Structure-Function Analysis of Transformation Events

At the beginning of the twenty-first century, critical reforms were outlined in biology. This was due to the fact that the increase of information garnered from the sequences of informational molecules (DNA, RNA and proteins) and their perception by the scientific community were incompatible with the narrow horizons of the dogmas and paradigms that shaped the ideology of biological knowledge at the end of the last century. The clear linear representations that were invoked during the initial period of the development of molecular biology were at first encountered with numerous exceptions to these "clear" rules and then lost in the avalanche of new representations that were incompatible with the linear schemes. As a result, new directions of study and even meta-directions (e.g., epigenetics, epigenomics and biosemiotics for reviews, see Allis et al., 2007; Ferguson-Smith et al., 2009; Hoffmeyer, 2008) have arisen, and functionally oriented divisions of biological science have formed that are named as various “–omics” (including the extravagant “biblioma”Abi-Haidar et al., 2007), the RNA machine (Amaral et al., 2008), and the molecular mechanisms of cell cycle regulation and individual development. In turn, these disciplines have demanded new theoretical implementations involving novel approaches from the theory of networks and systems (Barabasi et al., 2000; West & Brown, 2005; Zaretzky & Letelier, 2002). The last two decades have been particularly rich in discoveries concerning the mechanisms of the expression of biological information, such as new ways of alternative splicing (Rodriguez-Trelles et al., 2006), a variety of functions for non-coding transcripts and the role of short RNAs as forward and reverse regulators (Mattick et al., 2009). Presently, we have a situation in biology in which it would be nearly impossible to publish a book with the title “DNA Makes RNA Makes Protein” (Pentris et al., 1983). However, another book, with a title equally as concise and perfectly reflecting the new biological paradigm, has not yet been written. In other words, a revision of the old concepts has not been completed with a new and clear way of structuring the data from the quickly growing "body" of biological science. Theoretical biology is also at a critical state, which is characterized by attempts to formulate or reformulate the basic concepts and axioms of the discipline. Signs of such attempts may be the revival of interest in the definition of life, the revision of “sets” and even “types”, signs that distinguish the living from the non-living and increased attention to the genotypephenotype relationship.