Last week involved a couple of round tables hosted by Minister of Universities and Science David Willetts, the first on collaborations with China and the second on e-infrastructure (a topic that is a regular feature of this blog). Both are very important topics. BBSRC has long enabled collaborations with China through a number of schemes, such as the International Scientific Interchange Scheme and China Partnering Awards scheme. I myself was awarded one of the latter in 2004, and a number of papers, such as one on particle swarm optimization ensued. There is no doubt, that with a population some 23 times that of the UK, a buoyant economy and a large cadre of numerate scientists, China is likely to be a very important partner for the UK.
The report (pdf) at ArXiV claiming that neutrinos can behave as tachyons (i.e. particles travelling faster than light) has excited considerable interest, given that the standard version of Einstein’s theory of relativity places the speed of light as an upper limit on the speed of any particle or information transfer. While there has been evidence since at least the time of the Aspect experiment that Bell’s inequalities can be violated, and thus that superluminal (indeed ‘instantaneous’) information transfer can occur between entangled particles or states, the claimed precision and accuracy of the new experiments imply a difference in speed of the neutrinos and light (presumably in vacuo) of nearly 2.5 parts in 100,000.
Only two real outcomes are possible: the scientific community will find where the errors are and this incident will be confined to history, or the methods and findings will indeed stand up to scrutiny, be improved upon, and the lead authors rewarded with a trip to Stockholm. This is hardly my field, though I do have a strong interest in the philosophy or interpretation of quantum mechanics, wave-particle duality and entanglement, where I have long been attracted to de Broglie’s pilot wave explanation. Here I suspect– like Martin Robbins, Alok Jha and Ian Sample, New Scientist and many twitterati – that the former outcome – a ‘trivial’ explanation of one or more artefacts – is more likely.
Papers I enjoyed reading this week include one on a competition for short-read assembly, and two involving crowd-sourcing approaches, one for the production of enantiopure praziquantel and one involving a crowd-sourced online contribution to the solution of a retroviral protease structure. The last of these – predicting protein structure – is known as an NP-hard problem since in principle every possible tertiary structure might be produced from the amino acid sequence, and finding that of lowest energy (which anyway may not be the true structure), requires testing each of the possibilities.
I have long been musing about the general question of what, in an iterative scientific programme, and given that one has decided the general problem to tackle, is the best experiment to do next, how to find out, and the recognition that asking and answering this is – like the protein structure prediction problem – equivalent to tackling a combinatorial optimization problem. To this end I have just sent off a slightly philosophical piece that suggests that these questions are highly pertinent to all areas of biology. No superluminal particles were involved.
- Alon U: How to choose a good scientific problem. Mol Cell 2009; 35:726-728. Full text
- Aspect A, Grangier P, Roger G: Experimental realization of Einstein-Podolsky-Rosen-Bohm Gedankenexperiment – a new violation of Bell inequalities. Phys Rev Lett 1982; 49:91-94
- Earl DA et mult al. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Res 2011. Full free text as pdf
- Kell DB, Oliver SG: Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays 2004; 26:99-105
- Khatib F, Dimaio F, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I, Thompson J, Popovic Z, Jaskolski M, Baker D: Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nat Struct Mol Biol 2011
- Woelfle M, Olliaro P, Todd MH: Open science is a research accelerator. Nat Chem 2011; 3:745-748
- Yisu J, Knowles J, Hongmei L, Yizeng L, Kell DB: The landscape adaptive particle swarm optimizer. Applied Soft Computing J 2008; 8:295-304. Full free text at Citeseer