Contemporary concepts of homology in biology (a theoretical review)

A brief review of the contemporary theoretical concepts of homology being developed basically in systematics and phylogenetics as well as in developmental biology is presented. Ontologically, both homology and analogy represent a kind of correspondence considered from the standpoint of nominalism, realism, and conceptualism. According to their nominalistic treatment, both are described by a set-theory approximation which makes them classes (in the logical sense). The realistic treatment provides their holistic view according to which a homologue is an anatomical or evolutionary singular while analogue remains a class. The conceptualistic treatment means that there are real (objective) correspondences existing among real (objective) entities while fixation of any of them is based on certain theoretical presumptions adopted by a researcher; homology as a natural kind (including homeostatic property cluster) seems to be most consistent with such a treatment. Realistic view of homology makes it "absolute", while two others make discrimination of homology and analogy strictly relative. Two basic general homology concepts have been developed in recent literature--taxic and transformational ones; the first considers respective correspondences as structure relations, the second as process relations. The taxic homology is nearly the same as classical typological one (Owen), while transformational homology unites all its phylogenetic, ontogenetic (developmental) and transformation-typological definitions. Process-structuralistic approach seems to unite both taxic and transformational ones. The latter makes it possible to apply general homology concept not only to structures but to processes as well. It is stressed that homology is not identical to the similarity, the latter being just the means for revealing the former. Some closer consideration is given to phylogenetic, ontogenetic and genetic treatments of homology; significant uncertainty is shown to exist between them which causes the "homology problem". Epistemologically, any homology statement has a status of hypothesis which makes such a statement theory-dependent according to the hypothetic-deductive argumentation scheme. This dependence allows to stress once more the relative nature of homology and analogy correspondences. Some questions concerning operational concepts and criteria of homology are considered. A hierarchical concept of homology seems to be the most promising prospect of future development of the "homology problem".     

Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

Is a unified concept of species in ornithology possible? (An opinion of a practicing taxonomist)]

An analysis of current publications on species problem reveals the radical discrepancy between the statements of species reality in nature and different number of these "realities" in light of different species concepts. It has been shown, that the only realities are populations, and "species" is only logical construct--the notion. A concept of species is a system of interconnected notions, where the main element--ontology of species has been always given a priori to the real biodiversity. For that reason every concept of species creates its own "virtual reality". Various concepts of species are not mutually comparable, and can not be criticized from each other's views and from position of "reality". Biological and Phylogenetic Species Concepts competing in ornithology exclude each other completely, and the unified concept of species is principally impossible. But as generally accepted species "standard" is needed, the unified convention of species must take the place of the various concepts of species.     

Faith in Art

Individual creativity is ubiquitous. New technologies both enable and urge fresh approaches to creativity in the context of education. University-level education offers a natural place to adjust pedagogical structures in favor of a more individual approach to learning that organizes the intellectual community into new patters of interaction and time allocation. This direction is made possible by the vast improvements in access to information, data, knowledge, and opinion. College students live in this world of access, in an ever-expanding sea of material. Networking second-by-second is central to their zeitgeist. The result is far more than social. Interaction and collaboration are now important in most workplaces, and are expected to be even more important in the future. Higher education needs to use its natural resources in ways that develop content knowledge and skills in a culture infused at new levels by investigation, cooperation, connection, integration, and synthesis. Creativity is necessary to accomplish this goal. When central and culturally pervasive, creativity becomes exemplified and enhanced for every student. Problem solving becomes the driving pedagogy. Problem solving is a technique that can be advanced through practice, but practice takes time. Universities must meet the challenge of reapportioning time if suggested changes are to occur. These matters are important to P–12 arts education, because colleges prepare teachers and citizens who then provide leadership. Possibilities abound for changing paradigms that now hold arts education back in many policy situations. It is important to take advantage of opportunities inherent in the coincidence of present conditions, youthful energy, technological capabilities, and interest in creativity.     

Let the concept of trait be functional!

In its simplest definition, a trait is a surrogate of organismal performance, and this meaning of the term has been used by evolutionists for a long time. Over the last three decades, developments in community and ecosystem ecology have forced the concept of trait beyond these original boundaries, and trait-based approaches are now widely used in studies ranging from the level of organisms to that of ecosystems. Despite some attempts to fix the terminology, especially in plant ecology, there is currently a high degree of confusion in the use, not only of the term "trait" itself, but also in the underlying concepts it refers to. We therefore give an unambiguous definition of plant trait, with a particular emphasis on functional trait. A hierarchical perspective is proposed, extending the "performance paradigm" to plant ecology. "Functional traits" are defined as morpho-physio-phenological traits which impact fitness indirectly via their effects on growth, reproduction and survival, the three components of individual performance. We finally present an integrative framework explaining how changes in trait values due to environmental variations are translated into organismal performance, and how these changes may influence processes at higher organizational levels. We argue that this can be achieved by developing "integration functions" which can be grouped into functional response (community level) and effect (ecosystem level) algorithms.     

PHYLOGENETIC SYSTEMATICS AND THE SPECIES PROBLEM

Abstract— A tension has arisen over the primacy of interbreeding versus monophyly in defining the species category. Manifestations of this tension include unnecessary restriction of the concept of monophyly as well as inappropriate attribution of "species" properties, to "higher taxa", and vice versa. Distinctions between systems (wholes) deriving their existence from different underlying. processes have been obscured by failure to acknowledge different interpretations of the concept of individuality. We identify interbreeding (resulting in populations) and evolutionary descent (resulting in monophyletic groups) as two processes of interest to phylogenetic systematists, and explore the relations between the systems resulting from these processes. In the case of sexual reproduction, populations of interbreeding organisms (regardless of whether they are monophyletic) exist as cohesive wholes and play a special role in phylogenetic systematics, being the least inclusive entities appropriate for use as terminal units in phylogenetic analysis of organismal relationships. Both sexual and asexual organisms form monophyletic groups. Accepting the reality and significance of both interbreeding and monophyly emphasizes that a conscious decision must be made regarding which phenomenon should be used to define the species category. Examination of species concepts that focus either on interbreeding or on common descent leads us to conclude that several alternatives are acceptable from the standpoint of phylogenetic systematics but that no one species concept can meet the needs of all comparative biologists.     

Clonal and non-clonal chromosome aberrations and genome variation and aberration.

The theoretical view that genome aberrations rather than gene mutations cause a majority of cancers has gained increasing support from recent experimental data. Genetic aberration at the chromosome level is a key aspect of genome aberration and the systematic definition of chromosomal aberrations with their impact on genome variation and cancer genome evolution is of great importance. However, traditionally, efforts have focused on recurrent clonal chromosome aberrations (CCAs). The significance of stochastic non-clonal chromosome aberrations (NCCAs) is discussed in this paper with emphasis on the simple types of NCCAs that have until recently been considered "non-significant background". Comparison of various subtypes of transitional and late-stage CCAs with simple and complex types of NCCAs has uncovered a dynamic relationship among NCCAs, CCAs, overall genomic instability, and karyotypic evolution, as well as the stochastic nature of cancer evolution. Here, we review concepts and methodologies to measure NCCAs and discuss the possible causative mechanism and consequences of NCCAs. This study raises challenging questions regarding the concept of cancer evolution driven by stochastic chromosomal aberration mediated genome irregularities that could have repercussions reaching far beyond cancer and organismal genomes.     

Verity of beliefs in scientific cognition

Certain aspects of importance of scientist's convictions for cognition of the environmental are considered as exemplified by the analysis of formation of notions on mechanisms of protein synthesis on the basis of hereditary information. Special attention is attracted to problems on connection of convictions and ideology, on the absolute/relative truth relation as an initial position in the analysis of causes arousing prejudices, dogmatic thinking, groundless absolutization of the conception of "one gene--one polypeptide".     

A neural model of the dynamic activation of memory

We study an Attractor Neural Network that stores natural concepts, organized in semantic classes. The concepts are represented by distributed patterns over a space of attributes, and are related by both semantic and episodic associations. While semantic relations are expressed through an hierarchical coding over the attribute space, episodic links are realized via specific synaptic projections. Due to dynamic thresholds expressing neuronal fatigue, the network's behavior is characterized by convergence toward the concept patterns on a short time scale, and by transitions between the various patterns on a longer time scale. In its baseline, undamaged state, the network manifests semantic, episodic, and random transitions, and demonstrates the phenomen of priming. Modeling possible pathological changes, we have found that increasing the noise level or the rate of neuronal fatigue decreases the frequency of semantic transitions. When neurons characterized by large synaptic connectivity are deleted, semantic transitions decay before the episodic ones, in accordance with the findings in patients with Alzheimer's disease.     

Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.     

Modeling: optimal marathon performance on the basis of physiological factors

This paper examines current concepts concerning "limiting" factors in human endurance performance by modeling marathon running times on the basis of various combinations of previously reported values of maximal O2 uptake (VO2max), lactate threshold, and running economy in elite distance runners. The current concept is that VO2max sets the upper limit for aerobic metabolism while the blood lactate threshold is related to the fraction of VO2max that can be sustained in competitive events greater than approximately 3,000 m. Running economy then appears to interact with VO2max and blood lactate threshold to determine the actual running speed at lactate threshold, which is generally a speed similar to (or slightly slower than) that sustained by individual runners in the marathon. A variety of combinations of these variables from elite runners results in estimated running times that are significantly faster than the current world record (2:06:50). The fastest time for the marathon predicted by this model is 1:57:58 in a hypothetical subject with a VO2max of 84 ml.kg-1.min-1, a lactate threshold of 85% of VO2max, and exceptional running economy. This analysis suggests that substantial improvements in marathon performance are "physiologically" possible or that current concepts regarding limiting factors in endurance running need additional refinement and empirical testing.     

Classification of triplet periodicity in the DNA sequences of genes from KEGG databank

Totally, 472 288 regions of triplet periodicity were found in 578 868 genes from KEGG databank version 29 and classified. A new concept of triplet periodicity class and a measure of similarity between periodicity classes were introduced. Overall, 2520 classes were created and contained 94% of the triplet periodicity cases found. A similar correlation between the triplet periodicity and reading frame was observed for 92% of triplet periodicity regions contained in different classes. The remaining triplet periodicity regions displayed a shift of the reading frame relative to that common for the majority of genes belonging to the same triplet periodicity class. The hypothetical amino acid sequences were deduced from the periodicity regions according to the reading frame characteristic of the given triplet periodicity class. BLAST analysis demonstrated that 2660 hypothetical amino acid sequences display a statistically significant similarity to proteins from the Uni-Prot databank. It was supposed that 8% of the triplet periodicity regions contained in the classes have frameshift mutations. The triplet periodicity classes can be used to identify the coding regions in genes and to searching for frameshift mutations.     

The theory of phyllotaxis. II. Crystallographic interpretation of the interrelation between lower and superior phyllotaxis forms

Cross-opposite phyllotaxis forms are defined as superior with respect to the alternate ones and verticillate phyllotaxis forms as superior with respect to the opposite ones. Different phyllotaxis forms can be interpreted as a result of stretching of crystal-like structures of the embryo formed by dense packing of rudiments. Based on hypothetical concepts of the properties of plant rudiments and embryos, possible mechanisms of the formation of superior phyllotaxis forms from the lower ones have been analyzed. It was shown that the superior phyllotaxis forms can be considered as the results of additive summation of the lower forms. The theoretical conclusions are confirmed by the examples of polymorphic phyllotaxis in conspecific plants and by the facts of accidental splitting of superior phyllotaxis forms into the corresponding lower forms in nature and in experiment. The mechanisms underlying the formation of multiple forms of helical phyllotaxis have been proposed. The concept of a new type of mixed hexagonal-tetragonal phyllotaxis has been formulated and the mechanism of its formation has been considered. The forms of corn grain packaging in the corncob and leaf arrangement on the strawberry tomato stem are given as examples of true hexagonal-tetragonal phyllotaxis in nature.     

Cellular signaling: aspects for tumor diagnosis and therapy.

Cells are organic microsystems with functional compartments interconnected by complex signal chains. Intracellular signaling routes and signal reception from the extracellular environment are characterized by redundancy, i.e., parallel pathways exist. If a cell is exposed to an external "signal input", the signal processing elements within the cell provide a response that will be a pattern of reactions manifest as a metabolic, morphologic or electric "signal output". Cell-chip hybrid structures are miniaturized analytical systems with the capability to monitor such cell responses in real time and under continuous control of the environmental conditions. A system analysis approach gives an idea of how the biological component of these hybrid structures works. This is exemplified by the putative role of the microenvironmental pH as a parameter of the utmost importance for the malignant "mode" of tumor cells, which can be monitored and modeled on such hybrid structures.     

Transfer of genetic information in an organism

New knowledge in biology led us to a better understanding of organization and functioning of living organisms. Today, re-evaluation of our concept of human biology is taking place. Theoretical analysis shows that taking into account the complexity of the organism and frequency of spontaneous mutations, it is impossible to explain the real time of organismal life. Therefore, besides extant systems, other repair systems must also exist. There are three "levels" at which a cell population withstands mutational pressure. First - intracellular (repair), second - intercellular (all forms of informational flows), and third - cellular replacement. Stem cells undertake regenerative functions following damage at the level of the tissue. They are also influenced by mutations, and for stem cells, it is most important that they preserve and support their full activity.     

"Basic brown", a too little considered iris color]

The eye colour is mainly effected by the two components melanin and structural blue of the iris stroma which generally are present in various mixtures respectively combinations. Are these components lacking the dark pigment epithelium can produce a so-called "basic brown". The exact distinction between "brown" and "basic brown" is without doubt of considerable value for anthropological as well as for genetical examinations of eye colours.     

Spontaneous symmetry breaking in genome evolution

The quest for evolutionary mechanisms providing separation between the coding (exons) and noncoding (introns) parts of genomic DNA remains an important focus of genetics. This work combines an analysis of the most recent achievements of genomics and fundamental concepts of random processes to provide a novel point of view on genome evolution. Exon sizes in sequenced genomes show a lognormal distribution typical of a random Kolmogoroff fractioning process. This implies that the process of intron incretion may be independent of exon size, and therefore could be dependent on intron-exon boundaries. All genomes examined have two distinctive classes of exons, each with different evolutionary histories. In the framework proposed in this article, these two classes of exons can be derived from a hypothetical ancestral genome by (spontaneous) symmetry breaking. We note that one of these exon classes comprises mostly alternatively spliced exons.     

Motile chemosensory behaviour of phagotrophic protists: mechanisms for and efficiency in congregating at food patches

Phagotrophic protists are capable of congregating at point sources of food within a few minutes, from distances of up to several cm in the case of ciliates, or several mm in the case of microflagellates. This is exemplified by four ciliate species and a heterotrophic flagellate. Congregation is accomplished by the combined effect of more than one type of chemosensory motile behaviour including "kinetic responses", "temporal-gradient sensing", and "helical klinotaxis". The results are discussed in terms of microscale patchiness in nature.