Tag: darwin

  • Food and fuel for the next generation

    Uncategorized | Douglas Kell

    The beginning of the week marked the move of one of my postdocs, Irena Spasić, who – based on some very nice work recorded in papers such as this and this – has secured a lectureship in Computer Science at Cardiff.

    I then attended part of the programs of each of our 4 Research Committees, who were meeting near Windsor for the present grants round. It was as ever pleasing to see the high quality both of the great bulk of the applications and of the detailed discussions about the many proposals received. [...]

  • The world wide web foundation

    Uncategorized | Douglas Kell

    I had the privilege yesterday, on Darwin Day, of attending a breakfast meeting where the discussion topic was the development of the World Wide Web Foundation (W3F). Other discussants included Tim Berners-Lee, the revered inventor of the Web itself and now based at MIT, and Bob Geldof, the musician-philanthropist. The W3F has lofty goals (its slogan is ‘humanity connected’) as it ‘seeks to advance the Web to empower all people and benefit humanity’. Much has already been achieved with Web 1.0 as we transition to Web 2.0 and the Semantic Web, though a significant fact is that 80% of the world’s human population does not presently have internet access. [...]

  • Evolving new drugs – fragment-based lead discovery for all

    Uncategorized | Douglas Kell

    The search for new drugs with desirable properties has been likened by Robin Spencer (as cited) to the process of holing a golf ball from a great distance, in which several strokes (using different clubs) are required to get one ever closer to the target. This is because the search space of possible drugs is simply enormous. The field that deals with answering the question of this number is known as ‘enumeration’, and while not all possible molecules are likely to make drugs, thus introducing constraints, the number of ‘drug-like’ molecules containing up to 30 ‘heavy’ (non-H) atoms has been estimated at 1063.

    To face this challenge, pharmaceutical companies have acquired very large libraries (1 – 2 millions) of candidate substances that might produces hits in appropriate assays (screens), and which might then be developed into leads and finally into marketable substances. While many of these library molecules are proprietary, a lot of molecular diversity is already available to those without direct access to new synthetic chemistry. Thus, Williams points out that PubChem already contains data on more than 18M molecules, ZINC lists electronically 4.8M that are commercially available (see our recent analysis of its diversity as part of a separate analysis of the comparison between commercial drugs and intermediary metabolites, related to the role of carriers in cellular drug uptake), and the internet is a seriously useful resource for acquiring such molecules. [...]

  • How systems work (or not) – economics, delivery and more (…or some of what I read in the holidays)

    Uncategorized | Douglas Kell

    ‘How systems work’ is already a theme of these blogs, in that the general properties of systems – typically seen (mathematically) as ‘graphs’ of objects that interact with each other – are assumed by definition to have general applicability. While our focus is normally on biology, it is assumed from a systems perspective that the rules that we learn in biology can hopefully similarly be applied to other systems, and vice versa. One such class of system is the domain of what Carlyle famously called the ‘dismal science’ of economics – on which everyone, however amateur, is a Monday morning quarterback (and at some level a participant). So one of the books I read in the holidays was Paul Krugman’s short and masterful analysis of the lead-up to and unfolding of the present economic downturn. Now Krugman is no slouch – the book is an update of his predictions in 1999, and he received the Nobel Prize in Economics for 2008 – and his writing style is simple, effective, jargon-free and understandable. Some of his main conclusions (as I take them) are equivalently simple: [...]