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2

Genotype, Phenotype, and Environment

“Exterior” or phenotypic genes are those inherited from both parents that are

responsible for physical characteristics (traits) of an individual, such as the colours

of hair and eyes.

Those asserting the primacy of the genome will nevertheless concede that sending

the complete gene sequence of an organism to an alien civilization will not allow

the reconstruction of the organism (i.e., the creation of a living version of it—i.e.,

its phenotype). The phenotype is a composite of explicit and implicit meaning, the

latter being context-dependent (Stent 1975). Many things, including the principles

of chemical catalysis necessary for the genetic instructions to be read and processed,

may not even be implicit in the nucleic acid sequence (cf. Polanyi (2009)’s tacit

knowledge). As Bernal (1949) suggested, “any arrangement of atoms or molecules

necessarily carries with it complex possibilities of order and function, and those are

immanent in the structure of the molecules themselves”. The combinations actually

appear to depend on “the total play of universal forces” (Bernal) and are the result

of an evolutionary process; they may be considered as contingent. In a mechanical

system, the general character of what happens is governed by the laws of physics,

but specific features are determined by the initial or boundary conditions (Ramsden

2010); Polanyi (1968) has pointed out that the boundary conditions themselves are

not capable of being formulated in terms of physics and chemistry.

Contingency also ensures that differences exist between individuals of the same

species. Our identities are defined by the unique progression of personal acts and deci-

sions made throughout life (Ramsden 2001), rather than by our genetic endowment,

which merely specifies some boundary conditions. When we look in more detail, the

concept of the genome, or the complete set of genes, or chromosomes, or genotype

does not even adequately define a species, because of individual differences. Should

each species be represented by a canonical or standard genotype? ¹

It must also be kept in mind that, in the evolutionary process, natural selection

operates on the phenotype, yet the vehicle for its persistence is the genotype.

Bioinformatics started with computer-based methods for interpreting genomic

data, to decipher the genomic “text”. The computers were necessary to cope with the

vast amounts of data. But genotype is converted to phenotype by an epigenetic pro-

cess of, initially, embryonic development and continues as ontogenetic development

throughout the lifetime of the organism. These epigenetic processes can to some

extent be represented as regulatory networks, the complexity of which also requires

computers to cope with them, and the study of these networks constitutes a second

branch of bioinformatics.

Organisms are commonly characterized as species. Despite the pervasive use of the

term in biology, no entirely satisfactory definition of “species” exists. “Reproductive

isolation” is probably one of the better operational definitions, but it can only apply

under carefully circumscribed conditions. Geographical as well as genetic factors

play a rôle, and epigenetic factors are even more important. In any human settlement

of at least moderate size, there are almost certainly groups of inhabitants having no

social contact with other groups. Hence, these groups are as effectively reproductively

1 See Dupré (2005) for more discussion.