Home » Intelligent Design » Reconciling a Flawed Theory: Why Bother?

Reconciling a Flawed Theory: Why Bother?

Elliot Sober recently wrote a piece showing how Darwinian evolution and theism can be reconciled. It is interesting for two reasons. First of all, it never calls into question the premise – whether Darwinian evolution is itself true. Second, it’s primary purpose is political – to give Darwinian evolution political cover in the courts. For me, the more interesting of these is the first.

Sober basically asks if random mutations can be compatible with theism. But the bigger question is, are random mutations even the cause of evolution when it occurs? The evidence continues to gather that the evidence for that is no. It does not matter if the random mutation hypothesis is compatible with theism, or compatible with God’s participation in history, for the quite simple reason that this thesis is not itself true.

The primary example that is often propped up for random mutations causing evolution is in the somatic hypermutation process for the immune system. In this process, mutations are focused, not only on the right gene, but the right half of the right gene. The mutations are entirely focused on the part of the gene that attaches to the antigens, and not the part that signals the rest of the immune system.

It has long been known that most mutations occur in locations which deal with extracellular communication, rather than housekeeping genes that cells use for basic processing. There have been lots of systems which show mutations which are highly specific.

For those who want to know more about this, I give an overview of the situation in the following video, and other information in this series of posts.

So, why are the atheists so set to reconcile this dying theory with theism? One possible answer is that they are philosophically committed to the random mutation hypothesis, and, since it is failing on the evidence, they are looking for supporters. By pulling the theists into the random mutation hypothesis, it prevents them from looking on their own at the alternatives.

On another note, what’s absolutely hysterical is that Jerry Coyne is swearing up-and-down right now that the somatic hypermutation system really is an instance of random mutation. Let’s see if I’ve got this right. There are 3,000,000,000 base pairs in the human genome. The gene which needs mutating is about 1,200 base pairs long. The half that attaches to the antigen is about 600 base pairs long, and out of all 3,000,000,000 the mutation system focuses it in the right 600 base pair area. So, the process is .00002% random and 99.99998% non-random. But I guess we’ll call it a random process because it helps Jerry Coyne and Elliot Sober sleep better at night.

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23 Responses to Reconciling a Flawed Theory: Why Bother?

  1. Why does ‘random chance’ refine the (non)designs it haphazardly creates and sustains so brilliantly that the most towering geniuses of science of the modern age – all ID believers, of course – were in absolute awe of them; And I mean, ‘ABSOLUTE’ awe, of course, also, of this godlike genius, although they, evidently a little quixotically, attributed it to an omiscient and omnipotent creator-spirit, whether panentheist, as in Einstein’s case, or to the Judaeo-Christian God.

    Why was not ‘random chance’ content with (non)designs simply of the level of mankind’s greatest geniuses? Why did random chance have to be so fastidous and picky, and super-sophisticated and stuff, so that only Boffins like bornagain77 and Cornelius and could understand the stuff it non-designs? Why that constant goal of perfection? That’s what I want to know. I think we should be told.

  2. 2

    It has long been known that most mutations occur in locations which deal with extracellular communication, rather than housekeeping genes that cells use for basic processing. There have been lots of systems which show mutations which are highly specific.

    This hasn’t “long been known” for mutations. It sounds like something that might be true of *substitutions*, not mutations, and if you’re getting these two things confused, you’re making an absolute basic rookie mistake and your opinion on the validity of evolutionary theory is totally worthless.

    On another note, what’s absolutely hysterical is that Jerry Coyne is swearing up-and-down right now that the somatic hypermutation system really is an instance of random mutation. Let’s see if I’ve got this right. There are 3,000,000,000 base pairs in the human genome. The gene which needs mutating is about 1,200 base pairs long. The half that attaches to the antigen is about 600 base pairs long, and out of all 3,000,000,000 the mutation system focuses it in the right 600 base pair area. So, the process is .00002% random and 99.99998% non-random. But I guess we’ll call it a random process because it helps Jerry Coyne and Elliot Sober sleep better at night.

    Funny that this oh-so-excellent “nonrandom” hypermutation system produces so many silent or otherwise useless mutations when mutating a sequence. Why do millions and millions of receptors that don’t bind have to be tried in order to find one that binds well? If the system *really* had seriously guided mutations it wouldn’t bother with any of this, it would just know what the right mutations were to rationally design a receptor for the invader, make those mutations and those only, and be done with it with no waste.

  3. Nick matzke:

    Funny that this oh-so-excellent “nonrandom” hypermutation system produces so many silent or otherwise useless mutations when mutating a sequence. Why do millions and millions of receptors that don’t bind have to be tried in order to find one that binds well? If the system *really* had seriously guided mutations it wouldn’t bother with any of this, it would just know what the right mutations were to rationally design a receptor for the invader, make those mutations and those only, and be done with it with no waste.

    Strawman of the day. Nice job, Nick.

    Did you know that alleged silent muations really aren’t so silent?

    As for rookie mistakes, well saying that natural selection is non-random is a rookie mistake…

  4. Is nick saying substitutions are not mutations?
    That would be quite the rookie mistake.

  5. kaurtus -

    You are quite correct. For those tuning in, substitutions are merely a result of mutations, for which a given population no longer has the previous coding.

    In any case, for a good read on contingency loci in bacteria (i.e. mutation hotspots in non-housekeeping genes), you should read Adaptive Evolution of Highly Mutable Loci in Pathogenic Bacteria.

    As for the nonrandom somatic hypermutation system, I find it highly interesting that Nick only chose to mock, but never dispute, any facts given! As I said, it is, in fact .00002% random. And, it appears, that’s all that Nick cares about! He doesn’t seem to care at all about the fact that it is 99.99998% non-random. I guess that helps him sleep better at night, too.

    Of course, this is because Nick is facing a straw man. Instead of looking at reality, he is looking at fantasy-land. Only if the mutations are 100% directed will he bother to take notice – 99.99998% is not convincing enough! Of course, no one said that organisms were omniscient or perfect, only that the mutation system seems to be designed to generate mutations that are biased towards benefit – and that is both measurable and true. In the case of the somatic hypermutation system, you can calculate that the mutation space constriction contributes 22 bits of information per required base pair to the search. If I remember correctly the average number of base substitutions required for a target match is 3, so we can estimate it at 66 bits. Now, “bits” is an order-of-magnitude measurement. So, in other words, the mutations in somatic mutation are biased towards beneficial options by 66 orders of magnitude (note – power of 2, not 10).

    But, of course, Nick can’t see numbers or measurements, just like Coyne and Sober. Because, as Cornelius Hunter has pointed out numerous times, their objection isn’t really about the science.

  6. Freaking rookies:

    Evolution 101: Types of Mutations:

    Substitution

    A substitution is a mutation that exchanges one base for another (i.e., a change in a single “chemical letter” such as switching an A to a G). Such a substitution could:

    1. change a codon to one that encodes a different amino acid and cause a small change in the protein produced. For example, sickle cell anemia is caused by a substitution in the beta-hemoglobin gene, which alters a single amino acid in the protein produced.

    2. change a codon to one that encodes the same amino acid and causes no change in the protein produced. These are called silent mutations.

    3. change an amino-acid-coding codon to a single “stop” codon and cause an incomplete protein. This can have serious effects since the incomplete protein probably won’t function.

    :)

  7. Joe, it’s true that substitution is occasionally used to mean point mutation, but it’s pretty obvious that nick is referring to fixation of a new allele, the standard population genetic meaning…

  8. wd400-

    It is pretty obvious that there is more than one meaning of the word “substitution” wrt mutations. That Nick did not understand that is very telling and a rookie mistake.

  9. BTW, “fixation” already has a word for it. Why would we substitute the word “substitution” for the word that already works?

    Or are you saying that biologists just can’t keep things straight?

  10. Joe,

    The only thing that is “telling” here is the fact that your depth of knowledge on evolutionary biology goes about as far a as a google search. Nick was talking about the difference between a mutation happening and that mutation becoming fixed, a pretty major and important differnce I would think?

    And fixation applies to any allele, substitution describes the process of a new allele ariving by mutation and becoming fixed. A process that’s important in population genetics and phylogentics it’s provides the ground-up explanation of genetic divergence

  11. wd400:

    The only thing that is “telling” here is the fact that your depth of knowledge on evolutionary biology goes about as far a as a google search.

    Even if true it would be more than you or Nick knows.

    Nick was talking about the difference between a mutation happening and that mutation becoming fixed, a pretty major and important differnce I would think?

    I was pojnting out that the same word can be used for both- a mutation and it becoming fixed. It is very telling that you are too incompotent to understand that.

    And fixation applies to any allele, substitution describes the process of a new allele ariving by mutation and becoming fixed.

    So those other alleles didn’t arrive via mutation? They “just were”, I guess.

    A process that’s important in population genetics and phylogentics it’s provides the ground-up explanation of genetic divergence

    A process so important yet it has never been observed.

  12. A process so important yet it has never been observed.

    I think you forgot to google before this one…

  13. Then please, tell me when and where have we ever observed a new mutation become fixed.

  14. There are thousands of cases, but how about Behe’s comment on the Lenski experiments?

    ” After sequencing, they discovered a nonsynonymous point mutation in the spoT gene. When the researchers examined ten other populations that had evolved under the same conditions for 20,000 generations, they found that seven others also had fixed nonsynonymous point mutations in spoT”

  15. wd400-

    Nice bluff. Why can’t you reference one that occurred in nature.

  16. Really Joe?

    Apart from anything else, substitution is mathematical inevitability if we have finite populations and a non-zero mutation rate…

    Anyway, you wanted to “in nature” study so here’s one such. Shih et al (2007) found about 100 substituions which have all occurred since 1968 in a surface protein of one virus…

  17. Apart from anything else, substitution is mathematical inevitability if we have finite populations and a non-zero mutation rate

    Really wd400- do you have anything to support your bald assertions?

  18. BTW your link doesn’t work

  19. link is this: dx.doi.org/10.1073/pnas.0701396104

    Inevitability of substitution is from Kimura. Very simply.

    New alleles come in the population at the rate of mutation per individual (u) times the number individuals (N). Presuming neutrality the chance that any mutation becomes fixed is 1/N (i.e. it’s current frequency in the population) thus the rate of substituiton (K) is equal to the per-individual substitution rate

    K = Nu × 1/N = u

  20. I know the equation- no one has ever verified it- never.

    Haldane once said that a beneficial mutation will become fixed in 300 generations. Fruit fly experiments in the lab didn’t get one in over 600 generations. and they said it would even more difficult in the wild due to changing climates.

    And the site seems to confirm my PoV- design- with simulatneous amino acid substitutions. Not exactly what one would expect if the ToE was correct.

  21. Joe, just read up a little. The equation is the basis of neutral theory, it’s been tested thousands of times.

    Haldane was talking about the maximum rate of evolutionary change in a deteriorating environment presuming pre-adaptive alleles existed (not a shifting one in which mutations are required) not the normal background rate. It also turns out he was wrong.

    And you were wrong about observed substitutions, even if you are now trying to spin… something out of it.

  22. wd400, I have read up and it seems to me it is quite untestable. It appears that in order for any mutation to become fixed it takes a severe bottle-neck, design or in the case of the virus (I didn’t know they had a somatic hypermutation system), a limited genome that allows for the same mutation to occur in multiple members, which could be by design.

    Get a sexually reproducing population over 1000 and the equations can’t be tested.

    And what neither Haldane, Kimura, nor anyone even knows, is if any amount of mutational accumulation can account for the transformations required.

  23. Interesting to note near the end that E. Sober quoted M. Ruse from his article (2009) at BioLogos (“Why I Think the New Atheists are a Bloody Disaster”):
    “if science generally and Darwinism specifically imply that God does not exist, then teaching science generally and Darwinism specifically runs smack up against the First Amendment.”

    The quotation continues thus: “Perhaps indeed teaching Darwinism is implicitly teaching atheism. This is the claim of the new atheists. If this is so, then we shall have to live with it and rethink our strategy about Creationism and the schools. The point is however that the new atheists have lamentably failed to prove their point, and excoriating people like me who show the failure is (again) not very helpful.”

    Mind you, Ruse also wrote: “it is crucial to argue that Creationism, including its side kick IDT, is religion and not just bad science.”

    This makes it clearer why people at UD are so ardently opposed to any direct connection being made between IDT and religion/theology. Ruse is pushing them into a position they don’t want to have to defend, even if in their heart of hearts they know it and want it to be true (i.e. science, philosophy, religion cooperation).

    Relevant quotes from the Steve Fuller-ID thread:
    “For nearly all creationists and many intelligent design supporters, the legally relevant question here is whether restricting publicly funded science instruction to the pronounced anti-humanism of Darwin’s theory of biological evolution constitutes an encroachment of the state into matters that are constitutionally delegated to civil society. Thus, the legal mind behind intelligent design theory, Philip Johnson (1991), has accused the singular
    promotion of Darwinism in schools of fostering a naturalistic religion. And he is literally correct, as long as US courts insist on upholding the idea that science requires a belief that natural history is entirely the result of processes observable today under normal circumstances.” (176)

    “…[W]e should not be surprised if in the next few years Johnson’s worst fears are vindicated by a major lawsuit brought against some science instructor whose overzealous naturalism leads him [or her] to deny divine causation in a public school district whose tax base is funded mainly by religious believers.” (181)

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