Is REP a measure of “objective support”?

Grant and Kluge have recently stated that Bremer support and their own REP (“relative explanatory power”), are the only objective measures of group support. This paper discusses their claim, showing that their philosophical arguments have no basis, and that their own numerical examples actually serve to illustrate shortcomings of REP.     

Does hydrogen peroxide exist “free” in biological systems?

Hydrogen peroxide (H₂O₂) can diffuse far from the site of production to intracellular locations where biological effects may be greater. The diffusion range is extended by H₂O₂ carriers formed spontaneously by hydrogen bonding with monomeric and polymeric compounds, including amino and dicarboxylic acids, peptides, proteins, nucleic acid bases, and nucleosides. Hydrogen peroxide adducts (HPAs) are readily synthesized, e.g., crystalline histidine (His)-H₂O₂ adducts. An equilibrium exists between an adduct-forming compound and H₂O₂. The detection and relative stabilities of HPAs are measured by the degree of decomposition of H₂O₂ as influenced by test compounds in buffered solution competing with glucose or fructose for H₂O₂. The HPAs delay decomposition of H₂O₂ up to several hundredfold. The overall charge on an HPA, i.e., its ability to penetrate cell membranes, influences the cytotoxic and clastogenic effects of H₂O₂. Growth inhibition of Salmonella typhimurium LT₂ by H₂O₂ is enhanced by neutral HPAs but decreased by anionic HPAs. Addition of catalase 1, 10, or 30 min after inoculation of S. typhimurium LT₂ reduces or nearly eliminates partial growth inhibition by H₂O₂, but a neutral HPA, expecially his-H₂O₂, transported H₂O₂ into the cells within 1 min, and in about 10 min completely inhibited growth. The stability of HPAs decreases with increasing pH or increasing temperature, while added Fe(II) in the presence and absence of EDTA accelerates H₂O₂ and HPA decomposition. Calculations indicate H₂O₂ hydrogen bonds with nucleic acid-base pairs with no apparent bond strain and energy stabilization comparable to normal hydrogen bonding.     

Parrot claylick distribution in South America: do patterns of “where” help answer the question “why”?

Geophagy is well known among some Neotropical parrots. The clay apparently adsorbs dietary toxins and/or provides supplemental nutrients. We used location data and 23 environmental layers to develop a predictive model of claylick distribution using Maxent software. We related species characteristics to claylick use and examined how parrot assemblages using claylicks changed with distance from the centre of claylick distribution. Fifty‐two parrot claylicks were reported from an area of ca 4 million km² but over 50% were restricted to a 35 000 km² region of southeast Peru and northern Bolivia. Claylicks were strongly associated with moist forest on younger (<65 millions of yr) geological formations and exposed river banks. The predictive model of claylick distribution matched our reported range well, with precipitation of warmest quarter, land cover, temperature seasonality, and distance from the ocean being most important predictors of claylick presence. Twenty‐six of the region's 46 parrot species visited claylicks. Species differed greatly in their lick use, but body size, dietary breadth, abundance and other traits were poor predictors of lick use. We are confident that our survey identified the distribution of major parrot claylicks in South America, although less conspicuous parrot geophagy may occur elsewhere. We suggest that claylick distribution reflects both underlying geology (allowing claylick formation in only some regions) and the physiological need for geophagy among parrots in different parts of the continent. Data on the latter are inconclusive, but we argue that parrot claylick distribution supports the contention that geophagy is related more to sodium deficiencies than to protection from dietary toxins.     

TRH synthesis in “mute” thyrotropinomas: cause‐effect or coincidence?

In the pathogenesis of thyrotropin (TSH) immunopositive pituitary adenomas, trigger mutagenetic events are well recognized. However, the way towards a clinical significant tumor is followed under the pressure of growth factors, among which the intrapituitary synthesis of releasing factors could bring a significant contribution. In this study, the production of thyrotropin releasing hormone (TRH) and beta TSH chain was evaluated at the mRNA level by in situ hybridization and end product level by immunohistochemistry, in 18 patients submitted to neurosurgery for pituitary macroadenomas. The hormonal sampling showed abnormal secretion for FSH in 5 and TSH in 4 patients. Seven cases were immunopositive for TSH, and expressed TSH β mRNA. All but one out of these expressed also TRH mRNA. FSH immunoreactivity was documented in 12/ 18, only one of these being negative for TRH mRNA. Paracrine TRH could contribute to the patogenesis of these "mute" adenomas.     

Indole-3-ethanol oxidase in Phycomyces blakesleeanus. Is indole-3-ethanol a “storage pool” for IAA?

Indole-3-ethanol (IEt) was extracted from Phycomyces blakesleeanus Bgff. and purified by TLC and HPLC. Identification was performed by mass spectrum. The HPLC-purified compound showed an UV-spectrum typical for indoles, with absorption maxima at 220 and 281 nm. The IEt content varied between 1.5 nmol (g fresh weight)⁻¹ and 5.6 nmol (g fresh weight)⁻¹. The observed variations were strongly correlated with certain developmental stages of the fungus. Furthermore, the decrease of IEt between 60 and 84 h of fungal development coincides with a high IEt oxidase activity. The product of the enzyme reaction was indole-3-acetaldehyde, which was identified by co-chromatography with an authentic standard in several TLC and HPLC systems and by chemical conversion to indole-3-acetaldoxime.     

Are all grandmothers equal? A review and a preliminary test of the “grandmother hypothesis” in Tokugawa Japan

An unresolved question arising from human evolutionary research relates to the function of the postreproductive period in human females. If menopause is not merely an artifact resulting from the benefits of civilization, there must be an adaptive mechanism favoring the offspring of women who continue to thrive well past the time of their last ovulation. The "grandmother hypothesis" was developed on the basis of the original suggestion by Williams (1957 Evolution 11:32-39) that "stopping early" would benefit already-born children. This idea, combined with the concepts of kin selection (Hamilton 1964 J Theor Biol 7:1-52) and parental investment (Trivers 1972 Sexual Selection and the Descent of Man, Chicago: Aldine, p. 136-179), was expanded to suggest that postreproductive women (in contrast to males) contribute to their inclusive fitness by extending support to their grandchildren. We used discrete time event history analysis (Allison [1984] Event History Analysis, Newbury Park: Sage; Allison [1995] Survival Analysis, Cary, NC: SAS Institute) and logistic regression on data provided in population registers (Shūmon Aratame Chō, or SAC) from a village in central Japan, covering the period from 1671-1871, in a preliminary investigation of the effects of household grandparental presence on the probability of a child's death. We found that after accounting for the presence of other household members, the only grandparent whose presence exerted a consistent negative effect on the likelihood of a child's death was the mother's mother. Due to the small sample size of households that contained maternal grandmothers, these results failed to achieve statistical significance. Their importance, however, is in what they suggest about future research, i.e., census data from preindustrial societies can provide a basis for testing evolutionary proposals, including the "grandmother hypothesis."     

Does “supersaturated coexistence” resolve the “paradox of the plankton”?

In contradiction with field observations, theory predicts that the number of coexisting plankton species at equilibrium cannot exceed the number of limiting resources, which is called the "paradox of the plankton". Recently, Huisman & Weissing (1999 , 2000 ) showed, in a model study, that the number of coexisting species may exceed the number of limiting resources when internal system feedback induces oscillations or chaos. In this paper, we use the term "supersaturated coexistence" for this phenomenon. On the basis of these findings, they claimed that the paradox of the plankton is solved. We investigated the prerequisites for supersaturated coexistence in the same model. Our results indicate that supersaturated coexistence is a rare phenomenon in parameter space, requires a very precise parameterization of the community members and is sensitive to the introduction of new species and the removal of the present species. This raises the question of whether supersaturated coexistence is likely to occur in nature. We conclude that the claim by Huisman & Weissing (1999 , 2000 ) is premature.     

Was heißt “lebendig”?

“Life” means “being alive” of special entities, which we call “organisms”. From a physical point of view, living entities are open systems, which exchange matter as well as energy with their surroundings. Against disruptive influences permanently present, they maintain actively and autonomously a steady state far from the thermodynamic equilibrium. This dynamic state of living beings represents a functional order, an internal “organization”. That means that the involved processes one and all must be correlated in such a way that they in sum prevent the breakdown of the living state. Organization implies functionality, which in turn requires structural relationships, and structures require information for their specification. Information in turn presupposes a source, which is constituted in living systems by the nucleic acids. Organisms are unique in having a capacity to use information, which is stored in the nucleic acid and yields the basis for their specific internal organization in its perpetuation: Living beings, and only they, show a self‐maintained organization.     

“New”‐clear functions of PDK1: Beyond a master kinase?

Activation of cytosolic phosphoinositide-3 kinase (PI-3K) signaling pathway has been well established to regulate gene expression, cell cycle, and survival by feeding signals to the nucleus. In addition, strong evidences accumulated over the past few years indicate the presence of an autonomous inositol lipid metabolism and PI-3K signaling within the nucleus. Much less, however, is known about the role and regulation of this nuclear PI-3K pathway. Components of the PI-3K signaling pathway, including PI 3-kinase and its downstream kinase Akt, have been identified at the nuclear level. Consistent with the presence of a complete PI-3K signaling pathway in the nucleus, we have recently found that phosphoinositide-dependent kinase 1 (PDK1), a kinase functioning downstream of PI-3K and upstream of Akt, is a nucleo-cytoplasmic shuttling protein. In the present review, we update our current knowledge on the regulatory mechanisms and the functional roles of PDK1 nuclear translocation. We also summarize some of the kinase-independent activities of PDK1 in cell signaling.     

“The” genetic code?

The DNA‐based code for protein through messenger and transfer RNA is widely regarded as the code of life. But genomes are littered with other kinds of coding elements as well, and all of them probably came after a supercode for the tRNA system itself.     

Do leaf‐cutting ant nests make “bottom–up” gaps in neotropical rain forests?: a critical review of the evidence

We discuss the role of leaf cutting ant nests ( Atta sp.) on the formation of understory "bottom–up" gaps in tropical rain forests. We (i) describe the characteristics of Atta nests that qualify them as promoters of understory gaps; (ii) review the effects of Atta nests on the dynamics of systems other than tropical forests; and (iii) discuss the hypotheses that in neotropical rain forests Atta nests affect plant productivity, and also influence distribution and community composition of the flora. Finally, we discuss the importance of Atta nests in the dynamics of forests and compare their effects with the better-known effects of treefall gaps. Atta nests modify soil structure, soil nutrient content, light intensity at ground level, seed bank composition and understory structure. The presence of the nest and associated refuse also accelerates the soil nutrient cycles. The size, high frequency, turnover rate and duration of these nests could make them a good substrate for particular species of plants. In spite of their potential importance, little information exists on the effects of Atta nests on plant productivity and/or plant composition in neotropical rain forests.     

Are the gorillas in Bwindi Impenetrable National Park “true” mountain gorillas?

The gorillas that inhabit Bwindi Impenetrable National Park in Uganda are the least known of the eastern gorillas. Because they are an allopatric population living a minimum of 25 km from the well‐studied population of mountain gorillas (Gorilla beringei beringei) in Rwanda and have certain morphological and ecological differences from these gorillas, their taxonomic status has been in question in recent years. This study presents new craniodental metrics from Bwindi individuals and compares them to Virunga individuals as well as to eastern lowland gorillas, G. gorilla graueri. Multivariate statistics, including MANCOVA, least‐squares, regression, and principal components analyses, were used to evaluate how closely the Bwindi crania resemble the Virunga crania and how both relate to G. g. graueri. Results indicate that the Bwindi gorillas have generally smaller crania than the Virunga gorillas, but when metrics are log‐transformed, the only variable that distinguishes the Bwindi individuals is a longer face. When both populations are compared to G. g. graueri, they cluster together separately from the eastern lowland gorillas, sharing such features as higher rami, wider bigonia, longer mandibles, and wider and shorter mandibular symphyses in relation to G. g. graueri. Functional morphological explanations for these differences are discussed, but lacking measurements of the physical properties of G. g. graueri, they cannot fully be explained. Results clearly indicate that at least pertaining to the cranium, upon which most gorilla taxonomy is based, the Bwindi gorillas are proper mountain gorillas (G. b. beringei). Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.     

Activation of transmembrane cell‐surface receptors via a common mechanism? The “rotation model”

It has long been thought that transmembrane cell‐surface receptors, such as receptor tyrosine kinases and cytokine receptors, among others, are activated by ligand binding through ligand‐induced dimerization of the receptors. However, there is growing evidence that prior to ligand binding, various transmembrane receptors have a preformed, yet inactive, dimeric structure on the cell surface. Various studies also demonstrate that during transmembrane signaling, ligand binding to the extracellular domain of receptor dimers induces a rotation of transmembrane domains, followed by rearrangement and/or activation of intracellular domains. The paper here describes transmembrane cell‐surface receptors that are known or proposed to exist in dimeric form prior to ligand binding, and discusses how these preformed dimers are activated by ligand binding.     

Repeatability and correlation of physiological traits: Do ectotherms have a “thermal type”?

Across a range of taxa, individuals within a species differ in suites of correlated traits. These trait complexes, known as syndromes, can have dramatic evolutionary consequences as they do not evolve independently but rather as a unit. Current research focuses primarily on syndromes relating to aspects of behavior and life history. What is less clear is whether physiological traits also form a syndrome. We measured 10 thermal traits in the delicate skink, Lampropholis delicata, to test this idea. Repeatability was calculated and their across‐context correlations evaluated. Our results were in alignment with our predictions in that individual thermal traits varied consistently and were structured into a physiological syndrome, which we are referring to as the thermal behavior syndrome (TBS). Within this syndrome, lizards exhibited a “thermal type” with each being ranked along a cold–hot continuum. Hot types had faster sprint speeds and higher preferred body temperatures, whereas the opposite was true for cold types. We conclude that physiological traits may evolve as a single unit driven by the need to maintain optimal temperatures that enable fitness‐related behaviors to be maximized.     

Was “Lucy” more human than her “child”? Observations on early hominid postcranial skeletons

Fully adult partial skeletons attributed to Australopithecus afarensis (AL 288-1, “Lucy”) and to Homo habilis (OH 62, “Lucy's child”), respectively, both include remains from upper and lower limbs. Relationships between various limb bone dimensions of these skeletons are compared to those of modern African apes and humans. Surprisingly, it emerges that OH 62 displays closer similarities to African apes than does AL 288-1. Yet A. afarensis, whose skeleton is dated more than 1 million years earlier, is commonly supposed to be the ancestor of Homo habilis. If OH 62, classified as Homo habilis by its discoverers, does indeed represent a stage intermediate between A. afarensis and later Homo, a revised interpretation of the course of human evolution would be necessary.