Where's the evidence?

Science is in large part the art of careful measurement, and a fixed measurement scale is the sine qua non of this art. It is obvious to us that measurement devices lacking fixed units and constancy of scale across applications are problematic, yet we seem oddly laissez faire in our approach to measurement of one critically important quantity: statistical evidence. Here I reconsider problems with reliance on p values or maximum LOD scores as measures of evidence, from a measure-theoretic perspective. I argue that the lack of an absolute scale for evidence measurement is every bit as problematic for modern biological research as was lack of an absolute thermal scale in pre-thermodynamic physics. Indeed, the difficulty of establishing properly calibrated evidence measures is strikingly similar to the problem 19th century physicists faced in deriving an absolute scale for the measurement of temperature. I propose that the formal relationship between the two problems might enable us to apply the mathematical foundations of thermodynamics to establish an absolute scale for the measurement of evidence, in statistical applications and possibly other areas of mathematical modeling as well. Here I begin to sketch out what such an endeavor might look like.     

Sticking together? Falling apart? Exploring the dynamics of the interactome

Advances in techniques for the study of protein-protein interactions have dramatically improved our understanding of the interactome. However, we know little about the dynamics of this complex system. To better understand the dynamics of the interactome, it is important to consider what happens when single proteins are perturbed. Changes in protein abundance and post-translational modification can function as switches in the interactome, affecting protein-complex assembly and function. Changes in protein sequence or a dramatic increase in abundance might cause a promiscuous gain of interactions. These effects are not identical for all proteins and will differ depending on the number and type of interaction partners that a protein has.     

What is the function of the claustrum?

The claustrum is a thin, irregular, sheet-like neuronal structure hidden beneath the inner surface of the neocortex in the general region of the insula. Its function is enigmatic. Its anatomy is quite remarkable in that it receives input from almost all regions of cortex and projects back to almost all regions of cortex. We here briefly summarize what is known about the claustrum, speculate on its possible relationship to the processes that give rise to integrated conscious percepts, propose mechanisms that enable information to travel widely within the claustrum and discuss experiments to address these questions.     

Is the most frequent allele the oldest?

Exact and approximate expressions are obtained for the probability that the most frequent allele is oldest, in neutral allele models in which all mutations produce new alleles. The higher the mutation rate, the less likely is it that the most frequent allele would be oldest. The results are in agreement with simulation studies by Ewens and Gillespie (1974) (Theor. Popul. Biol.6, 35–57), and limit the range of validity of a suggestion made by Crow (1972) (J. Hered.63, 306–316) with respect to the statistical testing of the neutral allele hypothesis.     

Is the Octomacridae the sister family of the Diplozodae?

Diplozoidae and Octomacridae are usually considered as sister families. Essentially this is because they are the only polyopisthocotyleans parasitising primary freshwater teleosts. Because of the lack of phylogenetically informative morphological characters to explore the pattern of colonisation of the primary continental freshwater teleosts and in order to understand the appearance of the "natural parabiosis" of Diplozoidae, a molecular phylogeny was inferred by comparing newly obtained partial 28S and 18S rDNA gene sequences of Eudiplozoon nipponicum and Diplozoon homoion with other already available sequences. The phylogenetic analysis seems to show that Diplozoidae and Octomacridae are not sister groups. Thus, the colonisation of primary freshwater teleosts by these two families could be independent.