A very full week last week (ok, they are all ‘full’) started with the visit of Minister of Universities and Science David Willetts to a topping out ‘milestones’ ceremony celebrating partial completion of the ‘Development Phase 1’ building at the Institute for Animal Health at Pirbright. This is a major project for us, with this part alone costing rather north of £100M. It will allow a major expansion of our abilities to carry out research in this space, and will surely prove a magnet to other talented researchers. For reasons of biosecurity, the building itself includes many technical innovations, as well as high specifications even for more conventional materials like the concrete of which it is constructed. This kind of infrastructure is paralleled by e-infrastructure, another important part of scientific infrastructure for the development of which I attended another meeting.
I also fulfilled a long-standing engagement to give a seminar on pharmaceutical drug transporter, including the latest work, at Eisai pharmaceuticals in Hatfield, Herts, where I also enjoyed some very useful discussions about the pharmaceutical industry more generally. It was encouraging to note that the location of this unit reflected recognition of the strength of the UK science base.
I also participated in a ‘double header’ of Institute Assessment Panels on the Norwich Research Park, specifically at the Institute for Food Research and the John Innes Centre. Both were extremely ably chaired by Council Member John Coggins.
Two of my scientific papers have recently appeared online. The first, a result of the last grant proposal I (co)wrote before coming to BBSRC, exploits a modern and effective multiobjective evolutionary computing algorithm to find a small cocktail of pharmaceutical drugs (from a bounded search space of some 9 billion possible combinations) that inhibits the production of interleukin-1beta. Such cocktails, that reflect the emerging ideas of network pharmacology and included an iron chelator, might serve to be of importance in inflammatory diseases such as stroke. Another paper that just came out involved a multi-author perspective highlighting the virtues of the semantic annotation of systems biology models.
I quite enjoy statistical paradoxes. One typical such, with a Bayesian underpinning, is the so-called Three Doors Paradox, also known as the Monty Hall Problem. As phrased (roughly) in the Wikipedia link: A player in some kind of a game show is told that behind one of three doors lies a new car, but behind the others only a booby prize (a goat). The player is allowed to pick a door. In search of a new car, the player picks a door, say 1. The game host (who knows the answer – this is important) then opens one of the other doors, say door 3, to reveal a goat, and then offers – before the next door is opened – now to let the player pick door 2 instead of door 1. Should the player stick with the original choice or swap, or does it make no difference? The ‘obvious’ answer is that the odds are now 50:50 between the remaining doors 1 and 2 and that each guess thus has an equal probability of being correct and thus that there is no point in the player changing their choice. What do you think, before reading on?
As (like everyone else) I am a user of a considerable variety of software, both general and scientific, I am often moved to consider how the latter especially might best be funded. An interesting blog rehearses the disjunction between the needs of academic software development in bioinformatics and of career advancement; the conventions of the latter (involving publications) mean that more kudos is attached to producing your own software with functionality similar to what exists, rather than contributing to solving a difficult problem in a software program or environment that already exists. Obviously one really good SNP caller (or genome browser or whatever) is better than 3 or 10 less good ones! Collaborative activities such as those promulgated via Apache may be a way forward, but how best to organise them?
For the three doors problem: oddly enough (or not, if you have the correct perspective), the better strategy is always to swap from the original choice and if door 1 was the first pick indeed now change and pick door 2.
Finally, please note that the closing date for applications for our Innovator of the Year competitions is November 15th!
- Courtot, M., et mult. al. (2011). Controlled vocabularies and semantics in Systems Biology. Mol Syst Biol 7, 543. Full free text
- Hopkins, A. L. (2008). Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4, 682-690
- Kell, D. B. (2009). Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Medical Genomics 2, 2 Full free text
- Lanthaler, K., Bilsland, E., Dobson, P., Moss, H.J., Pir, P., Kell, D. B. & Oliver, S. G. (2011). Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast. BMC Biol, online manuscript. Full free text
- Small, B. G., McColl, B. W., Allmendinger, R., Pahle, R., Lopez-Castejon, G., Rothwell, N. J., Knowles, J., Mendes, P., Brough, D. & Kell, D. B. (2011). Efficient discovery of anti-inflammatory small molecule combinations using evolutionary computing. Nature Chem Biol., online