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The word 'gene' is quite ambiguous, hardly worth even using

Larry Moran lamoran at bioinfo.med.utoronto.ca
Tue Sep 16 09:26:24 EST 2003

On 16 Sep 2003 14:17:41 +0100, Bob <xyzbbruner at uclink4.berkeley.edu> wrote:
> On 15 Sep 2003 17:36:50 +0100, Larry Moran
><lamoran at bioinfo.med.utoronto.ca> wrote:
>>It's a stupid way of thinking. I define a gene as a DNA sequence
>>that is transcribed. (There are a few exceptions to this definition
>>but it works very well.) RNA editing and the rest don't have any
>>effect on my ability to recognize what I define as a gene.
>>You can try as many different definitions as you like but I think
>>I'll stick with one that works, thank-you very much.
> Well, ok, but that is something of a copout.

No it's not. Your original claim was that it's impossible to define
a gene. I gave you a definition that seems to work pretty well. Why
is that a copout?

> So you have defined the word gene to be a transcription unit.

Not exactly. I defined a gene as a region of DNA that is transcibed.
That may not be the same as a "transcription unit." I'd have to know
what you mean by "transcription unit" before I could agree. Do you
have a definition?

> But what we ultimately want is a unit of function (making a protein?)
> -- whatever you call it.

Okay. If that's what you want then try and come up with a word for
it. "Gene" is already taken. How about "protein-encoding region of

> Anyway... what do you mean by what is "transcribed"? Pol II
> transcription does not have a well defined terminus. Message end is
> determined not by transcription but by polyadenylation, which may
> vary. But actual extent of transcription goes beyond that.

This is only one of many difficulties with my preferred definition.
I think we all know how to criticize any definition of a gene since
we're all pretty knowledgeable about biology. The fact that there are
exceptions to every rule (and definition) in biology does not mean
that it's hopeless to try and come up with meaningful terms. There's
a useful molecular definition of "gene" and it seems to work well
in most cases. I don't think it's helpful to abandon the word just
because it can't be precisely defined to cover all possibilities in
every living species.

The real problem here is that you, and the authors you quote, want
to define a gene in terms of making a particular protein. This kind
of definition is a holdover from the olden days before the discovery
of functional RNA's. We need to recognize that some genes don't encode
proteins and any reasonable definition has to take this into account.
(Unless, of course, we want to stop talking about tRNA "genes",
ribosomal RNA "genes, or "genes" for snRNA's.)

Larry Moran


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