Is there a star tree paradox?

Concerns have been raised that posterior probabilities on phylogenetic trees can be unreliable when the true tree is unresolved or has very short internal branches, because existing methods for Bayesian phylogenetic analysis do not explicitly evaluate unresolved trees. Two recent papers have proposed that evaluating only resolved trees results in a "star tree paradox": when the true tree is unresolved or close to it, posterior probabilities were predicted to become increasingly unpredictable as sequence length grows, resulting in inflated confidence in one resolved tree or another and an increasing risk of false-positive inferences. Here we show that this is not the case; existing Bayesian methods do not lead to an inflation of statistical confidence, provided the evolutionary model is correct and uninformative priors are assumed. Posterior probabilities do not become increasingly unpredictable with increasing sequence length, and they exhibit conservative type I error rates, leading to a low rate of false-positive inferences. With infinite data, posterior probabilities give equal support for all resolved trees, and the rate of false inferences falls to zero. We conclude that there is no star tree paradox caused by not sampling unresolved trees.     

Is there a vitamin E paradox?

In addition to epidemiologic studies that suggest a benefit for high intakes of alpha-tocopherol, studies of supplementation in humans have clearly shown that alpha-tocopherol decreases lipid peroxidation, platelet aggregation, and functions as a potent anti-inflammatory agent. In the five large prospective clinical trials with alpha-tocopherol therapy, four have shown a beneficial effect on cardiovascular end-points (two studies on a primary end-point and two studies on other cardiovascular end-points). Thus, the totality of evidence based on the epidemiologic data, in-vitro studies and animal models, and the clinical trials appears to support a benefit for alpha-tocopherol supplementation in patients with pre-existing cardiovascular disease. However, definitive recommendations must await ongoing clinical trials.     

Is it a revolution?

Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence properties is also discussed.

Is it genomic imprinting or preferential expression?

Imprinted genes are monoallelically expressed in a parent-of-origin-specific manner, but for many genes reported to be imprinted, the occurrence of preferential expression--where both alleles are expressed but one is expressed more strongly than the other in a parent-of-origin-specific way--has been reported. This preferential expression found in genes described as imprinted has not been thoroughly addressed in genomic imprinting studies. To study this phenomenon, 50 genes, reported to be imprinted in the mouse, were chosen for investigation. Preferential expression was observed for 21 of 27 maternally expressed genes. However, only 5 of 23 paternally expressed genes showed preferential expression. Recently, it has been reported that a remarkable proportion of non-imprinted genes show differential allelic expression. If there is overlap between non-imprinted genes that are differentially expressed and imprinted genes that are preferentially expressed, we need to set new definitions of imprinted genes that, in turn, would probably lead to reassessments of the total number of imprinted genes in mammalian species.     

Human mitochondrial haplogroup H: The highest VO2max consumer – Is it a paradox?

Mitochondrial background has been demonstrated to influence maximal oxygen uptake (VO_2max, in mL kg^?1 min^?1), but this genetic influence can be compensated for by regular exercise. A positive correlation among electron transport chain (ETC) coupling, ATP and reactive oxygen species (ROS) production has been established, and mitochondrial variants have been reported to show differences in their ETC performance. In this study, we examined in detail the VO_2max differences found among mitochondrial haplogroups. We recruited 81 healthy male Spanish Caucasian individuals and determined their mitochondrial haplogroup. Their VO_2max was determined using incremental cycling exercise (ICE). VO_2max was lower in J than in non-J haplogroup individuals (P = 0.04). The H haplogroup was responsible for this difference (VO_2max; J vs. H; P = 0.008) and this group also had significantly higher mitochondrial oxidative damage (mtOD) than the J haplogroup (P = 0.04). In agreement with these results, VO_2max and mtOD were positively correlated (P = 0.01). Given that ROS production is the major contributor to mtOD and consumes four times more oxygen per electron than the ETC, our results strongly suggest that ROS production is responsible for the higher VO_2max found in the H variant. These findings not only contribute to a better understanding of the mechanisms underneath VO_2max, but also help to explain some reported associations between mitochondrial haplogroups and mtOD with longevity, sperm motility, premature aging and susceptibility to different pathologies.     

Pancreatic Incidentalomas: Is it Net or Not?

Abbreviations:FNA = fine-needle aspirateIPAS = intrapancreatic accessory spleenPNET = pancreatic neuroendocrine tumor     

Is it better to add taxa or characters to a difficult phylogenetic problem?

The effects on phylogenetic accuracy of adding characters and/or taxa were explored using data generated by computer simulation. The conditions of this study were constrained but allowed for systematic investigation of certain parameters. The starting point for the study was a four-taxon tree in the "Felsenstein zone," representing a difficult phylogenetic problem with an extreme situation of long branch attraction. Taxa were added sequentially to this tree in a manner specifically designed to break up the long branches, and for each tree data matrices of different sizes were simulated. Phylogenetic trees were reconstructed from these data using the criteria of parsimony and maximum likelihood. Phylogenetic accuracy was measured in three ways: (1) proportion of trees that are completely correct, (2) proportion of correctly reconstructed branches in all trees, and (3) proportion of trees in which the original four-taxon statement is correctly reconstructed. Accuracy improved dramatically with the addition of taxa and much more slowly with the addition of characters. If taxa can be added to break up long branches, it is much more preferable to add taxa than characters.     

Is it better to give information, receive it, or be ignorant in a two-player game?

The standard approach in a biological two-player game is toassume both players choose their actions independently of oneanother, having no information about their opponent's action(simultaneous game). However, this approach is not realisticin some circumstances. In many cases, one player chooses hisaction first and then the second player chooses her action withinformation about his action (Stackelberg game). We comparethese two games, which can be mathematically analyzed into twotypes, depending on the direction of the best response function(BRF) at the evolutionarily stable strategy in the simultaneousgame (ESS_sim). We subcategorize each type of game into two cases,depending on the change in payoff to one player, when both playersare at the ESS_sim, and the other player increases his action.Our results show that in cases where the BRF is decreasing atthe ESS_sim, the first player in the Stackelberg game receivesthe highest payoff, followed by both players in the simultaneousgame, followed by the second player in the Stackelberg game.In these cases, it is best to be the first Stackelberg player.In cases where the BRF is increasing at the ESS_sim, both Stackelbergplayers receive a higher payoff than players in a simultaneousgame. In these cases, it is better for both players to playa Stackelberg game rather than a simultaneous game. However,in some cases the first Stackelberg player receives a higherpayoff than the second Stackelberg player, and in some casesthe opposite is true.     

Is it functional?

This report describes the first scientific meeting of the British Society for Proteome Research (BSPR), which was organised jointly with the European Bioinformatics Institute (EBI) and held in July 2004. The focus of the conference was functional proteomics with an emphasis on possible clinical application. The main subjects described here are: the need to simplify samples, the use of biological fluids versus tissue, consideration of biological and experimental variation and the creation of databases to achieve meaningful functional analysis.     

Is infertility a disease and does it matter?

Claims about whether or not infertility is a disease are sometimes invoked to defend or criticize the provision of state‐funded treatment for infertility. In this paper, I suggest that this strategy is problematic. By exploring infertility through key approaches to disease in the philosophy of medicine, I show that there are deep theoretical disagreements regarding what subtypes of infertility qualify as diseases. Given that infertility’s disease status remains unclear, one cannot uncontroversially justify or undermine its claim to medical treatment by claiming that it is or is not a disease. Instead of focusing on disease status, a preferable strategy to approach the debate about state‐funded treatment is to explicitly address the specific ethical considerations raised by infertility. I show how this alternative strategy can be supported by a recent theoretical framework in the philosophy of medicine which avoids the problems associated with the concepts of health and disease.     

The gill of fish larvae. Is it primarily a respiratory or an ionoregulatory structure?

Based on surface area and chloride cell number, rainbow trout Oncorhynchus mykiss gills appear initially to be more important in terms of ion balance than gas exchange. Chloride cells appear on the gill 3–6 days before hatch at 10°C. This is about 9 days before secondary lamellae, the definitive adult gas exchange structure, begin to form. At hatch, 22% of all chloride cells but only 7% of total surface area are located on the gill. This discrepancy gradually diminishes but even at complete yolk absorption the gill still seems to be about twice as important in terms of ion balance (75% of chloride cells) as gas exchange (37% of total surface area represented by gill filaments and lamellae combined). Surface area measurements and chloride cell counts reported in the literature for larvae of other species show a similar pattern suggesting that this may be a general phenomenon. If true, the implications are profound not only for developmental physiologists but also for those interested in the evolutionary history of gills and their function in adult fish.