Phylogenetics. Huh! What is it good for? Absolutely nothing.

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.

335 Replies to “Phylogenetics. Huh! What is it good for? Absolutely nothing.”

  1. Alan Fox Alan Fox
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    Rumraket,

    And that inflatable snout! Adaptive or sexual selection?

  2. Rumraket Rumraket
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    Does this tiny tail constitute a remnant of a bigger one? Like on the Otters?

  3. Alan Fox Alan Fox
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    Manatees seem to have been a fruitful subject for phylogenetecists.

  4. Allan Miller
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    stcordova,

    Well, when you put it that way, the gap between Chimps and Man does look unbridgeable.

    So the big difficulty with the Common Ancestor hypothesis for Chimp/Man is that there are differences!

  5. Rumraket Rumraket
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    Phoodoo seems to be laboring under the delusion that evolution is over and nothing is in the process of changing. What a strange idea to have, one has to deliberately pretend to know nothing about extant biodiversity to entertain that crap. All he can do now is to just double down and staunchly assert that these organisms all are what they have always been and they will always be. But how can he know this?

  6. phoodoo
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    Its your theory Jock, not mine. I am just trying to give you a chance to show some examples.

    So do you want to claim that polydactylism is an example of evolution in action? Can this be an avenue for a new class of animals? Can this become a new gene with new functions? Because that’s what you need isn’t it. And then eventually these cats can’t breed with other cats right? Because they are no longer cats. They stopped being called felis catus, they are now felis catches.

    Its the same stupid reason why poodles are not an example of evolution. Because everything that forms the different dog breeds are just variations and mutations to existing genes with no new genes ever created. Dwarfism, hyperthyroidism, cleft palates, syringomyelia…

    A centuries worth of selective dog breeding has done nothing to “select” a new, viable animal. Instead what it has done is just taken a common wolf, and made it sicker and sicker. The more pure you try to make a dog breed, the more you destroy it. You can never reach the magic endgame of evolution, something new.

    So I guess polydactyls aren’t going to get it done. Sarcastic or not, your theory still isn’t working.

  7. Rumraket Rumraket
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    phoodoo: Because everything that forms the different dog breeds are just variations and mutations to existing genes with no new genes ever created.

    At what point does a gene become “new”. If a duplicate is spawned, does it take one, two or eight percent of the nucleotides to transform it from “the same” to “new”?

    Does a “new” morthological feature REQUIRE a “new” gene too, now? It only counts as “new” when it’s associated with a “new” gene? How many more goalposts can you erect in this idiotic whack-a-mole type argument?

  8. Rumraket Rumraket
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    phoodoo: The more pure you try to make a dog breed, the more you destroy it.

    The more you inbreed them the less variation there will be and the more prone they will be to errors in homologous recombination.

    OMG EVOLUTION MUST BE FALSE.

    phoodoo: You can never reach the magic endgame of evolution

    That’s because there is no “endgame” to it. Why the hell would you think so?

    phoodoo: something new.

    What is new? Define it.

  9. Allan Miller
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    phoodoo,

    Its your theory Jock, not mine.

    No, it’s yours. It bears no relation to evolution as commonly understood in biology, just some weird phoodoo version of ‘if evolution was true then …’. No-one expects part-populations of trees with kidneys or tigers with stings but you.

  10. phoodoo
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    Allan Miller,

    Then how did we get kidneys?

  11. Allan Miller
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    phoodoo,

    God just went ‘ping’ and created a whole bunch of organisms with kidneys, and some fossils to fool us. Don’t they teach you anything?

  12. phoodoo
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    Allan Miller,

    Since you can’t say how your theory did anything, don’t go blaming me by claiming I got it wrong.

    Pretty hard to evaluate when all you can say is, “well, you got a better idea? “

  13. Rumraket Rumraket
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    says:

    phoodoo: Since you can’t say how your theory did anything, ”

    Maybe we can actually say something about how kidneys evolved, but maybe bothering to do it so you can either ignore it or make another fatuous caricature is a waste of time?
    Look at the animal pictures I have posted. Those should be enough for you at your current crayon-level of “argument”.

  14. Rumraket Rumraket
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    Alan Fox:
    Manatees seem to have been a fruitful subject for phylogenetecists.

    Interestingly Manatees are also fully aquatic mammals, yet look much like seals or walruses. They don’t spend any time on land any more. Yet they retain a very seal-like head/face.
    Are they in the process of becoming like whales? Will their nostrils eventually migrate to the top of their heads? I don’t know. But phoodoo seems to think evolution has stopped and we can’t point to any organisms in the process of evolution. Aren’t otters, seals and Manatees actually perfect examples of what he’s asking for: multiple extant species of organisms that show various levels of adaptation to aquatic life? Why would anyone think they have “stopped” where they are now? How should they look if they were still evolving, then? (Phoodoo, you there?)

    In the fossil record similar transitions seem to have happened over timescales of 15 million years. How many gradations would that produce between the Otter and the Seal, say? Would phoodoo even be able to detect a specimen showing such gradations?

  15. Allan Miller
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    says:

    phoodoo,

    Since you can’t say how your theory did anything, don’t go blaming me by claiming I got it wrong.

    Pretty hard to evaluate when all you can say is, “well, you got a better idea? ”

    You show absolutely no inclination to ‘evaluate’. I’ve explained why large-scale incidence of partial populations in mid-adapt is not an expectation of evilutionary theory, nor the perennial generation of new adaptative structure regardless of necessity, developmental constraint and the role of gradualism. To all of which comes the same “Yurr well how come there aren’t X’s or Y’s”, just repeating the same strawman view as if I’d said nowt, getting more excitable all the while.

    Of course, I could discuss kidney evolution. I could put some effort in. But would you be listening? No, I don’t think you would.

    So I consider doing the same to you – taking the piss out of a strawman version of your notion (I hesitate to call it theory) – to be entirely appropriate.

  16. Allan Miller
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    Rumraket,

    My favourite example is the Sea Turtle. I think vivipary would be significantly adaptive, avoiding some of the massive attrition of babies and eggs. Of course that does not mean that we should necessarily expect to see vivipary evolve, even if it were adaptive. It may not be possible to get there from here without detrimental intermediates.

  17. Rumraket Rumraket
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    Few things are more clearly in an evolutionary process than soles. They’re also intrinsically comical.

  18. keiths keiths
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    That’s exactly how I picture phoodoo’s facial expression when he comments at TSZ.

  19. petrushka
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    keiths:
    That’s exactly how I picture phoodoo’s facial expression when he comments at TSZ.

    Don’t know what doodoo looks like, but that’s his argument.

  20. Alan Fox Alan Fox
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    toenailsRumraket,

    Manatee toenails hint at their ancestry.

  21. Rumraket Rumraket
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    Clearly that’s just what the designer wanted. It works in mysterious ways!

  22. John Harshman John Harshman
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    I think we have already established that you can only investigate what things are like, not how they got to be that way. Everything is the way it is because that’s what the designer (I mean Jesus) wanted, and that’s all the explanation you need or can get. Oh, and evolutionary biology is a science stopper, but ID is a fruitful source of new investigations.

  23. Alan Fox Alan Fox
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    Re manatees:

    I happened to stream a BBC program last evening with professor Brian Cox, which mentioned manatees in passing when discussing gravity-imposed shapes. The manatee’s body shape isn’t caused by blubber, the animal is not fat and suffers from hypothermia in water cooler than 20°C, but apparently has the lowest surface area to volume ratio of any large mammal. A good approximation to a spherical cow!

  24. John Harshman John Harshman
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    Alan Fox:
    A good approximation to a spherical cow!

    Spherical elephant.

  25. petrushka
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    says:

    Alan Fox:
    Re manatees:
    I happened to stream a BBC program last evening with professor Brian Cox, which mentioned manatees in passing when discussing gravity-imposed shapes. The manatee’s body shape isn’t caused by blubber, the animal is not fat and suffers from hypothermia in water cooler than 20°C, but apparently has the lowest surface area to volume ratio of any large mammal. A good approximation to a spherical cow!

    We have manatees in the river near my house. They needn’t worry about hypothermia.

  26. GlenDavidson
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    Alan Fox: A good approximation to a spherical cow!

    That’s what I assumed.

    Glen Davidson

  27. Allan Miller
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    Dissection of Denton’s cytochrome c arguments that might be worth a read.

    In spite of numerous refutations that immediately reached print and are still readily accessible, fallacious interpretations of cytochrome c data continue to circulate in creationist venues.

    This is, of course, a creationist venue.

  28. John Harshman John Harshman
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    I see that this thread has died, all without any response from the creationists to any of the questions raised or to the references cited. I had hoped for more.

  29. OMagain
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    says:

    John Harshman: I see that this thread has died, all without any response from the creationists to any of the questions raised or to the references cited. I had hoped for more.

    Ah, but therein lies the difference! Creationists prefer, as we know the ‘orchard’ model not only as a model for living things interconnectedness, but also their discussions. A discussion starts. They say some things. Some other people refute those things to the satisfaction of any reasonable observer. Creationist ignores this and continues to make original claim there or elsewhere.

    The orchard model, safely cocooning away those precious irrational beliefs where no argument can touch them, preserving them down the years.

    I bet FTK is still out there going on about how nobody has refuted Walt Brown yet, ffs.

    phoodoo: Pretty hard to evaluate when all you can say is, “well, you got a better idea? ”

    Evaluating it would take work, which you’ve shown no inclination to do.

  30. stcordova
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    Real phylogenetics is good for

    selecting model organisms
    tracing the origin disease
    figuring defenses to new viruses
    maximizing diversity of endangered species in an attempt preserve them
    tracing ancestry and population movements like that after the tower of babel (which by the way, does confirm the migration from the area of Biblical Babel)

    But just to set the record straight, John’s quotation of me was not me referring to these sorts of applications but to things like the prokaryote eukaryote transition, the fish to bird evolution, etc.

    That’s what I meant when I said there is not a lot of utility for that, especially since it may not be true given the barriers to macro evolution.

  31. OMagain
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    says:

    stcordova: tracing ancestry and population movements like that after the tower of babel

    What year did that happen? What can you point to in the scientific literature that supports that claim, specifically? Also, have you lost it totally?

  32. keiths keiths
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    He’s mangled biology, geology, astronomy, and physics. Why not linguistics too?

  33. John Harshman John Harshman
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    stcordova,

    Thank you for another non-response. At least you have expanded your concept of utility slightly from just medical research; now you allow that conservation biology may have some uses. But what is the utility of that last bit? Dare I hope that you display some interest in knowledge of history for its own sake, or was it just that you wanted to prove the bible true?

    Note the point of the Babel story (aside from not building anything tall enough to reach heaven — which incidentally is evidence for the concept that heaven is above the solid dome of the sky) is that all the people lived in one spot and that all languages originate there. But of course that isn’t true at all. People have lived all over the world long before any of the migrations from the Middle East that you may be talking about, which were toward Europe, more or less. And if those migrations correspond to any languages (questionable), it would be the Indo-European ones, a small fraction of all the world’s languages. Further, the Indo-European languages didn’t spring into existence all at once; they too have a phylogeny, some of it recorded by fossils (written documents).

  34. phoodoo
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    says:

    phoodoo:
    DNA_Jock,

    Leading somewhere Jock!Progressing, get it??

    Let’s take your implied premise of evolution, that this can go somewhere.That this can lead to novelty.

    First, can this mutation even be passed along.

    Second, many of you whacky evolutionists now subscribe to the neutral theory; that this can drift for a while, as long as it causes no harm (until the one day when it becomes really useful!).So show me Jock, where are the pockets of cats with these kinds of mutations, the beginnings of a new lineage? Are they out there, and we just haven’t studied them enough to know?is that what you believe Jock?

    We know that animals get mutations Jock.So since they have been getting mutations for centuries, where are some new lines that are forming, some new branches of evolution, that are in their infancy, just like the eyeball was?

    Maybe you are as bright as Robin, and you think poodles are that, huh?One day poodles can become a new class of animal, a big ball of fur that uses wind as a locomotion to tumble through the deserts and collect food on its fur.

    Your theory sure does its best to hide itself, until it becomes magically complete.Or maybe this cats descendants really will develop thumbs.Then they will be about as smart as you.

    Still waiting Jock. I have been waiting 3 million years. When are the new thumbs going to start shooting webs in some of the cats?

  35. OMagain
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    says:

    phoodoo: When are the new thumbs going to start shooting webs in some of the cats?

    https://en.wikipedia.org/wiki/Polydactyl_cat
    It seems fairly common for cats to gain additional digits. Out of interest, how many did the designer put on the original cat-kind?

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