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Author
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Topic: IC Chains, or back-to-back IC
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Mike Gene
Member
Member # 149
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posted 01. March 2002 23:37
Hi Jack,Interesting idea. But I don't think we can assume a "factory" is required for the synthesis of molecular machines. Most molecular machines are built from proteins and protein complexes can "self-assemble." The interactions between two or more protein chains are really no different than those that take place within any particular chain, apart from the consideration that two independent chains must find each other. However, your insight is interesting in that the synthesis of at least some molecular machines need help beyond the amino acid sequences of their components. Take the flagellum again. Its synthesis requires an orderly expression and presentation of the gene products, along with various chaperones that work only to synthesize the flagellum (thus, having no other known function). Another more intriguing example may involve nitrogenase, an ancient protein complex that fixes atmospheric nitrogen. In this case, a rather complex co-factor is synthesized on a protein scaffold that has very similar structure to nitrogenase and the scaffold is useless for other purposes. Then, with help from another protein, the co-factor is transported from the scaffold to nitrogenase so that it is now activated to work. [ 01 March 2002: Message edited by: Mike Gene ]
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James A. Barham
Member
Member # 50
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posted 18. March 2002 23:24
Jack:
On the thread dealing with the machine analogy for organisms, Jules suggested I contact you for more information about a theory called EAM (endogenous adaptive mutagenesis, I believe).
I have not heard this term used before, but it sounds intriguing and I would like to learn more about the idea---especially any bibliographical guidance you could provide would be welcome.
Jules seems to think that you support this idea, which sounds close to the sort of self-organization I have been developing. However, in your above comments on this thread, you seem to be supporting more the standard ID view that organisms are indeed machines, so perhaps Jules was mistaken (or I misunderstood him).
In reply to your posting above, I would very briefly say that you are absolutely right---the concept of a machine implies both an intelligent designer and a physical modality (a "factory") by means of which the parts can be assembled. From which I conclude that organisms cannot be machines.
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Jack Foster
Member
Member # 79
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posted 19. March 2002 17:29
Hi James:
Jules seems to think that you support this idea, which sounds close to the sort of self-organization I have been developing. However, in your above comments on this thread, you seem to be supporting more the standard ID view that organisms are indeed machines, so perhaps Jules was mistaken (or I misunderstood him).
I am open-minded and even sympathetic to the idea, but I’m not exactly a supporter. I think adaptive mutagenesis in e-coli is remarkable. To the extent that I understand it, what we see can be interpreted as an implementation of a search strategy. Still, I believe I am more of a Darwinian at this point than a Lamarkian regarding the phenomenon; feedback from the environment appears to be in the form of Darwinian selection.
I won’t quibble with you about whether biological molecular machines are truly machines or not. Suffice it to say that biological machines and man-made machines share some characteristics.
I’ve enjoyed your contributions to the site! They provoke thought.
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Janitor@MIT
Member
Member # 125
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posted 19. March 2002 18:24
But, Jack Foster, what if its neither?--Darwinian nor Lamarckian.
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Jack Foster
Member
Member # 79
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posted 19. March 2002 21:33
Hi Janitor (Rock? Is that you??)
janitor: But, Jack Foster, what if its neither?--Darwinian nor Lamarckian.
(Oh, I miss my jazzraptor handle already!)
(I presume the moderator will provide some leeway to the off-topic post rule for otherwise dead threads, especially when thread sponsor approves and partakes!)
In this case, janitor, of what alternatives do you speak?
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Janitor@MIT
Member
Member # 125
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posted 20. March 2002 15:47
Small world, huh, jazz? Presuming upon the indulgence of Mr. Moderator: I’ve just noticed a few things about the “design” of the code. E.g., how a highly degenerate code forces searches of neutral landscapes. (Which challenges the presumptions of a considerable body of research.) Or how the “design” of the code limits “revisiting” (“forward” mutations occurring 4X’s the rate of “back” mutations), which is (coincidentally?) an implementation detail for all genetic algorithms, distinguishing them from random searches. And how error-proofing of the genome represents a more significant negative control on evolution than natural selection (since only unproofed “errors” can be “selected”). So what I’ve done is, simply by pointing out these obvious and well-known features, to argue that a significant control over evolution exists in the genome at the most fundamental level possible, in the very design of the code itself. (This doesn’t even begin to enumerate the controls that exist!) A code whose “design” is not well accounted for on received theory. My approach is simply to take literally the code/program metaphor, and take metaphorically the RM&NS literalism (theomorphism?). Theorists are not inclined to posit any meaningful level control over evolution in the genome. And what “controls” or constraints exist over evolution is a long-standing dispute within the community. As I’ve described received theory, evolution is not something living things do, its something that happens to them. But isn’t it interesting that fixed-length code words, degeneracy, complimentarity, etc. evolved almost as if effective evolutionary searches were the “end” in mind? Or as you’ve wondered, how things have evolved so that evolution is possible. It’s the same “chicken and egg” question you asked. If an effective evolutionary search strategy (as implemented in the design of the code) can evolve from an ineffective one (presumably less effective codes), then another question occurs: Even if life began to evolve in a Darwinian mode than what is there to stop it from evolving out of that mode and into a more effective mode? I might even consider this the only true prediction that can be made from Darwin’s theory: the theory eats itself in the process of optimizing evolution. As life is optimized evolution is optimized! It ceases to be Darwinian. But once again, I am taking literally, optimization, what theorists only intend metaphorically. These metaphors taken to their logical conclusions become a bit of an embarrassment. I don’t think the traditionalists can fault me for seeing it this way, since they rely on four billion years of remarkable coincidences to account for the evolution of life. You could say that I’ve simply speculated that one of those “coincidences” was the “discovery” of more effective modes of evolution! (Even though they say the theory of evolution “evolves,” they never mean that evolution itself evolves. So the statement is really self-contradictory. Evolution itself is one of those “IC” systems that evolutionary theory presumes as given and can’t evolve! LOL My “hypothetical” scenario can only be precluded arbitrarily: “Evolution itself can’t evolve!” In the same way that Behe’s flagellum can’t evolve! Does Behe have a flagellum?! But now I’m just entertaining myself.) But I have to give the IDers their due. Since I can’t account for the evolution of the code itself, so marvelously “evolved for evolvability,” I can’t on any material, scientific, philosophical, or logical grounds reject their basic proposition.
You could say that well-designed “machines” (a code-program here) enables efficient manufacture of other machines. A basic presumption of Altenberg and Wagner above, and a blatant attempt to make any of this relevant to the topic.
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