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As evolutionary biologists slowly kill off Darwinism… hacking down the Tree of Life, even…

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Politicking about what is taught in schools and fronted in textbooks should start to morph into something more rational as key Darwinian assumptions are quietly abandoned. Get this:

Classic evolutionary theory holds that species separate over time. But it’s fuzzier than that – now we know they also merge…

In that southern California classroom, I told my students that once a species diverged from its ancestor – when it became unable to interbreed and form fertile offspring – those branches were separate, forever isolated. But, even as I spoke the words, I knew something wasn’t exactly right.

I was studying phytoplankton at the time. Single-celled creatures such as phytoplankton reproduce by cell division, which makes the question of what’s an offspring tricky. When you clone yourself, which one is the ancestor?

Graduate students down the hall in a microbiology lab regularly used viruses to transfer genes from one species to another. And gene shuffling wasn’t just happening by manipulation. I’d heard seminars about how different species of bacteria naturally perform a kind of sexual reproduction called conjugation, transferring genes from one to another. How did that kind of gene-hopping fit into the concept of a branching tree?

What I didn’t know then was that, even as I ambivalently placed the overhead film on the projector, the concept of the tree of life had begun to wilt. Four decades on, it’s morphed entirely.

‘That whole abstraction of evolution as being a tree, we always knew was a little inadequate,’ Rasmus Nielsen, a geneticist at the University of California at Berkeley and co-author of the book An Introduction to Population Genetics (2013), told me by video call. ‘But now we know it’s really inadequate.’

Juli Berwald, “The web of life” at Aeon (April 5, 2022)

And she can apparently keep her job. Wow.

You may also wish to read: A physicist looks at biology’s problem of “speciation” in humans

20 Replies to “As evolutionary biologists slowly kill off Darwinism… hacking down the Tree of Life, even…

  1. 1
    BobRyan says:

    They rely on evidence that was never there. Darwin’s dilemma remains problematic, only more so with less time. Not a single transitional fossil between completed species has been found. Speciation has never been witnessed by anyone.

    It is the only “theory” called fact. All other theories, including Big Bang, make it clear theories are not fact, but observances based on known facts.

    It is dogmatic, not scientific.

  2. 2
    DonaldM says:

    Rob wrote: “It is the only “theory” called fact. All other theories, including Big Bang, make it clear theories are not fact, but observances based on known facts. ”
    I’ve often said that evolution is a yet to be confirmed hypothesis. There are parts of evolutionary theory that are well confirmed, ie adaption. But the main parts of how natural selection acting on random variations accounts for the full tree of life…that’s still a working hypothesis needing confirmation, and many bits of it have been falsified.
    But that doesn’t stop the big guns of Darwinism, like Dawkins for example, from saying things like “evolution is as well established as gravity”. Funny, I never hear a physicist say that gravity is as well established as evolution.

  3. 3
    bornagain77 says:

    Of related note to killing off Darwin’s tree of life:

    Sara Walker and Her Crew Publish the Most Interesting Biology Paper of 2022 (So Far, Anyway)
    Paul Nelson – April 5, 2022
    Excerpt: We’ve just ended the first quarter of the year. It’s a long way to New Year’s Eve 2022. But this new open access paper from senior author Sara Walker (Arizona State) and her collaborators will be hard to top, in the “Wow, that is so interesting!” category.,,,
    The lesson that Gagler et al. 2022 draw from this discovery? The pattern is NOT due to material descent from a single common ancestor, LUCA. Indeed, under the heading, “Universality in Scaling of Enzyme Function Is Not Explained by Universally Shared Components,” they explain that material descent from LUCA would entail shared “microscale features,” meaning “specific molecules and reactions used by all life,” or “shared component chemistry across systems.” ,,,
    But what Gagler et al. 2022 found was a macroscale pattern, “which does not directly correlate with a high degree of microscale universality,” and “cannot be explained directly by the universality of the underlying component functions.”
    https://evolutionnews.org/2022/04/sara-walker-and-her-crew-publish-the-most-interesting-biology-paper-of-2022-so-far-anyway-2/

    Also of related note to killing off Darwin’s tree of life

    New Paper by Winston Ewert Demonstrates Superiority of Design Model – Cornelius Hunter – July 20, 2018
    Excerpt: Ewert’s three types of data are: (i) sample computer software, (ii) simulated species data generated from evolutionary/common descent computer algorithms, and (iii) actual, real species data.
    Ewert’s three models are: (i) a null model which entails no relationships between any species, (ii) an evolutionary/common descent model, and (iii) a dependency graph model.
    Ewert’s results are a Copernican Revolution moment. First, for the sample computer software data, not surprisingly the null model performed poorly. Computer software is highly organized, and there are relationships between different computer programs, and how they draw from foundational software libraries. But comparing the common descent and dependency graph models, the latter performs far better at modeling the software “species.” In other words, the design and development of computer software is far better described and modeled by a dependency graph than by a common descent tree.
    Second, for the simulated species data generated with a common descent algorithm, it is not surprising that the common descent model was far superior to the dependency graph. That would be true by definition, and serves to validate Ewert’s approach. Common descent is the best model for the data generated by a common descent process.
    Third, for the actual, real species data, the dependency graph model is astronomically superior compared to the common descent model.
    Where It Counts
    Let me repeat that in case the point did not sink in. Where it counted, common descent failed compared to the dependency graph model. The other data types served as useful checks, but for the data that mattered — the actual, real, biological species data — the results were unambiguous.
    Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent.
    Darwin could never have even dreamt of a test on such a massive scale. Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other.
    We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand.
    Ten thousand is a big number. But it gets worse, much worse.
    Ewert used Bayesian model selection which compares the probability of the data set given the hypothetical models. In other words, given the model (dependency graph or common descent), what is the probability of this particular data set? Bayesian model selection compares the two models by dividing these two conditional probabilities. The so-called Bayes factor is the quotient yielded by this division.
    The problem is that the common descent model is so incredibly inferior to the dependency graph model that the Bayes factor cannot be typed out. In other words, the probability of the data set, given the dependency graph model, is so much greater than the probability of the data set given the common descent model, that we cannot type the quotient of their division.
    Instead, Ewert reports the logarithm of the number. Remember logarithms? Remember how 2 really means 100, 3 means 1,000, and so forth?
    Unbelievably, the 10,064 value is the logarithm (base value of 2) of the quotient! In other words, the probability of the data on the dependency graph model is so much greater than that given the common descent model, we need logarithms even to type it out. If you tried to type out the plain number, you would have to type a 1 followed by more than 3,000 zeros. That’s the ratio of how probable the data are on these two models!
    By using a base value of 2 in the logarithm we express the Bayes factor in bits. So the conditional probability for the dependency graph model has a 10,064 advantage over that of common descent.
    10,064 bits is far, far from the range in which one might actually consider the lesser model. See, for example, the Bayes factor Wikipedia page, which explains that a Bayes factor of 3.3 bits provides “substantial” evidence for a model, 5.0 bits provides “strong” evidence, and 6.6 bits provides “decisive” evidence.
    This is ridiculous. 6.6 bits is considered to provide “decisive” evidence, and when the dependency graph model case is compared to comment descent case, we get 10,064 bits.
    But It Gets Worse
    The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450.
    In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450.
    We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data.
    https://evolutionnews.org/2018/07/new-paper-by-winston-ewert-demonstrates-superiority-of-design-model/

  4. 4
    Silver Asiatic says:

    And she can apparently keep her job. Wow.

    Yes it’s amazing. She says that evolution taught one thing (it was never presentedas an option. No alternative ideas were permitted: “there are no weaknesses in evolutionary theory”. But with contradictory findings she says: “Four decades on, it’s morphed entirely”.
    “Morphed” is the key word here. That’s how they can all keep their jobs and maintain the respect from each other and the media and the public. The theory just ‘morphs’ every once in a while. Not a big problem at all.

    Then the gentleman interviewed says:

    ‘That whole abstraction of evolution as being a tree, we always knew was a little inadequate,’ Rasmus Nielsen, a geneticist at the University of California at Berkeley and co-author of the book An Introduction to Population Genetics (2013), told me by video call. ‘But now we know it’s really inadequate.’

    He’s got the classic defense mastered: “We always knew this”. Thus, the believing public will think that the researchers are clearly very smart. They knew that the old-ideas were false decades ago. In fact, they always knew the tree of life was wrong. But,, they forced the public to believe it was correct, meanwhile knowing it was “a little inadequate”. I don’t recall that phrase in the caption to any of the thousands of tree of life diagrams students had to study.
    But now, the tree of life still hasn’t been falsified. The term “falsification” when applied to Darwin is not appropriate. Nobody should say it. Instead, he says “But now we know it’s really inadequate.”

    It’s never “wrong”, but just “really inadequate”. This means that the tree of life is still good enough to use in textbooks.

  5. 5
    Seversky says:

    If kf can quote Lewontin ad nauseam then I see no reason why we can’t do the same for Gould, courtesy of Laurence Moran:

    When non-biologists talk about biological evolution they often confuse two different aspects of the definition. On the one hand there is the question of whether or not modern organisms have evolved from older ancestral organisms or whether modern species are continuing to change over time. On the other hand there are questions about the mechanism of the observed changes… how did evolution occur? Biologists consider the existence of biological evolution to be a fact. It can be demonstrated today and the historical evidence for its occurrence in the past is overwhelming. However, biologists readily admit that they are less certain of the exact mechanism of evolution; there are several theories of the mechanism of evolution. Stephen J. Gould has put this as well as anyone else:

    In the American vernacular, “theory” often means “imperfect fact”–part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus the power of the creationist argument: evolution is “only” a theory and intense debate now rages about many aspects of the theory. If evolution is worse than a fact, and scientists can’t even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): “Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science–that is, not believed in the scientific community to be as infallible as it once was.”
    Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world’s data. Theories are structures of ideas that explain and interpret facts. Facts don’t go away when scientists debate rival theories to explain them. Einstein’s theory of gravitation replaced Newton’s in this century, but apples didn’t suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin’s proposed mechanism or by some other yet to be discovered.

    Moreover, “fact” doesn’t mean “absolute certainty”; there ain’t no such animal in an exciting and complex world. The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us falsely for a style of argument that they themselves favor). In science “fact” can only mean “confirmed to such a degree that it would be perverse to withhold provisional consent.” I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.

    Evolutionists have been very clear about this distinction of fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred. Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory–natural selection–to explain the mechanism of evolution.

    – Stephen J. Gould, ” Evolution as Fact and Theory”; Discover, May 1981

    Also, just to show Lewontin did actually write other things apart from the passage we all love and know so well. Moran quotes this in the same article:

    It is time for students of the evolutionary process, especially those who have been misquoted and used by the creationists, to state clearly that evolution is a fact, not theory, and that what is at issue within biology are questions of details of the process and the relative importance of different mechanisms of evolution. It is a fact that the earth with liquid water, is more than 3.6 billion years old. It is a fact that cellular life has been around for at least half of that period and that organized multicellular life is at least 800 million years old. It is a fact that major life forms now on earth were not at all represented in the past. There were no birds or mammals 250 million years ago. It is a fact that major life forms of the past are no longer living. There used to be dinosaurs and Pithecanthropus, and there are none now. It is a fact that all living forms come from previous living forms. Therefore, all present forms of life arose from ancestral forms that were different. Birds arose from nonbirds and humans from nonhumans. No person who pretends to any understanding of the natural world can deny these facts any more than she or he can deny that the earth is round, rotates on its axis, and revolves around the sun.
    The controversies about evolution lie in the realm of the relative importance of various forces in molding evolution.

    – R. C. Lewontin “Evolution/Creation Debate: A Time for Truth” Bioscience 31, 559 (1981) reprinted in Evolution versus Creationism, op cit.

    So, yes, evolution is both fact and theory.

  6. 6
    kairosfocus says:

    Sev, it seems that the root irritation is that Lewontin let the cat out of the bag, which you do not wish to be reminded of rather than addressing. Duly noted. KF

  7. 7
    bornagain77 says:

    Sev, quoting Gould, claims that, “So, yes, evolution is both fact and theory.”

    LOL, Darwinian evolution does not even qualify as a good ‘just-so story’. 🙂

    also per Gould,

    Sociobiology: The Art of Story Telling – Stephen Jay Gould – 1978 – New Scientist
    Excerpt: Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers “Just So stories”. When evolutionists study individual adaptations, when they try to explain form and behaviour by reconstructing history and assessing current utility, they also tell just so stories – and the agent is natural selection.
    Virtuosity in invention replaces testability as the criterion for acceptance.
    https://books.google.com/books?id=tRj7EyRFVqYC&pg=PA530

    “… another common misuse of evolutionary ideas: namely, the idea that some trait must have evolved merely because we can imagine a scenario under which possession of that trait would have been advantageous to fitness… Such forays into evolutionary explanation amount ultimately to storytelling… it is not enough to construct a story about how the trait might have evolved in response to a given selection pressure; rather, one must provide some sort of evidence that it really did so evolve. This is a very tall order.…”
    — Austin L. Hughes, The Folly of Scientism – The New Atlantis, Fall 2012

    Further note:

    Top Ten Questions and Objections to ‘Introduction to Evolutionary Informatics’ – Robert J. Marks II – June 12, 2017
    Excerpt: “There exists no model successfully describing undirected Darwinian evolution. Hard sciences are built on foundations of mathematics or definitive simulations. Examples include electromagnetics, Newtonian mechanics, geophysics, relativity, thermodynamics, quantum mechanics, optics, and many areas in biology. Those hoping to establish Darwinian evolution as a hard science with a model have either failed or inadvertently cheated. These models contain guidance mechanisms to land the airplane squarely on the target runway despite stochastic wind gusts. Not only can the guiding assistance be specifically identified in each proposed evolution model, its contribution to the success can be measured, in bits, as active information.,,,”,,, “there exists no model successfully describing undirected Darwinian evolution. According to our current understanding, there never will be.,,,”
    https://evolutionnews.org/2017/06/top-ten-questions-and-objections-to-introduction-to-evolutionary-informatics/
    Robert Jackson Marks II is an American electrical engineer. His contributions include the Zhao-Atlas-Marks (ZAM) time-frequency distribution in the field of signal processing,[1] the Cheung–Marks theorem[2] in Shannon sampling theory and the Papoulis-Marks-Cheung (PMC) approach in multidimensional sampling.[3] He was instrumental in the defining of the field of computational intelligence and co-edited the first book using computational intelligence in the title.[4][5]
    – per wikipedia

  8. 8
    martin_r says:

    Donald @2

    But that doesn’t stop the big guns of Darwinism, like Dawkins for example, from saying things like “evolution is as well established as gravity”. Funny, I never hear a physicist say that gravity is as well established as evolution.

    Dawkins should see this:

    A theory that challenges Newton’s and Einstein’s gravity and nixes dark matter passed its first test

    https://qz.com/876531/a-theory-that-challenges-newtons-and-einsteins-gravity-and-nixes-dark-matter-passed-its-first-test/

  9. 9
    martin_r says:

    Silver Asiatic @4

    Great post … so true…

  10. 10
    Silver Asiatic says:

    Martin – thanks.
    I was going to start going through Gould’s opinions about evolution as both fact and theory but there’s too much deception packed into just a few paragraphs. They’ll say evolution is a fact. It’s antibiotic resistance. But they don’t tell us they’re really claiming that bacteria evolved into every living species including humans. Then when observed evidence is impossible to explain, they’ll say that evolution is a theory after all, so it can’t be expected to be treated as a fact.

    Here’s a little bit of that word game played by Lewontin:

    It is a fact that all living forms come from previous living forms.

    There we have it. Lewontin says it’s a fact that all living forms came from previous living forms. So, the first life on earth must have come from God.
    That’s what I thought all along, glad to hear him finally admit it.

  11. 11
    Fasteddious says:

    SA @4: I was thinking the same think when I read that part!

  12. 12
    Fasteddious says:

    Sev @5:
    Dancing among the various definitions of “evolution” does not help your cause, it merely tries to obfuscate the situation. Here are various possible definitions:
    – change through geological time (fossil record) = ID accepted fact
    – minor shifts in allele frequencies within a population = ID accepted fact
    – “origin of the species”, per Darwin (just so stories) = controversial at best, more likely impossible
    – random mutation plus natural selection to yield new features = highly limited results
    – common descent and the “tree of life” = ID may accept, but controversial
    – development of new phyla from absent precursors = wishful thinking
    Next time you wave around “evolution is a fact”, you might want to say which evolution you are referring to, or feel free to use your own definition.

  13. 13
    Seversky says:

    So what life-form did God come from?

  14. 14
    Silver Asiatic says:

    Sev

    So what life-form did God come from?

    Exactly – a great question for Mr. Lewontin who proclaimed the “fact”. But that’s what passes for science.

  15. 15
    Fasteddious says:

    There was no mention of God in my post, if that is what you were responding to, Sev.
    Nevertheless, as you have been told often and repeatedly, God did not “come from” anything, but is self-existent and the original source of everything. Yes, that is a “Mystery”, but is a much simpler approach than the numerous mysteries (AKA miracles) inherent in full blown Naturalism (AKA materialism).

  16. 16
    Lieutenant Commander Data says:

    Seversky
    So what life-form did God come from?

    Lennox answer to Dawkins: Who created God? 😆
    https://www.youtube.com/watch?v=tM_sUy9RW-E&t=100s

  17. 17
    Silver Asiatic says:

    Fasteddious

    He was referring to this from Lewontin:

    “It is a fact that all living forms come from previous living forms.”

    So, Sev rightly wanted to know what life-form God came from. Lewontin’s “fact” doesn’t make a lot of sense.

  18. 18
    Seversky says:

    So an eternal God is okay but an eternal Universe is not?

  19. 19
    jerry says:

    an eternal Universe is not?

    An eternal universe exists in time and thus has an infinite number of self contradictions.

    Logic rules it out. Anything possible must have happened.

    The God postulated by Christians does not exist in time and thus, does not have theses same contradictions.

    Again the greatest mystery is existence itself.

    And again I recommend Asimov’s favorite story that he wrote, “The Last Question.”

    This is by far my favorite story of all those I have written.
    After all, I undertook to tell several trillion years of human history in the space of a short story and I leave it to you as to how well I succeeded. I also undertook another task, but I won’t tell you what that was lest l spoil the story for you.
    It is a curious fact that innumerable readers have asked me if I wrote this story. They seem never to remember the title of the story or (for sure) the author, except for the vague thought it might be me. But, of course, they never forget the story itself especially the ending. The idea seems to drown out everything — and I’m satisfied that it should.

    https://www.physics.princeton.edu/ph115/LQ.pdf

  20. 20
    Silver Asiatic says:

    The universe is limited by laws of physics and properties of matter and energy. An infinite universe then falls apart under those constraints. The universe is changing in time, has finite values and does not explain its own existence. It requires a cause.
    Because causes precede their effects and God is the first cause, then nothing can cause God.
    Because God exists before all else and cannot receive being from that which came after He already existed, God is complete in Himself, is not dependent on other substances or entities for existence, is the source and cause of existence of all things, is therefore unchanging and purely actual being and is is the author of the laws of physics and creator of matter and energy.
    So, yes – God is an absolute infinite beyond time and space and matter and energy – the cause of all of those things.
    Whereas the universe is not that, and therefore cannot be infinite and therefore requires a cause.

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