Startling Result–90% of Animals Less than 200 kya

One way to refresh your memory and move beyond your imagining of what was in the paper would be to read it. The figure you making the most of, 90% of animal species having a mrca for mtDNA btween 100ka and 200ka is simply not supported by any analysis at all. Why you feel the need to defend this paper's authors I do not know. To know if the level of diversity was consistent with the strict neutrality of mtDNA variants you would need some independent estimate of the effective population size of each species. They don't have that. FWIW, the fact mtDNA does not usually recombine means it is unlikely to evolve as if it were neutral, as selection effects the whole molecule and drags neutral variants along with it. Amblyrhynchus

Amby: If you are going to pay attention to the figure shouldn’t it come from data by way of some sort of calculation? If my memory serves me well, they make mention that 'neutral theory' would require that a much higher level of variation of mt-DNA be found that the very low levels GenBank returns. I imagine it's a straightforward calculation, almost trivial. PaV

as to: "If you are going to pay attention to the figure shouldn’t it come from data by way of some sort of calculation?" So the results of Mathematics now matter to Darwinists?

Darwinian Evolution vs Mathematics - video https://www.youtube.com/watch?v=q3gyx70BHvA

Mathematics is not a friend to Darwinian presuppositions in the least. Where Darwinian evolution is based on a materialistic view of reality which denies that anything beyond the physical exists, on the other hand, Mathematics, which provides the backbone for all of science, engineering and technology,,, mathematics exists in a transcendent, beyond space and time, (Platonic) realm which is not reducible any possible material explanation. Simply put, Mathematics itself, contrary to the materialistic presuppositions of Darwinists, does not need the physical world in order to exist. And yet Darwinists, although they deny that anything beyond the physical exists, need this transcendent world of mathematics in order for their theory to be considered scientific in the first place. The predicament that Darwinists find themselves in regards to denying the reality of this transcendent, immaterial, world of mathematics, and yet needing validation from this transcendent, immaterial, world of mathematics in order to be considered scientific, should be the very definition of self-refuting.

What Does It Mean to Say That Science & Religion Conflict? - M. Anthony Mills - April 16, 2018 Excerpt: In fact, more problematic for the materialist than the non-existence of persons is the existence of mathematics. Why? Although a committed materialist might be perfectly willing to accept that you do not really exist, he will have a harder time accepting that numbers do not exist. The trouble is that numbers — along with other mathematical entities such as classes, sets, and functions — are indispensable for modern science. And yet — here’s the rub — these “abstract objects” are not material. Thus, one cannot take science as the only sure guide to reality and at the same time discount disbelief in all immaterial realities. https://www.realclearreligion.org/articles/2018/04/16/what_does_it_mean_to_say_that_science_and_religion_conflict.htm An Interview with David Berlinski - Jonathan Witt Berlinski: There is no argument against religion that is not also an argument against mathematics. Mathematicians are capable of grasping a world of objects that lies beyond space and time…. Interviewer:… Come again(?) … Berlinski: No need to come again: I got to where I was going the first time. The number four, after all, did not come into existence at a particular time, and it is not going to go out of existence at another time. It is neither here nor there. Nonetheless we are in some sense able to grasp the number by a faculty of our minds. Mathematical intuition is utterly mysterious. So for that matter is the fact that mathematical objects such as a Lie Group or a differentiable manifold have the power to interact with elementary particles or accelerating forces. But these are precisely the claims that theologians have always made as well – that human beings are capable by an exercise of their devotional abilities to come to some understanding of the deity; and the deity, although beyond space and time, is capable of interacting with material objects. http://tofspot.blogspot.com/2013/10/found-upon-web-and-reprinted-here.html

bornagain77

Amb,

If you are going to pay attention to the figure shouldn’t it come from data by way of some sort of calculation?

You must be new here. :). Allan Keith

Their 90% figure comes, I’m rather sure, from what they see as an almost uniform lack of mt-DNA variation.

If you are going to pay attention to the figure shouldn't it come from data by way of some sort of calculation? Amblyrhynchus

Ambly: Is it "blunt-nosed," as in 'scissors'; or is it "snub-nosed" as in a 'revolver'? PaV

Ambly: I think I've followed their argument fairly well. I think it's simply a matter that you don't agree with them. Their 90% figure comes, I'm rather sure, from what they see as an almost uniform lack of mt-DNA variation. They might be onto something. But, I do agree, they haven't presented it as clearly and forcefully as they might have. But, then again, maybe they're afraid to speak their mind, or their article might be published anywhere. PaV

Origenes, You keep talking about this argument you have presented,but you haven't articulated it at all. Please try to do so in plain English. But bear in mind, we are talking about gene birth, then posts you've linked to are about evolution over 600 million years. Very hard to imagine they are relevant. PaV, This 90% of animals statistics simply isn't supported by anything in the paper. The idea that a recent common ancestor for mtDNA requires a clonal period is simply wrong. These authors are very confused (presumably why this ended up in such an odd little journal), and you're reading of them is only more confused. Amblyrhynchus

Amblyrhynchus (Blunt-Nose)[Viper?]: This is from Stoeckle and Thaler’s July 2014 paper:P

In contrast, direct measurements of mitochondrial mutation rate per generation are roughly similar in animals analyzed so far including organisms with very different population sizes and generation times such as fruit flies and humans [37]. The ad hoc modifications to neutral theory commonly proposed to account for low variation in individual cases, namely, recurrent bottlenecks or selective sweeps, struggle as general mechanisms. If bottlenecks limit variation, then a universal low ceiling implies recent population crashes for all species. This appears unlikely– almost a Noah’s Ark hypothesis–although perhaps long-term climate cycles might cause widespread periodic bottlenecks [38]. If selective sweeps limit variation, then a universal low ceiling implies a dynamic view of evolution, with all species adapting all the time [39], in contrast to the equilibrium model at the core of neutral theory.

This makes clear that they were struggling with the fact that mt-DNA clusters were showing that ‘neutral theory’ did not apply. This is a starting point for them. You’ll also note they reach the same conclusion in 2014 that I did in reading their paper: a “Noah’s Ark hypothesis.” They were obviously uncomfortable with this. From the Conclusion of the 2014 paper:

COI barcode variation within avian species is uniformly low regardless of census population size. This finding directly contradicts a central prediction of neutral theory and is not readily accounted for by commonly proposed ad hoc modifications. As an alternative model consistent with empirical data including the molecular clock, we propose extreme purifying selection, including at synonymous sites, limits variation within species and continuous adaptive evolution drives the molecular clock.

The obvious solution to neutral theory’s failure in regard to mt-DNA was to look for “extreme purifying selection.” And so they take up this view in their current, 2018, paper:

Codons that end in G are underrepresented by a factor of about ten in animal mitochondria. Previously we interpreted the lack of third position G’s in mitochondrial coding sequences is evidence of a role for extreme purifying selection in determining the COI DNA barcoding gap [20] but we now find this argument flawed. On the one hand there appears to be purifying selection against codons that end in G but this apparent selection is similar in neighboring species. With selection against G-ending codons in all animal species it could not be a source of species-specific adaptive peaks. Further insight into the lack of G in the third position follows from a focused review of the wobble hypothesis in the context of mitochondria.

So, the ‘neutral theory’ won’t explain the clustering of mt-DNA, nor will “purifying selection,” at least not for codons ending in G. So, now what? It appears that the authors look to “bottlenecks” as the answer to “speciation.”

Bottlenecks, founder effects, lineage sorting, and gene sweeps decrease genetic diversity in a population [111]. The question is how widespread these effects are in the context of defining animal species and if it is possible distinguish them in other than a rhetorical manner. Here we emphasize the overlap—in fact the near congruence—in the conditions that favor each of these mechanisms.

They quote Mayr---"(originally 1942, here quoted from a reprise based on interviews in 2004 [136])”:

The reduced variability of small populations is not always due to accidental gene loss, but sometimes to the fact that the entire population was started by a single pair or by a single fertilized female. These “founders” of the population carried with them only a very small proportion of the variability of the parent population. This “founder” principle sometimes explains even the uniformity of rather large populations, particularly if they are well isolated and near the borders of the range of the species.

Then, invoking Gould and Eldridge:

Models of allopatric or peripatetic speciation invoke a bottleneck with an additional feature: What emerges from the bottleneck looks or acts differently, i.e., it is a bona fide new species. It may be more frequent that what emerges from a bottleneck looks and acts like a middling representative of what went in.

So, Stoeckle and Thaler are saying it’s just a ‘winnowing down’ of what exists prior to a ‘bottleneck’ that counts. Immediately, they say:

If mitochondria are considered “honorary prokaryotes” then the dominant mode in prokaryotes of frequent processes that lead to clonal outgrowth either by selection or random processes [138] are not counterintuitive. A number of different processes could lead to the mitochondrial sequence becoming clonal. Candidate processes include bottlenecks and lineage sorting on three different levels: Within organelles, among organelles in the same cells, among cells in an organism (particularly in the germ line) and among organisms. Not certain is whether different processes have led to a similar result throughout the animal kingdom or if a single process operates throughout. Occam’s razor, the principle of parsimony, suggests that a single explanation should be considered.

In conclusion, their hypothesis seems to be that ‘speciation’ isn’t the result of either ‘neutral theory’ or of ‘natural selection (purifying)’, but of a kind of mitochondrial “cloning” wherein the mitochondria act as a kind of a “honorary prokaryote.” Hence, the whole notion that “90 percent of animal life, genetically speaking, is roughly the same age” is for Stoeckle and Thaler, an indication that some severe “bottleneck” event occurred within the past 200,000 years. And the lack of ‘neutrally’ induced variation ‘within species’ might represent a very new way of looking at how “speciation” takes place. Hence, their final paragraph:

Mitochondria drive many important processes of life [160-162]. There is irony but also grandeur in this view that, precisely because they have no phenotype, synonymous codon variations in mitochondria reveal the structure of species and the mechanism of speciation. This vista of evolution is best seen from the passenger seat.

Obviously the “grandeur in this view” phrase harkens to Darwin’s original conclusion in the Origin of Species and that Stoeckle and Thaler feel as though they've discovered a new, perhaps "the", mechanism for evolution. PaV

Amblyrhynchus @55 In #44 I quoted your idea of how genes can be explained. The arguments I presented show that your proposal is a non-starter as a full explanation of genes. Moreover, in certain cases, under discussion in GPuccio's OP's, the information jump in gene sequence, during the vertebrate transition, is so large and homology with pre-vertebrates so low, that the distinction between "old" and "new" gene becomes arbitrary. Origenes

In #44 I point out the glaringly obvious, namely that your archetypal fantasy about gene origination is a non-starter due to lack of probabilistic resources and your unwarrented assumption of integrability of new genes.

You'll note this is still not an argument. In 44 you linked to a post about BLAST bitscores and some calculation about the number of mutations occurring in a single population over time. Somehow I'm meant to conclude from this that evolution couldn't happen (?), but even then, none of this has anything to do with the de novo origin of genes. So... yeah. I find it all a little confusing (and, I'll admit, amusing too). Amblyrhynchus

In 45 Amblyrhynchus claims:

"Often the regulation comes before function, actually."

Because of course, as every Darwinists knows, regulating non-function is essential if you ever want to someday regulate function? :)

No Mere Bike Messenger, RNA Code Surpassing DNA in Complexity - March 21, 2017 Excerpt: In short, RNA has graduated from servant to master. The numerous RNA transcripts floating around in the nucleus, once thought to be genetic “noise,” may actually be the performance, like virtuosos in an orchestra bringing static notes written in DNA to life. This huge shift in thinking appears to be deeply problematic for neo-Darwinism. It sounds like a symphony of intelligent design. https://www.evolutionnews.org/2017/03/no-mere-bike-messenger-rna-code-surpassing-dna-in-complexity/

Amblyrhynchus then states:

"Random transcription makes lots of RNA, a few of them have a function."

Actually, RNA transcriptions are "highly non-random",,,

Toppling Another Evolutionary Icon, ENCODE Suggests Endogenous Retroviruses Are Functional - Casey Luskin - September 7, 2015 Excerpt: ENCODE didn't merely study the genome to determine which DNA elements are biochemically active and making RNA. It also studied patterns of biochemical activity, uncovering highly non-random patterns of RNA production--patterns which indicate that these vast quantities of RNA transcripts aren't junk.... ENCODE's results suggest that a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that "the majority of regulatory DNA regions are highly cell type-selective," and "the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types" studied increases. Thus, as two pro-ENCODE biochemists explain, "Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue-specific transcription in human cells." http://www.evolutionnews.org/2015/09/toppling_anothe099111.html

Moreover many classes of RNA transcripts are now shown to have function of some sort.

Shedding light on the 'dark matter' of the genome - May 19, 2016 - University of Toronto Excerpt: What used to be dismissed by many as “junk DNA” is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) — genome’s messages that do not code for proteins — in development and disease.,, ncRNAs come in multiple flavours: there’s rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA’s place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, nor how they do this. The new technology developed by Blencowe’s group has been able to pick up new interactions involving all classes of RNAs and has already revealed some unexpected findings. https://www.sciencedaily.com/releases/2016/05/160519120935.htm

Moreover, Darwinists certainly did not predict that the vast majority of the genome would be transcribed into functionally important RNA transcripts,.

Junk DNA not as worthless as once thought - 07/24/2014 Excerpt: As early as 2007,, Hackermüller, together with a number of colleagues, was able to demonstrate,, practically the entire genome (is transcribed into RNA—a template which normally serves the production of proteins),,, In their latest study,, Hackermüller and his team,, were able to bridge yet another knowledge gap. The transcription of non-coding regions in the genome is precisely regulated by cellular signaling pathways—and on a grand scale: up to 80% of the RNA copies were non-coding. "We did not expect such a magnitude," says Hackermüller. "This is not indicative of a chance product—it is highly likely that the non-coding RNAs perform a similarly important functions to that of protein-coding RNA." http://www.rdmag.com/news/2014/07/junk-dna-not-worthless-once-thought?et_cid=4064233&et_rid=653535995&location=top

In fact, Darwinists presupposed non-functionality for the vast majority of the genome because it was forced on them by the mathematics of population genetics. That is precisely the reason why Dan Graur said that “if the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.”

Dan Graur, Darwin’s Reactionary - June 21, 2017 Excerpt: In 2013, biologist Dan Graur criticized the “evolution-free gospel of ENCODE” and accused its researchers of “playing fast and loose with the term ‘function,’ by divorcing genomic analysis from its evolutionary context.”81 In a lecture at the University of Houston, Graur argued that “if the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.” In other words: “If ENCODE is right, then evolution is wrong.” But for Graur, evolution can’t be wrong. His solution to the problem? “Kill ENCODE.”82,,, Lots of evolutionists think that way but only the rare Darwinian atheist materialist is willing to state the matter as nakedly as this. No wonder Dr. Graur is among a list of individuals thanked by Dr. Wells in his Acknowledgments for “making embarrassingly candid or unwittingly humorous statements.” https://evolutionnews.org/2017/06/dan-graur-darwins-reactionary/

Amblyrhynchus then states:

"In general, young genes don’t have especially complex function,"

Actually, many 'young' genes are shown to have essential functions.

Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm

Amblyrhynchus then states:

"many of them make proteins that don’t fold in the way we are used to, for example."

Amblyrhynchus then links to Intrinsically Disordered Proteins (IDPs). IDPs are not as friendly to Darwinian concerns as Amblyrhynchus seems to believe.

Unfolded 'junk' Proteins have function - April 2014 Excerpt: In 2013 functions were identified for many of these (unfolded) “intrinsically disordered proteins” (IDPs), as they are sometimes called. Functions such as crucial roles in regulating ion channels and molecular hubs in intracellular signaling networks. A friend points us to: [1] Bozoky Z, Krzeminski M, Chong PA, Forman-Kay JD (2013) Structural changes of CFTR R region upon phosphorylation: A plastic platform for intramolecular and intermolecular interactions. FEBS J 280:4407-4416. doi:10.1111/febs.12422 [2] Ferreon ACM, Ferreon JC, Wright PE, Deniz AA (2013) Modulation of allostery by protein intrinsic disorder. Nature 498:390-394. doi:10.1038/nature12294 [3] Cumberworth A, Lamour G, Babu MM, Gsponer J (2013) Promiscuity as a functional trait: Intrinsically disordered regions as central players of interactomes. Biochem J 454:361-369. doi:10.1042/BJ20130545 https://uncommondesc.wpengine.com/intelligent-design/junk-proteins-hit-the-antiques-road-show-and/

Amblyrhynchus said ID was similar to a "Cargo Cult" which is interesting claim for him to make since he is the one that is found to be pretending that he has real evidence of some sort that will fly instead of him actually having any real evidence that will actually fly. https://cdn3.omidoo.com/sites/default/files/imagecache/full/images/bydate/201507/cargo-cult.jpg The shoe is squarely on the other foot, "Cargo Cult", is an extremely apt phrase for the unfalsifiable pseudoscience of Darwinian evolution

Darwin’s Theory vs Falsification https://www.youtube.com/watch?v=8rzw0JkuKuQ

bornagain77

Amblyrhynchus @ In #44 I point out the glaringly obvious, namely that your archetypal fantasy about gene origination is a non-starter due to lack of probabilistic resources and your unwarrented assumption of integrability of new genes.

Amblyrhynchus: No argument has been presented to me. ...

Well, good for you.

Amblyrhynchus: As I say, it’s an amazing place.

Don't worry, you will be escorted back to where you belong very soon. Origenes

Amb, no argument has been presented? I suspect, you mean no argument you are willing to take seriously. That reaction on your part is, as they say, interesting. KF kairosfocus

of related note to the handle "Amblyrhynchus" : It seems that Amblyrhynchus cristatus, which refers to "Galápagos marine iguana", remains "mutually fertile" with land iguanas which it supposedly separated from some 8–10 million years ago.

(Amblyrhynchus cristatus), Galápagos marine iguana, Excerpt: Researchers theorize that land iguanas (genus Conolophus) and marine iguanas evolved from a common ancestor since arriving on the islands from Central or South America, presumably by rafting.[8][9] The land and marine iguanas of the Galápagos form a clade, and the nearest relative of this Galápagos clade are the Ctenosaura iguanas of Mexico and Central America.[5] The marine iguana diverged from the land iguanas some 8–10 million years ago, which is older than any of the extant Galápagos islands.[10][11] It is therefore thought that the ancestral species inhabited parts of the volcanic archipelago that are now submerged. The two species remain mutually fertile in spite of being assigned to distinct genera, and they occasionally hybridize where their ranges overlap, resulting in the so-called hybrid iguana of South Plaza Island.[12]

In other words,the iguana is, like Darwin's finches, a fairly lame example of adaptation that is falsely claimed as proof for 'Darwinian evolution". And here is a picture of our new troll "Amblyrhynchus": https://depositphotos.com/106907528/stock-photo-the-marine-iguana-amblyrhynchus-cristatus.html Handsome little devil isn't he? :) bornagain77

No argument has been presented to me. PaV took a press release on face value, boranagin pasted a lot of quotes, Rob Sheldon pontificated on... something, jorronet lost the plot, Kaiser strung together a lot of words but produced no meaning and you have linked to giant posts that combine wikipedia-style summaries of particular proteins with some reification of BLAST bit scores to prove... well I'm stilll not sure what they are meant to prove. As I say, it's an amazing place. Amblyrhynchus

Amblyrhynchus: This place is kind of amazing though.

It must feel uncanny being outside the echo chamber. Meanwhile I note that you have failed to address the arguments presented to you. That is, I take it that you understand that your reference to IDP's is irrelevant to the issue of probabilistic resources. Also IDP's are not in any conceivable way an explanation for huge information jumps as we see in the evolutionary history of e.g. Ubiquitin system. Origenes

PaV @ 21 -

Was there a ‘flood’ 200 kya? Wouldn’t that be an acceptable hypothesis?

The flood would have to have lasted 100,000 years, so not really. Bob O'H

when you've seen a cargo cult before it doesn't take long to spot another one. This place is kind of amazing though. Amblyrhynchus

Amblyrhynchus @ Your "judgement" of two large OP's by GPuccio formed within a time frame of 11 minutes. Do not be offended when I say that your judgement has no value whatsoever. Origenes

Those linked posts are... really something. Often the regulation comes before function, acutally. Random transcription makes lots of RNA, a few of them have a function. In general, young genes don't have especially complex function, many of them make proteins that don't fold in the way we are used to, for example. Amblyrhynchus

Amblyrhynchus: So, you have a huge flux in lineage specific transcripts, most of which are doing nothing. Very occasionally, one takes on a biological function and then natural selectio acts to conserve that transcript. When that happen a lineage gains a new gene that will survive into all of its descendants. But the flux is much greatr than the accumulation of new genes.

Wishful thinking. First, we often see information jumps larger than 500 bits, while even the probabilistic resources of bacteria in 4 billion years of natural history, under a hugely optimistic estimate, are well under 140 bits — see here. Second, what are the odds that a new gene sequence can be incorporated by the organism? There are countless biological functions, but any specific organism has no use for the vast majority of them. Moreover, the new sequence needs to be regulated, what is the chance that a functional regulation system just happened to be in place at the advent of the new gene? Origenes

What? Amblyrhynchus

Amb, the issue is the informational import joined to the blind search for needles in a haystack. What is before us is evidence of deeply isolated islands of function -- scattered needles with a lot of haystack between. Where, a Hamming distance of just 500 bits is effectively insuperable for blind search mechanisms and the only empirically warranted cause for such is intelligently directed configuration. Where, 500 bits corresponds to a configuration space of 3.27 * 10^150 possibilities. And while I spoke to species above, the far more key cases are OoL and Oo Body Plans. The former requires 100k - 1,000 k bits, more or less and the latter 10 - 100+ M bits. 100 k bits is a space of 9.99*10^30102. Those are vastly beyond the search resources of our solar system or indeed the observed cosmos; which set a threshold at 500 - 1,000 bits. It does not take a lot of singletons to pass that threshold, and in any case the deep isolation of a lot of folds in AA sequence space is also highly relevant. So, while yes some of the phenomenon is explicable on artifacts, that does not credibly explain it away. Likewise, essentially random transcription etc does not escape the search challenge I outlined. KF kairosfocus

Kaisorfocus, Gene birth and turnover is actually one of my areas of reasarch. The existence of "singleton" genes in newly sequenced genomes is explained by two processes: (a) When we sequence a genome we focus on species that have not close relative already sequenced. The first sea squirt genome had thousands of singletons, but as we have sequanced more of this species relatives we have whittled that number of lineage-specific genes down. So "singleton" genes are partly an artefact of the way we prioritize genome projects, rather than a biologicl result. (b) None the less, there are a suprising (to me) number of totally new genes in some lineages. As we have studies these groups closely, the dynamics of gene birth and death have become clear. There is a lot of essentially random transcription going on in Eukaryotes. As long parrticular sequence motifs are present and chromatin is accessible then transcipts get made. As the sequences underlying these chromatin states and the motifs driving expression drift, the parts of the genome that are randomly transcribed differs among species. So, you have a huge flux in lineage specific transcripts, most of which are doing nothing. Very occasionally, one takes on a biological function and then natural selectio acts to conserve that transcript. When that happen a lineage gains a new gene that will survive into all of its descendants. But the flux is much greatr than the accumulation of new genes. It's a really interesting field at the moment. Amblyrhynchus

Amb, kindly read this: http://vixra.org/pdf/1105.0025v1.pdf , noting from abstract: "The predominant viewpoint appears incompatible with the finding that the sequenced genome of each species contains hundreds, or even thousands, of unique genes - the genes that are not shared with any other species. These unique genes and proteins, singletons, define the very character of every species." Reflect on the implication of isolated islands of function starting at molecular level and moving up through the diversity of body plans, then down to the requisites of a first living, metabolising, von Neumann self replicator using cell. Especially, on implications of codes and regulated, pretty exact stepwise functional processes. KF kairosfocus

I said in 25, the general statement that within-species diversity of mtDNA is generally low is well known and not a new result. But, if you actually read the paper, within species diversity varies beteen 0 and 0.8%, with humans at 0.1%. There is still considerable variation in this number. Precisely nothing you have quote about the yeast paper is about mtDNA, the numbers you have cited are not within-species diversity and the comment you made about the paper in 29 is completely unrelated to this point. Just stop. Amblyrhynchus

1.- For the planet’s 7.6 billion people, 500 million house sparrows, or 100,000 sandpipers, genetic diversity “ is about the same,” he told AFP. 2.- The data is in the paper. 3.- The same as in point 1. jorronet

What is the author's claim? How is it supported by data in the paper? How is it supported by this yeast paper? Amblyrhynchus

Not at all, the paper supports the author’s claim and yeast is just another example, you have not presented anything that proves the paper wrong except your disbelief. jorronet

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

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

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

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

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

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

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/s41586-018-0030-5 jorronet

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

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

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

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

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

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

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

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

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

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

OT: https://www.researchgate.net/publication/322896948_Where_is_in_2017_the_evo_in_evo-devo_evolutionary_developmental_biology OLV

OT: https://natureecoevocommunity.nature.com/users/30647-rui-diogo/posts/29886-where-is-the-evo-in-evo-devo-in-2017 OLV

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

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

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

Dinosaurs lasted millions & millions of years. Maybe recent animals don’t last long because of climate change. Ok, just kidding. ppolish

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

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

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

I’m more impressed with the animals (10%) that have been around for 200k+ years. Cockroaches? Water bears? Wayne Newton? ppolish

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://uncommondesc.wpengine.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

bornagain77

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://uncommondesc.wpengine.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

bornagain77

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

AK: Different methods. PaV

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

Maybe I am missing something, but are they not talking about a phylogenetic tree? Allan Keith

I have been arguing just that for a long while. A new "tree of life" will be shown through genetics. Also shows stasis and clear separation of species. buffalo

polistra:

Conclusion: The mitochondrial patterns aren’t a driving variable. They’re a secondary result, or a signal, of changes that don’t really affect speciesness.

Then how do you explain the fact that the 'DNA bar-codes' match the species definitions of paleontologists. That is, matching mitochondrial DNA to species looks to be a 'best-fit,' unlike phylogenetic trees. The mt-DNA almost seems to be the 'best' definition of species. Any thoughts? PaV

Hmm. We have a wide variety of artifacts (tools, paintings, etc) that are reliably dated back to 1.5 million years BC, using a variety of dating methods. But the current mitochondrial patterns have been stable for only 200k. Conclusion: The mitochondrial patterns aren't a driving variable. They're a secondary result, or a signal, of changes that don't really affect speciesness. polistra