Home » Intelligent Design » Francisco Ayala: “You’re a heretic and blasphemer, but don’t ask me what I am.”

Francisco Ayala: “You’re a heretic and blasphemer, but don’t ask me what I am.”

Darwin's Gift to Science and ReligionFrancisco Ayala has taken an aggressive theological stance against intelligent design, even using words like “blasphemy” and “atrocity” to characterize it (go here). But if Ayala feels entitled to make such strong accusations against ID, one might wonder what Ayala’s own theological views are. I therefore emailed him and copied Michael Ruse:

Dear Prof. Ayala,

I’m writing to inquire whether in any of your writings you lay out your present religious faith (and, if so, where?). I’m copying my friend Michael Ruse because I find his criticisms of ID parallel your own, and yet he makes clear that he himself is an atheist. You, on the other hand, regularly cite your background in the Roman Catholic Church as a priest. Yet you left the priesthood and it’s not clear what aspects of the Christian faith you retain. Do you, for instance, believe in a personal God who created the world? Do you believe that humans experience continued conscious existence after they die? Do you believe that Jesus was God incarnate? I would appreciate any clarifications you can provide. Thank you.

Blessings,
Bill Dembski

Ruse got back to me first and suggested that Ayala would not be forthcoming about his religious views, whereupon Ayala got back to me, agreeing with Ruse: “What Michael Ruse told you about my not asserting publicly my religious convictions is correct. I have stated that on numerous occasions, quoted in all sorts of publications from The New York Times and Scientific American to religious journals and periodicals.”

Interesting that Ayala is willing publicly to acknowledge his former theological views as a Roman Catholic priest (presumably he embraced RCC dogma). And yet his present theological views are off limits. Perhaps when Dover II rolls around, Ayala will be an expert witness and under deposition be required to state his theological views. In the mean time, Ayala’s reticence about his present religious faith (or lack thereof) is at best a convenient ploy.

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312 Responses to Francisco Ayala: “You’re a heretic and blasphemer, but don’t ask me what I am.”

  1. I don’t think there is any reason to believe Ayala is even a theist, for someone to go as far as he does, I would say is far less to pretend one is a theist. Clearly for people like Ayala political correctness is uber alles.

  2. The implication is clear enough. Like another well known Catholic Darwinian, Ken Miller, Ayala wants to wrap his theological credentials around his adherence to Darwinian dogma. Somehow, both he and Miller (and others of that ilk) mistakenly believe that they’ve somehow reconciled what they claim to believe as Christians (and aren’t Catholics Christians by definition) with naturalistic evolution. I’d like for Ayala to explain how he reconciles the Catholic (read: Biblical) teaching that “In the beginning was the Word (the Logos)…and all things were made by him, and without him nothing was made…” with “In the beginning were the particles…”

    Ayala’s reticence to discuss his current beliefs doesn’t surprise me. Either he’s abandon the core beliefs he claimed adherence to when he took his priestly vows, or he still retains them. If the former, then why the ruse in constantly referring to his Catholic credentials, as if that somehow makes his acceptance of and adherence to Darwinism more palatable? If the latter, then clearly he’s got a lot of explaining to do.

    Or, perhaps he’s taken a third route and modified (or rejected)just some of the core beliefs he once vowed adherence to. If so, why can’t he explain which ones those are and what criteria he uses to determine which beliefs may be safely adhered to, and which must be modified or rejected in order to maintain “scientific” respectability. And once he’s explained that, he can further explain why that criteria is correct and how he knows it is.

  3. I wish that you were either hot or cold…

  4. Ayala is screwed here because either his views are indistinguishable from atheist views, or he is like us, a heretic, Dembski asked him a clever little question here, what would Ayala choose? blasphemy or atheism?

    Ayala takes the lazy way out, and refuses to answer.

  5. 5

    DonaldM @2:

    I’d like for Ayala to explain how he reconciles the Catholic (read: Biblical) teaching that “In the beginning was the Word (the Logos)…and all things were made by him, and without him nothing was made…” with “In the beginning were the particles…”

    Well, setting aside the fact that the theory of evolution is not particle physics, and assuming for the sake of argument that he remains fully committed to Catholicism, I would imagine he reconciles himself with “naturalistic evolution” in much the same manner as, oh I dunno, the Pope?

    To wit, this fully Pope-approved text:

    In our own solar system and on earth (formed about 4.5 billion years ago), the conditions have been favorable to the emergence of life. While there is little consensus among scientists about how the origin of this first microscopic life is to be explained, there is general agreement among them that the first organism dwelt on this planet about 3.5-4 billion years ago. Since it has been demonstrated that all living organisms on earth are genetically related, it is virtually certain that all living organisms have descended from this first organism. Converging evidence from many studies in the physical and biological sciences furnishes mounting support for some theory of evolution to account for the development and diversification of life on earth, while controversy continues over the pace and mechanisms of evolution. While the story of human origins is complex and subject to revision, physical anthropology and molecular biology combine to make a convincing case for the origin of the human species in Africa about 150,000 years ago in a humanoid population of common genetic lineage.

  6. //Since it has been demonstrated that all living organisms on earth are genetically related, it is virtually certain that all living organisms have descended from this first organism.//

    But this is not evolution, Jerry Fodor explains:

    “it’s important to see that the phylogeny could be true even if the adaptationism isn’t . . . the classical Darwinist account of evolution as primarily driven by natural selection is in trouble on both conceptual and empirical grounds.”

    Bad Pope..

  7. Professor Dembski,

    Over at Biologos I made clear my vision for a “peace agreement” between them and ID:

    1) An acknowledgment by both sides that there are no major theological objections to either ID or Theistic Evolution.

    2) An acknowledgment that the major disagreements are merely scientific in nature.

    3) An agreement that the main spokespeople would refer to the “other side” with respect and love.

    It looks to me as if Biologos is attempting to institute (3), lately — for example, by allowing a positive review of your book. I think it would help if they disavowed Ruse’s and Ayala’s recent theological attacks.

    But meanwhile, do you think there are major theological problems with Theistic Evolution?

  8. But meanwhile, do you think there are major theological problems with Theistic Evolution?

    No there is no problem with theistic evolution, no more than there are theological problems with theistic alchemy, sure there might be scientific problems, but no theological problems no.

    Sorry I will let Professor Dembski answer, I just couldn’t resist.

  9. “I would imagine he reconciles himself with “naturalistic evolution” in much the same manner as, oh I dunno, the Pope?”

    The statement from a pope above, which we have seen a few times before, is 100% consistent with ID.

  10. @polanyi #6

    So the issue between darwinism and ID is not commond descent but on the machnisms of how things evolved?

  11. It’s safe to say that whatever faith Ayala has does not require sharing that faith — so he’s not an Evangelical! Also, with no evident sense of irony, the Templeton Foundation gave Ayala its most prestigious award — FOR ADVANCING THE DIALOGUE BETWEEN SCIENCE AND RELIGION — without inquiring into Ayala’s own religious views. This is rich.

  12. //So the issue between darwinism and ID is not commond descent but on the machnisms of how things evolved?//

    Darwin’s contribution was not evolution defined as change over time, not even descent from a common ancestor no. Darwin’s contribution was how this had to happened.

    It’s thanks to Charlie that we are now suppose to believe evolution is blind, purposeless, unintelligent, unguided. Darwin was convinced of this for religious and metaphysical reasons[you see cats happen to play with mice, this was all the evidence Darwin needed to rule out design].This is Darwin’s pathetic legacy, and then people have the nerve to reserve to theology to defend this.

  13. The point is people attack design for theological reasons, and then people try to ice the cake for evolution by trying to make it appear to be theologically appealing. Bu asking questions like “you think there are any major theological problems with theistic evolution?”.

    You can basically tag theism to anything without a problem if that is your goal, if I really believed for religious and metaphysical reasons that God would use alchemy to transform one metal into another, I can harmonize theology fairly easily with alchemy, but just because alchemy can be in harmony with theology this doesn’t mean I should try to sell alchemy because it appears to be in harmony with theology. Theistic Evolutionists don’t seem to be getting this.

  14. Why would Ayala’s (or anyone else)religious beliefs be relevant in a scientific discussion?

  15. I think some people might like this video. :)

    http://www.youtube.com/watch?v=fHQsaiMcPLc

  16. Critter @14 A person’s theological position is important because you need to believe in miracles if you choose to believe in Darwinian evolution.

  17. Why would Ayala’s (or anyone else)religious beliefs be relevant in a scientific discussion?

    Ayala rarely limits himself to scientific discussion – hence Dembski’s reference to the ‘heretic and blasphemer’ charges by Ayala. If he stuck to science and had nothing to say about theology, these questions would not be asked.

  18. Why would Ayala’s (or anyone else)religious beliefs be relevant in a scientific discussion?

    One reason is because it is Ayala himself (and Miller, too, for that matter) and others of that ilk who basically rely on some sort of “God wouldn’t have done it that way” kind of argument in order to justify their adherence to evolutionary dogma. They are the ones who insert a theological premise into what is supposed to be a scientific discussion.

    But in a larger context, it is science itself that brings religious belief into the discussion in the form of so-called methodological naturalism – the idea that whether or not philosophical naturalism is actually true, for the sake of doing science, we’ll pretend that it is. Adherence to MN implies a direct religious argument that basically says that any observed phenomenon in nature MUST have a natural cause. That introduces religion right into the heart of science.

  19. I am a bit troubled by the fact that private correspondence is being made public.

    That said, I tend to think Ayala is not being public about his religious views because they are not Christian, and yet he wants to hold traction in the Christian community. My guess is that he is either an atheist or a deist (maybe it was his radical theological views that caused him to leave the priesthood).

  20. Doomsday Smith wrote:

    “To wit, this fully Pope-approved text:”

    It seems that Mr Smith’s assertion that the quoted text is “fully Pope-approved” is not true.

    In fact, “The present text was approved in forma specifica, by the written ballots of the International Theological Commission. It was then submitted to Joseph Cardinal Ratzinger, the President of the Commission, who has give[n] his permission for its publication.”

    The ITC _approved_. Then Joseph Cardinal Ratzinger, Prefect of the CDF, _permitted_ the text’s publication.

    Permitting is not approving.

  21. jasondulle: I decided that Ayala’s one sentence email could be made public since he claims in it that he has publicly stated that he will not divulge his religious views, referring me to the New York Times, Scientific American, etc. Presumably this absence of public knowledge about his religious views is itself public knowledge, so I felt at liberty to share it.

  22. 22

    turandot @20:

    “Permitting is not approving.”

    *sigh*
    Fine: he was merely the president of the body that approved it. A body, by the way, which has only been given the duty “to promote and safeguard the doctrine on the faith and morals throughout the Catholic world: for this reason everything which in any way touches such matter falls within its competence.”.

    Given that, do you honestly imagine that he did not approve of the content of the text? Got any signs that since becoming Pontiff, that that position has changed or will do so in the forseeable future? If the answer to that is “No”, what might we infer from this?

  23. according to Cardinal Schonborn:

    EVER since 1996, when Pope John Paul II said that evolution (a term he did not define) was “more than just a hypothesis,” defenders of neo-Darwinian dogma have often invoked the supposed acceptance – or at least acquiescence – of the Roman Catholic Church when they defend their theory as somehow compatible with Christian faith.

    But this is not true. The Catholic Church, while leaving to science many details about the history of life on earth, proclaims that by the light of reason the human intellect can readily and clearly discern purpose and design in the natural world, including the world of living things.

    Evolution in the sense of common ancestry might be true, but evolution in the neo-Darwinian sense – an unguided, unplanned process of random variation and natural selection – is not. Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science.

    link

    the darwinists twist what the catholics say to suit their own purposes, just as they twist ‘science’ to match their atheist faith

  24. People should read the Pope’s statement. It is completely in sync with ID and does not endorse any particular mechanism for the appearance of new species. This statement has been presented here before so it is nothing new and nothing worth discussing.

    ID endorse naturalistic evolution in the sense that most evolution is through naturalistic means. Most evolutionary events never gets past the first decision point of the EF and thus is law like.

  25. Doomsday Smith wrote:

    “*sigh*

    “Fine: he was merely the president of the body that approved it. A body, by the way, which has only been given the duty ‘to promote and safeguard the doctrine on the faith and morals throughout the Catholic world: for this reason everything which in any way touches such matter falls within its competence.’”

    I’ll suggest that you read the ITC document from beginning to end, and I’ll suggest you consider that because then Cardinal Ratzinger _permitted_ the publication of an ITC document it cannot honestly be claimed that then Cardinal Ratzinger and now Pope Benedict XVI _approved_ its content.

    “Given that, do you honestly imagine that he did not approve of the content of the text? Got any signs that since becoming Pontiff, that that position has changed or will do so in the forseeable future? If the answer to that is “No”, what might we infer from this?”

    Having been an avid reader of now Pope Benedict’s published works for a good many years, I can quite honestly “imagine that he didn’t approve of several of the ITC’s claims.” See, for instance, Cardinal Schonborn’s _Creation and Evolution: a Conference with Pope Benedict XVI in Castel Gandalfo_ / Ignatius Press / 2008.

    Really, the question is whether Ayala is or is not a wolf in sheep’s clothing, so why the disingenuous b16 straw man?

  26. I wrote:

    “so why the disingenuous b16 straw man?”

    OOPS! I meant to write: “so why the disingenuous _B16_ straw man?”

  27. In his debate with William Lane Craig concerning the merits of ID, Ayala mentions throughout his beliefs about god (will remain lowercase since he clearly does not mean the God of his former Catholicism). If someone were willing to really parse the Q&A time, I think his beliefs would be more clear.

    At one point, he claims to view god as a grand programmer at one point who set things going, but “never needs to intervene” as he says in response to one of the questions. At another point (near the end), both are asked why they believe in God. Craig spent about five minutes giving the existential and intellectual reasons culminating in Jesus Christ. Ayala says in about twenty seconds that his religious faith comes from the immense beauty of the world. I think there was another point in the Q&A where Ayala mentioned fine tuning as well.

    I think it should be clear from these statements that Ayala clearly believes in a deistic god at best. In direct questions about Christianity and religious faith he often answered, “one could say…” instead of “I believe…” I personally find that somewhat telling.

    Of course, he could believe and worship the Christian God and simply go through this maneuvering because he doesn’t want to get skewered by his peers for holding to design arguments like fine tuning…one could even probably say that his “beauty of the world” reason invokes design, and his programmer statement clearly does.

    Who knows?

  28. Bilboe:But meanwhile, do you think there are major theological problems with Theistic Evolution?

    Speaking for myself (and not for Dembski), the “major theological [and rational] problem[] with Theistic Evolution” is that it is indistinguishable from materialism/atheism; and the major sociological problem with “Theistic Evolution” is that the so-called theistic evolutionists are generally indistinguishable from Dawkins.

    If words were always used rationally, these problems probably would not have arisen. But, reality is what it is, and in the only reality we have “Theistic Evolution” refers to an oxymoron.

  29. I am a bit troubled by the fact that private correspondence is being made public.

    Then, might I suggest that you look into growing up? You know, become an adult who thinks like an adult.

  30. As someone who accepts an old earth, common descent and limited amounts of evolution I find both Ayala and Miller’s popular books deplorable in terms of their treatment of ID! Over on Biologos Rich suggests that both of them are Christian Darwinists which is an oxymoron IMO but then their position is not intellectually sustainable either.
    Dave W

  31. Bill, I am so glad you asked Ayala this question and made his response public. He has publicly promoted his fading clerical collar as his confession of faith–and I, too, have wondered whether he could translate that gesture into words.

    For almost two thousand years, the confession of catholic (with a small “c”) Christians has been as follows: “I believe in God the Father almighty, creator of heaven and earth, and of all things visible and invisible…” This is the confession of John Polkinghorne in his book The Faith of a Physicist. The confession has never been as follows: “What Michael Ruse told you about my not asserting publicly my religious convictions is correct.”

    I must conclude that Ayala is not a catholic (let alone a Roman Catholic) Christian.

    The behavior of the Templeton Foundation with regard to i.d. has at least been intelligible to me, although I have not agreed with it. The awarding of the Templeton Prize 2010 to Francisco Ayala is not intelligible to me.

  32. Ilion,

    Your response is befuddling. I bring up an ethical issue, and your response is to tell me to “grow up” and think like an “adult”? Ironically, that response seems rather childish.

    I think it is ethically wrong to make private correspondence public without the consent of the person you are corresponding with. That is a valid, adult concern.

    With that said, I accept Bill’s explanation for why he posted it, and no longer find his actions ethically questionable.

    Jason

  33. If Ayala won’t say what he believes he isn’t a Christian.

  34. Ilion:

    Whether or not theistic evolution is an oxymoron depends on how the word “evolution” is defined.

    If evolution is understood as an unplanned and fundamentally unguided process, then the terms are incompatible. Otherwise, they aren’t.

    The problem with so many TEs is that they do understand evolution as fundamentally unguided, random, etc., yet insist this is compatible with the Christian conception of God. And the problem here is not the bare idea of evolution, but the Darwinian idea of evolution. It’s really theistic Darwinism that’s the oxymoron.

    However, getting old dogs like Ayala and Miller to question Darwin is impossible. He’s more than a scientific hypothesis to them; he’s become the symbol of naturalism, science, enlightenment, etc., and he’s their shibboleth against fundamentalism. They are simply not capable of dispassionate analysis of Darwinian mechanisms on the level of pure science. Until their generation passes away, evolutionary biology will remain mired in outdated concepts, and TEs will continue to do their schizophrenic dance, trying to pretend that evolution is simultaneously both guided and unguided and that there is no contradiction in saying this.

    T.

  35. Timaeus: If evolution is understood as an unplanned and fundamentally unguided process, then the terms are incompatible. Otherwise, they aren’t.

    The problem with so many TEs is that they do understand evolution as fundamentally unguided, random, etc., yet insist this is compatible with the Christian conception of God. And the problem here is not the bare idea of evolution, but the Darwinian idea of evolution. It’s really theistic Darwinism that’s the oxymoron.

    I think I disagree. I thought Miller argued persuasively in his book, Finding Darwin’s God, that it is possible that God allowed “free will” to nature, just as He allows free will to humans, knowing that eventually it would accomplish His ends. I think that is a theologically acceptable position, though I don’t think that appears to be what in fact happened.

  36. Ilion: Speaking for myself (and not for Dembski), the “major theological [and rational] problem[] with Theistic Evolution” is that it is indistinguishable from materialism/atheism; and the major sociological problem with “Theistic Evolution” is that the so-called theistic evolutionists are generally indistinguishable from Dawkins.

    But Christian beliefs about heliocentrism are indistinguishable from materialist/atheistic beliefs about it. Should we go back to geocentrism?

  37. Bilboe-

    Please grow up. Geocentrism is nowhere close to being a Christian doctrine.

  38. Bilboe:

    I know what Miller argued in his book. But what Miller argued in his book is not coherent.

    There’s no way God could possibly guarantee that nature would “accomplish his ends” if nature “evolves” through purely fortuitous events and purely stochastic processes. At the very least, he would have to bias nature from the outset, so that purely fortuitous events and purely stochastic processes would tend “upward” to produce higher life-forms, including man. But that view was not Darwin’s view, nor was it the view of the classic neo-Darwinists from whom Miller takes his science.

    The question of theological acceptability is another matter entirely. With Miller, I’m more worried about lack of intellectual coherence than heresy. However, he has argued for heretical positions, e.g., that naturalistic evolution must be true, because otherwise God would be responsible for physical pain and evil. But there is no requirement in Christianity that God *not* be responsible for physical pain or evil. The traditional Christian view is that God doles out good and evil, war and peace, curses and blessings, pain and pleasure, on whom he will. If he wills that lions shall eat lambs, that’s his prerogative. Miller and Ayala try to distance God from the killing of lambs, etc., by putting up “evolution” as a sort of plastic glove, to keep the blood off God’s hands. But their theological motivation is intrinsically heretical: they start from a notion of what they think God ought to be like, and re-tool the notion of Creation to suit that view. But neither God nor traditional Christian theology cares at all what Ayala and Miller think that God should be like.

    T.

  39. 39

    Bilboe,

    But Christian beliefs about heliocentrism are indistinguishable from materialist/atheistic beliefs about it. Should we go back to geocentrism?

    Did you miss the part called “Theistic” evolution? Have you ever heard of “Theistic” heliocentrism? Your response is a bad analogy.

  40. 40

    Bilboe,

    I think I disagree. I thought Miller argued persuasively in his book, Finding Darwin’s God, that it is possible that God allowed “free will” to nature, just as He allows free will to humans, knowing that eventually it would accomplish His ends.

    Humans actually have a will. Nature doesn’t. You might as well say that the oak tree has free will, that leaves after they’ve fallen, and inanimate objects have free will. It’s nonsense unless you’re a pantheist, which Miller apparently is.

  41. Hi Phaedros,
    Yes I keep trying to grow up, but having reached middle age, I find it more and more difficult to accomplish. Please pray for me. Yes, geocentrism is nowhere near a Christian doctrine. Your point?

    Hi Timaeus,

    It’s not clear to me that Miller’s position is incoherent. For example, God accomplished his purpose of allowing His Son to be crucified, even though this required the free choices of human beings. But I agree with you that Theistic Evolutionists are mistaken in thinking that evolution is theologically necessary to account for natural evil.

    Hi Clive,

    Yes, we don’t refer to theistic geocentrism. But Ilion’s point seemed to be that there was a theological problem with TEism because it was indistinguishable from Atheistic Evolutionism. I don’t think that’s a defensible position.

    As for nature having a free will, Miller was assuming the Copenhagen interpretation of Quantum Physics, which suggests that subatomic particles are indeterminate — similar to free will.

  42. One cannot be a Christian Darwinist and remain rational:

    If evolution knows where it is going and moves toward a specified end, it isn’t Darwinism; if it doesn’t know where it is going and produces a surprise, it isn’t Chrisianity.

  43. If evolution knows where it is going and moves toward a specified end, it isn’t Darwinism; if it doesn’t know where it is going and produces a surprise, it isn’t Christianity.

  44. Hi StephenB,

    I think a Christian Darwinist would say that what matters is that God knows where evolution is going.

  45. Bilboe:

    Yes, that’s what a Christian Darwinist would say, and I’ve argued this out many times with them.

    But God can’t know where evolution is going only because of his “foreknowledge”; that would imply that he is merely passively watching what happens in nature. But God *causes* what happens in nature; he’s no mere spectator-from-eternity. That’s what “creation” means, though TEs have trouble grasping this. God is fully responsible for the existence of every species. Even if naturalistic means are the vehicle for producing species, God has to set up nature so that it will run in the direction of certain species rather than others. That means design. But the TEs won’t allow that. They block design inferences at every turn. God only knows why.

    T.

  46. For my two cents the very idea of a “Christian darwinist” is logically incoherent. If darwinian/neo-darwinian evolution explicitly says that God did not do it, and it does, then to be a Theistic or Christian evolutionist is to literally say that “God did it by not doing it.” Right…

  47. Jasondulle @ 32:

    I *know* what you think. That’s why I said what I said.

  48. Timaeus # 34: “Whether or not theistic evolution is an oxymoron depends on how the word “evolution” is defined.

    … It’s really theistic Darwinism that’s the oxymoron.

    …Until their generation passes away, evolutionary biology will remain mired in outdated concepts, and TEs will continue to do their schizophrenic dance, trying to pretend that evolution is simultaneously both guided and unguided and that there is no contradiction in saying this.

    .
    Or, as I said: “If words were always used rationally, these problems probably would not have arisen. But, reality is what it is, and in the only reality we have “Theistic Evolution” refers to an oxymoron.

  49. Bilboe @ 36 (referencing me @ 28):But Christian beliefs about heliocentrism are indistinguishable from materialist/atheistic beliefs about it. Should we go back to geocentrism?

    Sophistry is not cute; and it is the opposite of wisdom.

  50. Clive Hayden @ 40:Humans actually have a will. Nature doesn’t. You might as well say that the oak tree has free will, that leaves after they’ve fallen, and inanimate objects have free will. It’s nonsense unless you’re a pantheist, which Miller apparently is.

    Moreover, to assert that “nature has ‘free will’” is logically to assert either:
    1) “nature” is a single entity … and thus, we are not real
    2) *all* components of “nature” have “free will” … you know, molecules, atoms, electrons …

    Why would anyone assert such things? The only reason I can come up with is as an (imagined) means to escape the commitments and/or implications of Christianity.

  51. Ilion @ 48:

    No, “theistic evolution”, in the basic meaning of “an evolutionary process planned or guided by God”, was not always an oxymoron, and need not be an oxymoron, and even today is not everywhere an oxymoron.

    To be sure, *most* American and British TEs of the last 20 years who are theistic evolutionists are in fact theistic Darwinists (and this includes some Catholics, including some who are trying to bend the ear of Pope Benedict). But there is still not complete acceptance of all aspects of Darwin among some Catholic evolutionists, and there are formulations of divinely-planned evolution that are not Darwinian, e.g., Denton’s. And of course, in the past, before modern TE arose as a reaction to YEC and ID, there were evolutionists who were critical of aspects of Darwinism, and thought of evolution as requiring either the action of a “life force” or some form of divine direction.

    What has happened — and to be fair, there are about half a dozen important TE exceptions to the generalization I’m about to make — is that a band of people with a very narrow focus (first, proving to their secular colleagues that they aren’t YECs or ID people by praising Darwin, and second, distancing themselves from all forms of fundamentalism, which in many cases was their own religious upbringing) have staged a sort of coup to take over the phrase “theistic evolution”. There is no reason why we should cede this phrase to them. Rather, we should mock their coup by calling them, incessantly and against their wishes, “theistic Darwinists”, until it drives them to fury. False advertising should be fought with truth in advertising.

    T.

  52. If evolution knows where it is going and moves toward a specified end, it isn’t Darwinism; if it doesn’t know where it is going and produces a surprise, it isn’t Chrisianity.

    Christians can’t be surprised? That surprises me. CS Lewis wrote a book titles Surprised By Joy.

    Of course, God can’t be surprised, but if we are talking about God’s perspective the first half of your idea fails. God’s omniscience doesn’t invalidate the change in allele frequencies over time.

  53. T:

    You have an interesting point.

    As a Platonist, I am sure you have Denton’s concept of forms and archetypes in mind.

    I do say that I was very impressed by his comparison of placental and marsupial animals that fit similar niches.

    And, Theistic Darwinists has just the little bite of highlighting a self-referentially incoherent irony that would make it fighting words indeed.

    But, in fact it is well justified as a descriptive term (as opposed to the self-chosen moniker of many prominent modern TE’s).

    My own thought is that for even the most strictly Biblical-literalist Creationist (up to of course the intra Creationist debates on dating and age estimates for the cosmos), there is a lot of room for flexibility on methods and dynamics in:

    Gen 1:1 In the beginning God created the heavens and the earth.

    2 Now the earth was [a] formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters.

    3 And God said, “Let there be light,” and there was light . . . .

    11 Then God said, “Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds.” And it was so . . . .

    20 And God said, “Let the water teem with living creatures, and let birds fly above the earth across the expanse of the sky.” 21 So God created the great creatures of the sea and every living and moving thing with which the water teems, according to their kinds, and every winged bird according to its kind. And God saw that it was good. 22 God blessed them and said, “Be fruitful and increase in number and fill the water in the seas, and let the birds increase on the earth.” . . . .

    24 And God said, “Let the land produce living creatures according to their kinds: livestock, creatures that move along the ground, and wild animals, each according to its kind.” And it was so. 25 God made the wild animals according to their kinds, the livestock according to their kinds, and all the creatures that move along the ground according to their kinds. And God saw that it was good.

    26 Then God said, “Let us make man [note the distinct shift in degree of explicit involvement] in our image, in our likeness, and let them rule over the fish of the sea and the birds of the air, over the livestock, over all the earth, [b] and over all the creatures that move along the ground.”

    27 So God created man in his own image,
    in the image of God he created him;
    male and female he created them . . .

    Where I think the specific, stringently empirically testable predictions of foundational Judaeo-Christian thought on Creation come in is:

    Jn 1:1In the beginning was the Word [Logos -- Reason, Intelligibility and Communication Himself, cf v 14 i.e. this is Christ], and the Word was with God, and the Word was God. 2He was with God in the beginning.

    3Through him all things were made; without him nothing was made that has been made. 4In him was life, and that life was the light of men . . . .

    Rom 1:19 . . . what may be known about God is plain to them, because God has made it plain to them. 20For since the creation of the world God’s invisible qualities—his eternal power and divine nature [i.e. in context plainly inclusive of morality] —have been clearly seen, being understood from what has been made, so that men are without excuse . . . .

    Col 1: 15He [Christ] is the image of the invisible God, the firstborn over all creation. 16For by him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things were created by him and for him. 17He is before all things, and in him all things hold together . . .

    Test 1: Do we have an ordered, intelligible cosmic system of reality that reflects a unified organisation that is intelligible and coherent? Physics, with particular reference to cosmology, says yes.

    Test 2: Does life reflect a similar pattern of intelligible coherent unified organisation? Molecular Biology and general biology have to acknowledge, yes.

    Test 3: Does human life reflect a significantly distinct level of life reflective of the characteristics of an in-stamped image of God? Across the ages of human culture the human spirit says a loud yes; from the yearning to worship, to the sense of self awareness and responsible choice, to the wonders of reason, logic, mathematics and philosophy to the awesome yet terrible power of moral choice implied in our ability to choose to love.

    Test 4: Do we have any signs that the same God may have redemptively tabernacled among us? Yes.

    Once we look at this this way, I think we can see that there is plenty of room to turn down the rhetorical voltage. And, we can see as well that there are many, many points where the Judaeo-Christian claims regarding God are open to empirical test, and that at these points there is at least good reason to believe that such a position is intellectually feasible. That is, there is no justification for the sort of hostile and even arrogant contempt that too many of today’s evolutionary materialistic atheists — who too often imagine themselves to have a monopoly on “brightness” [which is nothing like as important as either common sense based wisdom or virtue or just plain common good manners and decency] — are wont to exhibit.

    It is high time we turned dwen the voltage and allowed the atmosphere to clear of poisonous, polarising, mind-clouding smoke of burning ad hominem soaked strawmen.

    $0.02

    GEM of TKI

  54. Timaeus: But God *causes* what happens in nature; he’s no mere spectator-from-eternity. That’s what “creation” means, though TEs have trouble grasping this. God is fully responsible for the existence of every species.

    I agree that if what happens in nature is fully deterministic, then all of natural history is designed. It’s not clear that it is the case. Miller bases his argument on the Copenhagen interpretation of Quantum Physics, which suggests that what happens in nature is non-deterministic. In that case, it seems at least logically possible that God has been a spectator, though I would argue that He re-creates nature from moment to moment (every 10-44 second or so).

    Ilion: Sophistry is not cute; and it is the opposite of wisdom.

    I agree, though I don’t see the relevance, unless you’re admitting to sophistry.

    tgpeeler: For my two cents the very idea of a “Christian darwinist” is logically incoherent.

    Please see above.

    Kairo: It is high time we turned dwen the voltage and allowed the atmosphere to clear of poisonous, polarising, mind-clouding smoke of burning ad hominem soaked strawmen.

    Amen.

  55. Bilboe:

    I agree with you that Miller seems to accept the Copenhagen quantum school. But a couple of points must be borne in mind:

    a. There is a school of deterministic quantum mechanics. It’s the minority view, to be sure, but it exists. And Miller, not being a physicist, isn’t any more competent to judge between them than you or I. All he can do is go along with the majority of the physicists. And I’m sure it helps his decision along that the view of the majority of the physicists is exactly what he needs to fit together his neo-Darwinism and his liberal Christian theology.

    b. Even granting quantum indeterminacy, he says things that are completely bizarre, such as that the randomness of the movement of subatomic particles provides the basis of free will. But true randomness, if it existed in nature, would be just as opposed to free will as rigid necessity. If my moral choices are determined by lawless “blips” that happen randomly in the neurons in my brain, I’m no more free than if my moral choices are determined by utterly law-governed neural activity. Someone who drifts momentarily whichever way a sudden slight breeze blows is no freer than someone who is forced in a certain direction by gale-forced winds. Miller has problems reasoning things like this out, which is what one would expect from a cell biologist who has no training in non-scientific subjects. That’s why cell biologists, except in very rare cases, should not be writing about philosophy and theology. Miller is not one of those rare cases.

    Note: It may be that God recreates the universe every 10-44 seconds. There were medieval Muslim theologians who held roughly this view. I’m not posing as theological adjudicator. However, from a historical standpoint, it hasn’t been the orthodox Christian notion of creation. And Miller thinks that he is reconciling Darwinism with orthodox Christian teaching.

    T.

  56. —Billboe: “In that case, it seems at least logically possible that God has been a spectator, though I would argue that He re-creates nature from moment to moment (every 10-44 second or so).”

    Christian Darwinism, (not the traditional theistic evolution which allows for front loading), is, indeed, a contradiction in terms. God sustains the universe, God does not sustain the universe; man was a surprise outcome, man was not a surprise outcome; God reveals himself in Scripture, God hides himself in nature; evolution knows where it is going; evolution doesn’t know where it is going; God tinkers behind the scenes, God is merely a spectator; design is inherent in the evolutionary process; design cannot be observed or perceived; faith and reason are compatible; Scriptural teachings must be subordinated to scientific speculations; God’s handiwork is evident, God’s handiwork cannot be perceived; design is real (when speaking to Christians), design is an illusion (when speaking to Darwinists); a good God would not design a universe that allows suffering; a good God stacked the deck so that suffering would occur via secondary causes.

    Compared to the intellectual madhouse in which Christian Darwinists reside, Richard Dawkins is downright rational.

  57. Hi Timaeus,

    It sounds like you agree that if the Copenhagen interpretation is correct, then its logically possible that God has endowed nature with a sort of “free will” and allowed it to evolve (foreknowing what direction it would take). You and I both agree that though this is logically possible, the chances of nature randomly accomplishing the origin of life are too remote to be taken seriously. Nevertheless, there are Christian scientists who think it wasn’t that improbable. Though we disagree with them scientifically, should we accept them theologically? I wholeheartedly say, Yes.

    My idea of God re-creating nature comes from here:

    http://telicthoughts.com/steng.....ontinuous/

    Hi StephenB,

    I agree that Christian Darwinists are often inconsistent. But I think it’s possible for them to hold a consistent, theologically acceptable position.

  58. Hi Billboe:

    Which notable Christian Darwinist that we can analyze would you say holds a consistent, theologically acceptable position?

  59. —Nakashima: “Christians can’t be surprised? That surprises me. CS Lewis wrote a book titles Surprised By Joy.”

    So now you are comparing the sponteneity of a religious experience with the mindlessness, unguided emergence of a physical process? Did you have your coffee this morning?

    —”Of course, God can’t be surprised, but if we are talking about God’s perspective the first half of your idea fails. God’s omniscience doesn’t invalidate the change in allele frequencies over time.”

    Please rewrite that paragraph since I have no idea what you are talking about.

  60. If evolution knows where it is going and moves toward a specified end, it isn’t Darwinism; if it doesn’t know where it is going and produces a surprise, it isn’t Chrisianity.

    To the semicolon, seems to me to be a rational definition of Darwinian evolution.

    “…and produces a surprise…” Let us examine the question – to whom is it a surprise?

    Case 1: If it is the erstwhile Christian Darwinist, it would read like this:

    “…if it doesn’t know where it is going and produces a surprise to the Christian, it isn’t Chrisianity.”

    It seems to me that you are saying that Christians cannot be surprised and remain a Christian.

    Case 2: If it is God, it would read like this:

    “…if it doesn’t know where it is going and produces a surprise to God, it isn’t Chrisianity.”

    Okay, most people would agree that the God of Christianity is omniscient and cannot be surprised.

    So even though the natural flow of English would lead me to believe that it was the Christian who was surprised, I will accept case 2 for now.

    But it is perfectly rational for a Christian Darwinist to believe that God is omniscient, so now we have to go back and look at the phrase before the semicolon.

    If evolution knows where it is going and moves toward a specified end, it isn’t Darwinism; …

    Does God’s omniscience challenge this statement? Not the definitional statement, but the idea itself?

    Evolution isn’t a mindful entity, it is a natural process. Saying ‘evolution knows’ is like saying ‘fire knows’. The process of fire can be measured by the change in spectral lines over time. The process of evolution can be measured by the change in allele frequencies over time. The universal knowledge of God doesn’t impinge upon the process of evolution any more than it impinges upon the process of fire.

    Let’s call someone who thinks fire is a natural process a Flameist.

    Is a Christian Flameist rational?

    If fire knows where it is going and moves toward a specified end, it isn’t Flameism, if it doesn’t know where it is going and produces a surprise, it isn’t Chrstianity.

    By this line of argument, the Christian Flameist isn’t rational. Neither is the Christian Windist, the Christian Waveist, or the Christian Rustist.

    How about we step back and say that there are a lot of statistical, population based processes in nature, and while the Christian might hold as an axiom of their faith that God knows the all details, they personally do not. Therefore, the Christian studies these natural, statistical, population based proceses in the hope of understanding them better, to the glory of God. This is true of fire, of wind, of waves, of rust, and of evolution.

  61. Nakashima:

    Repeat after me:

    Divine foreknowledge is not divine predetermination.

    Say that to yourself every night before bedtime.

    The doctrine of Creation, if applied to evolution (for those who regard evolution as God’s mode of creation) does not mean that God, who sees the future as the present, merely *knows* what evolution will produce in the future. The doctrine of Creation means that God *makes sure* that evolution will produce certain things in the future.

    This means that *nothing pertaining to crucial evolutionary outcomes*, not even the smallest atomic motion, is left to chance by God. God does not throw out a bunch of hydrogen atoms, thinking: “I threw out lots of atoms, and I’ve got lots of time; Man will probably turn up sooner or later; and if he doesn’t, what the heck; I’ll just throw out some more hydrogen atoms. Large enough numbers of atoms and vast enough spans of time will make up for complete lack of planning and skill on my part. It won’t be as classy an operation as depicted in Genesis, but it’ll get the job done in a crude but effective way. And when Man finally does turn up, I’ll know the time and place, because of my divine foreknowledge. And I’ll inspire Moses to write it all up so that it looks like I was actually in control, instead of just looking down from eternity on a string of undesigned collisions that I neither planned nor executed.”

    This is the way some TEs seem to conceive of Creation. It allows them to have have their cake and eat it, too. But in orthodox Christian theology, God knows, from the moment of throwing out the first hydrogen atoms, exactly on what planet life will first occur, on what planet Man will first emerge, when all these events will occur, etc. And he doesn’t just know it because he sees it in advance; he knows it because he sees it, but he wouldn’t be able to see it if he hadn’t first ordained it. God is not just a video-camera that can see into the future. God is also a producer, director, scripter, actor, stage-hand, and special effects man. The video-camera can’t record the play if the others haven’t produced it.

    God doesn’t just foresee what will happen in nature. God acts in such a way as to determine the course of nature. That is not what Darwin said. That is not what Darwin intended. That is not what Gaylord Simpson, Mayr or Gould said, or intended. You can have orthodox Christian Creation doctrine, or you can have, uncompromising, honest Darwinism. You can’t have both.

    Is it clearer now? If so, then you know that StephenB was entirely right. If not, try these recommended authors: Augustine, Boethius. (In the originals, please, not Wikipedia summaries.)

    T.

  62. T:

    Wherever we go, we meet Plato, Socrates and Aristotle on the way back.

    GEM of TKI

  63. Mr Timaeus,

    Divine foreknowledge is not divine predetermination.

    Say that to yourself every night before bedtime.

    The doctrine of Creation, if applied to evolution (for those who regard evolution as God’s mode of creation) does not mean that God, who sees the future as the present, merely *knows* what evolution will produce in the future. The doctrine of Creation means that God *makes sure* that evolution will produce certain things in the future.

    You’ve just convinced me that you think divine foreknowledge _is_ divine predetermination! What else is “making sure” but determination?

    In any case, we’re still at the point that God isn’t surprised by the process of evolution, even if a Christian Darwinist has to work at gaining insight. God is personally pushing the atoms around to make fire, or wind, but for his own reasons has pushed those atoms in exactly the same way as if a-telic natural forces were at work. We’ve never detected God causing the decay of radioactive atoms in a way different than a predictable mathematical relationship over a large population.

    I suppose a Christian reserves the right to believe that since God is personally managing radioactivity, He could cause the decay of every radioactive atom in the granite of the Empire State Building. That’s nice. Doesn’t help us calculate the dosage for radiotherapy for cancer patients, though. All radiologists, including orthodox Christian radiologists, calculate the dosage the same way, according population statistics.

    The Christian Darwinist is no different than his brother in Christ, the Christian radiologist.

    Personally, I don’t know what Darwin said about how God acts to determine the course of nature. If he said anything at all, it is separable from the science of Darwinism, the importance of variation and selection in shaping populations over long periods of time.

    I thank you for the recommendation of Augustine and Boethius in the original. While I have read a good part of the Hebrew Bible in the original, I only have two years of Latin, and I am afraid they would be beyond me.

  64. Nakashima-San:

    Foreknowledge in the eternal present — as all longitudes come to a common pole* — is not to be equated to pre-determination of that which is future to us who live in time. (And BTW, certain features of experimental quantum mechanics on entanglement and erasure are pointing “suspiciously” in the direction of a domain of the eternal present.)

    The distinction becomes plain once we distinguish the mechanical necessity and stochastics of nature [which last varies within a pattern] from the moral government of creatures with “minds of their own.”

    That last category enfolds creatures capable of valuing the other and acting for the good of the valued other, i.e. of love. Love, the queen and root of the virtues, entails power of choice, thence moral government and the terrible yet awesome balance between the categorically different world of good that love opens up and the evils that come from those who abuse the power to love.

    GEM of TKI

    ______________

    * What is the time/longitude at the North pole?

    PS: And you are doubtless aware of Plantinga’s work on this subject. (Onlookers, 101 intro here.) A world in which such power to love exists and is actualised, is a world in which the necessary being and ground of contingent existence who is omniscient, omnibenevolent and omnipotent is a coherent concept. (Further down that road lies the dread balance between the goodness and severity of God: just, loving, redemptive and thus justifier. Thence, the force of the point that — on the blood of Him who was prophesied and came in love, healing, liberation and ever so costly redemption — there are in the end no “uncovered” evils. Nor does evil triumph in the end. Love, ever so costly but freely and agonisingly given love, triumphs.)

  65. Nakashima:

    I’m glad you have read some of the Hebrew Bible. It’s one of my favorite books. Love those cognate accusatives in Genesis! Love the Hebrew storytelling art! And of course, love the strong design themes in Genesis 1, Job, the Psalms, etc.

    I didn’t mean the original Latin of Augustine and Boethius. I meant their writings in translation, as opposed to internet articles about them, cobbled together largely from other internet articles, by hobbyists who generally understand less of what they read than they think they do.

    The “error” you think you detect in the long paragraph of mine that you quote is not an error. If you reread it carefully, you will see that I maintained my distinctions consistently. Foreknowledge alone would not give God control. God must be a doer as well as a knower.

    It’s irrelevant how Christian radiologists calculate decay. What they are obliged to believe if they hold to traditional Christian theology — and you know this if you’ve read as much of the Hebrew Bible as you’ve indicated — is that God is in control of what happens.

    Regarding design detection, the allegedly random nature of radioactive emissions, etc. is again irrelevant. Design detection does not work on the scale of individual atomic or subatomic events, but on macroscopic patterns. If a block of radium burned “Behe rocks!” into a piece of metal, even if we couldn’t prove that any individual atomic emission was anything other than random, we could be certain of intelligent design. Design detection is not “individual divine action” detection. It’s the detection of a degree of integrated complexity that’s beyond the reach of known stochastic processes.

    Since you mention it, I can tell you something about what Darwin said, since I’ve read all of the *Origin* and a considerable chunk of his other writing — unlike most of the TEs who glibly endorse his view as compatible with orthodox Christianity. He says that God works only through laws of nature, and does not perform special individual actions to generate new species. If that’s what you mean by his “science” being separate from his notion of God’s action, you’re right. But of course he had no proof whatsoever for that initial working assumption; it was just a naturalistic prejudice. Thus, he couldn’t credibly explain the origin of the camera eye, but gosh darn, he knew that *however* it came about, it was through through a series of tiny steps, somehow producing viable intermediate forms, all without any guiding design.

    TEs now try to back-read Darwinian naturalism into the Bible, but of course Darwin never claimed that his naturalism was compatible with the teaching of the Bible, and his remarks about religion make it clear that he did not think that it was. He kept opposing his view to the view he characterized as “creation”, an opposition which hardly fits in with the TE notion that “God creates through evolution”.

    Indeed, except for one or two obviously diplomatic remarks to Christian friends in private letters, Darwin’s writing about religion exudes a polite contempt. But TEs don’t see this as a problem. Like putting together a chimaera or a griffin out of two misfitting animals, they simply glue their teleological faith onto Darwin’s anti-teleological science, and declare that all is well.

    It’s been said here before that an evolutionary naturalism more suited to Christian orthodoxy is Michael Denton’s. I would agree. In Denton’s evolutionary scheme, God is in control from the start, since he programmed the entire process. But TEs illogically prefer to marry Christ to Darwin rather than to Denton.

    T.

  66. Mr Timaeus,

    It’s irrelevant how Christian radiologists calculate decay.

    I can’t agree. The radiologist is making the same kind of assumptions about an ensemble of large numbers of objects that the population biologist working on anti-biotic resistant bacteria.

    Thank you for your expression of Darwin’s religious views. You are correct, I find them irrelevant to his science. By the same token, William Shockley may have been an atheist, racist, eugenics supporter, but that doesn’t make his work on transistors any less an accurate description of reality, and one a Christian electronics engineer needs to follow.

    Our topic is – Christian Darwinism is not rational. I’ve argued that it is as rational as Christian radiology or Christian weather prediction. They all rely on large ensembles acting according to statistical rules. You haven’t told me anything about the Christian religion that would make me suspect that a Christian researcher should be more averse to applying a statistical rule to nature than F=ma.

    Statistics works for living entities as it does for atomic particles. It works for our species as it does for bacteria. I’m sure the life insurance provided by orthodox Christian institutions is calculated according to actuarial statistics, and not by prayer. That a Christian Darwinist should use the same approaches in a scientific pursuit, as a working assumption, is wholly rational, in my view. After all, the assumption works.

  67. Nakashima:

    I can tell that your training is in mathematics or physics or the like, not in the life sciences, because your examples of large-number effects, while appropriate in their contexts (radioactive decay, masses of particles in a movement of wind, etc.), do not translate directly into biochemical/genetic mechanisms. You are applying abstract reasoning about “large numbers” without taking into account the *very specific spatial and geometrical arrangements and rearrangements* of atoms, molecules, and DNA sections which are necessary if Darwinian evolution is to work. You need to read the very careful biochemical descriptions of Meyer and Behe and Denton before you simply apply the “if numbers are large enough, chance can have a directive effect” argument.

    Your argument is typical of Darwinians. The number one defensive rule of Darwinian apologetics is: “Always talk in big generalities about randomness, selection, etc. Never try to account for specific changes, or specific sequences of changes. Never specify what it would take, biochemically, genetically, developmentally, to turn a hippo ancestor into a whale. Never specify what it would take to turn a shrew ancestor into bat. Just assert that with great lengths of time, and large numbers of random mutations, anything can turn into anything. And throw in as much technical jargon as possible, even irrelevant technical jargon, to cause intelligent non-specialist critics to back off, even though their criticisms are good. Bluff. Exaggerate. Misapply analogies. Do whatever you can to stop the critic from asking ‘But exactly *how* could it be done?’ Because once they corner you in front of an audience, and you admit that you don’t know exactly how it could have been done, our theory will be in a very embarrassing position.”

    T.

  68. Nakashima:

    You analogy of the racist electronics wizard is faulty. The electronics and and the racism have nothing to do with each other, and that’s why they are separable, whereas in neo-Darwinian theory the *deliberate exclusion of design* is *an intrinsic part of the scientific theory*. You would know that if you had read Darwin, Mayr, Sagan, Gaylord Simpson, etc.

    The conflict with orthodox Christian theology (and I have no idea whether you are Christian, Jewish, agnostic, secular or whatever– your Hebrew studies are compatible with any of the above) is that in Christianity, design not only cannot be deliberately excluded, but must be insisted upon. So in trying to combine Darwin with Christianity one is trying to combine an account of origins that *in principle rejects design* with an account of origins which *in principle insists on it*. That TE’s cannot grasp this elementary logical incompatibility indicates that they suffer from “cognitive dissonance”. They deal with this by compartmentalization of the mind, and compartmentalization of truth: “scientific truths” versus “truths of faith”. ID people are unwilling to compartmentalize in these ways. They seek a unified picture of reality, and a unified understanding.

  69. Mr Timaeus,

    You are correct, I have degrees in computer science. But I have done field work, tramping about in the Okefenokee Swamp, for a population biology project. None of that is neither here nor there to the quality of the argument I am presenting. You are free to share your own training in biology, of course.

    I think it is amusing that you think bignum arguments are the province of Darwinists. Most ID arguments from improbability are bignum arguments.

    But what is relevant, and unaddressed by you, is that populations _are_, in fact, ensembles of large numbers of entities, and therefore statistical approaches are appropriate tools for their study. Are you arguing that life insurance companies shouldn’t use actuarial science?

    Your argument has morphed significantly away from the grounds originally given for why Christian Darwinism is not rational – a concept of surprise. OK, design must be included. How does that modify the Christian’s working hypothesis that God will insist/allow events to follow statistical distributions that are well known, when a large enough ensemble is studied? Juat as the Christian flame physicist knows not to apply the normal statistics to the fiery furnace of the Book of Daniel, the Christian geneticist does not apply population genetics to Noah’s family. But in everyday life, they do apply these statistics.

    You’ve read Darwin. You know Darwinism, or evolution, does not take a position on OOL. Thomas Cudworth is arguing on another thread that ID supporters can pick and choose positions ranging from active intervention by God in every speciation, to micro- and macro-evolution by natural means, to ID as cosmic fine tuning. It seems to me that some of those positions could be satisfying to a Christian who uses Darwinism as a working hypothesis. Or is Cudworth wrong?

  70. Nakashima:

    Not only is Cudworth not “wrong”; he agrees with me and with StephenB. I recommend you to this thread:

    http://www.uncommondescent.com.....-help-you/

    where Cudworth shows exactly why Christian Darwinism is incoherent. (As an added bonus, you get the objections of a TE embryologist, and some lengthy back-and-forth.)

    As for the rest, the stats arguments don’t work. I’ve already explained why. Would you expect a block of radium, if left on a chemically sensitive surface, to leave the message: “Pick up take-out chicken and your pressed trousers on the way home, Dear”? Even if that block were left there for 4 billion years? No, you wouldn’t. You might not find it incredible that the radiation left some simple geometrical pattern, but if you found an articulate message, you would never believe me if I told you that the cause was a block of radium, firing out particles randomly, would you? You would look for a cause capable of producing design. You would look for an intelligent cause.

    We know of no “large number” phenomena in nature capable of producing the sort of articulate changes required for macroevolutionary development. If you know of any, please tell us what they are, and *show us how* they can alter genomes in a constructive way, by using an *actual example* and giving us a *hypothetical evolutionary pathway*. I have yet to see this in any biological book or article, though I’ve repeatedly posed the challenge to Ph.D.s in biology who are absolutely certain that macroevolution has occurred by neo-Darwinian means.

    It is interesting that your biological background is in population genetics. The population geneticists are the stalwarts of neo-Darwinism among the biologists. They never get it. They don’t understand that ID’s challenge is an engineering challenge, not a statistical challenge. In evolution something new has to be *built*. You can no more expect random processes to build a mouse or a man than you can expect random processes to build Hoover Dam or the Statue of Liberty. Give yourself four billion years and an infinite number of sand particles, and lots of irregular wind currents, so you have lots of “random” motion. Hoover Dam and Lady Liberty will never be built. You have to have a designer. And a living cell is far more complicated than either of those structures, and the changes from one species to another require a far more complicated dance than is required to build those structures.

    Also, as a computer programmer, you ought to know that a word processor couldn’t be created by four billion monkeys randomly entering code for four billion years. (Though some of the irritating features of Word 2007 might give one pause on that point.)

    T.

  71. Mr Timaeus,

    Would you expect a block of radium, if left on a chemically sensitive surface, to leave the message:…

    The issue at hand is whether a Christian working with the radium has left open the possibility in their mind that God could start sending them a message using Morse code through the Geiger counter, or have they completely shut off everything but the statistical expectation? If their working hypothesis is always to expect the usual statistical distribution are they still Christians?

    Thank you for sharing your opinion on population genetics. You started down this path by opining that I did not have a substantial biological background, now you’ve shifted to criticzing the background that I’ve said I do have. Before I take this criticism very seriously, why don’t you share your background in the biological sciences? Or is it the case that while my background is relevant, your background is not? Just wondering.

    I think the demonstration of macroevolution by small changes is available in the form of what is known as a “ring species”. There are several examples of these. Around some barrier (such as a body of water) there are several populations. Each can breed with the ones next to it. But when the ring closes, there is a break – the two populations cannot interbreed.

    In this situation, what happens over time (in most macroevoltionary development) has been stretched out over space. Normally, we would not have each population preserved over time, and we would not be able to sample the DNA of each population to discover what were the changes. But in a ring species, we have the favorable situation that each stage is still alive, just shifted physically a little.

    Is this gradual change? Yes, each neighbor population can interbreed. Is this speciation (macroevolution)? Yes, two populations that don’t interbreed in nature is the definition of separate species. So one species has evolved into another species via gradual change. We can even estimate how fast evolution occurs by estimating how long it took the species to migrate around the barrier from the starting population.

    Given that these populations of salamanders or terns are all still alive today, all it takes is some enterprising biologist with enough grant money to go out, collect DNA from members of each population, sequence it, and we will be well on our way to having a change-by-change record of how macroevolution actually happened. But we don’t have to wait for the sequencing data to know that it has happened. The observed facts of interbreeding populations leading to a non-interbreeding result is all the data we need.

  72. Nakashima:

    I didn’t actually ask you what science background you had; rather, I inferred your background from your comments. You are welcome to do the same for me. In any case, it isn’t your background that matters, it’s your arguments, and they have been, and still are, inadequate to establish your conclusions.

    I’ll make another inference about your background. You have not done much formal study of either Christian theology (despite your knowledge of the Hebrew Bible) or philosophy. Your discussion of God, time, foreknowledge etc. indicates someone not used to operating fluidly in these subject areas. I am not seeing the sort of arguments I would expect to get from someone who, trained in Plato, Aristotle, Kant, Hume, Augustine, Aquinas, Ockham, Calvin, etc., was trying to reconcile Darwinian thought with the Christian doctrines of Creation and Providence. You seem to be improvising with the tools at hand, rather than speaking out of experience with the tools of the philosophical and theological professions. Am I correct again?

    Again, however, it doesn’t matter, because the only thing that is important is your argument, which I don’t find any stronger in theology than in the natural sciences.

    You evaded my question about the radium. If the message indicated was found, and I told you that it was caused by a block of radium, would you accept this as the causal explanation for the message? Yes or no? And why or why not? Until you can answer that question, and come to grips with your own answer, you won’t understand why the statistical argument you are using is inadequate when applied to explaining, say, the creation of new body plans via Darwinian mechanisms.

    Your example of ring species is old hat to me, and trivial. It’s straight microevolution, of the sort population geneticists always trot out. The further assumption you are making is that macroevolution is just microevolution writ large, i.e., carried out over a longer period of time, as if the difference between a marine worm and a lobster or cat is merely additive. But that assumption is far from certain, and in fact is precisely what remains to be proved. So to say that because seagulls can change slightly as they move around the world, and to infer from that that a bacterium can become Beethoven, is at this point of scientific knowledge sheer assertion.

    “With enough grant money” — you’ve hit the nail on the head there. That’s to a large extent what the Darwin lobby is about — bilking the taxpaying public out of hard-earned tax dollars to support its reckless speculations to discover alleged facts about the past which, even if determinable, are of little practical interest. It’s money that could be better spent on cancer research, research into genetic diseases, etc.

    DNA sequencing data alone would not tell us how evolutionary change took place. It would merely give us a full table of the degrees of similarity and dissimilarity of different genomes, i.e. a genetic version of the full table of similarities and dissimilarities of different morphologies. But there is no logical inference from the similarities and dissimilarities to a graded evolutionary pattern, unless you are already making the philosophical assumption of naturalism, i.e., that species could have emerged only out of other species, and only via entirely natural processes. But that would be assuming what is to be proved — that such transformations can happen.

    What you need is a mechanism which tells us how to get from one genome to another genome, in an orderly fashion which allows all the intermediate forms to have a selective advantage. Mapping all the genomes is necessary but nowhere near sufficient.

    We certainly do *not* know that macroevolution has happened, and cannot possibly know that, until a plausible mechanism has been found. Ring speciation is nowhere near a plausible mechanism. And even if we did know that macroevolution had happened, we would still be in the dark as whether it occurred entirely through natural processes or was influenced by the periodic input of an intelligent agent. The only way we could eliminate the need for input from an intelligent agent would be show the self-sufficiency of known biological processes to produce radically new organs, systems, and body plans — and we have no proof of such self-sufficiency. Ring species just don’t cut it.

    It appears to me that your acceptance of neo-Darwinian macroevolution is based on the evidence for limited microevolution, plus a heaping helping of faith in naturalistic mechanisms.

    Orthodox Christians, of course, do not place their faith in naturalistic mechanisms, but in God. An orthodox Christian can grant that God makes use of natural laws and mechanisms to accomplish much that we see; but, unlike atheist Darwinists and TEs, and orthodox Christian does not *require* that everything we see must be explicable naturalistically. Orthodox Christians take the dynamic Hebraic God — about whom you say you have read in the original texts — much more seriously than do TEs with their “hands off” God, who retires from active duty once he has established the laws of nature (which do all the creating on their own), then mysteriously comes out of retirement to do a few special miracles for Israel (but oddly, nowhere else), and, after that, sees to it that those miracles are recorded in the Bible, then retires again, this time for good.

    T.

  73. —Nakashima: “It seems to me that you are saying that Christians cannot be surprised and remain a Christian.”

    I am using the word “surprise” in the context of God’s omniscience. Whether a Christian is surprised or not isn’t really relevant. The issue is this: Does evolution produce a purposeless, unintended outcome: Darwinism yes; Christianity no.

    —“Okay, most people would agree that the God of Christianity is omniscient and cannot be surprised.”

    Right you are.

    [If evolution knows where it is going and moves toward a specified end, it isn’t Darwinism; …]

    —“Does God’s omniscience challenge this statement? Not the definitional statement, but the idea itself?”

    No. God’s omniscience is consistent with his knowledge of where evolution is going to go. It is inconsistent with the Darwinian model characterized by Simpson when he wrote, “man is the result of a purposeless and natural process that did not have him in mind.”

    One of the many excellent points that Timeaus was making is that, strictly speaking, God doesn’t really “foreknow” anything because He is outside of time. He just knows. All consequences are just as obvious to him as the preliminary events that gave rise to them. Timeaus is right, of course.

    We speak of God’s “foreknowledge” in an informal way so we can manage other questions that come up when non-Theists suggest that since God knows everything that is going to happen, God must have caused everything in a deterministic way. That is not the case. God knows if the stock market is going to crash, but that doesn’t mean that God caused it to crash.

    —“Evolution isn’t a mindful entity, it is a natural process. Saying ‘evolution knows’ is like saying ‘fire knows’.

    “Anthropomorphism” or “personification” is simply a linguistic tool. It is not to be taken literally. Notice that Simpson used the very same kind of language above [a process that did not “have man in mind.”]. He is using the technique of personification to dramatize the point of purposelessness just as I was using it to dramatize the point of purposefulness. The point is that evolution is [a] either moving toward a specified end [a purpose implanted by God] or [b] it is moving aimlessly with no specified outcome. The first point is consistent with Christianity; the second point is consistent with Darwinism. The two cannot be reconciled, which means that Christian Darwinists who try to have it both ways are militating against reason. [Or, as I like to put it, they live in an intellectual madhouse].

  74. I find it interesting that gradual change resulting in reproductive isolation is now considered to be trivial. I suppose the definition of trivial evolves over time.

    At any rate, I think there is a reason why Behe has not based his criticism of evolution on the differences between animals, be they worms or cats. There are few “inventions” separating them.

    Mostly changes in regulatory genes, and the changes are nested.

  75. Petruska states”

    “At any rate, I think there is a reason why Behe has not based his criticism of evolution on the differences between animals, be they worms or cats. There are few “inventions” separating them.”

    LOL… Why they (cats and worms) are almost in the same phylum Petruska,,, LOL

    “The likelihood of developing two binding sites in a protein complex would be the square of of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.” Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009
    Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
    http://www.evolutionnews.org/2.....hes_t.html

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-mic.....-evolution

    Multiple Mutations Needed for E. Coli – Michael Behe
    Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we’ve seen evolution do, then there’s no reason to believe evolution could produce many of the complex biological features we see in the cell.
    http://www.amazon.com/gp/blog/.....96N278Z93O

    Simulating evolution by gene duplication of protein features that require multiple amino acid residues: Michael J. Behe and David W. Snoke
    Excerpt: We conclude that, in general, to be fixed in 10^8 generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 10^9.,,,The fact that very large population sizes—10^9 or greater—are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 10^8 generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.
    http://www.pubmedcentral.nih.g.....id=2286568

    Waiting Longer for Two Mutations, Part 5 – Michael Behe
    Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years,
    http://behe.uncommondescent.co.....ns-part-5/

    An Atheist Interviews Michael Behe About “The Edge Of Evolution” – video
    http://www.in.com/videos/watch.....34623.html

  76. I’m not sure what your point is. Most of the genes found in animals are ancient, not new inventions. At any rate, they are found in single celled organisms.

    This seems to have been used quit often on this site as an an argument for front loading.

    The odds against “finding” a “needed” mutation may be enormous, which may be why species confronted with a sudden shift in the ecosystem tend to go extinct.

    On the other hand, finding a mutation that isn’t fatal seems to be rather common.

  77. How about us just finding a novel protein that would be “useful” Petruska:

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness – Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke – 2010
    Excerpt: In experimental evolution, the best way to permit various evolutionary alternatives, and assess their relative likelihood, is to avoid conditions that rule them out. Our experiments, like others (e.g. [40]), used populations of cells growing slowly under limiting nutrient conditions, thereby allowing a number of paths to be taken to higher fitness. We engineered the cells to have a two-step adaptive path to high fitness, but they were not limited to that option. Cells could reduce expression of the non-functional trpAE49V,D60N allele in a variety of ways, or they could acquire a weakly functional tryptophan synthase subunit by a single site reversion to trpAD60N, bringing them within one step of full reversion (Figure 6). When all of these possibilities are left open by the experimental design, the populations consistently take paths that reduce expression of trpAE49V,D60N, making the path to new (restored) function virtually inaccessible. This demonstrates that the cost of expressing genes that provide weak new functions is a significant constraint on the emergence of new functions. In particular, populations with multiple adaptive paths open to them may be much less likely to take an adaptive path to high fitness if that path requires over-expression.
    http://bio-complexity.org/ojs/.....O-C.2010.2

    “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed – along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering)

    A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells
    Excerpt: “Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division.”
    http://www.plosone.org/article.....ne.0007385

    The Origin of Biological Information and the Higher Taxonomic Categories – Stephen Meyer”Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.”
    http://eyedesignbook.com/ch6/eyech6-append-d.html

    Hopeful monsters,’ transposons, and the Metazoan radiation:
    Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable “hopeful monsters” render these explanations untenable.
    Paleobiologists Douglas Erwin and James Valentine

    “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan).” Michael John Denton page 172 of Uncommon Dissent

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells
    http://www.evolutionnews.org/2.....footnote19

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

  78. If, by Advantageous anatomical mutations, you mean easily observable structural differences that conveniently occur just when needed by a species, I’d probably agree with you.

    I don’t think biologists think of evolution that way, although pop science writers often do.

  79. Petrushka states,

    “I don’t think biologists think of evolution that way, although pop science writers often do.”

    You mean there actually is a difference between evolutionary biologists and pop science writers? LOL

  80. I’m not quite sure how you can argue that advantageous mutations are rare. I was just thinking about dog breeds, and that led to thinking about lions and tigers.

    There are certainly quite a few anatomical and behavioral differences between lions and tigers, and yet they can mate and produce healthy, even fertile offspring. They might even have been part of a ring species in which the geographical barriers eventually resulted in complete separation.

    Many people, like Ken Ham, who don’t accept evolution, seem willing to accept the likelihood that cats share a common ancestor. Some, if not most, of the differences between species of cats are going to be due to mutation (unless you would like to predict that cat species are the result of allele sorting, and all cats are really just one species).

    At what point would you argue that the accumulation of mutations can no longer occur?

  81. Petruska, A sub-species will always,/strong> lose genetic information in a “beneficial” adaptation away from a parent species. Yes there is great potential for sub-speciation from a originally created parent “kind” as clearly seen in this study:

    The following article is important in that it shows the principle of Genetic Entropy being obeyed in the fossil record by Trilobites, over the 270 million year history of their life on earth (Note: Trilobites are one of the most prolific “kinds” found in the fossil record with an extensive worldwide distribution. They appeared abruptly at the base of the Cambrian explosion with no evidence of transmutation from the “simple” creatures that preceded them, nor is there any evidence they ever produced anything else besides other trilobites during the entire time they were in the fossil record).

    The Cambrian’s Many Forms
    Excerpt: “It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.”"From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,”….(Yet Surprisingly)….”There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.” University of Chicago paleontologist Mark Webster; article on the “surprising and unexplained” loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago.
    http://www.terradaily.com/repo.....s_999.html

    Evolution vs. Trilobites – Prof. Andy McIntosh – video
    http://www.metacafe.com/watch/4032589

    In fact, the loss of morphological traits over time, for all organisms found in the fossil record, was so consistent that is was made into a scientific “law”:

    Dollo’s law and the death and resurrection of genes:
    Excerpt: “As the history of animal life was traced in the fossil record during the 19th century, it was observed that once an anatomical feature was lost in the course of evolution it never staged a return. This observation became canonized as Dollo’s law, after its propounder, and is taken as a general statement that evolution is irreversible.” http://www.pnas.org/content/91.....l.pdf+html

    A general rule of thumb for the “Deterioration/Genetic Entropy” of Dollo’s Law as it applies to the fossil record is found here:

    Dollo’s law and the death and resurrection of genes
    ABSTRACT: Dollo’s law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or “lost” developmental programs. Conversely, the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints;
    http://www.pnas.org/content/91.....l.pdf+html

    Dollo’s Law was further verified to the molecular level here:

    Dollo’s law, the symmetry of time, and the edge of evolution – Michael Behe
    Excerpt: We predict that future investigations, like ours, will support a molecular version of Dollo’s law: ,,, Dr. Behe comments on the finding of the study, “The old, organismal, time-asymmetric Dollo’s law supposedly blocked off just the past to Darwinian processes, for arbitrary reasons. A Dollo’s law in the molecular sense of Bridgham et al (2009), however, is time-symmetric. A time-symmetric law will substantially block both the past and the future,”. http://www.evolutionnews.org/2.....f_tim.html

    This following piece of Genetic Entropy evidence came to me from Rude on the Uncommon Descent blog:

    At one of the few petrified forests that sports ginkgo wood, I was told by the naturalist that ginkgos are old in the fossil record—they date from the Permian back when trees were first “invented”. She said that there are many species of fossilized Ginkgoaceae, but Ginkgo biloba, is the only living species left. – Rude – Uncommon Descent

    Petruska, even the races of humans follow this pattern:

    Even in the differences of human races we find that the younger races (Chinese, Europeans, American Indians, etc.. etc..) are losing genetic information when compared to the original race of humans which is thought to have migrated out of east Africa some 50,000 years ago.

    “We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.” Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.-

    I wonder what Hitler would have thought of that study?

    This following study is interesting in that it shows the principle of Genetic Entropy being obeyed for the estimated 60,000 year old anatomically modern humans found in Australia:

    Ancient DNA and the origin of modern humans: John H. Relethford
    Excerpt: Adcock et al. clearly demonstrate the actual extinction of an ancient mtDNA lineage belonging to an anatomically modern human, because this lineage is not found in living Australians. Although the fossil evidence provides evidence of the continuity of modern humans over the past 60,000 years,,, http://www.pubmedcentral.nih.g.....rtid=33358

    The author of the preceding paper offered a evolutionary “just so story” for how this loss of genetic information occurred. Yet, the result clearly falls within what we would expect from a Genetic Entropy perspective and doesn’t require any bending of evidence to fit the theory.

    Petruska, as you can see everything points to a loss of information. That is the problem for neo-Darwinism they have ZERO examples of the generation of functional information that would violate the principle of genetic Entropy. Do you care to provide an example?

  82. I haven’t really been arguing for the generation of functional information.

    I’ve been arguing that non-fatal change occurs, and presumably accumulates.

    I’ve given the cat family as an example of accumulated change that hasn’t involved degeneration. Even young earth creationists tend to believe that cats are related by descent.

    Dollo would seem to argue against the occurrence of any series of mutations that are specified in advance. (The obvious example would be a series of mutations occurring in reverse).

    I’m not aware that many evolutionary biologists try to argue that mutations occur because they are needed. I think the biologist would argue that many non-fatal mutations occur, and that they can accumulate.

    This offers no guarantee that a change necessary to prevent extinction will occur. It would seem that extinction is the most likely outcome in cases where sudden ecological change occurs.

  83. Petruska you state:

    “I’ve been arguing that non-fatal change occurs, and presumably accumulates.”

    Petruska if your are “presuming” “non-fatal change” will eventually become beneficial (i.e. will become functional information within a genome) there is no evidence to support that position that I know of. If you know of any evidence please present it for review for you will then be the first commenter on UD to ever show what neo-Darwinism claims for all of life on earth is actually true.

    As for the ID position:

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    http://mdpi.com/1422-0067/10/1/247/ag

  84. Mr Timaeus,

    We know of no “large number” phenomena in nature capable of producing the sort of articulate changes required for macroevolutionary development.

    My apologies. I assumed that ‘macroevolutionary development’ meant the same thing as speciation, and that speciation meant different species, and that different species meant ‘two populations that do not interbreed. Please point out to me where your definitions depart from these relatively common ones, and we can procedd.

  85. Mr Timaeus,

    You evaded my question about the radium. If the message indicated was found, and I told you that it was caused by a block of radium, would you accept this as the causal explanation for the message?

    We are dicussing the non-rationality of the Christian Darwinist. At the moment, I am not aware of being a Christian. Therefore my opinion is irrelevant. However, I assume you are a Christian, so please tell me if the Geiger counter next to the radium block started tapping out the Morse code for “What hath God wrought?”, what would your reaction be? What should be, in your opinion, the reaction of any Christian physicist?
    Is it… surprise?

  86. Petruska if your are “presuming” “non-fatal change” will eventually become beneficial (i.e. will become functional information within a genome) there is no evidence to support that position that I know of.

    I’m not sure what you are implying.

    Are you arguing that variation and diversity are unrelated to the ability of a species to survive change, or to extend its range? Are there no benefits in being larger or smaller, or having different fur patterns and densities, depending

    In the example of the cat family, are there no benefits to being a tiger rather than a lion, depending on the terrain and available prey?

    Or are you suggesting that cats are not related by descent?

    Or perhaps that the parent cat species had all the cat alleles, and that modern cats are just subdivisions of the parent genome?

    I’m not sure exactly what your position is, and how it comports with that of folks like Behe.

  87. Nakashima:

    If you can’t distinguish between “macroevolution” and “speciation”, I’m not sure you should be entering into these debates. You may need to do some more studying first. But I’ll try to help.

    An Arctic tern, after long geographical separation, becoming a distinct species, not interbreeding with the parent stock, is “speciation”.

    “Macroevolution” is the large sweep from bacteria to man, a process in which, allegedly, wholly natural mechanisms (for Darwinists, neo-Darwinian mechanisms) frequently generated radically new body plans and high-level distinctions such as kingdom, phylum, class, and order.

    There is *no proof whatsoever* that such mechanisms as can cause Arctic terns to diverge sufficiently that they can no longer interbreed, can rearrange the body plan of a marine worm into a lobster or a lizard or a cat. That is, there is no proof that the genetic mechanisms which drive *microevolution* (changes at the level of variety, species, and possibly genus) are capable of driving macroevolution. Such an extension is speculative.

    In other words, Darwinian mechanisms might be able to explain the evolution of lions and housecats from some wild common ancestor, but they haven’t yet explained the evolution of the order of bats from a non-flying primitive mammalian ancestor, or the evolution of a whale from a putative hippo ancestor, of the evolution of lobsters from marine worms, or the evolution of multi-celled animals from single-celled animals.

    The number of differences between a lion and a tiger are relatively small compared with the number of differences between a hippo and a whale. Asking random processes to produce a whale from a hippo is much more than asking them to produce one Artic tern from another, or a lion and tiger from a common wildcat ancestor. And it’s not just the number of individual changes, like a bigger eye or things of that sort; it’s the complex structural interrelations that have to be altered wholesale, not piecemeal, if there are to be viable intermediate forms.

    Random firings of radioactive nuclei are no more likely to produce co-ordinated, wholesale biological changes with survival value, than they are to spell out “Bring home the laundry, Dear”, or turn a chess-playing program into a spreadsheet program.

    If you think random changes have this power, the onus is on *you* to demonstrate it in the biological context. Tell me how a hippo was turned into a whale. Tell me how a marine worm became a lobster. Specify the genetic mechanisms employed at each step. Can you do this? Have you ever seen a book or article that has done this?

    T.

  88. Petruska, I’m saying all observed sub-speciation events within the cat family are the result of a loss of the information that was originally encoded in the parent kind. Such as the wolves to dogs example:

    ,,the mean sequence divergence in dogs, 2.06, was almost identical to the 2.10 (sequence divergence) found within wolves. (please note the sequence divergence is slightly smaller for the entire spectrum of dogs than for wolves)
    http://jhered.oxfordjournals.o.....0/1/71.pdf

    “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.” R. Milner, Encyclopedia of Evolution (1990)

    Natural Selection Falsified – Dr John Sanford – video
    http://www.metacafe.com/watch/4587204

    Natural Selection Reduces Genetic Information – Dr. Georgia Purdom – video
    http://www.metacafe.com/watch/4036808

    Natural Selection Reduces Genetic Information – No Beneficial Mutations – Spetner – Denton – video
    http://www.metacafe.com/watch/4036816

    EXPELLED – Natural Selection And Genetic Mutations – video
    http://www.metacafe.com/watch/4036840

    “…but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have…”
    Maciej Marian Giertych – Population Geneticist – member of the European Parliament – EXPELLED

    The Sheer Lack Of Evidence For Macro Evolution – William Lane Craig – video
    http://www.metacafe.com/watch/4023134

    etc.. etc..

    I don’t know how to make it any more clear Petruska.,,, There is variability within a created kind , such as the diversity seen within the cat family, but all variations from the original parent kind will always come at a cost of information. Material processes (neo-Darwinism) have never demonstrated a gain in functional information above what was already present in the parent species genome. i.e. if you were to sub-speciate a “new” species away from a lion or tiger, you would do so at a cost of the inherent information in the genome. Yet material processes cannot replace that lost information thus the sub-speciation events all “run into a wall” in which no more variation is possible, such as with extreme lack of genetic diversity found within cheetahs.

  89. I guess I’m asking a more specific question.

    Are you saying that the parent species had all the alleles now found in their descendants? Or has some of the variation arisen through mutation?

    It’s quite true that highly specialized creatures are likely to fail when the ecosystem changes. Particularly if population is small and there is little diversity.

    But not all species are rigid and unable to recover from overspecialization. Dog populations seem able to revert to a wild type when allowed to become feral.

    I can’t really see what specific predictions are being made by the concept of genetic entropy. There are species that seemed, based on gross morphology,to have existed unchanged for tens of millions of years. Things like alligators and cockroaches do not seem to have suffered from their relative stasis.

    What exactly happens to the genome when it degrades?

  90. 90

    Timaeus,

    I remember this basic question you ask from more than a year ago – then asked of professor of biology at Cornell.

    I wish you luck in getting a straightforward answer, but I believe Nakashima will punt into irrelevance just as the professor did.

    After all, what else could happen? Nothing else has happened so far.

  91. Mr Timaeus,

    You mentioned several higher level taxonomic categories. So, where for you does “macroevolution” leave off, and “microevolution” take up? What I hear you saying is that microevolution can cause speciation events, that Arctic terns are an example of such. Is that an accurate staement of your position?

  92. Petrushka you ask;

    “Are you saying that the parent species had all the alleles now found in their descendants? Or has some of the variation arisen through mutation?’

    I’m not saying anything. It is the evidence that says:

    Some bacterium spores, in salt crystals, dating back as far as 250 million years have been revived, had their DNA sequenced, and compared to their offspring of today (Vreeland RH, 2000 Nature). To the disbelieving shock of many scientists, both ancient and modern bacteria were found to have the almost same exact DNA sequence.

    The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    and this:

    Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber
    Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart,(thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution’s “genetic drift” theory requires.)
    http://www.sciencemag.org/cgi/...../5213/1060

    30-Million-Year Sleep: Germ Is Declared Alive
    http://query.nytimes.com/gst/f.....gewanted=2

    In reply to a personal e-mail from myself, Dr. Cano commented on the “Fitness Test” I had asked him about:
    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.

    Is Antibiotic Resistance evidence for evolution? – “Fitness Test” – video
    http://www.metacafe.com/watch/3995248

    According to prevailing evolutionary dogma, there “HAS” to be “significant genetic/mutational drift” to the DNA of bacteria within 250 million years, even though the morphology (shape) of the bacteria can be expected to remain the same. In spite of their preconceived materialistic bias, scientists find there is no significant genetic drift from the ancient DNA. I find it interesting that the materialistic theory of evolution expects there to be a significant amount of mutational drift from the DNA of ancient bacteria to its modern descendants, while the morphology can be allowed to remain exactly the same with its descendants. Alas for the materialist once again, the hard evidence of ancient DNA has fell in line with the anthropic hypothesis.

    Petruska you then state;

    “But not all species are rigid and unable to recover from overspecialization. Dog populations seem able to revert to a wild type when allowed to become feral”

    Does a “specialized” dog automatically become feral if returned to the wild? Or does that “specialized” dog, that has a extreme lack of genetic diversity, have to breed with other dogs that have more of the original genetic code which has more gentic diversity in order to accomplish variation? It is all about the information Petruska! IT IS THAT SIMPLE!!!

  93. My reading indicates that no significant DNA has been found that is more than a million years old. Claims of older DNA are generally regarded to be the result of methodological errors.

    Populations, dogs or otherwise, that have diversity, can adapt more readily than small, inbred populations, all else being equal.

    But even a single bacterium, given time, will develop into a diverse population.

  94. Sorry, Nakashima, I didn’t notice your #85 until just now. Here’s my answer:

    No, your opinion about the radium is not irrelevant. When I offered the example of the radium I was not addressing your claims about Christian theology and randomness, but your implied claim that randomness of mutations was not incompatible with building complex, integrated biological systems. And the point is that if you don’t believe that even in four billion years the radium would ever spell out “Bring home the laundry, Dear”, then you are being inconsistent in believing that random mutations, in the same time, could produce roses, aardvarks, and man, which contain orders of magnitude more integrated complexity than that simple message.

    So, would you believe me if I told you that the message was spelled out by a block of radium? And would you believe me if I told you that Microsoft Word was created by accident when a chess program was left exposed to input for ten years, and a random error was introduced into the code at the rate of five errors per second?

    And since I expect you to answer my question, I’ll answer yours:

    Yes, I’d be surprised, because I would not expect the radium block to produce specified complexity. I would therefore investigate further. I would first investigate all naturalistic alternatives, i.e, some kind of trickery or Candid Camera joke. After exhausting all of those, I would consider the possibility of miraculous intervention. I would never, not with my dying breath, believe that the message “just happened” to be meaningful, on the grounds that “it’s bound to happen” somewhere in the universe, if you have enough galaxies, etc. I would never accept that sort of irrational abdication of explanation. Miracle is more rational than that.

    Now, I’ve answered your question. If you answer mine, I’ll continue the conversation. If not, you won’t be discussing in good faith, and I’ll discontinue.

    By the way, if I may be permitted one more question: if you’re not even sure you are a Christian, why do you have such strong opinions about the compatibility of Christian theology with random mutations? Why are you concerned to defend the TEs’ desperate reasoning when you don’t even share their faith? Do you just like playing devil’s advocate here at UD?

    T.

  95. Nakashima:

    I didn’t see your question at 91.

    I’ll answer it after you’ve dealt with the questions I’ve already posed.

    T.

  96. Mr Timaeus,

    Please don’t worry about not seeing questions.

    My answer re radium is similar to yours. I would investigate natural causes first. This would include a quick calculation of just how unlikely such a message is. It would also include getting some other people to verify the message’s existence, on the theory that it was all in my head. I would posit space aliens communicating through rocks, and God, as a last resort.

    Having answered, I have to say I think your motivation for asking is mistaken. The random decay of the radium is analogous to only one aspect of the evolutionary process, variation. It says nothing about selection. The iterative combination of these two is what evolution is all about. But of course, you knew that, having read Darwin, Mayr, etc.

    On the question of why I’ve expressed such strong opinions, I have to say that I have been more motivated by the flawed nature of the argument, and the way this flaw has been used to slander a class of people in a way reminiscent of the use psychiarty by the Soviets. You don’t have to be the same religion as someone to come to their aid, as Jesus pointed out with a parable about a man from Samaria.

  97. Nakashima:

    I agree with you about the calculation. And would you not agree that there would be a number sufficiently low, after which you would infer that the result (for all practical purposes) could not have been produced by chance, and required design by agents unknown? If so, you agree in principle with the approach of ID theory.

    Yes, I know that natural selection is brought in, but natural selection creates nothing. All the heavy lifting is done by the variations. Natural selection can only accept or reject. It does not add one bit of new information to the genome; it only decides what will be preserved. So you still end up having to map out which variations would be necessary, and in which order, and how fast the creature reproduces, and how much time there is in the fossil record, etc., and do a probability calculation. And your admission above grants that at least in principle, one might come up with a number so low that it would be irrational to attribute the result to neo-Darwinian means. Of course, at present, we have nowhere near the ability to calculate these probabilities, so I am not claiming that ID has been proved; but by exactly the same token, neo-Darwinism has not been established either. No hard numbers, no proof. The objective scientist would vote for “insufficient data for a firm conclusion”. But that’s not what Darwinists do. They dogmatize and insist that their theory is as certain as Newton’s or Einstein’s.

    If you are so eager to come to the aid of people who are being slandered, you might consider coming to the aid of ID. ID’s arguments have been regularly misrepresented, caricatured, etc. by TEs and atheists alike. Every form of ad hominem argument has been used against ID proponents. TEs have regularly accused ID of being not only bad science but bad theology, accusing it of a false understanding of creation, a bad understanding of the problem of evil, a low view of God, etc. If you are so concerned to defend those who are repeatedly accused of false charges, maybe you can spare us some of that “justice for the underdog” that you are currently supplying to the TEs.

    T.

  98. Nakashima @ 91:

    It is not necessary for an ID person to hold that neo-Darwinian processes are entirely responsible for lower-level evolution (species, genus) and that miracles or interventions are needed for higher-level changes (kingdom, phylum, class). That is a possible view within ID, but it is not necessary. It seems more reasonable to me to imagine that the “design component” and the “chance component” are running in parallel all the way up and down, with the design component restricting the freedom of the chance component. Further, we must remember that “design” need not imply miracles or interventions, if the design is pre-programmed into the primitive genomes (which is not the Darwinian view, but is found in Denton’s writing). So there can be design “all the way down”, within a naturalistic framework. The intelligent designer’s work is thus taken out of the process by being pushed back in time to the origin, the first genomes (or in Denton further back, to the cosmic fine tuning). No miracles are necessary, but intelligence is definitely necessary. Thus, ID can co-exist with evolution, but not with pure neo-Darwinism. (ID can co-exist with a constrained, limited neo-Darwinism, but the Darwinists will not tolerate that option. They want it all their way.)

    T.

  99. …but natural selection creates nothing. All the heavy lifting is done by the variations. Natural selection can only accept or reject. It does not add one bit of new information to the genome; …

    But it does add information. Every selection event confirms or rejects a genome. It is negative feedback, and any system having negative feedback will be shaped.

    It constrains the content of genomes to a combination of exact replication and non-fatal changes, in general, very small changes.

  100. Petrushka:

    Call it new information if you want. I see the mutations as the new bricks, and natural selection as the mortar which holds the new bricks in place. But mortar isn’t a new brick, and I see no point in calling that information. It’s rather the fixing into place of the newly created information.

    But let’s not quibble over mere words. I don’t deny the importance of natural selection. The question is whether the thousands or millions of “very small changes” needed to create an eye or a new body plan are likely to occur in the right order and within the right timeframe, and no one has shown this in a detailed way for any major macroevolutionary change. We’ve been asking here for five years for the books and articles with the details, and we always get either silence or literature bluffs. So much for the science that is supposed to be as solid as the theory of gravity or electromagnetism.

    T.

  101. Petruska you state:
    “My reading indicates that no significant DNA has been found that is more than a million years old. Claims of older DNA are generally regarded to be the result of methodological errors.”

    And just how connected are you to evolutionary thought Petruska? Will you relinquish through reason or will you defend it no matter what the evidence says?

    Waiting Longer for Two Mutations, Part 5 – Michael Behe
    Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years,
    http://behe.uncommondescent.co.....ns-part-5/

    First study hints at insights to come from genes unique to humans
    Excerpt: Among the approximately 23,000 genes found in human DNA, scientists currently estimate that there may be as few as 50 to 100 that have no counterparts in other species.
    http://news.wustl.edu/news/Pages/11349.aspx

    The Evolution of Mammalian Gene Families – Jeffery P. Demuth
    Excerpt: Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences.
    http://www.plosone.org/article.....ne.0000085

    A recent, more accurate, human/chimp genome comparison study, by Richard Buggs in 2008, has found when he rigorously compared the recently completed sequences in the genomes of chimpanzees to the genomes of humans side by side, the similarity between chimps and man fell to slightly below 70%! Why is this study ignored since the ENCODE study has now implicated 100% high level functionality across the entire human genome? Finding compelling evidence that implicates 100% high level functionality across the entire genome clearly shows the similarity is not to be limited to the very biased “only 1.5% of the genome” studies of materialists.

    Chimpanzee?
    10-10-2008 – Dr Richard Buggs – research geneticist at the University of Florida
    …Therefore the total similarity of the genomes could be below 70%.
    http://www.idnet.com.au/files/pdf/Chimpanzee.pdf

    Moreover, when scientists did a actual Nucleotide by Nucleotide sequence comparison, to find the “real world” difference between the genomes of chimps and Humans, they found the difference was even more profound than Dr. Richard Buggs estimate:

    Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship?
    Excerpt: the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.]
    http://www.apologeticspress.org/articles/2070

    Chimp and human Y chromosomes evolving faster than expected – Jan. 2010
    Excerpt: “The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content.,,, The chimp Y, for example, has lost one third to one half of the human Y chromosome genes.
    http://www.physorg.com/news182605704.html

    The evolutionary scientists of the preceding paper offered some evolutionary “just so” stories of “dramatically sped up evolution” for why there are such significant differences in the Y chromosomes of chimps and humans, yet when the Y chromosome is looked at for its rate of change we find there is hardly any evidence for any change at all, much less the massive changes they are required to explain.

    CHROMOSOME STUDY STUNS EVOLUTIONISTS
    Excerpt: To their great surprise, Dorit and his associates found no nucleotide differences at all in the non-recombinant part of the Y chromosomes of the 38 men. This non-variation suggests no evolution has occurred in male ancestry.
    http://www.reasons.org/interpr.....lutionists

    Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005:
    The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1-2%. Recently, direct nucleotide sequencing confirmed this estimate. These findings generated the common belief that the human is extremely close to the chimpanzee at the genetic level. However, if one looks at proteins, which are mainly responsible for phenotypic differences, the picture is quite different, and about 80% of proteins are different between the two species. http://www.ncbi.nlm.nih.gov/pubmed/15716009

    etc…etc.. etc…

    Petruska just how committed are you to finding the truth?

  102. post note:

    If materialists were to actually try to account for the origination of completely unique genes, and proteins, between chimps and humans, instead of just ignoring them, they would find novel genes, and functional proteins, are exceedingly rare to “find”:

    Could Chance Arrange the Code for (Just) One Gene?
    “our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).”
    http://www.creationsafaris.com/epoi_c10.htm

    “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: – Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.”

  103. one more for you Petruska:

    “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009)
    Excerpt: Even among higher organisms, “the problem was that different genes told contradictory evolutionary stories,”,,,“despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” ,,,,Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”,,, “We’ve just annihilated the (Darwin’s) tree of life.”
    http://www.evolutionnews.org/2......html#more

  104. Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years,…

    I’ve already stipulated that the odds are against any string of mutations specified in advance. See my comment on Dollo.

    But biologist — at least most of them — do not assert that evolution foresees its direction or seeks specific solutions. The odds against a specific direction may be high, but the odds of change occurring approach certainty.

    I don’t think Woese means what you think he means. He certainty isn’t skeptical of evolution occurring, or skeptical that animals are cousins. He rearranged the branching at the base of the tree.

  105. Petrushka:

    But biologist — at least most of them — do not assert that evolution foresees its direction or seeks specific solutions. The odds against a specific direction may be high, but the odds of change occurring approach certainty.

    Just a comment on this point, because I believe it is a recurrent objection, whose logical and empirical difficulties are usually overlooked.

    The point is: how true is it that a complex system can “evolve” in many, many completely different directions? I believe that it simply is not true.

    Let’s start from OOL. We could argue that life, or something equivalent, is in principle possible in a completely different way from the system we know (nucleic acids, proteins, cells, etc.). In principle, that’s possible. But we:

    a) don’t know any example of that

    c) don’t have any idea or even the slightest vague model of how that could work

    So, empirically, we must stick to the fact that what we recognize for life needs, as far as we know, at least the minimal apparatus that we find in the simplest archea or bacteria (a genome, hundreds of funcional proteins, a cell membrane etc.)

    But let’s go on. Once we have a complex (very complex indeed) system like that, any further change must:

    a) be compatible with what already exists

    b) usually be of great complexity itself, if it has to add new original function to a very complex system. This is a very important point. Indeed it is perfectly possible that some relatively simple change may occur which changes some function in a positive way, but that will usually be just a “tweaking” of what already exists. Any really new, original function will work only if it is integrated in the high complexity of functions which already are working. There is not only a problem of function itself, but all the problems of connection, of interface, of regulation of the new function in the previous complex system.

    Let’s make an example from informatics: let’s say you want to improve Windows Vista, giving it new recognizable functionality. You can certainly just correct some little errors (which are always present in a complex system, however good the design has been), and in some very rare cases that could be accomplished by changing a few bits here and there. But, if you really want to achieve a new fucntional implementatin, even a minor one, you will have to right a lot of new code, and to insert it in the right places, and to change all the pertinent references in the old code. Just to make the work of development easier, modern programming is usually object oriented, andthat’s interesting, because that’s propbably the general programming philosophy of biological programming (see for instance how protein domains can be considered as the “objects” in the construction of the proteome). But even in object oriented programming, the complexity of the modifications you have to implement when you want to change a complex system is simply stunning. Here, more than ever, the problem of irreducible complexity arises at every corner. Each new “object” must be completely functional in itself to be added to the system, and its interface must be completely compatible with the existing interfaces of the existing objects.

    In other words, my point is that, if in principle some change in a generic system could point to positive modifications of the system of very different nature, the fucntional organizationa and complexity of an existing system creates an extreme narrowing of the potential for useful modification. Excluding the few examples where a small modification can correct some error, or just tweak an existing function (the conceptual equivalent of microevolution), new important modification will have to be complex, well integrated, well regulated, and point to few specific lines of change which have meaning in the context of what already exists.

    In other words, they will have to be designed.

  106. Mr Timaeus,

    I’ll respond to your points in approximately the same order as you make them, and also across multiple posts.

    I think you dismissal of selection is misguided. Each generation varies from a starting point that was slightly better at surviving than the previous one. That does make a difference across millions and billions of generations.

    Yes, I do accept that calculations can (in advance of a simulation being run) predict whether an outcome is likely or not. In the field of genetic algorithms, this is a very active research topic. If you told me that your problem involved optimizing 1,000 bits, but you could afford only 1,000 evaluations which would be better – one generation of 1,000 individuals, 10 generations of 100, 100 generations of 10, or 500 generations of 2? Choosing the right parameters involves making that calculation.

    I’m glad to here that you accept propability calculations as evidence to weighed. I’m sure you are familiar with Nilsson’s probability calculation on eye development – that sophisticated eyes can develop quickly. Rather than dismiss it for not being a simulation, I hope you can agree that it should be faced for what it says. Attack its assumptions, that is the good scientific way of critiquing, but don’t poo-poo it for being ‘just’ a calculation. If that criticism was valid, the key chapters of Signature in the Cell would crumble into dust.

  107. Petruska you state:

    ‘The odds against a specific direction may be high, but the odds of change occurring approach certainty.”

    Exactly, all biological change which is possible will always be at a cost of the original implemented functional information and this fact approaches as close to certainty as science will allow verification. The problem for materialists is to show just one example of material processes generating functional information above that already present in nature, instead of constructing elaborate just so stories of material processes generating functional information with absolutely no solid empirical basis to show for it. The burning unanswered question, as it currently sits in the laps of evolutionary biologists, is this, “Where Did The Information Come From?”

    The DNA Enigma – Where Did The Information Come From? – Stephen C. Meyer – video
    http://www.metacafe.com/watch/4125886

    Stephen Meyer is interviewed about the “information problem” in DNA, Signature in the Cell – video
    http://downloads.cbn.com/cbnne.....f?aid=8497

    Stephen C. Meyer – Signature In The Cell:
    “DNA functions like a software program,” “We know from experience that software comes from programmers. Information–whether inscribed in hieroglyphics, written in a book or encoded in a radio signal–always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source.”
    http://www.evolutionnews.org/2.....ligen.html

    The DNA Code – Solid Scientific Proof Of Intelligent Design – Perry Marshall – video
    http://www.metacafe.com/watch/4060532

    The Digital Code of DNA – 2003 – Leroy Hood & David Galas
    Excerpt: The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science.
    http://www.nature.com/nature/j.....01410.html

    A New Design Argument – Charles Thaxton
    Excerpt: “There is an identity of structure between DNA (and protein) and written linguistic messages. Since we know by experience that intelligence produces written messages, and no other cause is known, the implication, according to the abductive method, is that intelligent cause produced DNA and protein. The significance of this result lies in the security of it, for it is much stronger than if the structures were merely similar. We are not dealing with anything like a superficial resemblance between DNA and a written text. We are not saying DNA is like a message. Rather, DNA is a message. True design thus returns to biology.”
    http://www.arn.org/docs/thaxto.....gn3198.htm

    The Coding Found In DNA Surpasses Man’s Ability To Code – Stephen Meyer – video
    http://www.metacafe.com/watch/4050638

    Bill Gates, in recognizing the superiority found in Genetic Coding, compared to the best computer coding we now have, has now funded research into this area:

    Welcome to CoSBi – (Computational and Systems Biology)
    Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas.
    http://www.cosbi.eu/index.php/.....rticle/171

    Petruska, Since the programming found in life greatly exceeds man’s ability to program, and evolution is a fact like gravity is a fact, then why in blue blazes is Bill Gates not employing random number generators and selection software instead of 1000′s of software engineers?

  108. Mr Timaeus,

    If you are so eager to come to the aid of people who are being slandered, you might consider coming to the aid of ID.

    Yes, I might. I dislike stridency, and people who argue that disagreement equals psychlogical imbalance. I have argued against PZ Myers getting frothy mouthed on his blog, and against Nick Matzke on PT.

    But since I’m more interested in evolution than atheism, here I am.

  109. Mr Timaeus,

    It seems more reasonable to me to imagine that the “design component” and the “chance component” are running in parallel all the way up and down, with the design component restricting the freedom of the chance component.

    That does seem to be a reasonable exercise of the imagination, and one that could be espoused by a Christian Darwinist while remaing reasonable, remaining Christian, and remaining a Darwinist.

    If this is your position, I am a bit surprised that you see a need to challenge biology professors for pathetic levels of detail. You already accept that chance events could lead to a whole new phylum. I agree that it is nice to have evidence of particulars, but it would hardly ‘disprove evolution’ in your mind when such narratives are slow in coming.

    I also note that you have, in response to a question about micro- and macro-evolution, spun a hypothesis about ID that goes far beyond ‘detecting design in Nature’. You have imagined several processes which one or another ID advocate might prefer. How should we scientifically proceed to confirm or eliminate any of these?

  110. In other words, my point is that, if in principle some change in a generic system could point to positive modifications of the system of very different nature, the functional organization and complexity of an existing system creates an extreme narrowing of the potential for useful modification.

    I believe Ernst Mayr discussed in some detail the improbability of well adapted organisms improving significantly via random mutation and selection. The record of extinction supports the notion that species that are tuned to a particular niche are likely to go extinct when the niche disappears.

    But so far, no event has sterilized the earth, and the survivors of mass extinctions have branched to fill vacant niches.

  111. …then why in blue blazes is Bill Gates not employing random number generators and selection software instead of 1000’s of software engineers?

    Your assertion that he isn’t would come as a shock to some.

    The analogy of DNA as a computer program has some serious limitations, but if you wish to push it to its useful limit, it would be better to think of the cell and its machinery as the computer and operating system, and the genome as parameters passed to functions. The parameters would include such stuff as how big, how much, what shape, and so forth.

    The cell and its machinery are rather resistant to change, since change is likely to be fatal. There are elements of the genome that resist change also. We call them conserved regions. Changes to them presumably interfere with survival or reproduction.

    I would agree that most mutations are probably deleterious. Life deals with this in two basic ways. There are functions that correct copy errors, and there is tremendous wastage. Smaller species produce huge numbers of offspring, while population numbers tend to be stable.

    There’s tremendous wastage in mammal reproduction also, including human reproduction. It just tends not to be noticed.

    But for ever sperm cell that engages in conception, hundreds of millions fail. Looking at sperm cells under a microscope, it takes little interpretation to assert that many are defective. Perhaps they have some mutation that produces a fatal metabolic error. Of those that are not obviously defective, only one — as a rule — survives and wins. In terms of variation and selection, this is functionally equivalent to the huge population numbers of microbes.

    When you are counting generations and population size for the purpose of calculating odds, you need to take this into account.

    As for your software question, genetic algorithms are used to solve problems that are otherwise intractable. Having the program evolve along with the data will require new kinds of hardware, such as the “brains in silicon” being developed at Stanford. But it’s coming.

    http://www.stanford.edu/group/brainsinsilicon/

  112. Petruska I’m glad you finally decided to cite something:

    Evolution has no rigorous mathematical foundation with which we can rigorously analyze it in any computer simulation:

    Accounting for Variations – Dr. David Berlinski: – video
    http://www.youtube.com/watch?v=aW2GkDkimkE

    LIFE’S CONSERVATION LAW – William Dembski – Robert Marks – Pg. 13
    Excerpt: Simulations such as Dawkins’s WEASEL, Adami’s AVIDA, Ray’s Tierra, and Schneider’s ev appear to support Darwinian evolution, but only for lack of clear accounting practices that track the information smuggled into them.,,, Information does not magically materialize. It can be created by intelligence or it can be shunted around by natural forces. But natural forces, and Darwinian processes in particular, do not create information. Active information enables us to see why this is the case.
    http://evoinfo.org/publication.....ation-law/

    Conservation of Information in Computer Search (COI) – William A. Dembski – Robert J. Marks II – Dec. 2009
    Excerpt: COI puts to rest the inflated claims for the information generating power of evolutionary simulations such as Avida and ev.
    http://evoinfo.org/publication.....nt-reason/

    Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism – Dembski – Marks – Dec. 2009
    Excerpt: The effectiveness of a given algorithm can be measured by the active information introduced to the search. We illustrate this by identifying sources of active information in Avida, a software program designed to search for logic functions using nand gates. Avida uses stair step active information by rewarding logic functions using a smaller number of nands to construct functions requiring more. Removing stair steps deteriorates Avida’s performance while removing deleterious instructions improves it.
    http://evoinfo.org/publication.....gic-avida/

    The Problem of Information for the Theory of Evolution – debunking Schneider’s ev computer simulation
    Excerpt: In several papers genetic binding sites were analyzed using a Shannon information theory approach. It was recently claimed that these regulatory sequences could increase information content through evolutionary processes starting from a random DNA sequence, for which a computer simulation was offered as evidence. However, incorporating neglected cellular realities and using biologically realistic parameter values invalidate this claim. The net effect over time of random mutations spread throughout genomes is an increase in randomness per gene and decreased functional optimality. http://www.trueorigin.org/schneider.asp

    The Capabilities of Chaos and Complexity – David L. Abel
    Excerpt: “To stem the growing swell of Intelligent Design intrusions, it is imperative that we provide stand-alone natural process evidence of non trivial self-organization at the edge of chaos. We must demonstrate on sound scientific grounds the formal capabilities of naturally-occurring physicodynamic complexity. Evolutionary algorithms, for example, must be stripped of all artificial selection and the purposeful steering of iterations toward desired products. The latter intrusions into natural process clearly violate sound evolution theory.”
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Arriving At Intelligence Through The Corridors Of Reason (Part II) – April 2010
    Excerpt: Summarizing the status quo, Johnson notes for example how AVIDA uses “an unrealistically small genome, an unrealistically high mutation rate, unrealistic protection of replication instructions, unrealistic energy rewards and no capability for graceful function degradation. It allows for arbitrary experimenter-specified selective advantages”. Not faring any better, the ME THINKS IT IS LIKE A WEASEL algorithm is programmed to direct a sequence of letters towards a pre-specified target.
    http://www.uncommondescent.com.....n-part-ii/

    “Computer simulations of Darwinian evolution fail when they are honest and succeed only when they are not.” David Berlinski

    In the following podcast, Robert Marks gives a very informative talk as to the strict limits we can expect from any evolutionary computer program (evolutionary algorithm):
    Darwin as the Pinball Wizard: Talking Probability with Robert Marks – podcast
    http://www.idthefuture.com/201.....ard_t.html

    Mathematicians Offer Elegant Solution to Evolutionary Conundrum
    Excerpt: UBC researchers have proffered a new mathematical model that seeks to unravel a key evolutionary riddle–namely what factors underlie the generation of biological diversity both within and between species.,,, existing mathematical models that incorporate these ‘rare type’ advantages tend to have some serious shortcomings,”,,,,
    http://www.sciencedaily.com/re.....153931.htm

    translation,,, all the calculus level math, that has been taught to intimidated freshman biology students for decades, is, in fact, known to be wrong and, worse yet, has been known to be wrong for a long time. Massive bandages were applied to the existing evolutionary equations to hide the fact that evolution cannot explain the generation, nor spread, of novel functional information in biological forms. Worse still, this “new” model has not been tested against real world organisms though it is offered as a “elegant solution”.

  113. further note petruska:

    “… no operation performed by a computer can create new information.”
    — Douglas G. Robertson, “Algorithmic Information Theory, Free Will and the Turing Test,” Complexity, Vol.3, #3 Jan/Feb 1999, pp. 25-34.
    http://www.evoinfo.org/

    Here is a computer programmer’s article on the absurdity of Darwinism accounting programming logic (active information):

    Darwinism from an informatics point of view – May 2010
    http://www.uncommondescent.com.....t-of-view/

    On this following site, a computer programmer explains why computers are not truly “intelligent” even though they can can play (calculate) chess and checkers much better than humans:

    Epicycling Through The Materialist Meta-Paradigm Of Consciousness
    GilDodgen: One of my AI (artificial intelligence) specialties is games of perfect knowledge.
    See here:
    worldchampionshipcheckers.com

    In both checkers and chess humans are no longer competitive against computer programs, because tree-searching techniques have been developed to the point where a human cannot overlook even a single tactical mistake when playing against a state-of-the-art computer program in these games. On the other hand, in the game of Go, played on a 19×19 board with a nominal search space of 19×19 factorial (1.4e+768), the best computer programs are utterly incompetent when playing against even an amateur Go player. When it comes to true intelligence — even something as seemingly simple as evaluating the grammatical correctness or meaning of a trivial sentence — the best computer programs are less than worthless. I turn off my Microsoft Word grammar checker, because it is wrong almost all of the time, and its suggestions are almost universally laughably stupid. The notion that random errors filtered by natural selection created the human mind — which is capable of creating language and interpreting it — is laughably stupid raised to the 768th power.
    http://www.uncommondescent.com.....ent-353454

    Evolution vs. Genetic Entropy – video
    http://www.metacafe.com/watch/4028086

    Mutation Studies, Videos, And Quotes
    http://docs.google.com/Doc?doc.....ZnM5M21mZg

    Random Mutations Destroy Information – Perry Marshall – video
    http://www.metacafe.com/watch/4023143

    “There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter.” Werner Gitt, “In the Beginning was Information”, 1997, p. 106. (Dr. Gitt was the Director at the German Federal Institute of Physics and Technology) His challenge to scientifically falsify this statement has remained unanswered since first published.

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
    http://genetics.mgh.harvard.ed.....S_2007.pdf

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.metacafe.com/watch/3995236
    Entire video:
    http://vimeo.com/1775160

    etc,, etc.. etc..

  114. It is interesting to note petruska that information acts very “weird” in a computer:

    As well it should be noted that, counter-intuitive to materialistic thought (and to every kid who has ever taken a math exam), a computer does not consume energy during computation but will only consume energy when information is erased from it. This counter-intuitive fact is formally known as Landauer’s Principle. i.e. Erasing information is a thermodynamically irreversible process that increases the entropy of a system. i.e Only irreversible operations consume energy. Reversible computation does not use up energy. Unfortunately the computer will eventually run out of information storage space and must begin to “irreversibly” erase the information it has previously gathered (Bennett: 1982) and thus a computer must eventually use energy. i.e. A “material” computer must eventually obey the second law of thermodynamics for its computation.

    “information is physical”
    Rolf Landauer

    Landauer’s principle
    Of Note: “any logically irreversible manipulation of information, such as the erasure of a bit or the merging of two computation paths, must be accompanied by a corresponding entropy increase ,,, Specifically, each bit of lost information will lead to the release of an (specific) amount (at least kT ln 2) of heat.,,, Landauer’s Principle has also been used as the foundation for a new theory of dark energy, proposed by Gough (2008). http://en.wikipedia.org/wiki/L....._principle

    This ability of a computer to “compute answers” without ever consuming energy, until information is erased, is very suggestive that the answers/truth already exist in reality, and in fact, when taken to its logical conclusion, is very suggestive to the postulation of John 1:1 that the “information of Logos” is ultimately the foundation of our “material” reality in the first place.

    John 1:1-3
    In the beginning, the Word existed. The Word was with God, and the Word was God. He was with God in the beginning. Through Him all things were made; without Him nothing was made that has been made.

    (of note: “Word” in Greek is “Logos”, and is the root word from which we get our word “Logic”)

    This strange anomaly between lack of energy consumption and the computation of information seems to hold for the human mind as well.

    Appraising the brain’s energy budget:
    Excerpt: In the average adult human, the brain represents about 2% of the body weight. Remarkably, despite its relatively small size, the brain accounts for about 20% of the oxygen and, hence, calories consumed by the body. This high rate of metabolism is remarkably constant despite widely varying mental and motoric activity. The metabolic activity of the brain is remarkably constant over time.
    http://www.pnas.org/content/99/16/10237.full

    THE EFFECT OF MENTAL ARITHMETIC ON CEREBRAL CIRCULATION AND METABOLISM
    Excerpt: Although Lennox considered the performance of mental arithmetic as “mental work”, it is not immediately apparent what the nature of that work in the physical sense might be if, indeed, there be any. If no work or energy transformation is involved in the process of thought, then it is not surprising that cerebral oxygen consumption is unaltered during mental arithmetic.
    http://www.ncbi.nlm.nih.gov/pm.....4-0127.pdf

    The preceding experiments are very unexpected to materialists since materialists hold that “mind” is merely a “emergent property” of the material brain.

    Removing Half of Brain Improves Young Epileptics’ Lives:
    Excerpt: “We are awed by the apparent retention of memory and by the retention of the child’s personality and sense of humor,” Dr. Eileen P. G. Vining; In further comment from the neuro-surgeons in the John Hopkins study: “Despite removal of one hemisphere, the intellect of all but one of the children seems either unchanged or improved. Intellect was only affected in the one child who had remained in a coma, vigil-like state, attributable to peri-operative complications.”
    http://www.nytimes.com/1997/08.....lives.html

    Blind Woman Can See During Near Death Experience (NDE) – Pim Lommel – video
    http://www.metacafe.com/watch/3994599/

    Kenneth Ring and Sharon Cooper (1997) conducted a study of 31 blind people, many of who reported vision during their Near Death Experiences (NDEs). 21 of these people had had an NDE while the remaining 10 had had an out-of-body experience (OBE), but no NDE. It was found that in the NDE sample, about half had been blind from birth. (of note: This “anomaly” is also found for deaf people who can hear during their Near Death Experiences(NDEs).)
    http://findarticles.com/p/arti....._65076875/

    In The Wonder Of Being Human: Our Brain and Our Mind, Eccles and Robinson discussed the research of three groups of scientists (Robert Porter and Cobie Brinkman, Nils Lassen and Per Roland, and Hans Kornhuber and Luder Deeke), all of whom produced startling and undeniable evidence that a “mental intention” preceded an actual neuronal firing – thereby establishing that the mind is not the same thing as the brain, but is a separate entity altogether. http://books.google.com/books?.....8;lpg=PT28

    “As I remarked earlier, this may present an “insuperable” difficulty for some scientists of materialists bent, but the fact remains, and is demonstrated by research, that non-material mind acts on material brain.” Eccles

    “Thought precedes action as lightning precedes thunder.”
    Heinrich Heine – in the year 1834

    Genesis 2:7
    And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.

    “As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter.”
    Max Planck – The Father Of Quantum Mechanics – (Of Note: Planck was a devout Christian, which is not surprising when you realize practically every founder of a major branch of modern science also had a deep Christian connection.)

  115. Petruska, I went to fix a link on this paper

    Algorithmic Information Theory, Free Will and the Turing Test

    and found:

    Chaltin’s Algorithmic Information Theory shows that information is conserved under formal mathematical operations and, equivalently, under computer operations. This conservation law puts a new perspective on many familiar problems related to artificial intelligence. For example, the famous “Turing test” for artificial intelligence could be defeated by simply asking for a new axiom in mathematics. Human mathematicians are able to create axioms, but a computer program cannot do this without violating information conservation. Creating new axioms and free will are shown to be different aspects of the same phenomena: the creation of new information.
    http://www3.interscience.wiley.....8;SRETRY=0

  116. petruska as far as you insinuating that IDists have not taken into consideration all probabilities is ludicrous:

    Book Review – Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009.
    Excerpt: As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren’t chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.
    So, it comes down to this: Where did that information come from? The simplest known free living organism (although you may quibble about this, given that it’s a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.
    http://www.fourmilab.ch/docume.....k_726.html

    Petruska it all comes down to information! You can play games all you want but the fact of the matter is that no one has ever demonstrated the capability of material processes to generate information (and what is life to a materialists save “material with the ability to replicate?). Would you like to be the first to demonstrate that a mind is not needed to generate information?

  117. “… no operation performed by a computer can create new information.”

    I haven’t asserted that any operation or algorithm creates information.

    Selection provides a yes or no answer to the question of whether a change is lethal or not. That’s information.

    An algorithm that collects and stores such answers accumulates information.

    It’s obviously inefficient and wasteful, but it accumulates information. It doesn’t create it. No one says it does.

  118. off topic:

    Amazing Video of a Song Composed Entirely of 37 Cello Parts
    http://www.youtube.com/watch?v=gsavk0FX3Ro

    Petruska,
    Yes you will die, No you will not die, is not creating new information. I can see this is going to be pointless with you so I will waste no more time.

  119. Yes you will die, No you will not die, is not creating new information.

    Never said it was, but I agree that we’re talking past each other.

  120. Nakashima:

    Thanks for standing up against the bullying, insulting, and ultimately puerile behavior of Myers and Matzke. I wish more ID critics would do that.

    T.

  121. Nakashima @ 106:

    1. I have heard of Nilsson’s discussion of the eye. I have not seen it, nor do I know where it can be found. Can you direct me?

    Not having read Nilsson, I have not offered any objections to his views, and therefore am not guilty of any purportedly faulty arguments of the sort to which you refer.

    What I would look for in Nilsson is a specification of the number of morphological features that would require changing, and a specification of the genetic pathways that could conceivably had effected each morphological change, coupled with a discussion of the causes and frequency of the required mutations, and the environmental viability of the putative intermediate stages. I would count such a discussion as a genuine scientific discussion, worthy of scientific debate.

    2. I have not dismissed selection. I understand the “platform effect” you are talking about. Obviously once a favorable mutation is fixed by selection, future evolution doesn’t have to start from scratch. I am not claiming that the eye had to have been thrown together by the equivalent of a tornado in a junkyard.

    Nonetheless, each of the necessary mutations still has to have occurred. And selection does not have the power to evoke desirable mutations. In neo-Darwinian theory, they occur by chance (meaning not that they are utterly uncaused, but that they are “random with respect to the outcome”, as one TE has put it). So you still cannot avoid probablistic calculations regarding the occurrence of the necessary mutations in a viable sequence. Also, I would recommend you have a look at Behe’s example of the house with many staircases (in *The Edge of Evolution*), which is a good image for showing how, even with the aid of the “platform effect” of natural selection, the chance of finding one’s way to any given evolutionary goal by random search methods is very low.

    T.

  122. Nakashima @ 109:

    You appear to have misunderstood what I was driving at in my post. I don’t blame you for that, as we are talking in shorthand, about very speculative matters. Let me clarify:

    1. I don’t accept that “chance events could lead to a whole new phylum”. At least, not chance events *alone*. I think (and I mean this as a scientific comment, not a theological one) that the chance events would have to occur within the constraint of an overarching “directedness” of the evolutionary process. (And I add, as a wholly optional theological comment, that such overarching directedness is exactly what one would expect from a Creator God who has very definite goals for the evolutionary process.)

    2. I think we may be using “Darwinist” in slightly differing ways. Let me tell you where I am coming from. I have read Darwin’s major works with great care. I have also read some secondary scholarship about Darwin, and some of the history of post-Darwinian developments. I also grew up steeped in, and believing in, the neo-Darwinism of Gaylord Simpson, Sagan, etc. This view of Darwinism is exemplified in *The Blind Watchmaker* by Dawkins. So I have a certain notion of “Darwinism” and “Darwinian” that may be narrower and tighter than what you may be supposing by the term.

    The “Darwinism” that I have in mind is *utterly non-teleological*, and will not allow for any of the “overarching constraints” that I have spoken of. It would never submit to being merely a component, as it is in Behe and Denton, of a wider teleological process.

    Now, to switch from speaking of Darwinism as a scientific account of nature, to the theological question: it is precisely because Darwinism as I understand it will not consent to being enveloped within a wider teleological structure, that I think it is impossible to be a “Christian Darwinist”, as you suggest in this post.

    Let me be clear: I am not saying that it is impossible to be a Christian and to accept that Darwinian mechanisms may play a “local role” in evolution. I am saying that it is impossible to be 100% Darwinian and 100% orthodox Christian, as Ken Miller claims that he is. To be 100% Darwinian is to assume an anti-teleology which is plainly incompatible with the teaching of the Bible and the Christian tradition.

    Behe accepts a limited role for Darwinian processes, and he is an orthodox Christian.

    3. I never, at any point in this exchange with you, or anywhere else on UD, spoke of trying to “disprove evolution”. I don’t know how closely you follow my various comments on all the threads, but time and again I have insisted that there is no inherent incompatibility between believing in a process of macroevolution and believing in design. I have criticized only what I have called “Darwinian evolution”, understood as the combination of chance and natural selection, outside of any teleological constraint. And I have carefully separated my scientific criticism (i.e., that neo-Darwinism has not been very good at providing empirical evidence for major transitions) from my theological criticism (i.e., the antiteleology of neo-Darwinism is anti-Christian).
    So please do not impute “anti-evolution” to me. I am aware that some ID proponents oppose evolution itself; I am not one of them.

    T.

  123. I have criticized only what I have called “Darwinian evolution”, understood as the combination of chance and natural selection, outside of any teleological constraint.

    Despite the apparent exception of Behe, I find the majority of evolution critics do not accept common descent, even when it is coupled with the possibility that some change is the result of an agency other than chance.

  124. Petrushka:

    Despite the apparent exception of Behe, I find the majority of evolution critics do not accept common descent,

    I don’t think it is really so. I have always accepted common descent, not as a dogma, but as a reasonable theory, probably the best explanation at present for some data. I am sure it is not only Behe and me to have this approach in ID. I am certainly aware that many IDists think differently, and I respect their position, but not necessarily their arguments. I can’t say if they are the majority, but I am sure that many others have different ideas.

    The fact is, I really believe that ID must be based only on scientific reasoning. And my personal opinion is that ID theory gives us an extremely strong case for design as the cause of biological information, and only for that. The problem of common descent, instead, is completely independent on the problem of causal explanation.

    Frankly, I don’t think that the theory of universal common descent is at present either beyond reasonable doubt or falsified. It is at best debatable, even if I tend to accept it as the best explanation.

  125. Petrushka @ 123:

    I’m not responsible for the views of any ID proponent except myself. My comments to Nakashima were from my own perspective. I was trying to clarify for him where I was coming from, so that he would not mix up my views with those of other ID proponents he may have encountered here or elsewhere. I think (at least I hope) that I have now made my own form of ID crystal-clear to him, but we shall find out whether that is the case when he next replies.

    I agree with gpuccio’s remarks, and I adopt his general attitude toward the question of biological origins. I suspect that several of the veteran posters here have a position not far from mine and gpuccio’s. What many ID critics seem to forget is that “ID” is not just a dozen Fellows of the Discovery Institute. ID has thousands of explicit adherents, and probably millions of tacit adherents, worldwide. I wouldn’t be surprised if a large chunk of those supporters and adherents accept or are open to the notion of common descent. What ID is *in principle* against is not “evolution” but the notion that a primarily chance-driven mechanism could generate the integrated complexity of life.

    T.

  126. What ID is *in principle* against is not “evolution” but the notion that a primarily chance-driven mechanism could generate the integrated complexity of life.

    I certainly can’t change anyone’s mind about what they find plausible, but I do try to clear up the reasons for my own position.

    The algorithm embodied in mutation and selection can, in principle, compute or accumulate any string. The issue is time.

    Computations of time and probability seem to ignore the fact that most of the heavy lifting was done by microbes before the Cambrian. Even the basic genes that enable vision exist in microbes, and it’s not a stretch to assume they were “invented” during the 3,500,000,000 years before multicelled animals.

    Microbes have short generations and large numbers. Good soil may contain 10,000,000,000 microbes per gram. When you need astronomical numbers, microbes give them.

    Most of the calculations of probability assume there is a target, a configuration that must be reached. But even simple breeding experiments show that there are far more viable configurations than show up in “nature.” The target of evolution is much broader and more diffuse that just the list of creatures and plants we have seen.

    And there is no reason that structures, such as flagella, MUST arise. Looking at such oddments and wondering how they got there is a bit like looking at lottery winners and wondering how those particular people were fated to win.

    The only question that absolutely has to be answered by biology, regarding the invention of a complex structure, is whether there can be a continuous chain of living creatures between those that have the structure and those that don’t. It would be nice, but it isn’t necessary, to demonstrate that every step involves an increase in fitness.

    That’s my reasoning. Your mileage may vary.

  127. “I certainly can’t change anyone’s mind about what they find plausible, but I do try to clear up the reasons for my own position.”

    All your following comments are bogus are irrelevant except your last so they are not going to help you reason to anything coherent.

  128. P:

    Remarks re:

    The algorithm embodied in mutation and selection can, in principle, compute or accumulate any string. The issue is time . . .

    1 –> First, natural selection is demonstrably about the culling out of relatively “underperforming” sub-populations in the “struggle for life.”

    2 –> So, it is only capable of being responsible for REMOVAL , not origin of relevant bio-information.

    3 –> That leaves chance variation as the claimed source of bio-information, whereby allegedly incremental changes that have to be functional all the way are responsible for transforming say a 1 mn base pr microbe into several dozen phyla or the equivalent.

    4 –> Believe it or not, that means that the process of change from the one to the other is MORE constrained than with simple random chance — it is like transforming “Sue ran home,” into this post be adding a fee letters at random and having to maker a grammatically and contextually meaningful statement all along the way. [Or the equivalent in converting Hello World into say Open Office Draw.]

    5 –> So, you have not properly reckoned with the implications of the fact that with even 125 bytes [1,000 bits] worth of additional functional information, you face a situation where the whole cosmos acting as a search engine and with the 10^80 or so atoms changing state every Planck time for the thermodynamically credible lifespan of the observed cosmos, we cannot sample more than 10^150 states, or less than 1 in 10^150 of the 1.07 * 10^301 configurations specified by just 1,000 bits.

    6 –> In short, the search rounds down pretty well to zero-sized sample of the gamut that needs to be searched.

    7 –> That is the islands of function are far too isolated in the space of configs to be plausibly found by a process relying on effectively random walks to generate functionally specific, complex information.

    8 –> By contrast, posts in this thread and the underlying programs [not to mention languages, algorithms and data structures or implementing machines] that make them work show just how routinely intelligence can produce such FSCI.

    9 –> So, absent a priori imposition of materialistic blinders, and/or failure to look at he search space challenge, the best explanation jumps out: design.

    10 –> Meyer’s note on the challenge to be addressed on the Cambrian life revolution issue is therefore quite relevant (and BTW, had the sort of gradual evolution you envisioned happened across 3.5 BY, with countless transitionals, there should be abundant fossil record — missing of course from since before Darwin and even after 250+ k fossil species and with many soft bodied creatures in relevantly comparable rocks):

    the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. Molecular biologists have recently estimated that a minimally complex single-celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life (Koonin 2000). More complex single cells might require upward of a million base pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions. The genome size of a modern arthropod, the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart & Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells to complex animals represent significant (and, in principle, measurable) increases in CSI . . . .

    In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . [PBSW, 2004 . . . and the article passed proper peer review by renowned scientists (until the political reversal)]

    GEM of TKI

  129. Petrushka @ 126:

    I’m not interested in abstract arguments about large numbers of microbes and large amounts of time. Those are generalities which are very unsafe in scientific theorizing. How many is enough? How long is long enough? Without precise proposals for the *particular genetic and morphological changes* one has in mind, no numbers can reliably be attached.

    I’m interested in how integrated complex systems are built from scratch. I want to know how a cardiovascular system arises where there were nothing like it before. I want to know how all the complicated and interrelated changes in the bat’s ears, vocal apparatus, brain, nervous system, etc. are built up from a creature which has none of the relevant features.

    I’m interested in reading one, just one, book or series of articles which describes all the morphological changes required to produce a major new organ, system, or body plan, and the hypothetical clusters of mutations which could produce those specific morphological changes. It could be the vertebrate body plan emerging from the marine worm; it could be the bat’s wings and sonar emerging from an insectivore ancestor; it could be a whale emerging from a mesonychid or hippolike ancestor; it could be anything. Can you give me the reference to literature where such a hypothetical pathway can be found? And if no such detailed accounts yet exist, why should “science” regard neo-Darwinian mechanisms as capable of producing such change? Wouldn’t the proper term for such a claim be “speculation” rather than “fact” or “theory as solid as the theory of gravity”?

    T.

  130. I’m interested in reading one, just one, book or series of articles which describes all the morphological changes required to produce a major new organ, system, or body plan, and the hypothetical clusters of mutations which could produce those specific morphological changes.

    Such a series exists in the fossil record for the evolution of the mammalian inner ear.

  131. I’m not interested in abstract arguments about large numbers of microbes and large amounts of time.

    But time is in fact, the only argument offered by Behe and Dembski. Given sufficient time, variation and selection can produce anything. It’s a universal computing engine.

    So the argument does boil down to time.

  132. Petrushka @ 130:

    I know all these standard examples. I used to be a Darwinist and have been reading books on evolution for 45 years now. You’ll have to do better than this.

    The putative historical sequence you are referring to tells me nothing about the *mechanism* by which each form changed into the other. At the most (and if we apply rigorous philosophical criteria of argumentation, it can’t even do this) it would prove that macroevolution *happened*, but not *how* it happened.

    The result you point to, even if accepted as proof for “Form A became Form Z through intermediate morphological forms B, C, etc.” tells us nothing about what was happening at the biochemical/genetic level to drive the change in forms. The sequence itself, viewed externally, is compatible with not only neo-Darwinian or “chance” explanation, but also with Dentonian “necessitarian” explanation, or with various versions of supernatural intervention, guiding the process along. In other words, the sequence in itself does not prove that neo-Darwinian mechanisms were responsible for its existence. And this applies, mutatis mutandis, to the eye, the hippo-whale transition, the bat’s sonar, the development of winged flight in birds, or any other major macroevolutionary change.

    In short: no one has proved that neo-Darwinian processes are capable of turning a hippo ancestor into a whale. No one has even come close. If you think my conclusion is wrong, you are going to have to point me to, not a sequence of alleged transitional forms in the fossil record, but a detailed account of the macroevolutionary transitions at the level of genetics, development, selective fitness, etc. In other words, some Darwinist needs to write a book on the theory and evidence of whale evolution, with much more detail than I’ve yet to see assembled. If you know of such a book, regarding whales or anything else, let me know where it is. If you don’t, then surely you will see the reasonableness of my position, which is not “anti-evolution”, but merely a cautious empiricism that regards neo-Darwinism as a speculative hypothesis awaiting detailed confirmation.

    T.

  133. Petrushka @ 131:

    I disagree that time can produce anything, but that’s neither here nor there. The point is that just saying you have lots of time is meaningless; it’s a purely qualitative statement. Science is about quantity. You have to say “How much time would it take to perform evolutionary transition X, and is there enough time for that, given the fossil record?” You have to be specific. Unless you quantify the number of morphological changes, the number of genetic changes required for each morphological change, the probability of such genetic changes occurring in a favorable sequence, without cross-reactions which interfere, the number of generations, etc., any reference to “lots of time” is mere poetry, not science.

    To really grasp this point, I think Darwinians need to read Dembski’s *No Free Lunch* very slowly and carefully. He maps out the details which have to be considered. The issue is not merely absolute time, but the ratio of “probablistic resources” (including time) to the huge number of evolutionary dead ends which a “blind search” will produce. Without hard numbers based on empirical facts, this ratio cannot be computed. Thus, neo-Darwinians need to tie their mechanisms much more closely to hard numbers than they have done in the past, to meet the challenge posed by probablistic analyses. I haven’t seen this done yet, for anything other than piddling population genetics problems relating to the eye color of finches and so on. Show me where it’s been done for the whale, or any crucial macroevolutionary transition. If you can do this, you’ll have done better than Ayala, Miller, Collins, Dawkins, Gould, etc.

    T.

  134. 1 –> First, natural selection is demonstrably about the culling out of relatively “underperforming” sub-populations in the “struggle for life.”

    2 –> So, it is only capable of being responsible for REMOVAL , not origin of relevant bio-information.

    If underperforming individuals are culled, one might ask where their underperforming genes came from.

    The answer would be, from the same source that all variation comes from.

    A changed allele can result in the individual failing to reproduce, or it can affect the probability of the individual reproducing. The effect can be statistical rather than absolute, as you have indicated.

    Given time, this algorithm can produce any genome. For evolution to be true, all existing genomes must be placeable in a nested hierarchy, and historically, every individual must have exact or nearly exact copies of its parents genes.

  135. Timaeus,

    Regarding Nilsson’s and Pelger’s eye simulation, see http://www.discovery.org/a/1416
    where you can find all relevant links

  136. Science is about quantity. You have to say “How much time would it take to perform evolutionary transition X, and is there enough time for that, given the fossil record?” You have to be specific.

    Biologists since the 1930s have been quantifying the frequency of mutations and the mutational distance between species. This activity has been near the top of the priority list since we have been able to study biology at the molecular level.

    It’s a good question. It occupies the center.

  137. Show me where it’s been done for the whale, or any crucial macroevolutionary transition.

    Why not look at a well preserved sequence, such as the evolution of the mammalian inner ear?

  138. Petrushka,

    “Given time, this algorithm can produce any genome.”

    You might be satisfied with just-so stories, but that only demonstrates the strength of your faith.

    As Timaeus and others keep on pointing out to you, what is needed is empirical facts or theoretical pathway(s) describing evolutionary transitions.

  139. Petrushka @ 136:

    “Why not look at a well preserved sequence, such as the evolution of the mammalian inner ear?”

    I answered this in detail in 132. You must have missed it.

    Petrushka @ 135:

    “Biologists since the 1930s have been quantifying the frequency of mutations and the mutational distance between species. This activity has been near the top of the priority list since we have been able to study biology at the molecular level.

    “It’s a good question. It occupies the center.”

    Glad to hear it. Now let me know when they’ve learned enough to get me from a hippo ancestor to a whale, and let me know the venue the results are published in. Until then, as I’ve said, neo-Darwinian theory, at least as the primary explanation for major macroevolutionary change, remains for me a grand speculation – interesting, but utterly non-binding upon my intellect.

    I doubt we’ll get much further here, so if you don’t come up with a new angle, I’ll exit now.

    T.

  140. Petrushka,

    “Why not look at a well preserved sequence, such as the evolution of the mammalian inner ear?”

    This is perfect example of how your faith drives your conclusions.

    It is not scientifically legitimate to simply take the a series of structural similarities and declare that they constitute an actual evolutionary lineage.

    One is free to believe that two jaw bones migrated in the middle ear of the mammals over the course of time, although we have no fossil record of this miraculous process. To make it a scientific proposal, Darwinists would need to describe a stepwise, viable, theoretical pathways of such a process.

  141. Mr Timaeus,

    Thank you for your clarifications of your opinions. I feel we have been having a good dialogue.

    As much as I would like to continue, I am constrained by my impending marriage on Friday to stop at this point, however unsatisfactory that might be.

  142. Petrushka:

    Timaeus at 132 has raised some specific challenges that Darwinian theories of macro-level, body plan origins need to answer. In 128, I raised the point that once one talks about chance variation plus natural selection — which last is simply a culler not a source of information — as being able to move from a microbe with a genome ~ 1 mn bases, to body plans with ~ 10′s – 100′s+ mns of bases, we are running orders of magnitude past the credible information-generating capacity of random walks in genome space. (Indeed, we can add from Behe that in several decades, with more reproductive events than the vertebrate line can have had, malaria parasites responding to the severe pressure of antimalarial drugs, have only gone as far as 2 – 3 base pairs worth of more or less co-ordinated variation.)

    Your further points are therefore looking highly illustrative of a point made by Johnson, responding to Lewontin’s a priori evolutionary materialism:

    For scientific materialists the materialism comes first; the science comes thereafter. [Emphasis original]We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.” [Emphasis added.]

    . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses.[Emphasis added.] [The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

    So, I will comment on a few points:

    1] P,134: If underperforming individuals are culled, one might ask where their underperforming genes came from. The answer would be, from the same source that all variation comes from.

    What we generally observe is that existing, functioning organisms on a viable body plan reproduce, and sometimes there is relatively minor variation. Too often, that variation is inconsistent with life or with reproduction. In many other cases, we see loss of function or garbling of genes that may attract the eye of the artificial selector [e.g. with so-called fancy goldfish], or in the face of an unusual pressure like drugs or insecticides. Minor variation happens, and can be traced to actual mutations in some cases, in others to selecting out of existing varieties. (E.g. examination of bodies of arctic explorers from before the antibiotic era turned up antibiotic-resistant strains.]

    None of this addresses the issue of origin of novel body plans, and accounts for the origin of functional information in viable organisms well beyond 1,000 bits to achieve that.

    (And by the way, please notice I have discussed islands of function within which variations and selections can happily proceed; the issue is to get to the islands of function, or else to show beyond reasonable doubt on empirical data that the functional subset of the genomic config space is an interconnected tree. So far, after 150 years of trying and 1/4+ mn fossil species and millions more in the existing world, we still see the pattern of appearance, stasis and disappearance or continuation into today’s world. That is, the observations fit with islands of function, and that starts with the Cambrian revolution.)

    2] A changed allele can result in the individual failing to reproduce, or it can affect the probability of the individual reproducing. The effect can be statistical rather than absolute, as you have indicated. Given time, this algorithm can produce any genome.

    The evidence is that most variations are neutral to increasingly adverse, as would be expected from the requisites of an integrated, intricate functional basis for life. In short, the pattern supports the islands of function view.

    The proposed algorithm can explain the tendency of populations to remain stable in form — Blythian natural selection: the sports usually do not work so well as a rule and get weeded out. In other cases, it can explain minor variations, like relative dominance of light/dark moths [noting the problems with how observations were made and reported] or the switching off of a regulator on penicillinase production, or variation of an enzyme to eat a fairly closely related chemical to proteins, nylon, or the oscillating variation in finch beak sizes that were so celebrated a few decades back. It may explain specialisaiton and loss of variability to fit into a new ecological niche. But, it does not begin to explain and empirically substantiate the origin of relevant body plans by darwinian mechanisms.

    For, no plausible mechanism for origin of substantial quanta of functional information has been provided, nor has there been justification for the idea that the overall set of major body plans come in a continuum that can be incrementally scanned by a tree starting from its roots.

    3] For evolution to be true, all existing genomes must be placeable in a nested hierarchy

    A nested hierarchy antedates the creation of macroevolutionary theory [Linnaeus was in fact a Creationist], and fits in with say creation in an orderly pattern, or imposition of forms that serve as attractors for variations, or guidance of variation by intelligent direction through front-loading or even use of a library of parts. In this regard we should reflect on mosaics like the Platypus that has not only gross features from all across the animal kingdom, but genes and proteins etc too.

    In short, this is not a point that discriminates across relevant theories. It is only a priori ruling out of otherwise relevant alternatives that makes it seem to especially support the Darwinian model.

    4] and historically, every individual must have exact or nearly exact copies of its parents genes

    This is simply to say that variation must be incremental, to preserve viability. It begs the question of how then do we bridge the gaps between body plans, starting with unicellular organisms and ending with dozens of phyla [and equivalent in other kingdoms] worth.

    And this, in the teeth of strong evidence that complex functional information is not easily transformed incrementally from one form to another that is significantly different.

    Designers of course routinely adapt existing information to create novel systems.

    5] 135, Biologists since the 1930s have been quantifying the frequency of mutations and the mutational distance between species. This activity has been near the top of the priority list since we have been able to study biology at the molecular level. It’s a good question. It occupies the center.

    That is for 50 – 80 years, the question has remained stubbornly resistant to answers in a Darwinian frame. Especially when we move to the relevant level, not origin of species [which is often an arbitrary construct as say the inter-specific breeding of Finches in Galapagos showed], but instead the origin of body plans.

    6] Why not look at a well preserved sequence, such as the evolution of the mammalian inner ear?

    Let’s use Wiki’s summary to show the problem with this and other similar show and tell on the bones cases:

    The evolution of mammalian auditory ossicles is one of the most well-documented[1] and important evolutionary events, demonstrating both numerous transitional forms as well as an excellent example of exaptation, the re-purposing of existing structures during evolution.

    In reptiles, the eardrum is connected to the inner ear via a single bone, the stapes or stirrup, while the upper and lower jaws contain several bones not found in mammals. Over the course of the evolution of mammals, one lower and one upper jaw bone (the articular and quadrate) lost their purpose in the jaw joint and were put to new use in the middle ear, connecting to the stapes and forming a chain of three bones (collectively called the ossicles) which amplify sounds and allow more acute hearing. In mammals, these three bones are known as the malleus, incus, and stapes (hammer, anvil, and stirrup respectively).

    The evidence that the malleus and incus are homologous to the reptilian articular and quadrate was originally embryological, and since this discovery an abundance of transitional fossils has both supported the conclusion and given a detailed history of the transition.[2] The evolution of the stapes was an earlier and distinct event.

    The after the fact ad hocness of the account leaps out. Anatomically and embryologically, certain bones are related. A claimed ancestral sequence of fossils is laid out, and loss of function joined to emergence of new function is woven as the standard just so story. But at no point do we hear of a detailed genetic, developmental and biochemical pathway that credibly competently creates the new function based on the claimed dynamic principles.

    A library of adaptable anatomical parts that can be shaped to do different jobs in different animals is just as compatible with the evidence as is he standard narrative, but of course, such an alternative is not to be permitted to interrupt the neat little story.

    Not to mention, we do not see an explanation for how at each stage of minor variations, advantages drove change, leading to a continuum from reptilian to mammalian ears. Same for wings for birds and bats, same for all the diverse co-ordinated features needed to make a whale out of a bear or a wolf or a hippo or whatever ancestor de jour is in favour just now.

    Anyone who has had to design an audio amplifier and sensor system associated therewith can tell you that even with a generic block diagram or even a circuit level framework easily in hand, the trouble lies in the specific details, and in the careful matching and coodination of the several components to form an integrated functional whole.

    Just so, after the fact generality based tales of incremental changes resting on the question-begging assumed validity of the Darwinian framework — as opposed to level playing field inference to best explanation across relevant competing explanations — do not make the grade.

    What evidence do you have that the variation (assuming reptilian ancestry of mammals) was not built-in, or loaded in from a library of parts modified for the particular purpose in mind for the new group of animals? Etc?

    Or, that there is a credible continuous tree-of-life genetic and embryological path that generates the masses of coordinated functional information incrementally, generation by generation?

    Where in each hypothesised increment of advantageous change is there enough time and advantage to fix the small steps?

    In short, what demonstrated and calibrated mechanism can — per empirical data — credibly generate the required increments in DNA and epigenetic information [remember the 1,000 bit or 500 base pair threshold], for the culling out process to work to transform a reptile into a mammal complete with different reproductive system and ears, by chance variation and natural selection, in the supposed ~ 70 mn yrs “available” here on earth?

    7] OOL

    And of course all of the above come back with full force when we ask about the origin of the first life forms, bearing in mind that we have to account for spontaneous origin of codes, algorithms, coordinated molecular scale implementing machinery, and the sheer mass of relevant information stored in the DNA. Including in particular, origin of the irreducibly complex elements of the sort of von Neumann self-replication involved in a metabolic automaton that reproduces itself:

    (i) an underlying storable code to record the required information to create not only (a) the primary functional machine, but also (b) the self-replicating facility; and, that (c) can express step by step finite procedures for using the facility;

    (ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with

    (iii) a tape reader [called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling:

    (iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by

    (v) either:

    (1) a pre-existing reservoir of required parts and energy sources, or

    (2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment.

    Immediately, we are looking at irreducible complexity leading to islands of organised function for both the machinery and the information in the wider sea of possible (but mostly non-functional) configurations. In short, outside such functionally specific — thus, isolated — information-rich target zones, want of correct components and/or of proper organisation and/or co-ordination will block function from emerging or being sustained across time from generation to generation. So, once the set of possible configurations is large enough and the islands of function are credibly sufficiently specific/isolated, it is unreasonable to expect such function to arise from chance, or from chance circumstances driving blind natural forces under the known laws of nature.

    And as one moves form that root organism up the claimed tree of life, we keep on running into needs to jump vast informational increments to get to novel body plans, which come first before the variations into diverse types that the fossil record interpreted on the typical timelines shows — the Cambrian fossil life revolution being capital among these.

    Where did those dozens of major body plans come from in a short window of time relative to the multiplied megabits of information generation challenge? [And 3.5 BY is just as hopelessly inadequate to scan the sea o configs for just 1,000 bits [500 base pairs] as 5 – 10 my: our whole observed universe across a lifespan 50 mn times the usual timeline to date (13.7BY], would not sample as much as 1 in 10^150 of the configs of a space of just 1,000 bits. That is the search rounds down to zero.]

    ================

    Until we have solid, observationally anchored answers to questions like that, the dominant neo-darwinian school of thought will remain a hypothesis whose plausibility rests on a priori metaphysical impositions implicitly accepted by those who happen to dominate current science [based on the recent intellectual history of our civilisation], rather than a solid scientific theory backed up by bodies of relevant observational evidence. Evidence there may well be of common derivation and family resemblance across life forms, but is that by design or by undirected chance plus necessity?

    Onlookers, these questions have been on the table but not heard out, or even begged or ducked for decades. (And when someone as eminent as Hoyle — holder of a Nobel-equivalent prize — raised some of them in the context of origin of life on the cosmic scale, the issue was rapidly lost in the choking, blinding, polarising smoke of burning strawmen.)

    Let us see if P can provide cogent answers on the merits.

    GEM of TKI

  143. PS: Dr Hunter’s remarks on Horizontal Gene Transfer amplify the force of the point on the need to account for origin of complex functional information and implementing mechanisms in biological life forms.

  144. A claimed ancestral sequence of fossils is laid out, and loss of function joined to emergence of new function is woven as the standard just so story. But at no point do we hear of a detailed genetic, developmental and biochemical pathway that credibly competently creates the new function based on the claimed dynamic principles.

    I’m thinking the demand for transitional fossils is somewhat less than sincere. When a nearly perfect transitional series is available, it is unconvincing because it doesn’t include the complete sequence of DNA changes that produced it.

    When whale transitionals were entirely missing, creationists pointed to this gap as evidence against evolution. As transitionals have been found, the demand switches to DNA sequences, which must be complete — no gaps at all.

    I can only point out out that if this tactic were persuasive in courtrooms, where people’s lives and liberty were at stake, no one would be convicted.

    We know from animal breeding that the shape of facial bones is quite malleable and selection alone can take us from the long snout of sighthounds to the squished face of the Pekingese.

    But you guys are a tough jury. The prisoner will go free.

  145. There is absolutely nothing in the fossil record that supports a Darwinian mechanism. Yes, there is the appearance of new forms but nothing points to a gradual mechanism as its driver.

    The fact that one points to the inner ear is an admission of weakness. There must have been millions of transitions and this is all one has. There is no obvious mechanism for these changes. In the whales there are large gaps and no evidence of all the side branches that must exist in a Darwinian scenario.

    Every step is viable (and there are theoretically thousands of steps) and then each step can theoretically branch in many directions and we should thus witness branches that are several levels of magnitude greater in number than exist in the fossil record and also in the current suite of organisms on the earth. The absence of these branches indicates that the process did not work this way or that there was something within the organism that propelled it in specific directions. Either finding disproves Darwinian processes and most likely any naturalistic process.

    Micro evolution operates to refine species in small ways but there is nothing in the fossil record to indicate it can build complex novel characteristics nor is there anything in the current species on earth today to indicate such a capability.

    The fact that no one can provide it is telling and I often ask where does Richard Dawkins and Jerry Coyne do so in their books. These are two of the modern disciples of Darwin and they cannot do it.

  146. Petrushka

    First, the basic design inference is in principle quite easy to overthrow: provide a specific, credibly observed case where 125 bytes of functional information originated by chance and blind mechanical necessity.

    We can show 2 Zettabytes worth of cases in point on intelligent design, in the Internet. After years of asking, objectors cannot provide a single case where chance + necessity without intelligence give rise to a relevant case of FSCI.

    Also, factoring in:

    a: what we can easily see about the configuration space of 1,000 bits [2^1,000 => ~ 1.07 * 10^301 configurations] and

    b: the search capacity of the observed cosmos [~ 10^150 Planck time states for 10^80 atoms in 50 mn times the usual timeline since the Big bang], we see that:

    c: the cosmos acting as a search engine could not credibly sample 1 in 10^150th of the configs, thus

    d: the reason for chance + blind necessity not being able to access functional configs of a relevant degree of complexity is the swamping out of even a universe full of resources by the config space for just 1,000 bits.

    So, we have good empirical and analytic grounds for inferring that FSCI is an empirically reliable sign of design. In that context, on observing that cell based life rests on the DNA based information system, and that both the original and novel body plans will easily exceed the 1,000 bit threshold [500 base pairs, what a few reasonable proteins would take up], we have good reason to infer from FSCI to design as its best explanation.

    In the case of the evidence and claims usually cited to substantiate darwinist claims, we find that often the empirical evidence is well below the relevant threshold of complexity — point mutations and micro-evolution more generally. And when evidence is brought out to claim body plan level evolution by Darwinist mechanisms, we find that even if we accept the evidence as being explicable in terms of ancestry and descent, it fits at least as well with an intelligently guided process. Moreover, too often, when evidence is interpreted in Darwinist terms, it is by a priori, ideological, institutional or philosophical exclusion of otherwise relevant alternatives.

    So, we are asking for evidence that would truly substantiate the claim. But obviously from your dismissive reference to the usual darwinist claim of “incredulity” on our part, you do not have real evidence that can discriminate between Darwinist and non-darwinist mechanisms, including intelligence.

    Going further, you plainly do not have the chain of evidence that should be all over the animal and plant kingdoms: gradual development form unicellular to multicellular organisms and various forms. Instead we see islands of forms, which fit with the design insight that functional coded algorithmic information is going to come in islands.

    And, when we turn to the origin of the first life forms, we see that observed life is based on coded information interpreted and carried out by namomachinery that uses information to guide its actions step by step, e.g. in protein synthesis. Worse, we find nowhere the faintest trace of a credible account of how codes, algorithms and implem4enting machinery could credibly originate in a pre-biotic world by chance plus blind necessity. Indeed, we can see how the RNA and metabolism first views are mutually destructive, as say the recent Shapiro-Orgel exchange shows.

    So, if you are going to claim a demonstrative case of macro-evo by darwinist mechanisms, you need to give solid answers to serious challenges. A priori materialism that makes just so stories seem plausible by mere logical implication do not count.

    GEM of TKI

  147. PS: Darwinists do not like to hear me cite Lewontin on the point, but he makes the matter plain:

    ______________

    >>. . . To Sagan, as to all but a few other scientists, it is self-evident that the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test . . . .

    Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. >>
    ________________

    That is what you need to show us you are not falling into.

    Whether for the whale [and the Pakicetus blunder is a telling issue, one that happened within 20 years] or the inner ear or the Cambrian revolution or something else, you need to show us how it is credible t6hat chance variation plus natural selection, etc gave rise to novel and significant body plans. Including accounting for information, and the organization that emerges incrementally in competing populations that then allow for superior performing varieties to dominate. And remember, computer simulations do not count: we need real world data not someone’s fancy multimedia just so story.

  148. Nakashima:

    Congratulations on your upcoming marriage.

    Yes, now would be a good time to leave web debates aside for a while. Your new spouse will not appreciate sharing you with the computer on your honeymoon. And while I relish the image of you reading one of Behe’s or Denton’s books on the plane to Tahiti, I wouldn’t advise bringing along any ID literature, either.

    You perhaps have already heard the joke: “I can’t tonight, dear — someone on the Internet is wrong.”

    Best wishes for your new life, Nakashima.

    T.

  149. First, the basic design inference is in principle quite easy to overthrow: provide a specific, credibly observed case where 125 bytes of functional information originated by chance and blind mechanical necessity.

    In principle, Weasel is an example of chance and selection. I can see no rational argument demonstrating that Weasel’s algorithm for accumulating information is mathematically different from biological evolution. In both cases, the algorithm captures and accumulates information that exists independently of the operation of the algorithm.

    It would be an error though, to argue that biological evolution seeks a specific target or targets. All that is necessary for change to accumulate is that some changes are not so detrimental as to prevent reproduction. Other that that, it makes no difference whether the changes are trivial, such as hair color, or metabolically significant.

    I think it would bee interesting if ID proponents could demonstrate that all functional structures and objects are the result of intentionality.

    Is leishmaniasis the result of intentionality, or is it the result of chance and selection?

    Biological evolution may not provide a videotape of every point of change, but it does provide an observed mechanism of change, a mechanism that has been routinely exploited by human plant and animal breeders for thousands of years.

    I think it would be interesting for some ID advocate to demonstrate conclusively, that change cannot, in principle, accumulate — indefinitely, to use Wallace’s word.

    As for 125 Bytes, that is a bit of an escalation. Behe set the limit at approximately two bits. There are only a couple pf proteins that are bot essential to all flagella like structures and common to all known organisms that have such structures. There are, in fact, numerous pathways to similar functionality, and no cases where an exact sequence of data must be specified in advance.

  150. Nakashima-San:

    Congrats, mon. Best wishes!

    (And, don’t forget, you are now under new management!)

    GEM of TKI

  151. Petruska you state:
    “I think it would bee interesting if ID proponents could demonstrate that all functional structures and objects are the result of intentionality.”

    That is the whole point Petruska all functional structures (and information) that we do know the origination of have always arisen from intelligence (intention) and not from material processes. Including the post which you just posted which I can somewhat safely surmise arose from an intelligent being and not from a non-intelligent one and which exceeds the,,,

    The Universal Plausibility Metric (UPM) & Principle (UPP) – Abel – Dec. 2009
    Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, “Yes.”,,,

    c?u = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108

    c?g = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96

    c?s = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85

    c?e = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70

    http://www.tbiomed.com/content/6/1/27

    Petruska Instead of ID proponents having to prove every single functional structure arose by intelligence, as you are asking, the burden is on you to provide just one example of purely material processes doing as such:

    Petruska the materialistic argument essentially appears to be like this:

    Premise One: No materialistic cause of specified complex information is known.
    Conclusion: Therefore, it must arise from some unknown materialistic cause.

    On the other hand, Stephen Meyer describes the intelligent design argument as follows:

    “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
    “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
    “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.”

    As for you nonchalantly saying there are multiple paths to the bacterial flagellum that don’t involve intelligence all I can say is , Fine, Prove It!!!

    Michael Behe on Falsifying Intelligent Design – video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

    Bacterial Flagellum – A Sheer Wonder Of Intelligent Design – video
    http://www.metacafe.com/watch/3994630

    Genetic Entropy Refutation of Nick Matzke’s TTSS (type III secretion system) to Flagellum Evolutionary Narrative:
    Excerpt: Comparative genomic analysis show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal-body) have been kept…
    http://mbe.oxfordjournals.org/.....t/msn153v1

    “One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. ‘The most parsimonious explanation is that the T3SS arose later,” Howard Ochman – Biochemist – New Scientist (Feb 16, 2008)

    Genetic analysis of coordinate flagellar and type III – Scott Minnich and Stephen Meyer
    Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system.
    http://www.discovery.org/scrip.....php?id=389

    Bacterial Flagella: A Paradigm for Design – Scott Minnich – Video
    http://www.vimeo.com/9032112

  152. P:

    First, a corrective: Weasel is a classic example of design by smuggled in active information in the name of a non-designed process. It rewards nonsense — non-functional — strings on mere increments in proximity to target, which is thus shown to be pre-loaded and designed. As Dawkins says in so many words, but if you are not primed to spot the significance of that, you will miss it:

    It . . . begins by choosing a random sequence of 28 letters … it duplicates it repeatedly, but with a certain chance of random error – ‘mutation’ – in the copying. The computer examines the mutant nonsense phrases, the ‘progeny’ of the original phrase, and chooses the one which, however slightly, most resembles the target phrase, METHINKS IT IS LIKE A WEASEL . . . . What matters is the difference between the time taken by cumulative selection, and the time which the same computer, working flat out at the same rate, would take to reach the target phrase if it were forced to use the other procedure of single-step selection: about a million million million million million years. This is more than a million million million times as long as the universe has so far existed . . . . [TBW, Ch 3]

    He needs to openly acknowledge the blunder, and correct himself on this.

    On the bigger question, observe carefully that what has been pointed out is that complex bio-function is based on codes and implementation of coded algorithms and data in the cell, which is thus shown to rest in islands of function in the space of possible configurations of the data storage elements, here the GCAT elements of DNA.

    Putative blind chance plus necessity evolutionary mechanisms will have to start from an arbitrary config and plausibly get to shores of islands of function, starting with origin of life. That, in a context where observed life starts in the 100′s of k bases. (Autocatalytic molecules that do not code for associated metabolic functions and machines need not apply.)

    For the first life, that means implementing a version of a von Neumann self-replicator, which requires:

    (i) an underlying storable code to record the required information to create not only (a) the primary functional machine [here, a metabolic entity] but also (b) the self-replicating facility; and, that (c) can express step by step finite procedures for using the facility;

    (ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with

    (iii) a tape reader [[called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling:

    (iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by

    (v) either:

    (1) a pre-existing reservoir of required parts and energy sources, or

    (2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment.

    That such codes, algorithms and machines are spontaneously producable by chance molecular interactions and chemical forces in credible pre-life soups is highly dubious; for reasons already identified. And, by comparison with simplest observed life forms, we are looking at 100+ k bases, or over 100 times the threshold for information spaces that the whole cosmos we observe cannot credibly walk through enough of by blind chance and associated mechanical necessity to make happening on an island of function reasonable.

    Then, to create novel body plans, we are looking at increments of 10′s or more of millions of bases, for the sort of level of complexity implied by say the Cambrian fossils. And, the developments will have to be embryologically feasible and integrated, starting from early systems and structures unfolding from the initial cells of a new life form.

    The idea that by tiny increments this can be surmounted — the easy back way up Mt Improbable hypothesis — founders on the organisation and informational requisites to get to minimum functionality for say a wing. ESPECIALLY AS WE HAVE YET TO SEE OBSERVATIONALLY THAT CHANCE VARIATIONS IN A DATA STRINGS HAVE CAPABILITY TO GENERATE FUNCTIONAL CODE BEYOND A REASONABLE THRESHOLD.

    Of course, chance in principle can do any configuration. But beyond a point you are producing the materialistic equivalent of magic. E.g. as I have discussed here, the notion that by chance rocks falling down a hillside on the Welsh border would spontaneously form “Welcome to Wales” is strictly possible but so overwhelmingly beyond reasonable plausibility on the sea of possible configs that if we were to see an avalanche doing that we would suspect a trick.

    Your side is asserting that you can provide an easy back path up Mt Improbable. You need to show it, and on something a bit more credible than Weasel. In particular, as a frst step, you need to provide us a web of missing links that would turn the tree of life into a gradually evolving pattern of incrementally formed novel body plans. (Pleas about the paucity of the fossil record are wearing thin after 150+ years and 1/4+ millions of species with multiplied millions of individuals. And, with many or the “right” type and strata of rocks preserving soft bodied animals etc, just not the ones expected by Darwinists. For decades now it has been an open secret of paleontology that the fossil record pattern of gaps and stasis then disappearance or continuation into today’s world, is real. That’s why punctuated equlibria models were invented — to try to explain the systematic absence of desired and expected evidence.)

    What has been observed is minor variations within existing body plans, and not a mechanism that on the information challenge can credibly account for origin of body plans starting with the very first one.

    Overgenerous extrapolation from well inside the FSCI threshold to well beyond it is an implicit admission of want of a solid case. In that context, Behe’s observations on the limits with malaria parasites shows microevo and limits on it per observations in a context of more reproductions than the vertebrates can have had. 1,000 bits — which is far within the scope of DNA for the first body plan, and for observed DNA increments to move to complex multicellular body plans — is a threshold that identifies where the search capacity of the cosmos acting on a random walk till it can get a reproducing population going on an island of function so that incremental changes can move up the hill to optimality through differential reproductive success — becomes utterly inadequate for a plausible chance based information innovation mechanism. (Recall, natural selection works by culling out less successful sub populations in relevant environments, i.e by REMOVING information from the population. It is not and cannot be the source of the information.)

    So, please stop playing at burden of proof shifting and start showing that blind chance plus mechanical necessity acting on happenstance initial conditions can produce algorithmically functional, code based information beyond the FSCI limit. Posts in this thread are ample enough demonstration that intelligence is a routinely observed source of such FSCI as we are interested in.

    I have already shown the inference to best explanation on empirically known routine causes of FSCI and associated reasons why FSCI is not a credible product of chance + necessity.

    So, if there is a burden of proof for the design side, it has already been met in the relevant form: warrant on empirical and analytical evidence to best explanation.

    GEM of TKI

  153. Information is not “smuggled in.” The information about the relative value of variants is in the oracle, the selector. The algorithm merely accumulates or preserves information.

    Whether or not a variation in the genome results in a viable organism is determined by biochemistry, not an outside agent. The list of viable organisms is not in the mind of an agent, but is an attribute of physical laws.

    It really makes little difference how variations are generated, as long as the the rate of variation does not produce an entire generation of non-viable individuals.

  154. Petruska, seeing as the coding found in simplest life on earth greatly exceeds what man has done so far,,,,,,,,,,,

    “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?” – David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 http://www.biomedcentral.com/c.....2-2-29.pdf

    Stephen Meyer is interviewed about the “information problem” in DNA, Signature in the Cell – video
    http://downloads.cbn.com/cbnne.....f?aid=8497

    The Cell – A World Of Complexity Darwin Never Dreamed Of – Donald E. Johnson – video
    http://www.metacafe.com/watch/4139390

    Cells Are Like Robust Computational Systems, – June 2009
    Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,”We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail.”
    http://www.sciencedaily.com/re.....103205.htm

    ,,,,,,,, and you are convinced that random variation and natural selection can produce what teams of software engineers can’t, Please tell me exactly why Bill Gates does not employ millions of random number generators and selection software programs to produce staggering levels of computer coding? Maybe Bill Gates wants computers to do more than spit out “Me Thinks Its Like A Weasel? and better antennas? Just a thought petruska,,, I can tell you one thing that Random Number generators did that I found interesting:

    The Global Consciousness Project
    http://www.youtube.com/watch?v=GPUTA1a6KHk

  155. Mr Timaeus, KF-san,

    Thank you for your kind wishes. Having just returned recently from Malaysia, I won’t be heading off to Tahiti! My strategy is to dodge all the people I’d rather not deal with by saying that the wedding is in Budapest, when it is in fact in Prague. The happy but exhausted couple will be going no further than a spa in the Czech countryside. (Sorry, VMartin, not hiking the High Tatras this year.)

    Oh, and I downloaded “Trilobites: Eyewitness to Evolution” to my nook for those brief moments.

  156. P:

    Do you not see that by Dawkins’ own admission, Weasel works by comparing variations with the defined target and keeping whatever makes an increment to target, regardless of the fact that it is non-functional? [Which means that nothing remotely analogous to NS is a part of the situation in Weasel.]

    That he also acknowledges that this rewarding of non functional variations on increment to a preloaded target is what makes Weasel work with reasonable resources and time?

    Do you not see how this implies that the real problem is to get TO the shorelines of islands o function in the space of possible configs?

    And, that the way Dawkins did that was to implement a targetting procedure and cumulative selection process that are intelligent?

    And so, when you say:

    Whether or not a variation in the genome results in a viable organism is determined by biochemistry, not an outside agent. The list of viable organisms is not in the mind of an agent, but is an attribute of physical laws.

    It really makes little difference how variations are generated, as long as the the rate of variation does not produce an entire generation of non-viable individuals.

    . . . that rather gives the game away:

    1 –> You are begging the question of the amount of integrated, functional information and organisation to effect a body plan, starting with the first. (And when the observed quantity of information has been brought to your attention explicitly, you have glided over it in a telling silence.)

    2 –> You are begging the question of the observed structure of the space of known viable organisms: islands of function on distinct body plans that appear suddenly without the overwhelming number of transitionals that should be there on gradualist hypotheses.

    3 –> Similarly, you are ducking the question of origin of complex, embryologically sound, functional organisation and associated coded information by chance processes.

    4 –> We must note, again, that “natural selection” is little more than a label for the fact that if an organism is embryologically unsound, or is otherwise crippled from function in its environment, or cannot find viable mates etc, it will not have descendants.

    5 –> That is, the NS part of the darwinist expression CV + NS –> Evo is a REMOVER of information, not a SOURCE. And chance –the implied source of information — has strict limits to what it can credibly do as an information source, on the gamut of our observed cosmos.

    6 –> So, you have not bridged the gap between 1,000 bits as a generous upper limit on functional by happenstance, chance based variations in data strings, and observed simplest life forms with 100+ k bases in their DNA, or that complex life forms have counts in the 10′s – 100′s of millions of bases or more. [Not to mention, you have nor accounted for the credible origin of language as the framework of codes, of algorithms and data structures or implementing machinery, apart from the implication of materialistic statistical miracles by the warehouse- full.]

    (If you want to believe in statistical miracles, that’s fine; but please don’t then turn around and dismiss those who would believe that intelligence is a more credible account for the origin of complex functional organisation and information, in light of our experience of the routine source of such; especially not by making acid comments about inferring to the supernatural or Divine Feet in doors. That would show that materialistic ideological bigotry not reason would be driving the process; while hiding under the credibility of the lab coat functioning as the moral equivalent to evil masking itself in the ecclesiastical robes of yore. For, in every age, evil sneaks in by hiding in the robes of the most respected institutions and falsely claiming to act in the name of the good. Thankfully, we can always spott he woldf in sheep’s clothing by seeing the presence of the wolfish tactics of trying to promote “truth” by suppressing fair examination of evidence, and resorting to the tactics of doing evils in the name of promoting good. Sadly, resemblance to recent trends with appealing to “consensus” of the power brokers of key institutions, and backing this up by expelling dissenting scientists and thinkers is not coincidental.)

    7 –> In saying that viability of a variation “is determined by biochemistry” you have begged the question of how that biochemistry works.

    8 –> Namely, it is based on an information system that uses a definite digital code, step by step finite procedures with halting [i.e. algorithms], string based data structures, and associated implementing namomachinery.

    (And that is no mere “analogy” that one can airily dismiss without properly reckoning with how central reasoning by apt analogy is to inductive logic. For, as we can see in commonly available animations [or harder to understand detailed descriptions], DNA stores 4-state per base digital data, the mRNA transfers that data to the ribosome, in which with the aid of tRNA that uses key-lock matching anticodons and a nudged arm with active tip procedure to chain amino acids step by step, terminating with a stop codon and thus making the protein workhorse machines for the cell.)

    9 –> Thus, while the various machines and processes are indeed using the power of “physical laws,” those laws do not account for the organisation. Information bases systems and complex functional organisation do. (Back to Leibniz: when we see the wheels of a mill grinding away and with wheat coming in one end, flour going out the other, we do not explain the functionality of the organisation on the laws and forces and materials that are used as means to effect a purposefully organised, information-rich, onward useful and valuable end.)

    10 –> By utter contrast, we routinely see that intelligence produces complex functional organisation by design, and that functionally specific, complex information is a routine empirically recognisable signature of that effort.

    11 –> In short, it is plainly evident tha the reason why you refuse to allow a serious diswcussion o9n inference to best explanation with all the relevant possible causes of “variation” on the table is a priori materialism by the back door. Namely, imposition of so called methodological naturalism by which the only admitted sources of variation are chance and mechanical necessity; those that happen to sit well with evolutionary materialism as a dogma.

    12 –> Indeed, this set of materialistic blinkers plainly blinds you to the obvious — and author-admitted — facts on Weasel.

    ============

    P, please think again.

    G’day

    GEM of TKI

  157. 157

    KF remarks:

    …islands of function…

    This paper suggests there may be more than a few additional islands of function that reduce the odds a bit!

  158. Do you not see that by Dawkins’ own admission, Weasel works by comparing variations with the defined target and keeping whatever makes an increment to target, regardless of the fact that it is non-functional?

    The important question is not how the oracle works, or what specific information it contains. The question is whether random (non-foresightful) variation can supply changes which survive selection.

    From the point of view of the variation generator, the oracle is arbitrary.

    And in biology the oracle is sometimes arbitrary. There are some absolute selection criteria — biochemistry is not arbitrary — but there are thousands or millions of details that differentiate one individual from another.

    It strikes me that the discussion of Weasel tends to ignore the real issue — not where the information comes from, but where variation comes from.

    What Weasel does do is demonstrate that an algorithm using a completely random variation generator can accumulate information from any arbitrary oracle.

  159. P:

    An oracle is an intelligent signaler, like in the case of Weasel, where NONFUNCTIONAL strings are evaluated on increments of proximity to a target [Hamming Distance], and are rewarded on proximity through an intelligently designed warmer/colder algorithm..

    In the bio-world, the problem is not whether one may move around within an island of function through minor random variation of an already existing population, but the justification on adequate empirical evidence of the claimed chance plus blind mechanism origin of body plans requiring 100′s of thousands to tens or more of millions of bits worth of information; starting from the first one.

    Until that is answered decisively by darwinists, assertions and declarations of the wonderful power of darwinian mechanisms to create novel body plans are simply empty statements of belief backed up by a priori commitments to evolutionary materialism.

    GEM of TKI

  160. Petruska you state:

    “The important question is not how the oracle works, or what specific information it contains. The question is whether random (non-foresightful) variation can supply changes which survive selection.”

    Neglecting the fact that Weasel drives the variation to a predetermined “goal”, it seems to you that “random variation” is the “god” that creates everything in your worldview. Thus Petruska, why does it not fascinate you in the least when conscious intention is shown to influence random number generators?

    Scientific Evidence That Mind Effects Matter – Random Number Generators – video
    http://www.metacafe.com/watch/4198007

    Come on Petruska, if random (non-foresightful) variation is the be all, end all, “creator god” in your worldview, what in the heck is pushing your “creator god” around in the random number generator experiments?

  161. At any rate, the Weasel algorithm does not require a fixed target. It only requires an oracle that ranks individuals. If the oracle shifts criteria, the population shifts accordingly.

    It is rather easy to write an oracle that ranks the population by its conformity to another population, rather than to a fixed target.

    For example, the criterion could be nearness to words in general, rather than to a particular word. It doesn’t matter to the algorithm if the oracle switches languages. The algorithm will follow.

  162. Petruska you seem fairly confident in all this,, Do you mind falsifying Abel’s null hypothesis?

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    http://mdpi.com/1422-0067/10/1/247/ag

  163. 163

    Petruska begins by telling Timaeus that no evidence against materialism is sufficient, and with these last comments, is now telling Kairos and BA that no evidence for it is necessary.

    Garden variety scientism.

  164. Petruska:

    Frankly, I don’t know if it is worthwhile repeating again issues which should be well established, but let’s try:

    What Weasel does do is demonstrate that an algorithm using a completely random variation generator can accumulate information from any arbitrary oracle.

    Any algorithm using random variation can easily accumulate from any arbitrary oracle all the information which already is in the oracle. That is so obvious that there should be no need even to debate it. Take the weasel phrase. I already know it, you already know it, the oracle already knows it. All you have to do is to cycle randomly through the existing letters to find the first position, and check with the oracle until you find the right one, then fix it and pass to the second, and so on, until you have “found” the whole phrase. Piece of cake.

    But what do you think we have demonstrated? Only that we can “copy” information by a random writing, instead of copying it directly. If we wanted to be smarterm we could look at the oracle first, position after position, and just “write” the correct letter. Ah, but I forgot, we do love games!

    All so called “evolutionary” algorithms accomplish some variation, more or less brilliant, more or less explicit, of that same process. Even if the oracle does not know the solution explicitly, the system as a whole is designed to make the solution easy and possible.

    But it is not up to me to show that. Just read the papers of the evo informatics lab, and look at the very good work that is being done there.

    What is really strange is your convinction that, in that type of context, random search if finding the information. Well, a random search in a small search space, with the right oracle available to do intelligent selecion, can certainly find all that we want, from the whole works of Shakespeare to a detailed description of all known protein sequences. What do we need after all? Only a volume of Shakespeare’s works, possibly digitalized for easier use, and some good database of protein sequences downloaded from internet, and a very simple and patient search software, and the result is there. Why are those silly IDists complaining that random variation cannot do these things?

    But, as I really am one of those silly IDist, just show me one thing: try to find the primary sequence, let’s say, of human myoglobin (just 153 AAs), without knowing it in advance, and having only a lab instrument, let’s say, which can test available to evaluate if each newly generated molecule can bind the heme group and iron (but beware, only when the binding is really strong and efficient, in other words functional).

    And as you are so worried about the importance of time, I will be generous: I give you a billion years from now.

    But, in the end, you will have to admit that I was right :)

  165. Any algorithm using random variation can easily accumulate from any arbitrary oracle all the information which already is in the oracle.

    Fine. all that selection needs to do is rank differences in genomes according to fecundity. What accumulates is bits of genome that contribute to fecundity. Or at least don’t prevent reproduction.

    If one has a specific target, such as the works of Shakespeare, odds are that random variation and selection will not produce it.

    But viability is a cloud having gradations of density rather than a single island or point.

  166. gpuccio @ 163,

    What Petrushka is stating,

    At any rate, the Weasel algorithm does not require a fixed target. It only requires an oracle that ranks individuals. If the oracle shifts criteria, the population shifts accordingly.

    and Dawkins was trying to demonstrate, is biological feedback.

    The output is text because that’s easy to show on a computer display.

    The “Weasel” text is fixed so that we can monitor the progress of the algorithm, not because the algorithm requires a fixed output to function.

    The ID side is fixating on how the demonstration was set up, instead of the algorithm that was being demonstrated, which is, “biological feedback influencing selection”.

  167. The fundamental flaw in the ID analysis of evolution lies in the concept of target. It seems to imply that what is was destined. Evolution searched for complex structures.

    Things like the flagellum or the works of Shakespeare keep cropping up in the argument. But specific structures are not necessary to biology, just as Shakespeare is not an inevitable outcome of literature.

    As far as life goes, most of it is content being single celled, minus flagellum.

  168. Petruska, here are the results for evolution from the real world with no preordained “complex structures” in mind:

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-mic.....-evolution

    Dr. Behe states in The Edge of Evolution on page 135:

    “Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite.”

    That order of difficulty is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation.

    Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe – Oct. 2009
    Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
    http://www.evolutionnews.org/2.....est_s.html

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.” http://www.evolutionnews.org/2....._edge.html

    This following recent study solidly confirms the severe limit for evolution found by Dr Behe:

    Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness – Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke – 2010
    Excerpt: In experimental evolution, the best way to permit various evolutionary alternatives, and assess their relative likelihood, is to avoid conditions that rule them out. Our experiments, like others (e.g. [40]), used populations of cells growing slowly under limiting nutrient conditions, thereby allowing a number of paths to be taken to higher fitness. We engineered the cells to have a two-step adaptive path to high fitness, but they were not limited to that option. Cells could reduce expression of the non-functional trpAE49V,D60N allele in a variety of ways, or they could acquire a weakly functional tryptophan synthase subunit by a single site reversion to trpAD60N, bringing them within one step of full reversion (Figure 6). When all of these possibilities are left open by the experimental design, the populations consistently take paths that reduce expression of trpAE49V,D60N, making the path to new (restored) function virtually inaccessible. This demonstrates that the cost of expressing genes that provide weak new functions is a significant constraint on the emergence of new functions. In particular, populations with multiple adaptive paths open to them may be much less likely to take an adaptive path to high fitness if that path requires over-expression.
    http://bio-complexity.org/ojs/.....O-C.2010.2

    Shoot petruska I would be happy if you just provided even one example of the fitness test being passed by evolution by 3 point mutations or 4 functional information bits:

    Is Antibiotic Resistance evidence for evolution? – “The Fitness Test” – video
    http://www.metacafe.com/watch/3995248

    Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
    http://www.answersingenesis.or.....-drugstore

  169. Petrushka:

    Plainly, you are diverting. We have described islands of FunctIon in a sea of configurations, constrained by the requisites of codes, algorithms and data structures.

    We have pointed out that the resources of the universe are grossly inadequate to traverse even a tiny fraction of the implied config spaces. We have pointed out that there is abundant evidence that chance and necessity cannot credibly spontaneously reach islands of function for chance variation to begin to compete on differential performance of sub populations.

    We note that FSCI is routinely produced and observed as coming from intelligence.

    You appear unable to address that, instead trying to assert that “target” suggests purpose — well language and algorithms and data structures as we see in the cell more than merely suggest purpose.

    You speak about fuzzy clouds in a sky (most inapt as clouds are easily seen form way off; the problem is to ger=t the DNA, body plan and metabolic machinery to get TO an island of function, by drifting).

    Have you ever been on an island in the sea?

    If you have done so, you will know that the shoreline varies by the second, hour, day, month and year, and is considerably variable across the years. But that is immaterial to the relevant point: islands and even archipelagos isolated in a large ocean are notoriously hard to find unless you have intelligent guidance.

    And the relevant search resources of our observed cosmos are vastly inadequate to undertake the relevant search, or random walk if you will. Until you are ashore on an island of function, chance variation and natural selection on superiority of function are irrelevant.

    But we know that FSCI routinely comes from intelligence, as posts in the tread demonstrate.

    Think about that.

    GEM of TKI

  170. Petrushka:

    Fine. all that selection needs to do is rank differences in genomes according to fecundity. What accumulates is bits of genome that contribute to fecundity. Or at least don’t prevent reproduction.

    Yes, and for genomes to exist, and fecundity to exist, and enzymes and metabolism to exist, and so on, all that selection needs to do is to find the thousands of different individual functional protein domains that we observe in the proteome. Again I ask you explicitly: if evolution can only select existing function, how could it find thousands of independent configurations, each of them functional, in an ocean of non functional, non folding primary sequences? I invite you to read the recent review by Douglas Axe on Bio-Complexity, “The Case Against a Darwinian Origin of Protein Folds”.

    If one has a specific target, such as the works of Shakespeare, odds are that random variation and selection will not produce it

    Nor will they produce the proteome. Again, the argument of “evolution can take any direction” is a false argument. Once you have a basic structure for life (DNA, proteins, cells, etc.), directions are extremely narrow. You need proteins which fold and have active sites, and those active sites must do something useful in the context where they are supposed to arise, and must interact with what already exists, and the new proteins must be regulated in the correct way, and so on. Targets, targets everywhere!

    But viability is a cloud having gradations of density rather than a single island or point

    Viability is one thing, the information which can ensure viability is another. A long protein sequence has nothing to do with viability unless and until it acquires a specific, well integrated function which can be added to the existing function. Otherwise, no selection can take place.

    The fundamental flaw in the ID analysis of evolution lies in the concept of target. It seems to imply that what is was destined

    Wrong. It just implies that what is had to work. Funtion is a target. And in a specific context, specific functions (and not any possible function) are very specific targets. There may certainly be several possible functional targets in a specific context, but anyway always in a limited number. And practically all of them, in a complex context, require functional complexity. New functional complexity. And random search cannot find them. And, for the same reasonm NS cannot select what has not been found.

    Things like the flagellum or the works of Shakespeare keep cropping up in the argument. But specific structures are not necessary to biology, just as Shakespeare is not an inevitable outcome of literature.

    Wrong. Specific functional structures are necessary to biology, exactly as good, meaningful and beautiful works by gifted authors are necessary to literature. In your statement you meaningfully shift from “necessary” to “inevitable”. Individual events may not be “inevitable”, but authors are absolutely necessary to literature exactly as complex functional structures are necessary to biology.

    Would you affirm that a random search in the search space of letters can give us valid literary works, new valid literary works I mean, not the copy of the weasel? Please give me the reference of the evolutionary algorithm which has given us a new drama, meaningful and beautiful. It needs not be Shakespeare. Any good drama will do. Indeed, even a mediocre one.

    If that is possible, then certainly darwinian evolution could produce the proteome. So, I am here waiting for the reference to the drama creating algorithm.

    As far as life goes, most of it is content being single celled, minus flagellum.

    And, I suppose, minus DNA transcription and translation, cell membranes, metabolism, ATP synthase, rybosomes, etc? And the hundreds of very complex proteins and structures that even the simplest of archea or bacteria possess? Where did darwinists get this strange idea that the flagellum is the repository of all unexplainable complexity? Wake up. That is only one example, the example Behe used in his book a few years ago. One of thousands. One of millions.

    And, anyway, if I remember well, flagella do exist. Like multi celled beings. Like body plans. Like long distance cellular communication. Like nervous systems. Do these things exist, or are they ID myths?

    That prokaryotes are, still today, probably the best adapted form of life on earth is only evidence of what I have always affirmed: that there was no real reason for them to evolve, if the only driving principle is better survival or reproduction.

    But, if the driving principle is design and purpose, things change…

  171. “Islands” is a bad metaphor. There are not dead or impassable seas between variants. Gradients would be a better term.

    HIV managed the jump from one species to another in our lifetime.

    But there is no biological imperative for any species to change into something else, any more than there is an imperative for someone to win the lottery every week.

    Biological change simply doesn’t seek targets or goals. It follows, like a river, the path of least resistance.

    But even that is a limited metaphor, because species don’t always find a path. More often than not, they go extinct.

    As for mammals and their supposed innovations, I’m not aware of many inventions of metabolic machinery that distinguish one mammal from another. If there were, I suspect they would make a better mascot for ID than the flagellum.

  172. Petrushka-

    Just as anything would be a better mascot for for Darwinians than “Ida”?

  173. Better yet, “Junk” DNA?

  174. Petrushka

    I find it extremely disappointing that you are now playing art debating terms to describe realities, e/g/ clouds vs islands. (and thinly veiled assertions that just any and every config will have minimal functionality so its a smooth climb up a fitness landscape from just about anywhere.

    To correct this gross error, let us go back to the very first island of bio-function. That is, a metabolic automaton with self-replication, which must meet this functionality target, on the logical requisites identified in the late 1940′s by von Neumann:

    (i) an underlying storable code to record the required information to create not only (a) the primary functional machine [here, a metabolising automaton] but also (b) the self-replicating facility; and, that (c) can express step by step finite procedures for using the facility;

    (ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with

    (iii) a tape reader that reads and interprets the coded specifications and associated instructions; thus controlling:

    (iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by

    (v) either:

    (1) a pre-existing reservoir of required parts and energy sources, or

    (2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment.

    Parts (ii), (iii) and (iv) are each necessary for and together are jointly sufficient to implement a self-replicating machine with an integral von Neumann universal constructor. That is, we see here an irreducibly complex set of core components that must all be present in a properly organised fashion for a successful self-replicating machine to exist. [Take just one core part out, and self-replicating functionality ceases: the self-replicating machine is irreducibly complex (IC).] This irreducible complexity is compounded by the requirement (i) for codes, requiring organised symbols and rules to specify both steps to take and formats for storing information, and (v) for appropriate material resources and energy sources.

    Immediately, we are looking at islands of organised function for both the machinery and the information in the wider sea of possible (but mostly non-functional) configurations. In short, outside such functionally specific — thus, isolated — information-rich target zones, want of correct components and/or of proper organisation and/or co-ordination will block function from emerging or being sustained across time from generation to generation. So, once the set of possible configurations is large enough and the islands of function are credibly sufficiently specific/ isolated, it is unreasonable to expect such function to arise from chance, or from chance circumstances driving blind natural forces under the known laws of nature.

    So, your first challenge is to get from a reasonable prebiotic soup or vent or comet and credibly spontaneously get to a self-replicating cell or some reasonable analogue thereto. By blind chance and mechanical necessity starting from happenstance initial conditions.

    Suffice to say that as of the recent Shapiro-Orgel exchange, this has ended in mutual self destruction of the RNA world and metabolism first scenarios, and as to the actual requisite that BOTH metabolism and replication on stored info be put together to form life as we know it, that is a definite non-starter on chance plus necessity. But already serious pre-design studies on building self replicators have been done, in the context of galactic exploration.

    When we get to novel body plans, the problems do not vanish. As Meyer summarised in his well known paper in 2004 that left the NCSE activists foaming at he mouth with lynch-mob fervour that unfortunately targetted the Journal editor who had the integrity to publish a paper that critiques the magisterium’s favoured view, and passed peer review:

    One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93) . . . the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. Molecular biologists have recently estimated that a minimally complex single-celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life (Koonin 2000). More complex single cells might require upward of a million base pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions. The genome size of a modern arthropod, the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart & Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells to complex animals represent significant (and, in principle, measurable) increases in CSI . . . .

    In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . [PBSW, Aug 2004]

    Again, we find a functional target comprising a cluster of integrated complex entities that implement a novel body plan. And the credibility of getting to such on chance plus necessity plummets to a practical zero so soon as we — very rapidly — run past the 1,000 bit threshold.

    Summed up, the idea of islands of coordinated integrated, organised function is very well warranted. The problem, plainly is that you have no good empirical evidence of body-plan level macroevolution on CV + NS, so we find rhetorical challenges to an empirical issue: spontaneous generation of highly complex coordinated multipart information rich entities is extremely implausible as an explanation.

    But intelligence does this sort of thing all the time. Indeed, over the next few decades our own technology will be good enough to make a 3-D kinematic self-replicator. Already we can conceive what is needed.

    So, have you any good reason to infer that an intelligence to produce life or body plans for multicellular life forms is IMPOSSIBLE? Failing that, we have excellent reason to infer form known, reliable empirical traces of intelligence to intelligence as the best explanation of life.

    GEM of TKI

  175. OOL is certainly an interesting question, but I’ll have to stipulate that we don’t know much about it, and probably will never know the details.

    But from where I stand on this particular thread, the argument has been moved back from the question of whether dogs and cats are descended from a common ancestor, to questions from deep history that may never be resolved.

  176. I am not terribly surprised that most genes, most metabolic mechanisms and all body plans, seem to have been invented or discovered by microbes or very simple organisms, presumably having large numbers and short spans between generations.

    It is not surprising that few fundamental inventions have been made by larger and slower reproducing creatures.

  177. Petruska, you haven’t answered anything from any topic. You just dream fuzzy dreams and state them as if they are plausible and never go anywhere near any empirical evidence to prove any point, all the while you pretend you are being reasonable in all this. It would be funny save for the fact all of evolutionary biology is dreaming with you.

    Bring me to life by Evanescence
    http://www.youtube.com/watch?v=UKer9hry-Gg

  178. Petruska you state,

    I am not terribly surprised that most genes, most metabolic mechanisms and all body plans, seem to have been invented or discovered by microbes or very simple organisms,

    do you care to enlighten us to where the information for a body plan resides?

    This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show “exceedingly rare” major morphological effects from mutations to the DNA code.

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    The Origin of Biological Information and the Higher Taxonomic Categories – Stephen Meyer”Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.”
    http://eyedesignbook.com/ch6/eyech6-append-d.html

    Hopeful monsters,’ transposons, and the Metazoan radiation:
    Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable “hopeful monsters” render these explanations untenable.
    Paleobiologists Douglas Erwin and James Valentine

    “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan).” Michael John Denton page 172 of Uncommon Dissent

    Fearfully and Wonderfully Made – Glimpses At Human Development In The Womb – video
    http://www.metacafe.com/watch/4249713

    This includes the highly touted four-winged fruit fly mutations:

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells
    http://www.evolutionnews.org/2.....footnote19

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    As well as “cloning” studies:

    “There is now considerable evidence that genes alone do not control development. For example when an egg’s genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.) The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact.”
    The Design of Life – William Dembski, Jonathan Wells Pg. 50

  179. A bit off-topic, but it’s what we’ve come to.

    http://www.youtube.com/watch?v=isGrCmCFFmY

  180. do you care to enlighten us to where the information for a body plan resides?

    The genes for body plan seem to be rather ancient. They certainly go back to the era I discussed, which is characterized by large numbers and short generation spans.

    Are you suggesting there is some demonstrable discontinuity involved in the first body plans?

  181. I will stipulate that although cellular machinery is more conserved than genes, it is not entirely identical across species. It isn’t identical within species.

    But for the moment I think it would be interesting to discuss a point that you brought up, that evolution at the level of molecular machinery seems more likely in organisms that have high numbers and short generation times.

  182. What genes code for body plans?

  183. Petruska, neither you nor anyone else has a firm clue where the information for body plan morphogenesis resides. For you to pretend it resides in genes and leave it at that as if you have established your point and ignore the evidence I presented shows that you do not really want to know what the truth is. frankly it is ludicrous for you to think that your unsupported conjecture that essential conserved genes/proteins has any weight to explaining body plan morphogenesis. It is a non-explanation period!

    “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan).” Michael John Denton page 172 of Uncommon Dissent

    Riddick your youtube foray reminded me of this:

    Top 10 Excuses for Not Going to Church
    http://thedawghowse.blogspot.c.....hurch.html

    and the video also reminded me that it never was about the science with you anyway was it?

  184. Petrushka:

    By your pattern of exchanges over some days, we have to take it that ducking out of addressing the issue of the OOL conundrum of getting to the very first body plan from a plausible pre-biotic soup by spontaneous changes on chance and mechanical, chemical necessity, means that you have no good answer.

    In particular, you have no good explanation — and remember onlookers, if there was one, it would be all over the Internet on pro evolutionary materialism advocacy sites — for the claimed spontaneous origin of the very first body plan for a metabolising automaton with integrated self-replication facility that is based on coded information and organised complex molecular machinery. That is, the first cell-based life form.

    Indeed, neither do the major researchers, as we may see from the exchange between Shapiro and Orgel several years ago.

    But, based on the rise of information and communication technologies in the past half century and more, we have some very good, empirically anchored explanations for the origin of: codes, machinery for processing coded information, complex, organised machinery for carrying out resulting decoded instructions, and for manufacturing plants that convert components into intermediate or final products based on algorithmic control.

    Namely, design.

    In addition, we have excellent reason to see that chance contingencies and trial and error will not credibly account for such, as the set of possible configs is rapidly well beyond the random walk trial and error search capacity of the cosmos, and the tight co-ordination of integrated functional components and associated coded algorithmic instructions means that we have deeply isolated islands of function in vast config spaces of non-function. (Just check how many cars in junk yards are close to working but not working to see what this means.)

    (Notice onlookers, I went back to the OOL question to answer to the attempt to dismiss the concept of islands of function. Silence on the point tells us this was successful.)

    So, we have excellent reason to infer to intelligent design on empirically well supported signs of such design for the origin of life, once we reject the attempt to impose evolutionary materialistic ideological blinkers.

    But, once we see that, we have no good reason to reject the onward inference to similar design to explain the rise of major body plans, at the level of the difference between crabs, sea slugs, sea urchins, worms [of several quite distinct types], and fish, not to mention algae vs ferns or flowering plants and in this last group, a coconut tree vs a guava tree vs. a banana tree. (That is the sort of level of body plan differentiation we see in the Cambrian layer animal fossil diversity. Dogs vs cats is a much more minor level of differentiation. At a lower level, origin of birds, whales and bats with wings or underwater breathing and locomotion organs and associated body transformations is a similar cluster of cases in point.)

    The point is that the origin of Phyla and sub phyla or the equivalent across other kingdoms is again a matter of a huge jump in coordinated body development information, some genetic, some epigenetic [as BA 77 -- as usual -- reminds us with some apt quotes]. Jumps on the order of 10′s to 100′s of millions of bases, thus bits of information. Well beyond the FSCI threshold, again swamping the generous 500 – 1,000 bit estimate for the upper limit for what random walk trial and error can plausibly do.

    So, again, we see good reason to infer to design as the best explanation for origin of complex body plans.

    And in that context, we see that the origin of life and of biodiversity is thus best explained on intelligence, not random walk based trial and error; which is what darwinian style evolutionary materialism boils down to.

    So, on evidence we can see directly in the bodies before us and in the fossils we also can inspect, we have many, many reliable markers of design as the best explanation of origin of life and of body plans. And, once the evidence is acknowledged as having a designer’s foot in the door, then there is no good reason to dismiss design as a pervasive feature of life as we see it; including of the difference between dogs and cats, or the tabby sitting by the fire place and the puma roaming the hills behind.

    Briefly going beyond that, it is also quite evident that the physics of the cosmos is finely tuned for the existence of carbon chemistry cell based life, on dozens of co-ordinated parameters. That is, we have further evidence pointing to an intelligent designer and builder of the cosmos who is thus highly knowledgeable and intelligent, powerful and beyond the material cosmos we observe.

    It therefore seems quite reasonable to infer that the designer of life and its diversity up to and including ourselves, is the same designer who fashioned the heavens and the earth as a suitable habitat for such life. And in our civilisation, such an extra-cosmic designer echoes very tellingly of the God of Judaeo-Christian theism. Which brings science full circle to the pattern of thought of say Newton in Opticks, Query 31, nearly 300 years ago:

    In the two first Books of these Opticks, I proceeded by this Analysis to discover and prove the original Differences of the Rays of Light in respect of Refrangibility, Reflexibility, and Colour, and their alternate Fits of easy Reflexion and easy Transmission, and the Properties of Bodies , both opake and pellucid, on which their Reflexions and Colours depend. And these Discoveries being proved, may be assumed in the Method of Composition for explaining the Phaenomena arising from them: An Instance of which Method I gave in the End of the first Book. In this third Book I have only begun the Analysis of what remains to be discover’d about Light and its Effects upon the Frame of Nature, hinting several things about it, and leaving the Hints to be examin’d and improv’d by the farther Experiments and Observations of such as are inquisitive. And if natural Philosophy in all its Parts, by pursuing this Method, shall at length be perfected, the Bounds of Moral Philosophy will be also enlarged. For so far as we can know by natural Philosophy what is the first Cause, what Power he has over us, and what Benefits we receive from him, so far our Duty towards him, as well as that towards one another, will appear to us by the Light of Nature. And no doubt, if the Worship of false Gods had not blinded the Heathen, their moral Philosophy would have gone farther than to the four Cardinal Virtues; and instead of teaching the Transmigration of Souls, and to worship the Sun and Moon, and dead Heroes, they would have taught us to worship our true Author and Benefactor, as their Ancestors did under the Government of Noah and his Sons before they corrupted themselves.

    Such a full circle return to science in a genral design frame of thought that lives happily with theistic thinking generally, is of course utterly unwelcome in the more militantly ideologised evolutionary materialistic circles, some of which wield considerable power in the academy and institutional science. So the sort of bitter end resistance commonly seen in the teeth of where the evidence over the past 60 or so years has plainly been pointing is unsurprising.

    But, like any other bitter ender ideological campaigns, it will gradually falter and fail as the sheer accumulating weight of the evidence breaks it down.

    G’day

    GEM of TKI

  185. Petrushka:

    Considering that you like to make statements and never support them with data or reasoning, I will try to do the opposite.

    I am not terribly surprised that most genes, most metabolic mechanisms and all body plans, seem to have been invented or discovered by microbes or very simple organisms, presumably having large numbers and short spans between generations.

    It is not surprising that few fundamental inventions have been made by larger and slower reproducing creatures.

    Now, I will just give some data, to show that your affirmations are vague and inaccurate. I will refer to the paper “The Evolutionary History of Protein Domains Viewed by
    Species Phylogeny” , by Song Yang, Philip E. Bourne, freely available on the internet.

    This paper analises the distribution of single protein domains as derived from SCOP (the database of protein families) in the evolutionary tree, and even the distribution of their unique combinations.

    The total number of independent domains in the whole proteome is 3464 and the total number of combinations is 116,400.

    The first important point is that about half of the domain information was already present at OOL (or at least, at the level of LUCA, if you believe in a pre-LUCA life):

    Protein domains 1984;

    Combinations 4631.

    The mean domain content per protein, at this level, is 2.33

    So, the first point you have to explain is how 1984 protein domains were already working at the time of our common ancestor (supposedly 3.5 – 3.8 billion years ago), while not one of them can be found by a random search.

    The remaining half of the domains was discovered in the course of evolution, with the following pattern of new domains and domain combinations:

    Archea:

    Protein domains 31;

    Combinations 323;

    Bacteria:

    Protein domains 467;

    Combinations 4537.

    Eukaryota:

    Protein domains 520;

    Combinations 7192.

    Fungi:

    Protein domains 56;

    Combinations 3089.

    Metazoa:

    Protein domains 209;

    Combinations 12304.

    So, the next point is: about 1313 new domains arose after LUCA, and of them only 31 and 467 arose in archea and bacteria respectively, while the rest was “discovered” by more complex organisms. So, again, how do you explain the 209 new domains in metazoa?

    Another point: in the final parts of evolution, the search for new domains seems to be almost completed: for example, only about ten new domains appear in mammalia. On the contrary, the number of new combinations and the average complexity and length of the single protein definitely increase.

    So, to sum up:

    1) More than half of the information for the proteome is already present at the stage of LUCA (or, if you want, at OOL, unless you can explain how such a complex LUCA originated in a relatively short time from inorganic matter)

    2) The remaining new information was “discovered” during evolution, but certainly not only at the time of bacteria: at least half of the new domains appear in organisms more complex than bacteria, and about one quarter appear in metazoa.

    So, if it is true that the search for new domains “slows down” after OOL, and almost stops in the last stages, the successful search for new domains in the ocean of the search space definitely goes on for the whole evolutionary span.

    3) While the search for new domains slows down, the search for new combinations in more complex protein increases along the evolutionary tree. In other words, as the repertoire of elementary folds is almost completed (demonstrating that targets not only exist, but can be fully achieved), the search for function is moved to a higher logical level.

    4) Finally, we must remember that this analysis is only acoomplished at the level of protein genes (1.5% of the genome in humans). The non coding part of the genome constantly increases during evolution, and most of us (and, today, I would say most of the biologists) are convinced that non coding DNA is one of the keys to understanding genome regulation, and therefore body plans and many oyther things.

    Another, more complex level of abstraction and regulatory function which darwinists will have to explain after they have at least tried to explain the previous, simpler levels.

  186. Very interesting post gpuccio. Do you know the exact reason why the evolutionists pushed so many protein domains back to the origin of life?

    i.e. The first important point is that about half of the domain information was already present at OOL (or at least, at the level of LUCA, if you believe in a pre-LUCA life):

    Protein domains 1984;

    Combinations 4631.

    i.e. Was it loosely based on empirical evidence, or was the reason they grouped it as such based on necessity?

  187. BA (& GP):

    I would note that the requisites of a metabolic automaton that is self replicating a la von Neumann are not at all simple.

    G

  188. bornagain77:

    This is the method used in the pape I quoted:

    Mapping of domains and domain combinations to species trees is
    too time-consuming to do manually. Our approach (see methods),
    similar to the approach introduced by Snel et al. [30], aims to
    predict the presence or absence of protein domains in ancestor
    organisms based on their distribution in present day organisms.
    Four evolutionary processes govern the presence or absence of a
    domain at each node in the tree: vertical inheritance, domain loss,
    horizontal gene transfer (HGT) and domain genesis. (Domain
    duplication and recombination do not affect domain presence.)
    Each process is assigned an empirical score according to their
    estimated relative probability of occurring during evolution, and the
    minimum overall score depicts the most parsimonious evolutionary
    processes of each domain or combination (see methods).

    As you can see, it is based on empirical evidence, and not on functional reasoning.

    Obviously, it is only an estimate, and different approaches could give different numbers. The authors are well aware of that:

    Table 1 lists the predicted number of domains and domain
    combinations originated in the major lineages of the tree of life.
    1984 domains (at the family level) are predicted to be in the root of the tree (with the ratio Rhgt = 12), accounting for more than half of
    the total domains (3464 families in SCOP 1.73). This prediction is
    significantly higher than what is generally believed [5,31,32].
    There are several reasons to account for the discrepancy. First,
    previous attempts focused on universal and ubiquitous proteins (or
    domains) in LUCA [5], so one protein has to exist in the majority
    of species in each of the three superkingdoms (usually 70%–90%)
    to be considered as LUCA protein [32]. Second, the root of the
    tree is still not solved. Thus any domains that are shared by two
    superkingdoms are counted as originating in the LUCA.
    Endosymbiosis of mitochondria and chloroplasts and horizontal
    gene transfer across superkingdoms can result in the same effect,
    which is moving the origin of protein domains towards the root.
    Third is our limited knowledge of protein domains. On average
    nearly 40% of predicted ORFs in the genomes under study cannot
    be assigned to any known domain. When assigned in the future
    they may turn out to be species or lineage specific domains that
    emerged relatively late on the tree of life. There are also a
    significant number of domains which emerge at the root of
    bacteria and eukaryotes. Likewise, this can be explained by the
    unresolved early evolution at the origin of bacteria and eukaryotes.

    So, we are not taking these numbers as absolute, but it is perfectly reasonable that the general scenario will be something like that, even if the numbers can change.

    The conclusions of the authors appear reasonable:

    Notwithstanding, these data suggest that a large proportion of
    protein domains were invented in the root or after the separation
    of the three major superkingdoms but before the further
    differentiation of each lineage. When tracing outward along the
    tree from the root, the number of novel domains invented at each
    node decreases (Figure 4A). Many branches, and hence species,
    apparently do not invent any domains. As previously discussed,
    this might be a result of the incomplete knowledge of lineage
    specific domains.

    A functional approach is certainly possible too. That impllies having a model of the simplest living cell, and trying to estimate the number of necessary proteins and of necessary domains. The approach, anyway, is more conceptual, and not necessarily connected to evidence. Moreover, the definition of simplest living cell can vary, and a strictly reductionist approach, a la Venter, is certainly cutting down many of the naturally occurring functions. Therefore, I think that the empiric approach based on the vurrent distribution of damains and sequences is preferable, more scientific, and, I would say, perfectly “darwinian” (so that, for once, we could agree with our adversaries at least about one methodology :) ).

    Two facts cannot be questioned:

    1) A lot of the protein domains were “discovered” at the root of the evolutionary tree. So darwinists must not only find a vaguely credible theory for OOL, but also one which is extremely efficient in respect to time, much more efficient than all later darwinian evolution, in order to explain how approximately half of the basic protein information was avalable after, say, 200 – 300 My from the start (whatever the “start” was).

    2) Basic protein domain information is only the start, and definitely not the biggest part of the functional information to be explained. Then you have:

    a) The space of different protein functions in the context of a same domain (let’s remember that the same fold can have many different functions, and different active sites).

    b) The space of multidomain complex proteins, which implies a search in the combinatorial space of all domains.

    c) The fundamental space of protein regulation, maybe the biggest of all, which certainly implies at leat gene sequence, non coding DNA and epigenetic mechanisms.

    d) The space of multicellular integration.

    e) The space of body plans, system plans, organ plans, tissue plans, and so on.

    f) The space of complex integration to environment and higher cognitive functions (immune system, nervous system).

    That’s only a brief and gross summary. Each of these levels poses insurmountable impossibilities to the model of darwinian evolution. Unfortunately, most of these levels cannot yet be treated quantitatively for two reasons:

    1) They are too complex

    2) We know too little about them

    So, for the moment, let’s wait for answers about the first level, protein domain information, which is much easier to analyze.

    But I am not holding my breath.

  189. kairosfocus and gpuccio; My question for “exactly how did they arrive at the 1,984 number for protein domains present at origin of life?” arises from the estimates for the estimated complexity needed for the “first life”.

    “An earlier study published in 1999 estimated (not proven) the minimal gene set to fall between 265 and 350. A recent study making use of a more rigorous methodology estimated the essential number of genes at 382.”
    John I. Glass et al., “Essential Genes of a Minimal Bacterium,” PNAS, USA103 (2006): 425-30.

    Signature in the Cell – Book Review – Ken Peterson
    Excerpt: the “simplest extant cell, Mycoplasma genitalium — a tiny bacterium that inhabits the human urinary tract — requires ‘only’ 482 proteins to perform its necessary functions…(562,000 bases of DNA…to assemble those proteins).” ,,, amino acids have to congregate in a definite specified sequence in order to make something that “works.” First of all they have to form a “peptide” bond and this seems to only happen about half the time in experiments. Thus, the probability of building a chain of 150 amino acids containing only peptide links is about one chance in 10 to the 45th power.
    In addition, another requirement for living things is that the amino acids must be the “left-handed” version. But in “abiotic amino-acid production” the right- and left-handed versions are equally created. Thus, to have only left-handed, only peptide bonds between amino acids in a chain of 150 would be about one chance in 10 to the 90th. Moreover, in order to create a functioning protein the “amino acids, like letters in a meaningful sentence, must link up in functionally specified sequential arrangements.” It turns out that the probability for this is about one in 10 to the 74th. Thus, the probability of one functional protein of 150 amino acids forming by random chance is (1 in) 10 to the 164th. If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power.
    http://www.spectrummagazine.or.....ature_cell

    as you can see 382 and 482 is a far cry from 1984,, thus why the discrepancy?

  190. The first important point is that about half of the domain information was already present at OOL (or at least, at the level of LUCA, if you believe in a pre-LUCA life):

    There would be three billion years or so between OOL and the rise of metazoans. Is there some doubt about this?

  191. gpuccio, thanks for the background info

  192. Petruska asks:

    “There would be three billion years or so between OOL and the rise of metazoans. Is there some doubt about this?”

    The only doubt Petruska is in neo-Darwinians to account for the origination of even one protein domain.

  193. ,,, given all the time in the universe

  194. Petruska, neither you nor anyone else has a firm clue where the information for body plan morphogenesis resides. For you to pretend it resides in genes and leave it at that as if you have established your point and ignore the evidence I presented shows that you do not really want to know what the truth is.

    Aside from what is coming out of ongoing evo-devo research, do you have some additional facts and evidence?

    (sorry about my formatting. I have mistyped the blockquote tag on a couple of posts.)

  195. The only doubt Petruska is in neo-Darwinians to account for the origination of even one protein domain.

    I can’t do that, but it appears the argument has moved from the discussion of whether mammals are related by descent, back to origin of life issues.

    My original argument, the one that seems to have started down this path, was that compared to these early metabolic inventions, metazoans have been relatively uncreative.

    I believe my phrase was that microbes have done most of the evolutionary heavy lifting.

    Consistent with their numbers, their rate of reproduction, and their additional billions of years.

    As for the first replicator, I have no information. I would guess, however, that we will continue to synthesize and study very simple replicators.

  196. Petruska you ask:

    “do you have some additional facts and evidence?”

    Let’s see, extensive mutation studies to the DNA of micro-organisms and fruit flies that show ZERO ability to effect morphogenesis, and in the field studies of Malaria and HIV that also show ZERO ability to generate even trivial algorithmic functional complexity in population sizes that easily exceed all the populations of all mammals that have ever lived on earth, is as the evidence currently sits on this post. and You have presented zero evidence that neo-Darwinian evolution can produce even one protein, but instead of noticing this glaring defect in your evidential basis you want “more evidence” from me as if you have presented anything worth considering. Well OK petruska let’s pretend that you have a rational basis to work from and let’s go back as far in time and see what we can:

    Odd Geometry of Bacteria May Provide New Way to Study Earth’s Oldest Fossils – May 2010
    Excerpt: Known as stromatolites, the layered rock formations are considered to be the oldest fossils on Earth.,,,That the spacing pattern corresponds to the mats’ metabolic period — and is also seen in ancient rocks — shows that the same basic physical processes of diffusion and competition seen today were happening billions of years ago,,,
    http://www.sciencedaily.com/re.....152520.htm

    AMBER: THE LOOKING GLASS INTO THE PAST:
    Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms.
    http://bcb705.blogspot.com/200.....st_23.html

    Bacteria: Fossil Record – Ancient Compared to Modern – Picture
    http://www.ucmp.berkeley.edu/b.....riafr.html

    The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    and this:

    Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber
    Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart,(thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution’s “genetic drift” theory requires.)
    http://www.sciencemag.org/cgi/...../5213/1060

    30-Million-Year Sleep: Germ Is Declared Alive
    http://query.nytimes.com/gst/f.....gewanted=2

    In reply to a personal e-mail from myself, Dr. Cano commented on the “Fitness Test” I had asked him about:
    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.

    Is Antibiotic Resistance evidence for evolution? – “Fitness Test” – video
    http://www.metacafe.com/watch/3995248

    According to prevailing evolutionary dogma, there “HAS” to be “significant genetic/mutational drift” to the DNA of bacteria within 250 million years, even though the morphology (shape) of the bacteria can be expected to remain the same. In spite of their preconceived materialistic bias, scientists find there is no significant genetic drift from the ancient DNA. I find it interesting that the materialistic theory of evolution expects there to be a significant amount of mutational drift from the DNA of ancient bacteria to its modern descendants, while the morphology can be allowed to remain exactly the same with its descendants. Alas for the materialist once again, the hard evidence of ancient DNA has fell in line with the anthropic hypothesis.

    Petruska, we can also find that the ancient bacteria were not sitting around doing nothing for 3 billion years before the rise of metazoans, They were “terra-forming” the earth from a toxic wasteland into a place fit for habitation by higher lifeforms.

  197. I think I already pointed out that claims of DNA surviving more than a million years are regarded as due to contamination.

    As for DNA not affecting not affecting morphology, that’s just silly.

  198. bornagain77 #187:

    I have partially answered in #186. Moreover, those numbers of minimal protein repertoire (382, 482 etc) are referring to a reductionist calculation. Many of the simpler organisms are saprophytic, and would not represent well what LUCA was.

    Even so, considering a minimal number of 500 proteins in a very simple organism, and considering the mean of 2.33 domains per protein in the most ancient protein repertoire, we have anyway an higher theshold estimate of about 1200 domains, which is not so far from the estimate given by the other method.

    Obviously, LUCA was probably more complex than the simplest bacteria we observe now, because many bacterial species may have lost genetic information, instead of acquiring it. So, again I believe that data show that the original protein repertoire in the first living being was rich and complex.

  199. Petrushka:

    There would be three billion years or so between OOL and the rise of metazoans. Is there some doubt about this?

    Perhaps you have not read carefully the data I quoted. The statement in the paper was that hals of the domain information was present in LUCA, at the first node in evolution. Your 3 billion years came after that time, and nrought about a lower number of new domains.

    So, as LUCA is believed to have lived 3.5 – 3.8 billion years ago (according to wikipedia), and the age of the earth is estimated at 4.54 billion years (always according to wikipedia), and as there is general consensus that the first few hundred million years of the planet were not compatible with the start of life, that leave only a window pf about 100 – 300 My to generate the protein information of LUCA.

    After that, in the following 3 billion years, it seems that bacteria, for instance, “discovered” only 467 new protein domains. Don’t you think there is something to be explained here?

  200. petruska appeals to contamination,,, yet the evidence says:

    World’s Oldest Known DNA Discovered
    Excerpt: But the DNA was so similar to that of modern microbes that many scientists believed the samples had been contaminated.

    Not so this time around.

    A team of researchers led by Jong Soo Park of Dalhousie University in Halifax, Canada, found six segments of identical DNA that have never been seen before by science. Their work appears in the December issue of the journal Geobiology.

    “We went back and collected DNA sequences from all known halophilic bacteria and compared them to what we had,” Russell Vreeland of West Chester University in Pennsylvania said. “These six pieces were unique,,,
    http://news.discovery.com/eart.....vered.html

    Thanks again gpuccio.

  201. petruska incredulously states:

    “As for DNA not affecting not affecting morphology, that’s just silly.”

    I agree that DNA can affect morphology,, but all affects are found to be negative and none are found to be truly novel nor beneficial,,, the most popular example given by evolutionists, of a “beneficial” morphological change is the 4 winged fruit fly,,, yet when we look closer,,,,

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells

    Care to cite another example Petruska?

  202. Perhaps you have not read carefully the data I quoted. The statement in the paper was that hals of the domain information was present in LUCA, at the first node in evolution. Your 3 billion years came after that time, and nrought about a lower number of new domains.

    I didn’t see that in the article. We have zero information protein evolution in the first three billion years. And due to horizontal gene transfer, we are unlikely to be able to reconstruct it in any detail.

    At an rate, my point was that the invention (or creation, if you insist) of proteins and metabolic machinery is far more difficult and fundamental than gradual modifications of body plans, once metazoans exist.

    You seem to be agreeing with me.

  203. you know that whole horizontal gene transfer (HGT) thing Petruska? Could you please point to the literature demonstrating how the Bacteriophage, which is a major mechanism for what you are suggesting for massive HGT across kingdoms, originated?

    The Bacteriophage Virus – Assembly Of A Molecular (Lunar landing) Machine – Intelligent Design
    http://www.metacafe.com/watch/4023122

    The Bacteriophage Virus – A Molecular Lunar Landing Machine
    http://www.metacafe.com/watch/4205494

  204. Petrushka:

    Far from agreeing with you, I can’t even understand you any more!

    I didn’t see that in the article. We have zero information protein evolution in the first three billion years.

    Maybe I am tired, but can’t see what you mean here.

    And due to horizontal gene transfer, we are unlikely to be able to reconstruct it in any detail.

    So, due to HGT, all evolutionary biology is useless. That’s sad news for neo-darwinists…

    At an rate, my point was that the invention (or creation, if you insist) of proteins and metabolic machinery is far more difficult and fundamental than gradual modifications of body plans, once metazoans exist.

    Why creation? Invention is fine for me, and I have never insisted otherwise. Design is a fine word too, if you don’t insist…

    I don’t agree that the invention (or design) of proteins and metabolic machines is “far more difficult and fundamental than” anything which comes later. Fundamental it is, because it is the first level of design, and the following levels have to be based on that first level. So, it’s literally a “foundation”. But regarding the difficulty, I would not say that. We certainly know the difficulty of designing proteins (so much so, that we are still unable to do that). But as for designing body plans, not only we have no idea of how to do that, we also have no idea of how it is controlled or realized in what we observe in nature. Nothwithstanding all the evo-devo stuff, we really don’t know what generates, implements and controls body plans.

    And why do you speak of “gradual modifications of body plans, once metazoans exist”. First of all, as Belinski explains in that funny video, obtaining a whale from a cow could not be that simple. But my point is: don’t you want to consider how metazoan came to exist? After all, the cambrian explosion is not OOL. Darwin did not refuse to take that into consideration. Do you think that the ediacara and cambrian explosion are good examples of “gradual modifications of body plans”?

    In the end, while it is perfectly possible that I agree with you on something, please be more specific on that kind of statements, so that I can in case confirm or dissent.

  205. I agree that DNA can affect morphology,, but all affects are found to be negative and none are found to be truly novel nor beneficial

    It’s been tens of millions of years since the last mass extinction. I’d expect dramatically beneficial mutilations to be hard to come by.

    If you artificially jigger the selection criteria, you can get changes. Their benefit, however, is determined by those making the selection.

  206. Belinski explains in that funny video, obtaining a whale from a cow could not be that simple.

    I have trouble understind why that would be considered funny.

    No on has seriously suggested that whales evolved from cows or that they could.

    It’s likely that even if you started with an ancestor of whales you would not see it evolve into a whale. Too many contingencies.

    But stepwise modification of things like bone length is common. Many morphological features are like that.

  207. World’s Oldest Known DNA Discovered
    Excerpt: But the DNA was so similar to that of modern microbes that many scientists believed the samples had been contaminated.

    Not so this time around.

    Interesting development, but this time around it doesn’t support the claim that the organisms are unchanged.

    But it’s interesting.

  208. Petruska you state:

    “It’s been tens of millions of years since the last mass extinction. I’d expect dramatically beneficial mutilations to be hard to come by.”

    Actually mutilations are easy to come by just ask the 3% of human babies born with birth defects caused by the onslaught of Genetic Entropy:

    Evolution Vs Genetic Entropy
    http://www.metacafe.com/watch/4028086

    “Most babies are born healthy. In fact, 96 to 97 out of every 100 babies born are born healthy. About three or four out of every 100 babies born, however, have some type of birth defect.”
    http://genetics.emory.edu/docs.....efects.PDF

    the evidence for the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders.

    Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57 By John C. Avise
    Excerpt: “Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Humans.”

    I went to the mutation database website cited by John Avise and found:

    HGMD®: Now celebrating our 100,000 mutation milestone!
    http://www.biobase-internation.....mddatabase

    I really question their use of the word “celebrating”.

    (Of Note: The number for Mendelian Genetic Disorders is quoted to be over 6000 by geneticist John Sanford in 2010)

    “Mutations” by Dr. Gary Parker
    Excerpt: human beings are now subject to over 3500 mutational disorders. (this 3500 figure is cited from the late 1980′s)
    http://www.answersingenesis.or.....ations.asp

    Human Evolution or Human Genetic Entropy? – Dr. John Sanford – video
    http://www.metacafe.com/w/4585582

    This following study confirmed the “detrimental” mutation rate for humans per generation, of 100 to 300, estimated by John Sanford in his book “Genetic Entropy” in 2005:

    Human mutation rate revealed: August 2009
    Every time human DNA is passed from one generation to the next it accumulates 100–200 new mutations, according to a DNA-sequencing analysis of the Y chromosome. (Of note: this number is derived after “compensatory mutations”)
    http://www.nature.com/news/200.....9.864.html

    This mutation rate of 100 to 200 is far greater than even what evolutionists agree is an acceptable mutation rate for an organism:

    Beyond A ‘Speed Limit’ On Mutations, Species Risk Extinction
    Excerpt: Shakhnovich’s group found that for most organisms, including viruses and bacteria, an organism’s rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material.
    http://www.sciencedaily.com/re.....172753.htm

    What is funny Petruska is if you actually meant mutations instead of mutilations, then you are proposing that nothing we can find is demonstrating evolution right now because evolution has “topped out”. which is simply ludicrous to say!!! Have bacteria, or any other microorganisms, hit a brick wall that prevents them from becoming metazoans? Of course not!!! For you to suggest that they have just because you can present ZERO evidence for evolution is an shallow excuse not a solid reason. My question is “Why do you do this?” I surely don’t think You are that dumb as to actually believe the lies you spout, so why the grand facade? Of What possible payoff is it for you to fight against the God who created you?

  209. Petruska you state:

    “but this time around it doesn’t support the claim that the organisms are unchanged.” (I never said completely unchanged, I said the bacteria change in accordance with Genetic Entropy, which means a loss of molecular complexity)

    Actually Petruska if you want to get into details it does support unchanged in the context of Genetic Entropy for it proves their methodology is correct and renders the contamination objection moot. The fact is that the ancient bacteria they tested are no longer found in modern environments.

    Haloarchaeal diversity in 23, 121 and 419 MYA salts
    Older crystals contained unclassified groups and Halobacterium.,, The DNA demonstrates that unknown haloarchaea and the Halobacterium were key components in ancient hypersaline environments.,,,
    http://www3.interscience.wiley.....0/abstract

    Thus you have loss of a lineage(s) of bacteria that dated to 419 mya as well as corroborating confirmation that the 250 mya and 45 mya and 30 mya test are correct. Either way you want to take it Petruska you lose!

  210. Actually mutilations are easy to come by just ask the 3% of human babies born with birth defects caused by the onslaught of Genetic Entropy:

    Or the 10 to 50 percent of fetuses that miscarry (depending on the age of the mother). Or the hundreds of millions of sperm that are visibly malformed, and the vast majority of apparently healthy sperm that never fertilize an egg.

    Despite all this wastage, the population grows.

    Hundreds of notable species have gone extinct in historical times. Can you name one that went extinct due to infertility?

  211. Have bacteria, or any other microorganisms, hit a brick wall that prevents them from becoming metazoans?

    Only an ecosystem full of predators that have been engaging in an arms race for hundreds of millions of years.

  212. Petruska asks:

    Hundreds of notable species have gone extinct in historical times. Can you name one that went extinct due to infertility?

    Actually petruska Genetic entropy is the primary candidate to explain the mysterious “background extinction rate”;

    The Current Mass Extinction
    Excerpt:The background level of extinction known from the fossil record is about one species per million species per year, or between 10 and 100 species per year (counting all organisms such as insects, bacteria, and fungi, not just the large vertebrates we are most familiar with). In contrast, estimates based on the rate at which the area of tropical forests is being reduced, and their large numbers of specialized species, are that we may now be losing 27,000 species per year to extinction from those habitats alone. The typical rate of extinction differs for different groups of organisms. Mammals, for instance, have an average species “lifespan” from origination to extinction of about 1 million years, although some species persist for as long as 10 million years.
    http://www.pbs.org/wgbh/evolut.....32_04.html

    And Yes the species have a overall stable fossil record for as long as they persist in the fossil record before they go extinct:

    Ancient Fossils That Evolutionists Don’t Want You To See – video
    http://www.youtube.com/watch?v=jzFPhRzhMGs

    THE FOSSILS IN THE CREATION MUSEUM – 1000′s of pictures of ancient “living” fossils that have not changed in millions of years:
    http://www.fossil-museum.com/f.....8;limit=30

    as well petruska accelerated mutation rates were used here to push viruses “over the brink”:

    GM Crops May Face Genetic Meltdown
    Excerpt: Error catastrophe occurs when high mutation rates give rise to so many deleterious mutations that they make the population go extinct. For example, foot and mouth disease virus treated with mutagens (base analogues fluorouracil and azacytidine) eventually become extinct [1]. Polio virus treated with the mutagenic drug ribavirin similarly went extinct [2].
    http://www.i-sis.org.uk/meltdown.php

    Petruska for you to say that bacteria are limited in their ability to evolve because of a prolonged arms race (survival of the fittest) is a pathetic excuse not a scientific reason and in fact according to you reasoning, increased selection pressure should drive bacteria to greater heights of complexity. Thus again I ask, why do you act like you are being reasonable when you clearly are not?

  213. Petruska, please provide evidence that your philosophical basis (materialism) is true.

  214. Petrushka:

    I have trouble understind why that would be considered funny.

    Belrinski is funny. Intelligent amd funny. If we don’t agree on that, there is no hope!

    Only an ecosystem full of predators that have been engaging in an arms race for hundreds of millions of years.

    Do I understand you well? Predators are preventing bacteria from evolving into metazoa? Could you elaborate on that, please? Are they eaten each time evolution makes a step in that sense?

  215. Actually petruska Genetic entropy is the primary candidate to explain the mysterious “background extinction rate”;

    I assume this means that despite numerous extinctions in historical times caused by human activities, you can’t name a species that went extinct due to infertility. Perhaps you could name a species whose population is declining due to infertility.

    I’m aware that some species have gone extinct after their populations were severely reduced. That can happen due to lots of different causes. I’m interested in cases where extinction happened in a stable ecosystem, due to genetic entropy.

    I take your question regarding materialism to be a subtle form of name calling. If I disagreed with Isaac Newton in arguing that the planets do not require constant supernatural corrections to remain in stable orbits, would that make me a philosophical materialist?

    Science has a long and productive history based on seeking regularity and consistency in phenomena. I see no reason to abandon the search for regularity. I do not wish to posit miracles beyond necessity.

  216. Petruska for you to say that bacteria are limited in their ability to evolve because of a prolonged arms race (survival of the fittest) is a pathetic excuse not a scientific reason and in fact according to you reasoning, increased selection pressure should drive bacteria to greater heights of complexity. Thus again I ask, why do you act like you are being reasonable when you clearly are not?

    Everything we know about evolution indicates that radiation and diversification is most common after a mass extinction. Dinosaurs and many reptilians after the Permian extinction; birds and Mammals after the extinction of dinosaurs.

    Could be predation, could be competition for food. At any rate, specialized organisms are better competitors. That’s pretty much what we mean by specialized.

  217. petruska you state:

    “I assume this means that despite numerous extinctions in historical times caused by human activities, you can’t name a species that went extinct due to infertility. Perhaps you could name a species whose population is declining due to infertility.”

    PROS AND CONS OF INBREEDING
    Excerpt: Another animal suffering from the effects of inbreeding is the Giant Panda. As with the wolf, this has led to poor fertility among Pandas and high infant mortality rates.
    http://www.dogbreedinfo.com/inbreeding.htm

    90% of Cheetahs born die with in the first 3 months, 50% of which are destroyed by predators. The other 40% fall victim to lack of genetic diversity. This is the second reason for their inability to survive. This genetic peril is responsible for weak and underdeveloped immune systems. Disease and illness attack a weak immune system, which in turn causes death. Most cubs do not even make it past 1 month old when this is the case.
    http://www.bigcatrescue.org/cats/wild/cheetah.htm

    My first question to you is can you name even one species that has originated since man has appeared? Shoot can you name even one protein that has originated? as well, do you ever provide any evidence whatsoever for your claims besides bald face assertions? You never address the evidence presented. The fact of the matter is that you have no scientific foundation in which to make any claims whatsoever for Darwinism yet you act as if all is well in Darwinland and continue to make outlandish claims.

    Darwinism’s Last Stand? – Jonathan Wells
    Excerpt: Despite the hype from Darwin’s followers, the evidence for his theory is underwhelming, at best. Natural selection – like artificial selection – can produce minor changes within existing species. But in the 150 years since the publication of Darwin’s Origin of Species by Means of Natural Selection, no one has ever observed the origin of a new species by natural selection – much less the origin of new organs and body plans. http://www.evolutionnews.org/2......html#more

    “The closest science has come to observing and recording actual speciation in animals is the work of Theodosius Dobzhansky in Drosophilia paulistorium fruit flies. But even here, only reproductive isolation, not a new species, appeared.”
    from page 32 “Acquiring Genomes” Lynn Margulis.

    Selection and Speciation: Why Darwinism Is False – Jonathan Wells:
    Excerpt: there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of twenty to thirty minutes, and populations achieved after eighteen hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another.”
    http://www.evolutionnews.org/2.....why_d.html

    The problem for you petruska is you have no source for novel functional algorithmic information:

    Mutation Studies, Videos, And Quotes
    http://docs.google.com/Doc?doc.....ZnM5M21mZg

    The foundational rule of Genetic Entropy for biology, which can draw its foundation in science from the twin pillars of the Second Law of Thermodynamics and from the Law of Conservation of Information (Dembski, Marks), can be stated something like this:

    “All beneficial adaptations away from a parent species for a sub-species, which increase fitness to a particular environment, will always come at a loss of the optimal functional information that was originally created in the parent species genome.”

    You got a huge problem petruska, natural selection reduces genetic information and you have no source to replace it!

    you also state this petruska:

    I take your question regarding materialism to be a subtle form of name calling. If I disagreed with Isaac Newton in arguing that the planets do not require constant supernatural corrections to remain in stable orbits, would that make me a philosophical materialist?

    Since you disagree with Newton, arguably the greatest scientist who ever lived, Do you care to provide a materialistic solution for Gravity?

    The Mathematical Anomaly Of Dark Matter – video
    http://www.metacafe.com/watch/4133609

    Dark matter halo
    Excerpt: The dark matter halo is the single largest part of the Milky Way Galaxy as it covers the space between 100,000 light-years to 300,000 light-years from the galactic center. It is also the most mysterious part of the Galaxy. It is now believed that about 95% of the Galaxy is composed of dark matter, a type of matter that does not seem to interact with the rest of the Galaxy’s matter and energy in any way except through gravity. The dark matter halo is the location of nearly all of the Milky Way Galaxy’s dark matter, which is more than ten times as much mass as all of the visible stars, gas, and dust in the rest of the Galaxy.
    http://en.wikipedia.org/wiki/Dark_matter_halo

    Hubble Finds Ring of Dark Matter – video
    http://www.metacafe.com/watch/4133618

    The Elusive “non-Material” Foundation For Gravity:
    http://docs.google.com/View?id=dc8z67wz_38d7zmrn9v

  218. Petruska you state:

    “Science has a long and productive history based on seeking regularity and consistency in phenomena. I see no reason to abandon the search for regularity. I do not wish to posit miracles beyond necessity.”

    The fact is that there is a regularity, or order, imposed on creation which is a miracle in and of itself. And is what drove the Christian Theistic founders of modern science in that they were convinced that there was a rational “regularity of the universe” to be discovered that had been placed there by the “rational” mind of God. Whereas atheist, who are notoriously absent from the hall of fame for the founders of science, presuppose that at the basis of reality is merely chaos and chance with no mind to order it. Please tell me which group is more apt to make discoveries into the hidden order of things petruska?

    Mathematics is the language with which God has written the universe.
    Galileo Galilei

    The Unreasonable Effectiveness of Mathematics in the Natural Sciences – Eugene Wigner
    Excerpt: The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve. We should be grateful for it and hope that it will remain valid in future research and that it will extend, for better or for worse, to our pleasure, even though perhaps also to our bafflement, to wide branches of learning.
    http://www.dartmouth.edu/~matc.....igner.html

    How can it be that mathematics, being after all a product of human thought which is independent of experience, is so admirably appropriate to the objects of reality? — Albert Einstein

    “… if nature is really structured with a mathematical language and mathematics invented by man can manage to understand it, this demonstrates something extraordinary. The objective structure of the universe and the intellectual structure of the human being coincide.” – Pope Benedict XVI

  219. My first question to you is can you name even one species that has originated since man has appeared?

    I haven’t made any claims along those lines. You have made claims, and I asked you to support them.

    Out of all the species that have gone extinct in human history, can you name one that did so because of reduced fertility, rather than because of predation or loss of habitat?

    How about a species that is declining due to genetic entropy and loss of fertility?

    ID supporters seem to like engineering metaphors. Have you ever heard of negative feedback used to reduce distortion in amplifiers? It reduces amplification, but keeps the signal pure.

    Most species have far more offspring than survive to reproduce. Selection reduces the number of offspring, but also reduces the distortion of mutation. If it does not change, it guarantees compensating changes.

    Simple engineering.

  220. I suppose it’s worth mention that evolution is not regarded as a process that exists “in order to” produce new species.

    Evolution is a term denoting the observed phenomenon, descent with modification. This occurs even if there is no easily observed change in the appearance of species. It occurs even if there is no visible branching.

  221. Petruska,
    Believe what you want you will anyway. You have clearly been shown that you have no mechanism to generate functional algorithmic information by material processes, especially by kairosfocus, and you have not countered this evidence with any evidence at all, save for what you have imagined should be true. Yet just by you posting you have demonstrated, repeatedly, that intelligence can and does generate functional information. It is clear as day that this is as reality is constructed and yet you refuse to see the futility of your position. Thus since it is pointless to debate with someone who refuses to reason within the bounds of scientific inquiry, I will resign from trying any longer.

    http://docs.google.com/Doc?doc.....#038;hl=en

    Stephen C. Meyer – The Scientific Basis For Intelligent Design – video
    http://www.metacafe.com/watch/4104651

  222. 222

    Petrushka,

    No on has seriously suggested that whales evolved from cows or that they could.

    If not a cow, then something like a cow, a four-legged land-dwelling creature, has most certainly been seriously suggested, and not just suggested, but outright asserted.

  223. @bornagain + everyone else:

    -”My first question to you is can you name even one species that has originated since man has appeared? Shoot can you name even one protein that has originated? as well, do you ever provide any evidence whatsoever for your claims besides bald face assertions? ”

    I actually went on a biology forum recently and asked a similar question. Specifically I asked if we have any documented cases for macroevolution.

    The two main answers I got were chichlid fish and was given the link: http://www.newscientist.com/ar.....speed.html

    I was also referred to:
    http://www.talkorigins.org/faq.....ation.html
    for instances of speciation.

    I wanted to hear people’s opinions in regards to how valid these examples are in providing support for macroevolution.

    In addition to the opinion for the above examples I also wanted to pose the following question:
    Is speciation alone evidence to support macroevolution? It seems to me that in the case of the chichlid fish the main differentiator is the inability to interbreed as explain by on poster. Is that alone evidence enough to extrapolate the notion of going from cow to whale for example?

  224. Above, I’ve was hit with the cichlid example to and then I ran across this video:

    Cichlid Fish – Evolution or Variation Within Kind? – Dr. Arthur Jones – video
    http://www.metacafe.com/watch/4036852

    This following study is evidence of the “limited and rapid variation from a parent kind” predicted by the Genetic Entropy model using cichlid:

    African cichlid fish: a model system in adaptive radiation research:
    “The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory(of evolution).—-surprising implication of the study?—- the propensity to radiate was significantly higher in lineages whose precursors emerged from more ancient adaptive radiations than in other lineages”
    http://www.pubmedcentral.nih.g.....d=16846905

    More evidence for rapid radiations from a parent species can be found here:

    Biological Variation – Cornelius Hunter
    Excerpt: One hint that biology would not cooperate with Darwin’s theory came from the many examples of rapidly adapting populations. What evolutionists thought would require thousands or millions of years has been observed in laboratories and in the field, in an evolutionary blink of an eye. http://www.darwinspredictions......_variation

    Materialists may have trouble explaining such evidence for “robust and rapidly adapting genomes” from ancient parent lineages, but Genetic Entropy holds ancient parent lineages will always have a more robust genome than their sub-species. This is readily demonstrated by the rampant problems of inbreeding among “sub-species”, witnessed throughout animal husbandry.

    In fact Above all sub-speciation events which led to reproductive isolation are the result of the loss of genetic information. Thus staying within the overriding principle of Genetic Entropy. Evolutionists will always try to sell you on a limited variation within a kind and never let you “look under the hood” to see that actually is taking place. The fact is that there is no unlimited variation as evolutionists would like you to believe;

    “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.” R. Milner, Encyclopedia of Evolution (1990)

    Evolution? – The Deception Of Unlimited Variation – video
    http://www.metacafe.com/watch/4113898

    The following study shows Genetic Entropy being obeyed in humans:

    “We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.” Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.-

    I wonder what Hitler would have thought of that study?

    all the evidence turns out the same above. It all boils down to the fact that evolutionists have no way to generate information thus all radiations away from a parent species will always come at a loss of information.

  225. 225

    Petrushka,

    Evolution is a term denoting the observed phenomenon, descent with modification.

    That word means whatever any evolutionist wants it to mean anymore, i.e. descent with modification, micro, macro, change in allele frequencies, random variation, natural selection, lateral, horizontal or vertical genetic drift, genetic sifting, Thomas Malthus’s myth of competition for resources, differential inheritance, redistribution of wealth, convergence, deletion, insertion, Darwinism, and a hundred other words that have no meaning, in reality, within the context of “evolution”.

  226. Clive, please explain how competition for resources is a “myth”. It seems very clear that very few environment, if any, have abundant enough resources that all organisms in that environment have adequate resources without having to compete for them.

    So what about this is a “myth”?

  227. Believe what you want you will anyway. You have clearly been shown that you have no mechanism to generate functional algorithmic information by material processes…

    I’m a bit confused about how you quantify FAI. What units ins it measured in and can you give me an example of a measurement?

    Under what circumstances would a point mutation change the quantity of FAI? Does anyone else use this unit?

  228. Good luck, Petrushka – no one here has ever answered that, or any similar, question about a biological entity. Maybe Clive will surprise us, though.

  229. If not a cow, then something like a cow, a four-legged land-dwelling creature, has most certainly been seriously suggested, and not just suggested, but outright asserted.

    The phrase “land dwelling” covers a lot of territory, but alas, not cows.

    We’re really acquiring a good collection of fossils covering the transition to whales.

    http://en.wikipedia.org/wiki/E....._cetaceans

  230. Petrushka,

    Selection reduces the number of offspring, but also reduces the distortion of mutation. If it does not change, it guarantees compensating changes.

    “Selection” is nothing but a name for the fact that offspring differ in how many offspring they generate. It’s an outcome, not a process, no matter that guys like Lewontin have modeled it as an operator.

    There is no guarantee of compensating change. Almost all species that have ever existed have gone extinct. Under the theory of genetic entropy, a designer or designers must be revisiting Earth after mass extinctions to add genetic information for many new species.

  231. —Clive Hayden: “That word means whatever any evolutionist wants it to mean anymore, i.e. descent with modification, micro, macro, change in allele frequencies, random variation, natural selection, lateral, horizontal or vertical genetic drift, genetic sifting, Thomas Malthus’s myth of competition for resources, differential inheritance, redistribution of wealth, convergence, deletion, insertion, Darwinism, and a hundred other words that have no meaning, in reality, within the context of “evolution”.

    —Aleta: Clive, please explain how competition for resources is a “myth”.

    This is a perfect example of the daily Darwinist diversion [a little alliteration there]

    Responding to Petrushka’s attempt at “strategic ambiguity,” Clive provides a dozen or more examples of the Darwinist proclivity to morph defintions and terms as a means of avoiding debate. Aleta completely ignores the thematic context and promptly demands to know why the Malthus’ myth is a myth.

    This is typical.

  232. However, I’m still interested in whatever answer Clive may have to my question.

  233. That word means whatever any evolutionist wants it to mean anymore, i.e. descent with modification, micro, macro, change in allele frequencies…

    You might note that in my post, I narrowed it to descent with modification.

    I believe that is the common way to disambiguate a term that has many possible meanings.

  234. All complex theories have multiple component parts. Clive’s complaint that there are a lot of words that describe different aspects of that theory, and that therefore the word evolution is meaningless, is sophomoric. Almost every one of the terms Clive mentions (except Malthus’ myth and the part about re-distribution of wealth – how did that get in there?) are useful terms that describe specific aspects of evolutionary theory.

  235. Oops, my apologies to Clive in 228 above. The quote Petruska was responding to was from bornagain, not Clive.

    So 228 should read:

    Good luck, Petrushka – no one here has ever answered that, or any similar, question about a biological entity. Maybe Bornagain will surprise us, though.

  236. 236

    157

    Zach Bailey

    05/31/2010

    6:13 am

    KF remarks:

    …islands of function…

    This paper suggests there may be more than a few additional islands of function that reduce the odds a bit!

    As this comment of mine was held in moderation and then finally appeared waaay up thread maybe it got overlooked. I am still interested in the ID response to the possibility that there are many roads to Rome. Evolutionary pathways are the ones that successful lineages happened on. They may not be the only ones. Sort of impinges on the “islands of function” argument.

  237. 237

    Aleta,

    All complex theories have multiple component parts. Clive’s complaint that there are a lot of words that describe different aspects of that theory, and that therefore the word evolution is meaningless, is sophomoric. Almost every one of the terms Clive mentions (except Malthus’ myth and the part about re-distribution of wealth – how did that get in there?) are useful terms that describe specific aspects of evolutionary theory.

    Petrushka claimed that evolution “was only” descent with modification. I showed that the word means and implies much more, to whoever wants it to mean much more. Descent with modification doesn’t mean “evolution” of the kind normally meant among evolutionists. It’s a catch-all, a room full of smoke, that changes anytime any evolutionist is pressed as to exactly what the word means. I made up “redistribution of wealth, because there are plenty of “economic” terms that would fit as well; the word “economics” as a theory of “anything money ever does” has as much explanatory power as “evolution” does, which is none. By wanting everything in biology to be explained by virtue of evolution, it becomes vacuous, you get a deadlock.

  238. Petrushka (227) and bornagain77 (221),

    I’m a bit confused about how you quantify FAI. What units ins it measured in and can you give me an example of a measurement?

    Under what circumstances would a point mutation change the quantity of FAI? Does anyone else use this unit?

    I’m interested in the answer to this question as well. I lurk here semi-regularly and haven’t heard of FAI before. Understanding the units in which it is measured and how it is calculated would help in assessing bornagain77′s argument.

  239. Cassandra (et al.):

    May be there is some confusion here about this supposed new entity (FAI). I paste here the phrase by bornagain77, and I will try to comment on that (bornagain if I am interpreting wrongly your thoughts, please correct me).

    You have clearly been shown that you have no mechanism to generate functional algorithmic information by material processes, especially by kairosfocus, and you have not countered this evidence with any evidence at all, save for what you have imagined should be true.

    Now, IMO what BA is saying here is: “you have no algorithmic mechanism to generate fucntionally specified complex information”, because FSCI can be generated only by a conscious agent.

    That’s exactly the point of ID. So, please let’s go back to the classical concept of FSCI, or if you prefer (I definitely do) to its subset of digital functionally specified complex information (from now on: dFSCI).

    I have recently posted about that in another thread, debating alsio its measure (so please, those who say that we never go quantitative about that, please read more carefully).

    I paste here some pertinent comments I posted elsewhere:

    “2) Consciousness and ID.

    I did not realize for a long time the importance given in ID to “consciousness”. Its hard to fathom how you believe that some process has to experience its environment the way people do (what else could “consciousness” mean) in order for it to create complex specified output. Even bodily organs do incredibly complex things, without having to sense or understand the world the way that you or I do.

    Of course consciousness in central in ID theory. ID is about detecting design in things. Design is a process which originates in conscious intelligent beings (the designers). ID affirms that designed objects are recognizable with certainty as such if they exhibit a specific property, CSI. CSI is the main idea in ID. It is objectively recognizable, and in the known world it is always the product of design by an intelligent conscious being (leaving apart biological information, which is the object of the discussion).

    A special subset of CSI, digital functionally specified complex information (or, if you want, dFSCI), is specially useful for the discussion. It is easily definable as any string of digital information with the following properties: complexity higher than 10^150 (that is, length of about 500 bits); non significant compressibility (it cannot be generated through laws of necessity from a simpler string); and a recognizable, objectively definable function.

    That definition is very strong and useful. According to that definition, dFSCI includes language, software and practically all relevant biological information (in particular, the sequences of protein coding genes and the primary sequences of proteins).

    It is easy to show that no example is known of dFSCI (apart from biological information, which is the object of the debate) whic does not originate from a cosncious intelligent being (humans). And our common experience is that consciousness and intelligence are exactly the faculties used by humans in producing dFSCI.

    Biological information is dFSCI (any functional protein is). That’s why ID, with very sound inference based on analogy, assumes that some conscious and intelligent designer is the origin of biological information.

    That is, very quickly, the main idea in ID. Neo-darwinism cannot explain the emergence of dFSCI in living beings. The work of a designer can.

    I would like to mention that dFSCI originates from conscious intelligent beings directly; ot indirectly, through some non conscious machine which has received from an intelligent conscious being the pertinent dFSCI. In other words, Hamlet is dFSCI. Hamlet can be outputted by a PC, but only if someone has inputted it in the software. No computing machine can create Hamlet (or anything equivalent).

    Specification, function and purpose are definable only in relation to consciousness. Only consciousness recognizes them actively. So, consciousness is central to ID. Without consciousness, no function can be recognized. With consciousness, function can be defined, recognized and measured. And function is the only relevant form of specification in biological information.

    To go to your examples, bodily organs do not output dFSCI, even if they do complex things. A mchine can do complex things according to the CSI which has been inputted in the machine, but it cannot generate new dFSCI. The human body as a whole can generate new dFSCI (speaking, writing, programming) only because it is an interface for a conscious intelligent being.

    3) Types of digital information.

    But complex meaningful sequences will not be found in monotonic strings, only in the amount of variation provided by randomness.

    We have three types of digital information:

    a) highly compressible strings, like monotonic strings. These are not dFSCI.

    b) truly random strings (high complexity, no functional specification). These are not dFSCI.

    c) pseudo-random strings, where a recognizable meaning is superimposed to the random structure by an intelligent designer (Hamlet, any software, any long discourse). And, obviouisly, any functional protein. These are dFSCI.

    About that, I would suggest that you read the following paper:

    Three subsets of sequence complexity and their relevance to biopolymeric information

    by David L Abel and Jack T Trevors

    available at the following URL:

    http://www.ncbi.nlm.nih.gov/pm…..MC1208958/”

    And, about its quantitative measure, another post of mine from another thread:

    “As this is a fundamental issue, I will try to be more clear.

    There is a general concept of CSI, which refers to any information which is complex enough (in the usual sense) and specified.

    Now, while I think that we can all agree on the concept of complexity, some problems appear as soon as we try to define specification.

    There is no doubt that specification can come in many forms: you can have compressibility, pre-specification, functional specification, and probably others. And, in a sense, any true specification, coupled to high complexity, is a mark of design, as Dembski’s work correctly affirms. But the problem is, some kinds of specifications are more difficult to define universally, and in some of them the complexity is more difficult to evaluate.

    Let’s take compressibility, for instance. In a sense, true compressibility which cannot be explained in any other way is a mark of design. Take a string of 1000 letters, all of which are “a”. You can explan it in two different ways:

    1) It is produced by a system which can only output the letter “a”:in other words, it is the product of necessity. No CSI here.

    2) It is the output of a truly random system which can output any letter with the same probability, but the intervention of a conscious agent has “forced” an output which would be extremely rare and which is readily recognizable to consciousness. The string is designed to be highly compressible.

    In any case, you can see that using the nconcept of compressibility as a sign of specification is not without meaning, but creates many interpretational problems.

    Or, take the example of analog specified information, like the classic Mount Rushmore example. The specification is very intuitive, but you have two problems:

    1) The boundary between true form and vague resemblance is difficult to quantify in analog realities.

    2) It is difficult to quantitavely evaluate the complexity of an analog information.

    For all these reasons, I have chosen to debate only a very specific subset of CSI, where all these difficulties are easily overcome. That subset is dFSCI. A few comments about this particular type of CSI:

    1) The specification has to be functional. In other words, the information is specified because it conveys the intructions for a specific function, one which can be recognized and defined and objectively measured as present or absent, if necessary using a quantitative threshold. It is interesting to onserve that the concept of functional specification is earlier than Dembski’s work.

    2) The information must be digital. Tha avoids all the problems with analo information, and allows an easy quantification of the search space and of the complexity.

    3) The information must not be significantly compressible: in other words, it cannot be the output of an algorithm based on the laws of necessity.

    4) If we want to be even more restrictive, I would say that the information must be symbolic. In other words, it has to be interpreted through a conventional code to convey its meaning.

    Now, in defining such a restricted subset of CSI, I am not doing anything arbitrary. I am only willfully restricting the discussion to a subset of objects which can be more easily analyzed. The discussion will be about these objects only, and any conclusion will be about these objects only. So, if we establish that objects exhibiting dFSCI are designed, I will not try to generalize that conclusion to any other type of CSI. Objects exhibiting analog specified information or compressible information can certainly be equally designed, but that’s not my problem, and others can discuss that.

    And do you know why it’s not my problem? Because my definition of that specific subset of CSI includes anything which interests me (and, I believe, all those who come to this blog). It includes all biological information in the genomes, and all linguistic information, and all software.

    That’s more than enough, for me, to go on in the discussion about ID.

    So, to answer explicitly your questions:

    1) The presence of CSI is a mark of design certainly under the definition I have given here (dFSCI), and possibly under different definitions. I am not trying here to diminish in any way the importance of other definitions, indeed I do believe them to be perfectly valid, but here I will take care only of mine.

    2) I have no doubt that, under my definition, there is no example known of CSI which is not either designed by humans or biological information. Nobody has ever been able to provide a single example which can falsify that statement. And yet even one example would do.

    3) CSI in the sense I have given is certainly an objective measure. The measure only requires:

    a) an objective definition of a function, and an objective way to ascertain it. For an enzyme, that will be a clear definition of the enzymatic activity in standard conditions, and a threshold for that activity. The specification value will be binary (1 if present, 0 if not).

    b) A computation of the minimal search space (for a protein of length n, that would be at least 20^n).

    c) A computation, or at least a reasonable approximation, of the number of specific functional sequences: in other words, the number of different protein sequences of maximum length n which exhibit the function under the above definitions.

    The negative logarithm of (c/b) * a will be the measure of the specified complexity. It should be higher than a conventional threshold (a universal threshold of 10^150 is fine, but a biological threshold can certainly be much lower).

    For a real, published computation of CSI in proteins in the above sense with a very reasonable method, please see:

    Measuring the functional sequence complexity of proteins.

    by Durston KK, Chiu DK, Abel DL, Trevors JT

    Theor Biol Med Model. 2007 Dec 6;4:47.

    freely available online at:

    http://www.ncbi.nlm.nih.gov/pm…..ool=pubmed”

    Finally, for those who ask about units, it should be obvious that the complexity is measure in a way which is similar to the way we measure Shannon’s entropy, in bits, with the difference that specification must be present (must have value 1), otherwise there is no functional complexity.

    I must say that I will be very happy to discuss in detail these topics (usually, when we arrive at this level, nobody answers). It is also true that I don’t know if we can really do that here, at post 240 of an old thread.

  240. It has now been demonstrated Irreducible Complexity can be mathematically quantified as functional information bits(Fits).

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – video
    http://www.metacafe.com/watch/3995236

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
    http://genetics.mgh.harvard.ed.....S_2007.pdf

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    Excerpt: To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on wish-fulfillment, we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it:
    Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    The DNA Code – Solid Scientific Proof Of Intelligent Design – Perry Marshall – video
    http://www.metacafe.com/watch/4060532

    i.e. show me just one example of material processes creating coded information.

  241. Zach Bailey (#237).

    This paper suggests there may be more than a few additional islands of function that reduce the odds a bit!

    As this comment of mine was held in moderation and then finally appeared waaay up thread maybe it got overlooked. I am still interested in the ID response to the possibility that there are many roads to Rome. Evolutionary pathways are the ones that successful lineages happened on. They may not be the only ones. Sort of impinges on the “islands of function” argument.

    Frankly, I read the paper you linked, and I don’t understand how it supports your point (if I have understood well your point). Would you like to elaborate and give some detail?

    The paper is very interesting. It supports th ID point that protein sequences are “pseudo random” functional sequences, practically non compressible, undistinguishable for truly random sequences unless you can recognize the function encoded. That’s exactly the ID point.

    I quote from the paper:

    Already Monod (1969) expressed that protein sequences are not structured by any rules. The
    results observed for all measures of complexity applied in this study give support to the notion of
    protein sequences as “slightly edited random sequences” expressed by Pande et al. (1994), White
    & Jacobs (1993), and others. To express this in numbers: proteins have approximately 99% of the complexity of random polypeptides with the same amino acid composition.

    I believe this is not an ID paper, but it makes exactly the fundamental point of ID about the nature of information in proteins. Please, note the concept of “slightly edited random sequences”.

    This is also a very good answers to all those who want to believe that protein sequences could be in some way the result of necessity.

  242. Just a correction: in my previous post, both the first and the second paragraph are quotes from Zach’s post. I put my tag in the wrong place, I apologize.

  243. Thanks for the clarity once again gpuccio

  244. I hope this isn’t too off topic… In an attempt to dumb down this discussion so I can understand it, I reproduce a quote from an investment newsletter I get on new technologies.

    “Efforts are under way to fully map the 100,000 neurons in a fly’s brain, as reported in April’s issue of Nature Biotechnology. Once completed, the fly brain’s “circuitry” could possibly be reverse engineered with memristive circuitry. This would help us to better understand animal intelligence, and hence be able to develop true artificial intelligence. If sufficiently advanced, such computing devices would be able to easily recognize and differentiate between human faces and understand natural human language.”

    My question. For something to be reverse engineered, wouldn’t it have to be engineered in the first place??

  245. tgpeeler:

    My question. For something to be reverse engineered, wouldn’t it have to be engineered in the first place??

    I suppose so. Obviously, darwinists could always argue that an ancient non conscious process (darwinian evolution), given enough time (maybe not too much) can be smarter than they are :)

    But seriously, I would not gold my breath waiting that reverse engineering a nervous structure can explain a lot of things. I give you just a few reasons for that opinion:

    1) I don’t believe that nervous systems, even of simple animals, work in a completely algorithmic way

    2) I don’t believe that the working of nervous systems can be explained only at the level of gross structure and neural connections. The most important work happens probably inside individual cells, and even at quantum level (as suggested by John Eccles and others).

    3) We have the example of the very simple animal C. elegans: its nervous system is made of only 302 neurons (out of 959 total cells in the adult hermaphrodyte). Those neurons are known in detail one by one, numbered, and all their connections have been mapped. But I don’t think we understand how that simple nercous sustem control the somewhat rich behavious of this tiny worm (movement, nutrition, reproduction, etc.), or that we can reverse engineer anything from those data.

    Remember that, before the human genome was sequenced, there were huge expectations about the great knowledge that such an accomplishment would have given us. Without diminishing in any way the importance of the work which has been done, we can however acknoweldge that those expectations were not literally satisfied…

    The truth is that analytic knowledge is precious, and must absolutely be pursued, but while a reductionist approach expects that all truth must come from that channel, a different approach (we may call it “holistic”, but I don’t like the word) understands the importance of information, of consciousness, of organization, of thought, of meaning, and of many other entities which are daily denied by reductionists.

  246. gpuccio

    I don’t have any expectations about what they will be able to figure out. I was just poking a stick in the naturalist/materialist eye! :-)

  247. @gpuccio

    The thing that the reductionist daily denies is what we call reality.

  248. tgpeeler:

    I was just poking a stick in the naturalist/materialist eye!

    Always glad to help :)

  249. 249

    Petrushka,

    The phrase “land dwelling” covers a lot of territory, but alas, not cows.

    Your link says that the earliest ancestor was a wolf with hooves, so something like a carnivorous cow, is indeed “suggested”. Of course, we know that this animal is not the earliest ancestor, according to common descent the earliest (living) ancestor was a single cell, and even earlier was a self-replicating molecule, and even earlier was a rock, and even earlier was space dust, and even earlier was absolutely nothing.

  250. above:

    Reductionism is IMO a sort of masochistic approach to knowledge. The reductionist says: “I will know only “this” and believe only in “this”, and I will fiercely fight against anything which could be greater or more complex or richer.” And even if you try to reassure him, even if you demonstrate in all possible ways that you don’t want to take “this” from him, because “this” is certainly true and sacred and important, but you just want to show him that “this” is part of something bigger, of something more beautiful, more meaningful, and there is no reason in the world to stick tenaciously to “this and nothing else”, still he defends his position as though he were threathened, as though he could lose some fundamental treasure.

    Really, there is nothing to lose, and all to be gained. But fear is fear, and it is the greatest enemy of truth.

  251. gpuccio

    Help always gratefully accepted!

  252. Clive:

    Let’s just stick to people with first names. I think “LUCA” is a fine guy to be discussed (it’s the italian form for Luke).

    And could someone please explain me why “land dwelling” does not refer to cows? Am I missing something?

  253. For something to be reverse engineered, wouldn’t it have to be engineered in the first place??

    That’s awfully close to equivocation.

    If we could figure out the history of a thing by attaching a label. science would be a lot easier.

    But I can ask a question just as annoying:

    If you want to say a fly’s brain looks engineered, wouldn’t you need to compare it to something that you know was engineered, something whose history you know from observation?.

  254. 254

    #253

    You mean like an IF/AND/OR logic gate on a schematic…or perhaps a rotor/stator assembly from a motor?

  255. I don’t think IF is a kind of logic gate, Upright ;)

  256. Actually the reductionists are up a creek to since if you want to follow a purely reductionists route you will end up with “information” as well:

    leading quantum physicist Anton Zeilinger has followed in John Archibald Wheeler’s footsteps (1911-2008) by insisting reality, at its most foundational level, is “information”.

    “It from bit symbolizes the idea that every item of the physical world has at bottom – at a very deep bottom, in most instances – an immaterial source and explanation; that which we call reality arises in the last analysis from the posing of yes-no questions and the registering of equipment-evoked responses; in short, that things physical are information-theoretic in origin.” John Archibald Wheeler

    Why the Quantum? It from Bit? A Participatory Universe?
    Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: “In the beginning was the Word.” Anton Zeilinger – a leading expert in quantum teleportation:
    http://www.metanexus.net/Magaz.....fault.aspx

    Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh
    Excerpt: In contrast to a classical bit, the description of a (photon) qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1) — Concept 2. is used by Bennett, et al. Recall that they infer that since an infinite amount of information is required to specify a (photon) qubit, an infinite amount of information must be transferred to teleport.
    http://www.cas.umt.edu/phil/fa.....lPSA2K.pdf

    Single photons to soak up data:
    Excerpt: the orbital angular momentum of a photon can take on an infinite number of values. Since a photon can also exist in a superposition of these states, it could – in principle – be encoded with an infinite amount of information.
    http://physicsworld.com/cws/article/news/7201

    Ultra-Dense Optical Storage – on One Photon
    Excerpt: Researchers at the University of Rochester have made an optics breakthrough that allows them to encode an entire image’s worth of data into a photon, slow the image down for storage, and then retrieve the image intact.
    http://www.physorg.com/news88439430.html

    This following experiment clearly shows information is not an “emergent property” of any solid material basis as is dogmatically asserted by some materialists:

    Converting Quantum Bits: Physicists Transfer Information Between Matter and Light
    Excerpt: A team of physicists at the Georgia Institute of Technology has taken a significant step toward the development of quantum communications systems by successfully transferring quantum information from two different groups of atoms onto a single photon.
    http://gtresearchnews.gatech.e.....mtrans.htm

    and if you really want to go full tilt reductionism then you end up with the “mind of God” which is causing this “infinite information” to collapse to a bit/it state:

    “As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter.”
    Max Planck – The Father Of Quantum Mechanics – (Of Note: Planck was a devout Christian, which is not surprising when you realize practically every founder of a major branch of modern science also had a deep Christian connection.)

  257. semi off topic but related to information:

    Many people, including myself, argue that the Bible itself is proof of God’s supernatural and personal involvement with man because it is “alive”:

    Hebrews 4:12
    For the word of God is living and active. Sharper than any double-edged sword, it penetrates even to dividing soul and spirit, joints and marrow; it judges the thoughts and attitudes of the heart.

    The Word Is Alive – Casting Crowns – music video
    http://www.youtube.com/watch?v=f3ucyoy7sbk

  258. You mean like an IF/AND/OR logic gate on a schematic…or perhaps a rotor/stator assembly from a motor?

    No, I mean something like a fly’s brain.

    The simple fact is that the only engineers we have observed in action have been human, and humans have yet to build anything architecturally like a brain.
    If they succeed, the architecture will be a copy of something that arose through some other process.

  259. 259

    “No, I mean something …”

    I didn’t think so. Making comparisons between observed biological reality and those things we already know were enginieered is not a particularly profitable discussion for a materialist.

    “The simple fact is that the only engineers we have observed in action have been human…”

    That is not even close to being true.

    “If they succeed, the architecture will be a copy of something that arose through some other process.”

    Checkmate then, even if indulgently asserted.

    - – - – - –

    As I already noted, where you are concerned, no evidence against materialism is sufficient, and no evidence for it is necessary.

  260. The circularity of logic in the following statement is staggering:

    -”The simple fact is that the only engineers we have observed in action have been human, and humans have yet to build anything architecturally like a brain.
    If they succeed, the architecture will be a copy of something that arose through some other process”

    Notice how via the use of the semantic ‘other process’, this poster limits the explanatory scope within the myopic perspective of materialistic mechanism. Thus we see her assumption now pretend to be the explanation.

  261. There are certainly non-human builders, but engineers do not simply follow repetitive steps.

  262. Your link says that the earliest ancestor was a wolf with hooves, so something like a carnivorous cow

    It doesn’t say that at all.

    The traditional theory of cetacean evolution was that whales were related to the mesonychids, an extinct order of carnivorous ungulates (hoofed animals), which looked rather like wolves with hooves and were a sister group of artiodactyls. These animals possessed unusual triangular teeth that are similar to those of whales. For this reason, scientists had long believed that whales evolved from a form of mesonychid; however more recent molecular phylogeny data suggest that whales are more closely related to the artiodactyls, specifically the hippopotamus

    http://en.wikipedia.org/wiki/E....._ancestors

  263. Petrushka:

    Briefly:

    The simple fact is that the only engineers we have observed in action have been human

    the problem is that the property of humans which is connected to engineering is their being conscious and intelligent. So we associate engineering to being conscious and intelligent. And we have no right to assume that humans are the only conscious intelligent beings in reality. That’s why aliens are a valid candidate as designers, as Dawkins himself admits. That’s why a concious intelligent god is a valid candidate as designer, as Dawkins himself admits.

    Must I remind you that the existence of a conscious intelligent god has been considered a valid hypothesis in human thought for millennia?

    however more recent molecular phylogeny data suggest that whales are more closely related to the artiodactyls, specifically the hippopotamus

    So, it was a hippopotamus, and not a cow or a wolf… Staggering! So, if Berlinski had made his video about how to change a hippopotamus into a whale, you would have found it funny, I believe?

  264. 265

    “There are certainly non-human builders, but engineers do not simply follow repetitive steps.”

    Neither do spiders, nor beavers, nor …

    When you want to argue that they do, then humans follow repetitive steps as well.

    Give it a rest.

  265. So, it was a hippopotamus,

    Again, no.

  266. And we have no right to assume that humans are the only conscious intelligent beings in reality.

    Rights are irrelevant. When we assert that an object found in an archeological site is designed and made by humans, it is because we have observed humans making similar objects.

    The closest thing we have to seeing animals being designed is observing animal breeders using selection.

    If and when silicon brains are built, the final, critical wiring that makes them able to do useful things like recognize faces or human speech will be some form of trial and error learning — variation and selection.

  267. -”If and when silicon brains are built”

    It’s not like the brains are going to build themselves now are they?

    Humans will design them. That pretty much nullifies your argument.

  268. It’s not like the brains are going to build themselves now are they?

    Maybe not the first generation.

  269. Petrushka:

    So, it was a hippopotamus,

    Again, no.

    My compliments for your stubborness. You are really something…

    Rights are irrelevant. When we assert that an object found in an archeological site is designed and made by humans, it is because we have observed humans making similar objects.

    Maybe you assert that for that reason. I assert that because I can design things, and know that intelligent conscious processes are implicated, and understand that some features of designed things can only come from that kind of processes.

    Maybe not the first generation.

    Maybe not even the last. Your ability to shift from blind reductionism to blind faith is really remarkable. When have we observed silicon brains designing themselves?

    But, after all, maybe blind reductionism and blind faith are just the same thing.

  270. @gpuccio

    Actually they are the same thing. There is a book out by the atheist philosopher Quine called the “two dogmas of empiricism”. In it he refers to reductionism as a “metaphysical article of faith”.

  271. 272

    G Puccio

    I would love to elaborate but the result of moderated comments being eventually released with their original post numbers makes reasonable discourse impossible. May I request Clive consider lifting moderation.

  272. Cassandra, Aleta et al:

    In my post 239 I have answered in some detail to your request about quantification of functional information. BA and KF have given similar concepts in other posts. Would you like to comment on these things?

    I concluded my post as follows:

    I must say that I will be very happy to discuss in detail these topics (usually, when we arrive at this level, nobody answers).

    As I hate to be always right (not good for control of the ego :) ), I hope this time I can get some feedback from you, who seemed specially interested in the subject, and worried that “nobody” would address it…

  273. gpuccio writes, “I must say that I will be very happy to discuss in detail these topics (usually, when we arrive at this level, nobody answers)”

    I, and many others more knowledgeable than me (some of who are banned – hard to answer when you can’t post), have repeatedly pointed out the flaws in all these definitions of whatever acronym is currently in vogue about complex specified information. The fact that you don’t agree with the answer doesn’t mean that people haven’t answered.

    Let me point out the flaw again.

    You write, “It is easily definable as any string of digital information with the following properties: complexity higher than 10^150 (that is, length of about 500 bits); non significant compressibility (it cannot be generated through laws of necessity from a simpler string); and a recognizable, objectively definable function.” [my emphasis]

    All calculations of CSI et al are simple probability calculations that all the component parts of whatever is being considered came together simultaneously and entirely by chance. They do not take into consideration any causal chain of events that could have brought the thing under consideration into existence through a set of steps.

    Since no one believes that anything happens by a whole bunch of parts just coming to together by chance, such calculations of CSI are irrelevant: they eliminate a hypothesis (pure chance) that no one thinks happened anyway.

    That’s the answer that you don’t want to accept.

  274. WRT design, how can we determine whether a bird’s nest was intelligently designed by a bird – or a human?

    In other words, don’t we need objective criteria for determining the level/amount of intelligence required for various designs?

  275. Aleta you state:

    “They do not take into consideration any causal chain of events that could have brought the thing under consideration into existence through a set of steps.”

    Do you care to point out where Dr. Axe has failed to consider “climbing mount improbable” Aleta?

    Evolution vs. Functional Proteins (Mt. Improbable) – Doug Axe – Video
    http://www.metacafe.com/watch/4018222

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723

    further notes:

    In the year 2000 IBM announced the development of a new super-computer, called Blue Gene, which was 500 times faster than any supercomputer built up until that time. It took 4-5 years to build. Blue Gene stands about six feet high, and occupies a floor space of 40 feet by 40 feet. It cost $100 million to build. It was built specifically to better enable computer simulations of molecular biology. The computer performs one quadrillion (one million billion) computations per second. Despite its speed, it was estimated to take one entire year for it to analyze the mechanism by which JUST ONE “simple” protein will fold onto itself from its one-dimensional starting point to its final three-dimensional shape.

    “Blue Gene’s final product, due in four or five years, will be able to “fold” a protein made of 300 amino acids, but that job will take an entire year of full-time computing.” Paul Horn, senior vice president of IBM research, September 21, 2000
    http://www.news.com/2100-1001-233954.html

    “SimCell,” anyone?
    “Unfortunately, Schulten’s team won’t be able to observe virtual protein synthesis in action. Even the fastest supercomputers can only depict such atomic complexity for a few dozen nanoseconds.” – cool cellular animation videos on the site

    Networking a few hundred thousand computers together has reduced the time to a few weeks for simulating the folding of a single protein molecule:

    A Few Hundred Thousand Computers vs. A Single Protein Molecule – video
    http://www.metacafe.com/watch/4018233

  276. 277

    Cabal, instead of sidetracking into satisfying irrelevance, why not ask a fundamental question.

    How do we know a nest was not built by the wind?

  277. Bornagain, I do not watch your videos. If you personally have something to say, say it.

  278. At the risk of oversimplifying… The only objective criteria needed is the existence of information. Information requires the existence of a code (language) and a code can never be explained within a naturalist ontology that, by definition, relies solely on physical laws to explain everything. The mistake is glaringly obvious. Since physics is good at explaining material things then that must mean only material things exist. Hardly.
    The only thing in human history, on this planet, in this universe, that has ever explained a code is intelligence. Or, as some would say, a designer. I am continually mystified by people who cannot or will not see this. It really is interesting to see the lengths to which some people will go to deny the elephant in the room. Or to claim that indeed, the emperor is wearing a brand new spiffy set of clothes.

  279. Aleta: do you not read peer review either, you know the ones directly under the videos you didn’t watch?

  280. gpuccio (272),

    In my post 239 I have answered in some detail to your request about quantification of functional information. BA and KF have given similar concepts in other posts. Would you like to comment on these things?

    Thanks for the detailed response. Could you please point out the specific posts on the other threads where you provided a detailed mathematical definition of FAI or FSCI and where you have calculated this quantity for a real biological system of some sort?

    With this information, we can perhaps answer Petrushka’s question in 227:

    Under what circumstances would a point mutation change the quantity of FAI?

    I would also be interested in your response to Aleta’s 273 which identifies a significant problem with your definition from 239:

    b) A computation of the minimal search space (for a protein of length n, that would be at least 20^n).

  281. “Thanks for the detailed response. Could you please point out the specific posts on the other threads where you provided a detailed mathematical definition of FAI or FSCI and where you have calculated this quantity for a real biological system of some sort?”

    At the risk of oversimplifying, again, the KEY point is the existence of a CODE. If a code is present then so is design/intelligence. Why? Because there are NO naturalist/materialist explanations for a code.

    If I am wrong, if there is a code somewhere, anywhere, that can be explained by means of natural laws, then simply point it out and I will shut up. That should be motivation enough, I would think.

  282. tgpeeler (281),

    If a code is present then so is design/intelligence. Why? Because there are NO naturalist/materialist explanations for a code.

    You seem to be assuming your conclusion by saying that codes are only the result of intelligent design. If you define “code” in that way then your conclusion is trivially true but irrelevant to what we observe in DNA.

    If I am wrong, if there is a code somewhere, anywhere, that can be explained by means of natural laws, then simply point it out

    You seem to be asserting that DNA is a code that cannot be explained by means of natural laws, but that’s exactly the question under consideration. When we look at the internals of a cell, we see normal (bio)chemistry in action. You can model the nucleotides as a code, but what’s really happening is chemical reactions and physics. That’s as natural as it gets.

  283. Cassandra is exactly right. tgpeeler assumes the conclusion.

    And, he writes, “At the risk of oversimplifying, …”

    Yes, vastly oversimplifying.

  284. But aleta seems to so eager to ignore the blatant circularity of logic exibited by cassandra as indicated above by myself and others.

  285. ps. kairosfocus has repeatedly refuted the objections presented by cassandra. At some point it get’s rather boring to say and hear the same old stuff over and over again.

  286. Cassandra accuses Peeler of circular reasoning in #282, and then turns right around and begs the question in regard to the source of DNA code.

    The item on the table is the source of DNA’s coded information, and there are two explanatory paradigms in competition:

    1) Coded information is the result of known or unknown natural laws. If known, these laws should be demonstrated. If unknown, they are scientifically invalid until discovered.

    2) Coded information is the result of active input by an intelligent agent.

    There are two ways to confirm explanation #1: a) demonstrate/elucidate the laws which govern the spontaneous formation of coded information — absent intelligent input; b) Prove empirically that intelligence is purely the result of natural law.

    Explanation #2 has empirical support already: coded information is the result of intelligent intervention, and no known laws exist which can explain its spontaneous generation.

    Anyone is welcome to exercise faith in regard to finding a natural law, independent of agency, which governs/explains coded information. However until such faith is confirmed by hard evidence, design remains the best explanation for the presence of coded information.

  287. Apollos (286),

    To be perfectly clear, do you accept that the processes involved in gene expression are explained by chemistry and physics? Is your contention that the processes themselves could not have arisen without intelligent intervention?

  288. Cassandra-

    ” Is your contention that the processes themselves could not have arisen without intelligent intervention?”

    This is the whole point. :-/

  289. Cassandra, typically the phrase, “to be perfectly clear,” is followed by a clarifying statement, and not another question. ;-)

    Are you taking issue with any of my statements at #286? …

    1) that you were question begging in your accusation of circular reasoning;

    2) that there are two putatively plausible, basically opposing, and competing explanations for the source of coded information;

    3) that there are two ways of verifying empirically that chance acting in accordance with natural law is the best explanation for coded information (I’m open to any other explanations that would show why intelligence is an unnecessary component of abstract functional specification);

    4) that we have empirical evidence, already present and abundant, that intelligence is the only verifiable source of coded information apart from the phenomenon of subject?

    Or something else? Thanks in advance for any clarification.

  290. Aleta (#273):

    That’s the answer that you don’t want to accept.

    Wrong. I accept very easily what you say, only it is not an answer. I will try to clarify why.

    The problem is simple. The causal model of neo darwinisms assumes two different moments which happen sequentially: RV generates functional information, and NS fixes and expands it.

    It is obvious that the working of NS is based on necessity, and cannot be evaluated in terms of probability and statistics. Nobody denies that, least of all we at ID.

    But the fact is that NS can only select new function which is already present. Moreover, the function must be relevant enough to be selectable in terms of increased reproduction and survival. Any change which has not such properties cannot be even “seen” by NS for a positive selection. Obviously, NS acts also negatively, eliminating variation when it is “detectable” in terms of sufficient loss of function. But negative selection alone, while useful to mitigate genetic entropy, cannot help generate new information. Positive selection is necessary for that.

    Well, the point is that, while NS certainly acts according to necessity, RV is by definition random, and can certainly be evaluated according to a scientific, quantitative analysis, in terms of probability and statistics. In other words, a model which implies a random search as part of its explanation must be credible from a statistical point of view for the part of the model itself which implies a random search.

    It’s that simple. Nobody is trying to analyze the NS part in terms of probability. We are only trying to analyze the RV part, something that darwinists apparently do not to want to do.

    In my analysis, I have repeatedly stated that I was referring to the functional unit in proteins, protein domains. The work by Axe has the same approach. Our point is that protein domains are already complex enough to be beyond the possibility of a random search.

    When we measure the functional complexity of protein domains, or of simple domain proteins, it is perfectly correct to ask: how was that functional information discovered? How was the search problem solved?

    Darwinists have no credible answer. They continue to hope that there exists some path where single steps are selectable, but that is simply not true. They speak of smooth transitions form one island to another, but the primary sequences of proteins which we know tell us that such selectable transitions do not exist.

    So, the simplest problem in the proteome, the emergence of thousands of different protein folds and domains, has no credible answer in terms of RV and NS, simply because RV cannot find the information which NS ought to recognize. It’s as simple as that.

    Therefore, all our discourses about dFSCI are perfectly legit, because they apply only to the RV part of the model. As soon as, or as far as, darwinists can show clearly definable selective steps which are credibly selectable at the molecular level, we will happily restrict our quantitative analysis to the transition between such steps, in other words, again to the purely random part.

    Therefore, your objection:

    All calculations of CSI et al are simple probability calculations that all the component parts of whatever is being considered came together simultaneously and entirely by chance. They do not take into consideration any causal chain of events that could have brought the thing under consideration into existence through a set of steps.

    is simply not pertinent and not true. First of all, for a statistical analysis there is no need at all that the events happen simultaneously. You can have as many steps as you want, but if they are random they are random, and you can evaluate the probabilities of a specific result, given the search space and the probabilistic resources.

    A causal chain of events becomes non random only if specific laws, like NS, act on the events. In other words, the steps must be selectable (or obey to any other known law of necessity). Otherwise, the process remains perfectly random.

    You say:

    Since no one believes that anything happens by a whole bunch of parts just coming to together by chance, such calculations of CSI are irrelevant: they eliminate a hypothesis (pure chance) that no one thinks happened anyway.

    That’s not true. Darwinists do believe that the information in proteins, or genomes, originated by pure chance, until something could be selected. Darwinists do believe that new protein domains, new proteins, new functions, must be found by random variation, in random steps, until a new selectable step is achieved.

    Remember, NS is not like the Weasel algorithm: it does not know the solution. Otherwise, it would be intelligent selection.

    NS is blind to anything which is not a detectable function powerful enough to affect reproduction and survival. In all the rest of the procedure, RV is absolutely alone.

  291. Cassandra:

    First of all, I have answered Aleta’s “objection” in my previous post.

    You say:

    Thanks for the detailed response. Could you please point out the specific posts on the other threads where you provided a detailed mathematical definition of FAI or FSCI and where you have calculated this quantity for a real biological system of some sort?

    I have pasted in my #239 many significant points from two recent posts of mine in recent threads. I refer you also to my posts #185 and #188 in this thread for othe rimportant points.

    In the past, I have debated these things in great detail with many of different opinion, but as I have been absent form UD for a few months, I would not know how to point you to those old threads.

    A very interesting quantitative debate took place, some time ago, on Mark Frank’s personal blog, with some good darwinists, the best of which IMO (without offence for the others) was Zachriel. Those discussions were interesting, and I think they should be still available on Mark’s blog.

    KF, BA, StephenB and many others have debated these points many time, in great detail, and I must say with great patience, with all the kinds of interlocutors: strict darwinists, theistic evolutionists, religious people of all kinds, atheists of all kinds, or just with silly trolls whose only purpose was to provoke and blindly criticize.

    I have cooperated with KF and StephenB to the realization of the section “Frequently Raised But Weak Arguments Against Intelligent Design”, in the Quick Reference Resources of this blog, where you can again find our views about the quantitative problem of CSI.

    Axe, Abel, Trevors, Durston and others have published very good papers in peer reviewed literature about these points. I have referenced the most important in my posts in this thread. I would definitely add the non ID paper suggested by Zach Bailey at #236.

    We in ID have always been interested in a detailed discussion of the quantitative measurement of CSI in proteins. We have spent hours and hours debating that in as much detail as possible with everyone interested. Frankly, seeing people like Aleta jump here out of the blue, and happily stating:

    Good luck, Petrushka – no one here has ever answered that, or any similar, question about a biological entity.

    and similar false platitudes, in a thread where a lot of long posts had already been offered on the subject, in a blog where hundreds of long and detailed posts have been offered on the subject, is not a comforting sign.

    As you can see, Aleta has at least offered some reasoning, and I have offered my answer. That, for me, is constructive exchange, and I am ready to go on, even on the dangerous limit of 290 posts.

  292. Cassandra (#287):

    do you accept that the processes involved in gene expression are explained by chemistry and physics?

    First of all, I think that Apollos was talking about the origin of DNA code, and of DNA’s coded information, that is the origin of the information in the genes. That’s not the same thing as the “gene expression”, which seems to relate more to gene regulation and transcription.

    So, if we are speaking of the origin of protein genes, for instance, I would definitely say that it is not expalined by chemistry and physics. That’s usually a very well understood point.

    Chemistry and physics can explain well how nucleotides (or aminoacids) join to form long sequences, provided that the correct cell machinery for that is present. But they can in no way explain wht they form that specific sequence which is functional.

    For proteins, the only explanation is that the sequence is written in DNA. For DNA, the sequence was written in previous instances of DNA, and is copied down. Nobody knows how the functional sequences originated. That’s exactly the problem we debate here. There are fundamentally two approaches: one mechanichal, based on RV and NS, which for many reasons does not work. And one based on the concept of design, which has all the potentialities to describe correctly what we observe.

    That’s what all the debate is about.

  293. slightly off topic but not by much:

    Image of The invisible – Thrice (with LYRICS)
    http://www.youtube.com/watch?v=WWery1h7e1Q

  294. Aleta, Cassandra et al:

    I paste here another post of mine form another recent thread, which can be relevant to the present discussion. The main point I would like to emphasize here is the quantitative evaluation of the power which can be assigned to different causal models, on the basis of both theoretical and empirical considerations. The key concept is the number of coordinated mutations which are necessary for a new selectable trait to appear, in other words the number of random variation events which must be present at the same time (even if randomly generated in successive steps) for a new selectable function to be added to a previous context. Behe has shown very convincingly (in TEOE) that, on the basis of purely empirical data, the threshold of what RV can accomplish in the extremely favourable context of bacterial or protist environment (extremely big populations, extremely high reproduction rate) can be reasonably put at 2-3 coordinated mutations. That is a very important point, because it means that any supposed darwinist scenario for any specific moleculary macroevolutionary transition (if and when darwinist will care to offer one) will have to deconstruct the transition in single selectable steps which are not more than 2-3 coordinated mutations distant one from the other. Good luck!

    Anyway, here is my post (from the thread about neo-Lamarckism):

    To steer back to Lamarckism, a brief summary/proposal.

    Three procedures which can modify the genome:

    1) Random Variation + Natural Selection (RV+NS). Traditional neo-darwinist theory. Minimal power (small changes, usually acts mainly through negative NS of non functional mutations, but can fix and expand minimal, non complex mutations which can, in particular contexts, confer some benefits, usually through some concomitant loss of function: example, antibody resistance due to point mutation of target structures).

    2) Adaptation + NS. Adaptation takes place probably through pre-existing structures and algorithms of response which allow the incorporation and utilization of external information to create a selective genome modification. Power: discreet. Possible examples: antibody resistance or other functions obtained through HGT, including the algorithmic tweaking of existing information to accommodate new, slightly different targets (plasmid information, emergence of nylonase from penicillinase); antibody affinity maturation.

    The adaptational algorithms must be already present in the living being. They can be rigidly deterministic, or use partial random search in the context of a deterministic algorithm, and they usually incorporate external information: in antibody affinity maturation, for example, controlled random hypermutation acts on specific segments of the genome, and the information present in the external antigen is used to effect an intelligent selection of the results.

    3) Intelligent design. Power: limited only by the knowledge available to the designer and by his power of implementation. Here the input of information comes from an external source (the designer), who is a conscious intelligent being of some kind. The designer must have previous information about the result to be obtained, and must have access to some modality of manipulation of the physical support of biological information. The information inputted by the designer can be of different kinds (one does not esclude the others):

    a) Previous knowledge of the final information to be implemented (for instance, previous knowledge of the exact sequence of nucleotides/aminoacids which allows the desired function.

    b) Previous knowledge of the desired function, which can be used to effect intelligent selection after a controlled random search, especially if point a) is not available.

    c) Previous knowledge about the search space structure for the desired functional ouptut, which can allow a controlled and more efficient random search by defining specific constraints and procedures.

    In other words, some knowledge of the desired function must always be present (teleologism) for design to be implemented. Knowledge of the detailed information which confers the fucntion can allow a process of direct implementation of that information (point a). On the contrary, knowledge of the function but not of the detailed information needed in the output, and/or knowledge of the structure of the search space, will allow indirect design, with the use of intelligent search algorithms, incorporating possibly controlled random variation, and usually intelligent selection.

    Finally, if the indirect search algorithm is not used directly by the designer, but only incorporated in the genome for future use, if and when new external information will be available, then we are again in point 2, adaptation. In this case the role of the designer is only to design the algorithm, which will automatically produce the necessary output as soon as it is activated by the input of the pertinent external information.

  295. Cassandra:

    If you want, you can check the following old thread:

    http://www.uncommondescent.com.....-organism/

    and the discussion on Mark Frank’s blog, which I referred to previously:

    http://mark_frank.blogspot.com.....e-csi.html

  296. Cassandra @ 283

    “You seem to be assuming your conclusion by saying that codes are only the result of intelligent design. If you define “code” in that way then your conclusion is trivially true but irrelevant to what we observe in DNA.”

    And Aleta @ 284

    “Cassandra is exactly right. tgpeeler assumes the conclusion.

    And, he writes, “At the risk of oversimplifying, …”

    Yes, vastly oversimplifying.”

    I’ve probably got better things to do but because I care, I’m going to point out the egregious flaw in both of your statements. Cassandra for making it and Aleta for agreeing without, apparently, either of you actually bothering to read what I said.

    The argument is not circular. IF I said that a code was only intelligently designed and the way I knew something was a code was that it was intelligently designed, then that would indeed be circular. Unfortunately for you, that is not what I said.

    I said a code uses symbols and rules (look it up) and that there is no way to explain a code, any code, in terms of the laws of physics. Hardly the same thing, now, is it? Let me reiterate and use M-W so you don’t think I’m making this up.

    code: a system of signals or symbols for communication (note that I am not claiming a code is something that is intelligently designed, yet)

    Claim: there is no way natural processes, as described by the laws of physics, natural laws, however you want to say it, can explain a code (or a language) BECAUSE, BECAUSE the laws of physics describe, HELLO, physical things, the interactions of sub-atomic particles in energy fields. The laws of physics have NOTHING TO SAY about why a symbol, or set of symbols, means one thing and another combination of them means another. In other words, ABSTRACT things. Remember this little mantra, it may help. Physics explains physical things and minds explain abstract things.

    Let me spell it out for you in another way. Physics is all about the material world. Information is abstract. It is encoded into physical substrates by means of a code or language for transmission and decoding on the other end. It is a fundamental categorical mistake to expect to explain the abstract (information) in terms of the physical. It can’t be done. It can’t ever be done. It’s IRRATIONAL to try, or claim that it can be done. Particularly when it has been explained ad nauseum. NOW comes the part where I say that only a mind can explain a code, or a language.

    I offered you the opportunity to prove me wrong by giving us an example of a code described by physical laws, but NOOOO, you twisted what I said, making what is called a straw man argument, and completely ignored what the real argument was.

    You are both either extremely careless or lack any kind of intellectual integrity. Please address the argument if you care to continue with this discussion.

    p.s. Cassandra says: “You seem to be asserting that DNA is a code that cannot be explained by means of natural laws, but that’s exactly the question under consideration. When we look at the internals of a cell, we see normal (bio)chemistry in action. You can model the nucleotides as a code, but what’s really happening is chemical reactions and physics. That’s as natural as it gets.”

    What do you not understand? OF COURSE there are chemical reactions described and prescribed by physical laws. But the biological INFORMATION, which is expressed in the GENETIC CODE/LANGUAGE is not explained by the laws of physics. Get it? Information MUST BE encoded in a physical substrate of some kind but it’s APART from the physical substrate. I’m honestly pretty amazed that neither of you apparently grasp this elementary point. I don’t know how to make it any plainer.

  297. Apollow (290),

    Are you taking issue with any of my statements at #286? …

    1) that you were question begging in your accusation of circular reasoning;

    I ignored that as a silly and patently unsupportable attempt at a tu quoque.

    2) that there are two putatively plausible, basically opposing, and competing explanations for the source of coded information;

    You are here assuming facts not in evidence, to use lawyerly jargon. It is certainly possible to model nucleotide sequences as codes. That does not justify the equivocation of treating them as intelligently designed codes.

    3) that there are two ways of verifying empirically that chance acting in accordance with natural law is the best explanation for coded information (I’m open to any other explanations that would show why intelligence is an unnecessary component of abstract functional specification);

    I’m not asking about codes. I’m asking for a mathematically rigorous definition of CSI (or FSCI, or dFSCI, or whatever the acronym de jour might be) so that it is possible to determine if various known types of mutations can increase or decrease that quantity.

    4) that we have empirical evidence, already present and abundant, that intelligence is the only verifiable source of coded information apart from the phenomenon of subject?

    Let’s start with some rigorous definitions and measurements before skipping ahead to conclusions, shall we?

  298. gpuccio (292),

    First of all, I have answered Aleta’s “objection” in my previous post.

    I’m afraid you haven’t. It’s quite clear that the one calculation you provided is for the odds of a particular nucleotide sequence (or the protein it transcribes to) appearing ex nihilo. Any calculation that reflects observed evolutionary mechanisms will have a time component.

    Further, you have failed to answer my simple questions from my 238, echoing Petrushka’s 227:

    I’m a bit confused about how you quantify FAI. What units ins it measured in and can you give me an example of a measurement?

    Under what circumstances would a point mutation change the quantity of FAI? Does anyone else use this unit?

    What is the mathematically rigorous definition of FAI? Can you please provide an example or two of calculating FAI for a real world biological organism or even a subsystem?

  299. tgpeeler (297),

    Cassandra says: “You seem to be asserting that DNA is a code that cannot be explained by means of natural laws, but that’s exactly the question under consideration. When we look at the internals of a cell, we see normal (bio)chemistry in action. You can model the nucleotides as a code, but what’s really happening is chemical reactions and physics. That’s as natural as it gets.”

    What do you not understand? OF COURSE there are chemical reactions described and prescribed by physical laws. But the biological INFORMATION, which is expressed in the GENETIC CODE/LANGUAGE is not explained by the laws of physics.

    We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws. How, then, can you continue to assert that information cannot be explained by the laws of physics? What, exactly, is your definition of information and how, exactly, can it be measured in a nucleotide sequence?

    By the way, your implicit assertion that DNA contains a language comes dangerously close to assuming your conclusion (again). The fact that we can model certain processes using terms like “information” and “language” does not justify equivocating on those terms.

  300. 301

    “We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws.”

    Really? You can show the physical and chemical laws that lead to the origin of functional nucleotide sequences from their non-functional counterparts?

    Let me see it. Thanks.

  301. Upright BiPed (301),

    “We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws.”

    Really? You can show the physical and chemical laws that lead to the origin of functional nucleotide sequences from their non-functional counterparts?

    Let me see it. Thanks.

    Your restatement of my claim is inaccurate. I said nothing about the “origin of functional nucleotide sequences from their non-functional counterparts.” If you have a question about what I actually said, I’ll be happy to answer it.

  302. Cassandra:
    “We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws.”

    1. That makes no sense. Shannon information is merely a measure of decrease in uncertainty — basically measuring bit storage capacity. This does not tell us anything about the pattern in question either resulting or not resulting from physics or chemistry or from chance or anything else for that matter. The generation of the pattern is a completely separate issue.

    2. A nucleotide sequence is not defined by the physical properties of the nucleotides, in the same way that the sequence of letters in this paragraph of mine is not defined by the properties of the pixels used to “write” the letters.

    3. The fact that life operates according to laws of physics and chemistry does not mean that it can organize itself utilizing only physics and chemistry. A running, operational computer also operates according to the laws of physics and chemistry, yet its organization and sequencing is not defined by the physical properties of the material which is utilized in its construction. At the information processing level of life — especially concerning nucleotides — we also see the same type of “non-lawful” organization as is seen in the computer example. In fact, if a sequence of nucleotides were constrained by the laws of physics and chemistry there would be no degrees of freedom for it to carry information. We would merely have a rigid crystalline structure with no potential for variability and evolution.

    Is this making sense so far?

  303. 304

    Cassandra there was nothing particularly criptic in what you seem to imply.

    I simply wanted to establish that you haven’t even a conceptual clue as to a physico-chemical explanation for the existence of funtional nucleic sequencing.

    Telling us something can change over time is hardly an explanation for its existence. The hood on my car will rust away given enough time. I will be able to describe it’s demise by purely chemical laws, but there is nothing in the metal that will tell me how it came to be a hood on a car.

  304. Cassandra (#299):

    I’m afraid you haven’t. It’s quite clear that the one calculation you provided is for the odds of a particular nucleotide sequence (or the protein it transcribes to) appearing ex nihilo. Any calculation that reflects observed evolutionary mechanisms will have a time component.

    Wrong. The time component is not relevant. What is relevant is the number of trials in the random search, which is always taken in consideration in all ID discourses, usually under the term “probabilistic resources”.

    In other words, the model is simple:

    Let’s assume that you have to arrive to a new sequence (B), with a new fold and fucntion, from an existing sequence (A).

    Let’s assume that A and B have no significant homology (the standard case for two different folds and superfamilies).

    Let’s assume that the engine of variation is only random variation (random events of any type). That’s the standard neo darwinist assumption.

    Let’s assume, for simplicity, that A and B are of the same length (approximately).

    In this simple reference context, which must have happened, if any new protein fold has been discovered by darwinian mechanisms, RV acts on the starting sequence A by single random events (each of which can change one or more AAs) in time.

    Now, let’s assume that the intermediaries between A and B are not functional, or not functional enough to undergo positive selection. That rules out NS form this specific scenario. Obviously, NS can start to act as soon as we get B. At any moment, in a real scenario, anybody can prove that some intermediary is selectable. In that case, the scenario will be “resized” to the transition from A to, let’s say, A’, and then from A’ to B. But only on evidence, or at least reasonable assumnption, that A’ is selectable.

    Finally, please take notice that B is not a single sequence, but a subset of sequences in the search space: all sequences which exhibit the new fold and the new function. Let’s call it “the B target space”.

    That is the model. Now, each v ariation event, whenever it happens, can be considered as a random trial in the search space (you get a different sequence form the search space, in a random way). The result of that trial can be evaluated in a binary way, as a success (you got B; you found the B target space). Or a fialure (you didn’t).

    The probability of success in a single trial is simply the ratio between target space and search space (assuming a practically uniform distribution, which is the only reasonable assumption in this context).

    But you have time. Correct. And you can repeat your trials many times. Correct. Again, time is not the relev ant factor- The number of trials is the relevant factor. There is no difference if you toss a coin 1000 times in one hour or in one year, the probabilities of getting some specific result remain the same.

    You can get an estimate of the probabilities of getting B in n trials by a statistical calculation, taking into consideration the probability in each single trial and the number of trials. Again, time is not relevant, and nobody is modeling the new sequence as appearing ex nihilo (that would be true in an OOL scenario). The new sequence is modeled as emerging from a pre-existing, unrelated sequence.

    Time can be considered only when, after having calculated the probability of the supposed transition, we have to evaluate if the time available in our model is enough to allow sufficient trials to get to a vaguely reasonable probability of final success.

    Further, you have failed to answer my simple questions from my 238, echoing Petrushka’s 227:

    I’m a bit confused about how you quantify FAI. What units ins it measured in and can you give me an example of a measurement?

    Under what circumstances would a point mutation change the quantity of FAI? Does anyone else use this unit?

    What is the mathematically rigorous definition of FAI? Can you please provide an example or two of calculating FAI for a real world biological organism or even a subsystem?

    Strange, I would say I have done exactly that in my post 239, with further information in all ny following posts on this thread. Have we read different threads? I have also taken again the discussion in greater detail on the new thread on Andy MacIntosh’s paper, in answer to Petrushka. You can check that btoo, for reference.

    Please note that just from the start of my post 239 I have clarified that FAI does not mean anything, and that we should speak of CSI and of its subsets FSCI and dFSCI (and BA, who had in some way used the expression “you have no mechanism to generate functional algorithmic information by material processes” seems to agre that he was not trying to define a new category). So, all my discussion is about dFSCI.

    Of that I have given a rigorous definition, a way to measure it, examples of application of the measure to proteins and even to Hamlet! What can I do more? :)

    So, instead to just state that I have failed to answer, you could more correctly say that you don’t agree with my answers. That would be fair.

    And, if you want, you could also explain why.

  305. gpuccio @ 305,

    The new sequence is modeled as emerging from a pre-existing, unrelated sequence.

    Why unrelated?

    What is the probablity of getting from [stateN] to [stateN+1] in the following…

    [stateN]……..1011
    [stateN+1]……1111

    …if only one bit changes each generation?

    Your answer should 1 in 4, not 1 in 16.

    For a length of 32 bits it would be one in 32, while N bits would be 1 in N.

    Where is your decoder?

    If DNA is a code, something must convert that coded symbol to the real entity before use.

    If there is no decoder, then DNA is not a symbolic code for the component used in a chemical process, it already is that component.

    Are 2 hydrogen atoms and an oxygen atom in a molecule, a code for water, or is that water?

  306. 307

    Toronto,

    “If DNA is a code, something must convert that coded symbol to the real entity before use.

    If there is no decoder, then DNA is not a symbolic code for the component used in a chemical process, it already is that component.

    Are 2 hydrogen atoms and an oxygen atom in a molecule, a code for water, or is that water?”

    Keep going Toronto…you’d be an IDer soon.

  307. Toronto:

    Why unrelated?

    I thought I had specified why:

    “Let’s assume that you have to arrive to a new sequence (B), with a new fold and fucntion, from an existing sequence (A).

    Let’s assume that A and B have no significant homology (the standard case for two different folds and superfamilies).”

    In other words, I was modeling the transition which only could give rise to a new fold in a new superfamily. Is that clear. Again I quote from my post:

    “In this simple reference context, which must have happened, if any new protein fold has been discovered by darwinian mechanisms, RV acts on the starting sequence A by single random events (each of which can change one or more AAs) in time.”

    Proteins in different superfamilies are unrelated. You must remember that the primary sequence of many proteins is perfectly known. It is not a mystery. Everybody can use BLAST or any other similar tool to compare them.

    And protein domains and folds are unrelated. They have no significant homology. The ASTRAL SCOP Genetic Domain Sequence tool, version 1.75 (the latest) gives the following numbers:

    a) 1195 domains which represent each fold

    b) 1961 domains which represent each superfamily

    c) 6041 domains filtered with E values >=10

    d) 6258 domains with less than 10% identity

    All these criteria are guarantee that the structures are unrelated. Even if we take the strictest, the difference in folds, we still have at least 1195 independent structures whose emergence we have to explain. And remember two key points:

    1)About half of these domains seem to have been already present in LUCA

    2) The average single domain length is about 100 -150 AAs, with range 36 – 692

    I have to remind you that the two binary sequences you give in you post #306 are not only extremely short, but also heavily related (75% identity). I really don’t know what they were supposed to show.

    So, maybe you should stop playing tricks with binary sequences, and start discussing seriously.

  308. Toronto:

    Where is your decoder?

    If DNA is a code, something must convert that coded symbol to the real entity before use.

    If there is no decoder, then DNA is not a symbolic code for the component used in a chemical process, it already is that component.

    Are 2 hydrogen atoms and an oxygen atom in a molecule, a code for water, or is that water?

    I don’t understand why you ask such obvious things. Maybe you are not familiar with biology.

    The answers are very simple.

    DNA is a code (I am obviously sepaking of the protein coding genes). It contains in its sequence the information for the proteins, coded according to what is correctly called by everybody the genetic code.

    The real entity is the protein, not the DNA. The decoder is the translation apparatus. It is formed by about 100 proteins and the ribosomal RNA.

    But the part which specifically keeps the key to the translation of the code is formed by the “Aminoacil RNS synthases”, a set of 20 different proteins, each of them very long and complex and multidomain, which form two different classes of 10 each. Each protein of this set is specific for one aminoacid, and has, in a different part of the molecule, the correct anticodon to recognize the specific codons in mRNA. Without this very complex decoder system, the information in DNA is completely useless. And DNA, in itself, is a very inert molecule, its only real role is to be a mass memory for functional information.

    And finally, just to be clear, “2 hydrogen atoms and an oxygen atom in a molecule” are just a molecule of water. They don’t code for anything.

  309. Sorry, I messed with the tags again. In my previous post, Toronto’s quote is up to:

    “Are 2 hydrogen atoms and an oxygen atom in a molecule, a code for water, or is that water?”,

    while my post starts at:

    “I don’t understand why you ask such obvious things. Maybe you are not familiar with biology.”

  310. gpuccio @ 308,
    I appreciate the effort you put in your responses to me but keep in mind that I am in the moderation queue and can’t address long posts properly.

    Let’s try to come to agreement one single step at a time.

    Here is my re-labeled example.

    [DNA_1]=100….0….111
    [DNA_2]=100….1….111

    Notice there is a single-bit change in the “code”. The “codes” are 1 million bits long in my “lab-designed” life-form.

    Only one bit can change each generation.

    What are the odds of getting from DNA_1 to DNA_2 with a population of 1 million?

    I say it is likely that you will hit your target with the very next generation.

    Notice that there is no lower-level detail involving real-world chemistry required at all since the example works on the same level as the Dembski-Marks papers.

    This comment addresses only the one single ID point, that evolution cannot generate information without intelligent intervention.

    Here we see that the Evo position, that environmental feedback and random mutation are quite capable of modifying “information”, is viable.

    Any argument refuting the sudden appearance of a one million bit string of data from a “random starting point” is not refuting evolution, since it is addressing the random mutation component only.

    Evolution is not random at all, only mutation can be considered in some way, random.

  311. Cassandra @ 300

    “We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws. How, then, can you continue to assert that information cannot be explained by the laws of physics? What, exactly, is your definition of information and how, exactly, can it be measured in a nucleotide sequence?”

    Francis Crick, Of Molecules and Men, page 41. “The flow of information thus goes: DNA -> RNA -> protein.”

    OMM, page 43. “…we have, in effect, to translate the information from a four-letter language into a twenty-letter language, and this is by no means easy.”

    OMM, page 57. “…so that the language that is used in the nucleic acid polymers is universal.”

    Richard Dawkins, River Out of Eden, page 11. “You can treat the genetic code as a dictionary in which sixty-four words in one language (the sixty-four possible triplets of a four-letter alphabet) are mapped onto twenty-one words in another language (twenty amino acids plus a punctuation mark).”

    ROE, page 19. “Life is just bytes and bytes and bytes of digital information.”

    ROE, page 150. “Indeed, the whole DNA/protein-based information technology is so sophisticated – high tech, it has been called by the chemist Graham Cairns-Smith – that you can scarcely imagine it arising by luck, without some other self-replicating system as a forerunner.”

    Dawkins, The Selfish Gene, viii. “This reason is that we animals are the most complicated and perfectly designed pieces of machinery in the known universe.”

    Information Theory, Evolution, and The Origin of Life, Hubert P. Yockey, page 2. “The reason that there are principles of biology that cannot be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is much larger than the information content of these laws.

    ITEOOL, page 2. “The existence of a genome and the genetic code divides the living organisms from nonliving matter. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences.”

    ITEOOL, page 3. “Information theory and coding theory and their tools of measuring the information in the sequences of the genome and the proteome are essential to understanding the crucial questions of the nature and the origin of life.”

    ITEOOL, page 5. “The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences.”

    ITEOOL, page 6. “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.”

    ITEOOL, page 7. “The genetic information system is the software of life and, like the symbols in a computer, it is purely symbolic and independent of its environment. Of course, the genetic message, when expressed as a sequence of symbols, is nonmaterial but must be recorded in matter or energy.”

    ITEOOL, page 8. “Life is guided by information and inorganic processes are not.”

    ITEOOL, page 20. “The Central Dogma (ever hear of that???) states that information can be transferred from DNA to DNA, DNA to mRNA, and mRNA to protein.”

    ITEOOL, page 94. “…They find the genetic code to be very near or possibly at a global optimum for error minimization.”

    ITEOOL, page 118. “…no natural chemical procedure exists to form an optically active biochemistry.”

    ITEOOL, page 187. “Let us remind ourselves that the laws of physics and chemistry are much like the rules of grammar. They must be obeyed, but there is not enough information in the rules of grammar to produce Lincoln’s Gettysburg Address.”

    Should I go on??? All three of these authors are, or were, darwinists. They “get it.” Information and life are inextricably linked. Can’t have one without the other.

    Go argue with Crick, Dawkins, and Yockey. Well the alive one of the three, go argue with him.

    And lastly, you say: “The fact that we can model certain processes using terms like “information” and “language” does not justify equivocating on those terms.”

    Surely you jest. Equivocating? That’s rich. Go into any biology department in the country or world for that matter and tell them there is no such thing as biological information or a genetic language. hee hee. May I also suggest a Google search of the term “bioinformatics.” Pity. All these universities spending all this time, effort, and money to develop these programs. Be pretty embarrassing for them when they find out THERE’S NO SUCH THING AS BIOLOGICAL INFORMATION. You’re killing me. No really, you are. Nice… By the way, did you mention what universe you are from? I’d like to tell the other earthlings before it’s too late… Oh wait, there go Johns Hopkins and Boston University. Not to mention the Oxford journal of Bioinformatics. Darn. I’m sure there are others. Somebody help… We’ve got to stop them… They need to know… They’ll make fools of themselves…

    I have a solution. They all just need to go back and rewrite everything ala Richard Dawkins. You know, with him it’s all “apparent” design and the “illusion” of purpose. So now I suppose we’ll be treated to the “apparent” information in the genome and the “illusion” of a genetic language. They can use “find and replace” on the illusion of their copy of MS Word or the apparent Mac word processor. Shouldn’t take long. Let me know when they’re finished. I’m sure they’ll all be grateful to know this…

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