One of the most important ideas ever is the distinction between genotype and phenotype – between our genes and the traits they influence. It seems obvious to us now, but scarcely more than 100 years ago it wasn’t, which led to a lot of confusion.
The scientist who really clarified the distinction between genotype and phenotype (and who, along with the word gene, coined these terms), was Wilhlem Johannsen. I recently wrote about Johannsen for Pacific Standard, in the context of the recent discovery of the molecular basis of a European blond allele. Here I want to show why Johannsen’s key insight dispelled so much confusion.
Johannsen summed up his views in a 1911 paper, “The Genotype Conception of Heredity.” He starts out by saying that scientists have been confused because they are thinking about apparent heredity, or the “transmission-conception” of heredity. This transmission conception, which had been around since Hippocrates and Aristotle, was that “the personal qualities of any individual organism are the true heritable elements of traits!”
This is wrong, Johannsen wrote, because “the personal qualities of any individual organism do not at all cause the qualities of its offspring.” Instead, we should take the perspective of the “genotype conception”:
The qualities of both ancestor and descendant are in quite the same manner determined by the nature of the “sexual substances” — i.e., the gametes — from which they have developed. Personal qualities are then the reactions of the gametes joining to form a zygote; but the nature of the gametes is not determined by the personal qualities of the parents of ancestors in question. This is the modern view of heredity.
Unless you’ve thought about the alternative theories, it’s hard to realize how groundbreaking this is.
Once you have the distinction between genotype and phenotype, you can start to make sense of these particularly thorny facts of biological variation:
1. Organisms with identical genotypes can have different phenotypes.
2. Organisms with identical phenotypes can have different genotypes.
Try making sense of that without a genotype-phenotype conception!
Johannsen illustrates this with a figure showing variation in the bean plants he studied. Each row represents phenotypic variability in one genotype or “pure line;” the bottom row shows what happens when you combine them together in to a population. By looking only at the final population, making sense of heredity becomes really, really difficult.
DIAGRAMS SHOWING FIVE DIFFERENT PURE LINES OF BEANS AND A “POPULATION” FORMED BY THEIR UNION. In each case the beans enclosed in glass-tubes are marshalled in equidistant classes of length; identical classes are superposed. The pure lines show transgressive fluctuation: it is mostly impossible to state by simple inspection of any individual bean the line to which it belongs. — The fluctuations about the average length (the phenotype) within the pure lines as well as in the mixed population show no characteristic difference.
This means that the effects of environmental and genetic variation can be indistinguishable on inspection. That’s just one of many weird facts about heredity that makes genetics very hard.
Figure from Johannsen W. The Genotype Conception of Heredity. The American Naturalist 1911;45:129-159.
The Finch and Pea 
Dear Mike. A very good section on Johannsen. I enjoyed very much.
I would like to use the illustration in a book I am writing. Could you please guide me re copyright issue. Who should I apply to? Don’t know if 1911 requires permission now.
I would be very grateful to hear from you.
Thank you
Roy Andersen
Permission acquired. Problem solved. But thank you for a very clear and well meaning article. Roy