DNA Codes and Information: Formal Structures and Relational Causes
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DNA Codes and Information: Formal Structures and Relational Causes Richard v. Sternberg
Received: 10 August 2007 / Accepted: 9 March 2008 / Published online: 9 May 2008 Springer Science+Business Media B.V. 2008
Abstract Recently the terms ‘‘codes’’ and ‘‘information’’ as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any ‘‘DNA-centric’’ reductionism. In addition to the implications that are discussed, this approach validates the array of coding systems now recognized in molecular biology. Keywords DNA Genome Code Information Structural realism Structural attractors Mathematical structures
1 Introduction: The Problem of DNA ‘‘Codes’’ and ‘‘Information’’ For decades the prevailing assumption in genetics and molecular biology has been that DNA largely encodes information in the form of templates for RNA transcripts, transcripts that in turn are mainly translated into proteins. The encoded proteins do much of the heavy ontogenetic labor by effecting the self-assembly of the cell and, by extension, the organism. DNA thus has a necessary and sufficient causal role in specifying a bodyplan by providing only the one-dimensional layouts—the genes— for amino acid sequences and some structural RNA molecules. Genes are encoded
R. v. Sternberg (&) Biologic Institute, 16310 NE 80th Street, Redmond, WA 98052, USA e-mail: [email protected]
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information and are the genome in this framework, save for a few incidental sequences involved in their control plus those required for DNA replication, recombination, and genetic transmission. Perhaps nowhere is this assumption more evident than in the use of the label coding to refer to genes that specify proteins, and noncoding to refer to every other DNA sequence, including the loci for regulatory and structural RNAs (Rinn et al. 2007; Washietl et al. 2007; Xie et al. 2007). And even though we are now in the post-genomic era (Griffiths and Stoltz 2006) and now have ample empirical reasons for questioning this notion of DNA codes and information (Gerstein et al. 2007), it still has a hold on the biological imagination (e.g., Collins 2006). Recently though, the terms ‘‘codes’’ and ‘‘information’’ as used in conjunction with the words ‘‘DNA,’’ ‘‘genes,’’ ‘‘genetic program,’’ and the like have been critically examined (e.g., Fox Keller 2000b; Sarkar 2000). Those lines of inquiry have resulted in two general philosophical-theoretical reformulations. The first is an a
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