely a soft-tissue connection made of ligaments.</p>
<p>&quot;&quot;Tiktaalik had specialized ribs that would have connected to the pelvis by a ligament,&quot; Stewart said. &quot;It's astonishing really. This creature has so many traits -- large pair of hind appendages, large pelvis, and connection between the pelvis and axial skeleton -- that were key to the origin of walking. And while Tiktaalik probably wasn't walking across land, it was definitely doing something new. This was a fish that could likely prop itself up and push with its hind fin.'&quot;</p>
<p>Comment: the authors of this article see the purpose in evolution as they describe the advances related to walking</p>
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<link>https://agnosticweb.com/index.php?id=46227</link>
<guid>https://agnosticweb.com/index.php?id=46227</guid>
<pubDate>Sun, 07 Apr 2024 14:42:39 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: mummies with parasites (reply)</title>
<content:encoded><![CDATA[<p>A huge study:</p>
<p><a href="https://www.scientificamerican.com/article/ancient-egyptian-mummies-reveal-what-diseases-plagued-the-civilization/">https://www.scientificamerican.com/article/ancient-egyptian-mummies-reveal-what-disease...</a></p>
<p>&quot;Ancient Egypt—a civilization that was one of the most powerful the world has ever seen and which lasted for nearly 3,000 years—was among the first to mummify its dead, providing us a window into its people’s culture, language and politics, as well as their health. Now a new study has uncovered intimate details of the disease landscape that set this civilization apart from others of its time, including a surprising role played by the society’s lifeblood: the Nile River.</p>
<p>***</p>
<p>&quot;...anthropologist Piers D. Mitchell analyzed data from 31 studies of mummies from Egypt and neighboring Nubia—another early civilization, dating back to 2000 B.C.E., in what is today southern Egypt and Sudan. In one study, 65 percent of mummies had parasitic worms. In another, 40 percent had head lice. Of the mummies that were tested for Plasmodium falciparum malaria (the most dangerous and deadly form of the illness), 22 percent had it. And based on two other studies, Mitchell estimates that about 10 percent had leishmaniasis, a deadly parasitic disease that causes internal organs to enlarge. “Egypt and Nubia were heavily burdened by the kind of parasites that are likely to kill you or cause a chronic burden of illness,” Mitchell says.</p>
<p>&quot;While infectious maladies would likely have been common among any civilization millennia before vaccinations, treated water or antibiotics, the Nile River played a unique role in the types of illnesses that took hold in ancient Egypt. Despite the region’s arid conditions, vector-borne diseases such as malaria and leishmaniasis were common because mosquitoes bred in the marshlands of the river and sand flies on the drier savanna, Mitchell says.</p>
<p>&quot;By contrast, some sanitation-related afflictions, such as whipworm and roundworm—both of which are spread through feces and were common in other ancient societies—were conspicuously absent in ancient Egypt. Mitchell attributes this to the Nile’s reliable annual flooding and the fertile silt this provided, which would have reduced the need to use animal and human dung to fertilize crops. Aquatic snails in the river did carry some parasites, though. And the cult status of cats in ancient Egypt may have led to the spread of the parasite toxoplasmosis in humans who came into close contact with cats that were being mummified or used in religious offerings.</p>
<p>&quot;Many of the studies Mitchell reviewed used CT scans to analyze diseased tissue for parasites such as guinea worms, which could have formed cysts in the body. When soft tissue was present in mummified specimens, it was possible to use fragmented DNA to identify malaria and leishmaniasis. Similarly, a DNA analysis of muscle tissue was used in one study to detect toxoplasmosis. When working with specimens that had mummified naturally, researchers looked for intestinal parasites within the corpse. But in wealthier individuals, who were embalmed and properly mummified, researchers had to search out intestinal organs in canopic jars—containers the ancient Egyptians used to store organs separately after the mummification process.</p>
<p>***</p>
<p>&quot;Irrespective of social class, anyone using infected water sources is susceptible to infection,” says Ivy Hui-Yuan Yeh, a biological anthropologist at Nanyang Technological University in Singapore, who was not involved in the study. Yeh says this explains why even mummies from among the nobility were heavily burdened by disease. The young pharaoh Tutankhamun, for example, who lived from around 1341–1323 B.C.E., was infected with two different malaria strains (although scientists don’t know if either caused his death).</p>
<p>***</p>
<p>&quot;The disease burden in ancient Egypt and Nubia would have had widespread effects on society, says Marissa Ledger, a medical microbiology resident and biological anthropologist at McMaster University in Ontario, who was also not involved in the study.<strong> “Things like anemia [caused by malaria] make people tired. They also impact your ability to think and even how far you can walk in a day,” she says. “When you have such a high percentage of people in a civilization infected with chronic diseases like this, it has a huge impact on society functioning as a whole.'”  </strong></p>
<p>Comment: Thank goodness we know how to protect ourselves now. This was a major part of our civilized evolution. Big brains sure help.</p>
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<link>https://agnosticweb.com/index.php?id=46198</link>
<guid>https://agnosticweb.com/index.php?id=46198</guid>
<pubDate>Thu, 04 Apr 2024 20:37:21 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: giant armored species before crocodiles (reply)</title>
<content:encoded><![CDATA[<p>Literally like tanks and preceding dinosaurs:</p>
<p><a href="https://www.sciencedaily.com/releases/2024/03/240318164517.htm">https://www.sciencedaily.com/releases/2024/03/240318164517.htm</a></p>
<p>&quot;Dinosaurs get all the glory. But aetosaurs, a heavily armored cousin of modern crocodiles, ruled the world before dinosaurs did. These tanks of the Triassic came in a variety of shapes and sizes before going extinct around 200 million years ago. Today, their fossils are found on every continent except Antarctica and Australia.</p>
<p>&quot;Scientists use the bony plates that make up aetosaur armor to identify different species and usually don't have many fossil skeletons to work with. But a new study led by researchers at The University of Texas at Austin centers on an aetosaur suit of armor that has most of its major parts intact.</p>
<p>&quot;The suit -- called a carapace -- is about 70% complete and covers each major region of the body.</p>
<p>***</p>
<p>&quot;Reyes and his collaborators used the armor to identify the specimen as a new aetosaur species -- which they named Garzapelta muelleri. The name &quot;Garza&quot; recognizes Garza County in northwest Texas, where the aetosaur was found, and &quot;Pelta&quot; is Latin for shield, a nod to aetosaurs' heavily fortified body. The species name &quot;muelleri&quot; honors the paleontologist who originally discovered it, Bill Mueller.</p>
<p>&quot;Garzapelta lived about 215 million years ago and resembled a modern American crocodile -- but with much more armor.</p>
<p>&quot;'Take a crocodile from modern day, and turn it into an armadillo,&quot; said Reyes.</p>
<p>&quot;The bony plates that covered Garzapelta and other aetosaurs are called osteoderms. They were embedded directly in the skin and formed a suit of armor by fitting together like a mosaic. In addition to having a body covered in bony plates, Garzapelta's sides were flanked by curved spikes that would have offered another layer of protection from predators. Although crocodiles today are carnivores, scientists think that aetosaurs were primarily omnivorous.</p>
<p>***</p>
<p>&quot;Garzapelta is part of the Texas Tech University fossil collections. It spent most of the past 30 years on a shelf before Reyes encountered it during a visit. Bill Parker, an aetosaur expert and park paleontologist at Petrified Forest National Park who was not part of the research, said that university and museum collections are a critical part of making this type of research possible.&quot;</p>
<p>Comment: viewed from dhw's perspective, some horrible enemies had to exist to force this guy to require this degree of plate armor to survive.</p>
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<link>https://agnosticweb.com/index.php?id=46088</link>
<guid>https://agnosticweb.com/index.php?id=46088</guid>
<pubDate>Tue, 19 Mar 2024 17:28:29 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<item>
<title>Evolution: early strange forest (reply)</title>
<content:encoded><![CDATA[<p>With fascinating illustrations:</p>
<p><a href="https://www.sciencealert.com/earths-oldest-fossilized-forest-has-been-hiding-its-bizarre-trees-for-390-million-years?utm_source=ScienceAlert+-+Daily+Email+Updates&amp;utm_campaign=e07d1617ee-RSS_EMAIL_CAMPAIGN&amp;utm_medium=email&amp;utm_term=0_fe5632fb09-e07d1617ee-366098385">https://www.sciencealert.com/earths-oldest-fossilized-forest-has-been-hiding-its-bizarr...</a></p>
<p>&quot;The highest sea cliffs in England have been hiding the oldest fossilized forest yet found on planet Earth. The long-lost ecosystem's palm-like trees, called Calamophytons, are 390 million years old.</p>
<p>***</p>
<p>&quot;In southwest England, the red sandstone rock face where scientists found the imprints of logs, roots, and twigs was once considered &quot;barren of trace fossils&quot;.</p>
<p>***</p>
<p>&quot;Animals and primitive plants alike were quick to make use of the new environment. The first trees to colonize the supercontinents were unlike anything you'd see today. Initially, they didn't have roots, leaves, spores, seeds, or any vascular system to transport water and nutrients, forcing them to stick close to coastlines and rivers.</p>
<p>&quot;The Calamophyton trees discovered on the Somerset coastline near Minehead had evolved roots and strands of vascular tissue in their stems, but they were only two to four meters high, and their trunks were thin and hollow.</p>
<p>&quot;Others of their kind have previously been discovered in fossil form in Germany, New York, and China. When the Gondwana supercontinent existed, Germany used to be connected to this very part of England, so it makes sense that they'd share vegetation.</p>
<p>***</p>
<p>&quot;...some of the fossilized trees are preserved exactly where they grew or fell, giving scientists a first glimpse into the layout of the forest ecosystem. Unlike the fossil forest found in upstate New York, the trees in this ancient floodplain are shorter and appear to have grown close together, tightly packed in.</p>
<p>&quot;'This was a pretty weird forest,&quot; says geologist Neil Davies from the University of Cambridge.</p>
<p>&quot;'There wasn't any undergrowth to speak of and grass hadn't yet appeared, but there were lots of twigs dropped by these densely-packed trees, which had a big effect on the landscape.&quot;</p>
<p>&quot;Calamophyton trees had no leaves, but they were covered in hundreds of little twigs that were regularly shed. In fact, in one lifetime, Calamophyton trees may have shed as many as 800 branches.</p>
<p>&quot;That one tree's trash was likely another plant's treasure. As the woody debris accumulated on the forest floor, Earth's soil was infused with its first reserves of organic matter.</p>
<p>&quot;All those tens of millions of years ago, the forest ground would have been covered in &quot;exceptionally abundant plant debris&quot;, write geologists from Cambridge and Cardiff.</p>
<p>&quot;Surrounded by a network of rivers and channels, seasonal floods would have been common. The trees probably evolved deeper roots to survive bouts of water scarcity.</p>
<p>&quot;These roots, in turn, would have stabilized and sculpted the land to form the slopes of hills, river bars, and channels for other plants to then colonize.</p>
<p>&quot;As water washed through the floodplain, it deposited mud in ripples around the vegetation in ways that were later fossilized, preserving the plants and their position for millions of years.</p>
<p>&quot;'The Devonian period fundamentally changed life on Earth,&quot; says Davies.</p>
<p>&quot;'It also changed how water and land interacted with each other, since trees and other plants helped stabilize sediment through their root systems, but little is known about the very earliest forests.&quot;</p>
<p>&quot;The Devonian is sometimes called the 'age of fishes', but given how much plants like Calamophyton appear to have altered Earth's landscape, the time could just as well be known as the age of trees.&quot;</p>
<p>Comment: This is a marvelous example of how new life on Earth evolved the Earth itself adding organic matter to soil and making soil itself from decomposed rock. Do not miss seeing the illustrations!!</p>
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<link>https://agnosticweb.com/index.php?id=46068</link>
<guid>https://agnosticweb.com/index.php?id=46068</guid>
<pubDate>Sun, 17 Mar 2024 14:10:13 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: dinosaurs to birds (reply)</title>
<content:encoded><![CDATA[<p>Only one species based on feathers:</p>
<p><a href="https://www.sciencealert.com/scientists-discover-an-ancient-pattern-hidden-in-the-feathers-of-birds?utm_source=ScienceAlert+-+Daily+Email+Updates&amp;utm_campaign=b7195fb4bf-RSS_EMAIL_CAMPAIGN&amp;utm_medium=email&amp;utm_term=0_fe5632fb09-b7195fb4bf-366098385">https://www.sciencealert.com/scientists-discover-an-ancient-pattern-hidden-in-the-feath...</a></p>
<p>&quot;According to an analysis of hundreds of preserved bird specimens from museum collections around the globe, there's a specific set of feather rules behind the power of flight.</p>
<p>&quot;These newly discovered rules allow scientists to better predict which dinosaurs could fly too.</p>
<p>&quot;'Theropod dinosaurs, including birds, are one of the most successful vertebrate lineages on our planet,&quot; says Field Museum of Natural History paleontologist Jingmai O'Connor. &quot;One of the reasons that they're so successful is their flight. One of the other reasons is probably their feathers, because there's such versatile structures.&quot;</p>
<p>&quot;Their new data could settle some old paleontological debates over whether flight evolved in dinosaurs on more than one occasion.</p>
<p>&quot;Examining wing feathers of 346 different species of birds from museums around the world, Field Museum of Natural History ornithologist Yosef Kiat discovered an interesting trend. From the tiniest hummingbird to the fiercest eagle, all flying birds had 9 to 11 asymmetrical flight feathers called primaries.</p>
<p>***</p>
<p>&quot;'It's really surprising, that with so many styles of flight we can find in modern birds, they all share this trait of having between nine and eleven primary feathers,&quot; says Kiat. &quot;And I was surprised that no one seems to have found this before.&quot;</p>
<p>&quot;The number of primaries, along with feather symmetry and wing proportions accurately reflect the flight capacity of all known modern birds.</p>
<p>&quot;Looking at fossils up to 160-million-years-old the researchers identified which bird ancestors shared these traits, and were therefore likely to have been able to fly. Out of 35 different species of extinct birds, Kiat and O'Conner identified some that had the right feathers for flight, and others that did not.</p>
<p>***</p>
<p>&quot;'It was only recently that scientists realized that birds are not the only flying dinosaurs,&quot; explains O'Connor.</p>
<p>***</p>
<p>&quot;'Our results here seem to suggest that flight only evolved once in dinosaurs,&quot; states O'Connor.</p>
<p>***</p>
<p>&quot;Kiat and O'Connor point out claims suggesting flight evolved multiple times in dinosaurs were based on skeletal data alone.</p>
<p>&quot;'We argue it is impossible to assess flight potential in non-avian pennaraptorans without examining the structure of the feathers forming the wing itself,&quot; they write in their paper.</p>
<p>&quot;They believe we're still missing the earliest stages of wing evolution from our fossil records, so this is unlikely to be the final word in the debate.&quot;</p>
<p>Comment: this seems to solidify the story. Lots of feathered dinosaurs but only one bird ancestor.</p>
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<link>https://agnosticweb.com/index.php?id=45910</link>
<guid>https://agnosticweb.com/index.php?id=45910</guid>
<pubDate>Sun, 25 Feb 2024 15:59:50 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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<title>Evolution: explosion of birds (reply)</title>
<content:encoded><![CDATA[<p>Bechly again presenting the Big Bang of birds:</p>
<p><a href="https://evolutionnews.org/2024/02/fossil-friday-the-big-bang-of-tertiary-birds-and-a-phylogenetic-mess/">https://evolutionnews.org/2024/02/fossil-friday-the-big-bang-of-tertiary-birds-and-a-ph...</a></p>
<p>&quot;Indeed, modern crown group birds appear and diversify so abruptly that it has been called a “Big Bang of Tertiary birds” by some paleo-ornithologists (Feduccia 1995, 2003a, 2014, Ksepka et al. 2017). Some of their colleagues did not like such an explosive view for obvious reasons (e.g. Dyke 2003, van Tuinen et al. 2003), but Alan Feduccia addressed and rebutted all critics (Feduccia 2003b), and emphasized that “a rapid, explosive Tertiary radiation best explains why resolving phylogenetic relationships of modern orders remains intractable.”</p>
<p>***</p>
<p>&quot;Not just that rocks and clocks conflicted, but phylogenomic studies increasingly supported the Big Bang of Tertiary birds so that now molecular trees conflicted with molecular clocks. The Big Bang view was most strongly confirmed by the seminal study of Jarvis et al. (2014), a genome scale phylogenetic analysis by more than 100 authors (!), who found that “even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.” This result was widely reported by the popular science media with sensational headlines about the mapping of the “‘Big Bang’ of Bird Evolution” (AMNH 2014, Duke University 2014, BGI Shenzen 2014, Smithsonian Insider 2014), or as Time Magazine titled “There was a Big Bang for Birds” (Kluger 2014), or “Rapid bird evolution after the age of dinosaurs unprecedented, study confirms” (University of Sydney 2014). Casey Luskin (2014) then also reported for Evolution News how this “massive genetic study confirms birds arose in Big Bang-type of explosion.”</p>
<p>***</p>
<p>&quot;We can conclude that fossil and molecular data conflict in terms of the question when and how quickly modern birds originated, and molecular and morphological data conflict in terms of the reconstruction of the assumed bird tree of life. Why is there such a stark conflict, when Darwinism would naturally predict that different lines of evidence should converge towards one true evolutionary history of birds. Again, a quite obvious explanation could be that there just was no such history, or at least that totally different causal mechanism were at work.</p>
<p>&quot;The most important take home message from this article is this: in spite of the new study by Wu et al. (2024), there is overwhelming evidence, recognized by the vast majority of mainstream experts, that there was an explosive diversification of modern birds (Neoaves) in the Lower Tertiary (Paleogene). There was an abrupt origin, a burst of biological creativity with a genuine Big Bang of modern birds, which is <strong>best explained by an infusion of new information from an intelligent agent outside the system.</strong> What do evolutionary biologists suggest instead? They say that the global collapse of forest ecosystems after the end-Cretaceous impact killed off all arboreal bird lineages and the remaining ground-dwelling ancestors of modern birds experienced a rapid diversification afterwards (Field et al. 2018). Yet another description of the problem, rather than an explanation, which seems to be a recurring theme in evolutionary biology.&quot; (my bold)</p>
<p>Comment: Bechly's approach is that there are many Big Bangs in evolution, based on the fossil record. The bold is ehv whole point of intelligent design theory.</p>
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<link>https://agnosticweb.com/index.php?id=45908</link>
<guid>https://agnosticweb.com/index.php?id=45908</guid>
<pubDate>Fri, 23 Feb 2024 17:23:10 +0000</pubDate>
<category>Evolution</category><dc:creator>David Turell</dc:creator>
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