Saturday, July 14, 2012

Professor Confirms Evolutionary Equivocations

If anyone doubted that evolutionists equivocate, or that such equivocation is prevalent, they need doubt no more. I recently pointed out several examples of evolutionists equivocating on evolution. When they proclaim that evolution is an obvious fact, they are referring to the origin of species by random mutation, genetic drift, natural selection and a host of other explanatory mechanisms evolutionists employ when needed. This claim goes against the scientific evidence. Evolution may or may not have occurred. That is an ontological claim that can be argued. But there is absolutely no question the origin of species by evolution is not a fact. That is an epistemological claim which is undeniably false. The claim that evolution is a fact refers to our knowledge. It refers to the facts and theories of science. We may not know what happened in the distant past, but we do know exactly what is our current knowledge of what happened in the distant past. That knowledge indicates there are substantial problems with evolution. It is not something that likely happened, according to our current knowledge. It certainly is not a fact.

And so to justify and defend their false claim, evolutionists change the meaning of the word. To prove that evolution is a fact and indeed occurs, they switch from one end of the spectrum to the other. Evolution goes from the origin of the species to the incredibly trivial changing of gene allele frequencies or virus mutation.

I pointed out one example in the book Arguing for Evolution: An Encyclopedia for Understanding Science, where the evolutionists triumphantly asserted that the evolution of the species is a fact and then used an example of an allele frequency changing from 40% to 36% in a population of rock pocket mice.

Is this and other examples that I pointed out exceptions to the rule? Are these simply uninformed evolutionists making a blunder? Unfortunately such arguments are common in both the classroom and the literature.

If these were exceptions, then we might expect other evolutionists to reject such equivocations. Instead they supported and reaffirmed the equivocations. One evolutionist suggested that the book Arguing for Evolution: An Encyclopedia for Understanding Science, was merely referring to allele frequency change when it claimed that evolution is a fact. She commented: “I'd point out that evolution by Moore and Cotner's definition is also a fact by Gould's definition.”

The book had approvingly quoted Stephen Jay Gould who argued that while we may not know how evolution occurred, we do know that it occurred, based on the usual non scientific, metaphysical, arguments. In that context the book claimed that evolution is a fact. And throughout the book evolution was portrayed, not surprisingly, as the idea of the origin of species by random mutations, natural selection, and so forth.

A professor also defended the equivocation with yet more equivocation. He commented:

The mice example is mundane, but that's the nature of great scientific theories: they describe both the mundane and the profound. Theory of gravity applies equally well to a falling apple and the Moon in its orbit. The Earth keeps the Moon in a nearly circular orbit but barely deflects a comet's path. Both are still manifestations of gravity. So it is with evolution. It views small changes in populations through the same prism as the appearance of new species.

With gravity, one can adequately explain both a falling apple and the Moon in its orbit with the same simple law. The professor draws a false parallel with evolution: “So it is with evolution.”

No, it is not that way with evolution. Changing allele frequencies are not sufficient to explain the origin of species. Not even close. In fact evolutionists do not have a scientific explanation for the large-scale change their idea requires.

It is yet more equivocation, piled on top of the previous equivocation. These types of apologetic arguments are at the foundation of evolution. For if evolution were portrayed according to the science, it would lose all support.

205 comments:

  1. Hunter: No, it is not that way with evolution. Changing allele frequencies are not sufficient to explain the origin of species. Not even close. In fact evolutionists do not have a scientific explanation for the large-scale change their idea requires.

    That's silly, Cornelius. Here is a parallel from mechanics so that you could see why.

    Just observing the motion of a falling apple does not explain the circular orbit of the Moon. You need the whole theory: Newton's laws of motion and the law of gravitation.

    So it is with evolution. Observing changes in allele frequencies does not in itself explain speciation. You need to apply the actual theory, not its consequences.

    Silly category error.

    And I wonder along with Liz: what's with the professors shtick?

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    Replies
    1. oleg:

      That's silly, Cornelius. Here is a parallel from mechanics so that you could see why. Just observing the motion of a falling apple does not explain the circular orbit of the Moon. You need the whole theory: Newton's laws of motion and the law of gravitation. So it is with evolution. Observing changes in allele frequencies does not in itself explain speciation. You need to apply the actual theory, not its consequences.

      Silly category error.


      Thud. You didn't get much of a bounce on that one. Silly yes, category error no. Of course I did not mean you can't have theory along with your changing alleles. Your point is tendentious. It is beyond silly to equate the falling apple and the Moon with allele frequencies and the origin of species. You can have all the modern genetics theory, etc, that you want.

      Allele frequency changes and the origin of species do not come out of the same wash. That is the point you are laboring to avoid. You can have all the allele frequency changes you care to hypothesize and causes thereof, all the genetics theory available, etc., it's not going to get you nature's millions of species.

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    2. What??? There are separate theories describing a change in allele frequencies and speciation? That's a new word in evolutionary biology.

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    3. oleg:

      There is some tidy theory, as you pointed out, that explains both the apple falling and the Moon's orbit about the Earth.

      That is not true for allele frequencies and the origin of species. So while there is some theory to explain allele frequency changes (though probably more complicated than evolutionists thought), that same theory doesn't give you the origin of species.

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    4. oleg:

      Of course it does.

      No, that involves mutations, not mere allele frequency changes. Furthermore, even given the mutations, there's no scientific evidence that such speciation produces the massive changes evolution requires.

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    5. If evolution requires mutations, then that settles it. I mean, what evidence is there that mutations even occur?

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    6. Hunter: No, that involves mutations, not mere allele frequency changes.

      I addressed that in the very first comment on this thread. Can't you read, Cornelius?

      Hunter:Furthermore, even given the mutations, there's no scientific evidence that such speciation produces the massive changes evolution requires.

      Speciation does not require "massive changes." It requires two populations that diverge and lose the ability to interbreed. That's a gradual process, not some quantum leap.

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    7. CH: it's not going to get you nature's millions of species.

      If it's time for speciation you are concerned about, then don't forget that speciation is exponential. 30 rounds of dichotomous branching get you 1 billion species. We're working with a time scale for animals that is hundreds of million years long.

      If it's the quantity of genetic change you are concerned about, you are forgetting about the ubiquity and persistence of mutation and drift and that mutations involve larger changes like gene duplication, not just point mutations.

      If it's the quantity of morphologic change you are concerned about, you should read up about evo devo and the regulatory genome.

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    8. Cornelius: what do you understand by the word "speciation"?

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    9. I would venture a guess: crossing the baramin level. Amiright, Cornelius? :)

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    10. anaxyrus:

      If evolution requires mutations, then that settles it. I mean, what evidence is there that mutations even occur?

      It is not a matter of whether mutations occur, it is a matter of what we know about them. Let's try to stick to science here.

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    11. oleg:

      Speciation does not require "massive changes." It requires two populations that diverge and lose the ability to interbreed. That's a gradual process, not some quantum leap.

      But evolution does require such "massive changes." You are continuing with the same equivocation.

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    12. anaxyrus:

      If it's time for speciation you are concerned about, then don't forget that speciation is exponential. 30 rounds of dichotomous branching get you 1 billion species. We're working with a time scale for animals that is hundreds of million years long.

      If it's the quantity of genetic change you are concerned about, you are forgetting about the ubiquity and persistence of mutation and drift and that mutations involve larger changes like gene duplication, not just point mutations.

      If it's the quantity of morphologic change you are concerned about, you should read up about evo devo and the regulatory genome.


      The concern is equivocation. When you say (a) evolution, understood as the origin of all the species by mutation, selection, etc, is a fact, and (b) evolution is merely the changing of allele frequencies, then you are equivocating.

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    13. Cornelius,

      You're playing some interesting games.

      You first wrote: there's no scientific evidence that such speciation produces the massive changes evolution requires.

      I was quite puzzled by this statement and pointed out that speciation, as it is understood in theory of evolution, does not require "massive changes."

      Liz was also surprised, so she asked: Cornelius: what do you understand by the word "speciation"?

      It's obvious to anyone familiar with the standard concept of species that speciation is a rather unremarkable event. Two populations diverge and don't interbreed. Their genotypes and phenotypes become different as time goes one.

      You did not acknowledge that you were wrong about this fairly simple point and moved the goal posts: But evolution does require such "massive changes." You are continuing with the same equivocation.

      I did not equivocate—I used the standard concept of speciation. You did. You have never explained what you meant by speciation in this comment. Quite clearly not what it means in the evolutionary literature.

      So who's equivocating? Pot, meet kettle.

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    15. oleg:

      You're playing some interesting games.

      You first wrote: there's no scientific evidence that such speciation produces the massive changes evolution requires.

      I was quite puzzled by this statement and pointed out that speciation, as it is understood in theory of evolution, does not require "massive changes."


      Games? This discussion, with several evolutionists chiming in, is a good example of evolutionary thought in action. I point out a common equivocation by evolutionists, and the evolutionists not only remain in denial, but they rush to defend it with yet more irrationality. It is a consilience.

      In this interchange, I get accused of playing “games” by the evolutionist who is too deep into the equivocation to see it. I think we’ve reached that point in the discussion where the evolutionist’s irrationality reaches full bloom and meaningful discussion becomes impossible.

      Evolutionists literally see no difference between (a) allele frequency changes or viruses mutating, or moths changing colors, or populations becoming reproductively isolated and (b) the entire biological world spontaneously arising. So they are completely oblivious to their equivocating between the two.

      There’s no scientific evidence that allopatric speciation, to use the evolutionist’s example from above, produces the massive changes evolution requires. But that’s irrelevant to evolutionists, and pointing it out is puzzling to them, because after all, such speciation equates with all of evolution.

      Hence, evolutionists such as Moore and Cotner are certainly not equivocating when they say :

      These theories, in the words of the late Stephen Jay Gould, have been “confirmed to such a degree that it would be perverse to withhold provisional assent.” Evolution is one such theory. … Most simply, evolution is any change in a population’s genetic composition over time. … Evolution has occurred when any genetic change—even something that seems insignificant—happens to any number of individuals in a population. … consider a population of rock pocket mice living on the lava outcrop in the southwestern United States. At an initial observation, 40% of the mice possessed an allele (or genetic variant) that produces lightly colored fur when inherited from each parent. A few generations later, only 34% of the mice possessed this allele. This change in the genetic composition of the population means that evolution has occurred. For evolutionary biologists, the fact that evolution has occurred is often not as exciting as …

      It is an incredibly blatant equivocation, but when you point out this sort of equivocation, as we have many times, evolutionists will have none of it, and accuse the messenger of equivocating, games, etc.

      This is what happens when religion infects science. It is amazing how otherwise intelligent people have dug themselves into this bizarre rut.

      Continued …

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    16. oleg:

      It's obvious to anyone familiar with the standard concept of species that speciation is a rather unremarkable event. Two populations diverge and don't interbreed. Their genotypes and phenotypes become different as time goes one.

      You did not acknowledge that you were wrong about this fairly simple point and moved the goal posts: But evolution does require such "massive changes." You are continuing with the same equivocation. I did not equivocate—I used the standard concept of speciation. You did. You have never explained what you meant by speciation in this comment. Quite clearly not what it means in the evolutionary literature.


      Now you are even more confused. Remember, you guys are the evolutionists and we’re the skeptics. You have the ax to grind (evolution must be a fact), will twist science in whatever way you need to twist it, and must deny the mistakes you regularly have to make.

      We, on the other hand, just follow the science because our religion doesn’t mandate evolution being true or not. Therefore we're able to see that all of biology arising spontaneously is not a real good theory. So we only make mistakes at the regular rate, and readily admit to them.

      In this case, I’d be happy to clear up the mistake you are accusing me of. There’s just one problem, I didn’t say what you’re accusing me of. Hence I never “moved the goal posts” and I wasn’t “continuing with the same equivocation.”

      You're so confused by your own equivocations that anyone who says evolution requires massive change must be equivocating because, after all, you equivocate between allele frequency changes or populations going into reproductive isolation and all of evolution.

      Remember, evolutionists equivocate, not the skeptics.

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    17. That rant was long and content-free, Cornelius. Would you care to explain what you mean by speciation? That question was raised several times but you have refused to answer.

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    18. oleg:

      That rant was long and content-free, Cornelius. Would you care to explain what you mean by speciation? That question was raised several times but you have refused to answer.

      Refused to answer? I didn’t even bring it up. You evolutionists are the ones dwelling on speciation, remember?

      Delete
    19. Liz and others,

      I think I have figured this one out. Cornelius isn't really having a dialogue with the other side (i.e., us). His writing is directed at an invisible audience, most likely his Biola class. If you read his replies with that in mind it will all make perfect sense.

      Look at this:

      In this interchange, I get accused of playing “games” by the evolutionist who is too deep into the equivocation to see it. I think we’ve reached that point in the discussion where the evolutionist’s irrationality reaches full bloom and meaningful discussion becomes impossible.

      He is standing in front of a class commenting on the ongoing discussion. He goes on:

      Evolutionists literally see no difference between (a) allele frequency changes or viruses mutating, or moths changing colors, or populations becoming reproductively isolated and (b) the entire biological world spontaneously arising. So they are completely oblivious to their equivocating between the two.

      The poor evolutionists, thinking that this gibberish is directed at them, shake their heads at this silly description and wonder how Cornelius—a Ph.D. in biophysics from Urbana—can make such dumb pronouncements after being corrected so many times. They have no idea that the words are not directed at them. It's just another day at Biola. Nothing to see here. Move along.

      Cornelius concludes:

      Remember, evolutionists equivocate, not the skeptics.

      If you thought this was directed at you, it of course makes no sense. But it isn't. There is a class of future pastors and their wives, and they are the audience to whom all of this sheer nonsense is directed.

      We've been had.

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    20. Hunter: Refused to answer? I didn’t even bring it up. You evolutionists are the ones dwelling on speciation, remember?

      Oh, really? Let's see who brought it up first. Who wrote this?

      No, it is not that way with evolution. Changing allele frequencies are not sufficient to explain the origin of species. Not even close. In fact evolutionists do not have a scientific explanation for the large-scale change their idea requires.

      Hint: it's in the opening post of this thread.

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    21. oleg

      We've been had.


      No, not really. It's never been a secret that this blog is just fact free Creationist propaganda. That's what the DI pays Cornelius for, for Pete's sake.

      All we can do is point out his egregious misrepresentations and equivocations, and hope that some lurkers will have their eyes opened.

      Delete
    22. I don't think it's DI. It's Biola. Although, come to think of it, there is considerable overlap between Discovery Fellows and Biola adjuncts.

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    23. oleg

      I don't think it's DI. It's Biola. Although, come to think of it, there is considerable overlap between Discovery Fellows and Biola adjuncts.


      On second thought, you may be right.

      I wonder if all the mouthy Young Turks who've been posting here recently are Biola students of his?

      Delete
    24. You could be right, Oleg. That might explain why he keeps calling us "professors".

      And certainly why he never actually answers any of the questions addressed to him.

      I have now several times presented him with several concepts related to evolutionary theory, some of which are sometimes referred to as "evolution", and some of which are widely regarded as "facts" and asked him which of those he thinks is not a fact.

      He won't answer. Just keeps saying that "evolutionists" claim that "evolution is a fact" - i.e. equivocating with the word "evolution" - and then claiming that the equivocation is on the part of the "evolutionists"!

      I'm just not sure how much is genuine dishonesty, how much culpable ignorance (because if ignorance, it is definitely culpable, given his training) and how much self-deception.

      But Cornelius, if it is none of these things - please demonstrate that it is not by actually answering the very clear questions that have been put to you.

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    25. CH: But evolution does require such "massive changes." You are continuing with the same equivocation.

      No, Cornelius, you are. By what definition of "evolution", does "evolution" require "massive changes"?

      Universal common descent assumes "massive changes", certainly, over very long periods of time. But it does not assume a greater rate of change than is actually observed in real time, in living populations.

      And speciation does not require "massive changes" at all. Non-interbreeding populations of near-identical organisms, i.e. two species, are regularly found, as well as ring species, in which the differences are so slight that neighbouring populations can and do interbreed, but individuals from populations at the extremes and do not, even if they are introduced.

      You are therefore equivocating between "evolution" (defined as changes in a population over time), universal common descent (which you also call "evolution") and speciation (which you also call "evolution).

      Then there is also adaptation, which was Darwin's actual contribution, which is also sometimes called "evolution" (and which you often refer to as "random mutations" which it is not), and is the idea that if individuals inherit parental traits with variance, those traits that tend to contribute to reproductive success will become more prevalent in the population.

      All these ideas are different. We do not equivocate with them. You do.

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    26. CHGames? This discussion, with several evolutionists chiming in, is a good example of evolutionary thought in action. I point out a common equivocation by evolutionists, and the evolutionists not only remain in denial,

      We deny it because it is untrue.

      but they rush to defend it with yet more irrationality.

      Nobody has defended "equivocation". What we have pointed out is that the only person equivocating with different meanings of the word "evolution" is you. You apply it to:

      Universal Common Descent

      Changes in Allele Frequency over time
      Speciation

      Changes in in the phenotypic characteristics of populations over time

      The claim that there was no Intelligent Designer

      OOL

      Methodological naturalism.

      Neuroscience.

      Science.

      We don't.

      In this interchange, I get accused of playing “games” by the evolutionist who is too deep into the equivocation to see it.

      Look in the mirror, Cornelius.

      I think we’ve reached that point in the discussion where the evolutionist’s irrationality reaches full bloom and meaningful discussion becomes impossible.

      Consider at least the possibility that the problem lies with you.

      Evolutionists literally see no difference between (a) allele frequency changes or viruses mutating, or moths changing colors, or populations becoming reproductively isolated and (b) the entire biological world spontaneously arising. So they are completely oblivious to their equivocating between the two.

      This is completely false. Nobody, except in your fevered imagination, is conflating these two.

      There’s no scientific evidence that allopatric speciation, to use the evolutionist’s example from above, produces the massive changes evolution requires.

      Of course there isn't. Are you really this ignorant of evolutionary theory? Or is it, as Oleg suggests, just a show put on for your Biola studients?

      But that’s irrelevant to evolutionists, and pointing it out is puzzling to them, because after all, such speciation equates with all of evolution.

      No. It. Does. Not.

      For goodness' sake, Cornelius, crack open a basic biology text book. And look up the words "speciation" and "adaptation".

      Is it possible that your assumption that the two things are regarded by biologists as the same is due to simple ignorance?

      If so: please educate yourself pronto!

      Delete
    27. CH: It is an incredibly blatant equivocation, but when you point out this sort of equivocation, as we have many times, evolutionists will have none of it, and accuse the messenger of equivocating, games, etc.

      Please point out precisely where the authors are equivocating in the passage you cited.

      For example, annotate the passage, noting, perhaps in square brackets, where a word is being used in one sense, and where in another, and how the two meanings are being conflated to make a fallacious point.

      Delete
    28. CH: Now you are even more confused. Remember, you guys are the evolutionists and we’re the skeptics. You have the ax to grind (evolution must be a fact), will twist science in whatever way you need to twist it, and must deny the mistakes you regularly have to make.

      Why should we "remember" something that isn't true? And is actually meaningless? "Evolution is a fact" is a meaningless statement unless the speaker means by "evolution". For some definitions it is true. For some it is not. But either way, there is no "ax to grind".

      We have no vested interest either way. Religion plays no part in science (despite your unsupported insistence that it does) although religion often has to come to terms with science. All evolutionary theory could be true, and there could still be an Intelligent Designer. Unfortunately, the inverse is not the case - some religious beliefs depend on evolution being false.

      So who has the "ax to grind"?

      We, on the other hand, just follow the science because our religion doesn’t mandate evolution being true or not.

      Good. I know of no religion that mandates religion being true. I do know of some that mandates that evolution is false. I'm glad yours is not one of them.

      Therefore we're able to see that all of biology arising spontaneously is not a real good theory.

      It's not a theory at all.

      So we only make mistakes at the regular rate, and readily admit to them.

      You have made countless elementary mistakes on this blog, which have been pointed out to you. You rarely admit them.

      Remember, evolutionists equivocate, not the skeptics.

      I'll remember you said it, Cornelius. Doesn't make it true. Indeed, it seems to me self-evidently the inverse of the truth.

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  2. I wonder who these professors could be.

    Professor Moriarty?

    Professor Higgins?

    Professor Xavier?

    Professor Jones?

    Professor Dumbledore?

    Professor Venkman?

    Professor Challenger?

    Professor Quatermass? (My personal favorite)

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  3. CH: In fact evolutionists do not have a scientific explanation for the large-scale change their idea requires.

    Again, the underlying explanation behind evolutionary theory is that the knowledge of how to build adaptations, as found in the genome, was created using a form of conjecture and refutation. Specifically, conjecture, in the form of genetic variation, and refutation, in the form of natural selection.

    Yet, Cornelius has yet to present any sort of detailed criticism of this expansion. Period.

    So, apparently, I'm either not an "evolutionist" by Hunter's definition, despite thinking evolution is the best explanation for what we observe, or he objects to a theory despite having no criticism of it.

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  4. To illustrate the lack of criticism indicated above...

    Cornelius,

    Why don't you start out by explaining how knowledge is created, then point out how evolutionary theory doesn't' fit that explanation? Please be specific.

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  5. @CH: Off topic, but I've been wondering if you had seen the recent letter in Nature, Proto-genes and de novo gene birth (http://ge.tt/5iORITK/v/0). It offers a possible counter-argument to your post on protein space, http://darwins-god.blogspot.com/2012/03/these-new-protein-findings-are-problem.html by suggesting a gradual walk from non-coding regions to functional proteins. It would be good to hear your thoughts.

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  6. um, Cornelius, I'm very flattered and all, but I am not a professor.

    Also this is a weird conversation - why don't you actually respond to my comments, instead of anonymising my response to you and making oblique illusions (without naming me) in a new post?

    CH: evolutionists change the meaning of the word.

    No. They. Do. Not.

    YOU, you, Cornelius Hunter, take examples of DIFFERENT evolutionists using the word in DIFFERENT ways, ways in they make completely clear, and EQUIVOCATE by taking one statement by one person using the word in one way to set against a completely different person using the word in a different way!

    Not only that, but you often read the word "evolution" into a statement that doesn't even use it - as when I asked you some important questions about the following, very different, concepts:

    Universal common ancestry

    Adaptation by means of heritable variance in reproductive success in a given environment

    Evolution meaning change in populations over time, and sometimes, specifically, change in allele
    frequency over time

    Speciation.

    These are all different, Cornelius, and they are all facts.

    Separate facts.

    Which of them do you think is not a fact?

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    1. EL:

      CH: evolutionists change the meaning of the word.

      EL: No. They. Do. Not.


      Yes. They. Do.


      EL: YOU, you, Cornelius Hunter, take examples of DIFFERENT evolutionists using the word in DIFFERENT ways

      No, they are the SAME evolutionists using the word in DIFFERENT ways.

      This discussion is a good example of evolutionary thought.

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    2. Yes, it probably is.

      I am still waiting for an example of the SAME "evolutionist" actually equivocating with the word "evolution".

      None of your examples have been even close so far, as I have clearly demonstrated.

      What you ae clearly demonstrating is your inability to support your scurrilous allegations of dishonesty and lack of integrity on the part of scientists.

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  7. With gravity, one can adequately explain both a falling apple and the Moon in its orbit with the same simple law. The professor draws a false parallel with evolution: “So it is with evolution.”

    With evolution, as with gravity, there is the observed phenomenon and there are the explanations constructed to account for those phenomena.

    In the case of gravity, we observe that, for example, unsupported objects fall to the ground, which can be expressed more generally as any objects with mass are drawn towards each other. Newton explained this in terms of an attractive force operating between massive objects. Einstein's explanation was entirely different, as we know, accounting for the observed motion in terms of a spacetime continuum which is curved around massive objects.

    In the case of evolution, we observe that living things have changed and continue to change over time. This was known long before Darwin published his theory and was exploited to breed plants and animals that are better suited to human needs than their forebears. It is as much a fact, as defined by Gould, as gravity.

    Darwin proposed, in effect, that this observed phenotypic plasticity could be molded over time by natural forces just as much as by artificial selection and lead to the immense diversity of species we see today - a not unreasonable inference.

    What he lacked was a credible mechanism for this plasticity. Mendel's work on inheritance and that of Watson, Crick and Franklin which led to the discovery of DNA and the genome nicely filled that gap.

    Since then the evidence has just been piling up: industrial melanism in the peppered moth, the finches beaks, ring species of gulls, nylon-eating bacteria, antibiotic-resistant bacteria, the discovery of the Tiktaalik fossils exactly where they were predicted to be and so on.

    Of course, this is not enough for those who are predisposed, for whatever reason, to deny the theory of evolution and probably never will be. Even if it were possible to map out the step-by-step, molecule-by-molecule path between a complex modern protein and the Big Bang, it would still not be sufficient for the theological and ideological critics of evolution. They would still demand the evidence for evolution meet the "pathetic level of detail" criterion which they are unwilling and unable to apply to their own conjectures.

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  8. I have to say as an infrequent lurker (I suspect this blog would become extinct if not for the link from UD) how much I admire Dr Hunter's persistence in the face of logic and clarity. Keep it up, Cornelius.

    And be gentle with him, Lizzie!

    Seriously, I do at least acknowledge Cornelius's light hand on the moderation button!

    My 2 cents.

    I think Cornelius does not appreciate there are the facts of evolution; the fossil record, cladistics DNA homology etc. and the theory of evolution that attempts to explain them by the process of sifted variation. Or is it a case of equivocation over definitions?

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    1. Seriously, I do at least acknowledge Cornelius's light hand on the moderation button!

      Yes indeed. This blog is a shining beacon in that respect.

      Thanks Cornelius :)

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    2. Alan:

      I think Cornelius does not appreciate there are the facts of evolution; the fossil record, cladistics DNA homology etc.

      Can you elaborate on how the fossil record is a "fact of evolution"?

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    3. Cornelius Hunter

      Alan: I think Cornelius does not appreciate there are the facts of evolution; the fossil record, cladistics DNA homology etc.

      Can you elaborate on how the fossil record is a "fact of evolution"?


      They are facts that confirm evolution occurred.

      That the fossil record exists is an empirical observation. That there are specific patterns in the spatial and temporal distributions in the fossil record is an empirical observation. That the phylogenetic trees independently created from the fossil and genetic records correlate so amazingly closely is an empirical observation.

      Are you not aware of even those basic science fundamentals?

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    4. Hunter asked:

      Can you elaborate on how the fossil record is a "fact of evolution"?

      Thorn replied:

      They are facts that confirm evolution occurred.

      Wow. Thorn makes Hunter's point for him without even realizing it. Amazing.

      What Hunter means is that the fossil record is indeed evidence that there was some sort of progression or evolution over the years. However, it is not evidence for the common-descent type of evolution being preached by evolutionists whereby cow-like animals turned into whales by procreating. It could just as easily have been an evolution caused by progressive genetic engineering over hundreds of millions of years.

      Hunter just finished talking about equivocations and Thorn could not resist falling into Hunter's trap like a fool. It would be funny if it weren't so pathological.

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    5. I suspect this blog would become extinct if not for the link from UD

      Nah, Cornelius has the spirit of a Don Quixote. I'm sure he'd have no trouble going solo. Moreover, this little place is much more lively than UD, even without a "News department" ;)

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    6. Cornelius is doing a great job of exposing the dishonesty that, in the past, was not even recognized by otherwise intelligent people. The reality is that the so called theory of evolution is dead to real science. And all you delusional supporters, some who have actually been paid well for participating in the hoax, will find yourselves fighting against the ever increasing headwinds of scientific evidence that continues to make a joke out of your ridiculous claims.

      Delete
    7. "spatial and temporal distributions" As apposed to what, non-spatial and non-temporal distributions?

      Oh Thornty, Thornty, Come home now. It is time to go to bed! You have had enough time slinging irrelevant crap around on the internet for today. Oh by the way Thornty, You are a bit constipated. I am afraid mommy will have to perform an enema on you tonight before mommy tucks you in.

      Delete
    8. CH: Can you elaborate on how the fossil record is a "fact of evolution"?

      Yes, indeed. Fossils are a fact. They are part of the explananda of evolutionary theory.

      Their dating by stratigraphy is also a fact.

      These facts tell us that population changed gradually over time, in other words, support the case that populations evolve.

      That populations can be directly observed evolving today is also a fact

      That the genetic and phenotypic features of living organisms are distributed as a nested hierarchy is also a fact as is the fact that this nested hierarchy extends right back as far as we can see to an inferred common ancestral population.

      We can infer that common ancestral population with about as much confidence as we can infer Big Bang.

      Which is generally regarded as a fact.

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    9. CH: Can you elaborate on how the fossil record is a "fact of evolution"?

      Thorton: They are facts that confirm evolution occurred.

      Jeff: Fossilization is not an evolutionary mechanism.

      Thorton: That the fossil record exists is an empirical observation.

      Jeff: Indeed.

      Thorton: That there are specific patterns in the spatial and temporal distributions in the fossil record is an empirical observation.

      Jeff: Observed stratigraphic ranges are such that there is an observed fossil succession of that kind, yes.

      Thorton: That the phylogenetic trees independently created from the fossil and genetic records correlate so amazingly closely is an empirical observation.

      Jeff: They don't correlate well. This is what article after article CH has alluded to shows. But you are right that if they did correlate well, that would be hard, if not impossible, to explain by SA.

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    10. Jeff

      Thorton: That the phylogenetic trees independently created from the fossil and genetic records correlate so amazingly closely is an empirical observation.

      They don't correlate well. This is what article after article CH has alluded to shows. But you are right that if they did correlate well, that would be hard, if not impossible, to explain by SA.


      They correlate to better than 1 part in 10e6, or better than 99.999%

      Consilience of independent phylogenies

      Bye bye SA!

      Delete
  9. CH: If anyone doubted that evolutionists equivocate, or that such equivocation is prevalent, they need doubt no more. I recently pointed out several examples of evolutionists equivocating on evolution.

    Except you haven't actually illustrated where the *fallacy* of equivocation took place.

    Specifically, observations of the evolution of biology isn't the same as the explanation for those observations. Just because the same term is used doesn't mean that the *fallacy* of equivocation has actually taken place.

    So, what you're missing here are actual quotes that exhibit the *fallacy* of equivocation.

    CH: The claim that evolution is a fact refers to our knowledge. It refers to the facts and theories of science. We may not know what happened in the distant past, but we do know exactly what is our current knowledge of what happened in the distant past. That knowledge indicates there are substantial problems with evolution. It is not something that likely happened, according to our current knowledge. It certainly is not a fact.

    So some sort of fallacy must have taken place since "the science" conflicts with evolutionary theory?

    But we've corrected you on this time and time again. Specifically, you have yet to explain how it's possible to observations without fist putting them into an explanatory framework. A such, there is no theory neutral way of interpreting observations.

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  10. Also, I though the "truth" of evolutionary theory always boils down to theological beliefs?

    Yet, here, you seem to be suggesting that evolution is "true" because "evolutionists" are committing the fallacy of equivocation?

    Which is it?

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  11. When I was ten, I could long-jump nine feet; when I was fifteen, I could long-jump twelve feet; and when I was twenty-one, I could long jump fifteen feet. Obviously, when I'm ten thousand years old, I'll be able to long-jump 2,000 feet! It's obvious. It's a fact, like gravity.

    Such is the logic of evolutionists.

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    1. Pav Lino

      When I was ten, I could long-jump nine feet; when I was fifteen, I could long-jump twelve feet; and when I was twenty-one, I could long jump fifteen feet. Obviously, when I'm ten thousand years old, I'll be able to long-jump 2,000 feet! It's obvious. It's a fact, like gravity.

      Such is the logic of evolutionists.


      Actually Pav,that's a classic example of the ignorance and misunderstanding of Creationists.

      Genetic changes don't increase in magnitude each generation as a population ages. What happens is the rate of genetic change stays more or less constant in each generation, but the beneficial changes accumulate over time.

      In one day I can easily walk 10 miles.
      In two days I can walk 20 miles.
      In a week I can walk 70 miles.

      There are no known barriers that prevents me from walking 3650 miles in a year, or 36,500 miles in a decade.

      There are no known barriers that prevent small morphological changes from accumulating over time.

      There are no known barriers that prevent a land mammal's paws from evolving into a marine mammal's flippers in time.

      EDIT: moved to correct location

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    2. In The Edge of Evolution, Behe points out how the malarial parasite evades the effects of quinine by two a.a. mutations.

      Evolutionists extrapolate these two a.a. changes to entire genomes.

      It has nothing to do with rates; it has to do with the limits of random processes.

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    3. Pav Lino

      It has nothing to do with rates; it has to do with the limits of random processes.


      What limits would those be Pav? Behe's idiotic claims in "Edge of Evolution" were beaten into a fine pink mist by the practicing genetics community.

      You know of any other limits that prohibit genetic changes from accumulating over time?

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    4. Thorton:

      Behe's idiotic claims in "Edge of Evolution" were beaten into a fine pink mist by the practicing genetics community.

      Behe used a real, live experiment with a selection value of 1.0. After 10^20 replications---a number given by a scientist working in the field---the solution arrived at differed by two a.a.s. These are simply facts.

      But maybe that's what the "practicing genetics community" does: it "beats" facts "into a fine pink mist when that serves its purposes.

      You know--scientific consensus; otherwise known as "groupthink." (cf Smolin's "The Trouble with Physics", chapters 16 and 18)

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    5. Pav Lino

      Behe used a real, live experiment with a selection value of 1.0. After 10^20 replications---a number given by a scientist working in the field---the solution arrived at differed by two a.a.s. These are simply facts.


      No Pav, Behe cherry picked some values that had nothing to do with the claims he was making. It took the scientific community about 5 minutes to rebut and reject his idiotic bait-n-switch shenanigans.

      There's a reason Behe is considered such a laughingstock in the scientific community, and a reason he only self-publishes his crap instead of submitting it for proper peer review.

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    6. Thorton:

      "Cherry picked"???

      Behe thinks of a biological experiment pitting evolutionary forces working at fever pitch to gauge the power of said forces to evince genetic change.

      Based on a "peer-reviewed" article, he already had reasons to believe that neo-Darwinian mechanisms could not do much.

      He looked at the evidence, looked at the associated numbers, and discussed their implications.

      This is of what real science should consist.

      You simply dismiss it.

      It's called "hand-waving." And, in the land of the free, you can do that. But that simply means you're choosing to live in La-La Land.

      BTW, "he who laughs hardest is he who laughs last."

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    7. Thorton:

      There are no known barriers that prevent small morphological changes from accumulating over time.

      Well this must also mean that there are examples--plenty of examples--of mutations steadily accumulating over time. Do you have one?

      I think it is a paper by Orr where he shows that the utility of mutations falls off dramatically, and that by the third mutation, hardly any more phenotypic change occurs. I think he bases this on a Markov chain analysis using a special kind of assumption--the name of which I can no longer remember.

      This suggests a considerable limit.

      But, of course, this is only one half of the problem.

      The other half of the problem is that neo-Darwinism moves too slowly. This is the whole point of Behe's example of the malarial parasite: 10^20 generations and evolution gives you only TWO amino acid changes. Way, way, way too slow!!

      But, of course, reality is sometimes very hard to accept.

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    8. I'm sorry Pav - tell me again what peer reviewed scientific journal Behe published this work in? Its name escapes me.

      Delete
  12. CH: I pointed out one example in the book Arguing for Evolution: An Encyclopedia for Understanding Science, where the evolutionists triumphantly asserted that the evolution of the species is a fact

    Which it is - we can infer a deeply nested hierarchy of living things that indicates universal common ancestry, with evolution (where "evolution" means at least phenotypic change in population over time).

    and then used an example of an allele frequency changing from 40% to 36% in a population of rock pocket mice.

    Which is a good example of evolution in real time.

    Is this and other examples that I pointed out exceptions to the rule? Are these simply uninformed evolutionists making a blunder? Unfortunately such arguments are common in both the classroom and the literature.

    It's a perfectly valid argument for common ancestry.

    The blunder is yours.

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    1. EL:

      CH: the evolutionists triumphantly asserted that the evolution of the species is a fact

      EL: Which it is - we can infer a deeply nested hierarchy of living things that indicates universal common ancestry, with evolution (where "evolution" means at least phenotypic change in population over time).


      So evolution is a fact because of a "deeply nested hierarchy of living things that indicates universal common ancestry." Can you elaborate a bit on how the latter makes the former a fact?

      Delete
    2. Well, first tell me how you are defining "evolution" in that sentence.

      Delete
    3. Cornelius Hunter

      CH: the evolutionists triumphantly asserted that the evolution of the species is a fact

      EL: Which it is - we can infer a deeply nested hierarchy of living things that indicates universal common ancestry, with evolution (where "evolution" means at least phenotypic change in population over time).

      So evolution is a fact because of a "deeply nested hierarchy of living things that indicates universal common ancestry." Can you elaborate a bit on how the latter makes the former a fact?


      No one single piece of data makes evolution a fact. It's the consilience of all the evidence taken as a whole, consilient evidence that paints one clear coherent picture, that makes evolution a fact.

      Delete
    4. And while I am waiting, let me make my own meaning crystal clear:

      We can fit a family tree model to biological populations such that the tree shows evolution, where evolution is defined as change-over-time along each lineage. So the question arises: is there any evidence for changes-over-time along the lineage of a population?

      The answer is: yes - we see it happening in real time.

      Ergo, we have support for the hypothesis that all living things descended from a universal common ancestor, the lineages bifurcating and changing over time.

      Now the question is: what are the mechanisms that could bring about such a change?

      Possible answers: adaptation by Darwinian mechanisms; drift.

      Again, both these mechanisms have been observed in real time.

      And so we have evidence for UCA with evolution (where evolution means change-over-time) and we have a demonstrable mechanism by which this change could occur (Darwin's theory of adaptation).

      No equivocation involved.

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    5. EL:

      Well, first tell me how you are defining "evolution" in that sentence.

      Well you are the one who made the claim and the definition. I'm just going by what you said (i.e., where "evolution" means at least phenotypic change in population over time).

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    6. I have to tip my cap to you CH. Your continuing evasiveness would put a greased pig to shame.

      Delete
    7. Did you know pigs are supposed to be very intelligent creatures?

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    8. Cornelius Hunter

      Did you know pigs are supposed to be very intelligent creatures?


      No one questions your intelligence CH. It's your intellectual honesty that could use a reboot.

      If only you practiced a religion that emphasizes how wrong it is to lie...

      Delete
    9. Intelligent and tasty. Ever hear the joke about the three legged pig?

      Delete
    10. Well you are the one who made the claim and the definition. I'm just going by what you said (i.e., where "evolution" means at least phenotypic change in population over time).

      sheesh, Cornelius!

      YOU are the one accusing "evolutionists" of equivocation!

      I have given you my reasoning which involves no equivocation at all and which, I submit, is what the authors of Arguing for Evolution are saying, and which YOU paraphrase as: "evolutionists triumphantly asserted that the evolution of the species is a fact".

      OK, so if evolution means "phenotypic changes in species over time" - then in what sense is the assertion that species change over time not a fact?

      Or to put it another way, since you seem to be very slow on the uptake here:

      What is it that you think the authors are asserting is a fact that you think is not a fact?

      I await your answer with interest.

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  14. Evolutionists must be exhausted from moving those goalposts so often. UNfalsifiable.

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    1. NV, is it not clear to you that Cornelius is moving goalposts at something approaching the speed of light?

      He accuses "evolutionists" of equivocating with the word evolution, yet when asked to give an example, fails to produce one in which the writers he quotes actually use the word in an ambiguous way, and merely asserts that "evolutionists" have to maintain that "evolution is a fact" at all costs - without saying what he means by that word!

      And when challenged to do so, throws the burden on to the "evolutionists" - who have already, with great clarity, done so!

      If Cornelius is going to accuse "evolutionists" of saying that "evolution is a fact" when Cornelius thinks it is not, he needs to make it clear what precisely it is that he thinks is not a fact.

      Until he does so, the goal-posts will continue to oscillate at many megahertz.

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    2. E: We can fit a family tree model to biological populations such that the tree shows evolution, where evolution is defined as change-over-time along each lineage. So the question arises: is there any evidence for changes-over-time along the lineage of a population?

      J: How does the fact that a tree can be generated prove the tree is genealogical in nature? We can generate trees from character traits of non-living entities as well. You could say those trees show change over time. But it wouldn't be the relevant kind of change over time--genealogically-caused changed.

      So what about the tree tells you that the tree corresponds to traits caused by genealogical processes? If the tree doesn't do that on its on, you're just interpreting it the way you want to. Which is fine. But an interpretation isn't necessarily a fact, or even plausible.

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    3. Jeff,

      I would love to see the genealogical tree of the Honda Civic. Or the Toyota Prius. Feel free to take a stab.

      Delete
    4. E: We can fit a family tree model to biological populations such that the tree shows evolution, where evolution is defined as change-over-time along each lineage. So the question arises: is there any evidence for changes-over-time along the lineage of a population?

      J: How does the fact that a tree can be generated prove the tree is genealogical in nature?


      Well, if you find a dead body with gunshot wound, and you find a guy holding a smoking gun beside the smoking body, then you can infer with considerable confidence that the guy with the smoking gun made the wonds in the body.

      Similarly, if you find a tree-distribution of heritable features in a group of entities that inherit features from their parents, you can infer with considerable confidence that the tree you observe is genealogical in nature.

      We can generate trees from character traits of non-living entities as well.

      And as I've said several times, yes, you can fit a tree model to any dataset of entities with shared characteristics, just as you can fit a linear slope to any bivariate set of data. The issue is how good the fit is, and whether it is a better fit than some alternative model.

      That is why we produce goodness-of-fit estimates.

      In the case of a dataset to which we want to fit a tree, one approach might be to treat each item in turn as a root, fit the best tree to each root. If all roots give equally well (or poor)fitting trees, then the distribution of characteristics probably wasn't generated by a tree-producing process. If, in contrast, certain nodes produce coherent deeply nested trees, you probably can.

      And by using various bootstrapping or other techniques, you can test how likely it is or not that some other non-tree-producing process would produce the tree you observe by chance.

      You could say those trees show change over time. But it wouldn't be the relevant kind of change over time--genealogically-caused changed.

      What's not relevant about it?

      So what about the tree tells you that the tree corresponds to traits caused by genealogical processes?

      The fact that they are heritable.

      If the tree doesn't do that on its on, you're just interpreting it the way you want to.

      what?

      Which is fine. But an interpretation isn't necessarily a fact, or even plausible.

      You seem unfamiliar with the concept of hypothesis testing.

      Delete
  15. The tree can be generated. So what is the difference between the trees that tells you one is the product of genealogically-caused traits and the other isn't? There is nothing. Because you will resort to unproveable historical contingencies that are not known to explain anything to account for the particular phenotypes arising at the particular times. In short, there is nothing we know about genetics that tells us that the specific trees are genealogically-caused.

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    1. Then go ahead and do that. We'll see how much of a nested hierarchy you'll get.

      Delete
    2. Jeff: The tree can be generated. So what is the difference between the trees that tells you one is the product of genealogically-caused traits and the other isn't?

      The fact that the traits you are fitting are, as determined by independent means, heritable.

      There is nothing. Because you will resort to unproveable historical contingencies that are not known to explain anything to account for the particular phenotypes arising at the particular times.

      This is simply wrong. We know a huge amount about the genetic basis of phenotypes, and our knowledge is growing all the time.

      In short, there is nothing we know about genetics that tells us that the specific trees are genealogically-caused.

      Of course there is! For a start, there is the congruence between trees derived from genetics and trees derived from morphology! Then there is all the data we have that tell us about the genes, and protein products, that are implicated in various phenotypic features.

      You seem to be extrapolating from your own ignorance (which is entirely forgiveable) to the whole of biological science (which is less forgiveable!) Just because you don't know something doesn't mean that nobody knows.

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  17. And why does a deep nested hierarchy work only for descent with modification seeings how there's no predictive model that predicts the generated trees? Why can't it be a classification aid? For it surely is one.

    You keep indicating you're winning. But you're only winning in your own mind, because you're not considering other logical possibilities. We don't even know that the trees are logically-possible results of mutations given the time-limits and terrestrial environments that existed at the relevant times. But we do know that depth of nesting (as well as morphological gap size) is conducive to ease of human classification when you're dealing with large numbers of species.

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    1. Jeff,

      You wrote that the ancestral trees for the Honda Civic and the Toyota Prius can be generated. I am challenging you to do that. Once you have your trees, we can take a look at them.

      Delete
    2. And why does a deep nested hierarchy work only for descent with modification

      Well, it's essentially an inheritance model. But there could be other mechanisms of inheritance other than biological inheritance. However, as we know that biological organisms reproduce and pass on their traits to their offspring, we don't need to look far for the mechanisms in this case.

      seeings how there's no predictive model that predicts the generated trees?

      Yes there is: biological inheritance predicts trees. So does cultural inheritance - surnames are also distributed as a tree structure.

      Why can't it be a classification aid? For it surely is one.

      It's a useful classification aid, although thinking of taxonomic labels as representing discrete entities is a potential pitfall. Down each lineage we have continuous, not categorical, variation, and even between diverging species, the degree of inter-fertility is a continuous variable.

      You keep indicating you're winning. But you're only winning in your own mind, because you're not considering other logical possibilities.

      Well, you seem to be considering only "logical possibilities" and not those actually indicated by our observations. We know that biological organisms reproduce and pass on their traits. We know that they form family trees. So why should we think that some other mechanism is responsible for the observed tree? It's possible, but not parsimonious!

      We don't even know that the trees are logically-possible results of mutations given the time-limits and terrestrial environments that existed at the relevant times.

      And there you go again. You may well not be convinced that "mutations" are the mechanism responsible for the evolution of populations down bifurcating lineages. But what is as near a fact as science gets is that those bifurcating lineages exist. Perhaps an Intelligent Designer is responsible for adding key novelties at key times. Perhaps a whole team of designers.

      But whatever the reason, the family tree is blindingly obvious from the data.

      But we do know that depth of nesting (as well as morphological gap size) is conducive to ease of human classification when you're dealing with large numbers of species.

      What does this mean? I don't understand what you are saying here.

      Delete
  18. Other evolutionists have admitted that they can be. They, like you, just don't think the depth of nesting would be impressive. That's irrelevant since ID'ists typically attribute the depth of nesting to a designed fit to the human mode of classification. This inference goes back to Platonic times at least. But evolutionists conveniently ignore this.

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    1. In other words, ID proponents are claiming that deep nesting could just as easily be a product of design as of natural processes? Doesn't such a claim violate your principle of parsimony, though? You are positing an alien designer without having demonstrated the need for such an additional entity. We have evidence from observation and experiment of natural processes that could account for the diversity of life we see. It is certainly logically possible that naturalistic explanations are true since no one has demonstrated that they are impossible. What reasons are there, other than religious beliefs, for considering the possibility that extraterrestrial intelligences have influenced the course of life on Earth?

      Delete
    2. Jeff,

      Don't mind what "evolutionists" are saying. Mind your own words. You have said, in your own words, that the Honda Civic and Toyota Prius "can be generated."

      You can talk the talk, now walk the walk. Produce the trees. And we'll marvel at them.

      Delete
    3. Other evolutionists have admitted that they can be.

      Only in the sense that you can always fit the best tree to your data. That doesn't mean that your best tree isn't a terrible tree, with lots re-entrant cycles that you have to account for by other means.

      They, like you, just don't think the depth of nesting would be impressive.

      That's not the only criterion for a good tree fit.

      Let's do a simple worked example. Here are two sets of words:

      Pressure
      Expression
      Express
      Press
      Espresso

      Fin
      Fine
      Fineal
      Finally
      Final

      If we try to fit a tree to the first set we might get:

      Press
      Express Pressure Espresso
      Expression

      or

      Espresso
      Press
      Express Pressure
      Expression

      or

      Press
      Express Pressure
      Expression
      Espresso

      For the second, we get:

      Fin
      Fine Final
      Fineal Finally

      In the first case, no one tree is any better than any other, and a non-directed graph would be a more convincing model than a tree. For the second, a single tree stands out as the best fit.

      And we can actually do this mathematically, and determine whether the features of each item are distributed as a clear tree, with only a few ambiguities or violations to explain, or whether another model would be a better fit.

      That's irrelevant since ID'ists typically attribute the depth of nesting to a designed fit to the human mode of classification.

      Well, sure, but that would give the ID a very different method of working to the workings of the Intelligent Designers we are modeling him/her/it on, i.e. us. Our artefacts show frequent violations of the tree (as you will discover if you do the exercise oleg is waiting for), simply because we have foresight and can implement an innovation from one design "lineage" into another quite different one. Evolutionary processes can't, which is why that nested hierarchy is a much better indicator of evolutionary processes than of a foresighted designer. Unless of course the foresighted designer was smart enough to utilise evolutionary processes :)

      This inference goes back to Platonic times at least. But evolutionists conveniently ignore this.

      The do not "ignore" it - they reject it, on account of the evidence.

      Delete
  19. Branching speciation without hybridization and LGT will necessarily produce a genealogical nested hierarchy among living species. In eukaryotes, LGT and hybridization are not so overwhelming that we fail to find nested hierarchical structure in genetic and morphological data.

    In terms of our ability to fully resolve the eukaryote tree, we do indeed run into trouble with mutational saturation when we go back very deep in time. But that does not mean that the genealogical tree is not present.

    Observed evolution (not just mutation, but selection, drift, gene flow, etc.) is more than adequate to explain the observed diversity of life. When you limit evolution to a single mechanism, then yes, you would have a problem.

    As we gain more knowledge and fill more gaps, species level taxonomy is becoming trickier and trickier (see giraffes, elephants, gorillas, etc. for recent examples). When we add in fossils, there are arguments as to the composition of Homo sapiens as well.

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  20. Ian: We have evidence from observation and experiment of natural processes that could account for the diversity of life we see.

    Jeff: Actually, what we have is reason to believe that terrestrial species could evolve from single-celled organisms in SOME time-frame with SOME sequence of environments in that time-frame. We have NO reason to believe that terrestrial species would evolve in the POSITED time-frame in the ACTUAL sequence of terrestrial environments that occurred during that posited time-frame. We don't even have a theory that can model that as a POSSIBILITY yet.

    Ian: It is certainly logically possible that naturalistic explanations are true since no one has demonstrated that they are impossible.

    Jeff: I'm not saying historical UCA is NOT a logical possibility. I'm saying we don't know that it IS one. To know that is one, we'd have to do the deductions from the intial conditions in terms of the theory and deductively produce the tree in the right relative order at the posited times. That's not possible yet. Hence, we don't know that historical UCA is logically possible.

    That's why even Behe's front-loading theory is worthless as a competitor against SA. It, too, is not known to be logically possible. Every UCA approach has all the problems of SA plus plenty more that SA doesn't have. Thus, Behe isn't knowably solving his problem by positing extra front-loading.

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  21. SA has HUGE problems of convergence and parsimony that far outweigh any logical problems for UCA. UCA is certainly logically possible until proven otherwise.

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  22. J: Other evolutionists have admitted that they can be.

    E: Only in the sense that you can always fit the best tree to your data.

    J: Please tell Thorton this so he'll quit wasting disk space with his idiocy. LOL!

    E: That doesn't mean that your best tree isn't a terrible tree, with lots re-entrant cycles that you have to account for by other means.

    J: It's nice that you brought up the term means. Because any time you generate a tree using HUMANLY-selected criteria, you are doing teleological activity. So what would render the tree-generating means relevant to UCA? Simply that those means (i.e., rules of tree generation) accurately describe the rules of evolution AND that those rules somehow account for all the historical contingencies and evolutionary rates such that the tree would produce on the earth, genealogically, in the posited time-frame. We have no idea if that is possible or probable in the posited time-frame. No cladistic model takes that much complexity of event sequences and causality implications into account. Not even close. Heck, we don't even yet know the total complexity of it yet.

    E: And we can actually do this mathematically, and determine whether the features of each item are distributed as a clear tree, with only a few ambiguities or violations to explain, or whether another model would be a better fit.

    J: Note the equivocation, though. On the one hand, it's a tree. It just IS a tree, built by the relevant rules. Then you bring in the phrase "clear tree." At that point, we're not talking about WHETHER it's a tree. We're talking about whether it's a preferred tree. But that preference criteria has no known realistic correspondence to the complexity of biological evolution. And that's why cladistically generated trees have no know relevance to the possibility or probability of historical UCA.

    E: Well, sure, but that would give the ID a very different method of working to the workings of the Intelligent Designers we are modeling him/her/it on, i.e. us. Our artefacts show frequent violations of the tree (as you will discover if you do the exercise oleg is waiting for), simply because we have foresight and can implement an innovation from one design "lineage" into another quite different one.

    J: You're missing the relevant teleological point. Humans don't design successive car models with nesting depth as an objective. Thus, it's no wonder those trees don't have those kinds of characteristics. They're not even trying to accomplish that.

    E: Unless of course the foresighted designer was smart enough to utilise evolutionary processes :)

    J: And we don't know a designer isn't that smart. But I don't believe any designer can do the logically impossible. Once we have a predictive (which means naturalistic) theory that can predict the relevant events at the posited times with good probability starting with the posited initial conditions, then we have good reason to believe it's logically possible.

    E: The do not "ignore" it - they reject it, on account of the evidence.

    J: No, they ignore common design as a logical possibility. Whether that's for methodological reasons or not is irrelevant. Their beliefs about UCA, etc are not based on weighing ALL the evidence. No doubt UCA is the next best inference once you reject ID for methodological or other reasons. But it is not even remotely less implausible than ID-style SA.

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  23. Jeff

    I'm not saying historical UCA is NOT a logical possibility. I'm saying we don't know that it IS one. To know that is one, we'd have to do the deductions from the intial conditions in terms of the theory and deductively produce the tree in the right relative order at the posited times. That's not possible yet. Hence, we don't know that historical UCA is logically possible.


    Poor one-note Jeff, still cluelessly bleating his logic boner.

    When a process has a random component like evolution does, it is not necessary to predict a *specific* result for it to be logically possible to produce *some* result.

    It is logically possible for the Lottery Agency to produce new random lottery numbers from their drawing every week. No one could predict ahead of time what the numbers would be, and you can't look at the historical numbers and derive them from the original premise of a random drawing.

    It truly is amazing you're still too dense to grasp the concept.

    BTW, I notice you sure shut up quickly after seeing the statistical significance of the matching dual nested phylogenies. Why is that?

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  24. A: SA has HUGE problems of convergence and parsimony that far outweigh any logical problems for UCA.

    J: Let's say an SA hypothesis is that the ultimate common ancestor of mammals were 2 mammal parents. How, pray tell, are the convergence and parsimony problems of mammalian evolution not already entailed, for the most part, in the UCA approach? At least this SA approach for mammals avoids the other convergence problems of mammalian origins posited by evolutionists.

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    1. J:SA has HUGE problems of convergence and parsimony that far outweigh any logical problems for UCA. UCA is certainly logically possible until proven otherwise.At least this SA approach for mammals avoids the other convergence problems of mammalian origins posited by evolutionists.

      Within mammals, these two hypotheses would be identical. But SA produces, rather than avoids, convergence issues outside of and prior to Mammalia. Mammals are deeply nested phylogenetically within the otherwise extinct synapsids. These synapsids, from the Carboniferous through the Triassic, provide transitional fossils that link mammals to their amniote relatives, the Sauropsida (birds & "reptiles). Mammals as living sisters to sauropsids is one of numerous examples of congruence among extant morphology, fossils, and molecules that make separate ancestry so improbable to those with the relevant knowledge base. If mammals are a "holobaramin" then the creator sure went out of the way to fool us into thinking they share common ancestry with sauropsids, which in turn share common ancestry with amphibians, which in turn share common ancestry with lungfishes, etc. etc.

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    2. A: Within mammals, these two hypotheses would be identical.

      J:Exactly.

      A: But SA produces, rather than avoids, convergence issues outside of and prior to Mammalia. Mammals are deeply nested phylogenetically within the otherwise extinct synapsids.

      J: Nesting has nothing to do with known convergence unless nesting is known to correspond to some predictive theory that predicts the relevant phenotypes at the relevant times. There is no such predictive theory, thus the nesting is completely irrelevant, having no implications about convergence.

      A: These synapsids, from the Carboniferous through the Triassic, provide transitional fossils that link mammals to their amniote relatives,

      J: It doesn't follow because there are certain kinds of morphological stratographic-intermediates that they imply genealogical relationships. So the relevant question is, what's the probability that the stratographic-morphological-intermediate is a genealogical intermediate? That would be the probability that the currently known stratigraphic ranges for the relevant phenotypes correspond relevantly to their existential ranges TIMES the probability that the posited evolutionary trajectories would occur under the relevant contemporaneous conditions in the posited time-frame.

      Surely you realize there is no way to calculate that probability with any certainty whatsoever. Thus, we can't know the probability is greater than zero, much less good. So you have nothing in this regard that has to do with either deductive or inductive logic. You SEE what you WANT to see. You're not doing logic.

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    3. Jeff

      Surely you realize there is no way to calculate that probability with any certainty whatsoever. Thus, we can't know the probability is greater than zero, much less good.


      Your posts get dumber with each passing day. Not being able to calculate a probability with certainty doesn't make the probability zero. No one can calculate the probability that a six mile wide asteroid would hit Chicxulub 65 MYA, but we know for sure the probability was greater than zero because the event happened.

      So you have nothing in this regard that has to do with either deductive or inductive logic. You SEE what you WANT to see. You're not doing logic.

      We have empirically measured physical reality. That tends to trump idiotic Creationist attempts to disprove scientific finding with just logic.

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    4. J: Nesting has nothing to do with known convergence unless nesting is known to correspond to some predictive theory that predicts the relevant phenotypes at the relevant times. There is no such predictive theory, thus the nesting is completely irrelevant, having no implications about convergence.

      Evolution involving branching descent with modification predicts nesting. We would never expect to predict precise phenotypes at precise times, because there are far to many random inputs and contingencies. Assuming you had never seen a photograph or heard details, would you be able to produce an accurate rendering of your paternal great, great, great grandfather? Would you be able to pick him out of a group photo? Of course not.

      Inasmuch as non-mammals such a Thrinaxodon and Morganucodon are so mammal-like, if we require that they not be related, then this astounding similarity must be explained by convergence. No convergence necessary if we posit a genealogical relationship.

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    5. more reply off thread @ 3:14.

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    6. A: Evolution involving branching descent with modification predicts nesting.

      J: Yes, but depending on the evolutionary rules and historical contingencies, how do we rule out the possibility of a virtual infinite set of branching patterns and phenotype instantiations (assuming the mutated duplicated gene mechanism, etc, will work as advertised) if the time-span for the evolution is unlimited? IOW, the mere fact that nesting is a prediction doesn't help us if we don't have an evolutionary theory that can predict something specific enough to approximate the actual tree you're claiming occurred in the posited time-frame under the relevant terrestrial conditions. Any finite number divided by infinity is still basically zero.

      A: Inasmuch as non-mammals such a Thrinaxodon and Morganucodon are so mammal-like, if we require that they not be related, then this astounding similarity must be explained by convergence.

      J: There's apparent convergence (from a UCA perspective) leading up to mammals regardless, isn't there? So when you add on the convergence posited by UCA that we can't prove ISN'T common design, ID-style SA doesn't need to posit as much of that kind of inexplicable convergence.

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    7. Thorton: Not being able to calculate a probability with certainty doesn't make the probability zero.

      Jeff: I didn't say it did. You just can't read.

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    8. Jeff

      Thorton: Not being able to calculate a probability with certainty doesn't make the probability zero.

      Jeff: I didn't say it did. You just can't read.


      I didn't say you said it moron. I was just pointing out yet another battleship-seized hole in your logic.

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    9. Errata: "seized" = "sized"

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    10. J: Any finite number divided by infinity is still basically zero.

      FAIL - This just in: creationists still bad at math.

      But that's meaningless, as we do not have infinite time on our hands. A Precambrian rabbit really would falsify UCD. And if we have decent sampling of fossils, we should find congruence (not a perfect match, but congruence) with stratigraphy.
      Have a look at this chart: http://www.geol.umd.edu/~tholtz/G331/images/Synapsida.pdf

      Only one incongruence, where the more mammal-like Varanopseidae and Ophiacodontidae appears before the outgroup Caseasauria. Only three ghost lineages of any length (Caseasauria, basal Therapsida, Probainognathia). Note that all ranges are artificially lengthened in red to get the nodes and clade names in. Sure looks like evolution; even more so if you have familiarity with these taxa.

      Once we have a few good pieces to the puzzle, we can and do make predictions concerning what we expect to find in the fossil record in terms of combinations of character states and timing (see Shubin, Your Inner Fish for an example). But, if we were to lack any data whatsoever, why do you think we should be able to guess which characters changed first, and which changed later in time? That you expect perfect predictability is evidence that you have not given your ideas a whole lot of thought.

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  25. T: It is logically possible for the Lottery Agency to produce new random lottery numbers from their drawing every week. No one could predict ahead of time what the numbers would be, and you can't look at the historical numbers and derive them from the original premise of a random drawing.

    J: This has been explained about a million times. SO I can only assume you're idiocy runs much deeper than I realized heretofore. We know HOW lottery tickets are generated and selected. We know THAT they are generated and selected in a random way BY OBSERVATION. We have neither a "how" theory or observations that tell us that the posited evolutionary trajectories are even POSSIBLE in the posited time-frame. You are truly moronic, dude.

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  26. Jeff

    This has been explained about a million times. SO I can only assume you're idiocy runs much deeper than I realized heretofore. We know HOW lottery tickets are generated and selected. We know THAT they are generated and selected in a random way BY OBSERVATION. We have neither a "how" theory or observations that tell us that the posited evolutionary trajectories are even POSSIBLE in the posited time-frame. You are truly moronic, dude.


    Psst...hey clueless Creationist:

    We know HOW genetic variations are generated and selected. We know THAT they are generated and selected in a random way BY OBSERVATION. We DO have a "how" theory AND observations that tell us that the posited evolutionary trajectories are not only POSSIBLE but are HIGHLY PROBABLE in the posited time-frame.

    Besides being clueless in logic, you still have this silly habit of projecting your pitiful scientific ineptitude onto others. Just because Jeff is ignorant doesn't mean everyone else is ignorant also.

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  27. Thorton: We DO have a "how" theory AND observations that tell us that the posited evolutionary trajectories are not only POSSIBLE but are HIGHLY PROBABLE in the posited time-frame.

    Jeff: Like I said, you're a complete idiot.

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  28. Jeff

    Thorton: We DO have a "how" theory AND observations that tell us that the posited evolutionary trajectories are not only POSSIBLE but are HIGHLY PROBABLE in the posited time-frame.

    Jeff: Like I said, you're a complete idiot.


    Maybe you should tell the tens of thousand of colleges and universities and science labs that successfully use evolutionary theory every day that they're all complete idiots too, and that Jeff the ignorant Creationist philosopher knows the TRUTH! :D

    My side has the evidence. You don't. You lose.

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  29. We saw what became of your definition of evidence. As is typically the case with idiots, you prove WAY too much or WAY too little with your "evidence."

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  30. Jeff

    We saw what became of your definition of evidence. As is typically the case with idiots, you prove WAY too much or WAY too little with your "evidence."


    (Looks over hundreds of scientific disciplines that support evolution. Looks over thousands of college, university, and professional labs that research evolution. Looks over tens of millions of scientific research papers that document evolution.

    Then looks at simple minded Creationist on backwater blog claiming there's no evidence for evolution)

    Hey Jeff, what's the score?

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  31. Thorton: Hey Jeff, what's the score?

    Jeff: Let's see:

    UCA posits way more inexplicable convergence than SA.

    UCA posits more and greater inexplicable evolutionary trajectories than SA.

    SA is consistent with a teleological purpose for strong nesting while historical UCA is not known to account for it even probabilistically.

    The teleological perspective rendered the discovery of function in putative "junk" DNA plausible while while evolutionary theory didn't predict it at all in terms of historical UCA.

    It is plausible on analogical grounds that similar function causing sequences are either inherited or the result of common design. This is why SA need not posit near as much inexplicable convergence.

    So, I would say SA is the least speculative at this time. But that doesn't mean its true. It's just currently the least speculative in terms of the NUMBER of a-plausible auxilliary hypotheses required to render the higher level hypothesis intelligibly related to the events it attempts to explain.

    Of course, if you find ID objectionable on metaphysical grounds, that's fine. But then I would be curious as to how you think you know anything since you're not, by that approach, DESIGNED to inferentially approximate truth via some intuitively knowable hypothesis rejection criteria.

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  32. Oh yeah, and ...

    ID-style SA is consistent with the natural tendency for, as Dawkins said, the mind to perceive organisms as entities "that give the appearance of having been designed for a purpose."

    Evolutionary theory doesn't explain that tendency in terms of UCA. Because the human species is not predictable, even probabilistically, in terms of evolutionary theory applied to single-celled organisms in the precambrian.

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  33. Sorry to intrude, but the tendency of human to believe something is evidence in its actually happening? Really, I tend not to believe that.

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    1. When an inferential tendency is so natural, the burden of proof is on the disssenter. THat's all I'm saying. I'm looking for the evidence for the dissent.

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    2. In other words, it is not necessary to prove the existence of a designer because most people have a tendency to view purpose, one must prove the designer doesn't exist?

      I'll bite,the gambler's fallacy.

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  34. Again sorry for the interruption,what is the teleological purpose of a strongly nested hierarchy? Human design does not adhere necessarily to a strongly nested hierarchy,Neal found it a problem to construct such a tree for the iPod .

    To hypothesize a teleological end ,one must assume certain features of the "designer ",have you included these in your calculations which theory is more parsimonious?

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    1. When you have lots of species to classify, the more systematic gaps there are in the morphologies and the deeper the nesting of attributes, the easier it is for humans to retain the classification results.

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    2. So the designer created a strong nesting to help people classify his designs? He is both smart and kind,any other inferential attributes and motivations of the designer?

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  35. It doesn't follow because there are certain kinds of morphological stratographic-intermediates that they imply genealogical relationships.

    The nested, hierarchical structure used to infer recency of common ancestry is based upon cladistic analysis, not stratophenetics. We don't assume that individual fossil species in deep time are directly ancestral to one another (extinction and scarcity of fossil preservation guarantee this would be a fool's errand). Given the strength of genetic evidence for UCA, the probability of cousinship is as close to 1 as you would care to make it.

    In vertebrates (where there is much study and interest) we see strong congruence between cladograms using data from genetics and skeletal morphology. Anatomical homology is more than just superficial similarity; it was useful in producing a tree for vertebrates that is so strongly congruent with modern genetic data that we can induce it will be useful in the fossil record.

    Use of cladistics to infer genealogy in fossils has led to some interesting and precise predictions, including feathers in coelurosaurs and a digital frameshift in birds.

    The logic of science is fine; but it is you who are not doing science.

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  36. A: Anatomical homology is more than just superficial similarity; it was useful in producing a tree for vertebrates that is so strongly congruent with modern genetic data that we can induce it will be useful in the fossil record.

    J: But why would it not be congruent thus on the basis of common design in some cases? Unless the tree generates maximal nesting depth or something in a way that correlates well with known stratigraphic ranges, you need to be more clear on the relationship of the maximal-depth nesting to the fossil record.

    A: Use of cladistics to infer genealogy in fossils has led to some interesting and precise predictions, including feathers in coelurosaurs and a digital frameshift in birds.

    J: You use the word "infer." Inference is a discursive movement from grounds to conclusion via some kind of relationship. What is the relationship entailed in the generated cladistic tree that indicates something about genealogical causality such that those specific predictions could be made?

    I keep hearing cladistics provides the evidence. But no one yet has explained how cladistics corresponds to phenotype-predicting theories or the fossil record in any clear way. If it corresponds to the fossil record in some cases, for all I know it corresponds to common design inferences in some cases.

    No one is arguing that if you rule out common design as an explanation for similar sequences that inheritance isn't the ONLY non-arbitrary inference left. By how did you rule out common design? Methodological rejection? How?

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    1. Jeff

      By how did you rule out common design? Methodological rejection? How?


      Design isn't ruled out a priori you moron. It's still on the table, just as the Invisible Pink Unicorn created the entire universe last Thursday is still on the table.

      It's just that neither of those ideas have one speck of positive evidence, and both ideas are vacuous and completely useless as scientific explanations.

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    4. Thorton: It's just that neither of those ideas have one speck of positive evidence, and both ideas are vacuous and completely useless as scientific explanations.

      Jeff: How do you use the belief that UCA is true? How do you live your life different because of that belief? How does anybody?

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    5. Jeff

      How do you use the belief that UCA is true? How do you live your life different because of that belief? How does anybody?


      How do you use the belief that plate tectonics is true? How do you live your life different because of that belief? How does anybody?

      Sometimes having a piece of knowledge is useful merely because it helps fill in the details of the big picture, which can lead to further knowledge and understanding.

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    6. Thorton: How do you use the belief that plate tectonics is true? How do you live your life different because of that belief? How does anybody?

      Sometimes having a piece of knowledge is useful merely because it helps fill in the details of the big picture, which can lead to further knowledge and understanding.

      J: Then you're missing the point. If all you're saying is that researching the possibility of historical UCA might render it knowably plausible, I'm not arguing otherwise. But it is not known to be possible or plausible at the current time. As such, SA is less speculative at the current time.

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    7. Jeff

      But it is not known to be possible or plausible at the current time.


      It's known to be both possible and plausible to people who actually study the topic and understand the evidence.

      The scientific world doesn't much care if it seems not plausible or not possible to a willfully ignorant knob like you.

      As such, SA is less speculative at the current time.

      Except for the inconvenient fact that UCA has amassed a large amount of positive evidence, while SA has amassed exactly none.

      Reality wins out over Creationist personal incredulity every time.

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  38. J: But why would it not be congruent thus on the basis of common design in some cases? Unless the tree generates maximal nesting depth or something in a way that correlates well with known stratigraphic ranges, you need to be more clear on the relationship of the maximal-depth nesting to the fossil record.

    See my posting on the above thread for a stratigraphic chart. Earlier, you had written about separate ancestry (SA). If you invoke intelligent design, then there's no point in worrying about convergence or congruence. An intelligent designer could produce anything. But intelligent design is scientifically off limits for now, as it provides no testable hypotheses, is unfalsifiable, and there exists no objective evidence for it. There are numerous bad "designs" and in fact all intentional designs we know of arise from brains, which are found only in bilaterian animals. Bilaterians are a late result of evolution and cannot be the source of inspiration for it. Furthermore, the "good" designs we see are better explained by natural selection, as selection, unlike a designer, is demonstrable.

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  39. But no one yet has explained how cladistics corresponds to phenotype-predicting theories or the fossil record in any clear way.

    Cladistics can't be explained in a comment. To really understand it requires some serious study and at least some experience. But here goes: cladistics takes in no information from stratigraphy, but rather data that are morphological or genetic for a group of taxa. An outgroup (or multiple outgroups) are chosen to provide background polarity (information as to which traits [or character states] are ancient ancestral, and which are novelties). This is important because shared primitive traits are uninformative. Then assessing patterns of shared derived traits (synapomorphies), the computer program produces a tree that would optimally produce the character data, under either a criterion of maximum likelihood or parsimony. The generated tree, or cladogram, is a hypothesis of recency of shared ancestry. No taxon is taken to be a direct ancestor of any other under consideration.

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  40. A: An outgroup (or multiple outgroups) are chosen to provide background polarity (information as to which traits [or character states] are ancient ancestral, and which are novelties). This is important because shared primitive traits are uninformative. Then assessing patterns of shared derived traits (synapomorphies), the computer program produces a tree ...

    J: There's the circularity right there. Derived MEANS evolved, doesn't it? That's where you reject SA in the analysis. Thus, you're not comparing it to any other non-arbitrary explanation.

    A: The generated tree, or cladogram, is a hypothesis of recency of shared ancestry.

    J: Right, it's an hypothesis because of the circularity. It's not evidence FOR the UCA hypothesis.

    A: No taxon is taken to be a direct ancestor of any other under consideration.

    J: It matters not since you generate the tree in terms of putatively "derived" traits. The circularity is built into it if what you're saying is relevant to the analysis.

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    1. A: If you invoke intelligent design, then there's no point in worrying about convergence or congruence. An intelligent designer could produce anything.

      J: No, even intelligent designers can't use natural means to produce logically impossible event sequences. Natural laws constrain the LOGICAL possibilities. And ID'ists aren't positing non-natural means. Means in teleology are, by definition, NATURAL.

      A: But intelligent design is scientifically off limits for now, as it provides no testable hypotheses, is unfalsifiable, and there exists no objective evidence for it.

      J: What are the implications of positing single-celled organisms in the precambrian and whatever event regularities you wish which, if empirically verified, would corroborate UCA? NADA. Absolutely NADA.

      A: There are numerous bad "designs"

      J: How do you know they were designed that way?

      A: Bilaterians are a late result of evolution and cannot be the source of inspiration for it.

      J: Inspiration is irrelevant. It's about logical possibilites, calculable probabilities, and number of speculative hypotheses required.

      A: Furthermore, the "good" designs we see are better explained by natural selection, as selection, unlike a designer, is demonstrable.

      J: But the adaptive evolutionary trajectories you posit can not be demonstrated to be possible. They can only be inferred on the assumption that a competent designer did not do the adapting. Once we allow the possibility of competent design to account for the adaptation, there is no way of knowing that positing an evolutionary trajectory that is not known to be possible is plausible. That plausiblity derives from ruling out the only other known analogical inference for certain sequence similarities--common design. This is simply how the logic works since we haven't demonstrated the logical possibility or probability of UCA yet.

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    2. Most of these responses are incoherent. But in the first, it sounds like you are proposing the plot to Prometheus. If your designer is using the wholly natural means of evolution and you want to imagine him smiling and looking on from outer space, that's fine for you.

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  41. But no one yet has explained how cladistics corresponds to phenotype-predicting theories or the fossil record in any clear way.

    Cladograms can then be compared to stratigraphic ranges (see above), or can be used to make predictions about character state combinations.

    For example, computer based cladistic analysis of sauropsids from the 1980s on have confirmed the idea that Archaeopteryx (at the time, unambiguously considered a bird) is nested in (and thus descended from) theropod dinosaurs, more specifically coelurosaurs and more specifically yet a group called the eumaniraptorans. Archaeopteryx has feathers that are indistinguishable from those of flying birds today. It was deemed unlikely that flight feathers arose de novo, and that feathers and precursors of feathers should be found in those theropods most closely related to birds, the coelurosaurs. Restorations of these theropods by inspired paleoartists portrayed them as feathered before confirming evidence came in. That confirming evidence shows bristly to downy "proto" feathers in all major groups of coelurosaurs and vaned feathers (such as those found in the wings and tails of modern birds) in eumaniraptorans.

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    1. If nesting order corresponds to stratigraphic order in a statistically significant way, that would be something significant. You've given me a smidgen of correlation compared to the total possible correspondence of the whole generated trees to the whole fossil succession. How good is the correspondence over-all? How might the assumption of what are derived traits, etc affect the correspondence positively?

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    2. Jeff,

      Let's just say, it's a very good fit if we stick to organisms with mineralized hard parts; these are the only organisms with any sort of chance to have a representative fossil record. The whole history of life, the whole fossil record, and the big cladogram of life would be the subject of many, many, semester hours. You should, if you are interested in being an informed critic of evolution, get to know it a bit. Scientists listened to Stephen Jay Gould's critiques because he know something of which he spoke (although he wasn't always right, either). They are unimpressed with the DI crew because they so regularly make lower-level undergraduate mistakes (like pretending that evolution works through purely chance mechanisms).

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  42. J: There's the circularity right there. Derived MEANS evolved, doesn't it? That's where you reject SA in the analysis. Thus, you're not comparing it to any other non-arbitrary explanation.

    If life hadn't evolved, why indeed worry about derived? Why bother with cladistics in the first place?
    Cladistics was developed long after evolution was accepted based on the good fit of data to nested hierarchy that was perceived as far back before even Linnaeus, plus explanation of biogeography, structures that seemed to be exaptations, etc. Universal common descent was established on the basis of a common genetic code, ubiquitous genes shared throughout life, ribosomes, ATP, etc. etc. Under separate ancestry, all this and more would have to be explained by ridiculously massive amounts of convergence (see Theobald in Nature).

    Given the overwhelming evidence for common ancestry, cladistics was developed as an optimal technique for deriving phylogeny. It does indeed assume common ancestry (for all taxa under consideration, but unique patterns of common ancestry not for any particular subsets). Where you can assess the validity of common descent (if you like) is through comparison: against stratigraphy, morphological vs. molecular congruence, sequences vs. indels, etc. etc.

    You can indeed run a (meaningless) cladistic analysis on inanimate objects such as books, but the consistency index will be low (lots of convergence, little information explained by the model of branching descent).

    Cladistics is not employing circular reasoning; common descent had been established first. That is a model you must work to reject as either a null hypothesis or in competition with multiple scientific (no Goddidit) hypotheses.

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    1. anaxyrus:

      Cladistics is not employing circular reasoning; common descent had been established first. That is a model you must work to reject as either a null hypothesis or in competition with multiple scientific (no Goddidit) hypotheses.

      Since you rule out certain hypotheses a priori you must forfeit either realism or completeness. And since you are an evolutionist, it seems the latter is ruled out (even consciousness is explained by evolution, the hypothesis that seems to have no limits). So you must be forfeiting realism, right?

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    2. Ruling out the influence of the Easter Bunny doesn't seem unrealistic.

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    3. Or Russell's teapot if one wants to sound fancy.

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    4. CHSince you rule out certain hypotheses a priori you must forfeit either realism or completeness.

      1. No hypotheses are ruled out a priori
      2. Nevertheless, science opts for realism over completeness. Did you not know this?

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  43. A: Cladistics is not employing circular reasoning; common descent had been established first. That is a model you must work to reject as either a null hypothesis or in competition with multiple scientific (no Goddidit) hypotheses.

    J: Good. That's settled then. Cladistics is not the evidence for UCA. Now, convergence is an evolutionary interpretation of morphology or molecular sequence, so convergence is not an antithesis to UCA. And this is the point. The alternative to UCA is not convergence, contra Theobald, it's SA in terms of common design of function and the anatomy, genetics, etc that produces the function.

    If you reject common design, there are no non-arbitrary alternative hypotheses to UCA or something like it. It's all that's left inductively speaking. It wins for that reason alone. No evidence is necessary other than that similarity of sequence is caused by inheritance. This is the background AGAINST which convergence is inferred to have occurred where unobserved.

    SA apart from ID is not an explanation at all. What evidence is there for full blown ancestors arising to account for the SA? So why posit any more abiogenesis than necessary? We haven't even explained one case yet; not even close.

    But you have a huge problem as an atheist, agnostic or deist. How do you know anything to speak of? How do you know that analogy and, therefore, parsimony, etc are valid criteria for hypothesis rejection? There is no way to know there is such a thing as an evidentiary relation once you posit that evolution isn't teleological. For then you can't even rule out epiphenominalism, etc. There is no a priori way to know, in that case, that thought has any role in organismal adaptation. And therefore all thought could be illusory and have no impact on organismal survival.

    You can't prove there are proofs. And it is not conceivable how you could claim anything else is intuitive if the mind is not at least intuitively known to be designed to know in the first place.

    By ruling out the ID-style SA alternative, you've proven entirely too much--that knowledge is indistinguishable from blind faith.

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    1. Darn it anaxyrus, Jeff tricked you into disproving all knowledge. Now I will never find my car keys.

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    2. V, how do YOU distinguish between blind faith and knowledge? Let's say you believe your car keys are in your pocket. What's the difference in believing that blindly and knowing it, per your epistemology.

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    3. I may believe it but not blindly,since my Natural inferential tendency is to believe material object the size of keys do not posses the power in themselves of voluntary movement. Another inferential tendency is to believe in an external world and continuity of experience.

      As you say to burden of dissent falls to you

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  44. Jeff

    But you have a huge problem as an atheist, agnostic or deist. How do you know anything to speak of? How do you know that analogy and, therefore, parsimony, etc are valid criteria for hypothesis rejection? There is no way to know there is such a thing as an evidentiary relation once you posit that evolution isn't teleological. For then you can't even rule out epiphenominalism, etc. There is no a priori way to know, in that case, that thought has any role in organismal adaptation. And therefore all thought could be illusory and have no impact on organismal survival.


    Wow Jeff, that word salad is reaching batspit77 depths of incoherence. Maybe it's time to knock off the glue sniffing.

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  45. Cornelius Hunter:
    In fact evolutionists do not have a scientific explanation for the large-scale change their idea requires.

    This confirms what I have always believed. As I have scanned through the posts I did not see any explanation of how evolution really works. Do we not need to know how evolution really works before we can assert that it does work?

    I have asked this question before on various blogs including this one. I have phrased my question in various ways and have never gotten a direct answer. I will ask the question again.

    An evolutionary event, as I will call it, has to be one step in a long series of minor and major morphological changes that eventually result in significantly different body plan. The obvious example is the transition from land mammal to whale.

    Even a minor morphological change has to be the result of complex series of lesser changes. If a morphological change begins with a mutation that creates a new protein, we only have the fundamental building block of what ultimately will be built.

    A building block is one thing. Directing the assembly of proteins into tissues, tissues into organs, and organs into body plans is another. Stephen Meyer has said there is evidence that a genetic mutation does not affect the body plan. If that is true, then how is evolution by random genetic mutations even possible?

    This reminds of the series of complicated equations that a scientist writes on a blackboard. There is a big gap in the middle where he says, “Then a miracle occurs.” Another scientist says, “You should be more explicit here in step two.”

    Random mutation -> A miracle occurs -> New body plan.

    What do scientists really know about what happens in step 2? Do scientists have an explanation for the large scale change that their idea requires?

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    1. Doublee:

      Cornelius Hunter: In fact evolutionists do not have a scientific explanation for the large-scale change their idea requires.

      Doublee: This confirms what I have always believed. As I have scanned through the posts I did not see any explanation of how evolution really works. Do we not need to know how evolution really works before we can assert that it does work?

      I have asked this question before on various blogs including this one. I have phrased my question in various ways and have never gotten a direct answer. … What do scientists really know about what happens in step 2? Do scientists have an explanation for the large scale change that their idea requires?


      The response will be a series of bait-and-switch shell games. Here are some common types of responses that you’ll hear in various flavors and sequences:

      1. Random mutations, drift, selection and other such mechanisms can work wonders.

      2. In any case, evolution is an established fact that no serious biologist doubts.

      3. If evolution had any serious problems, believe me, it would have been jumped on long ago. That’s what science is all about.

      4. If you have a refutation of evolution, then great, let’s hear it.

      5. If you have a scientific alternative to evolution, then great, let’s hear it.

      These are all phony responses to distract attention from the absurd claim that evolution is a fact.

      Delete
    2. Doublee, please excuse CH his silly propaganda. He's just doing what he's paid to do.

      Please see my answer below for the correct, non-spun information.

      Delete
    3. Cornelius insist that evolutionists falsely claim that evolution is a fact.

      Even though he refuses to say which phenomena, sometimes referred to as "evolution", are not facts, in his view.

      i.e. he equivocates with the word evolution, while simultaneously, but without giving any supporting evidence, claiming that this is what "evolutionists" are doing.

      Delete
    4. Elizabeth:

      I really don't understand why you think Cornelius equivocates. Is it not clear that what we are talking about is major morphological transitions rather than minor genetic changes?

      Nobody argues with the changes that can be demonstrated by laboratory experiments.

      Michael Behe has defined the edge of evolution, which he places somewhere in the series of Genera, Families, and Orders. Those transitions beyond the edge of evolution are what I am asking about.

      If scientists do not yet know an answer to a question is there any harm in saying so?

      Delete
  46. Doublee

    Random mutation -> A miracle occurs -> New body plan.

    What do scientists really know about what happens in step 2? Do scientists have an explanation for the large scale change that their idea requires?


    Yes Doublee, for a lot of it they do. This book

    Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom

    by Sean Carroll is an excellent layman's description of the science of evolutionary development (evo-devo for short) that describes the evolution and development of new body plans.

    Another excellent book along the same lines is

    Your Inner Fish

    by Neil Shubin that traces the evolutionary development of the body's major organs.

    Hope that helps.

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    1. Thorton:

      I did find this in the introduction to Endless Forms Most Beautiful. using the Look Inside feature on Amazon.com.

      We now understand how complexity is constructed from a single cell into a whole animal. And we can see, with an entirely new set of powerful tools, how modifcations of development increase complexity and expand diversity.

      This book looks like it's worth a read.

      Delete
  47. J: Cladistics is not the evidence for UCA.

    But the hierarchy of the vertebrates, which was discovered before cladistics, and in part even before science, is part of the evidence, as is the fit between phylogeny and stratigraphy, the congruence of multiple data sets, and the superior consistency of true cladograms of organisms versus designed objects.

    J: The alternative to UCA is not convergence, contra Theobald, it's SA in terms of common design of function and the anatomy, genetics, etc that produces the function.

    Common "design" in anatomy and genetics that is not derived from common ancestry is analogy, rather than homology, and is explained by convergence. Saying this convergence is due to an intentional designer is an easy out, but without independent evidence of the designer, too easy a cop out for science.

    J: If you reject common design, there are no non-arbitrary alternative hypotheses to UCA or something like it. It's all that's left inductively speaking.

    Nope, there could indeed be evidence that infers separate ancestry. Non-carbon based life, life separated from (Bacteria + Eukarya) that lacks the shared traits, life that is not DNA/RNA based. In fact, common ancestry for viruses has not been established beyond reasonable doubt. Nor are they unified with our monophyletic tree of life.

    So common ancestry is a scientific inference, not a philosophical necessity.

    J: why posit any more abiogenesis than necessary?

    Exactly. But saying your baramins are designed doesn't get you out of this. Where did your hypothesized two original mammals come from? The Garden of Eden? Noah's ark?

    How do you know that analogy and, therefore, parsimony, etc are valid criteria for hypothesis rejection?

    Maximum likelihood is the preferred criterion for rejecting hypotheses due to low probability. Parsimony is used sometimes with morphological data. Maximum likelihood can be used with the same data to check for congruence, and we can also compare results of multiple authors.

    Because these techniques work with living organisms, and because they lead to the very predictions. There's no reason to find pennaceous feathers on dinosaurs if they are not ancestors of birds. No reason to look for flow-through lungs in alligators if they are not more closely related to birds than lizards. No reason to look for a frameshift mutation in the manus of a developing chick if birds are not dinosaurs. But, like Einstein's bent light, all of these predictions came true. Science works, even if we don't have philosophical "proof" of our ideas. Philosophy didn't put us on the Moon.


    J: And it is not conceivable how you could claim anything else is intuitive if the mind is not at least intuitively known to be designed to know in the first place.
    By ruling out the ID-style SA alternative, you've proven entirely too much--that knowledge is indistinguishable from blind faith.


    Wrong and wrong. Pretending the mind is purposfully designed rather than honed by natural selection doesn't change its function, which has worked well especially since losing the shackles of imaginary creators and designers. It takes no faith to infer that the processes we see going on today have gone on in the past, as the results of the scientific program based upon this assumption are remarkable. It takes great faith to infer a designer when known mechanisms that can do the job exist, and when the concept of designed life came from people who believe in gods

    ReplyDelete
  48. A: But the hierarchy of the vertebrates, ... is part of the evidence

    J: We have reason to believe significant evolution could occur with SOME succession of environments with SOME time-frame. But we have no reason to believe the the posited evolution occurred with the historical succession of environments in the posited time-frame. It's still more desparate to posit lots of a-teleological, abiogenetic origins of ultimate ancestors.

    A: as is the fit between phylogeny and stratigraphy,

    J: The phylogeny is not predicted from a predictive theory.

    A: and the superior consistency of true cladograms of organisms versus designed objects.

    J: Which designed objects have you done cladograms for that you know were designed with nesting depth as a design objective?

    A: Saying this convergence is due to an intentional designer is an easy out,

    J: If the sequences are due to a designer in the sense of SA common design, it isn't convergence at all.


    A: Nope, there could indeed be evidence that infers separate ancestry. Non-carbon based life, ...

    J: If you found a cat that wasn't DNA/RNA based, would you infer that it arose a-teleologically? Because if so, you are metaphysically committed in a very arbitrary way.

    A: Where did your hypothesized two original mammals come from?

    J: ID-style SA would have to place inferred ancestors prior to their descendants in the fossil record, at minimum. The logically relevant point is that libertarian causality either occurs or it doesn't. If it doesn't, I have no way of inferring that you are intentionally attempting to communicate via the words on this web page. If all belief is natural or uncaused, all belief is blind.

    A: Maximum likelihood is the preferred criterion

    J: But you're not using likelihood of evolutionary events in terms of an evolutionary CAUSAL theory. And that's the only likelihood relevant to the predictive claims.

    A: There's no reason to find ...

    J: Your tree has a hard beginning. There is no biological reason for any of it, ultimately, per your view.

    A: No reason to look for flow-through lungs in alligators if they are not more closely related to birds than lizards.

    J: From a teleological point of view, the reason is that the alligator lung adapts it (or did in the past) to its environment more parsimoniously with the rest of its intended functions than other lungs.

    A: ... all of these predictions came true.

    J: They're not predictions. There is no predictive theory applied to the relevant initial conditions that IMPLIES the effects. A scientific prediction is an IMPLICATION of a predictive theory applied to some initial conditions.

    A: Philosophy didn't put us on the Moon.

    J: If you don't think teleology, logical deduction and logical induction put us on the moon, you are very confused.

    A: Pretending the mind is purposfully designed rather than honed by natural selection doesn't change its function,

    J: You think you can infer accurately that the mind infers accurately. Huh? Dude, something has to be obvious for anything else to be inferrable. It is ridiculous to claim that UCA is what is intuitive rather than THAT there is a teleological causal relation.

    A: which has worked well especially since losing the shackles of imaginary creators and designers.

    J: You've just made my point. You're admitting that evolution is not known to depend on true beliefs. But that means you can't even know that whatever you believe effects any other being.

    A: It takes no faith to infer that the processes we see going on today have gone on in the past,

    J: On the contrary. By your view, it takes blind faith to believe most of your apparent memories are actual memories, etc. Because you can't prove evolution or biological life depends on apparent memories, etc at all. And it certainly isn't an intuitive given in your theory. Thus, to even believe that is to believe it blindly.

    ReplyDelete
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    1. Jeff,

      How is that Prius tree coming along? Lots of branches, I presume?

      Delete
    2. Jeff: We have reason to believe significant evolution could occur with SOME succession of environments with SOME time-frame. But we have no reason to believe the the posited evolution occurred with the historical succession of environments in the posited time-frame.

      Sure we do. We have the fossil succession, among other evidence.

      Jeff: The phylogeny is not predicted from a predictive theory.

      Of course it is. A nested hierarchy is the consequence of descent with modification and bifurcating descent.

      Jeff: If you found a cat that wasn't DNA/RNA based, would you infer that it arose a-teleologically?

      If you found a cat that wasn't DNA/RNA based, it would almost certainly be artificial.

      Jeff: ID-style SA would have to place inferred ancestors prior to their descendants in the fossil record, at minimum.

      Got it.

      Basically, you're claiming that some unknown designer using an unspecified mechanism did it that way for inscrutable reasons. A non-explanatory explanation.

      Jeff: There is no predictive theory applied to the relevant initial conditions that IMPLIES the effects.

      To repeat ourselves in other words, descent with modification and bifurcating descent *implies* a nested hierarchy.

      Delete
  49. Oleg, you are one confused puppy.

    ReplyDelete
    Replies
    1. Maybe I am, Jeff. Why don't you enlighten me?

      Can I see your Prius tree for starters?

      Delete
  50. This comment has been removed by the author.

    ReplyDelete
  51. Elizabeth has already explained it to you. Go above and read it. A, in turn, has rightly admitted that cladistic trees are not evidence for UCA. He has rightly admitted that the ASSUMPTION of UCA is used to infer derived traits which are, in turn, used in the cladistic analysis.

    Oleg, humans don't have nesting depth, etc as a design objective when they create new models of vehicles. Why, then, would you expect the trees generated therefrom to demonstrate such tree characteristics? The SA teleological inference works differently. We don't explain the cladistically-generated depth of nesting in terms of a predictive theory from initial conditions (because no one can). Rather, we see a conceivable purpose for the nesting depth--a fit to the way humans prefer to classify--and infer it as a purpose along with our other teleological inferences, like "eyes are for seeing," etc.

    Then, we interpret similarity of function-producing sequence as common design. And to the extent that phenotypes fall plausibly into lineages without radical, unpredictable saltational gaps, we interpret a lot of similar sequences as being inherited, as well.

    We don't assume that saltations occurred every time a significant morphological gap exists to the next most similar, but systematically different, lineage. Saltations for mammals, etc seem implausible analogically. And there is no predictive theory that predicts them from the intial conditions of other lineages in the posited time-frame in terms of descent.

    How A can say this approach implies the existence of more convergence is beyond me. Unless, i.e., he insists that SA must be a-teleological, thereby ruling out common design as an explanation of similar sequences. But that is utterly absurd for the reasons I explained to him above.

    ReplyDelete
    Replies
    1. May I see the Prius tree, Jeff? You wrote that it could be generated. Let's see it. Pretty please?

      Delete
  52. I don't have to generate it. Elizabeth has already admitted that such trees can be generated. She just doesn't like them. What's that got to do with a hypothesis being falsifiable? Nothing.

    State your hypothesis and tell me what the empirical predictions entailed therein are. Short of that, you don't have a falsifiable hypothesis. That means all we have is analogy. That's what ID'ists are using. That's all you have. But every time you posit convergence that is not predicted by the theory in terms of the relevant initial conditions, you're just rendering UCA more and more arbitrary (i.e., non-analogical). ID-style SA is MUCH, MUCH more analogical.

    ReplyDelete
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    1. Jeff,

      I don't think you understand what Liz wrote.

      And as I've said several times, yes, you can fit a tree model to any dataset of entities with shared characteristics, just as you can fit a linear slope to any bivariate set of data. The issue is how good the fit is, and whether it is a better fit than some alternative model..

      Let me unpack this for you. When one says that any data set can be fitted to any type of curve it does not mean that said curve describes the data well. Here is a set of points: (0,0), (1,1), (2,4), (3,9), (4,16). You can surely fit them by some straight line, but it will not be a good description of these data points. Because these points actually sit on a parabola. That has nothing to do with me not liking the linear fit. One can devise objective (i.e., observer-independent) criteria to compare the fits provided by different curves. The parabola will win over the straight line any day.

      So it is with trees. You can try hard to devise a tree for the Toyota Prius and its "ancestors" and "siblings" but the results will be comical because the tree model does not work all that well for cars. Your "tree" will be a short linear progression: Prius Generation I, Prius Generation II, Prius Generation III. And so it will be with Honda Civic. Instead of a universal tree of cars you will get a bunch of independent linear progressions, with an occasional branching when a hatchback model is added to a sedan line. They arise suddenly (saltation all the time), with no relation to previous models.

      In contrast, ancestry is well described by a tree (say, the patrilineage). Even in the absence of reliable genealogical records, paternity can be determined in an objective manner through a genetic analysis. Genomes of closely related individuals exhibit fewer differences than genomes of more distant relatives, which in turn have fewer differences than people of different ethnic origin etc. One can devise a simple metric that allows an objective determination of the degree of relatedness and thus enables one to construct a tree. There is no way to do this with cars.

      So a tree model does not always work well. Trees are suitable for patrilineages but not for car models. When one says that some relations are fit by a tree model your ears should perk up because it is a nontrivial statement. Not every collection of objects forms a tree. Just like not every set of data points lies on a straight line.

      Of course I knew that a Toyota Prius would not be found on a grand tree of cars. My repeated nudges were meant to get you to a simple but very important point: not every model is a good description of reality. Saying that phyletic trees work well is a nontrivial statement because they don't work well in most cases (e.g., cars). That they do work well suggests that the theory predicting such relations might be right.

      Delete
    2. O: ... with an occasional branching when a hatchback model is added to a sedan line. They arise suddenly (saltation all the time), with no relation to previous models.

      J: Right. No one is arguing that the branching will be the same. The question is, what kind of criteria are you using? Elizabeth mentioned nesting depth. What does nesting depth have to do with what phenotypes we would predict at the relevant stratigraphical points in the posited time-frame? Short of that correlation, how does the nesting depth, etc indicate a thing about UCA? Fossil succession does not equal evolution in terms of any conceivable logic unless just rule out final causes methodologically. That's fine, of course. But it leaves CH's point precisely intact--not to mention that you create the problem of being able to distinguish knowledge from blind faith (if you define blind faith as any belief that is acquired non-intuitively and non-rationally, inferentially speaking).

      For research guidance, of course we want to see what kinds and trajectories of variation are plausible in terms of time-frame and environments. But that is different than claiming we know that answer up front. We don't.

      Delete
    3. Jeff,

      You should reread Elizabeth's comment and pay close attention to the examples she gave.

      There is no requirement for a minimum nesting depth. What matters is not the number of layers but the right topology. A tree can be shallow (Liz's Fin "clade" has just tree levels) and still be a perfect tree. The two trees showin in this image individually have more depth but together they do not form a tree. You cannot start on one tree, move along its branches, and arrive on some branch of the other tree. It just doesn't work.

      The car example demonstrates the same. You can start with the latest Prius model (2009-today). It has a predecessor that looks almost exactly the same (2004-2008) and retains a large number of parts from it. These two models form a "clade." You can go deeper into the past and look at the first-generation Prius (1997-2003). It looks quite different on the outside, so one may or may not call it an ancestor just by the looks. But on the inside it is very much the same. Lots of parts were carried over, with minor modifications. So let's extend the lineage to include Prius I. We have a Prius "clade" that contains three levels. It even branches out somewhat at the top: the third generation includes Prius v and Prius c. But there is no way to extend the lineage any further into the past. There are no cars that resemble Prius I even remotely.

      So the Priuses arguably form a tree. Cars overall do not. It's a bunch of unconnected sticks or a grassy field, but not a tree.

      You can find faults with the car analogy, but this toy example is great because we know the history of cars pretty well. If we didn't, we could still try to classify them by inventing a metric that does not rely on our subjective impression (it looks like a Prius). That could be, for example, the percentage of identical parts shared by two cars. The score would be high for the latest Prius and its predecessor, quite small for the latest Prius and the Toyota Corola, close to zero for the Prius and the Ford Mustang.

      In fact, this is how phylogenetic trees are built on the basis of genome comparison. We share 99 percent of our genes with chimpanzees (which is a pretty close match if you compare it to cars). With gorillas, 98 percent. If the changes are due to mutations occurring at certain rates then the difference means that human and chimpanzee lineages parted way relatively recently. Gorillas are part of a clade that branched away (from us and chimpanzees) at an earlier point in time. That's roughly one of the methods used to establish evolutionary relationships.

      Delete
  53. Jeff, with some classic creationist quotemining:
    A, in turn, has rightly admitted that cladistic trees are not evidence for UCA. He has rightly admitted that the ASSUMPTION of UCA is used to infer derived traits which are, in turn, used in the cladistic analysis.


    While the fact that we can perform cladistics is not evidence for UCA, the congruence among data sets and superior consistency compared to cladograms of objects that lack inheritance (like books) IS evidence for nested hierarchical structure. The fossil record provides independent testing. Those primitive traits indeed show up earlier in the fossil record than derived traits.

    We end up with compelling evidence for evolution.
    If you were as honest as I was, you would acknowledge this.

    ReplyDelete
  54. Jeff: We have reason to believe significant evolution could occur with SOME succession of environments with SOME time-frame. But we have no reason to believe the the posited evolution occurred with the historical succession of environments in the posited time-frame.

    Wrong, again confusing evolution with a random search. The time scales available for macroevolution are vast, so that we have to posit stabilizing selection to have been historically much more common than positive selection.

    We have every reason to think evolution did indeed occur historically on Earth. We have already established that you don't seem to know anything about historical geology and the fossil record (prob. other than there are gaps), so why would you make bald assertions about it?

    ReplyDelete
  55. A: Where did your hypothesized two original mammals come from?

    J: ID-style SA would have to place inferred ancestors prior to their descendants in the fossil record, at minimum. The logically relevant point is that libertarian causality either occurs or it doesn't. If it doesn't, I have no way of inferring that you are intentionally attempting to communicate via the words on this web page. If all belief is natural or uncaused, all belief is blind.


    If the IRS comes asking about your taxes, I suggest that you don't try this word salad bluff approach. This type of obvious avoidance suggests fundamental dishonesty. If mammal ancestry is separate from all non-mammals, and if there were a pair of original mammals, then an honest answer from you might have looked like:

    "Yahweh spoke, and the first mammals appeared."

    ReplyDelete
  56. A: ... all of these predictions came true.

    J: They're not predictions. There is no predictive theory applied to the relevant initial conditions that IMPLIES the effects. A scientific prediction is an IMPLICATION of a predictive theory applied to some initial conditions.


    Those were obvious instances of evolution being a predictive theory. More dishonesty.

    ReplyDelete
  57. A: Those primitive traits indeed show up earlier in the fossil record than derived traits.

    B: There's your circular reasoning again. You infer to be evolution what you already know indicates evolution by mere stratigraphic order. Mere time passage is not a cause.

    A: The time scales available for macroevolution are vast, so that we have to posit stabilizing selection to have been historically much more common than positive selection.

    J: On the contrary, the number of possible DNA sequences is so vast that the time scales are not known to be anywhere near sufficient. Nor is positing tons of historical contingencies to save you from the theoretical obligation to predict phenotypes known to solve the problems. They're merely ASSUMED to solve them.

    A: We have already established that you don't seem to know anything about historical geology and the fossil record (prob. other than there are gaps), so why would you make bald assertions about it?

    J: My assertions have to do with what is not knowable. You seem to think mere fossil succession is evidence for natural causality over final causality. It's not. SA is MUCH, MUCH more analogical than UCA. You were being sensible when you just admitted that you reject ID causality on methodological grounds.

    The fact that you go back and forth is evidence that you really reject ID on metaphysical grounds as well. Either way, it's not induction at work for you on the two approaches. You reject one out of hand for personal preferences. Analogy, per se, works MUCH better for ID-style SA.

    ReplyDelete
    Replies
    1. A: Where did your hypothesized two original mammals come from?

      J: ID-style SA would have to place inferred ancestors prior to their descendants in the fossil record, at minimum. The logically relevant point is that libertarian causality either occurs or it doesn't. If it doesn't, I have no way of inferring that you are intentionally attempting to communicate via the words on this web page. If all belief is natural or uncaused, all belief is blind.

      A: If the IRS comes asking about your taxes, I suggest that you don't try this word salad bluff approach. This type of obvious avoidance suggests fundamental dishonesty. If mammal ancestry is separate from all non-mammals, and if there were a pair of original mammals, then an honest answer from you might have looked like:

      "Yahweh spoke, and the first mammals appeared."

      A: Notice how you changed the subject. Originally you asked where they came from in terms of a garden or an ark. Now you're meaning which designer. I answered the way I did to show that whoever the designer is, the ancestors have to proceed their descendants stratigraphic range, at minimum. As a causal hypothesis, it matters not who the designer is. It matters that design is a causal mode that produces intentional, purposed effects.

      But as to whether the causal agency is initiated by speaking, I'm good with that. Final causality is FREE. That alone means we can't constrain it in terms of antecedent conditions. So however it happens is FINAL in that sense.

      Are you free? If not, I won't bother arguing with you since you have no control over your attention to the question at hand. Clearly you demonstrate a difficulty avoiding gross circular reasoning.

      Delete
    2. A: Those primitive traits indeed show up earlier in the fossil record than derived traits.

      B: There's your circular reasoning again. You infer to be evolution what you already know indicates evolution by mere stratigraphic order. Mere time passage is not a cause.


      No, primitiveness for a character is determined by its distribution in the cladogram, completely independent of stratigraphy. You cry out "circular reasoning" yet again without having any notion of which you speak.

      On the contrary, the number of possible DNA sequences is so vast that the time scales are not known to be anywhere near sufficient. Nor is positing tons of historical contingencies to save you from the theoretical obligation to predict phenotypes known

      Technically, it is not known that the time scales are INSUFFICIENT, and plenty of reason to think that it is sufficient. It is actually deep conservation that requires explanation. Most genetic differences among species are explicable by drift without even any recourse to positive selection. Why do you pretend to know anything about genetics when it is obvious you don't.

      J:Notice how you changed the subject.

      Notice how you still don't answer the question. I didn't ask when the first two mammals appeared (before their descendants - duh). I asked how did they arrive on Earth (there's ZERO reason to think this pair would be fossilized, btw). You're good with a pair of mammals being "spoken" into existence. I guess that is about all I'll get for an answer. I'm free for the first two minutes, 99 cents each additional minute.

      Delete
  58. A: Those were obvious instances of evolution being a predictive theory. More dishonesty.

    B: State the predictive theory that is known to predict currently occurring phenotypes at the relevant times. Then apply it to the relevant initial conditions in the past and deduce the subsequent phenotypes. Can't do it. You have no predictive theory that has any KNOWN correspondence to real-world causality.

    ReplyDelete
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    1. This isn't a serious objection, Jeff. You might as well argue that statistical physics fails because it does not predict where and when each molecule of gas will hit the wall. The failure to predict everything does not make a theory a failure. The success metric is quite different. A theory must make some falsifiable predictions and survive these tests.

      Delete
  59. J: If the sequences are due to a designer in the sense of SA common design, it isn't convergence at all.

    Convergence of design or thought, if not convergent evolution. But much more easily explained away if we smuggle in imagined gods or space aliens.

    If you don't think teleology, logical deduction and logical induction put us on the moon, you are very confused.

    Philosophy was not sufficient, it required scientific investigation of the physical universe. Philosophy has contributed, and induction and deduction were incorporated into science. Teleology hasn't been as helpful and is not widely embraced.

    J: You think you can infer accurately that the mind infers accurately. Huh? Dude, something has to be obvious for anything else to be inferrable. It is ridiculous to claim that UCA is what is intuitive rather than THAT there is a teleological causal relation.

    Rational, evidence-based inference takes training, and indeed to progress in science we need to unlearn our naive sense of teleology. Most people don't unlearn this, hence it's a sticking point between scientists and broader society.

    it takes blind faith to believe most of your apparent memories are actual memories

    No, that's why we have witness corroboration, writing, photography, videography, and most importantly for science, peer review, replication, archival of data and specimens, and organization of knowledge.

    ReplyDelete
  60. State the predictive theory that is known to predict currently occurring phenotypes at the relevant times. Then apply it to the relevant initial conditions in the past and deduce the subsequent phenotypes. Can't do it. You have no predictive theory that has any KNOWN correspondence to real-world causality.

    That there are chance mechansims involved in evolution has not precluded the ability of scientists to make predictions. Just as we can make weather predictions, we can predict character state combinations for fossils and for living organisms. Your statement amounts to "Meteorology is not a predictive science because you can't predict the near future with perfect accuracy, or the far future with great accuracy at all. You can't even take weather data from a year ago and model weather and climate going forward. Can't do it."

    You seem to have a naive view of science as unmitigated causality due to steadfast natural law. Chance and stochastic behavior abound in nature and the natural sciences.

    ReplyDelete
  61. Jeff: He has rightly admitted that the ASSUMPTION of UCA is used to infer derived traits which are, in turn, used in the cladistic analysis.

    We assume a theory of gravity to infer movements of bodies which are, in turn, used in orbital analysis. If the observations fit the predictions, then it tends to support the theory. That's how hypotheses are tested.

    Jeff: Rather, we see a conceivable purpose for the nesting depth--a fit to the way humans prefer to classify--and infer it as a purpose along with our other teleological inferences, like "eyes are for seeing," etc.

    Hard to make sense of that. Why would the designer arrange the traits of organisms to fit the way humans prefer to classify? And if so, then why the exceptions?

    Let's try this: Do you understand that bifurcating descent with modification will result in a nested hierarchy of traits?

    Jeff: You infer to be evolution what you already know indicates evolution by mere stratigraphic order. Mere time passage is not a cause.

    The fossil succession supports descent with modification.

    Jeff: On the contrary, the number of possible DNA sequences is so vast that the time scales are not known to be anywhere near sufficient.

    Evolution doesn't search the vast majority of possible DNA sequences.

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    1. A: Evolution doesn't search the vast majority of possible DNA sequences.

      J: How is the search constrained to a minority of DNA sequences? How do you determine how long it's mode of search will take to produce trilobites from single-celled organisms by the posited time in terms of the succession of environments that occurred in that period?

      Mutations rates don't do it. Rates, per se, are insufficient. Mutations can occur with stasis. Mutation rates don't prevent extinction.

      Delete
    2. Oh, for crying out loud.

      Evolutionary search is not constrained to a minority of sequences. It just does not have enough time to sift through all of them.

      Stasis does not mean that mutations stop.

      Mutations rates don't prevent extinctions. Trivially true. In the same way as watching TV does not cause rain. So what?

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  62. J: mere fossil succession is evidence for natural causality over final causality. It's not.

    The fossil record provides support for the monophyly of cellular life on Earth that is inferred from shared genetics. If SA is much more analogical from your perspective, that's irrelevant in science because UCA explains the data better. ID on the other hand, is rejected due to lack of specific evidence in its favor, parsimony, and lack of falsifiability.

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  63. So, Oleg, is statistical physics successful at predicting statistical bounds and/or tendencies? If not, why is it called statistical physics. But with UCA, we can't even do that. You've already admitted that the historical contingencies render phenotypical trajectories (and/or extinctions) unpredictable from the initial conditions.

    We can't even describe the predicted tree statistically in terms of genetics alone. We have to make the blind assumption that such things as nesting depth, etc, just magically DO correlate with some non-observed, non-predictable, historical, evolutionary process. But blind assumptions are themselves hypotheses in need of evidence. Inferences from blind assumptions are also blind. The fact that fancy analysis is involved is irrelevant.

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    1. Jeff,

      Once again, you are using the wrong metric. A scientific theory is judged not by what it cannot do but by what it can.

      Statistical physics is unable to predict the trajectory of any given particle in a box containing molecules of gas. It cannot even predict in which half of the box this particular molecule will be in a few microseconds. What it can predict is the average number of molecules that will hit the wall per unit time.

      Likewise, theory of evolution makes statistical predictions such as the rate of divergence for genomes of two species that branch out from each other. See molecular clocks. Scientists do make assumptions that these rates remained the same in the past, but the assumptions of uniformity are made in other branches of science. For instance, in physics we assume that the speed of light (and other universal constants) remained the same in the past and that rates of radioactive decay were the same a billion years ago as they are today. You can question these assumptions, but you will have to explain why they are unreasonable and perhaps point out counter examples.

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  64. A: If SA is much more analogical from your perspective, that's irrelevant in science because UCA explains the data better. ID on the other hand, is rejected due to lack of specific evidence in its favor, parsimony, and lack of falsifiability.

    J: What does the UCA hypothesis explain? That there is an observed fossil succession? No, that's what UCA MEANS! That the inferred trajectories are explicable by known genetics, etc? No, because they're not. Just WHAT, then, does UCA explain? IOW, what observable fact that is not entailed in the very meaning of the hypothesis of UCA is implied BY it?

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    1. Again, wrong question. You are taking one part of a theory out of context and ask what it explains.

      To see the absurdity of your question, try it with Newtonian mechanics. What does Newton's first law of motion explain? The answer is nothing, of course. You can't take that part of mechanics and apply it with any degree of success. You need quite a bit more structure to make predictions. A theory, in other words.

      The UCA alone does not explain much. But it is not a standalone theory. It is part of evolutionary biology.

      Back to the drawing board.

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    2. Newtonian formulas predict (and therefore explain in that sense) observations by applying the formulas to intial conditions. That's what any causal (i.e., predictive) theory does. It allows deductions (i.e., predictions), when applied to initial conditions, that can be tested against the real world. We have no theory that works for historical UCA even probabilistically or statistically that way.

      That's why nesting DEPTH as opposed to nesting per se is made so much of. Descent with variation is consistent with an infinite set of nesting depths and branching patterns. So we need a theory that PREDICTS the nesting depth in terms of the relevant precambrian initial conditions. We have nothing remotely like that. So all we know from cladistics is the same thing we knew already--we can't empirically falsify UCA. Be we can't empirically falsify SA, either, so it matters not.

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    3. Jeff,

      You are not reading carefully or you are not thinking through your replies. Newton's first law does not contain any formulas or initial conditions. It allows no causal deductions. Read its formulation. Then ponder what I wrote above.

      That's why nesting DEPTH as opposed to nesting per se is made so much of.

      That's about the opposite of what Elizabeth and I have tried to tell you. Go back. Read slowly. Think. Then reply.

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  65. What does the UCA hypothesis explain?

    All the commonalities of cellular life on Earth, genetic and phenetic, from bacteria to birds. Why cladograms match up with stratigraphy, but also with geography (there are clades of South American dogs and cats, as just one of numerous examples). Why morphologically complex forms (vertebrates) from the deep past share so many traits with living, but are not identical to them.

    And before you hit "circular" on the findings of cladistics, recall that Darwin and other early naturalists found the same, and that there is zero geographic input into a cladogram.

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  66. What does the UCA hypothesis explain? That there is an observed fossil succession? No, that's what UCA MEANS!

    This is weapons grade ignorance. We could have UCA and no fossil record. Fossil succession was established long before common descent. It was presumed at the time that the slate was wiped clean after each epoch, and life started anew. Then later scientists started to observe surviving species and the greater similarities of stratigraphically adjacent layers.

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  67. J: What does the UCA hypothesis explain?

    A: All the commonalities of cellular life on Earth, genetic and phenetic, from bacteria to birds.

    J: No, A. That's not an implication. That's an inference you have made to minimize convergence, etc. But none of those trajectories are known to be possible or possible in terms of the actual history. ID-style SA doesn't even posit that most of the analogies are convergent.

    A: Why cladograms match up with stratigraphy,

    B: First of all, you've admitted that you feed the analysis what is "derived." Of course it would match to some extent. Second, to WHAT extent does it match when NO such information is used--when ONLY traits are used. THAT would be an interesting correspondence--not because it's predicted, but because it corresponds at all.

    A: but also with geography (there are clades of South American dogs and cats, as just one of numerous examples).

    J: How is this inconsistent with SA?

    A: Why morphologically complex forms (vertebrates) from the deep past share so many traits with living, but are not identical to them.

    J: That's not explained by UCA, that's ENTAILED in the meaning of UCA. Living things have existed. They have known similarities but they are not identical. They are posited to be genealogically related. THAT'S the hypothesis.

    A: And before you hit "circular" on the findings of cladistics, recall that Darwin and other early naturalists found the same, and that there is zero geographic input into a cladogram.

    B: That Darwin did it doesn't mean he didn't use the same kinds of primitive/derived inferences IN the "finding." That's circularity. Remove all assumptions of primitive/derived that can not be predicted by an independent theory. Then do an analysis based on nesting depth are whatever. Then how does that tree match fossil succession? And what would the match mean? Only that IF currently known fossil succession is a good fit to actual historical existential ranges and IF the posited trajectories are possible and reasonably probable, that the criteria used for the cladistic tree are high-level rules that apply to biological evolution over the posited history. It wouldn't be evidence FOR UCA. It would be evidence for what seem to be RULES of the UCA that occurred.

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  68. A: Then later scientists started to observe surviving species and the greater similarities of stratigraphically adjacent layers.

    J: You need more specificity. You have not said anything there that is known to be inconsistent with SA. This blog is about the fact that UCA or subsets thereof are not the only hypotheses in competition.

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    1. A formal test of the theory of universal common ancestry

      doi:10.1038/nature09014

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    2. Pedant

      A formal test of the theory of universal common ancestry

      doi:10.1038/nature09014


      I already showed this paper to Jeff a few weeks ago. He hand-waved it away with "well, that supports SA too!!"

      Jeff isn't the sharpest tool in the shed.

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    3. Theobald has an update:

      On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence

      doi:10.1186/1745-6150-6-60

      Delete
  69. J: No, A. That's not an implication. That's an inference you have made to minimize convergence, etc. But none of those trajectories are known to be possible or possible in terms of the actual history. ID-style SA doesn't even posit that most of the analogies are convergent.

    Common ancestry is always more parsimonious than convergence. All trajectories implied are possible; there is no reason to think otherwise. ID SA is ill defined. You have never stated which species share common ancestry and which do not. You have not stated what or who the designer could possibly be. You have not provided any evidence supportive of ID or SA. You have merely cried that we don't know that evolution is possible, when in fact, the sum of evidence we have shows that not only is it possible but that it really happened.

    First of all, you've admitted that you feed the analysis what is "derived." Of course it would match to some extent. Second, to WHAT extent does it match when NO such information is used--when ONLY traits are used. THAT would be an interesting correspondence--not because it's predicted, but because it corresponds at all.

    You have been told once before. Primitive traits are based upon distribution among taxa, not stratigraphy. There is NO inherent reason for them to match up. Much work has been done in the past with no attempt to put in polarity information: these include outgroup-free cladistics and phenetics. These techniques do not produce any support for SA, but they are not as accurate as cladistics with outgroups in resolving the branching order of phylogeny. For example, it is wrong to group humans with dogs to the exclusion of horses (due to possession of five fingers) because outgroups (like lizards and turtles) have five fingers too. That suggests five fingers is likely to be primitive for mammals. THEN we independently look at the fossil record, and indeed the earliest horses had five fingers too.

    How is this inconsistent with SA?
    Impossible to say, you have never specified exactly which groups have separate ancestry. If you allow CA for mammals separate from nonmammals followed by evolution as usual, then it's consistent. But the problem there is that the line is blurred between what is a mammal and what is not a mammal when we include fossils, and the whole therapsid sequence looks like it was placed there to fool us if these aren't ancestral to mammals.

    That Darwin did it doesn't mean he didn't use the same kinds of primitive/derived inferences IN the "finding."

    In the whole of On the Origin, there is not a single tree except an empty theoretical example. Darwin did not rip up Linnaen taxonomy (where shared primitive characters unite "Pisces" and "Reptilia"), but subsequent researchers did.

    There has been plenty of work without polarity, again the term is phenetics. Phenetics is mostly used in microevolutionary studies where the record is locally good. The original grouping of chimps and humans apart from gorillas was also based on phenetics (mixed melting point of DNA hybrids). But you can't test the potential validity of macroevolution using phenograms of morphological traits, because they do not reproduce the branching order of macroevolution the way cladistics does. AGAIN no stratigraphic information is taken in directly or indirectly, even if outgroups are used.

    If you want to test evolution as a hypothesis, you have to test it, not a strawman or failbot version.

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