Wednesday, April 28, 2010

New DNA Damage Repair Mechanism Must Have Arisen Early

DNA damage repair is a fascinating topic in cell biology. Fascinating because the cell's repair mechanisms are so incredible. What's more the mechanisms are coordinated in a sophisticated control network. As one researcher put it, "it’s almost as if cells have something akin to a computer program that becomes activated by DNA damage, and that program enables the cells to respond very quickly."

Now a new mechanism has been discovered which repairs DNA alkylation damage (the erroneous addition of carbon groups to DNA bases). The new mechanism links two previously known mechanisms. Here is how one science writer describes these two mechanisms:

The DNA repair process that removes such toxic "lesions" is known as base repair, and uses a protein called AGT (O6-alkylguanine DNA-alkytransferase) to remove the alkyl group before DNA replicates. The protein essentially sticks a chemical finger inside the DNA to flip the damaged [base] out from the DNA helix structure so that its adduct is exposed and can be transferred from the [base] to a part of its protein structure. The [base] is now repaired and can rejoin cytosine with three hydrogen bonds linking them.

AGT is believed to act alone, but there is another, unrelated repair process—nucleotide excision repair (NER)—that uses lots of proteins in its pathway. This repair occurs when bulky adducts stuck to bases distort the sleek shape of the DNA helix. Then a whole group of proteins come in and remove a patch of bases that includes the adduct, and DNA polymerase follows and fills in the patch while adding the correct base back.

The new mechanism uses alkyltransferase-like proteins (ATLs) which are similar to the AGT protein. Like AGT, ATL attacks the DNA base that has suffered alkylation damage. But the ATL protein distorts the DNA structure significantly, and thus triggers the nucleotide excision repair (NER) mechanism.

This sophisticated and coordinated repair sequence was found in all three domains of life (prokaryotes, eukaryotes and archaea). For evolutionists this forces the absurd conclusion that such a sophisticated DNA repair interaction evolved early on. Before there was so much as an amoeba, evolution had worked wonders. The earliest crude cells must not have been so crude after all. Evolution incredibly worked miracles in those heady days of early life. As the researchers write:

Our analysis of lesion-binding site conservation identifies new ATLs in sea anemone and ancestral archaea, indicating that ATL interactions are ancestral to present-day repair pathways in all domains of life.

This conclusion that complexity comes early is often forced on evolutionists, in spite of the evolutionary expectations to the contrary.

99 comments:

  1. Cornelius Hunter: This sophisticated and coordinated repair sequence was found in all three domains of life (prokaryotes, eukaryotes and archaea). For evolutionists this forces the absurd conclusion that such a sophisticated DNA repair interaction evolved early on.

    It's hardly an absurd conclusion. DNA is almost certainly not the original material of the genome, and even bacteria are complex organisms that require reliable replication. Genome repair would therefore be very ancient.

    Cornelius Hunter: This conclusion that complexity comes early is often forced on evolutionists, in spite of the evolutionary expectations to the contrary.

    Complexity has several different measures. Even a single ribozyme is an extremely complex three-dimensional structure, and a collection of related molecules contained in a lipid membrane as part of a community of such protocells would certainly be complex in terms of variety of interactions. Indeed, protocells may have been more complex in this sense than modern cells, though less well-integrated.

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  2. "DNA is almost certainly not the original material of the genome"

    I will be glad if you link to a prove.
    Please not stories or deductions.

    "Indeed, protocells may have been more complex in this sense than modern cells, though less well-integrated"

    is this Ok with darwinism?

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  3. Another failed perdiction of Darwin.

    First life was more than just a glob forming in Darwin's warm little pond. Perhaps if Darwinism had not warped the thinking of generations of scientists to see life as simple and accidental these complex and useful discoveries would have come sooner. But, fortunately good science and research continue inspite of Darwinian influence.

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  4. Think of the RNA World hypothesis.


    To Dr. Hunter: been reading the Uncommon Descent blog for 2 days now. I'm a anthropology student and I take part in an debate Pro/Con ID. The purpose is to get better in arguing. All of us are Anthro-students (we didn't find students who believe in ID to take part). Because of this, some of us have to take on the role of the Pro-ID.

    My assignment was to make a speech about some old book of Dr. Dembski but thanks to volcano ash the book didn't arrive in time.
    Now I'm working on a speech using blog entries by you and Dembski, playing the role of PRO-ID.
    As an Anthropology student I don't believe in ID but I will try to argue for it.

    After reading about 20 of the latest articles, including tons of comment discussions, I don't have much to say for ID.

    The main argument seems to be that the chance for life is so small - it just couldn't have happened.

    Besides that, most articles seem to tell the reader about new findings in science and ends with your conclusion that the new findings once more show that life is too complex, thus a designer must have done it.

    Could you link me to a summary of arguments for ID? Or mention some of the most striking ones? You seem to have some arguments against evolution. But mostly they seem to involve molecular biology, a field where scientists obviously still have a lot of research to do.

    For example, what would be some arguments supporting ID in the field of human ethology? What about sexual selection in human evolution?

    An answer would be much appreciated!

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  6. I'm not sure if you are role playing in your supposed pro/con ID debate, or if you are role playing on this blog as a serious poster. I'm willing to bet on the latter.

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  7. Zachriel: DNA is almost certainly not the original material of the genome

    Blas: I will be glad if you link to a prove.

    A single link won't do it. You might want to start with the Theory of Evolution and the discovery of ribozymes.

    Zachriel: Indeed, protocells may have been more complex in this sense than modern cells, though less well-integrated.

    Blas: is this Ok with darwinism?

    The use of the term "darwinism" can be ambiguous. It usually refers to the importance of natural selection. In this case, we refer to the time when evolution was posited to be primarily horizontal and organisms not well-defined as a pre-Darwinian period. Life then crosses a Darwinian threshold to begin orthodox phylogeny.

    Again, complexity is not a simple scalar. Protocells may have had more interactions, but more loosely defined, than in modern organisms.

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  8. Hi launzzz,

    You said: "The main argument seems to be that the chance for life is so small - it just couldn't have happened."

    I am no specialist in ID, but my encounter with the theories makes me belief that the probability (not chance) argument is simply part of the method to detect design. Inferring design is purely based on what we know about the phenomenon... called design... through science, that is. I simply understand design as the action of some form of intelligence. Everything would look like design if it weren't for scientific laws acting and allowing us to do science and thereby discern the act of nature vs. the act of intelligence. (Scientists do it all the time to make sure their observations were not influences by the observer or other intelligent agent, or even discerning the act of ancient intelligent actors in archeology.)

    Therefore we require the basic tenants of science, like the laws of logic and in particular the inductive principle to enable us to make accurate observations and predictions about design. (That is exactly what the SETI does. In all its complex endeavors.)

    Once you can successfully defend the principle of design detection in its pure scientific setting (like the SETI and ID) it will be easy to proceed and apply it to the entire body of knowledge regarding life sciences. The body of data and evidence should bring anyone with a basic understanding of design theories to conclude that the simplest and most powerful explanation for what we currently know about life is that it was caused by some form of intelligence. (Remember the starting point is science and the conclusion is still science. Transcendental consequences is not part of the argument... Remember naturalism (...evolution's default presupposition) has very clear transcendental consequences.)

    A final note is to remember that a design inference is falsifiable like any theory except maybe evolution that seems to be beyond falsification.

    Hope this will help your debate...

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  9. "a sophisticated DNA repair interaction evolved early on. Before there was so much as an amoeba, evolution had worked wonders."

    I guess this hinges on what you mean by 'early.' By the way, amoeba are Eukaryotes, with endomembranes and nuclei (N in your picture above), so evolution had maybe 2+ billion years to work wonders for their ancient ancestors.

    For a function to be present in all three domains, it has to be present in the inferred Last Common Universal Ancestor (LUCA), or spread by horizontal gene transfer after the fact.

    LUCA is already imagined to be very complex, with the universal genetic code, transcription, translation, etc., already in place. This repair system seems like a minimal addition compared to that!

    This is not to say the first cell was nearly as complicated as LUCA.

    Which is not to say the first replicating systems were as complex as that.

    In short, you're compacting the proposed timeline.

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  10. A single link won't do it. You might want to start with the Theory of Evolution and the discovery of ribozymes.

    That are proves of the capacity of RNA, I want proves of your statement:

    "Zachriel: DNA is almost certainly not the original material of the genome"

    ie. a proof that there is/was a genoma not made by DNA.

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  11. "In this case, we refer to the time when evolution was posited to be primarily horizontal and organisms not well-defined as a pre-Darwinian period. Life then crosses a Darwinian threshold to begin orthodox phylogeny"

    And only one organism crosses that threshold? Only one could become LUCA? Scientifically we can say that there are nor more than one similar LUCA?

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  12. Blas,

    You are correct. The evolutionary biologist Carl Woese thinks perhaps no individual organism could be considered a LUCA, but LUCA reflects the genetic heritage of all modern organisms as derived through horizontal gene transfer among an ancient community of organisms.

    Woese, Carl, The universal ancestor, Proceedings of the National Academy of Sciences, Vol. 95, Issue 12, 6854-6859, June 9, 1998, http://www.pnas.org/cgi/content/full/95/12/6854

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  13. Michael-

    Your problem in playing around with probabity is that an explanation invoking a supernatural agent is always less likely than one which calls only on natural forces.

    Saying 'God did it' may sound like a simple explanation, but it is not. It relies on God existing, which is phenominally unlikely. The explanation is, therefore, at least as unlikely.

    Similarly, ID relies on a designer - a being which must, by definition, be more complex (and therefore more unlikely) than life/the universe/whatever you want to credit him/her/it with designing.

    Supernatural explanations are always more complex, and therefore more unlikely than natural ones. And ID is indeed a supernatural explanation.

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  15. Zachriel: DNA is almost certainly not the original material of the genome.

    Blas: a proof that there is/was a genoma not made by DNA.

    Science doesn't deal in "proof," but evidence. If you want to make sense of the evidence, you need to start with the Theory of Evolution, in particular, the Theory of Common Descent.

    Blas: And only one organism crosses that threshold? Only one could become LUCA? Scientifically we can say that there are nor more than one similar LUCA?

    A population. But the boundaries are not necessarily distinct during the threshold period. If you were to look at life at that time, though, you may not recognize the universal ancestor as it was not a single organism, and there were probably many other competing populations that did not leave descendents.

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  16. Zachriel,

    There isn't any evidence which demonstrates that all living organisms owe their collective common ancestry to some unknown population(s) of single-celled organisms via an accumulation of genetic accidents.

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  17. Ritchie,

    You are sadly mistaken.

    ID does not require the supernatural.

    As for more complex it is your position that is the most complex- think about it- you rely on cosmic collisions, atomic accidents, chemical and genetic accidents.

    The reliance is so heavy you can't even test your position.

    What do you have besides "It just happened"?

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  18. I find it curious that Cornelius prides himself on somehow being "theory-neutral".

    But it's not hard to see of course that he really isn't. Just look at the language in the OP - "incredible", "sophisticated", "absurd".

    These are all value judgements of course - after all why is it "incredible" - incredible compared to what exactly? Just because it seems incomprehensible to us that simply makes it "incredible"?

    These subtle but revealing use of words, show that of course Cornelius thinks there is Some Other Explanation. That is not being theory neutral.

    So Cornelius, please don't trot out all that nonsense about you being "theory neutral" - we know you're not. On March 30th, you declared that you believe that there is a supernatural cause to evolution/origins - you also think that supernatural agent is the Christian God. You have provide absolutely no evidence to back up your claim. Curiously, you also said you talk about these beliefs "all the time", although it is quite clear you don't and possibly even regret what you've said. And repeated attempts to request you to elucidate the evidence fall on deaf ears.

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  19. Ritchie,

    I just wanted to give a perspective that does not isolate chance, or as I see it probability, from its setting within design detection. I made it very clear that it has nothing to do with the transcendental implications, only about the known and well established natural phenomenon... design.

    This was just to help launzzz and is as a matter of fact very off topic for this post.

    To conclude from my side, I just like to say that it seems as if you have a similar insight into logic than someone like Richard Dawkins. It is not clever to make an argument against ID by referring to the "...more complex (and therefore more unlikely)" concept, which, if I remember correctly, is something Dawkins used in "The God delusion". I am no philosopher but I know a self-defeating argument when I see one. This version of yours will bring any act of science to an abrupt halt, if you follow through with it, because the act of observing and describing something is an act of design in itself and according to you will necessarily fall into the spiral of endless complexity (regressive and progressive causal complexity). At least you seem to claim evolutionists can do science and they are exempt from this dilemma you (re)created here... Saying so does not make it so.

    I therefore urge you and launzzz, to stick to sound science that use what we know and observe to describe reality. Trying to exclude design from science is just stupid and no one claiming it can actually act according to such claims.

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  20. JoeG-

    Care to explain how the designer imagined by UD is not supernatural?

    Your brethren at UD have this posted on the front page:

    "Hence this designer, having exactly the same properties as Being, is identical to Being (as a consequence of the principle of “identity of indiscernibles”). Hence we arrive at the conclusion that the Designer of the universe is Being (God).

    There are two direct consequences of this argument. First, any attempt to make intelligent design compatible with atheism is incoherent. Conversely, ID is compatible with any orthodox theistic doctrine (Thomism included)."

    http://www.uncommondescent.com/philosophy/the-%E2%80%9Cdesigner-of-the-universe-is-not-god%E2%80%9D-error/#comments

    Why don't you engage them there, and prove them wrong?

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  21. Joe G -

    "ID does not require the supernatural."

    Does Intelligent Design not require an Intelligent Designer?

    "you rely on cosmic collisions, atomic accidents, chemical and genetic accidents."

    Probably not to the degree you imagine, but to a certain extent, yes. But then again, all these things do, in fact, happen. They are real. There is no reason to doubt the existence of these things, rare though they may be. Such cannot be said for any being worthy of being called an Intelligent Designer.

    "The reliance is so heavy you can't even test your position."

    Not so. Every time we discover a new fossil/animal species the theory of evolution is being tested - does it fit into the pattern of genetic/geological nested hierarchies which the theory of evolution absolutely necessitates? And since we have discovered thousands of species, living and fossilized, that equates to the theory of evolution being tested thousands of times. And guess what - they always do fit the pattern.

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  22. If I understand most of the anti-ID critics correctly, they disallow a theistic commitment to a transcendental implication of science because such a commitment by default disqualify the person that holds to such a commitment. This position just confirm my suspicion that ID critics is not seriously engaging the topic they want comment about.

    Wake up and smell the roses... Everybody holds to some metaphysical beliefs and claiming your belief is the only one compatible with science is just stupid and arrogant.

    If any anti-ID contributor to this blog would like to comment on the place of design detection in science as implied by ID... Is design detection part of science or not?

    Please don't say "Yes, it is ...except for biology."

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  23. Michael -

    I certainly take your point that we are drifting from the topic of this thread, but conversation is organic and I don't believe anyone really objects. If they do, I will hold my objections for a more relevant thread. I also accept that you are trying to enlighten launzzz - a worthy endeavour. I was not trying to belittle it. But I still believe your position is in error, and therefore while your defence of ID may be accurate, it is not scientifically coherant.

    Design is not, contrary to your claim, a 'known and well established natural phenomenon', let alone the only one. Not a single article has ever been published in any scientific journal which demonstrates design in nature (unless you want to refer to the accidental, unconcious result of natural forces, such as erosion and evolution, as 'design' which I believe you do not).

    As for your specific objection to Dawkin's train of logic, I don't think I follow it. But it seems to me that the way out of the complexity problem is to conclude that complexity built up from simplicity - which underpins the theory of evolution. If complexity is always the result of deliberate design, then it must always come from greater complexity - which leads to infinite regression unless the buck stops somewhere.

    "stick to sound science that use what we know and observe to describe reality. "

    Sound advice. And I offer it straight back to you.

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  24. launzzz:

    ===
    After reading about 20 of the latest articles, including tons of comment discussions, I don't have much to say for ID.
    ===

    That exercise sounds like fun. I think it is important for folks to learn the strengths of viewpoints they do not hold. I search for the strongest arguments for evolution.

    I think Michael makes good points, and you might want to consider representing the ID side by scrutinizing underlying philosophies, assumptions, etc.

    For instance, from your comments, it is not clear to me what would count as a good evidence or argument for design. So can you describe what type of evidence or argument would work?

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  25. Michael -

    Just to be clear, the metaphysical position of biology is the metaphysical position of all science - we must assume miracles do not happen. There may be a supernatural realm - but if there is, it does not affect the running of this one. This universe is run entirely by regular, measurable, natural laws.

    If we allow that the supernatural is real and miracles can happen, then we lose any reason to trust the results of our own experiments. Because the result of any given experiment might BE a miracle.

    So science makes the assumption that the universe is run by purely natural forces. That is the position of ALL fields of science. Yes, this is an assumption, and yes it may ultimately turn out to be wrong, but then again, science is incredibly productive. We have cars, computers, brain surgery, we have walked on the moon, decoded the human genome, etc. The achievements of science are far too numerous to list. But each one was achieved under the assumption that miracles do not happen. And the fact that science seems to be so productive is indeed indicative that science is probably an accurate representation of how the world works.

    That is the metaphysical position of science - not that there is no supernatural, but simply that the supernatural does not at all affect the running of the universe.

    It is the metaphysical position of physics, chemistry and biology - and more specifically of the theory of eovlution.

    Yet not the position of ID. Another reason why ID is simply not science.

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  26. Michael-

    SETI and anthropology rely on design detection. Biological ID could also be very important, for instance, in telling if a biological agent is designed (weaponized) by humans or not.

    But ID as in the ID movement, fails:

    1) Because of weak assumptions, and no supporting data, it doesn't have a functional design detector.

    You need: "X factors, found in Y phenomenon, are indicative of design for these reasons." That is, to separate design from non-design.

    Behe's irreducible complexity has been experimentally disproved, and Dembski’s assumes we can quantify the probability of phenomena
    occurring (independent of path, since mechanism is not considered). Dembski admits he cannot detect non-design, and excludes it!

    As others have put it, where is the field guide to detecting intelligence in biology? Can you name me something designed and something undesigned?

    2) It is not useful-it terminates further thought and research. We use model organisms, study homologous systems, etc. in biology. This produces useful model organisms. Deep homology take this a step further. Supernatural design and redesign does not allow such inferences.

    As Jill Schneider puts it: "Why is our intelligently designed physiology susceptible to microscopic organisms? The eternal answer is that we can never know the designer's hidden agenda. Things are the way they are because they were designed that way. The end. Supernatural explanations terminate the quest for further exploration, whereas a good hypothesis stimulates further exploration."

    http://www.lehigh.edu/~inbios/schneider/evolution.htm

    3) Insertion of the supernatural is not as science. For example, it is not parsimonious, and it is not falsifiable. ID as a theory has consistency depending on a understanding of the intent of the designer. ID is not dynamic and progressive. As we've mentioned before here, we consider meteorology in naturalistic terms. Should Pat Robertson's belief that God caused Katrina be presented as a scientific alternative? How would you test that? How would you disprove it?

    Most importantly, we know ID is just a stalking horse for the insertion of religion into the classroom. The origins history and politics of the movement suggest this.

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  27. Just a quick comment to Ritchie before I sign out from my time zone.

    You would very much like to have a simplistic causal regression into absolute simplicity, but that just does not work. Ask any "real scientist" playing with the pre-Big Bang scenarios... There is nothing simplistic about causal regression, not for evolution and not for any theory for that matter (Causal regression into nothingness has never been a logically acceptable position, that is why science are looking for something "before the Big Bang" and Nirvana is... well... Nirvana).

    So the preferred position remains "regressive and progressive causal complexity". I therefore have to challenge your "simplicity claim" and ask you to consider the fact that design detection is no more complex than any other scientific observation.

    In general I have to smile at the claim that no scientific paper ever claimed to use design detection. Did I not mention archeology. Again I have to say that anyone denying design as part of science is denying science itself.

    Live with it, ID is just science.

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  28. This is really addictive... but I will try to resist in the future ;)

    Ritchie,

    You said: "If we allow that the supernatural is real and miracles can happen, then we lose any reason to trust the results of our own experiments. Because the result of any given experiment might BE a miracle."

    That is just the big joke. If you know anything about David Hume and Karl Popper then you would know that it is not the supernatural that pose the big threat to science but the inductive principle itself. The uniformity of nature makes science possible and accepting this as an unchallenged axiom is exactly the same as saying miracles can happen, you just have to belief that things in nature will keep going the way it did.

    So if you think that denying miracles is your only metaphysical belief, then I have to refer you to the non-existence of a simplistic causal regression mentioned earlier... What is really your metaphysical commitments?

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  29. RobertC,

    I am not going to go into to much about your claims about ID because I don't know that much about it. What I do know is that both Behe and Dembski is still silencing their critics with fresh arguments that actually strengthen their positions.

    Having a slightly better understanding of Dembski's work, I can confirm that your statement about Dembski claiming that he "...cannot detect non-design" is misleading since the admission is, as I remember, that in the effort to detect design it is possible to have false negatives. (Please give me a reference to Dembski stating your point. As I said I know very little of the subject.)

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  30. Michael:

    The uniformity of nature makes science possible and accepting this as an unchallenged axiom is exactly the same as saying miracles can happen, you just have to belief that things in nature will keep going the way it did.

    No need to accept anything in science as unchallenged. One goes by experience. If the sun doesnt' "come up" tomorrow, that will be the day.

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  31. Michael-

    Not so much that it is possible to have false negatives, but that there is no way at all to rule out false positives.

    In Dembski's words:

    "As I’ve said (till the cows come home, though Thomist critics never seem to get it), the explanatory filter has no way or ruling out false negatives (attributions of non-design that in fact are designed). I’ll say it again, ID provides scientific evidence for where design is, not for where it isn’t."

    http://www.uncommondescent.com/intelligent-design/does-id-presuppose-a-mechanistic-view-of-nature/

    Personally, the three criteria I've listed above are in order of importance. If ID had a scientific, evidence supported, irrefutable designed-from-undesigned detector, that led to testable hypotheses that are useful to understanding biology, that would be game-changing. It would be on par with evolution.

    But its not there, and hell if anything I've seen in ID amounts to a controversy worth teaching.

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  32. Example: Environments change in an unpredictable way. Life has ways to adapt to a lot of changes.
    Van Valen hypothesized that the purpose of sex is part of an ongoing "war" between our immune system (IS) and parasites. Variability is the way to keep up with the parasites. This means parents must try to get a "super IS"(i.e. mother and father have very different IS's) for their offspring. The super-IS is able to fight against more types of parasites because it has more "weapons". Therefore, we must find a preference for different IS's in human mate choice.
    What studies suggest is:
    A man's "pheromone cocktail" is considered to be attractive (smell) to a woman if it differs a lot to hers, and vice versa.

    Just a short example but the theory of evolution fits by starting with Van Valen's "sex-war" followed by human mate choice by sexual selection.

    Now if I had to talk about this as a person pro-ID.

    I do not only want to say: Sexual selection does not exist and Van Valen was wrong.
    I want to have reasons to back this up.
    Furthermore, I want to be able to explain those things (i.e. Imune system vs. parasites, human mate choice, female choice, etc) by ID.

    Obviously noone knows everything, so if you cannot answer those questions, I'm sure you have other examples that involve ID and human life in contrast to what evolution says about that particular topic.
    I hope this was precise enough.

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  33. Michael -

    For when you return -

    Your point about causal regression is a strawman. Firtly, when it comes to life, all we need is a living, self-replicating organism and from that point on the theory of evolution neatly accounts for this giving rise to the amazing complexity and diversity of life we see around us. So go back further than this point and you are no longer talking about evolution. The theory of evolution only concerns how life adapts and devolps once it had already begun to exist. The theory of evolution is not at all challenged by asking what came BEFORE life.

    So where did this first organism come from? How did we get from inanimate chemicals to organic, living molecules? Well, that's abiogenesis - a different (though related) theory. Now it's true that we by no means have all the answers here, but real scientists are making tangible progress in this field. Scientists, it cannot be stated enough, who are decidedly NOT simply giving up and saying 'It's too complicated for us, let's just declare a miracle and go home', which ID is effectively doing.

    And going back further to the Big Bang? Well, logically, there is either an infintie regression of causes, or there was a first cause. The thing is, we already have a candidate for a first cause - the quantum vaccum. We know it exists and we know several of its properties. Did this have a cause? We have no way of knowing (yet). But deciding not only that it must, but also that it must be a specific agent - this intelligent designer - is falacous. We have no evidence that this being exists and it still does not solve the infinite causation problem. It is an unnecessary and unhelpful component.

    Let's be generous for a moment. ID is not necessarily an unscientific hypothesis IN PRINCIPLE. The idea that the universe/first living thing was zapped into existence by an external agent is a hypothesis that could be put to the test. But this would necessitate speculating about the desires, capabilities and motives of the designer - speculations we could then use to make predictions and formulate experiments.

    But is anyone actually doing this? Not to my knowledge. A common rebuttal is that the designer's capabilities/motives/desires cannot be guessed by us. Yet this leaves us without being able to test ID as a scientific hypothesis.

    Until it has been tested ID is not science. It is a hollow and unfulfilling catch-all explanation.

    And as for archaeology, the comparrisson is again, fallacous. When we discover ruins, artifacts in the ground, we know that there were people - agents capable of making them. So no supernatural agents are inferred. Archaeology poses NATURAL agents for its discoveries. ID poses SUPERNATURAL ones. The distinction may seem insignificant to you, but it is the difference between a scientific field and a non-scientific one.

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  34. Michael -

    Gosh, we do just keep on going, don't we?

    Science is built on inductive reasoning. It cannot be otherwise. Science formulates theories based on experiments and observations. That is inductive reasoning.

    And yes, this does rest on the assumption that natural laws are constant - an assumption which may be wrong, but science has been very productive making this assumption all the same, which kinda implies it is probably correct.

    But why do you say this assumption is the same as accepting a miracle? That makes no sense. A miracle is a VIOLATION of natural laws. To believe in constant natural laws is to believe miracles do NOT happen.

    Which, as I said, is science's metaphysical position.

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  35. Wouldn't an RNA based genome have the same requirement as a DNA based genome for a repair mechanism? So does saying life started with RNA solve the problem? And,if I'm not mistaken, RNA is less stable than DNA, so the need for a repair mechanism would be even greater. Please correct me if I'm wrong.

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  36. RobertC,

    Both Dr Behe and Dr Minnich testified at the Dover trial that ID does not require the supernatural.

    Also we have this ID faq:

    But Doesn't Intelligent Design Refer to Something Supernatural?

    And I will engage over on UD.

    Stay tuned to see if I get posted or not...

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  37. Ritchie:
    "Does Intelligent Design not require an Intelligent Designer?"

    Yes, but that doesn't mean the designer(s) were/ are supernatural.

    Ritchie:
    "Every time we discover a new fossil/animal species the theory of evolution is being tested - does it fit into the pattern of genetic/geological nested hierarchies which the theory of evolution absolutely necessitates?"

    The theory of evolution doesn't predict a nested hierarchy.

    Only design produces a nested hierarchy.

    That is a fact.

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  38. ID can be testaed and falsified.

    ID is based on our knowledge of cause and effect relationships.

    As with all design inferences- arachaeology and forensics included- all one has to do to refute it is to demonstrate that blind, undirected processes- ie nature, operating freely- can account for it.

    IOW all you ID critics have to do is to actually produce some positive evidence for your position.

    Not some general reference to "evolution" or "Common Descent".

    Everything Common Descent can explain Common DEsign explains better.

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  39. Joe G -

    "Yes, but that doesn't mean the designer(s) were/ are supernatural."

    ???

    I'm obviously being a bit thick here, so I'll illustrate my reasoning in the hope you can put me straight.

    The 'Intelligent Designer' is commonly invoked as a grand first cause, for life, the universe, and of course, natural laws. If he/she/it created natural laws, then how can he/she/it be subject to them?

    If he/she/it operates outside of the natural laws that he/she/it supposedly created, then that pretty much is the definition of supernatural.

    So how in Hades could an intelligent designer possibly be natural - that is, be subject to natural laws which he/she/it him/her/it-self created?

    "The theory of evolution doesn't predict a nested hierarchy."

    Another bizarre sentence which appears to make litle sense in English. Nested heirarchies are exactly what the theory of evolution predicts. The cat species is nested within the Felis genus, which is nested within the Felidae family, which is nested within the Carnivora order, etc. This is because of common descent. It is precisely what the theory of evolution predicts.

    "Only design produces a nested hierarchy."

    Again, che??? If everything was designed, why on Earth would creatures be arranged in nested hierarchies? Why wouldn't each species simply be an entirely unique and perfectly adapted to its environment without reference to other species which are, after all, unrelated to it?

    "ID can be testaed and falsified."

    Can it? How? Give me an example. A test which has actually been carried out would be preferable, but even something hypothetical would do. Exactly how would you test ID and what would falsify it?

    "As with all design inferences- arachaeology and forensics included- all one has to do to refute it is to demonstrate that blind, undirected processes- ie nature, operating freely- can account for it."

    You mean such as Lenski's bacteria study which meticulously detailed speciation occuring through blind, undirected processes?

    "Everything Common Descent can explain Common DEsign explains better."

    Let's put that to the test. Why do all mammals, from humans to cats, from whales to bats - creatures which have as varied lifestyles and habitats as you can imagine - all have the exact same arrangement of bones in the forearms, whether the forearms are legs, wings or flippers? Common descent says, 'Because they all evolved from the same common ancestor'. What is common design's 'better' answer?

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  40. Zachriel:
    "Science doesn't deal in "proof," but evidence. If you want to make sense of the evidence, you need to start with the Theory of Evolution, in particular, the Theory of Common Descent."

    If you have only evidence you can´t state:

    "DNA is almost certainly not the original material of the genome"

    Because evidence can be misleading.


    "A population. But the boundaries are not necessarily distinct during the threshold period. If you were to look at life at that time, though, you may not recognize the universal ancestor as it was not a single organism, and there were probably many other competing populations that did not leave descendents."

    This means that not all the life haas the same LUCA as the common ancestor hipotesis state.
    Maybe the plants derived from a part of that population and animals from another. Also maybe fishes and mammals evolved from different clusters of the primitive life. All the evidence for common ancestor could be convergent evolution.

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  41. "Yes, but that doesn't mean the designer(s) were/ are supernatural."

    Just something that was around billions of years ago till now, constantly tweaking biology in a way that looks like evolution to all scientists, that is light years ahead of us in technology. I think the (alien mother) ship has sailed on this one. I look forward to your engagement of the "Designer is God" orthodoxy. Chances are this line of logic will not be tolerated, and will remain unposted. ID knows what it stands for.

    "The theory of evolution doesn't predict a nested hierarchy."

    Why, yes, yes it does. In fact, the absence of clean phylogenies is often used here, in AIG, etc. as an assault of an evolutionary prediction.

    I can't think of a single human design that would truly form nested hierarchies based on multiple components, where the differences match with time of divergence. Prove me wrong and present one. Design allows breaks-stops, starts, replacement. It isn't contingent on the precursor. Evolution respects its history. Design doesn't.

    "As with all design inferences- arachaeology and forensics included- all one has to do to refute it is to demonstrate that blind, undirected processes- ie nature, operating freely- can account for it."

    Archeology and forensics have a design detector. They operates by analogy with human design. We recognize the types of things we can make, and when we see one, we say aha-a human made that. What is the design detector for life?

    And:
    "As I’ve said (till the cows come home, though Thomist critics never seem to get it), the explanatory filter has no way or ruling out false negatives (attributions of non-design that in fact are designed). I’ll say it again, ID provides scientific evidence for where design is, not for where it isn’t."

    http://www.uncommondescent.com/intelligent-design/does-id-presuppose-a-mechanistic-view-of-nature/

    So if you guys can't say what design isn't, how can we rigorously proof life isn't designed?

    Its a non-hypothesis, with a non-method, and you want us to rigorously and methodologically disprove it. Yikes.

    Until then, all evidence for common descent and evolution stands. I would especially focus on experimental proofs that random mutation and recombination plus selection yield successful, novel phenotypes (increased information, if you must). Selection is nature's 'designer'-it gives the appearance of fit.

    Take Darwin's finches-you could argue their beaks are perfectly designed to fit their food. No? Match perfectly. Complex-many genes go into their formation. But we know the genetic diversity in birds was selected by the pressure of their food to make this match. We even now know the genes. What does a design hypothesis add to our understanding?

    "Everything Common Descent can explain Common DEsign explains better."

    So if everything is designed, how can one separate design from nature? How is the process different? Have you reduced the position back to theistic evolution? Name one thing that common descent has explained that common design presents a hypothesis with greater explainitory and predictive power.

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  42. Joe G gets confused:

    "The theory of evolution doesn't predict a nested hierarchy."

    Nonsense. Special creation doesn't predict a nested hierarchy. Naturalistic common descent absolutely does. It is a hierarchy of the degree of divergence between species, based on the time since their divergence, whether morphological or molecular.

    "Only design produces a nested hierarchy."
    If a number of birds starting at the same point starting flying off at different times, in different directions, the distance between the birds could be modelled as a nested hierarchy that could be 'rooted' at the point of their release. No 'design' is needed. If physical distance is replaced with genetic distance and individuals with species, when exactly does design become invoked out of necessity?

    "Everything Common Descent can explain Common DEsign explains better.

    How does common design explain embryonic baleen whale teeth that are reabsorbed before before birth better than a toothed ancestor? The jaw needs to be spaced, just as terrestrial mammals need their jaws to be spaced. Common descent explains why ephemeral, embryonic teeth perform this role in baleen whales - how does common design better explain this, given that simpler means could be employed?

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  43. Hi Ritchie,

    I only have time to respond to the claim that my argument is a strawman argument. The best way is to point out to you that the foundation of the argument is the claim that a design inference will lead to insurmountable complexity (as you claimed). It is therefore a red-herring to try and bound this argument to origin of life and evolution. The argument is about the explanatory value of the study of all causes, known or inferred by science.

    Your attempt to minimize your dilemma of the an infinite causal regression is futile and make no sense when you claim that the scanty and metaphysical claims that evidence for the quantum vacuum brings an end to causal regression. Quantum Vacuum is purely speculative and has no bearing on the question of causal regress.

    You have not touched the hart of my argument that claims that it is not logically sound to argue the existence of an initial state of nothingness and countering the problem with an infinite causal regression just compound the explanatory complexity worse than any claim you or Dawkins made about a design inference. It is logically far better to talk about "Divine Simplicity" (google it...)

    It should be to your credit to investigate philosophy's fresh new thinking in this regards because Dawkins and your statement is one that can best be answered by philosophers, not biologists, in vainly trying to protect the notion of materialism.

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  44. abimer:

    Why does evolution predict a nested hierarchy? Life couldj have evolved in any direction.

    ReplyDelete
  45. Evolutionists talk about vestigal organs. I'm curious about nascient organs, organs that are in the process of formation. For example, a half-feather, or half an eye. Are there any known examples, in extant organisms, or in fossils. If not, why not?

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  46. Why is it that evolutionists love to bring up nested hierarchies yet they have no idea what a nested hierarchy is?

    Common Descent would expect a sequence.

    Darwin understood this and that is why he said if all the transitionals were still around we wouldn't observe the nested hierarchy that we do.

    Also nested hierarchies require a direction and evolution does not.

    IOW evos prove that tey are clueless by baldly claiming the ToE predicts a nested hierarchy.

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  47. Ritchie,

    No I have time to respond to:

    "But why do you say this assumption is the same as accepting a miracle? That makes no sense. A miracle is a VIOLATION of natural laws. To believe in constant natural laws is to believe miracles do NOT happen."

    Let me start by reminding you that both David Hume and Karl Popper (Philosophy of Science were considered by these renown scholars.) Both of them found the brute fact of the uniformity of nature very disturbing and challenging.

    What is very interesting is that Hume used a probability argument to claim the impossibility of violating the laws of nature. Its been thoroughly criticized and rejected by most modern philosophers. Popper use falsification as the basis for his arguments. (too complex for me to fully understand)

    What argument would you like to use as proof that the uniformity of nature is in fact immutable. Can you or anyone make accurate observations of all entities in our reality?

    There you have it... Probability does not support the exclusion of miracles simply because it is impossible to measure all events. It is pure faith you have in the odds you are looking at and funny enough you seem to reject the odds against evolution outright. How do you decide your bets?

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  48. Ritchie:
    "The 'Intelligent Designer' is commonly invoked as a grand first cause, for life, the universe, and of course, natural laws. If he/she/it created natural laws, then how can he/she/it be subject to them?"

    Well Ritchie your position regresses to the same point as ID.

    Your position required the laws to be created.

    Therefor, by your "logic", your position requires the supernatural.

    But I digress.

    Just because the designer designed the laws does not mean it is above them.

    The best we can say is the designer was PRE-natural.

    Nested hierarchies-

    Nested hierarchies require summativity.

    All nested hierarchies are constructed with defining characteristics,

    Descent is not a defining characteristic.

    The best we can hope for from Common Descent is a sequence.

    A sequence that includes transitionals.

    Transitionals which by their very definition would violate the distinct categories required by nested hierarchies.

    Reptile-like mammmals for example would have to be included in both sets- mammals and reptiles violating the nested hierarchy.

    NH must exhibit summativity.

    You don't get that from a lineage which is what we would expect from Common Descent.

    Testing ID-

    If it meets the criteria and cannot be reduced to matter, energy, chance and necessity then we infer design.

    The criteria for inferring design in biology is, as Michael J. Behe, Professor of Biochemistry at Leheigh University, puts it in his book Darwin ' s Black Box: "Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.”


    Now to refute that design inference all one has to do is demonstrate it is reducible to matter, energy, chance and necessity.

    IOW Ritchie all you have to do is to actually produce positive evidence for your position!

    BTW Lenski's experiment did not demonstrate blind, undirected processes are at work.

    And YECs accept speciation so you don't have anything there.

    As for Common Descent no one knows if the transformations required are even possible.

    No way to take a fish embryo, tinker with it until legs develop.

    IOW your position is untestable.

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  49. RobertC,

    If you don't like the design inference then all YOU have to do is to actually start providing positive evidence for your position.

    However it is obvious that you can't.

    Yes we have reliable design detection techniques.

    what is it that prevents us from using them in biology?

    Please be specific.

    As for nested hierarchies:

    If we start with a population A which gives rise to two other populations A1 and A2, does population A consist of and contain A1 and A2? No, therefor there isn;'t any nested hierarchy.

    It is that simple.

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  50. Michael -

    I should perhaps point out that I am not claiming the Big Bang (or whatever preceeded it by however many steps) came from absolute nothing. What I am saying is that we simply don't know what came before it, and have no way of finding out (currently). But postulating beings such as intelligent designers is utterly futile.

    It is unnecessary because we have no evidence for the existence of one, and it is unhelpful because it does not solve any regression problems. An intellegent designer is simply a totally hypothetical extra link in a chain of causes.

    Unless we accept an infinite chain of causes, there must have been a first cause. But an intellegent designer is both superflous and unhelpful as a first cause.

    As for the quantum vacuum I assure you it is not purely speculative at all. We have empirical evidence for it. Google it.

    "What argument would you like to use as proof that the uniformity of nature is in fact immutable?"

    You misunderstand. I don't think there is proof. I acknowledge that we cannot (or, at least, don't) know for certain that the laws of nature are immutable. Nevertheless, science in its entirety is built upon the ASSUMPTION that they are.

    It makes this assumption because it must. If the laws of nature are not immutable then we have no reason to trust the results of our own expetiments. What is true today might not be true tomorrow. So we wouldn't bother doing any experiments and science as a whole would come to a total stop.

    Perhaps this assumption is wrong. Which would pretty much invalidate the whole of science. But the fact that science gives us so many things which really do work kinda suggests it is an accurate representation of how the world works.

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  51. Blas: Because evidence can be misleading.

    Yes, it can. That's why all scientific claims are only tentative, why they are subjected to constant testing, and why they may be revised in the light of new evidence.

    Blas: And only one organism crosses that threshold? Only one could become LUCA? Scientifically we can say that there are nor more than one similar LUCA?

    Zachriel: A population. But the boundaries are not necessarily distinct during the threshold period. If you were to look at life at that time, though, you may not recognize the universal ancestor as it was not a single organism, and there were probably many other competing populations that did not leave descendents.

    Blas: This means that not all the life haas the same LUCA as the common ancestor hipotesis state.

    The other lineages didn't leave descendents.

    Blas: Maybe the plants derived from a part of that population and animals from another.

    The previous statement merely laid out the hypothesis, not the evidence, however, the evidence strongly indicates that all eukaryotes share a common ancestor.

    Blas: Also maybe fishes and mammals evolved from different clusters of the primitive life.

    There is no reasonable scientific doubt that fishes and mammals share a common ancestor. Indeed, we can watch the transition through the geological strata.

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  52. natschuster: Why does evolution predict a nested hierarchy?

    Uncrossed descent forms a tree structure. If we group twigs by branch and limb, they necessarily form a nested hierarchy. Each twig has one-and-only-one path to the trunk, but each limb can have any number of branches and twigs. Uncrossed descent with modification predicts a (reasonably consistent) nested hierarchy of traits (assuming rates of variation short of saturation). This is mathematical trusim.

    The question then is whether or not life forms such a nested hierarchy consistent with the hypothesis of common descent along uncrossed lines. And it does, for most taxa. In addition, this nested hierarchy applies across time!

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  53. JoeG-
    "Yes we have reliable design detection techniques."

    Well that settles it. Care to give me one designed and one undesigned structure? What is your criteria? Be quantitative-use 'design units' or whatever.

    The nested hierarchy in biology is:
    "Nested hierarchies are the organizational schemes behind taxonomies and systematic classifications. For example, using the original Linnaean taxonomy (the version he laid out in the 10th edition of Systema Naturae), a human can be formulated as

    {H. sapiens} subset {Homo} subset {Primates} subset Mammalia} subset {Animalia}

    Taxonomies may change frequently (as seen in biological taxonomy), but the underlying concept of nested hierarchies is always the same."
    http://en.wikipedia.org/wiki/Hierarchy

    Get it? Our phylogenies recapitulate these taxonomies. Individual molecules even form them:

    Oh, and what is the human-designed example that has multiple components that form such a phylogenetic trees?

    Still waiting for that diagram...

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  54. Joe G -

    "Your position required the laws to be created. Therefor, by your "logic", your position requires the supernatural."

    Ummm, no. Only if they were consciously created by some outside agent. Which is not my position at all. That's ID...

    "Just because the designer designed the laws does not mean it is above them. The best we can say is the designer was PRE-natural."

    Ummm, no. Any being that can be said to have designed natural laws must have... well... designed them. You cannot design something which is more complicated than yourself. The designer must be more complex and more complicated than the 'designed'. If not, then it was not designed.

    As for nested I'm afraid it is you who does not understand them.

    All humans are nested inside primates. All primates are nested inside 'mammals'. All mammals are nested inside 'vertibrates', etc.

    These are nested hierarchies. And common descent provides an explanation - a single vertibrate gave rise to all mammals, a single mammal gave rise to all primates, a single primate gave rise to all humans, etc.

    "The best we can hope for from Common Descent is a sequence."

    Sequence? You do realise common descent BRANCHES...?

    "A sequence that includes transitionals. Transitionals which by their very definition would violate the distinct categories required by nested hierarchies."

    Not at all. Why would they?

    "Reptile-like mammmals for example would have to be included in both sets- mammals and reptiles violating the nested hierarchy."

    Not at all. They would be placed at the overlap between the two groups. They would not, for example be placed in a 'fish' group or 'insect' group, would they? They still appear on the tree of life between reptiles and mammals.

    "If it meets the criteria and cannot be reduced to matter, energy, chance and necessity then we infer design."

    Give me an example. What, exactly, cannot be reduced to matter, energy, chance and necessity?

    "BTW Lenski's experiment did not demonstrate blind, undirected processes are at work."

    Elaborate.

    "If we start with a population A which gives rise to two other populations A1 and A2, does population A consist of and contain A1 and A2? No, therefor there isn;'t any nested hierarchy."

    Fail.

    If A gives rise to A1 and A2, then A1 gives rise to A1(a) and A1(b) and A2 gives rise to A2(a) and A2(b), then A1(a) and A1(b) are both contained within A1. A2(a) and A2(b) are contained within A2. And both A1 and A2 are contained within A. That is precisely what nested hierarchies are.

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  55. This comment has been removed by the author.

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  56. JoeG-

    "And I will engage over on UD.

    Stay tuned to see if I get posted or not... "

    Apparently not. That place is a bastion of free speech. Ironic for people who support lawsuits about free speech in the workplace, support teaching the controversy, etc.

    I understand the need to limit trolls, and abusive comments, but when one of their own supporters can't get a word in because they aren't on board with the orthodoxy, that is really telling.

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  57. natschuster -

    "Evolutionists talk about vestigal organs. I'm curious about nascient organs, organs that are in the process of formation. For example, a half-feather, or half an eye. Are there any known examples, in extant organisms, or in fossils. If not, why not?"

    What is an organ in the process of formation? If, in another million years, the human eye will have evolved to be twice as good as it is now, then our current eyes are 'half-eyes', aren't they? But then if, in another 2 million years, the human eye is twice as good again, then those eyes from a million years in the future will be 'half-eyes'...

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  58. "I'm curious about nascient organs, organs that are in the process of formation. For example, a half-feather, or half an eye. Are there any known examples, in extant organisms, or in fossils. If not, why not?"

    Good question. Ritchie is right-but I'll add a few systems.

    Essentially eye spots are an eye component. Patches of photoreceptors don't give binocular vision, but they allow some sense of light and allow phototaxis.

    Add little cups, like planarians, and you've got directionality. Then there are pinhole camera eyes without lenses and corneas, then ones like ours.

    All do a decent job for their host-but with respect to a vertebrate eye, they could be considered partial.

    Another example: tetrapod legs evolve from fins. They don't show up with cheetah legs-but each step (in the cheetah lineage, not all lineages, and not implying some 'goal') is s partial organ when compared to the final product.

    As for "half feathers," some fossils might show exactly that:

    http://www.sciencedaily.com/releases/2001/04/010427072701.htm

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  59. After years of arguing about nested hierarchies, Joe still haven't figured out what they apply to. Clades, Joe! Nested hierarchies apply to clades!

    If population A gives rise to populations A1 and A2 then clade {A,A1,A2} contains clades {A1} and {A2}. Write that down.

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  60. Natschuster:"abimer:

    Why does evolution predict a nested hierarchy? Life couldj have evolved in any direction. "


    Precisely because of common descent - life may evolve in any direction, as you say, but is constrained to do so from an ancestral state.

    The result is a series of branching lineages that share a common root at their base. The extant species form a nested hierarchy based on their degree of separation.

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  61. Wher did the fishes fins come from? And are there any eyespots in the procees of formation? Every example sited starts with a fully functioning organ. Are there any examples of a organ that is not yet functioning? If not, why not?

    And according to S.J. Gould, the Cambrian fauna had much more variability than modern animals. There was a much greater variety of basic body plans. The nested hierarchy might not hold up so well when applied to he Cambrain fauna. And if more of the Cambrian animals survived, then we might not have a clear nested hierarchy today.

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  62. And the dinosaur sited in the link above lived after the archaeopteryx, which had fully formed feathers. Where are the half feathers that lead to the archaeopteryx?

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  63. launzzz:

    ==========
    Example: Environments change in an unpredictable way. Life has ways to adapt to a lot of changes.
    Van Valen hypothesized that the purpose of sex is part of an ongoing "war" between our immune system (IS) and parasites. Variability is the way to keep up with the parasites. This means parents must try to get a "super IS"(i.e. mother and father have very different IS's) for their offspring. The super-IS is able to fight against more types of parasites because it has more "weapons". Therefore, we must find a preference for different IS's in human mate choice.
    What studies suggest is:
    A man's "pheromone cocktail" is considered to be attractive (smell) to a woman if it differs a lot to hers, and vice versa.

    Just a short example but the theory of evolution fits ...
    ==========

    It does? How does the theory of evolution fit this theory? Continuing ...



    ==========
    by starting with Van Valen's "sex-war" followed by human mate choice by sexual selection.

    Now if I had to talk about this as a person pro-ID.

    I do not only want to say: Sexual selection does not exist and Van Valen was wrong.
    I want to have reasons to back this up.
    Furthermore, I want to be able to explain those things (i.e. Imune system vs. parasites, human mate choice, female choice, etc) by ID.
    ==========

    You just did explain them by ID.

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  64. Timcol62:

    ======
    But it's not hard to see of course that he really isn't. Just look at the language in the OP - "incredible", "sophisticated", "absurd".

    These are all value judgements of course - after all why is it "incredible" - incredible compared to what exactly? Just because it seems incomprehensible to us that simply makes it "incredible"?

    ... So Cornelius, please don't trot out all that nonsense about you being "theory neutral" -
    ======

    It is "incredible" with reference to the evolution explanation, of course.


    ======
    On March 30th, you declared that you believe that there is a supernatural cause to evolution/origins -
    ======

    But of course I explained the basis of that belief, which unlike you and evolutionists, is empirical.


    ======
    you also think that supernatural agent is the Christian God. You have provide absolutely no evidence to back up your claim. Curiously, you also said you talk about these beliefs "all the time", although it is quite clear you don't and possibly even regret what you've said.
    ======

    No, I don't regret saying the Christian God created the world, any more than Francis Collins would be when he says the same.

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  65. natschuster -

    "Every example sited starts with a fully functioning organ. Are there any examples of a organ that is not yet functioning? If not, why not?"

    No, there are no 'not-yet-functioning' organs. Nature has no foresight. It does not plan to build organs in advance, and then slowly build them up until they eventually become functioning. Organs build up in a series of IMPROVEMENTS.

    The eye, for example. Let's imagine a time before eyes - worms, jellyfish and eyeless proto-fish living in the seas. Then imagine a single proto-fish which, through a random mutation, develops a single, light-sensitive cell. (The ACTUAL history of the eye is unimportant to the point I am trying to make here.) This puts this individual proto-fish at an advantage over his fellows because he can detect passing shadows - which may be approaching predators - or help him judge how deep he is in the water. So his chances of survival to reproduce have increased.

    Imagine he passes on his gene for a light-sensitive cell, and this becomes the norm in the species. Now, several such cells are better than just one since they can see more. So if any of these proto-fish with 'eye' cells are born with a few light-sensitive cells rather than just one, they are at an advantage over their fellows. Now if those cells formed a cup shape rather then a flat patch, that is even more of an advantage, since you can better detect where light comes from. If you find that hard to imagine, perhaps this will help: http://www.youtube.com/watch?v=7jEhzAn1hDc&feature=related

    I feel I should also point out that just because a cup is better than a patch, that will not influence the proto-fish developing a cup shape DIRECTLY. The fish won't decide to develop the cells in a cup, or actively try to do so. Random mutation is random. A random mutation would as likely arrange the cells in a bump as it would a cup - or scatter the cells further apart. It is just that such muations would be disadvantageous to the first individual which developed them, and so their chances of surviving and passing on such genes would go down. A cup IS an advantage, so the chances of this gene being passed on is much better.

    The point is that right from the start, the earliest feature which could reasonably be called the first precursor of the eye must have been an advantage over not having one - and at EVERY step of the eye's development, each tiny little step had to be an improvement on the last.

    A non-functioning organ is useless - worse than useless, for it is a needless waste of precious resources. So a non-functioning organ will be selected against, not for.

    This is not just applicable to the eye, but to every single natural organ you could name. They all were built via a series of improvements, not slowly and meticulously constructed like, say, a car enguine, which is useless unless fully complete.

    We do still find very primitive eyes in some creatures - particularly moluscs. Should we refer to them as 'half-eyes'? I say no. They function perfectly well. But moreover, they might never develop into more complex eyes. Simple though they are when compared to human eyes, there is no guarantee that natural selection will pressure the eyes of these creatures to become better. They may already be exactly as good as their host needs them to be.

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  66. natschuster -

    "And according to S.J. Gould, the Cambrian fauna had much more variability than modern animals. There was a much greater variety of basic body plans. The nested hierarchy might not hold up so well when applied to he Cambrain fauna. And if more of the Cambrian animals survived, then we might not have a clear nested hierarchy today."

    There were indeed more body plans back in the Cambrian seas. But that is not a challenge to nested heiracrchies. I don't really understand why you think it would be.

    All it really means is that certain body plans (for example chordata - having a backbone, which gave rist to all modern fish, amphibians, reptiles, birds and mammals) went on to dominate life, while other body plans went extinct. Wind back the clock and let other body plans dominate and they too would branch and inevitably form nested heirarchies. They wouldn't be the SAME nested heirarchies as the ones we have today, but they would form them all the same.

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  67. My point about nested hierarchies is that evolution deos notreuire or predict nested hierarchies.

    And are there actual fossils that show the evolution of, lets say, the trilboite eye from a primitive eyespot? And if not, why not?

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  68. sorry, typos

    should be "does not require or predict"

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  69. "My point about nested hierarchies is that evolution [does not require] or predict nested hierarchies."

    That's simply incorrect. It does. Related species share features of common ancestors. The more recent the ancestor, the more features will be shared. That's absolutely fundamental and presicely what the theory of evolution predicts.

    If you don't think so, then I challenge your understanding of the theory of evolution as a whole. What exactly do you imagine the theory of evolution IS? Please explain it to me in your own words.

    "And are there actual fossils that show the evolution of, lets say, the trilboite eye from a primitive eyespot? And if not, why not?"

    There is indeed. In fact trilobites developed three different types of eyes, all of which are widely represented enough in the fossil record to study: Holochroal eyes (packed hexagonal lenses with a single corneal membrane) Schizochroal eyes (fewer lenses, but seperate, and each with its own cornea), and Abathochroal eyes (far fewer lenses still but with a sclera seperate from the cornea).

    But going back as far as the very first creature with an eye spot, no the fossil record is virtually non-existant. This is because the very first eyes seem to slightly pre-date the Cambrian Explosion. Indeed, many biologists such as Andrew Parker have made convincing cases that the evolution of eyes could have been the great innovation which fuelled the 'explosive' biodiversity of the Cambrian.

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  70. Ritchie:

    ======
    "My point about nested hierarchies is that evolution [does not require] or predict nested hierarchies."

    That's simply incorrect. It does. Related species share features of common ancestors. The more recent the ancestor, the more features will be shared. That's absolutely fundamental and presicely what the theory of evolution predicts.
    =======

    It is more complicated than that. If we traveled to another planet and found no nested hierarchy evolution would not be harmed. It could explain it as many OOL events, or as temporarily rapid evolution at some previous time. Both explanations have been used in fact.

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  71. Dr Hunter:

    Both explanations have been used in fact.

    By whom?

    When?

    Where?

    Why don't you back up your assertions without being asked?

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  72. David:

    David Penny and co workers said that rapid evolution could be used to explain loss of phylogenetic signal.

    http://darwins-god.blogspot.com/2009/06/david-penny-religion-can-be-subtle.html

    And indeed that explanation has been used where useful. For instance, evolutionists used it to explain how proteins with highly constrained sequences (eg, histone IV) could have got a start. Rapid evolutionary rates have also been used as an explanatory device for problems with the molecular clock. And of course, this explanation is at the heart of punctuated equilibrium, to explain the sudden appearance of new forms in the history of life.

    As for multiple OOL events, that too has been suggested, but not as commonly. I don't have a good reference for you though. Sorry about that.

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  73. Ritchie:

    IF some of the Cambrian species survived and produced offspring that survived until today, we might see a greater variety of body forms. This would make it harder to arrainge them into a hierarchy. And if evolution can turn a bacteria into a blue whale, it is very powerful. Why can't it produce organisms that don't clusture into clear hierarchies? Why couldn't it produce something with a reptilian jaw that nurses its young, for example?

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  74. Cornelius -

    "If we traveled to another planet and found no nested hierarchy evolution would not be harmed."

    I am having trouble imagining a rich ecosystem which evolved through the process of evolution which does not produce nested hierarchies. How would that work, exactly?

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  75. Ritchie:

    ===
    I am having trouble imagining a rich ecosystem which evolved through the process of evolution which does not produce nested hierarchies. How would that work, exactly?
    ===

    As I said, one explanatory device is that you have spurts of rapid evolution (you know, due to environmental shift, etc, etc, the usual stories) which erase the phylogenetic signal. This is a tried and true explanation, so no problem invoking it again for our distant planet.

    OTH, another suitable explanation would be multiple OOL events. After all, if life can evolve once, why not many times. But once it got going, of course there would be strong conservative forces against too much deviation. Most mutations would be harmful, and strongly selected against, blah, blah, blah ... .

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  76. natschuster -

    "IF some of the Cambrian species survived and produced offspring that survived until today, we might see a greater variety of body forms. This would make it harder to arrainge them into a hierarchy."

    I'm not totally sure I know what you're saying.

    Consider this - small mammals lived in the shadow of the dinosaurs for tens of millions of years. Then could never get a foothold because the dinosaurs dominated pretty much every terrestrial ecosystem above a certain size. Then, suddenly, the dinsouars were gone and the surviving mammals had a chance to bloom and 'explode' in variety and body plan to take advantage of the empty niches left by the dinosaurs.

    My point? Well, with a clean slate experimental new body types compete for supremacy and the most sucessful ones go on to bloom in variety and dominate, thus stifling the development of others. It has happened several times - the slate is effectively wiped clean after huge mass extinctions which decimate ecosystems, such as the one which killed the dinosaurs and allowed mammals to bloom, or indeed the Permian-Triassic extinction which allowed the dinosaurs to come through.

    Nor do I find this a difficult concept to apply to the Cambrian seas - the oceans are teeming with new experimental life forms. The most successful ones dominate, blossoming in rich variety and stifling the development of other, less sucessful ones, which may well go extinct.

    I don't understand your objection to this. Nor do I understand why you seem to think that nested hierarchies would be less likely if different or more Cambrian species had survived until today.

    Unless perhaps you misunderstand the term nested hierarchies...? When we talk about them we are just talking about clades; that is, a single ancestor and all its descendants. So, for example. mammals are a clade. Rodents are also a clade NESTED WITHIN the mammal clade. Mice are another clade NESTED WITHIN the rodent clade. Doormice are then a clade NESTED WITHI|N the mouse clade, etc.

    "And if evolution can turn a bacteria into a blue whale, it is very powerful."

    Indeed.

    "Why can't it produce organisms that don't clusture into clear hierarchies?"

    The question is odd. It is simply the way evolution functions.

    "Why couldn't it produce something with a reptilian jaw that nurses its young, for example?"

    In theory it COULD. It just hasn't. There are many things evolution COULD POTENTIALLY produce - an almost infinite number of things, in fact. But being as there has only been a finite number of species, there will be a great many things evolution has not produced.

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  77. Cornelius -

    I'll happily admit I'm probably being thick on this one, but I still don't see.

    Indulge me in a thought experiment. Imagine we have a species. Lets say mice-like rodents. We plonk them down on an island free from animals but with some plants and food, etc.

    Over time we might see selection pressures changing certin groups of mice. For example, ones which live near rivers might adapt features to help them them cope with the water - webbed feet and thick thur, perhaps. Another group, say ones who live in hot open plains might develop other features - thin fur and long legs to raise their bodies a little from the hot ground.

    Whatever the case, if we put a single species in a variety of environments, we might well expect splinter groups of that species to adapt slightly to their specific environment.

    And viola; we have nested hierarchies. The aquatic mice are a clade nested within the whole mouse clade. The 'hot plains' mice and another clade within the whole mouse clade.

    If I try to imagine an alien world without nested hierarchies, I can only image the sort of world ID would create - where totally unrelated creatures lived in their ecological niche and no other - and shared no features with each other.

    Surely this is not the sort of world evolution could account for? However, it is also not the sort of world we live in.

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  78. Ritchie:

    "Surely this is not the sort of world evolution could account for?"

    Your narrative here is not a description of evolution in general, but kind of the clean, textbook version. To understand how evolution has a wider scope of explanations, it would help to consider that evolutionists resort to all kinds of explanations to describe the real world we observe. In particular, consider that temporarily rapid evolution is used liberally by evolutionists, and it will erase the nested hierarchy pattern. So yes, evolution very much does have the tools to explain a world without a nested hierarchy.

    In fact, our world does not reveal a nested hierarchy. We might say there is a partial nested hierarchy, in the sense that that pattern does show up quite a bit. But there are important deviations (deviations greater than mere biological noise).

    So if evolution predicts a strict nested hierarchy, then if is false, end of story. But of course that's not the end of the story. As usual, the prediction is not really a hard prediction. It is a soft prediction. Evolution can explain a wide range of outcomes. And there's no doubt they could explain a world where the nested hierarchy was apparent to a lesser degree than our world, or even altogether absent. The explanations have already been developed and used.

    Of course the real story behind the nested prediction is that evolutionary thinking states that God would not do it that way (ie, use the nested pattern, even partially).

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  79. Cornelius -


    Of course the real story behind the nested prediction is that evolutionary thinking states that God would not do it that way


    Or how about 'that there is absolutely no evidence to show that there is a God or designer who would do it that way, or any objective reason other than blind religious faith to believe such a being exists.'?

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  80. Ritchie:

    ===
    Or how about 'that there is absolutely no evidence to show that there is a God or designer who would do it that way,
    ===

    No, the argument is that god *wouldn't* do it that way.

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  81. Ritchie:

    ===
    Or how about 'that there is absolutely no evidence to show that there is a God or designer who would do it that way,
    ===

    Here are some examples of this metaphysical argument.

    "The several subordinate groups in any class cannot be ranked in a single file, but seem clustered round points, and these round other points, and so on in almost endless cycles. If species had been independently created, no explanation would have been possible of this kind of classification." --Darwin

    "If species are separately created there is no reason why they should be created in large groups of fundamentally similar structure." -- G. Carter

    "Could the single artisan, who has no one but himself from whom to steal designs, possibly be the explanation for why the Creator fashioned life in a hierarchical fashion—why, for example, reptiles, amphibians, mammals, and birds all share the same limb structure?"--N. Eldredge

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  82. Cornelius -

    "No, the argument is that god *wouldn't* do it that way."

    The problem with that is that the assertion itself presupposes the existence of such a God.

    We have ne evidence of a God. Therefore it is unscientific to invoke one to explain natural phenomenon.

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  83. Cornelius -

    If you want to hear an evolutionist say it is POSSIBLE that a God exists and that, assuming he does, it is POSSIBLE that he would have created the cworld the way it is, then I for one will gladly admit that.

    And by doing so I have not undermined the theory of evolution in the slightest.

    Invoking a God to explain natural phenomenon is still not scientific.

    And the theory of evolution remains the best explanation of the evidence.

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  84. Dr Hunter,

    Thank you for your response:

    David Penny and co workers said that rapid evolution could be used to explain loss of phylogenetic signal.

    http://darwins-god.blogspot.com/2009/06/david-penny-religion-can-be-subtle.html


    They may have said that, but their paper is lodged behind a pay-wall. Can you provide more documentation? Their abstract says only:

    The theory of evolution predicts that similar phylogenetic trees should be obtained from different sets of character data. We have tested this prediction using sequence data for 5 proteins from 11 species. Our results are consistent with the theory of evolution.

    Hunter:

    As for multiple OOL events, that too has been suggested, but not as commonly. I don't have a good reference for you though. Sorry about that.

    Thank you for your honesty. May I score that as “bluff called?”

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  85. Ritchie:

    ===
    If you want to hear an evolutionist say it is POSSIBLE that a God exists and that, assuming he does, it is POSSIBLE that he would have created the world the way it is,
    ===

    Why would I want to hear that?

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  86. Funny how most Darwinists don't understand their own theory.
    We see this all the time here with commentators like RobertC, Ritchie et al.

    Even funnier the way they swallow elephants yet sift out fleas.

    "Scientists are complaining that the new Dinosaur movie shows dinosaurs with lemurs, who didn't evolve for another million years. They're afraid the movie will give kids a mistaken impression.
    What about the fact that the dinosaurs are singing and dancing?" -Jay Leno

    That pretty much describes how Darwinians "reason".

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  87. This comment has been removed by a blog administrator.

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  88. Ritchie:

    First, please keep the language civil. Acronyms don't get a free pass.

    Second:

    "Merely because you seem rather distracted by the concept that evolutions insist God would not create the world as it is."

    "Distracted ...". That's an interesting way to put it. Evolutionary thought is based on metaphysical premises and I'm the one who is out of line.

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  89. Cornelius -

    Point taken. No offense meant.


    Evolutionary thought is based on metaphysical premises and I'm the one who is out of line.


    My point is that evolutionary thought is not based on those metaphysical premises.

    The only premise evolutionary thought is based on is that we cannot invoke supernatural agents/forces to account for natural phenomenon - the same premise every other theory in science is based on.

    You can very easily explain the theory of evolution without once mentioning God, an intelligent designer, or what they would or would not create. It simply does not need to enter into it at all.

    I think your problem is that you start out with the assumption (and that is the right word) that there is a God/intelligent designer, and then feel it is every competing theory's job to disprove your beliefs before replacing them with alternatives.

    But that is not how science works. By making observations and performing experiments, we collect data. Hypotheses are then formed which explain the data. Hypotheses, which must never assume supernatural forces or agents.

    It is not scientific to invoke the supernatural to account for the movement of the plants, it is not scientific to invoke the supernatural to explain illnesses and their cures, and it is not scientific to invoke the supernatural to explain the diversity and history of nature.

    The theory of evolution behaves no differently in this regard to any other scientific theory. You only think it does because it clashes with your pre-existing religious (again, the right word) beliefs.

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  90. David:

    The Penny et al. 1982 Nature paper is available online here:

    http://www.stanford.edu/~joelv/teaching/249/penny%20etal%20testing%20evolution%20using%20five%20protein%20sequences.pdf

    Google Scholar often brings up links to journal articles that are hosted on the author's personal or university website for those who don't have database access.

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  91. Ritchie:

    "I think your problem is that you start out with the assumption (and that is the right word) that there is a God/intelligent designer, "

    No, not at all. Unfortunately, your reading that in is a typical canard.

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  92. Ritchie:

    If evolution could produce a reptile that nurses, then it could have produced all life so that it does not fall into neat hierachies. I'm not convinced that evolution predicts or requires nested hierarchies. Since we happen to have nested hierarchies, we can say that evolution explains them. If we didn't see nested hierarchies, then we coudl also say that evolution explains that.

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  93. abimer,

    Thanks for the URL and the tip about Google Scholar.

    I see nothing in the Penny et al. paper that supports Dr Hunter's claim. Do you? Dr Hunter?

    Rather, I see a robust rejoinder to Popper's skepticism about the falsifiability of evolutionary hypotheses.

    Incidentally, I am grateful to Dr Hunter for bringing Penny's scholarship to my attention. Penny's Web site:

    http://awcmee.massey.ac.nz/people/dpenny/index.htm

    is a treasure-trove of information about evolution.

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  94. natschuster -

    "If evolution could produce a reptile that nurses, then it could have produced all life so that it does not fall into neat hierarchies."

    ????

    Huh? That's a thoroughly bizarre assertion. That's like saying 'If gravity could have kept a second moon in orbit around Earth, then it could function without pulling things down.' It's just a totally nonsensical non-sequiter.

    Again, I can only conclude you don't understand evolution, nested hierarchies or both.

    Let's try a thought experiment. Iimagine an island populated by just a species of mouse (and stuff for them to eat). There they are all happily living away. Random mutation necessitates that some babies born will have mutations. Most will hinder the individual's chances of survival, so they will die. But just every so often one will be born whose mutation is advantageous. That one will likely go on to survive and reproduce and thus pass on its mutation.

    Now from the very moment that first mutant was born we have a nested hierarchy. In time, perhaps the new mice with the mutation will form their own species. We then have two species of mouse on the island - one of which arouse from the other. So the new species is a clade within the island-mouse clade; a clade NESTED WITHIN a clade; a nested hierarchy.

    That is precisely how evolution operates. The only way I could see evolution NOT producing a nested hierarchy is if a new species always entirely killed off the parent species. Which would mean there was only ever one species of life on the planet.

    Which would be weird. And is clearly not how the world is.

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  95. But hwy couldn't the mice evolve into a whole variety of species that don't form a clear hierarchy? One species could evolve into hundreds.

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  96. The Cambrian fauna don't seem to form a clear hierarchy. And life had been around for 3 billion years. Why couldn't life have continues that way for another ~500,000,000 years?

    And why couldn't the mice in the example above evolve into something catlike, and something doglike, and something beaverlike for example? This would make the hierarchies harder to detect. Or why didn't other reptiles evolve hair and mammary glands, for example, and keep the reptilian jaws?

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  97. natschuster -


    But hwy couldn't the mice evolve into a whole variety of species that don't form a clear hierarchy? One species could evolve into hundreds.


    How can evolution operate without forming hierarchies?

    You have a population. An individual within that population has a mutation that is passed on and is the basis of a new species. That is how new species are formed. So new clades are formed 'within' old ones. And viola, you have nested hierarchies.

    That's just how evolution works.

    How could new species POSSIBLY arise without forming nested hierarchies?


    The Cambrian fauna don't seem to form a clear hierarchy.


    We are hampered with a lack of evidence before the Cambrian Exlposion. But rest assured the Cambrian life formed nested hierarchies. We're just not necessarily sure what they were.

    "And why couldn't the mice in the example above evolve into something catlike, and something doglike, and something beaverlike for example?"

    Theoretically they could. Eventually. But it would take long time, and a chain of many advantageous mutation. And every time a new advantageous mutation occurred, it would spawn a new clade - NESTED WITHIN an old one.

    Let's say it takes 100 mutations to get from mouse to cat. That's a nested hierarchy of 100 clades. Now probably not every clade in the sequence would be represented by the time cats emerged - some would have gone extinct. Nevertheless, by the time cats emerged there would probably be many surviving creatures from along that chain of 100 clades - species which historically fit INSIDE each other like a Russian doll. In other words, they form a nested hierchy.


    Or why didn't other reptiles evolve hair and mammary glands, for example, and keep the reptilian jaws?


    Some reptiles did evolve hair and mammary glands. They became mammals. It just so happened that in that particular line, they also evolved the mammalian inner ear - losing the reptilian jaw as a consequence.

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  98. natschuster -

    If you'll forgive me, with all due respect, I'm still not convinced you understadn what nested hierarchies are and how they work.

    I strongly recommend you watch this:

    http://www.youtube.com/watch?v=5Ev-2jN6MRU

    It is short, but very informative.

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