Information, Coding, and Biological Function: The Dynamics of Life.

In the mid-20th century, two new scientific disciplines emerged forcefully: molecular biology and information-communication theory. At the beginning, cross-fertilization was so deep that the term genetic code was universally accepted for describing the meaning of triplets of mRNA (codons) as amino acids. However, today, such synergy has not taken advantage of the vertiginous advances in the two disciplines and presents more challenges than answers. These challenges not only are of great theoretical relevance but also represent unavoidable milestones for next-generation biology: from personalized genetic therapy and diagnosis to Artificial Life to the production of biologically active proteins. Moreover, the matter is intimately connected to a paradigm shift needed in theoretical biology, pioneered a long time ago, that requires combined contributions from disciplines well beyond the biological realm. The use of information as a conceptual metaphor needs to be turned into quantitative and predictive models that can be tested empirically and integrated in a unified view. Successfully achieving these tasks requires a wide multidisciplinary approach, including Artificial Life researchers, to address such an endeavour.

Hierarchical pattern formation during amphibian limb regeneration.

In 1901 T.H. Morgan proposed in "Regeneration" that pattern formation in amphibian limb regeneration is a stepwise process. Since, biologist have continued to piece together the molecular components of this process to better understand the "patterning code" responsible for regenerate formation. Within this context, several different models have been proposed; however, all are based on one of two underlying hypotheses. The first is the "morphogen hypothesis" that dictates that pattern emerges from localized expression of signaling molecules, which produce differing position-specific cellular responses in receptive cells depending on the intensity of the signal. The second hypothesis is that cells in the remaining tissues retain memory of their patterning information, and use this information to generate new cells with the missing positional identities. A growing body of evidence supports the possibility that these two mechanisms are not mutually exclusive. Here, we propose our theory of hierarchical pattern formation, which consists of 4 basic steps. The first is the existence of cells with positional memory. The second is the communication of positional information through cell-cell interactions in a regeneration-permissive environment. The third step is the induction of molecular signaling centers. And the last step is the interpretation of these signals by specialized cell types to ultimately restore the limb in its entirety. Biological codes are intertwined throughout this model, and we will discuss their multiple roles and mechanisms.

Foundations of Intonational Meaning: Anatomical and Physiological Factors.

Like non-verbal communication, paralinguistic communication is rooted in anatomical and physiological factors. Paralinguistic form-meaning relations arise from the way these affect speech production, with some fine-tuning by the cultural and linguistic context. The effects have been classified as "biological codes," following the terminological lead of John Ohala's Frequency Code. Intonational morphemes, though arguably non-arbitrary in principle, are in fact heavily biased toward these paralinguistic meanings. Paralinguistic and linguistic meanings for four biological codes are illustrated. In addition to the Frequency Code, the Effort Code, and the Respiratory Code, the Sirenic Code is introduced here, which is based on the use of whispery phonation, widely seen as being responsible for the signaling and perception of feminine attractiveness and sometimes used to express interrogativity in language. In the context of the evolution of language, the relations between physiological conditions and the resulting paralinguistic and linguistic meanings will need to be clarified.

Interrogando as teorias sobre o arco-íris / Understanding the theories about the rainbow

Tentar entender as teorias do arco-íris é uma maneira de pensar sobre as argumentações entre a lógica científica e o pensamento mítico na história da ciência. Este trabalho segue três percursos relacionados: primeiramente, expõe um resumo das descontinuidades e recorrências históricas na explanação do arco-íris; em segundo lugar, examina registros de etnógrafos estrangeiros na Amazônia, na primeira metade do século XX; por último, aborda a 'teoria nativa' sobre o fenômeno nas terras baixas da América do Sul, visando compreender a lógica das classificações nativas, que opera como um pensamento mítico. A simetria das disciplinas permite uma complementaridade entre as teorias científicas e as humanidades, bem como analogias entre diferentes leituras dos códigos biológicos e sociais.

Trying to understand the theories of the rainbow we focus the debate between scientific logic and mythic thinking in the history of science. This paper follows three paths. Firstly, it presents a summary of the discontinuities and recurrences in the explanation of the fenomena in history of thinking. Secondly, registrations of foreign ethnographers in the Amazon in the first half of the twentieth century are examined. Thirdly, the approach is directed to the 'native theory' about the rainbow in the low lands of South America, trying to understand the logic behind the native classifications as mythic thinking. Symmetry among disciplines supposes complementarities between biological theories and humanities and allows for analogies involving biological and social codes.