Home » Intelligent Design » Unwitting Pro-ID Peer-Reviewed Articles on the Increase . . .

Unwitting Pro-ID Peer-Reviewed Articles on the Increase . . .

Here is an ID research paper published in PNAS. Note that some important principles of evolutionary theory are criticized in the abstract. This research shows how ID is capable of being applied in biology.

Genetics
The regulatory utilization of genetic redundancy through responsive backup circuits
( evolution | gene duplications | modeling | systems biology | noise )
Ran Kafri *, Melissa Levy *, and Yitzhak Pilpel
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Communicated by Marc W. Kirschner, Harvard Medical School, Boston, MA, June 12, 2006 (received for review March 6, 2006)

http://www.pnas.org/cgi/reprint/0604883103v1

Functional redundancies, generated by gene duplications, are highly widespread throughout all known genomes. One consequence of these redundancies is a tremendous increase to the robustness of organisms to mutations and other stresses. Yet, this very robustness also renders redundancy evolutionarily unstable, and it is, thus, predicted to have only a transient lifetime. In contrast, numerous reports describe instances of functional overlaps that have been conserved throughout extended evolutionary periods. More interestingly, many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. By manual inspection of the literature, we have compiled a list of such “responsive backup circuits” in a diverse list of species. Reviewing these responsive backup circuits, we extract recurring principles characterizing their regulation. We then apply modeling approaches to explore further their dynamic properties. Our results demonstrate that responsive backup circuits may function as ideal devices for filtering nongenetic noise from transcriptional pathways and obtaining regulatory precision. We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation. In this respect, we suggest that compensation for gene loss is merely a side effect of sophisticated design principles using functional redundancy.

Author contributions: R.K., M.L., and Y.P. performed research.
Conflict of interest statement: No conflicts declared.
Freely available online through the PNAS open access option.
*R.K. and M.L. contributed equally to this work.

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47 Responses to Unwitting Pro-ID Peer-Reviewed Articles on the Increase . . .

  1. Looking at biological features from a design perspective as opposed to a Darwinian perspective seems far more likely to stimulate research and discover utility and reason behind features that were previously not understood. Darwinism has a tendency to label such features as “vestigal” or just left over junk from evolution. In 1895 Darwinists claimed that there were at least 100 vestigal features on the human body. Now all of them are known to have function.

  2. 2

    Did any ID theorists predict this discovery?

  3. Indeed! Although regrettably, the paper is not overtly pro-ID nor am I aware the authors’ position on the issue. Perhaps this is an unwitting contribution to ID?….

    The authors describe the fact:

    this very robustness also renders redundancy evolutionarily unstable, and it is, thus, predicted to have only a transient lifetime.

    Absolutely, which really shows the theory (Darwinian evolution) was wrong in the first place to make the prediction!

    Redundancy by nature is resistant to Natural Selection, therefore, it’s evolution in the first place is difficult to account for.

    Andreas Wagner has a very good book on the issue (even though it has a highly pro-Darwinian emphasis with lots of circular reasoning), but in one of his sections it astonished me how weakly selectable redundancies like this are!

    However, increased mutational robustness caused by gene duplications pales in comparison to drift and selection as a cause for the fixation of gene duplicates, especially because the advantage of robustness is weak in many populations.

    page 268, Robustness and Evolvability of Living Systems

    I predicted the reasons these systems would be very difficult to discover through traditional Darwinian perspectives and those banal “knock-out” experiments in
    Airplane magnetos, contingency designs, and reasons ID will prevail.

    The EF has a better chance of detecting redundancy for the very reason that redundant systems are partially invisible to knockout techniques, but hopefully not to the EF.

  4. scordova:

    “The EF has a better chance of detecting redundancy for the very reason that redundant systems are partially invisible to knockout techniques, but hopefully not to the EF.”

    What does “detecting” mean here. It seems to me that this is a discovery made by somebody who most likely did not follow any ID reasoning but who decided to investigate this question. I have a hard time giving EF credit for predicting or explaining this observation. The retrospective that “EF has a better chance” does not strike me as a driving force to test anything.

    To explain, let me condense the sentence above: “The EF has a better chance because hopefully it does”

  5. ofro,

    The EF can detect linguistic constructs, that was the design detection I had in mind, though the EF is not limited to that. In fact, non-randomly distributed gene duplicates were suggestive of liguistic constructs. The EF succeeds in detecting fuction because, as Lewontin pointed out in a Winter 2003 SantaFe Paper, funcitonality has no inherent meaning or inherent detection by natural selection.

    See: Santa Fe, Winter 2003.

    How, then, are we to assign relative fitnesses of types based solely on their properties of reproduction? But if we cannot do that, what does it mean to say that a type with one set of natural properties is more reproductively fit than another? This problem
    has led some theorists to equate fitness with outcome. If a type increases in a population then it is, by definition, more fit. But this suffers from two difficulties. First, it does not distinguish random changes in frequencies in finite populations from changes that are a consequence of different biological properties. Finally, it destroys any use of differential fitness as an explanation of change. It simply affirms that types change in frequency. But we already knew that.

    In contrast, functionality has meaning (or at least recognition) in the world of the the EF.

    Salvador

  6. Salvador,

    A thought experiment for you: Say that x and y are redundant systems for performing function f. Function f has a high degree of specificity, but is not complex. System x is specified as a “doubly-redundant f” and system y is specified as an “n-fold redundant f” for some n > 2. Thus x and y have about the same (high) level of specificity. For straightforward choices of probability distribution, n-fold redundancy is less likely to arise by chance than double redundancy. Thus y has greater specified complexity than x, even if n is outlandish. It seems to me it is possible to reject x as intelligently designed and accept y as intelligently designed when n is much larger than anyone would reasonably attribute to intelligence.

    I don’t see that redundant design and the explanatory filter (not a term Dembski uses in his latest work, incidentally) are a match made in heaven.

  7. Stevie Steve is no longer with us. –WmAD

  8. “In 1895 Darwinists claimed that there were at least 100 vestigal features on the human body. Now all of them are known to have function.” – Jehu

    But, vestigial organs don’t have to be non-functional to still be vestigial.

    “The statement that vestigial structures are functionless is a convenient, yet strictly incorrect, approximation. It is analogous to the common, yet strictly incorrect, scientific claim that the earth is a sphere.”

    “A vestige is defined, independently of evolutionary theory, as a reduced and rudimentary structure compared to the same complex structure in other organisms.”

    Both quotes from: http://www.talkorigins.org/faq.....tion2.html

    Vestigial organs like eyes on blind cave-fish are direct predictions of evolution, this is why they are used as powerful evidence of evolution. Evolution does not predict that vestigial organs will have no function what-so-ever. It only predicts that they will exist.

  9. For the record…

    The Disemvoweler is triggered by two means and in the six months it has been installed has never gone off by accident.

    1) if the first line of any comment is

    [troll]

    then the remaining lines are disemvoweled. Theoretically a commenter could disemvowel his own comment if he knew that.

    2) by IP address – any comment coming from a list of IP addresses is automatically disemvoweled. To the best of my knowledge there were not more than 3 IP addresses in the list.

    I would guess the recent rash of disemvoweled comments is one person commenting under multiple names and furthermore that this one person’s IP address is one of the 3 on the disemvoweler’s list. Those three IP addresses have been on the list for almost 6 months so it’s someone testing the new moderator(s) to see what they can get away with. I think that person (and all the other disemvoweled aliases) is the poster who goes by Steve Story on ATBC. As I recall he was one of those 3 IP addresses. Possibly more than one if he has a fixed IP address in more than one location he accesses the internet from. I also had to put a block on his email address as he wouldn’t stop emailing me when asked.

  10. Tom English wrote:

    It seems to me it is possible to reject x as intelligently designed and accept y as intelligently designed when n is much larger than anyone would reasonably attribute to intelligence.

    Hey!

    Good to see you. It is permissible to have false negatives ( labeling a designed object as undesigned) in ID theory. The high complexity system you describe is like Michael Behe’s suggestion of Rube-Goldberg solutions. If anything, Rube-Goldberg screams design more strongly since it has many pitfalls for reproductive efficiency (i.e. the emergence sexual reproduction in the first place)….

    Distributed redundancy to accomplish the same function as a simple primary function may indeed be a gold-mine. As an analogy, flying an airplane under partial panel conditions (some instruments dead) requires more complex coordination of the remaining functioning distributed parts than normal. In fact, it takes foresight to prepare for such contingency and to design (as in teach pilots) for such contingencies.

    I can’t emphasize how difficult it is for natural selection to create such systems, since natural selection must have foresight into contingencies to create backup systems! In fact, Wagner showed that mathematically this is true, however he never really answered the question of why it came to be so, given these facts.

    Anyway, great to hear from you Tom.

    Salvador

  11. 11

    I can’t emphasize how difficult it is for natural selection to create such systems, since natural selection must have foresight into contingencies to create backup systems! In fact, Wagner showed that mathematically this is true, however he never really answered the question of why it came to be so, given these facts.

    Natural Selection having foresight? Please explain how this is possible.

  12. Hold it guys, in honor of Behe’s E.coli rotary motor should my new hyperIDist handle at yahoo be darwinshipyards or darwinmarinedrives?

  13. I am eagerly awaiting further peer-reviewed research from Dr. Dembski and his research assistant on this topic. If this falls sufficiently outside their area of Intelligent Design expertise, I assume that there are other robust ID research programs that will carry this forward. Can someone kindly provide links to the labs and researchers that have the capacity to carry this out?

  14. Tom English: “Thus y has greater specified complexity than x, even if n is outlandish. It seems to me it is possible to reject x as intelligently designed and accept y as intelligently designed when n is much larger than anyone would reasonably attribute to intelligence.”

    You seem to be saying that if x is “specified” but not “complex”–which sounds like the scenario you’re setting up–and y is n-fold redundant, x would be rejected as ‘designed’ since it is ‘specified’ but not ‘complex’, while y might pass the test of being ‘complex’ just because it’s n-fold redundant.

    If I’m understanding you correctly, then neither x nor y is ‘complex’, and hence neither is ‘designed’. The reason I say that is because simply repeating something doesn’t add information. Sometimes when posting at a blog your post doesn’t immediately go up, and it is not uncommon for multiple posts of your original comments to appear. But there’s no added ‘information’ contained therein, even if you posted a thousand times.

  15. I vote for ‘darwinmarinedrives’. It kind of has a ring to it.

  16. We’re thinking of laying off our blind-folded design engineers and replacing them with Denton’s primate linguists–monkeys.

  17. PaV,

    We went with darwinshipyards–since Darwin thinks cnc proramming is negotiable
    at ALL machining cells (roll forms, shears, brakes, horz and vert boring, lathes, gantry mills, cnc milling and turning. You ought to hear what some of our vendors say about our CEO! The Navy said “don’t go in to battle with that guy!”

  18. PaV,

    “The reason I say that is because simply repeating something doesn’t add information.”

    Functional redundancy in a design is not merely a matter of repetition of design elements. There generally has to be some coordination of functionally redundant elements. To go with Salvador’s example, you can’t just slap two magnetos on an airplane engine that previously had one and expect them to work together. And the magnetos do not have to be identical. There could be a primary magneto and a backup magneto.

    You seem to be mistaking Dembski’s complexity for Kolmogorov complexity or something similar. For Dembski, the complexity of an entity is related to its probability of arising by chance. High complexity corresponds to low probability, and low complexity corresponds to high probability. In most scenarios one would say that systems with high functional redundancy are less likely to arise by chance than those with low functional redundancy.

    Now let’s take another shot at what I want to say.

    Suppose we have a system that serves a highly specified function but exhibits low complexity. It will not trigger a design inference. Now let’s increase the degree of redundancy of the system without changing its function. The specificity of the system changes little. One would expect the complexity of the system to increase as the redundancy does. And as the complexity increases, so does the specified complexity.

    The upshot is that you can take a system that does not trigger a design inference, make it redundant, and obtain a system that does trigger a design inference. Intuitively, I have problems with the notion that simply increasing redundancy can increase the evidence for intelligent design. For instance, if the triply-redundant system does not merit a design inference, do we really want to accept that the quadruply-redundant system is designed?

  19. From Andreas Wagner’s book (perhaps the foremost on robustness and redundancy):

    However, fitness is hard to define rigorously and even more difficult to measure…..

    An examination of fitness and its robustness alone would thus not yield much insight into the opening questions. Instead, it is necessary to analyze, on all levels of organization, the systems that constitute an organism, and that sustain its life. I define such systems loosely as assemblies of parts that carry out well-defined biological function.

    In other words, to understand biology, one must forsake the perspective of natural selection and instead adopt the lens of Irreducible Complexity! If fitness cannot even be quantified, what good is it scientifically? How can science proceed without the capacity to measure something? How can natural selection be a good framework for biology when it’s influence cannot even be measured with respect to designed systems?

    In contrast, one can measure the fidelity of a design analogy. That was laid out in Bill’s work. Thus if there is a strong correlation to an engineering specification, we have high confidence in the predicted behavior of the system. And in addition, we have falsifiable and testable cybernetic laws.

    Thus again, the power of design analogy is a superior framework for investigating biology, mathematically and empirically.

    Biology has unwittingly adopted the central tenets of ID.

    Salvador

    PS
    Clarification: a holistic redundant system functions BECAUSE one can knock out a part and it still functions. In that sense it is still specified complex but not irreducibly complex. However, the individual back-up systems in a redundant system are IC.

  20. “But, vestigial organs don’t have to be non-functional to still be vestigial.”

    Then how can you prove that they are truly vestigial?

  21. This paper, although it probably does not willingly support ID principles, is extremely interesting. Indeed, if I am not wrong, the existence of duplicate genes has been used many times as an argument by Darwinists in two ways: 1) as a proof of evolution because the duplicate genes were considered “junk” burden from casual mutations. 2) as a mechanism to favour evolution, because the duplicate genes were considered as possible “neutral” genes where evoultionary “tentative” mutations could be tried by “nature” without affecting the function of the “true” gene, at least until a new “function” was dicovered (and I must admit that the latter mechanism, although probably only a fairy tale, looks very “designed” to me).
    Now, instead, it seems that duplicate genes are part of an informational control mechanism, probably very complex, whose main purpose is to “reduce genetic noise” and to compensate for random mutation!
    That certainly is a shift of attitude, and it really makes sense. It seems to me that it is a new step in the process of reevaluating “junk” DNA (that is, 99% of our genome), and finding that the more complex functions are just where we did not think anything was present.
    Now, the problem is not if IDers have predicted a specific finding. I don’t think IDers, although criticized for their religious attitude, have any obligation to behave as prophets! The important point is that if anyone (even a non-ID researcher) applies a type of reasoning which searchs for informational complexity in biology, instead of thinking it should not exist beyond a certain level compatible with naturalism, then that reasearcher is more likely to discover new things. In that sense, ID “attitude” is the greatest hope to increase our understanding.
    One more thought about “junk DNA”. If it is true (as most biologists now think) that junk DNA is where most regulatory activities are, that is in itself a major problem for Darwinist theory. Indeed, most evolutionary reasonings have been, up to now, in terms of “protein evolution”. If biological research can find out (and I think it will find out) that the real “code” for cellular functioning is written in a completely different way, that it relies mainly on non messenger RNA, and taht it is made of interactions so subtle and complex that, up to now, they could appear to us as “junk”, and that the protein mechanisms are only a tiny part of the global information, let’s say the “final effectory part”, then the whole naturalistic evolutionary theory appears even more unlikely, and it will have to be re-written, or, better still, discarded.

  22. Salvador,

    Wagner said it is *hard*, not impossible. In fact, Sir Ronald Fisher defined the concept of Reproductive Value (RV) already in 1930 (in his The Genetical Theory of Natural Selection), and RV is a rigorous measure of fitness that is widely used today in evolutionary biology. It is still hard to measure in practice because RV typically depends in a complictated way on demographic properties such as age-specific survival, fecundity, age of first reproduction, etc, all things which are hard to measure with precision in the field.

  23. Strangelove@8

    Vestigial organs like eyes on blind cave-fish are direct predictions of evolution, this is why they are used as powerful evidence of evolution.

    It all depends on what you mean by evolution. The fact that a fish lost the ability to see doesn’t say how the fish got here in the first place.

  24. Raevmo,

    I agree that Wagner did not say it’s impossible, but he only calculated how selection would act on a redundant architicture AFTER the architecture was in place, and it was very weak at that (dwarfed by the effects of genetic drift for example). He did not give an account of how the regulatory mechanisms for creating and controlling redundancy would emerge in the first place. And if the selection forces involved would be even much weaker for creation than maintenance, one has to wonder why it would be created in the first place?

    But another thought hit me today, if gene duplicates are vital for redundant functionality, this will pose and interesting question regarding the molecular clock hypothesis and interpretations of nested hierarchies of bio-polymer sequences such as that seen in the Dayhoff Diagram. The sequence divergences between species is almost like a periodic table. We thought that was consistent with some sort of “diffusion” (ala Kimura and friends), however, the redundant DNA’s throw a serious wrinkle in all of this. Why?

    If we find DNA sequences that participate in redundancy also follow the architecture suggested by Dayhoff’s bioinformatic diagram, this will lead to a serious contradiction in the molecular clock hypothesis. Why should duplicated, or redundantly tied sequences ‘tick’ in synchrony to create such beautiful inter-species equidistance?

    We have some scenarios:

    1. the sequence divergence in a single organismal between duplicates should be comparable to that divergence found between species, but this would contradict the findings of this paper since duplicated sequences are ideal for functional redundancy

    2. the sequence divergences ticked in synchrony in a species line to create the approximate equidistance we see in the Dayhoff diagram, but this would violate the concept of random walks of the neutralists, throwing doubt on the mechanisms which create the beautifully spaced sequence divergences as seen in Dayhoff Diagram.

    We need more sequence data to confirm this, but I have confidence (my prediction) this possible further enigma will be pervasive.

    Salvador

    PS
    Good to hear from you. Apparently copies of Sanford’s book are scare, and for whatever reason Amazon is delayed in shipping your order to your location. I placed it a month ago. I’m hoping it will eventually arrive. They tell me September!

  25. Ryan: “Then how can you prove that they are truly vestigial?”

    The example of vestigial organs in that link I posted were things like the wings of ostriches. Surely, the ostriches use those wings for courtship and balance. But they don’t use them to fly, like almost every other winged animal. “A vestige is defined, independently of evolutionary theory, as a reduced and rudimentary structure compared to the same complex structure in other organisms.” I’m puzzled as to what in that definition you think needs proving.

    Mats: “It all depends on what you mean by evolution. The fact that a fish lost the ability to see doesn’t say how the fish got here in the first place.”

    Vestigial organs are not used as evidence of origins, AFAIK. They are used as evidence of “change over time.” And these cavefish (and all of the other blind cave animals) seem to have descended from sighted ancestors. The fact that we have vestigial organs implies that even we descended from something. Mind you, vestigial doesn’t mean that those organs are functionless, just that they happen to be reduced versions of complex structures in other animals.

  26. Strangelove,

    The whole point is that assigning a biological feature as vestigial feature or “junk” or “left over from evolution” tends to limit research and inquiry as opposed to believing the feature was designed and has a purpose and then investigating that purpose. Now, nobody is going to search for the function of the eyes in blind cave fish, however, regarding the appendix and tonsils as vestigial and not useful proved to be a mistake. I expect, as do most IDers that, “junk” DNA actually has a function and that redundant features such as the one discussed in the above article are not merely left over from evolution but are the result of robust design. Robust design allows for features that do not confer selective benefit but merely make the organism better.

  27. 27

    Jehu: “The whole point is that assigning a biological feature as vestigial feature or “junk” or “left over from evolution” tends to limit research and inquiry as opposed to believing the feature was designed and has a purpose and then investigating that purpose.”

    I guess this is where I wholeheartedly disagree. I cannot think of a single scientist directly researching “junk DNA” (which is an unfortunate misnomer) and vestigial organs that doesn’t subscribe whole-heartedly to the theory of evolution. Correct me if I am wrong.

    I can understand why you would have that idea about scientists. You think that they call it Junk and toss it to the corner of the lab. But, this evidently is not the case.

    And furthermore, I have never heard of a discovery being made because a previously overlooked piece of DNA or organ was later re-analyzed by someone working with the “it was designed, hence it must have a purpose” assumption. Once again, correct me if I’m wrong. I certainly haven’t heard of every researcher out there.

    Look who is doing almost all of the lab work.

    Jesu: “Now, nobody is going to search for the function of the eyes in blind cave fish…”

    Here is an example of that faulty logic. Scientists should (and do) search for non-intuitive functions of DNA and organs. Perhaps the sightless eyes serve other functions for the cave-fish, maybe they work with bouyancy, blood regulation to the brain, etc. I can have those ideas without having to believe that the sightless eyes were designed.

  28. Jehu wrote:
    “I expect, as do most IDers that, “junk” DNA actually has a function and that redundant features such as the one discussed in the above article are not merely left over from evolution but are the result of robust design.”

    If Dembski is correct that “intelligent design is not optimal design”, why do so many ID supporters insist that “junk” DNA and vestigial organs must be functional?

  29. Strangelove: “{I cannot think of a single scientist directly researching “junk DNA” (which is an unfortunate misnomer) and vestigial organs that doesn’t subscribe whole-heartedly to the theory of evolution.”

    Wheather or not you can think of a scientist who does not subscribe whole-heartedly to evolution is totally irrelevant. I never said that no evolutionist will ever research junk DNA or vestigal organs, I said that the belief that such features are vestigal or left overs from evolution tends to limit inquiry and investigation as opposed to a belief that they are designed.

    As for blind fish, they have lossed the ability to see because natural selection did not weed out the fish born with defective eyes. Maybe there is some other function the eyes serve, however, if there is, I predict the eyes in fish with sight also serve the same function. The sightless eyes represent the degeneration of a designed feature not the evolution of a new feature. Feel free to investigate.

  30. Jesu: “Wheather or not you can think of a scientist who does not subscribe whole-heartedly to evolution is totally irrelevant.”

    Very true. I made an assertion: that no ID proponent does the research that you say they do, and that the less likely “evolutionists” actually do. And I’m asking you to prove me wrong.

    Jesu: “I never said that no evolutionist will ever research junk DNA or vestigal organs, I said that the belief that such features are vestigal or left overs from evolution tends to limit inquiry and investigation as opposed to a belief that they are designed.”

    Can you back this up with anything? You say “tends to limit” almost like you have some statistics. I’d be interested to see how worldview differences account for differences in what people research. If no one has done that study, that would probably be an interesting topic to pursue.

    Jesu: “As for blind fish, they have lossed the ability to see because natural selection did not weed out the fish born with defective eyes. Maybe there is some other function the eyes serve, however, if there is, I predict the eyes in fish with sight also serve the same function. The sightless eyes represent the degeneration of a designed feature not the evolution of a new feature. Feel free to investigate.”

    You are completely correct. The eyes of blind fish probably don’t serve many purposes nowadays. I picked a random example, and perhaps a poor one. Many vestigial organs, as you pointed out, do indeed have completely different functions than the fully working organs in other animals.

  31. Strangelove@25

    Vestigial organs are not used as evidence of origins, AFAIK.

    Vestigial organs are used as evidence for evolution, and then evolution is the suposed mechanism as to “how all biological complexity got here”. I don’t think it’s fair to use an example of loss of information as evidence for a mechanism that requires the aquisition of new genetic material.

    They are used as evidence of “change over time.”

    This is why I said “Depends on what you mean by evolution”. If by evolution you mean “change over time”, I don’t think that ID scientists have a problem with that (even though I would call that only “genetic variation”, or just “variation”, and not “evolution” per se).

    And these cavefish (and all of the other blind cave animals) seem to have descended from sighted ancestors.

    Yes, blind cavefish descend from sighted cavefish. Still a cavefish.

    The fact that we have vestigial organs implies that even we descended from something.

    1. Do we have vestigial organs?
    2. AS seen above, the fact that a system stopped working is not evidence for molecules-to-man evolution

    Mind you, vestigial doesn’t mean that those organs are functionless, just that they happen to be reduced versions of complex structures in other animals.

    If they are versions of a former complex structures, then that isn’t evidence for the full blown Darwinian theory. We can’t get rich by loosing money. Biological syste,s can’t get more and more complex by becoming less and less complex.
    Evolution says that systems were simpler and got complex. The vestigial organ framework says that systems used to be more complex, but now they are much simplier. You cannot use an example of the latter and evidence for the former, IMO.

  32. Just a few comments:
    1) The fact that most, or quite all, biological research is done by “evolutionists” is only a proof that most biologists, today, are evolutionists (or behave as such), and, even more, that most resources are owned by the official, evolutionist, scientific establishment. In no way it means that non evolutionist biologists do not exist, or that they don’t want to do research.
    2) The important point is not who makes what, but how he makes it. ID research could well be done by evolutionists, but they probably would never explain their results, even if they are strongly in favour of ID, from an ID point of view. In my opinion, ID and evolution are merely two different models of inerpretation of the same facts. So, there is not the problem of “evolutionist research”, or of “ID research”. Research should be done to find out facts. The conflict between interpretation models is more a cultural, ideological and political matter.
    3) Anyway, the interpretation model certainly does influence how you do research. It is a well known fact, for instance in biological statistics, that the model from which you start your research, or which you choose for the quantitative inerpretation of your data, is of fundamental importance, and it does affect your results. The model is the responsibility of the researcher, and it is not imposed by data. It is a pesrsonal choice of the individual scientist.
    4) Still, obviously, there are models which are vastly shared at a certain moment of history, and others which are not so popular, or which are definitely rejected.
    5) Scientific facts are objective, but scientific models are not. Science is always generated by a culture, and at any moment of history science is heavily influenced by the culture which generates it. Be it christian faith or naturalistic religion, be sure that science will be influenced by the expectations of the prevailing phylosophy. The evolution-ID conflict is a very good example.
    6) Regarding junk DNA, which is now known with the politically correct name of “non coding DNA”. I don’t know if Mattick and the other researchers, who have fought to change the prevailing interpretation of that kind of genetic code as an evolutionary burden, are evolutionists.They probably are, but I am in no way interested in that. I am very interested in the fact that a group of honest and intelligent researchers have tried to give a more satisfactory kind of answer to a very big problem, operating both at the level of research and at the level of interpretation model. There is no doubt that, as long as the prevailing interpretation was that non-coding DNA is useless, no great resources were assigned to research about its role, while now that the new paradigm about non-coding DNA is more fashionable, we will probably witness a lot of new work on that.

  33. Mats: “Vestigial organs are used as evidence for evolution, and then evolution is the suposed mechanism as to “how all biological complexity got here”. I don’t think it’s fair to use an example of loss of information as evidence for a mechanism that requires the aquisition of new genetic material.”

    Vestigial organs are luckily not the only evidence for evolution. You’re right, evolution requires the acquisition of new genetic information. The evidence for such processes is surely not vestigial organs.

    Mats: “1. Do we have vestigial organs?”

    Yes. Tailbones, nicitating membranes, appendices, etc. All of these fit the definition of: “reduced and rudimentary structures compared to the same complex structures in other organisms.”

    Mats: “If they are versions of a former complex structures, then that isn’t evidence for the full blown Darwinian theory.”

    Again, vestigial organs are not the ONLY evidence for evolution. They are required by the ToE, and we find them everywhere. Mutant whales born with legs are my favorite example. Such things are predicted and explained by the ToE.

  34. On cave fish:

    http://sciencenow.sciencemag.o.....004/1013/2

    When a body part is no longer needed, scientists usually assume that mutations accumulate in the genes controlling the structure, eventually preventing it from working or being made. “That was the dogma,” says Stephen Ekker of the University of Minnesota, Twin Cities.
    ….
    …new research suggests that for some cave-dwelling fishes, blindness results from the careful coordination of gene expression, not simply from lack of use.

    I also remember reading somewhere that the eyes are “turned back on” when conditions change. But I unfortunately cannot remember where I read this.

    On the supposed atavistic hindlimbs of whales:

    http://www.talkorigins.org/faq.....avisms_ex1

    http://www.answersingenesis.or.....le_leg.asp

    http://acs.ucsd.edu/~idea/pbsevolution.shtml

    Unfortunately I couldn’t find articles on the net that weren’t from Darwinists, Creationists, or ID proponents. Usually such articles only mention information that helps their argument, which is usually why I like to go to a 3rd party like I did with the Cave Fish. I haven’t seen anyone else mention it but could these “hind limbs” be accidental leftovers from temporary structures built during development? But answering that would require getting hold of an expert in whale development.

  35. 35

    Patrick, I must admit that I find the photo of the 2.5 foot legbone more convincing than the AIG rant.

    “I haven’t seen anyone else mention it but could these “hind limbs” be accidental leftovers from temporary structures built during development?” Wow!

    gpuccio: “It is a well known fact, for instance in biological statistics, that the model from which you start your research, or which you choose for the quantitative inerpretation of your data, is of fundamental importance, and it does affect your results.”

    Do you have a link or something?

  36. Heh. Maybe my off-the-top-of-my-head guess isn\’t so far off after all:

    http://digitallibrary.amnh.org...../N0009.pdf

    In a paper entitled \’Untersuchungen an walen,\” Professor W. Kukenthal has described external rudimentary hind limbs in three early embryos of Megaptera. These appear as two more or less caudally directed papillae on either side of the genital organ in the same relative position as the hind limbs which I have described in this paper. In Kukenthal\’s Stage I (an embryo 32 mm. in length) the rudiments are best developed and are 12 mm. long. In Stage II (an embryo 28 mm. long) the rudiments are somewhat less distinct, reaching a length of 9 mm. In Stage III (an embryo 30 mm. long) the hind-limb rudiments have still more decreased in size and appear as minute papillae.
    Kuikenthal has also discovered hind-limb rudiments in embryos of Phocaena communis and P. dalli, and Guldberg has recorded them in embryos of Lagenorhynchus acutus and Phocaena communis.
    Kukenthal states that the hind-limb rudiments are found in later embryonic stages of the Mystacoceti than in the Odontoceti and concludes that in the evolution of cetaceans the hind limbs lost their functional character in the Odontoceti earlier than in the Mystacoceti.
    Since Kiikenthal\’s and Guldberg\’s researches have shown that external hind-limb rudiments are still present in some cases in embryonic life, it is by no means impossible that, these vestigial organs should continue their growth and persist until the adult stage.

    Of course they\’re interpreting this evidence in an evolutionary framework, claiming it as \”rudimentary hind limbs\” present during development. Another interpretation would be to consider this structure as temporary \”scaffolding\” (extra-embryonic) that is \”normally\” removed as the creature grows. After all, many other creatures have temporary structures that have no apparent ultimate morphogenetic significance (as in, they disappear completely in later stages of development) but they DO serve a purpose. But again, we\’d have to get hold of an expert of whale development in order to be certain.

    EDIT1:

    As for gpuccio\’s assertion, you should check out this:

    http://www.uncommondescent.com.....chives/947

  37. OT as far as the latest comments on this post go, but on-topic as far as the post is concerned. Some more unwitting observation of design by mainline, non-ID scientists: as reported by the NYT. The key line being: “Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code.”

  38. Patrick,

    I cannot see the sciencenow link on cave fish, but I can read what you posted about it. It seems to be saying that the “micro-evolution” of the blind eyes of the cave fish was the result of NEW information, not a degeneration of existing information. Would ID then require to say that designer went out of his way to make these fish blind? Or perhaps the new information isn’t CSI?

    “Of course they’re interpreting this evidence in an evolutionary framework, claiming it as ”rudimentary hind limbs” present during development. Another interpretation would be to consider this structure as temporary ”scaffolding” (extra-embryonic) that is ”normally” removed as the creature grows.”

    I don’t know much about whale development. But a similar vestige closer to home, the human tail, has been more closely studied. http://www.ncbi.nlm.nih.gov/en.....t=Abstract

    The “scaffolding” argument loses alot of weight when the vestige is found to be 13cm long and outside of the body. “Scaffolds” rarely contain blood vessels, nerve tissue, muscles, sweat glands, hair follicles, etc. One really has to stretch the logic to suggest that these are anything other than vestigial tails from our primate heritage.

    Thanks for the link on gpuccio’s assertion. I heard a similar argument about convergence of the charge/mass ratio of the electron. Millikan’s data from his famous oil-drop experiment was a little off at first. All of the subsequent data from other scientists repeating the experiment caused the ratio to asymptotically approach the value accepted today. It goes to show you that scientists are humans, too.

  39. I quoted straight from the Science article. Where in the world did you get the idea that new information was being generated?? Did you miss the part about “blindness results from the CAREFUL COORDINATION of gene expression”?

    http://www.dimaggio.org/Archiv.....humans.htm

    Human “tails”…aka disarrangements that occurred during embryological development. I also highly doubt these “tails” are extra-embryonic features (“scaffolding” is just a common term I used for this discussion). That interpretation of the data is only a possibility with the whale leg; don’t attempt to confuse the two in an attempt to make a bad argument. I don’t believe the precise genetic basis for these examples of “tail” growth in humans is known, but I’d say the best bet is Hox (homeobox) genes. Mutations in these genes cause alterations in the development of the axial skeleton (vertebral column and ribs) and limbs, among other things. The Pax-6 regulatory group–which is about 130 amino acids long–shares a 94% similarity between humans and insects. They are conserved across all animal phyla, with similar or homologous functions (you can argue over the cause of this–designer reuse or common descent–later). Mutations in these regulatory gene sets can cause biological components to not be built (an animal losing their hind legs). They can result in more than the correct number of elements being built (as in the case of Hox-4.6 in chickens which create an extra “thumb”). They can even result in the construction of components in the wrong places. Ultimately, manipulations to these genes can only result in the rearrangement of elements already present in the biological development plan for a given organism. If I wanted to give someone’s child a tail, we’d need to know the exact pattern of expression of the correct gene(s) and how to achieve it by artificially engineering promoter-gene fusions and inserting them into the genome of an embryo. Otherwise you’d end up with these useless extensions as seen in the above pictures.

    But let’s ask some questions. Some human females are born with mammary glands under the armpits; does this mean they’re regressing to an earlier mammalian stage? After all, some mammals have mammary glands in their armpits. Does a second nipple on my right breast mean I’ve generated CSI? Of course not. Besides, if the bony tail is evidence that we evolved from tailed creatures, why also bother to insist that we evolved from a common ancestor with pan troglodytes, which doesn’t have tails? Just exactly who is stretching logic here?

    Also, you should read this:

    http://www.uncommondescent.com.....chives/875

    Obviously I’m in the search for the truth, not some tired attempt to defend an old framework. Whether humans came from pan troglodyte, or another route through convergent evolution, or were specially created…I don’t care. I just want to make certain it’s true.

  40. 40

    Patrick: “Where in the world did you get the idea that new information was being generated?? Did you miss the part about “blindness results from the CAREFUL COORDINATION of gene expression”?”

    It was previously discussed here that cavefish were descended from sighted fish. Let’s take that assumption at face value. Now, you point out that “blindness results from the CAREFUL COORDINATION of gene expression”. That sounds like to me that the cavefish has more genes being expressed than the sighted fish. I equated the idea of “CAREFUL COORDINATION” with new information. Is that wrong to do? Hence, under the assumption that these fish descended from sighted fish, that new information had to come from somewhere.

    Now we can consider that assumption false. If the new information is CSI, then doesn’t the theory if ID require that the designer blinded these fish, or designed them with useless eyes to begin with?

    If you see some holes in my logic, point ‘em out.

  41. 41

    Patrick: “Some human females are born with mammary glands under the armpits; does this mean they’re regressing to an earlier mammalian stage? After all, some mammals have mammary glands in their armpits.”

    I honestly know nothing about this. I’ve never even heard of mammary glands in armpits. I don’t need to further speculate on things I know nothing about.

    Patrick: “Besides, if the bony tail is evidence that we evolved from tailed creatures, why also bother to insist that we evolved from a common ancestor with pan troglodytes, which doesn’t have tails? Just exactly who is stretching logic here?”

    Why is it a stretch of logic to think that one of our common ancestors with the chimps had a tail? Just look at most other primates and land mammals. It does not have to be our most previous ancestor that was tailed for us to retain it’s mark.

  42. I equated the idea of “CAREFUL COORDINATION” with new information. Is that wrong to do?

    Yes. This has to do with changes in the regulation of one gene during development. They were able to restore sight in blind fish with different gene regulation induced artificially. Where exactly in this loss of functionality is this new information you’re talking about?

    And as I said before other scientists have posited that this change might be due to a responsive mechanism. Other senses are supposedly enhanced in addition to the loss of sight. Sounds Lamackian to me…but whatever, I cannot even remember where I read that.

    I don’t need to further speculate on things I know nothing about.

    Funny, you’re perfectly willing to do just that in your next paragraph: :P

    Why is it a stretch of logic to think that one of our common ancestors with the chimps had a tail? Just look at most other primates and land mammals. It does not have to be our most previous ancestor that was tailed for us to retain it’s mark.

    So, you’re claiming that this reversion to conserved tail information comes from an ancestor from before Ardipithecus ramidus–over 4.5 million years ago? Unfortunately Sahelanthropus tchadensis, dated at around 7 million years, is just a skull so we cannot tell if it had a tail. Or we can go back 20 million years ago to Proconsul heseloni, which lived in the trees of dense forests in eastern Africa. Proconsul is said to have had features that closely link it to the common ancestor of humans—for example, the lack of a tail. But fine, you go ahead and believe that if you want.

  43. 43

    Patrick: “Yes. This has to do with changes in the regulation of one gene during development.” And how does this regulation get passed down to the little blind cave-minnows? The genes perhaps?

    “They were able to restore sight in blind fish with different gene regulation induced artificially.” So an intelligent designer (man this time) had to change the gene regulation so the fish could see again. Hmmm….

    “Where exactly in this loss of functionality is this new information you’re talking about?” An eye that can’t see sounds like a loss in functionality to me. What would you call it?

    When’s the last time your nicitating membrane had a function? When’s the last time ostriches flew? When’s the last time whales walked on land? You’re throwing out these numbers, 4.5 million, 7 million, 20 million, as if they somehow disprove something. It does prove that you’re capable of looking up stuff. And for that I applaud you. But what do those numbers show? That it happened a long time ago. To which I reply, “So?”

  44. You must be under the misconception that I believe there CANNOT be vestigial organs or a loss in functionality…that is not so! I just have a distaste for repeated dogma disguised as poor arguments, especially arguments that don\’t even touch on ID. Be careful or I might go all DaveScot on you. ;)

  45. 45

    Patrick,

    I think we’ve both reached the point where we’re just plain ol’ arguing. And somehow I haven’t been able to get across my point effectively to you. And likewise I don’t get your point very well. Our previous comments stand for themselves. I’ll move on to more interesting threads.

  46. Agreed. I also must apologize for the tone of my last couple messages. While, yes, I do think your arguments are quite invalid I shouldn’t have let insults seep into my responses. Not to mention the main points of discussion are effectively finished with (unless you happen to know an expert in whale development ;) ).

  47. Sorry for answering so late.

    Stangelove:
    just for discussion, here is a very simple citation in favour of the importance of modeling. It is from the first chapter of a manual of statistics (Statistics for Research With a Guide to SPSS, 2nd.Edition).
    “The conceptualization and operationalization of variables
    Where do variables come from? Why do we choose to study particular variables and not
    others? The choice of variables to investigate is affected by a number of complex factors, three
    of which I will emphasize here.
    1. Theoretical framework. Theories are ways of interpreting the world and reconciling
    ourselves to it, and even though we may take for granted that a variable is worthy of
    research, it is in fact often a highly charged selection process that directs one’s attention to
    it. We may be working within an established theoretical tradition that considers certain
    variables to be central to its world-view. For example, Marxists consider ‘economic class’
    to be a variable worthy of research, whereas another theoretical perspective might consider
    this variable to be uninteresting. Analyzing the world in terms of economic class means
    not analyzing it in other ways, such as social groups. This is neither good nor bad:
    without a theory to order our perception of the world, research will often become a jumble
    of observations that do not tie together in a meaningful way. We should, though,
    acknowledge the theoretical preconceptions upon which our choice of variables is based.”

    I think hat subjectivity, conceptualization and modeling are constantly present in scientific research. In statistics, if you want to analyze the correlation between two variables, you have usually to decide first which, in your model, is the indipendent one. That is sometimes obvious, other times much less obvious, and it may critically depend on you pre-existing model of the phenomenon.
    More in general, modeling phenomena according to obligatory naturalistic mechanisms is a choice that has deep consequences on how one tends to make research or to intepret the existing data.
    The same problem is very obvious in sciences of men’s behaviour (psychology, sociology, psychotherapy, etc.), where fundamental beliefs about what a mind is or can be, or about free will or determinism, are very likely to deeply influence theories and research. For instance, a position of dependance from the theory of strong Artificial Intelligence will shut out a lot of models, leaving space only for purely algorithmic ones. That’s very important, because I think that strong AI has a role, corresponding to that of strict darwinism in biology, in supporting a purely naturalistic model of mind and brain in pshychological and mental disciplines.
    For instance, a mahematician and physic like Roger Penrose, who does not believe in strong AI, has generated a complex model of non algorithmic mental functions, based on his interpreation of Godel’s theorem (that model is obviously rejected by most, but it is very interesting and it is seriously debated. After all, I believe Penrose still has is job, and maybe that proves that mathematicians and physics are much more tolerant than biologists. Or am I being too optimistic?).

    Patrick:
    thanks for the link. I had already read that very interesting work, even in its extended form. The analysis is very complex, and the conclusions rather undefined and problematic, but it remains an extremely provocative article. I hope there is some follow-up on the same theme.

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