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?
Why “therefore”?
There are two ways of handling this situation.:
1. Define “fish” as anything descended from that common ancestor. Then, as PZ Myers said in his much-maligned post, we are fish, even though we don’t look like fish.
2. Define “fish” as anything that “looks like a fish”, Then “fish” are a paraphyletic group.
Either of these usages can be defended, and the which you use does not change your understanding of the phylogeny. It’s OK, as long as you make it clerar to the audience which sense of the word you are using.
Sal:
No one who understands the methods demands perfect congruence. What you and most creationists don’t realize is just how astoundingly good the congruence really is.
See this section of Theobald:
Prediction 1.3: Consilience of independent phylogenies
A key quote:
You mean those that merely look like bald assertion and arguments from personal incredulity?
Now I remember why I dismissed the essay, I saw equivocations like this. The only known branching pattern and actually obvserved is in micro evolutionary contexts, not in macro evolutionary contexts. He assumes the thing he is trying to prove, circular reasoning. Like I said, not worth trifling with.
He avoids the mechanical issues.
Besides, the birds nest (pun intended) in birdland, not inside the fish group. So even if UCA is true, the birds are not in the fish group. The only place birds are a subgroup of fish is in the imagination of evolutionists, not actual taxonomic and molecular data.
So even if macro evolution is true, the accepted evolutionary transitions (fish to amphibian to reptile to bird) are falsified by the molecular and morphological data. Fish nest taxonomically and molecularly within fish groups, birds don’t belong there.
So, even assuming there is macro evolution, the proposed phylogenies don’t make any sense and they don’t agree with the data.
Evolutionist: “fish are obviously a descendant of fish ancestor, look at all the similarities. Birds are obviously also a descendant of a fish ancestor, look at all the ….ahem …. we’re working on it, the PHYLYP program provies it. So does the 170 million dollar NSF funded Tree of Life project…”
stcordova,
You completely fail to address the ‘circular reasoning’ point. You just throw it into sentences like a talisman.
Why do you insist on leaping deep into the billion-year branches of the tree to support your contention? It should be possible to support the ‘circular’ case using dogs and wolves, or various member of the Compositae.
Pick two apparently homologous sequences that are inferred to be related by circular reasoning, and two that are not.
stcordova,
Why would isolated populations not produce a branching pattern?
Allan Miller,
I looked through John’s paper. It is a rigorous account of how to build an avian tree and the challenges to it. It shows comparative evidence including DNA comparison and shows tree nodes that have weaker and stronger relationships. How do you think this paper establishes common decent based on isolated populations or another mechanism?
Sal:
This earlier comment bears repeating:
Sal,
The hypothesis of unguided common descent fits the evidence of the objective nested hierarchy trillions of times better than “common design”. That in itself constitutes overwhelming evidence against your “mechanical infeasibility” argument, even if we don’t consider all of the known mechanisms by which evolution proceeds.
Your position is quite ridiculous. You have concocted an imaginary barrier to evolution, then invented an imaginary Designer to surmount your imaginary barrier. The end result is a pattern that matches exactly what you would expect if neither the barrier nor the Designer were real, and it doesn’t at all match what you would expect if common design were the correct hypothesis.
To overcome the trillions-to-one explanatory advantage of unguided evolution over “common design”, you’re going to have to do a lot better than “well, maybe evolution is somehow mechanically infeasible.” The evidence is massively against you.
stcordova,
You’re not forgetting embryology, are you. All your organisms start as single cells.
colewd,
It doesn’t establish mechanism. You have decided that this is a criterion of non-circularity; it is not demanded by any logical case I can see.
I am looking to see why you think the reasoning in that paper is ‘circular’, where your reasoning regarding dogs and wolves (or any other pair you care to name) is not. You and Sal seem to be avoiding addressing this point.
I don’t understand what experimental evidence you think shows either of these things. There is observational evidence, just as there is observational evidence for common descent of different species. I don’t understand why you think that experimental evidence is the only sort of evidence we should be paying attention to. (And incidentally, there are no ring species that appear to fit the requirements.)
And yet you are unwilling to commit yourself on any further details. You can’t tell me what the trees in your orchard are or how to recognize any of them. Whatever that may be, it isn’t science.
Let’s note that horizontal gene transfer and endosymbiosis are both examples of common descent, just not organismal common descent. And lineage sorting, which you probably should have mentioned, is common descent too. Convergence is something else. Again, you seem to be claiming that experimental evidence is the only sort. Why? And I’m still not getting the circularity. Perhaps if you directly responded to my arguments your ideas would be clearer.
No, that isn’t the answer. The answer is that we allow convergence when the evidence supports convergence, and descent when the evidence supports descent. If you would only read what I (and others) post, this would be a better discussion.
Again with the “experimental”. Why? We do know for sure, or as close as science ever gets, on a great many nodes in the tree. Of course you retreat to “UCA”, but most of what you say here is a denial of most of subsequent evolution. Chimps may give birth to chimps, but chimps and humans are descended from a common ancestor, and that has little to do with UCA.
I really would like an explanation of this constant use of “experimental” as a mantra.
This is exactly as we would expect from common descent, is it not? If changes happen on a tree, and changes could potentially happen more than once or in reverse, we expect to see homoplasy. If changes begin as polymorphisms in populations, we expect different changes to have slightly different histories. And we don’t expect small samples to resolve every node. Nevertheless, there is basic consistency, and conflicts do not obscure a central signal. Why?
I’m with you up to the “therefore”. Why can’t a fish be the ancestor of birds? Are you not assuming up front that evolution is impossible? Now that’s circular.
You also seem to be having trouble understanding paraphyly. There was once a taxonomic hierarchy that put birds and fish in separate groups. Not these days, though. Fish are paraphyletic. Any group that includes all fish must also include birds, as well as other tetrapods. The common ancestor of birds and fish was a fish, and nobody has to be pressed to say so. Have you, for example, ever heard of Neil Shubin’s book Your Inner Fish? How is any of this mechanically infeasible? And try not to pull your anatomical diagrams from creationist sources.
I assume that earthworms share a closer common ancestor with cabbages than with ragworms. I cannot for the life of me get any gene tree to match this assumption. But somehow I have proven it because … circular reasoning.
I’m trying to figure out how you think it doesn’t. Can you explain?
Physical common descent implies branching pattern, but branching patterns do not necessarily imply physical common descent.
If there are mechanical barriers to physical common descent, then the branching pattern cannot be explained by common descent. Evolutionists assert there is no sufficient barrier to common descent as evidenced by the branching pattern since they argue “branching patterns are only made by common descent” and thus they assume the claim (“branching patterns are only made by common descent”) they are trying to prove. Circular reasoning.
I provided a simple anatomical problem above with reptile hearts. I take it the phylogenists prefer to exercise confirmation bias than deal credible objections to the feasibility of common descent.
Sal,
You’re flailing, Sal.
The consensus phylogeny illustrated in Theobald’s Figure 1 is determined by the evidence — both morphological and molecular — to a precision of 1 in 10^38.
Would you be arguing against evidence that overwhelming if your brain weren’t addled by religion? I don’t think so.
Reality is under no obligation to prop up your goofy religious beliefs — and it doesn’t.
What is your objection?
stcordova,
If they were the only nodes, analysis might be inconclusive. Are they the only nodes? Is there any other data we can bring to bear on the question?
This is the sort of mindless comment that leaches away any respect for your arguments. Would you care to restore some respect by explaining why it isn’t mindless?
Let me explain why it is, just to set things up. Nobody ever claims that “group A is closer to group B than to group C” is evidence that group A descended from group B. It would, however, be evidence that any group BC was paraphyletic and that, if B and C were called by some single vernacular name, the common ancestor of A, B, and C, if we see it, would probably be called by that name too. Now, in the case of elephants and fish, there is no such name. But in the case of lungfish, carp, and sharks, there is such a name. Birds are descended from fish but not from elephants. See how that works?
Presenting reasoned scientific arguments to Sal and colewd is like casting pearls before swine, to borrow the Biblical metaphor.
stcordova,
How do relationships among the brassicas escape this charge? How precisely does mechanical feasibility avoid the charge of circularity?
Is it wrong for us to “believe in” the Indo-European language, even though no one has ever encountered it first-hand (roots have been reconstructed, but exact sounds will probably always be beyond our capacity for knowing), and no one has ever shown that languages can evolve that far? I mean, sure, Greek, Old English and Latin can evolve, but that’s micro-evolution, not the macro-evolution of Indo-European language evolving into a great many languages in Europe and some in Asia.
Of course the whole point of the above is that, like biologic evolution, it’s merely extrapolating known mechanisms to work beyond where we have actually seen them to work. Nothing odd about that, it’s just something creationists balk at when the “wrong results” show up.
So they won’t tell us why like producing like (with variation, as seen) hasn’t been demonstrated, why they don’t have to demonstrate anything about their cherished “cause of life-forms,” nor why normal scientific extrapolation fails with biology.
Same old creationism, same as it ever was, dull, anti-knowledge, ignoring any problem they don’t want to address, and failing to produce any knowledge. But they believe in it.
Glen Davidson
Or trying to reason with farm animals.
Glen Davidson
Ok, let’s try to settle this in a statistical way. PHYLYP is of great interest to YECs because they want to find the common ancestor of the animals on Noah’s ark. As I said, Joe Felsenstein’s work stands in a unique place in creationist theory (among creationist geneticists like those with actual academic credentials) because YECs want to use some of his theory to support YEC ideas.
Here are the distance models of PHYLYP, one I’ll note:
Note the bolded: Dayhoff PAM matrix
I provided one such matrix from Denton’s book. The matrix I provided unfortunately doesn’t have lungfish in it. I think we should re build it to include lungfish.
John Harshman objected to using smith-waterman. But note:
So I think John was wrong to say Smith-Waterman isn’t used for phylogenetic inference. It is, but it isn’t the only tool. But we can start by just looking at similarities. I assert birds will look more like other birds, not like lungfish and coelacanths according to molecular data.
It’s the only gap left.
stcordova,
Surely it’s all based on circular reasoning?
Total reworking? What the crap are you even talking about?
No, the nesting patterns of similarity. It is not mere similarity, it is the NESTING PATTERNS for fucks sake. They should simply not exist if common descent isn’t true.
Those nesting patterns can also be tested by deliberately testing reconstructed ancestral stages in the lab and seeing if they actually work, and HOW they work. This is ANOTHER type of work that should simply not be possible to do if common descent isn’t true.
stcordova: When pressed for answers how this is reasonable theoretically given the substantial problems of evolving new proteins and cell types and cellular inter-signaling
But those are NOT substantial problems, those are DEMONSTRABLY TRIVIAL problems. They have been addressed countless times and all your problems are entirely imagined and provenly false.
stcordova: , the objections are claimed to be moot because “we can build a phylogenetic tree”.
No, they’re claimed to be moot because in concrete empirical experiments they’re DEMONSTRATED to be moot. Look up ANCESTRAL SEQUENCE RECONSTRUCTION.
This method should simply not be possible if common descent isn’t true.
stcordova: Anyone can build a phylogenetic tree that shows elephants descended from birds since elephants are closer to birds than they are to fish.
Do you do thought, like… thought? Do you even have thoughts? Are you a creationist AI?
stcordova: Instead, the objection to the physical, statistical, mechanical barriers to evolving things naturally
What barriers? You have not demonstrated any barriers, you have assumed barriers and tried to argue for barriers, but you have failed in that effort. ¨¨
All the work is still ahead of you, waiting to be done.
stcordova:
is with the ability to construct phylogenetic trees. It’s circular reasoning.
No, it ISN’T circular reasoning as Allan’s Op demonstrates rather convincingly. An Op you have spectacularly failed to actually address in any sort of detail.
stcordova: Every anatomical
.. objection is shown to rest on a hypocritical double-standard. You accept the common descent of dogs and wolves, but reject the common descent of primates when humans are included, DESPITE THE ANATOMICAL DIFFERENCES BEING LESS BETWEEN MAN AND HIS CLOSEST PRIMATE COUSINS.
stcordova: chemical
There’s a CHEMICAL objection to common decsent?
stcordova: physiological
There’s a physiological one too? Do tell.
stcordova: population genetic
.. has been shown to rest on trivially false assumptions by, among others, Joe Felsenstein. No please, bring us those population genetic objections again so we can stare at another moron who should be practicing how to sort his crayons by colour, flailing around when one of the worlds foremost fucking experts tries to teach him the basics.
I get tired of watching you utter fucking lunatics work so unbelievably hard to preserve your manifest ignorance and stupidity. Do you HATE knowledge so badly?
stcordova,
I think we can probably give you that one.
We can without circular reasoning use hybridization to infer the mechanical feasibility of a recent common ancestor. Example: Lions, tigers, panthers in genus panthera can hybridize. YECs can prove feasibility by experiment or reference to experiments conducted by others.
YECs are interested in the question because they want to show the feasibility of fitting all those animals in the Ark. Ring species are obviously of interest too….
You can’t do that with rose bushes and sheep. You want to believe rose bushes and sheep descended from the same common ancestor, you’ll have to believe it in the absence of direct experimental evidence.
But we should probably ask him what point he thinks that would make.
keiths:
Sal:
It’s already been settled in a statistical way, Sal.
I repeat:
ETA: And yes, Theobald’s figure includes fish and birds.
stcordova,
Haha. Mostly the latter, I think you’ll find.
Like I said, you can’t use hybridisation to escape the charge because it depends upon sequence similarity.
How does hybridization show mechanical feasibility? Still not clear on this point. And when will you ever answer my repeated questions about your repetition of “direct experimental” as a necessary prefix to “evidence”?
The late Ronald Brady wrote a paper which IMO gives the big picture more suited to living form than current orthodox biology with its Darwinian speculations and laws borrowed from the physics of inanimate matter. I believe that these writings give us a better understanding of phylogeny.
Here are his opening words:
And here is a quote from the epilogue, although I would recommend that the whole article is read.
We shouldn’t be looking for the primal cause of the varios forms of nature in some unknown UCA but in the dynamic archetype of which the physical form is a specific instance apprehended by our senses.
…Which you precede by quotes about distance matrices and sequence alignment, as if each of those were equivalent to phylogenetic analysis rather than preliminaries. More evidence that you don’t understand much of what you read, when you bother to read at all.
And it’s PHYLIP. With an I.
Oh, one more thing. The protein similarity matrix you provided once upon a time was not a PAM matrix. You should learn the difference before posting again.
Sal:
Allan:
Only when it’s being used against creationism. When deployed in defense of creationism, it magically becomes non-circular.
With God, all things are possible.
You’re a hoot, Sal.
Well, the field is new to me, that’s why I’m here so you guys can set me straight and give me free-of-charge tutoring.
I came here to get some of my mis-understandings corrected, you guys show up and are so willing to help. What deal!
See, I already got my money’s worth in the school of TSZ.
So, onto PHYLIP, I want to compare some protein sequences from lungfish, coelacanths, chickens and elephants. Where do I start. Do I get some accession numbers and then cut and paste-the sequences.
Oh, well, let’s get the preliminaries right since it seems you can’t do phylogenetics without proper preliminaries like alignment algorithms which you roundly trashed as irrelevant and now admit are preliminary (dare I say essential first steps).
I know the game John, you just reflexively say “Sal doesn’t understand” even if I actually might. So now do you admit molecular phylogenetics won’t even get a start unless we have alignment algorithms like Smith-Waterman or Needleman–Wunsch. Far be if from you to admit you actually got caught having to back track before a creationist. 🙂
Sal,
That would be fine if you actually absorbed the lessons.
This is as circular as it gets: you claim macroevolution is impossible because of some arbitrary mechanical unfeasibility which you happen to define as whatever can’t hybridize, which precludes speciation in principle.
Sal’s into micro-learning.
Glen Davidson
Allan Miller,
I think the paper is a solid academic claim of similarities of species and how they relate. It discusses the difficulty of trying to assimilate all the data and make accurate trees.
I don’t think it is a detailed description citing evidence of how two specie of birds through isolated populations were the result of divergence form a common ancestor.
I read through it once and the author is discussing this with us so I am sure he can show where I am mis informed. Do you think that evidence of how one specie of birds diverged from another is well established in Johns paper?
My guess is that Sal is reflecting this creationist trope:
http://rationalwiki.org/wiki/Historical_and_Operational_science
colewd,
It’s not an analysis of ‘how’. What I am looking for is some support of the ‘circular reasoning’ argument beyond repeat assertion.
Why is sequence similarity acceptable as a non-circular inference of common ancestry at one taxonomic level but not another? If you just had the sequences, say, unlabelled.
So Sal would buy common decent between birds and fish if he found this with feathers? I really don’t get the creationist “logic” sometimes…
It seems clear to me that you didn’t. You are here to testify.
Depends. What do you mean by “compare”? Is that your euphemism for phylogenetic analysis, or is it something else?
Oh, well, let’s get the preliminaries right since it seems you can’t do phylogenetics without proper preliminaries like alignment algorithms which you roundly trashed as irrelevant and now admit are preliminary (dare I say essential first steps).
I know the game John, you just reflexively say “Sal doesn’t understand” even if I actually might.So now do you admit molecular phylogenetics won’t even get a start unless we have alignment algorithms like Smith-Waterman or Needleman–Wunsch.Far be if from you to admit you actually got caught having to back track before a creationist.🙂
Bit of advice: If you want my help, don’t insult me first. If you want to learn, actually read and try to understand what experts say. Don’t assume you always know better and don’t assume you have caught me in an error or forced me to backtrack. I don’t reflexively assume you don’t understand; I actually provide the evidence that you don’t understand. And apparently you still don’t understand, based on this post. Nor do you know “the game”.
First lesson: I never said alignment wasn’t important. I just said it wasn’t phylogenetic analysis. It isn’t. Alignment precedes phylogenetic analysis. So do a lot of things: gathering of data, character coding, choice of model, etc. None of them is phylogenetic analysis either.
If you want to do phylogenetic analysis the first step, as you seem to realize, is to get some data. If it’s protein data, you apparently know where to find it. Next you need to create a data matrix by aligning the proteins. There are a number of protein sequence alignment programs. PHYLIP, as far as I recall, will not do this step for you. You must also get your matrix into the PHYLIP format, which the accompanying documentation will tell you about. Once you have the matrix you need to pick an analysis algorithm. If that algorithm is a distance algorithm (which I don’t really advise), you will need to first create a distance matrix based on your sequence matrix. That’s what PROTDIST does. Then you analyze either the distance matrix, using a distance algorithm, or the sequence matrix, using a parsimony or likelihood algorithm. PHYLIP has all of those. My advice is to use a protein-likelihood method, e.g. PROML. If you want a distance method, PHYLIP has a number of choices. I’d go with FITCH. You may also want to test the strength of signal; I recommend bootstrapping (for which PHYLIP also has a program) as a first attempt. All these programs have a bit of a learning curve and you will need to understand why to choose among options.
But what is the point? None of these will be experimental evidence for anything, so to you they’re all meaningless, right?
Look, let’s assume macro evolution is true, the data don’t look to me like birds descended from fish.
So what does nested hierachies mean to you Keiths? Does that mean fish and birds nest within vetebrates? Why? Because all vertebrates share certain characteristics? Ok so do you think birds nest in something fish-like, because it share all the characters that define a fish… oops, there’s a problem there. That nested hierarchy suggests a common vertebrate ancestor (VCA), but it doesn’t suggest birds nest within a common ancestor line looking anything like a fish.
Since you swear so much by molecular phylogenies and hidden random markov models, here’s the chance to shine and show how we can infer from molecular data that birds descended from fish.
The Smith-Waterman Needleman-Wunch application of the Dayhoff Matrices does not agree with birds descending from fish unless a force-fit is applied, and I think I can demonstrate the force fit.
C’mon, we can argue or actually skeptically re-examine the data in a scientific way. I’m giving you guys a chance who swear by computer analytics of molecular data to actually walk through and example to prove your point. Do you guys want to explore phylogeny or go back to beating Dawkins weasel?
Do I have to try to get PHYLIP going or is John Harshman going to try to be helpful and provide data and some pointers. And let’s start with the preliminaries like alignments.
Does John have some suggestions for proteins or genes? How about you Keiths or anyone else who swears by the claims of talk origins. Surely you guys a skeptics won’t just buy into what someone else says without at least trying to investigate it yourselves. This is The Skeptical Zone after all, not “keep all your priors and not even consider different perspectives” zone.
So, I just dropped special creation for the sake of argument and accepted macro evolution as working hypothesis. Does your branching non-random hidden markov model when applied to genes and proteins of various species cause an ancient fish-like ancestor to split in to a branch that leads to extant fish and then birds and tigers and turtles? Or does the branching non-random hiden markov model support the idea fish and birds are sister groups that descended from some unspecified or uncertain VCA.
This bears emphasis. You don’t need to know how something happened to know that it happened. You don’t need a theory of gravity to know that apples will fall out of trees. The paper presents evidence for a particular pattern of common descent among a number of species of birds. It isn’t about mechanisms of speciation. It isn’t about mechanisms of evolution. Neither of these is relevant to the questions discussed.
The point is one can show even under the assumption of UCA, the data don’t support the claim birds descended from something that was a fish, which pretty much would show you can force fit phylogeny into whatever pre-conception you decided it should be unless you decide to try to be impartial.
The YECs could be very interested in PHYLIP and because it helped reconstruct Y-Chromosomal Aaron and the Abraham Modal Haplotype which is only 9 generations away from Noah.
See this here:
That’s garbage. John started out patiently explaining things to you. I hated seeing him put the effort into it that he did. It took a number of months for him to reach the point where he responds to you as he does now. I’ve been watching all the while.
Your worst problem is you. Stop impugning John’s integrity.
See, here’s more evidence that you don’t read. I’ve pointed out several times that your definition of “fish” is faulty, perhaps because you’re thinking only of teleosts, or perhaps because you think relationships are guided by overall similarity, and birds don’t look like fish to you. The actual data say that “fish” are paraphyletic, and if you understood that term you would know that it implies that the common ancestor of birds and fish was indeed a fish.
And I’ve also pointed out several times that alignment methods are not methods of phylogenetic analysis and that distance matrices are not phylogenies.
I’ve also cited actual phylogenetic analyses showing the relationships among birds, fish, and other vertebrates. You have always ignored them. None of this inspires confidence in your sincerity.
This is an interesting claim, which I would truly like to see you back up.