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Mailing List complex-science@necsi.org Message #9673 | |
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| Hi val, Thanks for your kind remarks. > Sung, > It is always a pleasure to read your very logical comments. > Let's try to place your logic in a "wider" context though. > > (Sungchul Ji) wrote: >> There is no doubt that cells are capable of transmitting information in >> space (e.g.,from the nucleus to the cytosol and to the adjacent cells) >> and in time (e.g., from one cell generation to the next in developing >> organisms or from one population of organisms to next in evolution). >> >> The molecular mechanisms underlying the information transmission in time >> (i.e., through transfer of DNA sequences) has been well established >> throughout the latter half of the 20th century following the discoveries >> of the double helical structure of DNA by Watson and Crick in 1953 and >> the genetic code in the 1960's. But the mechanisms responsible for the >> information transmission through space has not been widely discussed in >> the biological literature, despite the fact that the relevant experiments >> have been vigorously persued, for example, in the fields of cell-cell >> communications and signal transduction pathways in individual cells. >> Consequently, the contemporary concept of genetic information (i.e., >> genes) has been, it seems to me, unjustifiably biased in favor of the >> time dimension at the sacrifice of the spatial dimension. The main >> purpose of this post is to contribute to righting this bias, with the >> hope of defining genes in a more realistic manner for the post-ENCODE >> (Encyclopedia of DNA elements) genomics. > > It seems to me that even within that *highly simplistic* model there > were both temporal *and* spatial components; indeed, the > gene-controlled synthesis of proteins is the *sequence* of events in > time *and* in space - as any synthesis of mol. structures in chemistry. > So, to me, the "information transmission" in chemistry is always a > process in space and in time. I agree that all chemical processes involve changes is space and time of participating material entities. Although not all chemical changes need implicate information transmission, those chemical reactions involved in information transmission (e.g., molecular copying) must have spatial and temporal components. It may be important to specify the temporal and spatial scales when discussing spatiotemporal correlations. As already admitted, even though space and time cannot be separated on the molecular level (i.e., both spatial and temporal changes occur simultaneously at the molecular level), at higher levels of organization such as cells and multicellular organisms, spatial and temporal changes may not occur simultaneously and hence are separable. For example, during the life time of a cell (typically hours and days), the spatial sequence of nucleotides of DNA remains constant but its information can be transmitted in space (ie., from the nucleus to the cell membrane, for example) within a matter of minutes, a time period short relative to the lifetime of the cell. This is what I meant when I said that cells are capable of transmitting information in time and space. Cells use spatial (or equilibrium) structures to transmit information in time and concentration waves (or dissipative structures) to transmit information in space. The reason that dissipative structures cannot transmit information in time is because they have too short lifetimes. >> In 1988 [1] I proposed that there are two types of genetic information >> in >> the cell -- the traditional sequence-centered information >> (referred to as the Watson-Crick form) and the new, dynamic information >> encoded in concentration waves such as ion gradients and time-dependent >> RNA levels in the cell (referred to as the Prigoginian form). The >> Prigoginian form of genetic information (or Prigoginian genes, for >> short) can be identified with "intracellular dissipative structures" >> (IDSs), the final form of gene expression according to the Bhopalator >> model of the cell [2]. In [1] >> I have proposed the following ideas: >> >> 1) Watson-Crick genes => information transmission in time >> 2) Prigoginian genes => information transmission in space, >> >> where "=>" means "is responsible for" or "can mediate". >> >> Examples of information transmission in space and time are familiar to >> us through music and languages:. >> >> 1) Information transmission in time = Sheet music; written >> languages >> 2) Information transmission in space = Audio music; spoken languages >> >> We can summarize all these ideas in a tabular form: >> >> Table 1. The duality of the mechanisms of information transmission >> in linguistics, musicology, and cell biology. >> _____________________________________________________________________ >> >> Information Transmission in >> ____________________________________________________ >> >> Information Space Time >> Carriers >> (or Signs) >> ______________________________________________________________________ >> >> Macroscopic Audio music Sheet music >> Spoken language Written language >> >> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >> >> Microscopic Dissipative structures Equilibrium structures >> (e.g., concentration waves) (e.g., DNA segments) >> >> (Prigoginian genes) (Watson-Crick genes) >> _______________________________________________________________________ >> >> It is interesting to note that the information transmission in space >> utilizes waves of sounds or concentrations, whereas the information in >> space utilizes discrete material objects of either microscopic (e.g., >> DNA >> sequences) or macroscopic (e.g., words, musical notes) dimensions. Thus, >> it appears that the duality of spatial and temporal mechanisms of >> information transfer ultimately depends on the duality of waves and >> particles. Since DNA is a quantum mechanical object, it is not >> surprising >> that it should exhibit both particle and wave properties. >> >> Does anybody on this list know if a similar relation between the >> space-time duality and the wave-particle duality is observed in physics? > > Well, in (quantum) physics, a process, for example, a photo-induced > chemical reaction of dissociation (or association) is always a > spatio-temporal *and* wave-particle (quantum) phenomenon, say, the > dissociation of polar molecules by slow electrons (AB+e-->A+B-). > That the particle-wave duality is exhibited by (bio)chemistry is not surprising, since we are dealing with microscopic objects. But he notion that the concept of spacetime (ie.e., the inseparability of space and time) is also important in (bio)chemistry seems novel. The rationale for the "fusion" of space and time in biochemistry may be found in the following facts: (1) electronic transitions attending chemical reactions may occur with velocities comparable to the speed of light. (2) Although the nuclear rearrangements attending chemical reactions are much slower than electronic transitions (by a factor of 10^3 to 10^6?), they can be coupled to much faster electronic transitions through the Franck-Condon mechanisms. This so-called generalized Franck-Condon principle was formulated in 1991 and used to infer the space-time fusion in biochemistry/metabolism in [S. Ji, Molecular Theories of Cell Life and Death, Rutgers University, New Brunsiwck, N.J., 1991, pp. 49-51]. So it appears that both the wave-particle duality and the spacetime duality applies to biochemistry. The latter possibility was suggested by G. Welch and his student H. A. Smith from an entirely different perspective in the above reference [pp. 282-323]. > As to your introduction of process(P) genes, in addition to > structural(S) ones, well, a gene seems to be an inseparable structure > *and* function - in terms of chemistry and biology. My view is that "function" is not dichotomous with structure (as has been the tradition to assume in biology) but rather triadic in the sense that it requires both structure and process, which idea may be schematically represented as follows: Function (Gene) /\ / \ /____\ Structure Process (S-Gene) (P-Gene) Figure 1. A triadic definition of a gene. So a gene may be viewed as a functional entity, which can be observed either as a structure (e.g., a nucleotide sequence) or process (e.g., uncontrolled proliferation), depending on the experimental procedures employed (reminiscent of the wave-particle duality of light). > So, a gene cannot > be purely S-gene as well as it cannot be purely P-gene. Correct me if > im missing something here. See Figure 1. > > Sung, your analogy with sheet music is indeed nice and instructive, > demonstrating implicitly the critical/creative role of the *interpretive > environment*, the musician/performer. This is an insightful observation. >To me, in a cell, the DNA/genome > is a "dead stuff", a hi-tech punch-card, being (continuously) > *interpreted* by the cellular environment in terms of the > spatio-temporal tune ("protein expression") which is life. [feel free > to correct this speculation] > Although sheet music is "dead stuff" and come to life only when interpreted by a musician, the DNA/genome may be more active (or alive) than sheet music in that it can store free energy (received from topoisomerases and ATP-dependent chromatin remodeling factors, etc) in the form of mechanical deformations (i.e., conformons) and utilize it to expose or bury sets of genes as needed by the cell under a given environmental condition. In fact, I think the DNA/genome may be more like a sheet music, instrument, musician, and the conductor all rolled into one. We may refer to this view of the genome as the SIMC postulate, where S = sheet music, I = (musical) instrument, and C = conductor. With all the best. Sung > spatio-temporal-ly y'rs, val > >> >> With all the best. >> >> Sung >> >> >> Reference: >> >> [1] Ji, S. (1988). Watson-Crick and Prigoginian forms of Genetic >> Information. J. >> theoretical Biology 130:239-245. >> [2] Ji, S. (1985). The Bhopalator--a molecular model of the living >> cell >> based on >> the concepts of conformons and dissipative structures. J. theoret. >> Biol. >> 116:399-426. > > > -------------------------------------------------- > For information about this discussion group visit > http://necsi.org/discuss/discuss.html > |
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