The Logical fallacy
‘Phenotype’ is defined [by the poster] as the morphological expression
of characters on the basis of genetic constitution/genotype
There is no reason to accept this particular definition, but I find it reasonable enough. However I maintain that it is a logical fallacy to say — as the poster does — that it implies that if a morphological characteristic of an organism can, in certain circumstances, be caused by non-genetic factors, then it can never be a ‘phenotype’. To allow that implication the definition of phenotype would have to be something like:
A morphological expression of characters arising solely from the
genetic constitution of an individual.
which it is not what the definition states.
The term phenotype was coined and is used, solely in the relation to genetics. Hence, if the presence or absence of a particular gene causes a particular morphology, that morphology can be regarded as the phenotype of that gene or allele. This does not exclude the morphology also being the phenotype of another gene/allele, because the term is employed in relation to a specific gene. (Of course, some morphological features have a multigenic cause, and some genes have no observable phenotype, but that is irrelevant to the poster’s proposition.)
Incidentally, Mendel — who never used the term phenotype but a more cumbersome (Czech or German) phrase instead — would have been well aware that the size of peas could be affected by their access to nutrients and the weather. This did not invalidate his using size to access the effects of various breeding crosses and make conclusions about their origin in terms of invisible ‘factors’, only later called ‘genes’.
Footnote: Terminology in the biological sciences
Students from the numerical sciences (especially physics and mathematics) are in the habit of thinking in terms of definitions relating to the laws of the universe, and in this sphere a legalistic dissection of terms is often valid. The biological sciences are experimental sciences in which there are few, if any, universal laws. Ideas about biology develop from a limited number of observations (historically on whole organisms, rather than at the molecular level), and are refined as more observations are made and it becomes possible to provide molecular explanations for them. To communicate ideas it is necessary to make formal proposals and often to devise new terms to express them. Such proposals are not like laws or theorems in the numerical sciences. They frequently require modification as greater complexity is revealed and the anarchy of biology throws up exceptions. Biological scientists do not spend time debating the meaning of terms devised years previously. When new discoveries emerge they modify their picture of science and either modify or add riders to their terminology. They certainly do not spend their time shouting that a particular giant of the past had feet of clay. (Only seldom is there a complete revolution in ideas, or yesterday’s hero declared a charlatan.)
An example of the way genetics adjusts can be seen in Beadle and Tatum’s historic proposition: “one gene—one enzyme”. This was a made in 1941 at a time when the molecular nature of genes was still in debate (many, if not most, still thought that they were protein in nature) and not a single protein had been sequenced. The importance and originality of the proposal was in formulating a molecular relationship between nebulous entities, genes, and known molecules, enzymes.
Of course, we now know that not all proteins are enzymes, and some genes encode RNA (the structure and functions of which were unknown in 1941). Moreover with structural determination it became evident that some enzymes and proteins have more than one polypeptide chain, encoded by distinct genes (two genes—one enzyme). More recently, the discovery of alternative splicing means that in certain cases the situation is one genes—many enzymes.
Does this in any way diminish the contribution Beadle and Tatum made with their one gene—one enzyme hypothesis? I, for one, would wish to have half their insight.
