Biological ontologies

I've postponed really learning about ontologies in bioinformatics for a while now, but circumstances now dictate that I figure it out. It is a little bewildering. As just one example, the current Gene Ontology has the following processes as the top-level categories of "biological processes":

1. biological adhesion


2. biological regulation


3. carbohydrate utilization


4. carbon utilization


5. cell killing


6. cell wall organization or biogenesis


7. cellular component biogenesis


8. cellular component organization


9. cellular process


10. death


11. developmental process


12. establishment of localization


13. growth


14. immune system process


15. localization


16. locomotion


17. metabolic process


18. multi-organism process


19. multicellular organismal process


20. nitrogen utilization


21. phosphorus utilization


22. pigmentation


23. reproduction


24. reproductive process


25. response to stimulus


26. rhythmic process


27. signaling


28. signaling process


29. sugar utilization


30. sulfur utilization


31. viral reproduction

Most of these are reasonable, some seem odd. Pigmentation? A top-level process?

It reminds me of the fabulous first paragraph of Michel Foucault's "The Order of Things" (in my opinion his best book):

This book first arose out of a passage in Borges, out of the laughter that shattered, as I read the passage, all the familiar landmarks of my thought - our thought, the thought that bears the stamp of our age and our geography - breaking up all the ordered surfaces and all the planes with which we are accustomed to tame the wild profusion of existing things, and continuing long afterwards to disturb and threaten with collapse our age-old distinction between the Same and the Other. This passage quotes a ‘certain Chinese encyclopedia’ in which it is written that ‘animals are divided into: (a) belonging to the Emperor, (b) embalmed, (c) tame, (d) sucking pigs, (e) sirens, (f) fabulous, (g) stray dogs, (h) included in the present classification, (i) frenzied, (j) innumerable, (k) drawn with a very fine camelhair brush, (1) et cetera, (m) having just broken the water pitcher, (n) that from a long way off look like flies’. In the wonderment of this taxonomy, the thing we apprehend in one great leap, the thing that, by means of the fable, is demonstrated as the exotic charm of another system of thought, is the limitation of our own, the stark impossibility of thinking that.

Protein of the Day #17: mTOR

mTOR (mammalian target of rapamycin) does a whole lot of things, as the attempted pathway image below shows (from Wikipedia, which I am not ashamed to link to for biochemistry). My interest in it comes from its role in energy balance, particularly in synthesizing information in the hypothalamus. Since I am primarily focused on mammalian hibernation, the fact that mTOR is a serine-threonine kinase is intriguing - its known that transcription and protein translation are shut down during mammalian torpor bouts so the control mechanisms are likely to involve post-translational protein modifications such as phosphorylation. Perhaps mTOR is involved in these mechanisms.

Live from Cape Town

I arrived at AIMS (the African Institute for Mathematical Sciences) yesterday. Its a great place, right on the Muizenberg beach near Cape Town - quite a thrill after being in Duluth this time of year.

I have volunteered to teach a short course on bioinformatics algorithms here, using biopython and Sage as the computational platform. It will be very interesting to see how it goes over. I am using the Plasmodium species which cause malaria as a source of examples and projects.

Below is a satellite picture of the cape peninsula and a view of Muizenberg that includes the main AIMS building.

Protein of the Day #15: Adropin

Recently in Cell Metabolism there was a very interesting article on the newly characterized peptide Adropin. Adropin seems quite important in regulating the balance between sugar and lipid use as fuels; its one of several promising avenues to understanding and treating diabetes that have come out in the last year or two. The peptide is cleaved from the product of the gene Enho (energy homoestasis associated). Its extremely well conserved in mammals - for most species the amino acid sequence is 100% identical (a few ungulates have 1 amino acid difference). Here is a picture of the conservation from UCSC's genome browser:

Interactive coalescents

Genetic coalescents are interesting statistically; the variance in the time to coalescence is large, which is the kind of quantity I think human intuition has trouble with. So it helps a bit to be able to play with them (code can be found here):