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.
colewd,
In what way do experiments differ from observations?
John Harshman,
colewd,
This and your prior question on inference vs experiment are very valuable questions.
I will come up with a response tomorrow after some thought. Regarding your prior question on fused chromosome 2 I agree that if this is truly a pseudo gene then this is not a show stopper but the fact that so much of the telomere sequence is mostly eroded needs to be examined.
It has been pointed out that the paper your creationist got the telomere erosion from also proposed explanations for that erosion. You must ask yourself why, when asked to present evidence against common descent, you can only think of very feeble evidence (and some might uncharitably say it isn’t evidence at all). This is very similar to presenting as evidence that the moon is made of cheese a photo you took showing the moon to be the same color as white cheddar, while forgetting that several people have walked on the moon and even brought back rocks (not cheese).
reply
example
At that point, I mistakenly thought you were just a passerby with no professional qualifications, I didn’t realize you were varsity.
I don’t recall you ever made a retraction after you were called on it by the most respected phylogeneticist in the whole wide world:
Moved some posts to guano
colewd,
Sorry you’re having to get involved in the not-so-pretty side of discussions here. If you’re curious what I’m arguing for in this discussion it is this:
Even on the assumption of Universal Common Ancestry (UCA) being true and the acknowledgment that non-random nested hierarchical patterns in molecular data exist (such as what you saw in the diagrams I presented), the phylogenetic claims that argue fish evolved to birds is not a unique interpretation of the data, it requires auxiliary assumptions that are really based on circular reasoning, and if anything, it suggests the claim of fish evolving into birds is wrong. An impartial assessment of the data is that fish and birds have a sister-to-sister relationship not a mother (fish) to daughter (birds) relationship.
I don’t know how long this discussion will go because for it to conclude in a way that makes the point clear requires actual data. John is not really eager to dive into the actual data.
One thing I’ll point out that is simmering. For the longest time evolutionary biologists tried to justify their value to the scientific by its supposed contribution to medical science because evolutionary biology supposedly highlighted the similarities between creatures. In truth, there was no need for the assumption of common descent to see the similarities in the first place, and further, the phylogenies distorted and clouded and de-emphasized similarities that were anomalous to their story.
Worse yet, as you saw in one of the diagrams, there is an abundance of Orphan Genes, genes with no ancestors. What is really bad is that since Orphan genes don’t agree with evolutionary biology very well, an effort to actively erase them from databases is being recommended. This is a very bad move, there is nothing to gained from doing this, and lots to lose.
I reported it here when I managed the UD News desk while Denyse was working on another project:
Here is a case of evolutionary bias causing misrecognition of orphan genes in humans. Orphan genes are presumed protein coding genes that exist in only one species and have such non-similarity to anything in any other species they are called orphans (a play on words of the ORF acroym for Open Reading Frame).
This came up in the Nelson-Velasco debate where Velasco said there are 0 orphan genes, and Nelson pointed out the reason some say they are zero is because of their biases.
Nelson has been vindicated as I pointed out in New Mechanism of Evouion — POOF
Here’s is the proof of this cover up….
And now with the wars with ENCODE brewing, there is an active conflict between some evolutionary biologists and medical researchers.
So not only is evolutionary theory (the macro variety) not needed for medical science, it now starting to impede it. To retain their legitimacy they have to resort to equivocations where they argue finding ancestry trees among individuals in a population that can interbreed (hence the same species) is the same thing as the phylogeny of macro evolutionary change. But even assuming universal common ancestry, the phylogenies don’t make a lot of mechanical sense and it is a strained fit to the data.
I was hoping to have an easier time of showing the strained fit, but John is refusing to cooperate with the exploration of the genetic databases and providing accession numbers.
John doesn’t want to touch the Smith-Waterman algorithm as he insists it cannot show errors in phylogenetic reasoning which he deems above reproach. He only insists on using “phylogenetic methods” and will not accept that the method has flaws in it.
I held out hope he was going to cooperate with some data, but I guess I’m going to have to go to the public gene databases myself. This will be a bit tedious and I can’t guarantee a time line.
I have some interest in this topic, not so much to win a debate with John, but because I’m writing some material to teach high school and college students about these topics.
Neil:
The guanoed comments are here.
Sal, colewd,
I’m curious to hear your explanation of the following remarkable fact, described by Theobald:
Why is God so determined to make it appear that common descent is true? Why is he obsessed with mimicking evolution to a precision of dozens of decimal places?
And why not draw the obvious conclusion — the same conclusion drawn by intelligent and scientifically literate folks whose brains aren’t addled by religion? The evidence overwhelmingly supports common descent because common descent is true.
Separate creation, like the other forms of ID, is a fantasy. It’s completely undermined by science.
stcordova,
Nope, not true. She’s the MRCA of the mitochondria of all males and females. But she is most certainly not the MRCA of any other parts of anyone’s genome. Obviously, she’s an ancestor of everyone, but very unlikely to be the most recent common ancestor, even of all females. She is the most recent common ancestor of everyone through a strictly female lineage, but that’s not at all the same thing.
stcordova,
Based on this reply, I have to suppose that you have either not read or not understood almost everything I have said, as every bit of what you say is wrong, and I have responded to it many times. I don’t currently feel like responding again. Perhaps, instead of just dashing off a note to colewd, you could look up what I’ve said to you and deal with that explicitly. It’s conceivable that having my actual words in front of you would help you focus.
Let us assume for the sake of argument universal common ancestry is true, what patterns of similarity would you expect if the following groups were sister groups. Look at the sister groups of vertebrates for example below.
Suppose we had a common ancestor of all vertebrates which I will call VCA (Vertbrate Common Ancestor). I’m not going to describe what VCA looked like, but we can describe descendant sister groups based on grouping species into similar groups.
Now my drawing skills are not so good, but assume the arrows are actually the same length. Length of the arrow shows how dis-similar something is from the hypothetical VCA. Smith-Waterman can estimate the dissimilarity from the VCA by roughly cutting in half the similarity between groups. So let’s suppose we measured the dissimilarity of one mammal against a teleost fish and got 20%, the Mammal is then reasonably estimated to be 20%/2 = 10% different from the hypothetical VCA, and the teleost fish is assumed to be also 10% different from the VCA. The idealized result in this hypothetical scenario is that all the groups in the diagram are 10% different than the VCA. Obviously one would need mathematical refinement to deal with cases where this deviates from the ideal.
Now if, and “oh a big if” the VCA is a fish, the existing fish living today have to be different than the VCA by 10% for this molecular clocking to tick correctly. John Harshman suggested a close representative approximation of the VCA of all these groups is a lungfish. One is counting on the lungfish of today being about 10% different than the VCA-lungfish of the Devonian or whatever era the VCA was.
The figure of 10% is arbitrary at this point, but this what sort of number could be deduced from Smith-Waterman comparisons of individual genes.
In any case, the Smith-Waterman algorithm can in principle generate diagrams like the one below. So on what grounds will one argue a unique phylogeny given extant data? One could say a lungfish is a VCA, but on that diagram, one could argue “the VCA ain’t anything like any creature we know of”, in fact lots of common ancestors are described just that way because their physical structure is just plain absurd. See this essay on exactly that problem by Paleontologist Marcus Ross:
Problems Characterizing the Protostome Deuterostome Ancestor
So the first problem is that the molecular data may create nested taxonomic hierarchies from each gene, and creationist linnean taxonomists will also create nested taxonomic hierarchies from the morphological characters, but there is no formal way to assert what the common ancestor of all the sister groups is, and whether a representative of that group still exists — “TBD” could be the right answer.
So there is not a formal way of rigorously demonstrating what the VCA is without some level of just-so story telling even if common ancestry is true. That’s what I meant by unresolvable phylogeny, and that’s something that has little to no utility, certainly no experimental verifiability.
Like Matzke himself said:
But the unresolvability is on the beginning of problems. If one asserts some lungfishlike creature is representative of the VCA, and the intraspecific variation in lungfish species or the inter-group variation (like between coelacanth and lungfish) are small, this falsifies the phylogeny unless one invokes ad hoc kluges. This is because the molecular clock should still be ticking between coelacanths and lungfish since they diverged possibly 300 million years ago. I really saw the problems with microbial species.
1) Its infantile to speak about what science will or wont do in the future.
2) It’s churlish to want to ‘correct’ someone in this way. He’s an authority. You are famous for being wrong..
It’s always someone else’s fault why you can’t prove creationism is true ain’t it!
stcordova,
I think this highlights a problem evolutionists can never adequately deal with. if the molecular clock of change is always going on, why do we never see anything new. Never any new animals formed, never any new branches of evolution, even when we try our best to get one (like with selective dog or plant breeding, or long term bacteria cultures).
We never are on the way to anything, like to a new sense organ, a new use of a former function which will grow into a new feature. No new types of body plans, nothing. Just bacteria eating citrate, then going back to not eating citrate.
The clock keeps ticking and nothing ever happens.
Define “new”. How different must it be from the previous “thing” to be “new”?
How would that look? Should your dog shit out a cat?
By a new branch you mean a branch that splits in two? Then there are literally thousands of examples of that.
How do you know that none of the observed changes are “on the way” to something “new”? Have you been to the future to check?
What is a “new body plan”? How much must it be different from the previous body plan to qualify as “new”?
Eating citrate under aerobic conditions, when it could not before, is NOT new? Then what the fuck is? What do you expect to see? Should you grow wings on your ass and fly away in three generations? What?
phoodoo,
How fast do you think things should go? How long have we been looking at the watch as a percentage of its recording of time?
These are the most basic and foolish of creationist mistakes.
colewd,
Regardless what it is it is not a ‘show stopper’. Honestly, this is a pathetic argument against the fusion. Genes move.
It’s funny, though, that in this case the pseudogene’s paralogs are all telomere-associated. I mean, come on, own goal and all that …
What would it tell us? It is probable that many chromosomes arose from fusion events and their telomere and second-centromere sequences are no longer detectable. Evolutionists lose no sleep over this. Don’t you know why?
And I suspect Dr Matzke is unaware of Sal’s “correction”. Maybe someone should give him a headup.
stcordova,
I had a very similar discussion with you. If I recall correctly you thanked me for the correction when I said mtEve was not the MRCA of all humans.
Alan Fox,
He’s busy .. doing actual science.
stcordova,
Sal,
You should read the rest of Joe’s comment. His first sentence, which you interpret as ‘agrees with me’ is actually contradicted by the later paragraph. It is not possible to determine which DNA stretch coalesces upon our ‘true’ Most Recent Common Ancestor, among all the different MRCAs upon which different genomic stretches coalesce. But there is no special place for the mitochondrion in this, beyond the fact that it does not recombine.
It’s funny that you call Joe in as expert witness against John yet appear, by your arguments, to consider his significant contributions to the field of phylogenetic inference to be bunk.
stcordova,
The intraspecific variation in any species tells you little except the population’s recent history. It tells you knob-all about prior nodes of bifurcation, or deeper time.
Inter-group tells you a bit more, but just about that node, and you need to do more than just BLAST a coupla random exonic sequences. Why you would want to repeat analyses that the literature is full of, using plasticine and string, I don’t know.
No-one places the coelacanth-lungfish split in recent time. People have done the work. You think you can upend it with a couple of genes and BLAST?
Kenneth Miller: “• He [Tomkins] said there were too few telomere repeats in the fusion site. A “pristine” site would have 20,000 – 30,000 bases. But the fact is that “pristine” telomeres would prevent fusion, and treatments that dramatically shorten telomeres actually cause fusion, which is why there are so few repeats in chromosome 2. The small number of telomere repeats is exactly what should be expected at a fusion site.”
My bold.
Rumraket,
What did it look like when the first limbs appeared? When the first thumb? the first horn? The first tongue?
What about when that first thumb was just spreading through a population?
phoodoo,
I mean, its your alls theory, so I guess you know what new appendages and defense systems emerging would be like, so perhaps you can tell me what they would look like? Kind of like a rough patch of skin, or a deformity that doesn’t keep one from getting sex?
phoodoo,
So you’ll know how the Designer did things then – zebras, say? Maybe started with the stripes and worked inwards? Ears down? Hooves first? Grew little embryo zebras in a glass jar?
Allan Miller,
So you are admitting your theory is useless at describing it?
phoodoo,
At least in our theory we don’t have to imagine some half formed tongue, or new spleen just emerging as some accident.
Ah, but see, it’s our job to do science, and it’s their job to make fun of it.
It’s the Lord’s work–of making those who never troubled to learn things look bad.
Glen Davidson
GlenDavidson,
Awesome! So you learned what a new kidney starts off as? Any prospects for some new kidney like organs in some creatures in the near future?
I said no such thing, and I’ve told you this before. You have three main sources of confusion in those two sentences.
1. You assume that there is indeed a molecular clock ticking at an absolutely constant rate. This is closer to being true for some genes than for others, but it’s certainly not a reliable assumption. This is why phylogenetic analysis methods do not make that assumption.
2. You consistently confuse modern sister groups with ancestors. Lungfish are the living sister group of tetrapods, but lungfish (even the oldest lungfish) are not ancestral to tetrapods.
3. You equate the vertebrate common ancestor with the common ancestor of tetrapods and lungfish. They are not at all the same.
Everything you say subsequently about phylogenetics is nonsense.
Actually, there is a formal way, if you would just look at the literature. It falls under the general term of “optimization”. Given a tree, we can estimate the states at ancestral nodes. “Whether a representative of that group still exists” is again nonsensical; no, the common ancestor doesn’t exist any more. A “representative of that group” would mean any of its descendants. What I think you mean is something that looks to you rather similar to the ancestor. That’s your personal, subjective impression, so it isn’t really worth talking about. I will just point out here that, just as there is no perfect, universal molecular clock, there is also no perfect, universal morphological clock.
Your shameless misunderstanding of Matzke’s commonplace observation, even after having been corrected several times, is reprehensible.
They gradually transformed from fins to limbs. If you are talking about tetrapods. There’s a nice transitional fossil series.
At what point does it go from just another toe or finger to a bona fide thumb?
You know some humans are born with six or seven fingers on one hand, right? Is that new enough for you?
You tell me. How long do we have to wait to see some results?
???
We do “see” new creatures evolve. Here:
http://phys.org/news/2016-02-species-evolve-real.html
http://listverse.com/2011/11/19/8-examples-of-evolution-in-action/
It would be alarming, to say the least, if we did see any that. What you are describing above could only happen over hundreds, if not thousands, of human life times. As of 2016, we’ve had the tools to actually start looking at evolution in real-time for what…one hundred years? Maybe? So why would you expect to be able to see a new body plan or adapted organ?
Well things do happen. You just want something that can’t actually occur to happen.
phoodoo,
Hard to see what you do imagine. First nothing. Then zebras. Lots of ’em. Just like that. Curiosity fully assuaged.
phoodoo,
Kidneys never happened because kidneys do not continuously happen. Is that the meat of your argument, phoodoo?
Yea, but like Rumraket says, we do occasionally see people with six or seven fingers. So, you say it takes thousands of years, but they didn’t have to start today.
Shouldn’t we maybe see pockets of people with seven fingered hands, competing against those with five, to see which is more viable for more offspring?
Or something? Anything?
Peppered moths and Darwinian finches? Really Robin?
Polydactylism is an example of mutation Phoodoo, not fixation or even selection, so I have no idea what point you’re trying to make above. Rumraket’s point is that we do see the underlying working mechanics for new body plans, which is a wonderful confirmation of our understanding of evolution. I’m betting it’s not what you had in mind when you asked for new body plans however.
Two things: 1) for that to happen, there would have to be some selective pressure on six or seven fingers (or even four or three). Since we know there is no advantage, either mechanically or cost-wise to having more or less than five fingers, no one with some biological knowledge thinks humans will ever evolve into a six or seven (or four or three) digit species. It just isn’t physiologically or economically feasible. 2) assuming for the sake of argument that some environmental or…say sexual…issue favoring six or seven digits arose, then it would still take that hundreds if not thousands of human life times I mentioned above for the competition to establish one over the other. Heck, if would take hundreds of years just to start to see a trend towards fixation.
See above
Yeah…really. What’s wrong with either Pepper Moths or finches as examples of actual, documented evolution in action?
Robin,
What do you think they turned into?
Do you think poodles are examples of evolution?
I would say its more like, if kidneys happened the way you say they did (and brains, and scales and stingers), why have they all stopped?
phoodoo,
How do you know know it’s stopped? We are not observing processes taking thousands of years in our lifetimes. Hmm, wonder why that could be.
But anyway, why would a lineage furnished with one of these organs be expected to grow more?
But the problem you face saying stuff like that is that lungfish today look a lot more like the lungfish of the Devonian than they do like birds of today. I’m not confusing the modern sister group (modern lungfish) with ancestors (lungfish like), I am pointing out if you had the supposed lungfish-like VCA today and actual lungfish of today, a taxonomist or pheneticist would put them in the same group owing to their similar anatomical features. That’s why I referred to Matzke as “two faced”.
As far as the molecular clock, this is what I was saying about ad hoc klugery. The above drawing I made is astonishingly reflected by the Dayhoff Diagram provided by denton on the Cytocrome C protein.
I should first point out, there is a difference between a Taxonomic Nested Hierarchy and the supposed Phylogenetic Nested Hierarchy. The creationist since Linnaeus accepted the Taxonomic Nested Hierarchy. All of the non-random patterns of nesting in the taxonomic hierarchy are accepted even by creationists, in fact they were the ones to first start codifying it!
Evolutionists tried to explain how the Taxonomic Nested Hierarchy could be generated by a Phylogenetic Nested Hierarchy but the problem is that when one does a morphological comparison between lungfish today vs. lungfish of the Devonian, and then lungfish of today vs. birds, the lungfish of today look a lot closer to lungfish of the Devonian than to birds by large margin. And this suggests their genes didn’t change much, and this can be confirmed by looking at inteterspecific (within species) variation and seeing how the molecular clock is doing. If there is low interspecific variation, one has to kluge things with a recent MRCA and then some.
To settle the question further, we can go to creatures in the same group whose MRCA is far back like the coelecanth and lungfish that had supposedly already been diverged around the time of Devonian. The clocks should still be ticking for 300-400 million years between coelacanth and lungfish. But I suspect there isn’t much molecular distance in their genes as compared to birds. This is deeply problematic if one wants to maintain a semblance of a molecular clock. But one needs a molecular clock type to explanation the patterns of divergence between groups that are like my drawing above. To maintain the narrative that the taxonomic nested hierarchy is generated by the phylogenetic nested hierarchy, one needs ad hoc kluges to invoke molecular clocks when needed and then declare them broken (such as in the case of interspecific or inter group variation).
My drawing above reflects the distance matrix and taxonomic nested hierarchy below. For phylogenetic nested hierarchies concocted from supposed paleontological narratives to create taxonomic nested hierarchies, there is too much ad ho klugery needed. One can assert UCA to explain the patterns in my drawing which really are from the Smith-Waterman generatable Dayhoff matrix below. The problem is that “TBD” rather than some fish looking like creature is also a plausible candidate for the VCA, and invoking fish-looking creatures creates clocking problems where one has to apply the molecular clock in an arbitrary way to suit the narrative. This has no resemblance to experimental science and not even a coherent marginally self-consistent observational narrative.
Allan Miller,
Evolutionists always say this- it takes a long time….But its nonsensical. The time didn’t start today! It should have started 500 years ago, 1000 years ago…a few individuals started getting a new feature that others in the same population don’t have. So you need some animals in the population with five digits and others with seven. Some individuals in the population with three kidneys and some with only one. Pockets of new features. Pockets of new mechanisms.
Where in the heck are they? They don’t need to have started today. There should be a continuum of every possible progressions.
I’m not sure what you are asking about here. Are you asking what I thought pepper moths and finches “turned into”? If so, then I don’t think you have an accurate understanding of evolution.
Evolution is NOT some group of animals “turning into” something new. Evolution is simply the development of new traits within a species population that may or may not become fixated based on selective pressure (environmental advantages, sexual advantages, etc). Even IF a given trait becomes fixed, that doesn’t mean that the parent population will be out-competed by the “modified relatives”, so there’s rarely – if ever – any “turning into something new” in evolution. New species, genera, orders, families, etc emerge over time because changes in populations accumulate and compound the relative dissimilarities between populations, but this really isn’t a case of “something turning into something else”.
Of course they are. Any group of organisms that has traits that are different from some parent stock is an example of evolution. Do poodles have different traits from wolves? Why yes…yes they do! Do they have different traits from Great Danes, Irish Wolfhounds, Boxers, and Golden Retrievers? Why yes…they do indeed have that too! Are they a “fixed” population? Oh…why yes they are (within a human environment)! Then that would be an example evolution.
stcordova,
As I’ve said, I’m never sure whether you really mean interspecific or intraspecific when you use the terms. I assume inteterspecific is a typo, but anyway within-species is intraspecific. But you can’t use intra specific (within species) variation to ‘see how the molecular clock is doing’.
And, as a more general comment, over-reliance on the cytochrome c phylogeny is so 1970’s.
phoodoo,
While the feature is in process of formation, any potential candidate brought to you would be dismissed with “huh. That’s not a new organ”. When it has reached the stage at which you might be impressed, you’d say “huh. You never showed it evolving.”
What, like trees with kidneys? Or mammals with 2 perfectly functioning kidneys growing a completely different mechanism for doing the same thing? I’m not sure you’ve really thought this through in depth.
Rumraket,
Are you satisfied that Kens argument here closes the case? Why does he expect dramatically shortened telomeres? Do we have evidence of fusion events that would back up Kens claim?
What do you mean by “stopped” Phoodoo? And how do you know they have “stopped” according to what you mean by the term.
Again, I think you’re demanding something of evolution that no one who understands the process states could occur. Major organs within a species change really s l o w l y. I mean think about…what selective advantage would there be in changing an organ in the short term? So no human is likely to see a major organ change within a human life time.
Make no mistake…they do change. My kidneys did not grow from birth. That’s a change. Not a good one, but it’s a change. It’s a change that most definitely won’t be selected for at all, but again…it’s a change. And that’s the point. All sorts of things change within populations in every generation. The question is whether some change provides some sort of advantage in some given environment. That’s the part that’s key. But again, even if it’s an advantage, that doesn’t mean that parent group that does not have the change is suddenly at a disadvantage. Environments are generally large and have many varying conditions. So groups of organisms can have all sorts of variations and not necessarily promote one single dominant trait.
The point is, your claim that kidneys and brains and scales and stingers have “stopped” does not reflect reality. All sorts of traits change all the time. It’s simply a question of whether the environment sports a reason for the trait change to continue and spread through a population.
Some literature uses interspecific, but I like intraspecific better as a word. How about I use that.
Yes you can if the species members are geographically isolated. 🙂
The next best thing is to take a group whose members have diverged and then clock the variation like between coelacanth and lungfish.
It’s not a phylogeny, it is a taxonomy. Don’t confuse taxonomy with phylogeny, and if you want to claim that diagram is a phylogeny, “TBD” should be the common ancestor of all the taxonomic groups, but that would sort of break the spirit if phylogeny if one wants to say birds descended from creatures looking like fish.
You can generate the diagram on data today, and I see it in textbook in various incarnation.
And if you don’t like cytochrome-c, we can use other proteins if someone (hint hint) would be willing to provide sets of accession numbers.
stcordova,
Jeez, Sal. I point out what’s wrong with your claims, and your response is simply to repeat your claims. How can this be useful?
1. The common ancestor of all vertebrates is not the common ancestor of humans and lungfish; it’s a lot older than that.
2. Devonian lungfish are not the common ancestor of humans and lungfish. That ancestor would be the ancestral sarcopterygian, neither a lungfish nor a tetrapod.
3. There is no morphological clock. I will agree that modern lungfish, at least to human eyes, look more like Devonian lungfish than modern humans look like our Devonian closest relatives. So?
4. The cytochrome c in your table actually seems to show a pretty good molecular clock, so I have no idea why you think it supports some claim of yours. (And by the way, that isn’t a Dayhoff matrix, which would show the cost of transitions from one amino acid to another.)
5. There is no “creationist Taxonomic hierarchy”, just a taxonomic hierarchy. There is no creationist justification for a nested hierarchy of life other than “god decided to do it that way”, which is not very useful.
6. Genetic change is not very strongly linked to morphological change. Lots of genetic changes don’t affect morphology at all. Even many changes to proteins don’t affect morphology.
7. Some species differ by a lot, others not so much. Species that look similar may be genetically highly diverged. Is this too hard to understand?
8. It may indeed be that for many genes, lungfish and coelacanths are more similar to each other than to birds. Some groups evolve more slowly than others, though again molecules and morphology (or even different molecules) may not have correlated rates of evolution. This, again, is why real phylogenetic analyses do not a priori assume there is a universal evolutionary clock, as you do here.
9. No, your drawing reflects what we call a “star phylogeny”, and in fact a star phylogeny in which there is a perfect clock. If you took distances off that phylogeny, every species would be equidistant from every other species. That is not at all what your table shows. See how the distances vary across the table? And they do so in a systematic way that’s consistent with the known phylogenetic tree. Why, turtles are even closer to birds than to mammals, which the person who made the table may not have known.
10. The first step you need to take here is to gain a little humility. Don’t think you’re more of an expert on this subject than the actual experts. Be prepared to learn from them. As far as phylogenetic analyses go, that would be Joe and me. Apologies if anyone else here is a systematist.