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. OMagain,

    Yes, it’s quite clear. The claim is there is a “computer example” where an objective nested hierarchy can be demonstrated to exist in the relationships.

    This is your claim of a “computer example”.

    My claim is that computers can form nested hierarchies even objective ones. You wanted an independent example of which Theobald made in his 2003 paper. His example is that languages can form objective nested hierarchies, Languages are a human design.

    Computers use languages to form programs. You have heard of these languages like basic, fortran, pascal or the more modern C, C++, Java etc. They also have operating systems that have similarities and differences like Mac os, Windows, Unix etc. They also have different processing strategies like Intel core and RISC. If we start with the first PC as the Apple 1 that branches to the Apple 2 and the IBM PC. 2 Different computers with objective similarities and differences and the ability to create an objective nest between Apple os and PC os. We can continue this until present day with the current Mac family and the PC families.

    The interesting discussion is what about these products is forming the objective nests?

  2. fifthmonarchyman: You can objectively say crows have feathers if it can be known for certain that in fact crows have feathers.

    Well, what do you observe? Do crows have feathers? Is this really a point of contention? If we can’t agree that a crow objectively has feathers (have you looked?), then a discussion of an objective nested hierarchy seems rather futile.

  3. colewd: His example is that languages can form objective nested hierarchies, Languages are a human design.

    Language evolution is an example of small regional changes, some conscious, some not, leading to a global historical pattern, which was not designed. No one decided that Latin should diverge into many different languages.

  4. fifthmonarchyman: I’m not sure how an atheist can say any thing objectively.

    You’ve already acknowledged that people, regardless of being theists or atheists, can report a forest fire they see (the fire exists) and that report will be objective since, according to your criteria, the fire exists.

    fifthmonarchyman: The only way my report is objective is if there is actually a forest fire.

    this applies to the theist or the atheist or anyone in between.

    In reality you can see how an atheist can say something that is objective by your own criteria that you’ve outlined for us.

    feathers exist and crows are observed to have feathers. are you still going to argue that the atheist cannot state this objectively?

  5. fifthmonarchyman: If God does not exist then there there is no perspective that is free from personal bias and limitations.

    You believe in God, what is the objective nested hierarchy of life look like? How do you know?

  6. Zachriel: Well, what do you observe? Do crows have feathers? Is this really a point of contention? If we can’t agree that a crow objectively has feathers (have you looked?), then a discussion of an objective nested hierarchy seems rather futile.

    And that may be the objective.

  7. Zachriel,

    Language evolution is an example of small regional changes, some conscious, some not, leading to a global historical pattern, which was not designed. No one decided that Latin should diverge into many different languages.

    Interesting point. This does not happen with computer languages.

  8. PeterP: In reality you can see how an atheist can say something that is objective by your own criteria that you’ve outlined for us.

    Yes of course. We have been over thins

    Since God exists objectivity exists.

    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.

    PeterP: feathers exist and crows are observed to have feathers. are you still going to argue that the atheist cannot state this objectively?

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

    peace

  9. newton: what is the objective nested hierarchy of life look like?

    I don’t know.

    Then again I’m not using the claim that my position is objective to support an argument.

    peace

  10. newton: If we can’t agree that a crow objectively has feathers (have you looked?), then a discussion of an objective nested hierarchy seems rather futile.

    Right, Before you put forward the claim that your observations are objective reality you need establish that objectivity is possible given your worldview.

    First things first
    This is not difficult

    Thanks for the zach quote newton

    peace

  11. fifthmonarchyman: Right, Before you put forward the claim that your observations are objective reality you need establish that objectivity is possible given your worldview.

    This is silly.

    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”.

  12. Neil Rickert: If you think objectivity is impossible, then you have misunderstood the meaning of “objective”.

    If you think I’m arguing that objectivity is impossible, then you have misunderstood the meaning of my argument 😉

    Neil Rickert: People use “objective”, and they seem to communicate effectively with that word.

    Of course they do.

    That is because they assume that an objective perspective exists whether they want to admit it or not.

    The question is not whether objectivity exists but whether objectivity can exist in a world with out God.

    peace

  13. I really don’t want this topic to get mired in a philosophical ditch.

    been there done that

    I’d much rather folks here make their argument with out resorting to claiming that their personal observations infallibly reflect objective reality.

    that is all

    peace

  14. fifth,

    You haven’t answered the question I posed earlier.

    If humans (other than you) are bright enough to see that they can incorporate “continuity and flow” into their designs without slavishly adhering to the ancestor-descendant constraints we’ve been discussing, then why isn’t God?

    Why this divine blind spot? Why is he unable to see something that is obvious to his brighter creatures?

    And don’t you find it a bit, um, suspicious that your God is making the same dumb mistake that you’re making? It’s as if you’ve created him in your own image.

  15. fifthmonarchyman,

    Changing the overall temps just for testes is a bad idea when simply descending them will do just fine.

    So would making sperm tolerant of body temperature, as they are in birds – at a higher temperature than mammals, yet. The Designer of the Constraints seems unable to do much about them, other than design his way round them.

  16. fifthmonarchyman: I’d much rather folks here make their argument with out resorting to claiming that their personal observations infallibly reflect objective reality.

    No one claimed the necessity of infalliblity for objectivity except you.

  17. colewd:

    Different computers with objective similarities and differences and the ability to create an objective nest between Apple os and PC os. We can continue this until present day with the current Mac family and the PC families.

    LOL.

    Bill, you have no idea what an objective nested hierarchy is.

    Let me try to come up with an analogy for how far you are off the mark.

    OK, here’s one: It’s as if we’re discussing tax shelters and you are running around looking for buildings that protect tax returns from the rain.

  18. keiths: If humans (other than you) are bright enough to see that they can incorporate “continuity and flow” into their designs without slavishly adhering to the ancestor-descendant constraints we’ve been discussing, then why isn’t God?

    Once again if there is less continuity and flow in human design it’s because we are worse designers than God.

    What you are calling slavishly adhering to the ancestor-descendant constraints I would call optimally adhering to continuity and flow.

    The best designers do surprising unexpected new things while utilizing fully and smoothly what came before.

    keiths: And don’t you find it a bit, um, suspicious that your God is making the same dumb mistake that you’re making?

    I would find it completely and utterly amazing if an unthinking and uncaring “nature” would do it even remotely like I would do it but that is what we see.

    That is one of the reasons I infer design

    I realize that you claim you would do it differently if you could but that says more about your personal aesthetics than it does about God.

    peace

  19. newton: No one claimed the necessity of infalliblity for objectivity except you.

    objectivity in part means with out bias.

    With out God there is really no way to know for sure our opinions are with out bias. That is why I used the infallible qualifier.

    If by objective you only mean ——-with out bias as far as you know right now at this particular moment in time—— then I don’t have a problem.

    Is that all you mean when you say objective?

    peace

  20. fifth,

    What you are calling slavishly adhering to the ancestor-descendant constraints I would call optimally adhering to continuity and flow.

    And as I keep pointing out, they are not the same thing. For example:

    And one can easily show respect for conventions, such as the QWERTY keyboard layout, without being bound by ancestor-descendant relationships.

    Why not do the exercise I suggested for you? It might help you avoid silly mistakes like the one you’re making here.

  21. keiths: And as I keep pointing out, they are not the same thing.

    Claiming is not the same thing as demonstrating.

    keiths: one can easily show respect for conventions, such as the QWERTY keyboard layout, without being bound by ancestor-descendant relationships.

    Again this boils down to you thinking that less continuity and flow are good and my thinking that the more you have the better the design.

    The best designers would only abandon flow and continuity when it is absolutely necessary. When there is no possible way to accomplish your purpose with out abandoning it.

    keiths: Why not do the exercise I suggested for you?

    Because I’m not in third grade and I don’t need to put something like that on paper to visualize it.

    Why don’t you do your “exercise” then start a thread so that we can critique your work?

    peace

  22. keiths,

    Bill, you have no idea what an objective nested hierarchy is.

    Does Theobald understand what an objective nested hierarchy is? Thats the reference that you pointed me to. He claims that language can be organized in an objective nested hierarchy. Do you agree? If so, why?

  23. fifthmonarchyman: With out God there is really no way to know for sure our opinions are with out bias.

    Sure, there is. We compare our opinions with those of other people.

    By contrast, when you rely on God, you are comparing your own opinion with your own opinion, with a dubious assumption of “revelation”.

  24. newton,

    How do new languages come about?

    R and D labs in companies or universities. C was developed to program the unix operating system at Bell Labs. Fortran was developed at IBM and Basic was developed at a university possibly Cornel.

  25. colewd:

    Does Theobald understand what an objective nested hierarchy is?

    Yes.

    Does Theobald, or anyone who understands this stuff, think that computers form an objective nested hierarchy? No.

    You have no idea what an objective nested hierarchy is. Read what you wrote again:

    Different computers with objective similarities and differences and the ability to create an objective nest between Apple os and PC os. We can continue this until present day with the current Mac family and the PC families.

    The concept has completely evaded you.

  26. fifth:

    Again this boils down to you thinking that less continuity and flow are good and my thinking that the more the better.

    No, because of the obvious fact that those are distinct from a slavish adherence to ancestor-descendant constraints.

    keiths:

    Why not do the exercise I suggested for you?

    fifth:

    Because I’m not in third grade and I don’t need to put something like that on paper to visualize it.

    That’s just your ego talking. You do need that kind of help, at the very least. You’re making a lot of dumb mistakes, like thinking that honoring the QWERTY convention requires a slavish adherence to ancestor-descendant constraints. It doesn’t, and doing the exercise might help you see why.

    Don’t overestimate yourself. You’re struggling, and you’re not making progress. Winging it is not working for you; why not try a more disciplined approach and work out that exercise on paper a few times?

    Why don’t you do your “exercise” then start a thread so that we can critique your work?

    Because you’ll learn more by doing it yourself. There’s a reason that teachers, particularly of technical subjects, require their students to do homework as opposed to just attending lectures.

    I sense that you’re afraid of doing the exercise for fear of making more dumb mistakes. That’s a fear that you’ll need to overcome. Reassure yourself that mistakes are expected. You don’t understand this stuff, and you’re trying to learn from people who do. Making mistakes, and having them corrected, is part of the learning process.

    Don’t let your ego get in the way of learning. That happens far too often with you.

  27. A quote from the “Nested hierarchies” section of Theobald:

    Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern produced by a branching evolutionary process, such as common descent, is much more specific than simple similarity. [Sal, are you paying attention?] Real world examples that cannot be objectively classified in nested hierarchies are the elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc. [Bill and fifth, are you paying attention?]

  28. colewd:
    keiths,

    Does Theobald understand what an objective nested hierarchy is?Thats the reference that you pointed me to.He claims that language can be organized in an objective nested hierarchy.Do you agree?If so, why?

    By and large, this is the case. But whereas relationships due solely to inheritance MUST be nested, this is not true of language. People have invented entirely new languages tabula rasa.

    However, I think it’s possible that someday fairly soon, it will become possible to insert and/or modify so many genes in some organism, that inheritance will constitute a minority of the resulting genome. Nonetheless, the argument that such a thing MIGHT lie within human technology in the future, doesn’t imply the application of that hypothetical technology in the past.

    Descent with modification as understood here is biological descent. As of yet, human inventions don’t breed, not even natural languages.

  29. Neil Rickert: We compare our opinions with those of other people.

    Objectivity is not the same thing as popular.

    Unless you can compare your opinion with every possible opinion and unbiasedly choose the correct one. popular is as far as you can get

    Neil Rickert: when you rely on God, you are comparing your own opinion with your own opinion

    That’s only your opinion 😉

    Neil Rickert: with a dubious assumption of “revelation”.

    Revelation is not assumed it’s revealed. It’s person to person communication.
    If you are assuming revelation then by definition it has not occurred.

    peace

  30. keiths: because of the obvious fact that those are distinct from a slavish adherence to ancestor-descendant constraints.

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

    That is not what we see when we look at life. Despite your claims to the contrary.

    keiths: like thinking that honoring the QWERTY convention requires a slavish adherence to ancestor-descendant constraints.

    I don’t think that. I think you think that at least subconsciously.
    As I said before my keyboard has a QWERTY because of good design.
    Adhering to continuity and flow unless it’s impossible to do so is great design.

    keiths: You’re struggling, and you’re not making progress.

    I think I’m making a lot of progress.

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

    As long as you are actually trying to prove your argument then there still is work for me to do.

    Once you get to the “you disagree because you are an idiot” spiel I know I’ve got you right where I want you.

    All that is left for you to do is spout blasphemy bring up the problem of evil.

    peace

  31. Flint,

    By and large, this is the case. But whereas relationships due solely to inheritance MUST be nested, this is not true of language. People have invented entirely new languages tabula rasa.

    However, I think it’s possible that someday fairly soon, it will become possible to insert and/or modify so many genes in some organism, that inheritance will constitute a minority of the resulting genome. Nonetheless, the argument that such a thing MIGHT lie within human technology in the future, doesn’t imply the application of that hypothetical technology in the past.

    Descent with modification as understood here is biological descent. As of yet, human inventions don’t breed, not even natural languages.

    Thanks for the explanation, here are my concerns:

    By and large, this is the case. But whereas relationships due solely to inheritance MUST be nested, this is not true of language.

    This is circular as you are assuming your conclusion. If you look at John’s papers the one that looks like a real possible common ancestry has very little phylogenetic nesting as the sequences are very similar.

    Why do think cars do not nest but languages do?

  32. keiths,

    Here is the part from Theobald you did not include:

    Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between “subjective” and “objective” is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999).

    Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.

    While cars are subjective computers with specific operating systems are not. No one would argue that a laptop PC is more similar to a Mac air then a Mac book.

  33. fifthmonarchyman: As I said before my keyboard has a QWERTY because of good design.

    Nah. There’s more efficient arrangements for keyboards. It’s just adherence out of historical constraints (people would have to re-learn to type).

    But I think the discussion will not go anywhere, mainly because a magical “designer” could do whatever she wanted, whether that’d be bad or good design doesn’t matter. For a creationists any post-facto justification, no matter how ridiculous, will do. The issue is that the nested hierarchy is obvious from the evolutionary process, while a nested hierarchy would have to be put into the designs on purpose by the magical designer. That would make her a deceiving designer, but, as I said, for a creationist any post facto justification, no matter how ridiculous, will solve even that problem.

    Either way, I think that the non-believers are giving the creationists too much space. I would not consider a magical designer as a potential answer in the first place. It would be absurd.

  34. colewd:
    Flint,

    Thanks for the explanation, here are my concerns:

    This is circular as you are assuming your conclusion.If you look at John’s papers the one that looks like a real possible common ancestry has very little phylogenetic nesting as the sequences are very similar.

    I don’t think so. Modification through biological inheritance ENTAILS nesting. This is a logical requirement. Now, we do observe nesting in biology, but neither the logical requirement, nor the observation that it is being met, is an assumed conclusion.

    I’m going to guess here that your idea is that there COULD be common ancestry without nesting. If so, I think you are correct. But in that case, you would not have inheritance. There would need to be some entirely new way to make babies, every generation.

    Why do think cars do not nest but languages do?

    Except for the exceptions, in both cases. Languages tend to nest more than cars because languages are for communication, and entirely new ones communicate with nobody, defeating their purpose. Cars, on the other hand, may or may not borrow elements of design from prior versions, but in either case they provide transportation, so their purpose is not defeated by completely new designs.

    (And I think it’s worth noting that even if a car shares NO components with any prior model, it sells better if customers already know how to drive the prior models. This sort of “design inertia” exists in most technologies, where new inventions for common purposes try to minimize the aggravation pioneer buyers experience trying to figure out how to use the damn thing.)

  35. colewd: This is circular as you are assuming your conclusion. If you look at John’s papers the one that looks like a real possible common ancestry has very little phylogenetic nesting as the sequences are very similar.

    1) You appear not to know what “circular” means or what “assuming your conclusion” actually looks like.
    2) Both of John’s papers look like a real possible common ancestry.
    3) Both papers have lots of phylogenetic nesting; perhaps that’s something else you don’t know the meaning of.

  36. colewd,

    While cars are subjective computers with specific operating systems are not.

    You are presumably trying to claim that while cars do not fall into an objective nested hierarchy, computers do.

    That’s incorrect. Neither of them do, for the reasons that Theobald lays out in that very quote.

    Sorry, Bill, but these concepts — simple though they are — appear to be well beyond your grasp. Like fifth, you just don’t get it.

    This is not a surprise. Intelligence varies among persons. Some people enjoy more of it, and others less. It’s distributed quite unevenly.

    That’s easier for an atheist to explain than it is for you, but either way, it’s a fact. You and fifth got the short end of the intelligence stick, and it’s preventing you from understanding concepts that your opponents grasp easily.

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

  37. colewd:

    Why do [sic] think cars do not nest but languages do?

    Because language evolves through a branching process similar to that of life, with mostly gradual changes and primarily vertical inheritance. A process with those characteristics leads to an objective nested hierarchy.

    Cars and computers are formed through a completely different sort of process, and so it’s no surprise that they do not fall into objective nested hierarchies.

    Theobald makes this point in the very quote that you provided above. Didn’t you understand it?

    Here it is again:

    Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between “subjective” and “objective” is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999).

    Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.

  38. keiths,

    That’s incorrect. Neither of them do, for the reasons that Theobald lays out in that very quote.

    It appears to fit well with Theobald’s rational. Again you make assertions without argument and do not appear to understand what you are arguing.

  39. keiths,

    Cars and computers are formed through a completely different sort of process, and so it’s no surprise that they do not fall into objective nested hierarchies.

    Cars and computers are very different where computers build on ancestral layers of software and hardware constantly adding complexity. Dude you have no idea what you are talking about and your depth of thinking is not useful. Lets table this.

  40. Entropy:

    The issue is that the nested hierarchy is obvious from the evolutionary process, while a nested hierarchy would have to be put into the designs on purpose by the magical designer. That would make her a deceiving designer, but, as I said, for a creationist any post facto justification, no matter how ridiculous, will solve even that problem.

    Yes. The problem is obvious to the brighter folks, but not to guys like Mung, Sal, fifth, colewd, and Erik. They think (or hope, rather) that they can come up with an explanation for why a designer would be expected to produce the distinctive pattern we see — an objective nested hierarchy. The problem is that they can’t even grasp what that pattern is, much less give a plausible design explanation for it.

    There is a reason that creationism is regarded not just as wrong, but as a crackpot idea. Like flat-earthers or Scientologists, these guys can’t — or won’t let themnselves — see it.

    Creationism is literally trillions of times less likely to be true than common descent, and that’s an understatement. Yet these guys are dumb enough to bet against common descent.

    It’s a staggering display of incompetence.

  41. colewd:

    Dude you have no idea what you are talking about and your depth of thinking is not useful.

    Bill, can you think of anyone at TSZ whom you can legitimately condescend to, except perhaps Byers or J-Mac?

  42. Flint,

    I’m going to guess here that your idea is that there COULD be common ancestry without nesting. If so, I think you are correct. But in that case, you would not have inheritance. There would need to be some entirely new way to make babies, every generation.

    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.
    Flint,

    Except for the exceptions, in both cases. Languages tend to nest more than cars because languages are for communication, and entirely new ones communicate with nobody, defeating their purpose. Cars, on the other hand, may or may not borrow elements of design from prior versions, but in either case they provide transportation, so their purpose is not defeated by completely new designs.

    I agree with you here. This is well articulated. The issue appears to be continuity over time. This is why I think computers unlike cars may give us an interesting perspective to how design creates nesting. Computers also like cells are driven by translated code.

    (And I think it’s worth noting that even if a car shares NO components with any prior model, it sells better if customers already know how to drive the prior models. This sort of “design inertia” exists in most technologies, where new inventions for common purposes try to minimize the aggravation pioneer buyers experience trying to figure out how to use the damn thing.)

    Fair point.

  43. colewd:

    Cars and computers are very different where computers build on ancestral layers of software and hardware constantly adding complexity.

    No, Bill. You’re clearly not a technical guy. You don’t understand computers or how they are designed.

    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.

  44. John Harshman,

    1) You appear not to know what “circular” means or what “assuming your conclusion” actually looks like.
    1) You appear not to know what “circular” means or what “assuming your conclusion” actually looks like.
    2) Both of John’s papers look like a real possible common ancestry.
    3) Both papers have lots of phylogenetic nesting; perhaps that’s something else you don’t know the meaning of.

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

    3) Both papers have lots of phylogenetic nesting; perhaps that’s something else you don’t know the meaning of.

    Regarding number 3. I probably was taking too narrow a view.

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