In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted:
I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd rip into it and add a thousand qualifiers, and it would never get done.
Well, okay, technically speaking he didn't ask me for help. But, since I'm a biologist, as soon as I looked at the definition that he chose, from Modern Genetic Analysis (by Griffiths, Lewontin, Miller, and Gelbart), I couldn't help but find something wrong.
The definition from Griffiths, et. al. reads:
A gene is an operational region of the chromosomal DNA, part of which can be transcribed into a functional RNA at the correct time and place during development. Thus, the gene is composed of the transcribed region and adjacent regulatory regions.
But that sounds like a very nice definition and I know you agree with most of it. What is that you don't like?
I have a problem with the words "chromosomal," "DNA," and I guess even, the phrase "the correct time and place during development."
Why are they problems?
First, the easy part. I disagree with phrase "correct time and place during development" because of cancer cells. Cancer cells contain genes that do not behave nicely. The genes involved in turning a cell from the right path and onto the path of cancer are not getting transcribed at the correct time and place in development. Quite the contrary.
But they are still genes. So, it's easy to cut that part out of the definition.
Next, let's take the terms "chromosomal" and "DNA."
I object to those words because genes can be found on pieces of nucleic acids that are neither part of a chromosome, nor are they DNA. Sometimes the extra-chromosomal nucleic acids are plasmids, sometimes they are viruses. Sometimes they are made of DNA, sometimes they are made of RNA. But they still contain genes.
Alright, then, what's your definition?
A gene is a heritable string of nucleotides that can be transcribed, creating a molecule with biological activity.
[1/22/2007 Added the term "heritable."]
I think this works because it covers all the exceptions and tricky situations that I know about.
The most tricky thing that is up for debate in my definition of a gene, is whether or not we include the regulatory sequences. In practice, when we talk about cloning a gene, we consider a gene to be cloned when we've put the functional part of it into some other DNA molecule (a plasmid or virus). Cloning a "gene" doesn't require cloning the promoter, enhancer, or other kinds of regulatory sequences.
If we compare a gene to a light bulb, the regulatory sequences would be the switch that turns the light on and off, along with the dimmer mechanism that we use to control brightness. If I use a lamp as a metaphor, then, to me, the gene is light bulb, and the regulatory sequences are the pieces that determine whether or not the light gets turned on.
And a pseudogene would a light bulb that's missing the filament.