Recent work on gene concepts has been influenced by recognition of the extent to which RNA transcripts from a given DNA sequence yield different products in different cellular environments. These transcripts are altered in many ways and yield many products based, somehow, on the sequence of nucleotides in the DNA. I focus on alternative splicing of RNA transcripts (which often yields distinct proteins from the same raw transcript) and on 'gene sharing', in which a single gene produces distinct proteins with (...) the exact same amino acid sequence. These are instances of molecular pleiotropy, in which distinct molecules are derived from a single putative gene. In such cases the cellular and external environments play major roles in determining which protein is produced. Where there is molecular pleiotropy, alternative gene concepts are naturally deployed; molecular epigenesis (revision of sequence-based information by altering molecular conformations or by action of non-informational molecules) plays a major role in orderly development. These results show that gene concepts in molecular biology do, and should, have both structural and functional components. They also show the need for a plurality of gene concepts and reveal fundamental difficulties in stabilizing gene concepts solely by reference to nucleotide sequence. (shrink)

According to Conceptual Role Semantics ("CRS"), the meaning of a representation is the role of that representation in the cognitive life of the agent, e.g. in perception, thought and decision-making. It is an extension of the well known "use" theory of meaning, according to which the meaning of a word is its use in communication and more generally, in social interaction. CRS supplements external use by including the role of a symbol inside a computer or a brain. The uses appealed (...) to are not just actual, but also counterfactual: not only what effects a thought does have, but what effects it would have had if stimuli or other states had differed. The view has arisen separately in philosophy (where it is sometimes called "inferential," or "functional" role semantics) and in cognitive science (where it is sometimes called "procedural semantics"). The source of the view is Wittgenstein (1953) and Sellars, but the source in contemporary philosophy is a series of papers by Harman (see his 1987) and Field (1977). Other proponents in philosophy have included Block, Horwich, Loar, McGinn and Peacocke (1992). In cognitive science, they include Woods (1981) and Miller and Johnson-Laird (1976). (See references in Block, 1987.). (shrink)

Developments in the sequencing of whole genomes and in simultaneously surveying many thousands of transcription and translation products of specific cells have ushered in a conceptual revolution in genetics that rationally introduces top-down, holistic analyses. This emphasized the futility of attempts to reduce genes to structurally discrete entities along the genome, and the need to return to Johannsen's definition of a gene as 'something' that refers to an invariant entity of inheritance and development. We may view genes either as generic (...) terms for units of inheritance whose referents are pragmatic ad hoc and context-dependent, or as (epistemologically) representing entities of cell functions. It is cellular functions that determine the structural referents along the DNA. Structures that happened to secure specific functions that were essential for or conducive to the survival of cells were selected for. With natural selection being the etiological background of genes as functions, genes obtain again their theoretical role as intervening variables, abstractive variables that purely 'summarize' characters. The importance of DNA sequences is that of all possible phenotypes these are the most basic ones from which we can read off the genotype directly. (shrink)