I do think this site needs a thread to discuss phylogenetics and whatever the creationist alternative might be. Let’s start with this quote from Sal Cordova:
stcordova: Insisting on the truth of naturalism in the disguise of evolutionary theory could impede scientific progress in the medical sciences if the whims of some evolutionary biologists like Dan Graur are realized. The National Science Foundation (NSF) has invested 170 million dollars in unresolvable evolutionary phylogenies of little or no utility to medical science.ii To date, no therapies based on the 170 million dollar phylogeny project have come to market. By way of contrast, with the help of research like ENCODE, epigenetic therapies are already being delivered to patients with more such therapies in the pipeline. Therefore, a gambler’s epistemology that seeks to maximize reward in the face of uncertainty would seem a superior approach versus blind insistence on impractical naturalism.
This short paragraph raises a number of questions, a few of which seem like topics for discussion.
1. Assuming for the sake of argument that investing in phylogenetics doesn’t help medical science, why should we ignore other benefits? Is basic knowledge useless unless it contributes directly to human health? Should NSF be concerned only with medical sciences, and if so, shouldn’t it be folded into NIH?
2. Phylogenetics actually does have practical applications, even in medical research. Feel free to discuss that. Me, I’m into knowledge, regardless.
3. What is “unresolvable” intended to mean here? NSF grants, the AToL program in particular, have produced great amounts of phylogenetic resolution. My project, Early Bird, for example. Is it all somehow bogus? How much phylogeny is there, anyway, and how would a creationist tell where it begins and ends?
4. And a minor point: Where does this figure of $170 million come from? Is it the total amount awarded by the NSF Assembling the Tree of Life program from beginning to end? Or does it also count various other programs that have funded systematics research? I find it hard to pull any aggregate info from the NSF web site.
The mission to Pluto has yielded no practical benefits for humans.
Let’s scrap NASA.
Glen Davidson
Phylogenetics. Huh! What is it good for? Absolutely nothing.
Say it again.
Glen Davidson
That medicine doesn’t require knowledge of evolution is an old Ken Ham talking point.
Baby Faye notwithstanding.
Do we learn about the present by studying the past?
Well, creationists don’t.
Of course phylogenetics is of practical value because knowledge is of pragmatic value when it is related to practice, as phylogenetic knowledge is related to both research and to the practice of medicine. The trouble with explaining this to creationists/IDists, though, is that they have no practical or otherwise meaningful grasp of phylogenetics.
Glen Davidson
It is possible to be a successful medical practitioner simply by hiring good staff ang calling the drug reps on difficult cases.
Surgery is more of an art than a science, except possibly in the research phase of new procedures.
If you really are interested in the practical value of phylogenetics in medicine (which, actually, I am not), you could cite various studies of pathogens that were able to use phylogenetics to trace their spread from patient to patient, back to the original source. HIV is perhaps the most well-known. Now, of course, you could interpret this purely as clustering by similarity (which is isn’t, but never mind), but if you did, you would eliminate the utility, because unless interpreted as history it doesn’t trace anything.
I am currently too lazy to append a citation to the literature.
Medical doctors are sometimes asked whether they use evolutionary biology in their practice — they think for a second or two and say “no”, and creationists love to cite such surveys. The creationist neurosurgeon Michael Egnor claims that he does not need make any use of evolution.
But all these people are forgetting the biggest way that they make use of evolution. Their knowledge, their procedures, and the medicines they use all arise from investigation and testing on animals, the more closely related to humans the better. Monkeys, rats, mice, dogs, pigs, and frogs. If those were not at all genealogically related to humans, none of those investigations and tests would be at all relevant. A dog heart or a monkey brain would not be anything like a human’s.
And of course elementary knowledge about DNA replication, about cell growth, about tissue differentiation, about nerve transmission all come from bacteria, yeast, roundworms, and squid. Why would the biochemistry and biophysics of nerve transmission in the giant axon of the squid Loligo forbesi be worth studying? It was studied, beginning in 1939, and the study was incredibly important and received he Nobel Prize in 1963. A colleague in my department got the Nobel Prize for working out how genes controlled cell division in yeast. Was the committee for the prize in “Physiology and Medicine” deluded when it made that decision?
Given the relevance of model systems to humans, is it worthless to study how closely related to us they really are? It’s more than thinking evolutionarily about antibiotic resistance. Evolution is used, and phylogenies made relevant, any time a medical student dissects a dogfish or a neurosurgeon trains by looking at monkey brains.
Research into development, in particular, benefits from evolutionary insights. How anyone can make sense of human reproduction without understanding the evolutionary aspects I can’t even fathom. One simply has to take into account the fact that our ancestors laid eggs to understand the earlier processes of development involving yolk sacs and processes similar to that of embryos developing within eggs. Then there are the ways in which humans develop first a more ancestral form, changing to the current form as development proceeds, like the disappearance of the tail. Gonad movement from more ancestral positions occurs in both males and in females, but rather more noticeably in males.
When a human is born with a tail today, we understand that something went wrong with the suppression of tail formation. Amputate it, no big deal. No demons involved, it’s just a poorly formed tail occasionally appearing simply because we have much of the information for making tails from our evolution. Want to understand the coccyx? Some of the old muscle attachments remain, but certainly the fused vertebrae beyond that are pretty much the useless result of what evolution did with tail formation after we no longer had visible tails.
We understand form and function according to evolution, or we really don’t understand form and function all that well. I’m not saying that no understanding of the coccyx or descent of the testes could exist outside of our recognition of evolution and its effects, of course, because it could exist. But much would remain inexplicable that is explicable under evolution, and the explicable promotes both medical understanding and gives researchers insight into understanding DNA and its effects.
This will be lost on creationists/IDists, naturally, but it’s still the truth about how important evolution is to understanding our bodies and how they are formed. Evolution is the theory that lets us understand life, although clearly chemistry and physics are also important on their own. But chemistry and physics alone explain almost nothing about the complex forms that we know as life, while having these in conjunction with evolution we are able to gain considerable knowledge of why and how life and its parts exist and are formed.
Knowledge of life is practically important, while the ignorance pushed by creationists/IDists would undermine our knowledge of humans and their development.
Glen Davidson
I often compare putatively big government expenditures to the per-unit cost of weapons. Perhaps John was hinting at that sort of comparison with the title of the post.
The U.S. government spent at least $66.7 billion to obtain 187 operational F-22 Raptors. That’s $357 million per aircraft. So if we accept Sassy Sal’s figure of $170 million for whatever phylogenetics research it was that he meant to slur, then we’re looking at less than one-half the cost of a stealth air superiority fighter.
But phylogenetics is useless I tells ya.
Joe Felsenstein,
How does one determine what is most closely related to humans? By anatomy?
Which is a human closer to, a cow, a cat, a fox, a bat or a whale? Based on what?
Ideally you use genetics and anatomy.
phoodoo: Which is a human closer to, a cow, a cat, a fox, a bat or a whale? Based on what?
My guess would be bats of those. Based on anatomy alone.
Rumraket,
You mean because both have oversized brains and can fly?
Actually, all the animals Phoodoo mentioned are equally closely (or distantly) related to humans, all being part of Laurasiatheria, while humans are members of Euarchontoglires. Now, if he’d put in a mouse or a rabbit, that would have been the closer relative.
Sal is correct. We shouldn’t waste our time studying things without medical benefit.
Now if we could only go back in time to 1919 and tell Alexander Fleming to stop wasting his time studying soil fungus and start working on something useful!
Evolutionists view biology organized as one universal tree whereas creationists view biology as organized as an orchard. The word phylogeny in my paper was referring to Universal Tree phylogeny, but creationists (and implicitly the paper) accept Orchard phylogeny. Paternity tests in lawsuits are an example of orchard phylogeny. I’m just clarifying what I meant by phylogeny, I wasn’t talking about legitimate searches for ancestral relationships.
UCA phylogenetics should not be conflated with similarity comparisons. Similarity was known by creationists like Owen and Linnaeus even before Darwin.
One doesn’t need phylogenetics to see similarity, and phylogenies actually mask the anomalies of similarity not consistent with claimed phylogenies as shown in the diagram below.
What does it matter if humans some human genes are closer to zebrafish than to lampreys? One example is the BMP-2 bone morphogenetic protein. The human BMP protein is closer to zebra fish than the lamprey, but John says lampreys are closer to humans according to phylogeny. That’s what I mean by unresovable, there is also some chance the phylogeny is wrong because of such anomalies. Even invoking “incomplete lineage sorting” there is a finite chance the phylogeny is not correct even under evolutionary assumptions.
What difference does this assumption that lampreys are closer to humans than zebra fish in ancestry when with respect to the BMP-2 protein the zebra fish is closer to humans. One might be more inclined to study the zebra fish for BMP-2, and as a matter of fact zebra-fish are studied by medical researchers to study human kidney function and who knows what else.
Usually the decision to use non-human subjects in the labs is a matter of feasibility. If human cells (like HeLa or other lines) are closer in form than yeast, use them if feasible, but yeast are easy to study in various contexts. If one wants to study BMP-2, it’s better to study the Tasmanian devil than the lamprey at least as far as similarity goes. If one said “humans descended from Tasmanian devil like creatures” vs. “humans descended from lamprey-like creatures” does it make that much difference in what creature is studied? The decision is ultimately based on similarity and feasibility, not some story that humans came from lamprey-like creatures.
Even the word “homology” originally came from creationist, not evolutionist notions.
http://www.ucmp.berkeley.edu/history/owen.html
Ok, I’ve said ID should not be promoted as science. Some aspects of the study of creationism are not science, in fact many. I have no problem saying that.
But that does not mean I think most aspects of universal common ancestry (UCA) are science, in fact I don’t since it is not experimentally provable, they are speculations that can have no hope of affirmability compared to basic scientific questions like the “what is rest mass of an electron?”
When I look at similarity charts of DNA, proteins and anatomy this is what I see: it’s reasonable a fish like creature is an ancestor of another fish like creature, a bird-like creature is ancestor of another bird like ancestor, etc.
The issue with UCA phylogeny is whether one group (like fish) have a mother-daughter relation to birds (whereby the fish group is mother to bird group) or whether they have a sister/cousin relationship (whereby the fish group is sister/cousin to the bird group under a common vertebrate ancestor).
Given the tightness of grouping of the fish-like creatures, it seems absurd to me to claim that UCA necessarily dictates birds descended from some fish-like creature. The assumption of UCA would certainly permit, at least in principle, that fish-like creatures are sister/cousins of bird-like creatures. That’s what the physiological, anatomical, molecular data suggest.
Too bad the mainstream UCA phylogenetic story may not nicely agree with what the paleontologists speculate, but that’s what an impartial view of the data suggests : fish beget fish, birds beget birds, each kind (ahem, I mean phylogenetic group) begets after its kind (ahem, I mean phylogenetic group). Transformed cladism at least seems more honest with the data.
https://en.wikipedia.org/wiki/Transformed_cladistics
The question creationists have is “when is the homology purely conceptual (like vertebrates) or physical (such as with panther genus, maybe even the entire Felidae family)?” One way a physical ancestor is confirmed is via hybridization. If creatures hybridize (like lions and tigers), its easy to assume they proceeded from a common ancestor.
If something doesn’t hybridize or look mechanically feasible to have a common ancestor, it is reasonably assumed to be a separate line of ancestry and the similarities are conceptual only and not due to physical descent. For example, plants and animals are eukaryotes. It’s not mechanically feasible to have a plant/animal common ancestor — rose bushes and humming birds don’t look be mechanically related by physical descent, only conceptually related.
The exact same techniques used to infer relationship in paternity suits, forensics and pathogenesis are used to investigate the broader relationships. It is actually rather ridiculous to accept one while rejecting the other. There are known and, with some thought obvious, reasons why increasing genetic distance will result in increase in noise, even in a data set that really does arise from a true phylogeny. So this possibility needs to be eliminated rather than simply elided. An ‘orchard model’ would be expected to give detectable discontinuity. The methods of phylogenetics would shout ‘Creation’ if this were indeed at the base of ‘kinds’. But they shoot straight through this supposed boundary as if it weren’t there. So I’m prepared to bet it probably isn’t.
An alternatrive approach: name a created ‘kind’, and account for the hypermutation that must have occured since the origin of this clade in the time assumed available to give present variation.
Discontinuities are inferred from mechanical infeasibility not a small differences in genes. But even on the terms of genes, there are lots of orphan genes and taxonomically restricted genes.
Mammals are distinguished from other amniotes because of mammary glands. Evolution of mammary glands via natural selection, based on the necessary changes needed to transform sweat glands and keep the mother from sweating nutritious milk needlessly doesn’t seem mechanically feasible. Need I raise the staggering difficulty evolving a chromatin system from a bacteria-like creature (or some proto-eukaryote without chromatin).
For all the bragging of phylogenetic “proofs” they totally ignore mechanical feasibility of the transitional steps. If one wants to argue evolution proceeds by ordinary and typical steps, these difficulties in transition would appear to falsify the claim evolution proceeds by ordinary and typical steps. The alternative is to assume Hopeful Monsters which would resolve the mechanical problems of phylogeny with events indistinguishable from miracles. At that point, one could just as well be a creationist.
You’ll be demonstrating this “mechanical infeasibility” real soon now, I trust?
Mechanical infeasibilities are entirely imagined and exclusively in fundamentalist religious minds.
And surely those can’t arise in a natural stepwise manner, like a non-coding region turning coding, or HGT, or duplication and divergence.
Nope, can’t happen. They must have been created with divine magic powers, instantaneously, from no pre-existing material, at some point within the last 6000 years. *ALAKAZAM*
Because obviously it started with the mother leaking huge amounts of sweat 24/7. There’s just no other way it could have happened.
No, please don’t. You’d destroy evolution if you did. After all, the difficulty is staggering.
A pertinent question is why phylogenetic reconstructions are even possible if the purported transitions did not take place.
Of particular note are reconstructed ancestral stages, using phylogenetics. How come it is possible to use comparative genetics to reconstruct proteins with sequences that no longer exist in extant life, test them in the lab, and find them to be functional? If creationism was really true, this simply should not be possible.
What do these words detail, “ordinary” and “typical” steps? What is an “ordinary” and “typical” step and according to what principle are they ordinary and typical?
Does the reconstructed ancestral mutation I linked above constitute a Hopeful Monster? If so, since it patently really happened (otherwise the result would simply not be possible), it isn’t particularly miraculous.
So god made that mutation happen? How do you know that? What merits such a belief?
Clear as mud. “Orchard phylogeny” is oxymoronic. If you merely mean that there are separate kinds, within but not between which there are phylogenetic relationships, just say so. But then we are left to wonder what the kinds are and how to recognize them. I’m going to assume that you will avoid any discussion of such things.
Nobody does, except you.
John says no such thing. Lampreys are outside Gnathostomata, the clade that includes both humans and teleosts (what you are calling, wrongly, “fish”).
Now, what does it matter how species are related (i.e. the shape of the tree)? There are many possible answers. My answer is that knowledge is valuable for its own sake, even if it never improves our gas mileage or makes our teeth whiter.
As I have just said, this “anomaly” doesn’t exist. You imagined it. Arrogance arising from ignorance is no virtue.
Not sure Owen would be considered a creationist, but let’s go with it. He had a name for a concept, but we have the explanation for how it came to be that way. Surely that’s worth something.
Mini-Kennie Ham. Two Kinds of Science, operational and historical.
It’s entertaining to watch you move from the talking points of the Discovery Institute to those of Answers in Genesis.
Creationists think that science works like this: A guy with horn-rimmed glasses puts on a white coat. While complicated apparatus sparks and hums in the background, the scientist mixes green and purple liquids in a test tube, which gives off smoke and turns blue, thus proving his theory about potato salad.
Sal: Where does this figure of $170 million come from?
John,
The 170 million came from a paper by Change Tan and Tomkins. Tan is a cellular biologist in Missouri. Because of Keiths brought up the problem with the McAffe virus scan on my link to my paper, I could not post the MS-word document and the 60 end notes that included references to Tan and Tomkins, but it is in my paper, not in the excerpts I posted at TSZ.
The paper in question:
https://answersingenesis.org/biology/microbiology/information-processing-differences-between-bacteria-and-eukarya/
If you have other figures, that would be helpful to know.
As far as alternate phylogenies, I’m fine with stating the nested hierarichical nature of taxonomic data such as with the BMP protein. The problem is each protein or gene has a slightly different hierarchical pattern, this leads to inability to declare an absolute phylogeny.
But worse, as I showed for birds evolving for fish, the nested hierarchies can be used to argue against mother/daughter relationships and for sister/cousin relationships between groups, hence one can easily argue fish don’t likely descend from birds, but birds descend from birds.
The problem is one of believability. There maybe only relatively slight differences in the 16S ribosomal RNA or cytochrome-C between eukaryotes and prokaryotes (and other molecules used by phylogeneticists), but focusing on such a small sample size of differences glosses over the colossal gaps in architecture. The molecular phylogenetic comparisons erase away the substantial mechanical difficulties of assuming Universal Common Ancestry.
What has happened, as seen by the case of Dan Graur and the New Yorker article, is that when these mechanical differences in complexity are indirectly highlighted and staggering complexity is hinted at, the real problems of evolution by a series of ordinary events becomes less believable.
What the thesis of my paper really was is that we are getting to the point that some evolutionary biologists are now at odds with the medical research community. This is not a healthy state of affairs unless of course ENCODE is really a bunch of “crooks”, “ignoramuses…generating piles of excrement.”
If phylogeneticists and evolutionary biologists want to do their thing, I may cringe at taxpayer dollars going to the project, but I really cringe at the denigration of the NIH — that could affect all of us in terms of medical science.
My role in all this is passing on news to my ID colleagues who may have interest in developments at the NIH. My paper was to assemble a collection of information which may be later repackaged in various forms to various interested parties. I’ve been told by at least one prominent IDist that I probably have more knowledge of the details of the ENCODE project than anyone else in the ID/YEC community and that I should expend effort to disseminate the information.
I don’t, and in fact the number sounds about right for AToL. I just wanted to know.
This just isn’t true. The facts are complicated and differ from case to case, but your claim here is in general wrong.
I swear you don’t even read anything I write. I have explained at least three times why this is nonsense, but you never even acknowledge that I said anything.
The fossil record is the simplest counter to your claims here. Granted, your main example so far (lactation) doesn’t fossilize well. But you really can’t overlook the smooth procession of intermediate forms. Add in the extant monotremes (another thing you have ignored), and you have intermediates even for lactation. Perhaps more importantly, these “mechanical difficulties” are just another example of “god of the gaps”, which is just the assumption that your lack of imagination controls the universe.
stcordova,
Yeah, I dare say. But which forms the majority? It would be impossible to do cladistic analysis on molecular characters if exceptions were the norm. How do you account for the things that aren’t different? I hope you don’t say ‘common design’. That would be silly. Something you accept as common descent at low levels becomes common design at higher. Where does this happen? How would you identify it, using molecular genetics? Or is it impossible, because they look exactly the same?
stcordova,
Have you absolutely nothing to say on the use of the methods of phylogenetics and evolutionary biology in the analysis of pathology then? Never Happened? They Were Lucky?
You genuinely do not know how to generate PDF output?
There is no common ancestor between a PDF and a DOC file.
It’s likely a key point that Sal wants to get over to his students, and one that he wants to keep regardless of it’s veracity. That or he’s got you on ignore like me 😛
Sal really has quite a Graur obsession. In Sal’s revisionist history, Graur is all of evolutionary biology and he’s trying to get the NIH shut down. That is the story Sal is trying to construct so he can make it appear like evolutionary biology is a hinderance to science in medicine that can save lives. Sal knows it’s all a bullshit story he’s concocting.
Allan Miller,
Much harder than it is, I should say. It is rendered possible by the data, a curious fact in a world that did not in fact derive from phylogeny (beyond a certain, unspecified level).
stcordova,
Just to let you know I manfully resisted the opportunity to snark here. I deserve a medal or something.
Have to wonder why he’d put so much effort into cargo-cult science, it’s not as if he’s got much of an audience. Does he really think that his ‘paper’ is going to make a whit of difference? He’s only ‘published’ it here!
All Sal has to do is show a better way.
But he won’t of course. But he could try and that failure would be an invaulable lesson in reality I think.
So, c’mon Sal – give us the events as they actually really happened, step by step, from your POV.
stcordova,
Does this lead to the conclusion that there is NO underlying phylogeny?
One can generate artificial datasets, from real processes of copying. In fact that’s a way to test a method – generate a virtual phylogeny and let your method loose on it. If realistic enough, such datasets may well exhibit the same failure to converge on the One True Tree. But there is, nonetheless, a ‘true tree’ in such cases, because that’s how you generated the data. What leads us to conclude that natural datasets are different, when we see convergence on a set of equal-likelihood trees instead of one? And is there anything we can do to resolve the ambiguities?
Is it even necessary to know the one true tree, to be reasonably sure there is one? No.
The problem for you is that, given evolution with its chance component, that is what you’d expect. If it were exactly the same pattern from different proteins and genes, that would be miraculous.
As usual, you’re noting what’s expected and calling it a problem because the miraculous counterpart to your miraculous scenario doesn’t exist in science. That’s because it’s science, not creationist pseudoscience with its just-so claims.
Evolution has a real probabilistic component, which is what we find. It makes no sense–beyond creationism and its ignorance anyway–to fault evolution for yielding the probabilistic results expected of it.
Glen Davidson
Would that cure the McAffee warning if I converted it since macros are embedded in word files? If so, thanks for pointing that out.
I didn’t see the possible value of doing something like that, but if doing so will solve the problem, then participating in John’s discussion was worth the price of admission. Thanks Tom. 🙂
I second that. You’re a gentleman. 🙂
Then why are there conflicting phylogenies. Is it the incomplete lineage sorting (where zebra fish share genes with humans, but not with chickens)?
One thing that needs worth mentioning, the Smith-Waterman algorithm that drives the BLAST searches has a weighting matrix associated with it (like how much with is given to insertions and deletion in scoring identity). When alignments are particularly weak, the quality of comparison becomes dubious, not necessarily because of the algorithm but when does the concept of similar start to become virtually meaningless and phylogenies force fitted?
Protein phylogenies are particularly a problem since intron differences and the way stuff is spliced out can be very different, and focusing on the exons or the proteins hides a lot of important details. When I blastNed lysyl oxidase genes, the smith-waterman algorithm couldn’t even converge on a solution in some cases.
stcordova,
BLAST is probably the most coarse method one could use. No-one is going to publish a phylogeny based on BLAST. There is much cross-checking, using different methodologies and multiple alignments, trying to see the wood for the trees, heh heh. Every method has its advantages and disadvantages. It’s a matter of statistical inference, and there is not simply One Way. But none would work without some basic alignment.
Ok, I’ll acknowledge you didn’t even make a good showing interpreting a molecular taxonomy.
You said:
John was arguing over this diagram:
Here are some figures from the Dayhoff Diagram in Denton’s book that list the molecular taxonomic distances of cytochrome-C
Lamprey distance from Penguin : 18
Lamprey distance from Pekin Duck : 17
Lamprey distance from Pigeon: 18
Carp distance from Penguin : 14
Carp distance from Pekin Duck : 13
Carp distance from Pigeon: 14
Penguin distance from Penguin : 0
Penguin distance from Pekin Duck : 3
Penguin distance from Pigeon: 4
That tells me penguins descended from penguins, penguins descended from bird ancestors, birds descended from a vertebrate ancestor that was likely not a fish. If birds descended from fish, the more natural expectation would be something like the following hypothetical distance diagram:
Whereby lots of fish would be closer to birds than birds are to other birds. But that’s not the pattern we see, hence it is not believable to think birds descended from fish. But even that hypothetical diagram would be generous because one could just as easily say fish descended from birds!
Let’s not equate the actual fossil record with evolutionary interpretations of the fossil record. The BMP diagram shows a strong sister relationship between groups, not a mother/daughter relationship. Plain as day. Such diagrams suggest the evolutionary interpretation of the fossil record is wrong, and the creationists are closer to the truth.
The BMP (cytochrome-C, or name some deeply “conserved” protein) nested hierarchical diagram resists the interpretation of fish-to-amphibian-to-bird evolution. They are sister groups (fish, amphibians, birds) not grandmother-mother-daughter (fish, amphibians, birds) in relationship. One has to do a lot of over interpreting to insist on a grandmother-mother-daughter relationship between fish-amphibians-birds.
Even Nick Matzke had to finally come clean:
Even though I lost the original source of the following diagram, it has accession numbers that can be independently checked in places like Unirprot or the NIH NCBI databases. I don’t know what the outgroup was that generated the diagram, but lampreys (the supposed closest fish ancestor to birds) was so far below the similarity threshold it didn’t even appear in Uniprot searches, and I had to go to the NIH NCBI website and use a reasonable facsimile of BMP-2 protein for lampreys, hence likely the reason lampreys don’t even show up in the diagram.
[I had to do some digging to get a reasonable facsimile for lamprey BMP2 so I selected the lamprey BMP24/C because of this paper]
And even that protein just fell off the cliff when I used the NIH NCBI BLASTP comparison tool. So I believe the BMP diagram below is materially correct, and I expect for conserved vertebrate proteins (like cytochrome-C, or whatever) we will see similar non-random nested hierarchies highlighting the sister-sister rather than mother-daughter relationships.
Nick matzke was right and his admission and concession is well illustrated by molecular data below (not evolutionary interpretation of the fossil record).
I will insert my correction to Matzke’s statement:
First off, the “example” you mention here is not even a conflicting phylogeny. Second, gene loss in chickens (or somewhere in the lineage) is the obvious explanation. You keep trotting that out as if you knew what it meant. Now, there are conflicts among trees, though not to the extent you imagine. There are many reasons. Some are indeed due to lineage sorting. Others are due to inappropriate analytical methods. Others are due to just plain lack of decisive data. This is a big subject, and phylogenetic analysis isn’t merely a matter of looking at similarities and slotting them all into a single design. If that were true, the whole enterprise would have been done long ago. We could discuss some of the complexities if you liked, but we should at least start with the understanding that it isn’t all just made up to fit a preconceived notion. And you need to start with some knowledge of the conventional relationships, which apparently you now lack.
Force fitted to what? Do I sense a conspiracy theory?
One thing to realize at the start is that BLAST is not a phylogenetic analysis method or even an alignment method. It’s a quick and dirty assessment of similarity, not intended for prime time.
Rather than dipping your toe in the water without the requisite knowledge, why not study it at Univesity, Sal?
But I have some sharp guys here at TSZ very eager to teach me. 🙂 I mean, there is DNA_jock and John Harshman a professional phylogenticist and Joe and Tom English and Allan Miller and Neil R., etc.. Testing out and cleaning up and refining my ideas in this venue is priceless.
stcordova,
Talking of Joe, you might be interested in his book ‘Inferring Phylogenies’. Then you could tell him why it’s all ‘forced-fit’.
I am in University part-time evening classes, the NIH Foundation for Advanced Education in the Sciences graduate school. My classmates last semester were PhD students at Johns Hopkins, and a few were NIH post-docs. It’s not like I’m going to some 2nd rate venue to learn either.