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Evolution: Top notch studies commonly report contradictory genealogies today

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High profile studies in conflict/ Antonis Rokas, Vanderbilt University

A friend thinks confessions don’t get much better than this screed at ScienceDaily for this paper in Nature:

These days, phylogeneticists — experts who painstakingly map the complex branches of the tree of life — suffer from an embarrassment of riches. The genomics revolution has given them mountains of DNA data that they can sift through to reconstruct the evolutionary history that connects all living beings. But the unprecedented quantity has also caused a serious problem: The trees produced by a number of well-supported studies have come to contradictory conclusions.

“It has become common for top-notch studies to report genealogies that strongly contradict each other in where certain organisms sprang from, such as the place of sponges on the animal tree or of snails on the tree of mollusks,” said Antonis Rokas, Cornelius Vanderbilt Chair in Biological Sciences at Vanderbilt University.

And the further back they go, the less reliable the genetic data becomes.

Keep this story in mind when a coworker splinters the table insisting that Darwinian evolution is supported by “mountains of evidence,” or, better yet, “mountains and mountains of evidence,”or even just plain “fact! fact! FACT!”*

What is the mountain of evidence evidence for, specifically? Nothing the next paper won’t overturn, it seems.

*Michael Ruse, Darwinism Defended: A Guide to the Evolution Controversies, (Addison-Wesley, 1982) 1983, Third Printing, p.58. Emphasis Ruse’s.

Here’s the paper’s Abstract:

To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences. – Leonidas Salichos, Antonis Rokas. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature, 2013; 497 (7449): 327 DOI: 10.1038/nature12130

This was first reported over at crev.info - by David Coppedge of JPL Laboratories lawsuite fame. Here is his take on it:
Salichos and Rokas, in their Nature paper, had to resort to postulating rapid periods of diversification and long periods of stasis to keep Darwin’s vision intact against the onslaught of data. The press release continues,
In a study published online May 8 by the journal Nature, Rokas and graduate student Leonidas Salichos analyze the reasons for these differences and propose a suite of novel techniques that can resolve the contradictions and provide greater accuracy in deciphering the deep branches of life’s tree.… “The study by Salichos and Rokas comes at a critical time when scientists are grappling with how best to detect the signature of evolutionary history from a deluge of genetic data. These authors provide intriguing insights into our standard analytical toolbox, and suggest it may be time to abandon some of our most trusted tools when it comes to the analysis of big data sets. This significant work will certainly challenge the community of evolutionary biologists to rethink how best to reconstruct phylogeny,” said Michael F. Whiting, program director of systematics and biodiversity science at the National Science Foundation, which funded the study.
Problem is, the data looks more like a bush than a tree. The record is punctuated by rapid, sudden appearances of organisms. The authors acknowledged the problem of the Cambrian explosion:
In broad terms, Rokas and Salichos found that genetic data is less reliable during periods of rapid radiation, when new species were formed rapidly. A case in point is the Cambrian explosion, the sudden appearance about 540 million years ago of a remarkable diversity of animal species, without apparent predecessors. Before about 580 million years ago, most organisms were very simple, consisting of single cells occasionally organized into colonies. “A lot of the debate on the differences in the trees has been between studies concerning the ‘bushy’ branches that took place in these ‘radiations’,” Rokas said.
Calling this a “paradox,” the researchers found that even within yeast species a thousand genes did not match up to phylogenetic trees generated by standard software methods. The same conflicts were found in larger data sets involving vertebrates and metazoans. In response, they claimed that genetic dating becomes as unreliable as radiometric dating the farther back in time one searches, creating “considerable challenges to existing algorithms to resolve radiations” congruent with Darwin’s presumed ancestral tree. 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.” In conclusion, they had no solid answers for the conflicts. They called on other evolutionists to “to develop novel phylogenomic approaches and markers to more accurately decipher the most challenging ancient branches of life’s genealogy from the DNA record.”
This is scandalous! It’s also old news. Evolutionists have been concocting Darwin trees in spite of the evidence ever since Darwin acknowledged the Cambrian explosion as a real problem that lodged a valid objection to his theory (get the new book Darwin’s Doubt for details, and the film Darwin’s Dilemma). Darwinism is a classic case of Finagle’s Rule #3, “Draw your curves, then plot your data.” Guru Charlie drew his little tree sketch by faith, then sent his disciples out on a hopeless quest to find evidence to support it. Now, here it is May 15, 2013, and these guys are still telling us the tree vision is in conflict with the data! They have to finagle their methods (“novel approaches”) to try to force a match with the uncooperative genes. And here, we saw they are even willing to lie, 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? No; but you hear it here on CEH all the time, because we bring out into the open the dirty deals evolutionists whisper to themselves in the journals.
Please come set us straight and assure us that all the trees are actually very much in agreement, thank you very much, and that all is well with the Darwinian paradigm. That's pretty much right. Except, phylogeny and "Darwinism" aren't really related. The quoted passage is talking about a particular problem for phylogenetic reconstruction: how we deal with ancient and rapid splits (so called "star topologies"). The problem has existed as long as phylognetic reconstructions have been attampted, the only new thing is the among of data we can through at the problem. It turns out these problems are of type such that throwing more data at the problem won't fix it, rather, we need to improve our methods. But jumping from a finding that some of the most difficult areas of phylogenetics remain difficult even with genomic data, to some conclusion about the end of the tree of life would be... silly. wd400
DM: Here. Three days time, eight months and no serious takers. KF kairosfocus
KF in #2 - Where is that challenge mentioned? Not sure I saw that one. Thanks! DonaldM
Joe at 5, THAT is good news indeed. Family court would be even less civilized than it is now if ... ;) News
News, Paternity tests do not use the same DNA sequences that phylogenetics use. The DNA sequence(s) that demonstrate paternity wouldn't show any relationship to chimps. Just sayin' Joe
wd400: Please come set us straight and assure us that all the trees are actually very much in agreement, thank you very much, and that all is well with the Darwinian paradigm. Eric Anderson
I wonder how a paternity hearing would respond to a mess like this. PS, yes, Denyse O'Leary is now writing news again, but don't assume that just because the post is called News that she wrote it. ;) News
Hence, the request in the now almost eight month old 6,000 word free shot at goal UD Darwinist essay challenge, to resolve the TOL. Part of why, doubtless, no serious attempts to date. KF kairosfocus
Logically one would think that the plethora of genomic data would have clarified the family tree rather than make it more confusing. As we go deeper with our understanding of biological systems and how they work, the less credible the Darwinian story becomes. That seems to be true for both the so-called "Tree of Life" as well as irreducibly complex cellular structures. Just as we had with the fossil record, there can be conflicting sequences constructed. The point to be appreciated, however, is that there is nothing in the data itself, whether fossils or genomic data, to tell us which sequence is the actual one, or if there is any actual sequence at all. This problem is simply not going to go away with more data. If anything, it'll get worse for the Darwinian story. (Yes, that's a scientific prediction!) DonaldM

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