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. fifthmonarchyman: I can’t get John Harshman’s opinion by reading wikipieda

    What makes you think his opinion will diverge significantly from that page? At the level you are working at/capable of understanding I suspect not a lot of divergence.

  2. fifthmonarchyman: Sure it does we are looking for explanations of the pattern we see and we would not see the pattern if it weren’t for discernable lineages. Understanding why they exist gets us closer to an explanation

    An explanation of what? We were talking about nested hierarchy. That’s explained by common descent, and there’s nothing else that explains it. You could explain the mechanisms of common descent, and you could explain the mechanisms behind the mechanisms. There’s an infinite regress of explanations, but you only need the first explanation for this particular topic. The reasons speciation happens are not relevant to explaining the nested hierarchy.

    I might ask why does hydrogen fuses in the sun but not in the Goodyear blimp and why there is no much hydrogen available to fuse in the sun.

    You could ask that, but hydrogen fusion still explains the heat of the sun without going into why fusion happens in the sun or why there’s hydrogen in the sun. Especially the latter: you are demanding that we explain the entire universe in order to explain any part of it.

    I do wish you wouldn’t ignore my explanations of why nested hierarchy implies common descent and then complain that nobody has explained it to you.

  3. fifthmonarchyman: Again I’m not making an argument. I’m hoping that some one will provide a succinct cogent argument for common descent. preferably one that can be summarised in a couple of sentences

    no such luck as of yet.

    peace

    That sounds like you are making the argument that hasn’t happened repeatly.

  4. fifthmonarchyman: I would say baring another explanation that common descent is as good a guess as any but I would not want to be close minded about it.

    And herein lies the problem. You consider it a “guess” rather then something that can be supported with empircal facts.

  5. colewd:
    Walter Kloover,

    If both cases you would have multiple almost objective features or codes collaboratingthe nested structure.In either case it illustrates that design, based on base x codes, will create an almost objective nested hierarchy and explains the new innovations that common descent does not.

    .

    Okay, you seem to be trying to challenge my claim that computers cannot be placed in an objective nested hierarchy. But now you are talking just about the code in the computers.

    Just talking vaguely about a couple of features of code is not a substantive reason to doubt that computers cannot be placed in an objective nested hierarchy. You would have to include more features.

    Try making a spreadsheet with 10 rows, each a kind of computer, and 20 columns, each a feature of computers. Make an organization of the 10 computers based on the first ten features, then make an organization based on the second ten features. Compare the two.

    It will take some effort. Did you think overturning common descent would be easy?

    I’ll give you a start on the list of 20 features:

    Brand
    Model
    Year of manufacture
    Original Operating system
    Does it have Office loaded
    What kind of video card
    How much RAM

    There’s your mission, if you choose to accept it.

  6. fifthmonarchyman: Walter

    No, I don’t think categorizing by one trait would yield matching hierarchies. As I said in my comment you replied to, 10 features in each organization might be enough to get pretty close, depending on what features and what species you select.

  7. John Harshman,

    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?

    The Krebs and Calvin cycles produce ATP which is mission critical for cell division. So is transcription and translation which is the front end of the cell cycle. This has to do with standard methods which is evidence of design.

    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.

    The same would work for a nested group.

    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?

    Intellectually limited? Designed a diverse set of organisms that can self replicate. The software model is what we are observing in the form of DNA

  8. Neil Rickert,

    Yes, you are wrong.

    The Apple I was not, in any reasonable sense, an ancestor of the Mac. Rather, the Mac was a completely new design, though from the same people who designed the Apple I and Apple II.

    This is a good correction, thanks. The common ancestor is not the Apple 1 but Lisa which split into the pascal Mac and the objective C Next computer.

  9. Walter Kloover,

    Okay, you seem to be trying to challenge my claim that computers cannot be placed in an objective nested hierarchy. But now you are talking just about the code in the computers.

    This is following Theobald’s example of comparing phylogenetic with morphology. Your example is too subjective and would probably fail with living organisms like flying and swimming mammals.

  10. fifthmonarchyman: No what happened when the ancestor reproduced.
    My siblings and I are here because Mom and dad made a family not because of our common descent.

    Per the definition, siblings share at least biological parent, so your siblings are your siblings because of common descent. If your parents decided to make a family by adopting unrelated children what you consider siblings would not be siblings.

    We share the same color of skin (mostly) because mom and dad had skin of that color and passed it on to us not because of common descent

    How exactly did they pass a trait to you , if not thru heredity? Oh right you aren’t making any alternative arguments.

    One effect of mom and dad choosing to have a family is that my siblings and I share a common ancestor

    You are siblings because you share a common ancestor. The effect of your parents choice was one link in chain of causation (chain of causation – A series of events, each of which was caused by the immediately previous event. Just as whatever caused the effect of your parents choice to make a family, which might itself be an effect of your parents choice to get married.

    You are cherry picking the start of the chain of causation to avoid admitting common descent is a causative agent for some reason.

    You seem to be working really hard not to recognize an explanation for someone just looking for an explanation. What is the cause of that you think?

    peace

  11. colewd:The Krebs and Calvin cycles produce ATP which is mission critical for cell division. So is transcription and translation which is the front end of the cell cycle. This has to do with standard methods which is evidence of design.

    Yes, and atoms make up ATP, so atoms are crucial to understanding ATP. It’s turtles all the way down, and in order to understand anything we must understand everything. “Standard methods” seems to be your meaningless buzzphrase of the moment. What does any of that have to do with inheritance or nested hierarchy?

    Me: 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.

    Bill: The same would work for a nested group.

    Could you be a little more cryptic? There’s a danger that somebody might understand what you’re trying to say. Though it’s a slight danger.

    Intellectually limited? Designed a diverse set of organisms that can self replicate. The software model is what we are observing in the form of DNA

    Yes, intellectually limited for the reasons I said and you ignored. The software model limits god to human incremental modification, and there aren’t even any radical new designs, as in the mac example. Further, the design process is nonsensical, new parts being made from old parts with completely different functions. You can’t deal with that by ignoring it.

  12. colewd: This is following Theobald’s example of comparing phylogenetic with morphology. Your example is too subjective and would probably fail with living organisms like flying and swimming mammals.

    First, you are confusing “phylogenetic” with “molecular”. Morphological data is phylogenetic too. Second, no, the example doesn’t fail with flying and swimming mammals, and in fact the data are clear on these taxa. You persist in assuming that your speculation in ignorance can be taken as evidence for your claims.

  13. colewd:

    This is following Theobald’s example of comparing phylogenetic with morphology.Your example is too subjective and would probably fail with living organisms like flying and swimming mammals.

    Or in other words, the only thing that objectively explains the homologies that we see in flying and swimming mammals is common descent.

    What do you think evolution’s about? It’s about getting away from your fuzzy and generalist thinking to something that actually works.

    Glen Davidson

  14. colewd:
    Walter Kloover,

    This is following Theobald’s example of comparing phylogenetic with morphology.Your example is too subjective and would probably fail with living organisms like flying and swimming mammals.

    We are discussing computers now, not mammals. Focus. Make that spreadsheet and do the actual comparison. Then you can rub my nose in it if it turns out the two organizations are the same. Won’t that be satisfying? And if they don’t turn out the same you will have learned something. It’s a win-win situation.

  15. John Harshman,

    Yes, intellectually limited for the reasons I said and you ignored. The software model limits god to human incremental modification, and there aren’t even any radical new designs, as in the mac example.

    John, the software model is the model. The design is in the incredible flexibility of the components which are atoms and molecules. The evidence is this model can make radical new designs because of the unlimited sequence space and the flexibility of atoms and molecules.

    Could you be a little more cryptic? There’s a danger that somebody might understand what you’re trying to say. Though it’s a slight danger.

    If you look at Lisa as the common ancestor to the Mac pascal and the Next objective c we would expect the same software nesting as in the various versions of the Mac X family. The user interface and the binary code would show that Lisa is the ancestor to both the Mac pascal and the Next objective c.

  16. Walter Kloover,

    We are discussing computers now, not mammals. Focus. Make that spreadsheet and do the actual comparison. Then you can rub my nose in it if it turns out the two organizations are the same. Won’t that be satisfying? And if they don’t turn out the same you will have learned something. It’s a win-win situation.

    This is not how Theobald is showing an objective nested hierarchy for living organisms exists. It is your straw man. The most important issue is if the evidence points to design, inheritance or both. The computer example shows correlation between base 2 code and the user interface as Theobald’s model shows corralation between morphological and base 4 phylogenetic data.

    We are discussing computers now, not mammals. Focus.

    If you cannot show this for mammals then the point becomes mute as the objective nested hierarchy claim for living organisms would break down based on your straw man criteria.

  17. colewd: John, the software model is the model. The design is in the incredible flexibility of the components which are atoms and molecules. The evidence is this model can make radical new designs because of the unlimited sequence space and the flexibility of atoms and molecules.

    Atoms and molecules are your evidence of design? But then everything that has atoms and molecules must be designed. Rocks must be designed. Air must be designed. Mud must be designed. And in life there are no radical new designs.

    If you look at Lisa as the common ancestor to the Mac pascal and the Next objective c we would expect the same software nesting as in the various versions of the Mac X family. The user interface and the binary code would show that Lisa is the ancestor to both the Mac pascal and the Next objective c.

    There is no “software nesting”. You are still making up facts.

  18. John Harshman,

    Atoms and molecules are your evidence of design?

    They are one piece of the evidence so are:
    DNA
    Proteins
    The Genetic code
    The nuclear pore complex
    The spliceosome
    The citric acid cycle
    The electron transport chain
    The nuclear pore complex
    Transcription
    Translation
    Cell division
    Embryo development
    Gravity
    The strong/ weak force
    Electromagnitism
    etc.

    There is no “software nesting”. You are still making up facts.

    The Next and Pascal Mac software share the Lisa software as a common design ancestor.

    Please support your claim that there is no “software nesting” and I am making up facts.

  19. colewd:
    The nuclear pore complex
    The spliceosome
    The citric acid cycle
    The electron transport chain
    The nuclear pore complex

    The nuclear pore complex twice huh? Whoah!

  20. colewd: DNA
    Proteins
    The Genetic code
    The nuclear pore complex
    The spliceosome
    The citric acid cycle
    The electron transport chain
    The nuclear pore complex
    Transcription
    Translation
    Cell division
    Embryo development
    Gravity
    The strong/ weak force
    Electromagnitism

    Why are those evidence for design? What is it about them that makes them evidence for design?

  21. Rumraket,

    Why are those evidence for design? What is it about them that makes them evidence for design?

    All-have predictable outputs which are consistent with design.
    Many are the result of organized base 4 code. Translatable code is evidence of design.
    All appear to be the result of strict design rules.

  22. colewd,

    I think you need to focus on the nested hierarchy, rather than ‘things I think designed’ – especially if the list includes ‘everything’.

  23. colewd:
    John Harshman,

    They are one piece of the evidence so are:
    DNA, etc.

    So, literally everything is evidence of design. But you will have to show your work.

    The Next and Pascal Mac software share the Lisa software as a common design ancestor.

    I don’t know anything about that subject, and I suspect you don’t either.

    Please support your claim that there is no “software nesting” and I am making up facts.

    It’s impossible to support a negative claim of existence. You have to support a positive claim, which you have not done other than by vacuous assertion. Still, in support of “software nesting” you have previously used successive modifications of a single program, which is invalid.

    Could I ask that you stop ignoring most of my arguments?

  24. John Harshman,

    It’s impossible to support a negative claim of existence. You have to support a positive claim, which you have not done other than by vacuous assertion.

    If you cannot show the claim is false then calling it vacuous is non sense. I made an original proposal here that the Apple 1 was the common ancestor to the Mac. Neil corrected me and I modified it to the Lisa being the common design ancestor to the Mac pascal and the Next objective c.

    Neil’s criticism is that the software between the Apple 1 and the Mac was very different. Although that does not rule it out as a common design ancestor when I thought about it the Lisa was a much better fit as it shared the 68xxx processor and used the same graphical user interface.

    The most important issue here is if there is correlation between the base 2 code and the user interface. I am certain that we would see that the tree I described would be the same for the base 2 code and the user interface. This is inherent in how computers are designed and maybe inherent in how life is designed.

    What is interesting here is this supports the hypothesis that the correlation that Theobald got between morphological data and the base 4 phylogenetic data supports the design hypothesis.

  25. colewd: I made an original proposal here that the Apple 1 was the common ancestor to the Mac. Neil corrected me and I modified it to the Lisa being the common design ancestor to the Mac pascal and the Next objective c.

    I didn’t comment at the time. But, yes, I agree that seeing the Lisa as a common ancestor of the Mac and the Next computers does seem very reasonable.

  26. colewd: If you cannot show the claim is false then calling it vacuous is non sense.

    Or perhaps you don’t know what “vacuous” means.

  27. John Harshman,

    Or perhaps you don’t know what “vacuous” means.

    Calling a claim vacuous without support is circular reasoning. If you are doing this and admittedly do not understand the subject at hand very well this should be cause for self reflection.

  28. colewd:
    John Harshman,

    Calling a claim vacuous without support is circular reasoning.

    I don’t think so. It’s an assertion. You do say ‘circular reasoning’ a lot, but I don’t think you apply it correctly.

    If you are doing this and admittedly do not understand the subject at hand very well this should be cause for self reflection.

    That’s a keeper, in the broader context.

  29. Bill:

    If you are doing this and admittedly do not understand the subject at hand very well this should be cause for self reflection.

    Allan:

    That’s a keeper, in the broader context.

    Too bad we don’t have sigs here.

    Predicted Bill response: “Why is everyone laughing?”

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