Monday, April 17, 2006

Re: Do they expect that naturalistic methods will be able to explain a pathway to a minimum life form with 1000 genes?

AN (copy to CED minus your personal identifying information)

Thanks for your message and apologies for the delay in replying.

----- Original Message -----
From: AN
To: Stephen E. Jones
Sent: Tuesday, April 11, 2006 8:50 PM
Subject: 'More genes' needed to make life

>Regrading your last post in your blog I need to ask something. When we look at abiogenesis researchers we see two distinct type of researchs that are totally conflicting in my view. On one side we have researchers who claim that life can be reduced to structures as simple as RNAs and self-replicators, on the other side there are results showing that minimum requirements for something that we can call minimum life can't be less than 500-1000 genes as you mentioned in your last post. For example here we have a paper with various claims for first protocells and RNAs leading to more complex life.

This is a good point, but those who claim that "life can be reduced to structures as simple as RNAs and self-replicators" are, quite frankly, deluding themselves. There are no such things as "simple ... self-replicators." All replication takes place in a cell, by a coordinated system of ~50 molecular machines. The creationist chemist and early ID theorist Wilder-Smith makes this point, that "the synthesis of life has little to do with the clever synthesis of just one super molecule which self-replicates ... A real synthesis of life will more probably lie in the synthesis and ordering or arranging of the many component parts (i.e. molecules) of the von Neumann machine":

"To return to the technique required for abiogenetic in vitro synthesis: In the first place, there are probably no such things as single self-replicating molecules-although one speaks a great deal about them today. To achieve self-replication in general, one needs more than single molecules, the interaction of several different types of molecules with one another is mandatory. Maybe a DNA or RNA molecule might be able to replicate itself but it will be in the presence of certain other molecules - such as enzymes or replicases. Maybe the one molecule can act in several roles, of course. In this sense there have been reports, that some nucleic acids can act as their own catalysts. But it is usually the interaction of several molecules with one another that brings self-replication into play. The interacting molecules need not be all of varying analyses - as in the case of the molecules which act as their own catalysts. Varying roles are required for replication. We keep. then. in mind that the replication of one molecule entirely by itself is not yet known. Several molecules interact with one another to give the replication we ascertain in the von Neumann machine known as the biological cell. This interaction reminds us again of the machine nature of the self-replicating von Neumann machine, for the latter consists of an interacting multitude of component parts to achieve self-replication. The many different molecules correspond to the many different components of the replicating von Neumann machine. The above being the case, the synthesis of life has little to do with the clever synthesis of just one super molecule which self-replicates and hides the secret of life even though the literature speaks often of a primeval self-reproducing molecule arising. A real synthesis of life will more probably lie in the synthesis and ordering or arranging of the many component parts (i.e. molecules) of the von Neumann machine. By interacting with one another these components will produce the dynamic metabolic machine. Obviously the synthesis of a machine consisting of a multitude of mutually reacting component parts is an entirely different project to that which was formerly envisaged - the synthesis of one large macromolecule. It is for this reason that, although the DNA molecule is vital for biology in that it is life's information storage and retrieval system, yet it itself has to provide somehow the various different molecules with which it can react, as life starts to develop from the zygote. In the synthesis of the cell or the virus it is, then a question, not so much of the synthesis of any single macromolecule (although that will come into the solution of the problem) but the synthesis of a whole hierarchy of interacting molecules, that is, of a dynamically metabolizing, functioning machine." (Wilder-Smith A.E., "The Scientific Alternative to Neo-Darwinian Evolutionary Theory," T.W.F.T. Publishers: Costa Mesa CA, 1987, pp.94-95)

And as Von Neumann showed mathematically in the 1950's before the cell's replication mechanism was known in detail (and even then his was an oversimplification) that a minimum self-replication system (not just the one we have here on Earth but anywhere) is enormously complex (See my The Minimal Cell: A Problem of Evolution 2/2). As Cairns-Smith notes, "Von Neumann himself ... found the origin of life to be utterly perplexing'":

"So please respect the humble bacterium that is playing this game. It can reproduce, it can evolve. E. coli must have some sort of long-term memory about how to make itself that can outlast its substance. That means that an E. coli must be an automatic factory containing something analogous to control tapes and automatic manufacturing equipment. And that is only part of it. All the equipment must be contained, organised, fed. Pieces for it to work on, energy to drive it, must be provided by the E. coli cell. Apart from the manufacturing machinery that can follow instructions, there has also to be another kind of machinery that instead reprints them - something analogous to a Xerox machine or a tape copier. All these things have to be contrived through the manufacturing machinery duly instructed by appropriate bits of the Library tape. It may seem hardly surprising that no one has ever actually made a self-reproducing machine, even though Von Neumann laid down the design principles more than 40 years ago. You can imagine a clanking robot moving around a stock-room of raw components (wire, metal plates, blank tapes and so on) choosing the pieces to make another robot like itself. You can show that there is nothing logically impossible about such an idea: that tomorrow morning there could be two clanking robots in the stock-room... (I leave it as a reader' home project to make the detailed engineering drawings.) There is nothing clanking about E. coli; yet it is such a robot, and it can operate in a stock-room that is furnished with only the simples raw components. Is it any wonder that E. coli's message tape is long? (... about 10 kilometres long.) Is it any wonder that no free-living organisms have been discovered with message tapes below '2 kilometres'? Is it any wonder that Von Neumann himself, and many others, have found the origin of life to be utterly perplexing?'" (Cairns-Smith A.G., "Seven Clues to the Origin of Life: A Scientific Detective Story," Cambridge University Press: Cambridge UK, 1993 reprint, pp.14-15. Emphasis in original).

By the way, the above, "Is it any wonder that no free-living organisms have been discovered with message tapes" (DNA molecules) "below '2 kilometres'" is another way of saying that the minimum DNA molecule for a free-living organism is the equivalent of a 2 kilometre computer paper tape (p.11). So how can non-living chemicals get from zero length to 2 kilometres computer paper tape equivalent before they can even begin self-replication (assuming they also have the tape feeder, tape reader and convertor of the 2-D digital instructions into a 3-D machine, which can then repeat the process)?

AN>Now I want to ask, can't they see that there is a vast sea of conflictions between these two claims? Do they expect that naturalistic methods somehow will be able to explain a magical pathway from self-replicators and RNA to a minimum life form with 1000 genes which is much much more complex than a hypothetical protocell?

It is all decided at the metaphysical level. If 1) naturalism is true (which it isn't); and 2) we are here; then there simply must have been a naturalistic pathway from non-living chemicals to the first living cell. Actually finding that naturalistic pathway is not necessary. The Harvard chemist George Wald expressed this naturalist faith (actually I presume to the convinced naturalist it is more than a faith, it is a necessity - like 2 + 2 = 4 does not require faith):

"Organic molecules therefore form a large and formidable array, endless in variety and of the most bewildering complexity. One cannot think of having organisms without them. This is precisely the trouble, for to understand how organisms originated we must first of all explain how such complicated molecules could come into being. And that is only the beginning. To make an organism requires not only a tremendous variety of these substances, in adequate amounts and proper proportions, but also just the right arrangement of them. Structure here is as important as composition-and what a complication of structure! The most complex machine man has devised-say an electronic brain-is child's play compared with the simplest of living organisms. The especially trying thing is that complexity here involves such small dimensions. It is on the molecular level; it consists of a detailed fitting of molecule to molecule such as no chemist can attempt. ... One has only to contemplate the magnitude of this task to concede that the spontaneous generation of a living organism is impossible. Yet here we are, as a result, I believe, of spontaneous generation." (Wald G., "The origin of life," Scientific American, Vol. 191, No. 2, August 1954, pp.45-53, p.46)

Note that Wald can, because of "the magnitude of this task", "concede that the spontaneous generation of a living organism is impossible." Yet nevertheless he assumes it must have happened because: 1) "here we are"; and 2) naturalism is true.

The latter to Wald is an unquestioned ultimate premise. And as Johnson pointed out, "A system's ultimate premise is always beyond question; that is what it means to say that it is an ultimate premise":

"What Leff said is fascinating, but what he failed to say is more fascinating still. If there is no ultimate evaluator, then there is no real distinction between good and evil. It follows that if evil is nonetheless real, then atheism-i.e., the idea of the nonexistence of that evaluator or standard of evaluation-is not only an extraordinarily unappetizing prospect, it is also fundamentally untrue. Because the reality of evil implies the reality of the evaluator who alone has the authority to establish the standard by which evil can deserve to be damned. When impeccable logic leads to self-contradiction, there must be a faulty premise. In this case the premise is that because God is dead, `it looks as if we are all we have.' Why not reexamine the premise? Why not at least explain why you refuse to reexamine the premise? By not asking that last question, Leff in effect placed the death of God in the place of God. In his system, the absence of a supernatural evaluator was a premise so far beyond question that it could not be doubted even when it pointed to a conclusion Leff desperately wanted to escape, even a conclusion he acknowledged to be false. If we know that totalitarian mass murder is evil, and that those who acquiesced in it deserve damnation, then we know something about that absolute evaluator as well. Leff offered no reason for protecting modernism's founding premise from the brilliant skeptical analysis that he directed at everything else. To a theist this must seem indefensible, but Leff could not have done otherwise without ceasing to be a modernist. A system's ultimate premise is always beyond question; that is what it means to say that it is an ultimate premise." (Johnson P.E., "Nihilism and the End of Law," First Things, Vol. 31, March 1993, pp.19-25. Emphasis original)


Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

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