Translation

April 21, 2006 § 17 Comments

By way of background, a protein- any protein- is a complicated little machine. It is manufactured by a living cell, which initially produces it as a linear chain of amino acids, which (the “polypeptide chain”) then spontaneously folds up into a stable “native state”. There are twenty different amino acids, and a typical protein will be a few hundred amino acids long (many are longer, including many which are necessary for the process of making proteins in the first place). Now, just because a protein folds into a native state that doesn’t mean that it is useful for any particular purpose; but all life depends upon proteins folded into stable native states. (This includes viruses, prions – the little boogers that cause Mad Cow – everything living or close to living).

None of these things, including viruses or prions, grow independently of a preexisting living cell that has all the machinery (machinery which includes lots of complex preexisting proteins, among other things) required to make them.

But suppose random polypeptide chains did appear spontaneously in some primordial soup, or inside some primordial protected lipid bilayer which also formed spontaneously. How many random polypeptide chains have been shown to fold into a well-defined stable native state at all, let alone perform any useful function?

If you guessed “none”, you win the prize. Folding doesn’t make a protein useful for a particular purpose, but folding is necessary in order to get a useful protein at all. And random polypeptide chains don’t fold. Of the twenty to the power 100 polypeptide chains possible of length 100, only the ones already coded in DNA or designed by a person – an infinitesimally small fraction of all possible ones – will fold. Randomly generated ones don’t.

So the next time a materialist (or a functional materialist) tells you that all the diversity of life arose by random chance, natural laws, and natural selection, you will know for a fact that he is making a statement of faith, not a scientific statement.

And it isn’t the evidential faith of a Catholic – trust vested in a Person known to exist from the natural evidence. No.

It is a blind faith.

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§ 17 Responses to Translation

  • Rob says:

    “Now, just because a protein folds into a native state that doesn’t mean that it is useful for any particular purpose…”Zippy–Can you define “useful purpose”? From a strictly materialist point of view, what “useful purpose” is served by life?

  • zippy says:

    <>Can you define “useful purpose”?<>Sure: capable of performing any ordinary protein function at all. By analogy, metal can in contrived cases be useful in a liquid form in machines, but generally speaking in order to make a machine out of metal the metal has to be in the solid state when it is functioning as a part of a machine. Proteins have to be folded in order to be functional at all in biomolecular machines. The difference is that any old blob of metal will become solid at room temperature, whereas only designed polypeptide chains will fold into specific well-defined proteins under physiological conditions. Randomly ordered chains don’t fold.<>From a strictly materialist point of view, what “useful purpose” is served by life?<>Well, that is his problem not mine. Even a die-hard materialist generally won’t deny that particular objects perform particular functions (e.g. that RNA polymerase – a complicated multipart machine made of many proteins – functions to transcribe DNA into messenger RNA, which goes on to specify the building of a protein in a ribosome). Unfolded polypeptide chains don’t perform specific protein functions (indeed the body has many mechanisms to prevent the buildup of unfolded polypeptides because they are toxic), and random polypeptide chains don’t fold.All of this doesn’t “prove” much except that the materialist’s belief that life arose physically solely through natural laws, random chance, and natural selection is a blind faith – a blind faith that rejects/avoids evidence and reason in favor of its preferred explanation.

  • Rob says:

    Zippy–It seems to me that you have to go back far beyond the point at which carbon-based life became possible to launch an effective argument against chance, if that is your purpose.Is it possible to say that one unique randomly generated polypeptide chain didn’t fold, only because that has not been observed to occur since we’ve been watching?No, as you say, that would be a statement of faith, either way.To me, the only really interesting question is what caused The Big Bang.

  • zippy says:

    <>Is it possible to say that one unique randomly generated polypeptide chain didn’t fold, only because that has not been observed to occur since we’ve been watching?<>Strictly speaking, there is a finite number of possibilities – a finite permutation space of chains, if you will. Each link in the chain is one of the twenty different types. Someday we may know quite exactly which chains of a particular length fold under normal conditions and which ones don’t. Right now we only know that random ones don’t (just as, for example, a random blob of metal won’t fly but one designed in the shape of an airframe, chosen out of the permutation space of all possible shapes, will fly under certain conditions).And remember that just because a chain folds that doesn’t mean that it performs any particular function. Folding is just a prerequisite to performing a function, more like “the metal is solid” than “the metal is shaped like an airplane”.

  • Rob says:

    Zippy–I have no doubt that everything you say is correct, at least to the extent that it is possible for us to be correct about it. But, so many prior things had to have happened just so to even get to that point, that if you want to say that such-and-such strongly implies the conscious act of a Person, it seems to me that the Person in question could not have *started* at the point of polypeptide chains folding, so you need to take the argument back to the point at which the Person *first moved*.

  • zippy says:

    Again, Rob, I am not making an argument from design here. I am making an argument that the materialist (or the functional-materialist who says “God did it by these material means”) is expressing a blind faith that sets itself against the (current) physical evidence. Saying “that view over there is incoherent” isn’t the same thing as saying “this view over here is true”.

  • Rob says:

    Zippy–Yes, and I don’t disagree with your reasoning. But why pick that point in the natural history of the universe upon which to base the argument, when to move even in the general direction of a “proof” of anything involving matter, you inevitably (it seems to me) have to go all the way back to a Prime Mover.

  • zippy says:

    <>But why pick that point in the natural history of the universe upon which to base the argument…<>I don’t pick the battleground, I just do my own little part to litter it with the dismembered remains of bad arguments.

  • Rob says:

    Zippy–Fair enough.

  • Step2 says:

    Hello Zippy,You mention in the article that only proteins already encoded in DNA will fold into a native state. But RNA strands can also act as a source code, and mRNA does naturally fold into a functional state from its components. There are still some pieces missing from the puzzle to be sure, but it does not seem to be a matter of faith, just discovery.Relatedly, have you have heard about the mimivirus which some biologists think may have been the bridge between nonliving information carriers and living cells?

  • zippy says:

    Hi Step2,<>…but it does not seem to be a matter of faith, just discovery.<>I am not saying that it is <>irrational<> to wait for the Rapture, just that it is an anticipation based on blind faith.<>…have you have heard about the mimivirus which some…<>Yep. She’s a big sucker, to be sure, with a lot more parts than your average little squirt of RNA with a protein coat. But she does still require a host cell’s machinery to make functional proteins.

  • Charles Wynn says:

    I thought that some very simple i.e. uniform polypeptide sequences have been found to make beta-sheets, and have some catalytic effect. Now I flunked cell biology, so I was unable to evaluate my random-Internet-info source…possibly the catalytic effect was so entirely different from what happens at a real active site in a real protein, that there is no reason to regard this as a possible “first stage” in the origin of life. Such sequences were not picked at random in any case, that’s true, but then there’s no such thing as a “random” anything simpliciter, only certain things lack order with regard to certain principles.So, a sequence constructed “randomly” from all twenty biological acids may never fold…but a sequence constructed “randomly” from one or two?Then, of course, the question becomes: if the primeval earth had some region awash in amino acids, was it likely to be a broad spectrum of such acids or might you have concentrations of just a few, which might then polymerize?Then you have to ask if any such uniform polypeptides could catalyze their own polymerization, and then you have to ask how a complex sequence became possible. Almost nobody believes, I think, that it all began with RNA (nucleic acids don’t polymerize jack, and are obviously an info-storage device: they only encode proteins because there are proteins that facilitate the process) – so at what point did nucleic acids enter the picture? How?Yes, it’s all rather hard to buy as a random event – but is the particular point about lack of folding and consequence catalysis correct?

  • zippy says:

    <>…but a sequence constructed “randomly” from one or two?<>…is like a pathologically short sequence. Someone may say “maybe sequences of a hundred residues never fold, but a random sequence of five can fold” in response to my essay. In which case I reply “so what?” The belief that a short polypeptide sequence or a longer one made of just one or two residue types in fact self-ligased into a chain and transformed over geologic time into the first living cell is pure blind faith. It may even be <>true<>, but there is no more <>scientific<> reason to believe it than to believe that the first cell – or a Demiurge who subsequently created us in a lab – popped into existence whole as a purely random excursion in phase space.

  • Charles Wynn says:

    I meant “just one or two” as far as residue types, not length. Of course six or seven residues aren’t going to fold or catalyze anything.

  • zippy says:

    Indeed. That is exactly what I understood you to mean.

  • […] nuts and bolts of the day-to-day biological sciences even at the molecular/cellular level, and how terrifically oversold it is as an explanatory view of […]

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