Home » Intelligent Design » Friday Musings — Irrational Hatred of ID and a Scientific Sea Change

Friday Musings — Irrational Hatred of ID and a Scientific Sea Change

I think that one of the reasons for the irrational hatred of the ID movement is that in the last 50 years a scientific tide has reversed. The hard sciences (as opposed to Darwinian theory, evolutionary psychology and the like), which for centuries had demystified the world and made the transcendent seem increasingly irrelevant, suddenly started providing solid evidence that a materialistic worldview was untenable. The universe was fine-tuned for life, and living things were fundamentally based on highly sophisticated information and information-processing systems. The fact that those of us in the ID movement are promoting public awareness of this has enraged those with a philosophical commitment to materialism, those who counted on the hard sciences to provide ever-increasing support for their worldview.

What was thought to be their best ally is gradually becoming their worst foe, and this is a tough pill to swallow.

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78 Responses to Friday Musings — Irrational Hatred of ID and a Scientific Sea Change

  1. I’d agree with this. And I hope I don’t speak out of turn here.

    I still remember the stark difference between how young earth creationism was confronted by the materialism-minded – more or less joviality. Sure, they scoffed at the ‘Theory’ stickers on books, but generally they were all smiles. They considered science to be their turf.

    But ID was something different, and the tone changed in a noticeable way. No more smiles and dismissive humor. Suddenly the responses got angry and vitriolic. Rejecting large swaths of science was one thing. But having people with philosophical differences take a look at the same science they did and go “Actually, we see something special here. Something perhaps intentional.”?

    Unfair. Science is supposed to be theirs. They decide what people can and can’t consider to be a reasonable idea or theory. Accept their science with the philosophy attached, or reject it all – but anything else is forbidden. After all, if they’re forced to share, the results can be devastating.

    People may see the vastness of the cosmos and not accept Carl Sagan’s argument that the size proves how insignificant we are, but instead see a grand mission in a glorious creation.

    Evolution may not be the work of blind and purposeless forces of an uncaring universe, but a work brilliance in rules and programming with an intention of ascent – evidence that there is, in fact, an objective “better” and “good” in our world.

    And worst of all, all the past efforts on behalf of materialist and like-minded scientists may end up reinforcing a philosophy and worldview many of them wanted to see discarded entirely. Darwin shanghai’d to the side of the enemy, without any of the precious metaphysical concepts.

    Because, in the end, you can’t prove random and purposeless. Maybe you can’t prove brilliant design either – time will tell. But both can reasonably be seen as equally valid concepts, and paradigms to work by. Whether or not the materialists feel like sharing.

  2. This seems like an opportune time to bring up something that I think is a paradox in ID. IIRC, in Darwin’s Black Box, Behe says that Darwin was limited because he did not know about the inner workings of the cell. Darwin and his contemporaries thought that a cell was basically something like a blob of protoplasm, and we now know that it is full of molecular parts that interact so that the cell can function.

    Here’s my problem: isn’t the “blob of protoplasm” model harder to explain as a natural process than the “complicated molecules” model? Put more primitively, it seems more like “magic” that an undifferentiated mass of material could function like a cell.

  3. I think you hit the knail on its head. Materialists are upset that what they thought was their best ally (hard science) is in fact providing the scientific evidence AGAINST their religious/philosophical worldview. To them, this is unthinkable, thus, the emotional response to scientific criticisms to Darwinism.
    We have seen in another blog how one of Darwins’ contemporany bulldogs (PZ Meyers) is advocating physical violence against Darwin skeptics. Is this the response a rational scientist gives to opponents?

  4. 4
    sagebrush gardener

    What was thought to be their best ally is gradually becoming their worst foe, and this is a tough pill to swallow.

    I think of this whenever someone objects to the supposed lack of an “ID research program”. The hard scientists are doing an end run around the philosophers, albeit with an occasional perfunctory genuflection in their direction.

  5. Much of this irrationality against ID comes down to the fact that science will never know all the answers. If a being outside of time and space produced the universe and perhaps many of the complex systems in nature, it did so by means totally outside the grasp of our understanding. To admit as much must be agonizing to many interested in this debate (myself included). Yet to avoid this (or appear to avoid this) orthodox darwinians seem perfectly comfortable speculating ad infinitum; unfortunately, that is all any of us can do on such matters, speculate.

  6. I have learned first hand about this “irrational hatred” in the last few days since I posted an essay on my blog in support of intellignt design and kicked off a free-for-all discussion in the comment section. I wont repeat all the personal insults again, but suffice it to say, the reaction was a bit harsh, and more than a little emotional. I am very much a layman, but I was surprised to find that I was able to pretty-much hold my own intellectually against a gentleman who claims to have a PHD and to have written 30 scientific papers. Once you got through the emotion, the venom, and the insults,it turns out that he only had a couple of really good points that I hadnt already adressed. Also, he really didnt have any particulary convincing responses to my questions about the statistical improbability of the complex, specific information present in DNA coming about apart from design. Nobody seems to have knocked down the irreducible complexity argument either. I keep hearing about Selection as a counter to both problems-( it’s apparently some kind of magic genie that erases the need to confront statistical impossiblities as near as I can figure. ) At any rate, although my feelings may have gotten bruised a bit, in the end I think that free and open debate is worth the abuse.Everybody here has sugested that I moderate more strictly, but I just cant bring myself to do it. When our side has so often been the victim of academic censorship and derision, I just cant bring myself to censor anybody or shut anybody down. The irrational bomb-throwing on the part of some devout evolutionists probably says more about them and the strength of their ideas than it does about us, so I think that giving them equal time may help us in the long run. So I’m going try to just take my lumps like a man and stop whining about it. I came to this forum tonight to ask for direction and education on a SPECIFIC point put forward by the afformentioned critic of ID. The best argument he had was the statement that nested heirarchies infer common descent, not design. In the same way that he doesnt have the answer to some of the problems I raised regarding Evolution, I have to admit that I dont have an answer to his challenge on nested heierarchies. Would one or several of you brainiacs here who support ID be willing to pop in to the comments section and enlighten myself and the gentleman who raised the issue , as to how these nested heirarchies can be reconciled with ID? Since the name of this blog is “uncommondescent”, surely somebody here has the answer to this gentlemans’ challenge that these heirarchies prove common descent. The link is:
    http://tyharris.wordpress.com
    PS.- I know that my posts are too long, and that I need to work on my organization. I am new to all of this…

  7. Gil

    I was thinking along those same lines in a discussion I was having on another thread.

    Ty

    Keep at it.

  8. “…surely somebody here has the answer to this gentlemans’ challenge that these heirarchies prove common descent…” –Ty

    Ty, have you considered the possibility that common descent is actually true? Let us forget, for the moment, any further inference about the role of intelligence in evolution, etc. Many in the ID community accept common descent and, for me, it seems as difficult to deny common descent as it is to deny that the earth is over 10 thousand years old. Are you certain this is the battle you want to wage?

  9. GA – I’ll wage it. Common descent is only true if genetic similarity is in fact due to common descent – but that’s circular reasoning.

    But there’s something else that bugs me:

    The cosmological argument is a vacuous inference to design, if we have only Dembski’s design-detection criterion to work with. If you can’t demonstrate things could have been different, you can’t claim improbability.

    Please, someone, either fully address this argument on its own merits, or drop the cosmological argument.

  10. PS – I offer a constructive solution, and would appreciate a response: why should not algorithmic compressibility alone suffice for a design inference?

  11. tyharris said:

    Everybody here has sugested that I moderate more strictly, but I just cant bring myself to do it.

    It is equally important that you consider those friendly to the design argument, or curious of it, who to want to post comments and questions. If your blog is dominated by the carnivorous, then they will discourage those seeking information or reasonable discussion from contributing.

    If your blog is primarily a “Ty versus evolution” exercise, then this is not a concern.

  12. 12

    Is there any way to discriminate between hostility towards id that comes from, on the one hand, the need to preserve one’s identity as a professor of the profound truth, and on the other hand, the need to preserve one’s religious beliefs from attack by outside facts? Because I find it hard to ascribe one or the other to any evolutionist in particular, except of course, Dawkins, because I don’t know if the two motivations produce different behaviors.

  13. 13

    jaredl – the Darwinists are saying that evolution produces the appearance of design without design, and I think their understanding of apparent design would encompass algorithmic compressibility. A compressible sequence randomly formed through mutation, and then it continued to exist because it made the host more fit.

    Of course, the longer the compressible sequence, the lower the probability of random creation. But faithful Darwinists tend to ignore arguments based on stats, citing the classical physics truism that nothing is actually random, and thus, with a wish, declaring that evolution is not only not improbable, but in fact inevitable and certain. This mental state is known in criminal law as a heat of passion.

  14. Hi Ty et al:

    1] Nested hierarchies

    You may wish to take a look at what is now a fairly old book, Evolution, a Theory in Crisis, by Michael Denton. There, he analyses the resemblances across life forms based on typology — a design-based concept that goes all the way back to Plato.

    Now, too, common design also gives rise to nested hierarchies — within systems and across similar systems. That is, the observed architecture of classification is not a differentiating factor between common descent and common design, or even design for similar contexts and purposes. Indeed, Linnaeus, the originator of the modern classification system of life forms, was a Creationist.

    It is worth noting too that nested hierarchies are fairly common in designs and organisations etc. That is,the basic nested hierarchy system architecture is often found in indisputably design-based contexts. For example, consider a passenger jet as a cluster of nested sub-systems designed to achieve its goal. Software is often written that way too. And so on.

    Should we infer from the resemblances across aircraft, autos, trucks, adn even ships etc — which can be represented as a nested hierarchy — that these were not designed? [Similarly, there is a common taxonomy course exercise to classify paper clips and other similar fasteners using principles of taxonomy. One sees of course a nested hierarchy. Should we infer from that to common descent?]

    In short, the question at stake should not be begged. Nested hierarchies are possible and even expected on BOTH explanations, so the issue is not decisive between them.

    2] Climbing Mt Improbable:

    What is happening is that the level of complexity to get TO the first functioning life form is being ignored.

    For instance, we know that DNA strands range from about 500k to about 3 Bn in life forms. But, since the chemistry of chaining does not determine the genetic code, we are looking at a huge space for the various possible combinations of GCAT. But, on a reasonable basis we can see that 500 – 1000 bits of information [DNA chains of 250 - 500]cannot be accessed by random searches within the ambit of the observed universe. That is what the issue of functionally specified complex information is all about. [And BTW, the concept is NOT original to Dembski, but emerged from OOL studies by the early 1980's as Yockey, Wickens etc studied the nature of the informaiton base of life forms. Have a read of Thaxton, Bradley and Olsen's The Mystery of Life's Origins, the online chapters.]

    The idea that a simple information structure can be selected the n we go on tot he next one in sequence till we get to the fully functioning life form or system, in short begs the question of credibly irreducibly complex information.

    There is no “easy” back ways up Mt Improbable. [Cf the linked through my handle.]

    3] Probability vs sensitivity arguments and cosmology etc

    The issue on cosmological inference to design is principally on the SENSITIVITY of the relevant dozens of parameters, singly and in aggregate.

    In effect, according tot he General Theory of Relativity-derived equations — which have at least some significant empirical support — slight perturbation of key parameters gets us to a radically different cosmos that is not hospitable to life as we experience it. Similarly, the Goldilocks zone argument identifies that planets capable of harbouring intelligent life as we experience it are relatively rare int he observed cosmos, which can be a pretty hostile place.

    Probabilities are inferred from those sensitivities, based on the Laplacian principle of indifference that we use to say infer that a fair die will end up at 6 one out of six times on average. In short the frequentist approach is not the only legitimate one to the estimation of probabilities. [Here in Montserrat, expert elicitaiton is routinely used by the Scientific Advisory Commmittee to estimate likelihoods on the possible developments with the erupting volcano over the next year or so. While obviously the estimates are just that, they have a certain credibility and utility.]

    Of course, as soon as we are inferring to a probability other than 1 or 0, we infer to a certain degree of ignorance.

    Also, we should note that the fact of the common resort to an inferred quasi-infinite array of sub-universes is in part an acknowledgement that the probabilities as estimated have a point. Latterly, there is a tendency to scant such inferences, but it seems to me that much of that is self-servingly selective hyperskepticism. (In effect, “extraordinary claims demand extraordinary evidence” rests on the issue that one’s worldview assumptions and expectations lead one to selectively doubt what cuts across one’s comfort zone. We need to be aware that we could be wrong, so we shod insist on adequate not “extraordinary” evidence.)

    Hope that helps

    GEM of TKI

  15. Ty:

    “…surely somebody here has the answer to this gentlemans’ challenge that these heirarchies prove common descent…”

    Ty,

    I appreciate your courage to go on discussing with the crowd of darwinists, although I don’t think I would be able to do the same. The point is, it is very beautiful to discuss with those who have different ideas, but it is not beautiful at all to fight. If a lot of other people have no real intention to listen with a minimum of attention to what you say, and if the only goal of the “discussion” is to outnumber you with propaganda, then there is no fun.
    That said, I have tried to read the many comments to your essay on your site, and got immediately discouraged. There is only a certain amount of intolerance I can tolerate per day. So, if you could please give me the numbers of the posts you found interesting, and to which you would like some answer, we could be spared some useless suffering. Meanwhile, I will try to address what you say in your post here in a general way.

    You say: “The best argument he had was the statement that nested heirarchies infer common descent, not design.”
    I am not sure what he means by “nested hierarchies”. I suppose he means ordered level of omology at the DNA level. Any discussion at the morphological level is too vague to be worthwhile.
    First of all, I agree with great_ape: why can’t we accept that common descent may be the answer?. It is perfectly true that many here (including, perhaps, myself) accept or can accept common descent as a very good hypothesis. But it should be clear that:

    1) Homology in DNA, however nested, is not evidence of common descent, although it is certainly a strong support for it. Indeed, omology can be interpreted as reutilization of the code, even in absence of common descent. In other words, a designer could well reutilize solutions he has already used, even if he does not materially implement them in already existing “hardware”. So, if the designer modifies the code in already existing beings, we have reutilization/modification of the code and common descent is also true. On the contrary, if the designer implements the code, reutilizing parts he has already used, but on a completely new “hardware” (in other words, creating a new species not from an existing species, but, for instance, from inorganic matter), then homologies can just the same be explained as reutilization of the code, although common descent in that case is not true. Although, as I said, I tend to believe in the first hypothesis (designed common descent, with intentional modification of the code by the designer), both can be discussed.

    2) The darwinist hypothesis, instead, is one of unguided common descent. It is not true that there is any support to that hypothesis. Homologies, however nested, are not specific support to the hypothesis of unguided common descent (although they are compatible with it), because, as already said, they are also perfectly compatible with any design hypothesis. Besides, the “nesting” is far from being regular and corresponding to a specific “tree”. We all know the difficulties darwinists face each time they try to fix a specific “order”.

    Finally, even the arguments about “errors in the code repeated in different species” and “homologies in non coding parts of the code” have no meaning. Regarding errors, they are common in any code, adn they are perfectly compatible with the idea of reutilization of the code, especially in our first form, where not only the code, but also the implementation, is reutilized. Moreover, it is very difficult to establish what is really an “error”, when you don’t know all the intentions of the designer, and not even how most of the code works.
    Regarding the homologies in non coding DNA, now those are really interesting! We know that many parts of non-coding DNA are ultra-conserved. That is probably some difficulty for darwinists to explain, but luckily not for ID. Indeed, we have never thought that non-coding DNA is “junk”. We do believe it is code, and very important code indeed! And that can apply to any part of non coding DNA, including transposons of all kinds, until we understand how the living functions of regulation, differentiation, morphogenesis etc. are implemented.
    We should always remember that any fact observed by darwinists, from duplication of genes to all the similarities and differences between genetic code in various species, is by far best interpreted by design, while faces incredible improbabilities when interpreted as unguided common descent. This is the truth. That’s why there is no way to ultimately define research as darwinist or ID inspired. Research, although it may be inspired by specific ideas, is just research. It looks for facts. If it is done well, and with honesty, it usually finds them. And facts only support truth. So, if design is true (as I strongly believe), for me any good research is a pro-ID research. I read pro-ID reasearch every day, although the authors are rarely aware of that.

  16. I have a simple question. Isn’t this just an argument over the mechanism of the creation of new alleles?

    When objects (in this case biological organisms) are organized because of some type of similarity it is likely that there will be various forms of hierarchies used. If it assumed that the descent of the hierarchies on the paper used to show these hierarchies represents a time order then that can be checked against independent information.

    Assuming that time of appearance is not used in the original organization then this could be used to test the consistentcy of the hierarchical organization.

    I assume that is how it is done. Though I am sure there are attempts to reclassify based on the time order of appearance which then begs the question of the hierarchy having an independent verification.

    Even if all these procedures, which I assume are fairly complicated, indicate a general progression in life forms over time that reinforces the similarily, there is nothing said about how the individual life forms arose. We are still stuck with the lack of a mechanism no matter how consistent the hierarchies are and from what I understand there is lots to be desired in these hierarchies.

    So as gp has said. It could very well be common descent but common descent says nothing about the mechanism that produced the new organisms. Since no one has a clue about this, we are back to the basic question, how do new alleles arise?

  17. On my previous comment, I assume the procedure today is to use both time of appearance and physical similarity to classify and then use genetic information as the independent means of verification. If genetic information is also used to classify, then is there any other independent information source that could be used to verify.

    Since I am certainly not knowledgeable on this, maybe someone could comment using plain language to describe the procedures that are used to create these hierarchies.

  18. tyharris [6]

    Hierarchic classification is, by its very nature, an orderly groups within groups arrangement in which boundaries are distinct and the divisions in the system increase in a systematic manner as the hierarchy is ascended; absense of overlapping types implies the absence of sequential relationships.

    Therefore the contrast between hierarchic classification and gradualistic evolution, which would leave behind an overlapping blurred and fundamentally indistinct pattern, could not be more complete. Nature is fundamentally non-sequential, in other words, a discontinuous phenomenon.

    Furthermore, for gradualism to produce such hierarchic order it would be required that character traits once acquired can never subsequently be lost or transformed in any real sense and that the acquisition of new traits must leave previous traits essentially unchanged.

    Therefore, in other words, character traits (such as hair and mammary glands unique to mammals, or pentadactyl limb unique to all terrestrial vertebrates) must remain fundamentally immutable. But why should these traits have remained immune to change, after all, are we not talking about evolution?

    Put simply, gradualists who acknowledge hierarchic order are also acknowledging the fact that the crucial intergrading forms leading from one form to another are totally lacking. I have no idea how anyone can draw the conclusion of common descent from hierarchic classification.

    This also presumes that NS would direct evolution in this manner see comment:

    http://www.uncommondescent.com.....ent-109702

    And this also presumes complex systems can be produced gradually see comment:

    http://www.uncommondescent.com.....ent-110246

  19. “GA – I’ll wage it. Common descent is only true if genetic similarity is in fact due to common descent – but that’s circular reasoning.” -jaredl

    This was not my reasoning, but I note that your particular charge of circularity could be applied to most any statement whatsoever about the world. For example, “That the earth spins is only true if day and night are the result of the earth rotating…but that’s circular reasoning.” My reasoning, on the other hand, has more to do with how so very many things about molecular data make sense under common descent and do not under other interpretations. (i.e. inference to best explanation and the robustness of hypotheses based on common descent). This is particularly true in regard to the distribution of viral insertions among similar lineages, neutral mutations (including trivial insertions and deletions), patterns of decay in pseudogenes, and a multitude of other phenomenon, which, to explain by special creation would require either a) a deceptive designer or b) performing various intellectual contortions to assign utility to *every* genetic event in the genome, despite the fact that we now know a great many mutations have no consequence. I’m convinced that if people saw the molecular evidence that I’ve encountered, there would be far fewer doubters. One day I hope to compile some of the nitty gritty details into an accessible manuscript.

  20. What would it take to falsify common descent as an explanation for genetic similarity?

  21. great_ape,

    What would conserve a viral insertion? It seems that any coding region that has no function would within a few generations start to deteriorate because there is no reason for it to remain the same.

  22. I think the word “coding” should be dropped from my question because I beleive coding implies a function.

  23. What would it take to falsify common descent as an explanation for genetic similarity?

    Nothing can falsify common descent since it is not science, but a logical deduction from naturalism. If the fossil record, which is totally against common descent, the so called Cambrian explosion, the dowfall of homology and the lack of linages did not destroy common descent, nothing will.

  24. “What would conserve a viral insertion? It seems that any coding region that has no function would within a few generations start to deteriorate because there is no reason for it to remain the same.” –jerry

    They most certainly do start to decay, and this is observed, but it takes several million years for them to decay (in mammals) to the point where they are no longer discernable as what they are. The very fact that they decay in a predictable fashion further reinforces the notion that they (more often than not) have no function and thus serve as excellent markers to demonstrate common descent.

    “Nothing can falsify common descent since it is not science, but a logical deduction from naturalism.”
    –Mats

    I don’t know how you arrived at this conclusion, but it is wrong. Common descent makes a multitude of predictions, any number of which could be used to invalidate it. Let us take the example of the viral insertions discussed above. If a viral insertion is found to be decayed (by mutation) such that it is estimated (by a molecular clock) to have occurred sometime sufficiently *prior* to the speciation time of humans and chimps (i.e. in the *common ancestor*), then we should find it present in *both* species even if, so far, we have only observed one species’ genome. The empirical test is whether, when you look at the other species, you find the insertion in question. If it is not present, there will nearly always be some remnant of it or indication it has been removed via deletion, recombination, etc. To my knowledge, this prediction holds true in all cases except in situations where the insertion time is near the speciation time in which case the insertion can sort randomly among the two lineages. And this sorting of insertion polymorphisms is still *another* prediction of common descent. When you find insertions that date *near* speciation times, they sort randomly among lineages.

    It is not how functional things behave that demonstrates common descent, it is the behavior of spurious changes in retroviral sequence, pseudogenes, etc, that can be traced. These are the best markers and these tell a story that is only intelligible by positing common descent.

  25. Tribune, thanks for directing me to this thread. I haven’t seen anyone respond to Great_Ape’s points in a convincing way. The best argument is that God / the designer may have “re-used” code and that such re-use might incorporate earlier “mistakes,” “bugs,” or elements that are no longer functional. I think that is possible, but the question remains, is it the best inference given the data? We are not talking here about a few snippets of re-used code here and there, or a handful “bugs” or mistakes. We’re talking about “re-use” on a massive scale, with “bugs” and mistakes that fit elegantly into the hypothesis of common descent. At one level, the “re-use” explanation just seems like special pleading.

    At another level — and I think this is crictically important — the “re-use” hypothesis just seems like another way of viewing theistic evolution! After all, God is not absent from the process of evolution under the TE view. In effect, under the TE view, God is constantly “re-writing the code” via the secondary causes of natural selection and genetic drift. It seems to me, then, that the only reason for preferring the “re-use” hypothesis to TE is if there is some Biblical reason to do so — specifically, if the “kinds” of Genesis 1 require repeated acts of special creation. Personally, I don’t think that there is any exegetically or hermeneutically compelling reason to do so. But even more importantly to the ID discussion, there doesn’t to be any scientific reason to do so. So why not just admit that common descent is generally true?

  26. You’re welcome, Dave.

    A couple of points:

    The idea of the universal common ancestor many of us remember from the phylogenetic trees shown us back in junior high has been pretty much refuted.

    Now, back in the 50s60s70s this was taught as basically a slam-dunk sure thing, so it should be understandable that some would hold reservations about any common ancestor theory.

    And there is another reason that’s it’s defensible to hold these reservations. While it’s not irrational to infer a common ancestory based on genetic similarites (just as it wasn’t based on morphological ones in Darwin’s day), it can’t be shown how this evolution happened. It can’t be duplicated. All that’s offered are inferences and surmising.

  27. A question for everyone on common descent.

    Would multiple but similar origins of life be the same as common descent? Say there were two origins of the first life form – both on opposite sides of the planet. However, they both came from the same material source (Think 2 RNA World events, and yes, I know how unlikely that is.)

    Is this common descent? Or is CD strictly ‘There was exactly one origin-of-life event, and all life came from that’?

  28. First of all, let me join the others in praising great ape and his contributions to this blog. Some of the best discussions we have had have been motivated by his interventions, including this one.

    To dopderbeck, I would like to remark that in his intervention there seems to be some confusion of terminology (but if I have not understood correctly his intentions, I apologize). I have already said that common descent seems to me the most likely explanations for many observations, although it is not the only possible explanation, and always remembering that the observed facts are not always so consinstent as some want us to believe. Anyway, my idea of reutilization of the code can apply both to common descent scenarios and to “special creation” scenarios. The idea is that a designer can always reutilize his code, indeed designer always do that in a massive way. The common descent scenario only explains better the persistance of errors (including the viral insertions cited by great ape), because in that case the designer reutilizes his code “as it is already written in a previous implementation” (that is, in an existing species), and then modifies it as appropriate. The persistance of errors can be explained, outside of common descent, only if we assume that the designer has anyway reutilized a code “written” somewhere else, but I admit that I con’t find that explanation very convincing. And I agree with great ape on one other point, I don’t believe that “anything” in the genome needs have function, although I do believe that “most” of it has, including most of what has been considered functionless.
    That’s why I am happy enough with the common descent idea, although I think we must keep an open mind about that, and remember for instance that common descent could well be only “partial”.
    Anyway, of one thing I am absolutely sure. Common descent does not imply unguided evolution, and it does not imply, to cite dopderbeck’s definition of TE, that “God is constantly “re-writing the code” via the secondary causes of natural selection and genetic drift”. In my opinion, such a statement has no meaning. If the code is rewritten only by NS and/or genetic drift, there is no role for God there (except for having created the laws which imply NS and GD). Frankly, I can see no relation between such a view (which could be that of Ken Miller, approximately), and ID.
    Dopderbeck goes on: “It seems to me, then, that the only reason for preferring the “re-use” hypothesis to TE is if there is some Biblical reason to do so”.
    One thing is important for me: although I have my religious beliefs, I will never use them to motivate or justify a scientific discussion. Although our enemies like to represent ID as a pseudo-scientific, religious movement, I know that’s not true. I believe in ID for purely sciebtific reasons, not for religious ones. And I believe, and assume, that anyone in the ID frame should do so. I have never seen Dembski or Behe use a religious argument in a scientific context (although anyone can use religious arguments in a religious and/or philosophical context.
    Therefore, I am absolutely convinced that the ID arguments demonstrate, beyond any doubt, that biological information is designed. That it is in no way the product of natural selection, genetic drift, or any other combination of chance and necessity. That a designer had to design life from inorganic matter, and had to design each significant new implementation of life (such as species), through means which are open to discussion, and probably (but not necessarily) in a scenario of common descent. The presence of the designer(s) is an easy, constant, exciting, absolutely necessary inference whenever we look at any sifnificant aspect of the biological world.
    By the way, happy Easter to everybody!

  29. Great Ape:

    I entirely agree with GP’s point. You are no “troll.”

    speaking for myself: You have been civil and are a valuable participant in this forum.

    You also demonstrate that if NDT etc advocates will pull back on the incivility that too often mars their behaviour, they can participate productively in UD. [That sharply contrasts with the mantra about unjustified banning as a common tactic at UD. Of course, I say that, having not been banned despite a strong disagreement with the "banner in chief" himself. Though of course there is the minor matter of a pending in-filter comment for a while now . . . which may have something to do with a certain upcoming blessed event for Patrick, the filter-clearer in chief it seems.]

    Also, as the recent discussion on the sickle cell trait showed, the results from such a process of actual dialogue will not be one sided.

    GEM of TKI

  30. kairosfocus

    The moderation and spam queues are empty. The spam volume has been so high for the past two or three weeks that I’ve been emptying it without looking at the comments. Occasionaly a legit comment is in there but it’s like finding needle in a haystack amongst 500 advertisements for viagra, online casinos, and things of that nature. If there’s anything of yours that was in the spam queue it’s gone now.

  31. Great_Ape:
    They most certainly do start to decay, and this is observed, but it takes several million years for them to decay (in mammals) to the point where they are no longer discernable as what they are.

    LoL! We have NOT observed anything for millions of years. Therefore we don’t know how long viral insertions take to decay. We may be able to guess but that guess is goung to be based on one’s preconceived biases.

    Great_Ape:
    The very fact that they decay in a predictable fashion further reinforces the notion that they (more often than not) have no function and thus serve as excellent markers to demonstrate common descent.

    In order for Common Descent to have any weoght it must explain the DIFFERENCES observed- that is the physiological and anatomical differences- between alledged closely related populations, like chimps and humans.

    Also we do NOT know whether or not the allged viral insertions are viral insertions at all. All we have is “they LOOK like viral insertions”. Then there could be a cxommon mechanism. That is populations with similar genetic make-up that gewt hit with a similar virus, that virus will insert into similar DNA sequences.

    Ya see with the recombinations we know about there is NO way anyone should expect a useless viral insertion to stay intact enough over millions of generations all the while other changes are taking place throughout the genome. Changes that alter form and function.

  32. The following is a Creationist’s explanation of ERVs:

    ?Were Retroviruses Created Good?

    Abstract:

    Retroviruses that are not normally present in healthy hosts are called exogenous viruses, while DNA sequences in cellular genomes that are homologous to retroviruses are called endogenous retroviruses (ERVs). While the belief that all ERVs are remnants of germline infection seems logical, there are also facts against the endogenization theory, such as xenotropic ERVs and essentiality of some ERVs in host physiology. Syncytins, products of the env gene of HERV-W and HERV-FRD, contribute to human placenta development. Similar genes are also found in mouse and sheep. Indeed, the sheep ERV genes have been shown essential for sheep reproduction. Furthermore, regulation of the human syncytin-1 gene involves a complex regulation network including both viral and host factors. Conclusion: While intact ERVs with positional polymorphism are likely germline copies of exogenous viruses, ERVs with fixed locations and conserved beneficial genes may have been incorporated into the host genome at the time of creation. Exogenous retroviruses may have been created to help the ERVs and to transfer useful genes between hosts.

  33. nullasalus [27]

    It’s believed that every living organism can trace its ancestry down to a primitive single celled organism that spontaneously generated itself from inorganic matter. If you allow multiple origins, where does it end? One might as well believe in special creation.

    Orthodox darwinism has survived as long as it has because its proponents make it appear simplistic, elegant and yet paradoxically too complex for the moronic masses to understand. But break through the surface, dare to question the orthodoxy and you’ll discover that right from the offset the problems are insurmountable.

    The theory is not close to demise, it was stillborn. Look closely and you’ll see the strings and I don’t need to tell you who’s pulling them.

  34. “LoL! We have NOT observed anything for millions of years. ” –Joseph

    By “observed”, I mean that biologists have made frequent empirical observations of genetic sequence that are consistent with this working assumption. Say, for example, we examine a species’ DNA, species (w), and find a viral insertion (Or retroposon, etc.) If it was there a very long time–say since the common ancestor of species W,X,Y,Z–then when we look at the other species X,Y,Z at the same location, we should find copies of the virus that should have been degenerating for several million years. They should be battered with insertions/deletions, have base changes, etc. The open reading frames of their proteins should be disrupted disrupted. That is precisely what is seen. So yes, we make the inference that they were there millions of years and have been degenerating. Given a great deal of such data, I think it is by far the most reasonable inference.

    I will not argue that you can not come up with explanations that explain away this phenomenon under a creationist context. I will only say that such arguments are extremely awkward to make, as is the case with the paper you reference. If I had more time, I would detail some of the more egregious stretches there. Perhaps some other time.

  35. gpuccio — thanks for the thoughtful comments. You said this: that “God is constantly “re-writing the code” via the secondary causes of natural selection and genetic drift”. In my opinion, such a statement has no meaning.

    Why? Why are secondary causes irrelevant as evidence of God’s handiwork? In classical orthodox Christian theology, secondary causes certainly are not “meaningless.” Take a look at Aquinas’ intricate discussion of causation, for example.

    One good way to think about this is through another classic “natural theology” text, Psalm 139. The Psalmist says, “For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.”

    Notice the language here: each person is “created,” “knit together,” “fearfully and wonderfully made” — in other words, designed carefully by God — and this fact is a cause for wonder at God’s works.

    And yet, today we can explain the process of human birth from conception through every stage of fetal maturation entirely in terms of seconary causes. There are no “gaps” in our “scientific” knowledge of human conception of birth; no need to suggest there is something God had to do directly through primary causation.

    Is Psalm 139 thus falisfied? No, because natural theology pictures God as active within and through secondary causes. There is a layer to secondary causes, to use Pascal’s term, that is “hidden” from our direct observation — the will and power of God.

    Given this, I don’t see any reason why common descent through secondary causes must elide God. The question of God’s supervenience over secondary causes is a theological question, which scripture (as in Psalm 139) and Christian theology resoundingly answers in the affirmative.

    So, again, I haven’t seen any reason yet — scientific or theological — why the general notion of common descent should be rejected.

  36. dopderbeck:
    So, again, I haven’t seen any reason yet — scientific or theological — why the general notion of common descent should be rejected.

    What is the scientific reason it should be accepted?

    to Great_Ape-

    Again given what we know about chromosomal recombinations there is no way any viral insertion should remain, not only intact enough to be recognizable as a genetic marker, but also stay in the same location, over millions of generations is the most awkward claim there is to make.

    And perhaps what we see at X, Y, Z isn’t degeneration of the original (W), but only appears to be based on our ignorance and pre-conceived biases.

    IOW without confirming data that demonstrates such changes are even possible (to account for the physiological and anatomical differences observed between chimps and humans, for example), all this is is speculation based on the assumption. That is you have decided Common Descent and have set out to find what you think would be confirming data.

    And given the data that we do have Common Descent does NOT jive with it at all. Natural selection conserves and sexual reproduction produces wobbling stability. IOW to posit Common Descent would be an extraordinary claim and as such require some extraordinary evidence. Yet the best you can muster is speculation based on the assumption.

    And given what we are finding out about the genetic differences between chimps and humans there may have had to have been accumulating fixed mutations EACH GENERATION in each diverging branch just to account for them.

    Never mind the fact that the magical mutations just haven’t revealed themselves after all these years of looking…

  37. dopderbeck,

    I think what is being said is that common descent is a hypothesis that would explain a lot of the sequence of species we see. However, there are two problems, maybe more.

    Whatever criteria used to justify common descent has lots of holes and anomalies. I have no idea of the proportion of anomalies to consistency but there are many. In other words what has to spelled out is the information that supports and falsifies common descent.

    Given this approach and after we examine the evidence we find out that the support for common descent far outnumbers the anomalies we are no further along to finding the mechanism for the consistencies.

    We can argue fairly forcefully that gradualism could never have caused it. Also, there have been some here and in the literature who are evolutionary biologists and who say the ideas of Darwin are dead. Implying Darwinism would be long gone except that it would give solace to the creationists. And that is something they could never be allowed to do.

    But they have nothing to replace gradualism but pure speculation. So one man’s speculation without any evidence (Darwin) remains the basis for a major scientific area because other’s speculation have no evidence to back it up yet.

    You will understand the ID people when you understand none of have seen any evidence for gradualism or any other mechanism for species change. We recognize the fossil record shows a progression and while genetic markers for common descent may in fact be valid, it underlies no mechanism for these markers, not even circumstantial.

    If gradualism were true, you would expect to find a whole host of things, none of which appear in nature. If you disagree and think there is evidence for gradualism, then make your case. But common descent supported by genetic markers is not evidence for any mechanism let alone gradualism. In fact it is falsification for gradualism because if this was the mechanism one would expect to find a completely different suite of species in nature supported by a different set of genetic markers.

  38. dopderbeck, you said:

    So, again, I haven’t seen any reason yet — scientific or theological — why the general notion of common descent should be rejected.

    In a previous comment you said:

    So why not just admit that common descent is generally true?

    (Theological issues aside)

    Common descent certainly isn’t rejected here, just questioned. One of the beautiful things about Intelligent Design is that it isn’t trammeled by methodological naturalism. The benefit for ID proponents is that design becomes a valid explanatory mechanism for biological observations, including genetic similarities. Thus, common descent isn’t the only option. Still, it is an option in the ID universe (an ever expanding place).

    For NDE, common descent is a necessity. Without it, the likelihood for a neo-Darwinian explanation of observed biological systems shrinks away from even “vanishingly small.” NDE doesn’t even have the option of interpreting anything in nature as intentionally designed, nor does it appear to have the option of suggesting any alternatives to common descent, short of producing some kind of convincing chemical evolution scenario, or deferring to panspermia. It is fenced in to a materialistic world view: nothing else is allowed, nothing else is possible.

    From what I read on this blog, nobody here rules out common descent, nor does ID force anyone to do so; rather there are views on both sides of the issue. Since there are many who remain unconvinced that common descent is necessarily true, there’s nothing to “admit.” CD is not an “elephant in the room” for ID.

    So why not just admit that common descent is generally true?

    …because it isn’t necessarily true — ID doesn’t need to run things through the materialism filter.

  39. So why not just admit that common descent is generally true?

    Because the weight of evidence goes contrary to its claims. In fact, the most incredible discovery of modern science has to be the discontinuities in nature. Nature is fundamentally a non-sequential system whereby archetypes seem immune to radical change.

    There would be no doubt, and nobody here questioning common descent, if the fossil record showed the intergrading forms leading unambiguously from one form to the other, or even a detailed series of fossils showing the development of a complex organ.

    In respect to viral insertions, how have they managed to remain intact enough to be recognizable as a genetic markers? Is it realistic to believe as both lines diverged from a common ancestor, then travelled on their own path for millions of years, that these would remain?

    This argument seems very similar to the one gradualists use in repect to hierarchic systems in that many defining characteristics (i.e,. pentadactyl limb unique to all terrestrial vertebrates) must remain essentially unchanged during many millions of years of evolution.

  40. Dave Scott:

    Thanks for the note — I still puzzle over the strange parameters that seem to lurk in yon filter! (I note that even moderators complain or at least note on being “Caught” there.)

    I simply noted on a comment that did not seem materially different from one that got through but was blocked. [This is on our exchange on probability and estimations thereof.]

    My more basic point is that the Darwinist advocacy partyline that UD etc are unwilling to entertain healthy disagreement is plainly falsified by factual evidence.

    G-A is living proof of that.

    So, the challenge is obviously to the NDT — evo mat– secularist progressivism advocates: can you hold your own without resorting to uncivilised behaviour?

    GA has tried and we have had productive dialogue. Currently Pixie and I are having a good exchange on thermodynamics initiated by Sewell.

    More like that would help move the ball forward . . .

    GEM of TKI

  41. Would multiple but similar origins of life be the same as common descent?

    nullasalus, take the words as literal.

    In the situation you suggested let’s say one of those life forms evolved into all plants and the other into all animals. The plants would have a common ancestor but animals and plants would not.

  42. Joseph said: What is the scientific reason it should be accepted?

    Because it remains the most parsimonious and consistent explanation of the data; and because many of the predictions it makes about what we should expect to find in the data — including predictions about genomics, which was a black box when the theory of common descent was first posited — have generally been realized.

    Appolos said (Theological issues aside) … One of the beautiful things about Intelligent Design is that it isn’t trammeled by methodological naturalism.

    This seems directly contradictory to me. The best — I would say only — reasons for questioning methodological naturalism are theological ones.

    Appollos also said: …because it [common descent] isn’t necessarily true — ID doesn’t need to run things through the materialism filter.

    This seems to me to be part of the heart of the matter: a confusion of the general idea of common descent with the philosophy of materialism. Removing the materialism filter doesn’t excuse anyone from ignoring the evidence for common descent. The evidence remains; it remains compelling; and there remains no strong alternative explanation, except for a vague “God / the designer did it” — which really is a God of the gaps explanation. I have no problem with offering that explanation if it’s offered on the grounds of revelation (though I think it would remain a wrong understanding of revelation). I have a problem with the notion, however, that this is the sort of explanation that is separable from theological presuppositions. It just isn’t.

    Tribune said: In the situation you suggested let’s say one of those life forms evolved into all plants and the other into all animals. The plants would have a common ancestor but animals and plants would not.

    This highlights for me another disconnect in this discussion. Most of you seem to think “common descent” must mean “universal common descent.” Personally, I don’t use the terms so interchangeably, and I think that conflation of terms can be misleading.

    When I argue that “common descent” is well established, I mean that in general terms — that there is strong evidence for gradual organismal changes in natural history and a general pattern of coalescence as one goes farther back into natural history. The evidence, it seems to me, wipes out the artificial distinction between “micro-” and “macro-” evolution.

    That is not to suggest, however, that the history of life on earth is necessarily so simple that all of life coalesces to one point of ancestry. Even the materialist scientific community recognizes this, with considerable debate and disagreement, of course, in theories such as panspermia.

    Personally, I do find the notion of “front-loaded evolution” interesting in some ways — but I don’t see that as a rejection of common descent. OTOH, I don’t find even “front-loaded evolution” so compelling that I’d stake my life on it. It remains a bit of a “God fo the gaps” explanation, which I can’t see any strong reason to favor apart from theological reasons. And even with my theological presuppositions, I don’t see terribly strong reasons to favor it — after all, as the little study of Psalm 139 demonstrates, in theological terms, there are no no “gaps” for God to fill. Secondary causes are not “gaps” — they are themselves the exercise of God’s providential care for the creation.

  43. kairosfocus

    We use Akismet for anti-spam. You can look into the particulars of how it works at their website. In a nutshell; all comments, including the source information, are automatically sent to Akismet’s server farm. There the comment is scrutinized against a proprietary list of keywords, sender sources, and other factors which are known to be charateristic of spam. If suspected of being spam it is returned to us flagged as potential span and stored in a special queue pending further action by the blog adminstrators.

    Lately we have been getting over 1000 spam comments per day and Akismet has for us so far intercepted over 90,000 spam comments. Perhaps 1 in 100 of those were mistakes. A year ago we were getting only 100 – 200. A year ago I would conscientiously look at the entire spam list picking out the mistakes so they could be published. However, going through 1000 or more each day is too much. I might glance at the first page of 50 comments but when there’s hundreds of them queued up I usually just dispose of the whole lot en masse without examination. I expect as the popularity of the blog continues to rise so will its attractiveness to spammers and the spam problem will only continue to get worse.

    As an aside for you in particular I’ve noted that the longer a comment is the more likely it will flagged as spam. I believe that’s because the more words in a comment the more likely it is that one of them will be a suspicious keyword. Also as the length of the comment grows the more likely it is that it will hit the magic number of 5 embedded URLs which is a spam trigger. The overwhelming majority of spam comments are 3 lines or less so there may be good reason for Akismet to adjust its policy by weighting longer comments in favor of non-spam. The Akisment protocol learns through experience as well. Administrators have the option of flagging comments that we’re given a green light as spam and they are returned to Akismet so the system can analyze it and add any findings to their spam filter. This can effectively blacklist a prolific commenter who is considered a spammer by multiple blogs. We also have the option of tagging red lighted comments as non-spam and that is also returned to Akisment so that it can learn from its mistakes in both directions.

    One last item worth describing is we also have a private list of “blacklisted” words that when seen will direct the comment to the spam queue. In the past we had words in it such as “diet” and “pill” but because those words didn’t need to appear in isolation so that “pillow” would trigger the spam filter I removed all those keywords. That substantially reduced the number of mistakes and didn’t cause any spam comments to sneak through. The private blacklist is now composed strictly of email addresses of “banned” posters. So when someone gets banned here their comment privilege isn’t cut off entirely but rather their comments just get dumped to the spam queue. In the past when the spam queue was small enough for me to go through it all this effectively gave banned commenters a chance to reform and/or still have acceptable comments allowed through. Alas, because of the recent huge uptick in spam volume, they no longer get that courtesy.

  44. dopderbeck,

    you said

    “I mean that in general terms — that there is strong evidence for gradual organismal changes in natural history and a general pattern of coalescence as one goes farther back into natural history.”

    What evidence? We are all under the impression here that there is no evidence and have been asking for examples for years. And none has been forthcoming.

    Don’t you understand our problem? We have not seen any evidence let alone the overwhelming evidence Darwinist say exists. We are serious with this claim. We are like Diogenes looking for an honest man. We are looking for honest Darwinist who can provide some evidence to support Darwinism. So far the light has not found anyone and it gets embarrassing when you see what people like so called religious role models like Ken Miller resort to.

  45. dopderbeck:

    Thanks for providing the party propaganda line.

    You are confusing accomodations with predictions. Ya see there isn’t any genetic data that can account for the physiological and anatomical differences observed between chimps and humans.

    Heavy reliance on the future discovery of the magical mutation accumulation mechanism is hardly the stuff of science.

    Follow the link in comment 36- see wobbling stability. That is what the data and observations point to.

    And until one can explain the anatomical & physiological differences observed, then Common Descent, although interesting, does not qualify as a scientific effort. Similarities can be explained by a number of options.

  46. Jerry said: What evidence? We are all under the impression here that there is no evidence and have been asking for examples for years. And none has been forthcoming.

    Well, this is where the conversation just goes round and round. Great Ape pointed to a whole bunch of evidence concerning genetic markers and y’all just seem to ignore it or to brush it off with references to the designer / God “re-using” genetic material.

    Why are common genetic markers over the deep history of the genomes of different species not “evidence?” I understand that you can interpet this evidence in various ways, and you can approach it with differing presuppositions, but to say there is no “evidence” seems grossly overstated to me.

    Joseph said: Ya see there isn’t any genetic data that can account for the physiological and anatomical differences observed between chimps and humans.

    I’m not following you here. Differences in genes don’t produce differences in physiology and anatomy? Of course they do, depending of course on which genes are involved.

    If what you’re trying to argue is that there is no detailed map of exactly which differences in the genomes result in chimps rather than humans, well, so what? Maybe some day there will be.

    If you are trying to argue that there is no correlation between genetic and physiological / anatomical differences between species, is that a typical ID argument? I don’t think it is — at least I don’t think it’s an argument a careful ID proponent like Mike Behe would make.

    I don’t think this is even a typical creationist argument. I know that Hugh Ross’ organization, for example, likes to point out
    research that shows greater differences between the chimp and human genomes than previously supposed — suggesting a further separation between the chimp and human kinds. Or am I misunderstanding something?

  47. Rats, I messed up a tag. Joseph’s words end at “differences observed between chimps and humans”; the rest is my response.

  48. Joseph, I read that link on “wobbling stability,” and I honestly just don’t get it. Here is an excerpt:

    It is true that species may lose something on the way—the mole its eyes, say, and the succulent plant its leaves, never to recover them again. But here we are dealing with unhappy, mutilated species, at the margins of their area of distribution—the extreme and the specialized. These are species with no future; they are not pioneers, but prisoners in nature’s penitentiary.

    Is this a common line of ID reasoning? Again, I don’t think so. What does it mean to say that an organism that adapts to fill an ecological niche is “unhappy, mutilated” and has “no future?”

    This seems to make some kind of metaphysical statement about what sorts of ecologies are “normal” — that poor cave fish, it has gone to live in an “abnormal” environment and lost its eyes! This ignores the fact that the cave fish has likely adapted in ways that can be considered “positive” — in ways that make the organism better suited to its niche. The cave fish’s loss of sight isn’t a tragedy, it’s a beautiful extension of the seemingly endless flexibility of life. And if the cave fish adapted to life in the cave, why can it not adapt again to some other environment?

    It also ignores the multitude of organisms that do not represent other kinds of organisms “at the margins of their area of distribution”. What of the many unique organisms that are found only in the dark depths of the sea, or in the heat and sulphur of underwater volcanic vents? They aren’t at the “margins;” they’ve long since ceased being “marginal” and are instead right at the heart of where they belong.

  49. dopderbeck,

    Your discourse is getting very familiar. For example when asked to provide evidence for gradualism you replied

    “Well, this is where the conversation just goes round and round. Great Ape pointed to a whole bunch of evidence concerning genetic markers and y’all just seem to ignore it or to brush it off with references to the designer / God “re-using” genetic material.”

    We are not brushing off anything but asking for evidence. Great_ape said nothing about gradualism and was only commenting on common descent. Great_ape believes in gradualism but has never presented anything which supports it other than his faith that it happened. Maybe he will disagree with that assessment but he has been quite open about the lack of information available to support it.

    Several times the question has been asked and no reply forthcoming namely, what is there in common descent that points to gradualism. So do not mention genetic markers unless somehow you can show how it demonstrates gradualism. It is being used to demonstrate common descent which is a different issue. It does not demonstrate the mechanism for common descent.

    I do not think anyone here denies that parts of the genome can deteriorate over time in a gradual fashion but that in no way points to the generation of new biological capability in a gradual fashion. They are completely unrelated phenomena.

    Occasionally someone will bring up God’s hand in this but you seem fixated on religion and mentioning God while most of us here in the discussion of this particular topic seem fixated on scientific explanations.

    I get the feeling that you think we are a bunch of rubes who cannot understand the obvious. Well try fleshing out the obvious for us. Our experience is that no one has ever been able to do it. We have seen this attitude many, many times before. Nearly all end up the same way.

  50. dopderbeck:
    I’m not following you here. Differences in genes don’t produce differences in physiology and anatomy? Of course they do, depending of course on which genes are involved.

    Umm ants in the same colony have the same DNA yet can vary in physiology and anatomy. Bees in a hive- same DNA varying physiologies and anatomies.

    Dr Denton, through years of genetic research tells us that although genes may inflence every aspect of development but they do not determine it.

    Dr Sermonti, a geneticist, tells us:

    The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.

    IOW an organism is NOT the sum of its genome. Caterpillars and theor butterfly counterparts have the SAME DNA.

    Now if genetics could tell us what genetic differences can account for upright, bipedal walking, then Common Descent would be on to something.

    dopderbeck:
    Joseph, I read that link on “wobbling stability,” and I honestly just don’t get it.

    Of course you don’t. Population variation oscillates. That is it. No net Common Descent.

    That is what we observe in the lab and in the wild- wobbling stability.

    Those extremeophiles living near the deep sea vents- extreme and specialized. Senetenced to live out their lives in that little penetentiary of a niche. They are at the end of the dead-end road. Nothing more will come of them.

    And even a fish without eyes is still a fish. And if you are going to rely on Common Descent via the lose of functioning organs for your argument then you have already lost.

    Genetic markers over millions of are nonsense because of the observed chromosomal recombinations that occur during meiosis. IOW for some DNA sequence to stay not only ontact enough to be recognizeable, it also has to stay in pretty much the same position on the same chromosome, just goes beyond any credible explanation.

  51. dopderbeck:

    I still feel that there is some confusion in our mutual terminology, and therefore in our discussion. I wiil try to make some very short points, and if you want we can discuss them further if we at least agree on the definitions:

    1) Homologies in the code: the notion that there are similar, repeated features in the code of different species.

    2) Common descent: the notion that there is a continuity in the species (all or part of them), in the sense that one is derived “physically” from another. Common descent is probably the best explanation, at present, for point 1, and many of us here (but not all) accept it, at least as a tentative hypothesis.

    3) Mechanisms of derivation: Even accepting common descent, one has to postulate a reason for it, in other words a causal mechanism. Darwinists postulate various mixings of chance and necessity, the most classical of them being pure RM + NS. ID postulates one or more designer(s). Accepting common descent tells nothing about the cause of it. Discussion about the cause is much more important then discussion about common descent. You seem, instead, to unify the two problems, and that is not correct.

    4) Time modality of derivation: Essentially, if we accept common descent, we can think of two different modalities of its occurrence in time: gradual (continuous) or intermittent (discontinuous). Both darwinism and ID are compatible with both modalities. In darwinism, the classical vue is gradualism (Dawkins and most others), but punctuated equilibrium is a good example of a discontinuous model (although God only knows how you can justify it!). In ID, you may think of a gradual, continuous intervention of the designer in time, for instance through intelligent, guided mutation, or through intelligent, guided selection, or both. But you may also conceive that the designer has been acting at special times, either by special acts of “creation” (which would not allow common descent), or by special acts of modification (which is compatible with common descent). So, again, arguing for gradualism or non gradualism has nothing to do with the problem of cause. Again, the problem of cause remains the most important. The rest are details.

    Given, for clarity, these definitions, I will add a few reflections on some of the things you say:

    a) You say:
    “Notice the language here: each person is “created,” “knit together,” “fearfully and wonderfully made” — in other words, designed carefully by God — and this fact is a cause for wonder at God’s works. And yet, today we can explain the process of human birth from conception through every stage of fetal maturation entirely in terms of seconary causes. There are no “gaps” in our “scientific” knowledge of human conception of birth; no need to suggest there is something God had to do directly through primary causation.”
    Two objections here: first, you again are making a point from theology, and again I will not follow you on that plane, at least not in this context (a scientific blog, about ID, which is a purely scientific theory). I think that we have to be very firm on these point.
    The second objection, instead, is purely scientific: what you say is not true. I am sure you say iy in perfet good faith, but still it is not true. I don’t know if you have a professional education in biology and/or medicine, but believe me, it is not true, in any way, that “today we can explain the process of human birth from conception through every stage of fetal maturation entirely in terms of seconary causes”. I don’t understand where you got that strange idea. The opposite is true: today we can explain practically nothing of the process of human birth from conception through every stage of fetal maturation. That is, indeed, one of the greatest mysteries in science. The discussion could be long, and if you want we can have it in detail (that is my field, after all), but just to set the scenario, the greatest unanswered question in medicine today is probably wy and how the same genome, identical in all cells (made exception for the immulogical system), can express itself in myriads of different transcriptomes, each perfectly appropriated for the kind of cell, for its state of differentiation, for its functional moment, and so on. We have no reasonable idea of how that can happen. We have no idea of what makes a stem cell a stem cell, or a differentiated cell a differentiated cell. We have no idea of how ordered, sequential differentiation takes place, how it is controlled, how it conforms to a macroscopic multicellular plan involving billions and billions of different cells. If scientific ideology has given you the notion that we know that, well, I am sorry, but you have been cheated.
    So, it is a complete mystery. And you cannot use a complete mystery to argue anything.

    b) You say:
    “This seems to me to be part of the heart of the matter: a confusion of the general idea of common descent with the philosophy of materialism. Removing the materialism filter doesn’t excuse anyone from ignoring the evidence for common descent. The evidence remains; it remains compelling; and there remains no strong alternative explanation, except for a vague “God / the designer did it” — which really is a God of the gaps explanation. I have no problem with offering that explanation if it’s offered on the grounds of revelation (though I think it would remain a wrong understanding of revelation). I have a problem with the notion, however, that this is the sort of explanation that is separable from theological presuppositions. It just isn’t.”

    Many objections here. First of all, you are again speaking of common descent, but after it is evident that you are referring to the design inference. Again, you can’t do that. They are two separate things.
    So, let’s leave alone common descent. Let’s say we accept it, in the sense I have given. Let’s discuss, instead, the design inference. Here what you say is completely wrong, or at least it is different from what we argue in ID. Obviously, you are perfectly free not to believe what we say in ID, but you have not even tried to argue something about that.
    Let’s be clear about that. Let’s pretend I am an atheist and I believe in ID. I am not an atheist, but I have no problem to discuss and defend ID “as though” I were an atheist. I have no need of the idea of God (other than as a possible rational hypothesis)to demonstrate the ID points. And certainly I have no need of any scripture. Again, ID is a purely rational and scientific point of view. Indeed, it is much more rational and scientific than darwinism (OK, I know, that’s not very difficult to attain…). Darwinism does not explain anything about observed facts. ID can very well explain them all.
    You may dissent on that, but what I mean is that this is the point we should discuss. Not common descent. Not gradualism. Common descent and gradualism are important only as far as they can be used in a specific context about cause. But the discussion about cause is supreme.In that discussion, there is really no game: ID wins without even having to fight.
    You don’t believe that? You have not. It is not a scriptural revelation. Just come here, read this blog, read the many discussions about the main points (CSI, IC, abiogenesis, speciation, the fossil record, and so on), read the works of Dembski, Behe and others, read, if you care, the arguments of the “enemy” (on PT, pharyngula, or wherever you want: but beware, it will not be easy to find an argument, provided it exists, in the ocean of intolerance and personal attacks), and, above all, think for yourself. And if you want to discuss, we are here for that reason. We love discussion. You are welcome!

  52. gpuccio [51]

    Common descent is probably the best explanation, at present, for point 1 [homologies in the code], and many of us here (but not all) accept it, at least as a tentative hypothesis.

    I just don’t accept that common descent is probably the best explanation for homologies – far from it, we are talking about multiple lineages and millions of years of variations. Moreover, there are similarities (i.e,. echo location) in a wide variety of organisms which cannot owe their origin to a common ancestor.

    Essentially, if we accept common descent, we can think of two different modalities of its occurrence in time: gradual (continuous) or intermittent (discontinuous). Both darwinism and ID are compatible with both modalities.

    If ID is compatible with gradualism then so much for the main ID argument against naturalistic origins namely irreducible complexity – gradualism and irreducibility are at direct contradiction with each other. Punctuated equilibrium is not darwinism, and darwinism is not discontinuous.

  53. Acquiesce:

    I am not going into a detailed discussion about the plausibility of common or uncommon descent because, for me, it is not a fundamental issue, and indeed I have not definite, final reason to get to an irrevocable decision for myself on that issue. Indeed, that’s why I added “probably” in my statement. My real concern was to separate discussion about common descent from discussion about causal explanations. I think that ID is compatible with both common and non common descent. It is true, however, that darwinism is compatible only with common descent, at least partial.

    Instead, I don’t understand your objection about gradualism. Why do you say that ID or IC are not compatible with gradualism? I specified in my post that I meant “directed”, designed gradualism, that is a scenario where the designer implements his design step by step, possibly using as mucj as possible apparently natural means, like intelligent (guided) mutations or intelligent (guided) selection. That’s very different from the gradualism of darwinism, where random mutation and “natural” (that is unguided) selection are supposed to be the cause of information.
    So, that scenario is perfectly compatible with both ID and IC: the designer, knowing the design he wants to implement, is not obliged to implement it all at once. If he has a lot of time available, he can well decide to implement it “a bit at a time”, in long times. As the designer has to intereact with the material world to implement his design, he can well act by modifying slowly an existing implementation (a species) to transform it into another. The important concept is that the designer actively imparts information, for instance selecting each time a mutation which is compatible with his design, even if it is not useful at the moment. Such a process is very similar to writing a code, step by step, and it can perfectly explain irreducible complexity, because the complexity is imparted by the designer, gradually, and it needs not have any function until it is “ready”. The designer knows in advance the final goal, and so the information is imparted “from outside”, and Dembski’s law is not violated.
    Finally, I apologize that I included punctuated equilibrium into darwinism: that’s only because I was using the word “darwinism”, in that context, to define, for the sake of brevity, all “naturalistic” explanations of biological complexity relying only on natural laws and a mixture of chance and necessity, and in that sense puctuated equilibrium is certainly part of the group. I agree qith you that classical darwinism is gradualistic, but I think we should find some term to indicate all theories which deny design, just as we use ID for all theories which imply it.

  54. Acquiesce:
    If ID is compatible with gradualism then so much for the main ID argument against naturalistic origins namely irreducible complexity – gradualism and irreducibility are at direct contradiction with each other.

    Only blind, purposeless gradualism and IC contradict each other. Or at least appear to, as in goes against everything we understand and have experience with.

    Guided, pre-planned, pre-programmed, gradualism could very well be a design (ID) mechanism.

  55. gpuccio: we agree on more than we disagree on. Thank you for making the clarifications you did, which for the most part I agree with. I think, however, that there are many here who don’t agree because they reject common descent a priori on religious (young earth creationist) grounds. Note that I am not saying all ID folks are YECs, but the discussion, in my experience, continually gets muddled by objections to common descent on that basis (which I sense is where some of the objections to common descent are coming from here).

    You said: believe me, it is not true, in any way, that “today we can explain the process of human birth from conception through every stage of fetal maturation entirely in terms of seconary causes”. I don’t understand where you got that strange idea.

    I got that strange idea from the fact that I have three children. I know exactly how and when they were conceived down to pretty much the day of conception; in the case of my first child, I can even remember what I had for dinner that night. I observed the process of my wife carrying them, and I was there when they were born. I saw the “Miracle of Birth” on PBS; I saw my children in the womb on ultrasound. As far as I can tell, there was no direct intervention by a designer / God.

    Are you suggesting that, since we don’t know how the same genome “can express itself in myriads of different transcriptomes,” we should therefore infer that God / a designer does this directly? I don’t think you are. I think you would agree that the most reasonable assumption is that there are explanations for this sort of present lacuna about a detail of fetal development at the level of seconary or “ordinary” causes, without invoking direct action by God / a designer — though maybe I’m wrong about this?

    But the discussion about cause is supreme.In that discussion, there is really no game: ID wins without even having to fight.

    I don’t see how you can make a statement like this. The question of causes ultimately is a metaphysical question. I have never seen any argument by Behe, Dembski, or any other ID theorist I’ve read settle the question of ultimate causation on empirical grounds. I have seen them raise interesting questions about the sorts of causes proferred by Darwinism, and I have seen them suggest that design can be inferred largely by what is essentially the classical theological concept of the analogia entis; but that is quite different than demonstrating design affirmatively on empirical grounds.

    first, you again are making a point from theology, and again I will not follow you on that plane, at least not in this context (a scientific blog, about ID, which is a purely scientific theory).

    And for the reason that ultimate causes are never a “purely scientific” question, I think you are dead wrong about this. The question of ultimate causes is a metaphysical question. The inference of design by analogy to human design is essentially a restatement of the classical theological concept of the analogia entis. By eliding from that classical theological concept a thick conception of the designer as God, the strong ID program, IMHO, ultimately weakens the case for design and creates needless arguments about basic concepts such as common descent.

    “Design” is, and should be, an inherently theological concept, and we who are Christians should assert design on those grounds rather than caving in to the positivist epistemology of materialistic science. Moreover, I do not believe there is any adequate concept of “design” apart from the distinctives of the Christian God. Anything less is an unhealthy compromise.

  56. Joseph said: Guided, pre-planned, pre-programmed, gradualism could very well be a design (ID) mechanism.

    Joseph, if this is really your position, I would classify it as a type of theistic evolution. The theistic evolution folks I’ve met who hold to generally orthodox theology essentially hold the position you state here — assuming “guided, pre-planned, pre-programmed” can simply means “in accordance with God’s inscrutable sovereign will.”

  57. Acquiesce

    There have been billions of direct observations of life coming from life and none of life coming from non-life. Common descent is overwhelmingly supported by observation. The law of gravity is similar. Billions of observations, perfect record of prediction, and while it’s true that an apple might fall up from the tree into the sky it isn’t bloody likely based on past observations and neither is it likely that a new living thing will appear from a non-living thing. The only known source of living things is another living thing and there are so many confirmations of it it’s called the law of biogenesis. Common descent is beyond theory. It’s a law.

  58. Hi Dave Scott:

    Thanks for the notes on filtering. Perhaps, a policy page somewheres?

    I have said enough on my main point here, in support of G-A as a positive contributor.

    I note on Common Descent:

    There have been billions of direct observations of life coming from life and none of life coming from non-life. Common descent is overwhelmingly supported by observation . . . . The only known source of living things is another living thing and there are so many confirmations of it it’s called the law of biogenesis. Common descent is beyond theory. It’s a law.

    Of course, you may have your tongue firmly in cheek here, but for the sake of the uninitiated or ignoramuses like me, a few dumb Q’s:

    1] Common Descent, last time I checked, refers to claimed descent with modification capable of creating the body plan innovations seen in the fossil record and in the living world, going back a claimed 3.5 – 3.8 or so BY. Do the observations in question include that range of years, or just inferences to the projected past based on 150 – 250 years of actual observation and record?

    2] Has a clear case of descent with modification sufficient to create a novel body plan actually been DIRECTLY observed rather than inferred and/or reconstructed? [We do directly observe gravity at work, and Kepler's empirical laws came before Newton's theory in explanation. NLG then had the anomalies of perturbations etc, and the precession of Mercury's orbit. The former it solved, the latter, Einsteinian approaches have solved . . .]

    3] Has a mechanism credibly capable of creating more than say 500 – 1,000 bits worth of biofunctional information out of random forces been identified to drive the modification part? Or, to produce systems that have at least several interacting parts the absence of any of which will severely degrade or destroy functionality? Has such been directly observed in details, and independently confirmed in action? Published where?

    4] Similarly, to generate the initial life system?

    5] Wasn’t spontaneous generation of life from non-living matter regarded as a well established “unquestionable fact” for many centuries, based on duly performed scientific observations within the capabilities of the techniques, instruments and observers at the time?

    6] Are we sure we are not similarly misled today? Why or why not?

    7] How should such experiences and history guide us in how we present our findings in education and to the public today?

    GEM of TKI

  59. gpuccio [53]

    The important concept is that the designer actively imparts information, for instance selecting each time a mutation which is compatible with his design, even if it is not useful at the moment.

    This is totally in the realms of speculation and not to mention indistinguishable from orthodox darwinism. Are you saying that god(s) stores this information until workable (in which case it’s hardly gradualism), or that birds were at one point ‘flying around’ with just the barbs? then god(s) chose the barbules, then the hooks, ridges, controlling muscles, then the instincts etc?

    DaveScot [57]

    There have been billions of direct observations of life coming from life and none of life coming from non-life. Common descent is overwhelmingly supported by observation.

    Biogenesis has never been shown to produce organisms outside their type, the fossil record shows only discontinuities, natural selection takes evolution in the wrong direction and we are unaware of any random mutations producing new specified information. I apologize if your comment was made in jest but common descent is certainly not supported by observation.

    It has not been observed, we have not found a sequence of intergrading forms (either living or fossilized) leading unambiguously from one type to another, nor have we been able to reconstruct the intergrading forms hypothetically by providing an entirely plausible genealogy including all the intermediate forms and a thoroughly convincing explanation of how each stage of the transformation came about.

    Only the typological perception of nature accurately accomodates the evidence we have.

  60. Joseph said: Guided, pre-planned, pre-programmed, gradualism could very well be a design (ID) mechanism.

    dopderbeck:
    Joseph, if this is really your position, I would classify it as a type of theistic evolution.

    Is it my position that Guided, pre-planned, pre-programmed, gradualism could very well be a design (ID) mechanism? Yes Could very well be.

    BTW I am not a christian and ID does not require a belief in “God”.

    ———————————-

    DaveScot:
    Common descent is beyond theory. It’s a law.

    Then it the first law that no one knows about. We should call it “the magical mystery law”.

  61. BTW I am not a christian and ID does not require a belief in “God”.

    I also am not a christian (or any religion for that matter). My gripe with common descent is purely on empirical grounds.

  62. Acquiesce:

    “This is totally in the realms of speculation and not to mention indistinguishable from orthodox darwinism.”

    I agree that it is in the realm of speculation, like almost everuthing else on these specific subjects. To make things clesr, at present I don’t favour very much the hypothesis of “intelligent gradualism”, and I prefer the discontinuous hypothesis. I was only trying to show that the hypothesis of design is compatible with gradualism. I was not necessarily sponsoring the solution, only saying that it is a possibility. After all, it is possible that “birds were at one point ‘flying around’ with just the barbs”. It is just what most scientists believe now. I agree that the fossil record does not encourage gradualism, enyway. On that you are perfectly right. But for me, the real point where darwinism completely fails, and can be ruled out even on purely logical grounds (and, obviously, also on empirical grounds), is, as I have repeated many times, the problem of causes. Complex biological information cannot come out of chance and necessity. It needs a designer. Period. This is by far our strongest argument, and to this we should stick. Common descent and time modality are separate issues, and imo less important.
    I don’t agree, however, that modification by design, even in a gradual modality, would be “indistinguishable from orthodox darwinism.” First of all, gradual modification by design is possible, while orthodox darwinism is practically impossible. That is the core of the problem: the impossibility to get that kind of result by chance and necessity. I am sure that that issue, which in my opinion is already evident with our present knowledge, will soon be extremely evident to anybody, as our understanding of information, meaning, consciousness and similar concepts refines.
    Besides, I am sure that a further understanding of biological events at the subcellular level will give us empirical evidence of how and when design has been imparted to living beings. I have faith in scientific knowledge, and that the accumulation of new facts will allow us to distinguish between what is possible and what is not, and, further on, between what is probably true and what is not.

  63. Returning to the genetic markers.

    Imagine a table, and in the middle a perfectly stacked deck of cards ace to kings (call this the common deck). Either side of the table sits ‘Chimp’ and ‘Champ’ both with identical copies of the common deck. Both Chimp and Champ represent lineages to disparate organisms which share genetic markers.

    To represent evolution in time both Chimp and Champ are asked to shuffle their cards for a few second – after this they lay their cards down and examine the similarities. It would be expected that both would have small sequences identical to each others and also to the common deck.

    It might also be probable that one has a sequence, lets say of ace to king in diamonds remain. But both having this same sequence remain would be improbable. Both are then asked to shuffle their cards again, this time for a longer period, to represent the millions of years of variation.

    The more shuffling the more the original (common deck) pattern diminishes and the more disparate our players cards become from each others until the differences plateau. What peculiar rules of probability would have these sequences remain over the course of millions of years?!

    Furthermore, unlike my analogy, we are unable to cross reference two disparate types with their common ancestor because, by another peculiar rule of probability, these ancestors seem to vanish. Therefore, we simple do not know if the common ancestor contained the markers in the first place!

  64. I was only trying to show that the hypothesis of design is compatible with gradualism.

    Manmade systems such as a watch cannot be led up to gradually through functional intermediates because of the necessity of perfect coadaptation of all its components as a precondition to function, this holds even if intelligence is guiding the process.

    In short, there’s no functional continuum; just adding intelligence doesn’t change that fact. Unless what you’re saying is that god(s) or whatever helped the organism survive during these useless, selectively disadvantaged stages?

    Maybe I am totally wrong but it appears that many in the ID community are trying to provide stepping stones for gradualists to change sides. However, birds with only barbs for feathers will not fly!!

  65. dopderbeck:

    thank you for you reflections (#55). I think I understand your position better now, and that is always a good result. However, I still think I disagree with you in a few important points. For further clarity, I’ll try to sum them up:

    1)You speak, repeatedly, of “ultimate causes”. I speak, in the ID context, of “causes”. They need not be ultimate. That’s what makes the discussion scientific. Ultimate causes are, as you rightly suggest, the object of philosophy, religion, faith. Simple causes are the object of science. I understand that you maintain that the designer inferred by ID is probably God. I can agree on that. But that does not mean that ID infers God. ID infers a designer from an observed design. If we accept the hypothesis that God interacts with the world, and even if it is true that we cannot infer or observe the true nature of God (scientifically, I mean), if an interaction takes place, then our “side” of the interaction should be observable. Indeed, it must be observable. And to observe it, and analyze it, is the duty of science.

    2) You seem to believe that everything in the universe can be explained deterministically, provided we accept that God has put into motion the original laws, and that everything else can be considered an effect of “secondary causes”. But do you believe the same of man’s consciousness, free will, morality? Do you believe the same of beauty and purpose, of meaning and understanding? are all these things the effect of “secondary causes”, and did God only provide an engineering “consulence” in the beginning, defining the formulas of gravitation, electromagnetism, strong force, and letting these forces take care of everything else? Do you really believe that? I definitely don’t.

    3) But even if you believe that, at the scientific level you have to motivate your belief, or just keep quiet. This is, I think, the main difference between us. I have my philosophical and religious beliefs, but I am convinced that, if we are speaking scientifically, I have to speak to others as if “I were an atheist” (in a good sense, as one who has no prejudice in scientific discussion. My religious ideas can inspire me, give me good ideas about science, everything you want, but at the scientific level I have to find scientific motivation. That is in no way “caving in to the positivist epistemology of materialistic science”. This is, on the contrary, epistemological order, intellectual honesty. It is respect for all those who may not share our religious concepts, and who still deserve to discuss with us about our scientific ideas.
    So, I ask you: do you scientifically believe in determinism according to known natural law as the cause of biological complexity? Maybe you believe that for theological reasons, although God only knows what they could be, but I am not interested in that. If you believe in that “natural” mechanism, you have to motivate your belief. Technically, you are not different from proper darwinists, although you believe in God at the start. Technically, you are believing something impossible. You have to motivate why you don’t accept the scientific arguments of Dembski and Behe. You have to motivate how chance and necessity can build CSI or IC. You may think that darwinist have done that for you, but believe, that is not true.

    4) Let’s go to our discussion about fetal development. You say:
    “Are you suggesting that, since we don’t know how the same genome “can express itself in myriads of different transcriptomes,” we should therefore infer that God / a designer does this directly? I don’t think you are. I think you would agree that the most reasonable assumption is that there are explanations for this sort of present lacuna about a detail of fetal development at the level of seconary or “ordinary” causes, without invoking direct action by God / a designer — though maybe I’m wrong about this?”

    You wrote, in your previous post:
    ““today we can explain the process of human birth from conception through every stage of fetal maturation entirely in terms of seconary causes”. I simply remarked that it is not true. I am right on that, and nobody can deny it.
    But now you add:
    “I think you would agree that the most reasonable assumption is that there are explanations for this sort of present lacuna about a detail of fetal development at the level of seconary or “ordinary” causes”.
    No, I don’t agree. You are making two assumptions which can be described only as two acts of blind faith:
    a) That our present understanding of the laws of nature is complete, in other words that what you call “ordinary causes” corresponds to deterministic laws we already know.
    b) That no “out of ordinary” process takes place in fetal development.
    I accept none of these two assumptions. I do believe that we don’t understand nature, or understand it only partially, and never that gap was more evident than in our understanding of life. Our “laws of nature” don’t explain life. They don’t explain consciousness. They don’t explain purpose, meaning, design, intelligence. Probably, they don’t explain a lot of other things, but these are certainly the most prominent.
    In other words, we are ignorant. All our knowledge can’t explain how a bacterium may exist, and I am not speaking only of how it was designed originally (which is the ID problem properly), but also how it can exist and live now. Living things are totally unlikely, and present knowledge can’t explain them out.
    Fetal development is no exception. The reasearchers in Evo-devo are perfectly right in believing that understanding development can certainly help to understand evolution. I do agree. Only, I am not sure that the understanding they are looking for, and some day will certainly attain, will be exactly what they are expecting. It will, anyway, be precious and very, very interesting.
    My point is that, until we really understand something, the only honest position is to admit it is a mystery. Life is a mystery. Consciousness is a mystery. We have to look further, think further.
    In the meantime, we have gross cultural lies (darwinism, the theory of artificial intelligence) whose only purpose is to make the layman believe that science has understood what it has not even begun to understand, and to give scientists a pleasurable sense of omniscience. And, on the contrary, we have little oasis of rational thought, like ID, where intelligent people try humbly to find reasonable answers to some fundamental questions.

    To conclude, nobody has to believe in ID. But nobody has the right of dismissing it in principle, for “religious” reasons, be it a darwinism (ID is not science and similar racist arguments) or a religious man (“Design” is, and should be, an inherently theological concept…). If anybody wants to falsify ID, he has to do that at the right level, in the right context: very simply, demonstrating that what ID says is false.

  66. Acquiesce:

    I agree that there is no functional continuum. This is one of the strongest arguments against darwinian evolution!
    What I meant is that the designer could add gradually what is necessary for the new function, and fix it in the genome, before the function appears. That would not necessarily be a disadvantage. I agree that the hypothesis is a little bit awkward, but it has to be discarded on an empirical basis, not a logical one. I am in no way trying to “provide stepping stones for gradualists to change sides”. I am only trying to be fair to all possible hypotheses, provided that we really don’t have any clue of how design was practically implemented in new species. But again, I prefer a discontinuous model. Even in that model, however, the implementation of a new species needs not be instantaneous. It could take some time. We simply don’t know.
    You may prefer to believe in an instantaneous model (sudden creation from “nothing”), and I have nothing against that. But it is not the only possibility, and it has its cons too (more explicit violation of ordinary laws).
    The point is: we know living beings were designed (ID proves that), but we really don’t know how and when they were designed. Maybe the accumulation of new knowledge will allow us to answer even that question.

  67. gpuccio — thanks for those thoughts — again, I think we agree on more than we disagree on.

    Let me address this concerning secondary causes: But do you believe the same of man’s consciousness, free will, morality? Do you believe the same of beauty and purpose, of meaning and understanding?

    No, I do not. Secondary causes refer to the ordinary operation of the laws of nature. Human intentionality is not a secondary cause, as I view it. In theological terms, human beings have free will because they are made in the image of God. In biological terms, I suppose I might lean towards a nonreductive physicalist position — but whether human consciousness emerges from phyical structure or is part of a separate entirely non-material component of personhood (the “soul”), I think strong agent reductionism is incoherent and weak agent reductionism is irrational (BTW, an excellent book by Angus Menuge, an ID guy, called “Agents Under Fire,” has influenced my thinking substantially about this).

    I should note, that there are some TE’s who seem to want to accept sociobiology whole cloth as well. However, many don’t — as Francis Collins’ recent book makes clear.

    You said: My religious ideas can inspire me, give me good ideas about science, everything you want, but at the scientific level I have to find scientific motivation.

    You are right, this is our most basic disagreement. I don’t think it’s possible or wise to have such a “split personality” so to speak. Religious epistemology is holistic, I think, or it is not an epistemology at all — it becomes, as it has for so many people in the world today, merely a source of emotional comfort, rather than the fountain of Truth.

    You further said: You have to motivate how chance and necessity can build CSI or IC. You may think that darwinist have done that for you, but believe, that is not true.

    No, I do not think I have to explain things through “chance and necessity,” and I do not think any explanation of evolution based on “chance and necessity” understood metaphysically has any chance of succeeding. To the extent I accept evolution (and let me clarify again for the record that I don’t consider myself a fully-fledged “typical” TE) it is only theistic evolution.

    I reject as a foundational matter that there is any such thing as chance and necessity in a metaphysical sense. What appears to human eyes to be “chance and necesity” is the working out of God’s providential purposes through secondary causes. Moreover, nothing in creation is “necessary” in a metaphysical sense; rather, all of creation is “contingent” on God’s will. In this vein, I personally find some “soft” ID arguments — the anthropic principle, convergent evolution — very convincing and supportive of a theistic worldview.

    On fetal development — thank you for educating me a bit here. I evidently overstated my case. However, it seems to me that the basic point still remains: we can observe a fetus develop, and there is no apparent direct influence by a designer / God. If there is such influence, it is “hidden” from our sight. Thus, the natural theology of Psalm 139 isn’t based on direct empirical observations of God’s activity in literally “forming” the fetus.

  68. gpuccio — Could you elaborate a bit more on fetal development? Perhaps summarize where you think naturalism fails in explaining such a majestic process? I’m interested in this.

  69. dopderbeck:

    thank you for your intervention. I think we have explained our mutual differences (and similarities) satisfactorily. It has been a pleasure…

  70. Barrett1:

    As I said im my previous post, the development of a highly complex multicellular being (humans, for instance) from the single celled zygote is one of the least understood mysteries of biology. I am afraid many people think that, because we have developed technologies like cloning animals, that means we understand the process. That’s not the case. In cloning experiments, we just fertilize an egg with the nucleus of a somatic cell, but that’s just what we do. It’s interesting, it is somewhat amazing that it works, but we understand nothing more of what is happening.
    There are a lot of problems in understanding development, and they are strictly connected, in my opinion, to the deepest problems of the meaning of cellular life and, therefore, to that of evolution.
    Th gretaest problem as I said, is understanding the relationship between genome and transcriptome (and, obviously, proteome). We have in nature the rather amazing fact that, in multicellular organisms, all cells share the same genome, and yet all of them are different.
    Differences between cells are of various kinds:
    a) differences along the axis staminality -differentiation. We have different stages of staminality. Simplifying, we have the zygote, which is not only totipotent, but can generate a whole living organism. Then we have embrional stem cells (those you find in the morula, and which are at the center of moral debates today). These are totipotent (they can differentiate towards any kind of tissue) but cannot give birth to a whole organism. And then descending down on the ladder of staminality, we have fetal stem cells, cord blood stem cells, adult stem cells. And then we have differentiated cells, along different lines and tissues, and at different stages of differentiation. The problem is, all of these cells have the same genome. Out of the 20,000 genes which constitue human genome (protein coding, I mean), a specific subset id transcribed at each different occasion. It is as though you have 20,000 different words, or building blocks, and you have to choose every time a different subset of them (maybe one or two hundred) to realize adifferent discourse or model. And we are speaking of thousands, maybe millions, of different transcriptomes.
    This is a mystery in an adult being, but it is a cosmic mystery in the embryo. After all, the embryo starts as a single cell. Up to the morula state, we still have 20-30 cells which appear to be exactly the same.
    And there is more. Not only those first cells have to give birth to an immense progeny of different cells, each with its appropriate transcriptome and proteome, but they have also to arrange those myryad of differentiated cells in the precise pattern, in space and time, which gives birth to what we call the “form” of the body. And they have to connect everything with a myryad of regulatory functional networks: neurologic, immunologic, cytokines, etc.
    Just think: the central nervous system is made of approximately 10^11 neurons, each of them cennected by multiple connections, some of them at a really big distance for a cell (from a motor neuron in the cortex to its corresponding motor neuron in the spine, and then to the muscular fiber peripherically, we are in the order of magnitude of one meter).
    And the mystery is: what guides this extremely complex set of events? Where is the code, the procedures, the map for all that? We have no idea. We know those little 20,000 genes, many of them identical to those in the mouse or in some fish or plant. And we know there is another 99% of genome which is surprisingly “stupid” in its appearance: introns whose only purpose seems to be fragmenting proteic genes, non functional pseudogenes, repetitive sequences devoid of any known meaning, gtransposons which look more like parasites then like information, and so on. It’s a wild world, the non coding genome. An yet, there, in the jungle of the ex junk DNA, there must be something important. Perhaps not the whole answer, but something important.
    And that’s not all. Cloning has proved that we can reproduce a zygote (although not a perfect one) using the nucleus of a somatic cell plus an ovum (denucleated). Well, that’s really amazing! After all, we all have billions of somatic cell, of all kinds, and none of them seems able to operate miracles like becoming a zygote. And yet, each of them has all the necessary information, in its DNA. So, where is the miracle, in the cloning process? We don’t know, but I think we are well authorized to look with great interest at the ovum… But the ovum is cytoplasm, not nucleus. Is it possible that, in that tiny fragment of cytoplasm, no DNA, no apparent genetic information, there may be the key to unravel the whole complexity of a human being from the DNA of a somatic cell, usually relatively inert and static? It seems so… And remember, just after a few replications, at the morula state, this capacity of generating a complete organism is already lost.
    So, are these mysteries? You bet they are… Instead of letting people know that we have understood everything, we scientists should well admit our ignorance, and try to retrieve the sense of wonder that we lost a long time ago.

  71. gpuccio – thanks for taking the time to respond. Much appreciated.

  72. gpuccio: So, are these mysteries? You bet they are… Instead of letting people know that we have understood everything, we scientists should well admit our ignorance, and try to retrieve the sense of wonder that we lost a long time ago.

    Awesome! True! Amen! Spoken like a Polanyi-devotee? (I love Polanyi)

    But I’m curious — do you think this mystery in itself gives rise to a design inference, sort of like irreducible complexity? Or does that sense of wonder arise primarily from something inherent in natural processes that science is only beginning to understand — similar to the wonder produced every time our knowledge of physics is pushed deeper, revealing ever more fundamental layers of simplicity and elegance undergirding the universe?

  73. dopderbeck:

    You ask what I think, so I will, for once, speak freely. The following is not a scientific scenario which I can motivate in all the details, but is my personal view, for what it’s worth.

    I think that the mystery of life and the mystery of consciousness and the mystery of evolution are related.
    I think that all these deep and unsolved aspects of reality will be doors to understand new, higher laws that at present we don’t understand. I do think that our present understanding of the laws of nature is vastly incomplete.
    I think that the new laws and principles we are going to discover will have fundamental consequences in our model not only of life and biology, but of all reality.
    I think that the new laws we are going to discover will be different from those we already know, although they will not deny them. They will be different not only in details, but in principle. Indeed, they will probably bring new light even on classical problems of physics, like the meaning of quantum mechanics and so on.
    They will not be strictly deterministic, and will represent a new interface which will give a new picture of the relationship between consciousness and matter, mind and body, purpose and chance, life and non life.
    They will deliver us from all reductionist, pseudo-naturalist, determinist thought which has plagued our culture for more than one century, building completely false scenarios of reality, like evolution and artificial intelligence.
    They will give new meaning to the concept of God in relation to the world, at least from a human and scientific point of view, without subtracting anything to our traditional conceptions of His transcendence, or to our personal faiths.
    They will give us deep intellectual satisfaction, together with wonder and hope. And, thanks God, an ever new sense of mystery, because I think that it is true that reality has potentially infinite layers of complexity, and that our reason cannot possibly exhaust them.
    They will give new perspective to the theory of information, of meaning, of design, and will confirm the fundamental intuitions of people like Dembski and Behe. They will rely much more on biophysics and information theory, which will integrate ever more the classical approach of biochemistry and traditional genetics.
    And yes, they will “reveal ever more fundamental layers of simplicity and elegance undergirding the universe”.

  74. I regret that I’ve been swamped with work and have been unable to keep up with this thread.

    Aquiesce, Joseph, your statements contain so many empirical and philosophical points that I must take issue with that I don’t even know where to begin to address them. I suspect you are both relying on some woefully mistaken sources as your main source of information. I am a practicing biologist who is fairly well-versed in philosophy, yet I frankly have no idea what you two are talking about much of the time. If this does not concern you, it should.

    For example, here is Aquiesce regarding viral insertions:

    “Is it realistic to believe as both lines diverged from a common ancestor, then travelled on their own path for millions of years, that these would remain?”

    It is realistic. We know rough mutation rates both from empirical studies on extant species’ germlines in addition to molecular evolution studies. We know roughly how much DNA mutates in various taxa. Given these rates, the amount of time that something would require to mutate beyond recognition by sequence homology is rather large in mammals, somewhere on the order of 80-125 million years.

    To everyone else, I do suspect gradualism predominates, but I am not necessarily wedded to that stance. Certainly I believe in gradual changes in *nonfunctional* molecular regions; there is much empirical evidence towards that end.
    But as for what occurs at the time of speciations in functional DNA and in bone morphology, how fast it occurs, etc. I really don’t know. That is why I refrain from writing any lengthy defense of gradualism. Right now, as a molecular biologist, I simply think gradualism is the more conservative stance. Yet I can certainly understand how folks like Gould, from a palentological perspective, might arrive at a different position. I can tell you that there are active research projects going on concerning how reproductive barriers form between populations; studies that directly address how rapidly biological speciation could conceivably occur.
    Once species are isolated reproductively they continue on their own, independent, evolutionary trajectories. Just how fast they can substantially change subsequently is another fascinating question for which I have no good answer. I will venture an educated guess, though…To quote from a former computer science professor of mine, the best answer will be “it depends.”

  75. “I think that the new laws and principles we are going to discover will have fundamental consequences in our model not only of life and biology, but of all reality.” –gpuccio

    Your big-picture take on reality and a possible as-yet undiscovered reality is not very much different from my own. I suspect there may come a day when we be forced to fundamentally reinterpret most of what we now think we know. That may very well extend to chemistry, biology, evolution, etc. However, until that day, all we can do is doggedly and honestly apply the best techniques we know to arrive at the best model of the world that we can. Then should that new perspective on reality one day arrive–I doubt it will be in my lifetime–we will understand *why* it was that we saw the world as we did currently. And how, perhaps, there was no other way to see it at the time. It is my belief that if we do not engage reality through a process that goes to great lengths to avoid self-deception then we will never progress to the point where we have that fundamentally different perspective you refer to.

  76. great_ape:

    “It is my belief that if we do not engage reality through a process that goes to great lengths to avoid self-deception then we will never progress to the point where we have that fundamentally different perspective you refer to.”

    I absolutely agree with you!
    Obviously, as you know, in my opinion the darwinian framework is a big example of gross self-deception (not the only one), and we have to get rid of it to “doggedly and honestly apply the best techniques we know to arrive at the best model of the world that we can”. But that’s a detail on which we probably can’t, at present, agree. However, your principle is perfectly right, and I endorse it with all my heart!

  77. Gpuccio and Great_Ape,

    It seems we three are all Polanyi-ites of a sort. Good!

  78. dopderbeck,

    Most of us here at UD subscribe to what gpuccio in comment 76 has said.

    The big distortion propogated by those outside, is that we don’t.

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