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Author
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Topic: Error Correction Runs Deep
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Mike Gene
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Member # 149
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posted 25. September 2002 23:34
One of the biological universals of Life is proof-reading/error correction mechanisms on several levels. There are three primary nodes of information transfer (replication, transcription, translation) and all three are proof-read. At a deeper level, it appears the genetic code itself (where nucleotide codons represent amino acids) was designed to minimize deleterious mutations. However, a recent study suggests that error correction extends deeper yet, into the very fabric of the DNA molecule.
http://idthink.net/biot/error/index.html
[ 31. July 2003, 08:19: Message edited by: Moderator ]
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«¥» Plump-DJ® «¥»
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Member # 402
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posted 26. September 2002 13:36
I always find delvings into the inner sanctuary of life to be very Telelogical. It almost seems that the deeper you go the stronger the impression of design or teleology seems to get.
And I wonder how Evolution, driven by that immediacy for survival and advantage could ever hope to "come up" with as it were something that mirrors the parity bit used in data communications. Was there a 'non-parity-bit' stage in the evolution of life or maybe even a "half-parity-bit" stage? I personaly can't see how something like this could arise, step by pre-biotic Darwinian step.
-=-=-=-=-
[ 27. September 2002, 07:36: Message edited by: Moderator ]
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warren_bergerson
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Member # 262
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posted 27. September 2002 11:17
Mike,
Quote: In trying to understand the origin of the parity-code, Mac Donaill writes, "The critical question is whether the parity-code structure is accidental, or shaped by selection through evolutionary advantage." It is understandable that non-teleologists would frame this question in a binary fashion - chance or selection. But teleologists have a third option. That is, while they can agree with the selectionists that chance is not a good explanation, they propose an intelligent designer rather than the blind watchmaker.
In addition to looking at the ‘source’ or cause of error correction, it is also interesting to look at the result or effect of error correction on the processes of evolutionary change. Error correction is an example of what I call ‘selection acting directly on genes’. Many potential alleles or mutations are in effect selected out before they have any opportunity to produce any phenotype effects.
The simplest interpretation of error correction, is that it has the effect of reducing mutation rates. In the extreme case, completely efficient error correction would eliminate the effect of mutation. As should be obvious, with no source of diversity, evolutionary change could not occur.
Even incomplete or partial error correction can significantly slow down both mutation rates, and reduce the number of different ‘random mutations’ which are generated. If one assumes, as suggested that RM&NS, 1)that genetic change is the result of the interaction of natural or phenotype selection, and ‘net mutation rates’, and 2)that all genotype selection is error correction, then using techniques discussed in ‘selection acting directly on genes’, I believe, you can measure/estimate the speed, cost in lives, and the complexity/volume of genetic change produced by a genome.
I believe, (I haven’t actually done the calculations) that, adjusted for error correction and genetic selection, a biological systems using ‘Darwinian evolutionary processes’ would have a very limited, but measurable capacity to evolve.
Parity codes and other error correction mechanisms are powerful brakes applied to evolutionary change processes. Whether these brakes arose by chance, selection or external intervention, the existence of these brakes suggests that there must also exist some as yet unidentified gas pedal.
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Frances
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Member # 169
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posted 27. September 2002 12:42
If as you seem to suggest error correction is part of GSH and if error correction reduces evolution then it seems that it's not Darwinian mechanisms but GSH that suffers from problems explaining the facts of evolution.
Btw intelligent design is not a hypothesis limited to ID, in fact it could equally well be proposed and is sometimes proposed by scientists.
Thus ID perse is nothing new in science and in limited form ID can be quite succesful in some sciences. Things get more complicated if regularity hypotheses need to be considered in addition to chance.
[ 27. September 2002, 13:00: Message edited by: Frances ]
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Mike Gene
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Member # 149
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posted 02. October 2002 21:43
Hi DJ,
I do agree that the deeper you go, the stronger the impression of design or teleology seems to get. This is the primary thing that fuels my ID hunches. For it didn't have to turn out this way. On the other hand, maybe it did. Suffice it to say that non-teleologists did not anticipate such Deep Teleology. Check out how Science reports on this new finding - "The Genome Chose Its Alphabet With Care." The article quotes another scientist:
quote:
Mac Donaill's clever analysis shows how well different nucleotides could serve as matches in DNA and how much different pairs differ from each other. This analysis gives us reason to believe that the A-T and G-C choice forms the best pairs that are the most different from each other, so that their ubiquitous use in living things represents an efficient and successful choice rather than an accident of evolution.
The genetic code is not the "frozen accident" non-teleologists originally thought it to be. It was "chosen." Now, the use of A,G,C,and T is apparently not the "accident" non-teleologists originally thought it to be. It too was "chosen."
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yersinia
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Member # 324
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posted 02. October 2002 21:58
Mike writes,
quote:
The genetic code is not the "frozen accident" non-teleologists originally thought it to be. It was "chosen." Now, the use of A,G,C,and T is apparently not the "accident" non-teleologists originally thought it to be. It too was "chosen."
But then again...
quote:
Nat Rev Mol Cell Biol 2001 Feb;2(2):147-51
Confounded cytosine! Tinkering and the evolution of DNA.
Poole A, Penny D, Sjoberg BM.
Institute of Molecular BioSciences, PO Box 11222, Massey University, Palmerston North, New Zealand. a.m.poole@massey.ac.nz
Early in the history of DNA, thymine replaced uracil, thus solving a short-term problem for storing genetic information--mutation of cytosine to uracil through deamination. Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer. By keeping cytosine and replacing uracil the problem was never eliminated, returning once again with the advent of DNA methylation.
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Mike Gene
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posted 04. October 2002 23:04
Thanks for the cite, Nic. Scratch a little deeper than Poole et al. and these dynamics complement each other. More later....
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Janitor@MIT
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Member # 125
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posted 08. October 2002 10:49
In the design theory literature a self-correcting encoder-decoder is sometimes modeled as an observer-controller pair and the simple conception of a code as an information storage device becomes trivial. A code now becomes a sophisticated algorithm for controlling a process, e.g., by recognizing a pattern and inducing a path…
I noticed that the IDers are fretting over a research program: One of the outstanding problems, if not the most outstanding problem, in evolutionary biology is decoding the code. Until we’ve done that any confident statements about the process of evolution are going to be ridiculously premature. But this is going to be a difficult task, as any sufficiently advanced communications and control technology will appear to be “magic.” (LOL)
The IDers should have a “conceptual” advantage here, not being possessed of the “cargo cult” view of the design of life that prevails in evolutionary biology. (Sorry, Mr. Moderator, that was a shot, I know.) I think that even if their research program focused solely on the code they could be productively occupied for quite some time, with the very real possibility of making some fundamental contributions to biology.
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Mike Gene
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Member # 149
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posted 09. October 2002 06:58
Janitor: I noticed that the IDers are fretting over a research program: One of the outstanding problems, if not the most outstanding problem, in evolutionary biology is decoding the code. Until we’ve done that any confident statements about the process of evolution are going to be ridiculously premature.
I agree (although fretting over a research program doesn't really apply to me). As it stands today, evolution is still largely a black box. Take the well-documented reptile-to-mammal transition. We may know that it happened, but we have very little understanding of how it happened. The Darwinian "mechanism" offers only a vague heuristic perspective - something happened in some environment to increase the relative fitness of some vague,pre-mammal-like organisms. While such happenings may have been involved in such evolution, there is no reason to think they alone were the driving force. What were the molecular changes driving this evolution? How did they actually come about?
Deeply embedded in the non-teleological approach is an appeal to things that "just happen." In the case of such evolutionary explanations, we ultimately pose mutations that "just happen" in situations the organisms just happen to be. What should be encouraging to teleologists is the way these "just happen" explanations are being abandoned. The genetic code as a "frozen accident?" Nope, there is a design behind it. The choice of A,G,C, and T as an accident? Nope, there is a design behind it. The use of a particular nitrogenous base (cytosine) prone to deamination that just happens to spawn the other pyrimidine member of the parity code (thymine/uracil) is an accident overlooked by a myopic tinkerer? Hmmm. Sounds like a juicy TeleoLogic essay in the making. ![[Wink]](wink.gif)
[ 09. October 2002, 06:59: Message edited by: Mike Gene ]
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Janitor@MIT
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Member # 125
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posted 10. October 2002 13:29
If you’re interested, http://www.isi.ee.ethz.ch/publications/massey_cd/dir/pdf.html is a good resource. But sometimes you pay for an antiquarians interest in the origin and development of ideas so, Beware! Time-outs on excruciatingly slow scans of some of these older papers. David Forney, J. M. Schumacher, Joachim Rosenthal, Eric York, and a host of others have worked on this. See also Furhman’s http://www.nd.edu/~mtns/papers/18022_2.pdf (With apologies for the arcana of descriptor systems. Imagine what its like for me to read evolutionary biology! LOL)
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Mike Gene
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Member # 149
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posted 12. November 2002 00:33
Rarely do I get the chance to post a new essay that addresses so many issues simultaneously:
1. Would an engineer really preclude cytosine as Nic's citation asserts?
2. What might be a "gas pedal" behind evolution, as implied by Warren?
3. How about a few baby steps toward the "code" Janitor speaks of?
4. Another example where ID can guide research.
5. "Proponents" of MDT have been reluctant to apply their notions to the biological problem posed by cytosine. Features that might appear to indicate multiple designers at first glance make more sense when seen in the larger context of SDT.
http://idthink.net/biot/deam/index.html
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nobody
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Member # 145
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posted 12. November 2002 01:45
Janitor@MIT says:
quote:
One of the outstanding problems, if not the most outstanding problem, in evolutionary biology is decoding the code.
That will probably take years. Decoding what I call "God's software" will be very difficult indeed. However even that might not give us the complete picture. We need to somehow understand how all the interactions of life work. That seems to me to involve more than just breaking the code. I think this is what IBM is attempting to do with their reverse engineering project:
"The list of genes and proteins of an organism, however, constitute only the ground zero in a pyramid of biological complexity, whose top is life itself. This pyramid is a metaphor for the hierarchy of structures out of which biological function (such as metabolism or replication) arises. Elements at each level in this hierarchy interact with each other to produce a higher level of organization, thus climbing up one step in the pyramid of bio-complexity. It follows that the information of all the genome and all the proteome (which is roughly where we stand now) is insufficient to understand the subtleties of biological function. In order to get a handle to function we need to understand how the building blocks at a given level of organization interact with each other: how proteins interact with both genes and proteins to produce molecular circuits; how these circuits interact with each other to allow for cellular function; how cells interact to produce tissues; how tissues form organs; and finally how organs work together to create a living being."
http://www.research.ibm.com/FunGen/
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nobody
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Member # 145
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posted 12. November 2002 02:01
From the end of Mike's very interesting article:
quote:
One thing seems clear. Very early on, life became obsessed with error correction. The chemistry of DNA/RNA, the Genetic Code, and the proof-reading mechanisms behind information transfer are all biological universals. Apparently, one of the first "objectives" of evolution was to put a layer of constraints on evolution.
I have read somewhere that the error correction of DNA is superior to human programming. I'm sorry, but I can't locate the link right now.
A question for Mike:
How many generations of life, for even a "simple" life form, do you think would be possible without error correction?
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Mike Gene
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posted 12. November 2002 08:52
Hi nobody,
How many generations of life, for even a "simple" life form, do you think would be possible without error correction?
Who knows? No one has ever done such a simple experiment because there are no such "simple" life forms to experiment with. The fact that many layers of error correction are biological universals raises the possibility that life, without error correction, either cannot exist or cannot exist very long. But I think error correction goes deeper than this.
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Art
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Member # 179
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posted 12. November 2002 21:46
About error correction and life - I wonder what sorts of error correction mechanisms these living things have.
About MDT and error correction/the cytosine "problem": Off the top of my head, I think that the ideas regarding these subjects do not apply to the RNA World. This would seem to me to be a fertile subject for exploration vis-a-vis MDT, and a likely place where SDT would be less tenable a model than MDT. For example, the "need" of error correction, the multitude of ways that "errors" are avoided, the limited applicability of the parity code concept to mutifunctional RNAs (along with the myriad ways by which the parity is broken) all point to a pretty different mode of design, an entirely different "personality".
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