Phylogenetic Systematics

Let’s have a serious discussion about phylogenetic systematics.

What are the assumptions, the methods, and the inferences that can be drawn from phylogenetic analysis.

For example, is there anything to the creationist claim that phylogenetic systematics assumes common ancestry and does it even matter?

I’ll be using a number of different references such as Molecular Evolution: A Phylogenetic Approach and Molecular Evolution and Phylogenetics.

This thread will not be password protected, but it will be protected by angels.

1,034 thoughts on “Phylogenetic Systematics

  1. keiths,

    Honestly, Bill — do you truly think a guy of your modest abilities has spotted errors in the argument for common descent that the entire evolutionary biology has overlooked? Don’t you recognize how astronomically improbable that is?

    If you think the entire biological community would support that a nested hierarchy proves macroevolution you need to get out more 🙂

    As Mung says you need to support your claims. So far this is a hard failure.

    The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of “cladistic hierarchical structure” (also known as the “phylogenetic signal”) in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).

    Keiths, have you figured out yet what Theobald is statically comparing the phylogenetic signal to?

    Ok, here it is.

    subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a CHANCE PROCESS instead of a genealogical process

    Yes keiths you have been playing checkers while everyone else has been playing chess.

  2. colewd: If you think the entire biological community would support that a nested hierarchy proves macroevolution you need to get out more

    What does that statement mean and what sort of “get out more” were you thinking of? What members of “the biological community” would not agree that nested hierarchy supports common descent?

  3. Oh, Bill. So much struggle. So little progress. You must be incredibly frustrated.

    Chance is just the reference against which the objectiveness of the hierarchy is measured. This in no way changes the fact that organisms and natural languages fall into objective nested hierarchies, while cars and computers do not.

    Theobald is your lifeline. Stop thrashing and grab onto it.

    Yes keiths you have been playing checkers while everyone else has been playing chess.

    Bill, the bright folks have been playing chess. You haven’t. You’re still struggling to learn the rules, while confidently predicting an upcoming victory over Kasparov.

  4. Bill’s grandiosity is hugely entertaining.

    It reminds me of an experience I used to have. I lived with roommates who owned a beautiful, massive Harlequin Dane named Ed. (A different Harlequin is pictured below, but the photo will give you an idea of their size.)

    I enjoyed walking Ed, and we would typically encounter other dogs being walked by their owners. Often these other dogs were what I think of as “yip dogs” — small and excitable. Ed could have dispatched any of them with one bite of his massive jaw, but these idiot dogs would throw themselves at him with kamikaze ferocity, as if they stood a chance of defeating him in an actual dogfight. When Ed and I moved on, these dogs were beside themselves, thinking that they had scared the big brute away.

    Bill’s triumphant declaration…

    Yes keiths you have been playing checkers while everyone else has been playing chess.

    …reminds me of those idiotic yip dogs.

  5. colewd: Keiths, have you figured out yet what Theobald is statically comparing the phylogenetic signal to?

    Ok, here it is.

    subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a CHANCE PROCESS instead of a genealogical process

    Yes keiths you have been playing checkers while everyone else has been playing chess.

    Bill, there is only one other alternative that isn’t common descent: The consilience of independent phylogenies is because the designer wants to fake the evidence for common descent.

    There is no actual design-plan hypothesis (which is not itself an instance of a genealogical process) from which it is predicted that consilience of independent phylogenies will obtain.

    You’ve tried to make such design-plans up because you mistakenly believed that following these imagined design-plans would happen to produce consilience of independent phylogenies. But all the ways you could think of, failed to produce consilience of independent phylogenies.

    That means there are only three options left:
    1. The consilience of independent phylogenies is due to common descent.
    2. The consilience of independent phylogenies is due to deliberate deception.
    3. The consilience of independent phylogenies is due to chance.

    2. Is unfalsifiable conjecture, and I think to most theists also theologically problematic. And chance is, well it’s extremely unlikely.

    So, there must have been common descent.

    Happy new year!

  6. Rumraket: Bill, there is only one other alternative that isn’t common descent: The consilience of independent phylogenies is because the designer wants to fake the evidence for common descent.

    Actually, there is a third alternative: a severely limited designer who is capable of creating a new “kind” only by making slight tweaks to a previously existing kind. And in general the designer would appear to make two new kinds at a time and then to erase their model. And he frequently also gets rid of kinds that aren’t models. His skills are odd in other ways too. For example, if he wants to make a jaw, he repurposes part of a filter-feeding apparatus in the model, and if he wants an ear, he repurposes part of that jaw. To use Bill’s computer analogy, apparently the fan is made out of an old set of capacitors, and the capacitors were made out of chunks carved off the motherboard. Curious.

  7. keiths,

    Chance is just the reference against which the objectiveness of the hierarchy is measured. This in no way changes the fact that organisms and natural languages fall into objective nested hierarchies, while cars and computers do not.

    Thats fine keiths but thats not what your opponents are arguing and there is a lot of evidence that cannot be explained by reproduction and random variation alone.

    So what is the probability that the differences between Mac os and Windows is caused by a random change to the code? I would say these two groups are as different as mammals and birds, and no self replication occurred yet the probability the difference here is due to chance is zero.

  8. colewd:
    keiths,

    Thats fine keiths but thats not what your opponents are arguing and there is a lot of evidence that cannot be explained by reproduction and random variation alone.

    So what is the probability that the differences between Mac os and Windows is caused by a random change to the code? I would say these two groups are as different as mammals and birds, and no self replication occurred yet the probability the difference here is due to chance is zero.

    Oh, dear, that was inept. Theobald wasn’t trying to explain the evidence by chance alone. He was presenting chance as a null model. It isn’t the differences that Theobald’s method tries to explain but the similarities. The causes of differences are not relevant, and the causes of replication are not relevant either. And no, MacOS and Windows are not as different as mammals and birds; they’re as different as mammals and Jawas. All similarities are at the surface and are due to imitation.

    Now, there is a different null model that anyone is welcome to try out on Theobald’s data: a star tree, a model under which the creator started with a common model and then independently modified each kind. I expect it might do a bit better than the unconnected trees, but not better enough to be competitive with common descent.

  9. John Harshman: Actually, there is a third alternative: a severely limited designer who is capable of creating a new “kind” only by making slight tweaks to a previously existing kind. And in general the designer would appear to make two new kinds at a time and then to erase their model. And he frequently also gets rid of kinds that aren’t models. His skills are odd in other ways too. For example, if he wants to make a jaw, he repurposes part of a filter-feeding apparatus in the model, and if he wants an ear, he repurposes part of that jaw. To use Bill’s computer analogy, apparently the fan is made out of an old set of capacitors, and the capacitors were made out of chunks carved off the motherboard. Curious.

    Yes but it seems to me a designer who works like this is effectively playing the part of common descent. The designer’s actions are an instance of a branching genealogical process of descent with modification.

    I have a hard time imagining that a super-intellect that designs by such a process isn’t also aware of how this will look after the work is done. That would make it fraud.

  10. Rumraket,

    John Harshman,

    That means there are only three options left:
    1. The consilience of independent phylogenies is due to common descent.
    2. The consilience of independent phylogenies is due to deliberate deception.
    3. The consilience of independent phylogenies is due to chance.
    4. The designer who is limited (Harshman)

    5. A design based on atoms and molecules that was conserving resources so all energy conversion could by co2 o2 and glucose ultimately producing ATP. Just like keiths 80×86 instructions standards were used to conserve software engineering resources. As Flint mentioned we would expect some incremental change from design so phylogenetic convergence would be expected.

    So it turns out the design argument is not a “gaps” argument but what describes the whole show.
    The anomaly in the data is that some common descent has occurred, but how the whole show was created is common design.

    Thanks for sticking to chess 🙂

    Happy New Year

  11. newton: Without a belief in God breeding is impossible

    No, you don’t have to believe in God to breed. You can breed even if you don’t beleive anything at all

    I would say that God has to exist in order for us to expect accurate high quality reproduction to occur but that a discussion for another day.

    😉

    peace

  12. Rumraket: I have a hard time imagining that a super-intellect that designs by such a process isn’t also aware of how this will look after the work is done. That would make it fraud.

    Not necessarily! God could have the capabilities of omnipotence etc. but not have Homo sapiens’s interests in mind for a final outcome of the grand plan. Maybe what we see now is just a small blip.

  13. John Harshman,

    And no, MacOS and Windows are not as different as mammals and birds; they’re as different as mammals and Jawas.

    Take the code break it up into bit segments and compare.

  14. colewd: 5. A design based on atoms and molecules that was conserving resources so all energy conversion could by co2 o2 and glucose ultimately producing ATP.

    Why would that yield consilience of independent phylogenies?

    Bill, you’re just making stuff up. You’re just throwing out arbitrary examples of commonalities between different species.

    Those don’t yield consilience of independent phylogenies Bill.

    Again, please try to remember what the term refers to: Consilience of independent phylogenies. What does that mean? It means the trees you get from independent data sets (such as different sets of similar genes) exhibit similar branching orders. That they are consistently very similar. That the same species are overwhelmingly grouped together in the same groups.

    AJust like keiths 80×86 instructions standards were used to conserve software engineering resources.

    Bill, that is not a phylogeny. A phylogeny is a tree, Bill.

    You are supposed to explain why the trees are so similar. Why is the cytochrome c tree so similar to so many other trees?

    As Flint mentioned we would expect some incremental change from design so phylogenetic convergence would be expected.

    Please demonstrate this with concrete examples. MAKE the phylogenies Bill, from independent characters, and then show them to us so we can compare them.

    You keep just ASSERTING, which means you keep just SAYING, or CLAIMING, that this or that explains consilience of independent phylogenies. Stop just making claims, start demonstrating with examples, that your claims are true.

  15. newton: , however if we agree to measure on base percentage as “how often a batter reaches base.

    Yes if we agree on things like what to measure and the method we use and what our measurements tell us then we can say we agree on those things.

    Then Instead of objectivity as most folks would define it we have something like Neil’s intersubjective agreement. It might even approach unanimity in a given community. At that point “intersubjective agreement” might be a suitable analogue for objectivity but only in the particular community in question.

    I also think that given the proper relationship and the proper community it will reach the threshold of actual objectivity as most of us define it.

    This is a fascinating topic. I do wish some one would start a thread.

    I have been doing some thinking about objectivity, intersubjective agreement and the poker game called Blind man’s bluff or Indian poker.

    I’d like to kick it around but I don’t want to bog down a thread that should be about evidence for common descent

    peace

  16. colewd:
    John Harshman,

    Take the code break it up into bit segments and compare.

    The binary? I bet that if you do you will find no homologous segments more than a few instructions long. Certainly you won’t find the detailed similarities across long stretches that could be observed between mammal and bird genomes.

  17. John Harshman,

    You will see more similarity then you think because of the standard ascii characters especially at the operating system level. The instructions should be similar as both use Intel processors at this point. Older version macs used motorola. I do not expect a perfect correlation as life is working with molecules and computers are working with voltage levels but I think this will help us understand the grand design and what tradeoffs were made and why. The PC and Mac are different designs as far as the operating systems go so I would not expect nearly as much similarity as with closer generations comparing Macs or comparing PCs.

  18. keiths:

    Chance is just the reference against which the objectiveness of the hierarchy is measured. This in no way changes the fact that organisms and natural languages fall into objective nested hierarchies, while cars and computers do not.

    colewd:

    Thats fine keiths but thats not what your opponents are arguing and there is a lot of evidence that cannot be explained by reproduction and random variation alone.

    Christ, Bill. Chance is just the reference against which the objectivity of the hierarchy is measured.

    No one is assuming that cars and computers formed by chance. No one. And the use of chance as the reference does not imply it, either. Not in the slightest.

    Don’t latch on to every dumb idea that pops into your head. You’re as bad as fifth.

  19. colewd:

    You will see more similarity then you think because of the standard ascii characters especially at the operating system level. The instructions should be similar as both use Intel processors at this point.

    Holy shit. I despair of teaching anything to this person.

    My only solace is in imagining the laughter of the tech-savvy people out there who are watching this slow-motion train wreck along with me.

  20. colewd: You will see more similarity then you think because of the standard ascii characters especially at the operating system level.

    What you will see is more or less the same as different proteins repeating the same 64 codons, not something that can be extended for hundreds or thousands of instructions as in life. This is not the same thing at all, and you’re just fooling yourself in ignorance of real data.

  21. Rumraket,

    Why would that yield consilience of independent phylogenies?

    It drives a design based on standards and thats exactly what we see. As Flint said he expects incremental change which is what we saw in computer systems as the designers drove to keep them compatible as long as possible.

    The computer industry is driven by standards. Life’s design is driven by standards. Standards like how species process energy and how they reproduce. We see incremental change and with this I would expect gene trees to converge just like they would given inheritance.

    What inheritance does not account for is novelty but design covers this base. Common descent is certainly part of the history of life. The question is the line of demarkation between descent and design.

    The bible says that God created man in his own image. We now in less than 100 years created an industry that we can use as a benchmark against the grand design of life. Remarkable 🙂

    God left us with some incredible raw materials to work with.

  22. John Harshman,

    What you will see is more or less the same as different proteins repeating the same 64 codons, not something that can be extended for hundreds or thousands of instructions as in life. This is not the same thing at all, and you’re just fooling yourself in ignorance of real data.

    If you compare computers made by the same manufacturer you will see lots of familiar and comparable sequences. The similarity will be remarkable as you compare software upgrades to each other. Lots or redundant sequences with some novel ones that are new designs.

    The designer of life was more sophisticated and new the inter workings of atoms and molecules so it will be a while before we can design with such high standards and such consistent standards.

  23. Rumraket:

    Why would that yield consilience of independent phylogenies?

    colewd:

    It drives a design based on standards and thats exactly what we see.

    Bill, you have no idea what “consilience of independent phylogenies” means, just as you have no idea what “objective nested hierarchy” means.

  24. keiths,

    Christ, Bill. Chance is just the reference against which the objectivity of the hierarchy is measured.

    No one is assuming that cars and computers formed by chance. No one. And the use of chance as the reference does not imply it, either. Not in the slightest.

    Don’t latch on to every dumb idea that pops into your head. You’re as bad as fifth.

    Ok and based on that standard cars and computers are more objective then biology. We know for certain that both did not assemble by chance. Save yourself time here keiths. By driving to an objective standard your argument disappears.

  25. keiths,

    Bill, you have no idea what “consilience of independent phylogenies” means, just as you have no idea what “objective nested hierarchy” means.

    Sure I do keiths. What you cannot show is that it is not a by product of design. Your claim that no one understands you is juvenile and getting old.

  26. colewd: What inheritance does not account for is novelty but design covers this base. Common descent is certainly part of the history of life. The question is the line of demarkation between descent and design.

    The line of demarkation is where the action is.

    The “exceptions” Zach talked about in the nested hierarchy are like sign posts begging to be pondered and explored in depth. Too often we treat them like noise that merely distorts the overall signal.

    peace

  27. keiths:

    Bill, you have no idea what “consilience of independent phylogenies” means, just as you have no idea what “objective nested hierarchy” means.

    colewd:

    Sure I do keiths.

    Then you’ll be able to tell us, in your own words, what those terms mean. You’ll also be able to elucidate the distinction between mere nested hierarchies and objective nested hierarchies.

    Knock yourself out.

  28. colewd,

    Ok and based on that standard cars and computers are more objective then biology.

    No.

    First, the question is about the objectivity of nested hierarchies, not of objects (cars, computers) or fields of study (biology).

    Second, can you think of anyone besides yourself here at TSZ, other than perhaps Byers or J-Mac, who would make a category error of that magnitude?

    Third, nested hierarchies of computers and cars are not more objective than nested hierarchies of living organisms. The opposite is true.

    Fourth, you have no idea what an objective nested hierarchy even is, so how could you possibly judge whether computers and cars form them? (They don’t, and you can’t.)

  29. colewd:
    John Harshman,

    If you compare computers made by the same manufacturer you will see lots of familiar and comparable sequences.The similarity will be remarkable as you compare software upgrades to each other.Lots or redundant sequences with some novel ones that are new designs.

    Or sometimes you will see a shift to a completely different operating system, as MacOS 9 vs. MacOS X. This doesn’t compare in any way to what we see in life. And there is no nested hierarchy of computers or operating systems.

    The designer of life was more sophisticated and new the inter workings of atoms and molecules so it will be a while before we can design with such high standards and such consistent standards.

    This is you imagining what you would see if you had any knowledge of biology. You are imagining incorrectly. There are no standards, just inheritance and change. Even the genetic code isn’t a standard, since there are quite a few randomly sprinkled slight variations. If there’s a designer, he’s extremely nearsighted and can only make slight tweaks to whatever he begins with, though the tweaks can add up to radical difference over time. So, why are these tweaks arranged in a nested hierarchy? Since you don’t believe there’s anything like junk DNA, I won’t remind you that most of the tweaks are in junk.

  30. fifthmonarchyman: The “exceptions” Zach talked about in the nested hierarchy are like sign posts begging to be pondered and explored in depth. Too often we treat them like noise that merely distorts the overall signal.

    Strange they openly admit exceptions to their precious tree exist,silly biologists. What do you estimate as the acceptable as noise exception rate , maybe 5%, 1%?

  31. John Harshman: It seems that you are implying that you know where the line of demarcation is. Why not inform us?

    The line of demarcation is where the model fails to describe what we see but at the same time what we see is meaningful and not random.

    Any observable phenomena can be separated into three categories.

    1) Things explained by our model
    2) Random noise
    3) Things that are not random noise but not explained by our current model

    I think we can say two things about the third category

    1) It’s useful to take Daniel Dennett’s “design stance” for these things because it allows us to make predictions even with limited or no knowledge of the causes.

    2) Focusing on these areas will allow us perhaps to eventually improve our model (ie that is where the action is)

    I hope that makes sense to you.

    peace

  32. newton: Strange they openly admit exceptions to their precious tree exist,silly biologists. What do you estimate as the acceptable as noise exception rate , maybe 5%, 1%?

    This is exactly the point.

    Openly admitting is not the same thing as focusing on and automatically attributing those areas to “exception noise” is exactly the wrong approach in my opinion.

    peace

  33. fifth,

    Your self-image is comically inflated relative to reality.

    Scientists haven’t ignored the exceptions. They’ve studied them to determine the causes (including, for example, HGT).

    While scientists have been figuring things out, you’ve been running around quoting bible verses at people.

    So look at this realistically, instead of through the lens of your ego. You aren’t in a position to recommend a change of approach to scientists. You’re a rather slow guy with little understanding of, or aptitude for, science; a guy who gets his rocks off by pretending to be a thinker dispensing sage advice to the benighted scientists. You don’t know how scientists operate, and if you did, you wouldn’t be the guy to come up with a better approach.

    You claim to take the Bible seriously, but in reality you pick and choose which verses to pay attention to. Here’s one you carefully avoid:

    3 For by the grace given me I say to every one of you: Do not think of yourself more highly than you ought, but rather think of yourself with sober judgment…

    Romans 12:3, NIV

  34. As if to prove my point, fifth offers this boneheaded advice:

    Any observable phenomena can be separated into three categories.

    1) Things explained by our model
    2) Random noise
    3) Things that are not random noise but not explained by our current model

    I think we can say two things about the third category

    1) It’s useful to take Daniel Dennett’s “design stance” for these things because it allows us to make predictions even with limited or no knowledge of the causes.

    Dennett would not be very impressed — to put it mildly — by your suggestion, fifth.

  35. fifthmonarchyman: This is exactly the point.

    Openly admitting is not the same thing as focusing on and automatically attributing those areas to “exception noise” is exactly the wrong approach in my opinion.

    peace

    Your point was the even though scientists openly discuss possible issues with tree, it doesn’t follow that they try to discover why those exceptions exist? And you are pretty sure they don’t even if you don’t have an opinion on the tree itself

  36. fifthmonarchyman: I hope that makes sense to you.

    None whatsoever. Could you try harder to explain yourself? Perhaps you could try applying your line of demarcation in some real case. How about humans and chimps, for example?

  37. fifthmonarchyman: The “exceptions” Zach talked about in the nested hierarchy are like sign posts begging to be pondered and explored in depth.

    Sure. You might start with Darwin, Origin of Species, 1859, wherein Darwin discusses common descent, convergence due to Natural Selection, as well as hybridization; explaining the nested hierarchy as well as providing evidence of mechanisms that create exceptions. Of course, a lot has been learned since then, supporting and extending Darwin’s original theory.

  38. fifthmonarchyman,

    The line of demarcation is where the model fails to describe what we see but at the same time what we see is meaningful and not random.

    Can you describe what the model is and where it fails to describe what we see?

  39. John Harshman,

    Or sometimes you will see a shift to a completely different operating system, as MacOS 9 vs. MacOS X. This doesn’t compare in any way to what we see in life. And there is no nested hierarchy of computers or operating systems.

    Sure, life has been able to stay on the same architecture for 1.5 billion years. The design is rooted in atoms and molecules and the architecture is obviously quite scaleable. Since the beginning we have seen new architectural features pop up like alternative splicing, chromatin structure and the cell nucleus.

    The Mac OS x changed platforms and is written in C C++ and objective C where the prior Mac was written in Pascal. In human designs we do see saltation jumps when performance becomes more critical then compatibility.

    Since 2002 and the first release of the Mac os x the operating system has remained compatible.

    If we compare the code changes with the operating system features I would expect identical trees and we know that the cause of this is the overall design.

    I think Theobald has successfully eliminated chance as a hypothesis. The demarkation of common descent and design still remains murky.

  40. colewd:
    John Harshman,

    Sure, life has been able to stay on the same architecture for 1.5 billion years.The design is rooted in atoms and molecules and the architecture is obviously quite scaleable.Since the beginning we have seen new architectural features pop up like alternative splicing, chromatin structure and the cell nucleus.

    This is is just you making vague, invalid analogies between computers and life.

    The Mac OS x changed platforms and is written in C C++ and objective C where the prior Mac was written in Pascal.In human designs we do see saltation jumps when performance becomes more critical then compatibility.

    And we see nothing of the sort in life.

    If we compare the code changes with the operating system features I would expect identical trees and we know that the cause of this is the overall design.

    I wouldn’t expect trees at all, just a series of changes. No nested hierarchy there.

    I think Theobald has successfully eliminated chance as a hypothesis.The demarkation of common descent and design still remains murky.

    Can you think of any way to tell the difference? I can: common descent results in nested hierarchy, while there is no reason to think that design would do so.

  41. John Harshman,

    Sure, life has been able to stay on the same architecture for 1.5 billion years.The design is rooted in atoms and molecules and the architecture is obviously quite scaleable.Since the beginning we have seen new architectural features pop up like alternative splicing, chromatin structure and the cell nucleus.

    This is is just you making vague, invalid analogies between computers and life.

    The Mac OS x changed platforms and is written in C C++ and objective C where the prior Mac was written in Pascal.In human designs we do see saltation jumps when performance becomes more critical then compatibility.

    And we see nothing of the sort in life.

    If we compare the code changes with the operating system features I would expect identical trees and we know that the cause of this is the overall design.

    I wouldn’t expect trees at all, just a series of changes. No nested hierarchy there.

    I think Theobald has successfully eliminated chance as a hypothesis.The demarkation of common descent and design still remains murky.

    Can you think of any way to tell the difference? I can: common descent results in nested hierarchy, while there is no reason to think that design would do so.

    I don’t see any real counter arguments here. Do you see it differently?

    Can you think of any way to tell the difference? I can: common descent results in nested hierarchy, while there is no reason to think that design would do so.

    You continue to make the claim that common descent results in a nested hierarchy and you have failed to support this claim. How do you know that common descent will create a branching pattern?

  42. colewd: You continue to make the claim that common descent results in a nested hierarchy and you have failed to support this claim. How do you know that common descent will create a branching pattern?

    It would seem obvious and unavoidable, given that there is 1) inheritance, 2) branching of lineages, and 3) change within lineages. I’m puzzled why you think otherwise, particularly given that you have agreed that nested hierarchy within crocodylians results from common descent.

  43. John Harshman,

    It would seem obvious and unavoidable,

    This is not an explanation John. I said that the crocs in question may share a common ancestor not that they formed a nested hierarchy. The two are very different.

    As you pointed out in the computer example a nested hierarchy requires branching and branching requires speciation and speculation often requires new functional genes.

    Your claim is that common descent does not explain novelty. If this is the case it does not explain the nested hierarchy because novelty is part of the branching process. Design on the other hand explains this very well.

  44. keiths: Scientists haven’t ignored the exceptions.

    I never once said they had.

    I said that Too often “we” treat them like noise that merely distorts the overall signal.

    By “we” I mean folks like those who post here.

    colewd: Can you describe what the model is and where it fails to describe what we see?

    The model in this case is “common descent with variation” to use Zach’s phrase and one place that jumps to mind is the origin of eukaryotes. Where we have one descendant that “nests” into two separate kingdoms.

    Then there is my personal hobby horse hybrid speciation when two different twigs on the tree of life merge to form one new species.

    The are other examples as well and I’m sure some we have not discovered yet. I just wish we talked about them more.

    peace

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