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. Nonlin.org
    Ignored
    says:

    …bonus points: who can explain the picture and caption?

  2. keiths keiths
    Ignored
    says:

    Nonlin, to Rumraket:

    Your general frustration has been dully noted.

    “Dully”, indeed. You crack me up, Nonlin.

  3. keiths keiths
    Ignored
    says:

    Nonlin:

    keiths,

    Your empty statement is worthless. Now, do you have anything intelligent to say or not?

    Awww. I just realized that Nonlin is probably feeling left out. I wrote this:

    colewd:

    nested clad

    Whereas Bill, fifth, Mung, and J-Mac fall into a hierarchy of nested clods.

    My apologies for leaving you out, Nonlin. Yes, you too are a nested clod.

  4. Corneel Corneel
    Ignored
    says:

    Nonlin.org: As you might notice, I don’t like to make unsupported claims.

    must … resist … snarky … retort

    Nonlin.org: But once again, you’re trying to put words in people’s mouths. This tactic is a looser.

    I did not say ‘yes’ or ‘no’ to “independently created individual species”.

    Haha, yes silly me. For a moment I fooled myself into thinking that you were making a concrete statement. My bad.

    Nonlin.org: Why don’t you give an example of theme? I am sure you know a lot.
    The variation within themes seems built in by design. I see exactly what you see. The difference is that I would not venture a foolish “just so” story like your buddy Darwin.

    I have to give an example? My, what caution. Are you a bit scared to name one yourself? 😉

    If you will: how about Felidae (cats, panthers, leopards, lynxes, ocelots, servals, you know … cats). Independently created, yes or no?

    The “built in by design” is a bit too generic. I need you to confirm that these “variations” have a genetic basis (that ought to be a no-brainer). I also need you to make a statement on whether you believe these “variations” to be descended from some originally created primordial cat.

    Let me be clear on this: I will not discuss matters with you if you refuse to clearly articulate your own position. Otherwise we’ll just end up again in an endless loop with me trying to guess what you are saying and you accusing me of putting words in your mouth.

  5. keiths keiths
    Ignored
    says:

    Nonlin:

    As you might notice, I don’t like to make unsupported claims.

    Corneel:

    must … resist … snarky … retort

    Resistance is futile. Let it out, Corneel. You’ll feel better, and the rest of us can have a laugh at Nonlin’s expense.

  6. Corneel Corneel
    Ignored
    says:

    keiths: Resistance is futile. Let it out, Corneel. You’ll feel better, and the rest of us can have a laugh at Nonlin’s expense.

    This one was too easy, keiths 😉

  7. keiths keiths
    Ignored
    says:

    Corneel:

    This one was too easy, keiths 😉

    I see your point. You’d like more of a challenge.

    Carry on, then. 🙂

  8. keiths keiths
    Ignored
    says:

    petrushka,

    It’s just a small step on a slippery slope to octonions.

    My mouth watered when I heard about octonions. I’m already a huge fan of mononions and unigarlic.

  9. Corneel Corneel
    Ignored
    says:

    Nonlin.org: …bonus points: who can explain the picture and caption?

    I’ve got it: you are setting up a contest for the most jolly caption, right? Here is mine:

    -Hey Clarence, look down.
    -Why, what’s th- OUCH! DAMN YOU BARNEY!

  10. Rumraket Rumraket
    Ignored
    says:

    Nonlin.org: As you might notice, I don’t like to make unsupported claims.

  11. Mung Mung
    Ignored
    says:

    Corneel: must … resist … snarky … retort

    I think you’ve earned a few. Just call if ‘banter,’ if that helps. 🙂

  12. Mung Mung
    Ignored
    says:

    Corneel: Let me be clear on this: I will not discuss matters with you if you refuse to clearly articulate your own position.

    I appreciate you giving me special treatment.

  13. colewd
    Ignored
    says:

    Nonlin.org,

    …bonus points: who can explain the picture and caption?

    Does it support your claim that the tree of life is a subjective nested hierarchy?

  14. J-Mac
    Ignored
    says:

    keiths: My apologies for leaving you out, Nonlin. Yes, you too are a nested clod.

    keiths spends 16 plus hours per day at TSZ pretending that he knows something and we are all a nested clod to him…

    Speaking about having it all …including a purpose in life…
    keiths is a cream of cream of losers…

  15. Entropy Entropy
    Ignored
    says:

    colewd:
    Does it support your claim that the tree of life is a subjective nested hierarchy?

    Nope. Did you see the OP’s picture? Poor Nonlin thinks that’s a “clever” way to make fun of Darwin’s speculation about whale evolution starting with something that might have looked like a bear.

  16. Entropy Entropy
    Ignored
    says:

    ETA: This is not for Nolin, Nonlin doesn’t have enough intelligence to understand it.

    From the bullshit OP:

    “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution.

    Not Darwinist evolution, but evolution in general. Darwinian (not Darwinist) evolution had limitations because Darwin didn’t have as much information as evolutionary biologists have today, besides being mostly focused on natural selection effects.

    This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates.

    Curious, because I’ve seen evolutionary biologists being very careful about how they try and build their phylogenetic trees. They make test after test after test. Some branches are very difficult to get right, and, even more curious from such “zealots,” they openly declare that there’s difficulties. How come if this is so subjective, that these zealots cannot put a tree together and declare it to be perfect? I suspect that something is not right about the OP’s claims. As if it was written by someone who has no idea about science, in general, and evolution, in particular.

    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);

    Actually no. UCD is not an assumption. It started as a very bold speculation by Darwin, became a working hypothesis, and loads of data started making sense of the hypothesis to the point that we’re very convinced today that UCD might be true.

    b) There is a bifurcating pattern of cladogenesis;

    This was assumed until the data said otherwise. We now understand that there’s hybridization, endosymbiosis, horizontal gene transfer, etc. So, sorry, but those “zealots” seem more and more reasonable, while the OP looks more and more like written by an ignorant fool.

    c) Change in characteristics occurs in lineages over time.

    Not an assumption. This is irremediably true.

    Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism”

    As I said above, the OP was written by some very ignorant person. Evolution is not just Darwinian, and it’s not just natural selection. So, false. This is not an assumption in building phylogenetic trees.

    and not by a process generated by a designer that also happens to make use of biologic reproduction.

    This is so ridiculous I don’t know if it deserves anything else but mockery.

  17. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Entropy: Did you see the OP’s picture? Poor Nonlin thinks that’s a “clever” way to make fun of Darwin’s speculation about whale evolution starting with something that might have looked like a bear.

    It does show two species that have a common ancestor, the common ancestor of all the dogs, bears, and raccoons, which also includes all the Pinnepedia. It’s supposed to make fun of something, but it is mysterious as to what.

  18. Entropy Entropy
    Ignored
    says:

    Joe Felsenstein,

    Well, it backfires and makes fun of Nonlin’s self-inflicted ignorance and misunderstanding.

  19. Entropy Entropy
    Ignored
    says:

    2/7 (if I feel like finishing the series):

    Note: Not for Nonlin, but for those who might want to know.

    From the bullshit of an OP:

    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.

    This one comes from a deep misunderstanding. A misunderstanding that Nonlin would be very close to understanding if she could put two and two together, since she later mentions “curve fitting.” When building a tree, the hypothesis is that there’s common ancestry. If the hypothesis is false, trying to “fit” the data to the model will fail. Thus testing the hypothesis.

    An UCD “mechanism” has never been observed or proved elsewhere and is not “self-evidently true”, therefore not a valid axiom.

    Which is why it’s not an axiom, but something suggested by quite a lot of data.

    Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis.

    It neither an assumption, nor a conclusion from cladistic analyses. It’s a conclusion from lots of data that demonstrate that it is very, but authentically very, unlikely for the shared characteristics of extant life forms to have arisen independently.

  20. Entropy Entropy
    Ignored
    says:

    3/7 (If I feel like finishing this series).

    Again: Not for Nonlin, but for those who might be interested and able to read for comprehension.

    From the bullshit of an OP:

    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.

    Hum … close enough. Little tiny detail, the alternative hypothesis is the one put against the null hypothesis. They’re not synonyms.

    In the “cladistic analysis” case, the alternative hypothesis to UCD is “common design”,

    Oh shit. No. The null hypothesis is that the data fit some random distribution. Probabilities can only be calculated for random distributions.

    and of course UCD cannot be an assumption of such an analysis.

    Which is why it’s not an assumption of such analyses. Common ancestry is a hypothesis for the fucking data! The hypothesis is tested by checking of the data fit a model that assumes common ancestry. The fitting is the test.

    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.

    “Common design” is bullshit for god-did-it. It’s neither an alternative, nor a null hypothesis. It’s mere wishful thinking.

    This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD.

    Which is why UCD does not rest on cladistic analysis. Nonlin is mistaking evidence that there’s evolution with evidence for UCD. Phylogenetic analyses are performed to try and figure the order of separation between lineages, not to establish that they share common ancestry. The analyses happen to also support evolution because the order of lineage separation tends to be very similar when the analyses are performed at different levels: morphological, molecular, biochemical, etc. This point has a caveat, the only one worth checking in this whole bullshit of an OP. But we’ll visit that in the appropriate section (if I get there, since this OP is so obviously, and painfully, ignorant that I’m not sure that anybody is even interested in seeing some answers).

    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.

    If phylogenetic analyses are akin to “curve fitting”, it’s obvious that tests for the likelihood that the data fit the model would show if the model is right or wrong for the data. There’s data that fit a linear model, data that fit a hyperbolic curve, data that fit a power-law curve, etc. Linear data won’t fit very well to a log curve. Etc.

  21. Nonlin.org
    Ignored
    says:

    Corneel: must … resist … snarky … retort

    Haha, yes silly me. For a moment I fooled myself into thinking that you were making a concrete statement. My bad.

    I have to give an example? My, what caution. Are you a bit scared to name one yourself?

    If you will: how about Felidae (cats, panthers, leopards, lynxes, ocelots, servals, you know … cats). Independently created, yes or no?

    The “built in by design” is a bit too generic. I need you to confirm that these “variations” have a genetic basis (that ought to be a no-brainer). I also need you to make a statement on whether you believe these “variations” to be descended from some originally created primordial cat.

    Let me be clear on this: I will not discuss matters with you if you refuse to clearly articulate your own position. Otherwise we’ll just end up again in an endless loop with me trying to guess what you are saying and you accusing me of putting words in your mouth.

    I make and defend a lot of bold claims if you haven’t noticed. You have the list, so feel free to argue specifics. But you don’t want to discuss these claims. You want some foolish claims instead. Not happening.

    See, you know felidae. Now, what does “independently created” mean? I think they are a product of intelligent design if that’s what you mean. Of course this could happen in a thousand different ways and don’t ask for proof as I didn’t do it. One thing is for sure – they are not a product of the magical “natural selection”. Happy?

    Why would variations be genetic only? Do your genes change when you get a sun tan? Ridiculous.

    What “primordial cat” nonsense? Is your car a variation on this year base model or on the original Model T equivalent? Ridiculous question.

    Do you doubt that feral animals revert back to their wild type over time? Go check out the evidence. Same goes for “Darwin’s finches”, peppered moth, antibiotic and insecticide resistant pest out there. They all revert back with zero evidence of “divergence of character”. Are you denying the evidence?

  22. Nonlin.org
    Ignored
    says:

    Corneel: I’ve got it: you are setting up a contest for the most jolly caption, right? Here is mine:

    -Hey Clarence, look down.
    -Why, what’s th- OUCH! DAMN YOU BARNEY!

    How about “Darwinistas make those two ‘cousins’ for no other reason than a commitment to the ‘we’re all family’ nonsense”?

    You disappoint Corneel. Used to be one of the more logical Darwinistas out there.

  23. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: It does show two species that have a common ancestor, the common ancestor of all the dogs, bears, and raccoons, which also includes all the Pinnepedia.It’s supposed to make fun of something, but it is mysterious as to what.

    You get the prize! But where is that mythical “common ancestor”? And more importantly, how can you confirm without presupposing that those two are related?

  24. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Nonlin.org: how can you confirm without presupposing that those two are related?

    We don’t. We don’t assume that those two are more related than anybody else. We infer their relationships with one part of the genome. Then with another, and then with yet another, and so on. And look to see if there is any similarity of the resulting trees.

    And if someone says “well couldn’t that be Common Design” we laugh at them, because that is such a universally nonspecific and flexible hypothesis that it makes no predictions.

  25. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Nonlin.org: But where is that mythical “common ancestor”?

    Oh, so you do take a position, that the common ancestor is “mythical”.

    Perhaps you are of the “why are there still monkeys” persuasion since you seem to expect that. if polar bears and walruses had a common ancestor, it should be walking around, visible in the photo.

  26. Nonlin.org
    Ignored
    says:

    Entropy:
    ETA: This is not for Nolin, Nonlin doesn’t have enough intelligence to understand it.

    From the bullshit OP:
    Not for Entropy or his chimp cousins:

    1. Not Darwinist evolution, but evolution in general. Darwinian (not Darwinist) evolution had limitations because Darwin didn’t have as much information as evolutionary biologists have today, besides being mostly focused on natural selection effects.

    2. Curious, because I’ve seen evolutionary biologists being very careful about how they try and build their phylogenetic trees. They make test after test after test. Some branches are very difficult to get right, and, even more curious from such “zealots,” they openly declare that there’s difficulties. How come if this is so subjective, that these zealots cannot put a tree together and declare it to be perfect? I suspect that something is not right about the OP’s claims. As if it was written by someone who has no idea about science, in general, and evolution, in particular.

    3. Actually no. UCD is not an assumption. It started as a very bold speculation by Darwin, became a working hypothesis, and loads of data started making sense of the hypothesis to the point that we’re very convinced today that UCD might be true.

    4. This was assumed until the data said otherwise. We now understand that there’s hybridization, endosymbiosis, horizontal gene transfer, etc. So, sorry, but those “zealots” seem more and more reasonable, while the OP looks more and more like written by an ignorant fool.

    5. Not an assumption. This is irremediably true.

    This is not for Entropy or his chimp cousins:

    1. Who cares? Darwinist it is.
    2. They do their “best” to fudge the tree to match the UCD assumption. If Darwin fails they’re out of a job and out of luck.
    3. http://www.ucmp.berkeley.edu/clad/clad1.html
    4. Not my assumption. Same link as 3.
    5. Not my assumption. Same link as 3. Where’s the proof?

  27. Nonlin.org
    Ignored
    says:

    Entropy:
    2/7 (if I feel like finishing the series):

    Note: Not for Nonlin, but for those who might want to know.

    From the bullshit of an OP:

    1. This one comes from a deep misunderstanding. A misunderstanding that Nonlin would be very close to understanding if she could put two and two together, since she later mentions “curve fitting.” When building a tree, the hypothesis is that there’s common ancestry. If the hypothesis is false, trying to “fit” the data to the model will fail. Thus testing the hypothesis.

    2. Which is why it’s not an axiom, but something suggested by quite a lot of data.

    3. It neither an assumption, nor a conclusion from cladistic analyses. It’s a conclusion from lots of data that demonstrate that it is very, but authentically very, unlikely for the shared characteristics of extant life forms to have arisen independently.

    1. Assumption is different than hypothesis. Logically, UCD must not be both assumption and hypothesis. Note: logic is not a Darwinist strength
    2. “…assumptions have to be tested independently through an entirely separated method or be accepted as axioms.” UCD is not. “Suggested by quite a lot of data” is not proof, hence UCD is an untested assumption (= invalid axiom).
    3. It is an assumption: http://www.ucmp.berkeley.edu/clad/clad1.html also passed as conclusion: http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy …and the only reason we’re discussing cladistics here.

  28. Nonlin.org
    Ignored
    says:

    Entropy:
    3/7 (If I feel like finishing this series).

    Again: Not for Nonlin, but for those who might be interested and able to read for comprehension.

    From the bullshit of an OP:

    1. Hum … close enough. Little tiny detail, the alternative hypothesis is the one put against the null hypothesis. They’re not synonyms.

    2. Oh shit. No. The null hypothesis is that the data fit some random distribution. Probabilities can only be calculated for random distributions.

    3. Which is why it’s not an assumption of such analyses. Common ancestry is a hypothesis for the fucking data! The hypothesis is tested by checking of the data fit a model that assumes common ancestry. The fitting is the test.

    4. “Common design” is bullshit for god-did-it. It’s neither an alternative, nor a null hypothesis. It’s mere wishful thinking.

    5. Which is why UCD does not rest on cladistic analysis. Nonlin is mistaking evidence that there’s evolution with evidence for UCD. Phylogenetic analyses are performed to try and figure the order of separation between lineages, not to establish that they share common ancestry. The analyses happen to also support evolution because the order of lineage separation tends to be very similar when the analyses are performed at different levels: morphological, molecular, biochemical, etc. This point has a caveat, the only one worth checking in this whole bullshit of an OP. But we’ll visit that in the appropriate section (if I get there, since this OP is so obviously, and painfully, ignorant that I’m not sure that anybody is even interested in seeing some answers).

    6. If phylogenetic analyses are akin to “curve fitting”, it’s obvious that tests for the likelihood that the data fit the model would show if the model is right or wrong for the data. There’s data that fit a linear model, data that fit a hyperbolic curve, data that fit a power-law curve, etc. Linear data won’t fit very well to a log curve. Etc.

    1. There can be more than one hypothesis: https://www.stattrek.com/hypothesis-test/hypothesis-testing.aspx
    2. Not necessarily – see link at 1 above. Cladistics is not even hypothesis testing, it’s curve fitting, so statistics do not apply.
    3. Already shown to be both assumption and conclusion. Curve fitting will fit by definition. This is a retard combination: “Which is why it’s not an assumption” AND “a model that assumes common ancestry”
    4. Try this: “UCD is bullshit for Darwinism. It’s neither an alternative, nor a null hypothesis. It’s mere wishful thinking”.
    5. Already shown to be “an assumption: http://www.ucmp.berkeley.edu/clad/clad1.html also passed as conclusion: http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy”
    6. Not “akin”. It’s BS of the highest order: “if UCD were true, how would the tree look like? Hey look, this tree fits ‘UCD true’. Therefore UCD must be true”. It’s a tree – what BS hyperbolic curve, etc?

  29. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: We don’t.We don’t assume that those two are more related than anybody else.We infer their relationships with one part of the genome.Then with another, and then with yet another, and so on.And look to see if there is any similarity of the resulting trees.

    And if someone says “well couldn’t that be Common Design” we laugh at them, because that is such a universally nonspecific and flexible hypothesis that it makes no predictions.

    I should have said “how can you confirm without presupposing UCD”? Yes, you “infer their relationships” by presupposing UCD. Of course someone has to be someone else’s cousin.

    Why it’s so hard for you to see you can’t use UCD both as assumption and as conclusion?

    UCD makes no more predictions than Common Design. In addition, “design without a designer” is simply illogical.

  30. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: Oh, so you do take a position, that the common ancestor is “mythical”.

    Perhaps you are of the “why are there still monkeys” persuasion since you seem to expect that. if polar bears and walruses had a common ancestor, it should be walking around, visible in the photo.

    I am asking and you’re deflecting rather than answering. Nice try, but won’t fly.

  31. colewd
    Ignored
    says:

    Nonlin.org,

    What assumptions do cladists make?

    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 first assumption is a general assumption made for all evolutionary biology. It essentially means that life arose on earth only once, and therefore all organisms are related in some way or other. Because of this, we can take any collection of organisms and determine a meaningful pattern of relationships, provided we have the right kind of information. Again, the assumption states that all the diversity of life on earth has been produced through the reproduction of existing organisms.

    They are assuming the conclusion of universal common descent and validating it through what?

    So the eukaryotic cell is assumed to have evolved from prokaryotic cells?

    Multicellular organisms are assumed to have evolved from single celled organisms?

    All assumed true based on?

  32. DNA_Jock
    Ignored
    says:

    Nonlin.org: Cladistics is not even hypothesis testing, it’s curve fitting, so statistics do not apply.

    I claim this one as my sig line.
    Can’t wait to tell my daughter, the statistician.
    😀

  33. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    That must mean that when you’re actually doing curve-fitting, statistics don’t apply there either!

    So statistics doesn’t apply when you’re reconstructing evolutionary trees? Darn, now I’ll have to look up the two or three people who I’ve tried to tell to use statistics on that, and take back what I said.

  34. Corneel Corneel
    Ignored
    says:

    Nonlin.org: See, you know felidae. Now, what does “independently created” mean? I think they are a product of intelligent design if that’s what you mean. Of course this could happen in a thousand different ways and don’t ask for proof as I didn’t do it. One thing is for sure – they are not a product of the magical “natural selection”. Happy?

    Thanks. No, I am not happy yet. Please pay attention: Do you believe all felids to be related to each other, but not to any other organism?

    Nonlin.org: Why would variations be genetic only? Do your genes change when you get a sun tan? Ridiculous.

    When I walk in the sun, I tan. But when I release a tiger into the savannah, it does not turn into a lion. The variations of which you speak among felids breed true. Is this not obviously true?

    Nonlin.org: What “primordial cat” nonsense? Is your car a variation on this year base model or on the original Model T equivalent? Ridiculous question.

    To point out something which should be blatantly obvious: cats are not built in factories. They come from the womb of other cats. The “primordial cat” is the beastie that did not originate that way, but was built by the Designer and from which all other cats came forth. Did this animal exist?

    Nonlin.org: Do you doubt that feral animals revert back to their wild type over time? Go check out the evidence. Same goes for “Darwin’s finches”, peppered moth, antibiotic and insecticide resistant pest out there. They all revert back with zero evidence of “divergence of character”. Are you denying the evidence?

    It is rather amusing, but also a little bewildering that you do not understand the question I am trying to get you to answer. Organisms are brought forth by other organisms. I think that traces back to a single origin, you claim that that traces back to multiple origins. I need to know whether you believe all felids to trace back to a single originally created cat.

  35. Corneel Corneel
    Ignored
    says:

    Nonlin.org: You disappoint Corneel. Used to be one of the more logical Darwinistas out there.

    I’ll let Ellen Ripley answer this one:

  36. Corneel Corneel
    Ignored
    says:

    colewd: They are assuming the conclusion of universal common descent and validating it through what?

    So the eukaryotic cell is assumed to have evolved from prokaryotic cells?

    Multicellular organisms are assumed to have evolved from single celled organisms?

    All assumed true based on?

    I assume that this information can be easily found on the internet, or in books.

    I assume that most of the arguments have been explained to you before … multiple times … even on this very site.

    I also assume that you did not just selectively forget all this, knowing how open you are to arguments from both sides.

  37. Entropy Entropy
    Ignored
    says:

    4/7 (if I decide to go for the whole thing)

    Again, not for Nonlin, who is already showing either unwillingness, or incapacity, to even try and understand what I wrote.

    This one is a beautiful admission of defeat:

    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.

    1. “no designer” does not mean “Darwinist evolution.” As I already said, it’s evolution in general. There’s more to evolution than natural selection.

    2. Of course a magical being in the sky would be able to do things any way she wanted. After all, it’s a supermagical being in the sky. Thus, as others have said, the idea of a magical beings in the sky doesn’t help us understand anything about nature. Doesn’t make any predictions. From where I sit, since life looks evolved, since all the evidence shows signs of unplanned noise, of natural phenomena going one way then another, of “parts” that grow and shorten and stumble, and so on, all as if natural phenomena is all there is, then who cares if a magical being in the sky could do things any way she wanted? Until there’s evidence for the magical being in the sky, evolution works. No reason to go for something as ridiculous as god-did-it.

    3. It’s obvious from this piece of crap, that Nonlin thinks that there’s a need to “disprove” her magical being in the sky. One more sign of Nonlin’s mental problems. Sorry, but the existence of a magical being in the sky requires evidence.

    4. This claims works backwards to its intended effect. Since designers could do things any way they wanted, then we should see signs of magical beings in the sky doing things any way they wanted. Instead we see indifferent natural phenomena. Nonlin’s magical being in the sky has become indistinguishable from no magical being in the sky at all. Nonlin has thus admitted defeat.

  38. Nonlin.org
    Ignored
    says:

    Entropy is hereby forbidden to read this message:

    I rewrote these passages for better clarity:
    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, but UCD “mechanism” has neither been observed or proved elsewhere nor is it a valid axiom (“self-evidently true”). 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. Cladistic analysis is not really hypothesis testing since statistics are not essential to the methodology, but if it were it would need to compare against the alternative hypothesis to UCD which 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. Instead of hypothesis testing, “cladistic analysis” is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points.

    See? Entropy is not a totally useless dummy – don’t let them knock you down.

  39. Nonlin.org
    Ignored
    says:

    Entropy:
    4/7 (if I decide to go for the whole thing)

    Again, not for Nonlin, who is already showing either unwillingness, or incapacity, to even try and understand what I wrote.

    This one is a beautiful admission of defeat:

    1. “no designer” does not mean “Darwinist evolution.” As I already said, it’s evolution in general. There’s more to evolution than natural selection.

    2. Of course a magical being in the sky would be able to do things any way she wanted. After all, it’s a supermagical being in the sky. Thus, as others have said, the idea of a magical beings in the sky doesn’t help us understand anything about nature. Doesn’t make any predictions. From where I sit, since life looks evolved, since all the evidence shows signs of unplanned noise, of natural phenomena going one way then another, of “parts” that grow and shorten and stumble, and so on, all as if natural phenomena is all there is, then who cares if a magical being in the sky could do things any way she wanted? Until there’s evidence for the magical being in the sky, evolution works. No reason to go for something as ridiculous as god-did-it.

    3. It’s obvious from this piece of crap, that Nonlin thinks that there’s a need to “disprove” her magical being in the sky. One more sign of Nonlin’s mental problems. Sorry, but the existence of a magical being in the sky requires evidence.

    4. This claims works backwards to its intended effect. Since designers could do things any way they wanted, then we should see signs of magical beings in the sky doing things any way they wanted. Instead we see indifferent natural phenomena. Nonlin’s magical being in the sky has become indistinguishable from no magical being in the sky at all. Nonlin has thus admitted defeat.

    1. First establish that there is such thing as “natural selection. But there isn’t”: http://nonlin.org/natural-selection/. Of course there’s more Darwinist magic when the old one fails.
    2. And what predictions does “[more than] Darwinist evolution” make? None. And Darwinist “just so” stories “do not help us understand anything about nature”. And that’s the thing: evolution DOESN’T work.
    3. Incoherent rant
    4. You do see magic all around you! The miracle of life hits you in the face all the time.

  40. Nonlin.org
    Ignored
    says:

    Joe Felsenstein,

    DNA_Jock: I claim this one as my sig line.
    Can’t wait to tell my daughter, the statistician.

    Make sure to include these links:
    http://www.ucmp.berkeley.edu/clad/clad1.html assumptions
    http://www.ucmp.berkeley.edu/clad/clad2.html method

  41. Rumraket Rumraket
    Ignored
    says:

    This guy is like Bill Cole in the sense that he just says stuff and uses Big Words^{(TM)} he’s heard that sound technical and fancy without halfway understanding what they mean. Except that he’s also extremely arrogant too. Complete waste of time. You don’t even get the opportunity to explain where anything derails wrong because the train is not even on the track and it never was. It hasn’t been built yet. Or even invented.

  42. colewd
    Ignored
    says:

    Corneel,

    I also assume that you did not just selectively forget all this, knowing how open you are to arguments from both sides.

    Where would the theory of general relativity be if there was no model and experiment of mass-energy curving space-time.

    The explanation starts out with we assume mass-energy curves space-time. Assume based on what. The GR tensor equation validated by the eclipse experiment. ok.

    Again I ask: universal common descent is assumed based on what?

  43. colewd
    Ignored
    says:

    Rumraket,

    This guy is like Bill Cole in the sense that he just says stuff and uses Big Words^{(TM)} he’s heard that sound technical and fancy without halfway understanding what they mean. Except that he’s also extremely arrogant too. Complete waste of time. You don’t even get the opportunity to explain where anything derails wrong because the train is not even on the track and it never was. It hasn’t been built yet. Or even invented.

    Or your theory is based on an unsupported assumption.

  44. Nonlin.org
    Ignored
    says:

    Corneel: Thanks. No, I am not happy yet. Please pay attention:
    1. Do you believe all felids to be related to each other, but not to any other organism?

    2. When I walk in the sun, I tan. But when I release a tiger into the savannah, it does not turn into a lion. The variations of which you speak among felids breed true. Is this not obviously true?

    3. To point out something which should be blatantly obvious: cats are not built in factories. They come from the womb of other cats. The “primordial cat” is the beastie that did not originate that way, but was built by the Designer and from which all other cats came forth. Did this animal exist?

    4. It is rather amusing, but also a little bewildering that you do not understand the question I am trying to get you to answer. Organisms are brought forth by other organisms. I think that traces back to a single origin, you claim that that traces back to multiple origins. I need to know whether you believe all felids to trace back to a single originally created cat.

    1. Is your car related to all others but not to the bycicle?
    2. Variations do not have to be confined to DNA. Prove it if you believe they must.
    3. I see stasis everywhere – cats are cats and always have been. Same goes for “living fossils” croc, human, mosquito, etc. Can you POSITIVELY link some fossil that looks like a cat to your current pet? No! You’re only presupposing that link.
    4. I say PROVE: “traces back to a single origin”. I say cladistics cannot be that proof.

  45. Nonlin.org
    Ignored
    says:

    Corneel: Used to be one of the more logical Darwinistas out there.

    So you don’t like logic no more? Sad!

  46. DNA_Jock
    Ignored
    says:

    Nonlin.org,

    I was disparaging your claims that neither cladistics, nor curve-fitting, involve statistics. That’s funny.
    Your links to Berkeley Paleontology do not support your contention.

    Also, your claim #4 really is a complete admission of defeat. It is ‘telling’ that you cannot understand this.

  47. keiths keiths
    Ignored
    says:

    colewd:

    Again I ask: universal common descent is assumed based on what?

    The acceptance of common descent among biologists is a conclusion, not an assumption.

    Here’s where doofuses like you and Nonlin go off the rails: you think that if scientists assume something arguendo in order to test it, that their thinking must be fallacious.

    It’s exactly the opposite. To properly test a hypothesis, you need to know its entailments. To determine its entailments, you need to assume temporarily and for the sake of argument that it’s true. Once you have determined the entailments, you can test them against observation. In other words, once you know its entailments, you drop the temporary assumption that the hypothesis is true. Thus no fallacy.

    Having dropped the assumption of correctness, you look to see whether your hypothesis is supported by the evidence and fits it better than the alternatives. If so, you accept it (provisionally, as with all scientific positions).

    It’s therefore a conclusion, not an assumption.

    Anyone who understands science knows this. You and Nonlin don’t understand science (to say the least), so you are baffled by it.

  48. Entropy Entropy
    Ignored
    says:

    colewd: Again I ask: universal common descent is assumed based on what?

    I explained this above Bill. Please try and keep up. Don’t assume that because Nonlin pretends to have knowledge, and writes pretentiously, she actually has knowledge. With Nonlin you have to assume that she lacks the most basic understanding and doubt anything she says.

    In summary: UCD is not assumed. It’s inferred from several lines of data, meaning features shared by life forms that are similar enough that it’s pretty unlikely that they arose independently. None of the data is the phylogenetic trees. Again, as I explained before, phylogenetic trees attempt to figure out the order of lineage separation, not to establish that there’s common ancestry.

    The only reason trees also work as further evidence is because different lines of analysis, molecular, biochemical, morphological, biogeographical, etc, give very similar lineage separation histories. As Joe F said, it’s also because different parts of the genome, for example, also give similar trees. It goes further, since even viral insertions, transposon insertions, etc, all of which are independent of phenotype, also give similar trees. That consistency reinforces the notion of evolution and common ancestry between the organisms analyses, but we don’t start with the mere assumption. We start with inference of common ancestry based on the likelihood of similar features arising independently.

    ETA: Remember that Nonlin thinks that curve fitting has nothing to do with statistics. That alone should warn you against taking her seriously.

  49. Entropy Entropy
    Ignored
    says:

    DNA_Jock: I was disparaging your claims that neither cladistics, nor curve-fitting, involve statistics. That’s funny.

    I bet that you’ll repeat that a hundred times, and Nonlin will still miss it.

    In the meantime, I will contact all my prior professors to tell them to drop curve fitting from their statistics courses because I found a very wise guy on the webs, Nonlin, who says that curve fitting has nothing to do with statistics. My professors degrees in statistics mean nothing compared to Nonlin’s wisdom. Whenever they say things like “goodness-of-fit,” I’ll yell “curve fitting has nothing to do with statistics you idiot!”

  50. colewd
    Ignored
    says:

    Entropy,

    We start with inference of common ancestry based on the likelihood of similar features arising independently.

    So the null hypothesis is features rising independently how?

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