cumulative selection part IV

From: Josh Bembenek (
Date: Sat Aug 10 2002 - 16:26:31 EDT

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    > On a different line, what identity and sequence comparisons indicate that
    > globins are derivatives or relatives to the cytochrome B family? Is it
    > simply the ability to bind the porphyrin ring, or are there other
    > similarities? Obviously this type of evidence remains the most
    > data suggesting the reality of evolution and the ability of natural
    > selection to derive novel functions from precursor molecules. My
    > work is on a dual-specificity phosphatase. The dual-specificity class of
    > phosphatase is different structurally and mechanistically from the
    > phosphatases which use metal ions for catalysis. The phosphatases that
    > metal ions belong to a larger family of metallo-phosphoesterases that
    > in function from bacterial exonucleases to RNA debranching enzymes (Denu,
    > et al, Cell 87, 361-364). While these examples of similar fold/structure
    > proteins provide excellent insight into the hyptothetical path of
    evolution and variation
    > from precursor molecules, I have not yet seen any true insight into the
    derivation of
    > the original fold/structure, which is an essential component of the
    problem. Natural selection cannot act previously to the establishment of
    any function, however all current explanations assign function to any given
    sequence arbitrarily with NO support from documented established
    experimentation. Therein lies what I consider to be a huge gap between the
    evidence and the extrapolation of the theory.

    <Not to mention that vitamin A is a variation of a light sensitive chemical
    > used in eyes.>
    > ---Are there any similarities between the enzymes involved with making
    > vitamin A and those making retinal? And what about beta-carotene? How
    > these structurally related molecules indicate that the genetic sequences
    > derived to synthesize them are likely to evolve from random sequences?
    > does not appear that the existence of structurally related molecules
    > performing various different biological functions immediately minimizes
    > difficulty in finding molecules capable of synthesizing them in the first
    > place.

    I don't have time: you will have to be satisfied with the points I've
    made. You have my permission to quote my email on Usenet's ""
    if you wish to pursue the subject there.

    Donald C. Lindsay

    So, being that I was highly interested in whatever support there might be concerning this issue (that he simply didn't have time to inform me about) I forwarded the above conversation to the "experts" at the talkorigins archive (which is less biased than most sources concerning the evolution issue and I am truly impressed by it, which might surprise you!) The expert replied, again without the time (if you had seen the amount of time he has spent at talkorigins you might begin to wonder if they are simply avoiding the issue because they know that there is no suitable answer. Then again perhaps I'm not worth the time.)

    Dear Joshua Bembenek,

    I really don't have time for much discussion of your questions. I can just make a couple of points. First, you ask for evidence of the first proteins from which globins derived. I can't imagine how anyone might obtain such evidence of molecular events that probably occurred a billion years ago in an unknown location and environment. We have to make any deductions we can from available evidence. Our inability to access ancient biochemistry resembles somewhat the astronomer's inability to access the distant. If you choose to reject any principle that is not conclusively proven, you lose the pleasure of understanding a lot of stuff that it interesting, even if tentative, about our universe. Secondly, as I suggested in the Box in my essay, experiments searching for specific protein function among proteins containing random amino acid sequences have been successful. I don't have time to elaborate on this at present, but hope to summarize the evidence for this in a future essay. This kind of evidence implies that functional proteins can arise without their having been intelligently designed (though of course it doesn't prove that they weren't intelligently designed).

    Best wishes,

    Ed Max

    {Note} I would like to direct your attention to several words he uses, which are critical to my position: Imagine, deduction, somewhat, conclusively, tentative, implies. You see, if you don't agree with his presuppositions and assumptions, then everything he has said here can be interpreted in another fashion, that is not incongruous with the data, but disagrees with him (one possible alternate explanation off the top of my head: transition II occurs after a creator establishes transition I.) Just because he can't imagine how to derive evidence about ancient biochemistry doesn't mean we can't find it, hasn't Dawkins used this argument (i.e. not imagining something doesn't make it unlikely or unprobable)? I could easily imagine ways to prove or theoretically begin to discover data concerning ancient biochemistry (why exactly should this process have stopped- evolution should still be producing novel sequences with novel functions in novel pathways today? There should be some 50% complete biochemical pathways that we can find. We should also imagine some progression of biochemical systems that exist in bacteria into something more complex in mammals. If this was so prominent, we should be discovering evidence for it daily. As of now, I have not been directed to any such evidence. Additionally the issue of deriving functional sequences from random precursors should be possible experimentally using PCR or something along those lines. Any experimental establishment of these concepts could occur. He simply tries to create this dense fog around the issue as if there was no way to investigate it. Clearly folks in the protein folding field would not feel this way about the problem.) I would also like to draw a parrellel of his statement with Dawkins quote of Dr. Atkins' statement about the teapot orbiting pluto.

    The Richard Dawkins quote is listed here for reference:

    I once asked a distinguished astronomer, a fellow of my college, to explain the big bang theory to me. He did so to the best of his (and my) ability, and I then asked what it was about the fundamental laws of physics that made the spontaneous origin of space and time possible. "Ah," he smiled, "now we move beyond the realm of science. This is where I have to hand you over to our good friend, the chaplain." But why the chaplain? Why not the gardener or the chef? Of course chaplains, unlike chefs and gardeners, claim to have some insight into ultimate questions. But what reason have we ever been given for taking their claims seriously? Once again, I suspect that my friend, the professor of astronomy, was using the Einstein/Hawking trick of letting "God" stand for "That which we don't understand." It would be a harmless trick if it were not continually misunderstood by those hungry to misunderstand it. In any case, optimists among scientists, of whom I am one, will insist, "That which we don't understand" means only "That which we don't yet understand." Science is still working on the problem. We don't know where, or even whether, we ultimately shall be brought up short.

    Agnostic conciliation, which is the decent liberal bending over backward to concede as much as possible to anybody who shouts loud enough, reaches ludicrous lengths in the following common piece of sloppy thinking. It goes roughly like this: You can't prove a negative (so far so good). Science has no way to disprove the existence of a supreme being (this is strictly true). Therefore, belief or disbelief in a supreme being is a matter of pure, individual inclination, and both are therefore equally deserving of respectful attention! When you say it like that, the fallacy is almost self-evident; we hardly need spell out the reductio ad absurdum. As my colleague, the physical chemist Peter Atkins, puts it, we must be equally agnostic about the theory that there is a teapot in orbit around the planet Pluto. We can't disprove it. But that doesn't mean the theory that there is a teapot is on level terms with the theory that there isn't.

    Its possible that Dr. Max's deductions (and those that Dawkins trusts to the fullest extent) about ancient biochemistry are correct, but there's nothing to directly support it, and the deductions, implications and conclusions are flowing from other additional assumptions and presuppositions. If I said "God is Real" because "the creation" exists, evolution proponents tend to say that's simply wrong (and as ridiculous as a teapot orbiting pluto) with no other support than their presupposition that a God is quite unlikely. However, when folks like Dr. Max say evolution occurred because self-replicating systems exist and we have to make "any" deductions from available evidence, many will then say "I agree" and consider those who object to be clearly wrong and perhaps uneducated, when in fact they simply have different presuppositions on the likelihood of a creator. Whose deductions/ presuppositions are better appears to depend upon whose philosophical underpinnings you agree with. . Additionally, because I disagree that the fundamental mechanisms of evolution are sufficient for producing any protobiont/RNA world does not prevent me from understanding it!! Also, note that I never declared that I reject anything except the philosophical conclusions of atheists, as Max incorrectly implies. The tone of my letter is inquiry into the data, show me the money so to speak, not a rejection of all principles and data concerning evolution. It seems we're bankrupt for this data. As I mentioned in the body of the "inquiry," the current mechanism of darwinian evolution is insufficient to produce what we currently know about life on many levels. Someone pointed out to me that this means that some other theory must be found before we can account for the origins of life, similar to how Newtonian Physics became re-interpreted as a subset of principles within the framework of Relativity, and I think that is more accurate than supposing more evidence will prove the current dream of abiogenesis someday. We just don't have it figured out yet (which is a far cry from how Dawkins presents it in "The Blind Watchmaker)! Maybe Intelligent Design will win, maybe another completely naturalistic theory will come about. Either way, as I see it, natural selection and darwinian evolution are failing to answer some serious issues.

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