Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo

This article presents a statistical method for detecting recombination in DNA sequence alignments, which is based on combining two probabilistic graphical models: (1) a taxon graph (phylogenetic tree) representing the relationship between the taxa, and (2) a site graph (hidden Markov model) representing interactions between different sites in the DNA sequence alignments. We adopt a Bayesian approach and sample the parameters of the model from the posterior distribution with Markov chain Monte Carlo, using a Metropolis-Hastings and Gibbs-within-Gibbs scheme. The proposed method is tested on various synthetic and real-world DNA sequence alignments, and we compare its performance with the established detection methods RECPARS, PLATO, and TOPAL, as well as with two alternative parameter estimation schemes.

Incense and insensibility: Austin on the 'non-seriousness' of poetry

What is at stake when J. L. Austin calls poetry ‘non-serious’, and sidelines it in his speech act theory? (I). Standard explanations polarize sharply along party lines: poets (e.g. Geoffrey Hill) and critics (e.g. Christopher Ricks) are incensed, while philosophers (e.g. P. F. Strawson; John Searle) deny cause (II). Neither line is consistent with Austin's remarks, whose allusions to Plato, Aristotle and Frege are insufficiently noted (III). What Austin thinks is at stake is confusion, which he corrects apparently to the advantage of poets (IV). But what is actually at stake is the possibility of commitment and poetic integrity. We should reject what Austin offers (V).

Producing leisure spaces out of thin air: the case of the Countryside Stewardship Scheme

This paper examines the growing dysfunction between the apparently increasing significance of diverse leisure practices in the countryside and the largely unchanging official response towards them. Although there is recognition in the recent rural White Paper (DOE and MAFF, 1995) that access is essential to enjoying the countryside, the construction of this term is dubious, since paid access agreements, based on producer requirements, are favoured over any form of demand-driven freedom to roam. Using the Countryside Stewardship Scheme (CSS) as an example of the incentive structure developed to promote this policy, the paper applies Plato's simulacrum as a reading of how this process is being utilised to underpin the dominant rights associated with rural property interests. In particular, the paper makes the point that rather than representing the corollary of a market situation, as its supporters claim, the CSS involves government grant for the eclectic provision of short term licences over ground which remains unmapped as anything other than its continued agricultural use. In concluding, the paper asserts that rather than representing an increase in the availability of leisure sites in the countryside, the CSS and other schemes represent a diversion from the wider and deeper socio-cultural process of continued wealth and power redistribution.