Ontogeny and phylogeny in the evolutionary biochemistry space

The process of evolution is considered as the change of nucleotide sequence in an (N+1)-dimensional or 3-dimensional space. Restricting conditions may be represented by the shape of a tunnel, through which points or a rope representing nucleic acids move along with time, and may be similar for ontogenetic and phylogenetic development.     

Ontogeny and phylogeny in the evolutionary biochemistry space

The process of evolution is considered as the change of nucleotide sequence in an (N+1)-dimensional or 3-dimensional space. Restricting conditions may be represented by the shape of a tunnel, through which points or a rope representing nucleic acids move along with time, and may be similar for ontogenetic and phylogenetic development.     

Methodological problems in evolutionary biology

One of the major criticisms of optimal foraging theory (OFT) is that it is not testable. In discussions of this criticism opposing parties have confused methodological concepts and used meaningless biological concepts. In this paper we discuss such misunderstandings and show that OFr has an empirically testable, and even well-confirmed, general core theory. One of our main conclusions is that specific model testing should not be aimed at proving optimality, but rather at identifying the context in which certain types of behaviour are optimal. To do this, it is necessary to be aware of the assumptions made in testing a model. The assumptions that are explicitly stated in the literature up to now do not completely cover the actual assumptions made in testing OFT models in practice. We present a more comprehensive set of assumptions. Although all the assumptions play a role in testing models, they are not of equal status. Crucial assumptions concern constraints and the relation between fitness and currency. Therefore, it is essential to make such assumptions testable in practice. We show that a more explicit relationship between OFT modelling and evolutionary theory can help with this. Specifically, phylogeny reconstruction and population dynamic modelling can and should be used to formulate assumptions concerning constraints and currencies.     

Solving chemical problems through the application of evolutionary principles

Molecular evolution has been widely applied in the laboratory to generate novel biological macromolecules. The principles underlying evolution have more recently been used to address problems in the chemical sciences, including the discovery of functional synthetic small molecules, catalysts, materials and new chemical reactions. The application of these principles in dynamic combinatorial chemistry and in efforts involving small molecule-nucleic acid conjugates has facilitated the evaluation of large numbers of candidate structures or reactions for desired characteristics. These early efforts suggest the promise of pairing evolutionary approaches with synthetic chemistry.     

Some problems in the usage of Gibbs free energy in biochemistry

The usage of Gibbs free energy (G) in biochemistry is examined critically. The textbook formulation of the Second Law of Thermodynamics as applied to chemically-reacting systems is reviewed. Cognizance of the established theory and terminology of chemical thermodynamics leads to the conclusion that the symbol "delta G", as used in most biochemical calculations of free-energy change (e.g. in freeze-clamp study of steady-state metabolic processes), is erroneous. The instantaneous change, symbolized by the expression (delta G/delta xi) (with xi the degree of advancement of the reaction), is seen to be the correct form for describing the thermodynamic quality of the reactions of cell metabolism. Mathematical and graphical analysis of a sample reaction demonstrates the fundamental difference between delta G and (delta G/delta xi). Some problems in the application and interpretation of free-energy change in biochemical systems are reviewed: (1) Advances in protein dynamics have revealed the free-energy linkage properties of the enzyme molecule in binding/catalytic events of catalysis, demanding that we view the thermodynamics of elementary enzyme reactions with a finer eye. (2) The reality of metabolic microenvironments in vivo leads to equivocation in the significance of free-energy changes measured under macroscopic conditions in vitro. (3) The physicochemical character of reaction dynamics in the living cell may in some cases exceed the domain of validity of such thermodynamic state functions as Gibbs free energy.     

Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective

The evolution of new genes to make novel secondary compounds in plants is an ongoing process and might account for most of the differences in gene function among plant genomes. Although there are many substrates and products in plant secondary metabolism, there are only a few types of reactions. Repeated evolution is a special form of convergent evolution in which new enzymes with the same function evolve independently in separate plant lineages from a shared pool of related enzymes with similar but not identical functions. This appears to be common in secondary metabolism and might confound the assignment of gene function based on sequence information alone.     

Methodological problems in evolutionary biology VI. The force of evolutionary epistemology

Evolutionary epistemology takes various forms. As a philosophical discipline, it may use analogies by borrowing concepts from evolutionary biology to establish new foundations. This is not a very successful enterprise because the analogies involved are so weak that they hardly have explanatory force. It may also veil itself with the garbs of biology. Proponents of this strategy have only produced irrelevant theories by transforming epistemology's concepts beyond recognition. Sensible theories about knowledge and biology should presuppose that various long-standing problems concerning relations between the mental and the physical are solved. Such problems are wrongly disregarded by evolutionary epistemologists.     

SNP-detecting DNA technologies: Solving problems of applied biochemistry

The heterozygosity of CANP3, ACTN3, and GHR genes in specialized collections was studied using state-of-the-art DNA technologies for DNA analysis. A new dinucleotide deletion (AC) at the beginning of exon 21 was identified in five individuals with a heterozygous CANP3 gene. Analysis of polymorphism (1747 C T) of the ACTN3 gene demonstrated a positive association of allele C with high muscular performance. Real-time PCR assay of SNP1630 (A C) in the GHR gene suggested a putative negative association of allele C of this SNP with high muscular performance.__________Translated from Prikladnaya Biokhimiya i Mikrobiologiya, Vol. 41, No. 3, 2005, pp. 303–307.Original Russian Text Copyright © 2005 by Krakhmaleva, Shishkin, Shakhovskaya, Stolyarova, Plugov, Knyazev, Khomenkov, Shevelev, Chernov.     

NP-detecting DNA technologies: solving problems of applied biochemistry

Heterozygosity of CANP3, ACTN3, and GHR genes in specialized collections was studied using state-of-the-art DNA technologies for DNA analysis. A new dinucleotide deletion (AC) at the beginning of exon 21 was identified in five individuals with heterozygous CANP3 gene. Analysis of polymorphism (SNP1747 C-->T) of ACTN3 gene demonstrated a positive association of allele C with a high muscular performance. Real-time PCR assay of SNP1630 (A-->C) in GHR gene suggested a putative negative association of allele C of this SNP with a high muscular performance.