Nested Hierarchies (Tree of life)

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Do you want to be my cousin?
Sure. If not me, then who?

  1. “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution. This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates. The three basic assumptions of cladistics models are: a) Any group of organisms are related by descent from a common ancestor (UCD – universal common descent); b) There is a bifurcating pattern of cladogenesis; c) Change in characteristics occurs in lineages over time. Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism” and not by a process generated by a designer that also happens to make use of biologic reproduction.
  2. No assumption can be tested by the model that uses them. That is why they’re called ‘assumptions’ and not ‘conclusions’. Instead, assumptions have to be tested independently through an entirely separated method or be accepted as axioms. An UCD “mechanism” has never been observed or proved elsewhere and is not “self-evidently true”, therefore not a valid axiom. Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis. Furthermore the conclusions of any “cladistic analysis” will always and trivially be compatible with the UCD assumption in that model.
  3. Hypothesis testing requires an alternative (null) hypothesis and a procedure that demonstrates how the data available is compatible with the successful hypothesis and at the same time is statistically incompatible with the alternative hypothesis. In the “cladistic analysis” case, the alternative hypothesis to UCD is “common design”, and of course UCD cannot be an assumption of such an analysis. However this rule is violated twice, first by the use of an assumption also presented as conclusion, and second by the prejudiced rejection of the alternative “common design” hypothesis before analysis. This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD. What “cladistic analysis” is instead is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points.
  4. The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility. This is not surprising as designers are free to incorporate whatever mechanism they want, including intelligent “selection” (human breeders do!) and “common descent” (human breeders do!) if they so desire.
  5. The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false. On one hand, we do know the history of the automobile, so a proper classification must be able to reconstruct their unique “evolution”. Yes, vehicle share parts, so to get to the actual development tree, we must group them differently than organisms since mass production works differently than biologic reproduction. On the other hand, organisms may not be uniquely classified as demonstrated by the numerous revisions and exceptions to the “tree of life”, and in any case, “uniquely classified” is an absolute claim that can never be proven since it is impossible to compare the infinity of possible organism classifications.
  6. The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails. Anatomy is not independent of biochemistry. Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited. This is not to say that the fossil record is complete, or that fossils can be positively linked to one another and the living without – once again – presupposing UCD. The claim that “there is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry” is false as the ‘designer’ hypothesis produces the same result when one designer creates all morphologies, and furthermore “I cannot think of an alternative reason why…” is not a valid argument.
  7. A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure. To decide the position of a certain organism, the human creators of the “tree” have to decide which morphologic/biochemical/genetic characteristics to include and what weight to attach to each of those measures. This further supports the claim that “cladistic analysis” is ‘curve fitting’ rather than ‘hypothesis testing’ – if a tree must be built, a tree will be built as in this example: “The close relationship between animals and fungi was suggested by Thomas Cavalier-Smith in 1987, […] and was supported by later genetic studies. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants […].”

 

1,059 Replies to “Nested Hierarchies (Tree of life)”

  1. Entropy Entropy
    Ignored
    says:

    Nonlin.org: Swap “creationists” with “Darwinists” and it’s exactly my experience. And then they repeat their “argument” at infinitum as if nothing was ever said… See, we do have something in common

    Don’t flatter yourself, we have nothing in common. I answered your bullshit thoroughly only to see you jumping over the whole thing in ways that showed that either you didn’t read it, or, gasp, that you didn’t understand it at all. Yet here you are, making much more of a fool out of yourself. Pretending to know way better than professional scientists, while saying things as stupid as “because ancestry.com doesn’t do it that way, it doesn’t happen.”

    How your mind misfires so badly, I cannot understand. I’m still hoping that you’re just an arrogant teenager, and that you’ll learn better as life hits you with a few surprises about how little you really know. If you’re older, then I’m sorry, but there’s no hope for you and you’re damaged beyond repair.

    Repeating already defeated bullshit and jumping over explanations is your M.O. For example:

    Nonlin.org:
    UCD and “evolution” are assumptions hence cannot be proven by the curve-fitted tree. How many time do I have to repeat?

    You don’t have to repeat your misinformed piece of crap, you have to understand that your mere say so doesn’t make it so, and then understand that your view is poorly informed at best. I explained this many times, yet, you kept jumping over the explanations and repeating the very same crap.

    I explained why this is wrong. Somebody even posted links to courses on stats talking about curve fitting, and tests about whether the fitting was correct for the data, others explained some more. Yet, you didn’t care. That curve fitting is taught in stats courses, and that the stats courses include tests for how good the fitting is, didn’t hit your mind. So, sorry, but no, we’re very different. I can read for comprehension and understand when I’ve been shown to be wrong. You think you’re some kind of infallible god, while ridiculing yourself with astounding incompetence.

    I don’t expect you to do any better this time, and I’m not repeating my explanations. You’ve already shown that you cannot understand them anyway.

  2. colewd
    Ignored
    says:

    Joe Felsenstein,

    4. May I assume that nonlin.org has some substantial evidence, or some convincing argument, that changes in different genes are very strongly nonindependent?

    How about gene change being restricted from its original form?

  3. John Harshman John Harshman
    Ignored
    says:

    colewd:
    Joe Felsenstein,

    How about gene change being restricted from its original form?

    Why? How would that result in non-independence of changes across the genome? Before you ask a question like that, please think through what your implied claim is and whether it makes sense. (Yes, there was an implied claim: that restrictions on gene change would result in non-independence of changes at different loci.)

  4. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    colewd: How about gene change being restricted from its original form?

    To echo John, that, if it occurs, is essentially irrelevant to whether one can use the changes that do occur to infer phylogenies.

  5. colewd
    Ignored
    says:

    Joe Felsenstein,

    To echo John, that, if it occurs, is essentially irrelevant to whether one can use the changes that do occur to infer phylogenies.

    I got it but you asked NL to make a case that was not really relevant to the discussion.

    The bigger question is does similar gene trees among two or more genes differentiate common descent enough from design to infer common descent was the specific change mechanism?

  6. John Harshman John Harshman
    Ignored
    says:

    colewd:
    Joe Felsenstein,

    I got it but you asked NL to make a case that was not really relevant to the discussion.

    What does that mean?

    The bigger question is does similar gene trees among two or more genes differentiate common descent enough from design to infer common descent was the specific change mechanism?

    The answer is “yes”. We expect most sequences (not just “genes”) to tell the same story if they evolved on the same tree. We don’t expect that from “common design”. We don’t expect that from your scenario about “re-use”.

  7. colewd
    Ignored
    says:

    John Harshman,

    We don’t expect that from “common design”. We don’t expect that from your scenario about “re-use”.

    This is just an assertion.

    I showed a scenario where you would expect this. I don’t think you can reject design as the null here. You need to explain clearly why the data was unlikely the result of design to a statistical significance to reject it as the null.

    Is design in the position to reject common descent as the null?

  8. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    colewd: Is design in the position to reject common descent as the null?

    “Design” always explains everything better. Because it predicts exactly what is seen. Alas, it also predicts everything you don’t see. It predicts that elephants are big, lumbering, and gray. But it also predicts that they are small, pink, and flit from flower to flower pollinating them.

  9. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    colewd:… you asked NL to make a case that was not really relevant to the discussion.

    No, it is closely related to point 6 in the nonlin.org’s original post.

    nonlin.org keeps saying that analyses that assume universal common descent cannot be used to test universal common descent. But the common descent that is being inferred is the common descent of groups within the study, and there the consilience of phylogenies from morphology and from different parts of the genome is precisely relevant.

  10. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    This is just an assertion.

    I showed a scenario where you would expect this.

    No, you didn’t. Your scenario was vague, you ignored all attempts to get you to clarify it, and you didn’t actually examine the implications. I did examine them, and your scenario doesn’t have the consequences you imagine.

    I don’t think you can reject design as the null here.You need to explain clearly why the data was unlikely the result of design to a statistical significance to reject it as the null.

    You will again have to clarify what you mean.

    Is design in the position to reject common descent as the null?

    At a minimum you would have to have a coherent design model for comparison. So far you don’t. You just a few buzzwords like “design” and “re-use”.

  11. colewd
    Ignored
    says:

    Joe Felsenstein,

    “Design” always explains everything better. Because it predicts exactly what is seen.

    Then why is it not the hypothesis of choice? The reason is that you can get a tighter definition like gravity causing a ball to move from a table to earth or a differential charge causing electrons to move through a wire. Evidence here has eliminated both chance and design as the null.

    With common descent you are trying to get a tighter explanation for the tree. You need to eliminate design in addition to chance as the null. Why can I do this for a ball falling off a table and you cannot do this for the tree?

    If you use the tree to test the tree you have to eliminate design as the null.

  12. Rumraket Rumraket
    Ignored
    says:

    colewd: Then why is it not the hypothesis of choice?

    Because actually design predicts everything. You can always just reason that what you see is what the designer wanted to design. That’s a bug, not a feature.

    The reason is that you can get a tighter definition like gravity causing a ball to move from a table to earth or a differential charge causing electrons to move through a wire. Evidence here has eliminated both chance and design as the null.

    I’m sorry but none of that made any coherent sense. Try to explain what you wanted to say in different words.

    With common descent you are trying to get a tighter explanation for the tree.

    It isn’t clear what you mean by “tighter explanation”.

    Common descent is an explanation for there being tree-like structure in the data, and for the fact that different loci yield very similar trees. It’s what would follow if common descent was true. But it isn’t clear at all why those would follow on design.

    We’ve been over this before of course. You will remember this discussion yeah?.

    You need to eliminate design in addition to chance as the null.

    No, design proponents need to come up with a coherent, falsifiable explanation for why the data is the way it is. It is not our job to falsify an explanation that has not been given yet. I can’t prove to you that different genes weren’t created by invisible pixies.

    Why can I do this for a ball falling off a table

    You technically can’t. The designer is invisible and can create forces of nature. Now please go falsify the proposition that this designer made the ball fall off the table.

    If you use the tree to test the tree you have to eliminate design as the null.

    This makes zero logical sense.

  13. Entropy Entropy
    Ignored
    says:

    colewd:
    Then why is it not the hypothesis of choice?

    Because it’s philosophically untenable, and because it doesn’t actually explain anything. You missed Joe’s point.

    colewd:
    The reason is that you can get a tighter definition like gravity causing a ball to move from a table to earth or a differential charge causing electrons to move through a wire.

    That’s no reason to have something as absurd as “design” as a non-explantion for life.

    colewd:
    Evidence here has eliminated both chance and design as the null.

    Design is no null. Also, that you ignore the elegance and depth of evolutionary explanations doesn’t mean that the null, “chance,” hasn’t been “eliminated.” It just means that you lack the understanding.

    colewd:
    With common descent you are trying to get a tighter explanation for the tree.

    Nope. The tree is only about the order of lineage separation, and that helps reinforce common ancestry because different data sets give very similar patterns of lineage separation.

    colewd:
    You need to eliminate design in addition to chance as the null.

    No, you don’t. We don’t consider design because that’s philosophically backwards. Design cannot be a null. Come on Bill. If you don’t know what you’re talking about, better not to pretend. Nulls are about how much things approach what’s expected by chance. Not about magical beings in the sky.

    colewd:
    Why can I do this for a ball falling off a table and you cannot do this for the tree?

    Your inabilities are not a measure of what Joe can or cannot do. Your inabilities are yours to keep if so you choose. Just don’t project them onto others.

    colewd:
    If you use the tree to test the tree you have to eliminate design as the null.

    I cannot believe the confidence which with you propose such nonsense. Again, if you don’t know what you’re talking about, better to keep your eyes and ears open until you understand. Make questions where you get stuck, and stop pretending to know things that so obviously escape your understanding.

  14. colewd
    Ignored
    says:

    Entropy,

    Because actually design predicts everything. You can always just reason that what you see is what the designer wanted to design. That’s a bug, not a feature.

    Design may predict everything but we can get more specific solutions that eliminate it as the null as I mentioned before. The problem with common descent is that if your proof is a tree then design becomes the null as a random pattern will not generate a tree but design can.

  15. colewd
    Ignored
    says:

    Rumraket,

    We’ve been over this before of course. You will remember this discussion yeah?.

    So I assume you can eliminate design as a cause. Show how the patterns could not have been generated by design to a reasonable certainty. Eliminate design as the null. Your support here is hand waving at this point.

  16. colewd
    Ignored
    says:

    Rumraket,

    You technically can’t. The designer is invisible and can create forces of nature. Now please go falsify the proposition that this designer made the ball fall off the table.

    I don’t need a designer to explain the ball falling off the table. I can eliminate design as a primary cause. I can explain it by a repeatable mathematical model that we can test. A new set of species arriving from a common ancestor is a very different problem.

    I don’t have a mathematical model or an empirical test.

  17. Neil Rickert
    Ignored
    says:

    colewd: I don’t need a designer to explain the ball falling off the table. I can eliminate design as a primary cause.

    Actually, no, that does not eliminate design as the primary. What it does, is eliminate design as a useful explanation.

  18. Entropy Entropy
    Ignored
    says:

    colewd:
    Design may predict everything but we can get more specific solutions that eliminate it as the null as I mentioned before.

    What part of my explanation why it cannot be a null did you have trouble with? It’s nonsense statistically (aka by the very meaning fo the word “null”), it’s nonsense philosophically., and it’s nonsense scientifically. So what’s so hard to understand?

    colewd:
    The problem with common descent is that if your proof is a tree then design becomes the null as a random pattern will not generate a tree but design can.

    Again, no. Design cannot be a null. At best a competing explanation, but not a null. Then you’d have to demonstrate that it’s sensical for a designer to put things in motion in such a way that a “non-design” explanation works, solve the cart-before-the-horse problem, solve the problem of identifying a designer that would rather fool us into thinking that it’s all natural, and that designers, other than ourselves, can be non-natural, solve the problem that the designers themselves have to be explained, solve the problem that without plausible designers this is suspicious of being merely about the fantasies of religion, etc, etc, etc. So, sorry, but evolution wins this “contest” because it’s not philosophically and scientifically problematic. It’s you who needs to eliminate evolution from the picture before we could even conceive of a “design” explanation, which is why the IDiots focus on trying to do just that. They, like you, don’t realize that even if evolution as we understand it was taken out of the picture, design would still be enormously, deeply, flawed, leaving us at worst with an “I don’t know,” but still far away from a “designer.”

    So, start by thinking carefully about it, rather than haste into answering and repeating the very mistakes we’ve already dealt with.

  19. colewd
    Ignored
    says:

    Neil Rickert,

    Actually, no, that does not eliminate design as the primary. What it does, is eliminate design as a useful explanation.

    If we define the mechanism of design as, conscious intelligence, then it clearly is not required for the ball to fall to the ground although the origin of the mechanism that causes the fall might be.

    When we look at the different DNA sequences and other cellular changes that are required for the emergence of two separate species, conscious intelligence may be required.

  20. Entropy Entropy
    Ignored
    says:

    colewd:
    I don’t need a designer to explain the ball falling off the table.

    Just like we don’t need a designer to explain the divergence of populations into new species. It’s the very same situation, only that for evolution you don’t understand how well it works, while you understand the gravitation problem for being harmless to your beliefs. If the case was different you’d be as adamant about eliminating the designer “null” nonsense. A magical designer can bring things down as if it were a phenomenon related to the mass of the bodies under analysis. By being non-random designers “explain it,” and you have to deal with that “null.” See how basically foolish that is?

    colewd:
    I can eliminate design as a primary cause. I can explain it by a repeatable mathematical model that we can test.

    Just like we can explain evolutionary patterns by mathematical models that we can test. Again, you accept gravitation because it doesn’t conflict with your religious beliefs. But the same nonsensical excuse about design being a “null” can be made here.

    colewd:
    A new set of species arriving from a common ancestor is a very different problem.

    Only in the factors influencing the outcome.

    colewd:
    I don’t have a mathematical model or an empirical test.

    Well, that would be your problem, since many scientists do have mathematical models and empirical tests.

    Again, anything can be fit to a “the designer made it that way.” You just understand and accept gravitation because it’s simpler and because it doesn’t conflict with your religious beliefs. Thus you have no mental barriers and attitudes shielding you against trying to understand.

  21. John Harshman John Harshman
    Ignored
    says:

    colewd:
    Neil Rickert,

    If we define the mechanism of design as, conscious intelligence, then it clearly is not required for the ball to fall to the ground although the origin of the mechanism that causes the fall might be.

    When we look at the different DNA sequences and other cellular changes that are required for the emergence of two separate species, conscious intelligence may be required.

    Notice that you have elided from “possible” to “required”. That’s a big change which you seem not to have noticed. We can’t eliminate design as a possibility, because anything at all is a possible product of design, including a ball rolling off a table. That’s especially true if the supposed designer is omnipotent.

    But eliminating design as required, now that we can do. Trees, which if you recall are the subject, could be produced by design, but design is unnecessary because trees are a natural and inevitable result of evolution with branching. Perhaps you have once again confused common descent with the origin of variation? Oh, let’s face it: you have never not confused the two. It’s the basis of al your discussion.

  22. Neil Rickert
    Ignored
    says:

    colewd: When we look at the different DNA sequences and other cellular changes that are required for the emergence of two separate species, conscious intelligence may be required.

    But why must it be conscious?

    That’s the mistake there. Evolution itself is intelligent (in my opinion), but it is not conscious (again, in my opinion).

  23. colewd
    Ignored
    says:

    Entropy,

    Again, no. Design cannot be a null. At best a competing explanation, but not a null.

    Quote:

    Karl Popper (a philosopher) discovered that we can’t conclusively confirm a hypothesis, but we can conclusively negate one. So we set up a Null hypothesis which is effectively the opposite of the working hypothesis.

    We have common descent and its opposite design to explain a tree like pattern.

  24. John Harshman John Harshman
    Ignored
    says:

    colewd: We have common descent and its opposite design to explain a tree like pattern.

    Your problem with that is that a null hypothesis must be capable of being rejected by the data. “Design”, without any elaboration of the actual process, can’t be rejected by any conceivable data. You’re just using “null hypothesis” as a sciency-sounding buzzword.

  25. colewd
    Ignored
    says:

    Neil Rickert,

    That’s the mistake there. Evolution itself is intelligent (in my opinion), but it is not conscious (again, in my opinion).

    How do you get a DNA sequence that builds a eukaryotic cell without conscious intelligence?

  26. colewd
    Ignored
    says:

    John Harshman,

    “Design”, without any elaboration of the actual process, can’t be rejected by any conceivable data.

    Its mechanism, conscious intelligence, can. Electrons move through a wire without conscious intelligence. A ball drops to a floor without conscious intelligence. A complex sequence is built by ?

  27. Entropy Entropy
    Ignored
    says:

    colewd:
    How do you get a DNA sequence that builds a eukaryotic cell without conscious intelligence?

    It’s being happening for eons Bill. Without conscious intelligence to be seen anywhere around. We’re a very recent kind of life form.

  28. Entropy Entropy
    Ignored
    says:

    colewd:
    Its mechanism, conscious intelligence, can.

    Only very recently, and with a hell of a lot of help from the natural phenomena that started it all. Venter’s work is but a few years old. But Venter’s research group wasn’t there for most of the history of life in the planet.

    colewd:
    Electrons move through a wire without conscious intelligence. A ball drops to a floor without conscious intelligence. A complex sequence is built without conscious intelligence.

    See how easy it is to continue the trend?

  29. Neil Rickert
    Ignored
    says:

    colewd: How do you get a DNA sequence that builds a eukaryotic cell without conscious intelligence?

    I don’t claim to know where how the first eukaryotic cell originated.

    If you have trial and with evaluation of the results, then you have some kind of intelligence. It does not need to be conscious.

  30. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    Its mechanism, conscious intelligence, can.Electrons move through a wire without conscious intelligence.A ball drops to a floor without conscious intelligence.A complex sequence is built by ?

    How do you know electrons move or a ball drops without conscious intelligence? You don’t. In fact, people make electrons move and make balls drop all the time. How do you know God doesn’t personally make each electron and each ball operate? You don’t. And once again — as every single time you post on this subject — you are confusing common descent with mutation.

  31. Entropy Entropy
    Ignored
    says:

    Bill,

    If you are going to ignore explanations, then I’m leaving the discussion again. No point in continuing. It’s a tad sad that it’s so hard to get you to understand some very simple stuff. I don’t know what you think you contribute by ignoring so many attempts at explaining things to you, and then repeating old and plain nonsense. Maybe you just repeat it to yourself, as some kind of mantra or credo. But it won’t convince me that you’re thinking carefully about anything at all.

  32. Rumraket Rumraket
    Ignored
    says:

    colewd: Show how the patterns could not have been generated by design to a reasonable certainty.

    But I can’t, I outright admit that I cannot falsify the proposition “what we see is what the designer wanted to design”.

    But please understand that if you really advance the proposition that “what we see is what the designer wanted to design”, then you are advancing the proposition that the designer did it’s very best to make it look like common descent took place. It’s sort of like the idea that God put the fossils in the rocks to test our faith, or created starlight “with the appearance of age and distance”. I can’t prove to you that he didn’t. Not because that hypothesis is a good hypothesis, but because it is unfalsifiable. You can believe it if you want, but it isn’t science.

  33. Rumraket Rumraket
    Ignored
    says:

    colewd: I don’t need a designer to explain the ball falling off the table.

    I don’t need a designer to explain consilience of independent phylogenies, or stree-like structure in the data.

    I can eliminate design as a primary cause.

    No, you don’t seem to understand the difference between eliminating an explanation, and merely suggesting an alternative. To eliminate an explanation means to show with evidence and arguments that the explanation is either impossible, or very unlikely.

    How have you done that for an invisible designer with the power to create natural forces making the ball falling off the table? It seems to me that eliminating that option can’t actually be done. But again, that’s a bug, not a feature.

    I can explain it by a repeatable mathematical model that we can test.

    I can also explain consilience of independent phylogenies with a model of common descent.

    But again, your mere ability to come up with an explanation A for phenomenon X does not somehow eliminate explanation B for phenomenon X. You need to give evidence and arguments for why A is a more likely or more plausible option than B. For that you need a model that makes quantifiable predictions. There should be things it predicts to be a certain way, and things it does not predict, and things it predicts should not be a certain way. Then we can compare the predictions to the data and see whether A or B explains X better.

    A new set of species arriving from a common ancestor is a very different problem.

    I don’t see why. Do crocodylians not share common descent? Or rodents? Or primates?

    I don’t have a mathematical model or an empirical test.

    I do. It’s the common descent model, and it makes empirically testable predictions. There should be significant levels of consilience of independent phylogenies, and hierarchical structure in the data.

    Now I couldn’t prove to you that an invisible designer with magic powers couldn’t have made those. All I can do is ask why should anyone believe that it did? Why would the designer deliberately make the pattern expected from common descent?

  34. colewd
    Ignored
    says:

    John Harshman,

    How do you know electrons move or a ball drops without conscious intelligence? You don’t. In fact, people make electrons move and make balls drop all the time. How do you know God doesn’t personally make each electron and each ball operate?

    We observe these mechanisms operating independently. We can model their behavior. Science is tentative it is not about knowing.

    And once again — as every single time you post on this subject — you are confusing common descent with mutation.

    You are assuming the genetic change we see is caused by mutation and occurring during reproduction.

  35. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    We observe these mechanisms operating independently.We can model their behavior.Science is tentative it is not about knowing.

    How do you know they’re operating independently? How do you know that angels don’t push the planets, and merely choose to do so in a way that’s the same as if there were gravity?

    You are assuming the genetic change we see is caused by mutation and occurring during reproduction.

    Well, of course that’s what the data do show. Just as we see what seems to be gravity operating in the orbits of the planets, we see what seems to be spontaneous mutation (by well-known mechanisms) producing all the changes we see in the present day, and they’re exactly the same sorts of changes that we see between species. The great bulk of those mutations happen during either DNA replication or meiosis, and a few happen during DNA repair. It could all be God sticking his finger into your genome, but it could also be angels pushing the planets. Why do you accept the first as a live hypothesis when you reject the second?

    And I would also like to point out that, once again, you have confused the source of mutation with the cause of the nested hierarchy we’re supposedly talking about here. I keep pointing that out and you keep ignoring it. Are you capable of comprehending this simple fact?

  36. colewd
    Ignored
    says:

    John Harshman,

    How do you know they’re operating independently?

    Again, science is tentative. Your how do you know argument is not relevant to science, its for our philosophy friends. If you disagree please make an argument why it is.

    Well, of course that’s what the data do show.

    The data shows change. You need to isolate the cause of the change. Mutation is an assumption.

    Why do you accept the first as a live hypothesis when you reject the second?

    The first one I can observe and test an independent cause. The second one I can’t.

    And I would also like to point out that, once again, you have confused the source of mutation with the cause of the nested hierarchy we’re supposedly talking about here. I keep pointing that out and you keep ignoring it. Are you capable of comprehending this simple fact?

    Let me try again:

    You are assuming the genetic change we see is caused by mutation and occurring during reproduction.

    You have not shown the nested hierarchy is not likely the result of design by conscious intelligence independent of reproduction.

  37. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    Again, science is tentative.Your how do you know argument is not relevant to science, its for our philosophy friends.If you disagree please make an argument why it is.

    That’s just wordplay. “How do you know” is very important in science; it means “what enables you to come to a tentative conclusion and tentatively reject alternatives”, though of course there are various degrees of “tentative”, and we can work towards approaching certainty as close as possible. The main point is that your demands are asymmetrical; what you accept as good enough evidence to reject design in some situations is the same quality of evidence you reject in others.

    The data shows change. You need to isolate the cause of the change. Mutation is an assumption.

    Are you claiming that mutations don’t happen, or that we can’t know whether they happen? Even within populations? Even if you notice differences between parents and children or between cells in an organism?

    The first one I can observe and test an independent cause.The second one I can’t.

    Not true. You can observe and test each to the same degree. The movement of planets can be explained by gravity without recourse to angels, but you can’t actually test for the absence of angels. The differences between species can be explained by mutation and fixation without recourse to “design”, but you can’t actually test for the absence of design. It’s exactly the same situation. You just believe in gravity but want to deny evolution.
    Let me try again:

    You have not shown the nested hierarchy is not likely the result of design by conscious intelligence independent of reproduction.

    That’s a completely different claim from your previous one. Do you see that? Now of course it’s impossible to show that the nested hierarchy isn’t the result of design just as it’s impossible to rule out angels pushing the planets. How would you show that angels pushing the planets isn’t “likely”? By showing that you have no need of that assumption because there’s a simpler explanation, i.e. gravity. Similarly, I can show that design is not a likely source for nested hierarchy because there’s a simpler explanation: common descent. A designer could counterfeit gravity as well as common descent, but a deceptive designer isn’t the simplest explanation. We have no expectation that a designer would produce a fake phylogeny, and we have no expectation that angels would choose to follow Kepler’s laws. The reasoning in both cases is identical.

  38. colewd
    Ignored
    says:

    John Harshman,

    The main point is that your demands are asymmetrical; what you accept as good enough evidence to reject design in some situations is the same quality of evidence you reject in others.

    This is your assertion you keep repeating and not supporting.

    Are you claiming that mutations don’t happen, or that we can’t know whether they happen?

    I’ll ask you again how do you know differences are mutations unless you are in a controlled experiment.

    The differences between species can be explained by mutation and fixation without recourse to “design”,

    No, it can’t. This is false equivalence. This is where your argument fails.

    That’s a completely different claim from your previous one. Do you see that? Now of course it’s impossible to show that the nested hierarchy isn’t the result of design just as it’s impossible to rule out angels pushing the planets.

    I am asking you to show it is not likely the direct result of design. I know with reasonable certainty that you are not the direct result of design.

    The same requirement for the nested hierarchy. You need to show with REASONABLE CERTAINTY that it is not the direct result of design as I can show with REASONABLE CERTAINTY that you are not the direct result to design.

    The problem you are having is the process is underway to show with REASONABLE CERTAINTY the nested pattern is not the result of ancestry alone.

  39. Entropy Entropy
    Ignored
    says:

    colewd,

    It’s the other way around Bill. You have to prove that we’re the products of design. There’s too many problems to solve before even getting started. But try and understand: design has to be demonstrated. In the meantime, sorry, but that bullshit about considering design as some kind of default position doesn’t fly. It’s just excessively ridiculous.

    ETA: No amount of capital letters will change the situation.

  40. Nonlin.org
    Ignored
    says:

    Flint: What do you mean by “reconstruct”, and do you mean the same thing as Joe Felsenstein? If I can say with fair certainty that two (or more) people had the same great…..great grandmother, while two (or more) other people had a different one, does that count?

    How can anyone verify your “certainty”? And read the thread – DNA-ONLY is NOT how human genealogy is determined in real life.

  41. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    For context, let’s remember that the discussion here was using “genealogy” in the sense of tree diagrams of the descent of species, until nonlin.org brought in reconstruction of human genealogies, genealogies of individuals within the human species. This was done in this comment.

    But the original post, and the discussion up to that comment, was all about phylogenies.

    And I’m still waiting for nonlin.org to defend the assertion that changes in different genes are so tightly correlated, so nonindependent, as to lead us to expect highly similar phylogenies from different genes, when there is no common ancestry of subgroups of species within the group.

    So far just assertions.

  42. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: …

    1. Whatever you do, your model is fine as long as you’re not trying to use it to prove its underlying assumptions (circular logic).
    2. You should know that artifices can only do so much. Can you prove they can turn non-iid data into iid pseudo-samples?
    3. See 1. No doubt, once UCD is the main assumption, your curve fitting model can be optimized to that assumption. But the model will never validate its own assumption. This is elementary and quite frankly I am very surprised you have a hard time accepting it.
    4. Here we go again: “changes in different genes are very strongly nonindependent”… You’re just asking me to accept UCD without proof and to demonstrate “non-independence” when in fact the burden to demonstrate IID is on you. And regardless, see 1. and 3. Again.

  43. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: For context, let’s remember that the discussion here was using “genealogy” in the sense of tree diagrams of the descent of species, until nonlin.org brought in reconstruction of human genealogies, genealogies of individuals within the human species. This was done in this comment.

    Is this not your comment:

    Joe Felsenstein: That is very odd. Given people’s DNA sequences, yes, we can infer their genealogy without any “labels” to help us. All we have to know is which DNA sequence came from which person.
    “?
    This is false as shown.

    And no, the OP is not about “phylogenies” but about circular logic “proof” of UCD/evolution.

  44. Nonlin.org
    Ignored
    says:

    Entropy: I explained why this is wrong. Somebody even posted links to courses on stats talking about curve fitting, and tests about whether the fitting was correct for the data, others explained some more. Yet, you didn’t care.

    I keep track of all non-retard arguments (Con) and my replies (Pro) to this OP – if yours are not here, they are of the non-non-retard type 😊 or simply missed:
    Con: Every model contains assumptions, and the fit of the model to data can be used to test whether the assumptions are valid for the data. A chi square test is a simple example. And an inference made in one study can then be used as an assumption in another
    Pro: False. They’re called ‘assumptions’ and not ‘conclusions’ because they have to be tested independently through an entirely separated method or be accepted as axioms. as·sump·tion [əˈsəm(p)SH(ə)n] NOUN, a thing that is accepted as true or as certain to happen, without proof.
    Con: In the vitamin-C pseudogene being broken in the very same way in different primate species, like humans, chimps, gorillas. The probability of breaking a gene in the very same way in three independent lineages is so small, that the best explanation is that the gene broke once, in a common ancestor, and we all inherited that version of the broken gene from that ancestor.
    Pro: Are you saying that before this “proof” there was no UCD assumption whatsoever? Because I didn’t get the impression that Darwin knew about your “proof”, yet him and generations after him were already taking UCD for granted without knowing of your “proof”. And who said that UCD is “the best explanation” for this? What other explanations have you guys considered, and how is this “best” compared to the others? And these being said, the not so subtle point of this OP is not that UCD is true or not, but that cladistics cannot prove UCD when UCD is in fact an assumption of the cladistic analysis.
    Con: The genealogy of life could be a perfect tree (it isn’t a perfect one) without there being labels on life forms telling you where they fit into the tree.
    Pro: You won’t be able to build a genealogy without the labels: vital records, family records, interviews, etc. Yes, every person has a genealogy, but would you ever be able to build the family tree without the labels? And yes, the tree is an artificial human construct – lines and circles/squares of ink on paper or digital.
    Con: Fossils can be linked to one another and extant life forms without presupposing UCD. It’s enough if we can infer common ancestry among the organisms in question.
    Pro: Fossils can only be linked if one presupposes descent. Even between living, one has to presuppose descent or else it’s doppelgänger or whatever coincidence.
    Con: Formulate a hypothesis and look to see whether your hypothesis is supported by the evidence and fits it better than the alternatives.
    Pro: Yes, assume true only to make predictions that can verified by the hypothesis BUT NOT BY the alternative hypothesis. This is NOT happening with UCD as it makes no predictions whatsoever and alternative hypothesis is eliminated before analysis. Even if it were the case (IT IS NOT), this would only say “hypothesis 1 fits better than hypothesis 2”, but NOT “hypothesis 1 is thus proven true”. Furthermore, “Tree of life” is curve fitting and not hypothesis testing as shown.
    Con: What does “common design” mean and what would distinguish it from common descent?
    Pro: That would be “designed by the same designer or designing entity”. It recognizes that Toyota vehicles are not designed by Ford and that organisms resemble each other – another black eye for Darwinistas that cannot explain why LUCA would have happened once and only once.

  45. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: “Design” always explains everything better. Because it predicts exactly what is seen. Alas, it also predicts everything you don’t see. It predicts that elephants are big, lumbering, and gray. But it also predicts that they are small, pink, and flit from flower to flower pollinating them.

    No. Design predicts:
    1. intelligent biologic machines – we see that from hearts to flight, to sensors to whatever.
    2. It also predicts “unity of design” if one designer, duality if two designers (like Apple and Microsoft), etc. We see DNA – unity of design in all organisms
    3. and it predicts “similar solutions for similar problems” – we see that in the so called “convergent evolution”

    What does “evolution” predict?
    A. “Random creativity” – fails;
    B. “divergence of character” – fails;
    C. “gradualism” – fails;
    D. “most certainly not one single abiogenesis episode” meaning “no UCD” (why would you even use this assumption?)
    E. “small, pink elephants” – fails

  46. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: nonlin.org keeps saying that analyses that assume universal common descent cannot be used to test universal common descent. But the common descent that is being inferred is the common descent of groups within the study, and there the consilience of phylogenies from morphology and from different parts of the genome is precisely relevant.

    How so? Demonstrate.

    How would “morphology vs genome” change “analyses that assume universal common descent cannot be used to test universal common descent”?

    We know for a fact that morphology depends on the genome, so is it not stupid to be surprised that indeed morphology matches the genome?

  47. Nonlin.org
    Ignored
    says:

    Rumraket: No, design proponents need to come up with a coherent, falsifiable explanation for why the data is the way it is. It is not our job to falsify an explanation that has not been given yet. I can’t prove to you that different genes weren’t created by invisible pixies.

    Why can I do this for a ball falling off a table

    You technically can’t. The designer is invisible and can create forces of nature. Now please go falsify the proposition that this designer made the ball fall off the table.

    So “evolution” is false – witness the numerous FAILED attempts to abiogenesis, evolution (LTEE), infinite monkey random creativity, etc. etc. How is your hypothesis still standing if not a religious belief?

    What are “forces of nature”? Can you demonstrate they are not controlled by the Designer?

    Anyway, can we get back to this OP:
    Summary:
    1. “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution.
    2. No assumption can be tested by the model that uses them.
    3. Hypothesis testing requires an alternative (null) hypothesis and a procedure.
    4. The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative
    5. The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false.
    6. The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails.
    7. A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure.
    ?

  48. colewd
    Ignored
    says:

    Entropy,

    It’s the other way around Bill. You have to prove that we’re the products of design.

    Science is not about proofs. If you want to claim common descent based on a tree you need to show the alternative hypothesis (null) is highly unlikely.

    The only competing hypothesis that can create a tree is design. There is no way around this. You can use your philosophical/materialist limitations argument to make your case but thats about it. Those arguments have very little meat on the bone.

  49. Nonlin.org
    Ignored
    says:

    Rumraket: I do. It’s the common descent model, and it makes empirically testable predictions.

    What predictions? Examples?

  50. Nonlin.org
    Ignored
    says:

    John Harshman: The movement of planets can be explained by gravity without recourse to angels,

    We don’t know much about gravity. At best, gravity is just a step in the overall explanation but most certainly not “the explanation”.

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