Nested Hierarchies (Tree of life)

Moderator’s remark: this post is long enough to need a “more” tag.  But the wordpress editor will only allow me to add that at the very beginning or the very end.  So here it is at the very beginning.

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 thoughts on “Nested Hierarchies (Tree of life)

  1. Joe Felsenstein,

    I believe you have previously suggested that anyone interested in how this actually works might consider reading Inferring Phylogenies. It’s not a bad idea, except that despite its clarity and accessibility, I don’t think it would be either for Bill or nonlin. Maybe Mung could get something out of it.

  2. Joe Felsenstein,

    A discussion of how the rain runs off the roof can go forward without any discussion of what caused it to rain.

    Thank you for the analogy. When John discusses the tree and the nested hierarchy that is fine. His claim that this discussion is separate from mechanism is also fine.

    What becomes problematic is when he leaps to the claim that the only explanation of the nested hierarchy is common descent. He must have made this assertion without support 200 times in the famous 5000 thread op.

  3. John Harshman,

    If this means anything, and I’m not sure it does, it refers to your main confusion, the one between an explanation of nested hierarchy and an explanation of the various differences in features that happen within the hierarchy. Have you in fact learned absolutely nothing during all our conversations over a period of years?

    I think we agree that the nested hierarchy does not explain the origin of the spliceosome it only explains the pattern the spliceosome is a part of.

    Design does explain the origin of the spliceosome. It is a differentiating feature of the hypothesis.

    Both design and common descent explain similar genes being observed in different organisms.

    Design explains the same gene set being observed in two organisms that do not share a common ancestor that is not observed in the organisms that do share a common ancestor.

    The example is genes shared by chimps and rats that don’t exist in humans and mice.

  4. colewd:
    John Harshman,

    I think we agree that the nested hierarchy does not explain the origin of the spliceosome it only explains the pattern the spliceosome is a part of.

    Design does explain the origin of the spliceosome.It is a differentiating feature of the hypothesis.

    I’m afraid you are still hopelessly confused about what we’re talking about. That’s because you don’t actually have a design hypothesis. You only have the word “design”, which to you just means anything God might do anywhere at any time. If the spliceosome is designed, that’s fully compatible with common descent. That particular design is irrelevant to what we’re discussing here. We could argue about whether anything other than design could produce the spliceosome, but it’s still irrelevant.

    Both design and common descent explain similar genes being observed in different organisms.

    True, but only because design is just a word that could in principle apply to anything. If you try to set forth a real theory of common design, it fails instantly. Design doesn’t explain nested hierarchy, and it doesn’t explain why those supposedly re-used parts are different in different species.

    Design explains the same gene set being observed in two organisms that do not share a common ancestor that is not observed in the organisms that do share a common ancestor.

    The example is genes shared by chimps and rats that don’t exist in humans and mice.

    Genes shared by chimps and rats are also compatible with common descent; they just require two losses. But I don’t see how they’re compatible with design unless you just choose to interpret anything whatsoever as compatible with design. What design requirements could chimps and rats possibly share that they wouldn’t also share with humans and mice? And why, if this is re-use of parts, aren’t the genes identical in the two species? (One might also check to see if the genes in question are found in other species and if remnants of those genes are found in other species, including humans and/or mice.)

  5. colewd: What becomes problematic is when he leaps to the claim that the only explanation of the nested hierarchy is common descent. He must have made this assertion without support 200 times in the famous 5000 thread op.

    No, you just ignore the support. The support is simple: a nested hierarchy is exactly what we would expect from common descent (with branching). It’s not what we expect from separate creation of species, which is what you mean by “common design”. It’s not to be expected from your buzzphrase “re-use of parts”. It’s not to be expected from anything you have ever mentioned. There being no alternative that would produce such a pattern — if there were you would have come up with one by now — common descent is sole remaining hypothesis.

  6. John Harshman:
    Joe Felsenstein,

    I believe you have previously suggested that anyone interested in how this actually works might consider reading Inferring Phylogenies. It’s not a bad idea, except that despite its clarity and accessibility, I don’t think it would be either for Bill or nonlin. Maybe Mung could get something out of it.

    I plead innocent. I think I have referred people there for abstruse technical details, but I wouldn’t recommend it to people less interested in the minutiae. David Baum and Stacy Smith’s Tree Thinking: An Introduction to Phylogenetic Biology would be much more accessible. (Of course neither book is aimed at people who have difficulty with evolution, so they shouldn’t be surprised if their favorite criticisms are not covered).

  7. John Harshman,

    No, you just ignore the support. The support is simple: a nested hierarchy is exactly what we would expect from common descent (with branching). It’s not what we expect from separate creation of species, which is what you mean by “common design”.

    This is again just an assertion. Do you understand what supporting an argument means? It does not mean repeating this is what we expect and this is what we don’t expect it explains why and supports the argument with data.

    How do you know that we would not expect a nested hierarchy from special creation?

    Why do you expect a hierarchy from common ancestry?

    Thats what I would expect from special creation due to re-used genes base on basic design principals. I would not expect common ancestry to necessarily to create a hierarchy. Where we know common descent is likely there is very little hierarchical structure.

  8. colewd:
    John Harshman,
    How do you know that we would not expect a nested hierarchy from special creation?

    Because I can’t think of a model of special creation that implies a hierarchy. Can you?

    Why do you expect a hierarchy from common ancestry?

    I would have thought this was obvious. If events happen at particular times in particular evolving lineages, and those lineages split, the descendants will inherity the results of that event. If a fair number of such events happen at various points on a tree, the data will reflect that tree and will thus form a nested hierarchy. I would draw you a picture if I could, but hey, there’s a fine picture in the croc paper. Do you see Fig. 2? That actually shows all the changes in the sequence, mapped onto the tree, showing where each of them happens. See how that makes a nested hierarchy?

    Thats what I would expect from special creation due to re-used genes base on basic design principals.I would not expect common ancestry to necessarily to create a hierarchy.

    Why would re-used genes create a nested hierarchy? Why would re-used genes have different sequences in different species rather than the same sequence, and why would those different sequences themselves form a nested hierarchy? Why would different genes form the same nested hierarchy? Why would junk DNA form the same nested hierarchy?

    And why would you not expect common ancestry to create a hierarchy?

    Where we know common descent is likely there is very littlehierarchical structure.

    What do you mean by that?

  9. John Harshman,

    Because I can’t think of a model of special creation that implies a hierarchy. Can you?

    I think a normal design process using conservation of resources creates a hierarchical structure as components that can be shared are shared and different components are used where uniqueness of the design is specified.

    The ratio of unique components to shared comments grows as the design diverges.

    I would have thought this was obvious. If events happen at particular times in particular evolving lineages, and those lineages split, the descendants will inherity the results of that event. If a fair number of such events happen at various points on a tree, the data will reflect that tree and will thus form a nested hierarchy. I would draw you a picture if I could, but hey, there’s a fine picture in the croc paper. Do you see Fig. 2?

    I agree you can create a nested hierarchy among known ancestors at the sequence level but how about:
    -The gene level
    -Morphology level
    This is where the necessary differences for nesting may not be there.

    If a fair number of such events happen at various points on a tree, the data will reflect that tree and will thus form a nested hierarchy.

    You are having to rely on “events happening” in order to explain the connection between common descent and the hierarchal structure of the tree.

    How can you show that common descent explains the tree without discussing the “events happening”? The events are what is creating the hierarchal structure.

    Why would re-used genes have different sequences in different species rather than the same sequence, and why would those different sequences themselves form a nested hierarchy?

    Differences could be caused by
    -neutral or near neutral mutation
    -slightly different functional requirements

    And why would you not expect common ancestry to create a hierarchy?

    I agree that it would at the gene sequence level.

    I don’t think ancestry alone would create it at the gene and morphology level because there isn’t supporting evidence that reproduction can create new genes on its own.

  10. Rumraket: You have a model that, if true, says the data should lie ideally on a straight line.
    That’s your model, your assumption.

    Then you have the data you get by doing measurements.

    This is wrong. That’s why I asked for a link to a third party example from the hard sciences and not for your opinion.
    Excel will put a linear trend on ANY curve. That’s curve fitting and that’s what phylogeny is all about.

  11. Rumraket: The data can simply fail to conform to expectations. That’s how test your assumptions. There’s nothing mysterious about it.

    Go get a link to a third party example from the hard sciences!

  12. Entropy: Hum. Seems like assumptions can be tested despite Nonlin’s command that this shouldn’t be so! How dare them!

    Am I dealing with bots or retards? Is there any difference?

    From the same site the mindless bot quotes:
    “You can think of assumptions as the requirements you must fulfill before you can conduct your analysis. ”

    And it’s like someone can’t read: “I asked for a link to a third party EXAMPLE from the hard sciences and not for your opinion.” For those that don’t know, EXAMPLE is more than someone’s general yapping.

  13. Joe Felsenstein:
    1. My case is very different: adding new pairs of tosses we get new outcomes. The issue is whether the fraction of Heads will converge on the true probability of Heads. In your case it does not, in my case it does. So there is some issue of what sort of nonindependence occurs. I asked you to present an argument that the nonindependence between different genes is like your case instead of like my case. But you seemed to have missed the distinction between them. This calls into question your confident and dramatic assertions that nonindependence of outcomes in different genes shows that they do not help us check whether there is an underlying phylogeny.

    2. You did not understand my example.

    3. I mentioned the block-bootstrap, but it is not essential to my argument. Set it aside, no problem, just provide the argument that nonindependence is sufficiently strong that we routinely expect new genes to show the same phylogeny just because of the nonindependence.

    4. First, “curve fitting” is a vague analogy here. Inferring phylogenies is not “curve fitting”. Phylogenies are not curves.

    5. Your argument about Pinnepedia etc. compares apples to oranges. The issue is, when we take the same set of species (say carnivores plus pinnipeds) and use different genes (or regions of the genome) to infer phylogenies, what do we see, and is this evidence for there being an underlying phylogeny. Spoiler: consilience, and yes, it is.

    1. I did not say your example is identical to mine – that was just to make a point. “True probability”is simply unknowable just from a set of outcomes, so unless you assume that you have a perfect fair coin (unattainable ideal), your data converges to whatever bias, and if you know for sure it’s a fair coin, who cares about the data? You can’t ask me to disprove independence. It’s your argument and your burden.
    2. Maybe. Does it matter?
    3. Again, your argument, your burden. Yep, nonindependence will do that to you.
    4. Is ‘tree fitting’ better for you? Same idea.
    5. How is it apples to oranges? You just go back to “different genes (or regions of the genome)” but again without demonstrating independence – see 3.

    Can you explain this: “Just as well you can correlate shoe sizes with cloud shapes and automobiles. Does this tell you UCD applies to those three? No way!”

  14. Joe Felsenstein: The Berkeley Museum of Paleontology page does not say anything anything about the methods assuming that trees from different genes (or different character sets) are necessarily going to come out the same.

    Show me where it says that.

    The discussion was about assumptions, not what you now claim.

    There are three basic assumptions in cladistics:
    Any group of organisms are related by descent from a common ancestor.
    There is a bifurcating pattern of cladogenesis.
    Change in characteristics occurs in lineages over time.

  15. Joe Felsenstein: Totally wrong: there can be a comparison of phylogenies derived from different genes, to see whether they are similar.

    You need to demonstrate independence (an impossibility) – see earlier comment.

    Furthermore, the relation can certainly be wrong even if the same trees based on different criteria. Think shoe sizes, cloud shapes and automobiles in identical phylogeny by two or more different methods.

  16. John Harshman: You only have the word “design”, which to you just means anything God might do anywhere at any time.

    We have examples of design and the resulting automobile and many other implements evolution (if you want to call it that). This is experimental evidence that you lack for Darwinism. Not only that but you don’t even have a plausible mechanism. Darwinism falls apart everywhere including in logic, the biology lab and computer simulations; and that’s pathetic.

  17. colewd:
    John Harshman,

    I think a normal design process using conservation of resources creates a hierarchical structure as components that can be shared are shared and different components are used where uniqueness of the design is specified.

    Too vague to make any sort of prediction. WHat does “uniqueness of the design is specified” even mean? Why would this create a hierarchical structure?

    The ratio of unique components to shared comments grows as the design diverges.

    In this sentence, what does “diverges” mean? Would we expect a bat and a rat to share more “components”, or a bat and a bird? Why?

    I agree you can create a nested hierarchy among known ancestors at the sequence level but how about:
    -The gene level
    -Morphology level
    This is where the necessary differences for nesting may not be there.

    Why “among known ancestors”? How did that requirement slip in? When you say “the gene level”, what are you referring to — presence or absence of particular genes, perhaps? But in fact we do see nested hierarchy at that level, and also in morphology. The interesting thing is that it’s the same nested hierarchy we see from sequences. Why?

    You are having to rely on “events happening” in order to explain the connection between common descent and the hierarchal structure of the tree.

    You are confusing the fact that they happen with why they happen. We can infer the former without knowing anything about the latter. You are obsessed with how mutations happen, but that isn’t relevant to nested hierarchy. It’s enough that they do happen.

    How can you show that common descent explains the tree without discussing the “events happening”?The events are what is creating the hierarchal structure.

    Sure, but all we need is that they happen. We don’t have to talk about or know about why.

    Differences could be caused by
    -neutral or near neutral mutation
    -slightly different functional requirements

    We wouldn’t expect a nested hierarchy from either of these. So those hypotheses are falsified by the data.

    I agree that it would at the gene sequence level.

    Progress. So what explains the observed hierarchy at the gene sequence level?

    I don’t think ancestry alone would create it at the gene and morphology level because there isn’t supporting evidence that reproduction can create new genes on its own.

    Again, the cause of new genes is irrelevant to common descent. You can’t seem to escape that intellectual trap.

  18. John Harshman,

    You are obsessed with how mutations happen, but that isn’t relevant to nested hierarchy. It’s enough that they do happen.

    Yet it is relevant to your claim that the only explanation of the nested hierarchy is common descent. By claiming common descent you are violating your own rule by claiming HOW it happened.

    Your thesis is a walking contradiction once you connect the nested hierarchy to common descent.

  19. colewd:
    John Harshman,

    Yet it is relevant to your claim that the only explanation of the nested hierarchy is common descent.By claiming common descent you are violating your own rule by claiming HOW it happened.

    Your thesis is a walking contradiction once you connect the nested hierarchy to common descent.

    I have given up all hope that you will ever understand this one simple thing. Common descent is inferred from the pattern. The pattern is produced by common descent. Common descent is how the pattern happens. But it isn’t how the individual changes/mutations/differences/genes/morphological features happen. The reasons those happen are not relevant to the pattern. The fact that you can’t manage to distinguish the pattern from its individual elements is the reason you will never understand that one simple thing.

  20. Nonlin.org: 1. I did not say your example is identical to mine – that was just to make a point. “True probability”is simply unknowable just from a set of outcomes, so unless you assume that you have a perfect fair coin (unattainable ideal), your data converges to whatever bias, and if you know for sure it’s a fair coin, who cares about the data? You can’t ask me to disprove independence. It’s your argument and your burden.

    Nope. It was the argument of biologists starting in about 1700 (who, by the way, were creationists). They noticed that different parts of the anatomy all reinforced the same hieratchical classification.

    And perfect independence isn’t required. That’s the whole point of mixing conditions — they are the conditions required to have additional data cause you to converge on the right answer.

    And the analogy is not to bias in a coin, but to non-independence of tosses. Remember?

    The burden of proof is on nonlin.org, who is proposing a very strong nonindependence among changes in very different traits (foot anatomy versus kidney physiology versus cytochrome C sequence versus fibrinogen gene DNA sequence). Bizarre.

    Does any other ID advocate here, or any creationist, want to make that argument? Or do you think that it is as strange and nonobvious as I do?

  21. Nonlin.org: The discussion was about assumptions, not what you now claim.

    There are three basic assumptions in cladistics:
    Any group of organisms are related by descent from a common ancestor.
    There is a bifurcating pattern of cladogenesis.
    Change in characteristics occurs in lineages over time.

    The evidence that the phylogeny is real is from concordance of phylogenies from different sets of characters and different parts of the genome. Which the Berkeley UMP site is not discussing at that point. nonlin.org keeps pointing to that Berkeley page as showing that evolutionary biologists have assumed something rather than having evidence. But they have not assumed the concordance of phylogenies from different characters, they have checked it.

  22. Nonlin.org: Can you explain this: “Just as well you can correlate shoe sizes with cloud shapes and automobiles. Does this tell you UCD applies to those three? No way!”

    A thorough non-analogy.

    The issue is comparing the evidence from different sets of characters for the same set of species. What shoe sizes, cloud shapes, and automobiles have to do with that is beyond comprehension.

  23. Fair Witness,

    Bill, why would a god need to conserve resources?

    This is a good question. I think that what we live in is resource limited and perhaps there is a reason for this design. Working inside this entity he is actually limited by its design.

  24. colewd:
    Fair Witness,

    This is a good question.I think that what we live in is resource limited and perhaps there is a reason for this design.Working inside this entity he is actually limited by its design.

    Typical gibberish. Try harder.

  25. Nonlin.org:
    Am I dealing with bots or retards? Is there any difference?

    Yet you made a fool out of yourself, as usual.

    Nonlin.org:
    From the same site the mindless bot quotes:
    “You can think of assumptions as the requirements you must fulfill before you can conduct your analysis. ”

    Exactly! Which is why they say that you should test those assumptions. Did you miss that despite I quoted it directly? Here it goes again for your edification, maybe you’ll get it this time (as if you could):

    As you prepare to conduct your statistics, it is important to consider testing the assumptions that go with your analysis. Assumption testing of your chosen analysis allows you to determine if you can correctly draw conclusions from the results of your analysis.

    Did you see that? Assumptions can be tested! Now, who’s a mindless illiterate bot here?

    Remember that your claim was that assumptions are not testable. That once something is called an assumption it is accepted without question. I have given you plenty of explanations, even examples, that show that you’re interpretation of words is that of a dictionary robot, rather than one of a thinking being. Stop it already. You’re wrong about that. You don’t rule reality. Your preferred dictionaries don’t rule reality. Sorry, but that’s the way it is.

    Nonlin.org:
    And it’s like someone can’t read:

    Exactly! And that someone is you, as you were so keen to demonstrate. How can you write that after demonstrating that you cannot read? Are you really that self-unaware? Maybe mentally ill?

    Nonlin.org:
    “I asked for a link to a third party EXAMPLE from the hard sciences and not for your opinion.” For those that don’t know, EXAMPLE is more than someone’s general yapping.

    And posting from sites dealing with statistical analyses is neither mere opinion, nor yapping. Statistics are applied to every kind of field, from the hardest to the “lightest” sciences. Therefore I gave you a much better example than what you asked for. The problem is that you cannot read.

    As I said, your words end up backfiring, and you end up ridiculing yourself. You really should check your attitude by the door before commenting. You’re hurting your own image. Of course, we don’t know who you really are, but if you’re serious about your beliefs, then you’re ridiculing them as well. You’re making your beliefs into something only acceptable by illiterate buffoons. If that’s your goal, mission accomplished.

    You’re hopeless, and it’s sad to see that even when confronted with direct evidence of your mistakes, you could not care less. You double down on those very mistakes. Since you cannot read, I really don’t know who am I writing this for. Not you. You’ll redouble in your mindless, irrational, nonsensical, “answers.” Should I give it any more tries? Are you worth it? Nah. I think you’re beyond rescuing.

  26. Joe Felsenstein:
    1. Nope. It was the argument of biologists starting in about 1700 (who, by the way, were creationists). They noticed that different parts of the anatomy all reinforced the same hieratchical classification.

    2. And perfect independence isn’t required. That’s the whole point of mixing conditions — they are the conditions required to have additional data cause you to converge on the right answer.

    3. And the analogy is not to bias in a coin, but to non-independence of tosses. Remember?

    4. The burden of proof is on nonlin.org, who is proposing a very strong nonindependence among changes in very different traits (foot anatomy versus kidney physiology versus cytochrome C sequence versus fibrinogen gene DNA sequence). Bizarre.

    Does any other ID advocate here, or any creationist, want to make that argument? Or do you think that it is as strange and nonobvious as I do?

    1. What “it” are you talking about? Some dude 300 yrs ago was as wrong as you are now. So what?
    2. What does that even mean? Link to some third party proof if any (hard sciences only). Your opinion is predicated on you earning a living from this nonsense.
    3. I was making another point that was lost on you.
    4. Your model, your bad assumptions, your burden of proof. What does “strong” even mean? How does “weak” change anything? Nonsense! But you earn a living from it.

  27. Joe Felsenstein: The evidence that the phylogeny is real is from concordance of phylogenies from different sets of characters and different parts of the genome.

    Not cutting it. Since when is “concordance” of results based on the SAME flawed assumption evidence of anything? Will a gang of criminals vouching for each others in court be found innocent?

  28. Entropy: Remember that your claim was that assumptions are not testable. That once something is called an assumption it is accepted without question.

    This is the most retard thing from the most retard bot around.

    And still no “third party EXAMPLE from the hard sciences”. Of course NOT because there is NONE TO BE FOUND.

    At least the other bot blew a fuse and went away. Hint, hint.

  29. So what’s the conclusion to date?
    1. UCD is an unproven assumption of cladistics.
    2. Cladistics is curve (tree) fitting, not hypothesis testing.
    3. No model (analysis) can prove its own assumptions. A hard sciences example to the contrary was not found.
    4. Cladistics cannot be hypothesis testing until the proper alternative hypothesis is considered.
    5. Independence of DNA segments and morphology has not been demonstrated. Without proven independence of inputs, similar outputs (consilience…) are to be expected.

    Looks very much like where we started. Anything else missing?

  30. Nonlin.org: 1. UCD is an unproven assumption of cladistics.

    It is unproven, in the logical sense of “prove”. And that’s good. For a proof by logic does not, in itself, tell us anything about reality.

    It is, however, well supported by multiple lines of evidence.

  31. Nonlin.org:
    So what’s the conclusion to date?
    1. UCD is an unproven assumption of cladistics.
    2. Cladistics is curve (tree) fitting, not hypothesis testing.
    3. No model (analysis) can prove its own assumptions. A hard sciences example to the contrary was not found.
    4. Cladistics cannot be hypothesis testing until the proper alternative hypothesis is considered.
    5. Independence of DNA segments and morphology has not been demonstrated. Without proven independence of inputs, similar outputs (consilience…) are to be expected.

    Looks very much like where we started. Anything else missing?

    Any willingness of nonlin.org to explain the logic of nonlin.org’s assertions.

    Does any other ID advocate (or creationist) here agree with nonlin.org? If so, maybe you could explain nonlin.org’s logic to me.

  32. Nonlin.org: And still no “third party EXAMPLE from the hard sciences”. Of course NOT because there is NONE TO BE FOUND.

    Really Nonlin? Are you such a mindless idiot that you could neither reason, nor find an example by yourself? Aren’t you the google magician?

    Symmetric and asymmetric nuclear matter in the relativistic approach
    … Furthermore, we tested the assumption of a quadratic dependence of the asymmetry energy for a large range of asymmetries …

    All this time I resisted the urge of an easy “victory” because this is no victory. I feel ashamed for you Nonlin. Victory would have been to get you thinking instead of idiotically asking for an example, because this did not need an example. All this needed was for you to actually think. But thinking is not for you now, is it Nonlin? Remaining a creationist requires you to be a mindless idiot. Right?

  33. Neil Rickert: Nonlin.org: 1. UCD is an unproven assumption of cladistics.

    It is unproven, in the logical sense of “prove”. And that’s good. For a proof by logic does not, in itself, tell us anything about reality.

    It is, however, well supported by multiple lines of evidence.

    The point of this OP is that cladistics cannot prove it’s own assumptions including UCD and “evolution” in general. You seem to argue that UCD is supported by OTHER evidence, and that’s fine as the subject of a different discussion. Let’s debate that separately.

  34. Joe Felsenstein: Any willingness of nonlin.org to explain the logic of nonlin.org’s assertions.

    You can review all 1000+ comments to date and come to the same conclusion. But feel free to present your concise arguments yet again in case you think something got missed (unlikely).

  35. Entropy: Symmetric and asymmetric nuclear matter in the relativistic approach
    … Furthermore, we tested the assumption of a quadratic dependence of the asymmetry energy for a large range of asymmetries …

    Your cargo cult “example” is retard. And very doubtful there’s something useful beyond the paywall. Certainly nothing in the summary other than magic words in random order.

    And still no “third party EXAMPLE from the hard sciences”. Of course NOT because there is NONE TO BE FOUND…

  36. Nonlin.org: The point of this OP is that cladistics cannot prove it’s own assumptions including UCD and “evolution” in general.

    You are arguing for a form of skepticism that is so extreme that it is irrelevant to everything.

  37. Neil Rickert: You are arguing for a form of skepticism that is so extreme that it is irrelevant to everything.

    He’s not even arguing for any form of skepticism, he’s merely acting out a denial only seen in individuals of an extremely adverserial mindset.

  38. Neil Rickert: You are arguing for a form of skepticism that is so extreme that it is irrelevant to everything.

    Like it or not, this is the scientific method and has nothing to do with skepticism. If you think it’s wrong, go ahead and search for “third party EXAMPLE from the hard sciences” where a model tests its own hypothesis. Others have looked and failed to find any.

  39. Nonlin.org: And still no “third party EXAMPLE from the hard sciences”. Of course NOT because there is NONE TO BE FOUND…

    I didn’t write that article, thus it’s third party. The journal where it was published is on physics, and the article is on physics, which is hard sciences. You’re amazingly eager to ridicule yourself. I’ll never understand why. Maybe you feel that it’s ok to showcase your beliefs as proper of unreasonable idiots. Maybe you don’t really believe in any god, and what you’re looking for is to ridicule theism. I don’t know, and I don’t care. This is over.

  40. Been away on vacation this week, and can see that things are still in the same place. nonlin.org keeps repeating the mantra about UCD being assumed by phylogenetic methods, so therefore it can’t be tested. For over 1,000 comments nonlin.org has not clarified who exactly is assuming that the mere presence of an estimated tree validates UCD. (Hint: it is the similarity of the trees for different genes that validates the common descent of groups within the study).

    Then nonlin.org points us to these failures to clarify, and argues that somewhere in there we will surely find nonlin.org’s explation of the matter. Nope, it is not there. And the argument that changes in different genes are so tightly corrrelated that the genes do not corroborate each other is not there either — nonlin.org just asserts that this is so and demands we disprove that.

    So I too am done with this discussion. Perhaps I’ll start a new thread focused on the similarity of trees made from different genes, and try to get the discussion to be less silly. I am pretty sure any lurkers will have figured out from this thread what the score is.

  41. Joe Felsenstein: Perhaps I’ll start a new thread focused on the similarity of trees made from different genes…

    I (and I’m sure many others) hope you find the time. We’d all benefit from your knowledge and experience!

  42. Entropy: I didn’t write that article, thus it’s third party. The journal where it was published is on physics, and the article is on physics, which is hard sciences.

    Let me repeat for those that can’t read:
    Your cargo cult “example” is retard. And very doubtful there’s something useful beyond the paywall. Certainly nothing in the summary other than magic words in random order.

  43. Joe Felsenstein:
    1. nonlin.org keeps repeating the mantra about UCD being assumed by phylogenetic methods, so therefore it can’t be tested.
    2. For over 1,000 comments nonlin.org has not clarified who exactly is assuming that the mere presence of an estimated tree validates UCD. (Hint: it is the similarity of the trees for different genes that validates the common descent of groups within the study).

    3. Then nonlin.org points us to these failures to clarify, and argues that somewhere in there we will surely find nonlin.org’s explation of the matter. Nope, it is not there. And the argument that changes in different genes are so tightly corrrelated that the genes do not corroborate each other is not there either — nonlin.org just asserts that this is so and demands we disprove that.

    You have to read again all 1000+ comments
    1. Not what I said. Read again: “Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis”
    2. As said many times, you failed to demonstrate trees for different genes are independent. The burden is on you and not met in 1000+ comments.
    3. Very unclear. Rephrase.

  44. Nonlin.org: You have to read again all 1000+ comments
    1. Not what I said. Read again: “Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis”
    2. As said many times, you failed to demonstrate trees for different genes are independent. The burden is on you and not met in 1000+ comments.
    3. Very unclear. Rephrase.

    Nothing new here. Issue I am raising is whether the consilience of trees from different parts of the genome is evidence for common descent of groups within the study. Not just UCD. It is. nonlin.org asserts trees are so strongly nonindependent that such inferences aren’t valid.

    Called on that, nonlin.org demand that we prove total independence of these trees. And refuses to provide evidence that the trees are so strongly nonindependent that they can’t be used as evidence.

    Same old same-old. Boring!

  45. Joe Felsenstein: Nothing new here. Issue I am raising is whether the consilience of trees from different parts of the genome is evidence for common descent of groups within the study. Not just UCD. It is. nonlin.org asserts trees are so strongly nonindependent that such inferences aren’t valid.

    Called on that, nonlin.org demand that we prove total independence of these trees. And refuses to provide evidence that the trees are so strongly nonindependent that they can’t be used as evidence.

    1. Joe Falsenstein thinks that parts of the genome are independent but this is ILLOGICAL as parts of the genome are NOT separately inherited (acquired) and can NEVER be found separate from the genome (decomposition and lab experiments aside).

    2. Furthermore, an organism’s genome INCLUDING its genes is 100% (not 99.9…%) correlated with that organism’s morphology even in mules and other hybrids.

    3. Finally, cladistics based on different genes is SAME AS cladistics based on parts of the organism’s morphology like limbs, digestive, reproductive system, etc and is 100% RETARD as anyone knows there are no functional limbs, etc. independent of the organism with its morphology, genome and COMMON genealogy.

    And this is NOT the only point of this OP. Just as important is the issue of a model that pretends to prove its own assumptions (UCD and CD). This issue is totally ignored by Joe Falsenstein although others (SEVERAL!) tried to find a counterexample and couldn’t. In fact, there are a total of 7 major points of this OP that Joe Falsenstein and others could NOT counter in any way over 1000+ comments.

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