Startling Result–90% of Animals Less than 200 kya

_{May 28, 2018

Darwinism, Evolutionary biology, extinction, Intelligent Design, Tree of life}

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From PhysOrg this morning, in a study using “DNA bar-codes” (mitochondrial DNA, using a specific gene COI) and conducted around the world, here’s the verdict:

The study’s most startling result, perhaps, is that nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago.

“This conclusion is very surprising, and I fought against it as hard as I could,” Thaler told AFP.

The scientists can’t figure out what might have caused this. They ask:

Was there some catastrophic event 200,000 years ago that nearly wiped the slate clean?

Maybe a “flood”?

About “bar-codes” there’s this:

On the one hand, the COI gene sequence is similar across all animals, making it easy to pick out and compare.

On the other hand, these mitochondrial snippets are different enough to be able to distinguish between each species.

“It coincides almost perfectly with species designations made by specialist experts in each animal domain,” Thaler said.

IOW, this method works, unlike, say, ‘phylogenetic trees’!

Here’s the actual article. I haven’t had time to read it.

Enjoy!

Comments

The press release say 90% of animal species arose 200ka. The paper does not support this claim at all. This new paper says a particular species of yeast have SNPs. I'm finding it very hard to imagine how you think these things are related to each other. Perhaps you are simply an idiot who mistakenly started talking about a subject he knows nothing about but is now somehow unable to stop himself?Amblyrhynchus_{May 29, 2018
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Yes it relates , but you are cherry picking, both show the same exact pattern and the press release clearly says it, however your religious beliefs won’t let you accept the facts , even the paper about yeast that I posted shows that SNPs were prevalent and you dismissed it,so we have an example in non human animals also.jorronet_{May 29, 2018
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It does say that. Though this doesn't relate to anything in the paper in the OP or any claim you made earlier. So... what's all this about, exactly?Amblyrhynchus_{May 29, 2018
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Also the paper I posted says this ; “The comparison of genome content variation and levels of SNPs in domesticated and wild clades (Supplementary Fig. 28) shows higher SNP density (median 0.55% versus 0.41%) and lower genome content variation (median 115 ORFs that are not shared, versus 161 shared ORFs) in wild versus domesticated clades, respectively (Supplementary Fig. 28 and Supplementary Tables 9, 10). These findings suggest a shift in evolutionary mechanisms during the domestication process. The wild clades share similar genome content, and their evolution is mainly driven by the accumulation of SNPs. “jorronet_{May 29, 2018
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Amblyrhynchus; I’m just using what the paper you posted says , but you might not have read it : “Nonhuman animals, as well as bacteria and yeast, are often considered “model sys- tems” whose results can be extrapolated to humans.”jorronet_{May 29, 2018
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Is this some sort of world record attempt: The greatest concentration of error in one sentence? There is one species in this study, they found plenty of evolution, SNVs are not necessarily neutral and they found more than SNVs, the "species problem" has a couple of meanings but it's not clear that any of them relate to this paper or your misunderstanding of it. Now, if you want to slow down the Gish Gallop and get back to the point at hand please do.Amblyrhynchus_{May 29, 2018
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Amblyrhynchus; The species problem, more than 1000 species of yeast in this study and they found no evolution at all, just SNPs ( neutral mutations) , they didn’t evolve . https://www.nature.com/articles/s41586-018-0030-5jorronet_{May 29, 2018
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jorronet, The results don't exist. The things they have claim in the press release/article are not supported by any results in the paper. The finding they do report, that within-species diversity of mtDNA is often (but not always) shallow is well known and easily explained. Worryingly, the authors seem unaware of the basic background to this work. If you can point to a particular result that you think is unexpected or in need or explaining go for it.Amblyrhynchus_{May 29, 2018
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Amblyrhynchus; That is still no refutation, you might disagree with the results but you haven’t pointed where they are wrong except that you don’t like the results.jorronet_{May 29, 2018
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Jorronet
If I’m not mistaken, the authors of the paper used Tajima’s D
You are mistaken. It's pretty odd they didn't, since they are claiming these results are due to bottlenecks, and Tajima D is a test of this claim... Rob Sheldon
The net result of these competing processes of diversity and selection, is almost predictable–homeostasis. Nothing looks too different. Everything looks like it was made 200,000 years ago.
Do you have a citation for this, or are you just making it up as you go along?Amblyrhynchus_{May 29, 2018
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PAV,
Can you point to a phylogenetic tree that everyone is happy with? That was my point. Here, OTOH, there seems to be very good agreement between accepted groupings and genetic evidence.
The vast majority of phylogenetic questions are well-resolved and are agreed on by molecular and morpholgical types. Open an issue of Molecular Phylogenetics and Evolution or another solid mid-level journal and you'll see plenty. If you use press releases or creationists literature to filter the results then of course you'll only hear of the controversial studies. For most part, the remainin controversies relate to the evolutionary histories that are most difficult to recover: ancient rapid speciation giving rise to short internal branches, the ordering of which is difficult to reonstrcut.
I’m not in a position to evaluate the paper; however, what are the implications of “ . . . the time to the most common recent ancestor of mtDNA . . . ” being ‘one or several hundreds of thousands of year’ when it applies to 90% of extant species? Was there a ‘flood’ 200 kya? Wouldn’t that be an acceptable hypothesis? BTW, being Catholic, I have no vested interest in such a scenario since St. Augustine centuries before warned against taking the creation accounts as science. But, again, what are the implications of their findings? Or, are you disputing their findings as well?
There is no evidence for this claim about 90% of species having a mtDNA ancestor at 200ka. I think they are saying ~90% of animals are arthropods, the few arthropods they looked at have mtDNA diversity similar to that of humans, humans had mtDNA ancestor at 200ka so 90% of animals ahve a mtDNA ancestor at 200ka. Shoddy. There really is evidence that within species diversity of mtDNA is shallow (i.e. has pretty recent common ancestors), but that tells you that the effective population size of mtDNA is small and selection affects the whole molecule. There is not a requirement for a bottleneck to generate that pattern.Amblyrhynchus_{May 29, 2018
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Stepping back from this study one step, mitochondrial DNA is not the same as nuclear DNA. The mutation clock for the two DNA is very different, some 20X faster in mitochondria. Likewise, every cell has 1000-2000 mitochondria, and their life cycle includes fission, fusion and biogenesis. Older animals/cells have a different mtDNA than younger cells. Since all this is happening inside the cell, there are two effects superposed on one another---the "diffusion" of the species, and the "diffusion" of the mtDNA within an organism. Since the "DNA barcode" is taking swabs from many cells of single individuals, there is really no way to separate these two diffusion terms. Making things worse, mitochondria are essential for life. There isn't a lot of room for neutral mutations. That means most of the variations seen, actually are selected for. Once again, the aged cells tend to be populated with a mono-culture of mtDNA, having sacrificed their diversity for function. Some argue that this is a Darwinian effect of stress on that particular cell, so it optimizes the mtDNA. Others argue that it is a result of reactive oxygen species created by the necessary mitochondrial function itself, which eliminates the more agressive mtDNA. Whatever the reason, if few of the mutations are neutral, then there is no way to determine the "genetic clock" or age of the mtDNA distribution. The net result of these competing processes of diversity and selection, is almost predictable--homeostasis. Nothing looks too different. Everything looks like it was made 200,000 years ago. So the problem with this paper is not with its conclusion, but with its assumption: novelty is randomly accumulating. And that is probably a lot more damaging to evolutionary theory then saying something dramatic happened 200,000 years ago.Robert Sheldon_{May 29, 2018
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getting warmer ? More precise: all animal species are under 6K YA based on the strongest science (ie the highest probability explanation of the natural observations) as explained in/by RCCF framework for understanding science. 200k RCCF calibrates to just over 4K YA. Not long after the 1656 anno mundi Mabul impacts mass extinction events year that was the cause and effect for The ice ages to set in to begin with.Pearlman_{May 29, 2018
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If I’m not mistaken, the authors of the paper used Tajima’s D, if they considered that the conditions were the right ones for that method, I don’t see why not, a good scientist should consider all the options, now what the critics here should do is finding out if the method was correctly applied .jorronet_{May 29, 2018
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Amblyrhynchus: I had a link in the OP that could have taken you to the paper.
So not sure you assessment of other phylogeny studies adds up to much…
Can you point to a phylogenetic tree that everyone is happy with? That was my point. Here, OTOH, there seems to be very good agreement between accepted groupings and genetic evidence. #######+++++++++++++++++++++++++####### I’m not in a position to evaluate the paper; however, what are the implications of “ . . . the time to the most common recent ancestor of mtDNA . . . ” being ‘one or several hundreds of thousands of year’ when it applies to 90% of extant species? Was there a ‘flood’ 200 kya? Wouldn’t that be an acceptable hypothesis? BTW, being Catholic, I have no vested interest in such a scenario since St. Augustine centuries before warned against taking the creation accounts as science. But, again, what are the implications of their findings? Or, are you disputing their findings as well?PaV_{May 29, 2018
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I recall seeing an interesting formulation for evo-devo that was posted by somebody somewhere here, but can’t locate it now. Has anybody else seen it?OLV_{May 29, 2018
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Perhaps one problem that Rui Diogo doesn’t seem to realize is that the only evo that can be associated with evo-devo is microevolutionary. No matter how much he wants to push the issue in the direction of his preference.OLV_{May 29, 2018
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OT: https://www.researchgate.net/publication/322896948_Where_is_in_2017_the_evo_in_evo-devo_evolutionary_developmental_biologyOLV_{May 29, 2018
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OT: https://natureecoevocommunity.nature.com/users/30647-rui-diogo/posts/29886-where-is-the-evo-in-evo-devo-in-2017OLV_{May 29, 2018
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Moreover, the failure of the reductive materialism of Darwinian evolution to be able to explain the basic form of any particular organism occurs at a very low level. Much lower than DNA itself. In the following article entitled 'Quantum physics problem proved unsolvable', which studied the derivation of macroscopic properties from a complete microscopic description, the researchers remark that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, The researchers further commented that their findings challenge the reductionists' point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description."
Quantum physics problem proved unsolvable: Gödel and Turing enter quantum physics - December 9, 2015 Excerpt: A mathematical problem underlying fundamental questions in particle and quantum physics is provably unsolvable,,, It is the first major problem in physics for which such a fundamental limitation could be proven. The findings are important because they show that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, "We knew about the possibility of problems that are undecidable in principle since the works of Turing and Gödel in the 1930s," added Co-author Professor Michael Wolf from Technical University of Munich. "So far, however, this only concerned the very abstract corners of theoretical computer science and mathematical logic. No one had seriously contemplated this as a possibility right in the heart of theoretical physics before. But our results change this picture. From a more philosophical perspective, they also challenge the reductionists' point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description." http://phys.org/news/2015-12-quantum-physics-problem-unsolvable-godel.html
Thus, even if Darwinists could somehow disingenuously shoehorn the DNA sequences into some-type of preconceived tree-like pattern, that still, since the reductive materialistic foundation of Darwinian evolution is now falsified, would tell us absolutely nothing about how an organism achieves it basis form. In further falsification of the reductive materialistic foundation of Darwinian evolution, advances in Quantum Biology have now also further falsified the reductive materialistic foundation of Darwinian evolution,
Darwinian Materialism vs. Quantum Biology - video https://youtu.be/LHdD2Am1g5Y
As Jim Al-Khalili notes in the following video, Darwinists, with their with their balls and sticks models of molecules, i.e. with their reductive materialistic framework, are not even on the correct theoretical foundation to begin with in order to properly understand molecular biology
Jim Al-Khalili, at the 2:30 minute mark of the following video states, ",,and Physicists and Chemists have had a long time to try and get use to it (Quantum Mechanics). Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can't build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn't really require much in the way of quantum mechanics in the way to explain it." At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state: “To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate matter cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”. Jim Al-Khalili – Quantum biology – video https://www.youtube.com/watch?v=zOzCkeTPR3Q
Thus in conclusion, even though many lines of scientific evidence are devastating to the reductive materialistic presuppositions of Darwinian evolution, Darwinists constantly refuse to accept any empirical falsification of their theory. That refusal to deal forthrightly with empirical evidence against their theory is what makes their theory a pseudoscience instead of a real science. As others critics of Darwinism have often pointed out, Darwinism is a religion not a science.bornagain77_{May 29, 2018
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This paper. as well as the other papers listed in posts 7 an 8, show that the Darwinian expectation that the "comparison of anatomical and DNA sequences (should lead) to the same family tree of organisms" is falsified. As well, the poo pooing of this paper by Darwinists in posts 11, 12, and 14, is yet another example of the unfalsifiable, even pseudoscientific, nature of Darwinian claims:
Darwin’s Theory vs Falsification https://www.youtube.com/watch?v=8rzw0JkuKuQ
Moreover, even if Darwinists were somehow able to shoehorn the DNA sequences into some type of preconceived tree-like pattern, (which they, despite extreme cheery picking of data, have not been able to do),,
“The computer programs that analyze the sequence similarities, or differences, are programmed in advance to generate a tree-like pattern. In other words, the assumption of a common ancestor is built into the way in which the analysis is performed. So there is no way you would get anything other than the conclusion,,, It’s a question begging assumption.” Stephen Meyer – on the Cambrian Explosion – podcast (15:25 minute mark) http://intelligentdesign.podomatic.com/entry/2014-05-30T17_33_15-07_00 Richard Dawkins: How Could Anyone “Possibly Doubt the Fact of Evolution” – Cornelius Hunter – February 27, 2014 Excerpt: Not surprisingly evolutionists carefully prefilter their data. As one paper explained, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.” http://darwins-god.blogspot.com/2014/02/richard-dawkins-how-could-anyone.html Darwin’s Tree of Life is a Tangled Bramble Bush – May 15, 2013 Excerpt: ,,, One whole subsection in the paper is titled, “All gene trees differ from species phylogeny.” Another is titled, “Standard practices do not reduce incongruence.” A third, “Standard practices can mislead.” One of their major findings was “extensive conflict in certain internodes.” The authors not only advised throwing out some standard practices of tree-building, but (amazingly) proposed evolutionists throw out the “uninformative” conflicting data and only use data that seems to support the Darwinian tree: “the subset of genes with strong phylogenetic signal is more informative than the full set of genes, suggesting that phylogenomic analyses using conditional combination approaches, rather than approaches based on total evidence, may be more powerful.”,,, ,,,tossing out “uninformative” data sets and only using data that appear to support their foreordained conclusion. Were you told this in biology class? Did your textbook mention this? http://crev.info/2013/05/darwins-tree-of-life-is-a-tangled-bramble-bush/ That Yeast Study is a Good Example of How Evolutionary Theory Works – Cornelius Hunter – June 2013 Excerpt:,,, The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene. These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes or of the problem that gave the right evolutionary answer. They described those genes as having “strong phylogenetic signal.” And how do we know that these genes have strong phylogenetic signal. Because they give the right (preferred) answer. This is an example of a classic tendency in science known as confirmation bias.,,, http://darwins-god.blogspot.com/2013/06/that-yeast-study-is-good-example-of-how.html
,,, even if Darwinists were somehow able to shoehorn the DNA sequences into some type of preconceived tree-like pattern,,, that still would not tell us how the basic "form" of any particular type of organism was arrived at.
Darwinism vs Biological Form https://www.youtube.com/watch?v=JyNzNPgjM4w
Biological form simply is not reducible to DNA sequences. As Stephen Meyer states at the 5:55 minute mark of the following video, 'you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan.'
‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body-plan. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - Functional Proteins and Information for Body Plans – video – 5:55 minute mark https://youtu.be/hs4y4XLGQ-Y?t=354
bornagain77_{May 29, 2018
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Amblyrhynchus @ 12 - congratulations! It was hard work, wasn't it? I agree, it's a horrible paper: very arm-wavy and the evidence for the claim isn't really well supported. This is where the argument appears:
Mostly synonymous and apparently neutral variation in mitochondria within species shows a similar quantitative pattern across the entire animal kingdom. The pattern is that that most—over 90% in the best characterized groups—of the approximately five million barcode sequences cluster into groups with between 0.0% and 0.5% variance as measured by APD, with an average APD of 0.2%. Modern humans are a low-average animal species in terms of the APD. The molecular clock as a heuristic marks 1% sequence divergence per million years which is consistent with evidence for a clonal stage of human mitochondria between 100,000- 200,000 years ago and the 0.1% APD found in the modern human population [34, 155, 156]. A conjunction of factors could bring about the same result. However, one should not as a first impulse seek a complex and multifaceted explanation for one of the clearest, most data rich and general facts in all of evolution. The simple hypothesis is that the same explanation offered for the sequence variation found among modern humans applies equally to the modern populations of essentially all other animal species. Namely that the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.
The first problem is that if we have an APD of 0.1% and the average for animals is 0.2% then the average species should have speciated 200kya-400kya (if we assume, for the sake of argument, that the rest of the model is correct). Then, even within the 90% there is a lot of variation: a species with a divergence of 0.5% would have an estimated speciation 500kya - 1,000 kya. In addition, if the authors had actually looked at their figures (in particular Fig. 1) they would have seen that the APDs are not tightly clustered around 0.5, indeed most are much lower, suggesting much more recent speciation. And these criticisms can be made before we even consider how awful their argument is that APDs can be used (along with a single estimate of sequence divergence). APDs themselves are a stupid measure for speciation date: it should be obvious that for many pairs of individuals, their divergence is larger than the average, so they would have diverged before speciation(*). This contradicts that authors' contention that between-species divergence is much larger. The maximum divergence would be a better measure, but there are going to be all sorts of problems using that. (*) before someone else points this out: yes, in reality we can very easily find this, for perfectly good biological reasons. But in those case, you wouldn't expect to see much stronger divergence between species.Bob O'H_{May 29, 2018
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Dinosaurs lasted millions & millions of years. Maybe recent animals don’t last long because of climate change. Ok, just kidding.ppolish_{May 28, 2018
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I managed to find the actual paper: http://www.pontecorboli.com/digital/he_archive_articles/he122018/1_Stockle_Thaler.pdf It's remarkabl for how bad it is, and how little evidence there is for the grandiose claims in the press release. Pretty shoddy all around.Amblyrhynchus_{May 28, 2018
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I'm not sure you know what a palaeontologist is?
Most of the phylogenetic tree work I’m familiar with, generally, end up to be quite a mess, with one tree contradicting another. These authors seem to be reporting something quite different here, where clear correlations exist.
Well, you were wrong about this not being a phylogenetic method. So not sure you assessment of other phylogeny studies adds up to much...
All of this, of course, hugely distracts from the authors main point: according to them, “nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago.” Would you like to comment about their conclusion?
It's not one that is informed by knowledge of population genetics or phylogeny.... They seem to confuse the time to the most common recent ancestor of mtDNA with the time at which a species arose. These are different things.Amblyrhynchus_{May 28, 2018
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Amblyrhynchus: You wrote:
It’s absolutely not the case that “‘DNA bar-codes’ match the species definitions of paleontologists”, . . .
From the paper:
The pattern of life seen in barcodes is a commensurable whole made from thousands of individual studies that together yield a generalization. The clustering of barcodes has two equally important features: 1) the variance within clusters is low, and 2) the sequence gap among clusters is empty, i.e., intermediates are not found. Beyond the qualitative descriptor “low” for the variance within species there is a quantitative statement. The average pairwise difference among individuals (APD; equivalent to population genetics parameter ?) within animal species is between 0.0% and 0.5%. The most data are available for modern humans, who have an APD of 0.1% calculated in the same way as for other animals (See Fig. 2 in [34] and Fig. 7 in this paper). The agreement of barcodes and domain experts implies that explaining the origin of the pattern of DNA barcodes would be in large part explaining the origin of species. Understanding the mechanism by which the near-universal pattern of DNA barcodes comes about would be tantamount to understanding the mechanism of speciation.
Most of the phylogenetic tree work I'm familiar with, generally, end up to be quite a mess, with one tree contradicting another. These authors seem to be reporting something quite different here, where clear correlations exist. All of this, of course, hugely distracts from the authors main point: according to them, "nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago." Would you like to comment about their conclusion?PaV_{May 28, 2018
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I’m more impressed with the animals (10%) that have been around for 200k+ years. Cockroaches? Water bears? Wayne Newton?ppolish_{May 28, 2018
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Reviewing The Evolution Revolution, the NCSE Offers Uninformed Criticism that Misses the Point - Lee M. Spetner - January 13, 2016 Excerpt: Some researchers in the life sciences, who are not necessarily knowledgeable about evolution (including Levin), think that the various trees based on different biological systems or on protein- and DNA-sequence data yield the same tree. Life scientists once thought that trees based on anatomy and on the molecular sequences of proteins and DNA would be the same, but they were wrong (Nichols 2001; Degnan and Rosenberg 2006; Degnan and Rosenberg 2009; Heled and Drummond 2010; Rosenberg and Degnan 2010). They thought at least there would be consistency among the trees based on the DNA sequences of different genes, but again they were wrong. They then hoped that if they used the whole genome instead of individual genes, the data might average out and things would be better. In fact, it only made matters worse (Jeffroy et al. 2006; Dávalos et al. 2012). All this is discussed in my book. Levin is mistaken about what he calls the "cornerstone" of the evidence for common descent. He criticizes my rejection of common descent. I reject common descent because it is based on only circumstantial evidence. The drawback to circumstantial evidence is that it needs a valid theory to connect the evidence with the conclusion, and evolutionary theory is invalid, as I explain at length in my first chapter. There is thus no valid evidence for common descent -- and certainly not what Levin calls its "cornerstone." http://www.evolutionnews.org/2016/01/reviewing_the_e102281.html A New Model for Evolution: A Rhizome - May 2010 Excerpt: “Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations.” - Didier Raoult - has been referred to as 'Most Productive and Influential Microbiologist in France' http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html Extinct Four-Eyed Monitor Lizard Busts Myth of a Congruent Nested Hierarchy – Günter Bechly – April 23, 2018 Excerpt: We can safely conclude: it is an epic myth, willingly perpetuated by evolutionary biologists, that the similarities between organisms mostly fall in a hierarchic pattern of nested groups and thus suggest common ancestry and indicate phylogenetic relationship. In reality this claim is contradicted by a flood of incongruences and reticulate patterns that shed doubt on fundamental paradigms of evolutionary biology like the notions of homology and common descent. This inconvenient conflicting evidence is explained away with a pile of ad hoc hypotheses, correlated with more and more contrived and implausible evolutionary scenarios. https://evolutionnews.org/2018/04/extinct-four-eyed-monitor-lizard-busts-myth-of-a-congruent-nested-hierarchy/
Of supplemental note:
(March 2018) 1. The DNA similarity (between chimps and humans) is not nearly as close to 99% as Darwinists have falsely portrayed it to be. 2. Even if DNA were as similar as Darwinists have falsely portrayed it to be, the basic ‘form’ that any organism may take is not reducible to DNA, (nor is the basic ‘form’ reducible to any other material particulars in molecular biology, (proteins, RNAs, etc.. etc.. ,,), that Darwinists may wish to invoke. That is to say, ‘you can mutate DNA til the cows come home’ and you will still not achieve a fundamental change in the basic form of an organism. And since the basic ‘form’ of an organism is forever beyond the explanatory power of Darwinian mechanisms, then any belief that Darwinism explains the ‘transformation of forms’ for all of life on earth is purely a pipe dream that has no experimental basis in reality. 3. To further drive this point home, Dolphins and Kangaroos, although being very different morphologically from humans, are found to have very similar DNA sequences to humans. 4. Where differences are greatest between chimps and humans are in alternative splicing patterns. In fact ., due to alternative slicing, “Alternatively spliced isoforms,,, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,,” and “As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms,,” 5. Although the behavioral differences between man and apes are far greater than many Darwinists are willing to concede, the one difference that most dramatically separates man from apes, i.e. our ability to speak, is the one unique attribute that leading Darwinists themselves admit that they have no clue how it could have possibly evolved, and is also the one attribute that most distinctly indicates that we are indeed ‘made in the image of God’. https://uncommondescent.com/intelligent-design/comparing-human-and-chimp-dna-using-a-software-analogy/#comment-654633 Here is a video playlist of Dr. Giem's series reviewing John Sanford’s new book “Contested Bones”. The book “Contested Bones” (by Christopher Rupe and John Sanford) is the result of four years of intense research into the primary scientific literature concerning those bones that are thought to represent transitional forms between ape and man. This book’s title reflects the surprising reality that all the famous “hominin” bones continue to be fiercely contested today—even within the field of paleoanthropology. “Contested Bones” review by Paul Giem – video playlist https://www.youtube.com/watch?v=e6ZOKj-YaHA&list=PLHDSWJBW3DNU_twNBjopIqyFOwo_bTkXm “The unilineal depiction of human evolution popularized by the familiar iconography of an evolutionary ‘march to modern man’ has been proven wrong for more than 60 years. However, the cartoon continues to provide a popular straw man for scientists, writers and editors alike.” — Tim White, paleoanthropologist, in Current Biology Feb. 2013
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Looking past the primary conclusion of the paper that found “the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.”,,, The paper also adds another major piece of evidence falsifying Darwin's imaginary “tree of life”. Specifically, “1) the variance within clusters is low, and 2) the sequence gap among clusters is empty, i.e., intermediates are not found.,,,”
Why should mitochondria define species? - 2018 Excerpt: The particular mitochondrial sequence that has become the most widely used, the 648 base pair (bp) segment of the gene encoding mitochondrial cytochrome c oxidase subunit I (COI),,,, The pattern of life seen in barcodes is a commensurable whole made from thousands of individual studies that together yield a generalization. The clustering of barcodes has two equally important features: 1) the variance within clusters is low, and 2) the sequence gap among clusters is empty, i.e., intermediates are not found.,,, Excerpt conclusion: , ,The simple hypothesis is that the same explanation offered for the sequence variation found among modern humans applies equally to the modern populations of essentially all other animal species. Namely that the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.,,, https://phe.rockefeller.edu/news/wp-content/uploads/2018/05/Stoeckle-Thaler-Final-reduced.pdf
The preceding study, in over the top fashion, also confirms what Michael Denton had found over 30 years ago in his book “Evolution: A Theory in Crisis”. Specifically, “However, the most striking feature of the matrix is that every identifiable subclass is isolated and distinct. Every sequence can be unambiguously assigned to a particular subclass. No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of another group. Transitional or intermediate classes are completely absent from the matrix. 4”
Cytochrome C Excerpt: If the existence of cytochrome C in “higher forms” of animals is the result of evolution from a common ancestor, then one would expect to see a logical progression. That is, the cytochrome C of an invertebrate (like a worm) would be slightly different from a bacteria. A “primitive” vertebrate (like a fish) would have those same differences, plus a few more. As you progress along the presumed evolutionary path to amphibians, reptiles, mammals, primates, ending with humans, you should see the changes in cytochrome C accumulate. On the other hand, if cytochrome C is a commonly used component employed by a designer, you will not see that logical progression. You will just see minor differences which optimize cytochrome C for that kind of creature.,,, There is a way to distinguish evolution from design at the molecular level. Molecular biologist Michael Denton examined the molecular evidence in detail. He said,,, “,,,Where the fossils had failed and morphological considerations were at best only ambiguous, perhaps this new field of comparative biochemistry might at last provide objective evidence of sequence and of the connecting links which had been so long sought by evolutionary biologists. However, as more protein sequences began to accumulate during the 1960s, it became increasingly apparent that the molecules were not going to provide any evidence of sequential arrangements in nature, but were rather going to reaffirm the traditional view that the system of nature conforms fundamentally to a highly ordered hierarchic scheme from which all direct evidence for evolution is emphatically absent.”,, Dr. Denton then produced several tables and diagrams that show this. He showed, for example, that the cytochrome C in bacteria is 64% different from horses and pigeons, 65% different from tuna and silkmoths, 66% different from wheat, and 69% different from yeast. 2 He left it to the reader to realize that, according to evolutionary theory, one would expect the cytochrome C of a bacterium to be closer to the cytochrome C of a tuna (fish) than a horse (mammal). Furthermore, the horse should have the same mutations as the tuna, plus a few more. This is not what the molecular data shows.,,, Dr. Denton’s Figure 12.1, “The Cytochromes Percent Sequence Difference Matrix” 3, is an abridged version of the 1972 Dayhoff Atlas of Protein Structure and Function Matrix of nearly 1089 entries showing the percent difference between 33 species. Denton’s abridged matrix shows that molecular biologists can easily recognize which cytochrome C sample came from a fish and which came from a mammal. “However, the most striking feature of the matrix is that every identifiable subclass is isolated and distinct. Every sequence can be unambiguously assigned to a particular subclass. No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of another group. Transitional or intermediate classes are completely absent from the matrix. 4” If evolution were true, and creatures gradually evolved from one to another, there should be intermediate forms. Intermediate forms should be found in living creatures, in the fossil record, and in proteins. It should, in at least some cases, be hard to classify things because the boundaries are blurred. (But the boundaries are distinct as would be expected under the Design presupposition) http://scienceagainstevolution.info/v7i10f.htm of supplemental interest Transitional Metals And Cytochrome C oxidase – Michael Denton – Nature’s Destiny (Page 204) https://books.google.com/books?id=CdYpDRY0Z6oC&pg=PA204#v=onepage&q&f=false
Here are a few more references falsifying Darwin's imaginary 'tree of life':
Logged Out - Scientists Can't Find Darwin's "Tree of Life" Anywhere in Nature by Casey Luskin - Winter 2013 Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors. Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,, Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance: • A 1998 paper in Genome Research observed that "different proteins generate different phylogenetic tree[s]."6 • A 2009 paper in Trends in Ecology and Evolution acknowledged that "evolutionary trees from different genes often have conflicting branching patterns."7 • A 2013 paper in Trends in Genetics reported that "the more we learn about genomes the less tree-like we find their evolutionary history to be."8 Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled "Why Darwin Was Wrong about the Tree of Life."9 The author quoted researcher Eric Bapteste explaining that "the holy grail was to build a tree of life," but "today that project lies in tatters, torn to pieces by an onslaught of negative evidence." According to the article, "many biologists now argue that the tree concept is obsolete and needs to be discarded.",,, Syvanen succinctly summarized the problem: "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely. What would Darwin have made of that?" ,,, "battles between molecules and morphology are being fought across the entire tree of life," leaving readers with a stark assessment: "Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."10,,, A 2012 paper noted that "phylogenetic conflict is common, and [is] frequently the norm rather than the exception," since "incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."12,,, http://www.salvomag.com/new/articles/salvo27/logged-out.php The Biological Big Bang model for the major transitions in evolution - Eugene V Koonin - Background: "Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable; http://www.biology-direct.com/content/2/1/21 Darwin’s Tree of Life was uprooted in the Cambrian explosion - March 17, 2014 Excerpt: ,,,The study had sought to determine the evolutionary history of the animal phyla by analyzing fifty genes along seventeen taxa. He hoped that a single, dominant phylogenetic tree would emerge. Rokas and his team reported that “a 5-gene data matrix does not resolve relationships among most metazoan phyla” because it generated numerous conflicting phylogenies and historical signals. Their conclusion was candid: “Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved.”,,, Sean B. Carroll went so far as to assert that “certain critical parts of the TOL [Tree of Life] may be difficult to resolve, regardless of the quantity of conventional data available.” This problem applies specifically to the relationships of many of the animal phyla, where “[m]any recent studies have reported support for many alternative conflicting phylogenies.” Investigators studying the animal tree found that “ a large fraction of single genes produce phylogenies of poor quality” such that in one case, a study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom”,,, Steve Meyer - Darwin’s Doubt (pp. 120–21) https://uncommondescent.com/tree-of-life/darwins-tree-of-life-was-uprooted-in-the-cambrian-explosion/ “In 1965 one of the most important scientist of the last century, Linus Pauling, and biologist Emil Zuckerkandl, considered by some as the father of molecular biology, suggested a way that macroevolution could be tested and proved; If the comparison of anatomical and DNA sequences led to the same family tree of organisms, this would be strong evidence for macroevolution. According to them, only evolution would explain the convergence of these two independent chains of evidence. By implication, the opposite finding would count against macroevolution. So what were the results? Over the past 28 years, experimental evidence has revealed that family trees based on anatomical features contradict family trees based on molecular similarities, and at many points. They do not converge. Just as troubling for the idea of macroevolution. family trees based on different molecules yield conflicting and contradictory family trees. As a 2012 paper published in Biological Reviews of the Cambridge philosophical Society reported, "Incongruence between phylogenies derived from morphological versus molecular analysis, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species". Another paper published the following year in the journal Nature, highlighted the extent of the problem. The authors compared 1,070 genes in twenty different yeasts and got 1,070 different trees. An article in Quanta magazine, reporting on the paper in Nature, highlighted he challenge these findings pose for the Darwinian tree of life: "According to a new study partly focused on yeast, the conflicting picture from individual genes is even broader than scientists suspected. “They report that every single one of the 1,070 genes conflicts somewhat,” said Michael Donoghue, an evolutionary biologist at Yale who was not involved in the study. “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 [types of] yeast,” he said." A New Approach to Building the Tree of Life - June 2013 https://www.quantamagazine.org/a-new-approach-to-building-the-tree-of-life-20130604/ These results aren't what we should expect from a process of blind, gradual macroevolution.,,,, Evolutionary biologist Seirian Sumner describes the emerging problem, "These data are telling us to put to bed the idea that all life is underlain by a common toolkit of conserved genes. Instead, we need to turn our attention to the role of genomic novelty in the evolution of phenotypic diversity and innovation.,,, We can now sequence de novo the genomes and transcriptomes (the genes expressed at any one time/place) of any organism. We have sequence data for algae, pythons, green sea turtles, puffer fish, pied flycatchers, platypus, koala, bonobos, giant pandas, bottle-nosed dolphins, leafcutter ants, monarch butterfly, pacific oysters, leeches…the list is growing exponentially. And each new genome brings with it a suit of unique genes. Twenty percent of genes in nematodes are unique. Each lineage of ants contains about 4000 novel genes, but only 64 of these are conserved across all seven ant genomes sequenced so far. Many of these unique ('novel') genes are proving important in the evolution of biological innovations. Morphological differences between closely related fresh water polyps, Hydra, can be attributed to a small group of novel genes. Novel genes are emerging as important in the worker castes of bees, wasps and ants. Newt-specific genes may play a role in their amazing tissue regenerative powers." - WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? - Life Evolves Via A Shared Genetic Toolkit Seirian Sumner https://www.edge.org/response-detail/25533 - Matti Leisola, Heretic (2018), pages 83-84 and 118-119
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DNA barcoding is explicitly phylogenetic -- you have to make a tree before you can do the barcoding. It's absolutely not the case that "‘DNA bar-codes’ match the species definitions of paleontologists", in part because paleontologists study things that are very difficult to get DNA from... The authors quoted in the OP seem to be quite ignorant of population genetics and the biology of mtDNA. Of course all living members of a species will share a recent common ancestor, that doesn't meant that ancestor is the first of the species.Amblyrhynchus_{May 28, 2018
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