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PubMed1995

Evolution of biological regulation networks under complex environmental constraints.

This work investigates the influence of environmental inducers on the organization of cell regulation networks, using a connectionist approach. Protein interactions are modeled by an asymmetrical recurrent network, the units of which take continuous values. In contrast to classical models, we explicitly introduce a genome to encode the architecture of the system. This feature enables us to introduce an evolution model, in which a genetic algorithm that mimics the effects of evolution on proteins mutual interactions is used. We assume an efficient system to respond to persistent environmental stimuli, independently of their amplitude. Results are presented that show a structuration of the network with the emergence of specialized hierarchal structures. These structures seem to drive the system at the edge of chaos, so that it can present adapted responses to significant environmental changes.

Algorithms↗
PubMed2001

Primate evolution: a biology of holocene extinction and survival on the southeast Asian Sunda Shelf islands.

What biological traits distinguish taxa susceptible to extinction from less susceptible taxa? Substantiated island biogeographic theory suggests that after insularization, small islands lose more species than do large islands. Thus, susceptible taxa are those now found on only large islands. The traits of susceptible taxa can thus be found by comparing the biology of species found only on large islands with those also found on small islands. The islands examined here are those of the Sunda Shelf, created as a result of the Holocene rise in sea levels of 120 m. We use four statistical comparisons: comparative analysis by (phylogenetically) independent contrasts (N = 8 contrasts at the subgeneric or deeper level), Spearman correlations, stepwise regression, and principle components analysis (N = 9 subgenera/genera). The genera and one subgenus considered are: Hylobates, Macaca, Nasalis, Nycticebus, Pongo, Presbytis, Symphalangus, Tarsius, and Trachypithecus. Traits of risk appear to be large body mass, low density, large annual home range, and low maximum latitude. Expected traits that did not correlate with susceptibility were low interbirth interval, high percent frugivory, high group mass, low altitudinal range, and small geographic range. The risky traits also apply to just the anthropoids (i.e., prosimians excluded). The risky traits are explained if susceptibility is induced by requirements for a large extent of habitat, a small population size, and specialization. These findings, which indicate that efficiency and plasticity of use of the environment separate susceptible from successful primate taxa, might be relevant to an understanding of hominoid evolution.

Altitude↗
PubMed1999

Evolutionary changes reflected by the cellular amino acid composition.

Comparison of the amino acid composition of cell-proteins using 17 amino acids has been used to investigate the biological evolution of organisms such as bacteria, blue-green alga, green alga, fungi, slime mold, protozoa and vertebrates. The degree of difference in the amino acid ratios between any two groups reflects the degree of divergency in biological evolution. The amino acid composition of the Gram-negative bacteria (Escherichia coli, Klebsiella, Proteus, and Vibrio alginolyticus) was identical. However, the amino acid composition of Staphylococcus aureus and Bacillus subtilis, which are Gram-positive bacteria, differed from each other and from the Gram-negative bacteria. The amino acid composition of the blue-green alga (Cyanobacterium, Chroococidiopsis) was quite similar to that of E. coli. A marked difference in the amino acid composition was observed between E. coli and green alga (Chlorella), and significant differences were observed between E. coli and other organisms, such as fungi, protozoa (Tetrahymena), slime mold (Dictyostelium discoideum) and vertebrates. In conclusion, the change in cellular amino acid composition reflects the divergence which has occurred during biological evolution, whereas a basic pattern of amino acid composition is maintained in spite of a long period of evolutional divergence among the various organisms. Thus, it is proposed that the primitive life forms established at the end of prebiotic evolution had a similar amino acid composition.

Amino Acids↗
PubMed1989

Evolution, selection and cognition: from "learning" to parameter setting in biology and in the study of language.

Most biologists and some cognitive scientists have independently reached the conclusion that there is no such thing as learning in the traditional "instructive" sense. This is, admittedly, a somewhat extreme thesis, but I defend it here in the light of data and theories jointly extracted from biology, especially from evolutionary theory and immunology, and from modern generative grammar. I also point out that the general demise of learning is uncontroversial in the biological sciences, while a similar consensus has not yet been reached in psychology and in linguistics at large. Since many arguments presently offered in defense of learning and in defense of "general intelligence" are often based on a distorted picture of human biological evolution, I devote some sections of this paper to a critique of "adaptationism," providing also a sketch of a better evolutionary theory (one based on "exaptation"). Moreover, since certain standard arguments presented today as "knock-down" in psychology, in linguistics and in artificial intelligence are a perfect replica of those once voiced by biologists in favor of instruction and against selection, I capitalize on these errors of the past to draw some lessons for the present and for the future.

Antibody Formation↗
PubMed1993

Molecular biology and evolution of filoviruses.

The family Filoviridae contains extremely pathogenic human viruses causing a fulminating, febrile hemorrhagic disease. Filoviruses are enveloped, filamentous particles with a nonsegmented negative-strand RNA genome showing the gene arrangement 3'-NP-VP35-VP40-GP-VP30-VP24-L-5'. Genes are flanked by highly conserved transcriptional signals and are generally separated by variable intergenic regions. They are transcribed into monocistronic polyadenylated messenger RNAs which contain relatively long 5' and 3' untranslated regions. Seven structural proteins are encoded by the genome of which four form the helical nucleocapsid (NP-VP35-VP30-L), two are membrane-associated (VP40-VP24), and one is a transmembrane glycoprotein (GP). Comparison of filovirus genomes with those of other nonsegmented negative-strand RNA viruses suggest comparable mechanisms of transcription and replication and a common evolutionary lineage for all these viruses. Sequence analyses of single genes, however, showed that filoviruses are more closely related to paramyxoviruses, particularly human respiratory syncytial virus. These data support the concept of the taxonomic order Mononegavirales for all nonsegmented negative-strand RNA viruses and the classification of Marburg virus, Ebola virus, and Reston virus in the family Filoviridae, separate from the families Paramyxoviridae and Rhabdoviridae.

Animals↗
PubMed2004

Drug evolution concept in drug design: 1. Hybridization method.

A novel concept, "drug evolution", is proposed to develop chemical libraries that have a high probability of finding drugs or drug candidates. It converts biological evolution into chemical evolution. In this paper, we present "hybridization" drug evolution, which is the equivalent of sexual recombination of parental genomes in biological evolution. The hybridization essentially shuffles the building blocks of the parent drugs and ought to drug(s); no drug evolution can otherwise occur. We hybridized two drugs, benzocaine and metoclopramide and generated 16 molecules that include the parent drugs, four known drugs, and two molecules whose therapeutic activities are reported. The unusually high number of drugs and drug candidates in the library encourages high expectations of finding new drug(s) or drug candidate(s) within the remaining eight compounds. Interestingly, the therapeutic applications of the eight drugs or drug candidates in the library are fairly diverse as 38 therapeutic applications and 25 molecular targets are counted. Therefore, the library fits as a general chemical library for unspecified therapeutic activities. The hybridization of other two drugs, aspirin and cresotamide, is also described to demonstrate the generality of the method.

4-Aminobenzoic Acid↗
PubMed1993

Evolution of prokaryotic genomes.

Molecular genetics, which has its roots mainly in the development of microbial genetics in the middle of this century, not only greatly facilitates investigations of essential cellular functions, but also offers a means to better understand evolutionary progress. Spontaneous mutagenesis, the driving force of biological evolution, depends on a multitude of mechanistically distinct processes, many of which are already quite well understood. Often, enzymes act as variation generators, and natural gene vectors help to spread functional domains, entire genes and groups of genes across natural isolation barriers. In this overview, particular attention is given to comparing three selected natural strategies for the generation of genetic diversity: nucleotide substitution, DNA rearrangements, and gene acquisition. All of these mechanisms, as well as many others, appear to fulfill their specific roles in microbial evolution. Rather than being the result of an accumulation of errors, biological evolution may depend on a multitude of specific biological functions, as well as on a certain degree of intrinsic structural flexibility of biological molecules.

Biological Evolution↗
PubMedDate not supplied

[Biological and evolutive spectrum of patients ANCA present].

AIM: To analyse the immuno-biological profile of patients with antineutrophil cytoplasmic antibodies (ANCA) presents. This is a retrospective study of all ANCA positives cases from Nephrology Clinic Iasi during five years (1998-2003) on a cohort of 97 patients. RESULTS: pANCA was positive in 28, cANCA was positive in 60 and the others had pANCA and cANCA. The diseases ANCA associated were: systemic vasculitis, rapidly progressive glomerulonephritis (GNRP), chronic renal failure of an unknown etiology. ANCA presence was associated with inflammatory syndrome in 83.5%, anemic syndrome in 71.1%. From the patients with renal disfunction (71.1%), half of them presented an increased level of creatinine (>6 mg%). Renal biopsy proven especially crescentic glomerulonephritis. The complications and the diseases were more frequent in cANCA cases. CONCLUSIONS: cANCA presence is a negative prognosis factor in vasculitis; testing ANCA alone cannot be used to guide treatment.

Adult↗
PubMed2003

DNA and the revolutions of molecular evolution, computational biology, and bioinformatics.

The discovery of the structure of DNA was a necessary prerequisite for determining the sequence of DNA molecules. Technological advances have now made it possible to sequence DNA rapidly and has resulted in public databases with over 30 billion nucleotides of known sequence. The analysis of these data has lead to new fields of science and to amazing advances in our understanding of evolution.

Animals↗
PubMedDate not supplied

[Fractal structures in living beings and the evolutionary process ].

Fractal structures of living beings are discussed in the aspect of the directionality, i.e., programmed nature, of the evolutionary process. These theses are substantiated by analyzing the alternative views of Darwinism and Nomogenesis on the nature of biological evolution, in the context of the interdisciplinary approach, using the fractal concept, as well as based on the nature of the chaotic (fractal) attractors bearing non-random order-generating sequences. Apparently, along with the influence of natural selection representing the adaptive stage of evolution, the non-random order-generating sequences are the governing factor of the directionality and the programmed nature of biological evolution, thus representing its progressive form. A number of questionable and complicated problems and phenomena of the evolution of organic world that are difficult to explain by Darwinism, Nomogenetic theory, or by the Synthetic Theory of Evolution are discussed from this viewpoint. These are, in particluar, the nature of polymorphic series in plants and animals, M. Eigen's hypercycles, and Vavilov's homologous series in hereditary variation.

Animals↗