Julian's Polymath Explorations

[Updated Mar. 2022] Interactomics today bears a certain resemblance to genomics in the  1990s...  Big gaps in knowledge, but an explosively-growing field of great promise. If you're unfamiliar with the terms, genomics is about deciphering the gene sequence of an organism, while interactomics is about describing all the relevant bio-molecules and their web of interactions. A Detective Story Think of a good police-detective story; typically there is a multitude of characters, and an impossible-to-remember number of relationships: A hates B, who loves C, who had a crush on D, who always steers clear of E, who was best friends with A until D arrived... Yes, just like those detective stories, things get very complex with our biological story!  Examples of webs of interactions, familiar to many who took intro biology, are the Krebs cycle for metabolism or the Calvin cycle to fix carbon into sugars in plant photosynthesis. Now, imagine vastly expanding those cyc...

You might recall, around the year 2000, a Grand Breakthrough in biology: the complete sequencing of human DNA.   People hoped that proteins would be next.  But now, about 20 years later, we're not at that level of understanding when it comes to PROTEINS rather than DNA...  Why? Because proteins are devilishly complex . If you're managing a database (relational or semantic) featuring proteins, you might think that the entities (records) of your database are simply "proteins", and that you're just going to need a number of fields (attributes) to describe those records...  Right?  Wrong! A little basic biology brush-up for starters...  Recall that DNA is a sequence of 4 "letters" ( nucleotides .)  Proteins are sequences of 20 "letters" (amino acids. )  So, why the immense complexity of proteins? There are 20 200  possible amino-acid sequences for a 200-residue protein, of which the natural evolutionary process has sampled only an in...