They're tags and you end up with multiple names for the same gene. They might as well be replaced with an arbitrary string of numbers- those are equally easy to do a quick Google scholar or pubmed search with. You don't lose anything of value by changing the name. In chemistry amd organic chemistry, the proper IUPAC name of the compound also tells you its structure. It tells you what the compound is in a real physical sense. If you go to someone thats never heard of a compound d and you give them the full IUPAC name, they can draw it. You can't change those names without losing meaning.
You go to someone who's never hears of the hedgehog signaling pathway and ask them what SHH is, they're not gonna be able to give you much.
this does not negate the fact that these tags or lables actually do have meaning they are not arbitrarily made up.
if you do not have any understanding of rust and you read the source code it seems like meaningless tags but if you understand the idea of syntax you can see there is some underlying principle to the combinations of characters.
being unfamiliar with the scheme doesnt make it meaningless hash. the failure is not representation it is interpretation.
if we want to talk about absolutes the universal way to identify a gene is with its locus or loci depending on the nature of the gene, before we get there we use "tags" lables indexes to allow quick access to a particular character in a local store of data.
the whole thing about revising the standards of a genes identifying name is about getting the greatest benefit quickly with the least effort so we can get back to science and away from blaming the tools for the lack of craftsmanship.
Since when is the universal way to identify a gene its locus? The locus is just the position of a given gene in a particular chromosome. The function of a gene is not exclusively tied to chromosomal location. If I take the sequence for SHH and move it to a different location in the genome under the appropriate promoters, it will still express sonic hedgehog. If I go and shove some other gene sequence into where SHH is otherwise located on the genome, that new insert will not serve as a ligand in the hedgehog signalling pathway. The entire field of synthetic biology is predicated on moving bits of DNA to new locations.
The point is that there is no concrete, universal, IUPAC style scheme to naming these genes. I don't know what the comparison to a program language is supposed to imply. The syntax when programming has meaning beyond a meaningless hash. The syntax in gene naming barely has more meaning that a meaningless hash, because at least occasionally its related to a phenotype or function or keeps the same silly scheme for multiple members of the (e.g. hedgehog) pathway. That's not much.
>>the function of a gene is not exclusively tied to chromosomal location<< ...epigenetics, ultrastructure of expression systems
"Since when is the universal way to identify a gene its locus" since molecular genetics...and gene mapping.
this whole thing started with the idea that gene lables are arbitrary meaningless tags by extension not a problem to change labels to stop a spreadsheet program from mangling data. so now that we both know that genetic labels or tags or whatever you prefer to insert, are far from arbitrary thats the end of that.
You may note I used the word exclusively. TADs are hardly the end all be all of gene function. Epigenetics has more to do with gene regulation than function, and TADs aren't remotely close to the dominant force in epigenetics either.
Gene mapping through genetic linkage maps hasnt really been a major part of identifying and classifying genes for a while - not since sequencing became accessible. You could consider a genome sequence the ultimate physical (not linkage) map, but that's a couple decades out of fashion.
Edit: and im still not sure whether you're defending or attacking the naming of the hh family of genes, but yes, I'm intimately familiar with the hedgehog signaling pathway, and just because the hh loss of function makes fruit fly embryos look spiky doesn't mean that the name is justified or meaningful. Amd a basic problem in ontology is figuring out what that unifying theme should be to name all genes around, its not as easy as in chemistry. But until that's solved, the world loses nothing by changing shh to something less embarrassing so patients don't have to deal with being told their cancer has driver mutations in a pathway involving sonic the hedgehog.
Is your background in biology/molecular biology? I'm happy to share some links to resources if you'd like to read up on the state of the art now, including on gene ontology (GO). GO is an attempt to unify how genes are represented to give more meaning to the representations. I have my doubts about how successful these initiatives will be, but they're still really fascinating stuff. The field has come a long way since Morgan and Sturtevant developed that first linkage map back in 1913. And in epigenetics, there's so much more than TADs. There's the usual methylation/history acetylation etc, but also things like alternative splicing (perhaps not strictly epigenetics) that significantly change what genes do and what sequence even gets translated from the same locus. There's a lot of amazing stuff in happy to share some resources that I think are a good place to get caught up on the state of the art.
You go to someone who's never hears of the hedgehog signaling pathway and ask them what SHH is, they're not gonna be able to give you much.