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Author
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Topic: Error Correction Runs Deep
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Janitor@MIT
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Member # 125
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posted 13. December 2002 11:06
Now, I may be wrong, and I think there is room for accommodating a more traditional evolutionary perspective wrt uracil, but it was Darwin who insisted that such variations must be demonstrably beneficial, must somehow be “improvements.” Usually we have measured “benefit” in terms of a relative growth rate, and although this makes sense and seems to be a necessary corollary of Darwin’s idea, Gould (Wlliams and independently Pittendrigh also) has argued that Darwin, ironically enough, was really invoking a naïve design criteria of “benefit” or “improvement.” (And has pointed out some problems with the “growth rate” measure of evolution.) Uracil should therefore represent a “better design” over whatever it is that it replaces.
Improvements are no doubt important from a design perspective, but there is also a general and purely heuristic principle of design sufficiency or realizability and verifiability that introduces some level of arbitrariness into the selection of materials, etc. Any changes that are made to the design are hopefully not detrimental, but also don’t have to be improvements. (Also the concept of abstraction or seperability comes into play here.)
Engineers (and biologists) recognize that atoms and molecules are the ultimate “smart materials,” but we still design and build with comparatively simple bulk materials. This is because atoms and molecules are smart indeed, smarter than we are—we simply don’t know enough about their properties, especially in combination, to make effective use of them in design. (There are also technical limits to what we can do, unrelated directly to what we know about the materials themselves.)
Accordingly, we do something very interesting in designing a protein to hit a target, a drug, e.g. We employ evolutionary techniques to test many possible combinations/configurations, filtering out those combinations that are comparatively less effective for whatever object we have in mind. Obviously, atoms and molecules are ideal for such an approach. But notice that in doing this, improving an existing drug (or function) may be our object, but in inventing it is not. All that is required ab initio is that whatever we design-evolve is sufficient for our purposes, not that it be the “best.” (Over-designing and over-provisioning, etc. are natural tendencies to be avoided, and it often takes designers some time to learn this.) Later, if there is any impetus for improvement, or increased benefit, we find that the same evolutionary techniques are effective as well, but with refinements on the very process.
(You may have noticed that I’ve made this “refining” an important point: If evolution is conceived as an optimization process then there is reason to believe that there is every “natural impetus” for improving and refining the process of optimization itself. That is to say, the evolutionary process will evolve to “progressively” eliminate its less than optimal aspects. E.g., as in error-correction, it will in some sense systematically reduce the “randomness,” to tolerable (Manageable? Optimal?) levels, which is, of course, exactly what we do, quite intelligently I might add, when we “evolve” something. Which is just to make substantive and predictive what is usually offered as apologetic only: Evolution evolves. Ironic, isn’t it? Purely on a priori design principles I’ve predicted what evolution should look like. I keep forgetting that design has nothing, no insights, theories, predictions, or tests to offer.)
This is not to say that there is not some intrinsically “optimal” functional reason or logic for the selection of uracil. The fact that its usage is universal in this context is telling even from a “non-teleological” perspective.
However, that something “just happened” or is a “frozen accident” is the opposite of a scientific explanation in this context and is to be rejected on principle. These "accidentalist theories” are our last resort, when we’ve exhausted all other possibilities that we can imagine to test. They are not the first theory that we propose, but the last. How can you even test such ideas! Its absurd—anything can be “explained” this way!
Mike Gene’s teleological program is very interesting and recognizes a simple principle of design that is recognized implicitly by biologists: By the “proper” selection and combination of basic materials we can imbue designs with some amazing properties, as I’ve suggested, we can introduce a significant bias into a search or exploratory program, such as DNA. Hey, I can BS, uh, I mean, “brainstorm”…
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Mike Gene
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Member # 149
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posted 14. December 2002 12:11
Improvements are no doubt important from a design perspective, but there is also a general and purely heuristic principle of design sufficiency or realizability and verifiability that introduces some level of arbitrariness into the selection of materials, etc. Any changes that are made to the design are hopefully not detrimental, but also don’t have to be improvements. (Also the concept of abstraction or seperability comes into play here.)
I think that's an important point to keep in mind. The original question, "Why C?" was a more serious challenge to my ID hypothesis, as the high rates of deamination appear to contradict the error correction schemes that suggest some form of teleological explanation. The question, "Why U?" is not really a challenge, but an expression of curiosity. In other words, there was a problem with C, but no real problem with U.
Nevertheless, there do seem to be some potentially good "design reasons" for choosing U (as explained above). I found a link that better explains what I was discussing above:
Researchers unlock secret of RNA's versatility
It is thus interesting to note that hydrophobic amino acids and uracil both play "special" roles in structure formation and cytosine deamination can thus access both.
[ 14. December 2002, 12:13: Message edited by: Mike Gene ]
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Mike Gene
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Member # 149
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posted 17. December 2002 13:29
I think I'll close this thread out simply be restating what I stated near the beginning:
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
More good stuff to come....
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warren_bergerson
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Member # 262
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posted 18. December 2002 09:19
Mike,
Quote: 2. What might be a "gas pedal" behind evolution, as implied by Warren?
I believe your question relates to my comment that error correction provides a clear example of selection other than Darwinian Natural Selection. Error correction is an example of selection operating directing on a secondary form of variance (Natural Selection is assumed to act on the existence and reproduction of the entire organism.) If you assume as I do that 1)evolution is a by-product of biological information processing and that 2)biological information processing involves cyclical interactions between variation and selection (as I have discussed elsewhere, actually defining and modeling biological information processing involves cyclical interactions of more than two type of processes) then 3)the existence of non-Darwinian selection suggests that evolution can involve more than one selection occurrence and thus more than one cycle of information processing per life-time.
My model of evolutionary change suggests that evolution is the by-product of very, very large numbers of variation-selection cycles per life time. We can use the ‘assembly instruction’ or ‘design instruction concept’ to develop a rough estimate of the number of variation-selection cycles which need to occur during a lifetime for an organism to adaptive and to survive and reproduce.
Let us assume that 1)an organism contains 1 trillion cells, 2)that each cell during its life time generates 1 million assembly instructions 3)that each assembly instruction is 1 of 10 possible instructions, and 4)that 1 per thousand of the assembly instructions has to be modified during the organisms lifetime in order to be compatible with changing environmental conditions. Assuming the search for new assembly instructions is efficient, the number of cycles required would be something like (.001 *(1 trillion)*(1 million)*.5).
This is a number significantly greater than 1 per life time.
To answer your question, the ‘gas pedal(s)’ behind evolution in my model are changes in environmental conditions or changes in the adaptive landscape. Changes in the adaptive landscape change the ‘teleological or adaptive form of assembly instructions’. In order to survive, the organism must have the ability modify, adapt or evolve new ‘teleological’ assembly instructions compatible with the changed adaptive landscape.
The Darwinian/genetic model of evolution ‘assumes’ that the observed similarities between parent and offspring are the result of inheritance. Although dogmatically committed to this assumption, they have only mystical hand waving descriptions of how the inherited genes translate into a adaptive and adapting organism. In addition, they invoke mathematically impossible explanations of how the inherited code can change in order to change the organism.
My information processing model suggests that evolution and biological design are the results of very powerful biological information processing mechanisms. My model suggests that the ‘base-line’ expectation is for very rapid divergence from parent to offspring and for very rapid loss of species identity. The existence of groups or species with similar characteristics, and the appearance of heritability from parent to offspring, my model suggests, are the result of powerful stabilizing forces operating against powerful forces of divergence.
My model, it will be noted, provides a testable, materialistic explanation of how biological systems are capable of generating incredibly complex designs and design changes in very short periods of time. The gas pedal in my model is changes in the adaptive landscape. The changes in adaptive landscape requiring changes in teleological assembly instructions are assumed to occur ‘trillions’ of times per lifetime rather once or twice every 100,000 years.
Thanks for asking.
Warren
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Frances
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Member # 169
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posted 18. December 2002 12:46
Warren
quote:
The Darwinian/genetic model of evolution ‘assumes’ that the observed similarities between parent and offspring are the result of inheritance. Although dogmatically committed to this assumption, they have only mystical hand waving descriptions of how the inherited genes translate into a adaptive and adapting organism. In addition, they invoke mathematically impossible explanations of how the inherited code can change in order to change the organism.
Perhaps Warren could give some evidence to support his claims about hand waving, mathematically impossible explanations? So far we see a lot of wishful thinking on his part. May I be so bold as to ask for some supporting evidence for his claims?
I am asking because I believe that science has dealt quite well with his objections but I will give Warren the benefit of the doubt.
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