[Phylogenetic thinking in the modern biology]

I Ia Pavlinov
Zhurnal Obshcheĭ Biologii 2007, 68 (1): 19-34
Any research activity is conducted within the framework of a cognitive situation which is defined by certain basic assumptions about ontology of the portion of the objective world under investigation. From the standpoint of the non-classical scientific epistemology, a part of that situation is constituted by personal knowledge which is formed by a set of thinking (cognitive) styles. The scholastic thinking existing in taxonomy and phylogenetics is considered as an example showing unavoidability of such styles in the natural history knowledge. It is initially rooted in the antic, mythological by its essence, persuasion of isomorphism between movements of the objective reality and of the mind. The instrumentalism entailed by scholastic thinking is based on the mythologeme according to which the "right method" par excellence can lead to the "right knowledge". That is why any disputes between different numerical methods of phylogenetic reconstructions are vain: their validity could be assessed not formally but within particular cognitive situations formed by particular basic models of the phylogenesis. Phylogenetic thinking is of the key importance in evolutionary biology and has great impact on various fields of biology based on it. It is pretty mythological because of non-observability of the phylogenesis: the latter is rather "thinked-in" in the objective world then is induced from the observed facts. It constitutes a part of the evolutionary thinking considering mainly macroevolutionary trends and stressing the initial causes in the structure of causal relations in the analyses of the diversity of organisms. The "tree thinking" of O'Hara is its rough operational equivalent. Relation between phylogenetic thinking and some other styles are considered, which are population, phenetic, typological, and epigenetic ("developmental" of O'Hara). Phylogenetic thinking makes it obliged inclusion of the initial causes in the explanatory models which underlie adaptive and functional peculiarities of organisms, as well as of the entire structure of the biodiversity. It manifests itself in such kind of models through uncovering the phylogenetic signal. This thinking style has great effect on understanding of the ontology of taxa and acknowledges the objective status of the phylogenetic pattern. It is intrinsically included in the argumentation schemes of constructional morphology, comparative phylogenetics. The central metaphor of the phylogenetics is the Tree of Life. Emagination of its unity and uniquiness is of naturphilosophical nature. From the contemporary epistemological standpoint, it should be considered as a generalization upon partial hypotheses of evolution of particular structures each corresponding to certain consideration aspect of the global phylogenesis. Acknowledging of multi-aspectness of the phylogenesis constitutes one of the important points of modern phylogenetic thinking. As different semogeneses are incompletely congruent, the Tree of Life is less certain than each of the initial hypotheses. Any attempt to make it more resolved would lead to its reduction to any of the particular semogenetic scheme (i.e. to a "gene tree") or to its "decay" into several trees each corresponding to a particular consideration aspect of the global Tree.

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