Making sense of genotype-phenotype distinctions, version 2

The genotype-phenotype distinction—or, rather, the array of such distinctions—provides an entry point into the implications of the two foundational developments of modern biology—the theories of evolution by natural selection and the genetic basis of heredity—being built from the language, arguments, evidence, and practices of controlled breeding in agriculture and the laboratory.   Complexities get suppressed, which engenders new problems and complexity-recovering efforts.

When Johannsen (1911) introduced the terms genotype and phenotype, he was articulating an alternative to traditional accounts of heredity that, in his words, “tried to conceive or ‘explain’ the presumed transmission of general or peculiar characters and qualities ‘inherited’ from parents or more remote ancestors.”  More generally, he was promoting a shift from “morphological-descriptive” natural history, in which appearances could mislead, obscure, or be spun into speculative theories, to an “exact science,” using the experimental control of biological materials and conditions needed to establish repeatable outcomes and expose hidden mechanisms. In this endeavor, he recognized that “the objects for scientific research” are the “’types’ of organisms distinguishable by direct inspection or… by finer methods of measuring or description, [which] may be characterized as ‘phenotypes.’ Certainly phenotypes are real things.” The challenge, then, was to find phenotypes that would be a reliable basis for thinking about not-readily-observed processes of heredity.

Experiments on inbred lines of beans that Johannsen had undertaken provided his primary model. The plants in any line showed variation yet selection for some desired trait did not result in improvement from one generation to the next.  This result affirmed Weismann’s theory of the germplasm, which refers to cells that are sequestered early in the development of an organism, buffered from most of the interactions within the organism and with the environment that occur during the organism’s lifetime, and form a basis for development of an organism of the next generation. Whatever the germplasm was that seeds from a line shared and in whatever ways it “reacted” during the plant’s development, “interfering with the totality of all incident factors, may it be external or internal,” seeds of the next generation did not result in plants that matched their parent any more than any other seed. Plants from the inbred line were instances of a genotype; variation in the traits grown from the seeds was, borrowing from Wolterek, the norm of reaction (Reaktionsnorm) of that genotype; a plant’s relative position in the norm of reaction was not transmitted to its offspring.

Yet, even in Johannsen’s world of inbred lines, phenotypes, as he noted, might be heterogeneous, a mix of several genotypes (as illustrated by the one figure in Johannsen 1911). To remove the ambiguity of appearance, Johannsen needed a second model, Mendel’s experiments on peas, which can be summarized as follows:

  1. Conditions in which the peas were grown were as uniform as possible from one plant to the next.
  2. Inbred lines were established that differed one from the other in dichotomous ways, e.g., round or wrinkly peas; tall or dwarf plants.
  3. By preventing self-pollination, different inbred lines could be crossed to produce hybrids (F1) and then self-pollinated to produce the next generation (F2).
  4. The F1 hybrids all showed one of any pair of dichotomous traits. Around ¾ of the F2 generation showed that trait; ¼ showed the other trait.
  5. From the F1 and F2 ratios Mendel concluded that each pea had two “factors” influencing each trait, one from the pollen and one from the ovary (Law of segregation). When the two factors were of different kinds, the trait that resulted from development looked the same as the inbred line that looked like the F1 and more frequent F2 hybrids (Law of dominance).

In summary, although the F1 hybrids appeared the same as one of the inbred parents, by observing the ratios of the two traits in the F2 generation, the hybrids could be shown to belong to a different, in Johannsen’s terms, genotype—a heterozygote, not a homozygote.

Several features of Johannsen’s account are relevant to subsequent conceptual and methodological developments and debates about genotype and phenotype. First: Johannsen is not clear whether inbreeding, crossing, and self-pollination were to be seen as “finer methods of measuring or description” so that the inbred parent would be classified as a different phenotype from the F1 hybrid. If so, the study of heredity should find or generate phenotypes—classes of organisms distinguished by traits—that are identical to genotypes—classes of organisms that share germplasm. In any case, the character of the phenotype had become a secondary matter; what was important to Johannsen was to have a means to distinguish genotypes. Even if “differences between the phenotype-curves [that result from reactions of different genotypes under various conditions] may vary considerably or may even vanish entirely,” a specific “genotypical constitution always reacts in the same manner under identical conditions.” Having established this, it makes sense to shift the focus from the primacy of genotypes in heredity to the material basis of the shared germplasm shared by a genotype.

to be continued — or revised….

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