What is a Gene? The Definitive Answer

I think the GenBank file spec gets the definition just right:

gene: A region of biological interest identified as a gene and for which a name has been assigned.

That’s basically it. If people call it a gene, it’s a gene.

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They could mean:

  • a region in the genome that gets transcribed (or translated; but are introns no longer part of it?)
  • the nucleotide or amino-acid code in those regions
  • the “reference” nucleotide code that is expected in that region
  • the homologs of that (or othologs or paralogs or purposefully remaining fuzzy because it’s hard to say what’s what)
  • the regions of genome that cluster together across different organisms
  • a higher level concept that groups several proteins together through inferred orthology
  • (or perhaps even convergent evolution)
  • the protein encoded by the gene (or the general cluster of proteins)

In many discussions, gene is a good word to rationalist taboo. It clears up many mistakes when people are obliged to say what they mean by this tricky word.

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Another good word to taboo is species when the organisms are bacteria

To even use the same word as we have for animals is probably a mistake. We need a word for “bacteria whose rRNA clusters together in nucleotide space” without all of the baggage of species.

And so we would replace a veneral biological concept with a computational definition: progress!

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