Names and abbreviations in biology
Elsewhere on SE Biology I have answered a related question regarding enzyme names. Here I will restrict myself to genes, as it seems that this is the main concern of the poster. (In talking about ‘abbreviations’ I think he is referring to what are generally termed gene ‘symbols’.) The answer from @KarlKjer addressed current recommendations regarding gene nomenclature; mine addresses the causes of the current confusion.

Summary


Rules (actually recommendations) did not appear until a late stage in
the development of the field of genetics, when the problem was
already there and there was a need to do something about it.
Historically in animal systems the naming of new genes tended to
relate to mutant phenotypes as this was how they were discovered. The function of the gene that had been mutated was generally unknown.
Sometimes different mutants of the same gene caused different
phenotypes, either because of severity of damage to the protein, use
of animals from a different development stage, or different growth
conditions for bacteria. These mutants appeared to be of different genes, which
were given different names.
Sometimes the same gene was discovered at about the same time by
different workers and given different names in the laboratory while work was in progress and, hence, on publication.
Later it became possible in some cases to identify the products of
genes for which there was no clear mutant phenotype — perhaps just
lethality — and one method of naming was on the basis of the size of the
protein, preceded by the letter ‘p’ (e.g. p63)
The current trend is to try to rename genes according to the function
of their products, where these are known, i.e. to replace the name of a
mutant phenotype by the name of an enzyme or structural protein.
The implementation of such rules or recommendations is imperfect,
depending on the cooperation of authors and editors.


Illustration using some Drosophila genes

I shall use Drosophila melanogaster (the fruit fly) to provide some illustratations of the history of genetic nomenclature, because this was the organism used by Thomas Hunt Morgan (he of the centimorgan) to perform genetic studies after the rediscovery of Mendel’s work in 1900.  His laboratory was responsible for the discovery in 1910 of the first Drosophila mutant, a spontaneous sex-linked mutant that resulted in males having eyes that were white, rather than the normal red. The gene responsible for this mutant was named white, initiating the custom of naming genes after their mutant phenotype. (Drosophila gene names became italicized by convention.) What else could they have done? Not only was the protein product of this gene unknown, the whole idea of genes encoding proteins did not yet exist. The abbreviation (symbol) for this gene was merely w. Clearly, nobody anticipated that another 17,000 genes would follow, or suggested that a committee on gene nomenclature should be set up.

It is interesting to note that the product of the white gene was not identified until almost 90 years later. In 1999 it was established that this was a member of the ABC transporter family, responsible for bringing  into cells the guanine and tryptophan  needed to make the red pigment so characteristic of the eye of the wild-type Drosophila. The human version of white was identified roughly contemporaneously by sequence homology, and although it was initially referred to as hW (human homologue of white) is now named according to its gene product: ATP-binding cassette sub-family G member 1 (ABCG1). Its function in humans — who only have red eyes in flash photographs — is in lipid transport.

The era of of molecular genetics in the late twentieth century brought an avalanche of new genes, many not associated with a particular phenotype. The culture — accepted by scientific journals — was that if you discovered a new gene you had the right to name it as you pleased. A generation of young scientists were pleased to chose names that reflected twentieth century, rather than classical, culture. Flip through the names of Drosophila genes (try the autocomplete here) and you will find alien, bazooka, cactus, Dorothy, ether a go-go all the way to zucchini. Nor was it only the Drosophila geneticists that were responsible for this. The hedgehog segmentation gene, discovered in Drosophila, has three human homologues. One of these was named ‘sonic hedgehog’, which I am informed is the protagonist of a children’s video game. O tempora, o mores!

A couple of final points will be made to illustrate the problems of nomenclatue of Drosophila genes. Several other mutations of the white gene have been observed which have different phenotypes (e.g. result in different eye colour). This is because they involve insertions into the gene rather than its complete deletion. This also illustrates one historic difficulty that could result in several names for the same gene. The other point is that many of the genes identified by genome sequencing, at least initially, were associated with no mutant phenotype and had no known function, and were so named simply be an accession number (CG1234 etc.). As functions emerged they would be renamed. And an example of the nomenclature situation can be seen in the NCBI entry for Drosophila gene TfIIS (RNA polymerase II elongation factor):


  Also known as: BG:DS00929.12; br52; CG3710; Dmel\CG3710; DmS-II; DmSII; l(2)35cF; l(2)35Cf; l(2)br52; l35Cf; RnpSII; TFIIS; TFIISA; TFS-II