Nomenclature

Everyone is all up in arms about whether Pluto (+ other massive objects at the far end of our solar system) is a planet. It would seem like every ScienceBlog blogger expounded his/her opinion on the subject.

I thought this would be a one day affair in our ADD world, but again this morning I pick up the NYTimes and there is an Editorial entitled "Dissing Pluto and other Plutons". (The NYTimes used the word Dissing???)

The trouble is, the new definition of a planet will include an awful mélange of icy rocks found on the outer fringes of the solar system. It would be far better to expel Pluto from the planetary ranks altogether, leaving us to bask in the comfortable presence of the eight classical planets that were discovered before 1900 and have excited wonder ever since.

I just don't get it.

This phenomenon is not only limited to Astronomy, in Biology there apparently have been nomenclature wars (traditionalists vs. cladists). All of you should join the study of genes, or as we like to call it the Tower of Babel.

At the level of genes and proteins, the only rule is anarchy. Across species, orthologues gene may have several names and different genes may have the exact same name. I've already ranted on my frustration over the abbreviation "APC". Here's another story.

In my graduate thesis I studied the effect of a gene on microtubule dynamics. This gene used to be called mDia2 (for mammalian Diaphanous 2), a member of the formin family of proteins. In humans this gene was associated with deafness and was hence called DFNA1. Then at some point other formins started to appear. Names for these genes kept flying around. At some point it was announced that human hDia3 and not DFNA1 was the true orthologue of mouse mDia2, hence from that point on mDia2 was to be renamed mDia3 (and mDia3 would be converted to mDia2). So now if you read the formin literature, you're never sure what gene a manuscript is referring to.

Story #2. A couple of months ago, someone in lab presented a paper on bacteria signalling. In times of low nutrients, bacteria form hardy spores that can remain dormant until conditions change. To form the spore, the mother cell duplicates its DNA, then shoves one copy of its genome into a newly formed sac. Once the DNA transfer is complete, the spore signals the mother cell to activate the end of sporulation. This sac is then coated with a hardy cell wall and the mother cell commits suicide. The mechanism of this signalling is quite complicated ... but the nomenclature is even worse. (In fact it is so bad that the authors of the paper changed the nomenclature in attempt to simplify things, but in the end this just added to the confusion).

And so we have SpoIVA (as in Spo-4-A; forth stage of sporulation, gene A) SpoIVB, SpoIVCA, SpoIVCB, SpoIVFA, SpoIVFB ... and these are just of the SpoIV class ...

Try looking at this literature long enough and your head spins:

I think that the yeast researchers got it right. All genes in yeast genomes have a three letter abbreviation followed by a number. If you are writing about the protein, add a "p" to the end. Now the only problem with yeast is harmonization. For example, Cdc28 is probably one of the most important genes. It encodes a protein (Cdc28p) that regulates when cells divide (Cdc=cell division cycle) ... in S cerevisiae. But in S pombe the orthologue is called Cdc2p. What is worse than the two genes not having the same name, is having two genes with slightly different names. It drives me nuts.

So let them have Pluto, Plutons and all the rest. It's good PR. I can see kids talking about "the new planet". I'm sure that all these designation changes won't confuse astronomers. Just count your blessings that you're not trying to figure out bacteria sporulation ...