Monday, April 26, 2010

A "Malfunction" That Helps: Induced Adaptation in Yeast Cells

When yeast cells face environmental stress, such as exposure to hydrogen peroxide, their internal operations can begin to malfunction. For example, a particular protein misfolds and no longer functions as well. This hardly seems surprising, but as usual there is more to the story. It seems that the misfolded protein normally helps to terminate the synthesis of new proteins. But when it is misfolded, some of the newly formed proteins end up a bit longer, with more information added. And the added information is not just random garbage--it helps the cells adjust to the environmental stress which brought about the change in the first place.

Hints of this adaptation mechanism appeared with researchers found that yeast cells faced with environmental stress do not slow down or fail to function--they modify. As one writer put it, phenotypic variation in the yeast cells comes "out of the woodwork." It seems that previously hidden variation emerges, and sometimes it is advantageous in dealing with the new environmental conditions.

Furthermore, these design changes have been found to be inheritable. They can persist across generations. As one researcher summarized it, this adaptation mechanism and inheritance "allows yeast cells to exploit pre-existing genetic variation to thrive in fluctuating environments."

New research is now adding more details. It seems that the yeast has proteins that help to fine tune the process. They inhibit the protein misfolding until the environmental stress reaches critical levels. At that point the protein misfolding occurs and helps to adapt to the environmental stress. As the researchers concluded:

we find that [protein misfolding] provides yeast cells with an adaptive advantage under oxidative stress conditions, ... [protein misfolding] provides a mechanism for uncovering genetic traits that aid survival during oxidative stress conditions.

This story of yeast adaptation is one example of epigenetics--mechanisms that help organisms adapt to changing conditions, and that may pass that change along to later generations. And it is another example of the falsification of evolution's fundamental prediction that biological variation is independent of need. What we now must believe is that evolution produced sophisticated mechanisms by which evolution can occur. The absurdity of evolution is reaching new heights. Religion drives science and it matters.

25 comments:

  1. This was a seemingly interesting and informative article except for you having to slip in 'these design changes'. (facepalm)
    'evolution's fundamental prediction that biological variation is independent of need' - making stuff up again? This is not a general premise. Stop cherry-picking statements and facts to suit your purposes.
    'Religion drives science and it matters', no it doesn't, it drives denialists such as you, ant-vaxxers, right to lifers and homphobes. But yes, that does matter.

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  2. Dr. Hunter thanks again for clearly elucidating a major failure of neo-Darwinism

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  3. Actually Where's, Dr. Hunter is completely right in that evolution's primary prediction is that evolution predicts and expects the main driving force for evolution of greater functional complexity to be totally random variations which are completely independent of any organisms need at any given time. To find that an organism exhibits highly organized "pre-programmed" responses to any environmental cues is to be expected for the limited variation within kind model of Theism, and is totally unexpected, indeed crushing, for the atheistic/materialistic model of Neo-Darwinian evolution.

    Notes:

    Scientists Discover What Makes The Same Type Of Cells Different - Oct. 2009
    Excerpt: Until now, cell variability was simply called “noise”, implying statistical random distribution. However, the results of the study now show that the different reactions are not random, but that certain causes (environmental clues) lead to predictable distribution patterns,,,
    http://www.sciencedaily.com/releases/2009/09/090911204217.htm

    Bacteria 'Invest' (Designed) Wisely to Survive Uncertain Times, Scientists Report - Dec. 2009
    Excerpt: Essentially, variability of bacterial cells appears to match the variability in the environment, thereby increasing the chances of bacterial survival,
    http://www.sciencedaily.com/releases/2009/11/091102112102.htm

    De Novo Genes: - Cornelius Hunter - Nov. 2009
    Excerpt: Cells have remarkable adaptation capabilities. They can precisely adjust which segments of the genome are copied for use in the cell. They can edit and regulate those DNA copies according to their needs. And they can even modify the DNA itself, such as with adaptive mutations,,,,One apparent de novo gene is T-urf13 which was found in certain varieties of corn.
    http://darwins-god.blogspot.com/2009/11/de-novo-genes-evolutionary-explanation.html

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  4. bornagain77: So you keep saying, but not arguing. Please try to provide an actual argument.

    The term neodarwinism is ambiguous. It can refer to the century-old panselectionist school of thoughts, the mid-twentieth century modern synthesis, or the current theory of evolution. As this concerns so-called acquired traits, it seems you must be referring to the oldest of these.

    In any case, these capabilities can be considered as part of the phenotype and consistent with the basics of evolutionary theory.

    Altered translational fidelity in [PSI+] strains may provide a mechanism that promotes genetic variation and phenotypic diversity (True HL, Lindquist SL (2000) Nature 407:477–483). In agreement, we find that prion formation provides yeast cells with an adaptive advantage under oxidative stress conditions, as elimination of the [PSI+] prion from tsa1 tsa2 mutants renders the resulting [psi-] [pin-] cells hypersensitive to hydrogen peroxide.

    The biggest difference from orthodoxy isn't the phenotypic diversity, which is adaptive, but the promotion of genetic variation.

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  5. Thank you Dr. Hunter,

    This is a fascinating trait of nature and accolades should be given to the scientists that observed and described it!

    Your challenge to think about the implications of this finding should caution any true scientist to reflect before making any comment.

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  6. Looks like a clear example of natural selection at work, no problems there.

    However, is this type of mutation--the protein misfolding--an adding of *new* information to the genome, in the sense that it is an increase in the amount of information, or is it merely an example of more scrambling of pre-existing information?

    If it is the former, what are the limits? Could yeast become a higher organism, via one such advantageous mutation after another if given enough time?

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  7. Awesome stuff Dr Hunter. Thanks for bringing out discoveries of new research. Evolutionists are like the old uncle that never did anything constructive with his life except tell everyone how much he knows.

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  8. Neal Tedford: "Awesome stuff Dr Hunter. Thanks for bringing out discoveries of new research. Evolutionists are like the old uncle that never did anything constructive with his life except tell everyone how much he knows."

    The huge irony here is that the research is not being done by Cornelius or any of the ID camp but by the "old uncle" who does nothing constructive. And for the most part those who are doing this research have no fundamental issue with the basic concepts of evolutionary theory. It seems that the only contribution Cornelius makes is to take these articles, bold a few sentences and declare that they are "painfully obvious" that they contradict evolution. Is that doing science?

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  9. First, the prediction (of "Darwinian" or "neo-Darwinian" theories about what causes adaptive change, not of the idea that you share ancestors with gibbons and goldfish and yeast) is that variations arise without regard for need, not that they persist or spread without regard for need.

    Second, the articles you cite raise the problem of how to build up complex systems when the individual mutations, by themselves, might be detrimental. They then raise one occasional solution: the individual mutations might be of no effect except under stressful conditions. The authors are interested in the effects when such cryptic variants prove useful in concert under stressful conditions; presumably they're not so interested in the effects when they prove detrimental once stress brings out their effects. It's the fundamental principle of natural selection: bad mutations can outnumber good mutations by a great deal, and it won't matter much because the rare good mutations are the ones that survive and persist in the population.

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  10. Timcol: "It seems that the only contribution Cornelius makes is to take these articles, bold a few sentences and declare that they are "painfully obvious" that they contradict evolution. Is that doing science?"

    Do ever understand anything at all here?
    Apparently not.

    1) Dr. Hunter is acting as a scientist critically reviewing the nature and implications of science experiments.

    There are IDist and creationist scientists doing experiments. Now lets see why there aren't more...

    2) Consider the fact that you Darwinian prigs persist your fanatical attempts to squelch and slander every ID or creationist scientist that tries to get funds for experiments.

    It thus becomes all too clear that you have no business criticizing IDists for not being doing as much research as the Darwinists - indeed you yourselves are to blame for this situation!!

    What glaring hypocrites you are.

    It is truly amazing to see you dullards coming to blogs and forums, spitting out statements like yours all while being the very a**h's responsible for the very thing you criticize!

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  11. Hitch: "Do ever understand anything at all here? Apparently not."

    I am sincerely trying to understand it, but honestly without the "lens of faith" it doesn't make much sense.

    Hitch: "There are IDist and creationist scientists doing experiments. Now lets see why there aren't more..."

    That's good to hear - do you have examples or links to these experiments?

    Hitch: "It is truly amazing to see you dullards coming to blogs and forums, spitting out statements like yours all while being the very a**h's responsible for the very thing you criticize!"

    Nice Hitch. Real classy and so WWJD.

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  12. Timcol62, I don't understand your comment about Dr. Hunter's posts not being science. Would you prefer science not to ask what the impact of new evidence has on existing theories?

    It should be clear that a study into the research results contradicting evolution would be greatly helped by people like Dr. Hunter's ability to share his encounters with such research.

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  13. Michael: "Timcol62, I don't understand your comment about Dr. Hunter's posts not being science. Would you prefer science not to ask what the impact of new evidence has on existing theories?"

    I think the issue for me (and apparently others too), is that Cornelius has never once attempted to offer an alternative hypothesis. He has stated that he thinks that "supernatural causes" play a role in evolution and/or origins (he said so in the comments on March 30th). But he has yet to offer any evidence or hypothesis of why that is so. I have no doubt that the theory of evolution is not perfect - which of course goes for any scientific theory. The theory will always need to be modified and revised as new data is discovered - or perhaps even the theory may have to be thrown out and replaced with a new one. That would entail creating new hypotheses and experiments. That would be true scientific progress and something which Cornelius seems quite reluctant to participate in.

    It's easy to take potshots at what is wrong - it is harder to offer new ideas and new hypotheses. I wish the ID camp would have a bit more courage to put their money where their mouth is - offer us an alternative hypothesis and let's discuss it. Certainly what Cornelius is doing isn't "wrong" but in the end I don't think it really gets us very far. Is he going to be writing the same kind of blog articles as he is today in 10, 20 years, without any hint of an alternative hypothesis?

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  14. "Evolution's fundamental prediction that biological variation is independent of need."

    Evolution's fundamental prediction? Strange I never heard that one. Actually, Googling the phrase "biological variation is independent of need" turns up 6 hits. The first is the anti-science site www.darwinspredictions.com, the second and third are yours, the fourth and six are links to the first, and the fifth is krishnascience.com. Anyone see a trend here?

    The only evidence therein conflates the classic* understanding of production of genetic variation with biological and phenotypic variation.

    {And I mean classic. Like 1950's classic}

    In typical anti-science fashion, these sites mix references to variation (e.g. accumulation of random mutations), with phenotypic divergence due to selection, and things like stress response, which in a few organisms might actually increase mutation rates (bacterial SOS response).

    In this specific case, there is no genetic variation produced by need. There is pre-existing genetic variation unmasked by alteration of translation stop fidelity.

    From the paper: "Tsa1 and Tsa2 normally act to prevent oxidant-induced [PSI+] prion formation, but overwhelming this defense system provides an evolvable mechanism to survive the ensuing oxidative stress conditions. "

    Note the word EVOLVABLE. An evolvable stress response.

    Here's an actual Darwinian prediction for you:

    "Not only has life evolved, but life has evolved to evolve. … The rates at which the various events within the hierarchy of evolutionary moves occur are not random or arbitrary but are selected by Darwinian evolution."

    D. J. Earl, M. W. Deem, “Evolvability is a selectable trait,” Proceedings of the National Academy of Sciences 101 (2004): 11531-11536.

    Evolution of Evolvability produces what appears to you as design. Just as evolution produces complex features you wish to be designed.

    Are you arguing that species have been designed to more rapidly evolve under pressure? Wow, that is a twister, but the design arguement here actually relies on acknowledging evolution!

    What is the evidence that evolvability and resilience under pressure are not evolved traits subject to natural selection? Surely survival under stress is adaptive!

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  15. “This story of yeast adaptation is one example of epigenetics--mechanisms that help organisms adapt to changing conditions, and that may pass that change along to later generations. And it is another example of the falsification of evolution's fundamental prediction that biological variation is independent of need.”

    I think you might’ve misunderstood where the variation comes from.
    The prion formation is an epigenetic modification that allows expression of variation that is already present in the genome.
    The prion formation leads to a read-through of stop codons, which means that normally non-translated regions downstream of stop codons are translated as well on a genome-wide scale. Not the prion is adding variation, the variations were already present (downstream of stop codons).
    Of course, proteins with added amino acids will show altered stability and in case of proteins, altered folding and function. Because these downstream regions are not expressed normally, they’re not subject to natural selection and can accumulate variations.
    In most cases prion formation and read-through of stop codons is deleterious to the yeast but in up to 25 % of cases, according to this article (open access), the revealed variation is actually advantageous under the prion formation promoting conditions. Because the conditions that allow prion formation are normally pretty harsh, the chances of survival are higher with the normally deleterious read-through of stop-codons than without it.

    In any case, contrary to what you claim, the variation is independent of need. It is present in normally non-translated regions of the genome all the time.

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  16. @RobertC:
    "In this specific case, there is no genetic variation produced by need. There is pre-existing genetic variation unmasked by alteration of translation stop fidelity."

    Completely agree.

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  17. How is this example any different than the strains of antibiotic-resistent bacteria that result from beneficial mutations which don't add any new information to the genome but simply a recombination of existing information that happens to result in a benefit to the organism. This isn't caused by a need for change in bacteria on account of antibiotics, but rather merely revealed that the particular mutation happens to benefit the particular change in their environment--which is to say, natural selection. How are the yeast any different here in this example?

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  18. JLT:

    "I think you might’ve misunderstood where the variation comes from."

    No, I got it.


    ===
    The prion formation is an epigenetic modification that allows expression of variation that is already present in the genome.
    The prion formation leads to a read-through of stop codons, which means that normally non-translated regions downstream of stop codons are translated as well on a genome-wide scale. Not the prion is adding variation, the variations were already present (downstream of stop codons).
    ===

    Of course.


    ===
    proteins with added amino acids will show altered stability and in case of proteins, altered folding and function. Because these downstream regions are not expressed normally, they’re not subject to natural selection and can accumulate variations.
    ===

    The probability of such random additional segments usefully addressing the stress is remote, to say the least.

    ===
    In most cases prion formation and read-through of stop codons is deleterious to the yeast but in up to 25 % of cases, according to this article (open access), the revealed variation is actually advantageous under the prion formation promoting conditions.
    ===

    A non controversial falsification of the evolutionary expectation.


    ===
    Because the conditions that allow prion formation are normally pretty harsh, the chances of survival are higher with the normally deleterious read-through of stop-codons than without it.
    ===

    So next time a tornado comes folks should just start making random structural changes to their houses. That will help enhance their chances of withstanding the tornado.


    ===
    In any case, contrary to what you claim, the variation is independent of need. It is present in normally non-translated regions of the genome all the time.
    ===

    False, the yeast immediately responded with phenotypic variations that directly addressed the environmental stress, *in spite* of evolutionary predictions. The fact that the segments were "present in normally non-translated regions of the genome all the time" is not relevant to your claim that "the variation is independent of need." You must be an evolutionist.

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  19. RobertC:

    ===
    "Evolution's fundamental prediction that biological variation is independent of need."

    Evolution's fundamental prediction? Strange I never heard that one.
    ===

    Which is about the most absurd statement one could make. It would be like a physicist saying he never heard of Newton's laws of motion. This is what evolution is all about, protecting a silly theory. Here are three representative quotes from leading evolutionists:

    ---------------
    Mutation merely provides the raw material of evolution; it is a random affair, and takes place in all directions. Genes are giant molecules, and their mutations are the result of slight alterations in their structure. Some of these alterations are truly chance rearrangements, as uncaused or at least as unpredictable as the jumping of an electron from one orbit to another inside an atom; others are the result of the impact of some external agency, like X-rays, or ultra-violet radiations, or mustard gas. But in all cases they are random in relation to evolution. Their effects are not related to the needs of the organisms, or to the conditions in which it is placed. They occur without reference to their possible consequences or biological uses. --Julian Huxley

    We call these events [the various types of DNA sequence alteration] accidental; we say that they are random occurrences. And since they constitute the only possible source of modifications in the genetic text, itself the sole repository of the organism’s hereditary structures, it necessarily follows that chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is likely ever to be revised. --Jacques Monod

    The essence of Darwinian evolution is that populations [adapt] by producing mutations that are random with respect to the organism’s need, that is those that have random direction in phenotypic space. --Ronald Fisher
    ---------------

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  20. Dr. Cornelius *misrepresents* evolution when he says it requires that "biological variation is independent of need." Whether that is, or isn't, really evolutionary theory depends on how you define "biological variation." An artiodactyl giving birth to a fully-formed whale (in one step) is the kind of variation independent of need which would disprove evolution. In contrast, there are variations between queen bees and drones in a beehive, a variation that is *not* contrary to need, but that kind of variation does not disprove evolution.

    The kind of "biological variation" in yeast cells mentioned here is not the kind that disproves evolution; furthermore in Dr. Cornelius' list of alleged "falsifications" of evolution theory, several of his other examples also fall into the category of variations that support, rather than contradict, evolutionary theory.

    Regarding the variation in the yeast cells, here is what the authors really wrote, which Dr. Cornelius quote-mines:

    "Altered translational fidelity in [PSI(+)] strains may provide a mechanism that promotes genetic variation and phenotypic diversity [ref]. In agreement, we find that prion formation provides yeast cells with an adaptive advantage under oxidative stress conditions, as elimination of the [PSI(+)] prion from tsa1 tsa2 mutants renders the resulting [psi(-)] [pin(-)] cells hypersensitive to hydrogen peroxide. These data support a model in which Prxs function to protect the ribosomal machinery against oxidative damage, but when these systems become overwhelmed, [PSI(+)] prion formation provides a mechanism for uncovering genetic traits that aid survival during oxidative stress conditions."

    Note the phrase "promotes genetic variation." If this includes previously-existing genetic information, already present in the genome, but only expressed when the yeast cells are subject to oxidative stress, then evolution is not disproven, because those genetic sequences would have been subject to natural selection in the past.

    If this genetic variation includes new errors/mutations, then the fact that these errors/mutations are beneficial to the yeast cells when they are under stress, disproves the creationist argument that all mutations are detrimental. Why would an organism want to increase its error rate, the amount of errors in expressed codons, if, as creationists claim, all mutations are detrimental?

    The same thing goes with other things in Dr. Cornelius list of alleged falsifications of evolutionary theory. In particular, consider "Cairnsian" adaptive mutation, which Dr. Cornelius in his list also claims in a falsification of evolution. Cairnsian mutation involves bacteria, when stressed, overexpressing DNA Polymerase IV, which is an error prone polymerase. The fact errors in DNA copying are beneficial to stressed organisms disproves the creationist claim that mutations are always detrimental.

    These results imply that DNA copying errors are beneficial to organisms when stressed. The *error rate* is clearly higher when they are stressed, but the errors themselves appear uncorrelated with the resulting phenotype. And that is real evolutionary theory: information and complexity in the present resulted from past mutations that were, at the time, uncorrelated with the resulting phenotype.

    These types of experiments, if anything, disprove creationism and supports the evolutionary belief that "errors" are beneficial often enough to be useful to the species.

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  21. Among possible sources of variation/selection, Darwin included "use and disuse", a Lamarckian view which has since been almost entirely discredited (take that, Chuck!).

    However, epigenetics and similar phenomena now lend credence to vaguely Lamarckian situations whereby the environment can indeed direct genetic development beyond selection. It's pretty darn fascinating. Discovering and detailing this stuff is what science does. Whatever "religion" is "driving science" these days, well, it's doing an excellent job. :)

    What perpetually brings me down is how IDists act like new findings mean the whole structure of "Darwinism" as they define it (RM + NS, anything beyond that is not allowed to be considered naturalistic) is just a-tumblin' down.

    I can't help but imagine a blog post that made the following assertion: "The fundamental predictions of physics are to be found in Newton's Laws of Motion. Yet recent discoveries involving subatomic particles and masses moving at high speeds have utterly demolished these assumptions. Newtonism has nothing left to stand on, and applies only to the most minor of phenomena. The rest, clearly, is best explained by inferring non-naturalistic intelligent forces which leap the chasm of mechanistic causation. Heck, Newton himself said so!"

    And what about epidemiology? Germ theory asserts that diseases are caused by unfeeling microbes (which anyone who's been horribly sick can tell you is nonsense). Many discoveries have demonstrated dozens of non-microbial causes. Therefore, the hypothesis that nearly all disease is the result of malevolent forces, not ethically-neutral bugs, is the only reasonable inference remaining.

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  22. Excellent post Diogenes-

    To reiterate a key point:

    "Evolution's fundamental prediction that biological variation is independent of need."

    Is a vague statement, and contrived to bring about confusion. This is why we find it only on creationist sites. 'Biological' variation is not the same as 'genetic variation.' All the quotes from Dr. Hunter are discussing the accumulation of genetic diversity through random processes (mutation.)

    For example:

    "Mutation merely provides the raw material of evolution; it is a random affair, and takes place in all directions......Their effects are not related to the needs of the organisms, or to the conditions in which it is placed. They occur without reference to their possible consequences or biological uses."

    Great quote, but READ the difference. Hunter says BIOLOGICAL variation (which he then later chooses interprets as phenotype), while the quote is talking about accumulation of random GENETIC variation. Replacing the latter with the former allows muddling the water and intentional confusion.

    Take this post, where the yeast increase their phenotypic variation in response to stress, using evolvable genetic (and mechanistically understood) mechanisms--and Hunter gets to claim it is disproof of evolution.

    His confusion is most apparent in the comments, where he says: "False, the yeast immediately responded with phenotypic variations that directly addressed the environmental stress, *in spite* of evolutionary predictions"

    Baffling. Phenotype is predicted by evolution not to respond to selective pressure?

    Two problems here:

    1) The first related to the conflation of genotypic variation with phenotypic outcome discussed above*. There is NOT any biologist who would argue phenotype and need are uncoupled. Take Darwin's finches. Their phenotype is directly correlated to need. Beak size to food. The underlying genetic diversity that allowed this selection accumulated through years, independent of need, through random processes. Clear enough?

    Again, the response of phenotype or phenotypic variation to pressure is not the same as the random accumulation of genotypic variation. I'm not sure Dr. Hunter understands the difference-or doesn't wish his reader to consider the difference. The yeast did not remodel their genome. They read-through and translate regions of proteins reserved for stress conditions. This increases phenotypic diversity to allow survival.

    2) Directly: the response is generalized, and works only in certain kinds of stress. (Only 25%, I think). It is a shotgun approach to survival.

    Even in the rare cases where mutagenic rate is increased, such as SOS response in Bacteria, increased rates of mutation are not directed at certain genes. They increase the overall mutagentic rate but are RANDOM with respect to need! Gee, that still matches the quote exactly:

    "populations [adapt] by producing mutations that are random with respect to the organism’s need"

    My last point is that:
    1) Hunter tacitly accepts evolution, by pondering if yeast are designed to evolve.
    2) Hunter's acceptance that random mutation is not detrimental, but enhances survival and information content might conflict with core ID values.

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  23. Lenoxus:

    ===
    What perpetually brings me down is how IDists act like new findings mean the whole structure of "Darwinism" as they define it (RM + NS, anything beyond that is not allowed to be considered naturalistic) is just a-tumblin' down.
    ===

    Where did I say that?

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  24. Excellent post RobertC. You are right about this "baffling" quote from Dr. Cornelius:

    "False, the yeast immediately responded with phenotypic variations that directly addressed the environmental stress, *in spite* of evolutionary predictions"

    "Baffling" indeed, how does evolutionary theory predict no response to environmental stress involving a phenotypic change? The point is, there are some "biological variations" that evolution predicts or permits, some that it doesn't. If I exercise and build up my muscles, that is a "biological variation in response to need", but it does not disprove evolution. If an organism needs a characteristic, which can only occur if a T in its DNA mutates to C and not A or G, and it only mutates to C and never to A or G, and this bias for C is not due to a mechanism previously exposed to natural selection for the needed characteristic, that would disprove evolution.

    Dr. Cornelius is lumping all possible "biological variations" into one basket, but there are many kinds of "biological variations." The question is: how did the biological (presumably genetic, maybe epigenetic) variations that produce adaptive complexity *originally* appear? (Sequences in the genome that are expressed part of the time may not count.)

    And now, your testable ID prediction for the day. William Dembski is the gift that keeps on giving:

    "I predict that in the next five years [by 2003] intelligent design will be sufficiently developed to deserve funding from the National Science Foundation." [William Dembski, Mere Creation, 1998, p. 29.]

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  25. Diogenes:

    Maybe ID does deserve funding. It just isn't getting funding because of politics, bias, etc.

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