Output Stream of Consciousness

There is a site that summarizes many of the proteins that creatures have in common with one another. Most of the creatures listed are bacteria, but there are a few multicellular organisms with respective codes: Microsporidia [E], thale cress [A], a worm [C], the fruit fly [D], baker's yeast [Y], fission yeast [P], and humans [H]. "Coming soon", they have rice, the mosquito, chimpanzees, dogs, mice and rats.

The site is the COGs site, "Clusters of Orthologous Groups". If you click on the Eukaryotic Clusters link, you will get a cryptic looking list. What that list is, though, is a list of protein commonalities amongst a certain combination of organisms. So, by their code, "- C D H - - -" lists proteins that are common to just the worm, Caenorhabditis elegans, the fruit fly Drosophila melanogaster and humans. There are 1147 of them listed. Since these are down the animal family tree, this commonality shouldn't be too surprising. (There are 860 more in common between all of those organisms: yes, thale cress and you share proteins)

If you click on the KOGs column, you get a list of these proteins.

The first protein in the list, E3 ubiquitin-protein ligase, is pretty interesting. Oh, you are shocked, I know! It's called the Parkin protein for a reason.

We'll dig in a little deeper using the tools. If you click through, you get a list of the named and numbered proteins. The small tree on the left indicates that the gene encoding the protein duplicated twice somewhere between the common ancestor of fruit fly and human (getting more animal information sequenced will narrow when these happened down a bit!).

If you click on Hs4758884 the second human protein, you get a whole lot of visual hits, followed by text hits. You can see the worm, fruit fly and two other human matches - they have very, very low E values, indicating a very good match for this particular human protein. These are followed by the amino acid comparisons, so you can see what the difference in this protein is between fruit flies and humans, for example.

If you click on the the Genbank link up top, you get a list of abstracts of papers written about this protein. Here, you find some links to why it's called the Parkin protein: some mutations lead to a susceptibility to Parkinson's disease, specifically, a juvenile form.

One thing that struck me as neat is that mutations of this same protein in fruit flies has some of the same effects. Well, as much as a fruit fly can have. It's in this paper on PubMed:

Drosophila overexpressing parkin R275W mutant exhibits dopaminergic neuron degeneration and mitochondrial abnormalities

A lot of jargon, but just so you know, human Parkinson's disease has tremors and muscle control problems with a deficiency of dopamine from the brain. It even involves dopaminergic neurons, too.

Could we learn from fruit fly troubles with this protein? Probably. Certainly even more so from mouse and rat equivalents.

Here's the thing, though: we can do tests like this on animals and actually do something with the results because of common descent.

(Well, either that or something divinely set up to look exactly like common descent!)

Count common descent as not only true, but useful.