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Survival of the Sickest, Why We Need Disease

“It’s not a bug, it’s a feature!”

This is a phrase a software engineer will use to jokingly confess his software has a defect.

When Sharon Moalem wrote the NY Times Bestseller, Survival of the Sickest: Why We Need Disease, he probably did not intend to make a joking confession of flaws in Darwin’s theory, but he succeed in doing so.

Recall the words of Darwin:

Natural Selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good.

C.DARWIN sixth edition Origin of Species — Ch#4 Natural Selection

If Darwin’s claim is true, why then are we confronted with numerous, persistent, hereditary diseases?

Can it be that Darwin was wrong? The obvious answer is yes. But in the face of an obvious flaw in Darwin’s ideas, Moalem argues that what appears to be a flaw in Darwin’s theory is actually an ingenious feature! Moalem extols the virtues of disease, and since disease is virtuous, natural selection will favor it.

It is accepted that sickle-cell anemia persists because of natural selection, but what about other diseases? Moalem explores many other diseases like diabetes, hemochromatosis, high cholesterol, early aging, favism, obesity, PANDAS, CCR5-delta32, xenophobia, etc. showing how natural selection incorporated these “virtuous” diseases into our species.

Moalem is not alone in arguing that natural selection creates through the process of destruction. For example, Allen Orr suggests that natural selection is the cause of blindness in Gammarus minus. In the world of Darwin, what happened to Gammarus minus isn’t the loss of vision, it is the creation of blindness. And since selection favors blindness in Gammarus minus, blindness is a functional improvement! Once again, Darwinism is immune to any testability through the process of constantly redefining what is considered “good”.

The net result is that Moalem’s book becomes an unwitting critique of Darwinian evolution. It highlights numerous empirical examples of how natural selection actually goes against Darwinian ideas of constant progress, and instead demonstrates how natural selection can be an agent of demise.

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397 Responses to Survival of the Sickest, Why We Need Disease

  1. NOTES:

    In addition to Moalem’s findings, natural selection will fail to weed out the bad unless there are sufficient population resources. One example is the well known phenomenon of Mutational Meltdown.

    For all the supposed examples where natural selection is touted as “improving” a species, there are probably far more examples which illustrate natural selection fails to purge bad traits, or worse, ensure their persistence.

    Let us say for the sake of argument that there are Free Lunches (contrary to the ID claim of No Free Lunch), and that Behe’s Irreducible Complexity can be solved via gradualistic improvement, Darwinism still faces the barriers outlined in mainstream literature.

    I list below some links explaining some of the other considerations why natural selection doesn’t work in the way Darwin envisioned. These problems have not been lost on great geneticists like Motoo Kimura and NAS members like Masotoshi Nei.

    In my humble opinion, even based on accepted mainstream ideas, the hypothesis that Darwinian evolution as the primary mechanism of how life evolved has been theoretically and empirically falsified. Blyth’s view of the role of natural selection seems to have been vindicated over Darwin’s.

    Nachman’s U-Paradox

    Speed Limits of Evolution

    Fisher’s Fundamental Theorem of Natural Selection

    Airplane Magentos (the problem of contingency designs)

    Genetic Entropy

    Gambler’s Ruin is Darwin’s Ruin

    HJ Muller, unwitting pioneer of genetic entropy theories

    Walter ReMine surveyed 40 cases of the evolution of anti-biotic resistance, and in almost all cases, he reported to me that selection preserved a strain because of a functional defect, not because of novel

  2. In Orr searing critique of Dennett, Dennett’s Strange Idea

    Evolution is henceforth the magic word by which we shall solve all the riddles that surround us.– Ernst Haeckel

    and

    When does adaptationism stop being a useful research strategy and start being a silly exercise in cleverness? Dennett never confronts these legitimate worries. It is far easier for him to ridicule Gould and Lewontin’s rhetorical excesses.

    I suspect Dennett fails to appreciate these concerns in part because his thinking is guided by a subtly misleading picture of adaptation. Dennett is fond of speaking of selection as leading organisms through “Design Space”: Selection “lifts” organisms along “ramps” of good Design. Although this imagery is often useful, it invites two subtle misconceptions about adaptation. The first is that natural selection cares about Design. In reality, selection “sees” only brute birth, death, and reproduction, and knows nothing of Design. Selection — sheer, cold demographics — is just as happy to lay waste to the kind of Design we associate with engineering as to build it. Consider the eyes of cave organisms who live in total darkness. If eyes are expensive to make, selection can wreck their exquisite engineering just as surely as it built it. An optic nerve with little or no eye is most assuredly not the sort of design one expects on an engineer’s blueprint, but we find it in Gammarus minus. Whether or not this kind of evolution is common, it betrays the fundamental error in thinking of selection as trading in the currency of Design.

    Second, hazy imagery of selection lifting organisms along Design ramps makes it hard to see that selection sometimes moves individual traits down ramps. But this surely occurs.

  3. So far this thread has supported Gould and Lewinton’s 1979 critique of what they called the “adaptationist paradigm”. I hasten to add my voice of support to this critique, but would go on to point out that, if taken to its logical extension (which Gould and Vrba almost did in their 1982 paper on “exaptation”), this would not only undermine much of “Darwinian” evolutionary theory, but all of ID as well.

    The reason is quite simple: if (as Gould, Lewontin, and Vrba argue) adaptation isn’t legitimately part of what evolutionary theory is about, then the whole idea of “design” and “function” is read completely out of evolution, leaving only descent with modification. I believe that this is, indeed, the case, and have posted about it at my blog:

    http://evolutionlist.blogspot......-real.html

    I would strongly suspect that most ID proponents would disagree, and assert that the fact that adaptations aren’t “real” is precisely why guidance by an “Intelligent Designer” is necessary. However, I would counter by asking “Why is design necessary at all in explaining nature?” Simply asserting that it must be designed doesn’t make it so, nor does pointing to things we know are designed (i.e. by us) make it so.

    “If wishes were horses then beggars would ride…”

  4. Sorry, that should be Lewontin (as in Richard Lewontin, http://en.wikipedia.org/wiki/Lewontin ), not Lewinton

  5. This is why, rather than simply asserting that things are designed, I have consistently asked “what structural and functional characteristics do unambiguously designed objects and processes (such as heat-seaking missles or thermostats) have, which can then be used as criteria to determine which natural objects and processes possess such structural and functional characteristics and may therefore legitimately be considered to be the product of design?

    BTW, simply saying that something “has” CSI” or is “IC” does not qualify as a sufficient “structural and functional characteristic” of a designed object, IMHO. IOW, CSI and IC may be necessary characteristics of a designed object or process, but I do not think they are sufficient in and of themselves.

  6. While I believe that natural selection is part of an elaborate design process, the overall view of how it works is one of limitation. A great book that all interested in ID should get is

    “THE NATURAL LIMITS TO BIOLOGICAL CHANGE by Ray Bohlin, Ph.D.”

    While Dr. Bohlin, who has a Ph.D. in biology, is involved primarily now in a religious mission, this book looks at change in species according to a naturalistic paradigm. It finds the same thing that dog breeders or breeders of other animals do. Namely, that there is a limit past which naturalistic processes cannot go in terms of inward change.

    The Darwinist answer is that of course that is true but over long periods of time, mutations along with gradual small changes will break down this barrier and allow the grand suite of species that we have seen in the fossil record and on earth today. Because this assumption of long periods has certain obvious predictions that have never been observed, the Darwinian paradigm has been falsified and a large number of evolutionary biologists have looked elsewhere for an answer.

    There seems to be some obvious reasons why one designing the naturalistic processes would want limitations and a big one is that an ecology is necessary for life to work. But if each individual organism is under the natural selection guidance to maximize its individuality by being faster, stronger, smarter, older, more prolific etc, it would destroy the ecology. Natural selection does not see these limitations as barriers but in reality they exist. And the answer to why is a troubling one for any naturalistic paradigm.

    Just one, the role of age, seems to be a very persistent barrier. After all being older means having the opportunity to have more offspring and would according to the NS paradigm be one most likely to have more survivors. But we do not see organisms getting older as time goes on.

    If one were going to design a viable ecology these limitations on change or the ability of one species to dominate another or to use all the resources of an ecology would be paramount. The individual species does not know or the selfish genes do not know that they must be Politically Correct organisms or Politically Correct genes and behave in such a way so as to ensure that their neighbors also have a chance too.

    But if one wanted also to have these organisms to have the capacity to adapt to changing environments there would be built in a mechanism for some change. Thus we have another Goldilocks effect, not too much and not too little. Eventually individual populations run into an environment where they cannot adjust and they go extinct but lots of others are around to take up their place but are limited. The universe seems to have an abundance of these Goldilocks phenomena. Why?

    Natural selection exists but there definitely seems to be a built in regulator on how much change it can effect.

  7. As a first approximation to an answer to the question I posed in the previous comment, I would propose that Ernst Mayr’s requirement that a teleological object or process be produced and/or regulated by a program be perhaps the primary criterion by which design may be legitimately inferred. Furthermore, I would point out that such programs must have two characteristics:

    1) they must precede the objects and/or processes whose assembly and operation they specify and regulate, and

    2) like all forms of information, such programs must “run” in some kind of physical medium while specifying and regulating the assembly and operation of the object and/or process.

    That is, the program must consist of meaningful information, which must have a physical medium during at least part of its operation.

  8. In #6 jerry wrote:

    “After all being older means having the opportunity to have more offspring and would according to the NS paradigm be one most likely to have more survivors. But we do not see organisms getting older as time goes on.”

    Actually, we do observe precisely this correlation. That is, the larger and more complex an organism is, the older the average age of that type of organism. There is a well-established correlation between body size and average longevity in most organisms (not just animals). Furthermore, the largest fungi and plants (but not animals) are effectively immortal. That is, if nothing external kills them, there is no internal process that will kill them, and they effectively live forever. Obviously, given the vicissitudes of life on Earth, eventually something does kill even the oldest and largest fungi and plants, but this may not happen until they are tens of thousands of years old.

    Animals, by contrast, apparently have an “onboard” program that, if they are not killed by a particular age, will kill them via internal dysregulation. Find that program and alter it, and immortality is quite literally a possibility, and then human life becomes a true Hell on Earth…

  9. Allen,

    As always I’m so delighted to hear from you. I hope I haven’t started this thread at an inconvenient time since I know final exams are coming up. I know that is the case for me.

    With some degree of embarassment, for the 3 years that I’ve known you, I must admit I’ve been rather slow in understanding what you think is a correct view of evolution. Is it fair to say Spandrels De Saint Marco is closer to your position than that of Daniel Dennett or Modern Synthesis?

    If you are undecided, I think that is also a fair position, as I’m undecided on a few matters myself.

    I suppose in all my eagerness to attack Natural Selection, I forgot to ask you what paradigm you think is closest to the truth.

    Gould and Lewontin:

    An adaptationist programme has dominated evolutionary thought in England and the United States during the past forty years. It is based on faith in the power of natural selection as an optimizing agent. It proceeds by breaking an organism into unitary “traits” and proposing an adaptive story for each considered separately. Trade-offs among competing selective demands exert the only brake upon perfection; non-optimality is thereby rendered as a result of adaptation as well. We criticize this approach and attempt to reassert a competing notion (long popular in continental Europe) that organisms must be analyzed as integrated wholes, with Baupläne so constrained by phyletic heritage, pathways of development, and general architecture that the constraints themselves become more interesting and more important in delimiting pathways of change than the selective force that may mediate change when it occurs. We fault the adaptationist programme for its failure to distinguish current utility from reasons for origin (male tyrannosaurs may have used their diminutive front legs to titillate female partners, but this will not explain why they got so small); for its unwillingness to consider alternatives to adaptive stories; for its reliance upon plausibility alone as a criterion for accepting speculative tales; and for its failure to consider adequately such competing themes as random fixation of alleles, production of non-adaptive structures by developmental correlation with selected features (allometry, pleiotropy, material compensation, mechanically forced correlation), the separability of adaptation and selection, multiple adaptive peaks, and current utility as an epiphenomenon of nonadaptive structures. We support darwin’s own pluralistic approach to identifying the agents of evolutionary change.

    My own view is that Natural Selection cannot account for much more than 1% of the features of living organisms. That figure is from calculations by Haldane, Kimura, and others. There is simply a shortage of population resources.

    Darwin’s “pluralistic view” suggested Natural Selection as the primary agent (accounting for 50% or more). I don’t think that is possible.

    Sal

  10. In #6 jerry wrote:

    “Natural selection exists but there definitely seems to be a built in regulator on how much change it can effect.”

    Indeed, there is; it’s called the environment. So long as environments are limiting, then stabilizing selection (the kind recognized by Edward Blythe) tends to predominate among all populations, and ecosystems reach a condition of stable equilibrium.

    However, if something happens so that environments are not necessarily limiting (as would typically happen to the survivors of a local, regional, or global mass extinction event), then there is little or no limit on the amount of variation that may arise among the members of such surviving populations. As is quite clear from the analysis of the “engines of variation” (see the list here: http://evolutionlist.blogspot......awman.html ), there is far more than enough variation to get almost anywhere you can go in “evolutionary design space”.

    Ergo, new, stable forms arise not by means of natural selection, but rather as a consequence of the necessarily temporary relaxation of stabilizing selection as a result of changes in the environment.

  11. Life has a specific design characteristic as described by Allen MacNeill above, namely the transcription and translation process. Such a process is found nowhere else in nature and while not exactly like the guidance system of a heat seeking missle, it does direct very complicated processes.

    They fit the two criteria set up

    1) they must precede the objects and/or processes whose assembly and operation they specify and regulate, (protein assembly but other processes too)

    2) like all forms of information, such programs must “run” in some kind of physical medium while specifying and regulating the assembly and operation of the object and/or process. (A very good description of DNA)

    ID has given a name to this phenomenon, namely FSCI or functionally specified complex information.

  12. sal asks:

    “Is it fair to say Spandrels De Saint Marco is closer to your position than that of Daniel Dennett or Modern Synthesis?”

    Yes, indeed, except that I believe that Gould, Lewontin (and later, Vrba) were, like Darwin, unwilling to take their principles to their logical conclusion: that adaptations (like species) are a figment of the human imagination, and do not actually exist in nature (or, to be even more precise, do not have to exist in nature).

  13. “Animals, by contrast, apparently have an “onboard” program that, if they are not killed by a particular age, will kill them via internal dysregulation.”

    It seems fairly wide spread and there is no non design reason for it. Why. I gave a design reason and it fits what we see.

  14. jerry:

    Insofar as FSCI is applied to the translation functions of the genetic code, I agree. That is, unless it can be convincingly shown that it is the case that there is a necessary relationship between the various levels of the genetic code and translation machinery, I believe that the origin of this code and the machinery that translates it is a genuinely open question.

    I also believe that, being “open”, such questions do not have answers that can be decided using empirical methods.

    Given the foregoing, however, it is still clearly the case that virtually the whole of biology is completely untouched by an ID theory that addresses only the origin of the FCSI of the genetic code and its translation machinery. After all, Darwin never mentioned these, and yet his theory (albeit in highly modified form) still adequately explains virtually all of the descent with modification that has occurred since the origin of the genetic code and its translation machinery.

    At least that’s the way it seems to me and to virtually all other evolutionary biologists (and most other scientists).

  15. The theory of evolution cannot even explain the evolution of the eye/ vision system…

  16. This is why, rather than simply asserting that things are designed, I have consistently asked “what structural and functional characteristics do unambiguously designed objects and processes (such as heat-seaking missles or thermostats) have, which can then be used as criteria to determine which natural objects and processes possess such structural and functional characteristics and may therefore legitimately be considered to be the product of design?

    Personally I don’t think you’ve gotten good answers.

    My answers:

    1. The Edge of evolution, which suggests protein-protein binding is a good example.

    2. Abel’s paper which argues for a non-trivial computer as a necessary requirement for life

    3. Convergent architechtures with good degrees of complexity (such as that described Homology a Concept In Crisis

    The reason I like convergence, is that one is alleviated of worries of post-dictive mental projections. The similarites in convergent lines are suggestive of design (much like how we recognize when a melody is being repeated, we know their is a great degree of deliberation versus mindless improvisation).

    Nelson and Wells use this example:

    Since homologies cannot be explained by equating developmental information with DNA sequences, some biologists have attempted to explain it by attributing it to similar developmental pathways. Although DNA determines the amino acid sequence of proteins essential for development, such pathways also involve other factors, such as the localization of cytoplasmic constituents in the egg cell, physical constraints resulting from the size of the embryo, and so on. (Wells, 1992)

    Efforts to correlate homology with developmental pathways, however, have been uniformly unsuccessful. First, similar developmental pathways may produce very dissimilar features. At the molecular level, it is well known that virtually identical inducers may participate in the development of non-homologous structures in different animals. (Gilbert, 1994) At the multicellular level, the pattern of embryonic cell movements which generates body form in birds also generates body form in a few species of frogs. (Elinson, 1987) And even at the organismal level, morphologically indistinguishable larvae may develop into completely different species. (de Beer, 1958) Clearly, similar developmental pathways may produce dissimilar results.

    Second, and more dramatically, similar features are often produced by very different developmental pathways. No one doubts that the gut is homologous throughout the vertebrates, yet the gut forms from different embryonic cells in different vertebrates. The neural tube, embryonic precursor of the spinal cord, is regarded as homologous throughout the chordates, yet in some its formation depends on induction by the underlying notochord while in others it does not. (Gilbert, 1994) Evidently, “structures can owe their origin to different methods of induction without forfeiting their homology.” (de Beer, 1958, p. 151) Indeed, as developmental biologist Pere Alberch noted in 1985, it is “the rule rather than the exception” that “homologous structures form from distinctly dissimilar initial states” (see Figure 2). (Alberch, 1985, p. 51)

    Production of similar forms from dissimilar pathways is also common at later stages of development. Many types of animals pass through a larval stage on their way to adulthood, a phenomenon known as indirect development. For example, most frogs begin life as swimming tadpoles, and only later metamorphose into four-legged animals. There are many species of frogs, however, which bypass the larval stage and develop directly. Remarkably, the adults of some of these direct developers are almost indistinguishable from the adults of sister species which develop indirectly. In other words, very similar frogs can be produced by direct and indirect development, even though the pathways are obviously radically different. The same phenomenon is common among sea urchins and ascidians (see Figure 3). (Raff, 1996)

    Even the classic example of vertebrate limbs shows that homology cannot be explained by similarities in developmental pathways. Skeletal patterns in vertebrate limbs are initially laid down in the form of cartilage condensations, which later ossify into bone. The sequence of cartilage condensation is the developmental pathway which determines the future pattern of bones in the limb. Yet similar bone patterns in different species (i.e., homologies) arise from different sequences of cartilage condensation. (Shubin, 1991) In the words of biologist Richard Hinchliffe: “Embryology does not contribute to comparative morphology by providing evidence of limb homology in the form of an unchanging pattern of condensation common to all tetrapod limbs.” (Hinchliffe, 1990, p. 121)

    The constancy of final patterns despite varying pathways has prompted developmental biologist Günter Wagner to suggest that homology might be due to conserved developmental “constraints”. (Wagner, 1989) Wagner’s critics, however, object that this notion is too vague to be useful. Although developmental constraints emphasize the fact that embryos are capable of producing similar end-points by a variety of routes, they do not constitute a naturalistic mechanism accessible to empirical investigation.
    So embryology has not solved the problem of homology. In 1958, Gavin de Beer observed that “correspondence between homologous structures cannot be pressed back to similarity of position of the cells in the embryo, or of the parts of the egg out of which the structures are ultimately composed, or of developmental mechanisms by which they are formed.” (de Beer, 1958, p. 152) Subsequent research has overwhelmingly confirmed the correctness of de Beer’s observation. Homology, whether defined morphologically or phylogenetically, cannot be attributed to similar developmental pathways any more than it can be attributed to similar genes. So far, the naturalistic mechanisms proposed to explain homology do not fit the evidence.

    The list of what would include, but not be limited to:

    1. protein-protein binding
    2. computer systems
    3. examples of convergence

    Sal

  17. To follow up on #14, would some ID supporter please explain why it is necessary to use ID to explain all of evolution, when it seems clear that all that is really necessary for evolution to occur is:

    1) variety (for which there more than enough “engines of variation” to do the job)

    2) heredity (does anyone wish to argue that this doesn’t happen?)

    3) fecundity (again, does anyone wish to argue that this doesn’t happen?)

    and

    4) demography: differential survival and reproduction

    Given a genetic code and the machinery to translate it into biological structures and functions (i.e. given 1, 2, 3, above), then it seems to me that 4 necessarily follows. Ergo, it is up to ID to show empirically that somehow it does not. That is, despite the fact that all three prerequisites are met, that somehow they just aren’t enough to produce the demographic changes that form the foundation for descent with modification.

  18. In #15 joseph asserts:

    “The theory of evolution cannot even explain the evolution of the eye/ vision system…”

    This is a baseless assertion. Unless you can produce or cite valid and convincing evidence to the contrary, it is no different from saying that the Eye Fairy produced the eye/vision.

  19. In #16 sal wrote:

    The Edge of Evolution, which suggests protein-protein binding is a good example.”

    A good example of what? Please elaborate…

  20. Alternatively, the similarites in convergent lines are also suggestive of similar developmental mechanisms, as indicated by evo-devo. So, what kind of empirical evidence must one have to decided between these two hypotheses? Simply showing that convergence happens doesn’t count; you have to show how such convergence happens (mechanisms, please, not airy speculation).

  21. Allen, just as an aside while we have your attention here. One of the many anti ID commenter’s here said that punctuated equilibrium only produces micro evolution and no macro evolution resulted as a result of it.

    Now I know our definition of macro evolution is different from what many who support Darwinian processes hold. Many of us define it as the origin of novel complex capabilities. We recognize that large morphological changes can happen with small changes to a genome but would not consider such a change as macro evolution.

    So is it your experience that PE is just micro evolution but done more quickly when a split-off population with a more limited gene pool produces morphological changes and essentially just produces a new variant.

  22. In other words, once again it seems to me that you are pushing back the problem of the origin of design to the origin of the mechanisms of developmental convergence, which (like the origin of life and the genetic code) are probably permanently beyond our reach (developmental mechanisms do not fossilize).

    So, we are left with the developmental mechanisms as they exist now, and must explain how they produce the convergent (and divergent) structures and functions for which they are the ultimate regulating mechanisms.

    Notice that word mechanisms. That’s what it all comes down to. Unsupported and untested (and probably untestable) hypotheses about the origins of those mechanisms isn’t science. When (and if) such mechanisms can and have been tested, they will then (and only then) be considered part of science.

  23. Allen, ID accepts all of micro evolution. ID is limited to a very small subset of evolution and to OOL and to the origin of the universe.

  24. I should say that ID does not dispute all of micro evolution. It has no quarrel with natural selection or your engines of variation. Only what they are capable of producing.

  25. In #21 jerry wrote:

    “One of the many anti ID commenter’s here said that punctuated equilibrium only produces micro evolution and no macro evolution resulted as a result of it.”

    I completely disagree, and would argue that this is a long-undermined (and continually weakening) position among die-hard holdouts for the mid-20th century “modern evolutionary synthesis”.

    jerry also wrote:

    “…large morphological changes can happen with small changes to a genome but would not consider such a change as macroevolution”

    In which case, your definition of “macroevolution” is so different from that used by evolutionary biologists as to be essentially useless. Clearly, if large phenotypic changes resulting from relatively small genetic changes do not qualify as macroevolution, then essentially nothing would. Ergo, if your assertion about ID supporters is correct, then they (like the old holdouts for the “modern synthesis”) are simply asserting (without evidence) that microevolution is all there is.

    That and magic, that is…

  26. in #21 jerry asks:

    “…is it your experience that [punctuated equilibrium] is just micro evolution but done more quickly when a split-off population with a more limited gene pool produces morphological changes and essentially just produces a new variant?”

    No; not necessarily. I believe that punctuated equilibrium is a “fact”. That is, it appears that evolutionary novelty originates during relatively brief periods of rapidly increased variation, interspersed among relatively long periods of evolutionary stasis during which stabilizing selection is the norm. How brief such periods of increased variation and novelty are can be as short as a single generation (as happens in polyploid plants) or a few thousand generations (a very short time indeed, even for sequoias).

    In other words, my understanding of the evidence for macroevolution indicates to me that it operates by fundamentally different mechanisms than microevolution, over time scales that are not necessarily correlated with the timescales of microevolution. The “modern evolutionary synthesis” was almost entirely focused on the mechanisms of microevolution, to the point that some of its adherents refuse to recognize macroevolution to this day. This doesn’t mean that it doesn’t exist; it only means that those individuals who deny its existence either don’t understand the evidence for it, haven’t encountered such evidence, or disbelieve it.

    I am currently working on a much more detailed examination of the mechanisms of macroevolution, which I will post on my blog. However, as sal pointed out, it is final exam time, and my students come first (after my family, of course). Also, I am producing a series of videotaped lectures on the Darwinian revolutions for Cornell, plus a new course on the evolution of the capacity for religion (also for Cornell), and so will have less time to participate here for the next two months.

    That is, if I can only tear myself away…

  27. To follow up on #14, would some ID supporter please explain why it is necessary to use ID to explain all of evolution, when it seems clear that all that is really necessary for evolution to occur is:

    1) variety (for which there more than enough “engines of variation” to do the job)

    2) heredity (does anyone wish to argue that this doesn’t happen?)

    3) fecundity (again, does anyone wish to argue that this doesn’t happen?)

    That is a good question, and I will attempt an answer since I think it is on the minds of many.

    You’ve actually forced me to clarify my thinking.

    There is no question Dennett’s algorithm (as you describe) will induce change. Certainly, Moalem has given good evidence that natural selection can induce changes in a population (like sustaining the frequency of sickle-cell anemia, diabetes, high colesterol, favism, etc.).

    The illustration I like to use is that of an intelligently designed car. Throwing rocks at the car will damage it. This is unquestionably a “change over time”. But is it the sort of change that explains the other features of the car?

    We might argue, based on population genetics and Kimura’s math, that Dennett’s algorithm applies to maybe 1% at most to the population. But even granting that, we still have no requirment to invoke ID. So why invoke ID.

    My best answer at this time is that ee are still confronted with the appearance of design. The neutralists (like Nei) have suggested the apperance of design is merely an artifact of our imagniation, a postdictive projection. Thus, in their mind, there nothing that is need to be explained in the first place. This is very close to Shermer’s view.

    But the problem of convergence and that of computers seems to resist the post-dicitive viewpoint.

    Let us say for the sake of argument, design in OOL and computers should be a separate question to that of the rest of biological evolution.

    Granting that, I think the problem of convergence still circumstantially suggests design. That was not lost upon Simon Conway Morris

    believe the topic of convergence is important for two main reasons. One is widely acknowledged, if as often subject to procrustean procedures of accommodation. It concerns phylogeny[supposed evolutionary lineage], with the obvious circularity of two questions : do we trust our phylogeny and thereby define convergence (which everyone does), or do we trust our characters to be convergent (for whatever reason) and define our phylogeny? As phylogeny depends on characters, the two questions are inseparable

    Even so, no phylogeny is free of its convergences, and it is often the case that a biologist believes a phylogeny because in his or her view certain convergences would be too incredible to be true.

    During my time in the libraries I have been particularly struck by the adjectives that accompany descriptions of evolutionary convergence. Words like, “remarkable”, “striking”, “extraordinary”, or even “astonishing” and “uncanny” are common place…the frequency of adjectival surprise associated with descriptions of convergence suggests there is almost a feeling of unease in these similarities. Indeed, I strongly suspect that some of these biologists sense the ghost of teleology looking over their shoulders.

    Selection has been used to explain convergence, but if selection can be shown to be a minor mechanism, then is strengthens (not necessarily proves) the case for ID.

    It should be apparent then, why I have put a lot of stake in Kimura and Nei’s mathematical arguments against selection being a large component of evolution. They have shown that perhaps Dennett’s algorthim is applicable to only a small portion of evolution. I put the figure at around 1%, but I’m quite willing to amend that view as more information arrives.

    If I may say, even if ID is true, aside from philosophical or theological considerations, “so what?”

    My view is that convergence will help us advance medical science. If ID proponents are able to exploit convergences or species comparisons to advance medical science, then ID might have a legitimate place in empirical science. Until such time, I think ID will mostly be outside the official mainstream.

    Philosophy and theology have a way of being divisive, but useful medicine and healing will have a way of fostering cooperation, imho.

  28. Hi Allen,

    I was inteersted in this snippet from an earlier comment–#26–(my emphasis):

    No; not necessarily. I believe that punctuated equilibrium is a “fact”. That is, it appears that evolutionary novelty originates during relatively brief periods of rapidly increased variation, interspersed among relatively long periods of evolutionary stasis during which stabilizing selection is the norm.

    Are you saying that these punctuations are due to actual increased levels of variation? Could it also be possible that what we are seeing (especially in the fossil record) is not actual increases in levels of variation, but instead periods of increased levels of ecological opportunity for variation to be “segregated” into unique populations?

  29. In #27 sal wrote:

    The neutralists (like Nei) have suggested the apperance of design is merely an artifact of our imagniation, a postdictive projection. Thus, in their mind, there nothing that is need to be explained in the first place. This is very close to Shermer’s view.

    It is also very close to mine. However, if this position is the most warranted, given the evidence available now, this means that the core of both ID and the core of the “modern synthesis” – that all significant evolution is adaptive – is gone, and all that remains is descent with modification, about which most of us agree.

  30. For myself, I would prefer not to hazard a numerical estimate of the percentage of a given organism’s phenotype that is the product of “adaptive” selection. On the contrary, what is interesting to me is why some components of the phenotype (and some components of the genotype, not necessarily correlated) seem stable over time, while others “drift” at velocities close to those predicted by the neutral theory. If the former are what “Darwinists” refer to as “adaptations”, then what makes them such is semantics, not science.

    Unless, of course, one believes that science is completely reducible to semantics…

  31. In #28 Dave Wisker asked:

    “Are you saying that these punctuations are due to actual increased levels of variation?”

    No; just the other way around – that increased levels of variation (due to the relaxation of stabilizing selection) are a consequence of the event that initiated the “punctuation”, rather than the cause.

    At least most of the time. There are cases of “punctuation” in which a new adaptive zone was opened by the formation of a novel variation (the origin of eukaryotes and the origin of multicellularity come to mind). In such cases, the novelty precedes (indeed, drives) the “punctuation”.

    “Could it also be possible that what we are seeing (especially in the fossil record) is not actual increases in levels of variation, but instead periods of increased levels of ecological opportunity for variation to be “segregated” into unique populations?”

    Exactly.

  32. 19

    Allen_MacNeill

    04/27/2009

    9:16 am

    e In #16 sal wrote:

    “The Edge of Evolution, which suggests protein-protein binding is a good example.”

    A good example of what? Please elaborate…

    I think you’ve scored a point on me with that one. I think it deserves more elaboration on my part, but I don’t think I have a strong answer at this time.

    Alternatively, the similarites in convergent lines are also suggestive of similar developmental mechanisms, as indicated by evo-devo. So, what kind of empirical evidence must one have to decided between these two hypotheses? Simply showing that convergence happens doesn’t count; you have to show how such convergence happens (mechanisms, please, not airy speculation).

    We might be able to eliminate one hypothesis, but estabilishing ID outside of a circumstantial case, I don’t think is possible. The ID case can be overturned (falsified) by the discovery of a mechanism, but formally proving it is another story.

    So I think you score another point.

    Perhaps a more basic question, and one that I should have asked you earlier. Does biology look designed to you. If it doesn’t look designed to you, then it explains why we may be talking past each other. If it doesn’t look designed, then all the other ID arguments would appear moot.

    So, what kind of empirical evidence must one have to decide between these two hypotheses?

    We have to show that Evo-Devo doesn’t explain the majority certain convergences. Body plans may be realized by some of the same control genes but as Nelson and Wells argue, the developmental pathway (the order and mechanics of construction) are different. Evo-Devo might argue that development occurs with the same vocabulary, but I think ID proponents will argue that the same features are arrived at using different recipes.

    Perhaps this is legitimate topic of much more elaborate discussion and learning. Certainly for me.

    Formally speaking, elimintating Evo-Devo wouldn’t establish ID anymore than it would establish the Flying Spaghetti monster as a cause.

    Empirically speaking, I think we can legitimately argue whether something looks designed (in as much as things look analogous). Ultimate causes and mechanism would probably be formally inaccessible.

    In such cases, some like Trevors and Yockey, have opted for declaring questions of mechanisms as “undecidable”.

    I think all that can be formally done is establish the strength of analogies and falsify possible mechanisms.

    Suggesting that intelligence is a mechanism is a tough call since there are good arguments against the idea that intelligence is reducible to mechanism in the first place.

    So you may ask “why do you,Sal, defend ID as science”. Answer: I usually don’t. I think ID is true, but you won’t see me attempt to make formal case, only a circumstantial one.

  33. I should mention this aritcle by Lewontin:

    Santa Fe Winter 2003

    The difficulties of the concept of fitness are, unfortunately, much deeper than the problem of frequency and density dependence. The problem is that it is not entirely clear what fitness is. Darwin took the metaphorical sense of fitness literally. The natural properties of different types resulted in their differential “fit” into the environment in which they lived.
    The better the fit to the environment the more likely they were to survive and the greater their rate of reproduction. This differential rate of reproduction would then result in a change of abundance of the different
    types.

    In modern evolutionary theory, however, “fitness” is no longer a characterization of the relation of the organism to the environment that leads to reproductive consequences, but is meant to be a quantitative expression of the differential reproductive schedules themselves.
    Darwin’s sense of fit has been completely bypassed.

    Moalem’s book has basically shown that Darwin’s original notion of fitness has been bypassed, and reinforced the objection Lewontin has put forward about the nebulous definition of fitness.

    Sickness has become a virtue, and that is contrary to Darwin’s conception of virtue.

  34. Allen and jerry,
    i think we have a misunderstanding, mainly due to the strange definitons of terms used here on UD. first, Punct eq is fundamentally about species-level changes in the fossil record. this fits the definition of macroevolution (evolution at species level and above) used by evolutionary biologists. However it does not fit that used by jerry et al, who define macroevolution as evolution of novel complex traits (let’s call the former macroEB and the latter macroUD.) thus, all of the patterns described by GOuld would fit under jerry’s terms as microevolution. GOuld pointed out that separation of higher level taxa occurred in a graded manner with lots of intermediates between, for example, orders, that may contain novel complex traits. thus evolution of higher level taxa did not fit the pattern of PE. in other words evolution at the species level is jumpy but at the higher levels is smooth. bc novel complex traits are almost always associated with higher level divisions, the “jumpy” pattern of PE applies to macroEB but not to macroUD. FOr example, feathers didn’t appear all at once but by a gradual accumulation of branches in different families and genera of theropods. but there are v few transitionals at the species level. so there were “jumps” between species but smooth gradations between higher taxa and the novel complex trait.

  35. David Wisker said

    ““Could it also be possible that what we are seeing (especially in the fossil record) is not actual increases in levels of variation, but instead periods of increased levels of ecological opportunity for variation to be “segregated” into unique populations?””

    And Allen MacNeill said

    “Exactly”

    This is just micro evolution and not dissimilar than what artificial selection could create with a specific gene pool.

  36. But I am getting the feeling that Allen is saying that in addition to just a reshuffling of the genetic elements during punctuated equilibrium we are also getting a lot of intense variation creation to the gene pool during the supposedly punctuated equilibrium events.

    And somehow this is also facilitated by the small populations and isolated gene pools which are more limited.

  37. Allen,

    “Given a genetic code and the machinery to translate it into biological structures and functions (i.e. given 1, 2, 3, above), then it seems to me that 4 necessarily follows.”

    That’s one of the big issues I have with this whole arguement. Given a genetic code then…..

    How can we just say that? The genetic code is information and meta-information of specified complexity. The only thing we have discovered that can produce similar information and meta-information of specified complexity is intelligence.

    The genetic code is the biggest reason to believe there is intelligence behind what we see. How can we ignore that fact, skip past it and then just discuss the items you listed?

  38. Sal, consider:

    Is design part of reality, a phenomenon, an observable event?

    Yes (Let’s just all agree to this and not have a silly argument about semantics or metaphysics.)

    Can design be detected?

    Yes, if one accepts the utility of the scientific method. To say that it can’t be is to put a strange and sad limitation on science.

    Should design be limited to humans?

    Ironically, if one is an hard-core Darwinian one should insist on a big, loud “no”. After all, if man developed an ability to design via evolution what would keep some other life form? Dolphins, maybe, or sea otters LOL.

    Does ID succeed in ascertaining design for certain complex objects and events?

    That’s the question to discuss.

  39. “The theory of evolution cannot even explain the evolution of the eye/ vision system…”

    This is a baseless assertion.- Allen MacNeill

    Geez then all YOU would have to do is demonstrate otherwise.

    However I can offer the following:

    Andrea Bottaro said the following over at the panda’s thumb:

    Eyes are formed via long and complex developmental genetic networks/cascades, which we are only beginning to understand, and of which Pax6/eyeless (the gene in question, in mammals and Drosophila, respectively) merely constitutes one of the initial elements.

    IOW the only evidence for the evolution of the vision system is that we have observed varying degrees of complexity in living organisms, from simple light sensitive spots on unicellular organisms to the vision system of more complex metazoans, and we “know” that the first population(s) of living organisms didn’t have either. Therefore the vision system “evolved”.

    Isn’t evolutionary “science” great!

    I say the above because if Dr Bottaro is correct then we really have no idea whether or not the vision system could have evolved from a population or populations that did not have one.

  40. In #27 sal wrote:

    The neutralists (like Nei) have suggested the apperance of design is merely an artifact of our imagniation, a postdictive projection. Thus, in their mind, there nothing that is need to be explained in the first place. This is very close to Shermer’s view.

    It is also very close to mine. However, if this position is the most warranted, given the evidence available now, this means that the core of both ID and the core of the “modern synthesis” – that all significant evolution is adaptive – is gone, and all that remains is descent with modification, about which most of us agree.

    Allen,

    In the event I’m pulled away from this thread because of other committments, I hope we can resume this fruitful discussion. It has been a delight!

    Let me relate an experience that has enlightened me toward your view of the the ID/EB debate.

    I had studied classical piano performance before changing my undergraduate degree to the engineering disciplines.

    I was listening to my piano teacher playing Bach, and I thought to myself, “what a mindless conglomeration of sounds”. I’m sure my teacher would be horrified, as well as many Bach enthusiasts for my heretical view of Bach.

    To this day, I fail to hear any semblence of genius in certain Bach pieces. Yet to others, what strikes me as mindless randomness, is divine Genius! In contrast when my teacher played Wagner-Lizt’s Liebestod, I thought “Genius!”.

    Here is an interesting anectdote about Joshua Bell playing Bach in the Subway on a 3.5 milliion dollar violin. This proverbial story is very applicable to the ID/EB debate.

    It seems to me we computer engineers at UD and the ID movement look at life and think to ourselves: “Genius, the designer is a computer genius!” while others are less astonished. I think getting others to view ID though the lense of an ID-sympathetic engineer is like getting me to learn to appreciate Bach (yes, I know that is heresy for a classical musician like myself to admit).

    I have stated that the strongest circumstantial case for design is in the area of computational and information processing systems involved in the Origin-of-Life.

    I’m not as versant in the fields of biological evolution that are of interest to you. And I will concede that I cannot articulate a defense of ID in the area of convergent evolution and protein-protein binding sites to a degree I feel comfortable with. Suffice to say, it is an idea think is true, but hold more tentatively than the ideas I put forward regarding OOL.

  41. Allen MacNeill:

    In which case, your definition of “macroevolution” is so different from that used by evolutionary biologists as to be essentially useless.

    LoL!!! With their use of macroevolution no one debates it!!!

    Therefor using it to defend some position is deceptive at best.

  42. Sal:

    Addressing your original point about Meloim’s book, NS is nothing more than the “Better Machine”. What I mean is this: put something in the machine, it scours for a slight improvement, then amplifies it, producing in the end—its output—something that is “better”. With endless repititions of this cycle, ALL THINGS are possible.

    So, if I compare A and B, for me to say that NS is involved only two things are necessary: First, that A and B are alive, since being alive means, as with all living organisms, it can replicate; and Second, A is “better” than B in some respect. In this second condition ANY aspect of organisms A and B can be considered.

    Let’s note that under these conditions, it is IMPOSSIBLE to negate NS if a third condition is invoked: the correlation of parts; that is, if Part A becomes worse, than Part B “might” become better. It’s a zero-sum game: each plus balanced by a minus, and vice versa. So, if a fish goes “blind”, no problem for NS, this simply means that the organism is “better” for its environment since this “loss” is, presumably(!), balanced by a “gain” in some other, more needed function.

    Thus, this “Better Machine” can explain ALL things. Isn’t it wonderful. You see, it’s ALL-powerful, and so, we should simply bow to the majesty of NS. It’s a shame we just don’t get it here at UD!

    Alan, as to “adaptations”, I’ve said for a long time that if Darwin’s book was entitled the “Origin of Adaptations” that I would be 100% behind it. Does that mean I subscribe completely to NS? No. Why? Because I think there are “adaptionist” programs “built into” the genome that really run the show. If this is the case (which I believe, and think will eventually be demonstrated), then NS is a outcome, not a cause (per Wm. Provine).

    I haven’t read all of the above posts, but if you want to refer me to one or the other, that’s fine.

  43. Hi jerry,

    But I am getting the feeling that Allen is saying that in addition to just a reshuffling of the genetic elements during punctuated equilibrium we are also getting a lot of intense variation creation to the gene pool during the supposedly punctuated equilibrium events.

    Not exactly. Allen is not saying he thinks the events involve intense periods of variation “creation”. He is saying he thinks relaxation of stabilizing selection allows more of the existing variation to be expressed.

    And somehow this is also facilitated by the small populations and isolated gene pools which are more limited.

    Not quite, as I see it. The expanded ecological opportunities (i.e., new niches) allow the variation to be segregated in these unique gene pools. It has nothing to do with mechanisms of increasing the generation of variation.

  44. jerry writes:

    This is just micro evolution and not dissimilar than what artificial selection could create with a specific gene pool.

    Pretty much. However, I may differ from Allen in the following, so I don’t want to be seen as putting words in his mouth. Divergence depends primarily on reproductive isolation. Once the divergence has been established, novel variation (be it mutational or recombinational) that occurs in one lineage will not occur (with rare exceptions of convergence) or be transferred to another–only to its own descendants. Clusters of closely related, recently developed lineages become higher taxa such as genera and families, and are often so similar due to recent ancestral relationships that they generate intense taxonomical debate. Even higher taxa such as orders and classes are easier to discern due to the extinction of older, intermediate lineages.

    That’s how I see it. It’s very close to what was argued in that paper on macroevolution by Charlesworth et al.

  45. This is why, rather than simply asserting that things are designed, I have consistently asked “what structural and functional characteristics do unambiguously designed objects and processes (such as heat-seaking missles or thermostats) have, which can then be used as criteria to determine which natural objects and processes possess such structural and functional characteristics and may therefore legitimately be considered to be the product of design?

    In a phrase: “they look like machines”.

    Other objects such as rocks, clouds, rivers, storms, hurricanes, planets, stars — they don’t look like machines.

    You’ve certainly forced me to consider why something looks like a machine. That perception certainly isn’t unique to ID propoenents.

    Formalizing the reasons why seem difficult, but I’m sure it relates to the issue of analogies and metaphors.

    You’d think an engineer could articulate the reasons why they look like mahcines, but perhaps the perception seemed so intuitively obvious, that its been difficult to state formally.

  46. “what structural and functional characteristics do unambiguously designed objects and processes (such as heat-seaking missles or thermostats)

    A place to start is with man-made objects.

    I’ve sometimes suggested to chemists, “make a polymer that will obviously suggest to a chemist that it is man-made”.

    A very strong tell-tale sign is that it is realtively easy to form analogies and metaphors with other objects. Furthermore these analogies and metaphors shouldn’t be the sort that arise spontaneously. It would even be better that nature would generally work against the formation of such analogies.

    A good example: Sand Castles.

    The “cell as a computer” I blogged about considerably.

    Flying birds, their analogy to aiplanes seems hauntingly compelling. The Wright brothers used their study of birds to create airplanes. They copied the designs of nature.

    It seemed that only a limited number of architectures are permissible to enable flight. So even in the case where man copies nature, the machine analogy still applies. Only certain architectures seem to work.

    We recognize a controlled-flying vehicle from a drop of water or a meteor dropping from the sky. The architectures have recognizable features amenable to making analogies.

    It is hard if not possible to project the salient features of controlled flight onto meteorites or clouds, but it is readily easy to identify systems between:

    1. airplanes
    2. butterflies
    3. birds

    We have common elements of:

    1. controlled propulsion
    2. guidance
    3. steering
    4. navigation
    5. sensing
    6. lifting systems
    These concepts are completely inapplicable to most other macroscopic objects, even things that are alread airborne.

    Is the assessment subjective? Yes, imho. Does the subjective element invalidate it from scientic inquiry? That would appear to be a subject of debate, but I’d say, “no”.

    The same considerations apply to whether we label something as “sickness” or “disease” or “broken”.

    Are the labels scientifically justified? I’d say yes, although, formally speaking nothing in physics or chemistry or mathematics demands we use such anthropcentric labels.

    I think science would be at a standstill if we did not permit (dare I say encourage) usage of such subjective labels.

  47. Quite a number of engineers in the areospace industry are sympathetic to ID.

    Even though much of modern aviation owes itself to immitation of nature, there is still a strong sense that birds have a design that enables them to fly. It wouldn’t take a lot of deviation from that design to preclude birds from flying.

    Anyone who has worked in the aerospace field appreciates how tight the constraints are to create a flying machine. Not so easy.

  48. Regarding man imitating machines found nature, it seems that there are certain platonic forms that achieve certain functions.

    These constraints are defined by physics (as D’Arcy Thomspon asserted). However, the fact that physics constrains the architecture of a controlled flying vehicle to be a certain way, it does not imply the architecture will spontaneously emerge.

    We can scientifically say:

    1. whether a physical object is analogous to a platonic ideal

    2. whether that realization of a platonic ideal is probable by unguided processes

    I don’t think we formally say intelligence was the cause, but we can assert the above two considerations scientifically. In such case, we can say something is “designed”, even in the sense that an physiologist or engineer would argue something has a design or architecture.

    Asserting the above two considerations constitutes detection of specified complexity in an informal sense.

  49. Dave Wisker in #43 and #44:

    Exactly! Couldn’t have written it better myself…indeed, I apparently didn’t write it as well as Dave did.
    Thanks for the clarification!

  50. sal in #45:

    “You’d think an engineer could articulate the reasons why they look like mahcines, but perhaps the perception seemed so intuitively obvious, that its been difficult to state formally.”

    Exactly, Sal! It’s always the things that seem most “obvious” to us that are the most difficult to actually analyze and explain. This is one of the basic principles of evolutionary psychology: that the things we do without thinking about it are often the most complex things we do (i.e. require the most sophisticated and rapid computational resources). As just one example, it takes an immense amount of computing power to make it possible for a computer to accomplish (and accomplish badly, with many false negatives) what a nearly new-born infant can do literally without thinking about it: recognize if something in their visual field is “behaving intentionally” or not. Lots of research has gone into this, and all of it points to the hypothesis that our minds (and probably the minds of all animals, if not all living organisms) include an “innate agency detector”. It is likely that this detector is a combination of analog processors (i.e. “hard-wiring”) and digital programs (i.e. algorithms), the overall output of which is an almost effortless identification of potentially intentional “agents” in our environment. So good is this detector that it very rarely produces false negatives (i.e. it very rarely mistakes intentional agents for non-intentional processes), but it does so at the price of many false positives (i.e. paranoia/pareidolia, and – perhaps – ID).

  51. In #48 sal pointed out:

    We can scientifically say:

    1. whether a physical object is analogous to a platonic ideal

    Easy!

    2. whether that realization of a platonic ideal is probable by unguided processes

    Very, very difficult.

    How, exactly (and using empirical methods) can one do this, without simply arguing via analogy?

  52. sal asserted:

    In such case, we can say something is “designed”

    But this is precisely the point: how (in the absence of direct or indirect empirical observation of the action of a designer) can we say this? You have provided no empirical criteria for doing so, and neither has any other ID supporter (beyond arguments by analogy and assertion).

    Asserting the above two considerations constitutes detection of specified complexity in an informal sense.

    Again, this exactly the problem: asserting something doesn’t make it true, especially if one is only trying to “constitute” something in an informal sense. In science we require more than assertions and arguments by analogy. We require empirical tests that unambiguously distinguish between opposing hypotheses. Until ID can provide such, it will not be considered to be science by the people who actually do science for a living and as an avocation.

  53. It is likely that this detector is a combination of analog processors (i.e. “hard-wiring”) and digital programs (i.e. algorithms), the overall output of which is an almost effortless identification of potentially intentional “agents” in our environment. So good is this detector that it very rarely produces false negatives (i.e. it very rarely mistakes intentional agents for non-intentional processes), but it does so at the price of many false positives (i.e. paranoia/pareidolia, and – perhaps – ID).

    Unlike some of my colleagues, I take no offense that you might suspect there are physiological causes that incline some toward accepting ID than others. This almost seems blatantly apparent by the over-representation of engineers in the ID community. So I have already tentatively accepted there is a physiolgoical relation (ah, yes I’ve made another heretical statement for the day).

    When I was in flight school, aspiring pilots receive special training to ingrain in them not to trust their ordinary sensory perceptions of motion. The human mind and sensory organs can play serious tricks on one’s perception, and for pilots flying at night and in clouds, the misperceptions rooted in our natural physiology could be deadly. Pilots have to learn to distrust their intuition, their physical sense of motion, and trust their instruments (made by engineers like me.) :-)

    So I take no offense in attempts to discern where our perceptions may be misleading. People should value the inquiry.

    The question then is whether the engineering mindset would be an asset or liability in assessing if something is designed. One might argue, it would be a liability since an engineer would be more inclined to describe things in terms of design.

    But the problem is that engineers are a respected discipline that share close kinship with empirical scientists. Even if you were to prove conclusively that engineers might have physiological dispositions, it would be hard to convince them that their perceptions of design are completely wrong.

    So what is the resolution? I have attempted, informally, to argue for the importance of analogies and metaphors. At least these are somewhat more amenable to empirical investigation.

    Even granting that the analogies can be scientifically demonstrated, the ultimate question of whether “God did it” is probably out of the reach of science. But the exploration of analogies and metaphorse seems amenable to empirical inquiry.

  54. Salvador says,

    It seems to me we computer engineers at UD and the ID movement look at life and think to ourselves: “Genius, the designer is a computer genius!” while others are less astonished.

    But I have invoked here at UD a theorem that students learn in a first course in the theory of computation, and have sketched a simple proof that there is no algorithm to decide if the function of a program is designed. No IDer has challenged my argument.

    I feel wonder at the physical universe, including life, and choose to attribute the existence of all to a Creator. But I must oppose claims that one person can prove to another that design is a property of the cosmos. There are modes of understanding that are more valuable, in terms of individual human experience, than math and science.

    It seems that Jesus never proved a theorem or tested a hypothesis.

  55. 55

    Sal Gal,

    “It seems that Jesus never proved a theorem or tested a hypothesis.”

    That’s true, but we should also remember that Paul told us that the natural world speaks to God’s design, and that all know God through it, so that all are without excuse.

  56. But this is precisely the point: how (in the absence of direct or indirect empirical observation of the action of a designer) can we say this

    To clairfy, this is an assertion of “design” in the common sense that a biologist might refer to the “design” of an organ.

    It makes no formal claim that the origin was intelligence.

    ID offers the falsifiable assertion that only intelligence makes certain designs. The assertion is not provable, but is falsifiable in principle for various specific artifacts.

    To claim “D” (design) that a design of some sort exists can often have broad agreement even by opponents of ID. It is customary to refer to the “design” of the cell, etc.

    There are somethings where we can’t agree if something has a design. For example, certain parts of “junk DNA”.

    You are correct to say that the claim of “ID” (as opposed to just “D”) is merely an assertion.

    The claim of “ID” is not a provable assertion, but it is falsifiable at least with respect to specific artifacts (i.e., the genetic code).

    I suppose in that sense ID can be labeled scientific, but you won’t see me make that case vigorously.

    So I recognize your concern that the claim of “ID” is a merely an assertion of a hypothesis, it is not a proof of a hypothesis. In otherwords, I agree with you.

  57. Sal Gal,

    Pardon my intrusion, but I just read your post about Rice’s Theorem you linked to. ID in general and the explanatory filter in particular don’t claim to be able to sort design from non-design perfectly: they fail when designed objects appear to be not designed (false negatives), and can theoretically fail on a false positive (therefore ID is falsifiable), although no known example of a false positive has been shown.

    Therefore, the explanatory filter just claims to be highly reliable, not a formally complete method of sorting objects into two classes.

    Just my two cents. Thanks for your contributions, btw, I enjoy them.

    Atom

  58. But I have invoked here at UD a theorem that students learn in a first course in the theory of computation, and have sketched a simple proof that there is no algorithm to decide if the function of a program is designed. No IDer has challenged my argument.

    I’m inclined to agree that, “no algorithm to decide if the function of a program is designed” in ALL cases.

    It does not mean we can’t detect design in some cases. If we find bit patterns that are copies of known designs, we have detected designs.

    The Explanatory Filter does not detect all designs:

    Masters of stealth intent on concealing their actions may successfully evade the explanatory filter. But masters of self-promotion intent on making sure their intellectual property gets properly attributed find in the explanatory filter a ready friend.

    Bill Dembski
    Mere Creation

    There is reason I have staked a lot on the question of analogies and metaphors rather than some hypothetical algorithm that can universally detect intention or design.

    Given that “masters of stealth” can evade detection, I would agree that “no algorithm to decide if the function of a program is designed” in ALL cases.

  59. 59

    Allen MacNeill,

    “So good is this detector that it very rarely produces false negatives (i.e. it very rarely mistakes intentional agents for non-intentional processes), but it does so at the price of many false positives (i.e. paranoia/pareidolia, and – perhaps – ID).”

    Take the first part of your sentence that reads “So good is this detector that it very rarely produces false negatives (i.e. it very rarely mistakes intentional agents for non-intentional processes)”, which is contradictory to Darwin’s claim that events such as the dog noticing the wind moving the parasol and mistakenly thinking it was an agent moving it, and through more of the same error produced religion in an ongoing false negative until the world’s religions were hard-wired into us. Of course, you’re right, we don’t produce such false negatives, as you pointed out, so Darwin’s theory about more of the same false negatives accounting for religion is not likely, for if it were continued, as he thought it was, the false negative would have become more acute, if it really was more of the same. No, somewhere along the line, even taking such a ridiculous idea at face value, humans did an about face, and started acting the opposite in producing false negatives and correctly not seeing agency when there was none, so Darwin’s idea of the infancy and growing stages of religion (which are based on false negatives) is shabby. Remember, Darwin said “In the distant future I see open fields for far more important researches. Psychology will be based on a new foundation, that of the necessary acquirement of each mental power and capacity by gradation.”
    And as far as the second part of your sentence “but it does so at the price of many false positives (i.e. paranoia/pareidolia, and – perhaps – ID)” is to beg the question, for the question at hand is whether ID is recognizable–and that is an ongoing debate, to answer it in the negative and assume it a finished question is not an answer.

    And, I’ll ask you again, pertaining to Darwin’s quote above, how do we, by successive gradations, produce the ought from what was and is?

  60. Clive says,

    That’s true, but we should also remember that Paul told us that the natural world speaks to God’s design, and that all know God through it, so that all are without excuse.

    A slide presentation of Bob Marks reminds me of this passage from Paul’s first letter to the Corinthians:

    For since in the wisdom of God the world through its wisdom did not know him, God was pleased through the foolishness of what was preached to save those who believe. Jews demand miraculous signs and Greeks look for wisdom, but we preach Christ crucified: a stumbling block to Jews and foolishness to Gentiles, …

    I see ID as a program of “wise” identification of “miraculous signs.” In my opinion, the scientism of ID contributes to spiritual ills, rather than remedies them.

  61. 61

    Allen MacNeill,

    And secondly, using this line of thinking “In the distant future I see open fields for far more important researches. Psychology will be based on a new foundation, that of the necessary acquirement of each mental power and capacity by gradation,” I can see why Darwin had his “horrid doubt” that his thoughts were invalid, because they were the end result of dog-like thinking. This line of thinking, of course, includes this line of thinking. It becomes self-refuting. It is, itself, subject to the same doubt that hangs about any of the other “false” thinking that it supposedly produces. It sounds like special pleading to me. And, to be honest, all of evolutionary psychology’s supposed answers for the wrong-ness of any developed thought, that somehow do not also apply to those thoughts, is a perpetual special pleading.

  62. 62

    Sal Gal,

    Nope. Nothing is being expected except looking at ordinary nature. No sings or visions, just good ol’ natural processes. Signs are, by definition, deviations from the natural account. Do you really think that’s what ID is about? Miracle detection?

  63. Clive:

    Take the first part of your sentence that reads “So good is this detector that it very rarely produces false negatives (i.e. it very rarely mistakes intentional agents for non-intentional processes)”, which is contradictory to Darwin’s claim that events such as the dog noticing the wind moving the parasol and mistakenly thinking it was an agent moving it, and through more of the same error produced religion in an ongoing false negative until the world’s religions were hard-wired into us.

    You seem to be confusing false positives with false negatives.

  64. Clive:

    Apparently I was insufficiently clear; what I meant to infer was that religion has been explained by several anthropologists and evolutionary psychologists as a side-effect of an “innate intentional agency detector/algorithm” that produces multiple false positives, not false negatives. That is, the tendency to infer agency in objects/processes in which such agency does not, in fact, exist (not the other way around).

    There is, of course, yet a third possibility: that our “innate intentional agency detector / algorithm” did indeed evolve via non-guided processes, but that once in place it made it possible for us to detect what would otherwise be undetectable: God/the Intelligent Designer. This third alternative would probably satisfy those who enjoy irony and what appears to be the very twisted sense of humor on the part of an Intelligent Designer who would put so much effort into creating beetles, but so little effort into creating roses that we had to finish the job for Her).

  65. Darwin’s expression of “horrid doubt” was specifically about the idea that we might find that humans and monkeys use essentially the same kinds of mental processes. Rather than causing most primatologists “horrid doubt”, this idea presents an interesting and testable research hypothesis (which, BTW, has been mostly – but not entirely – refuted by their research).

  66. Clive asks:

    “…how do we, by successive gradations, produce the ought from what was and is?”

    We do not, neither by successive gradations nor by sudden, large leaps. That is, one cannot derive an “ought” from an “is”.

  67. Clive:

    Your comments about evolutionary psychology appear deeply incoherent to me, a trained evolutionary psychologist. What exactly are you trying to assert about evolutionary psychology, and upon what empirical evidence are you basing such assertions? And please be patient, I’m slow and need all of the logical steps filled in…

  68. Salvador says,

    We can scientifically say:

    1. whether a physical object is analogous to a platonic ideal

    2. whether that realization of a platonic ideal is probable by unguided processes

    1. Unlike Allen, I have problems with the notion that Platonic ideals are in the scientific domain of discourse. Contemporary science (though not every living scientist) eschews metaphysics, and I don’t know what could be more metaphysical than a discussion of the relation of physical observations to unobservable ideals.

    2. As a matter of basic epistemology, it is impossible for us to rule out through inferences on physical observations the possibility of a deterministic universe. To be a bit more concrete, there is no scientific “proof” that we will not eventually learn to control quantum experiments in such a way that apparent indeterminism vanishes. There are, in fact, physicists who entertain the notion that “randomness” is actually high-dimensional, deterministic chaos. You should be aware that quantum mechanics has been re-derived in terms of algorithmic information theory.

    I have posed to Bill Dembski and to Paul Nelson the question “What is the probability of the universe?” Neither replied, and I would suppose that it is because they are both strong enough philosophers of science to know that we cannot, as scientists, step outside the domain of discourse of science — the physical universe, whatever that is — to speak of a universe-generating mechanism.

    Cosmological ID based on arguments from improbability (say, the improbability of “fine tuning” of physical “constants”) cannot get off the ground as science, simply because scientists qua scientists cannot associate a probability distribution with the one and only universe. (Here I treat a “multiverse” as a universe.) I believe that this problem carries over to biological ID.

    We have no way of saying, ultimately, whether randomness is real. Most physicists believe at present that it is, on the basis of their collective experience, but they have no “proof.” Perhaps a physical system evolving deterministically in 11 dimensions looks random in 4 dimensions. This is a case in point that scientific belief is necessarily tentative.

  69. I support the concept of “Platonic ideals” only insofar as this term refers to the concepts that we form regarding regularities that we perceive in the objects and processes in the universe around us. I do not believe that such “ideals” are somehow separate from those objects and processes, nor that they can somehow exist in the absence of such objects and processes. Indeed, I believe that it would be literally impossible to verify any of these ideas except the very first, which is the only one I support.

  70. Ergo, asserting that some object or process is “analogous to a Platonic ideal” is merely to say that the object or process is sufficiently similar to an already established regularity in nature that we can confidently subsume it in same concept.

  71. Personally, I prefer the term “unpredictable” to the term “random”. The first actually includes the criterion by which one would classify an event using it, whereas the second is neither obvious nor includes any criteria whatsoever to decide to which processes it might be applied.

  72. In such case, we can say something is “designed” . . .But this is precisely the point: how (in the absence of direct or indirect empirical observation of the action of a designer) can we say this?

    One branch of ID says that if something made of many interacting parts the removal of any which causes it to cease to function indicates that something to be designed.

    Another branch says that if a pattern is discerned with a disqualifying low probability of it occurring, that would indicate design.

    Others might suggest function and low probabilities as being a solid indicator.

    Now, you might say these methods are flawed — and dadgummit you are gonna show how they are — but they certainly are potential ways of showing that something was designed without observing the designer.

    Further to dismiss attempts to objectively determining design, appears, well anti-science.

  73. Sal Gal:

    , I have problems with the notion that Platonic ideals are in the scientific domain of discourse. Contemporary science (though not every living scientist) eschews metaphysics, and I don’t know what could be more metaphysical than a discussion of the relation of physical observations to unobservable ideals.

    But what about the notion of “sickness” and “health”, or “broken” vs. “functional”.

    The notion of ideals is consistent with the topic of this thread.

    How can on define sickness without some inhrenent notion of what it means to be well.

    Moalem has implicitly shown, from the standpoint of population biology, we could just as well label sickle cell anemia as selectively advantaged trait in a malalaria environent. But that doesn’t seem extremely fruitful from a scientific standpoint.

    Perhaps it is more fruitful to argue for the notion of calling sickle-cell anemia a “disease” and that environments that are favorable to sickle cell anemia (such as high malaria) are not consistent with the platonic ideals of a healthy environment for humans.

    This may seem like a trivial argument, but once we begin classifiying parts of biological systems as :

    “pumps”
    “decoders”
    “motors”
    “wings”
    “systems”
    “codes”

    we begin to oprationally invoke subjectivism into science. We also subtly define what it means when a system is functional or broken. For example, we say someone’s respiratory system is damaged, or his immune system is damaged. These are subjective labels.

    I respect you reluctance, but the fact is the practice of biology is finding itself amenable to defining itself in the language of engineers, and less so in terms of selective advantage.

    We could call blindness “a feature not a bug” in the case of blind creatures like Gammarus Minus. But somehow characterizing blindness as a feature instead of a bug doesn’t seem to advance scientific understanding.

    It would appear the medical profession operates under the presumption that health is defined by some set of implicit ideals. This seems completely agreeble to me. Rather than hurting science, here is a case, where there is some degree of sensible operational metaphysics is perfectly legitimate

    Trying to define biology in terms of selection and adaptation alone leads to ideas like “survival of the sickest”. One is certainly free to look at biology through the lens of selection metaphors and analogies, but it sure doesn’t seem as operationally effective as the traditional platonic views we implicitly operate under already (whether we’re willing to admit it or not).

    In the world of design, the notion of “sick” and “well” or “broken” and “functional”. In the world of adaptationist stories, these notions don’t fit quite so well, hence we have ideas like survival of the sickest.

  74. 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 functions.

    Andreas Wagner
    Robustness of Evolving Systems

    “I define such systems loosely as assemblies of parts that carry out well-defined biological functions.” This sounds and awful lot like Behe’s description of systems!

    But the notion of function, suggests purpose. It matches platonic notions of what it means to function.

    We don’t really use such metaphors to describe rocks lying around on the ground. We don’t say, “the function of rain is to water plants”. Even if true, it doesn’t seem scientifically legitimate.

    However, it seems perfectly legitimate to say that the purpose of the heart is to pump blood. This is a subjective description, but it seems perfectly appropriate for science.

    The following are subjective phrases that are appropriate for medical and biological science:

    “The purpose of eyes is in order to see.”

    “The eyes of Gammarus Minus are dysfunctional.”

    “sickle-cell anemia is a disease”

    And as Wagner pointed out, trying to view biology in terms of adaptation and fitness seems clumsy.

    And imho, forcing purely adaptationist language onto biology is just as much a metaphysical intrusion as using functional machine metaphors and analogies.

  75. Allen,

    We infer design given our current state of knowledge pertaining to nature, operating freely vs what agencies can do with nature.

    IOW if complexity and specification are observed then design is infered.

    And we can empirically check tat by reducibility- that is we can find out what it would take to duplicate what we observe.

    If no agency involvement is required the design inference is taken away.

    With the theory of evolution the best you can provide is “it evolved” without any determining factors other thahn you refuse to accept design.

    And what is the big deal?

    Well experience demonstrates it matters to any investigation whetrher or not that which is being investigated arose via agency involvement or nature, operating freely.

  76. Clive asks,

    Do you really think that’s what ID is about? Miracle detection?

    Without the least sarcasm, I answer yes. Material events with unobservable causes are miracles in my book. For non-material intelligence to create complex specified information out of nothing is a miracle.

    The primary way in which I see myself as a Child of God is that I witness my own acts of creation. But there is no way to make this private apperception into public science.

    I have spent many years working hard at science, engineering, and math. Nothing I have learned in those fields has been of any spiritual significance. Religion, philosophy, and the arts, along with solitary contemplation, have made an enormous difference. And I say this as someone who was struck by chronic illness long ago.

    I have seen that the Kingdom of Heaven is within me, just as Jesus said, though there’s no proof of it. And I am sure that unless we change and become like little children, we will not enter into the Kingdom. Thus I say we should regard science as a game of prediction and control, not a hallowed path to Truth.

  77. Dave Wisker and Allen MacNeill,

    Since Allen has seconded Dave’s discussion of punctuated equilibrium and Dave has said it is what is in Charlesworth et al’s paper, we have what may be a foundation for a further discussion of macro evolution. If such a paper exists in pdf form it would be good if everyone could have it so it could be the basis for debate in the future.

    I am not sure if anything said solves the problem of information creation but it sounds like macro evolution is being depicted sort of like elaborate artificial selection or that nearly all changes are from within the gene pool. If that is true, then the debate will probably be easily settled as more and more genomes get mapped and more is understood about how genetic elements control the various life processes and whether they could have arisen from such a process.

  78. 78

    Very nice comment Sal Gal [76].

  79. Dave Wisker:

    Divergence depends primarily on reproductive isolation.

    That is not (entirely) so and once I re-locate the paper I will post it.

  80. Sal Gal:

    For non-material intelligence to create complex specified information out of nothing is a miracle.

    That’s not ID’s position.

    However for non-intelligent processes to create intelligence is nothing short of a miracle.

  81. Allen (69-70):

    What distinguishes your “ideal” from a model?

    (71):

    I would tweak slightly by saying that what we regard as “random” is what cannot presently predict, not what is “unpredictable.” I see no way to decouple unpredictability from present scientific ignorance. This is a key point in analysis of the argument from specified complexity. Dembski can only reject the best extant model in favor of design. I would not call this argument from ignorance, but there is always the possibility that subsequent scientific learning will reveal that apparent unpredictability (“complexity”) was largely ignorance. Of course, Dembski retreated from his promise of “no false positives.”

    Perhaps this is what you had in mind. I apologize if I seem to be picking at words.

  82. In #74 sal points out:

    “…forcing purely adaptationist language onto biology is just as much a metaphysical intrusion as using functional machine metaphors and analogies.”

    I agree. John O. Reiss, at Humboldt State University in California, has written a book about this very subject, Not by Design: Retiring Darwin’s Watchmaker, in which he argues strongly against Darwin’s teleological arguments for adaptations. It is due for publication in August, 2009. See:

    http://www.amazon.com/Not-Desi.....038;sr=8-1

  83. No problem, Sal Gal; you’ve written it much better than I did.

  84. I have posed to Bill Dembski and to Paul Nelson the question “What is the probability of the universe?” Neither replied, and I would suppose that it is because they are both strong enough philosophers of science to know that we cannot, as scientists, step outside the domain of discourse of science — the physical universe, whatever that is — to speak of a universe-generating mechanism.

    That is not the complete issue. If we could theoretically demonstrate that a universe capable of hosting information-processing systems (and life is an information processing systems) was easily achieveable with a wide range of possible values of physical constants, then it would be easy to dismiss the design argument for the universe.

    The problem is that we know theoretically that fine tuning in at least one of the supposed multi-verses is necessary for the ability of computation (such as found in life) to arise.

    The hypothesis of cosmological ID is formally unprovable, but it is falsifiable. It could have easily been falsified if we determined that we didn’t need fine tuning in any of the multi-verses, but this wasn’t the case.

    And even if we don’t formally know the probability distribution for the chemical formation of the first life, the ID hypothesis could have easily been falsified of Pasteur’s swan neck experiments failed.

    The ID hypotheses maybe formally unprovable, but certain claims are falsifiable, therefore on Popperian grounds ID could be called science. Whether ID is science or not is less my concern than whether it is reasonably true.

    Natural selection has been posited as an explanation, but unlike evolutonary algorithms in a computer, life is constrained by very serious limitations as defined by population genetics. I don’t think selection can be the cause for the appearance of various designs because of the population resource issues in play.

    The Mendels Accountant Team composed of Ivy League talent might actually be able to help decide the issue decisively.

    All this to say, attempts to falsify or defend the ID hypothesis could be very fruitful scientifically. We don’t have to accept ID as true in the ultimate sense in order for it to be scientifcally fruitful.

    The crucial question for science is whether design helps us understand the world, and especially the biological world, better than we do now when we systematically eschew teleological notions from our scientific theorizing. Thus, a scientist may view design and its appeal to a designer as simply a fruitful device for understanding the world, not attaching any significance to questions such as whether a theory of design is in some ultimate sense true or whether the designer actually exists. Philosophers of science would call this a constructive empiricist approach to design. Scientists in the business of manufacturing theoretical entities like quarks, strings, and cold dark matter could therefore view the designer as just one more theoretical entity to be added to the list. I follow here Ludwig Wittgenstein, who wrote, “What a Copernicus or a Darwin really achieved was not the discovery of a true theory but of a fertile new point of view.” If design cannot be made into a fertile new point of view that inspires exciting new areas of scientific investigation, then it deserves to wither and die. Yet before that happens, it deserves a fair chance to succeed.

    Bill Dembski
    No Free Lunch

  85. As a very preliminary approach to a discussion of macroevolution, I am in the process of compiling a list of the various mechanisms by which macroevolution has been shown (or at least hypothesized) to occur. As you can see by reading the following list, these mechanisms have some overlap with the mechanisms for microevolution. However, there are very significant differences. Also, please keep in mind that at this stage, this is only a list (i.e. there are no explanations provided; you will have to google them). Finally, some of the following are not so much “mechanisms” as they are “descriptions of mechanisms”; the actual mechanisms themselves remain to be elucidated:

    1) Exaptation
    2) Neutral genetic drift (especially founder and bottleneck effects)
    3) Allopatry / vicariance / divergence
    4) Convergence / phylogenetic anastomosis / horizontal gene transfer
    5) Contingency / historicity
    6) Heterochrony (both developmental and evolutionary, which includes punctuated equilibria dynamics)
    7) Macroscopic changes in homeotic gene regulation
    8) Partial or complete genome reorganization / duplication
    9) Relaxation of stabilizing selection/ecological “release” (which includes / results in adaptive radiation)
    10) Extinction, especially mass extinction
    11) Large-scale ecological change / disruption
    12) Inter-specific competition / species selection / species sorting
    13) Inter-specific cooperation and symbiosis, especially endosymbiosis
    14) Partial or complete genome fusion / developmental cooptation / diversification
    15) long-term neutral “drift”
    16) Neo-activation of formerly non-functional genome components
    17) Internal variance/”complexification”

    Some will want to condense this list (pointing out that some processes are subsumed under others), while others will undoubtedly feel that I’ve left some important items off the list. If you feel either way, please comment to that effect. Thanks!

    Also, if the moderators feel that posting this list constitutes “hijacking” this thread, please feel free to post it as the OP for a new thread on macroevolution (sal, you could do this yourself, right?)

    Again, thanks!

  86. That was weird; I don’t know where the “sunglasses guy” came from in #7. Maybe it was the unseasonably sunny and hot weather we’ve been having today in Utopia…

  87. In #84 sal wrote:

    “The problem is that we know theoretically that fine tuning in at least one of the supposed multi-verses is necessary for the ability of computation (such as found in life) to arise.”

    Actually, this isn’t the case. All you really need for “fine-tuning” (i.e. coordinating the various physical fine structure constants) is “cosmic inflation”. The inflationary process itself produces a “flat” universe, which is essentially the universe in which we live.

    Ergo, the problem is not coordinating a whole set of unrelated constants, the real problem is explaining “cosmic inflation”.

    So much for the “fine tuning” argument…

  88. In #84 sal also wrote:

    “We don’t have to accept ID as true in the ultimate sense in order for it to be scientifcally fruitful.”

    Here, I agree. As I pointed out in the introduction to my notorious evolution-design seminar at Cornell in 2006, Darwin’s search for a “natural” explanation for teleological adaptations led him to his theory of evolution by natural selection. In the same way, Ernst Mayr’s reintroduction of the argument for design in biological development has stimulated a renewed interest in the topic of teleology and teleonomy in evolutionary biology. The publication of John O. Reiss’s forthcoming book, Not by Design: Retiring Darwin’s Watchmaker is an extension of this philosophical research project, stimulated at least in part by the current debate over ID.

    For my own part, I have found that debating the question of design with my colleagues/opponents like Hannah Maxson and Sal Cordova has greatly improved my own clarity on these issues, and led to my initiating work on a book-length treatment of the “problem” of teleology in evolutionary biology.

  89. In #84 Sal also wrote:

    “The Mendels Accountant Team composed of Ivy League talent might actually be able to help decide the issue decisively.”

    I believe you are referring to John Sanford and his colleagues, who have developed the “Mendel’s Accountant” software program to model his theory of genetic entropy. Unfortunately, his model is completely based on the old “modern evolutionary synthesis” paradigm, as first worked out by R. A. Fisher, H. B. S. Haldane, and Sewall Wright. As I have repeatedly noted, while this paradigm was useful when we didn’t know much about evolution and development or genomics, it has now been almost completely superseded by those fields, thereby rendering Dr. Sanford’s software program a quaint curiosity with little or no relevance to current evolutionary theory.

  90. BTW, when Dr. Sanford made a presentation in our evolution course at Cornell (at Will Provine’s invitation), he freely admitted that the evaluation that I posted above was essentially correct.

  91. Moderators: If you will, please pass along this message and delete it from this thread. Thanks!

    Dr. Dembski:

    I have been encouraged by several ID supporters (including my good friend, Hannah Maxson, founder of the Cornell IDEA Club) to correspond with you on several of the issues that have recently been raised here. I realize that we may have gotten off on the wrong foot years ago, and freely admit that much of that may have been due to my own, rather intolerant attitude.

    Ergo, if you are amenable to starting up a correspondence now, please rest assured that I will endeavor to account myself with all the civility and courtesy due a fellow academic. If this proposal meets with your approval, please send me an email at the following address (say it out loud; it’s phonetic):

    [public display of e-mail address has been removed by scordova with permission from Allen MacNeill 4/28/09 20:50 in order to protect Allen from spam]

    Thank you for your understanding; I’m looking forward to hearing from you!

    –Allen MacNeill
    Introductory Biology and Evolution
    Cornell University

  92. if the moderators feel that posting this list constitutes “hijacking” this thread,

    Hi Allen,

    Feel free to discuss macro evolution here. I think the material is too technical for our readers, and I personally feel uncomfortable starting a thread where I feel completely incompetent regarding the subject matter. I have little knowledge about macro evolutionary theories. Please accept my apologies, but feel free to discuss it some here in this thread.

    And if I may explain the reasoning for loosening up what is discussed on this thread:

    It seems that you had some sympathy for the point I was making about “survival of the sickest”.

    You said:

    So far this thread has supported Gould and Lewinton’s 1979 critique of what they called the “adaptationist paradigm”. I hasten to add my voice of support to this critique,

    After that, it didn’t seem that we had much grounds to argue regarding my reactions to Moalem’s book.

    It didn’t seem like anyone was really objecting to what I said in characterizing Moalem’s book.

    You put forward a far more interesting question:

    but would go on to point out that, if taken to its logical extension (which Gould and Vrba almost did in their 1982 paper on “exaptation”), this would not only undermine much of “Darwinian” evolutionary theory, but all of ID as well.

    This a shocking, heretical statement. I like it as it raises important questions.

    Furthermore, as a matter of policy. If a commenter, like yourself, has added to our understanding and has taken time to help educate the reader, I think he has earned the right to offer a post or two that is not the main point of the thread, especially after there is broad agreement about the original posting.

    I mean,you really took the cake when you suggested an idea in Reiss’s book:

    More than two centuries ago, William Paley introduced his famous metaphor of the universe as a watch made by the Creator. For Paley, the exquisite structure of the universe necessitated a designer. Today, some 150 years since Darwin’s On the Origin of Species was published, the argument of design is seeing a revival. This provocative work tells how Darwin left the door open for this revival–and at the same time argues for a new conceptual framework that avoids the problematic teleology inherent in Darwin’s formulation of natural selection.

    So Darwin is partly to blame for the revival of the design argument!! That’s a good one.

    It seems my Original Post has some sympathy from you (but perhaps for totally different reasons), especially in light of your citation of Reiss.

    It didn’t seem that I got much disagreement with my claim:

    The net result is that Moalem’s book becomes an unwitting critique of Darwinian evolution. It highlights numerous empirical examples of how natural selection actually goes against Darwinian ideas of constant progress, and instead demonstrates how natural selection can be an agent of demise.

  93. I would only add that, as generally understood by most evolutionary biologists, natural selection is neither progressive nor regressive. On the contrary, since both of these terms include an evaluative component, natural selection (as a “natural” process) literally can’t be either of these things.

    After all, if one is a tapeworm, then evolutionary “regression” has been quite “beneficial”, as it has made it possible to live quite well while shuffling off almost all of this mortal coil.

  94. I would also point out that Stephen Jay Gould relentlessly criticized the idea that evolution was “progressive” in any way. That, among many other things, is why I tend to agree with Gould, to the point of thinking of myself as a “Gouldian”, rather than a strict “Darwinian”.

  95. BTW, when Dr. Sanford made a presentation in our evolution course at Cornell (at Will Provine’s invitation), he freely admitted that the evaluation that I posted above was essentially correct.

    Allen,

    I’ve been working with members of the Mendel Team. I met Dr. Sanford over the summer.

    I very much welcome your comments and criticisms on the project.

    As I mentioned, a new website is being constructed as a repository of more scholarly inputs and exchanges. The participation is by invitation only, and some of the discussions will be restricted from public view in order prevent ideas being quoted out of context or other complications.

    There is not a lot that is secret about the project as it is now very much in the public domain and published in a conference proceeding on computing.

    Of interest however, is whether the model will accurately predict genomic deterioration in humans. Notwithstanding the good objections you put forward, I think at least some of the Mendel Team’s findings are amenable to empirical testing and falsification. I think everyone has something to gain from the project.

    Oddly enough, we might actually be able to tell if the “sickest are surviving” through research inspired by the Mendell Team.

    My view is it can’t hurt to go out into the field and actually see if a hypothesis is correct. That would probably be the next phase of work inspired by the Mendel team.

    Sal

  96. Hi joseph,

    Dave Wisker:

    Divergence depends primarily on reproductive isolation.

    That is not (entirely) so and once I re-locate the paper I will post it.

    I look forward to reading it.

  97. That was weird; I don’t know where the “sunglasses guy” came from in #7. Maybe it was the unseasonably sunny and hot weather we’ve been having today in Utopia…

    An 8 followed by a parentheses creates the sunglass.

    “It’s not a bug, it’s a feature” of UD software. :-)

  98. It’s something you use when you want to take the sting out of something since web communication is often misconstrued for the worse :-)

  99. Allen writes:

    I would also point out that Stephen Jay Gould relentlessly criticized the idea that evolution was “progressive” in any way. That, among many other things, is why I tend to agree with Gould, to the point of thinking of myself as a “Gouldian”, rather than a strict “Darwinian”.

    Well, I’m still only a grad student, but right now I’m not much of a “Gouldian” in my outlook, especially when it comes to some of the mechanisms on Allen’s list like species selection. However, reading Gould and Lewontin’s Spandrels paper was one of those defining moments in my education, and I think Gould, along with Dawkins, is relentlessly misrepresented and misunderstood. He was also one of the most graceful writers in English.

    So maybe this can be fun. As for the pdf of the Charlesworth et al paper, since Allen has given us his email address, may I send it to him as point of contact?

  100. sal wrote:

    “This a shocking, heretical statement. I like it as it raises important questions.”

    That’s the spirit! No sacred cows…

    I often say to my students that our intro evolution course consists of a series of “rug-pullings”. That is, we spend a significant period of time laying out a particular piece of “received wisdom” (e.g. the “modern synthesis”) and then pull the rug out from under it by showing how its basic assumptions have been undermined by further empirical research.

    When you first have the rug pulled out from under you, the usual result is that you fall on your ass. However, once you’ve had several rugs pulled out from under you, it is possible (if one is nimble-footed) to develop a certain equanimity, and thereby save your ass a lot of nasty bruises.

    To me, that is the chief value of skeptical iconoclasm.

  101. sal also wrote:

    “My view is it can’t hurt to go out into the field and actually see if a hypothesis is correct.”

    Indeed, that’s the whole basis of the empirical sciences; it ain’t science until you’ve tested it against nature itself…which usually means that you’ve gotten a bunch of confusing data, some of which supports your hypothesis, a lot of which supports absolutely nothing, and (if you’re incredibly lucky) some of which suggests something you (and everyone else) has never thought of.

  102. Gotta go to bed; it’s been a blazing hot day here in Utopia, and the bedroom is finally cool enough to contemplate sleeping.

    Later, y’all…

  103. 103

    Allen,

    “Actually, this isn’t the case. All you really need for “fine-tuning” (i.e. coordinating the various physical fine structure constants) is “cosmic inflation”. The inflationary process itself produces a “flat” universe, which is essentially the universe in which we live.

    Ergo, the problem is not coordinating a whole set of unrelated constants, the real problem is explaining “cosmic inflation”.”

    Neither the fine-tuning nor the flat universe, (which makes me laugh, because it was first thought that the world was flat, now we’re saying it’s just the universe that’s flat, and not the world), will be “figured out” in the respect that we can ever get behind the laws and know their relation and inner synthesis. We can see the relationship between laws of logic and reason, but we have no equivalent “inside” information with the laws of nature. All we can do is record their effects, we can never say why they are the way they are.
    But that’s not to say that the laws don’t seem awfully fine tuned, because they certainly are fine tuned, the question is why? The obvious answer, to me, is that there was a fine-tuner. But there is a deeper, more conceptual reason for believing in, what is essentially, a fine-tuning argument, which credits an intelligence for the laws of nature. But this concept would apply even if the laws of nature were not fine tuned. It has to do with the nature of laws in themselves. Since we cannot see why the laws of nature are the way that they are, we cannot see why they shouldn’t have been otherwise.

    “It discredits supernatural stories that have some foundation, simply by telling natural stories that have no foundation….But the scientific men do muddle their heads, until they imagine a necessary mental connection between an apple leaving the tree and an apple reaching the ground. They do really talk as if they had found not only a set of marvellous facts, but a truth connecting those facts. They do talk as if the connection of two strange things physically connected them philosophically. They feel that because one incomprehensible thing constantly follows another incomprehensible thing the two together somehow make up a comprehensible thing. Two black riddles make a white answer.

    A law implies that we know the nature of the generalisation and enactment; not merely that we have noticed some of the effects. If there is a law that pick-pockets
    shall go to prison, it implies that there is an imaginable mental connection between the idea of prison and the idea of picking pockets. And we know what the idea is. We can say why we take liberty from a man who takes liberties. But we cannot say why an egg can turn into a chicken any more than we can say why a bear could turn into a fairy prince. As IDEAS, the egg and the chicken are further off from each other than the bear and the prince; for no egg in itself suggests a chicken,
    whereas some princes do suggest bears. Granted, then, that certain transformations do happen, it is essential that we should regard them in the philosophic manner of fairy tales, not in the unphilosophic manner of science and the “Laws of Nature.” When we are asked why eggs turn to birds or fruits fall in autumn, we must answer exactly as the fairy godmother would answer if Cinderella asked her why mice turned to horses or her clothes fell from her at twelve o’clock. We must answer that it is MAGIC. It is not a “law,” for we do not understand its general formula. It is not a necessity, for though we can count on it happening practically, we have no right to say that it must always happen. It is no argument for unalterable law (as Huxley fancied) that we count on the ordinary course of things. We do not count on it; we bet on it. We risk the remote possibility of a miracle as we do that of a poisoned pancake or a world-destroying comet. We leave it out of account, not because it is a miracle, and therefore an impossibility, but because it is a miracle, and therefore an exception. All the terms used in the science books, “law,” “necessity,” “order,” “tendency,” and so on, are really unintellectual, because they assume an inner synthesis, which we do not possess. The only words that ever satisfied me as describing Nature are the terms used in the fairy books, “charm,” “spell,” “enchantment.” They express the arbitrariness of the fact and its mystery.

    I deny altogether that this is fantastic or even mystical. We may have some mysticism later on; but this fairy-tale language about things is simply rational and agnostic. It is the only way I can express in words my clear and definite perception that one thing is quite distinct from another; that there is no logical connection between flying and laying eggs. It is the man who talks about “a law” that he has never seen who is the mystic. Nay, the ordinary scientific man is strictly a sentimentalist. He is a sentimentalist in this essential sense, that he is soaked and swept away by mere associations. He has so often seen birds fly and lay eggs that he feels as if there must be some dreamy, tender connection between the two ideas, whereas there is none. A forlorn lover might be unable to dissociate the moon from lost love; so the materialist is unable to dissociate the moon from the tide. In both cases there is no connection, except that one has seen them together. A sentimentalist might shed tears at the smell of apple-blossom, because, by a dark association of his own, it reminded him of his boyhood. So the materialist professor (though he conceals his tears) is yet a sentimentalist, because, by a dark association of his own, apple-blossoms remind him of apples…

    This proves that even nursery tales only echo an almost pre-natal leap of interest and amazement. These tales say that apples were golden only to refresh the forgotten moment when we found that they were green. They make rivers run with wine only to make us remember, for one wild moment, that they run with water. I have said that this is wholly reasonable and even agnostic. And, indeed, on this point I am all for the higher agnosticism; its better name is Ignorance…

    We have all forgotten what we really are. All that we call common sense and rationality and practicality and positivism only means that for certain dead levels of our life we forget that we have forgotten. All that we call spirit and art and ecstasy only means that for one awful instant we remember that we forget.”
    ~”The Ethics of Elfland”–Orthodoxy, G.K. Chesterton.

    Lets be honest with ourselves. We have no inner knowledge of why the laws of nature are as they are. Recording their effects won’t get us one bit closer to answering this more fundamental question either. Nor will recording their effects tell us why they should be one way and not another. We are in the unfortunate position for the materialist who wants a complete picture, and the fortunate position for the spiritualist who likes the mystery and awe of nature to be maintained, when we admit that we will never “get behind” these laws of nature as we can get behind laws of reason and understand their connection and reasonableness or lack thereof. And I see no reason to not accept this world as being anything except just as wonderful and mysterious as a fairy tale is. The only difference is that we’ve gotten used to this one.

  104. Footnotes:

    1] Cosmic inflation itself raises further issues of itself being finetuned.

    2] Many finetuned parameters — e.g. the near balance of charge in the observed universe — are independent of such inflation.

    GEM of TKI

  105. Allen,

    I asked a question back in #37 and didn’t see a response. I might have missed it but was just curious what your thoughts were.

  106. 106

    hi ellijacket,

    I’m not speaking for Allen, but I can give something of an answer to your question:

    That’s one of the big issues I have with this whole arguement. Given a genetic code then…..
    How can we just say that? The genetic code is information and meta-information of specified complexity. The only thing we have discovered that can produce similar information and meta-information of specified complexity is intelligence.
    The genetic code is the biggest reason to believe there is intelligence behind what we see. How can we ignore that fact, skip past it and then just discuss the items you listed?

    I don’t think Allen is “just saying that”. There are hypotheses for the origin and evolution of the genetic code. Here is one, accessible to all:

    http://www.pnas.org/content/103/28/10696
    .abstract

    Vetsigian K, C Woese & N Goldenfield (2006). Collective evolution and the genetic code. PNAS 103(28): 101696-1071

    From the abstract:

    A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early communal life generically lead to refinement and selection of innovation-sharing protocols, such as the genetic code. Our proposal is illustrated by using a simplified computer model and placed within the context of a sequence of transitions that early life may have made, before the emergence of vertical descent.

  107. Re #103 by Clive Hayden:

    The word “why” occurs in your long post eleven times, whereas the word “what” appears only three times and the word “how” appears in it only once. This is very interesting, as science can only be concerned with “what” and “how” questions. When a scientist asks the question “why”, the answer is exactly the same as the answer to the question “how”. Ergo, in scientific explanations, there is only the question “how”.

    Scientific “what” questions are asking for a description of something observable in nature. for example, a scientist might ask “what” is that muscular structure in the center of the chest cavity of mammals? To answer such a “what” question, s/he would measure this muscular structure, dissect it to determine its fine structure, perhaps measure its electrical nature, its rate of contraction, its “ejection fraction”, etc. All of these empirical observations, taken together, would constitute an answer to the “what” question. That is, they would constitute a description of the heart. What all of these descriptions add up to is that “the heart is a hollow muscular organ regulated by the autonomic nervous system that pumps blood through the circulatory system”.

    Scientific “how” questions are asking for an analysis of something observable in nature. For example, a scientist might ask “how” does the mammalian heart pump blood through the circulatory system? To answer that “how” question s/he would measure the fluid dynamics of cardiac contraction, the conduction of motor endplate potentials in the sino-atrial and atrio-ventricular nodes, the Purkinje fibers and the bundles of Hiss, the effects of laminar versus turbulent flow through vessels and valves, etc. All of these empirical observations, taken together, would constitute an answer to the “how” question. That is, they would constitute an analysis of the heart. What all of these analyses add up to is that “the heart pumps blood through the circulatory system according to the following principles und so weiter“.

    The peculiar and most interesting thing (to me) about the empirical sciences is that if a scientist asks the question “why” about the heart, her/his answer is exactly the same as the answer to her/his “how” question. To be very specific, there is no separate and epistemologically superior appeal to teleological explanations. The object/process simply does what it does, period, end of story. About the question “why” the universe and its natural laws are the way they are, as Wittgenstein says, “we must remain silent”.

    The reason we remain silent in the face of “why” questions about any “ultimate” explanation for natural objects and natural laws is that such questions cannot be answered using the empirical methods of science. Furthermore, any attempts to answer “why” questions in science produce no new information, as they simply reiterate the answer to “how” questions about the same phenomena. Nothing whatsoever is added to a scientific description by attempting to answer the question “why” about the subject under study.

    This is most especially the case when we talk about evolutionary explanations for the origin and evolution of particular biological characteristics. A scientist might ask “how did the mammalian heart come to have its particular structural and functional characteristics?” The answer would involve references to comparative vertebrate anatomy: in fish, there is a two-chambered heart, augmented by the sinus veinosus and the conus arteriosus. With the separation of the pulmonary and systemic circulations in amphibians (the first terrestrial tetrapods), and additional circuit evolved by the separation of the common atrium of ancestral Ripidistians into the two atria found in amphibians. This separation was correlated with the increased oxygen demand associated with terrestrial locomotion, which is in turn associated with the increased availability of oxygen in the air. This same separation of the pulmonary and systemic circulations was extended to the ventricles in birds and mammals. There is increasing evidence that this configuration of the hearts in birds and mammals evolved independently in these two clades, especially as we learn more about the evolutionary developmental biology of the vertebrate circulatory system.

    And the answer to the question “why did the mammalian heart come to have its particular structural and functional characteristics?” The answer: the exact same information as contained in the previous paragraph.

    Ergo, the eleven questions “why” contained in your long post are either not answerable using empirical science, or they reduce to the answer to the question “how”.

    To be as succinct as possible,

    There are no “why” questions that are separably answerable by the empirical sciences.

    How do birds come to have feathers?

    They inherit the developmental capability to produce feathers from their parents.

    Why do birds come to have feathers?

    They inherit the developmental capability to produce feathers from their parents.

    And so forth, ad infinitum

  108. Re the question in #37:

    Fascinating as it is, the question of how the genetic code and its translation machinery originally evolved (or, alternatively, was created) appears to me to be entirely beyond the scope of the empirical sciences. Molecules do not (indeed, cannot) fossilize, and even if we could somehow “recreate” the various steps in what we might assume to be the “logical” evolutionary pathway to the origin of such systems, there is absolutely no way (short of time travel) to verify that this pathway was, indeed, the way it actually happened.

    Ergo, it is one of those “Wittgensteinian undecidables” about which I prefer to remain silent.

  109. Allen,

    Since we know intelligence can produce information just like the genetic code how can we so easily discount that intelligence was behind the original?

    The scientific method will verify over and over again that our only known way to produce this type of information is through intelligence. It seems then that, scientifically, it’s safe to say that intelligence is needed to produce a genetic code.

    Let’s say you disagree. What if we flipped it? What if we couldn’t produce a genetic code through intelligence but everytime we mixed certain elements together a genetic code appeared on it’s on? I think materialists would jump on that as proof that there is no need for any kind of creator.

    I guess my point is that it seems dishonest for materialists to ignore what we currently know about producing specified information of the type found in a genetic code. If the tables were turned as above I don’t think they would ignore it because it would fit what they want to see.

  110. Fascinating as it is, the question of how the genetic code and its translation machinery originally evolved (or, alternatively, was created) appears to me to be entirely beyond the scope of the empirical sciences.

    The empirical sciences can offer information as to which way the balances may tip.

    One question that seems quite reasonable to me is that the genetic code could not have occurred in gradualistic steps. At some point partially formed organisms will not be viable. This is very obvious with dead creatures. They have large amounts of biotic material, in some cases a higher concentration of the kinds of chiral materials than all the OOL labs have ever produced.

    It would seem that when life first appeared it would have to have been farily intact. As Gould said, “what good is half an arm”, this is especially true of a computer program, “what good is a partially formed computer program running on a partially formed computer?”

    Formally speaking, sudden emergence on its own does not necessarily imply ID, we might just simply say it was an improbable, unique, unrepeatable event.

    But at some point stochastically improbable events are indistinguishable from miracles.

    The goal of most OOL researchers is to try make a case that the conditions for first life were not all that improbable. But the reason ID has grown has been the spectacular lack of success by the OOL community despite their valiant and talented efforts.

    Some, faced with the empirical evidence became ID proponents.

    The most well known story was that of Dean Kenyon who wrote the premiere graduate textbook on OOL. After reading Cybernetic Evolution by Oxford chemist AE Wilder Smith, Dean Kenyon eventually became an ID proponent. He struggled with this for almost 20 years after publishing his OOL textbook. Kenyon was most well-known for his other textbook Pandas and People prominently featured in the Dover trial.

    Allen is correct that the exact details are probably beyond our reach, but sudden emergence of fully functional, Irreducibly Complex life seems like the most reasonable inference.

    Whether God was involved, I suppose is a matter of faith, but sudden emergence seems theoretically difficult to refute. Everything we’ve discovered in the lab doesn’t suggest falsification of sudden emergence will ever happen.

    I can understand the separation of OOL from the rest of evolution. Indeed, most of my ID focus has been OOL. But even generously granting Darwinian evolution after the first life emerged, sudden emergence of the first life strikes me as undeniable.

    And this sudden emergence certainly made ID believable on a personal level.

    One may argue that religious motives may drive ID, but even granting that, from an intellectual standpoint, the convictions run deep, especially among computer engineers and physicians. The machine metaphor is just too compelling, and nothing in labarotory experience suggests machines can spontaneously emerge fully intact nor even through gradualitic steps.

    If the machine metaphor were not so compelling, I would not be in the ID movement. I’d probably be an agnostic (as I nearly was in 2001).

    And perhaps to tie this to the original post, the notion of sickness (which is non-funtioning) makes the most sense when one accepts the machine metaphor. If we exorcise teleological metaphors from biology, it would cause biology to disconnect with the implicit way the medical industry views biology.

    The metaphysical viewpoint of teleology seems too useful for technology and medical science.

    The fact that Moalem and others have suggested the ways Natural Selection favors diabetes, doesn’t seem to remove the intuition that diabetes is fundamentally a bad thing.

  111. …there is absolutely no way (short of time travel) to verify that this pathway was, indeed, the way it actually happened.

    If extraterrestrial evidence turned up, say, on Mars, with bacteria that had a

  112. …there is absolutely no way (short of time travel) to verify that this pathway was, indeed, the way it actually happened.

    If extraterrestrial evidence turned up, say, on Mars, with bacteria that had a similar structure to earth bacteria, but with opposite chirality, for example, or utterly different chemistry, or identical, that would give us a few clues.

  113. Sorry about 111, hit wrong key!

  114. In #109 ellijacket asked:

    “Since we know intelligence can produce information just like the genetic code how can we so easily discount that intelligence was behind the original?”

    Because we cannot show using empirical methods that this is, in fact, the case. Once again, arguments by analogy have essentially no logical validity. See:

    http://evolutionlist.blogspot......gical.html

  115. In #112 Alan Fox suggested:

    “If extraterrestrial evidence turned up, say, on Mars, with bacteria that had a similar structure to earth bacteria, but with opposite chirality, for example, or utterly different chemistry, or identical, that would give us a few clues.”

    The problem with Mars is that it’s too close to Earth; one cannot rule out cross-contamination as a source of similar biochemistries. However, you do have a point if what we discover is life with very different biochemistries. What this would imply is that the “frozen accident” hypothesis for the origin of biochemical homochirality and the genetic code was a more parsimonious model given such observations.

    On the other hand, finding similar biochemistries in other stellar systems would support the opposite conclusion: that the chirality and genetic code that characterizes life on Earth is probably “necessary”, rather than “accidental”. And please note that neither of the two explanations outlined here includes any reference to a supernatural Intelligent Designer, because one isn’t necessary for either explanation.

  116. 116

    Allen,

    I’m sorry, but I don’t think you really grasp what is at issue. I’m not talking about effects of natural “laws,” such as birds having feathers because of x, I’m talking about the “laws” themselves. This is not a question of teleology. It is a question of knowledge about the “laws” themselves. I appreciate your long answer, but it doesn’t address my post.

  117. Allen,

    Because we cannot show using empirical methods that this is, in fact, the case. Once again, arguments by analogy have essentially no logical validity.

    So you would also say that if we could stir up some elements in a pot and get DNA that we could not infer anything for the same reasons? If so, I appreciate your consistency.

  118. [93] Allen wrote:

    would only add that, as generally understood by most evolutionary biologists, natural selection is neither progressive nor regressive. On the contrary, since both of these terms include an evaluative component, natural selection (as a “natural” process) literally can’t be either of these things.

    Allen, if we couple the “neutral theory” of mutations with this, your understanding of NS as basically “neutral”, then we have two components of change that are both “neutral”.

    Here is an analogy of such a combined, neutral mechanism of change:

    Imagine a wide, very sharp-edged cutting blade locked in position. Next, imagine an immensely large holding bin positioned directly above this edge filled with an inumerable quantity of bust-sezed blocks of wood. Now imagine that beneath the cutting edge is a collection basin, having within it a conveyor belt that returns the blocks of wood to the bin overhead after being dropped over the cutting edge.

    In such an imagined scenario, the only forces at work are gravity and resistance, with gravity providing velocity to the blocks, and the edge providing shear (resistance). Would you expect that this process of dropping the blocks of wood over the fixed edge (at either a fixed, or, randomly changing heighths) and then returning them to the bin above once they have been dropped, carried out over an immense amount of time, would produce the figure of an animal, for example?

    My point here is that if everything is “neutral”, then I don’t believe anyone would expect an ‘art’ form to emerge from such a process. And, if such a ‘form’ did emerge from such a process, then wouldn’t all of us be curious about the ‘non-neutral’ force that must have surely brought it about? Wouldn’t it be natural to ‘intuit’ such a force or power?

    IOW, even if you don’t want to go so far as to posit a designer, then surely you must posit that NS is ‘not’ neutral. (Dawkins argues thusly.)

  119. Am I to understand that the ONLY evidence for ID t6hat will be accepted is a meeting with the designer?

    Why can’t we just look to experiments like Tracey and Joyce with their RNA?

    They synthesized RNA and all it could do was make ONE new bond connecting two other pre-synthesized parts together.

    ONE new bond in ideal conditions.

    Shouldn’t that give us an indication on the powers of nature, operating freely?

  120. #118 You mean like clouds that have similar shape and form to objects? Are you suggesting that a god is responsible for those coincidental shapes?

  121. 121

    Perhaps the metaphysical materialists on this thread would venture to answer an inconsistency in their conclusions.

    When as rock falls away from the side of a cliff it has no meaning. It is simply acting upon chance, gravity, erosion, etc.

    The same applies to water evaporating off the sidewalk on a coolish day. Its a mixture of lowered air pressure acting upon established elements – but there is no meaning.

    Following the materialists paradigm, there is no meaning in the material world. Chance cannot create meaning, and neither can physical necessity.

    Yet, prescriptive algorithms are the exact opposite. Intructions inherently have meaning. They mean something.

    There is nothing in the physical laws of this Universe that says that instructions have to physically exist. Also, there is also nowhere in the Universe that it can be demonstrated that chance can formulate meaning or create instructions within any material object whatsoever.

    Metaphysical materialists must then deny that instructions have meaning. Or, they must deny that nucleic sequences are instructions. Or, perhaps they can simply deny that meaning is meaning, after all.

    So which is it?

  122. Mr MacNeill,

    I’m not sure why you quibble about knowing the exact history in 108. There is plenty of good research on the evolution of the genetic code, such as recent study.

  123. 123

    I am enjoying this thread and don’t want to derail it with an extended discussion of the relationships between ID and engineering. But let me just point out that although you started out well, as this thread progresses you seem to increasingly imply that you are speaking for the majority of engineers. Based on my engineering experience, you are not.

  124. Your argument is based on things which are metaphors, not actual. You use the words “telling,” “instructions,” “information,” “meaning,”– talk to a molecular biologist and they will speak of “cellular machinery” and “intracellular communication.” The only have such “properties” because someone was there to decide such things were like instructions, relating a phenomenon to something they have familiar experience with. RNA transcription to protein translation (another metaphor) is not literally translating the language of RNA to the language of proteins. It is a series of chemical processes of high specificity which result in a peptide. Without an observer to apply meaning, because the molecules cannot do it themselves (unless you are suggesting the molecules are capable), there is no meaning—it is a human contrivance.
    It does not strengthen the ID position—would you say the axle is telling the wheel to move? IDists have a tendency to use the metaphorical language in biology as “evidence” for ID. I would hope some would be smarter….
    Good job scordova on the quote min. Perhaps next time you will include the “It may be metaphorically said,…”

  125. Joseph: [119]

    They synthesized RNA and all it could do was make ONE new bond connecting two other pre-synthesized parts together.

    ONE new bond in ideal conditions.

    Shouldn’t that give us an indication on the powers of nature, operating freely?

    By way of answering some of the questions posed earlier on on this thread, I agree, Joseph, that we should note the limitations of mutational power on the part of nature.

    In fact, some have discussed algorithms and such, and how we should look to nature for confirmation or negation. Well, isn’t that exactly what Behe has done? First, with a mathematician by the name of Snoke, he did a computer simulation designed to elicit the evolutionary firepower needed to produce a simple peptide through duplication events combined with recombination and immediate fixation of the changes (this is often invoked by the intelligentsia as the mechanmism by which evolutionary progression occurs in nature). Behe found—rather, the mathematical model found—that only small changes in amino acid sequences can be searched out when invoking the gene duplication/recombination/fixation scenario, and only using huge population numbers and huge numbers of generations.

    Then he found an example in nature with which he could compare the evolutionary firepower of nature versus what his model told him. Nature confirmed his model: at most, after huge numbers of generations, only two a.a. substitutions were found to take place in the Plasmodium farmecium, the malarial parasite, amidst its life and death struggle with quoinone.

    eligoodwin [120]

    Please notice the questions I asked. I asked how one would react if the shape of a squirrel came out from a process I described. I asked the question: ” . . . wouldn’t all of us be curious about the ‘non-neutral’ force that must have surely brought it about? Wouldn’t it be natural to ‘intuit’ such a force or power?

    Now, if I asked the question: Is it possible for clouds to assume shapes that we’re familiar with simply through changing wind currents and air pressure? how would you answer? I don’t think you’d be invoking God would you? I don’t think you could as easily dismiss the necessity for some kind of intervention in addition to natural forces if what I decribed above were to happen.

    As to invoking God, how do you know that I’m not describing a toy factory?

  126. 126

    Hi Mr Nakashima,

    <i.Mr MacNeill,

    I’m not sure why you quibble about knowing the exact history in 108. There is plenty of good research on the evolution of the genetic code, such as recent study.

    I mentioned a similar hypothesis in #106, but since I am in perpetual moderation, it was probably missed.

    That being said, I think Allen is simply saying we most likely will never be able to figure out the exact process by which the genetic code arose. However, it’s my opinion we have several hypotheses that can at least demonstrate the plausibility of the code’s evolution through natural means. The basic stereochemical affinity of specific tRNA’s with certain amino acids suggests to me that intelligent design is not necessary to explain the origin of the code.

  127. PaV–You are curious of the bias in the machine which chops wood, I am curious of the bias contained in weather, producing clouds of familiar shape.
    My point: what is the difference?

  128. In #110 sal wrote:

    “…diabetes is fundamentally a bad thing.”

    Not exactly. Type I diabetes is indeed a bad thing; everyone who had it before the discovery of insulin and the development of insulin treatment died from it, quite horribly.

    Type II diabetes, however, is quite different. There is quite good evidence to indicate that certain phylogenetic lines in humans are strongly predisposed towards the development of Type II diabetes. Furthermore, it is also quite clear that Type II diabetes is primarily an “environmental” disease. That is, if one has the requisite genetic predisposition, one develops it only if one is exposed to the right environment. To be specific, people with a genetic tendency toward Type II diabetes will develop it if they are in an environment in which they
    1) get relatively little exercise, and
    2) consume a diet in which a large fraction of their calories are derived from foods with a high glycemic index (sugars and easily digested starches). Under these conditions, such people develop a tendency to produce too much insulin in response to the ingestion of high glycemic index foods, which has the effect of “burning out” their insulin receptors (the physiology of this reaction is complex and doesn’t really involve “burning”; I would be happy to explain it if there is sufficient interest). This is a bad thing, as it eventually causes them to be unable to regulate their blood glucose concentrations.

    However, having a tendency toward “hyperinsulinism” is actually a good thing, if one lives in an environment where foods with a high glycemic index are rare and only intermittently available, and in which periodic starvation is common. Under such conditions, people who can very rapidly mobilize the glucose in those rare foods that contain a lot of it would be at a definite advantage over people who could not do so. Furthermore, having a slightly elevated blood concentration every now and then also means that when everyone who does not have the same tendency is semi-comatose from hypoglycemia, the people with slightly elevated blood glucose are “feelin’ just fine”.

    So, in the case of Type II diabetes, what causes a disease in us today (in our overly sugared, under-exercised environment) had exactly the opposite effect in our under-sugared, over-exercised evolutionary past.

    This is just one example of how particular physiological adaptations that had the effect of increasing fitness in past environments can have the opposite effect in our current environment. Our tendencies to consume too much sodium and too much fat can also be explained by very similar evolutionary circumstances, as can the genetic predisposition toward such nasty genetic diseases as sickle-cell anemia (and related thalasemias), cystic fibrosis, and even such mental diseases as depression and schizophrenia. What is maladaptive today can very well have been adaptive in our evolutionary past, and that seems to me to be the main point when one is considering those diseases that have evolutionary underpinnings.

  129. Nakashima in #122 and Dave Wisker in #126:

    Don’t get me wrong; as a stated in my comment to which you are reacting, I find the question of the origin of life and the genetic code to be quite fascinating, and would certainly encourage those biochemical geneticists with an interest in the subject to investigate possible scenarios.

    That said, however, I would find even the most robust evidence that particular tRNAs “naturally” (i.e. spontaneously and without enzymatic assistance) associate with particular amino acids to be indirect evidence at best. One could infer that this is a plausible explanation for the origin of the genetic code, but plausibility is not the same as entailment.

    The real problem here is that we have no direct or indirect evidence analogous to the fossil record to indicate that such a mechanism is indeed how it actually happened. This is not the case with most of evolutionary biology. Unless one is a YEC, the fossil record is a direct record of what organisms lived in the past. Yes, the relationships between fossil organisms must still be inferred (as must the absolute ages of the strata from which they were obtained), but the fossils are there, to be examined by anyone who wishes to view the evidence.

    To me the difference between the laboratory recreation of the OOL and the reconstruction of phylogenies using evidence from fossils, comparative anatomy, and comparative genomics seems to me to be analogous to the difference between circumstantial and direct evidence in criminal justice. Defendants are indeed convicted on the basis of circumstantial evidence, but there is always a lingering doubt, compared with convictions obtained through the use of direct evidence.

    And, of course, in neither case can one ever be certain. In evolutionary biology, like all of the empirical sciences, the criterion is always “beyond a reasonable doubt”, not absolute certainty.

  130. Clive hayden in #116:

    It is clear to me now that we don’t so much have a “disagreement” as a “failure to communicate”. You seem to be using the terms “natural” and “law” in a fundamentally different way than these terms are usually used by most scientists. This is why I have suggested that someone with posting privileges initiate a thread on the various meanings of these terms. I think all of us would find this illuminating, and might clear up quite a few of the misunderstandings that seem to have dogged our discussions so far.

  131. 131
    AmerikanInKananaskis

    This was one of the books that got me thinking about my personal theory of ID, where design “flaws” actually turn out to be the things that were designed.

  132. In #121 UprightBiped wrote:

    “Perhaps the metaphysical materialists on this thread would venture to answer an inconsistency in their conclusions.”

    Not being a metaphysical materialist, I must defer to those on this thread who would willingly ascribe to this moniker (if any). As I have pointed out repeatedly in the past and in other venues, metaphysics has literally nothing to do with the empirical sciences. Like Newton, “I make no hypotheses!”

    To be as clear as I can, I believe that asserting a position of “metaphysical materialism” is just that: a metaphysical assertion, not a scientific one. Confusing metaphysics with science is nearly as pernicious as confusing “ought” and “is”. The former makes for questionable science and the latter makes for questionable ethics.

  133. Why is Dave Wisker in permanent moderation? As far as I can tell, his comments have always adhered to the rules of courtesy and argumentation supported by evidence outlined in the moderation rules. Indeed, his comments have often been more concise and to the point than mine, and are at least the intellectual equivalent of those posted by David Kellogg and Nakashima. Once again I am forced to ask, is there a double standard at work here, and if so, why?

  134. On a related note, Upright Biped writes,

    Perhaps the metaphysical materialists on this thread would venture to answer an inconsistency in their conclusions.

    Perhaps if the person who was defending materialism hadn’t had his posts inexplicably deleted you might still have a materialist to try to answer that question.

    Back to waiting for consistent moderation …

  135. Once again I am forced to ask, is there a double standard at work here, and if so, why?

    Allen,

    I’m not involved in decisions as to who is placed in the moderation queue, but if I may offer a consideration in terms of pure numbers.

    In order for UD to succeed as a weblog serving the ID community, some equalization of numbers of participants in the comment section should be in order.

    The weblog could be shut down by swarming tactics, and such attempts have been made.

    I think a 60/40 balance (60 pro-ID, 40 anti-ID) would keep UD alive. If that balance is destroyed, I think readership will fall off.

    These informal discussions have their value, but I don’t consider internet blogs necessarily the best venue for careful scholarly discussion.

    So, I would not fault the moderators with double standards. The essentially serve as editors for the benefit of our readers.

    As a matter of experience, ID proponents will lose the numbers game quite easily if there were not any filtering.

    Many of our readers come here to hear the pro-ID position, and we have some obligation to deliver that.

    Consider that I created a thread like the one regarding David Abel’s paper. I was swarmed with almost 100-200 opposing postings, most of which were directed at me. Even if I felt competent to answer many of the biggest concerns, it’s a fairly substantial workload.

    For the record, I’ve not deleted any comments from this thread.

    So I plead a little forebearance in light of the fact that the ID proponents are probably outnumbered on the net. My personal experience puts the figure at about 20 to 1. Remember we are vastly outnumbered by qualified evolutionary biologists like yourself.

  136. Mr MacNeill,

    Please do not compare anyone to me! I am sure Mr isker has accomplishments far beyond mine in his own area. We should all be heard on the basis of a shared concept of human dignity – which is what is so sad about these problems of inconsistent moderation. If the forum mods just took everyone out of moderation who has ever posted a rational comment, pro or con, they would be reducing their own burden and at the same time improving the level of discourse by keeping it on point.

  137. 137

    Allen and Hazel,

    Both of you share something in common – neither of you addressed the question raised.

    A metaphysical materialist is one who operates under the unquestioned assumption that the empirical evidence will indefinitely – or even currently – supports chance and necessity as being the manifest cause of a non-physically-contingent, poly-functional, convention-based symbol system of instructions being embedded (with inherent, detectable, obvious meaning) inside of a physical object.

    I think that describes both of you, so you’ll have to forgive me if I am wrong.

    - – - – - – - – -

    Start with the nose on your face and follow its existence back through time, back through all of the material-chemical changes and origins, back through everything, and you will come to a point where you can go no further. That spot is where the material-chemical changes do not describe the next step along your way. The line of physicality has come to an end. That spot also happens to be the point where inanimate materials are powerless to become living tissue. Such are the facts. You ignore them to badger about twentieth-century tyrants and theological shortcomings, the anthropic principle, forum moderation, and computer simulations that know in advance the targets they seek.

    Let’s start a new thread about ID being the science-stopper and see if either of you have anything to say.

  138. Mr MacNeill,
    That said, however, I would find even the most robust evidence that particular tRNAs “naturally” (i.e. spontaneously and without enzymatic assistance) associate with particular amino acids to be indirect evidence at best.

    Why insist on a lack of enzymatic assistance? The motif of ‘scaffolding’ has reappeared many times in OOL discussions. Ahh, perhaps catalytic is a more general term, and more apt?

  139. Allen MacNeill @132 wrote:

    —-”As I have pointed out repeatedly in the past and in other venues, metaphysics has literally nothing to do with the empirical sciences.”

    This statement is false. As E. A. Burtt put it, “The world view is the final controlling factor in all thinking whatever.”

    Metaphysics has everything to do with empirical science. It was the Christian metaphysics that launched the entire scientific enterprise in the first place, and there can be little doubt that metaphysical beliefs are just as important today as they were centuries ago. Indeed, it is metaphysics of monistic atheism that introduced this novelty approach to science called “methodological naturalism.” Prior to Darwin and the world view that he inspired, no one had ever approached science in this way. Atheist Darwinists didn’t choose methodological naturalism because they were science purists. They chose it because allowed them to practice atheism openly while, at the same time, enjoying the benefits of “strategic ambiguity” of “plausible deniability.” [“What? Me an theist? Why no! My methodological naturalism has nothing at all to do with my metaphysical naturalism.”]

    One of the reasons why Darwinists will not budge from their position is because their global world metaphor, materialism or some metaphysical equivalent, rules out any possibility of interpreting patterns of information as evidence for design. Why argue design with someone who would not accept it under any circumstances? Also, notice the way they completely ignore or rationalize away the evidence for the “anthropic principle.” Only a firmly held world view of the most bizarre kind could prompt someone who is familiar with the evidence for a fine-tuned universe to discount the design explanation and speculate about infinite multiple universes. If, tomorrow, a pattern was found in a DNA molecule that read, “Yahweh was here,” monists would find a way to rationalize it away. Since it is their metaphysics calling the shots, it almost seems fruitless to argue science with them.

    Possibly the most destructive world view of all is the one which questions reason’s foundational principle, the proposition that we have rational minds, that we live in a rational universe, and that there is a correspondence between the two. It is this intellectual harmony between the investigator and the object of investigation that sustains rationality. Without a correspondence between the mind and the real world, there can be no rationality. Put another way, unless there is a vehicle [mind] and a destination [truth], there obviously can be no intellectual journey. I have never yet met a Darwinist who accepts this principle. Given that kind of myopia, what hope is there that they could appreciate the even more important fact that a supernatural agent [God] had to set up such a correspondence in the first place? How can we expect them to make the intellectual journey to truth, when they don’t believe that there is any destination at the end of the journey? In keeping with that principle, what can we say about the rationality of those who question very conditions necessary for rationality? Can we not say that they have chosen irrationality?

  140. StephenB,

    Crank it up man. Your on a roll.

  141. Stephen

    Well said. All reasoning — including scientific reasoning — has worldview roots.

    1] Whyzatt?

    One way to see that is the old “why accept A” argument:

    Take a generic claim A

    Why do we accept it?

    Because of B, some body of further evidence of the senses, argument, assumptions, models/explanations etc that make A plausible. (Often B is called background knowledge — which in effect is warranted, credibly true belief. But, given our finitude and fallibility — not to mention intellectual blind spots — that is not in turn certain beyond all question.)

    But, why accept B?

    Well, C. Thence, D, etc . . .

    So, we either face an infinite regress [which is impossible for us, as we are FINITE and FALLIBLE], or else we stop at a set of first plausibles, F.

    F is the core of our worldview, our faith point.

    To avoid begging the question, we may then look at live options F1, F2, F3, . . . Fn, and compare them using methods of philosophical inquiry such as comparative difficulties across factual adequacy, coherence and explanatory power [elegantly simple, but not simplistic; and certainly not an ad hoc patchwork].

    Thus, since science in particular is based on the abductive pattern of inference to best explanation, wiorldview level considerations and provisional warrant based on comparative difficulties of alteranticve explanations, is deeply embedded in the core of all scientific research programmes.

    And, of course, as Lakatos pointed out, such cores are partly protected by a belt of auxiliary models and theories, which serve to articulate the core view and couple it to empirical data. However, as protective implies, these also serve to insulate the core from critique, to a significant extent.

    Lewontin in 1997 gives us a classic illustration . . .

    2] Lewontinian materialism:

    In a now notorious 1997 NY review of Books article on Sagan’s last 9appar posthumously published) book, this leading scientist and member of the US NAS wrote:

    >> . . . to put a correct view of the universe into people’s heads we must first get an incorrect view out . . . the problem is to get them to reject irrational and supernatural explanations of the world, the demons that exist only in their imaginations, and to accept a social and intellectual apparatus, Science, as the only begetter of truth . . . . To Sagan, as to all but a few other scientists, it is self-evident that the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test . . . .

    Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen. >>

    Of course, this rests on a strawman caricature of the older teleological view of science: a world created by the Judaeo-Christian God as presented in the Bible and in Jewish and Christian thought over the ages is one of “order not confusion.”

    That order speaks of his glory and nature.

    Also, miracles, if they are to stand out as signs that point beyond the general run of nature, MUST contrast sharply to the general predictable order of Creation.

    Thirdly, if we are to be morally accountable creatures, actions must have predictable consequences in general, so that we make responsible choices.

    And so it is no surprise to see that in say Newtgon’s General Scholium to the Principia — the greatest work of modern science, and by the greatest modern scientist — we see a view that reflects just this frame of thought. indeed, Newton grounds his order of reality and the foundaiton of the space-time matrix in which his laws act, in the judaeo-Christian view of God.

    But, thanks to the dominance of materialism as Lewontin documents so tellingly, few learn of that today.

    Indeed, few even know that such a document as the General Scholium exists.

    But, it is plain that worldviews play a key role in the way science is done in any era.

    And right now, a priori imposed materialism is dominant but under serious challenge.

    _______________

    GEM of TKI

  142. 142

    Hi allen,

    That said, however, I would find even the most robust evidence that particular tRNAs “naturally” (i.e. spontaneously and without enzymatic assistance) associate with particular amino acids to be indirect evidence at best. One could infer that this is a plausible explanation for the origin of the genetic code, but plausibility is not the same as entailment

    Oh, I agree 100%. I doubt if we will ever be able to recreate the actual conditions and events.

  143. So Allen, here’s where the “worldview” comes in.

    There is reasonable doubt about whether purely natural processes can produce the information necessary to life.

    There is reasonable doubt about whether purely natural processes can produce the fine-tuning that has been demonstrated in the universe.

    There is reasonable doubt that purely natural processes can produce complex structures like a cell or a body plan.

    There is reasonable doubt that purely natural processes can produce the excellence of form seen in the species, and indeed in everything that exists.

    A worldview is evident when reasonable doubts are suppressed in order to protect the reigning paradigm.

    After all, Allen, what’s wrong with simply admitting that these are reasonable doubts?

  144. Allanius,

    That’s my point as well. Not only is there reasonable doubt that the genetic code could arise naturally there is evidence pointing to the fact that it requires intelligence.

    “What’s wrong with simply admitting that these are reasonable doubts?”. Great question.

  145. 145

    Ellijacket,

    “What’s wrong with simply admitting that these are reasonable doubts?”. Great question

    The reason it is never answered (in a straight and forthright manner) is because of the position it protects. The rules of opposing force apply. If the position can only be maintained by power, and not by reason – then zero tolerance is its only refuge.

    In other words, materialism cannot attack itself to improve its position – the reasoning behind its support.

  146. I’ve been corresponding via email with a former member of our argument here. I thought that some of her/his comments might be useful or interesting to those still engaged on this topic:

    I’ve been following the ‘Survival of the Sickest’ thread and have some comments on it and on your essay on the (un)reality of adaptations.

    First, a major area of agreement between us is that Salvador’s OP is fatally flawed by 1) his assumption that “Darwinism” implies “constant progress”, and 2) his failure to understand that fitness is always defined relative to a particular environment, and that environments change over time. You made the latter point quite cogently in your comment on Type II diabetes.

    Now, on to some points of disagreement:

    You mentioned Gould and Vrba’s 1982 paper on exaptation, and wrote:

    The reason is quite simple: if (as Gould, Lewontin, and Vrba argue) adaptation isn’t legitimately part of what evolutionary theory is about, then the whole idea of “design” and “function” is read completely out of evolution, leaving only descent with modification.

    I was very strongly influenced on this topic by Warren Allman, director of the Paleontological Research Institute here in Ithaca. He asserted that all adaptations are actually exaptations. His rationale for this assertion was that the term “adaptation” has built into it an assumption of teleology: literally translated, it means “toward usefulness”. It’s the “toward” part that is the problem. As you and I both understand it, evolution (including natural selection, but not artificial selection) does not tend toward anything. It has no goal as far as we can tell. Ergo, it builds on what has gone before, but without any specific goal “in mind”.

    This is why “exaptation” expresses better how we understand natural selection. It builds “away from” non-functionality (or even away from previous functionality), but never really “toward” anything at all as far as we can tell. And, if Sewall Wright’s “shifting balance” theory is a reasonable model of evolution, then it never really “arrives” anywhere at all, since the “goal” is constantly shifting anyway.

    I’m wondering why you think that Gould and Vrba regard adaptation as being outside the legitimate scope of evolutionary theory. My take on the paper is not that they regard the concept of adaptation as illegitimate, but just that it has been typically construed too broadly and should be broken down into the categories of true ‘adaptation’ and ‘exaptation’, where they define a true adaptation thusly:

    “Following Williams, we may designate as an adaptation any feature that promotes fitness and was built by selection for its current role.”

    The problem I have with this definition is the inclusion of the words “promotes” and “for”. “Promotion” means exactly what it says: “motion towards” something. Ergo, using this word immediately suggests teleology, and as I have pointed out above, teleology cannot be a valid assumption in the origin of the products of evolution at any level. This is not because including teleology allows for “a divine foot in the door” (Lewontin), but rather because it requires that the “plan” for the teleological process must exist prior to the realization of that process. When we do things, this assumption is perfectly valid, but when something happens in nature, such an assumption is entirely unwarranted. Where, in nature, would such a pre-existing plan exist?

    As for the word “for, I always point out to my students that teleological explanations virtually always reduce to sentences that include the phrase “in order to”. This can be shortened even further to “to” (leaving out the “in order”). However, the entire phrase “in order to” can be replaced with the word “for” without changing its meaning. Ergo, the definition quoted above is still irreducibly teleological, and therefore includes an assumption that we should not make in evolutionary biology.

    In my paper on the evolution of the capacity for religious experience, I began with a succinct definition of “adaptation”, from which I lay out four criteria that a characteristic (i.e. a “trait”) must meet to be considered a genuine adaptation.

    An evolutionary adaptation is any heritable phenotypic character whose frequency of appearance in a population is the result of increased reproductive success relative to alternative versions of that heritable phenotypic character.

    Here are the four criteria that I believe must be met for a characteristic to be considered to be an adaptation:

    1) An evolutionary adaptation will be expressed by most of the members of a given population, in a pattern that approximates a normal distribution;

    2) An evolutionary adaptation can be correlated with underlying anatomical and physiological structures, which constitute the efficient (or proximate) cause of the evolution of the adaptation;

    3) An evolutionary adaptation can be correlated with a pre-existing evolutionary environment of adaptation (EEA), the circumstances of which can then be correlated with differential survival and reproduction; and

    4) An evolutionary adaptation can be correlated with the presence and expression of an underlying gene or gene complex, which directly or indirectly causes and influences the expression of the phenotypic trait that constitutes the adaptation.

    I would now modify criterion #4 to state that such genes/gene complexes must be shown to have been conserved, relative to other sequences in the genome. However, one must keep in mind that such conservation, while necessary, is not sufficient. As we know now, some sequences are conserved, but can be knocked out, with no discernible effect on phenotype. Ergo, to fully satisfy criterion #4, a characteristic must be shown to be associated with a particular gene or gene complex, the knocking out of which can be shown to have significant negative effects on fitness.

    Obviously, this means that a great many characteristics that we observe in living organisms will not qualify as adaptations. I believe that this is fully justified, following Williams’ assertion that the concept of adaptation is “onerous” and should only be resorted to “in the last resort”. It is only by doing so that we may avoid the otherwise almost inevitable pitfall of appealing to teleology in our explanations.

    They close their paper with this:

    “The argument is not anti-selectionist, and we view this paper as a contribution to Darwinism, not as a skirmish in a nihilistic vendetta. The main theme is, after all, cooptability for fitness. Exaptations are vital components of any organism’s success.”

    There’s that nasty little word “for” again! Fitness is immediately measurable as relative differential reproductive success, but “adaptation” can only be legitimately inferred retrospectively. We can’t say that something is a genuine adaptation until it already is, and this seems to me the kind of logical circularity that has also plagued Herbert Spencer’s phrase “survival of the fittest”. If we stick to the four criteria listed above, we will rarely fall into the trap that teleological thinking always sets for us.

    Also, you later wrote the following, which seems to acknowledge that Gould and Vrba did regard adapation as a legitimate part of evolutionary theory:

    “Yes, indeed, except that I believe that Gould, Lewontin (and later, Vrba) were, like Darwin, unwilling to take their principles to their logical conclusion: that adaptations (like species) are a figment of the human imagination, and do not actually exist in nature (or, to be even more precise, do not have to exist in nature).”

    What I meant by this is that the only way we can actually “detect” the presence of adaptation is by inferring it. In that sense, adaptations are not “primary” characteristics; that is, characteristics that can be directly observed (such as differential reproductive success). Rather, such “secondary” characteristics must be indirectly inferred. In that sense, they are indeed “imaginary”; we must “imagine” that they exist (as the result of our application of inferential logic), as we cannot observe them directly.

    Am I missing something?  Are you trying to say that although Gould and Vrba regarded adaptations as real, they nevertheless thought they should be excluded from evolutionary theory?

    No, I’m saying what Williams was saying, only I’m saying it more strongly and consistently: that we should never include any hint of teleology in our explanations, as such inclusion includes the biological equivalent of that old bugaboo of physics: “action at a distance” in physics is the equivalent of “goals preceding causes” in biology.

    When I reread Williams’ famous 1966 book, Adaptation and Natural Selection, which supposedly read teleology out of evolutionary biology, I was astonished to find it shot through with the same kind of teleological reasoning that he was supposedly trying to eliminate. I think I could find all the “hidden teleology” in Williams because I have spent so much time debating with ID supporters. They are the ultimate teleologists, and can always find where we have subtly woven teleological assumptions into our biology.

    Finally, you wrote:

    “To be as clear as I can, I believe that asserting a position of “metaphysical materialism” is just that: a metaphysical, not a scientific assertion. Confusing metaphysics with science is nearly as pernicious as confusing “ought” and “is”. The former makes for questionable science and the latter makes for questionable ethics.”

    I would agree that science has no say on metaphysical questions that don’t have observable consequences (although I would argue that even then, Ockham’s razor should cause us to prefer simpler metaphysical systems to needlessly complex ones). However, some metaphysical assertions do have observable consequences. For example, I consider the existence of the YEC God to be a metaphysical assertion that has nevertheless been decisively falsified by science.

    I agree, but the same cannot be said for the more subtle versions of teleology found in Behe or Dembski. Their books (especially Dembski’s) present a much more subtle and less easily refuted version of teleological explanation, one that is easily reinforced by our own unwitting resort to teleological explanations.

    Evolutionary adaptation is where the rubber of both evolutionary theory and ID hit the pavement.

    Now on to your essay “Are Adaptations ‘Real’?” You wrote:

    “That is, although there are characteristics of organisms that are correlated with relatively high reproductive success (and would therefore be considered by most evolutionary biologists to qualify as “adaptations”), it becomes problematic to decide exactly which of those characteristics are the “real” adaptations and which are merely ‘accidental’”.

    The problem, of course, is the words “real” and “accidental”. If we are genuinely dedicated to rooting out teleology in all of our explanations of the origins of biological objects and processes, then all adaptations are “accidental”, in the sense that they are all unplanned. We perceive them as having “functions” because our naive viewpoint of reality is always teleological. We can think non-teleologically only with very great difficulty. It’s like special relativity and quantum mechanics; we have to twist our minds to be able to even begin to conceive of them, and even then we constantly slide back into our naive (and unwarranted) views of reality.

    True, if by “accidental” adaptations you mean exaptations. But while it may sometimes be difficult to tell whether an adaptation is “real” or “accidental”, that is not evidence that “real” adaptations don’t exist. Indeed, the only scenario I can envision in which “real” adaptations would not exist would be one in which every fitness-enhancing feature was an exaptation.

     

    Exactly!

    But that would mean, among other things, that every incremental improvement to the eye would have to have been the accidental result of changes that were selected for some reason other than improved vision. That seems far-fetched to me. Am I misunderstanding your position?

    It’s not that that every incremental improvement to the eye would have to have been the accidental result of something, it’s that every incremental change to the eye would have had to originate accidentally, but then be “caught” by natural selection. If we think the way you worded it (and we almost always think that way), then the teleological trap is that all of the incremental changes are somehow “predestined” and that complex eyes must be the inevitable result.

    But this just plays into the hands of the ID supporters. When we argue that “half an eye is still adaptive” we unwittingly include the assumption that “half an eye” is just that: half of what will ultimately evolve by natural selection. But our knowledge of the natural history of vision has shown us over and over again that “half an eye” is the whole thing in many cases. We can only say that the eyes of, say, flatworms, are “half an eye” because we already know that such a thing as a “whole eye” exists in cephalopods and vertebrates. We have to disabuse ourselves of the idea that any characteristic is only partially the whole deal. All characteristics of all organisms are the whole deal for those organisms, period, end of story, that’s all She wrote. Anything else contains the beginnings of teleology, and that way lies error, endlessly compounded.

    We now have the ability to selectively delete individual characteristics from many different organisms. This makes possible something that natural selection does not: the precise determination of the selective “value” of particular characteristics. This has already been done, and the surprising outcome has been that even some gene sequences that were thought to have been very important in selection (due to having been “conserved” over deep evolutionary time) are apparently insignificant or useless. We know this because knocking them out of the genome has no discernible effect on the survival or reproduction of the “knock-out” progeny.

    Precisely my point, above.

    That interpretation seems to depend on the hidden assumption that the environment hasn’t changed significantly in the recent history of the organism, and that the experimental environment is fully representative of the historical environment over the entire time during which the features in question evolved. In the case of knocked-out sequences that have no apparent effect on fitness, how sure are we that the experimental environment is fully representative in this way?

    No, but to assume that we are making the opposite mistake – assuming that some characteristic really has some function, even if that function is entirely unobservable – is once again to fall into the “teleology trap”. This is essentially the same argument that ID people make about “junk DNA”. Just because we haven’t found any function for it, doesn’t mean that all of it has no function. They argue that all of it must have some function. They are, like the evolutionary biologists for whom Williams, Gould and Lewontin, and Gould and Vrba wrote their warnings about assuming teleology in evolution, “pan-adaptationists”.

    As a hypothetical example, imagine a bacterial DNA sequence that is expressed only during the formation of spores to protect the organism during periods of extreme environmental conditions. Knock out the sequence and test the viability of the resulting variant. If the experimental environment doesn’t include the extreme conditions that induce spore formation, the organism will never attempt to express the knocked-out sequence, and so its absence will not be noticed. If the experimenter concludes that the sequence is insignificant or useless, she is mistaken.

    True, but I would strongly prefer that adaptation be considered a “diagnosis by exclusion” rather than our first and most important resort. By focusing on adaptation and natural selection, we teeter on the edge of the “teleology trap” and often (maybe even usually) fall in, despite our best efforts to avoid doing so.

    Too bad I couldn’t post all of this on the thread at UD, where it belongs. Oh well.

    I’ll see if there is something I can do about that. Barry (and especially Sal) don’t seem to view themselves as censors/keepers of the faith. Having been shot down several times, and risen each time from “bannination/moderation hell”, the only thing I can suggest is to keep telling them that you will henceforth always “play nice”, and would they please let you rejoin the argument?

    This is part of my bedrock philosophy of life: if you don’t ask, it won’t happen. If you do ask, it may still not happen, but if you don’t ask, it definitely won’t happen. So, if you want to stay in the argument, keep asking to rejoin it. The worst that can happen is that they will say no.

  147. In #139 stephenB wrote:

    As E. A. Burtt put it, “The world view is the final controlling factor in all thinking whatever.”

    It’s very interesting that you would bring up my old friend/Friend Ned Burtt. He was one of the founders of the Ithaca Monthly Meeting of Friends, of which I am a member. He ans his wife, Marjory, were long-time Friends, and I recall fondly many, many meetings in which Ned spoke “to the Light” and “in the Spirit of Truth”. I consider him to be one of my personal mentors, and miss his calm, loving presence in meeting very much.

    And I agree that all worldviews are ultimately founded on a metaphysical choice. In my case, I have chosen methodological naturalism as the most reliable guide for doing science. That said, I personally believe that this choice is not logically connected in any way to my choice to not accept ontological naturalism as valid. To do the latter, one must use completely different logical criteria than to do the former, and I do not (contra Dawkins, et al) think that asserting that methodological naturalism necessarily requires ontological naturalism

  148. eligoodwin:

    If you can’t tell the difference between the two scenarios, then you’re not being thoughtful enough—or, perhaps honest enough. What you propose that clouds can do, clouds actually do—you and I have both eexperienced it. Now the question is: would you expect the machine I described to ‘randomly’ produce the image of a squirrel. This question is for you to honestly consider and answer.

  149. Nakashima:

    Please forgive me for comparing you with someone else. We are all of us, incomparable, all of the time, in all conceivable circumstances.

    I shall in the future attempt to forgo all attempts at invidious comparison…

  150. In #137 UprightBiped wrote:

    “A metaphysical materialist is one who operates under the unquestioned assumption that the empirical evidence will indefinitely – or even currently – support chance and necessity as being the manifest cause of a non-physically-contingent, poly-functional, convention-based symbol system of instructions being embedded (with inherent, detectable, obvious meaning) inside of a physical object.”

    Given your definition, then I am definitely not a “metaphysical materialist”. And so, you are indeed forgiven for being completely wrong.

  151. Nakashima-san in #138:

    Indeed, “catalytic” was precisely the word I was searching for, but failed to find. Once again you have shown superior discernment! My humblest and most heartfelt thanks…

  152. In #139 stephenB asserted:

    “Prior to Darwin and the world view that he inspired, no one had ever approached science [using methodological naturalism].”

    This statement is demonstrably false. Indeed, that was Ned Burtt’s whole point in his monumental book, The Metaphysical Foundations of Modern Physical Science. In that book professor Burtt emphasized precisely this point: that Newton adhered to methodological naturalism in his science, while hewing to metaphysical theism in his personal beliefs. Hence, his famous dictum “I make no hypotheses!” refers only to his science, as anyone who has read his meandering and ultimately fruitless musings on alchemy can attest.

    This is basic history and philosophy of science, stephen, and you have clearly gotten it completely and demonstrably wrong.

  153. To follow up, this is also the reason why Darwin is often referred to as the “Newton of biology”. He extended Newton’s methodological naturalism to biology, by proposing an hypothesis (i.e. natural selection) in which the origin of the teleological characteristics of living organisms (i.e. adaptations) could be fully explained by a non-teleological process.

    So, why is teleology such a “bad” thing, so bad that it seems to invalidate all of methodological naturalism? Simple: without teleology, there is no need for an Intelligent Designer. If one has a prior (i.e. metaphysical) commitment to the existence of such an entity, then one cannot, on principle, push the Divine foot out of the door.

  154. Sorry, I should have referred to teleology as a “good” thing in the previous comment. ID supporters see teleology is not only “good” but as irremovably rooted in “that which is the source of all goodness”.

    Empirical scientists (at least those who do not have a prior commitment to ontological naturalism) see teleology as unnecessary, not “bad” (those who – like Dawkins et al – have a prior commitment to ontological naturalism assert, without evidence, that it does not exist).

  155. Atheist Darwinists didn’t choose methodological naturalism because they were science purists. They chose it because allowed them to practice atheism openly while, at the same time, enjoying the benefits of “strategic ambiguity” of “plausible deniability.” [“What? Me an theist? Why no! My methodological naturalism has nothing at all to do with my metaphysical naturalism.”]

    Again, false. As you have studiously avoided acknowledging, there is no necessary connection between being an evolutionary biologist and being an atheist. I have repeatedly cited famous examples to the contrary, and you have consistently ignored them. Indeed, you have asserted in your parenthetical statement at the end of the comment that you, like Dawkins, think your opponents are either deluded, insane, or lying (and since all of us recognize the reference, evil as well).

    You have, in other words, consistently put words in other people’s mouths, charged them with misguided and/or negative intentions and motivations, and deliberately mischaracterized all arguments and evidence to the contrary.

    Why, exactly, do you do this, stephen?

  156. On a roll, indeed, but toward what?

  157. “I have never yet met a Darwinist who accepts this principle.”

    Have you ever had an actual conversation with an evolutionary biologist? To me, your constant, unsubstantiated charges against us, and your consistent mischaracterization of all of us (apparently on the basis of your hatred for Richard Dawkins) indicates that you haven’t actually met anyone who disagrees with your position.

    This, of course, makes for powerful polemics, but is death to rational argument.

  158. 158

    Allen,

    You do not question the efficacy of chance and necessity in formalizing the algorithmic instructions that are required by Life. You do this in the face of substaintial empirical evidence to the contrary.

    You are a metaphysical materialist, even as you attempt to parse the issue.

  159. Allen.

    Maybe you wan to summarize your thoughts on your blog on all this. I haven’t had to time to read everything let alone digest it. But when you post on your own blog, it can be analyzed with less time spent by everyone. I know this imposes a burden on you and you can certainly take your time to do it since I know you have other responsibilities especially current ones.

    However, I want to say one thing. And that there is a direction in evolution. To say there isn’t is absurd. You can argue that it was not a pre planned direction but there is definitely a direction. Just take the number of cell types and extrapolate that out from the Cambrian to now and you will get a direction. Take the various capabilities and extract that out. The main one being neural or mental capability. There is definitely a direction.

    I suggest you read Brosius again in the Vrba and Eldredge book and see what he thinks about direction. As I said you can argue that it not a pre planned direction but it definitely exists.

    The very process of whatever evolutionary theory you pick will if it includes fitness will have a direction. You can point to the idea that no one knows what the current environment will do but some of your supposed explanations for macro evolution will lead to organisms with more capabilities surviving. You yourself have even invoked it in the past when it was convenient for you to do so. For example, in the origin of multi-cellular organisms and their increased size.

    And as far as this direction to evolution is concerned, is it as prevalent in other phyla as it is in vertebrates especially in the last 100 million years.

  160. In #142, allanius asserts:

    There is reasonable doubt about whether purely natural processes can produce the information necessary to life.

    There is reasonable doubt about whether purely natural processes can produce the fine-tuning that has been demonstrated in the universe.

    There is reasonable doubt that purely natural processes can produce complex structures like a cell or a body plan.

    There is reasonable doubt that purely natural processes can produce the excellence of form seen in the species, and indeed in everything that exists.

    A worldview is evident when reasonable doubts are suppressed in order to protect the reigning paradigm.

    After all, Allen, what’s wrong with simply admitting that these are reasonable doubts?

    On the contrary, I heartily agree with Augustine of Hippo, who asserted:

    “Si enim fallor sum”

    I strongly believe that there is “reasonable” doubt in both directions, on all of these points. The only way to reduce such doubts is to follow the evidence wherever it leads. This means that one must be able to find empirical evidence; that is, evidence that is “self-evident”, that anyone can observe and evaluate.

    Ergo, the most warranted position is one of consistent skepticism, evenly applied on both sides of the issue. In the case of ID, this means that there must be empirical evidence that unambiguously supports the ID hypothesis, and simultaneously falsifies the evolutionary hypothesis. Simply showing that both hypotheses are possible isn’t doing science, it’s doing apologetics (and shades into propaganda).

    Furthermore, for our inferences about nature to be as reliable as possible, such skepticism should be pursued without limit. The empirical sciences are founded on exactly this kind of skepticism. Indeed, since the empirical sciences are ultimately grounded in inductive reasoning, they literally cannot be otherwise.

    To be a scientist, one must be ready and willing to give up one’s most cherished preconceptions about nature. To paraphrase the Bard of Avon:

    “Doubt thou the stars are fire, Doubt that the sun doth move, Doubt truth to be a liar, And always doubt your love!”

    To do otherwise is to open the door to credulity, which opens the door to error, which opens the door to madness, which opens the door to great evil.

  161. In #158 jerry suggests:

    “I suggest you read Brosius again in the Vrba and Eldredge book and see what he thinks about direction. As I said you can argue that it not a pre planned direction but it definitely exists.”

    I have read Brosius, repeatedly, and agree that he makes a strong case for directionality in macroevolution. However, as you suggest, directionality is most emphatically not the same as teleology. Simply observing that there is an overall increase in complexity over deep evolutionary time does not necessarily mean that this process is either planned or progressive.

    On the contrary, a later article by McShea in the same anthology proposes a very interesting hypothesis that “complexification” can evolve without natural selection, via a completely natural process he refers to as “internal variance”. I strongly recommend that you read this article, so that we may discuss its implications further, perhaps in later threads.

  162. jerry suggests that I might want to summarize my thoughts on all of this at my blog. I don’t think that blogs are the best place to do this, and so I am currently writing a book on the subject (that is, trying to write a book on the subject while teaching seven courses, raising four children, being a good husband, and trying to get some sleep). It will come, eventually, and I will keep everyone posted as to developments.

    BTW, I have been helped immensely in the writing of my forthcoming book by our discussions here, and especially by the criticisms brought against my views by my dedicated opponents. This is the true value of lively debate; it helps us come to clarity about what we understand, and to find the weak points in our own arguments. So, to all who have made rational arguments, supported by evidence (and generally free of ad hominem attacks, my heartfelt thanks!

  163. In #144 UprightBiped asserted:

    The reason it is never answered (in a straight and forthright manner) is because of the position it protects. The rules of opposing force apply. If the position can only be maintained by power, and not by reason – then zero tolerance is its only refuge.

    In other words, immaterialism cannot attack itself to improve its position – the reasoning behind its support. [Emphasis and the prefix "im" added]

    I couldn’t have said it better myself (with the slight correction noted in my emphasis, above).

  164. In #158 UprightBiped asserted:

    “You do not question the efficacy of chance and necessity in formalizing the algorithmic instructions that are required by Life. You do this in the face of substaintial empirical evidence to the contrary.

    You are a metaphysical materialist, even as you attempt to parse the issue.

    I assume that your are once again referring to the origin of life and the genetic code, here. And what might that “empirical” evidence be? And please, don’t resort to arguments by analogy (i.e. some of the information produced by us is the product of intelligence; ergo, all information must be the product of intelligence). Simply repeating the same analogy over and over again adds nothing to its credibility.

    And I could just as easily assert that you are a metaphysical inmaterialist, even as you attempt to parse the issue. How, exactly, does such name-calling advance either side of the argument?

  165. If you think that arguments by analogy are valid, consider this one:

    “Some of the pollution in our environment is produced by us, as a by-product of our intelligence; ergo, all of the pollution in our environment must be a by-product of our intelligence.”

    Clearly false, unless one can show empirically that volcanic eruptions and other “natural” sources of pollution are somehow the product of human intelligence.

  166. Allen, Allen, you are worried about many things. “Error…madness…great evil”…it’s amazing you can grade all those exams while laboring under such a terrible burden.

    Allowing the little children to think even for a moment that there might be a designer—one can see why you might be haunted by this horrible thought. But my dear friend, don’t allow yourself to be so distracted by your grief that you keep on changing the subject.

    The question is whether “science” really can be pure, as you claim, or whether it is mingled inevitably with one’s worldview. The witchhunt against ID, which includes the kind of furious resistance to reasonable doubt seen in so many of your posts, indicates that Darwinism is not merely pure science but also “entails” a worldview that you want to preserve.

    In other words, the very fervor of your comment disproves your own disclaimer. But let not your heart be troubled. We don’t plan on throwing you in jail.

  167. At least not until you’re done grading those papers.

  168. This statement is demonstrably false. Indeed, that was Ned Burtt’s whole point in his monumental book, The Metaphysical Foundations of Modern Physical Science. In that book professor Burtt emphasized precisely this point: that Newton adhered to methodological naturalism in his science, while hewing to metaphysical theism in his personal beliefs. Hence, his famous dictum “I make no hypotheses!” refers only to his science, as anyone who has read his meandering and ultimately fruitless musings on alchemy can attest.

    This is basic history and philosophy of science, stephen, and you have clearly gotten it completely and demonstrably wrong.

    Allen,

    I’m a pragmatist. I generally avoid debates about demarcation as I don’t think it necessarily brings us closer to understanding what is true.

    Yockey (an agnostic) and Trevors (an atheist) have made strong suggestions that properties of the natural phyiscal universe are outside of scientific inquiry. That is, one can even be a materialist and acknowledge that truths about the physical universe may be out of the reach of empirical science.

    On a personal level, there may be true statements about the world where all we can offer might be an educated guess. The challenge is that it seems the most important truths often seem the most hidden. As Yockey said, quoting the Apostle Paul, “we see through a glass darkly”.

    That said, I think teleological metaphors being introduced into biology is a metaphysical intrusion. I think this is perfectly legitimate from an operational standpoint, it seems this intrusion seems to work.

    Even granting my advocacy of teleology in biology might have nefarious motives (wink), can we agree that it is a metaphysical intrution of subjective ideas creeping slowly into science? And this not necessarily because of the ID movement. Actully the revival of the ID movement is a symptom of this metaphysical intrusion as perpetuated by non-ID proponents.

    I think you’ve answered the question before, but I just want to make sure I understand your position.

    Is teleology in biology a metaphysical intrusion? And has this metaphysical intrusion continued to persist, partly due to those who are not even favorable to ID?

  169. In #168 sal notes:

    “…one can even be a materialist and acknowledge that truths about the physical universe may be out of the reach of empirical science.”

    One can also be a methodological naturalist and acknowledge precisely the same thing. At least, that’s what I do, and see no logical contradiction whatsoever.

    Sal also asks:

    “Is teleology in biology a metaphysical intrusion? And has this metaphysical intrusion continued to persist, partly due to those who are not even favorable to ID?”

    To the first question, I answer unequivocally, yes. The invocation of teleology in nature is the invocation of something that cannot be empirically demonstrated. Indeed, I would assert that teleology (i.e. “final causes”) cannot be observed, on principle. Final causes can only be inferred. The same would be true for “formal causes” as well.

    It was very fruitful to me to review Aristotle’s four causes, in the light of what I understand to be the foundations of modern empirical science. When I did, it became clear to me that modern science simply ignores both formal and final causes, and sticks strictly to material and efficient causes. This is because the former can only be inferred, whereas the latter can be directly observed.

    In answer to the second question, I would say that evolutionary biologists (including Darwin himself) are at least partially to blame for the persistence of teleological explanations in evolution. There are many “mined” quotes to this effect, and I readily admit that they are unfortunate.

    This is why I have argued that it may be necessary to jettison the entire concept of “adaptation” in favor of Gould and Vrba’s concept of “exaptation”. While the latter still includes some echo of functionality, it places the emphasis on the perspective from which one infers such functionality: retrospective, rather than prospective.

    As I once wrote in an entirely different context, the only thing that makes mortality tolerable is its absolutely intolerable uncertainty.

  170. Mr MacNeill:

    Analogies are obviously not demonstrative proofs. But, neither are scientific theories, models or definitions — for all of which analogous reasoning is deeply embedded.

    We do not treat them as pretended proofs but as to be validated empirically on a case by case basis. then, we use that which is empirically reliable as rtrustworthy until shown falsified.

    And, I include definitions in there as these in the first instance are based on concept formation by identified examples and family resemblance thereto.

    That is, by analogy.

    And, in fact we develop definitions in terms of precising necessary-sufficient statements by testing them against cases that accord with that concept. (Similarly, on genus-difference.)

    A classic case in point is the definition of the subject matter of your discipline, life.

    There is no one size fits all generally accepted definition, and so a list of major typical characteristics has been identified and is used to assess possible cases on family resemblance.

    So, to make a broad brush dismissal of reasoning by analogy is selectively hyperskeptical; and even self referentially inconsistent.

    It would be far better to examine the cases and see if the family resemblance claim is warranted.

    When it comes tot he claimed origin of complex digital information that functions algorithmically by lucky noise; we have not analogy but instantiations of such digital information on a very large inductive data base. There are ZERO cases where such have originated by lucky noise within our observation.

    And, by turning to the mathematics of large contingency spaces we see why easily enough: islands of function (notice the simplifying analogy to make a valid point) are deeply isolated in the wider space of all configs so that random walk based searches are hopelessly challenged to get to shores of initial function before they can apply hill climbing algorithms. (And of course notice how deeply analogies are embedded in the technical not just the popular level language. No prizes for guessing why.)

    The real first challenge is for you to show that within the reasonable probabilistic resources of a planet, or a deep sea vent or a comet’s ball of ice or whatever, we can on the gamut of our observed cosmos reasonably get to spontaneous formation of first life. Thereafter, you need to show how innovations of body plans — on teh gamut of several thousand millions of years on a planet of our scale — would plusibly get to docverns of times over 10′s – 100′s of mega bits of further bio-functional informaiton required to specify body plans. Without intelligent intervention.

    We know that intelligent agents can produce 100′s k bits to 100′s or 1,000 of mega bits of digital functional information all the time. And, we know that in the heart of the cell is a digital, data storing, code using [i.e language using] structured, algorithmic [thus logical-phsyical] information system with flexible programs. That is, a computer implemented with molecular nanotechnologies.

    Instantiation, as observed, not mere analogy. [Four-state digital systems are digital systems. Digital systems that act in accord with codes and algorithms to effect flexible sequences of actions that lead to definite predictable outcomes, are computers. just as Babbages’ machine built in the end with gears etc was a computer, and just as relay machines are computers, as well as valve based ones or transistor or IC based ones. just as it is possible to do so with other technologies. Molecular technologies, we have not yet learned how to implement but on the density of DNA info storage, that looks like it may be well worth doing.)

    GEM of TKI

  171. To the first question, I answer unequivocally, yes. The invocation of teleology in nature is the invocation of something that cannot be empirically demonstrated. Indeed, I would assert that teleology (i.e. “final causes”) cannot be observed, on principle.

    I agree that teleology in biology is a metaphysical intrusion.

    My sense is that this intrusion is less because of religious motives and more so because the intrusion helps the scientific enterprise so well.

    Let me explain. There is close kinship between empirical science, engineering, and medical science.

    In engineering, teleology is the order of the day, albeit the intelligent designer is well known in that case.

    The language of engineering is being imported into biology,and this has only been speeded up because of the cross-disciplinary exchange of ideas.

    Medical science treats biology as collection of systems, thus they reinforce the teleological metaphors. Thus medical science together with engineering are sustaining the importation of teleology into empirical science.

    My view is that this metaphysical intrusion is not damaging the advance of biology. But my opinion counts for little in the scheme of things. The decision will be made by biologists whether to perpetuate or even further these metaphysical intrusions.

    I suspect teleology can’t be successfully removed from biology. It’s too useful operationally.

    And to make a weak tie to the original point, the notions of “sickness” and “wellnes” are best appreciated with reference to teleology.

  172. 172

    Allen, you are gaming again.

    I have asserted nothing immaterial (or un-natural or teleological for that matter) I accept (and depend upon) the material world exactly as it presents itself through observation. It is you who is demanding something more from material that material can deliver.

    And Allen, there are no analogies needed. The transcription and translation system of DNA isn’t like a symbol system – it is a symbol system. It is not like a conventional code, it is a conventional code. If the convention in nucleic sequencing was physically contingent, then it would be a chemical reaction that is like a symbol system – but it is not contingent, nor is it merely as chemical reaction. There is nothing in the physical laws of this Universe that says this information has to exist the way it does, in fact, as far as the physical laws of the Universe are concerned, it doesn’t even have to exist at all. In other words, there is absolutely nothing in the physical laws that makes it exists – but it exists anyway, without physical laws to explain it.

    This leaves you with only pure random chance to explain how these non-physically-caused instructions and algorithms came to exist in a physical object. This is like asking random chance to explain any other language or instructions – it simply can’t. Nowhere in the history of the Universe can science demonstrate that random chance created a language or formulated instructions in any material object whatsoever. As far as anyone knows, it’s never happened, and there is no scientific reason to believe it ever has, or ever will.

    Also, there is nothing in the combination of physical law and chance that can explain this evidence. The two acting together cannot even begin to explain the factual existence of complex algorithmic instructions existing in a linear digital code (with meaning) within a material object. (The data even going so far as to say the coding is polyfunctional, creating even further barriers to a chance emergence).

    To require a priori assumption that chance and necessity are the causes of embedded complex algorithms in a material object – when the evidence is 100% opposite to that conclusion – is patently irrational. And, sticking your head in the sand and assuming that the answer to an intractable physical problem will be forthcoming, therefore it is safe to make an assumption (against the evidence) is…above the physical, it is meta-physical.

  173. I would only agree if it could be conclusively shown, using empirical methods, that there is no necessary relationship between the various levels of the genetic code (that is, between the nucleotide sequences in DNA, RNA, and amino acids). That is, to eliminate the “necessity” alternative, one would have to show that there is no tendency, based on physical chemistry alone, for particular RNAs to be associated with particular amino acids.

    I assume even you would agree that there is, indeed, a very simple physical/chemical reason why particular RNA nucleotides are associated with particular DNA nucleotides – this was, after all, the realization for which Watson and Crick were awarded their Nobel Prize.

    By the same argument, it is relatively easy to show that on purely physical/chemical reasons alone, particular protein active sites are associated with particular substrate molecules. This is, after all, how enzymes function; they violate no known rules of physical or stereochemistry.

    Ergo, the real “hinge” of the OOL debate is the relationship between the sequence of nucleotides in the anticodons of tRNA and the amino acids that are specifically associated with those anticodon sequences. Until this issue is resolved, there will be no resolution to the question of “chance” versus “necessity” versus “design” in the origin of the genetic code.

    In brief:

    IF: there is some empirically demonstrated necessary relationship between anticodon sequence and amino acid specified, then a purely “natural” explanation for the origin of the genetic code will almost certainly be forthcoming.

    However,

    IF: there is no empirically demonstrated necessary relationship between anticodon sequence and amino acid specified, then there are two alternatives: “frozen accident” (i.e. pure “chance”) versus “design”.

    I’m not really certain how these two could be empirically distinguished, although I suspect that an approach similar to that of Dr. Dembski might prove useful.

    In this context, it is very interesting to me to discover that the question of homochirality (indeed, levorotary homochirality) in biotic amino acids seems now to have been shown to have an entirely “natural” basis. See:

    http://www.newscientist.com/ar.....-asteroids

    One down, one to go…

  174. Kairsofocus:

    Analogies are obviously not demonstrative proofs. But, neither are scientific theories, models or definitions — for all of which analogous reasoning is deeply embedded.

    Agreed.

    To add to the idea of analogies being used in science.

    From Lewontin, Triple Helix page 71:

    If the animal is like a mchine, as Descartes claimed in Part V of the Discourse on Method, then it is made up of clearly distinguishable bits and pieces, each of which has determined causal relation to the movement of other bits and pieces.

    But Decartes’s machine model is not only a description of how the world operates but also a manifesto for how to study natural phenomena.


    Such an analytic mode of understanding and study of biological systems, appropriate to a machine, is implied in the very word organism, first used in the eighteenth century. The analogy is between the living body and the musical instrument composed of separte parts that work together to produce a variety of final functions.

    To be fair, it appears Lewontin was critical of the Cartesian approach, but this seems to be the very manifesto of Systems Biology!

    I’m not necessarily saying how science ought to be run. As I’ve said, my opinion counts for little. I leave the running of science to the scientists.

    I’m merely observing that it seems reasoning-through-analogy is par for the course in empirical science. Further, it seems its going to be impossible to exorcise the machine metaphor from empirical science. Subjectivism is becoming the order of the day in empirical science, particularly biology.

    This sort of subjectivism is par for the course in engineering, and it looks like it is bleeding over into biology.

  175. —-Allen: And I agree that all worldviews are ultimately founded on a metaphysical choice.

    Well, then, you ought to retract your earlier statement in which you held that metaphysics has nothing at all to do with empirical science, when it is clearly the case that it has everything to do with empirical science.

    —-In my case, I have chosen methodological naturalism as the most reliable guide for doing science. That said, I personally believe that this choice is not logically connected in any way to my choice to not accept ontological naturalism as valid. To do the latter, one must use completely different logical criteria than to do the former, and I do not (contra Dawkins, et al) think that asserting that methodological naturalism necessarily requires ontological naturalism.

    The institutional motive, (I can say nothing of your personal motive) for establishing methodological naturalism [in the 1980s] was to rule out the design paradigm. It isn’t any more complicated than that.

    —-“This statement is demonstrably false. Indeed, that was Ned Burtt’s whole point in his monumental book, The Metaphysical Foundations of Modern Physical Science. In that book professor Burtt emphasized precisely this point: that Newton adhered to methodological naturalism in his science, while hewing to metaphysical theism in his personal beliefs. Hence, his famous dictum “I make no hypotheses!” refers only to his science, as anyone who has read his meandering and ultimately fruitless musings on alchemy can attest.”

    You misread history in the most profound way. Here is the crucial distinction that you miss, [notice I didn’t say ignore (this is the kinder, gentler me)]: To say science is “primarily” about natural causes is not at all the same thing as to say that science is “exclusively” about natural causes. Methodological naturalism is a recent arbitrary rule which holds that science is “exclusively” about natural causes. Newton did not and could not have embraced such a position. He was well aware that only the individual scientist knows which problem he wants to solve, and therefore only the individual scientist can choose methods appropriate to the problem. The scientist’s methods are either rigorous or they are not, but they need not follow a set of “rules.” If a scientist needs institutional supervision to practice his discipline, he is hardly worthy of being called a professional. Anyone who does not understand this either has never practiced science or is doing it the wrong way.

    —–Allen: “This is basic history and philosophy of science, stephen, and you have clearly gotten it completely and demonstrably wrong.”

    Sorry, but the error is on your part. As far as I know, the term “methodological naturalism” is in no book about the history of the philosophy of science or in any treatment of the philosophy of science prior to 1980. If you can provide me with evidence to the contrary, I will modify my position. Meanwhile, it is obvious that Newton was not an advocate of “methodological naturalism,” nor is there any that he could have been. At no time did Newton declare that science is “exclusively” about natural causes, and he was obviously aware of the fact that it need not be so. If that was the case, the Catholic Church could not investigate miracles attributed to saints during the canonization process. Are you prepared to tell the entire medical community that they are not doing science when they distinguish between natural causes and supernatural causes, when that is precisely what they have been called on to do in the name of science?

    This entire discussion began when you contended that metaphysics have nothing to do with science. Obviously, that is not the case. You are now agreeing with the same point which you attempted to refute in an earlier post. The correct response should not be, “I agree,” but rather, “I stand corrected.” When you finally come to agree with me on this second point, the proper response at that time should also be, “I stand corrected.”

  176. at 173 Allen MacNeill helpfully endorses negative evidence and the validity of at least the one node of Dembski’s EF.

    Unfortunately, he makes a rather blatant error wrt DNA and code. It is not that there is some necessary relationship between DNA and RNA, RNA and AA, etc. But rather, that there is no necessary relationship (via physics and chemistry) exhibited in the ordering of the DNA nucleotides which, ultimately, are responsible (as far as we know) for the AA ordering and the protein product.
    This is like saying that there is a relationship between how we sound out written letters, and how those sounds are interpreted as words, and how those words form sentences as though this could explain the meaningful ordering of the letters in the first place.

  177. In this context, it is very interesting to me to discover that the question of homochirality (indeed, levorotary homochirality) in biotic amino acids seems now to have been shown to have an entirely “natural” basis.

    That was one big easy gulp from speculation to fact.

  178. 178

    Allen,

    “It is clear to me now that we don’t so much have a “disagreement” as a “failure to communicate”. You seem to be using the terms “natural” and “law” in a fundamentally different way than these terms are usually used by most scientists.”

    That is exactly right, and my quote from Chesterton explains that how the terms “natural” and “law” are usually used are unintellectual, for they assume an inner synthesis between the “laws,” and pertaining to the “laws” that we don’t possess.

  179. 179

    Allen,

    What? There is no physical relationship between nucleic sequences and the amino acids that transpire thereafter. This is not even a question.

    The sequencing of nucleotides in DNA also prescribes highly specific regulatory micro RNAs and other epigenetic factors. Thus linear digital instructions program cooperative and holistic metabolic proficiency.

    Not only are symbol systems used, but a bijection must occur between two independent symbol systems. Bijection (translation; a symbol system to symbol system correspondence) is rule-based, not physical law-based. No cause-and-effect necessity exists in the linking of anticodons, amino acids, tRNAs, and amino acyl tRNA synthetases with codons. The anticodon is located on the opposite end of tRNA from the amino acid. The correspondence between the two languages is arbitrary and abstract. By arbitrary, we do not mean random. Arbitrary means free from physicodynamic determinism. Bijection rules are freely selected. Translation of this linear digital prescription into functionally specific polyamino acid chains cannot be explained by physicodynamics.” (The Capabilities of Chaos and Complexity – Abel – Journal List > International Jopurnal of Molecular Sciences > v.10(1); Jan 2009 : Received November 6, 2008; Revised December 27, 2008; Accepted January 4, 2009

    Your argument holds no water Allen.

  180. “…let us not play into the hands of ID propagandists. For instance, be careful about using teleological words to describe biological entities in our teaching and writing. Calling cells “machines that do X” or describing biological structures as “well designed to do Y” will be duly cited in ID propaganda as one more biologist-supporting design.” –

    Rudy Raff,
    Indiana University
    “Stand up for evolution”
    Evolution and Development, 2005

  181. Re UprightBiped in #179:

    “Your argument holds no water Allen.”

    On the contrary, it’s the current (i.e. last month) argument from empirical science:

    ABSTRACT: In distinction to single-stranded anticodons built of G, C, A, and U bases, their presumable double-stranded precursors at the first three positions of the acceptor stem are composed almost invariably of G-C and C-G base pairs. Thus, the “second” operational RNA code responsible for correct aminoacylation seems to be a (G,C) code preceding the classic genetic code. Although historically rooted, the two codes were destined to diverge quite early. However, closer inspection revealed that two complementary catalytic domains of class I and class II aminoacyl-tRNA synthetases (aaRSs) multiplied by two, also complementary, G2-C71 and C2-G71 targets in tRNA acceptors, yield four (2 × 2) different modes of recognition. It appears therefore that the core four-column organization of the genetic code, associated with the most conservative central base of anticodons and codons, was in essence predetermined by these four recognition modes of the (G,C) operational code. The general conclusion follows that the genetic code per se looks like a “frozen accident” but only beyond the “2 × 2 = 4” scope. The four primordial modes of tRNA–aaRS recognition are amenable to direct experimental verification.

    Read the entire article here:

    http://www.pnas.org/content/94/10/5183.full

    The reference you quoted (Abel, 2008) has no empirical foundation, and is merely a theoretical analysis, which has now been falsified.

    If you disagree, please cite references from reputable peer-referenced scientific journals that support your position.

  182. In #177 Charlie notes:

    “That was one big easy gulp from speculation to fact.”

    Indeed, that’s what happens when you find empirical evidence; unverified hypotheses become verified “facts”.

  183. Mr MacNeill,

    The only quibble I have is your phrase “has now been falsified”. If I read that PNAS paper correctly, it is from 1997. Perhaps the falsification occured deeper in the past.

  184. Re stephenB in #145:

    Your assertion that no one in the sciences used methodological naturalism to investigate nature until the 1980s is laughable. It may indeed be the case that no one called it “methodological naturalism” until fairly recently, but the worldview subsumed by that term has been used by philosophers and scientists for almost 3,000 years.

    The pre-Socratics of Ionia (circa 7th century BC) are generally credited with initiating “methodological naturalism” as a viewpoint from which to investigate the natural world. Virtually all historians of philosophy and science agree that Thales, Anaximander, Leucippus, Democritus of Abdera, Empedocles, Heraclitus, and most of the other pre-Socratics were doing exactly what you assert wasn’t done until the 1980s.

    “The modern emphasis in methodological naturalism primarily originated in the ideas of medieval scholastic thinkers during the Renaissance of the 12th century:

    “By the late Middle Ages the search for natural causes had come to typify the work of Christian natural philosophers. Although characteristically leaving the door open for the possibility of direct divine intervention, they frequently expressed contempt for soft-minded contemporaries who invoked miracles rather than searching for natural explanations. The University of Paris cleric Jean Buridan (a. 1295-ca. 1358), described as “perhaps the most brilliant arts master of the Middle Ages,” contrasted the philosopher’s search for “appropriate natural causes” with the common folk’s habit of attributing unusual astronomical phenomena to the supernatural. In the fourteenth century the natural philosopher Nicole Oresme (ca. 1320-82), who went on to become a Roman Catholic bishop, admonished that, in discussing various marvels of nature, “there is no reason to take recourse to the heavens, the last refuge of the weak, or demons, or to our glorious God as if He would produce these effects directly, more so than those effects whose causes we believe are well known to us.”

    Enthusiasm for the naturalistic study of nature picked up in the sixteenth and seventeenth centuries as more and more Christians turned their attention to discovering the so-called secondary causes that God employed in operating the world. The Italian Catholic Galileo Galilei (1564-1642), one of the foremost promoters of the new philosophy, insisted that nature “never violates the terms of the laws imposed upon her.” [Ronald L. Numbers (2003). "Science without God: Natural Laws and Christian Beliefs." In: When Science and Christianity Meet, edited by David C. Lindberg, Ronald L. Numbers. Chicago: University Of Chicago Press, p. 267.]

    There’s more:

    Isaac Newton, when asked about the lack of mention of God in his works on physics, is said to have replied, “Hypotheses non fingo.” (“I do not make hypotheses.”) Similarly, Pierre Simon de Laplace, when asked about the lack of mention of God in his work on celestial mechanics, is said to have replied, “I have no need of that hypothesis.”

    During the Enlightenment, a number of philosophers including Francis Bacon and Voltaire outlined the philosophical justifications for removing appeal to supernatural forces from investigation of the natural world. Subsequent scientific revolutions would offer modes of explanation not inherently theistic for biology, geology, physics, and other natural sciences.

    Here, apparently is the source of your confusion:

    The term “methodological naturalism” for this approach is much more recent. According to Ronald Numbers, it was coined in 1983 by Paul de Vries, a Wheaton College philosopher. De Vries distinguished between what he called “methodological naturalism,” a disciplinary method that says nothing about God’s existence, and “metaphysical naturalism,” which “denies the existence of a transcendent God.”

    [...de Vries, then at Wheaton College,...it at a conference in 1983 in a paper subsequently published as “Naturalism in the Natural Sciences,” Christian Scholar’s Review, 15(1986), 388-396. De Vries distinguished between what he called “methodological naturalism,” a disciplinary method that says nothing about God’s existence, and “metaphysical naturalism,” which “denies the existence of a transcendent God.” (p. 320 of: Ronald L. Numbers, 2003. “Science without God: Natural Laws and Christian Beliefs.” In: When Science and Christianity Meet, edited by David C. Lindberg, Ronald L. Numbers. Chicago: University Of Chicago Press, pp. 265-285.)

    The term "methodological naturalism" had been used in 1937 by Edgar Sheffield Brightman in an article in The Philosophical Review as a contrast to "naturalism" in general, but there the idea was not really developed to its more recent distinctions.[ http://www.calvin.edu/archive/asa/200603/0501.html ]

    In a series of articles and books from 1996 onwards, Robert T. Pennock wrote using the term methodological naturalism to clarify that the scientific method confines itself to natural explanations without assuming the existence or non-existence of the supernatural, and is not based on dogmatic metaphysical naturalism as claimed by creationists and proponents of intelligent design, in particular Phillip E. Johnson. Pennock’s testimony as an expert witness at the Kitzmiller v. Dover Area School District trial was cited by the Judge in his Memorandum Opinion concluding that “Methodological naturalism is a “ground rule” of science today”

    Methodological naturalism by Christians is historically supported:

    Despite the occasional efforts of unbelievers to use scientific naturalism to construct a world without God, it has retained strong Christian support down to the present. And well it might, for (…) scientific naturalism was largely made in Christendom by pious Christians. Although it possessed the potential to corrode religious beliefs — and sometimes did so — it flourished among Christian scientists who believe that God customarily achieved his ends through natural causes. [Numbers 2003, op cit, p. 284]

    I don’t know where you learned the history of the philosophy of science, but if you paid tuition to do so, I’d try to get my money back if I were you.

  185. Thank you, Nakashima; as usual, you are correct.

  186. “one can even be a materialist and acknowledge that truths about the physical universe may be out of the reach of empirical science.”

    I have to disagree, Sal. Once the materialist admits to this he confesses to a faith, and it is impossible for faith to be material. This would mean that the materialist admits to believing in the immaterial, which would put him in a permanent spin.

  187. Thank you for the well documented post at 184, Allen. The idea that we learn a certain kind of thing by examining natural causes only, and by explaining natural things in terms of natural causes, has a long history that is compatible with a belief in God. Many of the great founding fathers of modern western science believed in God, but they were also aware that the explanations they were devising did not invoke him as a proximate cause.

    And to tribune7: I think it is quite wrong to think that a materialist can’t have faith because, in your opinion, faith is immaterial. You may think faith is immaterial, but it is precisely on this point – that ideas and our cognition in general is grounded in the material world – that the materialist disagrees with you. You are put into a spin by trying to contemplate being a materialist when you aren’t really one, but the materialist himself does not have this problem.

  188. Allen, you are hilarious. Don’t you know that I have debated others on this subject and all of them go to that same website to copy those same references?

    In any case, the fact that many philosophers and scientists, including pre-Socratics preferred to study nature without reference to God is well-known and not very hard to explain. Atheists don’t generally go looking for God-like explanations. So, the point is completely irrelevant to the discussion. It is also known that Plato, Aristotle and others began to emphasize teleology and the advance of reason began.

    More to the point, your extended discussion in cyberspace was totally wasted since you ignored the main distinction. Here it is again, and I ask you to please pay special heed. Methodological naturalism is a RULE which forbids any scientist to consider anything other than natural causes. There has never been any such rule until the 1980’s.

    Also, your expansive comments about medieval scholastic thinkers was improperly framed. Everyone knows that early scientists began to distinguish “superstition” from “natural causes,” but that doesn’t mean that they established an institutional rule to forbid anything else. This is a serious logical error that fails to account for the two extreme positions and the one common sense position:

    Extreme [A] = Radical “Union” of science and religion [anti-intellectual superstition]

    Extreme [B] = Radical “Separation” of science and religion [anti-intellectual secularism]

    The ideal [C] = Moderate “Intersection” of religion and science. [free and responsible intellectual inquiry]

    You labor under the illusion that [A] and [B] are the only two alternatives, so you choose [B] without acknowledging the existence of [C]

    By the way, here is telling paragraph from your references that you seem to have glossed over: “Although characteristically leaving the door open for the possibility of direct divine intervention, they frequently expressed contempt for soft-minded contemporaries who invoked miracles rather than searching for natural explanations.”

    Even this Darwinist, whoever he is, admits that scientists “left the door open.” So, clearly, methodological naturalism was not being practiced because, as one of your guys defined the term, “We can’t allow a Divine foot in the door.” That is what methodological naturalism is. Are we clear yet?

    So, if you find an ancient scientist who says that he has “no need for that hypothesis,” [God] he is saying that he prefers to explore naturalistic explanations as the default explanation as we all do. He is not saying that anyone who disagrees with him ought to be “expelled” from the academic community.

    —-You write: “Here, apparently is the source of your confusion:”

    —–The term “methodological naturalism” for this approach is much more recent. According to Ronald Numbers, it was coined in 1983 by Paul de Vries, a Wheaton College philosopher.

    I am not the one who is confused, and you are not telling me anything that I don’t already know. In the 1980’s Darwinists decided to get serious about the business of persecuting design thinkers, so they got serious about using the term “methodological naturalism,” which was a new idea formed as an institutional rule to be used against ID dissenters.

    —-“In a series of articles and books from 1996 onwards, Robert T. Pennock wrote using the term methodological naturalism to clarify that the scientific method confines itself to natural explanations without assuming the existence or non-existence of the supernatural, and is not based on dogmatic metaphysical naturalism as claimed by creationists and proponents of intelligent design, in particular Phillip E. Johnson. Pennock’s testimony as an expert witness at the Kitzmiller v. Dover Area School District trial was cited by the Judge in his Memorandum Opinion concluding that “Methodological naturalism is a “ground rule” of science today”

    Yes, that is a true statement, and I salute the author, whoever he is. Methodological naturalism is a “ground rule.” Did the pre-Socratics have an institutional rule to use as a weapon of expulsion? Of course not. Did scientists in the middle ages have any such mandate? Not on you life.

    —-“Methodological naturalism by Christians is historically supported:”

    As I have made abundantly cleaer, that simply is not true. Secularism and materialistic monism have always been with us, but you can’t pass that off as methodological naturalism. The latter is strictly a 20th century novelty. You continue to miss the distinction. Here it is again: To say that science is “primarily” about natural causes [common sense] is not “to say that science must be “exclusively” about natural causes [methodological naturalism]. The difference is only everything.

    —-“I don’t know where you learned the history of the philosophy of science, but if you paid tuition to do so, I’d try to get my money back if I were you.”

    Once again, you are making me laugh. It is not I who feels the need to go Googling, since my investigation on this matter long preceded our discussion. As one who must resort to changing definitions and historical rewrites to defend an indefensible position, you can’t afford to take that tone. All that you have proven with your latest foray into the history of science is that you will twist facts and change definitions for the purpose of distorting the truth. The truth is that methodological naturalism, as it is understood and practiced today, has no pre-20th century history. None.

  189. Methodological naturalism is a RULE which forbids any scientist to consider anything other than natural causes. There has never been any such rule until the 1980’s.

    Well, to quote that pirate captain in Pirates of the Caribbean, it’s not so much of a rule as it is a guideline.

    Searching for natural causes has been successful, and searching for other types have causes has not, so scientists go with what works. If someone could show how to look for, and test, something other than natural causes in a way that led to a increase in fruitful knowledge, then at least slowly that procedure and those causes would become adopted.

    But such attempts have failed to impress the world of science, not because they break a rule, but because they don’t successfully tell us anything that we can explore and test about the world.

  190. Two quotes from 188:

    Everyone knows that early scientists began to distinguish “superstition” from “natural causes,” but that doesn’t mean that they established an institutional rule to forbid anything else.

    and

    So, if you find an ancient scientist who says that he has “no need for that hypothesis,” [God] he is saying that he prefers to explore naturalistic explanations as the default explanation as we all do.

    So let’s assume that all the great religious scientists since, say, Galileo, accepted the above two statements.

    Doesn’t it tell us something important that not a single one of them ever seriously advanced, much less found, an explanation involving other than natural causes? If they were open to the possibility of finding explanations involving other than natural causes, then why didn’t they find any?

    Perhaps it’s because that approach doesn’t work, and looking for explanations involving natural causes does.

    And if that’s the case, maybe it’s reasonable to generalize from their experience and adopt the limitation of science as looking for natural causes as a “working ground rule” of science. If all those great scientists who were not against explanations involving non-natural causes never actually found any such explanations, then it seems reasonable to me that we should learn from their experience, and stick with what has worked.

  191. Allen (184):

    Fantastic comment. Methodological naturalism was part of my indoctrination in experimental psychology, back in the Seventies, though no one called it that. I remember exclaiming “What a fine way to put it!” when I first saw the term.

    Are biology undergrads at Cornell required to get an introduction to the philosophy of science? If so, what do they read?

  192. —Allen: “If you had turned this in as an essay in an introductory history of philosophy ……blah, blah, blah.

    Are you cuckoo! I am not writing essays, I am correcting Darwinist fanstasies, and, I am sorry to say, calculated distortions. In any case, I would not subject myself to a classroom environment to one who has less formal education than I do. So, you can get off that high horse.

    You are not in a position to weigh anyone’s arguments, because you are not sufficiently informed on the matter.

    Even your guy admits I am right.

    From Ron Numbers, who is your main source and the one who pushes MN back as far as he can get away with, said this to Paul Nelson [Ron numbers, methodological naturalism, and the rules of baseball]

    “If you’re going to have a game, he continued, you’ve got to have some rules. For a long time now — really from the middle of the 19th century — one of the rules in science has been that the hypothesis of supernatural design is excluded from scientific discourse as a candidate explanation. Just as in baseball, where the first and third base lines define the field of play, in science one of the defining rules has been that the hypothesis of design, although quite possible, falls wholly outside the lines of admissible discourse.”

    So, this is the most radical view from any historian and it comes from the one most likely to push it back to the earliest date that he thinks he can get away with. Even by his biased, anti-ID standard, he confesses that Methodological naturalism does not predate the mid-nineteenth century. Even at that, it is clear that such a “rule” was not enforced, so you have no case. All these attempts to attribute MN to ancient Greece, the middle ages, or even at the time of Francis Bacon, are obviously made up for the purpose of providing historical cover for an arbitrary rule that really has no history at all. Even with your guy pushing it all the way back as far as he can, you have no case. As I pointed out much earlier, it all began with Darwinian ideology and started festering from that point. About 1980, it finally occurred to someone to use it as a tool for oppression and then rewrite history to cover it up. Give it up. Googling will not help you because you have no place else to go.

    By the way, are you clear now on the relationship between metaphysics and science? I haven’t heard from you on that one for a while. If someone came to one of my classes and told me that metaphysics has nothing to do with science, I wouldn’t just flunk him, I would sent him to detention.

  193. —-Hazel: “Doesn’t it tell us something important that not a single one of them ever seriously advanced, much less found, an explanation involving other than natural causes?”

    No. It doesn’t tell us anything at all. Michael Faraday’s religious belief in a single Creator [God's unity], for example, encouraged his scientific belief in the “unity of forces.” What that means is that that magnetism, electricity and the other kinds of forces would have had a common origin.

    I could provide dozens of similar stories. Doesn’t anyone care about facts anymore, or is everything about idealolgy at all costs? Good grief!

  194. Michael Faraday’s religious belief in a single Creator [God's unity], for example, encouraged his scientific belief in the “unity of forces.” What that means is that that magnetism, electricity and the other kinds of forces would have had a common origin.

    I could provide dozens of similar stories. Doesn’t anyone care about facts anymore, or is everything about idealolgy at all costs? Good grief!

    The fact that scientists then, and now, have religious beliefs about why the world is orderly, and are thus motivated to look for that order, is a different matter entirely then including religious concepts in those explanations. Faraday’s religious beliefs were a motivation, but he practiced science as we understand it today – explaining natural things with natural explanations, invoking measurable and testable concepts.

    God to him and others was the creator and sustainer of the universe – the ultimate cause – but the proximate causes he studied and invoked are entirely contained in the material world without reference to any direct involvement in God. He practiced methodological naturalism as a theist. Perfectly reasonable thing to do and done every day by thousands of religious scientists.

  195. BTW, stephenB, in your exhaustive research into the history and philosophy of science, did you happen to read Karl Popper’s two-volume masterwork, The Open Society and Its Enemies, and if you did, which side did you find more congenial? Just curious…

  196. —–Allen: “You seem completely unable to recognize the difference between the term “methodological naturalism” and the concept to which it is applied. The former has been in common use since the 1980s, but it is the general consensus of virtually all reputable historians of science (including Ned Burtt, Paul Feyerabend, Carl Hempel, Thomas Kuhn, Imré Lakatos, and Karl Popper, not to mention Ludwig Wittgenstein) that “methodological naturalism” has, in fact, been a basic assumption of almost all empirical scientists and “natural philosophers” since the origin of western philosophy in Ionia in the 7th century BC.”

    I think that we need to take a break and cool down a bit. In any case, your assessment is not correct. It was the starting point of investigation, but it was not the end point. There was no rule as is evident that all the geniuses would have broken it.

    It might just be easier to just refute your arguments with example after example. Do you think Michael Faraday practiced methodogcal naturalism when he sucessfully concluided that God’s unity informed the universe and effected the “unity of electricity?”

    Let’s move on. Robert Boyle believed that, as a Christian, it was part of his service to seek God’s purposes in nature. It was in his important work, Skeptical Chemist, that he advanced chemistry from the world of alchemy into the realm of science. Boyle believed the orderliness of the universe reflected God’s purposeful design. Did you get that? His belief in a Christian God helped him rescue chemistry from superstition. Does that sound like methodological naturalism to you? Is anyone getting this yet?

  197. I see we’re having debates about history of science.

    But, for the sake of argument, let us say methodological naturalism was the norm practiced even by religious scientists.

    The question I pose: “is methodological naturalism being eroded away by the mingling of teleology into biology?”

    I echo Raff’s idea, that the machnine metaphors used by biologists are helping ID proponents and creationists. The subjectivism in engineering is now being imported into biology, and this is making the ground fertile for consideration of ultimate and supernatural causes, or at the very least, causes that are outside the reach of empirical science.

    Is that a fair statement?

    PS
    I certainly think that religious impulse was vital to inspiring science.

    That was the thesis by Alfren North Whitehead.

    One can argue that the idea of miracles is most meaningful when they are the exception rather than the rule, thus operationally speaking many scientific theories will presume “natural” (as in ordinary causes), even by religious scientists.

    But when we are dealing with origins (of life and the universe), it seems we are dealing with causes that are inaccessible to direct empirical inquiry. If the origin of the universe and life were singular events, then by definition they are not natural. It doesn’t formally mean “God did it”, but on the otherhand it seems rather futile to argue the events were natural in the sense that they were ordinary.

    My personal educated guess is that God did it. It seems that an intelligence far beyond anything we know created life. If life did not look like it had many machines within it, I’d probably be an atheist.

  198. In #200 sal asks a good question:

    “Is methodological naturalism being eroded away by the mingling of teleology into biology?”

    It is if one assumes that teleology has no place in biology. However, this is manifestly not the case. Biological organisms areteleological entities, and are shot through with anatomical features and physiological processes that have all the hallmarks of teleology.

    Hence, Francisco Ayala and Ernst Mayr both asserted that teleology is legitimate in biology, but only when it is applied to the development and operation of living organisms. This is because living organisms, like all teleological entities, are constructed and operated according to a “plan” or “design” that precedes their construction and operation. Part of this “design” is encoded in their genomes, and part of it is “impressed upon them” by their ecological circumstances.

    Furthermore, it is most assuredly possible to investigation this kind of teleology using empirical methods. One can explore the genome to find out what kinds of “designs” are encoded therein, and can study the developmental processes by which such “designs” are realized in the structures and functions of the organism whose characteristics they specify.

    However, none of the foregoing applies to the processes by which such teleonomic “designs” come into being. These processes are all subsumed under evolutionary biology, and as Ayala, Mayr, and all other evolutionary biologists (including Darwin) have pointed out, teleology is unnecessary in evolutionary explanations of the origins of biological teleonomy. [1]

    As I have now repeatedly pointed out, there is no contradiction between teleology and biological causation, so long as there is some “natural” medium for the storage and expression of the “designs” that precede (or “pre-exist”) the construction and operation of living organisms. The problem comes in when one asserts that the same is true for the evolutionary processes by which the “designs” themselves come into being. Such processes exhibit no signs of being teleological (as far as we can tell). Furthermore, there is no place outside of the genomes and ecosystems in nature for the “designs” for evolution itself to reside. One could argue (and indeed, many ID supporters do argue, that they reside “outside” of nature in the mind of God/the Intelligent Designer. However, they also assert (correctly , in my opinion) that God/the Intelligent Designer cannot be studied via empirical methods, nor can His motives or means of operation be studied either.

    Ergo, since the role of God/the Intelligent Designer in the origin of biological teleonomy has not been (and probably cannot be) shown to be necessary to evolutionary explanations for the origin of biological teleonomy, evolutionary biologists simply don’t mention them. Some go further and deny they exist, but they do so using metaphysics, but not science.

    [1] Ayala and Mayr, following Monod, Pittendrigh, and Wimsatt, both referred to the “internal” teleology of living organisms by the term “teleonomy”, to distinguish it from the “external” form of teleology of Aristotle, Paley and what we would now call ID supporters.

  199. from Stephen at 199:

    Boyle believed the orderliness of the universe reflected God’s purposeful design. Did you get that? His belief in a Christian God helped him rescue chemistry from superstition. Does that sound like methodological naturalism to you? Is anyone getting this yet?

    Yes, it does sound like methodological naturalism to me. Boyle’s work involved explaining natural phenomena in terms of other natural phenomena – he did not reference God in his explanations.

    His overlying religious perspective motivated him to believe that the material world is an orderly, investigateable place, and his investigations confirmed that. Other people have different reasons for believing that the material world is an orderly, investigateable place, and they too, like Boyle, have found that treating the material world as such has been successful.

    But both the theist (Boyle in this case) and someone else with a different perspective come to the same conclusions because they agree that the studying the material world in terms of its constituent parts is highly successful.

    Boyle practiced methodological naturalism (irrespective of the actual term used).

    So back to my question: can you show us an example of a religious scientist who advanced and investigated a natural phenomena in terms of some non-natural cause – that is, who didn’t practice methodological naturalism?

    Note well, and I hope you get this, my question does not have to do with the religious beliefs that motivated their search, but with the actual science they performed, and the type of explanations they offered.

    Can you give an example of some real science advanced by these religious scientists that did not follow the guideline of methodological naturalism?

  200. But, for the sake of argument, let us say methodological naturalism was the norm practiced even by religious scientists.

    Sal, you are asking us to imagine away the sticking point of the problem.

    If meth-nat is accepted as a standard, we would have to specifically reject the possibility that God might have designed life for ID to be considered a science, rather than to leave it as an unanswered question.

    And if meth-nat were the standard in the 19th century Pasteur’s disproof of spontaneous generation would never have been accepted. If it were the standard in the first half of the 20th century Lemaître’s Big Bang idea would have been rejected on semantic grounds.

  201. sal:

    It may very well be the case that God/the intelligent Designer “created life”. Darwin himself said as much in the last paragraph of the Origin of Species. He recognized what virtually all evolutionary biologists (indeed, virtually all empirical scientists) recognize: that following the origin of life, the evolution of life on Earth could (and therefore probably did) proceed according to “the fixed laws” of nature acting around and within us.

    As I have pointed out many times, evolutionary biology assumes that life already exists, and proceeds to explain how it has come to be the way it is now. Questions about the origin of life (like the origin of the universe, and time, and natural laws, and so forth) are probably beyond the scope of the empirical method, and may remain forever unanswered.

    I can live with that; can you?

  202. Let me be more explicit about what I mean by “real science”: One of Boyle’s laws states that for a certain amount of an ideal gas kept at a fixed temperature, the pressure and the volume are inversely proportional, which can be expressed simply as P•V = k, k a constant.

    This law falls under the umbrella of methodological naturalism: it explains the relationship between things in the material world. The fact that Boyle was a Christian when he derived this, and that his Christian beliefs motivated him to look for a simple mathematical relationship is not a part of the result itself: Christians and materialists and Hindus and flaming New age hippies can all agree about the law despite the fact that they have different ideas about why such laws might exist.

    That is the value of methodological naturalism: it provides a common background within which people of all sorts of metaphysical perspectives can work and come to agreement.

  203. (Boyle’s) law falls under the umbrella of methodological naturalism: it explains the relationship between things in the material world.

    That’s not what meth-nat is, Hazel.

    Meth-nat is the requirement that “all causes are empirical and naturalistic — which means they can be measured, quantified and studied methodically”

    Boyle (or Faraday or Thomson or Planck) would have axiomatically assumed God did it and not worried about a cause in describing the aspect of nature that was their interest.

  204. Johannes Kepler’s works on astronomy contained writings about how space and heavenly bodies represent the Christian Trinity. Oops, someone forgot to tell him that methodological naturalism forbids such things. I wonder how it was that he didn’t get the message. Could it be that there was no such message? Good guess.

    Do we neet more? How many more?

  205. —Sal: “But, for the sake of argument, let us say methodological naturalism was the norm practiced even by religious scientists.”

    Why would we want to assume something that clearly isn’t true?

  206. If meth-nat is accepted as a standard, we would have to specifically reject the possibility that God might have designed life for ID to be considered a science, rather than to leave it as an unanswered question.

    It is standard practice in mathematics to assume for the sake of argument a hypothesis you actually believe to be untrue in order to prove the argument you believe to be true. This is fundamental to the technique of “proof by contradiction”. Some of the most important theorems in math came about by assuming as true the hypothesis that was actually false.

    But my aim with posing the question about methodological naturalism was less ambitious. Rather than taking sides on the issue, I viewed it as a moot point because, I have specualted, the hypothesis of ID will persist because of teleology in biology. My personal opinion is that the design hypothesis is alive and will persist because God is helping it along. No peer-review committee on Earth can prevail over ID if God is for it. But that is a personal opinion, not a scientific one.

    My view is that Allen feels ID is outside of empirical science, and prefers to be realtively quiet on the question ultimate causes.

    Trying to argue if methodological naturalism is good or bad might be a moot point if the scientic enterprise begins to discard it for practical reasons. I sense a slight capitulation in the questions of origin of the universe and the origin of life.

    Personally, I stay from arguments about whether ID should be part of empirical science or not. That is somewhat the position of Stephen Meyer. The real question is not whether ID should be a part of empirical science, but whether ID is true.

    I concluded after remotely participating in the debates surround Allen notorious “Evolution and Design Class”, that arguing over whether ID should be a part of empirical science will not be of great benefit to the ID community.

    What I think will benefit the ID community:

    1. a serious contribution to the understanding of evolutionary biology. I consider the work by Sandford and the Mendel team potentially in that category. Medical science could be overturned by their findings (if indeed genomic deterioration is as bad as they suppose).

    2. Stegonography. The ability to use comparative anatomy and DNA sequencing to uncover “user manuals” in life. I firmly believe God made the Apes and the snails and butteflies for a reason. They are artifacts like the Rosetta stone. Why they have been made will eventually be known. Their purpose is not completely evident, but one day they may be vital to scientific understanding.

    I decided that philosophical debates were not for me, and to some extent Allen’s class in 2006 sort of motivated me to go back to school. I felt he was correct to argue that for ID to succeed, it would do them well to have people working in field research. I decided that I wanted to acquire the skills to at least be an amateur field researcher. My chosen field is physics.

    PS

    As a side note, I think it would be better to dialogue with Allen than try to debate. He has decades of knowledge in the area of biology and many other disciplines. I think we can learn a lot from him.

    Actually, he has introduced a new word I’m completely unfamiliar with: “teleonomic”

    One may wonder why I feel on such friendly terms with Allen. Recall I study and continue to study in secular schools. Many of my professors despise ID. I had to learn to feel comfortable being instructed by people who totally rejected my ID leanings.

    Demonization and attempts to humiliate people who disagree with us can be counter productive.

  207. If meth-nat is accepted as a standard, we would have to specifically reject the possibility that God might have designed life for ID to be considered a science, rather than to leave it as an unanswered question.

    Actually if one accepts philosophical naturalism as true, it leads to an incoherent view of reality. There is a contradiction.

    If one evolves methodoligical naturalism to be philosophical naturalism, then that will result in a contradiction. But many will stop short of doing that because they know it will lead to contradiction. Mark Perakh of all people saw the futility of trying to argue all causal agencies are natural. If everything is “natural” then the word “natural” will lose any meaning!

    I think one can invoke miracles as causes of natural phenomena, but in so doing, one will admit it cannot be studied in the lab, since by definition, miracles would not be subject to direct laboratory repeatability. Hence one has a good argument to say miracles can’t be a part of empirical science by definition, even if miracles are the fundamental cause of much of the physical universe.

    Trevors and Abel and others have used “proof by contradiction” to make a persuassive case that the emergence of life on Earth was a very unique event. Imho, miracle is the appropriate description.

    One can use empirical science to make a circumstantial case that a miracle happened. But to make miracles a part of empirical scence? That’s tough sell. I’m not going to try.

    PS

    To undstand the technique of “proof by contradiction”

    See:
    Proof by Contradiction

  208. —-Sal: “To undstand the technique of “proof by contradiction”

    I understand the principle. My question was rhetorical.

  209. 209

    Allen,

    “Questions about the origin of life (like the origin of the universe, and time, and natural laws, and so forth) are probably beyond the scope of the empirical method, and may remain forever unanswered.”

    Exactly right, especially the “natural laws,” which was what I was trying to illustrate, in part, with the quote from Chesterton. The natural repetitions, which I think is more accurate than calling them “laws,” are like first principles, in a way. You have to assume them from the outset, and work forward. They do not have prior premises, and by “premises” I mean any “reason behind” the repetitions where we can see or understand the “chain of reasoning” leading up to them that makes them what they are. We cannot see it, even if the chain of reasoning existed, we have no insight into it. Does this make sense? We can see what just has to be assumed, and what we can otherwise infer, natural repetitions just has to be assumed. The idea that we van ever reason within them and see their inner synthesis like we can real laws, such as laws of logic, is just false, because we have no power of inference between the repetitions like we do between the laws of logic. Now I understand that this is an obscure way of looking at what we call laws of nature, but it is important to understand and remember, for it maintains the arbitrariness, in principle, that seems to be the case with the weird repetitions, and the following inference that something intended them, and if nothing else to awaken someone out of the spell of scientism and put things into the proper perspective.

  210. Gentle Folks:

    Sometimes, it is necessary to remind ourselves of what the informed consensus on science and its methods was only “yesterday”:

    science: a branch of knowledge conducted on objective principles involving the systematized observation of and experiment with phenomena, esp. concerned with the material and functions of the physical universe. [Concise Oxford, 1990]

    scientific method: principles and procedures for the systematic pursuit of knowledge [”the body of truth, information and principles acquired by mankind”] involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses. [Webster's 7th Collegiate, 1965]

    For, science at its best is the unfettered (but ethically and intellectually responsible) pursuit of the truth about our world based on empirical evidence, and theorising, analysis and discussion constrained by that evidence, towards building up a growing body of open-ended knowledge of our world.

    And, discovery of such knowledge may occur in a “pure” or “applied” context. [For instance, Edison -- on exploring the physics of the light bulb -- discovered a form of the photoelectric effect; and, patented it. (Typical . . . )]

    On that premise, methods and rules of inquiry are warranted based on their ability to contribute to the success of that programme of inquiry. Inference to best empirically anchored explanation passes that test. Logic passes that test. Statistical techniques pass that est. Probability based reasoning passes that test.

    For that matter, the explanatory filter used by design theorists passes the test:

    (i) chance, necessity and design are all empirically warranted causal forces,

    (ii) they have characteristic manifestations,

    (iii) we can cluster them based on an analysis of factors and aspects of phenomena

    (iv) on seeing the disjunction between regularity and high contingency we can identify law-like mechanical necessity,

    (v) on seeing high but stochastic contingency we can identify chance based causal factors

    (v) on seeing high contingency that fulfills functionality joined to complexity we can identify a strong association with design per a massive database of observed cases,a nd a statistical rationale as to why chance is unlikely to get to islands of function on the available search resources.

    In fact, such techniques are extensions of well known statistical and forensic approaches that are routinely used to make momentous decisions and just as routinely understood to be applications of the scientific approach. For excellent reason.

    But, in certain cases, the design inference runs across a strongly institutionalised worldview’s preferred origtins story, one that is well described by Mr Richard Lewontin:

    It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.

    So, the issue is not whether science is primarily about exploration of chance and mechanical forces, over the past several centuries. [For, it has equally been applied to detection of design for the past 150 years, and has routinely been used to make very serious decisions indeed.]

    The real issue is as Stephen B has raised: the imposition of a worldview by institutional power and associated censorship and career busting, backed up by propagandising of science education and public policy debates. Sorry if such sounds harsh, but it is unfortunately a well warranted description of what has been done, and done on the record.

    This has to stop, and it has to stop now.

    Or we will pay a terrible price as a civlisation for our folly. For, eternal vigilance is the price of liberty.

    GEM of TKI

    PS: I strongly suggest a careful reading of Newton’s general Scholium to his Principia, for those who imagine that methodological naturalism was the dominant view of science in the past.

    PPS: Mr Lewontin goes on to reveal his ignorance of theistic thought, showing just how deep the gap is on the required knowledge base fort understanding the true history of modern science. For, the belief in the Judaeo-Christian God as exemplified by Newton, Pascal, and up tot he likes of Faraday, Maxwell and Kelvin etc, is marked by the understanding that God is a God of order not chaos, so we have reason to expect that there will be an intelligible general order to the operations of the cosmos.

    And indeed even chance follows laws — statistical distributions. Further to this, miracles are NOT chaotic: for a miracle to stand out as a sign, it must be in a context of an orderly and predictable pattern to nature, so it must be inherently rare, pointing to the imposition f a higher order on the usual course. Also, in a world of accountable moral choice, such only is possible when actions have predictable consequences as a rule. So, the notion that the Judaeo- Christian frame of the founding scientists was chaotic is a strawman distortion fed by — at best — disqualifying ignorance.

  211. @ StephenB

    A forrmer poster Keiths/ribczynski points out elsewhere that you have had this discussion before with him.

    In his book Science and the Study of God, p. 79, Alan Padgett quotes Jean Buridan:

    Natural philosophers like Roger Bacon (ca. 1220-1292) and Jean Buridan (ca. 1292-1358) examined the secondary causes by which God upheld the common course of nature. Buridan wrote, for example, that “in natural philosophy we ought to accept actions and dependencies as if they always proceed in a natural way.”

    That’s practically a textbook definition of methodological naturalism.

    Padgett adds:

    We should note, however, that Buridan was devoutly Christian and that his natural philosophy was framed within a Christian worldview. After the quotation just given, for example, Buridan goes on to state, “Nevertheless God is the cause of this world.”

    So Buridan is a perfect example of how one can embrace methodological naturalism without being a philosophical naturalist.

    Link

  212. Also:

    I think we would profit from a reading of Plantinga’s discussion here.

    GEM of TKI

  213. Mr Fox:

    That science is in the main about the exploration of the regularities of nature is not the same as that it cannot infer to design per empirical data, as a factor of explanation in the empirical world.

    Methodological naturalism imposes a distorting, censoring rule that entails that where it is inconvenient to materialism [a particular worldview], scientific work may not use empirical evidence that would otherwise warrant a design inference to so infer.

    That is censorship not science, and it is very different from how the founders of modern science have thought. “Reinterpretations” of Buridan et al notwithstanding.

    GEM of TKI

  214. Though I am flattered that you address a comment to me, Mr. M, I doubt I have the stamina to respond in detail.

    You mention censorship. There are several former posters, more articulate and better-informed than me, who are prevented from commenting here notwithstanding the new, improved moderation policy.

    To me the issue is simple, neither you, I nor anyone else is limited in thinking what they like about ultimate causes, and science does not have the tools to examine ultimate causes. Philosophy encompasses science, science does not encompass philosophy.

    …scientific work may not use empirical evidence that would otherwise warrant a design inference to so infer.

    Rubbish! Any evidence that is amenable to scientific study (i. e. capable of being detected, observed, directly or indirectly, measured)can be looked at. Any real phenomenon is available for scientific scrutiny and analysis. Give me an example of evidence (that is visible to the scientific method) that is barred from scientific study.

  215. PS: This will also repay a read.

  216. How does Professor Delfino propose that scientists should study the supernatural, which, by definition, is invisible to the scientific method?

  217. Mr Fox:

    It seems, regrettably, you have not followed the case of the imposition of methodological naturalism in recent decades closely enough.

    As Mr Lewontin documents and as the US NAS et al have now sought to impose up to the level of career busting and forcing eduction policy [not to mention Journal editorial policy . . . ], MN is being imposed as a censoring rule on science.

    And that, in a context where if it were not so imposed, there would be excellent reason to see that the evidence of — say — the data structures and contents of DNA, with associated codes and implementing mechanisms are strong indicators of design.

    (Have you got handy cases of algorithm-implementing, coded data storing, flexibly programmed entities that are known per observation to have resulted from chance plus mechanical forces? I would think that there is a large number of instances showing that computers routinely originate by design, and that there are no known exceptions; with an excellent statistical, search resource exhaustion reason why that is so.)

    GEM of TKI

  218. …MN is being imposed as a censoring rule on science.

    And that, in a context where if it were not so imposed, there would be excellent reason to see that the evidence of — say — the data structures and contents of DNA, with associated codes and implementing mechanisms are strong indicators of design.

    Nobody is prevented from conjecture that the DNA code etc. is too complex to to have come about other than with some supernatural input. Suggest a scientific way of examining the hypothesis.

  219. Mr Fox:

    Scientists may and often do study empirical phenomena that — per abundant direct observation — show reliable signs of design.

    That is not a study of “the supernatural” [whatever that is], but of the empirical and the observationally warranted: signs of intelligence.

    On the case of life and its origin, the cell strongly suggests design as just discussed, but we have no basis on currently available empirical — i.e properly scientific — evidence to infer to a designer as being within or beyond the observed cosmos. [remember, I am an advocate for research towards the creation of real artificial intelligences and if we can mange it, self-replicating ones, though under control so we don't do a Frankenstein.]

    On the origin of said cosmos, we see a finetuning for life that suggests that a designer beyond our observed cosmos is a credible candidate, but that is different from inferring to that there is design. [Whodunit is different from seeing that tweredun.]

    Taking the two together it is a reasonable worldviews conclusion that the author of the cosmos intended to create cell based life and so is the most credible candidate for that, but that is not a scientific conclusion. (Which does not mean that is is an unreasonable one.)

    GEM of TKI

  220. Mr Fox

    The mere denial of the sad facts of imposition of methodological naturalism and its resulting censorship as Mr Lewontin so clearly documented, does not disestablish them.

    And, the pathway in which said investigations of DNA as data storing entities have now long been undertaken.

    We are dealing with the implications — or at any rate, warranted inferences therefrom — of that longstanding discovery in light of the significance of signs of intelligence.

    As to the idea that the contrast is made between “natural” and “supernatural, I must add that it is at least as well warranted to draw the contrast natural vs artificial [or intelligent]. And, much less metaphysically or rhetorically loaded. And, we have many many methods of investigating what is spontaneous in nature from what is art that stands above the probabilistically credible reach of undirected chance and necessity.

    GEM of TKI

  221. Scientists may and often do study empirical phenomena that — per abundant direct observation — show reliable signs of design.

    If this were true, Intelligent Design would already be science. But it is just wishful thinking, unfortunately.

  222. And, the pathway in which said investigations of DNA as data storing entities have now long been undertaken.

    I think you may have omitted a word or two, as this statement makes no sense to me.

  223. We are dealing with the implications — or at any rate, warranted inferences therefrom — of that longstanding discovery in light of the significance of signs of intelligence.

    ?

  224. As to the idea that the contrast is made between “natural” and “supernatural, I must add that it is at least as well warranted to draw the contrast natural vs artificial [or intelligent]. And, much less metaphysically or rhetorically loaded.

    A definition of something natural that makes sense to me is “available to scientific scrutiny” It is a foible of human thinking to assume dichotomies, and it seems to follow there must be something “non-natural, super-natural imaginary”. By definitions any of these things may be there, but as they are invisible to scientific scrutiny, there’s an end of it.

  225. Oh BTW, Mr M.,

    How does Professor Delfino propose that scientists should study the supernatural, which, by definition, is invisible to the scientific method?

    I ask because I saw nothing in his article that suggested a practical way forward.

  226. Mr Fox:

    As of this point, you are simply rep[eating the already adequately answered. for instance, one does not study “the supernatural” empirically, but one may freely study signs of art or intelligence; as was already pointed out.

    I suggest that you review from 16 on in the WACs above, and in particular no 19.

    GEM of TKI

  227. Sal–It is standard practice in mathematics to assume for the sake of argument a hypothesis you actually believe to be untrue in order to prove the argument you believe to be true.

    And there is nothing wrong with this, as long as the false position doesn’t become the norm.

    My view is that Allen feels ID is outside of empirical science, and prefers to be realtively quiet on the question ultimate causes.

    And this would be my concern, albeit not necessarily directed at Allen. ID is argued not to be science due to the meth-nat definition i.e. it’s arbitrarily rejected due to semantics.

    For instance, ID does not even address a cause. Granted it raises questions it cannot answer, but so does the Big Bang (or neo-Darwinism for that matter).

    Trying to argue if methodological naturalism is good or bad

    Actually, I think there are times when the standard is quite appropriate. For instance, if you want to learn why the bridge collapsed you want to reject before hand the possibility of angry leprechauns.

    OTOH, to use it as the arbiter of all truth is a perversion of it as is the demand that it be applied to descriptions of nature rather than causes.

    And I have no problem with dialoguing with Allen, although both parties should endeavor to understand the positions of the others. For instance, is Idist synonymous with creationist?

    And I certainly hope Allen and Dr. D. have hooked back up and begun to dialogue.

  228. 19] Science does not address the “Supernatural”

    But this is not correct. A better statement would be “Science has no tools with which to examine the supernatural. Of course science can look at natural results produced by supernatural inputs”. It is all a matter of definitions.

  229. This whole discussion would go away if one group admitted that there are some phenomena that science may not be able to explain. I use the word “admit” because that is issue.

    No one is saying not to use scientific processes to investigate any phenomenon but that only that there may be some that may not be the result of the laws of nature and chance. And that there is a third possibility of agency which is actually investigated by many scientific disciplines but limited arbitrarily to certain things.

    So what we have is an arbitrarily declared stricture that a certain subset of phenomena can not be due to agency. And any conclusion that these phenomena are due to agency is forbidden. And in addition specious conclusions are substituted in place which have no basis in fact.

    This is what the discussion is about. Short and simple. So we argue over the belief or lack of belief of some scientists in God or not when the real issue is over this arbitrary dictum on the possible range of conclusions to the methods and findings of science.

    I have said here many times what would an ID scientist do differently from a non-ID scientist and answered little would be done differently. But what they would differ on is the conclusions of the findings and not necessarily the methods and phenomena examined.

  230. It has been suggested by others here before, and by me elsewhere, but an avenue for ID research would be to look for the interface where the supernatural input impinges on the real world. There you must see discontinuity, a reaction without an opposite. Why isn’t anyone trying this?

  231. Hayden-san,
    The natural repetitions, which I think is more accurate than calling them “laws,” are like first principles, in a way. You have to assume them from the outset, and work forward. They do not have prior premises, and by “premises” I mean any “reason behind” the repetitions where we can see or understand the “chain of reasoning” leading up to them that makes them what they are.
    I fnd it difficult to agree with this. It may be that the first phase of scientific inquiry is the stamp collecting phase, in which a large number of measurements are made. And then a second phase, in which a line is fitted to this set. Engineers might be happy to stop there. Science does want to get at what underlies the regularity – why is that line a better fit than another?
    In the Boyle’s Law example earlier, we can hypothesize at least two explanations for the pressure/volume relationship.

    1 – that a gas is a continuous entity than is infinitely compressible
    2 – that a gas consists of a large but fixed number of small particles that are themselves incompressible

    Experimentation would show that the line ceases to be a good fit in some range of high pressure, leading to a preference for one hypothesis over the other.

    Accepting the fitted line as the ultimate description of an arbitrary reality is not the natural end-state of scientific inquiry. This is why QM irritates so many people! Very few people are happy that QM is the most useful and precise engineering description of reality. Science still wants to know “why?”

    In this sense, scientists are like anorexics. An anorexic teenage girl is never happy being thin, she is obsessed with “thinner”. Similarly, the scientist is never happy with the line fitted over a range of values. It can always be fitted over a wider range, or with more precise measures, etc.

    Thinking about science as line fitting also gives a clear definition to what is called Occam’s Razor. We know that it is possible to draw an infinite number of lines through any set of observations. Occam’s Razor is the preference for the lowest order polynomial in that infinite set.

  232. Nakashima-san:

    Your analogy between Occam’s Razor and “least squares” method of line-fitting is one I have never read before, but one that seems quite useful. With your permission, I would like to use it my forthcoming book on evolution.

    Occam’s Razor is widely misunderstood, even by scientists. There is a tendency to think that it’s equivalent to a “natural law”, when in fact it is only a “useful rule of thumb” for scientists who are trying to focus on a particular empirical problem. Nothing at all in standard (i.e. Aristotelian) logic rules out the infinite number of possible explanations of any observable phenomenon.

    One can hypothesize that solar eclipses are indeed caused by giant dragons eating the sun, who then regurgitate it upon being propitiated by priests interceding on behalf of their congregations. Nothing prohibits the construction of a fully logical syllogism concerning such an explanation of solar eclipses.

    Furthermore, one can study the various explanations that people in different cultures have proposed for such phenomena. When one does so, one notices immediately that there is a virtually infinite variety of such explanations, ranging from giant dragons to angry gods to competing sky deities.

    However, when one uses purely empirical methods to investigate such phenomena, one generally discovers that, despite the variation in proposed explanations,there is an underlying similarity (i.e. regularity) in those empirical observations.

    This is what Occam’s Razor focuses our attention upon: those underlying regularities that “cut through” all of the varieties of culturally-based explanations and point to the simple, unadorned nature of nature itself.

    Does Occam’s Razor ever “prove” anything in science? No, and neither does science “prove” anything at all in the Aristotelian/mathematical sense. All we ever have in science (and all we can ever have) is a tentative explanation that is “good enough” and “simple enough” that anyone, from any culture, using any form of inductive logic, can agree upon as a useful (i.e. not absolute) explanation.

    And what does “useful” mean? Useful for guiding further empirical investigations; nothing more (and nothing less).

  233. It has been suggested by others here before, and by me elsewhere, but an avenue for ID research would be to look for the interface where the supernatural input impinges on the real world. There you must see discontinuity, a reaction without an opposite. Why isn’t anyone trying this?

    If you mean by supernatural: “extraodinary”, then by definition it cannot be directly measured in the lab.

    If you mean by supernatural: everything inaccessible to science, then by definition it cannot be directly measured in the lab.

    So it would seem futile to try to directly investigate this interface except through circumstantial, indirect arugments.

    Besides, that would be closer to creationism than ID. An ID oriented creation would by “Biotic Message” or PEH.

    A circumstantial case can be made. Such as:

    1. origin of the universe
    2. origin of life
    3. Heisenberg Uncertainty

    This [quantum uncertainty] is something biologists, almost universally, have not yet come to grips with. And its consequences are enormous. It certainly means that we should wonder more than we currently do about the saying that life is made of “mere” matter….

    This means that absolute materialism, a view that control and predictability and ultimate explanation are possible, breaks down in a way that is biologically significant. It means that after we have obtained understanding of so much of the world around us, the ultimate mastery of even the tiniest bit of matter in the universe will always elude us….

    [Thus] The core assumptions supporting the “scientific” disbelief [atheism] of the absolute materialist are wrong, even by the terms of science itself…

    What matters is the straightforward, factual, strictly scientific recognition that matter in the universe behaves in such a way that we can never achieve complete knowledge of any fragment of it, and that life itself is structured in a way that allows biological history to pivot directly on these tiny uncertainties. That ought to allow even the most critical scientist to admit that the breaks in causality at the atomic level make it fundamentally impossible to exclude the idea that what we have really caught a glimpse of might indeed reflect the mind of God.
    ….

    In the final analysis, absolute materialsm does not triumph because it cannot fully explain the nature of reality.

    –Ken Miller
    pages 208-209, 214, 219 Finding Darwin’s God

    and

    We thus see how quantum theory requires the existence of God. Of course, it does not ascribe to God defined in this way any of the specific additional qualities that the various existing religious doctrines ascribed to God. Acceptance of such doctrines is a matter of faith and belief.

    If elementary systems do not “possess” quantitatively determinate properties, apparently God determines these properties as we measure them. We also observe the fact, unexplainable but experimentally well established, that God in His decisions about the outcomes of our experiments shows habits so regular that we can express them in the form of statistical laws of nature. this apparent determinism in macroscopic nature has hidden God and His personal influence on the universe from the eyes of many outstanding scientists.

    F.J. Belinfante
    department of Physics
    Purdue University

    and

    Something peculiar has been going on in science for the past 100 years or so. Many researchers are unaware of it, and others won’t admit it even to their own colleagues. But there is a strangeness in the air.

    What has happened is that biologists, who once postulated a privileged role for the human mind in nature’s hierarchy, have been moving relentlessly toward the hard-core materialism that characterized nineteenth-century physics. At the same time, physicists, faced with compelling experimental evidence, have been moving away from strictly mechanical models of the universe to a view that sees that mind as playing an integral role in all physical events. It is as if the two disciplines were on fast-moving trains, going in opposite directions and not noticing what is happening across the tracks.
    ….
    During the period in which psychologists and biologists were steadily moving toward reducing their disciplines to the physical sciences, they were largely unaware of perspectives emerging from physics that cast an entirely new light on their understanding. Toward the close of the last century [the 1800s], physics presented a very ordered picture of the world, in which events unfolded in characteristic, regular ways, following Newton’s equations in mechanics and Maxwell’s in electricity. These processes moved inexorably, independent of the scientist, who was simply a spectator. Many physicists considered their subject as essentially complete.

    Starting with the introduction of the theory of relativity by Albert Einstein in 1905, this neat picture was unceremoniously upset. The new theory postulated that observers in different systems moving with respect to each other would perceive the world differently. The observer thus became involved in establishing physical reality. The Scientist was losing the spectator’s role and becoming an active participant in the system under study.

    With the development of quantum mechanics, the role of the observer became an even more central part of physical theory, an essential component in defining an event. The mind of the observer emerged as a necessary element in the structure of the theory. The implications of the developing paradigm greatly surprised early quantum physicists and led them to study epistemology and the philosophy of science. Never before in scientific history, to my knowledge, had all of the leading contributors produced books and papers expounding the philosophical and humanistic meaning of their results.

    Werner Heisenberg, one of the founders of the new physics, became deeply involved in the issues of philosophy and humanism. In Philosophical Problems of Quantum Physics, he wrote of physicists having to renounce thoughts of an objective time scale common to all observers, and of events in time and space that are independent of our ability to observe them. Heisenberg stressed that the laws of nature no longer dealt with elementary particles, but with our knowledge of these particles – that is, with the contents of our minds. Erwin Schrodinger, the man who formulated the fundamental equation of quantum mechanics, wrote an extraordinary little book in 1958 called Mind and Matter. In this series of essays, he moved from the results of the new physics to a rather mystical view of the universe that he identified with the “perennial philosophy” of Aldous Huxley. Schrodinger was the first of the quantum theoreticians to express sympathy with the Upanishads and Eastern philosophical thought. A growing body of literature now embodies this perspective, including two popular works, The Tao of Physics by Fritjof Capra and The Dancing Wu Li Masters by Gary Zukav.

    The problem faced by quantum theorists can best be seen in the famous paradox, “Who killed Schrodinger’s cat?” In a hypothetical formulation, a kitten is put in a closed box with a jar of poison and a triphammer poised to smash the jar. The hammer is activated by a counter that records random events, such as radioactive decay. The experiment lasts just long enough for there to be a probability of one-half that the hammer will be released. Quantum mechanics represents the system mathematically by the sum of a live-cat and a dead-cat function, each with a probability of one-half. The question is whether the act of looking (the measurement) kills or saves the cat, since before the experimenter looks in the box both solutions are equally likely.

    This lighthearted example reflects a deep conceptual difficulty. In more formal terms, a complex system can only be described by using a probability distribution that relates the possible outcomes of and experiment. In order to decide among the various alternatives, a measurement is required. This measurement is what constitutes and event, as distinguished from the probability, which is a mathematical abstraction. However, the only simple and consistent description physicists were able to assign to a measurement involved an observer’s becoming aware of the result. Thus the physical event and the content of the human mind were inseparable. This linkage forced many researchers to seriously consider consciousness as an integral part of the structure of physics. Such interpretations moved science toward the idealist as contrasted with the realist conception of philosophy.

    The views of a large number of contemporary physical scientists are summed up in the essay “Remarks on the Mind-Body Question” written by Nobel laureate Eugene Wigner. Wigner begins by pointing out that most physical scientists have returned to the recognition that thought – meaning the mind – is primary. He goes on to state: “It was not possible to formulate the laws of quantum mechanics in a fully consistent way without reference to the consciousness.” And he concludes by noting how remarkable it is that the scientific study of the world led to the content of consciousness as an ultimate reality.

    A further development in yet another field of physics reinforces Wigner’s viewpoint. The introduction of information theory and its application to thermodynamics has led to the conclusion that entropy, a basic concept of that science, is a measure of the observer’s ignorance of the atomic details of the system. When we measure the pressure, volume, and temperature of an object, we have a residual lack of knowledge of the exact position and velocity of the component atoms and molecules. The numerical value of the amount of information we are missing is proportional to the entropy. In earlier thermodynamics, entropy had represented, in an engineering sense, the energy of the system unavailable to perform external work. In the modern view, the human mind enters once again, and entropy relates not just to the state of the system but to our knowledge of that state.

    The founders of modern atomic theory did not start out to impose a “mentalist” picture on the world. Rather, they began with the opposite point of view and were forced to the present-day position in order to explain experimental results.

    We are now in a position to integrate the perspectives of three large fields: psychology, biology, and physics. By combining the positions of Sagan, Crick, and Wigner as spokenmen for various outlooks, we get a picture of the whole that is quite unexpected.

    First, the human mind, including consciousness and reflective thought, can be explained by activities of the central nervous system, which, in turn, can be reduced to the biological structure and function of that physiological system. Second, biological phenomena at all levels can be totally understood in terms of atomic physics, that is through the action and interaction of the component atoms of carbon, nitrogen, oxygen, and so forth. Third and last, atomic physics, which is now understood most fully by means of quantum mechanics, must be formulated with the mind as a primitive component of the system.

    Harold Morowitz
    Director of the Krasnow Institute for Advanced Study

  234. And what does “useful” mean? Useful for guiding further empirical investigations; nothing more (and nothing less).

    Yes, and using Allen’s definition, Intelligent Design would advance if someone could demonstrate that it was useful!

  235. Alan Fox, this same worn-out example that you allude to [Buridan as a defense of historical MN], and which has already been attempted on this thread, does itself prove the point. That you can navigate through the entire history of science and find only one instance of what you hope to be the case, dubious on its own merit, does itself refute your point. You cannot hope to compete with names, times, and places, which is the substance of the debate. I have already provided three counter examples, and can provide a hundred more.

    Even the Buridan example is suspect. Wikipedia and Panda’s Thumb draw everything from Ronald Numbers, who, as I have already shown contradicted himself in his discussion with Paul Nelson, confessing that MN cannot be traced any further back than the mid-nineteenth century, which in itself is a stretch.

    Let’s get back to reality with two more examples: (numbers #4, #5 and counting)

    John Ray, scientist and author of “The Wisdom of God Manifested in the Works of the Creation,” [1691] believed that nature was a worthy subject for study and reason, and that such activity was pleasing to God. He believed that living things showed adaptations to their environments, which for Ray were signs of God’s design.

    Temple Chevallier wrote, “Of the proofs of the divine power and wisdom derived from the study of astronomy in 1835.” Does that sound like methodological naturalism to you?

    If those who claim to be educated on this matter would simply think the matter through, we would not be having this discussion. The Catholic Church, for example, when it initiates is canonization process, calls on medical science to verify miracles attributed to saints. During the process, these same medical scientists are called on to distinguish natural healings from supernatural healings. Has anyone from your group informed them that they must cease and desist from that tradition because it violates your 1980ish rule that you have dubbed, “methodological naturalism.”

    How often do I have to say this. You have no case. Give it up.

  236. If you mean by supernatural: everything inaccessible to science, then by definition it cannot be directly measured in the lab.

    Well, exactly!

  237. How often do I have to say this. You have no case. Give it up.

    My case is that Intelligent Design, by proposing supernatural input, excludes itself from scientific scrutiny. It is a matter of definitions. There may be a way forward. I can’t imagine what it might be, but it is not my problem.

  238. “It has been suggested by others here before, and by me elsewhere, but an avenue for ID research would be to look for the interface where the supernatural input impinges on the real world. There you must see discontinuity, a reaction without an opposite. Why isn’t anyone trying this?”

    One reason is that ID says nothing about the supernatural, only intelligence or agency.

    Second, ID is doing research into the involvement of agency but it is research that other scientists who are not pro ID would also do. See the work of Abel and Durston.

    Third, as I said above, ID researchers would not do things much different than what other researchers would do. It is only the conclusions that would be different. In fact you could take all the research done to date in the history of the world and it would be ok with ID. ID would just come to more reasoned and logical conclusions on some of the studies.

    You seem to want to start some special discipline but ID does not want to do something different from what other scientists have been doing, only do it more intelligently. Somebody who believe in ID could study dark matter and dark energy, genetics, mutations to microbes over time, plate tectonics, string theory etc. Why shouldn’t they? Tell me what an ID scientist can not do or would not do. There is nothing.

  239. —Alan Fox: “It is all a matter of definitions. {natural, supernatural}

    Yes, of course. You do get it. When ID defines reality in terms of law, chance, and agency, then the natural, supernatural paradigm is inappropriate [and even maliciously applied] because the methodology, as formulated, does not incorporate natural, supernatural as definitions, because in that context, natural cannot be defined. Science employs definitions, constructs, and assumptions. Once they are in place, the ground cannot be shifted as in, shifting law, chance, agency to natural, supernatural.

    On the other hand, when the natural vs. supernatural paradigm is employed in other contexts, as in ordinary healing vs. miraculous healing, then the terms can be employed because natural, by definition, means without Divine assistance, or extraordinary. Everything does turn on definitions and the practice of being consistent with them IN CONTEXT.

  240. My case is that Intelligent Design, by proposing supernatural input,

    Where does it do that?

  241. If there were supernatural input into our universe, begging the question of just what supernatural means, this could mean that there may be phenomena that would have no explanation through natural laws or chance. So when we see such phenomena we don’t cease to study them on the chance that they could be explained by natural laws, but “admit” that they may not have an explanation that is due to the operation of known natural laws.

    How hard is that. Nothing changes in science except this “admission.”

  242. stephenB:

    You consistently and relentlessly confuse the motivations of scientists and natural philosophers of the past with their methods. Science is founded on the empirical method, and none of the scientists and natural philosophers whom you have cited have used a non-empirical method to conduct their research.

    Ergo, the fact that they may have been motivated by their beliefs in the supernatural ultimately had no effect on the method with which they studied the natural.

    This is all that “methodological naturalism” is prescribing: that the most fruitful way to study nature is to observe it, and to ground one’s conclusions in one’s observations and solely in one’s observations.

    Hypotheses non fingo!

    Longer quote (translated from the Latin):

    “I have not as yet been able to discover the reason for these properties of gravity from phenomena, and I do not feign hypotheses. For whatever is not deduced from the phenomena must be called a hypothesis; and hypotheses, whether metaphysical or physical, or based on occult qualities, or mechanical, have no place in experimental philosophy. In this philosophy particular propositions are inferred from the phenomena, and afterwards rendered general by induction.

    – Isaac Newton (1726). Philosophiae Naturalis Principia Mathematica, General Scholium. Third edition, page 943 of I. Bernard Cohen and Anne Whitman’s 1999 translation, University of California Press ISBN 0-520-08817-4, 974 pages.

    Oddly enough, that was written in the 18th century, not the 19th. But you keep trying, stephenB, those goalposts aren’t that heavy…

  243. —-Alan Fox: “My case is that Intelligent Design, by proposing supernatural input, excludes itself from scientific scrutiny. It is a matter of definitions. There may be a way forward. I can’t imagine what it might be, but it is not my problem.”

    No, your case was that methodological naturalism is historical, which it obviously is not. That was the context of my remark, “you have no case.” If you are going to respond to my comments, then please honor the context. With regard to natural/supernatural, see my commmet at 239.

  244. Where does it do that?

    Have I misunderstood? I thought the core idea was that natural phenomena such as variation sifted by differential survival and reproduction was insufficient to explain the observed diversity of life on Earth, and that additional information had to be injected into the system by some unobservable process. If the process is observable, then the problem goes away.

  245. Here’s a place to try to put your goalposts, stephenB:

    “Nothing exists except atoms and the void.

    and

    “All things are the fruit of chance and necessity.”

    - Democritus of Abdera
    7th century BC

  246. Democritus may also not have been the first to articulate this particular version of “naturalism” (Leucippus comes immediately to mind), but unfortunately we don’t have written records that go much further back than that.

    So, was Democritus prescribing a “supernaturalist” viewpoint, or a “naturalist” one? And if your answer is the second, how do you square this with your assertion that scientists and philosophers have only been using “naturalist” assumptions to guide their investigations into nature since the 1980s?

  247. 247

    I’ve returned to find this thread has moved on…but…I have to respond to Allen at 181.

    You must be kidding.

    You post a quote from a paper, calling it the “current” “last month” falsification of Abel. Well hallelujah, the information paradox was solved and no one knew it!

    Oddly enough, I read that paper about 10 years ago. I really have to wonder if you even read it when you posted it. By the authors own conclusions they could not find a physical relation beyond the trivial. This is what you call a falsification?

    Allen, even for you, this is weak.

  248. —-Allen: “You consistently and relentlessly confuse the motivations of scientists and natural philosophers of the past with their methods. Science is founded on the empirical method, and none of the scientists and natural philosophers whom you have cited have used a non-empirical method to conduct their research.”

    I know what science is as well as anyone since I have experience with it. What my examples proved, and I have a hundred more if you need them, is that the scientists of antiquity did not employ methdological naturalism, which Intrudes anti-design ideology APRIORI. According to MN, the scientist MAY NOT DRAW ANY CONCLUSION ABOUT DESIGN. This is news to you?

    —-Allen MacNeill: “This is all that “methodological naturalism” is prescribing: that the most fruitful way to study nature is to observe it, and to ground one’s conclusions in one’s observations and solely in one’s observations.”

    No, methodological naturalism goes beyond that. ID grounds its conclusions in its observations and SOLELY IN ITS OBSERVATIONS. Methodological naturalism goes one step further and insists that it MAY NOT DRAW CERTAIN CONCLUSIONS BASED ON THOSE OBSERVATIONS. Stop misrepresenting your own arbitrary law.

  249. @ StephenB

    I think Allen MacNeill has already answered you about the history of empiricism.

  250. stephenB:

    Your case at #239 is deeply incoherent: what, exactly, is “the natural, supernatural” supposed to mean? You use this phrase three times in the first paragraph of #239 and each time it makes no sense whatsoever.

    Indeed, both paragraphs in #239 (but especially the first paragraph) do not even scan as standard English syntax.

    If this is the best you can do, I would suggest you try some other hobby…

  251. 251

    Oh…and Allen

    As Charlie tried to get you to realize…its the sequencing of nucleotides that has no relation to physical necessity. They are physico-dynamically inert.

    Try to keep that in mind.

  252. And Stephen:

    Beware all caps.

  253. Hi Allen,
    Please post another lecture on civil discourse.

  254. —-Allen: “Here’s a place to try to put your goalposts, stephenB (Democritus)

    History is replete with philosophers and scientists who studied nature without reference to a Diety. What they did not do is institutionalize their approach and declare that no one else but they were doing real science. In fact, the line between philosophy and science was blurred. There was no such thing as “demarcation.” It just wasn’t there.

  255. Macneill-san,

    The analogy (or perhaps definition) of Occam’s Razor as the preference for the lowest order polynomial to fit the data, only occured to me as I was writing the post. So I am sure it must have occured to others who have thought more deeply than I have on these subjects. Nevertheless, you certainly have my permission to reference our discussions as a starting point for any fuller investigation into the idea that you might undertake for your book, with no claim made for priority, just “examining shells on the beach” level amusement while walking unaware next to the oceans of wonder and knowledge.

  256. Alan and Allen, you are both misrepresenting your own doctrine. You need to reread 248 and respond. Hint: read carefully the part about forbidding certain conclusions prior to the investigation. Try to focus.

  257. Methodological naturalism goes one step further and insists that it MAY NOT DRAW CERTAIN CONCLUSIONS BASED ON THOSE OBSERVATIONS. Stop misrepresenting your own arbitrary law.

    Is there a list of conclusions that are forbidden? Usually conclusions gain acceptance on being found to be useful.

    >a href=”http://redwing.hutman.net/~mreed/warriorshtm/allcaps.htm”>Sorry messed up All Caps link. :)

  258. H’mm:

    Seems we need to present a bit more from Newton’s General Scholium, which is a classic statement of a design thought, and that within the greatest work of modern science, his Principia, by of course the greatest modern scientist:

    __________________

    . . . This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent and powerful Being. And if the fixed stars are the centres of other like systems, these, being formed by the like wise counsel, must be all subject to the dominion of One; especially since the light of the fixed stars is of the same nature with the light of the sun, and from every system light passes into all the other systems: and lest the systems of the fixed stars should, by their gravity, fall on each other mutually, he hath placed those systems at immense distances one from another.

    This Being governs all things, not as the soul of the world, but as Lord over all; and on account of his dominion he is wont to be called Lord God pantokrator , or Universal Ruler; for God is a relative word, and has a respect to servants; and Deity is the dominion of God not over his own body, as those imagine who fancy God to be the soul of the world, but over servants. The Supreme God is a Being eternal, infinite, absolutely perfect; but a being, however perfect, without dominion, cannot be said to be Lord God; for we say, my God, your God, the God of Israel, the God of Gods, and Lord of Lords; but we do not say, my Eternal, your Eternal, the Eternal of Israel, the Eternal of Gods; we do not say, my Infinite, or my Perfect: these are titles which have no respect to servants. The word God usually signifies Lord; but every lord is not a God. It is the dominion of a spiritual being which constitutes a God: a true, supreme, or imaginary dominion makes a true, supreme, or imaginary God. And from his true dominion it follows that the true God is a living, intelligent, and powerful Being; and, from his other perfections, that he is supreme, or most perfect. He is eternal and infinite, omnipotent and omniscient; that is, his duration reaches from eternity to eternity; his presence from infinity to infinity; he governs all things, and knows all things that are or can be done. He is not eternity or infinity, but eternal and infinite; he is not duration or space, but he endures and is present. He endures for ever, and is every where present; and by existing always and every where, he constitutes duration and space. [root of the Newtonian view of space and time] Since every particle of space is always, and every indivisible moment of duration is every where, certainly the Maker and Lord of all things cannot be never and no where. Every soul that has perception is, though in different times and in different organs of sense and motion, still the same indivisible person. There are given successive parts in duration, co-existent puts in space, but neither the one nor the other in the person of a man, or his thinking principle; and much less can they be found in the thinking substance of God. Every man, so far as he is a thing that has perception, is one and the same man during his whole life, in all and each of his organs of sense. God is the same God, always and every where. He is omnipresent not virtually only, but also substantially; for virtue cannot subsist without substance. In him are all things contained and moved [i.e. cites Ac 17, where Paul evidently cites Cleanthes]; yet neither affects the other: God suffers nothing from the motion of bodies; bodies find no resistance from the omnipresence of God. It is allowed by all that the Supreme God exists necessarily; and by the same necessity he exists always, and every where. [i.e accepts the cosmological argument to God.] Whence also he is all similar, all eye, all ear, all brain, all arm, all power to perceive, to understand, and to act; but in a manner not at all human, in a manner not at all corporeal, in a manner utterly unknown to us. As a blind man has no idea of colours, so have we no idea of the manner by which the all-wise God perceives and understands all things. He is utterly void of all body and bodily figure, and can therefore neither be seen, nor heard, or touched; nor ought he to be worshipped under the representation of any corporeal thing. [Cites Exod 20.] We have ideas of his attributes, but what the real substance of any thing is we know not. In bodies, we see only their figures and colours, we hear only the sounds, we touch only their outward surfaces, we smell only the smells, and taste the savours; but their inward substances are not to be known either by our senses, or by any reflex act of our minds: much less, then, have we any idea of the substance of God. We know him only by his most wise and excellent contrivances of things, and final cause [i.e from his designs]: we admire him for his perfections; but we reverence and adore him on account of his dominion: for we adore him as his servants; and a god without dominion, providence, and final causes, is nothing else but Fate and Nature. Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. [i.e necessity does not produce contingency] All that diversity of natural things which we find suited to different times and places could arise from nothing but the ideas and will of a Being necessarily existing. [That is, implicitly rejects chance, Plato's third alternative and explicitly infers to the Designer of the Cosmos.] But, by way of allegory, God is said to see, to speak, to laugh, to love, to hate, to desire, to give, to receive, to rejoice, to be angry, to fight, to frame, to work, to build; for all our notions of God are taken from. the ways of mankind by a certain similitude, which, though not perfect, has some likeness, however. And thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy.
    ____________________

  259. MacNeill-san,

    as a post-script in re Occam’s Razor, I would note that the preference for low order polynomials is explicit in the Latin phrase “entia non sunt multiplicanda praeter necessitatem”! ;-P

    #punning in a dead language must be the absolute lowest form of humor!

  260. I wrote:

    I think one can invoke miracles as causes of natural phenomena, but in so doing, one will admit it cannot be studied in the lab, since by definition, miracles would not be subject to direct laboratory repeatability. Hence one has a good argument to say miracles can’t be a part of empirical science by definition, even if miracles are the fundamental cause of much of the physical universe.

    In other words, I’m probably closer to Allen’s position of methodological naturalism with respect to causal agencies that can be studied direcly by empirical science.

    We can indirectly suggest testable predictions as to whether a naturalistic cause will succeed in creating a certain feature: i.e. predictions about the success of OOL.

    Abel correctly framed how an ID-sympathetic hypothesis can be framed:

    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it:

    “Physicodynamics cannot spontaneously traverse The Cybernetic Cut [9]: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.”

    This is the correct approach since we are dealing with undeniable observables.

    We can use science to lead to promising inferences about ID, but formally speaking it is still only a reasonable inference, it is not a direct observation.

    But this cuts two ways, we can also argue macro-evolution has not been observed in the lab. The same two-edge swords can be applied to evolutionary psychology or any of the inferences made with the sketchiest of data.

    In fact, some naturalists have suggested independent origin of organisms versus macro evolution (Senepathy). There are some controversies surrounding theories in evolutionary psychology, precisely because of the problem of direct observables.

    So if we applied the same strict standards to paleontology, or cosmology, etc., we might rule their inferences out of empirical science as well, since their inferences are not directly observable.

    The sword of strict methodolgical naturalism cuts both ways.

    But as I said, I try not to concern myself with big discussion about labels and definitions. I’m more interested in what is reasonably true given what little evidence we have, and we have very little!

    The evidence suggests to me that the emergence of life was a spectacularly unique event. Miracle would be an appropriate term.

    Some ID proponents do not share my view about miracles, so in deference to them, I don’t want to suggest that my appeal to a miracle for the first life represents their view, but it is my view.

  261. —-”Allen Fox: Beware all caps.”

    That was a cute example. I liked it. Of course, using caps also reflects on the authors perception about the readers sensibilities and willingness to understand a point that has already been made, say, twenty or thirty times. Sometimes, a megaphone really is the way to go for audiences who evade, distract, and obfuscate.

    Example:

    [a] Faraday’s religious belief in a single Creator [God's unity], informed his scientific belief in the “unity of forces.”

    [b] Methodological naturalism: “We must nevertheless …..”investigate nature as if nature is all that there is” “We cannot allow a Divine ‘foot in the door.’”

    Now, most rational people understand that [a] cannot be reconciled with [b]. However, Allen MacNeill and you obviously either do not accept the point or else will not face it. So, naturally, I must, from time to time, resort to caps in order to dramatize that which should already have been apparent.

    With each new example, I make the point anew, and each time, the two of you evade it. Allen now wants to hearken back to ancient Greece again. Well, first things first. Let’s first understand that methodological naturalism was not in force during the middle ages and post middle ages, the very time when scientists were appealing to the Bible as their source for scientific wisdom.

  262. Scordova, When the Catholic Church attempts to canonize a saint, it must, among other things, attribute a miracle to that saint’s intervention. Usually, it is a medical miracle. In order to prove that a supernatural healing has taken place, for example, as opposed to a natural healing, the Church brings in some of the best medical scientists in the world to confirm the fact. According to methodological naturalism, those scientists, who certainly regard themselves as scientists, are not really doing science at all. You seem to agree.

  263. Alan–

    Where does it do that? . . .Have I misunderstood?

    It appears so.

    I thought the core idea was that natural phenomena such as variation sifted by differential survival and reproduction was insufficient to explain the observed diversity of life on Earth, and that additional information had to be injected into the system by some unobservable process.

    No. Although you raise an good point: is “variation sifted by differential survival and reproduction” sufficient to explain the observed diversity of life on Earth?

    That is not ID, however.

    ID is the claim that design is a real and observable part of nature, has qualities that can be determined objectively, and that by using an almost hyper-skeptically rigorous methodology for finding such qualities in lifeforms it is indicated that inherent parts of life are designed.

    And ID, btw, in no way prohibits a belief in evolution.

  264. Sal –I don’t want to suggest that my appeal to a miracle for the first life represents their view, but it is my view.

    Somewhere along the line anyone will have to invoke a violation of the laws of physics for anything to make sense.

  265. What Stephen hasn’t addressed is that doing anything other than applying methodological naturalism has been spectacularly unsuccessful. As Stephen said earlier, early scientists helped move science away from superstition: invoking Kepler’s reference to the Holy Trinity in respect to elliptical orbits or Newton’s forays into alchemy merely highlights that this transition took time, and that scientists continuing to mix superstition (Stephen’s term) with science.

    What is important to note is that the testable explanations in terms of material processes are what have endured, and the religious speculations have become footnotes in history. As I’ve said, I don’t believe that Stephen can provide an example of real science advanced and tested by the world’s great religious scientists that actually involved their religious beliefs.

    No matter how religious a scientist is, the science he or she does involves explaining the material world in terms of its constituent material parts, and is no different than the science an materialist scientist would do.

    What we call methodological naturalism has proven itself to work extremely well. It’s adoption as a “working rule” – a strong guideline – is entirely justified.

    However, there is a sense in which the whole discussion of methodological naturalism is misleading, or at least hides some of the real issues. Science starts with some fundamental concepts. The first is that it is based on observable (and in many cases measurable) sensory phenomena that are common to all human beings. Second, scientific explanations have to be testable in the sense that there are further observations that are capable of aiding in the confirmation or disconfirmation of the explanation.

    In a sense we define natural (or at least material) in reference to whether something can fall under the two criteria listed above: it is these component parts of science that are truly what distinguish it. Methodological naturalism is an umbrella term for the whole set of things which make up the scientific method, but it is a somewhat misleading term because it implies that what is natural can be defined separate from, or prior to, the process of scientific investigation.

    That is, one can propose what at first glance might be a non-natural explanation or a non-natural phenomena, but if in fact we could test that hypothesis using empirical evidence, then the phenomena would be better considered “natural.”

    So the big question is not whether proposal X is natural or not, but whether it is testable or not. Focussing first on “natural” is somewhat misleading, and perhaps has the cart before the horse.

  266. Was alchemy based upon superstition and a violation of naturalism?

  267. Scordova, When the Catholic Church attempts to canonize a saint, it must, among other things, attribute a miracle to that saint’s intervention. Usually, it is a medical miracle. In order to prove that a supernatural healing has taken place, for example, as opposed to a natural healing, the Church brings in some of the best medical scientists in the world to confirm the fact. According to methodological naturalism, those scientists, who certainly regard themselves as scientists, are not really doing science at all. You seem to agree.

    My point is that if someone wants to call it science, they are welcome to, if someone else doesn’t want to call it science they are welcome to.

    What is more important is whether the miracle took place.

    If you think I’m avoiding addressing the issues, I already confessed I try to avoid the issue since it strikes me as a moot point.

    If Christ was raised from the dead, isn’t it sort of a minor point whether the inference is scientific or not. The truthfulness of the account seems to be far more important.

    Their is a blood-type bombay blood “h-h”. Is that a miracle since it is so rare?

    We can say scientifically an event is inferred to be extraordinarily rare or unrepeatable or singular. Labels of “supernatural” or “miracle” are philosophical.

    But how will we ever dis-entangle or delineate “miracle” from “rare” or “unusual” scientifically?

    One of the world’s most respected physicists said:

    the laws of physics are not from everlasting to everlasting

    –John Wheeler

    That conclusion was a direct consequence of Quantum Mechanics. Wheeler’s idea, by the way, is a mainstream view.

    Is the suspension of the known laws of physics a miracle?

    There are many statements which are true, but have no logical connection.

    For example, I can say, “2+2=4″ and “the sky is blue today”.

    But to say, “2+2=4 implies the the sky is blue today” is not a logical construction, even though both the premise (“2+2=4″) and the conclusion (“the sky is blue today”) are both true. What is false is to say the premise necessarily implies the conclusion.

    Thus, we can say:

    1. the origin of life was a rare event

    2. God did it

    Both statements may be true, but the conclusion may not follow directly from the premise. Hence it is a suspect statement to say “the origin of life is rare, therefore God did it”.

    Even though both statements may well be true. The issue in such cases is not whether God did it, but whether the inference follows from the proper rules of logic.

    And that is why I’m sympathetic to Allen’s characterization of methodological naturalism.

    One can say, “structures like mount rushmore cannot be created except through intelligent agencies”.

    That is an empirically falsifiable statement.

    One can say, “computers like the cell cannot be created except through intelligent agencies”.

    That is an empirically falsifiable statement. But formally speaking, that is different than saying, “intelligent agencies created the cell”.

    Methodological naturalism I think can admit statements like: “computers like the cell cannot be created except through intelligent agencies”.

    But this is still a weak construction since, I could also say: “computers like the cell cannot be created except by the flying spaghetti monster”.

    The statement is scientifically falsifiable, but somehow it doesn’t seem quite right.

    Something to consider:

    Wm. Dembski pg 36 of The Design Inference:

    The principal advantage of characterizing design as a complement of regularity and chance is that it avoids committing itself to a doctrine of intelligent agency.

    Defining design as the negation of regularity and chance avoids prejudicing the causal stories we associate with the design inference.

    So even design recognition is preferred to be done without making a commitment to a “doctrine of intelligent agency”. That approach can fit with the framework of methodological naturalism, even though the underlying motivation is to strenghthen the case that an intelligent agent was involved.

  268. “Methodological naturalism” only comes up when scientists want to be philosophers and put in their two cents about the nature of being. It never comes up when nature is being studied purely for its own sake. It’s not needed.

  269. It was both superstition and failed science. To the extent that alchemists were trying to work with substances to produce gold they were in fact doing science – certain aspects of chemistry build upon some of their failures.

    On the other hand, alchemists were also interested in philosophical and spiritual matters that were analogous to some of their physical experiments, such as purifying the soul so as to achieve immortality. I think these would fall under the superstition category.

  270. —-Hazel: “As I’ve said, I don’t believe that Stephen can provide an example of real science advanced and tested by the world’s great religious scientists that actually involved their religious beliefs.”

    That suggests that you have not been paying attention. It was their religious beliefs that helped them decide what exactly needed to be tested and why. Don’t you remember the example of Faraday? His belief in God’s unity informed his conviction that God’s created forces also have unity. Thus, he discovered the principle of unity in electricity.

    In any case, you are shifting the ground to a new issue. The issue on the table is not how much progress these scientists did or didn’t make, but whether or not these scientists practiced methodological naturalism, which they obviously did not.

  271. Interesting.

    So, motivated by superstition (apparently) they developed a science, made many important discoveries, advanced technology, relied on physical experimentation and empiricism, invented lab techniques and apparati, and relied upon the current state of knowledge of physics and chemistry.

  272. And to the extent that they were interested in, and experimenting with, the the transmutation of lead to gold did they not, like Edison with his failed lightbulbs, successfully demonstrate how the process didn’t work?

    By the way, as far as the possibility of turning lead into gold goes, they weren’t wrong, were they?

  273. To Charlie: I think I made clear that the superstition part had to do with philosophy and religion. Trying to turn substances into gold was an empirical project that did aid the development of chemistry, but I think you overstated the relative importance of their contributions. At the same time they were trying to do alchemy, many more people were working more directly to understand the nature of chemical substances.

  274. Yes, Hazel, you did assert that special plea.
    It undoes your theory, unfortunately, that so much was accomplished, empirically speaking, by people with such un-natural motivations.

  275. That suggests that you have not been paying attention. It was their religious beliefs that helped them decide what exactly needed to be tested and why. Don’t you remember the example of Faraday? His belief in God’s unity informed his conviction that God’s created forces also have unity. Thus, he discovered the principle of unity in electricity.

    Stephen, I have been paying good attention, and have responded three times to your point. That fact that Faraday had a religious belief in unity motivated him to look for underlying similarities, but the actual science he did – the experiments he ran and the conclusions he reached HAD ABSOLUTELY NO RELIGIOUS CONTENT! In practice, he was a methodological naturalist, studying the material world and seeking to explain it in terms of material processes.

    One can be, and millions are, a theist and still practice methodological naturalism.

    These are some points that you don’t seem to be paying attention to.

  276. —-Sal: “And that is why I’m sympathetic to Allen’s characterization of methodological naturalism.”

    But Allen has misrepresented methodological naturalism.

    Allen writes: “This is all that “methodological naturalism” is prescribing: that the most fruitful way to study nature is to observe it, and to ground one’s conclusions in one’s observations and solely in one’s observations.”

    If that is all MN was, then ID would be welcome in the scientific community, because all its conclusions are “grounded solely in its observations.”

    What is MN really? Well here are a couple of examples: From Wikipedia “We must nevertheless …..investigate nature as if nature is all that there is”…. From Lewontin: “We cannot allow a Divine foot in the door.”

    Do you not see the difference? ID cannot proceed as if nature is all there is. If nature is all there is, then, by definition, God [or anything or anyone else] could have designed it. Allen’s definition, either consciously or unconsciously, left out that information.

  277. —Hazel: “That fact that Faraday had a religious belief in unity motivated him to look for underlying similarities, but the actual science he did – the experiments he ran and the conclusions he reached HAD ABSOLUTELY NO RELIGIOUS CONTENT!”

    ****Of course they didn’t. But that is not what is at stake. Methodological naturalism forbids any conclusions or assumptions that may even hint at religious content.

    —-”One can be, and millions are, a theist and still practice methodological naturalism.”

    Totally irrelavent.

    —-These are some points that you don’t seem to be paying attention to.

    It isn’t you that is making the points, it is me. The point is that methodological naturalism, the doctrine that we must approach science AS IF NATURE IS ALL THERE IS, [wikipedia] was not practiced in the middle ages and post middle ages.

    What you need to pay attention to is the comment after*******

  278. But MN (short cut for a much bigger idea) doesn’t say that nature (that which science can study) is all there is. What it says is that the techniques of science are limited to studying certain kinds of things in a certain way. The theist believes there is more to the world than science can study and the materialist says there isn’t, but that is a disagreement that science itself can’t address.

    Short version: science isn’t everything.

    Trying to make it everything both weakens the power of science within its domain and deflects us from addressing those issues that are beyond science in appropriate ways.

  279. I get to make points, too, Stephen. Why do you think you are the presumed leader of this discussion?

  280. By the way, science does not actually practice methodological naturalism but rather methodological theism as the scientist must presume cause and effect, regularity and order, rationality and logic, in order to do science. He is then relying upon the metaphysics of theism when doing science whether – he so justifies it or not.

    What is more, lest we lose our sense of proportion, we should bear in mind that science done on atheistic presuppositions will lead to the same results as science done on theistic presuppositions.
    For example, when trying to find out in practice how an organism functions, it matters little whether one assumes that it is actually designed, or only apparently designed. Here the assumption of either ‘methodological naturalism’ (sometimes called ‘methodological atheism’) or what we might term ‘methodological theism’ will lead to essentially the same results. This is so for the simple reason that the organism in question is being treated methodologically as if it had been designed in both cases.

    John Lennox, God’s Undertaker
    pp. 27-36

    John [Lennox] and I agree that much of current biology (in so far as functional and teleological claims are still current) is in fact methodologically theistic. As the theistic paradigm develops, there is every reason to hope that it will be joined by scientists who are personally agnostic but who recognize good and successful science when they see it.

    Indeed, historians of science like Duhem and Whitehead have argued that the development of modern physical theory in the 14th through 18th centuries would have been impossible without the Christ-engendered conviction that the physical universe might prove to be intelligible to us.

    Robert Koons
    http://www.origins.org/article.....ebate.html

  281. But this cuts two ways, we can also argue macro-evolution has not been observed in the lab. The same two-edge swords can be applied to evolutionary psychology or any of the inferences made with the sketchiest of data.

    The fact that the “junk DNA” meme persisted only demonstrates that strict methodological naturalism was not itself practiced in the field of evolutionary biology. Inferences were made without direct observable evidences.

    I don’t fault the community, as they tried their best, but suffice to say, a lot of things are presumed with no direct evidence and accepted as fact.

  282. —-Charlie: “By the way, science does not actually practice methodological naturalism but rather methodological theism as the scientist must presume cause and effect, regularity and order, rationality and logic, in order to do science. He is then relying upon the metaphysics of theism when doing science whether – he so justifies it or not.”

    That is exactly right. Although Darwinists and monists enforce methodological naturalism as a tool for disenfranchisement, they do not practice it in any real sense. They [quietly] assume just as the early scientists did that the universe is a rational place with ordered laws. They don’t start, nor could they possibly start, with a clean slate. Of course, they plant artificial barriers to the research by refusing to follow where the evidence leads, but that is another matter.

    The relavent point is just as you say: To begin research with no metaphysical assumptions would be both irrational and impossible. On the other hand, to deny those metaphysical assumptions, as do the Darwinists on this blog, is also irrational. I have raised this issue many times, and with each new installment, they all claim that metaphysics has absolutely nothing to do with science. incredible.

  283. —-Hazel: “I get to make points, too, Stephen. Why do you think you are the presumed leader of this discussion?”

    Yes, of course. Welcome to the party.

  284. They [quietly] assume just as the early scientists did that the universe is a rational place with ordered laws.

    Assuming that the properties of the observable universe are consistent has been useful scientifically so far. What are the alternatives?

  285. “Assuming that the properties of the observable universe are consistent has been useful scientifically so far. What are the alternatives?”

    A universe that is not designed.

  286. 287

    Charlie, Stephen, you are making me rethink my use of the term metaphysical materialists – a term I picked up from Abel’s work.

    I see it as describing a materialist that patently assumes their conclusion that there is nothing beyond a material cause.

    I would like to hone the description, but have no desire to argue over it. There are already plenty of side arguments to comfort the adversaries of ID – as can be seen repreatedly in the skirting responses given on any of these threads, or on any university campus, and throughout the media.

  287. —-Alan: “Assuming that the properties of the observable universe are consistent has been useful scientifically so far. What are the alternatives?”

    The point is that the scientific process does not begin with an empirical observation; it begins with a world view assumption. In other words, everyone acts as if the universe was rationally ordered even though many deny that fact with their words or their public proclamations. Their actions do not match their stated beliefs or, more precisely, their non beliefs.

  288. Charlie writes,

    By the way, science does not actually practice methodological naturalism but rather methodological theism as the scientist must presume cause and effect, regularity and order, rationality and logic, in order to do science. He is then relying upon the metaphysics of theism when doing science whether – he so justifies it or not

    No, because theism (or design) is not the only possible explanation for why the universe exhibits “cause and effect, regularity and order,” etc, and the subject of why the universe is such is a matter of metaphysics that is itself not addressable by science.

    This is not the place to revisit that metaphysical topic, I don’t think. People of many various philosophical perspectives accept, based on experience, that the universe exhibits orderly properties: why the universe is that way is not part of science. People can disagree about why the universe is as it is and yet agree completely on the science itself.

  289. “Assuming that the properties of the observable universe are consistent has been useful scientifically so far. What are the alternatives?”

    A universe that is not designed.

    Ah! I think I am beginning to see. If there are consistent properties of matter, for example, someone must have specified them, or they would be random? Therefore design?

  290. Upright Biped: You are on solid ground. You write: “I see it as describing a materialist that patently assumes their conclusion that there is nothing beyond a material cause.”

    Sure, that’s it. Charlie’s point was just that materialists are not consistent. That’s all. It’s like the solipsist who says nothing exists but himself, but then looks both ways before crossing the street.

    We all understand materialism exactly as you do, so I don’t think you should rethink anything.

  291. The point is that the scientific process does not begin with an empirical observation; it begins with a world view assumption.

    The assumption is made that the properties of, say, matter are consistent.

    In other words, everyone acts as if the universe was rationally ordered…

    That is the working hypothesis, if you mean that it is assumed that the properties of the observed universe are consistent.

    …even though many deny that fact with their words or their public proclamations.

    An example would clarify your meaning, I’m sure.

    Their actions do not match their stated beliefs or, more precisely, their non beliefs.

    In what way?

  292. —-Alan: “That is the working hypothesis, if you mean that it is assumed that the properties of the observed universe are consistent.”

    While I agree with Charlie’s point, I am not sure that I want to get into a long discussion defending it at the expense of abandoning my argument about MN, which I consider to be more important. Nor do I want to put words in Charlie’s mouth since he may see it differently than I do.

    I am guessing, though, that he meant something like this: It seems that, on the one hand, materialist Darwinism negates meaning or purpose in the universe but on the other hand, quietly conducts its business as if there was something meaningful and purposeful to discover.

  293. I am guessing, though, that he meant something like this: It seems that, on the one hand, materialist Darwinism negates meaning or purpose in the universe but on the other hand, quietly conducts its business as if there was something meaningful and purposeful to discover.

    That’s what I thought he meant. I, for one, don’t immediately make the connection between consistent properties and design. So if I make assumptions based on consistency, I don’t feel the need to attribute that consistency to design. I have no need for that hypothesis. [/Laplace

  294. 295

    StephenB,

    “I am guessing, though, that he meant something like this: It seems that, on the one hand, materialist Darwinism negates meaning or purpose in the universe but on the other hand, quietly conducts its business as if there was something meaningful and purposeful to discover.”

    That sums it up nicely.

  295. to Stephen:

    In other words, everyone acts as if the universe was rationally ordered even though many deny that fact with their words or their public proclamations. Their actions do not match their stated beliefs or, more precisely, their non beliefs.

    Like Alan, I would like to see examples. Who denies that the universe is ordered? You say this is true of “many” – can you name someone and give a quote?

  296. StephenB @ 283

    That is exactly right. Although Darwinists and monists enforce methodological naturalism as a tool for disenfranchisement, they do not practice it in any real sense. They [quietly] assume just as the early scientists did that the universe is a rational place with ordered laws. They don’t start, nor could they possibly start, with a clean slate. Of course, they plant artificial barriers to the research by refusing to follow where the evidence leads, but that is another matter.

    The accusation that the biological establishment ruthlessly suppresses dissenting opinion is political complaint not a scientific criticism. It is belied by the example of how the theory of punctuated equilibria won acceptance and the continuing vigorous debates between the various contending factions within evolution.

    Is there also any necessity to point out yet again that proponents of Intelligent Design are publishing books and magazine articles, running websites, appearing on radio and TV shows and have even established their own research and advocacy body in the Discovery Institute? That does not suggest oppression.

    As for an rational and ordered Universe, it is not an assumption, it is an observation. We do not assume things fall to the ground unless something holds them up, we know it – as much as we know anything – because that is what we see all around us. It has happened all our lives and at least as far back as recorded history goes. If the Universe were not rational and ordered not only would science not be possible but neither would the Universe. That order calls for explanation. Methodological naturalism assumes there is an explanation but makes no assumption about it beyond that such an explanation exists.

    As for barriers to research, they seem to exist within the ID community not outside it. There seems to be a curious reluctance to even propose specific research projects let alone commit resources to carry them through. It seems to be not so much that they are prevented from following the evidence wherever it might lead as that the are hesitant about walking down that road.

  297. —-”Like Alan, I would like to see examples. Who denies that the universe is ordered? You say this is true of “many” – can you name someone and give a quote?”

    If something is ordered, it is ordered for a purpose. I have never met a Darwinist who thinks that there is purpose in the universe. Notice that Alan, thoughtfully and judiciously, used the word “consistent” and carefully avoided the word “order,” knowing that order implies purpose and design. If something is ordered it is ordered to something or for the sake of something.

    In terms of quotes, here are a couple:

    George Gaylord Simpson: “Evolution is a purposeless, mindless process that did not have man in mind.”

    In his earlier work, Ken Miller used the same quote, but then, in his latest book, he reversed his position, saying that man’s arrival was inevitable, carrying on as if he had not changed his position at all.

  298. If something is ordered, it is ordered for a purpose.

    Nope, not necessarily, but we have argued this enough, I think.

    For the purposes of this discussion, it is in fact true that virtually everyone – theist, materialist, whatever – believes that the material world is orderly and that through empirical investigation we can learn things about the material world that everyone – theist, materialist, whatever – accepts as true (in the sense that word is used in science.)

    So back to the main point: people of all philosophical and religious perspectives accept MN as a well-established guideline for doing science because it has worked. However, if someone wants to offer a non-material e

    If something is ordered, it is ordered for a purpose.

    Nope, not necessarily, but we have argued this enough, I think.

    For the purposes of this discussion, it is in fact true that virtually everyone – theist, materialist, whatever – believes that the material world is orderly and that through empirical investigation we can learn things about the material world that everyone – theist, materialist, whatever – accepts as true (in the sense that word is used in science.)

    So back to the main point: people of all philosophical and religious perspectives accept MN as a well-established guideline for doing science because it has worked. However, if someone wants to offer a non-material explanation that can in fact be tested in reference to empirical observations, let them do it. Complaining that there is a rule against doing so is not persuasive, because if such a testable hypothesis were actually offered and confirmed then people’s minds would change. Conversely, the reason that hypotheses that want to explain the material by the non-material are not adopted is because they are not convincing because they can’t be tested, not because of some rule. Focussing on the purported existence of some rigid rule is a distraction from the fact that hypotheses that fall outside the scope of MN fail to useful – they are neither testable nor lead to further productive investigation.xplanation that can in fact be tested in reference to empirical

  299. Whoa – what a mess is 298. Let me try again.

    If something is ordered, it is ordered for a purpose.

    Nope, not necessarily, but we have argued this enough, I think.

    For the purposes of this discussion, it is in fact true that virtually everyone – theist, materialist, whatever – believes that the material world is orderly and that through empirical investigation we can learn things about the material world that everyone – theist, materialist, whatever – accepts as true (in the sense that word is used in science.)

    So back to the main point: people of all philosophical and religious perspectives accept MN as a well-established guideline for doing science because it has worked. However, if someone wants to offer a non-material explanation that can in fact be tested in reference to empirical observations, let them do it.

    Complaining that there is a rule against doing so is not persuasive, because if such a testable hypothesis were actually offered and confirmed then people’s minds would change. Conversely, the reason that hypotheses that want to explain the material by the non-material are not adopted is because they are not convincing because they can’t be tested, not because of some rule. Focussing on the purported existence of some rigid rule is a distraction from the fact that hypotheses that fall outside the scope of MN fail to be useful – they are neither testable nor lead to further productive investigation.

  300. —Hazel: “So back to the main point: people of all philosophical and religious perspectives accept MN as a well-established guideline for doing science because it has worked.”

    Not if you define it the way that is adherents want to enforce it: “investigating nature as if nature is all there is.” That definition has been used many times by many evolutionary scientists.

    To define it accuractely is to immediately realize that it has not always been so, especially during the middle ages and thereafter until at least the neo-Darwinism era.

    That is why folks on this thread are now changing the definition to something softer, something that even ID would qualify for.

    Since you don’t acknowledge that point, we are, as they say, stuck on defintions.

  301. Ergo, this thread is now over. See you all later…

  302. Mr StephenB,

    Not to delay a pleasant end to the thread, but your confusion of order, purpose and evolutionary process is atypical of your usual careful thinking. You said you gave two quotes but only gave one, repeated.

    Hexagonal cracks in the mud are orderly, as are snowflakes. Energy minimization effects often are. These effects are not governed by the evolutionary process of your quotation of Simpson. Order is a static description, 1-entropy. No purpose involved.
    I’m happy to let the thread die on a difference of definitions also. I accept that there are multiple definitions to a word. None of them is privileged.

  303. 304

    SB@291

    Thnx

  304. Nakashima-San:

    Order and organisation are significantly different.

    From The Mystery of Life’s Origin, 1984 [the first technical design theory book], ch 8:

    “a periodic structure has order. An aperiodic structure has complexity.” . . . .

    “Nucleic acids and protein are aperiodic polymers, and this aperiodicity is what makes them able to carry much more information.” . . . .

    “only certain sequences of amino acids in polypeptides and bases along polynucleotide chains correspond to useful biological functions.” . . . .

    [Citing Orgel, 1973:] Living organisms are distinguished by their specified complexity. Crystals fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity.6 [Source: L.E. Orgel, 1973. The Origins of Life. New York: John Wiley, p. 189.]

    They then gave an example:

    >>1. [Class 1:] An ordered (periodic) and therefore specified arrangement:

    THE END THE END THE END THE END

    Example: Nylon, or a crystal . . . .

    2. [Class 2:] A complex (aperiodic) unspecified arrangement:

    AGDCBFE GBCAFED ACEDFBG

    Example: Random polymers (polypeptides).

    3. [Class 3:] A complex (aperiodic) specified arrangement:

    THIS SEQUENCE OF LETTERS CONTAINS A MESSAGE!

    Example: DNA, protein.>>

    Hurricanes, columnar jointed basalt, etc are orderly and are driven by various constraints, energy flow throughs and boundary conditions, they do not store the kind of high information functionally specific, dynamically inert, logical switch-/ decision node- bearing aperiodicity that functional sequence complexity requires.

    Maybe, my notes here will be helpful (from Appendix 3, my always linked).

    GEM of TKI

  305. 306

    Seversky,

    —-”The accusation that the biological establishment ruthlessly suppresses dissenting opinion is political complaint not a scientific criticism. It is belied by the example of how the theory of punctuated equilibria won acceptance and the continuing vigorous debates between the various contending factions within evolution.”

    No it isn’t belied by factions “within” evolution. If it were to be belied, it would be belied by folks “without” evolution.

    —-”As for an rational and ordered Universe, it is not an assumption, it is an observation. We do not assume things fall to the ground unless something holds them up, we know it – as much as we know anything – because that is what we see all around us. It has happened all our lives and at least as far back as recorded history goes. If the Universe were not rational and ordered not only would science not be possible but neither would the Universe. That order calls for explanation. Methodological naturalism assumes there is an explanation but makes no assumption about it beyond that such an explanation exists.”

    “Here is the peculiar perfection of tone and truth in the nursery tales. The man of science says, “Cut the stalk, and the apple will fall”; but he says it calmly, as if the one idea really led up to the other…But the scientific men do muddle their heads, until they imagine a necessary mental connection between an apple leaving the tree and an apple reaching the ground. They do really talk as if they had found not only a set of marvellous facts, but a truth connecting those facts. They do talk as if the connection of two strange things physically connected them philosophically. They feel that because one incomprehensible thing constantly follows another incomprehensible thing the two together somehow make up a comprehensible thing. Two black riddles make a white answer.

    A law implies that we know the nature of the generalisation and enactment; not merely that we have noticed some of the effects. If there is a law that pick-pockets
    shall go to prison, it implies that there is an imaginable mental connection between the idea of prison and the idea of picking pockets. And we know what the idea is. We can say why we take liberty from a man who takes liberties. But we cannot say why an egg can turn into a chicken any more than we can say why a bear could turn into a fairy prince. As IDEAS, the egg and the chicken are further off from each other than the bear and the prince; for no egg in itself suggests a chicken,
    whereas some princes do suggest bears. Granted, then, that certain transformations do happen, it is essential that we should regard them in the philosophic manner of fairy tales, not in the unphilosophic manner of science and the “Laws of Nature.” When we are asked why eggs turn to birds or fruits fall in autumn, we must answer exactly as the fairy godmother would answer if Cinderella asked her why mice turned to horses or her clothes fell from her at twelve o’clock. We must answer that it is MAGIC. It is not a “law,” for we do not understand its general formula. It is not a necessity, for though we can count on it happening practically,
    we have no right to say that it must always happen. It is no argument for unalterable law (as Huxley fancied) that we count on the ordinary course of things. We do not count on it; we bet on it. We risk the remote possibility of a miracle as we do that of a poisoned pancake or a world-destroying comet. We leave it out of account, not because it is a miracle, and therefore an impossibility, but because it is a miracle, and therefore an exception. All the terms used in the science books,
    “law,” “necessity,” “order,” “tendency,” and so on, are really unintellectual, because they assume an inner synthesis, which we do not possess. The only words that ever satisfied me as describing Nature are the terms used in the fairy books, “charm,” “spell,” “enchantment.” They express the arbitrariness of the fact and its mystery.

    I deny altogether that this is fantastic or even mystical. We may have some mysticism later on; but this fairy-tale language about things is simply rational and agnostic. It is the only way I can express in words my clear and definite perception that one thing is quite distinct from another; that there is no logical connection between flying and laying eggs. It is the man who talks about “a law” that he has never seen who is the mystic. Nay, the ordinary scientific man is strictly a sentimentalist. He is a sentimentalist in this essential sense, that he is soaked and swept away by mere associations. He has so often seen birds fly and lay eggs that he feels as if there must be some dreamy, tender connection between the two ideas, whereas there is none. A forlorn lover might be unable to dissociate the moon from lost love; so the materialist is unable to dissociate the moon from the tide. In both cases there is no connection, except that one has seen them together.”
    ~G. K. Chesterton, Orthodoxy.

    It doesn’t matter one whit that these weird repetitions continue to occur. We do not know that they exist in any way as a necessity. It is an assumption that the universe is rational, for if it were anything less than an assumption, it would be a proper knowledge of these weird repetitions. But we don’t have proper knowledge. We should be able to demonstrate proper knowledge of it in the way we can with laws of reason and logic. But we cannot. We assume it. I’m going to continue quoting Chesterton until this fact sinks-in.

  306. Hmmm. What if we don’t agree with Chesterton, and don’t think that his point of view is a “fact.” Just repeating the quote won’t help.

    We come upon the key issue again: many people don’t believe that what you call “proper knowledge” of the nature of the universe is attainable, nor that some outside source and cause of the universe is what justifies and upholds it. In this case, the inductive evidence that things happen with regularity is sufficient – the question of whether there is some metaphysical necessity for that is not particularly important.

  307. 308

    Mr Hayden,

    I delight in Mr Chesterton’s prose even as he flies to cloud cuckoo land.

    So ‘law’ should be reserved for situations where we understand the relation, as well as we understand pickpockets and prisons? What about pickpockets and being whipped? Standing in the stocks and having garbage, rocks and sewer waste thrown at you? Having you hands cut off? Being sold into slavery?
    GKC hasn’t looked at the tax code recently has he? Having warmed on those, I’m sure he’ll be ready to explain the Law of the Red Heifer. Chesterton seems to think the universe is run by the Mikado, and that the “punishment fits the crime”. I suppose he never saw the guilty go free on a technicality, or the innocent wrongly imprisoned. If he doesn’t like the term, ‘law of nature’, he would do better than to point at the uniformity, regularity, justice, and purpose of human laws.

    But all that aside, I see that you and Seversky agree that science works by assumption of regularity. So we don’t need GKC to be wheeled out any more, thank you.

    Actually, I’ve said before that science works by finding the lack of regularity. Engineering might be happy with the line fit between dependent and independent variables, but science never is.

  308. Mr. Nakashima, let me explain why the problem of definitions is important. This blog is primarily about drawing inferences to design based on observation. By way of the “anthropic principle,” we infer a designed universe, and by way of FSCI [and other patterns] we infer the design of life. Now according to the arbitrary and intrusive principle of “methodological naturalism,” we may not draw these inferences because, according to this principle, science must study the universe “as if nature is all there is.” Well, obviously that rules out drawing inferences about a designer who may transcend the natural universe, so that would mean that ID is not science.

    This is very bad reasoning because science has never limited itself in this way. Obviously, all the great scientists of the past assumed the very opposite, that is, they insisted that since a rational and comprehending God created the universe, the universe must also be rational, and comprehensible. Indeed, that assumption not only undergirds science reasoning, it undergirds all reasoning period. If we don’t believe that our rational minds correspond to a rational universe, we can’t reason in the abstract. So, it should be clear that Newton, Faraday, Boyle, and all the other greats did not proceed on the assumption that nature is all there is. It was, in fact, the opposite point of view that informed them and gave these men the courage to persist in the face of many frustrations, failures, and disappointments.

    Now, when I explained this point to the Darwinists on this blog, they began by denying these facts, telling me that these men really practiced “methodological naturalism,” which of course they did not. When I began to provide example after example of scientists who held the opposite view, my adversaries realized that they had no argument. Rather than concede the point, however, they began to soften their definition of methodological naturalism in order to make it seem more historical. Indeed, their revised definition was so radical from the one that they attempt to enforce in the academy, [and the one they use to declare intelligent design invalid] that Intelligent Design would actually fit into it. Then, with this new softened definition, [MN as a “preference for natural causes,”] they wanted to go back in time as say that it has always been so.

    So, here is the way the game is played. If Darwinists want to persecute ID, they define methodological naturalism as meaning that “nature is all there is.” But, if they want to argue irrationally that this new outrageous doctrine is not new, they simply change the definition to something else and then say the new definition has always be so. This is the kind of irrational nonsense I have to deal with regularly on this blog.

  309. I don’t believe you have accurately portrayed the position of many of us in this discussion, and certainly not me. In particular, I can find no place on this thread where the phrase “preference for natural causes” appears.

    Also, you have persistently ignored the point I have made that one can be a theist and still practice MN, which is what the scientists mention did: the fact that their motivation and their belief in an ordered universe was religiously based does not change the fact that when they actually did the science, they practiced MN.

    In fact, when I wrote that “One can be, and millions are, a theist and still practice methodological naturalism,” your response was,

    Totally irrelavent.

    That’s not a very strong argument. Perhaps you should address the issue rather than just repeating yourself and declaring us irrational for not agreeing with you.

  310. Mr StephenB,

    Yes, I can feel that this is a very wearisome discussion. I am not a big fan of this kind of stuffs – ‘what was in the mind of the Founding Fathers’.

    If there is a witch hunt in the academy today, that can be addressed without the side issue of whether definitions have been read back into the historical record. My father was an academic, and I grew up with a ringside seat on academic backbiting and politics. As with letting a guilty man go free to avoid imprisoning the innocent, my personal preference is to allow “the feeling of being stared at” to be studied.
    The biggest lesson to be drawn from Newton is that he feared his private religious opinion would cost him his job. How sad if we have not progressed since then.

  311. Mr StephenB,

    I disagree, of course, that “sucess of anthropic principle = design” but I did not want to distract from the thoughts of my previous post! ;)

  312. —-Hazel: “Perhaps you should address the issue rather than just repeating yourself and declaring us irrational for not agreeing with you.”

    Here is the way it works. “Metaphysical” naturalism is the dogmatic assumption that nature is all there is. “Methodological naturalism” is the academic rule of doing science “as if nature is all there is,” while withholding comment about ultimate reality. That is why the word “naturalism” follows the word “methodological.” It means, do science as if metaphysical naturalism was true without asserting that metaphysical naturalism is true.

    [Wikipedia] Methodological naturalism means studying nature “as if nature is all there is.” [Lewontin] It means science cannot “allow a Divine foot in the door.” I can provide a dozen more examples if you need them from Eugenie Scott to Ken Miller. Now, it is this definition that disqualifies ID is science, which is, of course, is the reason that it was formulated that way. Please try to learn this and you will not fall into some of the more unfortunate lapses in logic that I will now illustrate:

    —Hazel: “But MN (short cut for a much bigger idea) doesn’t say that nature (that which science can study) is all there is. What it says is that the techniques of science are limited to studying certain kinds of things in a certain way.”

    The first sentence is demonstrably false as I have just indicated. With regard to the second sentence, what does “certain things in a certain way” mean? Excuse me, but it means nothing.

    —-Allen MacNeill: “This is all that “methodological naturalism” is prescribing: that the most fruitful way to study nature is to observe it, and to ground one’s conclusions in one’s observations and solely in one’s observations.”

    That statement is calculated to soften the idea that we should “study nature as if nature is all there is.” By MacNeill’s new definition, the one that attempts to evade the real definition which disqualifies ID as science, ID would, in fact, qualify as science. ID’s conclusions are, after all, grounded solely in observation. And, for that matter, so were most of the earlier scientists. [Of course, here you must also understand that, even at that, they are not, strictly speaking, grounded “solely” in observation because an assumption of a rational universe must precede even the observation. (But you are not ready for that subtler point yet, because you are still lagging too far behind even on the surface issue)]

    —-Hazel: “Boyle practiced methodological naturalism (irrespective of the actual term used).”

    Excuse me again, but that statement really is, [here it comes] “irrational.” The definition or the term used is only everything as I have just indicated. Further, it is clear that Boyle did not practice methodological naturalism. He and his collegues of that era believed that they were “thinking God’s thoughts after him,” an idea that is totally unacceptable from the standpoint of methodological naturalism.

    Now please take this information and reread my comments @309 with what I trust will be improved comprehension.

  313. to Stephen at 313: I’m sure my comprehension is just fine. I understand your point, and I understand mine, but I don’t think the reverse is true. Therefore I am not hopeful that trying to explain again will help. I also think that if you would stop initiating these judgments about our rationality, reading comprehension, etc, and just make your points, we might all be happier.

    Science studies nature “as if nature is all there is” means that science limits itself to a certain kind of investigation (details can be found in many places – try googling “scientific method.”)

    Science doesn’t say that nature is all there is – such a determination is outside the scope of science: science says that what science does is study nature in terms of itself. Science is a limited way of knowing the world – it does not encompass nor address all knowledge.

    I haven’t addressed your point about ID because that is a topic that I haven’t been very interested in discussing, but I will now because you continue to repeat it.

    You write that MN would disqualifies ID as science. If ID posits a non-natural cause that cannot be tested by reference to empirical observations, then ID isn’t science, not because of the first issue (non-natural) but because of the second issue (cannot be tested by reference to empirical observations.) However, as far as I can tell there is no statement of what ID is that is specific enough to apply this criteria: ID appears to be way too broad of an idea.

    For instance, theistic evolutionists believe that God guides every moment of the world, and that all is because of his will. This may be true, but it is not a statement that science can even begin to address. On the other hand, the belief that little green space people dropped life on earth many billions of years ago and then periodically returned to make new additions is a testable hypothesis, although no evidence for it has been found.

    So for ID to even begin to be considered science it needs to provide some empirically testable hypotheses. If those hypotheses were to posit non-natural causes but were yet testable by the methods of science, then they could be studied – although I think if the hypotheses were confirmed we would probably reclassify the causes as natural.

    (And, as an aside, I prefer the word material to natural, because I think there are some natural things, such as each person’s private internal experiences, that are not accessible to communal science.)

    ==========

  314. It’s possible, of course, to define “methodological naturalism” as simple observation of nature. Tons of basic research papers are published every year that do just that.

    But Allen and band of merry mates have something else in mind. They make the metaphysical assumption that evolution occurred by purely natural means and use “methodological naturalism” as a club to suppress all other viewpoints.

    We’ll go with Kant. The question of origins lies outside of pure science because origins cannot be seen. Darwinism is based on a metaphysical assumption.

  315. Hazel, I don’t have any more time to wade through your nonsense and correct your multi-dimensional errors. Anyone who reads our recent exchanges thoughtfully will soon discover that you are impervious to reason and ever so prone to change the subject. I merely ask onlookers to go back and read posts 301 forward to get my point.

  316. —-allanius: “It’s possible, of course, to define “methodological naturalism” as simple observation of nature.

    What matters is how the academy defines it and what they do with that definition. Consult the Kansas City standards for education in the sciences.

  317. Stephen, I am willing to leave judgments up to the onlookers. I always write with the general audience in mind. I am not trying to convince you of anything, but rather to use discussion (if you can call it that) as a springboard to clarifying the extent of the issues and to expressing myself on those issues.

  318. 320

    StephenB,

    Forgive me if this seems a basic and/or naive question, but…

    I get that you see methodological naturalism as flawed, and I get why.

    If you were to “re-write” or revise the definition of methodological naturalism – including its name – how would you do it? That is, what is the better formulation of the methodological approach scientists should follow?

    Thanks.

  319. 321

    Stephen, methinks you’ll just have to give up on Hazel.

    It would be hard to imagine anyone with their head shoved more deeply into the sand. There is seemingly no end to the length she will go to ignore what is in directly in front of her.

    As I stated earlier upthread, mataphysical materialism cannot attack itself to improve its position, thereofere, zero tolerance is the only refuge left to it.

    While Hazel’s comments are sometimes interesting, she is a poster child for a defense lead by obfuscation (masquerading as a search for clarity).

  320. —Larry Tanner: “If you were to “re-write” or revise the definition of methodological naturalism – including its name – how would you do it? That is, what is the better formulation of the methodological approach scientists should follow?”

    [A] Science: a branch of knowledge conducted on objective principles involving the systematized observation of and experiment with phenomena, esp. concerned with the material and functions of the physical universe.

    [B] Scientific method: principles and procedures for the systematic pursuit of knowledge [”the body of truth, information and principles acquired by mankind”] involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses.

    Beyond that, the scientist must devise his own methods because only the scientist knows which problem he is trying to solve. Hence, Einstein could not have arrived at his theory of relativity if he had been told that he must use exactly the same methods employed by Charles Darwin. Similarly, ID cannot employ information theory to argue on behalf of intelligent design if some bureaucratic interest goup declares that ID’s methods, however rigorous and appropriate, do not conform to some petty rule that was calculated to rule out ID in the first place.

    If a scientist does not know enough about his discipine to choose the right methods, then he is not worthy of his profession. One thing sure, no institutional rule can help him since no institutional rule can anticipate the problem in advance and cannot therefore say anything meaningful about which method should be used. The explanatory filter, for example, is appropriate for one thing and one thing only, detecting complex specified information. How could an institutional rule provide that system.

    On the other hand, if the ID scientists are so stupid and so methodologically sloppy as to bootleg their religious faith into their methodology, which is what they are often accused of doing, how could the “rule” of methodological naturalism make them any less stupid? We don’t need an administratively enforced rule to tell us that smuggling a religious presupposition into a scientific conclusion constitues bad scientific practice. We already know that. What we need is for ID critics to learn the difference between a religious presupposition and a design inference. If those who presume to make the rules are too naive to distinguish one from the other, then it is they that need watching and monitoring.

  321. 323

    hazel,

    —-”You write that MN would disqualifies ID as science. If ID posits a non-natural cause that cannot be tested by reference to empirical observations, then ID isn’t science, not because of the first issue (non-natural) but because of the second issue (cannot be tested by reference to empirical observations.) However, as far as I can tell there is no statement of what ID is that is specific enough to apply this criteria: ID appears to be way too broad of an idea.”

    The designer doesn’t have to be non-natural. But even if it were, radio waves were once considered non-natural. I reckon it just depends on your lines of what constitutes nature, and on this question, which is really the central question, methodological naturalism presupposes an answer, but that presupposition is itself not a conclusion of MN, but rather a philosophical one. If MN were all that one started with as a basis for methodology, you could never come to the conclusion using MN that you should use MN, for it doesn’t justify itself as a philosophical stance.

  322. Upright biped writes,

    While Hazel’s comments are sometimes interesting, she is a poster child for a defense lead by obfuscation (masquerading as a search for clarity).

    Thank you – I hope to be at least sometimes interesting.

    I have a philosophical position quite different than that held by the ID supporters on this thread – one which many of you consider irrational, blind to the facts, etc., so it is no wonder that you and others feel the way you do.

    This doesn’t bother me. I’m trying to learn, and perhaps in some cases to teach. I feel it is valuable to hear the arguments of people with whom I disagree, and to explore those so as to better understand what I myself think. Perhaps for some of you the same is true – perhaps not.

    But everyone needs to just put their best case forward, and if you, or I, are successful in influencing others, then good for us; and if we come across as sticking our head in the sand, obfuscating, being irrational or dogmatic, attacking the person instead of the idea, etc., then not so good for us.

    So if Stephen is trying to “win” arguments with me, then I think he should take your advice and give up on me. However, if he is trying to be a convincing representative for his point of view to the world at large, then he ought to continue doing the best he can and hope he is effective and influential.

  323. 325

    Hazel,

    Your position is well understood.

    It is exactly why I added “masquerading as a search for clarity” to the end of my comment.

  324. Hazel, @324, you are right of course. In the end, it is our beloved audience of onlookers that we hope to reach.

  325. Hazel, why don’t you think ID is meth-nat?

  326. The debate is quite simple. It is over the conclusions one can/is allowed to make from the practice of science. Practicing methodological naturalism means examining the natural world. It does not imply what conclusions one makes based on that examination. Now some have made a coercive attempt to limit these conclusions.

    The assertion that it works is a fatuous argument because there are some obvious places where it hasn’t. So the search goes on but that search should not limit the possible conclusions.

  327. Clive writes,

    The designer doesn’t have to be non-natural. But even if it were, radio waves were once considered non-natural. I reckon it just depends on your lines of what constitutes nature, …

    I have agreed with both these things. In particular my point has been that focussing on some supposed dividing line between natural and non-natural obfuscates the more important point: that scientific explanations have to be testable in terms of further empirical observations. If there is nothing we, humankind at large, could observe to help us know whether a particular explanation is true or not, or to help us know what further refinements we might make in our explanation, then the explanation is not scientific.

    I think this distinction is more useful than saying science can only study nature in terms of its constituent parts, so I think the MN argument is perhaps a distraction unless one just takes it as shorthand for the scientific method as a whole (observations, testing hypotheses, etc.).

    Clive also writes,

    methodological naturalism presupposes an answer, but that presupposition is itself not a conclusion of MN, but rather a philosophical one. If MN were all that one started with as a basis for methodology, you could never come to the conclusion using MN that you should use MN, for it doesn’t justify itself as a philosophical stance.

    MN is a practical conclusion based on many hundreds of years of science. The fact that science can’t itself prove that science is the way to go about things is not relevant: that is a conclusion that human beings have reached using more than just scientific reasoning.

    So I don’t think that your argument that MN can’t justify itself is important. Science is a tool devised by human beings for purposes that are themselves broadly based – purposes that go beyond science itself. This is an interesting issue, but not one that fundamentally calls into question the nature of science.

    Hope that was somewhat interesting. :)

  328. Jerry, what appears to be going on is an attempt to exclude ID from the debate via arbitrary definitions.

    ID involves solely the natural world, does not attempt to invoke causes and in no way addresses the supernatural.

  329. —-Jerry: “Practicing methodological naturalism means examining the natural world. It does not imply what conclusions one makes based on that examination.”

    Actually, it means a great deal more than that. I means disallowing any evidence from the natural world that might hint of supernatural or divine activity, insisting that any such information violates the standards of science. It means doing science “as if nature is all there is.”

    Here is the way Alvin Plantinga puts it:

    —–”The philosophical doctrine of methodological naturalism holds that, for any study of the world to qualify as “scientific,” it cannot refer to God’s creative activity (or any sort of divine activity). The methods of science, it is claimed, “give us no purchase” on theological propositions–even if the latter are true–and theology therefore cannot influence scientific explanation or theory justification. Thus, science is said to be religiously neutral, if only because science and religion are, by their very natures, epistemically distinct. However, the actual practice and content of science challenge this claim. In many areas, science is anything but religiously neutral; moreover, the standard arguments for methodological naturalism suffer from various grave shortcomings.”

  330. @331 should be, “[It] means disallowing….”

  331. Here is Paul Kurtz definition of methodological naturalism: (Plantinga is ID; Kurtz is anti-ID

    “Naturalism is committed to a methodological principle within the context of scientific inquiry; i.e., all hypotheses and events are to be explained and tested by reference to natural causes and events. To introduce a supernatural or transcendental cause within science is to depart from naturalistic explanations. On this ground, to invoke an intelligent designer or creator is inadmissible….

    Both sides understand the meaning.

  332. StephenB,

    “Both sides understand the meaning.”

    Our know nothings here seem to claim other wise. You have show that some people are explicit in the limitations on conclusions from a study. No one is obliged to follow these dictums and we have a host of people here including hazel, Allen MacNeill, Nakashima, Alan Fox and Seversky who will join us in fighting this edict.

    I assume they will fight with us to oppose it. Otherwise we should ask them why and see how they wiggle out of support.

  333. Here is a question for both pro ID and anti ID alike. Name one study that an anti ID person would do that a pro ID wouldn’t? If you cannot name any, then why should there be any prohibition of pro ID people in science?

  334. Everyone,

    StephenB said the following about Paul Kurtz

    ““Naturalism is committed to a methodological principle within the context of scientific inquiry; i.e., all hypotheses and events are to be explained and tested by reference to natural causes and events. To introduce a supernatural or transcendental cause within science is to depart from naturalistic explanations. On this ground, to invoke an intelligent designer or creator is inadmissible”

    Who here supports this dictum about science; rejects it? Speak or forever hold your peace.

  335. I have expressed some reservations, or at least qualifications, about MN at 266, 314, and 329.

  336. —-Jerry: “Our know nothings here seem to claim other wise. You have show that some people are explicit in the limitations on conclusions from a study. No one is obliged to follow these dictums and we have a host of people here including hazel, Allen MacNeill, Nakashima, Alan Fox and Seversky who will join us in fighting this edict.”

    Jerry, I wish you had read my earlier posts, because when folks come in late, I have to repeat points that I have perhaps overemphasized to the point of excess.

    First, methodological naturalism has an official definition and it is the one that I have explained several times. That definition rules out ID in principle. So, there isn’t really anything complicated about how ID should respond to it.

    Now it does get complicated when some folks try to justify methodological naturalism by saying that it has always been the scientific method and even go to the extreme of saying that earlier scientists, like Newton etc, practiced it, when they obviously did not.

    In order to pull that off, they change the definition from the stringent anti-ID formula to one like the one you presented earlier to make it seem benign so that they can use that new definition to claim that MN has always been the default scientific position. I have been laboring to explain this for a long time on this thread and it is very difficult to sum up at the last minute. I have just had a long battle with Allen and an extended discussion with Hazel on this matter, so there is a great deal that has gone on that you don’t know about. I would ask you to at least read my summary post at 309 to get caught up.

  337. Jerry, when I say “Both sides” understand the meaning of methdological naturalism, I don’t mean both sides on this site. I mean both sides among those who are acquainted with the matter. In other words all the heavy hitters on both the ID side and Darwinist side understand the point. You will recall the context that I made that statement was in my references to Plantiga and Kurtz. I assume that Allen MacNeill was also aware of it.

  338. —-Hazel” I have expressed some reservations, or at least qualifications, about MN at 266, 314, and 329.”

    No you have not. You stated several times the MN is the only thing that works and has ever worked. Of course, you didn’t know what it was when you were saying that, which is why you are not retreating from that position.

  339. that should read, “why you are [now] retreating from that position.”

  340. Stephen says that I have not expressed any reservations, or qualifications, about MN.

    I have. Here are parts of posts I made at 266 and 329.

    I don’t expect Stephen to agree with them. I’m just pointing out factual evidence that I have expressed some reservations.

    266

    However, there is a sense in which the whole discussion of methodological naturalism is misleading, or at least hides some of the real issues. Science starts with some fundamental concepts. The first is that it is based on observable (and in many cases measurable) sensory phenomena that are common to all human beings. Second, scientific explanations have to be testable in the sense that there are further observations that are capable of aiding in the confirmation or disconfirmation of the explanation.

    In a sense we define natural (or at least material) in reference to whether something can fall under the two criteria listed above: it is these component parts of science that are truly what distinguish it. Methodological naturalism is an umbrella term for the whole set of things which make up the scientific method, but it is a somewhat misleading term because it implies that what is natural can be defined separate from, or prior to, the process of scientific investigation.

    That is, one can propose what at first glance might be a non-natural explanation or a non-natural phenomena, but if in fact we could test that hypothesis using empirical evidence, then the phenomena would be better considered “natural.”

    So the big question is not whether proposal X is natural or not, but whether it is testable or not. Focussing first on “natural” is somewhat misleading, and perhaps has the cart before the horse.

    329

    In particular my point has been that focussing on some supposed dividing line between natural and non-natural obfuscates the more important point: that scientific explanations have to be testable in terms of further empirical observations. If there is nothing we, humankind at large, could observe to help us know whether a particular explanation is true or not, or to help us know what further refinements we might make in our explanation, then the explanation is not scientific.

    I think this distinction is more useful than saying science can only study nature in terms of its constituent parts, so I think the MN argument is perhaps a distraction unless one just takes it as shorthand for the scientific method as a whole (observations, testing hypotheses, etc.).

  341. Hazel, there is not one word in those lengthy passages critical of MN. The only thing you have done there is provide an extended discussion about your perception of what science is. Why will you simply not acknowledge the fact that you didn’t know what methodological naturalism was until I explained it. Indeed, I am not at all sure that you even know what it is now.

  342. 344

    Hazel at 342 has done a superb job of making my point at 321/325.

  343. re 343: I didn’t say “critical” of MN – I said I’d expressed reservations or qualifications.

    My point is, and here I am somewhat in agreement with Jerry, that someone might offer a hypothesis that posited what appeared to be a “supernatural” phenomena (say, radio waves when they were first being proposed), but we might later discover that they can be investigated with the tools of science. Have we now admitted the supernatural into science, or have we incorporated what we thought was supernatural into the natural world?

    To some extent the supernatural/natural distinction causes some semantic confusion, and therefore the statement from Kurtz – “all hypotheses and events are to be explained and tested by reference to natural causes and events” – does not as clearly demark science from non-science as Kurtz may want to claim.

    The distinction I am making is not just my own – I know of others who make the same argument that I am making. That is why I stress a more complete look at the scientific method rather than a short encapsulation such as MN.

  344. For what it’s worth, I see over on the FAQ thread here Diffaxial is making specific points that support what I am saying: that the natural/supernatural distinction is not what is important, but rather whether the hypothesis in question has any specific empirically testable entailments by which the hypothesis can be confirmed or disconfirmed. That is what demarks something as amenable to scientific investigation or not, not whether it falls on one side or another of some natural/supernatural definitional line.

  345. @345: I am afraid that if I enter that fog I will never get back out. So, you get the last word.

  346. @346: If you ever do find your way to a reasoned argument, or if you somehow experience a moment of clarity, cling to the one and hope that the other follows.

  347. Thanks for the encouraging words, Stephen, and so long for now.

  348. Hazel: I know that you don’t want any advice from me, but here is a tip. You have the ability to put words together in a credible way, a gift that not everyone has. You also have the capacity to probe beyond that which is obvious. That too, is good. Here is the thing: Build your sophistication around the argument; don’t try to build an argument around your sophistication.

  349. Well, thanks Stephen, and this time my thanks are more genuine.

    I don’t, however, agree with the distinction you are making about me. My main goal is to refine my understanding of what I believe through dialog with others. Since you don’t agree with me on some very fundamental things you see my arguments as faulty, and thus see my skills as poorly serving my understanding, but, as I have stated a number of times before, I see my position as solid (although growing as I learn) and therefore I see my skills as enhancing my arguments. In general I hope to make sophisticated arguments, but I don’t think that I am sacrificing one quality at the expense of the other.

    But I understand and accept that you think otherwise about me, and I appreciate your efforts to try to make your assessment of me clear.

  350. OK, Hazel: Meanwhile, I will work at improving my tone and strive to exercise more self control.

  351. StephenB,

    I have read your post at #309 and you are probably right about the people here. My point is that science only investigates natural phenomena. The hypotheses have to be based on the observation of or manipulation of natural phenomena. We have no way to do anything else. But people are failing to distinguish between this and the explanations for the phenomena or the conclusions. There is no necessary logical reason to limit the explanations for these natural phenomena a priori so the scientist should not be compelled to use only natural explanations especially when these conclusions do not make sense. Now in reality, natural explanations will make sense nearly all of the time but in some cases they will not.

    So what do we call this more reasonable type of science. This is the science practiced by nearly everyone until recent times. I personally have no problem with the term “methodological naturalism” because all these words are referring to is the methods used and that they be natural. I understand the imposition of the constrained conclusions is now part of the use of this term. But when one forces a set of conclusions, one is admitting weakness because they do not think the conclusions will stand on their own but must load it in their favor. If a non natural explanation, Zeus throwing lightning bolts, is seen as absurd and weak it will disappear and be laughed away. So what are they afraid of? We know the answer.

    But what do we call this type of research?

    That was the point of my questions as to who supports the usual definition of methodological naturalism and who doesn’t. It all depends on what is allowed as a conclusion.

  352. Jerry wrote @ 336

    StephenB,

    “Both sides understand the meaning.”

    Our know nothings here seem to claim other wise. You have show that some people are explicit in the limitations on conclusions from a study. No one is obliged to follow these dictums and we have a host of people here including hazel, Allen MacNeill, Nakashima, Alan Fox and Seversky who will join us in fighting this edict.

    I assume they will fight with us to oppose it. Otherwise we should ask them why and see how they wiggle out of support.

    Neither Kurtz nor Plantinga are Ultimate Arbiters of what constitutes methodological naturalism (MN) although I believe Kurtz’s view is widely held.

    MN should not exclude any investigable explanation by fiat but, as a method of deciding between competing explanations, it can only work with those that offer at least the possibility of being tested.

    Proposing as an explanation a god or other supernatural being who exists in some domain entirely separate from our Universe such that we can know nothing about them, even in principle, is of no use because we have no way of testing the accuracy of any claims about them.

    If, on the other hand, some sort of god or Intelligent Designer is being proposed that is actively involved in the world then, to that extent at least, it is part of the natural order and is accessible to scientific investigation. It is also no longer supernatural by definition.

    In one sense, MN does no more than what many here have urged as the proper course which is to follow the evidence wherever it may lead. This, to me, raises an interesting question.

    Although this website is dedicated to Intelligent Design as a scientific theory, there are a number of regular commenters here who make no bones about their religious sympathies and affiliations and I suspect that there are more who are not so open. It is also fairly obvious that much of the animosity expressed here towards evolution and materialism stems from a perceived conflict with – and even threat to – those strongly-held beliefs.

    On The Panda’s Thumb website there is this quote from an essay by Richard Dawkins about creationist Kurt Wise:

    Kurt Wise doesn’t need the challenge; he volunteers that, even if all the evidence in the universe flatly contradicted Scripture, and even if he had reached the point of admitting this to himself, he would still take his stand on Scripture and deny the evidence. This leaves me, as a scientist, speechless. I cannot imagine what it must be like to have a mind capable of such doublethink.

    My question to the believers here is: do you agree with Wise? Do you stand foursquare on the overriding Truth of Scripture regardless of any and all contradictory evidence that might be discovered by science?

  353. An interesting discussion, and resolved in the way that most such discussions are resolved: with the participants agreeing to disagree.

    I apologize for having departed early, but it’s final exam time, two of my six children are home with the flu (not the porcine variety, thank goodness!) and there are other threads to which I wished to contribute.

    That said, I think it would be interesting for both sides in the debate around methodological naturalism (MN) to consider why this term has become so widely used in recent times. For the sake of argument, let us assume that, indeed, the entire concept of MN only became “solidified” following Paul de Vries’ coinage of the term in 1983. For the sake of argument, let us concede stephenB’s assertion that prior to that time the use of “non-natural” assumptions was indeed legitimate for at least inspiring scientific research (as, indeed, history shows us was clearly the case). Let us then further assume that the current application of MN does indeed exclude any reference to “non-natural causes”, either in the design of experimental tests of hypotheses or in their interpretation.

    One might then reasonably ask, “What happened in the early 1980s that prompted such a dramatic shift in the perception of scientists, so dramatic that it led most scientists to reject what had previously been allowable: that is, the use of “non-natural” hypotheses as an inspiration for scientific research (if not necessarily also in the interpretation of the results of such research)?

    I believe that if one examines what was happening the early 1980s vis-a-vis evolutionary biology, the answer to this question is obvious: the rise of “scientific creationism” (especially of the “young Earth” variety) as a political force in the U.S., culminating in the SCOTUS’ decision in Edwards v. Aguillard (482 U.S. 578) in 1987. During the 1960s, American science was promoted very hard, both by government and by scientists themselves, as a reaction to scientific advances by the Soviet Union. Part of this promotion involved the formulation of the Biological Sciences Curriculum Study (BSCS) protocol and its associated textbooks (the “blue”, “green”, and “yellow” versions). All three versions stressed evolutionary theory as providing a foundation for the biological sciences. This was virtually the first time since 1925 (and the conviction of John T. Scopes for having violated Tennessee’s Butler Act by teaching evolution in a public school classroom) that evolutionary theory had been so prominently featured in biology textbooks that were widely promoted in the American public school system.

    This caused an immediate negative reaction among American evangelical Christian groups. Legislative bans on the teaching of evolution similar to the Butler Act were either reinstated or promoted in several states. At the same time, Henry Morris and other “scientific creationists” founded and promoted the “scientific creationism” movement, which sought to provide scientific evidence for their version of “young Earth creationism” (YEC). Not much actual science was done by these self-described YECs, but strenuous political efforts were undertaken to have their YEC reinterpretations of existing scientific information incorporated into public school curricula in several states (most notably Arkansas and Louisiana).

    In reaction to these efforts by YECs, the scientific community partnered with the ACLU and allied organizations to bring such efforts to the attention of the SCOTUS, with the intention of having them outlawed as violating the first amendment to the US constitution. These efforts were ultimately successful, as both laws banning evolution from public school science classes and the attempts to insert YEC in public school science classes were struck down as unconstitutional by the SCOTUS. These events, and not the subsequent rise of ID, are the context within which the adoption of MN by the scientific community in the 1980s can most effectively be viewed.

    From my interactions with them, I have found that some ID supporters are very strongly in sympathy with the YECs, and view ID as a way of getting their version of YEC back in the public schools. This was clearly the case in the Dover Area school board’s 2005 attempt to provide students with alternative biology textbooks incorporating ID, as shown by the sworn testimony by several of the members of that school board and other members of the board who were present at meetings at which this plan was discussed and approved.

    However, in my interactions with other ID supporters (and especially the members of the Cornell IDEA Club and some commentators at this website), I have come to understand that a significant fraction of ID supporters do not accept that YEC is a legitimate empirical science, nor support it’s incorporation in public school science curricula.

    The dispute that has occurred in this thread (and similar recent disputes elsewhere) seem to me to be examples of people “fighting the last war” rather than dealing with the situation as it exists today. ID supporters who are not YECs need to understand that most evolutionary biologists lump the two together, partly because of the behavior of the Dover Area school board and similar, more local situations in which YECs have persisted in pushing their views into the public schools. At the same time, evolutionary biologists and their political supporters need to understand that there is no necessary connection between YEC and ID, nor are they united in their conviction that YEC and ID must be incorporated into the public school curriculum today.

    A recognition of the political contexts within which both EBers and IDers have come to their positions, and what these contexts imply about the value of possible further actions would be valuable for both sides in this debate. I have had many ID supporters say privately to me that Dover was a disaster for ID, and especially for its quest to be accepted as a legitimate empirical science. I have also had many evolutionary biologists express to me their opinion that there is essentially no difference between YEC and ID, a viewpoint that I have learned through experience is clearly in error.

    Ergo, I have concluded that the most effective way to move forward in this debate is the way I have been conducting it since the mid-1990s. That is, to invite supporters of both sides of the debate to make presentations in my evolution courses and seminars at Cornell and to conduct such debates in public forums such as this website. Ironically, I find this venue to be much more congenial to such debates than places like AtBC, in which character assassination is the order of the day, rather than the last resort of people who are either confused about their own position or uncertain about its logical force.

    And so, I recommend that all participants in this debate emulate hazel (bless her heart!) in the avoidance of name-calling and ad hominem arguments. As hazel has pointed out, for each committed commentator here there are many thousands of quiet observers who are trying to come to their own conclusions about the issues being debated here. While mud-slinging is fun, it’s fun in the same way that smoking or drinking heavily is fun; it provides short-term personal gratification, but in the long term it undermines everything one is trying to accomplish.

    I believe that clarity should be our goal, not necessarily agreement. If we come to clarity about our positions and agree to disagree, then we have accomplished a great deal more than we would have accomplished if our goal was simply to attack our opponents’ characters or to question their personal motives. Going forward I will do my best to pursue this course of action, and recommend that all who genuinely wish to come to clarity on these issues and, by doing so, help the “silent watchers” of this forum to do so as well, treat each other as colleagues (in the “collegiate” sense of that word) in their pursuit of what they perceive to be the truth, rather than as enemies in a culture war.

  354. Thanks, Allen – many interesting comments – and thanks for the support for my thoughts about the value and purpose of such discussions. I know that the important lurkers – those that are really trying to sort out where they stand – are more likely to be influenced when comments are on-topic and not personal attacks. There may be those that silently cheer when someone is put down, but they are usually firmly in one camp anyway, and are here for entertainment, not growth.

  355. Allen,

    I have been one of the ID people here that has been very critical of YEC science. In fact I have said that YEC science is a millstone around the neck of ID because of the conflation of the two. I have nothing against YEC’s personally and in fact a few who comment here are very bright and insightful and nearly all are polite and respectful.

    About 8 months ago I wrote something about the confusion that people have with ID and asked a YEC person here to comment on it and since that time a couple anti ID people also have commented. None found anything wrong with it except for a small nit on terminology.

    it is here

    http://www.uncommondescent.com.....ent-296129

    If you have time, maybe you could read it and offer any comments on how to make it clearer or better or more consistent with your understanding. The purpose obviously is to present to anyone who tries to conflate the two positions so we do not waste time on useless debate.

  356. ID as a way of getting their version of YEC back in the public schools.

    Allen, you make some very good points. If you recall the movie “Inherit the Wind” you will remember Spencer Tracy packing the Bible with Darwin at the end. Of course, the movie was made pre-Engel v. Vitale, which is where I think the problem started.

    With regard to YEC, the solution is to teach the methodology rather than the conclusion.

    It is quite appropriate to require a young Evangelical to understand how radiometric dating works or how the inferences are arrived at from geological strata. OTOH, it is wrong to demand that he be required o accept the results as the final truth.

    Conversely, it is appropriate to require one raised as a non-Biblical literalist to read an OT genealogy — without sneering — and to understand how the YEC calculation is arrived at, and why it shouldn’t be mocked.

  357. I think it was Chesterton who once said, “Grant me this one assumption and all the rest will be easy.” Naturally, if I grant that the YEC fiasco was the impetus for establishing the “rule” of methodological naturalism, then sure, everything falls right into place for the Darwinists. [Define Darwinist as anyone who thinks that naturalistic forces can create new information]. What could be more rewarding for their side than to think that evolutionary biologists saved science from the anti-science YECs. However, there is one little problem with that thesis: YEC was never really a significant threat to their paradigm because they could always dismiss it as a faith based methodology. Indeed, the YECs served the Darwinist community very well, providing it with an easy target for ridicule.

    No, it wasn’t the YEC approach that motivated the academy to establish this arbitrary and intrusive rule of methodological naturalism. Religion masquerading as science can hardly compete with evolutionary biology, even if the latter model makes unwarranted scientific claims for itself. The real threat came from the ID paradigm and the introduction of information-oriented, empirically-based models. It was at this juncture that Darwinists lost their sense of humor. With the advent of intelligent design, there was a new game in town, or, more precisely, a reformulation of the old natural theology reworked as empirically based science. It had been easy enough in the past for Darwinists to militate against natural theology and its allusions to “final causes” by simply shrugging it off as non-science. But what were they to do with this new formulation that could actually detect design using scientific methodologies.

    The answer wasn’t long in coming. The good old boys got together in the smoke filled rooms of academia and established a new rule called methodological naturalism. According to this formulation, science must approach nature as if “nature is all there is.” Now this stretch was not hard to make. While science was never “exclusively” about natural causes, it had, indeed, always been “primarily” about natural causes. Christians in the middle ages understood that God was not capricious or prone to arbitrarily throw thunderbolts out of the sky. Quite the contrary, God was rational and comprehending and, proper to his character, had created a rational and comprehensible universe. That fact prompted the early scientists to look for and study rational elements in the universe, various manifestations of order expressed in terms of regularities and laws. So, to get at that one aspect of rationality and order, they searched “primarily” for natural causes. At the same time, they hardly assumed that naturalistic forces are the only manifestation of God’s order, meaning that science was not “exclusively” about natural causes.

    So, the strategy was easy enough. All the Darwinist community needed to do was claim that science was “exclusively” about natural causes. Suddenly, the pesky problem of a competing paradigm is solved, design inferences are reduced to non-scientific status, and ID is out of business. Never mind that natural laws were only a part of God’s rational order. What did reality have to do with anything when perception was the name of the game? The real issue was to disfranchise ID from the community of researches and scholars by making it appear as non-scientific and the only way to do that was to establish a new scientific standard that had never been heard of before, and they called it methodological naturalism.

    Of course, that wasn’t their only strategy for killing the ID movement. There was this other little thing called slander. Everyone knew that the ID community is populated with Christians, and everyone also knew that many Christians accept YEC. Why not, they reasoned, conflate the two and put the “creationist” brand on ID. In other words, tell everyone that ID is nothing more than “creation science” in a cheap tuxedo. Not only is that a very effective lie; its one hell of a metaphor. That’s important, because, as everyone knows, metaphors travel with the speed of light. Now did it matter to them that creationism is faith based and that intelligent design is empirically based? No. Why allow the truth to get in the way of a self-serving strategy? Did it matter that both creation science and intelligent design each had a pedigree that goes back two thousand years, and therefore could not possibly be the same thing. No. Why would that matter if it complicates their plan to destroy ID?

    Meanwhile, there was a problem on the methodology front. It appears that someone figured out that if Intelligent Design is not really science, then none of the earliest scientific geniuses could possibly be scientists either since they were all design thinkers. In other words, Richard Dawkins is a scientist, but Sir Isaac Newton was a fraud. That is a hard line to sell to anybody. So, a new strategy emerged, [Darwinists never design anything]. They said this: Newton and company grounded their methodology in nature, which distinguishes them from ID scientists. The strategy was conceived in the hope that everyone concerned would forget a small little fact: ID scientists ground their methodology in nature as well, so the point is irrelevant. But if one fantasy doesn’t work, try another. So, they presented the same mischievous argument in another form: Newton, Faraday, Boyle, and all the others, we are told, all “practiced” methodological naturalism. Of course, that is ridiculous on the face of it because you can’t practice methodological naturalism while you are “thinking God’s thoughts after him.”

    Ah, but they were just getting started, especially over at Panda’s Thumb. Evidently, someone must have come up with the idea of using two definitions for methodological naturalism so that it could be both new and old at the same time. On the one hand, they use the first definition, [studying nature as if nature is all there is] to discredit ID and label it as non-scientific; on the other hand, they use the second definition [studying natural causes] to associate methodological naturalism with the earlier scientists and give it a phony history and instant credibility. So, when someone points to their outrageous habit of persecuting ID researchers by appealing to their arbitrary, pseudo-scientific methodology, they can smugly retort, “Oh, I suppose Newton, Faraday, and Boyle were using pseudo-scientific methodologies as well.” So, for Darwinists a methodology can be old or new, true or false, existent or non-existent—whatever works. It is simply a case of using whatever definition is needed for the moment. How sweet it is.

  358. In #357 tribune7 wrote:

    “…it is wrong to demand that he be required o accept the results as the final truth.”

    Indeed, I would go further than this: it would be wrong to demand that anyone accept the results of any scientific analysis as “the final truth” about anything at all. As I have pointed out many, many times, science isn’t about “truth”, final or otherwise. It’s inherently provisional and always open to revision as the result of new empirical findings.

  359. Feel better now, stephen? I hope so. Perhaps now you might actually get on with the discussion at hand, now that you’ve finished venting your spleen against the “bad guys” in their “smoke-filled rooms”.

    However, you won’t be doing it with me. I didn’t put up with John A. Davison’s apparent compulsion to forgo reasoned argument for ad hominem arguments, character assassination, rampant speculation about motives, demonization of one’s opponents, and guilt by association, nor will I respond to yours. If you can someday bring yourself to make arguments based on evidence using a collegial tone, I will respond in kind. Until then, I will no longer respond to you at all.

  360. 362

    360 is a perfect response by Allen.

    Smug, minimalizing, absolutely perfect.

    Bravo

  361. I am particularly taken at the vast influence of the guys at the Panda’s Thumb, although they only inhabit a virtual smoke-filled room. :)

    On a more serious note, Stephen says,

    Of course, that is ridiculous on the face of it because you can’t practice methodological naturalism while you are “thinking God’s thoughts after him.”

    When I have pointed out that in fact thousands of Christian scientists who do believe in God and would assent to the idea that they are “thinking God’s thoughts after him” also would say that they practice methodological naturalism, Stephen responded,

    Totally irrelavent

    I presume then that Stephen dismisses these thousands of Christian scientists as “ridiculous” and “irrelevant”. Not only are atheists like me part of this conspiracy to outlaw ID, but so, it seems, are many of Stephen’s presumably fellow Christians.

  362. Thank you, UprightBiped. If your sentiments are genuine, indeed, my sincere thanks. If they are meant as sarcasm, then please read comment #354, especially the last paragraph.

  363. There’s more than one way to make an ad hominemargument, but all of them are both illegitimate and self-defeating…

  364. jerry in #356:

    I have read the link you posted, and this caught my eye:

    “…the evolutionary debate is mainly about the mechanism for the development of new complex functional capabilities and secondarily about how fast some of these complex functional capabilities can permeate a population once they arrive.”

    I completely and wholeheartedly agree, and would go on to point out that this means that the real focus of evolutionary studies in the future should be on the “engines of variation” about which I have written much lately. The answer to the question of “where do genuinely new biological forms (and the information that underlies them) come from” is to be found in the 50+ mechanisms of phenotypic variation that I have listed at my blog:

    http://evolutionlist.blogspot......awman.html

    If there is an answer to the core question that lies at the heart of both evolutionary biology and ID, I am confident that it will eventually be found there. Looking for the answer should keep several generations of scientists busy for at least the next century. I wish them luck!

    P.S. I hope by this answer to your question I have made it clear that I believe that the question posted above is still an open one.

  365. Indeed, I would go further than this: it would be wrong to demand that anyone accept the results of any scientific analysis as “the final truth” about anything at all.

    Very true!

  366. P.S. Has anyone else received a message that “comments are closed” on the thread discussing Dr. Dembski’s upcoming paper on “Life’s Conservation Law”:

    http://www.uncommondescent.com.....formation/

    or is it just me?

  367. Allen, I just posted on it.

  368. What a strange response @361. I explain that ID scientists have been persecuted through the arbitrary rule of methodological naturalism, in conjunction with the “creationism” slander, and Allen says that I, the bearer of that bad news, am the character assassin.

    For what it is worth, I believe that Allen has been quite tolerant in his own community in terms of allowing freedom of speech. So I happily qualify my statements with that nuance.

    On the other hand, the facts I report are true about the Darwinist academy in general, whether Allen has ever ratified that policy or not. The movie “Expelled” was not a lie and Ben Stein was not a character assassinator.

    At the same time, one can indirectly contribute to the problem by continuing to promote the big lie. Now, there is a way around this. Allen can simply say, I renounce that arbitrary rule of methodological naturalism, I promise never to attribute it to Sir Isaac Newton again, and, in the name of truth, I promise I will never conflate creationism and intelligent design on my website again.

    What is unreasonable about what I have just said? I attack the Darwinist community in general for real crimes against free speech and that makes me guilty of character assassination. But Allen calls me a character assassin and compares me to John Davison, but that is not character assassination. What kind of bizarre thinking is this?

  369. @370 Ben Stein is not a character [assassin.]

  370. —-Hazel: “When I have pointed out that in fact thousands of Christian scientists who do believe in God and would assent to the idea that they are “thinking God’s thoughts after him” also would say that they practice methodological naturalism.”

    OK, yes, I get the point. Yes, theistic evolutions are definitely part of the persection. Thanks for bringing that up again. Insofar as they refuse to allow the ID scientist to draw a design inference in the name of science they are far worse than the Darwinists, because they claim to believe in Christianity, which holds that design in nature is evident. So, yes they are even worse, far worse.

  371. Hazel, @363 Thanks again for raising that issue about my comment, “totally irrelevant.” I just glossed over it too quickly the first two times. It is totally relevant.

  372. Wow – I’m glad that’s cleared up.

    That’s a quote to remember:

    Thanks for bringing that up again. Insofar as they [theistic evolutionists] refuse to allow the ID scientist to draw a design inference in the name of science they are far worse than the Darwinists, because they claim to believe in Christianity, which holds that design in nature is evident. So, yes they are even worse, far worse.

  373. Yes, and here is a little something to chew on while Allen and hazel bristle at my relelations:

    Timothy White, president of Idaho University, established a speech code which banned any criticism of Darwinian evolution.

    Nancy Bryson, chemistry professor, was fired from a state university for giving a lecture on scientific criticism of Darwin’s theory.

    Bryan Leonard, graduate student at Ohio State, was accused of “unethical human subject experimentation” for criticizing Darwin’s theory.

    Robert Hart, high school teacher was fired from a public school teaching position for “wanting” to teach both sides of the issue.

    From PZ Myers, at the University of Minnesota, “Our only problem is that we aren’t martial enough or vigorous enough, or loud enough, or angry enough. The only appropriate responses should involve some form of righteous fury, much butt-kicking, and the public firing and humiliation of some teachers, many school board members, and vast numbers of sleazy far-right politicians.”

    So, according to Allen, I am a character assassin for pointing out these things. How exactly does that work? Can someone explain it to me?

  374. 375 [Revelations]

  375. In #370 stephenB wrote:

    “Allen can simply say, I renounce that arbitrary rule of methodological naturalism, I promise never to attribute it to Sir Isaac Newton again, and, in the name of truth, I promise I will never conflate creationism and intelligent design on my website again.”

    I will take stephenb’s three requests one at a time:

    1) “Methodological naturalism: I’m not certain I have ever claimed that I myself have ever adhered to the rule of “methodological naturalism” as stephenB defines it in doing my own research. Indeed, I don’t think I’ve even thought about it much at all until very recently. In this thread, I have asserted that, at least since the time of Francis Bacon, most scientists have based their conclusions on empirical evidence only, inferring such conclusions using inductive reasoning. So, if by “renouncing methodological naturalism” (MN) stephenB means his definition of MN (with which I clearly do not agree, as shown by our comments in this thread) – that is, a version of MN in which non-natural causes for empirically observable phenomena are ruled out a priori – then I will indeed cheerfully rule out applying his version of MN when doing my own science, and in describing it to others.

    2) Isaac Newton: I believe that this is the very first debate in which I have ever characterized Isaac Newton’s declaration of “hypotheses non fingo” from the General Scholium to his Principia Mathematica as adhering to the principle of MN. Having finally understood what stephenB means by his definition of MN, I can once again declare that, to the best of my knowledge, Newton indeed never applied stephenB’s definition of MN to his physics. Ergo, if the subject ever comes up again, I will henceforth simply quote in full Newton’s “hypothesis non fingo” declaration, as translated from the General Scholium (“I have not as yet been able to discover the reason for these properties of gravity from phenomena, and I do not feign hypotheses. For whatever is not deduced from the phenomena must be called a hypothesis; and hypotheses, whether metaphysical or physical, or based on occult qualities, or mechanical, have no place in experimental philosophy. In this philosophy particular propositions are inferred from the phenomena, and afterwards rendered general by induction”), and include a reference to the whole of the Principia and the General Scholium, and let readers willing to read both conclude from them what they may.

    3) Conflating creationism and intelligent design: This one is easy: I have already agreed with my good friend and colleague (and intellectual opponent), Hannah Maxson, that such a conflation is both inaccurate and inflammatory. Henceforth, I shall not conflate the two, neither in by blog or in my other writings. In return, I would hope that stephenB and the rest of the ID supporters here will refrain from asserting that “all evolutionary biologists are atheists who conceal their real beliefs” and “all evolutionary biologists have conspired to exclude ID theorists (such as Michael Behe, William Dembski, John Sanford, etc.) and ID supporters (such as Hannah Maxson, Rabia Malik, etc.)” from either publishing, speaking about, or pursuing their investigations into the possibility that teleology might, in fact, be part of the causal process in evolution. They now know my position on all three of these issues, and to continue to make assertions to the contrary would therefore be to perpetuate a lie, plain and simple. And please note that just leaving off the numerical qualifier “all” in the sentences above does not substantively change their meaning.

  376. And here’s something for stephenB to chew on while considering my response to his “demands”:

    I have been teaching introductory biology at Cornell for 32 years and evolution for 14 years. In every single one of those years, I and/or my colleague Will Provine have invited (and supported) the following individuals to come and make presentations in our evolution courses (without censorship, prohibitions, or pre-conditions):

    Michael Behe
    John Grehan
    Phillip Johnson
    Hannah Maxson
    John Sanford

    Indeed, in the case of Hannah Maxson, I invited her to be a co-presenter in my notorious “evolution and design” seminar at Cornell in the summer of 2006.
    You can read about it here:

    http://evolutionanddesign.blogsome.com/

    Furthermore, in every single case we have encouraged students to make up their own minds about which side of the debate they supported, and required them to defend those positions to the best of their abilities, in class discussions and on essays and research papers.

    So, while making blanket characterizations such as these:

    “The good old boys got together in the smoke filled rooms of academia and established a new rule called methodological naturalism.”

    “The real issue was to disfranchise ID from the community of researches and scholars by making it appear as non-scientific…”

    “So, for Darwinists a methodology can be old or new, true or false, existent or non-existent—whatever works.”

    isn’t exactly “character assassination”, it isn’t exactly the truth, either. In my opinion, making ad hominem arguments is never justified in scientific debates, and is also ultimately self-defeating.

    Personally, I disagree with the assertion that teachers of evolutionary biology (or science in general) should prohibit discussion of creationism or ID in their classrooms or lecture halls. On the contrary, I believe that when all sides of the debate are given a fair chance to make as complete a presentation of their views as possible so that students can make up their own minds where they stand on the issues, the most common outcome is that students tend to side with those who advocate evolutionary biology as the most convincing explanation for the underlying cause of biological diversity and functional adaptation.

  377. Hi Allen MacNeill,
    Can you refresh our memory on the actual breakdown of students’ beliefs, pre/post term, as per your questionnaire?
    I remember you saying that a significant number move toward creationism after your lectures.

  378. Every once in a while I read the ASA forum and in April there was a long discussion of methodological naturalism there. Many of the points brought up here were brought up there.

    There was one interesting comment about the supernatural and it was that it is frequently studied by science but only in the negative, that is to debunk it. So telepathy or the power of prayer etc are fair game in science as long as the objective is to disprove it. My guess a study showing that prayer is effective would be sent off to another non scientific journal or would start a mass spending for studies to disprove it.

    One telling comment was that methodological naturalism that defines it as only allowing natural causes is of itself not neutral on the separation of church and state issue. My guess is that the definition that allows non natural explanations is more of a neutral position.

  379. Re #379:

    “I remember you saying that a significant number move toward creationism after your lectures.”

    Nope; the only significant changes have been a move away from the “God-guided” and “ID-guided” statements toward evolutionary and YEC statements (in almost equal frequencies). Interestingly, over the years the proportion of the class that has chosen the “non-guided evolution” statement at the very beginning of the course has steadily grown, while the proportion choosing the “God-guided” and “ID-guided” statements have steadily declined. Also, the proportion that has chosen the YEC statement at the beginning of the course has remained almost constant at around 10%. I can provide the actual statistics to anyone who is interested; just drop a comment at my blog ( http://evolutionlist.blogspot.com ), along with contact information.

    This outcome squares with the recent observation that there has been a significant increase in atheism in the United States as a whole. However, I want to make it very clear that I do not cite this trend as “proof” that people who accept the non-guided evolutionary explanation are necessarily atheists, only that the two phenomena are correlated.

  380. Nope?
    Nope; the only significant changes have been a move away from the “God-guided” and “ID-guided” statements toward evolutionary and YEC statements (in almost equal frequencies).
    I thought that’s what I said.
    At any rate, thank you very much for responding and clarifying.

    Did you mention how many days Behe would lecture in your class on the ID side throughout the term, as opposed to how many days you lectured on the validity of the non-teleological explanation?

  381. Take Two:
    Nope?

    Nope; the only significant changes have been a move away from the “God-guided” and “ID-guided” statements toward evolutionary and YEC statements (in almost equal frequencies).

    I thought that’s what I said:

    I remember you saying that a significant number move toward creationism after your lectures.

    At any rate, thank you very much for responding and clarifying.

    Did you mention how many days Behe, for instance, would lecture in your class on the ID side throughout the term, as opposed to how many days you lectured on the validity of the non-teleological explanation?

  382. 384
    Barry Arrington

    Allan writes: “I believe that when all sides of the debate are given a fair chance to make as complete a presentation of their views as possible so that students can make up their own minds where they stand on the issues, the most common outcome is that students tend to side with those who advocate evolutionary biology as the most convincing explanation for the underlying cause of biological diversity and functional adaptation.”

    The best explanation for your data has nothing to do with the student’s actualy beliefs. It has everything to do with the fact that students tend to tell their professors (who hold their academic success in their hands after all) what they want to hear. You know that, and your pretense that you are “just reporting the facts” is risible.

  383. 385

    Allen’s quote seems to be pitting evolutionary biology against ID but ID can in fact go hand in hand with EB. Bottom line is that EB needs ID to make it reasonable- but ID does not necessarily need EB- though empirical evidence and good science can in fact shape the need for EB in life’s explanation.

  384. Allen MacNeill says:

    Personally, I disagree with the assertion that teachers of evolutionary biology (or science in general) should prohibit discussion of creationism or ID in their classrooms or lecture halls.

    MacNeill claims that because of his personal experience and feelings stephenB would not be justified in making statements such as this (by MacNeill):

    “all evolutionary biologists have conspired to exclude ID theorists … and ID supporters … from either publishing, speaking about, or pursuing their investigations into the possibility that teleology might, in fact, be part of the causal process in evolution.

    Even if someone like stephenB were not actually to say “all”. Because Allen MacNeill has made his personal feelings known one would be “lying” in making such statements that contradict MacNeill’s own position.

    As he further asserts:

    And please note that just leaving off the numerical qualifier “all” in the sentences above does not substantively change their meaning.

    as though his experience entails that the sentiments are lies (“plain and simple”) even if one is not saying all evolutionary biologists.

    Too bad Allen MacNeill doesn’t really seem to be representative of the all:
    http://toledoblade.com/apps/pb.....33/-1/NEWS

  385. 387

    Allen,

    —-“I believe that when all sides of the debate are given a fair chance to make as complete a presentation of their views as possible so that students can make up their own minds where they stand on the issues, the most common outcome is that students tend to side with those who advocate evolutionary biology as the most convincing explanation for the underlying cause of biological diversity and functional adaptation.”

    My experience is the complete opposite.

  386. Mr MacMeill:

    In citing the “I feign no hypotehses” excerpt from Newton’s General Scholium, you need to give the overall context, as I have excerprted at say 259 above.

    I think that gives a very different picture formteh one you are painting: for in that, Newton made his Hebraic-Christian framework very plain. [Yes, I know he was a "heretic" but he is OUR heretic.]

    In particular, he considered it entirely appropriate as an integral part of natural philosophy — which when it established findings produced “science” i.e knowledge — to infer from the lawful, unified order and observed frame of the cosmos to its Designer, Creator and PANTOKRATOR; as that necessary being who is intelligent and wise, also being in part knowable from his works that are studied by what we now call science.

    GEM of TKI

  387. —-AllenMacNeill:)

    “Methodological naturalism: I’m not certain I have ever claimed that I myself have ever adhered to the rule of “methodological naturalism” as stephenB defines it in doing my own research. Indeed, I don’t think I’ve even thought about it much at all until very recently. In this thread, I have asserted that, at least since the time of Francis Bacon, most scientists have based their conclusions on empirical evidence only, inferring such conclusions using inductive reasoning. So, if by “renouncing methodological naturalism” (MN) stephenB means his definition of MN (with which I clearly do not agree, as shown by our comments in this thread) – that is, a version of MN in which non-natural causes for empirically observable phenomena are ruled out a priori – then I will indeed cheerfully rule out applying his version of MN when doing my own science, and in describing it to others.”

    The definition that I put forth is not my definition and you know it. I provided several examples from other writers including ID advocate Plantinga and Darwinist advocate Paul Kurtz. Indeed, the definition that you offered originally on this thread was different from the real definition, and you tried to get some mileage out of it. The real definition, the one which you now put at the end of your paragraph, [non-natural causes ruled out apriori] is the one used to invalidate ID. I am not asking to refrain from using it yourself, which would be a meaningless gesture. I am asking you to renounce it as unfair as put forth by your colleagues. Please stop with the posturing.

    —-Isaac Newton: I believe that this is the very first debate in which I have ever characterized Isaac Newton’s declaration of “hypotheses non fingo” from the General Scholium to his Principia Mathematica as adhering to the principle of MN. Having finally understood what stephenB means by his definition of MN, I can once again declare that, to the best of my knowledge, Newton indeed never applied stephenB’s definition of MN to his physics.”

    How can you say that you finally understood what I meant by methodological naturalism? Are you telling me that this is the first time you have had it presented to you? There is only one definition of methodological naturalism and it is not MY definition. In any case, if you believe the first sentence, why would you bother to write the second sentence? Why do you continue to evade the subject by refusing to acknowledge the one and only definition of methodological naturalism? The word “naturalism” follows the word “methodological” for a reason. Either you are just now learning this [hard to believe] or you have been stonewalling. Have you so soon forgotten that you insisted that methodogical naturalism goes all the way back to ancient Greece and passed through the middle ages? Please!

    —“Conflating creationism and intelligent design: This one is easy: I have already agreed with my good friend and colleague (and intellectual opponent), Hannah Maxson, that such a conflation is both inaccurate and inflammatory. Henceforth, I shall not conflate the two, neither in by blog or in my other writings. In return, I would hope that stephenB and the rest of the ID supporters here will refrain from asserting that “all evolutionary biologists are atheists who conceal their real beliefs” and “all evolutionary biologists have conspired to exclude ID theorists (such as Michael Behe, William Dembski, John Sanford, etc.) and ID supporters (such as Hannah Maxson, Rabia Malik, etc.)” from either publishing, speaking about, or pursuing their investigations into the possibility that teleology might, in fact, be part of the causal process in evolution. They now know my position on all three of these issues, and to continue to make assertions to the contrary would therefore be to perpetuate a lie, plain and simple. And please note that just leaving off the numerical qualifier “all” in the sentences above does not substantively change their meaning.”

    So, now you are resorting to strawmen? When did I ever say that ALL evolutionary biologists are atheists who conceal their beliefs? In fact, 95.8% of evolutionary biologists are either atheist or agnostic. For your informatin, Eugenie Scott has gone on record of asking them to conceal their beliefs, but I have no way of knowing whether they comply or not. I have pointed that out in the past and I will continue to point it out. Also, I wish that you would read more carefully. In a previous post, I went out of my way to point out that I don’t believe that your personally suppress freedom of speech. I did, however, point out that you add to the circle of confusion by refusing to acknowledge the true definition of methodological naturalism. Please observe the relevant nuances. The world of evolutionary biologists is bigger than your classroom, so to say that you personally don’t persecute, which I am sure is true, does not change the sad state of the big picture. Being a scientist, I am sure that you can appreciate how unscientific it is to appeal to your own situation as counter evidence.

  388. I wrote: “The good old boys got together in the smoke filled rooms of academia and established a new rule called methodological naturalism.”

    “The real issue was to disfranchise ID from the community of researches and scholars by making it appear as non-scientific…”

    “So, for Darwinists a methodology can be old or new, true or false, existent or non-existent—whatever works.”

    —-Allen: …”isn’t exactly “character assassination”, it isn’t exactly the truth, either. In my opinion, making ad hominem arguments is never justified in scientific debates, and is also ultimately self-defeating.”

    Well, the scientific community has indeed established methodological naturalism as its official scientific methodology. [The stringent definition]. The definition did not write itself. I know that many evolutionary biologists believe in “emergence” but, as far as I know, no formal definition has ever emerged without an intelligent designer. So, if you don’t like the metaphor or “smoke filled rooms,” we can just say Darwinist cabal. I still don’t understand why explaining that fact constitutes an ad hominem argument, although I can understand how accusing the bearer of bad news [me] of resorting to ad hominem arguments is an ad hominem argument.

  389. Dave Wisker,

    My apologies but I was very busy last week.

    The paper that demonstrates that divergence can and does take place without geological separation is:

    “How the Species Became” by IanStewart- New Scientist” 10/11/2003

    The basic premise is that there is variation in a population- for example the beaks of finches.

    Some have longer beaks, some have shorter beaks and some have medium length beaks.

    The selection pressure occurs in the middle, taking out all the medium length beaks. You are left with short and long beaked finches.

  390. Hi Frost at #385,
    Indeed he does. In fact, Allen MacNeill has recently said on another thread that to argue against teleology (design, purpose) is to argue for evolutionary biology. Notice how he has necessary infused metaphysics with his evolutionary biology. He also tells us that Darwin did just the same in OOS (i.e. argued against purpose/ends/design).
    [aside; Darwin knew full well he was making a metaphysical claim and was intent that his science would reshape the entire metaphysic of society]
    So evolutionary biology is not merely an empirical science but also a metaphysical claim.
    Likewise MacNeill redefined “random” a while back, for its use in evolutionary biology as “without foresight.

    Ergo, Allen MaNeill believes that evolutionary biology speaks towards ends and purpose and he is necessarily making metaphysical claims when he advances his case.

  391. I am going to amend this comment I made to Allen @389: “Either this is the first time that this information has been presented to you or else you are stonewalling.”
    That’s a little too strong. Let’s just say that certain conflicting accounts need to be resolved.

  392. 394

    joseph writes:

    The paper that demonstrates that divergence can and does take place without geological separation is:

    “How the Species Became” by IanStewart- New Scientist” 10/11/2003

    The basic premise is that there is variation in a population- for example the beaks of finches.

    Some have longer beaks, some have shorter beaks and some have medium length beaks.

    The selection pressure occurs in the middle, taking out all the medium length beaks. You are left with short and long beaked finches.

    That’s interesting, but I never said divergence depended primarily on geographical separation. I said it depended primarily on reproductive isolation, which can occur in many different ways, geographic isolation being only one of them.

  393. 395

    Hi joseph,

    To amplify on my previous comment, the phenomenon you are talking about is called divergent or disruptive selection. This leads to reproductive isolation between the two divergent phenotypes (and their underlying genotypes) because the heterozygote, or hybrid phenotype, is selected against, preventing or severely reducing gene flow between them. Here is a paper that does a great job discussing the phenomenon in light of speciation:

    Schluter, D (2001). Ecology and the origin of species. TRENDS in Ecology & Evolution 16(7): 372-380.

    From the article:

    ECOLOGICAL SPECIATION (see Glossary) occurs when DIVERGENT SELECTION on traits between populations or
    subpopulations in contrasting environments leads directly or indirectly to the evolution of REPRODUCTIVE ISOLATION.

    As always, I apologize in advance for the delays my comments have in appearing. It is due entirely to the fact that all my comments are held up by moderation, sometimes for many hours.

  394. In the paper I referenced Ian Stewart says that “even though creatures can choose mates from the other group, the clusters tighten up and remain separate from each other.”

    Sympatric speciation…

  395. 397

    In the paper I referenced Ian Stewart says that “even though creatures can choose mates from the other group, the clusters tighten up and remain separate from each other.”

    Sympatric speciation…

    Yes, that is one way sympatric speciation can occur. There is still reproductive isolation between the two groups because there is selection against the intermediate (hybrid) phenotypes which significantly reduces gene flow between them. If the hybrids have significantly reduced fertility (i.e., lower fitness), then gene flow between the groups will be reduced. Individuals with one of the two selected phenotypes who mate with individuals in their own group will have significantly more offspring than those who mate with individuals from a different group. Gene flow is considerably reduced between the groups this way. That is one form of postzygotic reproductive isolation. And, as I said, divergence depends primarily on reproductive isolation.

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