BA77 and a vid on FOXP “1/2/3” molecular trees vs Dawkins’ claim of “You get the same family tree”

_{kairosfocus

January 23, 2016

Atheism, Genetics, rhetoric}

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BA77 often posts clips of citations and links here at UD. ~~After a recent noticeable break (we missed you),~~ he has ~~just~~ [–> correction: he posted in a thread some time ago which just got a comment from TJG . . . ] posted a link to a video on objections to prof Dawkins’ claims that FOXP 2 (let me be exact) etc trees give the same structure:

[youtube IfFZ8lCn5uU]

Key clips include a transcript:

Plus, several family trees, such as FOXP1, showing:

With FOXP2:

FOXP3:

The three trees seem to be quite divergent, one putting chimps with squirrels and the like, another putting gorillas on a different branch, and only one putting the three on neighbouring twigs.

This seems to be consistent with the objection that molecular trees are both inconsistent with traditional trees and that they are mutually inconsistent.

So, has Mr Dawkins erred, or is this the grand-daddy of all elaborate Creationist quote mines and hoaxes?

If you assert or imply the latter, what is your evidence? END

Comments

Mung: "I would also say that common descent is what allows us to make sense not just of similarities, but also of dissimilarities." I absolutely agree, as I have tried to explain in detail in my last posts. :)gpuccio_{January 26, 2016
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Eric: You say: "The fact is that no-one has any good knowledge about what it takes to get from organism A to organism B. What we do know is that what it takes is always grossly underestimated by facile, naive evolutionary relationship stories." I must disagree. I believe that I have a very good knowledge about what it takes "to get from organism A to organism B": it takes design, the input of new original functional information. And you may probably agree with that. The point is: when I say that there is strong evidence for CD, in no way I am saying that CD explains the evolution of species. What I am saying is: a) There is CD and b) New species appear by design, and reuse some previous information by CD. IOWs, CD is guided CD, engineered CD. It is like developing Windows 11 by working physically on the code of Windows 10 in a disk which contains that code. IOWs, the designer does not start from scratch to design Windows 11: he takes the code of Windows 10, and changes what has to be changed, writes from scratch what is really new, and keeps what remains more or less the same. Now, if there is some minor error in Windows 10, which is not important for the basic work (let's say a quasi-neutral error), and the designer is not aware of that error, or simply is not really interested in taking the time to correct it, he will "bring" that error into Windows 11. That is evidence of physical descent of Windows 11 from Windows 10. But Windows 11 is a new design, with inertial parts derived from the previous system. OK, I will wait for your comments.gpuccio_{January 26, 2016
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Eric: However, if you read carefully my post #11, you will see that I don't believe that all differences in homologue proteins are due to neutral variation. My point is, some of the differences are certainly due to neutral variation, and my example of myoglobin is a good example of the. Those differences are an argument for CD. But many other differences are due to different functional constraints in different species. That is the case, IMO, with transcription factors. As I have said, usually TFs are made of two different "parts": at least one DNA binding domain, and the rest of the molecule. In general, the DNA binding domain in very conserved. Not so the rest of the protein. Does that mean that only the DNA binding domain is functionally constrained? I don't think so. Usually, the "rest" is the greatest part of the molecule, and often no conserved domains can be recognized there. My point is: TFs are regulatory proteins, which act combinatorially to change the transcriptome not only in different species, but also in different cells of the same species. IOWs, they are master actors of the epigenetic landscape. So, while the DNA binding site works in similar ways in different species, the "rest" regulates different procedures in different species. That's why the "rest" changes so much: not because it is not functional and neutral variation acts on it, but because its functions vary from species to species. So, restricting function to conserved sequences is a potential error. Different functions require different sequences. However, we cannot deny that neutral variation happens: we see it happening even in the human genome, and generating functional polymorphisms, exactly as negative variation generates genetic diseases. We know that not all protein sequence have the degree of functional constraints that we see in histones. Myoglobins certainly behave very differently. Some kinds of proteins can be even less constrained. So, neutral variation, when it is really neutral variation, tells us that proteins pass from one species to another, and bring with them the neutral differences which have accumulated through time. More in next post.gpuccio_{January 26, 2016
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Eric: Thank you for your interesting comments. Discussing CD here is always a little difficult for me, because it seems that I cannot easily explain what I think about the issue. I will try to clarify. I have said many times that, IMO, the strongest argument at the molecular level for CD is not the homologies, but the differences. My point is: I accept that neutral variation happens, if there is not a strong functional constraint which translates into negative (purifying) selection. IOWs, take histone H3, a 136 AAs protein which is practically the same in all eukaryotes: it does not change, except for really trivial differences, throughout something like 1 - 2 billion years (impossible to say exactly when eukaryotes first appeared). Is that an argument for CD? Yes and no. It is an argument for a very strong functional conatrint on histone H3, and if we accept CD it is an argument for extremely strong purifying selection on the protein. IOWs, it is an argument for the designed origin of the protein (a sequence of 136 AAs which has to be, in some way, almost exactly that specific sequence has a lot of functional information in it). But the fans of common design could simply argue that, exactly because there is such a functional constraint, a designer who redesigns each living species can only use that sequence. So, simple strong homology and conservation is not the best argument fro CD. Now, tale myoglobin. Human myoglobin is 154 AAs long. Globins are rather "simple" globular proteins, whose 3D structure is rather well conserved even in presence of great differences in sequence. Now, if we blast human myoglobin against chimp, we have 153/154 identities (99%), expect 2e-108. IOWs, almost the same sequence. And a few million years of chronological split. Let's go to mouse. Against human, we have 129/154 identities (89%), expect 1e-89. The two proteins are still very similar, but less. And we have 80 - 100 million years of chronological split. Let's go to bony fishes. We have 71/149 identities (48%), with an expect of 6e-37. And a time split of about 400 million years. And so on. Now, my point is: these molecules are rather similar. They do more or less the same thing in different species. They have similar 3d structure. OK, there could be different functional constraint to explain some of the sequence differences, but... frankly, the best explanation for the growing differences at sequence level between homologue molecules with the same function and 3d structure is simply: neutral variation through time. And indeed, as the time split grows, so grows the sequence difference. This is a good argument for CD: not the homologies, but the differences in similar molecules, differences which are proportional to time separation between species. OK, this is the first point. I will go on in next post.gpuccio_{January 26, 2016
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Thanks for the compliment (at #23) Dionisio!GaryGaulin_{January 26, 2016
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Eric Anderson
Nobody has a clue how to get from A to Z.
Well, the situation gets even worse when they try to explain in detail how to get from Z* to B**. :) (*) Zygote (**) BirthDionisio_{January 25, 2016
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VJT From Joe's paper cited: Thus, a more stringent and rigorous way to test the common ancestry for more than two proteins would be to model the possible relationships among the proteins, which may conflict. It is plausible, then, that the extra INFORMATION IMPARTED BY A PHYLOGENETIC MODEL MAY FAVOR INDEPENDENT ORIGINS OVER COMMON ANCESTRY, even for a set of proteins with low BLAST E-values. SO INDEPENDENT ORIGINS A POSSIBLE CONCLUSION.... DNA data is just part of the story. Must also look a splicing patterns and gene expression for multi cellular species.bill cole_{January 25, 2016
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Mung, as I said in 20, if we assume common descent, then similarities seem helpful in putting together the tree of descent. But wouldn't it be a little strange to say that similarities are evidence of common descent (because, the thinking goes, certain characteristics will tend to be preserved), but then to ignore the other side of the coin, namely, if there are lots of dissimilarities, then perhaps we do not have common descent. We don't just get to say common descent will produce similarities . . . except when it doesn't. I admit, that is a standard approach in evolutionary thinking, but it is unbecoming anyone who is serious about rational thought. Furthermore, what most people mean when they say "common descent" is a purely naturalistic and materialistic storyline. And it is a storyline without a realistic mechanism, as bill cole notes @25. Obviously some on this site and elsewhere in the Darwinian-skeptical realm take the view that common descent is true, but that some other mechanism, such as front-loading or guided evolution, is in play. Even setting aside for a moment that this desire to conclude common descent is often driven by a philosophical/religious preference, a proposal of some kind of pre-programmed or guided evolution is certainly far preferable to the facile, materialistic evolutionary approach of stuff-happens-and-here-we-are. However, it still begs the question. We are still left with all the dissimilarities and discontinuities, the questionable and contradictory trees. We can't simply ignore them. They are real evidence, just as much as the similarities. Common descent may indeed be true (though we would need to tighten up our definitions a lot to determine whether we are talking about limited common descent, universal common descent, or something else), but there is certainly no known mechanism to go from organism A to B to C to Z. Nobody has a clue how to get from A to Z. Without a realistic mechanism, without knowing how it could occur, and without evidence that such a thing is even possible in the real world, a conclusion of common descent becomes, at very best, a tentative idea. I, for one, am singularly unimpressed with our ability to identify so-called "homologous" characteristics by scouring the realm of nature. Searching for similarities and cataloging and labeling and nesting and drawing trees are interesting exercises, but we must not lead ourselves to believe that they necessarily represent reality.Eric Anderson_{January 25, 2016
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Hi VJT The opinion I shared with Dr Moran about common decent is that it does not have meaning without an identified cause of change or mechanism. Common decent implies that the change happened in nature. If we can mathematically model these changes then common decent becomes a credible argument. Until then it remains an untested hypothesis. I think the evidence is strong for common biochemistry.bill cole_{January 25, 2016
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Eric Anderson and gpuccio Your insightful comments confirm my enormous ignorance. Is the below referenced paper somehow related to your interesting discussion? Maybe not. Based on that paper, could HFGT+epigenetics+DNA recombination gene exchange+RM+NS+T+...+(anything else someone could think of in the future) eventually help to change the mentioned fish spatiotemporal developmental process into the spatiotemporal developmental process for a different kind of biological system? How? Thank you.
Further investigations will lead to a more complete understanding of the biological functions of this gene.
Horizontal functional gene transfer from bacteria to fishes Bao-Fa Sun1, 2 n1, Tong Li3 n1, Jin-Hua Xiao1, Ling-Yi Jia1, Li Liu4, Peng Zhang1, Robert W. Murphy5, Shun-Min He1 & Da-Wei Huang Scientific Reports 5, Article number: 18676 (2015) doi:10.1038/srep18676 http://www.nature.com/articles/srep18676#discussion

Dionisio_{January 25, 2016
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GaryGaulin Thank you for sharing your interesting software here. Seems like an impressive work you've done.Dionisio_{January 25, 2016
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If similarity is evidence for common descent, then is it not the case that dissimilarity should be evidence against common descent? In other words, why do we get to invoke common descent when we see similarity, but don’t question common descent when we see dissimilarity, even significant dissimilarity?
Personally I don't follow the logic that says that if you accept that similarities are explicable in terms of common descent that therefore dissimilarities are evidence against common descent. I would also say that common descent is what allows us to make sense not just of similarities, but also of dissimilarities.Mung_{January 25, 2016
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gpuccio @11:
The interesting thing is that, in this long and highly conserved proteins, only a short conserved domain is clearly recognized: the DNA binding site, about 70 AAs long. That is often the case in transcription factors: only the DNA binding site represents a clearly recognizable and highly conserved domain, while the rest of the molecule is much less understood.
The part I highlighted above is another significant part of the issue. I may be getting cynical, but anytime I hear "poorly understood" or some similar statement with respect to a scientific claim, particularly with respect to evolutionary biology, I can take it to the bank that it means, "not understood at all to the level necessary to draw any rational conclusion," or, more often, "no-one even has a clue about X." The fact is that no-one has any good knowledge about what it takes to get from organism A to organism B. What we do know is that what it takes is always grossly underestimated by facile, naive evolutionary relationship stories. Casting about the whole of biology to find similarities is, to roughly paraphrase David Berlinski, perhaps more useful for keeping cladists employed than for finding actual answers. :)Eric Anderson_{January 25, 2016
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gpuccio: Not necessarily arguing with you at this point, just wanted to get your take and play devil's advocate for a moment. As to this:
I agree with our neo darwinian interlocutors that the evidence for Common Descent is very strong.
If similarity is evidence for common descent, then is it not the case that dissimilarity should be evidence against common descent? In other words, why do we get to invoke common descent when we see similarity, but don't question common descent when we see dissimilarity, even significant dissimilarity? I'm not just talking about so-called homologous genes (a definition based essentially on circular reasoning anyway). What about completely different genes? For example, organism A shares a "homologous" gene with organism B. Common descent, we shout! Yet organism B has, say, a dozen completely unique genes from organism A. Do we acknowledge the significant dissimilarity and infer that there is no way a dozen non-homologous genes could have arisen in only organism B, thus casting doubt on the common descent idea? Or do we just ignore the dissimilarities? Do we bring in some other justification, horizontal gene transfer and such, to salvage the common descent story? The inference to common descent by looking at similar structures, whether genetic or phenotypic, seems to be so heavily invested with the pre-suppositions of (a) common descent, and (b) only purely natural and material causes allowed, that it begs the question as to whether such similarities actually provide evidence for the presuppositions. Unless we are willing to count dissimilarities and discontinuities as evidence against common descent, it seems we should not be saying that similarities constitute evidence that helps prove common descent. What really seems to be happening is that if (a) we assume common descent by purely natural causes is the cause of the organisms we see, including A and B, then (b) we can infer that organism A might have a descent relationship with organism B, because we've stumbled upon an interesting case of similarity.Eric Anderson_{January 25, 2016
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I was able to upload a version that has all the required Fasta files still in it. Each of the .fa files for each ChromoType only needs to be clicked once (then be patient it might take half a minute for the biggest our human 2) to compile to DNA files. It's 294 megs and after unzipping is a 1.7 gigabyte folder named BandChromosomesFromFastaFiles. The .zip file is then no longer needed and can deleted. Since no files are saved or installed outside of the BandChromosomesFromFastaFiles folder deleting it from your hard drive completely removes everything, including illustrations that were saved to the BitMaps folder so first move any you want to keep to a safe place. A downward pointing arrow should be right above for downloading the .zip file at this link: https://drive.google.com/file/d/0ByxeUHZcTIhgazNQcWF0MUJFRnc/view I just downloaded and tried it out, works well on at least my Windows 10 machine. This should make it easier for anyone who wants to get started on their own comparison using the newer fasta file assemblies available for download on the internet. There is also a place to write your name so it will display in the credit line at the bottom left of each bitmap you make. Then please make sure to give me a link so I can show them around to others who would be genuinely interested in seeing your work. This very visual method for comparing the genetic data of chromosomes does not draw a tree showing what came from what and what "split" from another is not shown. Only what we became after long ago going off on our own to become what we now are is shown in the picture. You see what things look like in the year 2016, not what was around when the split occurred. Showing what existed at the time of the chromosomal fusion (estimated to have occurred up to around 6 million years ago or so) should lead to what I can best describe as a backtracking of what all the chromosomes learned over time, leading to a morphing where at some point the next thing that happens is the fusion event never happened and there is suddenly a Human "A" and "B" half to our now single chromosome 2. That would require converting the fasta files to new fasta files, then same way compare the banding. I expect that at the point in time when the Adam and Eve moment occurs the halves they came from would still not exactly match any of the others shown. A common ancestor would still be further back in time, where at that point what we see is more human looking than chimp. Our common ancestor might even have more smarts than chimps now do, but (not to pick on them) it's too early to know for sure what went wrong for their lineage. I'm eager to see what bonobos look like, which is at least a step up in social responsibility and civility skills even though all run around naked while thinking about sex all day. The lack of common human sense to run for clothes certainly rules them out as being described by Genesis. It's in a way funny but according to where the scientific evidence leads that works as an indicator of what our Adam and Eve moment looked like. All of a sudden having 46 chromosome (human) thoughts and a brain that makes the tree of the knowledge of good and evil worth getting kicked out of the more living in trees type Eden that all the other animals are happy with. To us that is a cruel thing to have happen. We even soon enough pave paradise then put up a parking lot, in a way our own worse enemy. But not getting kicked out of that paradise would require us to have been less than we now are, which sets us back to still being an animal happy running around naked all day in a forest like the others. Scientific theory that is this much in agreement with Genesis is at least a big improvement over the Darwinian world view, which normally instead ridicules what I consider to be the oldest of origins theory, even though some call it "scripture". There was not even supposed to an Adam and Eve moment to be found in the scientific evidence. What it takes to go even further is to compare chromosomes and other things that do not require a fancy lab or necessarily writing science papers. And where it came from does not matter, so regardless of your possibly not having academic "credentials" all are now scientifically equal. So no matter who you are, have fun trying to make a PhD+ sized dent in science, of your own. At this point we just need more chromosome comparisons that look at biology from the perspective of intelligence, which should not be all that hard for those who are NOT looking at everything from the perspective of "natural selection" that in this case only stops progress. It's best to not even once mention it, at all.GaryGaulin_{January 25, 2016
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If molecular data means anything then why not just mean a atomic parts department number for a common blueprint from a creator?? Its fine with me to have perfect matches for bio itams that are a match. If a creator did have a common blueprint with a parts department dna number THEN one would predict likeness in dna relative to likeness in parts. Evolutionism is using a line of reasoning that not only denies this option but the better option. In fact Darwin had to defeat the piont in his book and possiblt the modern dna scores would cause him distress and not happiness. We should have almost perfect dna scores with apes because we look almost alike. What else would it be? Yet don't assume the likeness is EVIDENCE SETTLED for common descent. Its not evidence for anything but likeness. its another presumption that connects the dots. Yet another also connects the dots. there is no bio sci evidence for evolution as it never happened. Its funny Dawkins embraces this stuff ass his top evidence. A other error.Robert Byers_{January 24, 2016
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I found it! Software is now at: https://sites.google.com/site/digitalchromosomebanding/home/BandChromosomes.zip To make the size of the zip file small enough to upload to Google the software does not include the fasta (.fa) files the program generated DNA files (.DNA) were made from. The .fa files are available in .gz compressed form here: ftp://ftp.ncbi.nlm.nih.gov/genomes/ For example Human chromosome 2 is at: ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens There may be updated assemblies but the software also used: Pan_troglodytes.CHIMP2.1.4.68.dna.chromosome.2A.fa Pan_troglodytes.CHIMP2.1.4.68.dna.chromosome.2B.fa Gorilla_gorilla.gorGor3.1.68.dna.chromosome.2a.fa Gorilla_gorilla.gorGor3.1.68.dna.chromosome.2b.fa Pongo_abelii.PPYG2.68.dna.chromosome.2a Pongo_abelii.PPYG2.68.dna.chromosome.2b Into the "DNA" folder: decompress the .fa.gz to a folder you created and named, or use the now empty ones files were once in that are already there. The way it works is in the top file list box you select which ChromoType (such as Human or Gorilla) then click on the downloaded .fa file to compile it to a DNA file the program will use. Repeat for all of the chromosomes needed. Human has one. The others have two chromosomes each, a part "A" and "B". After having all the required .DNA files showing up in the middle file list box: select which ChromoTypes to compare together then press the "Create Illustrations" button. The new bitmap will be saved to the "BitMaps" folder. The "Codons" directory contains the text files that the earlier linked to software had generated. Since the code was written in VB6 and Microsoft no longer supports it there is a small chance you will need something no longer shipped with Windows. If there is a problem then please let me know so I can try to work around it, or where necessary rewrite in the newer VB.Net that replaced VB6. There is now a bonobo genome to add to the comparison and other possibilities for this way figuring out what came from what, where when how and why, according to ID. In that case the methodology would be based upon how intelligent systems learn over time, as opposed to selection acting upon this or that approach. A living genetic system then reduces down to sensory, memory (its genome letters that allow reading its mind), confidence (in cells called homeostasis) and motor (protein) force that controls itself and its environment. It's then clear why the "natural selection" variable and all the "evo" words are only useful in Darwinian theory. For cognitive science related work regardless of whether a (multicellular development) human baby or (genetic/molecular development) new species everything "develops" over time, we just have to add a qualifier in front to indicate which intelligence level is being discussed. After this way being as scientifically precise as possible even the word "evolution" is made irrelevant, don't need it. And the "evo-devo" phrase was created after realizing "development" has to be considered, which caused further bloating of the Darwinian model. It in way creates its own science world that has to link back to the real science world that would now still go on just fine without its metaphors.GaryGaulin_{January 24, 2016
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I have to add that there is another program that goes with it to draw the images, which I'm having trouble finding on the computer I now use after the one I wrote the software with broke down. I'll see what I can do to recover the files or find a backup somewhere. It will only make the same images already linked to in my previous reply, but I would like to find it.GaryGaulin_{January 24, 2016
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VJT, it is interesting that it is Dawkins who chose this as his named example and asserted that there were consistent trees across the molecules. Crevo headlines comments revealingly about algorithms (which will doubtless be adjusted over time given what is about to be cited), in the context of the Doolittle & Bapteste PNAS paper I cited above:
Darwin’s “Tree of Life” is a myth. It’s based on circular reasoning. It is a pattern imposed on the data, not a fact emerging from the evidence . . . . Homologies, for instance, do not comprise independent evidence for a tree of life: [D & B:] “homologies are more often deduced from trees than trees are from homologies,” they explain. “Thus, explanans melds with explanandum, and neither is tested.” The reasoning is circular. The fossil record and biogeography cannot be used to infer a universal tree except by extrapolation of limited evidence from “specific groups, areas, or times.” No evidence, in short, produces a tree pattern necessarily; biologists should be open to other patterns, like networks. Growing realizations that lateral gene transfer (LGT) is rampant in biology, at least among the prokaryotes, render the discernment of a tree pattern impossible. One cannot draw a tree out of a scrambled egg. Is it justifiable to infer a tree when only 5% or less of the data conform to the expected pattern? Some evolutionists have tried to dispute the extent of LGT, but commit another circular argument in doing so. Doolittle and Bapteste explain: “to make ‘vertical descent’ the null hypothesis against which claims for LGT must be tested is to assume that which is to be proved: that an inclusive hierarchy exists independently of our beliefs.” In addition, the authors complain that a “phylogenetic signal” in the genetic data is often weak at best. Despite what students have been led to believe, “there is no strong expectation that a universal hierarchy that embraces all life should be produced with molecular markers.” . . . . this paper clearly argued that there was no reason inherent from the data that the pattern of relationships we observe must look like a branching tree. It could look like a web, or a network, or something else.2 In fact, some evolutionists have argued for a ring instead of a tree (09/09/2004). The possibility of “pattern pluralism” arising from multiple mechanisms requires that evolutionary biologists rid themselves of the predilection for “tree-thinking.” . . . . Carl Woese, the one who reorganized taxonomy into three kingdoms (archaea, bacteria, and eukarya), wrote an article with Nigel Goldenfield in Nature last week that is even more radical.4 They even call it revolutionary. “The emerging picture of microbes as gene-swapping collectives demands a revision of such concepts as organism, species and evolution itself” they said in a Connections article called, “Biology’s next revolution.” . . . . The Tree of Life is arguably the central icon of evolution. From the single illustration in Charlie’s book till now, the image of a branching tree from a single root emerging from a primordial soup has been the symbol of evolution. Papers are regularly published with phylogenetic trees. There are whole journals devoted to tree-building. Phylogenists employ elaborate software programs that take genomes and try to decipher the hidden tree within. Is this all for naught? Is it nothing more than playing games, tilting at windmills that don’t fight back and aren’t even aware of you? These authors basically said that tree-thinking evolutionists are dreaming. Data don’t build trees, people do! The software programs only succeed in finding a “consensus tree” or “maximum likelihood tree” or “maximum parsimony tree” because that is what biased programmers told them to find (see 07/25/2002). If the program’s job is to find a tree, then find a tree it will. It may have to throw out long-branch attraction (04/30/2005), massage the data to account for molecular clock heterogeneity (05/02/2006), and select between a dozen equally-valid results or whatever, but out pops a tree – whoop-de-doo! The scientist gets a nice graphic to publish in his paper, and everyone is happy except Mother Nature. If you doubt this, look at what they do with evidence in the 06/13/2003 and 04/30/2005 entries.
CEH should give us sobering pause. KFkairosfocus_{January 24, 2016
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I found it useful to compile a visual side-by-side comparison of electronically banded chromosomes. This is my comparison of Orangutan, Gorilla, Chimp and Human chromosomes that correspond to our number 2 which evidences chromosome fusion speciation, hence chromosomal Adam and Eve who were alive in the period of time before chimps existed and our "split" from a common ancestor is estimated to have occurred. There is a separate comparison for each possible base pair triplet combination, codon to show in the picture. Clicking on the image will greatly enlarge it: https://sites.google.com/site/digitalchromosomebanding/home/RevComplimentTripletAbundancesForChr2OrangutanGorillaChimpHuman900Bands150kBasesBrightness20.png Brightness adjusted: https://sites.google.com/site/digitalchromosomebanding/home/RevComplimentTripletAbundancesForChr2OrangutanGorillaChimpHuman900Bands150kBasesBrightnessAdusted.png Source Code: https://sites.google.com/site/digitalchromosomebanding/home/Codons.zipGaryGaulin_{January 24, 2016
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VJT, this is the site he was using: http://www.ensembl.org/index.html As far as human genes I found a link to this from the above site: FASTA: Homo SapiensMung_{January 24, 2016
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VJT, we should ponder the fate of the Ptolemaic and Copernican epicycles when Brahe then Kepler then Newton came along. KFkairosfocus_{January 24, 2016
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VJ: For what it's worth, I will restate here a few points which I have always sticked to: a) The similarities and differences between homologous genes in different species are an argument in favor of Common Descent, not an argument against ID. Indeed, they are usually a very good argument in favor of ID, because the similarities allow to quantify in some way the functional constraints of proteins. b) As an argument for Common Descent, those similarities and differences are in general a very good argument. I agree with our neo darwinian interlocutors that the evidence for Common Descent is very strong (maybe not "overwhelming", but very strong). That's why I have always accepted CD as the best explanation for those observations. c) I am not an expert (or fan) of trees and nested hierarchies. However, as far as I can understand, the existence of different trees from different genes is not a strong argument against CD, even if it deserves attention. I believe that Joe Felsensteins thoughts, as reported by you, are essentially correct in that regard. d) Tom Mueller's objection is definitely more interesting. I have always argued that differences in homologous genes are probably of two different kinds: d1) Differences due to neutral evolution: these are the differences which can be used to build molecular clocks and trees, with some hope of success. They can also help us understand how much of a protein is functionally constrained by purifying selection, which is a basic point for ID theory. d2) Differences due to different functional constraints in different species: IOWs, those differences which represent optimizations of the protein in different contexts. Here we have an opposite perspective: the diffferences are evidence of functional constraints, exactly as the homologies. These differences, if unrecognized, will cause strong anomalies in the building of molecular trees. e) As far as I can understand, the second type of differences are vastly underestimated. Many "evolutionists" go on with an attitude which seems to assume that almost all differences are due to neutral evolution. That is, IMO, a big mistake. HAR are a rare exception to that, one of the few cases where the problem has been faced explicitly. f) The problem is that it's not easy to distinguish between the two cases. The only "objective" tool, as far as I can understand, could be the Ka/Ks ratio, which has many problems. However, I believe that this issue deserves better understanding, and not only in relation to HARs. We need to understand how much the differences between homologous proteins are due to functional reasons.That is especially important for regulatory proteins, like transcription factors. g) Just to make an example: the cited FOXP 2. In humans, it is a 715 AAs long protein. It is a transcritpion factor, with important high level functions, not exactly well understood. It is absolutely true that it is highly conserved in mammals, and I would say in vertebrates: Humans - mouse: Identities: 711/715(99%) Similarities: 713/715(99%) Expect: 0 Humans - shark: Identities: 632/715(88%) Similarities: 673/715(94%) Expect: 0 That would already cover a span of about 400 Million Years of "neutral" evolution. And most differences here are due to poli-Q sequences whose length varies in different species. The interesting thing is that, in this long and highly conserved proteins, only a short conserved domain is clearly recognized: the DNA binding site, about 70 AAs long. That is often the case in transcription factors: only the DNA binding site represents a clearly recognizable and highly conserved domain, while the rest of the molecule is much less understood. Indeed, if we go outside the vertebrates, the protein is much less conserved: Humans - Drosophila: The Drosophila protein is shorter, 442 AAs, and only part of it (295 AAs) can be aligned to the human form: Identities: 152/295(52%) Similarities: 187/295(63%) Expect: 1e-90 Humans - C. Elegans: The protein is even shorter (262 AAs). This is the best alignment: Identities: 102/181(56%) Similarities: 123/181(67%) Expect: 2e-53 OK, 2e-53 is still a strong homology: the protein is certainly in some way the same, and what is most conserved is the DNA binding site, as it always happens with transcription factors. But what about the rest of the protein? Are those big differences between humans and C. Elegans just the result of Neutral Evolution? Are those very strong identities in all vertebrates non functional? I really don't think so. The point is: transcription factors are regulatory proteins. While the DNA binding site remain almost the same, because it does more or less the same things, the rest of the molecule changes a lot (or very little) in different species and sets of species, because it probably regulates different things in different ways. We understand too little of these problems, and I hope that the growing knowledge about epigenetic regulation of cell differentiation will help.gpuccio_{January 24, 2016
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Thanks very much for posting the very interesting video linked to by BA77, kairosfocus. It was quite an eye-opener. I notice that Professor Larry Moran stated in his post that "the FOXP2 example was a bad one for many reasons," but he didn't say what they were, which is not very helpful. Over at the Sandwalk blog, a commenter named Tom Mueller wrote: "FOXP2 is one of several interesting genes that constitute an EXTRAORDINARY EXCEPTION to the rule when expecting the inexorable ticking of some presumed neutral molecular clock – to wit Human accelerated regions (aka HARs)." Professor Joe Felsenstein made another point: "Trees from different genes are not all exactly the same. There is noise owing to accidental convergence, reversals, and parallelism. But they do come out very similar, and when you look at many loci in eukaryotes the signal of an underlying evolutionary tree becomes overwhelming. See, for example, Doug Theobald's papers on formal tests of common ancestry (here, for example)." What do readers think of these points? By the way: what's the name of the Website where you can check out these gene trees, and does anyone have a list of the names of all human genes? (Is there such a list?)vjtorley_{January 24, 2016
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KF, I have good reason to believe that the "theory of intelligent design" can in fact add to what is shown, which is the result of the theory being properly premised to start at the forces powering the "behavior of matter" that causes a trinity of conscious intelligence levels each in our image/likeness to show in a different color or whatever. Darwinian theory is premised for a "natural selection" generalization, not the bigger-picture that Alfred Wallace spoke about that has to account for conscious intelligent minds. I can here recommend this video summary: http://www.discovery.org/multimedia/video/2013/07/alfred-russel-wallace-a-rediscovered-life/GaryGaulin_{January 23, 2016
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GG, looks to me like there may be a question of a little gash down the side of the ship due to an impact with a floating ice mountain. Under such circumstances, other priorities may be advisable. KFkairosfocus_{January 23, 2016
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Then the question is now: what does your well advertised "theory of intelligent design" add to this? http://www.zo.utexas.edu/faculty/antisense/tree.pdf More: http://www.science20.com/news_articles/earliest_date_placental_mammals_discovered-103142GaryGaulin_{January 23, 2016
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PS: In response to one of LM's commenters, I have headlined a comment BA77 made in the context of a fresh remark by TJGuy, and have therefore laid it on the table for serious discussion i/l/o the trend of quote mining accusations and associated projection of claims that are under reasonable doubt as though they were settled. There is an issue there that needs to be faced, whether BA77 commented in 2014 or more recently (as I had initially thought). Mr Spearshake would do better to refrain from outing tactics and accusations.kairosfocus_{January 23, 2016
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F/N: Luskin's critique here will also be helpful. I clip, for reference:
Evolutionists often claim that universal common ancestry and the “tree of life” are established facts. One recent opinion article argued, “The evidence that all life, plants and animals, humans and fruit flies, evolved from a common ancestor by mutation and natural selection is beyond theory. It is a fact. Anyone who takes the time to read the evidence with an open mind will join scientists and the well-educated.”1 The take-home message is that if you doubt Darwin’s tree of life, you’re ignorant. No one wants to be ridiculed, so it’s a lot easier to buy the rhetoric and “join scientists and the well-educated.” . . . . The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified. Some of these ad hoc rationalizations may appear reasonable — horizontal gene transfer, convergent evolution, differing rates of evolution (rapid evolution is conveniently said to muddy any phylogenetic signal), fusion of genomes — but at the end of the day, we must call them what they are: ad hoc rationalizations designed to save a theory that has already been falsified. Because it is taken as an assumption, evolutionists effectively treat common ancestry in an unfalsifiable and unscientific fashion, where any data that contradicts the expectations of common descent is simply explained away via one of the above ad hoc rationalizations. But if we treat common descent as it ought to be treated — as a testable hypothesis — then it contradicts much data . . . . When speaking to the public, evolutionists are infamous for overstating the evidence for universal common ancestry. For example, when speaking before the Texas State Board of Education in January, 2009, University of Texas evolutionist biologist David Hillis cited himself as one of the “world’s leading experts on the tree of life” and later told the Board that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. But this is not accurate. Indeed, in the technical scientific literature, one finds a vast swath of scientific papers that have found contradictions, inconsistencies, and flat out failures of the molecular data to provide a clear picture of phylogenetic history and common descent. Indeed, the cover story of the journal New Scientist, published on the very day that Dr. Hillis testified, was titled, “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’ gross oversimplification of molecular systematics, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:
“For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.2
Of course, these scientists are all committed evolutionists, which makes their admissions all the more weighty. To reiterate, the basic problem is that one gene or protein yields one version of the “tree of life,” while another gene or protein yields an entirely different tree. As the New Scientist article stated:
The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.3
[--> this looks a lot like what was just highlighted in the OP from a different set of molecules used in evidence, among primates] Likewise, leading evolutionary bioinformatics specialist W. Ford Doolittle explains, “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.”4 Hillis (and others) may claim that this problem is only encountered when one tries to reconstruct the evolutionary relationships of microorganisms, such as bacteria, which can swap genes through a process called “horizontal gene transfer,” thereby muddying any phylogenetic signal. But this objection doesn’t hold water because the tree of life is challenged even among higher organisms where such gene-swapping does not take place. As the article explains:
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.5
Even among higher organisms, “[t]he problem was that different genes told contradictory evolutionary stories,” leading Syvanen to say, regarding the relationships of these higher groups, “We’ve just annihilated the tree of life.” This directly contradicts Hillis’ claim that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence.” Other scientists agree with the conclusions of the New Scientist article. Looking higher up the tree, a recent study published in Science tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.”6 Likewise, Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”7 Likewise, National Academy of Sciences biologist Lynn Margulis has had harsh words for the field of molecular systematics, which Hillis studies. In her article, “The Phylogenetic Tree Topples,” she explains that “many biologists claim they know for sure that random mutation (purposeless chance) is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk, dichotomously branching-phylogenetic-tree pattern!” But she dissents from that view and attacks the dogmatism of evolutionary systematists, noting, “Especially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don’t study ancestors.”8
In short, there is a serious problem to be addressed on the merits rather than the dismissals. KFkairosfocus_{January 23, 2016
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Folks, It is worth noting the following revealing 2006 remark in the journal, PNAS, by W. Ford Doolittle and Eric Bapteste:
Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation . . . [[Abstract, "Pattern pluralism and the Tree of Life hypothesis," PNAS February 13, 2007 vol. 104 no. 7 2043-2049.]
While these researchers do try to suggest a new evolutionary alternative (much as the punctuated equilibria advocates did in the 1970's), the basic message is plain. Namely, the premier icon of macro-evolutionary theory, the tree of life -- one long presented in the august name of science as almost indubitable truth -- is in serious trouble and is now unlikely to be sound, once the molecular evidence has spoken. All of this grand -- even, visionary -- tree of life picture, then, has always been a sweeping, extrapolated explanatory inference; one long since projected unto a significantly recalcitrant gap-filled fossil record and now even more recalcitrant genetic/molecular evidence. KF PS: Worse, there are hints that your tree-form results will vary based on how you parse and process the sequences.kairosfocus_{January 23, 2016
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