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You Won’t Believe This New Epicycle: Congruence Incongruence is a Powerful Phylogenetic Signal

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Remember how evolution was confirmed by congruence and proven by parsimony? The idea was that different anatomical comparisons lead to the same evolutionary tree. Even at the genetic level, different genes told the same evolutionary story. Similar evolution trees are derived from completely different genes. Such congruence of independent data was predicted by evolution and evolutionists have consistently proclaimed it as a powerful confirmation of the fact of evolution. It is, as evolutionists like to say, a powerful phylogenetic signal. There’s only one problem: all of this is false. It is yet another example of evolution’s theory-laden science where the findings are dictated not by the data but by the doctrine. There is no powerful phylogenetic signal. That is a myth. For when evolutionists construct their phylogenies, they first filter out the anatomical comparisons that don’t cooperate. But that is not enough so after their first try they filter some more. As one evolutionist admitted, “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 [types of] yeast.” And so it is good to see a new paper that admits that data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.  Read more

Comments
ow you have two things that don’t exist: “noise” and “signal” Which is which? Really... If there is signal then of course there is lack of signal, that's called noise. Which is which? What objective criteria are you using to determine there is a signal at all between two fundamentally different classes of organisms? I don't know what "fundamentally different classes of organisms" have to do with it. But phylogenetics is a statistical process, there are various ways to estimate the uncertainty of a phylgenetic estimate. Genes that give well supported trees have signal, those that don't do not. I've never seen the papers you link to, but not PLoS one uses whole genomes sequences with no filtering and very few taxa. I'm not very inclined to believe that sort of paper. That is an amusing statement, considering the “noise” is subjectively identified as the data causing the incongruence But, of course, that's not how signal is measured. You really ought to try an understand the basis of the theory you are so opossed to...wd400
October 9, 2013
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wd400
The approach is not to match gene trees to a “favoured” topology, but to find the gene trees that have phylogenetic signal.
There's no such thing as a "phylogenetic signal". That's only a theoretical construct that comes from inference.
This is a pretty standard practice in science – remove the noisey data and focus on the bits that have signal.
Now you have two things that don't exist: "noise" and "signal" Which is which? What objective criteria are you using to determine there is a signal at all between two fundamentally different classes of organisms? http://www.pnas.org/content/103/26/9929/F2.expansion.html This phylogeny from 2006 based on transposon data placed Humans closer to mice and rats than to dogs http://www.ncbi.nlm.nih.gov/pubmed/17206860 This phylogeny from 2007 found that humans and dogs are more closely related than mice and rats. Please tell me which study was following the phylogenetic signal, and which study was hampered by noise.
The trees were not filtered on their topology, but on how much signal they have. As it happens, when you filter out the noisey data you get rid of some incgrunence. That’s hardly a surprise – noisey data makes for uncertain estimates.
That is an amusing statement, considering the "noise" is subjectively identified as the data causing the incongruence in the first place... and gee, wouldn't you know when you remove the incongruence, the incongruence is removed. Now that's science.lifepsy
October 9, 2013
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semi related: Darwinists Grapple with Findings on Convergent Evolution - podcast http://intelligentdesign.podomatic.com/entry/2013-10-09T14_26_36-07_00bornagain77
October 9, 2013
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So, wouldn’t the “concatenated data set” be the target or “favoured” topology that they measured against No. The trees were not filtered on their topology, but on how much signal they have. As it happens, when you filter out the noisey data you get rid of some incgrunence. That's hardly a surprise - noisey data makes for uncertain estimates. You other quote (I don't know where it's from, so can only guess context) is talking abut something different - conflicting by well supported topologies in gene trees. This is expected to happen, especially when speciation is recent or rapid. That's because population genetic processes like incomplete lineage sorting make gene-trees different than species trees. New methods, like those reviewed in the TREE paper Hunter linked to, can take advantage of population genetic models to reconstruct species trees and even population genetic parameters (like population size) from ancient populations.wd400
October 9, 2013
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You may be completely right - I'm not an expert, but it doesn't seem like a question noise in the signal but rather whether there's the correct tree structure in place. There was some expectation about the pattern that they were going to find -- but were "shocked" that "trees from individual genes were in conflict with the tree based on a concatenated data set". So, wouldn't the "concatenated data set" be the target or "favoured" topology that they measured against? Elsewhere it says:
... if different sets of genes support two different architectures equally, it is much less likely that either structure is accurate.
It's not that there is noisy signal from the genes, but that the architectures or structures are incorrect. When they remove the genes that conflict with their architectures, then you get "the correct tree". That's the way it seems to me, anyway.Silver Asiatic
October 9, 2013
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Cornelius Hunter stated that they’re only taking the samples that match the prediction. I don’t get it. Hunter doesn't get it. The approach is not to match gene trees to a "favoured" topology, but to find the gene trees that have phylogenetic signal. This is a pretty standard practice in science - remove the noisey data and focus on the bits that have signal.wd400
October 9, 2013
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lifepsy -- thanks for your reply. Your sounds sarcastic, but isn't that exactly what they did -- fudge the data? If so, that's why I still can't understand it. As I see this, the researchers blatantly admitted that they were going to bias the sample towards their pre-determined conclusion and disregard information that contradicted it (and such a huge amount was incongruous that they were "shocked"). I don't understand how they could get away with that. I also don't understand why their findings are not a massive problem for evolutionary theory and even for claims of common descent. I think I must be misreading it, or exaggerating something. I don't understand how they could report things like:
“Just about all the trees from individual genes were in conflict with the tree based on a concatenated data set,” says Hilu.
similar methods have produced trees of life that are rife with contradiction
The result, published in Nature in May, was unexpected. Every gene they studied appeared to tell a slightly different story of evolution.
... and how could those statements say nothing at all about the validity or predictive power of evolutionary theory? This just remains just an ordinary bit of science research. And that is aside from the fact that they openly state that they kept only the results that matched their expectations.Silver Asiatic
October 9, 2013
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OT: Study shows alpine swift (bird) can stay aloft for 200 days - Oct. 8, 2013 Excerpt: In analyzing the data captured by the sensors, the researchers found that the test birds stayed in the air at one point for 200 days, covering approximately 10,000 kilometers in the process. This, the researchers report, is the longest flight duration ever recorded by a bird, and is only equaled by some sea-going creatures who need only propel themselves forward—birds of course also have to keep themselves in the air, a process that consumes a lot of energy. Some of the most obvious questions that come to mind regarding the birds are: how do they eat and drink? When do they sleep? Prior research has an answer for the first, they eat what is known collectively as aerial plankton—a mix of fungus spores, small insects, seeds and even bacteria that float about in the sky. The water in their food is apparently enough to sustain the birds indefinitely. As for how and when they sleep, scientists are still divided. Data from the sensors in the study indicated slow-downs, or periods of reduced activity where the birds glided more than flapped, but that clearly isn't enough evidence to prove that the birds were sleeping. Some suggest that the birds, like some other organisms, don't have to sleep, or only do so during certain periods of their lifecycle, such as during mating season. http://phys.org/news/2013-10-alpine-swift-aloft-days.htmlbornagain77
October 9, 2013
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OT: Blood Vessel Cells Can Repair, Regenerate Organs - Oct. 8, 2013 Excerpt: Damaged or diseased organs may someday be healed with an injection of blood vessel cells, eliminating the need for donated organs and transplants,,, the researchers show that endothelial cells -- the cells that make up the structure of blood vessels -- are powerful biological machines that drive regeneration in organ tissues by releasing beneficial, organ-specific molecules.,,, The researchers also found that organs dictate the structure and function of their own blood vessels, including the repair molecules they secrete. Together, the studies show that endothelial cells and the organs they are transplanted into work together to repair damage and restore function,,, "Our work suggests that that an infusion of engineered (immature) endothelial cells could engraft into injured tissue and acquire the capacity to repair the organ,",,, http://www.sciencedaily.com/releases/2013/10/131008152218.htmbornagain77
October 9, 2013
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If the genes supported the model, then they accept them as accurate, if they don’t — then they exclude them. That seems like a very strange way to test results.
Well the researchers already *know* that evolution is true. When you start with your conclusion, it's okay to fudge the data until it is in agreement.lifepsy
October 9, 2013
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I didn't understand this story and the articles related to it. There was little reaction from the usually-outspoken Darwinist commentators. But it seemed like it deserved a lot more attention.
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.
The only thing I was was an attempt to minimize by stressing the word "somewhat". But what about the self-depreciating quote at the end? It seems like something a critic of evolution would say. (???) And does "somewhat" really minimize the fact that every one of the 1070 genes contradicted the expected tree and was incongruent with each other?
The resulting tree was accurate according to standard statistical analysis. But given that similar methods have produced trees of life that are rife with contradiction, Rokas and Salichos decided to delve deeper. They built a series of phylogenetic trees using data from individual yeast genes and employed an algorithm derived from information theory to find the areas of greatest agreement among the trees. The result, published in Nature in May, was unexpected. Every gene they studied appeared to tell a slightly different story of evolution.
"Rife with contradiction"? I guess the answer to that is, "Obviously, evolutionary theory predicts that there will be contradictory findings. That's why it's so powerful."
“Just about all the trees from individual genes were in conflict with the tree based on a concatenated data set,” says Hilu. “It’s a bit shocking.”
I think the concatenated data set is the one built to model common descent, and "just about all the trees" conflicted with that. Really??? Mr. Hilu then says "It's a bit shocking". So, again with the minimizing. I would think that on the scale of emotional values, "a bit shocking" is more than "extremely surprising". Or let's put it this way: he was shocked by what the data shows -- but this is really not a problem, apparently. ???
They concluded that if a number of genes support a specific architecture, it is probably accurate. But if different sets of genes support two different architectures equally, it is much less likely that either structure is accurate. Rokas and Salichos used a statistical method called bootstrap analysis to select the most informative genes.
If the genes supported the model, then they accept them as accurate, if they don't -- then they exclude them. That seems like a very strange way to test results.
In essence, “if you take just the strongly supported genes, then you recover the correct tree,” said Donoghue.
Cornelius Hunter stated that they're only taking the samples that match the prediction. I don't get it.Silver Asiatic
October 8, 2013
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I call it the Darwin of the gaps theory. All roads must lead to Darwin, no matter how logically contradicting they are.wallstreeter43
October 8, 2013
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Another example of the unfalsifiability of Darwinian evolution. Opposite results are both claimed as supporting evidence. It's like the convergent evolution argument. Heads I win. Tails you lose.tjguy
October 8, 2013
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A bit more on the onion test. I think it's possible that the information content to build an organism, whether it leads to building blocks or instructions is still not clear. The notion that DNA is everything is still a popular idea or feeling - even for those that know better. So... another question... 1) Let's call the sum of ALL information for development in an organism is S. The value of which varies per organism {onion, human, rabbit, worm, amoeba..etc..} 2) Let's call the idea of a metric based on an arbitrarily small amount of genetic information as B. e.g. it can be set to equal 100,000 sequence of base pairs or some other number. So, if it was 100k bp, a human's DNA would be approx. 30,000B (3Giga base pairs). 3) Let's call the sum of all the other information that is either (a)NOT contained in an organisms DNA OR (b) it is part of the known coding portion of the organisms DNA as E. i.e. This is all the information that isn't called junk DNA; it is either known coding or nonDNA information involved in developmental information. So, if we assume B is equal to the size of all claimed non coding portions of human DNA, then this follows: For humans S = B + E. For onions S = 5*B + E. For the Onion Test to have any of it's intended meaning, it needs to prove that E is not significantly greater for humans than for the E in onions. For example, it might be that the human S value is ten or twenty times larger than the onion's S value. Leaving the the onion test in tears. :P Even so, I still have an affinity for the idea that the extra DNA could benefit other organisms outside of the onion, or it could make the onion more adaptable to more environments.JGuy
October 7, 2013
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The Onion Test seems more like an argument from ignorance. "Can I explain why an onion needs about five times more non-coding DNA for this function than a human?" Maybe instead ask or explain first why an onion actually has five times more non-coding DNA. From ID, it could be that onion provides nutritional or health benefits to non onions. e.g. of a non onion: a human. :) related: http://www.evolutionnews.org/2011/11/why_the_onion_test_fails_as_an052321.htmlJGuy
October 7, 2013
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Alan, I've heard "just look at the onion" too many times already.Mung
October 7, 2013
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OT: Stephen Meyer continues his reply to Charles Marshall's critique of Darwin's Doubt: To Build New Animals, No New Genetic Information Needed? More in Reply in Charles Marshall - Stephen C. Meyer - October 7, 2013 http://www.evolutionnews.org/2013/10/to_build_new_an077541.htmlbornagain77
October 7, 2013
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Ah mung the mereticious! As Professor Moran can't post here, let me refer you to this post at his blog which may go some way to helping you.Alan Fox
October 7, 2013
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Lot's of "junk DNA" gives a strong signal in proof of evolution. Very little "junk DNA" gives a strong signal in proof of evolution. How much "junk DNA" is "just right"?Mung
October 7, 2013
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