Eugenio Andrade

From external to internal measurement: a form theory approach to evolution

The point of view of external observers has led to an explanation of life based on digitally encoded information. In contrast, the existence of natural internal observers, or agents that belong to the same scale of the observed objects, explains the appearance of form centered approaches. The main controversies in thermodynamics and evolution are due to the changes of perspective, so as to speak, if measurement is considered to be external or internal. Equilibrium theories developed for closed systems under ideal conditions are analogous to external measurements. On the other hand, morphogenetic perspectives as far from equilibrium thermodynamics applicable to open systems allow to imagine self-organizing agents that perform local measurements. Chaitins algorithmic approach would help to elucidate the relation between digitally encoded information and active forms, because forms and shapes are responsible for specific pattern recognition and play a major role in the process of finding the proper measuring standard. The predominance of form over digital records is illustrated by studying the mapping between genetic descriptions and functional shapes, originally suggested for RNA, by Schuster. Therefore, interactions between living entities are seen as reciprocal measurement processes that bring about couplings (shortened descriptions and local decreases of entropy) that are paid by partial record erasure (increase of entropy). To conclude, this approach centered on the inner dynamics or form is appropriate for understanding how Lamarckism and the modern neutral theory of evolution can be integrated for expanding the neoDarwinian perspective.

A semiotic framework for evolutionary and developmental biology

This work aims at constructing a semiotic framework for an expanded evolutionary synthesis grounded on Peirces universal categories and the six space/time/function relations [Taborsky, E., 2004. The nature of the sign as a WFF--a well-formed formula, SEED J. (Semiosis Evol. Energy Dev.) 4 (4), 5-14] that integrate the Lamarckian (internal/external) and Darwinian (individual/population) cuts. According to these guide lines, it is proposed an attempt to formalize developmental systems theory by using the notion of evolving developing agents (EDA) that provides an internalist model of a general transformative tendency driven by organisms need to cope with environmental uncertainty. Development and evolution are conceived as non-programmed open-ended processes of information increase where EDA reach a functional compromise between: (a) increments of phenotypes uniqueness (stability and specificity) and (b) anticipation to environmental changes. Accordingly, changes in mutual information content between the phenotype/environment drag subsequent changes in mutual information content between genotype/phenotype and genotype/environment at two interwoven scales: individual life cycle (ontogeny) and species time (phylogeny), respectively. Developmental terminal additions along with increment minimization of developmental steps must be positively selected.

Designing a methodology to estimate complexity of protein structures

This paper proposes a methodology to estimate the information content of protein structures by using: an alphabet of local microenvironments obtained from a set of protein domains with equivalent function, a modification of the physical complexity concept [1], the measures of mutual information (I(seq; str)) and conditional entropy (H(str|seq)). between sequence and structure. The kinase domain catalytic subunit was used as a specific example. Our results are in accord with the hypothesis that proteins are information gathering and using systems [3], and suggest that protein structure depends less on protein sequence than biologists have historically supposed.