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Author
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Topic: Self-Disclosive Design (SDD) as an ID Research Program
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charlie d.
Member
Member # 159
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posted 12. April 2002 20:01
Hi David:
thanks for posting this. I am still having problems understanding the essence of your findings at a biological level (unfortunately, the original sources are not readily available in my med school library, but I will have a better chance to look on monday. If anything is available online, let us know).
From your ref #1, you seem to discuss finding structural information from tRNA and rRNA sequences, which of course is expected for such molecules (as opposed to proteins). I imagine this is a more of a description of the function of the basic algorithm.
#2 and #3 are less clear: what kind of higher-order information is it that you are using for groupings, and how does it relate to protein structure? What is your hypothesis as per the functional significance of these higher-order groupings?
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YZ2
Member
Member # 91
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posted 22. April 2002 14:35
Some clarifications are needed, because some previous discussion may sidetrack your thinking:
In reference 1: Tertiary bondings are found from the primary sequences alone, without any other inputs. My algorithm is based on statistical interdependency between sites from different species, that is, the tertiary bondings (of course secondary bondings as well) are reflected as common attributes of the different species (and from multiple sites), and cannot be generated from the primary sequence of one single species alone in my algorithm. If this is so, then I call this a higher-order formation, because the secondary and tertiary bondings are formed from sequences of multiple diverse species. Of course, these are tRNA and rRNA and not proteins. I do not know whether similar algorithm can be designed and worked on proteins, neither an algorithm that infer secondary and tertiary structure from a single sequence without additional inputs. (From your posting, you appear to say that it cannot be done.) In any case, the conclusion is the same. That is, there is a close relationship (or what I previously called unity) between sequence and molecular structure and can be discovered if we work hard enough.
For reference 2, I am not sure I understand your question. I did not use any high-order information to generate the groupings. The groupings emerge from sequences of different species and from multiple statistical evidences (based on the primary sequences alone). Since groupings are formed from multiple sequence characteristics alone and this is the most natural way without any other inputs or assumptions, I call these inherent groupings from the sequences. The formation is thus a higher-order formation. That is, high-order formation is formed due to these multiple sequence characteristics and cannot be inferred from a single characteristic, or from a single sequence.
What does it mean to biology? I think understanding how biomolecules are formed is a basic research problem in biology. It is more relevant if there are close relationships between sequences, molecular structure, taxonomy and biological functions, and less so if there are no relationships. That is, if biomolecules are fairly random, then there isn't much value in studying them. Are these points new? Probably not. It just turns out that evolutionary interpretations did not focus on the unity of biomolecules.
I did not deal with the relationships between RNA and proteins, and have no comment on this topic. Hope that this clarifies what I mean by higher-order formation and some of your questions.
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YZ2
Member
Member # 91
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posted 24. April 2002 11:24
Some qualifications for my previous posts:
1) I am not a theorist, ID or Darwinian, even though I do theorize when drawing conclusions. I consider myself more an 'empiricist'. That is, my approach is data-driven, rather than model-driven. It suits me well in my research area of bioinformatics.
2) In my previous comments, they indicate my current experimental results can be explained better using the design approach. That is, the design explanation carries fewer restrictions in explaining the data. Design explanation to me, involves investigating how design works and what factors determining the design. It does not require explanation of the source. In particular, it is usually not necessary to impose additional time-dependent factors on statically-oriented data.
3)Should the data-driven rather than the model-driven approach be used in education in biology? I leave this important subject for others to explore.
[ 13. June 2003, 10:45: Message edited by: YZ2 ]
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