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. colewd:
    Flint,

    Where it is likely common descent occurs due to same specie type we get very little nesting as sequences are similar.As far as I can tell nesting requires differences.

    I confess I don’t know what you intend here. Of course sequences are similar. Biological nesting has always involved very small differences from one generation to the next. But given (mostly) genetic isolation and enough generations, you get larger differences. But no matter how different our very distant descendants are from us, they will STILL be mammals, and still be apes. Just the way tuna and trout are still fish, and eagles and wrens are still birds.

  2. colewd:
    John Harshman,

    The disconnect here is at this point I don’t think the nested hierarchy points only to common descent.

    In theory, you can have common descent without nesting, but you could not have inheritance. Also in theory, you can have nesting without common descent, but it won’t be biological as we know it.

  3. keiths:

    A Core i7, like the one in my computer, does not have an ancestral 8086 at its center.It can run 8086 code, but it does so using hardware that is completely different from the 8086.

    Well, yes and no. The 8086 code opcodes are decoded “natively” – that is, your i7 is not running a simulation (the way, for example, a 68000 processor “ran” 8086 code).

    As for “ancestral” software, this is problematic. I spent several years porting code written in one language, to very different environments (including unrelated processors) in nominally the same language. It was NOT just a simple matter of recompiling the code on the appropriate compiler. Important chunks of the original code simply could not be translated, and the target functionality had to be recoded at a high enough level that no trace of the original remained.

    Windows running on an Atom processor in a tablet has no more than a vague cosmetic similarity to windows on the i7.

  4. Flint:

    Well, yes and no. The 8086 code opcodes are decoded “natively” – that is, your i7 is not running a simulation (the way, for example, a 68000 processor “ran” 8086 code).

    They are decoded natively by hardware that is completely different from that of the 8086. There is no ancestral 8086 buried at the core of modern X86 processors.

    Hence my statement:

    A Core i7, like the one in my computer, does not have an ancestral 8086 at its center. It can run 8086 code, but it does so using hardware that is completely different from the 8086.

  5. fifth:

    Slavish adherence to ancestor-descendant constraints would entail that nothing new happens descendants would be just like their ancestors.

    No, that’s just your misunderstanding. Those constraints do not entail that nothing changes.

    What those constraints actually entail is that variations arising in an ancestor can be passed down to descendants, but they can’t pop up willy-nilly in unrelated parts of the hierarchy.

    I think I’m making a lot of progress.

    No, and your confusion may even be deepening, judging by your misconstrual of the nature of the ancestor-descendant constraints.

    I know I’ve got your goat and made my point when you stoop to this sort of schoolyard belittlement.

    It isn’t “schoolyard belittlement.” Some people are genuinely more intelligent than others, and some are markedly less intelligent. That’s a fact that even Christians acknowledge. Here’s Paul, commenting on the unequal distribution of “gifts”:

    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, in accordance with the faith God has distributed to each of you. 4 For just as each of us has one body with many members, and these members do not all have the same function, 5 so in Christ we, though many, form one body, and each member belongs to all the others. 6 We have different gifts, according to the grace given to each of us. If your gift is prophesying, then prophesy in accordance with your faith; 7 if it is serving, then serve; if it is teaching, then teach; 8 if it is to encourage, then give encouragement; if it is giving, then give generously; if it is to lead, do it diligently; if it is to show mercy, do it cheerfully.

    Romans 12:3-8, NIV

    Your gift, if you have one, is clearly not in the arena of logical thinking and argument. The sovereign God, according to Paul, decides how to distribute his grace, and he has clearly decided to deprive you of the gifts of intelligence and level-headedness. Hence your chronic failures in debates here at TSZ.

    Your ego balks at this, of course. You think that you’re entitled to be a smart guy, and if God has deprived you of this gift, it must be some kind of cosmic mistake. Balance must be restored. Anyone who denies your intelligence must be resorting to “schoolyard belittlement”, since it is a law of nature that “fifthmonarchyman must be intelligent.”

    It simply isn’t possible, according to you, that your sovereign God has granted intelligence to others and not to you. It’s not permissible.

    Get over yourself, fifth. You happen to be significantly less intelligent than most of your opponents here at TSZ. That’s just the way it is, and it’s revealed by the poor quality of your arguments and your numerous mistakes.

    Them’s the breaks. Now why not set aside your ego and try to learn, instead of fighting in futility to save face and to defend an unsustainable self-image?

  6. keiths: What those constraints actually entail is that variations arising in an ancestor can be passed down to descendants, but they can’t pop up willy-nilly in unrelated parts of the hierarchy.

    Is not “willy-nilly” another word for random as in random mutation?

    Are you saying that “Slavish adherence to ancestor-descendant constraints” means that random mutation is not possible?

    perhaps you need to batten down what you mean by “Slavish adherence to ancestor-descendant constraints” because it sounds like you need a tighter definition.

    keiths: It simply isn’t possible, according to you, that your sovereign God has granted intelligence to others and not to you. It’s not permissible.

    You aren’t understanding my point. There are lots of folks who are smarter than me. I’m not even the smartest person in my household.

    There are lots of folks here at TSZ who are smarter than me as well on both sides of the debate.

    Usually the smart folks folks don’t go around saying in effect.

    “The reason you don’t agree with me is because you are so stupid”

    Instead it’s often folks who are not able to formulate a cogent argument for their position who retreat to such tactics

    get it now?

    When I hear folks claiming that “you are too dumb to understand the argument for common descent” I can’t help but think of this.

    https://www.youtube.com/watch?v=rMz7JBRbmNo

    😉

    peace

  7. newton: And that may be the objective.

    It turns out that fifthmonarchyman’s problem with the objective nested hierarchy isn’t to the hierarchy, it isn’t to the nesting, but his problem is with objectivity. We have reached a point where fifthmonarchy man won’t even agree that crows do, in fact, have feathers.

  8. fifthmonarchyman: Usually the smart folks folks don’t go around saying in effect. “The reason you don’t agree with me is because you are so stupid”

    Fifthmonarchyman is certainly not unintelligent nor is he insincere. Rather, he is convinced of a certain point of view, but when that point of view comes into contradiction with the facts, in order to hold onto his viewpoint, he has to ignore or distort the facts. If admitting that crows have feathers would threaten his viewpoint, then crows may or may not have feathers. It’s just an opinion.

  9. Allan Miller: Well, I wasn’t, which is why I can’t think of one. Doesn’t mean there isn’t one, I’m just not aware and doubt it is bookworthy.

    It doesn’t have to be the whole book. But a chapter or two at least. 🙂

    As you are probably aware I have a decent library that includes such titles as Why Evolution Is True. You’d think they would cover it. But no.

    ETA: I added The Ancestor’s Tale.

  10. Zachriel:

    Fifthmonarchyman is certainly not unintelligent nor is he insincere.

    Intelligence is (at the very least) a continuum, with no bright line demarcating “intelligent” from “unintelligent”. The question here is not whether fifth is unintelligent in some absolute sense, but rather whether he is capable of grasping the concepts that are essential to the topic being discussed here.

    The evidence suggests that he is not, at least not without a protracted effort of the kind he has been unwilling to make so far. His egotistical refusal to do the exercise I suggested (“I’m not a third-grader”) is certainly not helping.

    More on this shortly.

  11. Zachriel: That’s because designs don’t branch neatly, but are subject to rampant crossings, as well as saltation.

    What is endosymbiosis if not a saltation? How rampant is/was HGT at the “root” of the tree of life?

    So you have to hope that the designer has done enough to wipe out the vertical signal and that’s just ad-hoccery.

    ETA:

    Zachriel: Human artifacts simply don’t form into objective nested hierarchies. With human artifacts, we can form many different equally valid classification schemes.

    All equally objective. 🙂

  12. fifthmonarchyman: The problem is in claiming that God does not exist while at the same time claiming that objectivity exists. That is what the atheist is doing.

    We can objectively say that God does not exist when 51% of the population agrees.

  13. Mung,

    I am reading it keiths. Have you answered yet any of the questions I’ve asked you?

    If I think you’re actually making a good-faith effort to understand Theobald, but are still confused, I’ll step in to help you. Your behavior so far hasn’t convinced me.

    I certainly won’t spoon-feed you. You need to try a lot harder than you have so far.

  14. Neil Rickert: People use “objective”, and they seem to communicate effectively with that word. If you think objectivity is impossible, then you have misunderstood the meaning of “objective”.

    The word “objective” has multiple meanings.

    ETA:

    Neil Rickert: That’s only a question because you have the wrong meaning for “objective”.

    Better to ask which meaning of objective fifth is using.

  15. keiths: I certainly won’t spoon-feed you.

    Did you come to accept universal common ancestry before or after you read Theobald? It’s a very simple question. No spoon feeding required. Just a willingness to engage in honest dialogue. Can you do that?

  16. fifth,

    Are you saying that “Slavish adherence to ancestor-descendant constraints” means that random mutation is not possible?

    Of course not. See why I despair of getting you to understand what an objective nested hierarchy is?

    You aren’t understanding my point. There are lots of folks who are smarter than me. I’m not even the smartest person in my household.

    There are lots of folks here at TSZ who are smarter than me as well on both sides of the debate.

    Then why not take that into account? When you find yourself disagreeing not only with your smarter opponents at TSZ, but with the entire evolutionary biology community, why not remind yourself of the disparity in intelligence?

    Who is more likely to be correct?

    a) people of modest intelligence who are struggling and failing to understand the basic concepts, but are nevertheless convinced that the eggheads and the experts have it all wrong; or

    b) brighter folks, technically trained, who understand and deploy the concepts competently and with ease; some of whom — the evolutionary biologists — have spent their entire careers working with these concepts — concepts that the people in (a) don’t even grasp?

    The obvious rational answer is that the folks in category (b) are overwhelmingly more likely to be correct. Yet you continue to cling to the fantasy that you are mounting an actual challenge to the argument for common descent. Erik, Mung, Sal, and Bill indulge in that same fantasy. It’s mental masturbation, and an enormous amount of time is wasted in these discussions because of it.

    It’s vanishingly improbable that you guys, of all people, have discovered an error in the arguments for common descent — errors that have escaped the notice of the entire evolutionary biology community. You are not here to overturn the tenets of evolutionary biology. You are confused people who are here to learn — or at least you ought to be.

    In the overwhelmingly unlikely event that you turn out to be correct, that will come out in the discussion. But it is so ridiculously improbable that it should not be the starting assumption, regardless of its ego-soothing effects.

  17. Mung:

    Did you come to accept universal common ancestry before or after you read Theobald?

    I accepted common descent long before I read Theobald. The content of 29+ Evidences is not revolutionary, Mung. What makes it useful is that it collects and summarizes the evidence and arguments so well.

    Keep reading.

  18. keiths: The obvious rational answer is that the folks in category (b) are overwhelmingly more likely to be correct. Yet you continue to cling to the fantasy that you are mounting an actual challenge to the argument for common descent. Erik, Mung, Sal, and Bill indulge in that same fantasy. It’s mental masturbation, and an enormous amount of time is wasted in these discussions because of it.

    It’s vanishingly improbable that you guys, of all people, have discovered an error in the arguments for common descent — errors that have escaped the notice of the entire evolutionary biology community. You are not here to overturn the tenets of evolutionary biology. You are confused people who are here to learn — or at least you ought to be.

    I really wish you’d back up these unfounded allegations of yours. Any chance of that actually happening in my lifetime (or yours)?

  19. keiths: I accepted common descent long before I read Theobald.

    Likewise, keiths. Are you under the impression that I am trying to overturn common descent?

    You remind me of the Creationists, but like in reverse. You think I am questioning the fact of evolution. I am not. (Not unless you define evolution in such a way as to exclude the possibility of divine action.)

  20. Mung: What is endosymbiosis if not a saltation? How rampant is/was HGT at the “root” of the tree of life?

    Endosymbiosis probably happened in stages, but does represent a significant cross. It’s thought that HGT was common, especially before the last universal common ancestor. Since then, branching descent has been far more common, leading to the observed nested hierarchy.

    Mung: The word “objective” has multiple meanings.

    Sure, but in science, objectivity refers to testability and reproducibility of results. So, if someone observes that a crow has feathers, another observer should be able to verify the claim through independent observations. The more independent methods by which a claim can be verified, the more confidence we have in the result.

  21. fifthmonarchyman: Yes of course. We have been over thins

    I doubt it. Otherwise you would not be writing this nonsense. Maybe you went over this, but never stopped to actually think. Your claims are self-defeating.

    fifthmonarchyman: Since God exists objectivity exists.

    Nonsensical bullshit. Objectivity is independent of the existence, or lack thereof, of magical beings. However, a god would make objectivity very difficult to assert, since she could change whatever she wanted at any time. But it would still be objective that at least that magical being existed.

    fifthmonarchyman: The problem is in claiming that God does not exist while at the same time claiming that objectivity exists. That is what the atheist is doing.

    You’re just repeating your nonsensical claim. You’ve got it wrong. Objectivity is independent on the existence of magical beings. Only the magical beings would make it pretty hard to decide what’s objective in a mess of magic going on all around us.

    fifthmonarchyman: Again, If the atheist is correct then there are no objective facts whatsoever.

    Again a non-sensical, self-defeating claim. Your nonsense translates into: “if the atheist is correct, then it would be an objective fact that there are no objective facts whatsoever.”

    Noticing the nonsensical nature of your claims already?

    fifthmonarchyman: peace

    Whatever.

  22. keiths: Of course not.

    Then you need to tighten up your definition. What exactly do you mean by “Slavish adherence to ancestor-descendant constraints” if it does not exclude variation?

    keiths: Who is more likely to be correct?

    The person with the better argument.
    Correctness is certainty not dependent on IQ.
    Some of the smartest folks in the world are hopelessly incorrect

    keiths: It’s vanishingly improbable that you guys, of all people, have discovered an error in the arguments for common descent — errors that have escaped the notice of the entire evolutionary biology community.

    If appeal to authority is the reason you accept common descent just say so.

    There are things that I accept on the basis of authority.

    But I generally don’t try and convince others of the correctness of my position based on the fact that the “authorities” find it to be convincing.

    Instead I try and present evidence and argument.
    Why not give that approach a try?

    peace

  23. keiths: None of this is difficult, but it baffles guys like you and fifth (and Mung, and Sal).

    Remind me again of what it is that baffles me? Please be specific.

  24. Entropy: Objectivity is independent of the existence, or lack thereof, of magical beings.

    Of course that is only your subjective opinion. Right?

    Entropy: “if the atheist is correct, then it would be an objective fact that there are no objective facts whatsoever.”

    exactly !!!!!!!

    the atheist position results in absurdity

    since there are objective facts the atheist necessarily is incorrect.

    peace

  25. keiths: It’s a staggering display of incompetence.

    Indeed it is. Please stop. Intellectual superiority based upon a foundation of falsehoods is nothing for you to be proud of. If you keep making these false allegations and failing to back them up with any actual evidence I will put you back on Ignore. That will be strike two and you’ll find yourself on the brink of Adapa territory. But at least Glen will have company.

  26. Mung: https://www.biblegateway.com/passage/?search=Genesis+11:1-9

    Like this part
    “ But the Lord came down to see the city and the tower the people were building. 6 The Lord said, “If as one people speaking the same language they have begun to do this, then nothing they plan to do will be impossible for them. 7 Come, let us go down and confuse their language so they will not understand each other.”

    Wonder how high you can construct a building using mud bricks with tar for mortar? Couple hundred feet?

    God was a bit of a hothead in those days

  27. Zachriel: Sure, but in science, objectivity refers to testability and reproducibility of results.

    So if I submit the same data to the same algorithm and get the same result, and then my co-worker submits the same data to the same algorithm and gets the same result, we can all agree that the result produced by the algorithm is objective?

    Does that mean the data and the algorithm are likewise all objective or do we also need independent testability and reproducibility for the data, the algorithm, and the results?

  28. keiths: It’s vanishingly improbable that you guys, of all people, have discovered an error in the arguments for common descent — errors that have escaped the notice of the entire evolutionary biology community.

    It’s vanishingly improbable that you guys, of all people, have discovered an error in the arguments for geocentrism — errors that have escaped the notice of the entire natural theology community.

    😉

    peace

  29. Mung,

    this one needs a bump

    Mung: So if I submit the same data to the same algorithm and get the same result, and then my co-worker submits the same data to the same algorithm and gets the same result, we can all agree that the result produced by the algorithm is objective?

    Does that mean the data and the algorithm are likewise all objective or do we also need independent testability and reproducibility for the data, the algorithm, and the results?

    Did you all get that???

    I hope you did

    peace

  30. fifth:

    It’s vanishingly improbable that you guys, of all people, have discovered an error in the arguments for geocentrism — errors that have escaped the notice of the entire natural theology community.

    Um, fifth — I hate to break it to you, but the theological community — aside from a very few crackpots — has accepted heliocentrism for some time now. The errors in the arguments for geocentrism have hardly escaped their notice.

  31. keiths: The errors in the arguments for geocentrism have hardly escaped their notice.

    So if the authorities see the errors now that means that they always did?

    There never was a time when the authorities were incorrect and errors escaped their notice ?

    Peace

  32. There never was a time when the authorities were incorrect and errors escaped their notice ?

    I’m not making an argument from authority, fifth. That’s just your confusion.

    Go back and read my comment again.

  33. Alan,

    Your characteristically poor moderation decisions, such as this one, are harmful to TSZ. Show some restraint.

  34. keiths:
    Flint:

    They are decoded natively by hardware that is completely different from that of the 8086.There is no ancestral 8086 buried at the core of modern X86 processors.

    Hence my statement:

    And hence my comment of “yes and no.” The i7 core really DID evolve, stepwise with modifications, from the 8086. It morphed through the 286, then 386, the Pentium, etc. SOME of the internal decoding mechanisms were retained, and some were changed, at each iteration. There has been, in fact, a good deal of inheritance here. The internal hardware of the i7 resembles the 8086 analogous to the way your internal genetics resemble a sponge.

  35. FMM is once again trying to win an argument by mere stipulation instead of by reasoning.

    Of course it would be incoherent for an atheist to urge a conceptual distinction between the concept of God and the concept of objectivity if she were to also accept that the two ideas mutually imply each other. But that’s exactly what has always been at issue here. FMM has always insisted that the concept of God and the concept of objectivity cannot be disentangled, but that’s only because of how he insists on defining his terms.

    The atheists are under no obligation to use the terms as FMM wishes, no matter how he insists that are irrational if they do not.

    I urge that anyone exasperated with FMM just ignore him. There’s no hope of reasoning with him.

  36. Flint,

    And hence my comment of “yes and no.” The i7 core really DID evolve, stepwise with modifications, from the 8086. It morphed through the 286, then 386, the Pentium, etc. SOME of the internal decoding mechanisms were retained, and some were changed, at each iteration.

    No. That’s not how it works.

    Successive generations of X86 processors are backward compatible with the instruction sets of earlier generations, but that is emphatically not because they retain portions of the hardware of those earlier generations. You will not find residual pieces of the 8086 hardware buried in the Core i7.

  37. fifthmonarchyman: the atheist position results in absurdity

    since there are objective facts the atheist necessarily is incorrect.

    “fifthmonarchyman: Since God exists objectivity exists.” Does it follow since God exists subjectivity exists?

  38. : So if I submit the same data to the same algorithm and get the same result, and then my co-worker submits the same data to the same algorithm and gets the same result, we can all agree that the result produced by the algorithm is objective?

    We can agree it more objective than if they disagree. Better yet if we get the same result from another line of reasoning.

  39. newton: “fifthmonarchyman: Since God exists objectivity exists.” Does it follow since God exists subjectivity exists?

    God is tripersonal so———- yes.

    peace

  40. John Harshman: So you’re saying that causes can’t be inferred from effects? Bye bye, science, if so.

    The analogies are just not reaching you.

    From the given effects, how do you know that your claimed causes are the causes? If the analogies apply, then the effects do not tell you the causes. The ink marks on the manuscripts do not tell you how they came about. You know on totally independent grounds how ink marks come about. Causes are known, no probabilistic-statistical inference needed in this case.

    The other option is that the analogies actually do not apply, in which case you should detail where the analogy breaks down and how common descent really works, according to you.

    John Harshman:
    The mechanism of descent can be determined in other ways, and we know that mechanism in all three cases: copying by scribes, transmission from individual to individual, and reproduction. We may not know everything that causes the various changes that accrue, but we don’t have to.

    Oh, so now you say you do not have to know the causes? What a scientist! Okay, this ends about here.

    John Harshman:
    We are not, in this particular thread, talking about the causes at of evolution at all. We’re talking about the causes of nested hierarchy.

    And either way you don’t have to know the causes?

    John Harshman:
    Ah, but living things do self-replicate, don’t they? That’s the form that descent takes in living things. Do you have reason to suspect anything else? If so, what?

    I suspect that living things replicate according to their species, displaying only minor variations. The common descent claim is that modern species came from different species by means of ordinary self-reproduction, crossing the lines of phylums and kingdoms and what not. Pretty bold claim.

    But I got it: You don’t have to know the causes! Happy New Year!

  41. keiths: I’m not making an argument from authority, fifth. That’s just your confusion.

    now would be a good time for you to succinctly spell out your argument for common descent so as to illustrate my confusion

    hint pointing to a web-page does not count

    peace

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