I just wrote a very long semi-ranting comment over on Pharyngula that I decided to put it here as a post to be considered along with Basics: What is a Gene?

MartinCL: Greg, that definition is SO twentieth century. A gene doesn’t necessarily have to encode a protein. What about non-coding RNA genes like microRNAs or cis-antisense genes ?

Greg thusly rants: The more I think about it the more I deeply disagree with you. To be fair (to myself) the definition I posted here is the watered down simplified version without the details which is the one being requested. The fuller definition is on my blog, and addresses your issues with a sort of compromise. (that I don’t actually like)

But here is why I don’t agree with expanding the definition of a gene to include non-coding RNA etc. etc.:

That expanded definition is a dog being wagged by the tail. Once upon a time, in the 20th century, we figured out that the units of inheritance were stored in the DNA molecule. So, the definition of the gene included DNA, details of the encoding of the gene in the DNA, and details of the expression of the DNA as a product related to the traits that we knew were inherited … in other words, gene expression roughly equaled the information end of protein synthesis.

Everything was fine until science progressed, so now in the 21st century we know that the DNA system is more complex.

The dog is the definition of the gene, the tail that is wagging it is comprised of two things: Anything anybody figures out that DNA does, and every detail and exception to any central definition or model. Forget about the second aspect and focus on the first.

Do you know that the total amount of DNA in a species-typical cell correlates (no, not just correlates, relates functionally to, so I don’t wanna hear any “correlation does not equal etc… remarks”) to the size of the cell, and thus to the metabolic efficiency of the cell, and thus with metabolic implications for the whole organism? This is probably why some animals have genomes where the genes take up most of the space and there is little or no “junk” etc. Even some of their genes may be shorter and they may nave fewer functional duplicate genes. Birds that fly have nil junk DNA, birds that don’t fly have junk DNA. Bats have nil junk DNA. Etc.

If the definition of the gene requires that everything known about DNA is included in it, then this apparent fact needs to be somehow shoehorned into the definition of a gene. How the heck do you do that? What does that get you?

If you find out (the following is very made up:) that some DNA is used to store energy… so in a muscle cell that is stressed for energy some of the DNA is sliced out and used for energy … would you feel the need to incorporate that into the definition of a gene? I would hope not. That would be included in your definition or description of DNA.

It is simply not the case that the definition of a gene needs to be the definition or description of all of the properties of DNA. The genes are the units of inheritance. In order for a gene to be expressed there needs to be a supply of amino acids, there needs to be a bunch of enzymes, there needs to be specific features of organelle structure and arrangement to get at the DNA, build the protein … The nucleic membrane, even the cell membrane are involved in some way in this expression. Among this list of things are the non-coding RNA’s There are many things related ultimately to expression. We don not include foraging behavior that leads to ingestion of specific amino acids in our definition of a gene. Yet, by not including that in the definition of a gene, it is not the case that we don’t know it is happening. We do not feel the need to incorporate all of biology into the definition of the gene!

If the non-coding RNA’s were actually separate organelles that simply duplicated themselves during cell division and had no template in the DNA, the approach you are taking would not require their existence to be accounted for in the definition of the gene other than in their functional role. If DNA was used for energy sometimes then according to the way you are building a definition you would have to include energy storage in the definition of a gene.

The DNA tail is wagging the gene definition dog.

Genes are units of inheritance. DNA is a big-’ol molecule. They are not exactly the same thing. This is not a 20th century idea!

Requiring every single thing that DNA does in the definition of the gene is like … requiring our definition of intestines to include tape worms and sausages. We can certainly discuss tape worms and sausages in along side intestines, but they are not part of the basic description.