The question of heredity was formulated by August Weismann in 1883 when he asked how a single germ cell is capable of reproducing the entire body in all of its details. For Weisman and his successors, the answer was to be found in the action of the genes.
The distinction between genotype and phenotype, introduced by Wilhelm Johannsen in 1911, separates the issues of hereditary transmission from issues of embryonic development. The genotype is the genetic constitution of an organism, which it has inherited from its parents. (In A-life terms, it is the specification of the machinery.) The phenotype is the actual appearance of an organism; its manifested attributes, (or the behaviour of the machinery.) There are thus two separate spaces of description, the genotypic space for the state of the internal factors, which describes the processes of inheritance, and the phenotypic space for the manifest state of the organism, which describes the processes of development.
Ever since Mendel, the genotypic status of the organism has been considered to be causally prior to it phenotypic state. In What is Life?, Erwin Schrödinger describes chromosome structures as the code script of life, which are instrumental in bringing about the development they foreshadow. For Schrödinger, "they are law-code and executive power -- or, to use another simile, they are architect's plan and builder's craft -- in one." (p.22) Individual genetic instructions, or genes, are short stretches of DNA of the right length and base sequence to specify a protein. Each gene is made up of a number of three-base-long codons, each of which specifies an amino acid, the building blocks of proteins. Sequences of amino acids specify a polypeptide chain, which folds up in a complex shape to form a protein. It is this shape which confers phenotypic (functional) properties on the protein. While genes are often described as information, they are understood more as instructions. These instructions are executed, or "expressed", when their DNA sequence is used as a template for transcription, in protein synthesis, for example. "DNA makes RNA, RNA makes proteins, and proteins make us." (Fox Keller) Evelyn Fox Keller describes this as "the discourse of gene action."
Genetics is concerned with the replication and variation of genes in a population (and their impact on adaptation), while embryology studies the expression of the genotype in the phenotype of an individual. The development of the phenotype from the genotype is also called morphogenesis. In contemporary biology, the processes of genetics (the effects of the nucleus) are far better understood than those of development. (relating to the cytoplasm) The separation between genetics and development has been contested by "organismic" geneticists such as Conrad Waddington, for whom the problem of gene activity "is essentially an embryological problem." (see epigenesis / preformation)
While the " big science" projects of genetics such as the human genome project receive enormous attention and funding (and are the object of enormous capitalist speculation), a number of biologists are critical of the suggestion that the genotype determines the phenotype.
Francisco Varela and Jean-Pierre Dupuy note that although molecular chemistry seemed a model success case of reduction, the genetic program needs its own product in order to be executed. Every step of DNA maintenance and transcription is mediated by proteins, which are precisedly what is encoded. They call this the "logic of the supplement," but they could have equally invoked the circular logic of the cybernetic paradigm. (Fox Keller)
Critics of the causal discourse of the gene ("whenever X, then Y.") point out that while one-to-one correspondence between genes and traits may well occur, it is not the general rule, and that specific genetic makeup should not be thought of as either the necessary or sufficient cause for the production of a specific morphology. (see Gerry Webster and Brian Goodwin, Form and Transformation.) In fact, there can also be morphological invariance despite variation in genetic makeup. Part of the difficulty of mapping genotypic space into phenotypic space derives from the fact that the latter are temporal fluxes. Also, mapping in the direction from genotype to phenotype may not be symmetrical when going back from phenotype to genotype. Gerald Edelman proposes "topobiology" as the place (and time) dependent links between the mechanical events leading to the rearrangement and specialization of cells with the sequential expressions of the gene.
Phenotypic plasticity (also called polyphenism) is the ability of a genotype to produce various phenotypes. Increasingly, biologists are becoming aware that organisms, including primates, can develop along different pathways, even assume different forms or exhibit quite different behavioral profiles, depending upon what developmental track they find themselves on. (cf chreod )
Adaptive plasticity describes an actual phenotypic distribution which is affected by environmental demands, so that a given phenotype is more likely to occur in environments where it is more adapted, and less likely to occur where it is less adapted. High plasticity tends to reduce genetic responses to selection. "Norms of Reaction" are graphs showing the phenotype properties of organisms of a particular genotype as a function of the environment. Richard Lewontin uses the complex and unpredictable variations in norms of reaction to criticize the notion that genotype determines phenotype. In addition, he points out that much developmental variation is "developmental noise" -- a consequence of variations from cell to cell in the number of molecules that are being synthesized. "The organism does not compute itself from the information in its genes nor even from the information in the genes and the sequence of environments. The metaphor of computation is just a trendy form of Descartes's metaphor of the machine. Like any metaphor, it catches some aspect of the truth but leads us astray if we take it too seriously." (The Triple Helix, p.38)
The field of artificial life could easily be described as taking metaphors too seriously. It trades on both the metaphor of life as computation and of computation as life. When Christopher Langton discusses development, he qualifies the implications of centralizing control of the "discourse of gene action" by describing the genotype as a largely unordered "bag" of instructions. In general, phenotypic traits at the level of the whole organism will be the result of many non-linear interactions between genes, and there will be no single gene to which one can assign responsibility for the vast majority of phenotypic traits. But as R. B. Goldschmidt pointed out in relation to the gene, "If we wish to express this factual situation by saying that a phenotypic trait is the product of action of many or all genes, we must realize that this facon de parler is nothing but a circumscription, in terms of the atomistic theory of the gene, of the fact of the unity and integrity of the organism".
Langton abstracts the notions of genotype and phenotype into general concepts of GTYPE and PTYPE, noting that for simulations of life, PTYPES should be complex and multilevel, and that their nontrivial properties are not predictable. If this leads to a process of trial and error, natural selection is held up as the only truly efficient general procedure for searching. (see evolution)
Richard Dawkins proposes to consider human artifacts as part of the "extended phenotype"
(for an architectural interpretation, see John Frazer arch theories)