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.
No, read again. He wanted a candidate basal osteichthyan (though he didn’t exactly know that’s what he wanted; he asked for the common ancestor of a bird and a fish, when by “fish” he meant a teleost).
Not that I know of. Unfortunately, the big genomic sequencing projects have focused almost entirely on other birds. Given how cheap this stuff is all getting, it will happen some time.
I get the distinct impression that you’re building up to the old creationist “What use is half an eye?” argument.
What do you consider “mechanically feasible” vs “mechanically infeasible”? What evidence do you have for any “mechanically infeasible” transitions in the history of life? How does your argument differ from the usual creationist argument from incredulity?
Patrick,
Or perhaps he was going to ask what is the use of two optic nerves and only one eye?
Nope. I did, when I complained about your BMP2 tree not having the proper taxa.
No, that isn’t what I’m complaining about. You really have no clue, I’m afraid. Not sure why. I was complaining that you said evolutionary theory asserted birds descended from teleosts (your first claim) and then lampreys (your second claim) and finally from Latimeria (your third claim). You haven’t got it right yet. Again, not sure why. But it shows you have little understand of what evolutionary biology actually claims.
I’m beginning to think you have no idea what you mean by “sister relationships” and, most particularly, “fish”. The fact that we can check pathogen evolution (sometimes) with laboratory samples is actually good evidence that phylogenetic analysis works, not a problem for it. “Mechanically feasible” to you is just a buzzword meaning “Sal can personally imagine it happening”. I’m also starting to think you haven’t thought about the meanings of “observable” and “testable”.
Once again, the problem here is that you don’t know what you mean by “fish”. I’ll say it again for perhaps the fifth time, just in case you read it this time. Your BMP2 tree shows only teleosts. Teleosts are not ancestral to birds or any other tetrapods. No living species is ancestral to any other (with a few exceptions we can ignore for now). Ancestors are all way in the past. Lungfish are not ancestral to birds. Coelacanths are not ancestral to birds. Sharks are not ancestral to birds. Lampreys are not ancestral to bird. However, the paraphyletic group to which teleosts, lungfish, coelacanths, sharks, and lampreys belong is commonly referred to as “fish”, and an ancient member of that paraphyletic group is ancestral to birds as well as all other tetrapods. Panderichthys, while probably not this ancestor, is certainly a close relative of the ancestor. Panderichthys was a fish. Tiktaalik was a fish, sort of. Ichthyostega was pretty close to being a fish, except that it had legs. Pretty sure each of those species was mechanically feasible, too. If you want “fish” to be a monophyletic group, you have to include birds and other tetrapods. Is any of this sinking in?
No I didn’t. I said that a lungfish (most likely) or a coelacanth (less likely) was the closest living fish relative to birds.
I love how you add “supposed” and “for the sake of argument”. It’s good to be reminded that you’re a YEC. We really should discuss geology some time. This really is the “why are there still monkeys” argument. Are you sure you want to make it? I’ll give you a chance to reconsider.
Nope. Because that’s what both the fossils and the phylogeny (based on living species, especially their genes) tell us. There was no predetermined conclusion, just conclusions based on data. Again, you seem to be unclear on what “fish” means, and keep imagining that teleosts are the only fish.
Lots. They separated from each other way back, probably in the Devonian.
Actually, it would mean that at least one of the assumptions I mentioned a while ago was wrong: 1) that BLAST is a measure of genetic distance; 2) that genetic distances are patristic distances; 3) that evolution is precisely clocklike. Still, I suspect that most sequences would show approximately equal distances among the three groups, since the branch connecting the apparent lungfish-tetrapod clade to coelacanths is probably short, and the molecular clock is often not a bad approximation. Note that real phylogenetic analyses do not use BLAST, do not in fact generally use genetic distances, and do not assume a molecular clock.
Are you acquainted with the term “word salad”? I am unable to determine what you mean here. What does infraspecific variation have to do with this? And did you know that there are at least two species in the genus Latimeria and at least three genera of lungfish? You really should stop talking about “the coelacanth”.
Again, BLAST is not phylogenetic analysis. How about I cite a real such analysis?
Here is the first one I found that wasn’t paywalled (again, representative of a great many I could have cited): Shen X-X, Liang D, Wen J-Z, Zhang P. 2011. A case study of tetrapod phylogeny focusing on the position of turtles. Mol Biol Evol 28 (12): 3237-3252.
That just isn’t the proper way to go about it. Phylogenetic analysis is what you need here, not BLAST searches.
By the way, I don’t know how to upload images. How does that work?
Heh. Though I have seen my share of obtuse creationist questions about evolution around here, to be fair, the all time most stupid question was erected by Ray “Banana Man” Comfort at his appearance on Pat “Fraud” Robertson’s TV show.
Behold, the Dumbest Creationist Question of All Time: This is nothing if not painfully stupid.
Rumraket,
Comfort actually seems to be criticizing special creation. Let’s see, can we think of any hypothesis in which a male of a species appears without a female, and problems ensue as he looks fruitlessly for a mate, until someone steps in and finally (after exhausting all other options) makes one for him?
Imagine God taking credit for designing Ray. Or Dembski.
It seems self-defeating for these people to speak for ID/creationism–except that they have many ignorant folk to baffle with their bull, and, the more they can keep them ignorant, the better.
Glen Davidson
John Harshman,
Are you aware of the eclipse experiments? John, these are experiments that allow repeatable data collection. Do you have an experiment that can show repeatable evidence that man and apes split from a common ancestor?
Yes, historical science requires an inference based of evidence but this makes it much more difficult to get an accurate hypothesis.
BTW thanks for the paper. I hope to finish it tonight when I get home.
Again with the creationist trope that experiment is the only real model of science. No, I don’t know of experiments, but I do know of repeated, independent data collection and analyses. In one sense, sequencing the same genes and species again is repeating. In another sense, sequencing different genes, or scoring morphological characters, or finding new fossils is repeating. Yes, repeatable observations do establish common ancestry of humans and other apes. This is evidence of a caliber that only a committed creationist would deny, so you might as well come clean.
By the creationist “historical science” standard, we can’t convict murderers beyond reasonable doubt, since we can’t travel back in time and experimentally reconstruct the murder taking place.
Which just goes to show the double-standard creationists have, because in the vast majority of cases they really do think we can know “beyond reasonable doubt” who the murderer is, despite not having been present to directly witness it ourselves.
In Sal’s parlance, joining the ends of this bridge is “mechanically infeasible”.
colewd,
Could you indicate the kind of thing you have in mind? Designing experiments that would satisfy you might be too tall an order for anyone. Do you actually want to see a single species split into man and ape clades [eta – yes, I know, man is in the ape clade …] in the lab?
And yet, textual analysis shows that the Bible is correct, don’t you know. You can figure out the phylogeny of Biblical texts, you know, by comparing how similarities and differences appear and propagate through time, and figuring out the textual families that way. Sort of like clades–human clade and chimp clade, for instance.
I guess that’s because we can observe what happened 1500 years ago when some anonymous scribe made an error.
Glen Davidson
Those are observations, not “experiments” in the classical sense. You collect data (observations of the position of mercury), then you make a model that accounts for that collected data, then you calculate additional predictions from the model (what you should expect to see at a later time if the model is correct), then you wait until the opportunity is good and do your observations again and see if they fit the model.
This is EXACTLY how the theory of common descent works.
You collect data (genetic, morphological, fossil chronology etc. etc.), then you make a model that explains that data (common descent), then you derive predictions from the model (undiscovered organisms, unsequenced loci should fit into the hierarchy in such and such a way), and then you make your observations and compare them to your model.
Common descent is AT LEAST as well attested as General Relativity. It just is, and by the same method. Get over it.
Yeah one wonders what the hell he has in mind. Does he think we put a Rhesus monkey in a cage and wait until it gives birth to a Gorilla and Ken Ham?
He means experiments with all of the rigor of the experiments indicating design by an unknown designer, of course.
No, wait, it can’t be that…
Glen Davidson
Rumraket,
Now that looks like photographic evidence of Chromosome 2 in the actual process of fusion to me. I’m convinced.
Just click on “upload file” in the message box and select the file you want to upload. It should then appear at the end of your comment.
It does need to be less than 200 Mb.
John,
There’s a box above the combox that says
Click there. The image you select will be placed at the end of your comment.
Allan:
You evolutionists are so gullible. It’s obviously photoshopped.
Don’t represent your misinterpretation of what I said as what I actually said. Like others here you reassure yourself that I don’t understand by appealing to arguments I actually wasn’t making.
I put up diagrams of stuff like teleosts because they are representative of fish, and now you said you don’t even know for sure what fish birds descended from.
You’re the one who mentioned lampreys, and if you’d knew of my writings from even 3 years ago you’d realize, contrary to your false claims, I actually do understand some things. I was just humoring your unclear communications by mentioning lampreys since you brought lampreys up.
Note what I actually wrote about 3 years ago, July 22, 2013:
You’re just so quick to criticize arguments I’m not making. Is that because you’re having a hard time actually dealing with the actual arguments I am making? And don’t presume that because I misinterpret something you say, it’s because of my lack of understanding of evolutionary theory, you’ve said things in a confusing way and you even have said some outrightly wrong things as witnessed in our discussions here at TSZ.
So before you throw around accusations, think first if you’re just listening to your own misrepresentations of what I said vs. what I actually said.
But I’m not here as part of a public advocacy as some of you might think I am, I here to get review of what I actually think and test out my ideas.
BLAST/Smith-Waterman is an impartial comparison of similarity not polluted by phylogenetic reconstructions. How do you think this similarity diagram below was generated, certainly not by those real [sic] phylogenetic analyses. Those factual comparisons such as derived by NIH tools like BLAST are more important to medical science then the claim “fish evolved into birds”.
You’re so steeped in phylogenetic reconstructions and story telling you’ve stopped looking at molecular data impartially without preconception. That’s one reason you think birds are a credible descendant of fish (whatever fish of your choosing, and as of right now, you’ve said evolutionary biologists may not even know what that fish was, lungfish or coelacanth being a reasonable facsimile).
Think about what the diagram below and the molecular taxonomies I’ve provided (BMP-2, Cytochrome C). Compare that real data to your mythical phylogenetic reconstructions, and it will indicate there is a conflict between the phylogenetic reconstruction and the similarity data as measured impartially by the Smith-Waterman algorithm, and for that matter plain old common sense – birds don’t look like fish!
So how about you suggest some accession numbers and we’ll settle this the scientific way, with testable computations. Maybe you’ll see the light, maybe not, but this would be a worthwhile exercise in using real data with impartial comparison methods like the Smith-Waterman algorithm.
Zachriel directs my attention to one of John’s comments:
Zachriel,
We’ve been over this already. From our original 2012 discussion:
keiths:
And:
And:
I tried that just now. I see that it worked, but only after posting. More feedback would be nice. But here, for Sal, is a tree of relationships among some vertebrates, constructed from protein sequence data, taken from the paper I cited just a while ago.
Possibly because common ancestors no longer exist and cannot provide genomes.
Since you are the biggest jesus fucking mary expert on biology, you are no doubt aware that genomic evidence occasionally overturns or clarifies relationships among extant species. Birds are among the leading examples of this.
We won’t bother with this here, as it is off-topic, and you weren’t able to follow the forum rules, anyway. We’ll return to lurking.
Such a great argument you were making there, too. Ooh, see dat, tuna look more like lungfish than they look like humans.
It’s hard to care what you write about these matters, since it rarely rises above the abysmal.
Glen Davidson
If you weren’t making those arguments, you are either a very bad writer or you misunderstand the implications of what you say.
Either that was very bad writing or you have no clue about phylogeny. Teleosts are representative of one group of fish, but, as you claim now to know, some fish are more closely related to tetrapods than to others. But if you know that, it’s hard to see how you could have said much of what you have previously claimed. Such as your claim that the evidence is as good for descent of fish from birds as birds from fish, or your weird ideas about what a molecular clock ought to show.
Not sure what you meant by “what fish birds descended from”. Are you referring to a species or a group? As I’ve explained several times, it’s impossible to identify ancestral species. They’re all way in the past, so no extant species will do. It’s unlikely that any known fossil is an ancestor given the spotty fossil record. And if it were an ancestor, there’s no way to affirm that with confidence. But we can certainly narrow down the node on a phylogenetic tree that ancestor occupies and use the tree to determine what it looked like. None of this should be a surprise to such an expert on phylogenetics as yourself.
Ah, blame the victim and “I was just kidding”, both in one sentence. Bravo.
Note what I actually wrote about 3 years ago,July 22, 2013:
A snide comment with no argument other than an implied “hey, two fish look more similar to each other than to Indiana Jones”? That’s the sort of thing you want me to see? I’m afraid that shows just the opposite of what you’re trying to demonstrate to me. It shows your arrogant ignorance.
Such as? Seriously, I don’t know what you’re referring to here.
Your obsession with medical science to the exclusion of all else is one of the things this thread is about. Now, if by “this similarity diagram below” you refer to the BMP2 tree you have put up many times, I don’t actually know how it was generated, and neither do you, because you can’t tell me where it came from so I can look at the methods section of the paper. But BLAST does not build trees. BLAST does pairwise comparisons of sequences. This notion you have of “polluted by phylogenetic reconstructions” is odd, and suggests that, once more, you have no idea how phylogenetic analysis works; if you disagree, could you explain what pollution you’re talking about?
Once again you say things that tell me you have no clue about phylogeny. No, lungfish and coelacanths are not reasonable facsimiles of the common ancestor of “fish” and birds. You appear not to be able to distinguish between ancestors and living sister groups. Lungfish (or conceivably) coelacanths are the latter, not the former.
There is no diagram below. Apparently it isn’t the BMP2 tree. Nor have you ever provided any taxonomies, molecular or otherwise. Put that down as another word whose meaning you don’t know. You provided a tree using BMP, and you gave a table of pairwise comparisons among cytochrome-c sequences. Neither in any way contradicts the standard phylogeny. That you imagine they do is yet more evidence that you know nothing about phylogenetics. That you also imagine “birds don’t look like fish” to be an argument is evidence that you know little about reasonable discussion too.
“Testable computations”? It’s this sort of word salad that helps make you a laughingstock. Once more: BLAST is not a method of phylogenetic analysis; it does not determine relationships among taxa. Real (yes, real) phylogenetic analysis does not involve story-telling but algorithms that objectively compare the fit of different trees to data. It’s not a question of impartiality; it’s a question of function. You can try to repair a pocket watch using butter, but even if it’s the best butter it won’t repair the watch. For that you need to use watch repair tools. I have explained previously the assumptions you would have to make in order to turn BLAST results into a hypothesis of relationships, but you have ignored that as you ignore most of what I tell you.
Zachriel,
Because you weren’t able to remain honest. Besides, when did you become such a delicate flower? You’ve experienced far worse at UD without bailing out of the conversation.
Feel free to delurk if you come up with an answer to this:
John Harshman,
This is not my claim. My claim is that a tested hypothesis carries a higher scientific standard than an inference.
W.H. Newton-Smith (ed) A Companion to the Philosophy of Science (Blackwell, 2000) 184-193.
Inference to the Best Explanation PETER LIPTON
colewd,
Relevant observations are tests of a hypothesis.
The hypothesis of common descent has been tested thoroughly, and it has passed the tests with flying colors.
keiths,
I agree, so why don’t we claim the evidence is so overwhelming that it is a fact.
Oh yea, some evolutionist marketers already beat us to the punch.
My claim is that a tested hypothesis is an inference. What’s the difference?
Well, that is what “fact” tends to mean: a hypothesis for which the evidence is overwhelming. And I see no difference between a “tested hypothesis” and an inference. What is that difference?
By the way, I’ve looked at your reference, and I find nothing in it to support (or even mention) the claim you make above.
Quite.
Here’s Lipton commenting on ID:
Looks like he covers a lot of the problems of ID in a short space, although the fact that organisms apparently exhibit the constraints of unintelligent evolution alone counts for more than what he mentions, imo.
Glen Davidson
Well, this is just plain wrong. The simple fact is, “an inference” is essentially the outcome of “a tested hypothesis.” There’s no such thing as one without the other.
http://www.sjsu.edu/faculty/gerstman/StatPrimer/hyp-test.pdf
http://isites.harvard.edu/fs/docs/icb.topic129780.files/Lecture_4/Evans_lecture4.pdf
https://en.wikipedia.org/wiki/Statistical_hypothesis_testing
Well, we rely on free plugins. If it would help, I can increase the file-size limit.
No, the file was only 64K or so. It’s just that there was no visible result from clicking to upload. Nothing appeared in the post until it had already been posted. But I guess now I know that it works.
You just gotta have faith! 😉
Alan, Keith: Get a room.
Sorry for the derail.
John:
There’s already a room, if Alan insists on indulging his grudge.
colewd,
Sure, why not? The evidence for common descent really is that overwhelming.
Why don’t you read (actually read) Theobald so you’ll know why I say that?
The theory of common descent has been tested literally millions of times.
Yep. It’s a fact because the support is so overwhelming it would be perverse to deny it(once actually understood).
Did you start reading Theobald yet?
Miller’s response:
“Most of the genome databases show the DDX11L2 sequence as off to one side of the fusion site, so it really doesn’t span it. However, in some of the databases there are transcript variants that include the head-to-head telomere sequence motifs as one of the introns in the primary transcript. That is basis on which Tomkins claims that the gene spans the site. But the very same data are easily explained by variability in the termination of transcription so that occasionally a somewhat longer RNA is produced. This is exactly what I pointed out to Tomkins….So that any claim that I “admitted” he was right about his interpretation is bogus.”
My emphasis. Read for comprehension.
Rumraket,
I did.
Look, it’s a pseudogene, not a gene, that’s occasionally transcribed, never translated, and then occasionally transcribed with the sequence extending into the ex-telomere repeats. In what way is that an argument against fusion?
Rumraket,
Rumraket,
This is not the experiment that validated general relativity. per wiki
The first validation was Eddington in 1919 and several experiments later validated the theory by predicting the amount of deflection of starlight during an eclipse. This validate the curvature of spacetime was repeatable and could be predicted by Einstein s General Relativity equations.