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 Replies to “Nested Hierarchies (Tree of life)”

  1. keiths keiths
    Ignored
    says:

    Theobald:

    This term [the “twin nested hierarchy”] is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.

    Mung:

    When I say it, it’s false. When Theobald says it, it’s true.

    If you ever actually managed to say the same thing that Theobald does here, then you were correct.

  2. colewd
    Ignored
    says:

    Corneel,

    You have never shown that Mac computers can be arranged into a (objective) nested hierarchy,

    Can you support this claim?

    Will you please, pretty please, ponder for a moment the absurdity of all eukaryotes being related by common descent, while a dog and a bird are not.

    We have consensus this is absurd 🙂

  3. keiths keiths
    Ignored
    says:

    Corneel:

    You have never shown that Mac computers can be arranged into a (objective) nested hierarchy,

    colewd:

    Can you support this claim?

    Yeah, Corneel. How do you know he didn’t do it last Wednesday while sitting on the toilet (assuming he knows how to operate one)? Prove it! Checkmate, evilutionists.

  4. Mung Mung
    Ignored
    says:

    Joshua Swamidass:

    Common descent does not predict that data will fall perfectly in nested clades. Common descent does not produce DNA that falls into a tree. This is well known by experts, but “popularizers” have been wrong.

    here

  5. keiths keiths
    Ignored
    says:

    Mung,

    Here are the sentences you left out:

    So Ewert’s [paper] might be understood to dispatch a cartoon version of evolution. This has nothing to do with evolution as understood in mainstream science.

  6. Rumraket Rumraket
    Ignored
    says:

    colewd: Can you support this claim?

    Since you’re the one claiming they can, but have only ever claimed it, not actually done the sorting, how about you proceed to do that and shut us up?

    I remember asking you to do that like 20 times in the common descent thread. You made the Mac-computer claim over and over again, you never actually showed someone sorting them objectively into a nesting hiearchy.

    Enough with you claiming it can be done. Proceed to ACTUALLY DOING IT. You wouldn’t be making claims you can’t support right?

  7. Rumraket Rumraket
    Ignored
    says:

    Mung:
    Joshua Swamidass:

    here

    There’s a lot of rather imprecise statements being made. I think I know what Swamidass intends to say, but the problem is he’s making a sort of universal statement when the reality is just much more complicated than that.

    Common descent does predict that genetics will produce tree-like patterns, given all sorts of caveats and constraints. All of those constraints and caveats can be violated under special circumstances. Very long periods of time (or very high mutation rates, or both) will erase phylogenetic signal as all sites eventually mutate multiple times. Convergence (whether just due to chance, or due to adaptation) will make disparate sequences or physical characteristics appear more similar. Genes can be lost or replaced. There can be horizontal gene transfer. And so on. These are all observed phenomena that can happen and they have different likelihoods of occurring.

    It would be more correct to say that common descent predicts that tree-like structure in a subset of the data should be detectable up to a certain point, but that not all the data should be expected to conform.

  8. J-Mac
    Ignored
    says:

    Rumraket: Enough with you claiming it can be done. Proceed to ACTUALLY DOING IT. You wouldn’t be making claims you can’t support right?

    Exactly!
    You should have made that comment on the “Help the gliding snake grow wings” OP…
    I agree with your comment 100%. I’m tired of evolutionists claiming it can be done by evolution… Proceed to actually doing it and showing that evolution can do what Darwinists claim it can…

  9. Mung Mung
    Ignored
    says:

    keiths: Here are the sentences you left out:

    So?

  10. Mung Mung
    Ignored
    says:

    Rumraket: There’s a lot of rather imprecise statements being made. I think I know what Swamidass intends to say, but the problem is he’s making a sort of universal statement when the reality is just much more complicated than that.

    Yes, reality bites. Now it’s beginning to bite evolutionists.

  11. keiths keiths
    Ignored
    says:

    keiths:

    Here are the sentences you left out:

    So Ewert’s [paper] might be understood to dispatch a cartoon version of evolution. This has nothing to do with evolution as understood in mainstream science.

    Mung:

    So?

    Heh. I knew you’d say that.

    You’re just pitiful, Mung.

  12. Mung Mung
    Ignored
    says:

    keiths: Heh. I knew you’d say that.

    Presumably, you think it’s relevant. Care to share why it’s relevant?

  13. keiths keiths
    Ignored
    says:

    Mung:

    So?

    keiths:

    Heh. I knew you’d say that.

    Mung:

    Presumably, you think it’s relevant. Care to share why it’s relevant?

    It’s Mungese for “Crap. I got caught. I’d better try to minimize this.”

  14. Nonlin.org
    Ignored
    says:

    keiths:
    Someone needs to explain to Nonlin what “LUCA” means.

    I see they caught on to the ridiculousness by claiming:
    “LUCA is not thought to be the first living organism on Earth , but only one of many early organisms, all but one of which died out.”
    You do realize that “only one of many early organisms, all but one of which died out.” is just as ridiculous, right?
    Darwin’s “…the littlest creature (or “four or five” of them)…” is also very much ridiculous.
    More importantly, none of these assertions is supported by any evidence. Unless… do you have the “evidence”?

  15. Nonlin.org
    Ignored
    says:

    Alan Fox: Hi, nonlin. Pleased to see that you are defending your OP. I have popcorn.

    Join the party. You can start by elaborating on “full of errors and misconceptions”. I also have popcorn:)

  16. Mung Mung
    Ignored
    says:

    keiths: It’s Mungese for “Crap. I got caught. I’d better try to minimize this.”

    So, no. You can’t explain its relevance. Exactly as expected.

  17. Nonlin.org
    Ignored
    says:

    Corneel: BTW: Out of curiosity. Do you believe that each and every species is independently created?

    What you or I believe is of no consequence without evidence, right? What I see is variations around fixed themes. I would not use the word “species” since we don’t have a clear definition for it – http://nonlin.org/speciation-problems/. Agree?

    The ‘themes’ sure do look independently created to me. One thing is for sure, they do not flow from one into another. You can take this to the bank: “we observe that even unicellular organisms with huge populations and short-lived generations do not occupy a biological continuum.”

  18. colewd
    Ignored
    says:

    Rumraket,

    I remember asking you to do that like 20 times in the common descent thread. You made the Mac-computer claim over and over again, you never actually showed someone sorting them objectively into a nesting hiearchy.

    I did and modified it based on Neil’s corrections. The common ancestor to the current Macs (laptop and desktop) is the next computer. The original Mac I believe is extinct. I think what we are seeing is that there are good reasons for design to create a nested pattern.

    I do think that Winston’s argument is better then this using software alone. Software as in biology connects code (functional information) directly to function. In the Mac case you have to explain hardware which is an intermediary or support structure between the code and the function.

  19. Nonlin.org
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    says:

    keiths: Some more questions for the ID supporters out there:

    1. Bob is walking through the desert with his friend, a geologist. They come across what appears to be a dry streambed. After some thought, Bob states that every rock, pebble, grain of sand and silt particle was deliberately placed in its exact position by a Streambed Designer. His friend says “That’s ridiculous. This streambed has exactly the features we would expect to see if it was created by flowing water. Why invoke a Streambed Designer?”

    Who has the better theory, Bob or his friend?

    2. Bob is invited to the scene of an investigation by a friend who is an explosive forensics expert. They observe serious damage radiating out in all directions from a central point, decreasing with distance, as if an explosion had taken place. Bob’s friend performs some tests and finds large amounts of explosive residue. Bob says, “Somebody went to a lot of trouble to make it look like there was an explosion here. They even planted explosive residue on the scene! Of course, there wasn’t really an explosion.”

    Who has the better theory, Bob or his friend?

    3. Bob and another friend, an astronomer, observe the positions of the planets over several years. They determine that the planets are moving in ellipses, with the sun at one of the foci. Bob says, “Isn’t that amazing? The angels pushing the planets around are following exactly the paths that the planets would have followed if gravity had been acting on them!” The astronomer gives Bob a funny look and says “Maybe gravity is working on those planets, with no angels involved at all. Doesn’t that seem more likely to you?”

    Who has the better theory, Bob or his friend?

    4. Bob is hanging out at the office of a friend who is an evolutionary biologist. The biologist shows Bob how the morphological and molecular data establish the phylogenetic tree of the 30 major taxa of life to an amazing accuracy of 38 decimal places. “There couldn’t be a better confirmation of unguided evolution,” the biologist says. “Don’t be ridiculous,” Bob replies. “All of those lifeforms were clearly designed. It’s just that the Designer chose to imitate unguided evolution, instead of picking one of the trillions of other options available to him.”

    Who has the better theory, Bob or his friend?

    This is fun:
    1. Flowing water has a cause that has a cause and so on to First Cause. Otherwise, “flowing water” would be like: “John died because the bullet hit his heart”. Well, duh!
    2. This has nothing to do with anything. One observes the aftermath of an explosion but questions the motives – happens all the time. No one ever leaves the investigation at “yes, there was an explosion”.
    3. Wrong question again, and this scenario is plain stupid. What is gravitation? Where is gravitation coming from? Who gave you gravitation? These are the right questions.
    4. You clearly did not read the OP. Otherwise you would see the answer or at least challenge the explanations provided

    Now, where’s my prize?

  20. dazz dazz
    Ignored
    says:

    Nonlin.org: I see they caught on to the ridiculousness by claiming

    I see you didn’t catch on to the stupidity of your question “why the Last Universal Common Ancestor would have happened once and only once.”

  21. Nonlin.org
    Ignored
    says:

    Corneel: If you nor any other IDer are willing to commit to this particular version of common design and defend it, then keiths’ criticism still stands as common design proponents leave the door open for any of the thousands of alternative versions of common design.

    Forget Ewert. Many ID proponents make the mistake of complicating matters. Luckily you have in this OP seven claims that destroy “nested hierarchies common descent”, yet you have not even attempted to argue against. Get to work! If you have not figured out, this is a compliment for you, one of the more intelligent Darwinistas out there.

  22. keiths keiths
    Ignored
    says:

    colewd:

    I think what we are seeing is that there are good reasons for design to create a nested pattern.

    Demonstrating, yet again, that you don’t understand the difference between a nested hierarchy and an objective nested hierarchy.

    It matters. Hugely.

  23. keiths keiths
    Ignored
    says:

    Nonlin.org:

    Now, where’s my prize?

    Your prize for misunderstanding examples that even Robert Byers, of all people, was capable of grasping?

    Here you go:

  24. Nonlin.org
    Ignored
    says:

    Rumraket: Common descent does predict that genetics will produce tree-like patterns, given all sorts of caveats and constraints. All of those constraints and caveats can be violated under special circumstances. Very long periods of time (or very high mutation rates, or both) will erase phylogenetic signal as all sites eventually mutate multiple times. Convergence (whether just due to chance, or due to adaptation) will make disparate sequences or physical characteristics appear more similar. Genes can be lost or replaced. There can be horizontal gene transfer. And so on. These are all observed phenomena that can happen and they have different likelihoods of occurring.

    I make seven claims in this OP that destroy your “nested hierarchies common descent” and that you ignore and then re-state your nonsense. Are you just doing a monologue here? If so, be my guest, but your credibility is shot.

  25. Nonlin.org
    Ignored
    says:

    keiths,

    So you’re a sore looser. Got it. You know, I’m not your enemy – just the one that brings bad news for your religion. But not your personal enemy…

  26. Nonlin.org
    Ignored
    says:

    dazz,

    You know, I’m not your enemy – just the one that brings bad news for your religion.

    Now enlighten me – do you have any evidence for “LUCA is not thought to be the first living organism on Earth , but only one of many early organisms, all but one of which died out.” No? I thought so.

    How about for Darwin’s “…the littlest creature (or “four or five” of them)…” No? I thought so once again.

  27. dazz dazz
    Ignored
    says:

    Nonlin.org: You know, I’m not your enemy – just the one that brings bad news for your religion.

    Fuck religion, that’s your thing, and as I keep responding to all the religious fucktards that attack us for supposedly being religious, that only puts your inferiority complex on display.

    Nonlin.org: Now enlighten me

    I can’t, no one can, you’re far too stupid and lacking in reasoning skills to even figure out what LUCA means and entails, let alone evaluate the evidence for it’s existence

  28. keiths keiths
    Ignored
    says:

    Nonlin,

    It’s true. Robert Byers, of all people, grasped those examples (except for the last one), while you failed.

    It seems that I’m the one bearing bad news to the religious.

  29. Robert Byers
    Ignored
    says:

    keiths:
    Robert writes, concerning my four examples:

    To see why the “evo bio guy” is right, you will need to read and comprehend the following, taken from Theobald’s “29+ Evidences for Macroevolution”:

    Good luck.

    I understand their point.
    The error continues in simply presuming only one option for these relationships.
    If the morphologies are divergent then it could only be that the molecular score would be a copy.
    The differences in morphology must have a equal foundation in the molecular level.
    A option for a design would mimic this/even be a prediction.
    its not two nests but one. Yet not a nest but instead a design allowing variation.

    my point is that common design easily would include likeness in morphology and likeness in a drift from it. mechanism within a design in biology would allow exactly what is seen in molecular studies.
    they are convincing themselves too quick about common descent because of two trails matching.
    it would be this way from common design.
    Why not?

  30. Corneel Corneel
    Ignored
    says:

    Nonlin.org: The ‘themes’ sure do look independently created to me. One thing is for sure, they do not flow from one into another. You can take this to the bank: “we observe that even unicellular organisms with huge populations and short-lived generations do not occupy a biological continuum.”

    No independently created individual species then, that’s good.

    Could you give an example of such a “theme” (= baramin, I guess)? Where does the variation within the themes come from?

  31. Corneel Corneel
    Ignored
    says:

    Mung: Corneel: “It fits the data better”

    That’s an understatement.

    It’s getting harder and harder to understand your jokes.

  32. Rumraket Rumraket
    Ignored
    says:

    Mung: Yes, reality bites. Now it’s beginning to bite evolutionists.

    Thank you for your vacuous commentary.

  33. Rumraket Rumraket
    Ignored
    says:

    colewd: I did and modified it based on Neil’s corrections. The common ancestor to the current Macs (laptop and desktop) is the next computer. The original Mac I believe is extinct.

    That’s not an objective hierarchy. You don’t even understand what you’re being asked to do.

    Bill, anyone can just draw a tree and put items at the leafs and nodes. That’s not an objective nested hierarchy. The hierarchy has to be inferred from patterns in the data. In the case of mac computers, you have to show that the physical characteristics of mac computers can be used to sort them objectively into a nesting hierarchy. That means you group them by their properties, not by simply taking something you *think* belongs together.

    I do think that Winston’s argument is better then this using software alone. Software as in biology connects code (functional information) directly to function.

    Please dont’ pretend you even understand what Winston is doing. Or what it’s supposed to explain. Or what it leaves out.

    In the Mac case you have to explain hardware which is an intermediary or support structure between the code and the function.

    Oh gee that sure sounds technical, clearly you are an expert.

  34. Corneel Corneel
    Ignored
    says:

    colewd: We have consensus this is absurd 🙂

    Capital! Now you have to choose between common descent of all eukaryotes which includes dogs and birds OR maintain that dogs and birds do not share a common ancestor, so the same goes for all eukaryotes.

    Or you can keep contradicting yourself every other sentence, but I have to warn you that this looks a bit silly.

  35. Rumraket Rumraket
    Ignored
    says:

    Fuck but do I get tired of seeing this brigade of clueless IDcreationist gimps trying to pelt away at a wall of science they don’t even half-way understand.

    Between J-mac, Nonlin, and Bill Cole, I doubt they could find their way out of a doorless phone booth with a map and compass. In broad daylight. And Mung is just plain content-less one-liner trolling.

    You people have nothing. Nothing. What a colossal joke.

  36. Corneel Corneel
    Ignored
    says:

    For those interested: it appears Winston Ewert has made his appearance at Joshua Swamidass’ blog. In the comment thread, Steve Schaffner made a remark that resonated very closely with my own suspicions about the “better fit”. This objection will immediately occur to every bio-informatician and computational biologist: variation in the quality of curation.

    Without going into the details of the models, here’s my understanding of the situation: given a set of N species and a set of gene families, any gene family that appears in more than one species and in less than (N-1) species can contribute to the comparison of the two models. If the gene family appears only in a subclade of the full set of species, or is missing only in a subclade, then it is consistent with both models. If its presence or absence is not consistent with a single subclade, then it is improbable under the simple tree model but still probable under the dependency model. (And the dependency model is penalized for its extra degrees of freedom.)

    Is my summary accurate? (If not, you can probably ignore the rest of my comments.)

    If so, then it seems to me that this kind of comparison is critically dependent on the completeness and consistency of the dataset, since missing data in more than one species appears as a signal for one of the models. Comparative genome sequence data is typically typically come from independent sequencing projects with different degrees of completeness and accuracy, so the issue is particularly severe for this test.

    If it were my study, the first thing I would want to do is understand the completeness of the data. For the case of the closely related fish, for example, how many gene families are there in total? How many are missing from a single species? How consistent is this number from species to species? Is there a correlation between the number of singleton missing gene families and the number of shared missing gene families, when assessed across species? (These would be good numbers to post here, by the way.)

    The second thing I would absolutely, positively do – and would insist on an author doing if I were reviewing a study like this – is look at some of the genes that are supposedly missing (in a way not consistent with common descent) and confirm that they are really are missing genes and not missing (or different annotations. What’s in the genome where they should be, based on related species that have them?

    Steve Schaffner

    That perfectly explains the wonky stuff, like the finding that lancelet and a species of sea anemone uniquely share dozens of gene families (modules) found in no other metazoan.

  37. Rumraket Rumraket
    Ignored
    says:

    In any case, I’m still glad to finally see Ewert at least try to do what no other ID theorist has done before, which is to make an actual model that attempts to account for data, with an actual explanation.

    I completely agree with Swamidass here:

    However, this is also head on addressing one (of many) important patterns in the data, at least in part. He has proposed a mathematical model. He is testing this model. Such efforts are almost unheard of in anti-evolution arguments. I might be able count the number of comparable attempts on one hand. In that sense, it is not merely a negative effort to poke holes, but a positive effort of model building. It is not full of errors of computing the “probability of X by natural processes” either. So this is a legitimate effort to engage the data, whether or not it pans.

    It is also typical of ID to overstate what is happening, which is why Cornelius huffing and puffing is not helping Ewert. If they can correctly frame their results, actually engage with critique, they MIGHT be able to refine this into something workable for PART of the data. Then they have to find a way to deal with the REST of the data.

  38. colewd
    Ignored
    says:

    Rumraket,

    That means you group them by their properties, not by simply taking something you *think* belongs together.

    The properties that group Mac’s are the operating system, functional usage such as desk top or laptop, and performance. The most important criteria is the operating system.

  39. Rumraket Rumraket
    Ignored
    says:

    colewd: The properties that group Mac’s are the operating system, functional usage such as desk top or laptop, and performance. The most important criteria is the operating system.

    Make the groups then.

    Group them by what operating system they run, then group them desktop and laptop, then by performance.

  40. colewd
    Ignored
    says:

    Corneel,

    Capital! Now you have to choose between common descent of all eukaryotes which includes dogs and birds OR maintain that dogs and birds do not share a common ancestor, so the same goes for all eukaryotes.

    This logic is absurd.

    OR maintain that dogs and birds do not share a common ancestor, so the same goes for all eukaryotes

    Have you thought of the possibility that some eukaryotes share a common ancestor and some don’t?

  41. colewd
    Ignored
    says:

    Rumraket,

    Make the groups then.

    The original Mac laptop and desktop in one group with the Lisa as the common ancestor and the objective c Mac os in the second group with the Next computer as the common ancestor.

  42. colewd
    Ignored
    says:

    Rumraket,

    Group them by what operating system they run, then group them desktop and laptop, then by performance.

    The major group is by operating system. Within the group we separate by laptop and desk top then within those groups by performance.

  43. Corneel Corneel
    Ignored
    says:

    colewd: Have you thought of the possibility that some eukaryotes share a common ancestor and some don’t?

    WHAT?!? Are you serious?

    Can you really not see that, if dogs and birds do not share a common ancestor, this also rules out common descent of ALL eukaryotes? How can you possibly maintain a single independent origin for the spliceosome if it had to be created multiple times for different eukaryotic lineages?

    Oh, and all those times when we were discussing purifying selection and talking about exploring sequence space, you were assuming that proteins within tetrapods were not homologs? If you want to claim that the beta chain of ATP synthase was preserved by purifying selection for 400 million years, then you MUST accept common descent of all tetrapods, including birds and mammals. You cannot just collect the arguments that you happen to like as if you are doing your groceries.

  44. keiths keiths
    Ignored
    says:

    Corneel:

    Will you please, pretty please, ponder for a moment the absurdity of all eukaryotes being related by common descent, while a dog and a bird are not.

    colewd:

    We have consensus this is absurd 🙂

    Corneel:

    Capital! Now you have to choose between common descent of all eukaryotes which includes dogs and birds OR maintain that dogs and birds do not share a common ancestor, so the same goes for all eukaryotes.

    colewd:

    Have you thought of the possibility that some eukaryotes share a common ancestor and some don’t?

    Corneel:

    WHAT?!? Are you serious?

    Can you really not see that, if dogs and birds do not share a common ancestor, this also rules out common descent of ALL eukaryotes?

    Bill, do you understand why Corneel is incredulous? You’ve made a logic error so basic, and so extreme, that it induces astonishment in the brighter members of your audience. (It might even astonish Mung, but I wouldn’t bet on it.)

    This is the intellectual equivalent not only of being unable to tie your shoes, but of not knowing which appendages the shoes go on. You are earnestly trying to stick your shoes on your ears, all the while wondering why people are laughing.

  45. keiths keiths
    Ignored
    says:

    Rumraket,

    Between J-mac, Nonlin, and Bill Cole, I doubt they could find their way out of a doorless phone booth with a map and compass. In broad daylight.

    You’re giving Bill too much credit. I don’t think he could even find the phone booth.

  46. keiths keiths
    Ignored
    says:

    colewd:

    The properties that group Mac’s are the operating system, functional usage such as desk top or laptop, and performance. The most important criteria is the operating system.

    Yet again demonstrating that you have no clue what an objective nested hierarchy is. How many frikkin’ times has this been explained to you?

    How many times has the following passage from Theobald been quoted to you?

    Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between “subjective” and “objective” is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.

    The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.

    Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.

    If you cannot, through repeated study (and I mean repeated study), come to understand what Theobald is saying there, then there is simply no hope that you will ever be able to participate in this conversation — in any role other than as the buffoon, that is.

    Don’t pretend to understand what you cannot, Bill. It just makes you look even more ridiculous than before.

  47. Mung Mung
    Ignored
    says:

    Corneel: It’s getting harder and harder to understand your jokes.

    That one wasn’t a joke. 🙂

    The dependency graph model was a better fit, by far.

  48. Mung Mung
    Ignored
    says:

    Rumraket: Thank you for your vacuous commentary.

    Just call me keiths! Or dazz.

  49. Mung Mung
    Ignored
    says:

    Rumraket: In any case, I’m still glad to finally see Ewert at least try to do what no other ID theorist has done before, which is to make an actual model that attempts to account for data, with an actual explanation.

    Yes, it probably really does deserve its own OP here. Maybe someone will create one.

  50. Mung Mung
    Ignored
    says:

    keiths: (It might even astonish Mung, but I wouldn’t bet on it.)

    That’s right. Nothing that Bill says astonishes me.

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