Molecular semantics and the origin of life

The physical origin of life addresses itself to a semantic process on material grounds, in which causation toward contextualization is at work. Physically semantic process of whatever kind is specific in that every material participant is searching and modifying the material context to be fitted in. Fundamental to the physical semantics is the process of measurement proceeding internally among the constituent material participants, whereas the molecular syntax alone as embodied in the form of the quantum-mechanical equation of motion supplemented independently by exogenous boundary conditions cannot cope with the material process underlying the origin. A basic physical attribute of the phenomenon called life is variable duration, in contrast to invariant duration of Galilean inertia. In fact, moleculars replication thought as a harbinger of the phenomenon of life is a concrete form of variable duration and could be established unless internal measurement being instrumental to physically semantic process is forcibly eliminated by some external means. Physical experiments on the onset of molecular replication could become feasible only when external controllability over the intended experiments even at nano-meter scales is abandoned so as to save the room of internal measurement on the part of participating molecules.     

Phenomenon of life span instability in Drosophila melanogaster: I. Nonrandom origin of life span variations in successive generations

The dynamics of life span (LS) and fecundity in Drosophila melanogaster, strain D-32, were analyzed in a series of successive generations. Highly reliable variations in both fitness components were found. On initial inspection the variations would be characterized as random or irregular wherein mean values differed up to threefold. The variance in longevity is greater in females than in males. By use of mathematical procedures we have shown a scale regularity in LS distributions for all generations. Such regularity, in spite of considerable differences in absolute values (mean and maximum LS), suggested that the origin of LS instability is nonrandom.     

Asymmetrical DNA replication promotes evolution: disparity theory of evolution

Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication. This contradiction existing between heredity and evolution cannot be resolved in an individual organism, but only in terms of a population, in that a delicate balance exists between wild type and variants in a population which is necessary for the survival of the species. Namely, there seems to be a key in the mechanism of DNA replication to solve some problems of evolution. DNA is replicated semiconservatively using the leading and discontinuous lagging strands. According to our 'disparity theory of evolution', the existence of a sufficient fidelity difference between the leading and lagging strands is advantageous in terms of evolution, because the diversity of genotypes is enlarged but genotypes that have occurred in the past are guaranteed. In theory, by artificially increasing the fidelity difference between the leading and lagging strand ('disparity mutator'), evolution is accelerated while avoiding the extinction of the population. Using a disparity mutator, we should be able to improve living things, including multicellular organisms, within constrained conditions. A double-stranded algorithm, which mimics the structure and replication manner of DNA, is promising for solving optimization problems.     

Molecular complementarity II: energetic and vectorial basis of biological homeostasis and its implications for death

The energetic basis of molecular complementarity is presented. In biological systems requiring both homeostasis and non-equilibrium state maintenance, molecular complementarity provides a framework for the co-existence of these states within an organism. Smoothly changing homeostatic and thermodynamic systems, such as regulation of pH or an ensemble of asynchronous muscle crossbridges, are modeled using Liapunov functions. When biological systems undergo discontinuous state changes, such as the initiation of the heartbeat, life/death transition or the detachment of molecules, alternative analytical systems such as catastrophe theory provide information that continuous analytical methods cannot. Catastrophe theory produces a model of biology in which death can occur by two distinct mechanisms: loss of homeostatic control or loss of sufficient free energy. Molecular complementarity buffers molecules from temporal and physical changes. The usefulness of molecular complementarity is limited to association energies near the ambient energy, kT. Within this range, complementarity will alter molecular functions and will convert scalar biochemical reactions into vectorial physiological processes. Both thermodynamic and catastrophic models can be used to link energetic and homeostatic processes: the former providing quantitative information from continuous systems; the latter providing qualitative information from discontinuous systems involving state changes.     

Historical origin and evolution of the agents of infectious diseases

Data on the establishment and further evolution of the causative agents of human infectious diseases were systematized. Saprophytes proved to be the initial stage of this evolution for all the parasitic species. It was demonstrated by concrete examples that evolution of parasitism was the result of an interaction of many factors (the mechanism of transmission of the causative agents, the immunity formation in the population, hereditary resistance, etc.) and not only the sequence of a unilateral action of the transmission mechanism. The author considers that some properties of the causative agents of the infecticus diseases of man (spore formation, the capacity to reproduction on the objects of the external environment) were not newly acquired in the process of the parasitic species formation, but atavistic signs which persisted from saprophytic ancestors. The dialectics of progressive and regressive processes in the acqisition of the parasitic properties by saprophytes is considered.     

A suggested principle of complementarity for psychology: In theory, not method.

A distinction between the Copenhagen Interpretation and complementarity is underscored, with the former based on methodological effects (i.e., disturbance) and the latter on nonmechanical theoretical understandings of empirical findings. Psychology cannot have a Copenhagen Interpretation per se because it lacks clear experimental data comparable to the wave-vs-particle findings on the nature of light. Psychology's problems do not stem from method but from the uncertain and confusing grounds that predicate its theories. Physikos, Bios, Socius, and Logos are presented as complementary grounds for theoretical explanation. It is advised that a theorist try to stay within just 1 ground at a time, although he or she can then shift to a complementary ground to explain the same target without being inconsistent. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Quality of life: theory and methodology in rehabilitation

Validity studies of neuropsychological tests have typically examined individuals with neurological disorders. The present study was designed to investigate the construct validity of neuropsychological measures in patients with schizophrenia. We used Wechsler Adult Intelligence Scale Revised (WAIS-R) factor scores that were generated from the population of interest as marker variables in the present analysis. The current study included 39 patients with schizophrenia who were evaluated with a battery of neuropsychological tests assessing attention, memory, and abstract reasoning abilities. Pearson correlations indicated significant relationships between (a) WAIS-R Verbal Comprehension factor and tests of sustained attention, verbal memory and remote memory; (b) WAIS-R Perceptual Organization factor and tests of visual memory and abstraction and problem solving; and (c) WAIS-R Freedom From Distractibility factor and neuropsychological measures of attention and concentration. These results provide support for the construct validity of the neuropsychological tests in patients with schizophrenia, and indicate that these tests evaluate essentially the same constructs in patients with schizophrenia as they do for patients with structural neurological disorders.     

Molecular evolution of olfactomedin

Olfactomedin is a secreted polymeric glycoprotein of unknown function, originally discovered at the mucociliary surface of the amphibian olfactory neuroepithelium and subsequently found throughout the mammalian brain. As a first step toward elucidating the function of olfactomedin, its phylogenetic history was examined to identify conserved structural motifs. Such conserved motifs may have functional significance and provide targets for future mutagenesis studies aimed at establishing the function of this protein. Previous studies revealed 33% amino acid sequence identity between rat and frog olfactomedins in their carboxyl terminal segments. Further analysis, however, reveals more extensive homologies throughout the molecule. Despite significant sequence divergence, cysteines essential for homopolymer formation such as the CXC motif near the amino terminus are conserved, as is the characteristic glycosylation pattern, suggesting that these posttranslational modifications are essential for function. Furthermore, evolutionary analysis of a region of 53 amino acids of fish, frog, rat, mouse, and human olfactomedins indicates that an ancestral olfactomedin gene arose before the evolution of terrestrial vertebrates and evolved independently in teleost, amphibian, and mammalian lineages. Indeed, a distant olfactomedin homolog was identified in Caenorhabditis elegans. Although the amino acid sequence of this invertebrate protein is longer and highly divergent compared with its vertebrate homologs, the protein from C. elegans shows remarkable similarities in terms of conserved motifs and posttranslational modification sites. Six universally conserved motifs were identified, and five of these are clustered in the carboxyl terminal half of the protein. Sequence comparisons indicate that evolution of the N-terminal half of the molecule involved extensive insertions and deletions; the C-terminal segment evolved mostly through point mutations, at least during vertebrate evolution. The widespread occurrence of olfactomedin among vertebrates and invertebrates underscores the notion that this protein has a function of universal importance. Furthermore, extensive modification of its N-terminal half and the acquisition of a C-terminal SDEL endoplasmic-reticulum-targeting sequence may have enabled olfactomedin to adopt new functions in the mammalian central nervous system.     

Molecular evolution of viruses: an interim summary

The origin and molecular evolution of viruses in this issue is dealt with at two levels: (1) tracing the past evolutionary pathways of viruses belonging to RNA virus families, retroviruses, and small and large DNA viruses; (2) tracing current changes in the RNA and DNA viral genomes that lead to the evolution of new virus mutants. In this interim summary, a time scale for the evolutionary processes is given, based on the accumulated published knowledge concerning the postulated origins of life on planet Earth, and the hypothesis that living cells with RNA genomes may have emerged (the "RNA world hypothesis") that then developed into cells with DNA genomes in eukaryotic and prokaryotic cells (1-3). The ideas about the evolution of RNA and DNA viruses from ancient cellular RNA and DNA molecules over a period of 3.5 billion years are discussed. It may be possible that by studying virus genes and molecular processes in virus-infected cells, and their involvement in the shaping of the genomes of bacteria, yeast, plants, insects, mammals, and humans, it will be possible to understand the importance of viruses in past evolution and to predict their possible impact on current and future evolutionary trends in biology.     

Eriksonian lifespan theory and life history theory: An integration using the example of identity formation.

Furthering the cause of consilience in the social sciences a model is proposed in which Eriksonian life span theory and life history theory are integrated. The model explains individual differences in the Eriksonian developmental stages as a function of the individual differences in developmental trajectories of life history theory as conceptualized by Belsky, Steinberg, and Draper (1991). Erikson's fifth stage of identity formation is used to examine the model, with the results of three studies presented to illustrate the viability of the model. Future research should examine other aspects of the model and the relationship between the developmental trajectories in life history theory and the Eriksonian stages in greater detail. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Molecular evolution of the photolyase-blue-light photoreceptor family

The photolyase-blue-light photoreceptor family is composed of cyclobutane pyrimidine dimer (CPD) photolyases, (6-4) photolyases, and blue-light photoreceptors. CPD photolyase and (6-4) photolyase are involved in photoreactivation for CPD and (6-4) photoproducts, respectively. CPD photolyase is classified into two subclasses, class I and II, based on amino acid sequence similarity. Blue-light photoreceptors are essential light detectors for the early development of plants. The amino acid sequence of the receptor is similar to those of the photolyases, although the receptor does not show the activity of photoreactivation. To investigate the functional divergence of the family, the amino acid sequences of the proteins were aligned. The alignment suggested that the recognition mechanisms of the cofactors and the substrate of class I CPD photolyases (class I photolyases) are different from those of class II CPD photolyases (class II photolyases). We reconstructed the phylogenetic trees based on the alignment by the NJ method and the ML method. The phylogenetic analysis suggested that the ancestral gene of the family had encoded CPD photolyase and that the gene duplication of the ancestral proteins had occurred at least eight times before the divergence between eubacteria and eukaryotes.     

Molecular phylogenetics and the evolution of antarctic notothenioid fishes

The monophyly of the antarctic fish suborder Notothenioidei and the monophyly of its earliest family the Bovichtidae have been investigated with 12S and 16S mitochondrial DNA sequences. New data from Cottoperca, Pseudaphritis, Harpagifer and several outgroups, in addition to available sequences, show that the bovichtids are paraphyletic. Pseudaphritis is the sister group of all the non-bovichtid notothenioids. The same results are found from two independent genetic markers, the nuclear 28S rDNA and the 12S and 16S mitochondrial rDNA. This reliably refutes a previous hypothesis that placed Pseudaphritis as the sister group of all the remaining notothenioids (including Cottoperca and Bovichtus). Bootstrap analyses show that the Notothenioidei are monophyletic (although members of the suborder Trachinoidei have not been surveyed). Subsequent data from hemoglobin composition confirm the present relationships. After discussions between members of the European Science Foundation (ESF) network during its last two meetings, we point out here some fundamental aspects of comparative biology to improve understanding between the physiologist community and phylogeneticists. The most important points are differences in how the concept of homology is used and differences in the consideration of adaptation. When adaptation is evoked or questioned, endless speculations and untestable scenarios are often developed. We strongly advocate the use of phylogenetic trees for testing hypotheses of adaptation (through multiple character mapping). Such a "research program" in comparative biology has the power to improve knowledge because it can potentially lead to new experiments for testing adaptive hypotheses.     

Molecular evolution of the family Camelidae: a mitochondrial DNA study

We report the first molecular evolutionary analysis of the family Camelidae by analysing the full DNA sequence of the mitochondrial cytochrome b gene. Estimates for the time of divergence of the Old World (Camelini) and New World (Lamini) tribes obtained from sequence data are in agreement with those derived from the fossil record. The DNA sequence data were also used to test current hypotheses concerning the ancestors of the domesticated llama and alpaca. The results show that hybridization has occurred in the ancestry of both domesticated camelids, obscuring the origin of the domestic species.