Last week began with a meeting of the Heads of Research Council of the G8 nations, the G8HORCs of the title. This is an annual meeting that moves between member nations, and this time was held in the UK at and near the University of Warwick. This was a very useful opportunity to hear, in a closed setting that allowed a degree of frankness, the thoughts of equivalent leaders of research funding agencies around the world. Many of the issues are common to us all, of course (the increasing costs of doing science, open access, data floods, upskilling our communities, etc.), but the opportunity to share solutions that work was both welcome and taken. Subra Suresh, the relatively new Head of the US National Science Foundation, stayed on for further meetings with the RCUK Chief Executives both as a group and individually, and this allowed a longer and deeper discussion.
It is not news that man-made systems, as systems, share properties of natural systems, such as being selected for by processes describable as evolution. A well-known recent paper by Haldane and May made this very explicit in terms of the knowledgebase of ecologists that has evidently not penetrated the systems of financial regulation. Having been thinking along these lines for some time, I enjoyed some discussions of how we might take forward a programme in this area in due course. It seems that the models of mainstream economics still make unsupportable assumptions about ‘efficient markets’, while folk who model biological and other highly nonlinear system have never sought to and thus might have methods better suited to the modelling of economic systems.
Another meeting concerned the EU ICT Future Emerging Technologies Pilot projects, to help ensure a suitable UK involvement in the next stages.
I spent a thoroughly interesting day at the Centre for Process Innovation in Wilton, necessarily concentrating on aspects surrounding the National Industrial Biotechnology Facility, and enjoying a tour of the fermentation and related facilities, while also learning about other aspects such as printable electronics. Process Technologies represent a substantial fraction of the UK manufacturing sector, and this facility seems to be an excellent model of how to help take technologies through the ‘valley of death’ between early promise (‘technology readiness levels’ 1-3) and full commercial application (levels 8-9). Continuing a previous example, I learnt another new chemical engineering processing word: prilling.
Synthetic biology, with potential applications in industrial biotechnology, continues to develop new and exciting tools. A stunning paper published last week described methods for large-scale genome replacement, a harbinger of the many others we shall need in order to do synthetic biology in vivo. I also much enjoyed a lecture by Prof Jean-Louis Reymond from the University of Berne. Nature makes polypeptides as linear chains that fold up, but in an unusual series of applications of combinatorial synthetic biology, Prof Reymond has enjoyed considerable success in synthesising polypeptides as dendrimers (‘like broccoli’). These had enjoyed application as catalysts and binding agents, inter alia.
An interesting question concerns how many molecules of a particular chemical formula might exist, and Prof Reymond has also done some very interesting work in this area. Recent developments include a searchable map of PubChem, including from a drug discovery point of view, and an open online database that allows one to discover what other real or conceivable molecules are (in a specified sense) ‘close to’ the structure of a particular starting molecule, an area that has attracted my own interest.
Finally, I was pleased to note our announcement of the publication of the genome sequence of a strain of potato. Although for various genetic reasons this was a variety rather different from those commonly cultivated, it will serve as a reference for sequencing those, with a view to uncovering the genetic basis for the considerable variation observed at the phenotypic and metabolic levels.
- Blum, L. C., van Deursen, R. & Reymond, J.-L. (2011). Visualisation and subsets of the chemical universe database GDB-13 for virtual screening. J Comput Aided Mol Des., online
- Catchpole, G. S. et mult al. Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. Proc Natl Acad Sci 2005; 102:14458-14462. Full free text
- Dobson, P. D., Patel, Y. & Kell, D. B. (2009). “Metabolite-likeness” as a criterion in the design and selection of pharmaceutical drug libraries. Drug Disc Today 14, 31-40
- Fink, T. & Reymond, J.-L. (2007). Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physicochemical properties, compound classes, and drug discovery. J Chem Inf Model 47, 342-53
- Haldane, A. G. & May, R. M. (2011). Systemic risk in banking ecosystems. Nature 469, 351-5
- Isaacs, F.J. et mult al. (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348-353
- Maillard, N., Biswas, R., Darbre, T. & Reymond, J.-L. (2011). Combinatorial discovery of peptide dendrimer enzyme models hydrolyzing isobutyryl fluorescein. ACS Comb Sci 13, 310-20
- Uhlich, N. A., Natalello, A., Kadam, R. U., Doglia, S. M., Reymond, J. L. & Darbre, T. (2010). Structure and binding of peptide-dendrimer ligands to vitamin B12. Chembiochem 11, 358-65
- van Deursen, R., Blum, L. C. & Reymond, J.-L. (2011). Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem. J Comput Aided Mol Des., online
- van Deursen, R., Blum, L. C. & Reymond, J.-L. (2010). A searchable map of PubChem. J Chem Inf Model 50, 1924-34
- Xu, X. et mult al. (2010) Genome sequence and analysis of the tuber crop potato. Nature 475, 189-195
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