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A lot of people are attacking excel in this thread, just remember to give a fair share of the blame to people naming genes as well. These are meaningless names

A lot of people are attacking excel in this thread, just remember to give a fair share of the blame to people naming genes as well. These are meaningless names and changing them is frankly easier than changing a feature in excel (that the finance folk probably don't want changed). And its a good excuse to clear up some of the egregiously silly disease related names as well so we don't tell parents their kid is suffering from a debilitating mutation in luke-Skywalker-like upside-down cantaloupe 12b or whatever.

rolph 6y ago
no these are not meaningless names, there is undue confusication in the case of the more contemporary names such as [Sonichedgehog] these are not meaningless lables https://en.wikipedia.org/wiki/Sonic_hedgehog https://en.wikipedia.org/wiki/Sonic_hedgehog mentioned eslewhere in this thread is a nomenclature that allows one to easily find notes referring to the gene from your research library. It was a new cadre of young upcoming scientists that decided to break with tradition and use something familiar to lable genes according to game characters or pop icons.
- vikramkr 6y ago
  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.
  - rolph 6y ago
    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.
    - vikramkr 6y ago
      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.
      - rolph 6y ago
        do you know why HH is named such ? >>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.

rolph 6y ago

no these are not meaningless names, there is undue confusication in the case of the more contemporary names such as [Sonichedgehog] these are not meaningless lables https://en.wikipedia.org/wiki/Sonic_hedgehog https://en.wikipedia.org/wiki/Sonic_hedgehog mentioned eslewhere in this thread is a nomenclature that allows one to easily find notes referring to the gene from your research library. It was a new cadre of young upcoming scientists that decided to break with tradition and use something familiar to lable genes according to game characters or pop icons.

vikramkr 6y ago
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.
- rolph 6y ago
  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.
  - vikramkr 6y ago
    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.
    - rolph 6y ago
      do you know why HH is named such ? >>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.