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Can someone explain a bit more about "horizontal transfer"? It would seem that a gene is simply a symbol in relation to the DNA it is a part of, and so there i

Can someone explain a bit more about "horizontal transfer"? It would seem that a gene is simply a symbol in relation to the DNA it is a part of, and so there is no reason to believe that a particular gene would mean the same thing in two different species DNA. The context for the meaning of the gene would seemingly be completely accidental. But then if a horizontal transfer resulted (by chance) in something with selection value, it would be likely to remain in the population. Do horizontally transferred genes typically do something novel? Or do they interact with other (distantly, vertically shared) genes in their resulting expressions? Is my description of a gene in the context of DNA being a "symbol" accurate? Or is there a more accurate programming metaphor. I would hesitate to liken it to a subroutine, but I am curious if it might be more analogous to a type class or something like that.

thaumasiotes 9y ago
"Gene" is often used as a technical term to refer to a stretch of DNA that produces a protein. If it's being used that way here (no opinion), then in a pretty raw sense it would mean exactly the same thing in two different species. Specifically, it would mean that both species produced e.g. lactase. The overwhelming majority of DNA is not "genes" in this sense, which confuses a ton of people.
- grandalf 9y ago
  > Gene" is often used as a technical term to refer to a stretch of DNA that produces a protein. How does something like pleiotropy happen if a gene simply codes for a protein? Is the thing that is pleiotropic actually the protein?
  - thaumasiotes 9y ago
    Well, in the first place, I think my original comment was pretty clear that the word "gene" is used in multiple senses. For example, the words immediately following your quote are "if it's being used that way here...". In the much less important second place, it shouldn't be hard to imagine that two different phenotypical processes might both be cued by the presence of the same chemical.
  - dekhn 9y ago
    The ontology of genetics is not isomorphc with the actual physical methods by which phenotypes are expressed. Think of genetics (and the content that a gene codes for proteins) as a first order approximation to the actual underlying mechanics, or as the primary component in a multidimensional, nonlinear, feedback driven system.
21 9y ago
Not a biologist. Most genes code for proteins, so in a programming sense, the genome would be a directory and the genes files. Obviously, the raw order and position of files on disk doesn't matter if you just want to run them. But it seems that there is also information in the genome which is position dependent, which is more of what you alluded, that moving stuff around would break things.

thaumasiotes 9y ago

"Gene" is often used as a technical term to refer to a stretch of DNA that produces a protein. If it's being used that way here (no opinion), then in a pretty raw sense it would mean exactly the same thing in two different species. Specifically, it would mean that both species produced e.g. lactase. The overwhelming majority of DNA is not "genes" in this sense, which confuses a ton of people.

grandalf 9y ago
> Gene" is often used as a technical term to refer to a stretch of DNA that produces a protein. How does something like pleiotropy happen if a gene simply codes for a protein? Is the thing that is pleiotropic actually the protein?
- thaumasiotes 9y ago
  Well, in the first place, I think my original comment was pretty clear that the word "gene" is used in multiple senses. For example, the words immediately following your quote are "if it's being used that way here...". In the much less important second place, it shouldn't be hard to imagine that two different phenotypical processes might both be cued by the presence of the same chemical.
- dekhn 9y ago
  The ontology of genetics is not isomorphc with the actual physical methods by which phenotypes are expressed. Think of genetics (and the content that a gene codes for proteins) as a first order approximation to the actual underlying mechanics, or as the primary component in a multidimensional, nonlinear, feedback driven system.

21 9y ago

Not a biologist. Most genes code for proteins, so in a programming sense, the genome would be a directory and the genes files. Obviously, the raw order and position of files on disk doesn't matter if you just want to run them. But it seems that there is also information in the genome which is position dependent, which is more of what you alluded, that moving stuff around would break things.