the bone is “fractured” or “broken”. While orthopaedic surgeons consider these terms synonymous, patients appear tocomprehend the terms as having different meanings. Given the commonality of this frequently posed question, it may beimportant for providers to assess patients’ level of understanding in order to provide optimal care. The purpose of thisstudy is to evaluate patients’ comprehension ...

Observing differences between DNA or protein sequences and estimating the true amount of substitutions from them is a prominent problem in molecular evolution as many analyses are based on distance measures between biological sequences. Since the relationship between the observed and the actual amount of mutations is very complex, more than four decades of research have been spent to improve mo...

Most methods for estimating the rate of synonymous and nonsynonymous substitution per site define a site as a mutational opportunity: the proportion of sites that are synonymous is equal to the proportion of mutations that would be synonymous under the model of evolution being considered. Here we demonstrate that this definition of a site can give misleading results and that a physical definiti...

Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the patter...

We present a new computational method to identify positive and purifying selection at synonymous sites in yeast and worm. We define synonymous substitutions that change codons from preferred to unpreferred or vice versa as nonconservative synonymous substitutions and all other substitutions as conservative. Using a maximum-likelihood framework, we then test whether conservative and nonconservat...

In a paper devoted to problems of synonymy and translation between modal logics [2], the authors attempted to show that there are two modal logics so that each is exactly translatable into the other, but they are not translationally equivalent. Unfortunately, there is an error in the proof of Theorem 4.7 of this paper, that purports to prove this result, as Lloyd Humberstone discovered [1]. In ...