A defense of syntax-based gene concepts in postgenomics: ‘Genes as modular subroutines in the master genomic program’

The purpose of this article is to update and defend syntax-based (conserved DNA-sequence motifs) gene concepts. I show how syntax-based concepts can and have been extended to accommodate complex cases of processing and gene expression regulation. In response to difficult cases and causal parity objections, I argue that a syntax-based approach fleshes out a deflationary concept defining genes as genomic sequences and organizational features of the genome contributing to a phenotype. These organizational features are an important part of accepted molecular explanations, provide the theoretical basis for a large number of experimental techniques and practical applications, and play a crucial role in in annotating the genome, deriving predictions and constructing bioinformatics models