Genotype–phenotype mapping and the end of the ‘genes as blueprint’ metaphor

Abstract

In a now classic paper published in 1991, Alberch introduced the concept of genotype -phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch's approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened the need for a different conceptual treatment of how phenotypes are produced. Old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading about the nature of G!P, and are being replaced by an algorithmic approach emerging from the study of a variety of actual G!P maps. These include RNA folding, protein function and the study of evolvable software. Some generalities are emerging from these disparate fields of analysis, and I suggest that the concept of 'developmental encoding' (as opposed to the classical one of genetic encoding) provides a promising computational -theoretical underpinning to coherently integrate ideas on evolvability, modularity and robustness and foster a fruitful framing of the G!P mapping problem.

A Model of Artificial Genotype and Norm of Reaction in a Robotic System

“…In other words, genes determine phenotypes. This sort of answer bypasses the process of development, which is treated as an incidental blackbox with no direct causal relevance to the evolutionary process [11]. From this point of view, changes in the species are produced by isolated changes in the individuals.…”

The mismeasure of machine: Synthetic biology and the trouble with engineering metaphors

“…Contemporary biology too is steeped in engineering metaphors (Pigliucci, 2010;Pigliucci & Boudry, 2011): genes are said to carry information that constitutes a ''blueprint'' for the organism; cells and sub-cellular organelles are talked about in terms of factories full of molecular machines. When the human genome project got started, the hope was to be able to have the information necessary to ''read off'' a human being stored on a CD or hard drive, thereby allowing biologists to pinpoint with precision where to intervene to cure a number of diseases.…”

Epigenetic Operators and the Evolution of Physically Embodied Robots

“…These developmental models were designed with the understanding that the process by which a phenotype is constructed is as critical to an individual's fitness as the information coded in its genome. However, in biological systems, this construction process is not fully specified in the genome (Pigliucci, 2010). Instead, epigenetic processes, together forming the genetic regulatory network (GRN), alter how the genotype is expressed through physical interactions.…”

“…Keywords: epigenetic operators, evolutionary robotics, development, genotype-phenotype mapping, physically embodied robots inTrODUcTiOn In biology, understanding how development-the mapping of genotype-to-phenotype (G → P)-shapes the creation of phenotypic variation has created a paradigmatic shift in evolutionary theory (Wagner and Altenberg, 1996;Pigliucci, 2010). The long-standing "adult transformation" paradigm treated development as if it were absent, invariant, or instantaneous, in spite of Garstang's (Garstang, 1922) early hypothesis that ontogenies, not fully formed adults, evolve (Northcutt, 2002).…”