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. newton: How is the implementation of these innovations explained beyond someone did something ,somehow?

    Is the fact that we don’t understand a process completely make attributing an outcome to that process incorrect?

    For example is it incorrect explain why the Universe appears to be the same in all directions, why the cosmic microwave background radiation is distributed evenly, why the Universe is flat, and why no magnetic monopoles with cosmic inflation…….

    until we can go beyond “inflation happened at the beginning somehow” ?

    peace

  2. fifthmonarchyman: Is the fact that we don’t understand a process completely make attributing an outcome to that process incorrect?

    Not at all ,however if you object to an alternate explanation for the same reason
    then the same objection should apply to your explanation as well.

    For example is it incorrect explain why the Universe appears to be the same in all directions, why the cosmic microwave background radiation is distributed evenly, why the Universe is flat, and why no magnetic monopoles with cosmic inflation…….

    If the answer is therefore design, you should be able to answer the same questions before “therefore design” .

    until we can go beyond “inflation happened at the beginning somehow” ?

    Not knowing happens,I don’t see where explaining the same thing as “ design happens somehow” is more useful.

    peace

  3. Mung: But we do not know what sort of data common descent would produce if it existed.

    Of course we do: nested hierarchy. It would be difficult to avoid. How can you not see that?

  4. keiths:

    Imagine trying to get through life using Mung logic.

    Mung:

    With God, all things are possible.

    Merry Christmas keiths.

    Merry Christmas, Mung. Here’s hoping Santa brings you a brand new cerebrum.

    ETA: Hope you have fun mimicking Santa Claus tonight.

    The very possibility of which proves Rumraket’s point. I really hope Santa brings you that new cerebrum.

  5. Mung: Not sure I understand the question. I think descent with modification serves as an explanation for the nested hierarchy. I find it superior to “common descent” as an explanation because it at least attempts to explain the origins of the innovations that lead to the nesting pattern. The twiddling bits that the supporters of “common descent” are trying to avoid lest they have to explain what they cannot explain.

    When you say “descent with modification”, what do you mean? Clearly you don’t mean what Darwin meant.

    As for the accusations that supporters of common descent are avoiding anything, that’s just wrong. Common descent explains what it can, which is the pattern. Common descent can’t explain the origin of differences and has never claimed to. But that doesn’t say that evolutionary biology can’t explain them. Still, that explanation doesn’t belong in a discussion of common descent.

  6. fifth,

    From your comment, it appears that you don’t understand the difference between a mere nested hierarchy and an objective nested hierarchy. Have you read Theobald?

  7. There is no such thing as an objective nested hierarchy.

    There is, presumably, one true tree, and many attempts to try to find something that might resemble it, all of which are subjective.

  8. keiths: From your comment, it appears that you don’t understand the difference between a mere nested hierarchy and an objective nested hierarchy.

    From your comment It appears that you don’t understand my comment.

    Or what objective means

    😉

    peace

  9. Well, while I did not ask Santa for a new cerebrum, I did ask for snow. And it’s snowing! Whee!

  10. Mung: With God, all things are possible.

    … which of course is the very point so many of us have been making. If God is the Designer, she can do anything, and there is no predicting what she will do. Any outcome can be rationalized as Common Design.

    Which is why Common Design is not a scientific theory.

    Git yontiff to all.

  11. newton: If the answer is therefore design, you should be able to answer the same questions before “therefore design” .

    1) what questions exactly?
    2) Design is not an answer to a question it’s an inference that is drawn from the available evidence.

    newton: Not knowing happens,I don’t see where explaining the same thing as “ design happens somehow” is more useful

    I think this is an interesting comment. in the future I’d like to explore the usefulness of adopting Dennetts “Intentional stance” over assuming an accident.

    Do you think that inferring design when you are not yet sure of the details is ever useful?

    For example would it under any circumstances be helpful to infer that Churchill saved England before you knew exactly how he did it?

    peace

  12. Joe Felsenstein: Which is why Common Design is not a scientific theory.

    I’ve not been arguing for or defending “Common Design” because I don’t know what it means. (Actually, I think I came across something the other day that says what is meant by common design. I’ll have to look that up.)

    Git yontiff to all.

    Thank you. I think. 🙂

  13. Joe Felsenstein: If God is the Designer, she can do anything, and there is no predicting what she will do.

    Of course you can predict what God will do.
    Just like you can predict what any person will do based on what you know about them. other things that they have done etc..

    omnipotence does not equal arbitrariness or inscrutableness

    peace

  14. Part 3 of 3:

    At present the methodology of phylogenetic reconstruction is quite controversial. There seem to be at least three reasons for this controversy…

    Third, in phylogenetic analysis, the true tree is almost always unknown, and it is difficult to test the accuracy of the trees obtained by different tree-building methods. Currently, there are several statistical criteria for evaluating the accuracy, but all of them depend on a number of simplifying assumptions. Therefore, none of them is perfect. Furthermore, the theoretical basis of the statistical methods currently used for phylogenetic reconstruction is not well established, as mentioned above. The mathematical models used for describing sequence evolution are crude approximations to reality, and a sophisticated model does not necessarily give better results. Therefore, there is plenty of room for controversy.

    – Molecular Evolution and Phylogenetics (2000). p. 84-85

    I like these authors. They pull no punches. But none of this matters as long as we can find more than one tree that agrees. Right?

    Somehow, building trees is a test of common ancestry even though “it is difficult to test the accuracy of the trees.” Someone will need to explain that to me.

    As we are talking about models here. the old spectre of confusing the map with the territory needs to be considered.

    Part 1 of 3
    Part 2 of 3

  15. dazz: I can predict what god does at any time: not exist

    See there Joe Felsenstein even dazz acknowledges that predicting what an omnipotent designer will do is not a problem.

    All that is left for him to do is for him to come up with some entailments for that prediction and he has the makings of a hypothesis. 😉

    peace

  16. Joe Felsenstein: … which of course is the very point so many of us have been making.If God is the Designer, she can do anything, and there is no predicting what she will do.Any outcome can be rationalized as Common Design.

    Which is why Common Design is not a scientific theory.

    Git yontiff to all.

    which of course is the very point so many of us have been making.If Evolution is the Designer, she can do anything, and there is no predicting what she will do.Any outcome can be rationalized as Common Descent.
    Which is why Common Descent is not a scientific theory

    unless obviously the following have been predicted:

    1. Alternative splicing of RNA that produces multiple
    proteins from one gene.
    2. Duons – Overlapping sequences that code for both protein expression and transcription factor binding sites simultaneously (simultaneous evolution prediction)
    3. Dual coding genes in which one sequence is read in multiple frames to produce completely different proteins

    The conclusion is she can write genetic code resembling two different stories that can be read forward and backwards and still make sense…

    She is one hell of the writer and designer that sheer dumb luck…
    You should try it… 😉

  17. Mung: I’ve not been arguing for or defending “Common Design” because I don’t know what it means. (Actually, I think I came across something the other day that says what is meant by common design. I’ll have to look that up.)

    I find Purposeful Design more accurate and specific than Common Design…

    What are your thoughts?

  18. Mung: I’ve not been arguing for or defending “Common Design” because I don’t know what it means. (Actually, I think I came across something the other day that says what is meant by common design. I’ll have to look that up.)

    Common design, as we’ve been using it here, is an alternative to common descent. It’s separate creation of “kinds” (whatever those may be) unrelated by descent to other kinds. And the “common” part refers to a single entity responsible for multiple kinds.

    As far as I can tell, you are defending some kind of common descent in which changes result from theistic evolution, i.e. poofing of mutations. But that isn’t clear, since you have never clearly expressed what you think, whether by accident or, dare I say, design.

  19. John Harshman: Common design, as we’ve been using it here, is an alternative to common descent. It’s separate creation of “kinds” (whatever those may be) unrelated by descent to other kinds. And the “common” part refers to a single entity responsible for multiple kinds.

    So, Harshman wrote the entire OP and tens of comment exchanges with Sal and others and he still doesn’t know what kinds are…How could he know the crocs have evolved if he doesn’t know where the boundaries of KINDS are?

    If a wolf and coyote can breed leading to hybrids called coywolfs ( I saw a few recently), how does he know the crocs he has been blathering about can’t interbreed? Has he experimented with the crocs in his birdie lab?

  20. John Harshman: Common design, as we’ve been using it here, is an alternative to common descent. It’s separate creation of “kinds” (whatever those may be) unrelated by descent to other kinds. And the “common” part refers to a single entity responsible for multiple kinds.

    As far as I can tell, you are defending some kind of common descent in which changes result from theistic evolution, i.e. poofing of mutations. But that isn’t clear, since you have never clearly expressed what you think, whether by accident or, dare I say, design.

    Merry Christmas to all(and it is only Christmas please).
    I’m gifted and stuffed up but before the year ends LETS get things ACCURATE.
    Common design, YEC, would first be KINDS, yet thats not the point.
    The KINDS have the same common design for eyeballs.likewise tongues.
    A common blueprint if you will. THEN biology is segregated.
    THEN after the fall, the design , in the blueprint/dna allows more adaptation as needed for survival. So THEN there is a spectrum in biology of likeness within closely related types. Even kinds.

    the analagy is human beings. in our colours/body plans we are quite segregated though, all admit, we come from a original population.
    So the spectrum either shows common descent or common design or both or neither.
    Evolutionists, by this analogy, are saying the colours/bodyplans of man show branching back to a original population.
    YEC creationism says it doesn’t show this. instead a design in the dna allowed colours/bodyplans to change as needed upon migration from a first population.

    Creationism does it still better. it admits both positions would seem to be a option.
    Evolutioniosm doesn’t admit this or historically intellectually scientificaly comprehend the concept

    We win this and I think it will become a bigger criticism of common descent EVIDENCE claims.
    They can’t just say HOW ELSE would similarity in traits/characters occur!!.

  21. John Harshman: As far as I can tell, you are defending some kind of common descent in which changes result from theistic evolution,

    FWIW

    I don’t have a dog in this hunt but I would like to see folks defend common decent for a change

    I think it too often is treated as an assumption when in reality should be a conclusion.

    That is the reason I asked the questions I did. No one bothered to answered so I’ll ask again in case you all missed it.

    1) Do nested hierarchies automatically entail common decent?
    2) Are there any possible systematic groupings that would rule out common decent while still facilitating categorisation into ever smaller groupings ?

    peace

  22. fifthmonarchyman: FWIW

    I don’t have a dog in this hunt but I would like to see folks defend common decent for a change

    I think it too often is treated as an assumption when in reality should be a conclusion.

    What, srsly?

    If one determines from phylogenetic analysis that a particular node gathers together in a single ancestor species several descendant lines, how is that an assumption not a conclusion? It could be that there is no phylogenetic signal at all. You don’t assume things are related if there isn’t one (ignoring other, non-phylogenetic evidence for now). You conclude it if there is.

  23. fifthmonarchyman: 1) Do nested hierarchies automatically entail common decent?
    2) Are there any possible systematic groupings that would rule out common decent while still facilitating categorisation into ever smaller groupings ?

    1) Nested hierarchical data does, unless you can find an alternative explanation. A deity who simulates common descent is one, but it’s hard to find anyone who proposes that explanation, and Occam’s razor is its enemy.
    2) If by this you refer to a nested hierarchy, I can’t think of any. But it’s unclear what you’re talking about.

    Incidentally, the thread What’s Wrong with this Paper? discusses a test of common descent, not just an assumption. Every phylogenetic analysis that incorporates any test of hierarchical structure in data does the same.

  24. fifthmonarchyman: 1) what questions exactly?
    2) Design is not an answer to a question it’s an inference that is drawn from the available evidence.

    The same questions the alternative is asked to provide answers for ,of course.

    newton: Not knowing happens,I don’t see where explaining the same thing as “ design happens somehow” is more useful

    I think this is an interesting comment. in the future I’d like to explore the usefulness of adopting Dennetts “Intentional stance” over assuming an accident.

    Not sure they are mutually exclusive positions.In human design chance often plays a role as does the principle of selection. What is your prediction of how the divine choose to design?

    Do you think that inferring design when you are not yet sure of the details is ever useful?

    Design by an unknown designer with unknown abilities can never be eliminated. It seems to me saying “inflation happened somehow “ includes intentional design in the “somehow”. I am open to the possibility, when one infers design how does one go about answering the question ,beyond saying it was designed , how did inflation happen?

    For example would it under any circumstances be helpful to infer that Churchill saved England before you knew exactly how he did it?

    Did he or was it bad strategy on the part of the Germans or the scientists who developed the radar or the designer of the Spitfire or the improved tactics which overcame the wolf packs or the code breakers at Bletchley Park or just chance?

    All those hows answer the question who

  25. fifth:

    I don’t have a dog in this hunt but I would like to see folks defend common decent for a change

    We’ve defended it at great length, particularly in the following thread (in which you have participated):

    Common Design vs. Common Descent

    Instead of demanding a personalized spoon feeding, why not read through that thread?

    Also, as I pointed out earlier:

    From your comment, it appears that you don’t understand the difference between a mere nested hierarchy and an objective nested hierarchy. Have you read Theobald

    Once you understand the difference, you’ll get why the two hierarchies you cited do not entail common descent.

    See in particular this section of Theobald.

  26. Allan Miller: If one determines from phylogenetic analysis that a particular node gathers together in a single ancestor species several descendant lines, how is that an assumption not a conclusion?

    It would be an assumption if you assumed that just because a node gathers together together in a certain way means that you have one ancestor species and several descendant species.

    In order for it to be a conclusion you would need to demonstrate that the only possible reason for it to gather in that way is because it was one ancestor species and several descendant species.

    You could possibly demonstrate that the most likely reason it gathered that way was that it was one ancestor species and several descendant species.

    But that would involve defending your position and no one here seems to be willing to do that as far as I can tell.

    peace

  27. John Harshman: Nested hierarchical data does, unless you can find an alternative explanation.

    No, Just because no other explanation has been offered does not mean that a nested hierarchy automatically entails common decent. That is what I mean by assumption rather than an conclusion.

    If a theist here was to claim that the big bang entailed creation unless a alternative explanation was offered. You all would blow a gasket

    John Harshman: Incidentally, the thread What’s Wrong with this Paper? discusses a test of common descent, not just an assumption.

    I might have to check it out

    John Harshman: Every phylogenetic analysis that incorporates any test of hierarchical structure in data does the same.

    Not unless you demonstrate that a hierarchical structure entails common decent.

    peace

  28. keiths: Instead of demanding a personalized spoon feeding, why not read through that thread?

    Why not just answer the two simple yes or no questions I asked more than once? Is that too difficult?

    peace

  29. newton: The same questions the alternative is asked to provide answers for ,of course.

    I really have no idea what you are talking about

    newton: Not sure they are mutually exclusive positions.In human design chance often plays a role as does the principle of selection.

    chance can play a role but n ever the ultimate role.

    quote:

    If you choose not to decide you still have made a choice

    end quote:
    Geddy Lee

    newton: What is your prediction of how the divine choose to design?

    to paraphrase Dr Seuss

    “a person’s a person no matter their divinity”

    peace

  30. newton: . I am open to the possibility, when one infers design how does one go about answering the question ,beyond saying it was designed

    again what question exactly?

    newton: How did inflation happen

    as far as I know no one has a clue. Do we have to know before we can say it happened?

    newton: All those hows answer the question who

    Possibly. Just as likely before the how comes the who.

    Again channeling Dr Seuss. 😉

    newton: Design by an unknown designer with unknown abilities can never be eliminated.

    Why do we always need to be concerned with elimination?

    Isn’t it possible that inferring an intentional stance can be at times useful even if we could be wrong?

    peace

  31. fifthmonarchyman: No, Just because no other explanation has been offered does not mean that a nested hierarchy automatically entails common decent.

    Do you have the slightest clue about what’s being said? The point is that common descent entails the nested hierarchy (assuming some changes occur) as a mere “mechanistic fact” of descent (with change). No one said that the lack of entailment by common design, or some other rot, means that common descent entails the nested hierarchy. That’s your lack of understanding cropping up yet again.

    That is what I mean by assumption rather than an conclusion.

    Quite an assumption on your part.

    If a theist here was to claim that the big bang entailed creation unless a alternative explanation was offered. You all would blow a gasket

    Too bad this only shows how poorly you understand the issues.

    Not unless you demonstrate that a hierarchical structure entails common decent.

    Well it doesn’t. Common descent is just the only process that can be expected to produce the results seen. Intelligence produces, well, more intelligent, less constrained by the past, results.

    Glen Davidson

  32. fifthmonarchyman: It would be an assumption if you assumed that just because a node gathers together together in a certain way means that you have one ancestor species and several descendant species.

    In order for it to be a conclusion you would need to demonstrate that the only possible reason for it to gather in that way is because it wasone ancestor species and several descendant species.

    Do you know of another reason? If common descent is the fact, one would expect a branching pattern. If one finds such a branching pattern, particularly the same or similar branching pattern from independent data sets, common descent is supported. The latter is a conclusion, after examining the data. If you think another cause should be considered, what is it, and why does it better explain the data?

    Why would people do phylogenetic analysis if they already knew what the answer was?

    But that would involve defending your position and no one here seems to be willing to do that as far as I can tell.

    That, my friend, is pure bullshit. The entire common design common descent thread has consisted of people defending that position. You choose not to access it, I don’t blame you, it’s a bloated mess, but that is not because no-one on the evolution side is willing to defend common descent.

  33. Allan Miller: Do you know of another reason?

    Perhaps but instead of focusing on other possible reasons why not support your own preferred reason?

    Allan Miller: If common descent is the fact, one would expect a branching pattern.

    Why exactly? Is there any pattern that would rule out common decent?

    Allan Miller: Why would people do phylogenetic analysis if they already knew what the answer was?

    Do people do phylogenetic analysis to establish common decent? I thought phylogenetic analysis was only possible if we assume common decent

    peace

  34. Allan Miller: The entire common design common descent thread has consisted of people defending that position.

    When I look basically all I see is folks appealing to a nested hierarchy and demanding critics produce another explanation.

    It’s highly possible that there is some actual defending of common decent going on but I never seem to see it.

    Allan Miller: You choose not to access it, I don’t blame you, it’s a bloated mess,

    Why not provide a single paragraph synopsis of some of the evidence that does reduce to appeals to the nested hierarchy.

    That would at least give me the impression that there is some actual “there” there amongst the bloat

    peace

  35. GlenDavidson: No one said that the lack of entailment by common design, or some other rot, means that common descent entails the nested hierarchy.

    ORLY?

    John Harshman: It begins as an assumption for the sake of argument. If there’s common descent, we expect to see this. Do we see this? Yes, we do. Would we expect to see this absent common descent? No, we would not. Ergo, common descent.

    Unless you can come up with some other process that results in that sort of nested hierarchy, we can’t avoid the conclusion of common descent.

  36. GlenDavidson: Common descent is just the only process that can be expected to produce the results seen.

    Wrong again.

    John Harshman: If you want to say that the designer creates species from scratch by copying existing species but making little errors in the copying process, go ahead. That is indeed an alternative explanation that would produce exactly the same results as common descent. Do you want to advance that as a hypothesis?

  37. GlenDavidson: No one said that the lack of entailment by common design, or some other rot, means that common descent entails the nested hierarchy.

    I never said they did.

    On the other hand I would like to know if a nested hierarchy entails common decent? Does it?

    GlenDavidson:Common descent is just the only process that can be expected to produce the results seen.

    Now perhaps we are getting somewhere. Why exactly can no other possible process be expected to produce the results seen?

    GlenDavidson: Intelligence produces, well, more intelligent, less constrained by the past, results.

    1) Is “intelligence” the only alternative process to common decent?
    2) Why is it not intelligent to rely what has worked in the past?

    peace

  38. Mung:
    I get the distinct impression that Glen hasn’t really been paying attention.

    The only reasonable explanation, yes.
    The Designer could also have some angels push planets around the Sun to mimic gravity. Why believe gravity as an explanation for the planet orbits?

    GTFO

  39. dazz: The Designer could also have some angels push planets around the Sun to mimic gravity.

    Those are not two different processes, they are the same process merely described in different ways

    😉

    peace

  40. What dazz thinks is due to gravity is really due to angels. So he has things reversed, and it is actually his “gravity” that is mimicking angels. He just prefers to call it “gravity” because it somehow sounds more atheistic.

Leave a Reply