Problems with using RNA to build tree of life

wd400 claims,,,

overturned that result by doing a better job with miRNA and using other data.

and by 'better job' wd400 means doing a better job of 'explaining away' the data than the initial analysis of raw data did, as was pointed out in post 2:

MicroRNAs Still Do Not Support an Evolutionary “Tree of Life” – July 31, 2014 Excerpt: Nature News,,, ended on a despairing note: “For Ken Halanych, an evolutionary biologist at Auburn University in Alabama, today’s paper provides a critical analysis of a method that he has long doubted. Why did microRNAs get so much attention? “Because we are hopeful,” he says. A simple tool to decode how animals have evolved over hundreds of millions of years would certainly be nice — but it is looking unlikely that one exists.” At best, this “explains away” the microRNA mismatch. But if a “simple tool to decode how animals have evolved” does not exist, evolutionists are left with a collection of methods that either disagree with one another, or rely on ad hoc fudge factors to bring the data into agreement with expectations. That’s hardly a good situation to be in for arguing the empirical reliability of any scientific theory. http://www.evolutionnews.org/2014/07/micrornas_still088431.html

And as was also pointed out in post 2, All in all, genetic tree of life studies are a huge embarrassment for Darwinists instead of being any kind of proof for Darwinism that many think that they are:

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

I would like to point out that the, 'annihilation' of Darwin's genetic tree of life, article came out on the very day that Dr. Hillis, a self-proclaimed 'world leading expert' on the genetic tree of life, testified before the Texas State Board Of Education that the genetic tree of life overwhelmingly confirmed gradual Darwinian evolution. One could almost argue it was 'Intelligently Designed' for him to exposed as a fraud on that particular day of his testimony instead of just any other day of the year.

Why Darwin was wrong about the (genetic) tree of life: - 21 January 2009 Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. ."We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?" http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html

bornagain77

Turtles probably aren’t really closer to birds than to lizards and snakes, like RNA studies reported. No one else noticed News is exactly wrong, again? The only recent molecular papers supporting the (turtle lizard),(archosaur)) tree were based on miRNA, the paper in the earlier post overturned that result by doing a better job with miRNA and using other data. So, turtles are closer to birds (and crocs) and it was onl an eariler RNA study that claimed otherwise. wd400

This got me wondering. Just how much RNA does it take to build a tree of life? On each side of the river stood the tree of life, bearing twelve crops of fruit, yielding its fruit every month. And the leaves of the tree are for the healing of the nations (NIV). Mung

It is good to remember Peterson's exact words in his initial assessment of trying to construct evolutionary trees from micro-RNA's;

Phylogeny: Rewriting evolution - Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. - Elie Dolgin - 27 June 2012 Excerpt: “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. "...they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist - Kevin Peterson) Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says. Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885 pdf: http://www.nature.com/polopoly_fs/1.10885!/menu/main/topColumns/topLeftColumn/pdf/486460a.pdf

ENV recently reported on the failed attempt by Darwinists, in this present study, to 'fix' Peterson's initial analysis:

MicroRNAs Still Do Not Support an Evolutionary "Tree of Life" - July 31, 2014 Excerpt: Nature News,,, ended on a despairing note: "For Ken Halanych, an evolutionary biologist at Auburn University in Alabama, today's paper provides a critical analysis of a method that he has long doubted. Why did microRNAs get so much attention? "Because we are hopeful," he says. A simple tool to decode how animals have evolved over hundreds of millions of years would certainly be nice -- but it is looking unlikely that one exists." At best, this "explains away" the microRNA mismatch. But if a "simple tool to decode how animals have evolved" does not exist, evolutionists are left with a collection of methods that either disagree with one another, or rely on ad hoc fudge factors to bring the data into agreement with expectations. That's hardly a good situation to be in for arguing the empirical reliability of any scientific theory. http://www.evolutionnews.org/2014/07/micrornas_still088431.html

And this is certainly not the only time Darwinists have tried to 'fix', i.e. 'explain away', incongruent genetic evidence:

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 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

All in all, genetic tree of life studies are a huge embarrassment for Darwinists instead of being any kind of proof for Darwinism that many think that they are:

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 podcast - Molecular Data Wreak Havoc on (Darwin's) Tree of Life - Casey Luskin - March 2014 http://intelligentdesign.podomatic.com/entry/2014-03-14T16_17_31-07_00 More Fossil-Molecule Contradictions: Now Even the Errors Have Errors - Cornelius Hunter - June 2014 Excerpt: a new massive (phylogenetic) study shows that not only is the problem (for Darwinist) worse than previously thought, but the errors increase with those species that are supposed to have evolved more recently.,,, "Our results suggest that, for Aves (Birds), discord between molecular divergence estimates and the fossil record is pervasive across clades and of consistently higher magnitude for younger clades." http://darwins-god.blogspot.com/2014/06/more-fossil-molecule-contradictions-now.html etc.. etc..

Moreover, there is simply no way to rigidly falsify Darwinism from the genetic evidence since, (besides Darwinism having no rigid mathematical basis in the first place), Darwinists rely on any number of rescue devices, (i.e. 'just so' stories), to prevent Darwinism from ever being falsified from the genetic evidence:

Shark Proteins Contradict the Standard Phylogeny of Vertebrates - Casey Luskin - January 6, 2014 Excerpt: there's almost no dataset that can contradict (falsify) common descent. Every time you find that one trait predicts one phylogeny, and another trait predicts a conflicting phylogeny, you can effect a reconciliation by invoking at will more evolutionary steps of convergent loss or gain of traits, or invoking a host of other ad hoc explanations. In a worst case scenario, if genes were distributed in the most un-treelike manner imaginable, I suppose you could take all the known genes present in the most recent presumed common ancestor of that group, and then simply invoke losses (and gains) of genes to reconcile the observed distribution with a tree. - http://www.evolutionnews.org/2014/01/shark_proteins_080781.html

bornagain77

Perhaps we should go back to looking at gross anatomical features and guesswork. Mung