Last week began with the viva voce exam of my last research student, Eva Zelena, who emerged from a 3.5h discourse based on her work on developing and exploiting methods for metabolomics with flying colours. The first use of the word ‘metabolome’ was in 1998, a year in which I was invited to join domain experts in Streptomyces biology to help develop tools for the emerging field of ’omics, as part of a BBSRC Initiative called Functional Genomics Technologies. This was one of our earliest initiatives as the world learned to adapt to and make use of the post-genomic era, and was followed, for instance, by two rounds of the Investigating Gene Function initiatives (a review of which will appear this year).
Streptomycetes (and other actinobacteria) are responsible for the production of many natural products of pharmaceutical importance, and are thus of applied interest in industrial biotechnology, as well as a model for studies in developmental biology. Our sustained funding of the UK Streptomyces community, especially based on the model organism S. coelicolor A3(2), has helped it maintain the UK’s world-leading pre-eminence, and I was pleased to attend part of a meeting in which we are seeking to establish the details of how and why this programme has been so successful, both before and after the sequencing of the S. coelicolor genome.
As part of the developing Food Security programme, we had a very useful meeting with Prof John Beddington, the Government Chief Scientific Adviser, to exchange information on where we were and where we need to get. Following our Strategic Plan that is being launched on Thursday, we anticipate further announcements.
I also had a very interesting and useful visit to UCL, both to rehearse our own strategic thinking and its potential alignment with theirs, and to enjoy some fascinating scientific presentations, for instance in the area of healthy ageing (one of our strategic interests) and including in the basic biology of ageing (biogerontology). (My next University visit is to Newcastle, another hub of expertise in that space.) One of our discussion topics was around the securing of grants by early and mid-career applicants. Given a fixed pot of money, there is clearly a disconnect between the expectations that young investigators have their ‘own’ (presumably small) projects to establish their careers while (presumably) older investigators join larger multi-disciplinary consortia. Evidently we need to encourage younger investigators to join these consortia, while ensuring adequate means of identifying their contributions to the research.
One interesting paper that I just picked up analysed the dynamics of abstracts published at annual meetings of a learned society (in this case the Society for Neuroscience), which allowed the authors to determine geographical concentrations of researchers, co-authorships, the logarithmic distributions of scientific productivity (see also an earlier blog), trends in subject areas and, interestingly, the transient nature of much of the contributing population (fully two thirds of the authors contributed in only one of the 6 years studied). These kinds of study give wonderful insights into the way science evolves, and we can anticipate many more.
I also see the blogosphere expanding to include books. While it is possible to publish anything on the web, this may be without any kind of peer review. Equally, full-blown commercial books may be inaccessible to a large potential readership (although an increasing fraction are made available of the Web, including that just published on Science and Innovation for Development by Sir Gordon Conway and Jeff Waage with Sara Delaney). A new publishing experiment is designed to combine the merits of books and blogs in order to overcome their shortcomings. This will apparently involve getting a small group of about twenty people (mostly bio-ontologists) together, and writing openly but with peer review about what an ontology is, why you would want to a biomedical ontology, how to build one, and so on. The experiment can be followed at http://ontogenesis.knowledgeblog.org.
Finally, to reprise the metabolomics theme, I was pleased to see that our 2005 paper comparing GM and conventionally bred crops is my latest (of 29) to reach 100 citations. This paper showed that the variation of the metabolome between different conventionally bred cultivars of potato exceeded substantially the variation occasioned by introducing into one such cultivar transgenes involved in inulin production. As I remarked at the House of Commons Science and Technology Bioengineering inquiry, the important issues for regulating biological organisms should be based on what they are and not how they are created.
- Bentley, S. D., Chater, K. F., Cerdeno-Tarraga, A.-M., Challis, G. L., Thomson, N. R., James, K. D., Harris, D. E., Quail, M. A., Kieser, H., Harper, D., Bateman, A., Brown, S., Chandra, G., Chen, C. W., Collins, M., Cronin, A., Fraser, A., Goble, A., Hidalgo, J., Hornsby, T., Howarth, S., Huang, C.-H., Kieser, T., Larke, L., Murphey, L., Oliver, K., O’Neil, S., Rabbinowitsch, E., Rajandream, M.-A., Rutherford, K., Rutter, S., Seeger, K., Saunders, D., Sharp, S., Squares, R., Squares, S., Taylor, K., Warren, T., Wietzorrek, A., Woodward, J., Barrell, B. G., Parkhill, J. & Hopwood, D. A. (2002). Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141-147
- Catchpole GS, Beckmann M, Enot DP, Mondhe M, Zywicki B, Taylor J, Hardy N, Smith A, King RD, Kell DB, Fiehn O, Draper J: Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. Proc Natl Acad Sci 2005; 102:14458-14462. Full text pdf
- Lin JM, Bohland JW, Andrews P, Burns GA, Allen CB, Mitra PP: An analysis of the abstracts presented at the annual meetings of the Society for Neuroscience from 2001 to 2006. PLoS One 2008; 3:e2052. Full text pdf
- Oliver, S. G., Winson, M. K., Kell, D. B. & Baganz, F. (1998). Systematic functional analysis of the yeast genome. Trends Biotechnol. 16, 373-378.
- Zelena, E., Dunn, W., Broadhurst, D., Francis-McIntyre, S., Carroll, K., Begley, P., O’Hagan, S., Knowles, J. D., Halsall, A., HUSERMET Consortium, Wilson, I. & Kell, D.B. (2009). Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum. Anal Chem 81, 1357-1364.