Molecular evolution theories

Molecular evolution theories have been discussed in detail in a number of textbooks e.g., Nei, 1987 Gillespie, 1991 Hartl and Clark, 1997 Graur and Li, 2000 Ridley, 2004). Here we will, therefore, only sketch out the selection theory, the neutral theory and the nearly neutral theory, in order to ask whether they can account for, or at least be compatible with, our observations on the structural and evolutionary genomics of vertebrates. 

The nearly neutral theory of Ohta (1971,1987, 1992) (t ig. l. C) desaibed how the rate ofnwleatlar evolution could vary not only with changes in the mutation rate (as postulated by the neutral theory), hut also through the changing balance between selection and drift . As still phrased by Bromham and Penny (2003), the nearly neutral theory considered three categories of mutations mtnaikmsfar which selection is the predominant force 3  

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These studies raise the same two problems for modern molecular evolution theory that we have already encountered in the chapter 4 discussion of the evolution of the diving response—how to account for conservative and for adaptable traits in the evolution of complex physiological systems. 

Pogliani, L. The evolution of the valence delta in molecular connectivity theory. Internet Electron. J. Mol. Des. 2006, 5, 354-375. 

How can negative fluctuations in entropy production occur or be triggered As Manfred Eigen shows in his evolution theory, fluctuations in entropy production can be caused by the coming into being of a self-replicating molecular species which is capable of selection. Autocatalytically active mutants can also have the same effect. Looked at this way, the phenomenon of evolution consists of a continuous series of instabilities, i.e., collapses of stationary states. 

Kimura, M, (1983) The Neutral Theory of Molecular Evolution (Cambridge Univ. Press, Cambridge, U.K.). 

Gillespie, J. H. (1994). Alternatives to the neutral theory. In Non-Neutral Evolution Theories and Molecular Data. (B. Golding, ed.) pp. 1-17. Chapman Hall, New York. 

The study of chemical reactions requires the definition of simple concepts associated with the properties ofthe system. Topological approaches of bonding, based on the analysis of the gradient field of well-defined local functions, evaluated from any quantum mechanical method are close to chemists intuition and experience and provide method-independent techniques [4-7]. In this work, we have used the concepts developed in the Bonding Evolution Theory [8] (BET, see Appendix B), applied to the Electron Localization Function (ELF, see Appendix A) [9]. This method has been applied successfully to proton transfer mechanism [10,11] as well as isomerization reaction [12]. The latter approach focuses on the evolution of chemical properties by assuming an isomorphism between chemical structures and the molecular graph defined in Appendix C. 

The Bonding Evolution Theory, briefly presented in Appendix B, provides a description of the bonding features of a system, along with their evolution accompanying a reaction path. It relies on the variation of the ELF topological profile as a function of nuclear coordinates. The ELF makes a partition of the molecular space into open sets having a... 

In the previous equation, the sum runs over all critical points of the gradient dynamical system. In the Bonding Evolution Theory, the critical points form the molecular graph. In this graph, they are represented according to the dimension of their unstable manifold. Thus, critical points of / = 0, are associated with a dot, these with I = 1 are associated with a line, these with / = 2 by faces, and finally these with 7=3 by 3D cages. 

A. Greenberg, Stereochemistry and the ether in the evolution of molecular structure theory the musings of a chemist on Moeller s supplanted screw theory , beginning with a view of the obnoxious and equally outdated cod-liver oil , J. Chem. Educ., 1993, 70, 284-286. 

In this chapter, we review important concepts regarding vibrational spectroscopy with the STM. First, the basis of the technique will be introduced, together with some of the most relevant results produced up to date. It will be followed by a short description of experimental issues. The third section introduces theoretical approaches employed to simulate the vibrational excitation and detection processes. The theory provides a molecular-scale view of excitation processes, and can foresee the role of various parameters such as molecular symmetry, adsorption properties, or electronic structure of the adsorbate. Finally, we will describe current approaches to understand quenching dynamics via internal molecular pathways, leading to several kinds of molecular evolution. This has been named single-molecule chemistry. 

The theory to calculate these relationships, particularly in the context of applied molecular evolution, is still sparse. The remainder of this section highlights some potentially very useful concepts and approaches for experiment protocol design. The summary of literature here is by no means complete. 

The theory of molecular evolution and the in vitro evolution experiments suggest practical applications to the design of biopolymer molecules as they were proposed already in the 1980s [4], The basic principles of the so-called irrational design of biomolecules are indeed identical with Darwin s natural law of variation and selection. Molecular properties are improved iteratively in selection cycles in order to achieve an optimal match with the predefined target function. The process is sketched in Fig. 5. Every selection cycle consists of three phases amplification, diversification, and selection. In these experiments, the fitness of genotypes is tantamount to their probability to enter the next selection round. 

One of the problems with DNA is that it is essentially a linear code that stores information. The functional groups (nucleotides) only interact with each other and, while this can lead to the elegant double helix, it limits the ability of DNA to form different secondary and extensive tertiary structures. RNA is rather more amenable to forming other structural motifs, hence the RNA World theory of molecular evolution, but it appears that only proteins with their varied side chains are able to adopt truly complex structures. 

Kimura, M. (1982). Molecular Evolution, Protein Polymorphism, and the Neutral Theory Springer-Verlag, Berlin and Japan Scientific Societies Press, Tokyo. 

More than 30 years of experimentation on the origin of life in the fields of chemical and molecular evolution have led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution. At present all discussions on principal theories and experiments in the field either end in stalemate or in a confession of ignorance.2... 

Publish or perish is a proverb that academicians take seriously. If you do not publish your work for the rest of the community to evaluate, then you have no business in academia (and if you don t already have tenure, you will be banished). But the saying can be applied to theories as well. If a theory claims to be able to explain some phenomenon but does not generate even an attempt at an explanation, then it should be banished. Despite comparing sequences and mathematical modeling, molecular evolution has never addressed the question of how complex structures came to be. In effect, the theory of Darwinian molecular evolution has not published, and so it should perish. 

In addition to mutation rate, even the other molecular parameters turned out to be different from the expectations of selectionism. It was discovered, for example, that neutral mutations are not in the least a tiny minority with respect to adaptive mutations, and the actual ratio is probably the other way round. At the molecular level, in other words, the dominant mechanism of evolution is not natural selection but genetic drift, and this led Motoo Kimura to formulate the neutral theory of molecular evolution (1968, 1983). 

Kimura s theory has not been universally accepted, and the debate between selectionism and neutralism is still going on, but the experimental data have changed for good our view of molecular evolution. Today, biologists are aware that neutral mutations are a fact of life, and that genetic drift is, at the molecular level, at least as important, if not more important, than natural selection. It must also be noticed that this does not diminish in the least the key role of natural selection in phenotypic evolution, and Kimura himself explicitely acknowledged that The basic mechanism of adaptive evolution is without doubt natural selection. He added however that Underneath the remarkable procession of life and indeed deep down... 

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