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: 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.

    How does design introduce novelty in organisms?

  2. John Harshman: Perhaps you could try applying your line of demarcation in some real case. How about humans and chimps, for example?

    I think that there is more to humans that can be explained by simple genetic variation in the subfamily Homininae.

    If you want to get an idea of the sorts of things I’m talking about you might take a look at the recent Adam and Eve thread.

    peace

  3. newton: 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?

    No my point is that “we” meaning folks interested in biology should focus more on the exceptions because that is where the action is.

    I also think that we don’t necessarily have to understand exactly what physically caused the exceptions before we can glean some value from them.

    peace

  4. newton: How does design introduce novelty in organisms?

    Design does not introduce novelty any more than common descent prevents it.

    Design is a inference we might draw from observing novelty in certain circumstances. Just as we might infer common descent from observing the lack of novelty in certain other circumstances.

    Get it?

    peace

  5. fifth:

    Design does not introduce novelty any more than common descent prevents it.

    You actually think that design doesn’t introduce novelty?

    Unbelievable.

  6. To my confrères: We have a low opinion of ID supporters, and rightfully so. But did any of you imagine that you would hear an ID supporter denying that design introduces novelty?

    The mind boggles.

  7. keiths: You actually think that design doesn’t introduce novelty?

    Design does not introduce novelty designers introduce novelty

    Design is not a person or a force.
    It’s a description of what persons do

    After all these years you really still don’t know what is being argued?

    peace

  8. keiths: Design is a process. A process that introduces novelty.

    LOL

    That is like saying hammering built a house.
    Or painting created the Mona Lisa.

    peace

  9. No, it’s like saying that

    a) the process of contamination introduces impurities; or
    b) the process of corrosion produces structural weakness; or
    c) the process of making dumb mistakes produces embarrassment.

    All of which are obviously true.

    Fifth, you put the capital “I” in Incompetent.

    ETA: Which brings great glory to Jesus, of course.

  10. keiths: All of which are obviously true.

    If he would of said the “process of design” produces novelty he might of had a point. The “process of design” implicitly includes the designer.

    Just like the “process of contamination” includes the thing doing the contaminating.

    On the other hand

    If I asked you why the water has impurities and you said because of contamination.

    I would reply LOL

    The same goes if I asked you why did the steal beam rust and you said because of corrosion.

    by the way

    A) How exactly does contamination introduce impurities into the water?

    B) How exactly does corrosion cause iron to rust?

    peace

  11. newton,

    How does design introduce novelty in organisms?

    Stating this slightly differently, the design process results in novel organisms. I agree with keiths that design can be described at a high level as a process but its execution is often not completely repeatable and takes the form of a project. Novel organisms are created by unique biochemical organization some of which we understand like novel DNA sequences, alternative splicing patterns and post translation protein modification.

  12. fifth,

    Learn to cut your losses. You claimed that design does not introduce novelty. It was a dumb mistake. You are embarrassed.

    Accept it and move on.

  13. colewd:
    John Harshman,

    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.

    What in the paper led you to believe that the crocs may share a common ancestor? And are you claiming that the croc sequence data do not form a nested hierarchy? I chose that paper because the data are so absurdly obvious that even you should be able to see it.

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

    I disagree. Branching doesn’t require speciation, though it helps, and speciation very seldom requires new functional genes. You have been misinformed.

    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.

    Common descent doesn’t have to explain the branching process. It only has to explain the nested hierarchy. Design doesn’t explain nested hierarchy, and as far as I can tell it doesn’t explain the branching process either.

  14. fifthmonarchyman: I think that there is more to humans that can be explained by simple genetic variation in the subfamily Homininae.

    If you want to get an idea of the sorts of things I’m talking about you might take a look at the recent Adam and Eve thread.

    I am unable to recognize this as an answer to the question I asked.

    The original comment by Bill said this: “Common descent is certainly part of the history of life. The question is the line of demarkation between descent and design.”

    Bill was referring to the spot in a tree of putative descent where fiat creation of kinds occurs, below which there is no common descent among kinds. You seem to be talking about something else entirely. I want to know how you can tell whether, in any particular case, a nested hierarchy results from common descent or from some unknown and unexplained feature of common design without descent.

  15. John Harshman,

    I disagree. Branching doesn’t require speciation, though it helps, and speciation very seldom requires new functional genes. You have been misinformed.

    Then explain to me how all the Mac os versions past os 10.0 do not branch?

    speciation very seldom requires new functional genes

    Very seldom says it ultimately requires them. Your explanation of the nested hierarchy is at best incomplete and at worst does not work at all.

    Common descent doesn’t have to explain the branching process. It only has to explain the nested hierarchy.

    Sure it does. Heredity is part of reproduction and a process. Common descent is the result of heredity. Claiming common descent explains the nested hierarchy is saying that the nested hierarchy is explained by heredity. If you cannot demonstrate that the heredity process results in branching then it does explain the nested hierarchy.

  16. colewd:
    John Harshman,

    Then explain to me how all the Mac os versions past os 10.0 do not branch?

    They don’t branch because they’re linear. Is it necessary to explain the difference between branching and linearity?

    Very seldom says it ultimately requires them.

    No it doesn’t. What are you talking about?

    Sure it does.Heredity is part of reproduction and a process. Common descent is the result of heredity. Claiming common descent explains the nested hierarchy is saying that the nested hierarchy is explained by heredity. If you cannot demonstrate that the heredity process results in branching then it does explain the nested hierarchy.

    Word salad. Common descent is the result of heredity within lineages, branching of lineages, and changes within lineages. That’s all you need to explain nested hierarchy, and the details of how each works are irrelevant. I don’t know what you mean by “the heredity process”. So what do you think explains the nested hierarchy of life? Be specific.

  17. John Harshman: Bill was referring to the spot in a tree of putative descent where fiat creation of kinds occurs

    That is not how I understood his comment

    I was talking about the exceptions we see in the nested hierarchy , places where nested hierarchy does not fully describe the pattern we observe. It’s those places that interest me.

    IOW “the line of demarkation between descent and design”

    John Harshman: I want to know how you can tell whether, in any particular case, a nested hierarchy results from common descent or from some unknown and unexplained feature of common design without descent.

    It’s my tentative opinion that observing a nested hierarchy in the absence other information does not tell us much at all. It’s the other information that helps you decide what caused the pattern you see.

    If we have good reason to infer design it doesn’t matter the pattern that is left.

    I really don’t have a problem with common descent however I came to this thread hoping for some convincing explanation as to why we should infer common descent when we observe a nested hierarchy.

    I was hoping for a succinct argument something like

    P1: Common descent (in isolation) entails a nested hierarchy
    P2: life can only be categorized into a nested hierarchy
    Conclusion: therefore common descent

    no such luck so far

    peace

  18. fifth,

    Do you know what an “objective nested hierarchy” is? Do you know what “consilience of independent phylogenies” means?

    Be careful. Bill got caught lying about his own (lack of) knowledge of those concepts. He looks pretty pathetic right now.

    Let’s see if you can do better. Here’s what I requested of Bill:

    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.

    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.

    colewd:

    [complete and utter silence, despite repeatedly being asked to answer the questions]

    Can you do what Bill could not, and honestly say that you understand those concepts? Can you rise to the challenge he fled from?

  19. fifthmonarchyman: Design does not introduce novelty any more than common descent prevents it.

    You should tell Bill. But OK, since design is incapable of novelty, who is the designer and how do we know he is capable? Assuming he is ,how did he he create the novelty in physical organisms?

    Design is a inference we might draw from observing novelty in certain circumstances.

    Shouldn’t that be the process of design or the process of the designer is a the result of the process of inference we might use the process of drawing a conclusion from the process of observing novelty in certain circumstances?

    Just as we might infer common descent from observing the lack of novelty in certain other circumstances.

    You mean the process of common descent? Care to elaborate on that process of inference?

    Get it?

    peace

  20. fifthmonarchyman: It’s my tentative opinion that observing a nested hierarchy in the absence other information does not tell us much at all. It’s the other information that helps you decide what caused the pattern you see.

    What other information, and how?

    If we have good reason to infer design it doesn’t matter the pattern that is left.

    Why do you not care about the main pattern in the data? Doesn’t it need an explanation as much as or more than the exceptions? What, if anything, is your explanation?

    I really don’t have a problem with common descent however I came to this thread hoping for some convincing explanation as to why we should infer common descent when we observe a nested hierarchy.

    I was hoping for a succinct argument something like

    P1: Common descent (in isolation) entails a nested hierarchy
    P2: life can only be categorized into a nested hierarchy
    Conclusion: therefore common descent

    no such luck so far

    What do you mean by “in isolation”? Other than that, your syllogism looks fine to me. In fact I think I’ve said it in almost the same words on several occasions, though I’d use “implies” rather than “entails”.

  21. fifthmonarchyman: I really don’t have a problem with common descent however I came to this thread hoping for some convincing explanation as to why we should infer common descent when we observe a nested hierarchy

    You have any convincing evidence beyond your statement that was your intent ?

  22. fifthmonarchyman,

    I was talking about the exceptions we see in the nested hierarchy , places where nested hierarchy does not fully describe the pattern we observe. It’s those places that interest me.

    This assumes that common descent is the only explanation for the nested hierarchy and I am not sure it is at this point. John is right I think the points that are caused by descent may be limited to a few where the rest is caused by design.

    If we look at the design history of personal computers all known branching was the result of design. The apple 1 with a basic operating system (os) was the ancestor to the apple 11 basic and the first pascal os Mac. The branching in this case we know was caused by design.

    If we were to look only at the user interface the branching would be as stated. If we looked at all the bits of the operating system the branching would also be consistent with the user interface branching. This consistent branching is confirmation in this case that the nested hierarchy confirmed by the user interface and the code is caused by design. Chance or inheritance ( common descent) are not possible causes in this case.

    In life we see this same pattern where the nested hierarchy of phylogenetic data matches the nested hierarchy of morphological data more often then not. Could the cause of this matching be from design as it is in the computer example? Is it possible that common descent does not explain the nesting. The nesting may simply be slow design changes with the strategy of keeping the common designs compatible. As all multicellular organisms use glucose oxygen or co2 to generate ATP to power the cell compatible designs are important for living systems.

  23. Bill,

    Consider the current sad state of affairs:

    1) You are so convinced that you don’t understand what “consilience of independent phylogenies” and “objective nested hierarchy” mean that you are afraid to even try to explain them when asked.

    2) This, despite telling us last night that you did understand them.

    3) That means you were deliberately lying last night.

    4) Now, despite being convinced that you don’t understand the concepts, you continue to ignore the people who do, including me, John, and Theobald.

    5) And yet your confidence in yourself has evaporated. You’ve gone from baldly declaring

    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.

    …to timidly asking:

    Could the cause of this matching be from design as it is in the computer example? Is it possible that common descent does not explain the nesting.

    6) Your lack of confidence makes sense. Who would trust a guy who is (correctly) convinced that he doesn’t understand the concepts, who was so ashamed of that that he lied through his teeth about it, and who has gone from confidently declaring victory to timidly asking whether it’s at least possible that design might explain the pattern? (It doesn’t.)

    How much lower will you have to sink, Bill, before you see the value of the advice I gave to fifth?

    Follow the example of brighter folks: learn first, and once you understand, then challenge if you think you have a case.

    You know that you don’t understand. Why are you wasting time on your challenges, when you could be learning instead?

  24. colewd: Is it possible that common descent does not explain the nesting. The nesting may simply be slow design changes with the strategy of keeping the common designs compatible.

    Bill, you are tilting at windmills. If we were to grant you, for the sake of the argument, that both the branching process and the introduction of novel features were by design processes (it doesn’t matter whether they occur simultaneously), how would your scenario differ from common descent?

    It wouldn’t, because in the end all traits are inherited along a lineage and shared by the daughter lineages after a split. As long as there is no cross porting, your scenario becomes indistinguishable from common descent.

  25. newton: You have any convincing evidence beyond your statement that was your intent ?

    Does my repeated asking for a succinct argument or a short summary of the evidence for common descent count? 😉

    peace

  26. keiths: Do you know what an “objective nested hierarchy” is?

    No,

    I know what a nested hierarchy is but I don’t know what you mean when you use the word objective.

    I’ve repeatedly asked for your definition but you just ignore me and point me to a website and crow that I’m too stupid to understand.

    peace

  27. colewd: This assumes that common descent is the only explanation for the nested hierarchy and I am not sure it is at this point.

    I don’t think it’s the only explanation but it is an explanation.

    peace

  28. fifthmonarchyman: colewd: This assumes that common descent is the only explanation for the nested hierarchy and I am not sure it is at this point.

    I don’t think it’s the only explanation but it is an explanation.

    Did you know we have a dedicated thread running well over 5000 comments where we collect all alternative explanations to common descent? Care to add yours?

    So far we have … let me count …

    one

    1) The Designer deliberately faked a nested hierarchy.

  29. fifthmonarchyman: Does my repeated asking for a succinct argument or a short summary of the evidence for common descent count?😉

    Not if you had repeatedly been given both. Evidence might be the same level of scrutiny for any alternate explanations for the data if they exist. Just saying, that would be convincing.
    peace

  30. The objective nested hierarchy is “objective” because if you take a group of species and categorize them based on 10 traits, and then categorize the same group of species based on ten other unrelated traits, the two hierarchies will resemble each other. If you add ten more traits to each categorization, the resulting hierarchies will be even closer to each other. And the more traits you take into account, the more the hierarchies will match.
    For computers or cars, this will not happen.

  31. keiths:

    Do you know what an “objective nested hierarchy” is?

    fifth:

    No,

    I know what a nested hierarchy is…

    You do? So you now acknowledge that the hierarchy of quadrilaterals you presented was not a nested hierarchy at all, and that you were badly mistaken about that, despite insisting otherwise?

    …but I don’t know what you mean when you use the word objective.

    I’ve repeatedly asked for your definition but you just ignore me and point me to a website and crow that I’m too stupid to understand.

    No, I point you to a website that explains, in simple and clear language, what an objective nested hierarchy is. I urge you to study it. You refuse. Learning is not of interest to you, particularly if it involves effort of any kind. You are here to glorify yourself while hypocritically pretending that the aim is to glorify God. It’s the worst kind of public mental masturbation.

    You are a huge liability to your faith, fifth.

  32. Corneel,

    It wouldn’t, because in the end all traits are inherited along a lineage and shared by the daughter lineages after a split. As long as there is no cross porting, your scenario becomes indistinguishable from common descent.

    Common descent does not explain how new features arise which is important to nesting where common design does. Common descent is an incomplete explanation of the pattern. Common design also explains all the standard methodologies used in the biological process.

  33. keiths,

    There’s a huge, but I mean huge, problem to communicate with filthymonarchyguy. The problem resides in how filthy defines “objective.” Unlike normal human beings, filthy defines objective as the subjective beliefs of his imaginary friend (aka “God”). That makes filthy’s claim that objectivity doesn’t exist for an atheist trivially true: we don’t believe in the magical being, therefore nothing can be the subjective belief of the magical being.

    In order to communicate, several people have attempted to explain what objective means in the contexts discussed, but filthy is unable to shake his absurd religiously-motivated definition and use the ones provided even if just for understanding the point. Of course, I doubt that filthy wants to understand at all, but that’s yet another issue.

  34. Walter Kloover,

    If you add ten more traits to each categorization, the resulting hierarchies will be even closer to each other. And the more traits you take into account, the more the hierarchies will match.
    For computers or cars, this will not happen.

    Can you support this claim?

  35. newton,

    Not if you had repeatedly been given both. Evidence might be the same level of scrutiny for any alternate explanations for the data if they exist. Just saying, that would be convincing.

    Why don’t you try to give him an explanation. I am curious if you can articulate the difference between an objective hierarchy and a subjective one. When Theobald ultimately tried he compared the nested hierarchy to chance. Is this the test your mind that allows for an objective categorization of a nested hierarchy.

    Walter just made a claim about what a biological objective an hierarchy is. Do you think he can support that claim with an example?

  36. colewd: Common descent does not explain how new features arise which is important to nesting where common design does. Common descent is an incomplete explanation of the pattern. Common design also explains all the standard methodologies used in the biological process.

    Common descent doesn’t need to explain the origin of derived characters. I am pretty sure John mentioned this a few times, but OK I’ll play along.

    Would you agree that, going by your criteria, common design is also an incomplete explanation of the nested hierarchy because it fails to explain how, where, when and why the Designer created new features? Or perhaps you are going to give us a detailed description of those “standard methodologies”?

  37. colewd: Common descent does not explain how new features arise which is important to nesting where common design does. Common descent is an incomplete explanation of the pattern. Common design also explains all the standard methodologies used in the biological process.

    How new features arise is not important to nesting. Why would you think so? Common descent is a complete explanation of the pattern, but only of the pattern, not of the differences that make up the patter. Common design explains what again? What are the “standard methodologies used in the biological process? And what do you mean by “also”, when common design doesn’t explain the nested hierarchy at all?

  38. John Harshman,

    How new features arise is not important to nesting. Why would you think so?

    Because common descent is a claim that heredity caused the pattern. The pattern is nested and the some of nesting we observe is caused by new features.

    What are the “standard methodologies used in the biological process?

    Cell division and the entire process involved, the Krebs cycle, the Calvin cycle, transcription, translation, alternative splicing etc.

    And what do you mean by “also”, when common design doesn’t explain the nested hierarchy at all?

    I think common design is the only reasonable explanation of the pattern. In the computer example we show that design creates nesting where there is correlation between the nesting of the computer code and nesting of the user interface.

  39. Corneel,

    Would you agree that, going by your criteria, common design is also an incomplete explanation of the nested hierarchy because it fails to explain how, where, when and why the Designer created new features?

    I would patricianly agree with this, however I think it is a far superior explanation of the pattern to common descent and stimulates more interesting discussion. Some of the why can be explained by observing the overall design concept as it is logical WHY PLANTS ingest co2 and animals ingest o2.

  40. colewd: Because common descent is a claim that heredity caused the pattern. The pattern is nested and the some of nesting we observe is caused by new features.

    Please speak English. And no, nesting isn’t caused by new features. Nesting is the pattern of distribution of features. The features don’t “cause” the nesting.
    What are the “standard methodologies used in the biological process?

    Cell division and the entire process involved, the Krebs cycle, the Calvin cycle, transcription, translation, alternative splicing etc.

    How are these considered “methodologies”? How are the Krebs cycle and the Calvin cycle involved in cell division? How are transcription, translation, and alternative splicing involved in cell division? What does any of that have to do with inheritance or nested hierarchy?

    I think common design is the only reasonable explanation of the pattern. In the computer example we show that design creates nesting where there is correlation between the nesting of the computer code and nesting of the user interface.

    Common design isn’t an explanation at all. In the computer example you showed that design creates linear sequences of “descent”, not nested hierarchy, and that even the linear sequence is broken by radical gaps, including complete discontinuity.

    Further, if you’re proposing computer software design as a model for life, have you considered how intellectually limited that would make your designer, who is able only to produce slight changes in a previous model and even makes new structures out of old structures with completely different functions because he’s incapable of real innovation? Is that the sort of god you think exists?

  41. colewd:
    Walter Kloover,

    Can you support this claim?

    The claim that there is such an objective nested hierarchy of organisms/traits in nature, or the claim that there is no such objective nested hierarchy in cars and computers?

    I’m not an expert, so I would guess that you are as aware of the supporting evidence for each of those claims as I am. You just weigh it differently.

    Can you give a substantive reason to doubt either claim?

  42. The really important point about nested hierarchies and the other related phenomena, is that the unthinking evolutionary processes that have been identified are necessarily derivative, mostly vertically derivative (with varying amounts of horizontal derivation). Morphology is simply always derivative of the past.

    That just doesn’t happen in technology. Colewd tries to narrow things enough to make it fit with computers, but it still doesn’t even with Apple computers in isolation, let alone in context. Languages and manuscripts always are better analogies than technology, mainly because they are phenomena involving common descent, even if via substantially different means. More importantly, nothing entails the derivative nature of life except for common descent.

    It just never works. Evolution is stuck being derivative, and that’s just what we see in life. Technology simply lacks the limitations in change that we see in life, and so this is one of the telling differences between life and technology.

    Glen Davidson

  43. colewd, to newton:

    I am curious if you can articulate the difference between an objective hierarchy and a subjective one.

    Why are you asking? Remember, two nights ago you lied through your teeth and told us that you knew the difference:

    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.

    I asked you to elaborate:

    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.

    Your response: total silence. You haven’t responded to a single comment of mine, including that one, since then. You might as well hang one of those “guilty dog” photos around your neck so that people can laugh at the resemblance between it and the look on your face. You got caught, and you are ashamed.

    Isn’t it time to come clean about your dishonesty? What will your grandchildren think about you if they stumble across this after they’ve grown up? Do you want to be remembered by them as a pitifully incompetent religious fanatic, one so embarrassed by his lack of understanding that he lied about it, and then refused to acknowledge the lie, even when confronted by incontrovertible evidence of it?

    I’m curious — having behaved so poorly, how do you feel about yourself, Bill?

  44. I wish we could make this the Analogy Free Zone. They serve a useful, occasional purpose for illustration of concepts, but when page after page is devoted to discussion of the analogy, it becomes a massive yawn. It seems to be all we ever do, nowadays.

  45. Allan:

    I wish we could make this the Analogy Free Zone.

    It’s a dilemma. With brighter students, analogies work well, enabling them to better understand the thing being analogized. With poor students, the analogy becomes a stumbling block (I’m looking at you, Erik.) They can’t distinguish what’s analogous from what’s disanalogous, and their confusion only deepens.

    What are we to do? Come up with an analogy for the analogy? And when that analogy is misunderstood, introduce an analogy for the analogy of the analogy?

    At some point you just have to shrug and say “That dog ain’t gonna hunt, and it ain’t gonna learn calculus.” You resort to analogy, in other words. 🙂

  46. keiths,

    Yes, It’s like trying to ride a hippo with a shoelace rein. Or cook steak in a chocolate frying pan. Or something!

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