Last week I attended the annual Science Foo camp (twitter hashtag #scifoo) ‘unconference’, held at the Googleplex outside San Francisco. Just as last year, topics were determined by attendees offering sessions in one of 14 rooms they considered appropriate to the anticipated audience size.
The first session I attended was on the evolution of beauty, and topics discussed ranged from the natural world (e.g. bird feathers) via language and the co-evolution of art and its appreciation. We also saw a demo of some linguistic analyses of various writers, that allows one to discover whether one’s style if more like that of Shakespeare or of Beatrix Potter (for instance). I then attended one by Hod Lipson on the automation of science, including various strategies for automated reasoning and scientific discovery, similar in essence to the Robot Scientist project, and including a useful site for generating equations or rules from data, based on what is usually referred to as genetic programming.
I then led a couple of presentations myself, the first on “How can we feed 9 billion people sustainably by 2050?”. This elicited a good crowd and much useful and thoughtful input, including some very interesting thoughts by Richard Jefferson of Cambia on the hologenome (review) and specifically the contribution of the soil ecosystem to plant root size. This implies that we need to seek genes not only in crops but in the soil ecosystem with which they are in mutually beneficial contact; according to this view, ‘plant breeding’ (including the genomics-driven approach) should imply improving both plants and their symbiotic microflora, with the latter possibly being easier. (I also sent off a minireview on the role of deep roots in carbon sequestration, just before reading a nice piece on roots in a survey of agriculture published in the July 29th Nature.)
A second session that I led concerned the role of iron in various diseases, where among others I met Hugh Rienhoff of Ferrokin, who have an interesting and novel iron chelator undergoing trials.
Other sessions I attended were one on the reproducibility of digital experiments led by Carole Goble and Victoria Stodden, one on new media led by the BBC’s Andrew Marr and by Aleks Krotoski (presenter of a BBC series on the Virtual Revolution), one on the human (and other) microbiomes led by David Relman and Richard Jefferson (mentioning lots of papers new to me, such as this and this), privacy issues surrounding the online availability of data, including genomics data, led by Tim Hubbard, and one on The Academic of the Future, led by Nigel Warburton and Sarah Caddick. I also managed to join a couple on the Big Data challenge, including one led by Mario Caccamo from TGAC.
In discussion, I was alerted to a variety of interesting ‘Open Innovation’ types of websites, such as patientslikeme, a novel and ‘crowd-sourced’ way of doing Phase III clinical trials much more cheaply and effectively, and the Open Knowledge Foundation’s wheredoesmymoneygo showing just that for UK Treasury Data. This, and a lovely site at DECC, allow one to play citizen scientist or citizen policymaker and see quite quickly what might be sensible strategies for solving grand challenge problems such as those in energy. There is also an interesting and well-written report from Nesta on how best to rebalance the economy.
I also enjoyed a walk-through of the updated scientific visualisation exhibition that I visited last year, as it reminded me of several wonderful visualisations (like this one on the value of research). Visualisation remains extremely important, and a 6-screen joystick-controlled version of Google Earth gave much food for thought as to how one might wish to explore scientific knowledge in a similar kind of way. The data are largely available, but the software is not! To this end, we are co-organising with AHRC a workshop on the challenges of visualising biological data, for which applications are still open. A driver of this is the need to understand large volumes of data, and I read a nice method for the combinatorial optimisation of biochemical networks for biotechnological overproduction.
A huge number of visionary people (some 330) were invited this year, including Nobelists, Royal Society Presidents, Eco-pioneers, a man who flew across the English Channel without a plane, journalists from Scientific American, New Scientist and The Economist, experts in cosmology, multiverses, quantum gravity, many computer scientists, and so on, and thus the chance of meeting them all was remote. Some of the many sessions I could not attend (amusingly, two were proposed for multiverses, but they were merged…) were tweeted at #scifoo, which contains some fascinating links to many other blogs. Overall, an inspiring and useful meeting that it would be nice to see emulated in the UK. Any takers?
- Dethlefsen, L., Huse, S., Sogin, M.L. & Relman, D.A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6, e280 (2008). Full free text.
- Gewin V: An underground revolution. Nature 2010; 466:552-553.
- King, R. D., Whelan, K. E., Jones, F. M., Reiser, P. G. K., Bryant, C. H., Muggleton, S. H., Kell, D. B. & Oliver, S. G. (2004). Functional genomic hypothesis generation and experimentation by a robot scientist. Nature 427, 247-252.
- Ranganathan S, Suthers PF, Maranas CD: OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput Biol 2010; 6:e1000744. Full free text.
- Zhao, L. & Shen, J. Whole-body systems approaches for gut microbiota-targeted, preventive healthcare. J Biotechnol (2010).
- Zilber-Rosenberg I, Rosenberg E. (2008) Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev. 2008 Aug;32(5):723-35.
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