Biochemical systems, evolution

There are scores of journals devoted to biochemical research. Although JME carries articles concerning molecular evolution exclusively, other journals carry such articles also, mixed in with research on other topics. Perhaps, then, it is a mistake to conclude too much based just on a survey of JME. Perhaps other nonspecialized journals publish research on the origins of complex biochemical systems. To see if JME is simply the wrong place to look, let s take a quick look at a prestigious journal that covers a broad range of biochemical topics the Proceedings of the National Academy of Sciences. 

Gillespie was published in 1991 with the enticing name The Causes of Molecular Evolution. But it does not concern specific biochemical systems. It is, like Kauffmans, a mathematical analysis that leaves out all of the specific features of organisms, reducing them to mathematical symbols and then manipulating the symbols. Nature is blanched. (I should add that, of course, mathematics is an extremely powerful tool. But math is useful to science only when the assumptions the mathematical analysis starts with are true.)... 

The search can be extended, but the results are the same. There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems. 

Many students learn from their textbooks how to view the world through an evolutionary lens. However, they do not learn how Darwinian evolution might have produced any of the remarkably intricate biochemical systems that those texts describe. 

Molecular evolution is not based on scientific authority. There is no publication in the scientific literature—in prestigious journals, specialty journals, or books—that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred. There are assertions that such evolution occurred, but absolutely none are supported by pertinent experiments or calculations. Since no one knows molecular evolution by direct experience, since there is no authority on which to base claims of knowledge, it can truly be said that—like the... 

Incidentally, scientists who believe in God or a reality beyond nature are much more common than popular media stories lead one to believe— there is no reason to think that the figure of 90 percent of the general population that believes in God is much different for scientists. Ken Miller, whose argument from imperfection I analyzed in the last chapter, is like myself a Roman Catholic, and he makes the point in public talks that belief in evolution is quite compatible with his religious views. I agree with him that they are compatible.4 The compatibility or lack of compatibility, however, is irrelevant to the scientific question of whether Darwinian evolution of biochemical systems is true.)... 

One would have hoped that finding proteins with similar sequences would lead to the proposal of models for how complex biochemical systems might have developed. Conversely, the fact that such sequence comparisons do not help us understand the origins of complex biochemical systems weighs heavily against a theory of gradual evolution. 

Darwinian accounts of the evolution of any biochemical system, only a variety of wishful speculations. ... 

Hence, any chemical and biochemical transformations of practical importance occur usually far from thermodynamic equilibrium— that is, far from the region of applicability of the relations of linear nonequflib rium thermodynamics. As a result, thermodynamic analysis of these pro cesses is considerably complicated and usually requires the application of direct kinetic methods for describing the system evolution in terms of differential equations. 

As has been discussed in the introduction, the possibility of a relation between parity violating energy differences and the biochemical homochirality observed on earth has been noted by Yamagata [11] a decade after the discovery of parity violation in nuclear physics. Various different kinetic mechanisms have been proposed which could possibly amplify the tiny energy difference between enantiomeric structures to result in an almost exclusive chiral bias on a time scale relevant for the biochemical evolution. This aspect as well as other hypotheses regarding the origin of the biochemical homochirality have been discussed and reviewed multiple times (see for instance [33,37-39,190-193] and literature cited therein) so that we can concentrate here on the computational aspects of molecular parity violating effects in biochemical systems. 

Volume 29. Comparative biochemistry, molecular evolution I. Comparative biochemistry, (a) Basic concepts, (b) Autotrophic metabolism, (c) Chemical needs in heterotrophs. (rf) Biochemical cycles in the biosphere, (e) Biochemistry and taxonomy. II. Molecular evolution, (a) Molecular adaptations to the physical environment, (b) Molecular adaptations to the biological environment, (c) Heteromor-phic aspects of molecular evolution, (d) Evolution of biochemical systems, physiological radiations, (e) Biosynthesis and phylogeny. (/) Paleobiochemistry. (g) Chemical evolution and prebiological evolution. Subject index. 

Several groups have also made relevant contribution to the evolution of the original PCM. A related model based on conductor-like screening (COSMO) has been developed recently by Klamt and Schuiirmann [13]. Likewise, another approach to the PCM has been proposed in which the cavity surface is determined in terms of an electronic isodensity surface [14]. Olivares del Valle and coworkers [15] have focused their attention on aspects such as the inclusion of correlation effects in the PCM, or on the role of nonadditive effects in solute-solvent interactions. Pascual-Ahuir et al. [16] have paid most attention to the problem of the definition of the cavity surface. The work done in Barcelona has focussed mainly on the parametrization of the PCM to treating aqueous and nonaqueous solvents, as well as the application of the PCM to the study of biochemical systems [17, 18]. Finally, we and others have made new methodological developments to allow the implementation of the PCM in molecular dynamics or in Monte Carlo calculations [19]. 

Harborne J B 1977 Flavonoids and the evolution of the angiosperms. Biochem System Ecol 5 7-22... 

M. Laurent and N. Kellershohn, Multistability A Major Means of differentiation and evolution in biological systems. Trends Biochem Sci. 24(11), 418 422 (1999). 

In the biochemical network, the processing elements do not learn from task examples, but the knowledge is already built in. For example, an enzyme recognizes a specific substrate and applies a specific rate for the catalytic reaction, as a function of the particular conditions, pH, temperature, and so on. Therefore, in such systems, adaptation is implemented by adjusting the catalytic characteristics according to environmental conditions and following laws already built in by evolution. 

From a mathematical point of view, the onset of sustained oscillations generally corresponds to the passage through a Hopf bifurcation point [19] For a critical value of a control parameter, the steady state becomes unstable as a focus. Before the bifurcation point, the system displays damped oscillations and eventually reaches the steady state, which is a stable focus. Beyond the bifurcation point, a stable solution arises in the form of a small-amplitude limit cycle surrounding the unstable steady state [15, 17]. By reason of their stability or regularity, most biological rhythms correspond to oscillations of the limit cycle type rather than to Lotka-Volterra oscillations. Such is the case for the periodic phenomena in biochemical and cellular systems discussed in this chapter. The phase plane analysis of two-variable models indicates that the oscillatory dynamics of neurons also corresponds to the evolution toward a limit cycle [20]. A similar evolution is predicted [21] by models for predator-prey interactions in ecology. 

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