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 […].”

 

1,009 thoughts on “Nested Hierarchies (Tree of life)

  1. keiths: Where did you get that idea? Damn, Mung.

    You obviously think that I am trying to use Ewert to refute your nonsense.

    keiths: You couldn’t refute my argument, so you went around looking for someone or something you hoped would be able to.

    No, that’s silly. And wrong. FFS.

    My posting of Ewert was done for its own sake. I’ve been aware of it for a number of days. It has nothing to do with trying to refute you or your silly unjustified claim [you know the one].

  2. keiths:

    Okay, Mung. In your own words, tell us why my argument fails.

    Mung, in desperation:

    Easy. Your argument fails because it is false.

    And neither you nor Bill can say why.

  3. Mung,

    My posting of Ewert was done for its own sake. I’ve been aware of it for a number of days. It has nothing to do with trying to refute you or your silly unjustified claim [you know the one].

    …says Mung, who specifically cited Ewert against my argument:

    BIO-Complexity Presents Better Model than Common Ancestry for Explaining Pattern of Nature

    In other words, roughly two-thirds of all data do not fit the common ancestry model.

    So much for that nonsense post by keiths that he refuses to defend. Who can blame him.

    Oops.

  4. keiths:
    Follow the link I gave, Robert.

    I read it. Trillions poped up billions of time. Then the word literally.
    Anyways you don’t actually make a point about why common design doesn’t better/same explain biology?
    You bring up about the creators options and why its unlikely he would make biology as if common descent was true.
    I don’t see this point at all.
    A creator would make a common blueprint for biology to fill the earth in all good ways. Just like a common blueprint in physics. Why not biology like physics from the same thinking creator???
    Then YEC must have creaton/gods hands on end on creation week.
    After the fall biology7 radically changed YET by innate biological systems.
    We need this. The blueprint contains within it glorious ability to bring body plan changes.
    We see no reason to deny this option just because we don’t see it happening today.

    IF there is a biology system within biological entities , however hidden. it would be logical and consistent in its results.
    There would be spectrums of body plan differences.
    People being case in point. All the species of humans gained their different body plans from sudden innate triggering events upon migration to areas. No selection with the demise of the unworthy ones. GOD never allowed anyone to die because they were the wrong colour for the climate.
    ‘People changed as quick as arctic critters do today going from brown to white for the winter. Or those sea creatures that change upon moving a few feet.
    The nested tree thing evolutionists convince themselves about has a better alternative.
    Its still just scoring likeness in traits of body plans.
    its not biological evidence in any way. Just a line of reasoning.
    In fact you brought up lines of reasoning to try to say common design is not a option.

  5. Byers:

    Anyways you don’t actually make a point about why common design doesn’t better/same explain biology?

    Sure I do. Common design is a poor fit to the pattern we see. Common descent fits beautifully.

    When one hypothesis is a poor fit to the data, and a second is an excellent fit, we prefer the latter over the former. And in this case common descent fits the evidence trillions of times better, so it would be idiotic to reject it in favor of common design.

    Yet that’s what creationists do.

  6. Once again we see that keiths was just giving us nonsense and expecting us to believe it because he said it.

    Mung,

    Are you actually claiming to understand my argument, and Ewert’s, well enough to render that judgement? That would be rather remarkable, given your bafflement over why evolutionary biologists accept common descent while rejecting common design.

    But if so, then please make your case — in your own words.

  7. keiths,

    Are you actually claiming to understand my argument,

    You mean the argument that the designer had a lot more choices then the pattern that the observed data formed. I have to admit this is air tight.

    As Mung says. Eyes are easy to evolve. Look how many times eyes have evolved 🙂

  8. keiths: Are you actually claiming to understand my argument…

    Does your argument rest on the claims you made? Because if it doesn’t, then I would not claim to understand your argument. I do, however, understand your claims. I also observe your consistent refusal to back them up with actual facts.

    Why don’t you just drop the claims you’re not willing to defend?

  9. As far as the Ewert paper is concerned, I have to wonder if keiths has even looked at it. It’s not an anti-evolution paper. It’s not a paper that argues against common descent.

  10. keiths: That would be rather remarkable, given your bafflement over why evolutionary biologists accept common descent while rejecting common design.

    What bafflement. I already accept common descent as the current best explanation. And I would say that they reject common design because they lack a model for it, not because they created a “common design” model and tested it.

    Contrary to your unsupported claims about scientists creating models and testing them. In the same way that you cannot produce the “creationism” model that was tested, you likewise cannot produce the “guided evolution” model that was tested, nor can you produce the “common design” model that was tested.

    Now it would be a simple enough thing for you to prove me wrong if what you have said is true. So why haven’t you? Are you afraid to put your claims to the test?

  11. Mung,

    As far as the Ewert paper is concerned, I have to wonder if keiths has even looked at it. It’s not an anti-evolution paper. It’s not a paper that argues against common descent.

    Along with gpuccio Ewert has done some interesting empirical work to support the case for a conscious intelligence model. I hope to see more from those guys.

  12. Here is your claim keiths:

    keiths: Scientists routinely test their assumptions (and their models) by asking “What would I expect to observe if these assumptions (or this model) were true?”, and then comparing that to what they actually observe.

    This has been done for both common descent and creationism.

    According to you, scientists have created a “creationism” model and tested it.

    And to this, based on additional comments you’ve made, we can add the following claims as well:

    Scientists have created a “guided evolution” model and tested it.

    Scientists have created a “common design” model and tested it.

    If you can’t support these claims just say so, and then explain how your “argument” doesn’t depend on them anyways.

  13. colewd: Along with gpuccio Ewert has done some interesting empirical work to support the case for a conscious intelligence model.

    Ewert does the sort of thing that critics of ID say IDists don’t do. But I predict they won’t change their tune, lol.

    I’ve always rejected “common design” as an explanation because I had no idea what someone meant when they said it and what would distinguish it from common descent.

  14. Mung,

    I’ve made an argument against creationism and guided evolution. You and Bill can’t refute it.

    It’s the usual story: evolutionary theory succeeds and ID fails.

  15. keiths,

    I’ve made an argument against creationism and guided evolution. You and Bill can’t refute it.

    It’s the usual story: evolutionary theory succeeds and ID fails.

    I wonder if keiths player/referee model is sustainable 🙂

  16. colewd:

    I wonder if keiths player/referee model is sustainable 🙂

    Bill, you’re making the same dumb mistake as before:

    colewd:

    This is an assertion you continue to make. You’re putting yourself as the judge and authority. A logical fallacy which renders the statement meaningless.

    keiths:

    By Bill’s inane logic, no one can ever decide that someone else is wrong. That would be a logical fallacy. So when Bill criticizes evolutionary theory, he is, by his own standards, spouting fallacious nonsense.

    Bill couldn’t pour water out of a boot with instructions on the heel.

  17. keiths: It’s the usual story: evolutionary theory succeeds and ID fails.

    Please be more specific. Which model of ID was tested and found wanting, and by whom? Where was the research published? Or is this just yet another claim of yours that you are going to decline to support.

    Bring back the old keiths please.

  18. Neil Rickert: Christianity is refuted.

    The basis for Christianity is supposed to be evident to those who are born again.But that would constitute testing them by the model that uses them.

    Christianity is a religion like Darwinism, not an assumption that would test itself.

    keiths: Scientists routinely test their assumptions (and their models) by asking “What would I expect to observe if these assumptions (or this model) were true?”, and then comparing that to what they actually observe.

    They test the model and compatibility with assumptions. Not the same.

    keiths: Scientists routinely test their assumptions (and their models) by asking “What would I expect to observe if these assumptions (or this model) were true?”, and then comparing that to what they actually observe.

    Doesn’t matter. Lack of objectivity has always been an issue.

    Acartia: Since nobody has claimed that this is proof of UCD, I guess we are OK.

    Yes, they did: http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy

    Rumraket: Almost everything in the OP is wrong and incredibly ignorant. But it isn’t worth it to argue with the person who made the OP, because this individual denies there’s a correlation between phenotype (the physical characteristics of an organism, like it having camouflage, or eyes, or wings) and it’s ability to survive and reproduce.

    Prove “wrong and incredibly ignorant” if you can.

    I did not deny “a correlation between phenotype and its ability to survive”. This is what I said with a very clear and undeniable example that nonetheless you don’t seem to grasp:

    “No. Natural Selection fails since survival is not directly tied to phenotype and “survival of the best adapted” is tautological. In a small farm, only organisms closely related to their wild cousins survive, but agribusinesses select for chickens with oversize breasts and research labs select for populations with specific genetic mutations requiring tight environments to survive. As shown, all these different organisms may or may not survive regardless of their phenotype. The only measure of “selection” is survival – we only know if and organism was selected if it survives and reproduces. “Best adapted” is also unknowable separate from survival“

    Not my problem that you can’t defend your positions and hide away in desperation.

  19. Mung:
    I thought about starting a new OP, but since this thread is already generating so much interest I may as well post it here.

    BIO-Complexity Presents Better Model than Common Ancestry for Explaining Pattern of Nature

    So much for that nonsense post by keiths that he refuses to defend. Who can blame him.

    http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2018.3

    Interesting, thanks for that.
    As they say:
    “Ewert’s article represents only the first step in evaluating and developing his framework. Still, the significance of this research cannot be overstated. The dependency graph model explains why subsets of the biological data crudely fit a tree pattern and why so much of the data is incongruent. “

  20. keiths:

    I’ve made an argument against creationism and guided evolution. You and Bill can’t refute it.

    It’s the usual story: evolutionary theory succeeds and ID fails.

    Mung, in effect:

    But I don’t want that. I don’t want it! Therefore, you have to jump through a bunch of arbitrary and irrelevant hoops which I will now proceed to invent.

    Um, no. I’ve presented an argument against ID that you cannot refute. Evolutionary theory succeeds, and ID fails. Again.

    And of course, you and Bill are on the failing side.

  21. keiths,

    Bill:You’re putting yourself as the judge and authority.

    kieths; By Bill’s inane logic, no one can ever decide that someone else is wrong:

    Positioning yourself as an authority and making a personal decision based on evidence are not the same.

    As a player you can make a personal decision.

  22. colewd:

    Positioning yourself as an authority and making a personal decision based on evidence are not the same.

    As a player you can make a personal decision.

    I’m not “positioning myself as an authority.” I’ve made an argument. You and Mung can’t refute it.

    Evolutionary theory succeeds, and ID fails.

  23. keiths,

    I’m not “positioning myself as an authority.” I’ve made an argument. You and Mung can’t refute it.

    So this pivot signals you understand you created a straw-man fallacy and that Entropy committed an appeal to authority fallacy. Progress.

    Yes. It is challenging to refute nonsense except to call it nonsense.

  24. Mung: I’ve always rejected “common design” as an explanation because I had no idea what someone meant when they said it and what would distinguish it from common descent.

    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.

  25. colewd:

    So this pivot signals you understand you created a straw-man fallacy and that Entropy committed an appeal to authority fallacy.

    It’s not a “pivot”, and it signals no such thing.

    You’re pitiful, Bill.

  26. Nonlin.org:

    another black eye for Darwinistas that cannot explain why LUCA would have happened once and only once.

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

    Too funny.

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

    Too funny.

    What’s the point? these retards aren’t equipped to grasp the simplest of concepts

  28. keiths: You’re pitiful, Bill.

    Yet you’re the one running away from backing up his claims with anything that even remotely resembles evidence. Hell, now you’re pretending like you didn’t even make them. But you did make them, and they are now a part of the record.

    Given that your premises are untrue your argument isn’t worth spit.

  29. Nonlin.org: Not my problem that you can’t defend your positions and hide away in desperation.

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

  30. keiths:
    Byers:

    Sure I do.Common design is a poor fit to the pattern we see.Common descent fits beautifully.

    When one hypothesis is a poor fit to the data, and a second is an excellent fit, we prefer the latter over the former.And in this case common descent fits the evidence trillions of times better, so it would be idiotic to reject it in favor of common design.

    Yet that’s what creationists do.

    Then its about the fit.
    Intellectually i see common design not only easily explain any spectrum in biological patterns but it makes great sense. its what i would do as a creator.
    your side is asking a creater to be straitjacketed by KINDS with no option for adaptation . your not allowing a design that includes mechanisms to react to needs.
    Then in spectrums going from this to that.
    its just like my prople analagy.
    Your insisting human colour/other bodyplan details could only be in a nested tree due to common descent of a same original bodyplan.
    Yet creationism insists colour/other details are more likely due to sudden body changes from innate mechanisms. this fits better what we see with peoples looks.

  31. Robert,

    I think the abstractness of the argument is befuddling you, so let me offer some concrete analogies taken from the 2012 thread:

    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?

    Share your answers with us. Did your answers to the four questions differ? If so, please explain exactly why.

    And ponder this: If you are an ID supporter, then you are making exactly the same mistake as Bob does in the four examples above, using the same broken logic. Isn’t that a little embarrassing? It might be time to rethink your position.

  32. Nonlin.org: I hope you will agree with me that a lot of TMZ comments simply show frustration rather than valid arguments.

    And your hope is not in vain. I agree wholeheartedly with this statement.

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

  33. Mung: As far as the Ewert paper is concerned, I have to wonder if keiths has even looked at it. It’s not an anti-evolution paper. It’s not a paper that argues against common descent.

    Not explicitly, but it sure waggles its eyebrows suggestively. “It fits the data better”, wink wink, nudge nudge.

    More importantly, nobody is willing to commit to it. You stick with common descent, EN calls it “a first step” and Bill thinks it is “interesting” (and we all know what THAT means). 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. The only person that can be said to be off the hook is Ewert, but he has his work cut out for him to prove that those “dependencies” are real. Good luck with that.

  34. Corneel,

    then keiths’ criticism still stands as common design proponents leave the door open for any of the thousands of alternative versions of common design.

    To what extent are you supporting keiths argument?

  35. colewd: To what extent are you supporting keiths argument?

    Given the undefined nature and motivations of the Designer, there is no particular reason to expect her to have produced the nested hierarchy. This is a well-known weakness of the common design hypothesis; It is compatible with anything, and therefore it explains nothing. This is old hat, I suppose, and you won’t be surprised that I fully agree with that.

    The Ewert paper actually presents a concrete model of how common design is supposed to have produced the nested hierarchy. It’s sure nice to finally see such a thing, but I haven’t seen anyone embracing it yet. Mostly everybody on the ID side just seems happy that “common design” supposedly beats common descent as an explanation. But it is still one version out of a multitude, and when Ewerts dependency theory at some point gets trashed, as it surely will, it will just be interchanged for the next version.

    colewd: What do you think this means?

    Well, I think it means that you are unsure what to make of it. Am I mistaken? Are you still “open” to common descent, or are you willing to defend the idea that novel gene families require pre-installed dependencies?

  36. Corneel: The Ewert paper actually presents a concrete model of how common design is supposed to have produced the nested hierarchy

    Really? How so? What are the causal links between dependency graphs and anything biological? how do dependency graphs explain anything in biology?

  37. Corneel,

    Given the undefined nature and motivations of the Designer, there is no particular reason to expect her to have produced the nested hierarchy.

    Sure there is. For design efficiency. That is why the Mac family of computers produces a nested hierarchy. Macs have constraints like compatibility and available components.

    Living organisms have constraints like compatible energy sources.

    The Ewert paper actually presents a concrete model of how common design is supposed to have produced the nested hierarchy. It’s sure nice to finally see such a thing, but I haven’t seen anyone embracing it yet.

    It’s complex and new. It will take people time to evaluate it. I agree it is a pretty cool concept whether it has legs or not.

    and when Ewerts dependency theory at some point gets trashed, as it surely will, it will just be interchanged for the next version.

    Bold prediction 🙂

    Well, I think it means that you are unsure what to make of it. Am I mistaken?

    Yes. Not enough time to think through the issue so I would rather not comment whether I think it is real or not.

    Are you still “open” to common descent, or are you willing to defend the idea that novel gene families require pre-installed dependencies?

    I think there is common descent in the history of life the question is how much. Universal common descent is a failed concept in my view as there are several events that are best explained by independent origin such as the eukaryotic cell. I am clearly open to discuss where the lines of demarkation are. I would not bet against a wolf and a dog sharing a common ancestor, however I would bet against a dog and a bird sharing one.

    There is no experimental evidence that I know of that a unique protein can be created by reproduction. Their has been identified paths (Thornton labs) but it is still known if one has actually taken the journey as a freely mutation living organism.

  38. keiths:
    Robert,

    I think the abstractness of the argument is befuddling you, so let me offer some concrete analogies taken from the 2012 thread:

    Yes the friend is right in the first three cases.
    The last case the evo bio guy has it wrong.
    The errtor is as follows.
    The evo biologist did not show how morphological and molecuoar data fit a nested tree to 38 decimals.
    All he shows is data of likeness in biological entities.
    Thats it. So a design model better fits the data. why not?
    THEN you have these graduations/spectrum due to common descent. WELL that just means there is a need to be in this stage of graduations/spectrum. SO the need is supplied by a design that allows mechanisms to react as needed.
    Just like my people colour etc analagy.
    so need to see colours evolving from each other but instead just appearing in areas as needed. Other biological mechanisms however hidden.
    There is another option and a better one.

    Your evo biologist is not doing what the geologist/astronomer are doing.
    He is rejection as a first step the most obvious origin for likeness in biology.
    your evo biologist is far too quick to see eyeball likeness as the only possible from a original pair of eyeballs. When a design of eyeballs from a creator would better fit biology including mechanisms that allow eyeballs to change when needed to change.
    you can’t just say things looking alike is proof they come from a original.
    its not showing imagination open to a creator. Its too simple and exclusive option.

  39. Robert writes, concerning my four examples:

    Yes the friend is right in the first three cases.
    The last case the evo bio guy has it wrong.
    The errtor is as follows.
    The evo biologist did not show how morphological and molecuoar data fit a nested tree to 38 decimals.

    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”:

    So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 10^38 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439). Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree, as shown in Figure 1, to better than 38 decimal places. This phenomenal corroboration of universal common descent is referred to as the “twin nested hierarchy”. This term is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.

    Good luck.

  40. dazz: Really? How so? What are the causal links between dependency graphs and anything biological? how do dependency graphs explain anything in biology?

    Yeah, I know. I am being pretty lenient here. The model has been developed to explain presence/absence patterns in gene families. It is the usual “DNA is computer code” nonsense in which gene families represent modules that are required for compiling a program. If we accept that, say the “giraffe” module requires the “artiodactyl” module as a dependency, etcetera, that will actually work, and we get nested patterns. As to how well it is going to describe actual biological systems, I share your skepticism.

  41. colewd: Sure there is. For design efficiency. That is why the Mac family of computers produces a nested hierarchy. Macs have constraints like compatibility and available components.

    You have never shown that Mac computers can be arranged into a (objective) nested hierarchy, nor demonstrated to us that that would be the most efficient solution, nor given us any reason to accept that living organisms are in any way comparable to computer hardware (available components? WTF?). This is just you typing stuff again, I am afraid.

    colewd: I think there is common descent in the history of life the question is how much. Universal common descent is a failed concept in my view as there are several events that are best explained by independent origin such as the eukaryotic cell. I am clearly open to discuss where the lines of demarkation are. I would not bet against a wolf and a dog sharing a common ancestor, however I would bet against a dog and a bird sharing one.

    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.

    Thanks

  42. 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.

    LoL.

  43. keiths: This term is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.

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

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