During recent discussions on phylogeny, we saw a distinct failure to communicate, probably felt by both sides. The ‘evos’ attempted to consider the role of molecular data in determining relationship. Given that an obvious cause of common sequence is common descent, due to the significant but not perfect fidelity of the DNA replication process, the phylogenetic inference is that sequence similarity is indicative of common descent. This, critics feel, is a circular argument.
In this, they may be following Jonathan Wells in Icons of Evolution. His criticism is that “homology is inferred from common ancestry, then turned around and used as evidence for common ancestry”. Yet in molecular genetics, the term ‘homology’ tends to be used to indicate sequence similarity alone, not a descent relationship. DNA probes and separate-strand annealing rely upon ‘high homology’, meaning only complementary sequence. The similarity is an observation, not an inference. If one had two sequences, XXXXXXXY and XXXXXXXZ, they certainly aren’t inferred to be similar: they really are similar. The retention of similarity (with variations) in a line of descent is also an observation. It is not clear to me where the circularity comes in in putting those two observations together and inferring that sequence similarity is supportive of common descent. Particularly when other sites are brought in to the analysis. Each site verifies the assumption for the other(s); Creationists on the other hand lump the whole into a composite sequence, and expect ‘independence’ to come from something other than sequence identity. You can’t verify genes using genes, or something.
Well, if the argument is circular, we must apply that razor to within-species comparisons as well – paternity testing, forensics, molecular genealogy and ethnic investigations must all be based upon circular reasoning too. Which I suspect no-one would try and argue in court. Broadening this out to between-gene-pool sequence similarity, among species that are even termed ‘closely related’, we presumably don’t have a major problem with sequence being commonly derived from a common ancestor there either. So the question is: as one goes ‘upwards’ in the Linnaean classification system, where does the circularity arise, if it is not there throughout? The differences identified between higher taxa are inevitably greater than those at lower, as one would expect from the same process of descent with modification that explains similarity among relatives, extended in time. As time goes on, the similarities erode and the differences increase. But there is no boundary detectable, no clear transition at which ‘circular reasoning’ comes in, nor where there is an abrupt difference as would be expected from separate origins. Differences remain a matter of degree, albeit confounded by rare events and inevitable statistical artefacts.
The Creationist alternative for sequence similarity is ‘Common Design’. I confess I can never make any sense of this. At what point does Common Descent stop and Common Design take over? In a process whereby a Designer generated in initial version of a sequence, and then allowed nature to take its course, the similarities between subsequent lineages would actually be due to Common Descent, not the initial Design.
OK, we might propose a Designer making separate taxa. The similarities in sequences between any two such taxa could be termed Common Design. But members of Taxon A and Taxon B are still commonly descended from that point on, from the moment of creation. So you can never separate out Common Design completely from Common Descent. In any process where similarities were initiated by Common Design, residual within-taxon similarities still indicate Common Descent from those points. The exact same kind of data has two completely different explanations across that assumed boundary, which is extravagant and inconsistent. The boundary is not a real boundary in the data.
If we follow the differences in Taxons A and B back, attempting to reverse out evolutionary history, we get to a point where the ‘ur-sequences’ exhibit a high degree of sequence similarity. Something which, if we observed it today, would strongly support a genetic relationship. So what would persuade us that, at that point in history, the relationship was not, in fact, genetic?
Common Design is sometimes invoked as ‘like creatures need like DNA’. But if we envisage the Design occurring at a high enough taxonomic level, we are saying that some very unalike ‘creatures’ had like DNA, at the moment they were … created. They only have unalike DNA now, after a few million years of separate change.
Further, none of this helps explain genetic similarities at loci that have little to do with phenotypic difference. One of the principal markers used in paternity testing are SINEs – a kind of transposon. Intergenic examples have no apparent phenotypic effect, and vary in humans (obviously, or they’d be no use). But there are also SINE inserts that are held in common between humans and chimps, others that are diagnostic at still higher taxonomic levels. They can’t all be essential to the form of the members of the clade they are restricted to – can they?
I’ve taken a somewhat circuitous route to my point, and the reason for the title. Consider the following not-very-treelike tree.
It represents the result of extensive phylogenetic analysis of the entire eukaryote clade. Reminiscent of those ‘you are here’ pictures of the Milky Way, ‘animals’ are all stuffed in the red box at bottom right. That’s everything: vertebrates, insects, sponges, nematodes … Fungi are just above, and land plants, seaweeds and Volvocales at about 11 o’clock. That’s pretty much it for multicellular life. The tree overwhelmingly consists of unicellular eukaryotes of bewildering diversity – what used to be called protists, and still are when we aren’t being cladistically rigorous. Never mind beetles, thats what the designer has an inordinate fondness for! If we had no place on this tree, I suspect people would have no problem with it, or the methods used to infer it. Of course we notice the multicellular life more than anything else. They’re bigger. It’s us, it’s our pets, food, materials and enemies. But most of the tree is minute, and does not indulge colonial clumping, amendments of which cause the ‘mechanical impossibility’ arguments ranged against phylogeny.
The discussions involved in resolving and testing these ‘protistan’ branches are surprisingly heated. It’s not just a question of assuming a relationship; the relationships are teased out of the data. If there were no relationship, that too would be apparent from the data. So where, in the progression to the interior of this diagram, and trying not to be bamboozled by the contents of that little red box, does circular reasoning come into it? Likewise, where does Common Design take over from Common Descent as the cause of similarity?
stcordova,
Still more evidence that you don’t read. None of those fossils is “missing”. As I said, we are unlikely to have found any of them, but if we have there’s no way to tell. Perhaps, say, Probainognathus is actually our direct ancestor. How could you say that it is or is not?
Many people have told you this before, many times. You don’t read.
Hi Allan – help me out here. “Fossil DNA” as described above cannot fall under the rubric of “Common Design” because by definition, there is no “design” to non-functionality (teeth for chickens?!). Wherein lies purpose, planning, or intention that exists or is thought to exist behind non-functional “Fossil DNA”?! …unless the Creator is possessed of perverse sense of humor, who also needed to create marijuana for those of us who failed to get the joke!
No matter how you slice this creationist baloney, intelligent design is no longer an option!
I have yet to meet any high school student, who when presented facts along these lines, fails to “get it”! And may I add, my clientele represent quite a conservative bible-belt constituency.
So does that mean they’ve been found?
You can start with the mother-of-all Sarcopterigii, then the Rhipidistia (which as I showed, some don’t even think Rhipdistia is even a real clade!
C’mon guys, you said common descent is for real, how about some discovered missing link in the direct line to humans. I just showed, the direct line of the lungfish from 300 million years ago today. No problem because the 300 million year old ancestor of a lungfish is — A lungfish!
Tom Meuller.
Well well well, look who showed up, Tom Mueller, the guy who speaks untruth by claiming I promised to invite my professors to this mud slinging website. Still can’t find proof of your false claims about me. Still unwilling to retract after being called on your false claims?
stcordova,
The ice is getting thin, Sal!
If there is no way to tell, then say “we don’t know if the theory is therefore true”, than insult real scientific disciplines like physics and claim that UCA and the requisite transitionals are proven as gravity. It is not.
But you can find rabbits in the Cambrian, or other fossils out of place or sequence in the strata and this would be strong evidence against common descent. The theory is open to falsification. Yet we find likely candidates like Probainognathus in strata where they should be, if evolution was true.
Alan, Tom said something untrue. If you suggest a wording for how to make him correct his untruth I’ll use your suggested wording, but changing my wording doesn’t change the fact that after three months he never retracted a falsehood about something he claims I said, but which I never said. He’s never proven it because it is false. Until he retracts, I see no reason to let him off the hook because he said something false about me personally. If this were an argument about common ancestry, I’d let it slide.
stcordova,
It’s water under the bridge regarding a moderating issue and off-topic here. I suggest you invite Tom to noyau, though of course he’s under no obligation to follow you.
ETA I’ve relinquished actively moderating comments. This is just friendly advice.
So they’ve been found? How many in this list in the direct line to humans would you say have been found? This is the skeptical zone you know, not believe-whatever-evolutionary-theory says-is-true-in-the-absence-of-direct-and-contrary-evidence Zone.
You could provide the mother-each-clade.
I tell you what, the ancestor of all humans is a….tada…a human! You can call her Eve, heck the evolutionists call her Eve. Till the missing links are conclusively found, you should say, “we don’t know for sure” rather than advertise it as Darwin’s truth.
So which of these has been found?
ETA I’ve relinquished actively moderating comments. This is just friendly advice.
In deference to you old friend, I’ll try to just provide a link in the future. FWIW, I appreciated your service to TSZ. I hope you are well. Take care.
TomMueller,
Tom.
I agree. It makes no sense to prefer ‘common design’ for non-functional indels, inversions, scars, ancient centromeres, telomeres, pseudogenes and the like. And yet they do.
Given that pairwise common ancestry coalesces upon a speciation node, and speciation is necessarily a somewhat local phenomenon, the lack of these demanded ‘missing links’ (I call ‘house’ on my Creationist Bingo card) is in no way a surprise if evolution is true. It is an expectation.
Finding a close fossil member of the clade depends upon the fairly close (in time) widespread success of branches of that clade, close to the node, which is hardly a universal expectation.
More circular reasoning, not proof! Furthermore, some claims may have been falsified.
Example: pseudogenes may generate long-non-coding RNAs that serve as microRNA sponge targets. One is less likely to find function if one insists on the evolutionary story rather than actually doing experiments like those that discovered the role of the PTEN pseudo gene.
My example is not as far removed from evolutionary relationships as you believe.
The genomes of the leaves will confirm that they all descended from a common source, the seed or runner. And the cells of the leaves don’t always reproduce perfectly, there are somatic mutations. So here also there are the equivalent of genealogical relationships to consider, the history of the sustance of the leaves over the life of the plant. Without any knowledge of the history of the leaves in front of us all we have is comparisons of the forms and the genetics.
So we see before us lobed fins, flippers, wings, legs and arms all built on a similar plan. But this does not tell us that any of these is descended from any other. If we believe that arms have emerged due to a series of genetic mistakes then we can imagine a series of limbs progressing from fins to terrestrial supporting limbs to the dexterous forelimbs of humans all being selected from chance alterations to some original structure. But from the available evidence we do not have to believe this. Alternatively they could all be the physical expression of an overarching type which suits the organism to which they belong. At some stage in our evolution humans may have possessed fin like appendages but this is not obtained from observation, it is speculation.
Well you can’t expect Sal to do research in order to learn, can you? After all, he already possesses The Truth.
Ghee whiz – it has been a while and I had forgotten my earlier antipathy to this forum & no… I do not want this matter to “slide”
OK – I have just been accused of “untruth”
Let me see if I understand this all correctly:
Sal shamelessly impresses us all with his bona fides by expounding on his ground-breaking efforts in NIH not to mention glowing accolades from his mentors/professors.
Here is just one example:
… and another.
The shameless list continues, but let’s leave it there…
Sal then continues to contradict himself – does not realize he is contradicting himself and then even goes on to say that Allan, I and others present are all wrong because he is faithfully reiterating what his own professors say to be the “truth”.
For example:
There is more – much more… but this post is already too long!
Of course such contention cannot go unchallenged and this is where I believe the accusation of my own “untruth” originates:
Sal’s failure to respond to this more than reasonable (and I can only suspect enticing) challenge has somehow rendered me the purveyor of “untruth”. Indeed, I am still unclear where my own “untruth” lies. Sal was less demure when he declared Alan, myself and others incorrect because he was in the camp of “truth” together with his admiring professors.
Perhaps we should put this nagging question to rest once and for all and I put it to the community:
Should we contact Sal’s declared mentor(s) at NIH and inquire whether or not Sal is representing their own views correctly?
I suggest we start with Gary Felsenfeld garyf@intra.niddk.nih.gov and get to the “truth” of the matter.
It is a slow summer day, but I am somewhat curious whether Sal has indeed blipped on the NIH’s radar. I suspect the fruits of our scientific curiosity may prove amusing.
Your thoughts?
Take it somewhere else. That’s my thought.
Allan – can you refer me to creationist literature where they claim “intelligent design” for the non-functionality of “Fossil DNA” that can only be reasonably construed as lost functionality (an interpretation of course, they cannot brook)? How do they wrap their heads around chickens having non-functional genetic information for teeth (for starters)?
Remember it’s not just chance variation, it is variation plus selection in the niche environment. Environments change and move. Organisms stray into new environments. Fish don’t do well on land normally. But mudskippers are well adapted to their niche where they pursue an effectively amphibious lifestyle.
Tom,
I responded here:
We have noyau. It is is intended for “gloves-off” discussion.
ETA I see Sal has posted a link.
WTF?
Hi Alan – Hi John
Thank you… but to cite a wise Zen proverb: The sage concerns himself not with the barking of a dog…
I apologize if I stepped out of line and best moving on…
best regards
No, that’s not circular reasoning, it is EVIDENCE of common descent. There simply shouldn’t BE these structures if common descent is false.
May, oh cool they MAY do it. How many of them ACTUALLY do it? You have the “divide by 10.000” problem.
Besides, having a long stretch of DNA sit around and accumulate mutations over hundreds of thousands of generations can eventually mutate into something that secondarily acquires a function. From this alone you’d expect SOME small fraction of pseudogenes (and lots of other forms of junk-DNA, such as retrotransposons) to also have acquired functions over evolutionary time. Common Design doesn’t explain why there’s a broken protein-coding gene in the first place, nor why they can ALSO be used to build phylogenies that support each other, common descent does.
Not to mention the fact that even the pseudogenes of multiple species can be sequenced and a phylogenetic relationship inferred therefrom, all the way back to a split from a species sitting in a lineage that retained a functional version. Case in point: GULOP.
You keep making up this synthetic revisionist picture of evolutionary biologists running around telling people to stop doing medical research because they have decided what pieces of the genome are and aren’t functional. This simply doesn’t happen. You cannot cite one single instance of someone deciding to do important medical research and evolutionary biologists coming around succeeding in changing their minds. This has literally NEVER happened.
Sal, if your creationist views are really true, why do you have to LIE to support them? Why do you HAVE to tell FALSEHOODS to support what you believe?
Did you even read my post? I’m telling you why it is almost never claimed that the direct ancestor of anything is found.
Since no one has been forthcoming with mothers-of-the-clade fossils that are in the direct line of humans as I listed here:
How about just imagining the mother of the clade of reptiles with the following circulatory systems below. Which circulatory system do you propose is closest to the mother-of-the-clade, and then suggest how there were gradual changes that permitted the thing to live in the adult stage without dying.
For example, suppose the mother of the clade had a heart like the crocodile heart where the right aorta is on the left ventricle and the left aorta is on the right ventricle. How then did it evolve into a lizzard heart where the left AND right aortas are on the left ventricle! Or how then did the mother-of-the-clade-of-reptile hearts evolve the snake heart where the left AND right aortas are on the right ventricle!
Phylogenetic reconstructions don’t provide mechanically feasible explanations for such enigma of how something like that would evolve even in principle because it relies on circular reasoning as justification in the face of contrary evidence.
Or you could just use published data sets, or even cite published analyses. As I have done several times. Also, you don’t know what a PAM matrix is. Your proposed study is a distance matrix. A PAM matrix is a 20×20 matrix of transition costs between pairs of amino acids. You can use that to help construct a distance matrix, which you could then use for your study. However, I advise you that a likelihood method operating directly on the sequence matrix would produce a better result.
In other news, you need to stop with the triumphant revelations you think will show me to be a fool and you to be the true expert. It’s already been pointed out that the study you cited used BLAST for exactly what I have suggested it’s good for, not for phylogenetic analysis. For that analysis the study used Mr.Bayes, which is in fact a phylogenetic analysis program. BLAST is not.
Similarly, the exact relationships among lungfish, coelacanths, and tetrapods are not completely clear, which I have mentioned before. But all that is irrelevant to the main point, which is that all three groups are sarcopterygians, while teleosts are actinopterygians, and thus the group “fish” is paraphyletic to tetrapods (even without bringing up sharks, cyclostomes, and various extinct groups).
Finally, I just can’t seem to get you to understand that we don’t need to identify actual ancestors in the fossil record in order to be confident of common descent or in order to use the record to understand the history of life. Cousins are good enough. The fact that some of those cousins might be ancestors (again, we can’t tell them apart) is also irrelevant. The point is that separate creation can’t explain the nested hierarchy or the existence of a those intermediates. Why, you’re even a YEC. You don’t believe that there’s a temporal succession of life at all. You think the fossil record is of species that all lived at once. There’s probably no point in discussing fossils with you at all.
Anyway, I appeal to you once more: have just a little more humility and a little less arrogance. Don’t assume that you must be right and the experts all wrong, easily caught out in error, and just plain foolish. You will only embarrass yourself, assuming you are capable of embarrassment.
And you have been told why but didn’t get it apparently.
A couple of minutes googling finds an enormous number of popular and scholarly articles on the evolution of hearts. Here’s one from 2004, for instance.
ETA and a Pim van Meurs article at Pandas Thumb
stcordova,
Regarding the heart diagram: it’s a cartoon that doesn’t adequately represent the natures of the organs shown. Crocodiles have complete septa dividing the ventricle into two unconnected left and right sides (just as birds do, incidentally). The others do not. They have various incomplete septa of complex conformation that help to channel the flow of blood. Whether you want to consider those septa to create separate left and right ventricles is a matter of opinion. Any decent comparative anatomy text might help you there.
Never mind – I found it!
Nobody can make this sh!t up!
http://creationwiki.org/Chicken_teeth
Chicken ancestors were born with a huge repertoire of unused but functional genetic potential.
The ancestors for chickens lost the functionality of all this somehow latent genetic information for grasping talons, long tails, teeth and other accouterments common to dinosaurs
… and this is the good bit…
…any such postulated lineage-based accumulation of differential genetic changes represents a CONTRADICTION to evolution.
Imagine that, I learned something today!
I attempted to read their incoherent gobbdygook on pseudogenes which somehow ignored pseudogene commonalties within and across lineages. Convenient that!
That’s it… I’ve had enough.
Best regards to one and all.
I can’t believe what I’m seeing. So many challenges to evolution, impossible crocodile hearts, impossible citrate metabolism, unbelievable phylogenies, fossils, etc, etc… and not a single attempt to explain any of those pieces of evidence in light of the Grand Theory of Intelligent Design! (patent pending) I thought I was about to witness a major scientific revolution in ID. What’s going on here?
Distraction?
It’s just Sal’s way of exhibiting the fact that ID/creationism rests upon no evidence whatsoever. Not thinking about things, other than to try to tear down evolution (ignorantly), creationism is supposed to win just because it’s their belief (and you’re not supposed to die in that scenario–nice if it were true) and they cling to it.
No, no science, no furtherance of knowledge, just a desire to crush whatever disagrees with him.
Glen Davidson
There is you’re usual reflexive answer that I don’t understand. I do understand the difference between a distance matrix and the cost matrix that is used generate the distance matrix. I was the one who provided the citation of how the Smith-Waterman Needleman-Wunch algorithm utilizes a variety of cost matrices of which Dayhoff PAM is but one.
Like I said, you’re usual reflexive response of attributing claims and arguments to me that I didn’t make, and then using those mischaracterizations as supposed evidence I don’t understand.
But in any case, you’ve not provided unequivocal references to fossils that are mothers of the clades in the direct line to humans, neither did anyone here bother to even describe a viable evolutionary trajectory of the heart of the mother of the reptile clade to extant reptile hearts.
So says the expert who said mtEve is not the MRCA of all female humans.
BLAST establishes similarity. Claims of common descent are driven by patterns of similarity and diversity. BLAST comparisons on newly sequenced molecular data are potentially falsifying circularly reasoned phylogenies, therefore it is good for phylogenetic analysis as it helps falsify them.
It doesn’t surprise me at all that despite the claims of the Early Bird project that Rhipidistia is a clade, there have been those that object to Rhipidistias status as a clade, not to mention there isn’t a fossil that would qualify as the mother of Rhipidistians.
Furthermore comparisons between species force phylogenies to invoke epicycles such as with the case of shark DNA looking closer to human DNA than ray-fin fish DNA. The phylogenies have to be ad hoc kludged with the assumption of the mother of the overarching clade having all the genes that are then selectively appearing in some lines and not in others all the while avoiding the problem of the absurdity of the mother-of-the clade having more genes and uses for those genes than she can handle.
The BLAST comparisons show the absurdity of various phylogenies and the need to support the phylogenies with epicyclic kluges like assuming the mother of the clade started with tons of genes that got lost. Diagrams like the one below which are generatable by BLAST Smith-Waterman show the problem.
It also shows graphically the another problem, that of large amounts of Orphan Genes and Taxonomically Restricted Genes. The mother-of-the-clade had to have an abusrd number of genes to support even the ad hoc kludges necessary to make a phylogeny viable:
stcordova,
Sal, you are reminding me of the Gish gallop. It is much easier to hurl out random criticisms than it is to respond substantively, and it is exasperating when many of these criticisms have been dealt with many times in other venues. And doubly exasperating when you ignore substantive responses from professional scientists such as John Harshman.
Treat it as entertainment.
I’m impressed with Allan’s patience, repeatedly explaining in detail to deaf ears.
I’m willing to run a few BLAST runs to put this to the test.
Would Ray-finned fish be Actinopterygii and sharks selachii?
http://www.uniprot.org/uniprot/?query=Actinopterygii&sort=score
http://www.uniprot.org/uniprot/?query=Selachii&sort=score
Not trying to be exasperating. I’ll summarize the points:
1. Universal Common Ancestry (UCA) descent is challenged by mechanical feasibility. I gave an example of the reptile heart. The common ancestor mother of the clade doesn’t exist in the fossil record and doesn’t exist even in principle as evidenced by the structure of existing reptile hearts.
2. The evolution of lobe-finned fishes to humans or lobe-finned fishes to birds is stated in terms of nested clades, but the mother of each of the clades is missing in the fossil record.
3. There are conflicts in terms of asserting which supposed phylogenetic tree should take priority as it requires sometimes ignoring conflicting data or kludging it with untenable explanations. Example. Humans share genes with zebra fish that they don’t share with mice as shown in the diagram above. Not to mention the mother of the clade needs an absurd number of genes to explain the orphans or taxonomically restricted genes — the other explanation is they poofed or converged into existence.
4. There is the mother-of-all lobe-finned fishes. There were 3 lines descened from the mother-of-all lobe-finned fishes: Lunfish (Dipnoi), Coelecanths, Tetramorpha (birds, humans, turtles giraffes, elephants, frogs….a huge number of forms etc.).
So two of the descendants (lungfish and coelecanth) of the mother-of-all-lobed finned fishes didn’t diversify at all, whereas the other line (tetramorpha) became all the plentitude of tetrapods (birds, humans, turtles giraffes, elephants, frogs….a huge number of forms etc.). There is a serious incoherence as far as a theory that explains no change and abundant change at the same time.
Rather than galloping around, I could just keep repeating the questions above till someone admits evolutionary theory doesn’t have good answers. 🙂
According to your own diagram:
About 2500 genes shared with mice that are not shared with Zebra fish
About 180 genes shared with Zebra fish that are not shared with mice
What’s so strange about that? Remember the title of the post: Look at the big picture
TomMueller,
I can’t point to any literature as such. It is something I have seen retreated to by numerous commenters of the type we have here, is all. Most either ignore the issue altogether, or just repeat the mantra ‘common design’, with some lame crap about ‘you don’t know it isn’t’, or hastily start talking about something else, such as … hearts.
Evolutionary convergence is common design, so even evolutionists use the concept, just by a different name.
Hearts have been covered many times by others in other venues. I already linked to Pim van Meurs article. Here is a BioLogos article that emphasizes the developmental aspects. What is mechanical feasibility and how is it a problem for the evolution and embryology of vertebrate hearts?
But I’d never have glanced at some of the fascinating stuff on the web without being prompted. There are some great expositions on evolutionary pathways.
stcordova,
More assertion on the matter of circular reasoning, without one iota of reasoning in support. There is nothing circular about inferring that centromeric sequence to which kinetochores no longer attach is indicative of an ancient centromere.
Sal’s famous ‘some-therefore-all’ gambit. Also known as ‘the anomaly is the signal’.
What on earth does that have to do with common descent? You’ve just seen the word ‘pseudogene’ and responded with ‘here’s something I know about pseudogenes’. If something is not, in fact, nonfunctional, it can simply be removed from the pile of nonfunctional sequences and placed on the other. It does not take all the other nonfunctional sequences with it.
stcordova,
No it isn’t.
Sal – do you have an example of molecular convergence, beyond the inevitable statistical fact of homoplasy, and a reference to anyone calling it ‘common design’?
That’s molecular convergence, not phenotypic btw.
That means the mother-of-the-clade that includes zebrafish and humans had a large number of genes and presumably uses for those genes such that there is this similarity between humans and zebrafish and for that matter all such anomalous numbers of shared genes — we might say taxonomically restricted genes (TRGs), but who knows where that definition is going. Assuming the mother of the clade containing all these creatures had all the TRGs this would be an absurdly high number for the ancient mother-of-clade to have appear in the history of evolution with so many genes, especially in light of the evolutionary story of simplicity evolving complexity. This would look more like complexity devolving away.
The problem is acknowledged in the literature, I’m not saying something original here.
John Harshman,
Really? I feel the Crocoduck Project may be just weeks away from a breakthrough, then.