Home » Intelligent Design » Questioning the Tree of Life: International Workshop Series

Questioning the Tree of Life: International Workshop Series

One cause (of many) delaying the completion of On Common Descent, my monograph examining the theory of the universal common ancestry of life on Earth — Darwin’s monophyletic Tree of Life, rooted in LUCA (the last universal common ancestor) — has been the explosion of publication on the topic. In 1998, when I submitted my dissertation, only a handful of researchers openly doubted monophyly, and only generally-known-to-be-crazy philosophers of science, like me, cared much about it.

Now an international workshop series on the question has been organized, to culminate in a major meeting in London in July 2010. The first workshop in the series was held on November 7th, 2008, at the Philosophy of Science Association biennial conference, in Pittsburgh. Massimo Pigliucci provides a helpful summary of much of the discussion.

For those who like to think about all this, here’s a thought experiment to try. Imagine two, or more, places on the early Earth where life is coming to be, contemporaneously [i.e., at the same slice in time]. Suppose, in addition, that those places are distant from each other: in the northern and southern hemispheres, let’s say. The physical distance between the locations ensures no direct causal interactions between them.

Now — will the biomolecules being formed in these independent settings be ‘the same,’ or ‘different’? How would you know? What does your answer, either way, do to the post-Darwinian understanding of “homology” as meaning “descended from a common ancestor?”

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57 Responses to Questioning the Tree of Life: International Workshop Series

  1. This series of conferences provides a striking refutation of the notion that evolutionary biologists are a bunch of hidebound dogmatists who refuse to consider anything that contradicts their ideology.

    Instead we see an initially radical idea — a network of life instead of a tree — gaining acceptance as the evidence for it mounts.

    The lesson for ID supporters is clear: if you want ID to become part of the mainstream of science, then make a genuine scientific case for it. Scientists will listen if the evidence is there and the arguments are valid.

  2. if you want ID to become part of the mainstream of science, then make a genuine scientific case for it.

    Yeah, like how the tree of life used to be :-)

  3. Scientists will listen if the evidence is there and the arguments are valid.

    ROTFLMAO!!!

  4. Scientists will listen if the evidence is there and the arguments are valid.

    *Scientists find four letter digital-code within DNA*

    First scientist talking to colleague: “Hey, we’ve found a code within DNA, much like a computer code, but it’s far more advanced than anything man has ever invented. As far as I know codes only come from intelligence. This looks like the result of an intelligent agent to me.”

    Colleague’s response: “No we haven’t. We’re not archeologists, we cannot possibly have found a language or code. This isn’t design. This is the result of random activities. Now be quiet and find a way that this could have happened by chance!”

    I’m suuuuure they’d listen. :P

    PS:

    *Thousands of experiments later*

    1st scientist: “Dude, we still haven’t found anything. I still think that an intelligent agent is a much better idea!”

    Colleague: “Shut up! Keep experimenting!”

  5. The lesson for ID supporters is clear: if you want ID to become part of the mainstream of science, then make a genuine scientific case for it. Scientists will listen if the evidence is there and the arguments are valid.

    The ONLY “evidence” anti-IDists will accept is a sit-down meeting with the designer.

    IOW they are not intertested in science.
    BTW the easiest way to make ID go away is to actually substantiate the caliams of ID opponents.

    That is demonstrate the power of accumulated genetic accidents.

    However as it stands the best they can do is point to slight variations and then throw eons of time at it and say “See!”.

  6. We are so often told by Darwinists that no scietists seriously question that evolution occured. Rather, any controversies within evolutionary biology are over the details of how evolution occured. But as Paul’s post indicates, here’s another example of another of the fundamental hows of evolution under serious debate. There’s not a single area of evolutionary biology from RM/NS to genetic drift to homology to convergent evolution to punk eek and now the supposed tree of life that is not swirling with controversy and disagreement. In other words, there’s not a single mechanism of evolution that biologist can claim is “well understood” or “confirmed” in the same way that, say, the inverse square law of gravity is. I’m reminded of a quote from the late S.J. Gould

    Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world’s data. Theories are structures of ideas that explain and interpret facts. Facts don’t go away when scientists debate rival theories to explain them. Einstein’s theory of gravitation replaced Newton’s in this century, but apples didn’t suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin’s proposed mechanism or by some other yet to be discovered.

    From Evolution as Fact and Theory Discover Magazine May 1981.

    Of course the fallacy in Gould’s comment here is obvious. We know by direct observation and experiment that apples fall to the ground every time they are dropped. We do not know how or if common descent explains our arrival on the planet by any direct observation on or even near the same level. Indeed, whether or not humans did arrive via some distant common ancestor is part of the main issue itself. Apples falling to the ground is not. The only issue of apples falling to the ground is how not if.

    Gould cleverly tries to put them in the same category to make his point. But they aren’t. When every single explanatory hypothesis of how evolution was supposed to work its magic is highly contoversial, claiming that evolution itself is not in doubt rings hollow.

  7. The following is my rendition of an evoltionary response:

    Now — will the biomolecules being formed in these independent settings be ‘the same,’ or ‘different’?

    Yes

    How would you know?

    My answer, as with the theory of evolution, is all encompassing.

    What does your answer, either way, do to the post-Darwinian understanding of “homology” as meaning “descended from a common ancestor?”

    The real question is, what does the post-Darwinian understanding of “homology” do for you?

    :)

  8. DonaldM,

    Either humans evolved from ape-like ancestors, or Someone wanted to make it appear that they did.

    Serious scientists don’t doubt the fact of evolution because the evidence doesn’t make sense unless evolution has occurred.

    Look at the data regarding human chromosome #2 and ask yourself how it can be explained other than by a) evolution, or b) an attempt by the Creator to make it appear that evolution has occurred.

    The facts are presented in this video, starting at 35 minutes:

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

  9. ribcyzinski – I’ve seen this argument 100+ times before…there’s nothing new here. Throwing Ken Miller at the question resolves nothing.

    There’s all sorts of ways to “make sense” of the evidence. Nearly all the evidence cited for common ancestry could also be evidence for common design. Pointing out the issue with chromosome 2 proves little (Ken Miller’s pontifications not-with-standing). There’s all sorts of evidence you could point to as “evidence” of common ancestry. The point you want to make is that evolution must explain it, because ID so “obviously” does not. But that is not a scientific argument…but a theological one. It is just another version of the “God wouldn’t have done it that way” argument. I’ve not read or heard a Darwinist yet who could tell me scientifically how they know what God would or would not have done. All such speculations are theological.

  10. Either humans evolved from ape-like ancestors, or Someone wanted to make it appear that they did.

    Could it be it only “appears that way” to people who refuse to consider anything else?

    Because it doesn’t appear that way to me. And I challenge any one on this planet to link the genetic differences to the physiological and anatomical differences.

    Unless there is some way to confirm that genetic changes can produce the physiological and anatomical differences observed, the “theory” is of no practical use. And the only people who accept it already assumed it.

  11. DonaldM wrote:

    ribcyzinski – I’ve seen this argument 100+ times before…there’s nothing new here.

    The question isn’t how many times you’ve seen the argument; it’s whether you can refute it.

    There’s all sorts of ways to “make sense” of the evidence.

    Beyond the two I’ve already mentioned? If so, could you share them with us?

    Nearly all the evidence cited for common ancestry could also be evidence for common design.

    True, but only if you accept that the designer specifically chose a design that makes common ancestry appear to be true.

    It is just another version of the “God wouldn’t have done it that way” argument.

    No it isn’t. I’m perfectly willing to entertain the possibility that God would have done it that way. It just means that if he did, he did so knowing that he was making common ancestry appear to be true.

    I’ve not read or heard a Darwinist yet who could tell me scientifically how they know what God would or would not have done. All such speculations are theological.

    I’m not saying I know what God would or wouldn’t have done. I’m saying that if he designed us, he made it appear that we are descended from ape-like ancestors, as the chromosomal evidence vividly demonstrates.

    And note that this remains true even if (as ID supporters suggest) we don’t assume the designer is God.

  12. Joseph wrote:

    And I challenge any one on this planet to link the genetic differences to the physiological and anatomical differences.

    Joseph,

    The chromosomal argument for common ancestry would still stand even if there were no link between genetic differences and anatomical differences.

    For the chromosomal argument to succeed, all that matters is for the genetic material itself to be heritable.

    This has been amply demonstrated, over and over again.

  13. The chromosomal argument for common ancestry would still stand even if there were no link between genetic differences and anatomical differences.

    The real question is whether Darwinian mechanisms are capable of transversing the informational divide. They apparently are not so now it comes down to the competing ID-compatible hypotheses…which ones make the most sense in light of the evidence?

  14. Patrick,

    Does that mean that you believe the designer made humans in a way that makes common ancestry appear to be true?

  15. ribczynski

    No it isn’t. I’m perfectly willing to entertain the possibility that God would have done it that way. It just means that if he did, he did so knowing that he was making common ancestry appear to be true.

    Again, you’ve introduced a theological statement into what is supposed to be a scientific argument. You have neither theological nor scientific basis for this claim…and THAT is the point of what I’m saying. You are making huge, sweeping assumptions about what God would or would not have done based solely on your interpretation of certain bits of data. But since your interpretation isn’t a scientific one, you have no basis for the claim beyond your own personal sense that this must be so.

    Contrary to what your write, you are inserting a theological premise into what is supposed to be a purely scientific argument. Unless, of course, you can explain to me how you know scientifcally what God would or would not have done.

    True, but only if you accept that the designer specifically chose a design that makes common ancestry appear to be true.

    There’s a hidden assumption built into this claim: naturalism. This claim assumes that things came to be the way they are by virtue of the blind, purposeless combination of chance and necessity (RM/NS). Therefore, if they really are the way they are because of common design, then the designer (or God) must be being deceptive making things appear to be the result of a “natural” process, when in fact they are not. Beides the theological implicatios of this assumption, it also implies that we are required to frame things in purely naturalistic terms, as if naturalism is true, whether or not it is.

    Why is it the case that we must see everything first as if they were the end result of the blind, purposeless forces of matter and energy evolving over eons of time through chance and/or necessity? That is the hidden assumption in the claim that things appear as if common ancestry is true. One of the main things about ID is that it challenges the very idea of whether or not things actually do appear to be the result of common ancestry. In making that the starting point of your argument you are assuming the very point at issue. In other words, begging the question. I therefore reject your premise.

  16. Hi Paul. I read the blog you linked to and didn’t see anything related very much to the thought experiment you mentioned. It appears to me that what these guys are saying that is that because of lateral gene transfer and because notions of species are hard to apply to bacteria (since they don’t reproduce sexually, for one thing), the start of life can’t be simplified into a tree. Rather the very beginnings of life can be pictured as composed of DNA or its precursors transferring and grouping in multiple novel ways, and only after this period stabilized into more coherent groups of organisms did it become more tree-like.

    I don’t think any of the people at the conference are finding evidence for two separate starts to life, but rather just that the start of life was very decentralized and amorphous rather than centralized on a unique first organism.

    Is this an accurate summary of what the people at the conference are trying to say?

    Disclaimer: I know some here don’t particularly believe in all this, and even more don’t believe that this couldn’t have happened with design, but those are not the issues I am interested in bringing up. I just want to know if I understand the general conclusion of the people at the conference correctly.

  17. Donald,

    My argument does not assume the truth of naturalism.

    Whether naturalism holds or not, the following statements are true:

    1. Human chromosome #2 is either designed, or it isn’t.

    2. If it is not designed, then it overwhelmingly supports the notion that humans and apes share a common ancestor.

    3. If it is designed, then the designer has created the appearance of common ancestry (to a rational person looking for the most likely explanation, whether a naturalist or not).

    Suppose you’re walking down the street one day when you come across an anvil resting on a banana skin, with the banana’s contents sprayed across the pavement as they would be had the anvil been dropped onto the banana from above.

    What would be the likeliest explanation? Would you assume that the banana had already been smashed before the anvil was lowered gently onto it? Or would you conclude, rationally, that the anvil had fallen onto the banana? Both are logically possible, but one is more likely than the other.

    The question is always this: Given the evidence, what is the most probable explanation?

    P.S. If the fused chromosome is designed, why do you think the designer kept the non-functional centromere and telomeres? He must have really wanted us to think that common ancestry was true.

    P.P.S. If you think there are other more plausible alternatives that fit the evidence, then please describe them for us and explain why they make sense.

  18. ribczynski:

    I have not followed the thread (I have just written a long answer to you on the other thread), but let me just ask:

    Why are you assuming that design is incompatible with common ancestry?

    Why not say that human chromosome 2 is designed, and that the designer derived it from the apes chromosomes?

    And it is possible that the designer kept the non-functional centromere and telomeres (if they are really non functional) not to give the “appearance” of common ancestry, but because he worked through common ancestry, and that was probably the simplest and most functional way to do that.

  19. gpuccio asks:

    Why are you assuming that design is incompatible with common ancestry?

    I’m not. My three statements remain true without assuming that design is incompatible with common ancestry:


    1. Human chromosome #2 is either designed, or it isn’t.

    2. If it is not designed, then it overwhelmingly supports the notion that humans and apes share a common ancestor.

    3. If it is designed, then the designer has created the appearance of common ancestry (to a rational person looking for the most likely explanation, whether a naturalist or not).

    However, if you read the thread, you’ll see that the issue being debated is whether the chromosomal evidence supports common ancestry. I claim that it does, overwhelmingly. DonaldM and Joseph claim that it does not.

  20. In answer to #14 and #17 I’d just add a fourth option:

    4. If it is designed, then the designer(s) used a mechanism that resulted in Intelligent Evolution.

    I don’t have any personal preference. A fifth option where the “appearance of common ancestry” is based upon a misunderstanding of the system and/or designer reuse is fine with me, IF true.

    In general I’m agnostic when it comes to the competing ID-compatible hypotheses. I just think it’s way too early to tell, although it’s obvious that intelligence is involved at some level. Basic engineering principles don’t allow for any leeway on that issue.

    Although, as I’ve said it before I do allow that it’s “possible” that there is “something” about the design of the overall system that allows non-foresighted mechanisms to function. As such the only direct design was involved at OOL and not the rest of evolution. The only reason I allow for this possibility is since scientists are still struggling to understand how the entire system works so there is still the potential that both Darwinists and ID proponents are overlooking “something”.

  21. The chromosomal argument for common ancestry would still stand even if there were no link between genetic differences and anatomical differences.

    It doesn’t stand for anything if it cannot be objectively tested by linking the genetic differences to those physiological and anatomical differences.

    For the chromosomal argument to succeed, all that matters is for the genetic material itself to be heritable.

    That is false. You don’t know what caused the chromosomal rearrangement.

    However it is obvius that you don’t understand the implications of such an arrangement.

    Do you think the chimp-like individual who had said arrangement could succesfully mate with one who did not?

    Very unlikely.

    And just what advantage did the rearrangenment offer sio that it would be kept?

    Don’t know do you.

    IOW all you have is a speculation based on the assumption.

  22. ribczynski,

    Human chromosome 2 represents a case of Common Design to IDists and perhaps even with Creationists.

    IOW it is NOT exclusive evidence for common ancestry.

  23. Patrick:

    “In general I’m agnostic when it comes to the competing ID-compatible hypotheses. I just think it’s way too early to tell, although it’s obvious that intelligence is involved at some level.”

    Me too. I am really open to all possibilities on that. It is true, however, that at present I would accept as “best explanation” an intelligently designed common descent. But we must wait foe further evidence: after all, genomes are only now being sequenced in significant numbers, and their analysis is very slow and often unsatisfying, also because it is usually performed form a very dogmatic darwinistic point of view, which could be a serious obstacle to a true understanding of the data.

    “The only reason I allow for this possibility is since scientists are still struggling to understand how the entire system works so there is still the potential that both Darwinists and ID proponents are overlooking “something””

    That’s right, but, as I have recently argued with ribczynski, everything remains theoretically “possible” in science, because any existing scientific theory could some time be partially or totally falsified by new facts. But scientific theories should be “empirically” possible before they are seriously considered, in other words they should be, if not the best explanation for existing data, at least some kind of explanation. Unfortunately, that’s not always the case, as can be said of two of the most successful scientific theories of our times (guess which?).

    PS: Answer: darwinian evolution, strong AI.

  24. Does that mean that you believe the designer made humans in a way that makes common ancestry appear to be true?

    Evolution explains — and is maybe the best explanation — as to why some things are more alike. Just because a theory works for one circumstance, however, doesn’t mean it is true. Evolution fails terrifically — fatally, I think it’s fair to say — on other important points.

    Even though an idea was good at the time, thinkers must be objective about it and be willing to walk away from it when it becomes clear it fails.

  25. Joseph:

    I think that ERVs, pseudogenes and human chromosome 2 are good arguments in favor of common ancestry. But I don’t believe they are absolutely compelling. As you say, they could be explained in a common design scenario, but that requires some more adjustments to be done: in particular, we should be able to prove the functional necessity of those features, at least in some measure.

    I am aware that there is some evidence in that sense at least for ERVs, I don’t know about chromosome 2. That’s why, for me, the question of common ancestry should realistically remain open, and anyone is free to choose his favourite position.

    Moreover, let’s remember that human chromosome 2 is not, anyway, evidence of universal common descent. Common descent could well be true, but not be universal. That’s a possibility which should always be considered.

  26. ribczynski

    My argument does not assume the truth of naturalism.

    Whether naturalism holds or not, the following statements are true:

    1. Human chromosome #2 is either designed, or it isn’t.

    2. If it is not designed, then it overwhelmingly supports the notion that humans and apes share a common ancestor.

    3. If it is designed, then the designer has created the appearance of common ancestry (to a rational person looking for the most likely explanation, whether a naturalist or not).

    For #1 – not quite. We can’t assume that the current state of the chromosome is the original design. My grandfather had an old piece of farm equipment out behind the barn on the farm. It was clearly designed, but was also in a state of decay (rust, missing parts, etc) from long dis-use. From a theological perspective, many believe (as do I) that we live a fallen world, thus what exists is not in its original perfect state…far from it.

    #2. I agree it could be evidence for common ancestry…but deny the “overwhelming” part. I see no reason why a designer wouldn’t use common parts in creating structures that have some similarities. And, if common parts are used, it is likely that they will exhibit similar or even identical features, even in a state of decay. My grandfather had a second piece of equipment (an old horse drawn hay rake as I recall) next to the other one, and most of the nuts and bolts on the 2nd one were rusted and decayed almost exactly like the 1st one. But the nuts and bolts themselves were in many cases identical — same size, shape, etc. But, the rust and decay in the two pieces of equipment, and specifically in the nuts and bolts can not be traced back to a common ancestral nut and bolt that had the same features and passed on its rust and decay to the nuts and bolts in my grandfathers machinery. Rather, they independently responded to identical enviromental conditions with the same results.

    #3 – As I said, it could be evidence for common ancestry, but could also be evidence for common design.

    P.S. If the fused chromosome is designed, why do you think the designer kept the non-functional centromere and telomeres? He must have really wanted us to think that common ancestry was true.

    P.P.S. If you think there are other more plausible alternatives that fit the evidence, then please describe them for us and explain why they make sense.

    As I said earlier, the original design may have been somewhat different than the current state due to the effects of decay in the system. Common parts exposed to similar or identical enviromental conditions could produce remarkable similarites in a decayed state. It does not necessarily mean that those similarities were inherited from some third common ancestor.

    The problem I see with the logic applied is it conflates the assumption of common ancestry with the evidence for it.

  27. gpuccio:

    I think that ERVs, pseudogenes and human chromosome 2 are good arguments in favor of common ancestry.

    I know that they are arguments for universal common descent, but how “good” they are depends on if you have already assumed it or not.

    As for ERVs what if they are really remnants of a once living organism? IOW they are very similar to prions except that the protein enveloped these DNA sequences in the decaying organism. That kept the thing “alive” until it was consumed and then evolution, as in variation, took over.

    As for chromosome 2 do you realize the bottle-neck, involving incest, that has to be overcome?

    First the mutation has to be in the germ line. Then that particular germ cell has to be able to successfully merge with another that doesn’t have it, which would produce a mix.

    The offspring with the mix would then have to successfully mate and hopefully pass down that fusion to one of its offspring.

    Then it mates with that offspring to provide two sets with the fusion.

    Then those with both would have to die off and only those with two sets of fused or non-fused would have to survive bit also become isolated.

    Or can you provide a better scenario?

  28. Joseph:

    “Or can you provide a better scenario?”

    Well, I just thought that if the fusion happened by design, the scenario could have been different, although I don’t really know how. I never thought that the transition could have happened in an uncontrolled way, and I think that, if it happened, it must have been designed and have a functional reason.

    I am not especially interested in the problem of common descent, just think that it is fair to recognize empirical arguments for and against it. I really think we have not a satisfying answer on that point, yet.

  29. “I’ve not read or heard a Darwinist yet who could tell me scientifically how they know what God would or would not have done. All such speculations are theological.”

    Which is exactly why ID is not science. ID claims that they do know what God (or some other intelligent agent) would or would not have done because it says that he DID do it in just the way that we see it. By your own admission, a theological speculation rather than a scientific one.

    (Sorry I’m a little behind with my posts…I just got here today)

  30. Which is exactly why ID is not science. ID claims that they do know what God (or some other intelligent agent) would or would not have done because it says that he DID do it in just the way that we see it.

    To limit semantic argument, let’s say science here is using an objectively consistent, clearly defined methodology capable of producing duplicable results.

    Is using geometry to give the square footage of tile on a floor not “science” because that methodology will not tell you the tile’s color, or who laid it down or conceived its pattern?

    Why would you demand ID tell you the designer?

  31. “Why would you demand ID tell you the designer?”

    I demanded no such thing. The claim by DonaldM is that speculation about what a designer would or would not do is theological in nature, as opposed to scientific. Once you invoke a designer, you implicitly state that the designer chose to design things in exactly the way that they appear to us, which is necessarily a speculation about what s/he would or would not do…namely that s/he WOULD design things in just this way.

  32. “Why would you demand ID tell you the designer?” . . .I demanded no such thing.

    Well, you did and do. But I’ll rephrase to allow less wiggling: why would you demand ID identify the designer to be considered science while allowing geometry or metallurgy or archaeology or forensics to considered science without a requirement that a designer be identified?

    Once you invoke a designer . . .

    ID does not “invoke a designer”. It describes the characteristics of an object.

  33. Kris

    Which is exactly why ID is not science. ID claims that they do know what God (or some other intelligent agent) would or would not have done because it says that he DID do it in just the way that we see it. By your own admission, a theological speculation rather than a scientific one.

    This is not accurate. ID’s main claim is that certain features of nature provide evidence of having been designed. By what or by whom is an interesting but completely separate question. It may very well be theological in nature, but that doesn’t change the fact that certain observations and phenomenon in nature provide evidence of actual design. Recognizing, describing and understanding those features is the science part. Speculating on the nature or identity of the designer is not.

    The difference here is that Darwinists frequently make claims about what the designer or God would or would not have done as part of what is supposed to be a scientific argument. Darwin himself did this in ToS. S.J. Gould opened his book “The Panda’s Thumb” with a little essay on why certain features of the biological world are just not the stuff of “a wise creator”. The conclusion, of course, is that therefore it must be the work of nature. But the premise is theological not scientific…God wouldn’t have done it that way.

    ID, on the other hand, isn’t saying God did or should have or would have done this or that one way or another. Rather it is saying, these phenomenon have features of actual design. That’s a very different thing. These are not equivalent statements as you want to make them out to be.

  34. Just as a clarification, ERV’s, pseudo-genes, SINES and LINES are evidence of common ancestry which is not common descent. Common descent is Darwin’s idea that we all descended from the same single celled organism.

    Common ancestry in terms of chimps and humans are often discussed using the term common descent but the meaning of common descent is much broader than this. I do not think anyone in ID denies common ancestry for many species. It only gets sticky when humans are part of analysis.

  35. “Well, you did and do.” – tribune7

    I am not demanding any information whatsoever about who or what the designer is. It is perfectly irrelevant. DonaldM mentioned a designer in the context of scientific speculation, and I followed up on that. He has since made clear the context of that statement, and my follow up was, it seems, out of said context. For that, I apologize.

    That being said, I am quite interested in what the evidence is for design in nature. It seems to me that all of the evidence essentially boils down to variations of “it can’t be evolution, or any other scientific process, and so we are left with design as the last viable option.” Please keep in mind that this is in large part due to the fact that most of the information I’ve gotten about ID is through the popular media (books like Darwins Black Box, Intelligent Design: The Bridge Between Science and Theology, and of course The Complete Idiot’s Guide to Intelligent Design).

  36. Nevermind. This was fun for a few minutes.

  37. For that, I apologize.

    I apologize too then, for taking your comments in the wrong way.

    It seems to me that all of the evidence essentially boils down to variations of “it can’t be evolution, or any other scientific process, and so we are left with design as the last viable option.”

    No. No. No.

    ID is methodology advanced by Dr. Dembski and others that notes “design” is a reality and a phenomenon that can be studied methodologically; and that it has characteristics that can be objectively defined.

    And that when this methodology is applied to biology it registers a positive for design.

    And since it is a methodology with concisely defined filters and mathematical backing it can be falsified.

    Now with regard to Behe, I’m inclined to agree with you that what he’s doing is mostly falsifying neo-Darwinism rather than showing design — although some say IC is solid evidence of design.

    There is a whole side to ID that you seem to be missing, though.

    Check out Dembski’s Design Inference site for a first-hand explanation.

  38. Ignore that “nevermind”. I’m a third shifter and it’s way past my bedtime.

  39. “There is a whole side to ID that you seem to be missing, though.”

    I suspected as much. I didn’t think it could be that simple, otherwise it would have faded away long ago, I think.

  40. Kris, You may want to take a look at the post that Dave Scot just made here called “Some Thanks for Professor Olofsson”. you wrote:

    That being said, I am quite interested in what the evidence is for design in nature. It seems to me that all of the evidence essentially boils down to variations of “it can’t be evolution, or any other scientific process, and so we are left with design as the last viable option.”

    That’s not quite how its stated. Take some feature of a biological system f. Its perfectly legitimate to ask does f exhibit features that can be explained by unintelligent, undirected processes (ie chance and necessity). Note that the issue here is one of explanation in scientific terms. For something to be explained in science means that we have good reason based on testing, models, and repeated experimentation to hold that the explanation is true or approximately true. Imagined explanations, no matter how scientfically stated, that have not been tested, repeated, confirmed or modelled are little more than untested hypotheses that might explain f.

    But suppose f is such that in every case where we observe it in some other system f1 and we know the actual cause, it is only caused by intelligence. Then it does not seem problematic to say that as far as we know all f1‘s are the result of ID so its highly likely that f is as well, even if it is in a biological system.

    To falsify that, we only need to show how 1 unintelligent, undirected cause produced f. So it isn’t merely saying “it isn’t evolution, therefore its design”. It is saying we know that only intelligence produces these sorts of features, so it is reasonable to assume this was produced by an intelligence. The two most prominent examples of this in biological systems are irreducible complexity (IC) and specified complexity (SC). IC could be said to be a special case of SC. We know that intelligence can and regularly does produce IC systems. We don’t know of any unintelligent, undirected process that can do so. it is therefore reasonable to infer that a biological system that exhibits IC is produced by an intelligence.

    Questions of when, where and how that occured are separate and interesting questions that open up avenues for future research.

  41. KRIS– check out DesignInference.com It has works going back to the 90s, related to this discussion. It’s kind of neat to see the responses to the responses etc.

  42. Joseph wrote:

    As for chromosome 2 do you realize the bottle-neck, involving incest, that has to be overcome?

    Joseph,

    Incest is not necessary. An individual with a fused chromosome can mate with a normal partner and produce viable offspring.

    Meiotic sorting will produce some gametes with a lethal karyotype, but other gametes will be fine, which allows the fused chromosome to persist in the population.

  43. Judging from the comments in this thread, it appears that there is still some misunderstanding of the details and significance of the chromosomal fusion evidence.

    Let me stress a couple points:

    1. The fusion event per se is not evidence for common ancestry. What the fusion event does is show that common ancestry continues to fit the evidence even though apes and humans have a different number of chromosomes. It nullifies what would otherwise have been evidence against a common ancestor.

    2. Assume for the moment that common design is true and common descent is false. Of all of the ways in which a designer could employ common design, the vast majority do not give the appearance of common descent. Yet wherever we look, the evidence of ERVs, pseudogenes, chromosome numbers, etc., matches overwhelmingly with a hypothesis of common descent.

    Which of the following is a better explanation of the evidence?

    1. Common design is true, and the designer just so happened, in every case, to pick a style of common design that is indistinguishable from common descent, when the vast majority of styles he could have chosen would have given the opposite impression.

    2. Common descent is true.

    Which explanation fits the facts better? And if you choose #1, how much is your choice influenced by your desire to believe that a certain ancient book, written by members of a scientifically illiterate nomadic tribe in a backward part of the Middle East, is literally true?

  44. And if through torturous attempts to reason you claim Dembski’s method provides false positives how much is it due to your desire not to accept the teachings of a certain ancient book?

  45. None. There is plenty of evidence apart from Dembski that the Bible is scientifically inaccurate.

    I knew that long before I had even heard of Dembski.

  46. As for chromosome 2 do you realize the bottle-neck, involving incest, that has to be overcome?

    Joseph,

    Incest is not necessary. An individual with a fused chromosome can mate with a normal partner and produce viable offspring.

    Yes, viable offspring with a mixture- 23/24. In order to get a 23/23 incest is indeed necessary.

    Or else there has to be another family with an offspring with the same fusion. Very, very doubtful, unless it was directed.

  47. 1. The fusion event per se is not evidence for common ancestry. What the fusion event does is show that common ancestry continues to fit the evidence even though apes and humans have a different number of chromosomes. It nullifies what would otherwise have been evidence against a common ancestor.

    Yeah and it used to be that chimps and humans DNA was 98.5% similar.

    Now we know it is closer to 70. But for some reason that isn’t evidence against common ancestry.

    2. Assume for the moment that common design is true and common descent is false. Of all of the ways in which a designer could employ common design, the vast majority do not give the appearance of common descent. Yet wherever we look, the evidence of ERVs, pseudogenes, chromosome numbers, etc., matches overwhelmingly with a hypothesis of common descent.

    There isn’t any real evidence for universal common descent unless scientists can link the genetic differences to the physiological and anatomical differences.

    Otherwise the “evidence” for UCD amounts to no more than “I wouldn’t have seen it if I didn’t believe it.”

    Of all of the ways in which a designer could employ common design, the vast majority do not give the appearance of common descent.

    1- How do you know that?

    2- The evidence for common descent is only in the minds of those who have already assumed it.

    BTW I don’t care if the Bible is refuted. ID is an areligious approach to our origins.

    We exist and your optionm means it was all just an accident- an accumulation of accidents.

    That takes quite a bit of faith.

  48. Joseph wrote:

    Yeah and it used to be that chimps and humans DNA was 98.5% similar.

    Now we know it is closer to 70. But for some reason that isn’t evidence against common ancestry.

    Actually, we don’t know that the number is closer to 70. You’re probably getting that number from this post by Denyse O’Leary, which links to an an article by Richard Buggs.

    In the article, Buggs takes it upon himself to “correct” the methods used by his predecessors for quantifying genetic similarity between species. His “corrections” are misguided, if not downright dishonest. For example, he writes:

    We also find places where two pieces of human genome align with only one piece of chimp genome, or two pieces of chimp genome align with one piece of human genome. This ”copy number variation” causes another 2.7% difference between the two species.

    This is absurd. Buggs is suggesting that a second copy of a matching sequence should be counted as a mismatch. That means the second copy cancels out the first, and it’s as if there were no match at all!

    I was surprised at his naivete or dishonesty, whichever it is, until I discovered a couple of things:

    1. Buggs is an ID supporter and creationist who is interested in denying that humans share a common ancestor with apes.

    2. His article isn’t published in a scientific journal, but in the Reformatorisch Dagblad (“Reformational Daily”), a Dutch Protestant newspaper whose website, believe it or not, is actually closed on Sundays.

    Now I’m not so surprised about Buggs’s behavior.

    Buggs’s 70% number can’t be trusted, but in any case it’s not so much the absolute numbers that are important — it’s the pattern of differences between the numbers when a bunch of species are compared to each other. Contrary to Buggs’s desire, a number of 70% by itself would not rule out a common ancestor of apes and humans. You’d have to look at the pattern of numbers to make that determination, and of course all of the numbers would have to be calculated using the same, accurate algorithm.

    There isn’t any real evidence for universal common descent unless scientists can link the genetic differences to the physiological and anatomical differences.

    This is the third time in this thread that you’ve made that claim. Repeating the claim doesn’t make it any truer, Joseph.

    I’ve already explained this to you, but let me try again: Even if the genetic differences we observe had no phenotypic effect, common ancestry would still be detectable from the pattern of those differences.

    I wrote:

    Of all of the ways in which a designer could employ common design, the vast majority do not give the appearance of common descent.

    Joseph asks:

    How do you know that?

    Because in most cases it doesn’t matter where on a chromosome a gene appears, or even on which chromosome, or whether the genes are grouped onto a larger or smaller number of chromosomes.

    A designer drawing on a common pool of genes therefore has zillions of alternate arrangements to choose from, most of which would rule out common descent if they were observed.

    Yet if common design is true, as you claim, then it means that the designer just so happened to choose from the tiny fraction of possible arrangements that don’t rule out common descent. How convenient.

    BTW I don’t care if the Bible is refuted.

    Got it. Right. It’s all the same to you, either way. No skin off your back.

  49. 1- No one knows what the exact genetic difference is between chimps and humans. The 98.5% was based on similar stretches of DNA. That similar stretch was 98.5% similar.

    The 98.5% can’t be trusted.

    [b]There isn’t any real evidence for universal common descent unless scientists can link the genetic differences to the physiological and anatomical differences.[/b]

    This is the third time in this thread that you’ve made that claim. Repeating the claim doesn’t make it any truer, Joseph.

    Wel you have had more than one opportunity to refute it but yet you have FAILED to do so.

    That tells me that you can’t match the genetic differences to the anatomical and physiological differences. And it also means that you have had ample time to find the proper peer-reviewed papers that would refute my claim, and yet again you have FAILED.

    I’ve already explained this to you, but let me try again: Even if the genetic differences we observe had no phenotypic effect, common ancestry would still be detectable from the pattern of those differences.

    Yeah but just because those who see a “pattern of common ancestrty” had already assumed it.

    Ya see without a way to test the premise- that the genetic differences can be linked to the anatomical and physiological differences- universal common descent is outside of the realm of science.

    Of all of the ways in which a designer could employ common design, the vast majority do not give the appearance of common descent.

    How do you know that?

    Because in most cases it doesn’t matter where on a chromosome a gene appears, or even on which chromosome, or whether the genes are grouped onto a larger or smaller number of chromosomes.

    How do you know? We knmow there are complex interactions between genes- Sean Carroll called in “combinatorial logic”. And that means it does matter where the genes are.

    A designer drawing on a common pool of genes therefore has zillions of alternate arrangements to choose from, most of which would rule out common descent if they were observed.

    That is nothing but a bald asserttion built on ignorance of biology and genetics.

    Yet if common design is true, as you claim, then it means that the designer just so happened to choose from the tiny fraction of possible arrangements that don’t rule out common descent.

    One more time- the alleged pattern of common descent exists only in the minds of those who have already assumed it.

    Over 95% of the fossil record is of marine inverts. Just what we would expect knowing the fossilization process. Yet is that vast majority there isn’t any pattern of universal common descent.

    And also if we didn’t see a common pattern then common design would be refuted.

    PS if there is a 70% genetic difference between chimps and humans it would rule out universal common descent. That is because at 70% the pop[ulation would have to accumulate mutations in every generation to make up that difference.

  50. ribczynski,

    Dr Richard Buggs is a research geneticist.

    What are YOUR qualifications?

    ribczynski has a problem with the folloowing:

    We also find places where two pieces of human genome align with only one piece of chimp genome, or two pieces of chimp genome align with one piece of human genome. This ”copy number variation” causes another 2.7% difference between the two species.

    I bet he (she?) misunderstands what Dr Buggs is saying. And it only counts as another 2.7%.

    This is absurd. Buggs is suggesting that a second copy of a matching sequence should be counted as a mismatch.

    EVERY difference must be counted.

    That means the second copy cancels out the first, and it’s as if there were no match at all!

    That is a stupid inference. It does no such thing. One of the copies matches the one in the other genome. The leftover copy is the only copy that gets counted as a difference.

    And in the end if no one can link the genetic differences to the anatomical and physiological differences what you are doing isn’t science.

  51. I’m sorry, Joseph, but there are just too many mistakes and misconceptions in your comment. I don’t have the time or energy to correct them all.

    Perhaps you could find a fellow ID supporter who understands and accepts common descent and is willing to explain it to you.

  52. Joseph,

    in the end if no one can link the genetic differences to the anatomical and physiological differences what you are doing isn’t science.

    To be fair no one can currently do this to a large extent, so the information you are demanding of ribczynski is impossible to obtain. Whether the similarity in the code is 98.5% or 76% or 70% or whatever the key is–as Dr. Buggs put it–that “there is a huge amount [of] exciting research still to be done in human genetics.” You guys are arguing over the accuracy of rough estimates!

    if there is a 70% genetic difference between chimps and humans it would rule out universal common descent. That is because at 70% the population would have to accumulate mutations in every generation to make up that difference.

    Not completely. It would only serve as evidence against common descent via Darwinian mechanisms, which have observed to work slowly, but not necessarily Intelligent Evolution. But I admit that this would require not only Intelligent but Rapid Evolution which would also then be self-terminating since we do not observe such rates currently AFAIK.

  53. I’m sorry, Joseph, but there are just too many mistakes and misconceptions in your comment.

    Nice bald assertion.

    I don’t have the time or energy to correct them all.

    translation:

    I cannot provide the evidence of the mistakes and misconceptions so I will just post that they exist and leave it at that.

    BTW I unstand univrsal common descent and I used to accept it.

    However I know that common desgn AND convergence can explain the SAME data as universal common descent can.

    So the bottom line is ribczynski cannot support his (her?) position and cannot find the peer-reviewed papers that do so.

  54. in the end if no one can link the genetic differences to the anatomical and physiological differences what you are doing isn’t science.

    Patrick:
    To be fair no one can currently do this to a large extent, so the information you are demanding of ribczynski is impossible to obtain.

    Don’t blame me if ribczynski’s premises are un-testable and do not allow for experimental scrutiny.

    And besides if we knew the combinatorial logic involved in making body parts and body plans, then we would be able to test the premise.

    Patrick:
    Whether the similarity in the code is 98.5% or 76% or 70% or whatever the key is–as Dr. Buggs put it–that “there is a huge amount [of] exciting research still to be done in human genetics.”

    That is obvious and goes without saying.

    if there is a 70% genetic difference between chimps and humans it would rule out universal common descent. That is because at 70% the population would have to accumulate mutations in every generation to make up that difference.

    Patrick:
    Not completely.

    30% x 3.2 billion = 960,000,000

    If the split took place 7.5 million years ago that leaves 15 million years between chimps and humans since the divergence.

    So you are right. It wouldn’t be per generation it would be per YEAR!!!!

    Or do you think that 960 million differences can arise in 15 millin years? If “yes” what is your justification for that?

  55. Joseph,

    My point was that to argue over the accuracy of these estimates is pointless…we know without a doubt they are not accurate! We must first understand the system better. For example, within the genome there is likely to be a percentage of “true junk”. But until we understand the system in detail we cannot tell what is junk and what is not.

    But you are correct that the estimates in the high 90s are likely not accurate and thus we can examine the implications of newer estimates based upon better data.

    The estimates for a split vary, with some pushing it back further based upon a tooth. And then others place it at around 4.1 million based upon another analysis.

    But I would bias the numbers just to be certain. So let’s assume 20 million years and 85% similarity.

    480,000,000 / 20,000,000 = 24 bases per year must be fixated within a population (of course, this is on average since any beneficial functional complexity will almost certainly exceed 24)

    That still presents quite a challenge for non-foresighted mechanisms. According to Nachman and Crowell, “[t]he average mutation rate was estimated to be ~2.5 x 10-8 mutations per nucleotide site or 175 mutations per diploid genome per generation.” (I’ve read more recent studies, but I forget where they are.)

    EDIT(Found a quote from Sanford summarizing some studies):

    One of the most astounding recent findings in the world of genetics is that the human mutation rate (just within our reproductive cells) is at least 100 nucleotide substitutions (misspellings) per person per generation (Kondrashov, 2002). Other geneticists would place this number at 175 (Nachman and Crowell, 2000). These high numbers are now widely accepted within the genetics community. Furthermore, Dr. Kondrashov, the author of the most definitive publication, has indicated to me that 100 was only his lower estimate — he believes the actual rate of point mutations (misspellings) per person may be as high as 300 (personal communication). Even the lower estimate, 100, is an amazing number, with profound implications. When an earlier study revealed that the human mutation rate might be as high as 30, the highly distinguished author of that study, concluded that such a number would have profound implications for evolutionary theory (Neel et al. 1986). But the actual number is now known to be 100-300!

    EDIT2 (As an admin I love being able to clarify my thoughts :P )

    960,000,000 (70%) / 4,100,000 = 234.15 (which is barely within high estimates of human mutation rates)

    But that does not consider functionality and the ratio of deleterious-to-beneficial mutations, which is very roughly estimated to be one in one million by Gerrish and Lenski. So even if we presume that only 1% of that 960k is functional that still leaves 2.4 constructive (non-deleterious) beneficial mutations per year on average.

    As for Intelligent Evolution you know very well that research into related hypotheses has barely begun. So I could only posit potential mechanisms and not identify any specific data as a justification.

  56. Thanks Patrick,

    I have some questions though:

    One of the most astounding recent findings in the world of genetics is that the human mutation rate (just within our reproductive cells) is at least 100 nucleotide substitutions (misspellings) per person per generation (Kondrashov, 2002).

    Is that per gamete? Or is that per all the gametes?

    From the link you provided (Nachman & Crowell) it looks like they first assume that chimps and humans shared a comon ancestor then looked at the differences to provide the rate of mutations:

    We investigated the rate and pattern of mutations at the nucleotide level by comparing pseudogenes in humans and chimpanzees to (i) provide an estimate of the average mutation rate per nucleotide, (ii) assess heterogeneity of mutation rate at different sites and for different types of mutations, (iii) test the hypothesis that the X chromosome has a lower mutation rate than autosomes, and (iv) estimate the deleterious mutation rate.(bold added)

    That is NOT how to go about estimatimg mutation rates- that is it is incorrect to first assume a common ancestor then go back, count the differences and then estimate the rate.

    Also even intelligent evolution needs to account for the physiological and anatomcal differences observed. However I do understand that is a more likely scenarion than evolution via an accumulation of genetic accidents.

  57. Good point. We need an observed mutation rate. I tried looking for just that the other day but I could only find references to these studies. But I can imagine it would be difficult to get an accurate observed human mutation rate since there are hotspots and other variances that confuse the issue.

    I notice that the estimated mutation rate has increased dramatically with time. Perhaps this correlates with research that shows the increasing differences between chimp and human?

    Another data point is that I remember reading about a comparison of the genome from the Human Genome Project and a more recent complete sequence whose source I forget (Venter?). The interesting part is that the similarity was only around 98-99% if I remember correctly.

    As for the Sanford quote, you can try asking him directly.

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