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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.
Continue reading: Technology development as an evolutionary process
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.)
Continue reading: Large-scale directed evolution of microbial pathways for biotechnology
In the previous blog, I wrote about directed evolution for the discovery of variants of proteins with desirable properties (and that this is a multiobjective combinatorial optimisation problem). The usual metaphor for understanding the relationship between sequence and structure is that of a ‘landscape’, in which one moves about through sequence space seeking a high peak (of fitness). A danger here is of premature convergence, where one rushes up the nearest hill (‘Snowdon’) while failing to search in regions that might ultimately prove more fruitful (‘Mont Blanc’ or ‘Everest’). Because the number of experiments one can typically do at one time (a batch or ‘generation’) is very small relative to the size of sequence spaces, it is common to favour the selection of ‘good’ variants, which means that mutations that on their own are deleterious (as most are) will be lost before helping one get across a valley to a higher mountain range (very high mutation rates may help here).
Continue reading: Of directed evolution and downturns
One would have to be very removed from access to the media not to be aware of the 2009 outbreak of swine flu (influenza). Although it presently appears that this outbreak is barely (if at all) more dangerous than are the seasonal outbreaks of ‘traditional’ human flu (that may yet change), it raises questions about both our preparedness against pandemics (a word that implies only a widespread distribution; of itself it says nothing about virulence) and our understanding of the means by which such strains arise, transmit, infect and display virulence in humans.
Continue reading: If pigs had wings; what we know and what we don’t know about swine flu and bird flu
“Actually, the orgy of fact extraction in which everybody is currently engaged has, like most consumer economies, accumulated a vast debt. This is a debt of theory and some of us are soon going to have an exciting time paying it back – with interest, I hope.”
In Theory, in Loose Ends, Sydney Brenner, Current Biology, 1997, p. 37
Physics differs from biology in many ways, a particularly striking one being the status typically accorded to theory and theoreticians. To quote Danny Hillis from Brockman’s book, “…A theoretical biologist [is] almost an oxymoron. In physics there are the theoretical types and the experimental types, and there is a good understanding of what the relationship is between them.
Continue reading: In praise of theory
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