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PubMed2002

Coexistence of sexual and asexual conspecifics: a cellular automaton model.

Most previous models of populations mixed for reproductive mode have omitted important local interactions between sexual and asexual individuals. We propose a cellular automaton model where local rules focus on fertilization and colonization. This model produces rich sets of data which are then studied by means of spatial statistics. Results point to the fixation of one of the two reproductive modes in the landscape. However, some examples of coexistence of sexual and asexual conspecifics over long periods of time are also found. This model is an example of a CA that diverges from its mean field approximation. The formation of sexual and asexual clusters reduces effective colonization rate in the CA and may account for this behaviour.

Biological Evolution↗
PubMed1976

A critical review of the 'neugliederung' concept in relation to the development of the vertebral column.

The literature on the early embryonic development of the vertebral column in various animal species was analyzed to evaluate so many unrelated or contradictory observations. The recurring problems are described. One of the first was the lack of correspondence between the metameric boundaries of the 'primitive vertebral bodies' arising from the somites and those of the adult vertebral bodies, as presumably shown by their relationship to the vertebral processes and spinal nerves. A century ago, Remak introduced the concept of 'Neugliederung', according to which the ultimate vertebral body boundaries are determined by a shift of a half segment in comparison with the earlier segment boundaries. Another question was about the nature of the structures the primitive segments give rise to (axial skeletal tissue and/or muscular tissue and/or nervous tissue), which led to the fundamental problem which system (skeleton or musculature) retains its segmentation. The observation of what was called the intervertebral fissure led to a far-reaching modification of the 'Neugliederung' concept, making a regrouping of parts of the primitive vertebral bodies both possible and probable. The functional necessity for the alternation of muscle and skeleton primordia was also assumed. Although the difference in rostro-caudal level between the boundaries of the somites and the definitive vertebral bodies, measured for instance in relation to the position of the intersegmental vessels, does not support a resegmentation of the vertebral column, because the somite is not a precursor of the adult vertebra, few authors have rejected this view. Subsequently, the discussion focussed on the problem of a) the animal species in which and b) the time at which the intervertebral fissure occurs, and the relationship of this fissure to the primitive vertebral cavity. Under the influence of comparative embryology, a number of authors concentrated mainly on identifying certain embryonic primordia as homologues of phylogenetic vertebral elements, and also on attempting to determine the recombination by which such elements could form a definitive vertebra. According to these authors, not only the vertebral bodies but also the arches and ribs undergo a 'Neugliederung'. Another variant of the 'Neugliederung' concept envisages a gradual shift of the original boundaries of the somites with respect to the transverse level of the definitive vertebrae with or without migration of cellular material. A critical consideration of the concepts at issue, and notably of the 'Neugliederung' concept, is presented. Certain phenomena held to be pillars of the 'Neugliederung' theory could not be confirmed. The functional interpretation of the resegmentation was also reduced to its proper proportions by the analysis. A development of the axial skeleton without resegmentation is just as conceivable in functional terms as one in which resegmentation occurs. A functionally meaningful relationship between muscles and skeletal elements is possible in both cases...

Animals↗
PubMed1994

The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments.

How to sample alignments from their posterior probability distribution given two strings is shown. This is extended to sampling alignments of more than two strings. The result is first applied to the estimation of the edges of a given evolutionary tree over several strings. Second, when used in conjunction with simulated annealing, it gives a stochastic search method for an optimal multiple alignment.

Algorithms↗
PubMed1977

When are two qualitative taxonomic characters compatible?

A proof is given of a procedure that has previously appeared claiming to determine when two amino acid positions on a protein could both possibly be divergent taxonomic characters. An algorithm for executing this procedure is described.

Amino Acid Sequence↗
PubMed1981

Formation of the thioester, N,S-diacetylcysteine, from acetaldehyde and N,N'diacetylcystine in aqueous solution with ultraviolet light.

The thioester, N,S-diacetylcysteine, is formed during the illumination of phosphate buffered (pH 7.0) aqueous solutions of acetaldehyde and N,N'-diacetylcystine with ultraviolet light. The yield of N,S-diacetylcysteine relative to N-acetylcysteine and unidentified products progressively increases as ultraviolet light below 239 nm, 253 nm and 281 nm is cut off with optical filters. When ultraviolet light below 320 nm is removed with an optical filter, there is no detectable reaction. Illumination of 0.025 M N,N'-diacetylcystine with 0.5 M and 1.0 M acetaldehyde with filtered ultraviolet light gives, respectively, 20% and 80% yields of N,S-diacetylcysteine. In the reaction with 1.0 M acetaldehyde, N-acetylcysteine forms early in the reaction and later decreases with its conversion to N,S-diacetylcysteine. The prebiotic significance of these reactions is discussed.

Acetaldehyde↗
PubMed1990

Was there a universal tRNA before specialized tRNAs came into existence?

It is generally true that evolving systems begin simply and become more complex in the evolutionary process. For those who try to understand the origin of a biochemical system, what is required is the development of an idea as to what simpler system preceeded the present one. Here we present an hypothesis that a universal tRNA molecule, capable of reading many codons may have preceeded the appearance of individual tRNAs. Evidence seems to suggest that this molecule may have been derived from a common ancestor of the contemporary 5S rRNAs and tRNAs.

Biological Evolution↗
PubMed2005

Homology and ontogeny: pattern and process in comparative developmental biology.

In this article the interface between development and homology is discussed. Development is here interpreted as a sequence of evolutionarily independent stages. Any approach stressing the importance of specific developmental stages is rejected. A homology definition is favoured which includes similarity, and complexity serves as a test for homology. Complexity is seen as the possibility of subdividing a character into evolutionarily independent corresponding substructures. Topology as a test for homology is critically discussed because corresponding positions are not necessarily indicative of homology. Complexity can be used twofold for homology assessments of development: either stages or processes of development are homologized. These two approaches must not be con-flated. This distinction leads to the conclusion that there is no ontogenetic homology "criterion".

Animals↗
PubMed2006

Unburdening evo-devo: ancestral attractions, model organisms, and basal baloney.

Although flourishing, I argue that evo-devo is not yet a mature scientific discipline. Its philosophical foundation exhibits an internal inconsistency that results from a metaphysical confusion. In modern evolutionary biology, species and other taxa are most commonly considered as individuals. I accept this thesis to be the best available foundation for modern evolutionary biology. However, evo-devo is characterized by a remarkable degree of typological thinking, which instead treats taxa as classes. This metaphysical incompatibility causes much distorted thinking. In this paper, I will discuss the logical implications of accepting the individuality thesis for evo-devo. First, I will illustrate the degree to which typological thinking pervades evo-devo. This ranges from the relatively innocent use of typologically tainted language to the more serious misuse of differences between taxa as evidence against homology and monophyly, and the logically flawed concept of partial homology. Second, I will illustrate how, in a context of typological thinking, evo-devo's harmless preoccupation with distant ancestors has become transformed into a pernicious problem afflicting the choice of model organisms. I will expose the logical flaws underlying the common assumption that model organisms can be expected to represent the clades they are a part of in an unambiguous way. I will expose the logical flaws underlying the general assumption that basal taxa are the best available stand-ins for ancestors and that they best represent the clade of which they are a part, while also allowing for optimal extrapolation of results.

Animals↗
PubMed2006

Introduction--development and phylogeny of the arthropods: Darwin's legacy.

In the present essay, I first recall the genealogical concept of classification settled by Charles Darwin in the "Origin of Species". Darwin tightly linked what we now call phylogeny and development. He often insisted to take into account embryonic and larval characters, most often using as examples his favourite animals, the cirripedes. Then I discuss remaining problems, and also perspectives, to address the link between phylogeny and development in the modern terms of molecular and cladistic phylogenetics and of molecular and genetic developmental biology.

Animals↗
PubMed2001

Recent findings in the modern RNA world.

It is assumed that modern life forms arose from a molecular ancestor in which RNA molecules both stored genetic information and catalyzed biochemical reactions. In modern cells, these functions are carried out, respectively, by DNA and proteins, but diverse cellular RNAs are also involved in key cellular functions. In this paper, we review the cellular RNAs that are ubiquitous and/or that perform essential biological functions, and we discuss the evolutionary relationships of such RNAs with a prebiotic RNA world. This unexpected biological diversity of cellular RNAs and the crucial functions they perform in cellular metabolism demonstrate the complexity of an RNA-driven metabolism in an ancient RNA world and in modern life. Cellular RNAs are involved in translation (tRNA and rRNA) but also in ribosome maturation (snoRNA) and more generally in RNA processing (snRNA and snoRNA), replication (telomerase RNA), editing, protein translocation (SRP RNA), cellular transport (vRNA) and translation quality control (tmRNA). In addition, the function of many other cellular RNAs has not yet been determined. Future investigations of RNA function will allow us to better understand not only early evolutionary biological processes but also the central metabolism of modern cells.

Biological Evolution↗
PubMed2006

Novel approach to evolutionary neural network based descriptor selection and QSAR model development.

Capability of evolutionary neural network (ENN) based QSAR approach to direct the descriptor selection process towards stable descriptor subset (DS) composition characterized by acceptable generalization, as well as the influence of description stability on QSAR model interpretation have been examined. In order to analyze the DS stability and QSAR model generalization properties multiple random dataset partitions into training and test set were made. Acceptability criteria proposed by Golbraikh et al. [J. Comput.-Aided Mol. Des., 17 (2003) 241] have been chosen for selection of highly predictive QSAR models from a set of all models produced by ENN for each dataset splitting. All QSAR models that pass Golbraikh's filter generated by ENN for each dataset partition were collected. Two final DS forming principles were compared. Standard principle is based on selection of descriptors characterized by highest frequencies among all descriptors that appear in the pool [J. Chem. Inf. Comput. Sci., 43 (2003) 949]. Search across the model pool for DS that are stable against multiple dataset subsampling i.e. universal DS solutions is the basis of novel approach. Based on described principles benzodiazepine QSAR has been proposed and evaluated against results reported by others in terms of final DS composition and model predictive performance.

Benzodiazepines↗