Tag: sequencing

  • Complexity, networks and reductionism

    Uncategorized | Douglas Kell

    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). [...]

  • Insect pollinators, anniversaries, global science and emergency budgets

    Uncategorized | Douglas Kell

    A long-heralded and especially interesting engagement last week involved the launch of the funded outcomes of the multi-agency Insect Pollinators Initiative of which we were a significant part (and for which we provided the secretariat). This initiative – part of the Living with Environmental Change programme – was developed in response to the recognition that bees and other insect pollinators may well be in decline. What their true dynamics are is something we need to keep monitoring, and their numbers certainly exhibit potentially alarming annual fluctuations. Consequently, given the huge influence of insects as pollinators of major crops (most fruit and veg, forage legumes such as beans, and oleogenic crops such as oilseed rape) – potentially worth over £440M p.a. at a primary level (much more, I suspect if our crops actually fail, since such estimates are based on the results of present productivity) – it was very timely to improve what turns out to be a rather meagre scientific understanding of the details. [...]

  • Technology development as an evolutionary process

    Uncategorized | Douglas Kell

    In my blogs of last week and the week before, I discussed the use of evolutionary methods for improving biotechnological processes. I have also blogged, more than once, about the concept of the economy as an evolutionary ecosystem. The question then arises as to whether the development of technology in general might be seen in this way. While it is clear that minor improvements in existing products or technologies can be seen as ‘evolutionary’ advances derived from their ‘parents’ or precursors, it is not so clear how this metaphor might be applied to the arrival of novel and disruptive technologies that have no obvious precursors. That the evolutionary metaphor does work is the theme of a new book by Brian Arthur. The chief recognition is that all kinds of complex products (and these can include ‘products’ like musical symphonies!) arise largely by the combination or recombination of existing modules. These existing components may also provide novelty by processes akin to horizontal gene transfer, something that genome sequencing methods have shown us is far more common than was previously anticipated. [...]

  • Large-scale directed evolution of microbial pathways for biotechnology

    Uncategorized | Douglas Kell

    Most genes individually contribute little to complex phenotypes (although small subsets often can when mutated in the right combinations), which is why the traditional methods of strain improvement – largely random mutation and selection for higher yields – are still effecting improvements after 50 years in the penicillin process. (A couple of recent examples from maize – with commentary – show the similarly complex genetic architecture of maize flowering time.) In last week’s blog, I discussed some new methods for laboratory evolution, that speeded up the fluxes (to mevalonic acid) severalfold, in this case in well-understood pathways. Clearly if we have a network model, as is the case in E. coli and is emerging in e.g. baker’s yeast, we might hope to understand the system and thereby direct evolution along favourable paths. (Similar approaches will, most desirably, assist our understanding of humans, e.g. by bringing together the UCSD and Edinburgh models.) [...]

  • Animal health, digital biology, yeast, and iron

    Uncategorized | Douglas Kell

    The week began (leaving aside a historic victory at Lord’s) with a meeting with several other funders designed to ensure joined-up strategies for the funding of research into animal health, a topic of considerable importance to BBSRC. Other activities included a useful dinner with the Technology Strategy Board, a monthly meeting of the RCUK (Chief) Executive Group, a talk from John Wilbanks (Executive Director of the Science Commons and a leading light at Creative Commons) at the British Library on Scientific findings in a digital world, and co-chairing a session on Systems Biology at the major biennial Yeast Genetics and Molecular Biology meeting, held this year in Manchester. [...]