Last week, I enjoyed reading a couple of books on what is known as complexity or complex systems, the first by Melanie Mitchell and the second by Stuart Kauffman. The concept of complexity has a very particular kind of meaning in systems science, and though definitions abound, Mitchell’s version captures the essence: a complex system is “a system in which large networks of components with no central control and simple rules of operation give rise to complex collective behaviour, sophisticated information processing, and adaptation by learning or evolution” (although I’d quibble with the necessity for large networks).
While it is often quipped that there is no noun that cannot be verbed, Kauffman purposively, on several occasions, uses situated as an adjective – a usage I rather like. Kauffman’s thesis is a strongly anti-reductionist view of biology (I agree), in which we should not separate existence from function (are genes or functions selected during evolution?). Kauffman has an astonishingly fertile mind, and some of the cute ideas that flow from quite fundamental concepts of random Boolean networks that he sets down include one in which the number of human cell types (macrostates) is approximately the square root of the number of genes (true) and one that describes a power law distribution (with slope -1.5) of the effects of gene deletions, a fact observed by two groups.
Another interesting book was a ‘popular’ version of an extended nutritional assessment of diet and health in China – “The China Study” – that covered 65 rural locations sampling 100 individuals from each. The considerable variance in both the concentrations of biochemicals (e.g. cholesterol levels were typically far lower than in the West) and disease prevalence was very notable. Consequently, the book contained some striking statistics on the relationships between dietary practices and disease susceptibility. Some were evidently causal, as mechanisms could be proposed and checked.
As part of my vacation, we enjoyed an all-day visit to Kew Gardens. Plenty of wonderful displays of all kinds of plants, as well as some outstanding examples of botanical art and garden photography, and extensive reminders about the economic importance of plants and their diversity. Another visit was to the Design Museum, which included an exhibition of the recent Designs of the Year. Design is something that is often ignored but great (and sometimes iconic) designs – think of the London tube map) – contribute hugely to the success of products and services. One that caught my eye was a project creating sustainable furniture from bamboo – one wonders whether other grasses such as Miscanthus might be suitable.
There are some areas in which computers are better than humans and some in which the converse is true; we do not in all cases know which area is which, however. A recent elegant crowd-sourcing effort has shown that in some cases computers and people collaborating iteratively, in this case on the ab initio protein folding problem, do better than either alone, since humans will tolerate – better than will most search algorithms – intermediate states that are considerably less good than are their progenitors. Clearly this kind of approach could be applied to many other problems of biology, most of which are also combinatorial in nature
It is said that some 50% of proteins are metalloproteins, but that is on the basis of those that we know about. Although some metal-binding protein motifs are well established, our knowledge is likely far from complete. A recent exploratory experimental paper in Pyrococcus furiosus finds 343 proteins that bind metals, of which 158 were neither known nor predicted to bind metals effectively. This kind of data-driven strategy will soon increase greatly our knowledge of this field.
Finally, the announcement and open data availability of the draft 5-fold coverage of the wheat genome by a BBSRC-funded consortium attracted considerable media interest, such as this and a leader in the Independent, and places the UK firmly at the forefront of wheat research. The release is a step towards a fully annotated genome and is part of an international effort to develop a complete genome. Further work will include UK research teams and scientists collaborating across the world, particularly through coordination via the International Wheat Genome Sequencing Consortium (IWGSC).
- Campbell, T.C. & Campbell II, T.M. The China Study. (Benbella Books, Dallas, TX; 2004).
- Cooper, S. et al. Predicting protein structures with a multiplayer online game. Nature 466, 756-760 (2010)
- Cvetkovic, A. et al. Microbial metalloproteomes are largely uncharacterized. Nature 466, 779-782 (2010)
- Kauffman, S.A. Reinventing the sacred:a new view of science, reason and religion. (Basic Books, New York; 2008)
- Mitchell, M. Complexity: a guided tour. (Oxford University Press, Oxford; 2009)
- Rämö, P., Kesseli, J. & Yli-Harja, O. Perturbation avalanches and criticality in gene regulatory networks. J Theor Biol 242, 164-170 (2006)
- Serra, R., Villani, M., Graudenzi, A. & Kauffman, S.A. Why a simple model of genetic regulatory networks describes the distribution of avalanches in gene expression data. J Theor Biol 246, 449-460 (2007)
- Waldron, K. J., Rutherford, J. C., Ford, D. & Robinson, N. J. (2009). Metalloproteins and metal sensing. Nature 460, 823-30
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