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Darwinian time trees don’t really work

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They are “deeply flawed,” say two researchers:

Two theorists have caused a stir in evolutionary circles, claiming to have proven that Darwinian phylogeny efforts (tree-building) cannot be constrained to one “best” answer. In fact, any proposed tree is no better than an infinity of other trees. They can’t see the tree for the forest. p1 The theorists are Stilianos Louca, biologist at the University of Oregon, and Matthew W. Pennell, evolutionary biologist at the University of British Columbia. Their paper that started the controversy was published in Nature, “Extant timetrees are consistent with a myriad of diversification histories.” A timetree is a phylogenetic tree supposedly calibrated by the appearance and disappearance of organisms. An extant timetree is a timetree calibrated using living organisms. The news from the University of Oregon, “Researchers find flaws in how scientists build trees of life,” sums up the paper’s thesis that “long-used approaches for reconstructing evolutionary paths are deeply flawed.”

Evolution News, “Controversy Arising: Timetrees Unconstrained” at Evolution News and Science Today

The paper is paywalled.

We hope those people’s careers are safe.

The controversy arising about timetrees is something to think about when hearing confident-sounding presentations about the history and evolution of life. When scientists speak glibly about adaptive radiations, early bursts of diversification, global extinctions and all the rest, what do they really know? They weren’t there. They take bits of bone, molecules from eye of newt and bat wing, and conjure up fantastical scenarios of an evolving world of universal common ancestry driven onward and upward by natural selection alone. But if the model is just one of an infinite number of congruent timetrees held together by unrealistic adjustments, the world picture may never have existed except in the crystal ball of the imagination.

Evolution News, “Controversy Arising: Timetrees Unconstrained” at Evolution News and Science Today

Well, sure, but is it safe to say that?

The article goes on to talk about refutations but so far it seems like a civilized discussion. That’s evidence that Darwinism is losing its chokehold on thought.

Comments
Orthomyxo.... don't fight :))) i went to University of Oregon website, look at this, it is brutal: Article title (not my words): "Researchers find flaws in how scientists build trees of life" some brutal quotes (from Darwinians): "In a new paper placed online April 15 ahead of print in the April 23 issue of the journal Nature, they argue that long-used approaches for reconstructing evolutionary paths are deeply flawed." "deeply flawed" :))) "“Our finding casts serious doubts over literally thousands of studies that use phylogenetic trees of extant data to reconstruct the diversification history of taxa, especially for those taxa where fossils are rare, or that found correlations between environmental factors such as changing global temperatures and species extinction rates,”" "thousands of studies" :))))) and this is very brutal: "The results, Louca said, do not invalidate the theory of evolution itself. They do, however, put constraints on what type of information can be extracted from genetic data to reconstruct evolution's path." invalidate of the theory of evolution ? :)))))) it seems, like he thinks that this is so serious, it can eventually invalidate the theory of evolution :)))))) This guy is very brutal :)))) Lets see whether he gets fired :)))) University of Oregon article: https://around.uoregon.edu/content/researchers-find-flaws-how-scientists-build-trees-lifemartin_r
January 17, 2021
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What a mess Darwinism is. Is homology due to common ancestry or convergence? This question up the thread hits right home.EugeneS
January 17, 2021
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So, your position is that "any proposed tree is no better than an infinity of other trees"is not a statement about trees?orthomyxo
January 17, 2021
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LoL! No, it isn't clear at all. YOU are reading something into it that just isn't there. Perhaps you should contact them as I have and ask. They do not think the paper is about estimating trees.ET
January 17, 2021
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What the hell is wrong with you two? Here's the first paragraph of the piece , ,Two theorists have caused a stir in evolutionary circles, claiming to have proven that Darwinian phylogeny efforts (tree-building) cannot be constrained to one “best” answer. In fact, any proposed tree is no better than an infinity of other trees. They can’t see the tree for the forest. It's clear the author thinks the paper is about estimating trees. The paper is not about estimating trees. It doesn't matter how many times that use the word "estimate" of that get the thing being estimate wrong. Why in earth are either of you objecting to surfing so simple ?orthomyxo
January 16, 2021
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The first paragraph doesn't support your claim.ET
January 16, 2021
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Orthomyxo: Two things: first, the word "estimate" in the ENV is used 9 times, of which 7 are direct quotes from the various papers under discussion. When "estimate" is used (I believe they might use the word "estimating") by the author/s of the ENV post, they are basically repeating what the papers' authors were saying. Second, I notice the word "identifiability" has been dropped.PaV
January 16, 2021
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The first paragraph, for a startorthomyxo
January 15, 2021
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Where does the ENV story say "this paper is about how we estimate phylogenetic trees"?ET
January 15, 2021
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I don't how it can be said more plainly PaV, the ENV story days this paper is about how we estimate phylogenetic trees. This paper is not about how we estimate phylogenetic trees.orthomyxo
January 15, 2021
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The question immediately arises: "What is causing these "mechanical forces" to be applied 'where' and 'when' they are applied.?" There has to be a 'feedback' system at work, so, what is 'monitoring' what forces are applied and how and what shapes are being assumed. Conversely, the shapes are influencing cell function/protein formation. That's an awful lot of information. Whence the information?PaV
January 15, 2021
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ET: The thought did cross my mind that Orthomyxo hadn't read the article. I'm guessing that he's already read it and formed an opinion and is giving us his 'remedy' for overcoming the perceived difficulty. I don't find his suggestion satisfactory as the last post indicates.PaV
January 15, 2021
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Orthomyxo: You've characterized this issue as one of "identifiability,' however, the question that I see being posed is this: "If you have an infinite number of models with different variables that can give rise to the your "tree," then why is any model you use a true description of the history you're trying to analyze? In mathematical terms: 1/infinity = 0. That is, each putative "model" has zero probability of being the "right" one. This is problematic if clearly demonstrated since it strongly suggests that there's no real trajectory to evolutionary history as might be expected if NS was truly the guiding force. Remember, we're told that it is NS that makes evolution 'non-random.' These 'experimental' results (simulations) suggest that evolutionary history looks to be 'random.'PaV
January 15, 2021
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I doubt that Ortho read the article on ENVET
January 15, 2021
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Classic example of underdetermination. That's is something many people need to know more about: https://en.wikipedia.org/wiki/UnderdeterminationRalph Dave Westfall
January 14, 2021
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Orthomyxo, the whole Darwinian theory of evolution is a big misunderstanding.martin_r
January 14, 2021
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You’ve addressed what you see as the ‘issue’ in regards to the author’s first paper. However, there was a response made to their claims and to which the authors themselves respond. So, we’re way beyond the first paper.
It's not really an issue with the paper, it's what the paper actually says. The authors would not object to my summary of it. The subsequent papers are about the topic of the first one, so not related to Evolution News and Science's misunderstandings of it.orthomyxo
January 14, 2021
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Here's the original paper from the OSU website. The second paper is on BioArxiv and is publicly accessible. Orthymyxo: You've addressed what you see as the 'issue' in regards to the author's first paper. However, there was a response made to their claims and to which the authors themselves respond. So, we're way beyond the first paper. As to 'identifiability,' this seems to be the same 'identifiability' issues that string theory has. Stipulate a model and there are an infinite number of 'backgrounds' (how you construct the vector space within which your model operates) that can support your model. It appears that the scale of the problems are equally bad.PaV
January 14, 2021
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not to mention viruses... viruses do not fit Darwin's tree of life at all... a quote from a mainstream source Virology.ws, the following is saying a mainstream virologist: "In a phylogenetic tree, the characteristics of members of taxa are inherited from previous ancestors. Viruses cannot be included in the tree of life because they do not share characteristics with cells, and no single gene is shared by all viruses or viral lineages. While cellular life has a single, common origin, viruses are polyphyletic – they have many evolutionary origins." this is interesting: "....Viruses have many evolutionary origins ..." yeah, i can imagine, all looks unique..... yet, NOBODY ON EARTH knows, where all these viruses come from... MANY EVOLUTIONARY ORIGINS ????? SO WHERE ARE HIDING ALL THESE ORIGINS ????martin_r
January 14, 2021
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finally someone takes this subject seriously... finally... in regards to family trees, let me add a quote from a mainstream magazine: "Bats and Dolphins Evolved Echolocation in Same Way" this part is somehow disturbing: "The discovery that molecular convergence can be widespread in a genome is "bittersweet,” Castoe adds. Biologists building family trees are likely being misled into suggesting that some organisms are closely related because genes and proteins are similar due to convergence, and not because the organisms had a recent common ancestor. No family trees are entirely safe from these misleading effects, Castoe says. “And we currently have no way to deal with this.”" let me repeat this one: "No family trees are entirely safe from these misleading effects," Full article: https://www.sciencemag.org/news/2013/09/bats-and-dolphins-evolved-echolocation-same-waymartin_r
January 14, 2021
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The actual funny thing is that the author of the Evolution News and Science Today doesn't understand the paper. This is not about time trees (i..e dated phylogenies) but about inferences drawn from those trees. Specifically about rates of speciation and extinction at different times and in different parts of the tree. The paper shows that if you only use modern species (not fossils) then a given time tree is compatible with infinately-many birth-death models of speciation and extinction, and that sometimes the models in the supported set are quite different from each other (it's worth remembering that data can support infinately many models without supporting all models). In short it is an idenfiablity issue (https://en.wikipedia.org/wiki/Identifiability) about a secod order analysis sometimes performed on time trees.orthomyxo
January 13, 2021
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The funny thing is this: When evolutionists spend decades creating thousands of these alleged trees using (a while back now) organismal characteristics, and (more recently) DNA, and then something like THIS comes along, they don't go back and retract all those papers even though the basis for them is totally undermined. Heck, they'd have to retract entire _journals_.EDTA
January 13, 2021
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