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.     

Are the Kow Swamp hominids “archaic”?

Initial reports of hominids recovered at Kow Swamp, in the Murray Valley of Victoria indicated that, on the basis of cranial analyses, there was a "survival of Homo erectus features in Australia until as recently as 10,000 years ago (Thorne and Macumber, 1972, p. 316). This claim was later refuted by others, who suggested that artificial cranial deformation may have been responsible for at least some of the distinctive and "primitive" traits seen in the Kow Swamp individuals. Previous research by this worker and others has indicated that taxonomic traits at both specific and subspecific levels are present in hominine femora. Therefore, it may be possible to evaluate the "primitiveness" of the Kow Swamp sample on the basis of their femoral anatomy. Morphometric analyses were undertaken, using as controls femora of Romano British, Tasmanian, and other Murray Valley populations. On the basis of bivariate and multivariate analyses it was found that, at least in this single element of the postcranium, no primitive features were present. The Kow Swamp sample, in fact, shows a very close morphometric relationship with all included Homo sapiens controls and is significantly distinct from Homo erectus.     

How “representative” is the Terry collection? Evidence from the proximal femur

The work reported here is the beginning of an attempt to determine whether data on skeletal aging changes derived from the Terry collection (Smithsonian Institution) can safely be applied to present-day clinical and forensic problems. Measurements made on radiographs of the proximal third of the right femur below the greater trochanter were compared in three groups of American white females: Terry collection “regulars,” Terry collection willed, and GW (George Washington University Medical Center) willed. Mean birth year for the Terry regulars was 1883, whereas the mean birth year for Terry and GW willed was 1910. Terry willed femora are longer than those of Terry regulars, but not more robust. The two groups show opposing secular trends in femoral length, and in this respect the Terry regulars appear closer to the general U.S. population. In two indices of relative medullary cavity size (which reflect changes in cortical thickness as well as internal and external diameters) all three groups agree in showing age-related increase of medullary diameters, greater increase in the anterior–posterior dimension, and greatest amount of increase at diaphyseal levels. The major difference between groups is in timing, with medullary cavity expansion becoming evident at least a decade earlier and leading to greater eventual loss of cortical thickness in the willed groups.     

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.     

Does the “C3 effect” offset the Δ2 effect,as regards the solution flexibility of aldoses?

The solution flexibility of carbohydrates influences a variety of molecular recognition and regulatory processes. For aldoses and other monosaccharides, this flexibility is dictated by the orientations of the various hydroxyl (OH) groups present, which influences conformer and anomer ratios, interactions among these OH groups, and interactions between them and the surrounding solvent. Depending on the number and position of axial OH groups, a variety of structures can coexist in solutions at equilibrium. In 1950, as part of his pioneering studies on the shape of pyranoside rings, Reeves described the Δ2 effect, the greater destabilization of the pyranose ring conformation when the OH group on carbon 2 (C₂) is in the axial position. It was later proposed by Angyal that the Δ2 effect could be cancelled by the presence of an axial OH on C₃, termed here the “C₃ effect.” Employing size‐exclusion chromatography, an entropically‐controlled separation technique, we have investigated whether or not the C₃ and Δ2 effects indeed do compensate for one another with respect to their influence on the solution flexibility of select aldohexoses and aldopentoses. As will be seen, while qualitatively and semiquantitatively this mutual cancellation of effects does occur in aldohexoses, it does not appear to do so in aldopentoses. An explanation for the latter appears to lie in the variety of anomers and conformers present in equilibrium solutions of those aldopentoses studied and in the relative entropic contribution of individual conformers or anomers to the total solution flexibility. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 703–711, 2014.     

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.     

“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.     

What does body size mean,from the “plant's eye view”?

Alternative metrics exist for representing variation in plant body size, but the vast majority of previous research for herbaceous plants has focused on dry mass. Dry mass provides a reasonably accurate and easily measured estimate for comparing relative capacity to convert solar energy into stored carbon. However, from a “plant's eye view”, its experience of its local biotic environment of immediate neighbors (especially when crowded) may be more accurately represented by measures of “space occupancy” (S–O) recorded in situ—rather than dry mass measured after storage in a drying oven. This study investigated relationships between dry mass and alternative metrics of S–O body size for resident plants sampled from natural populations of herbaceous species found in Eastern Ontario. Plant height, maximum lateral canopy extent, and estimated canopy area and volume were recorded in situ (in the field)—and both fresh and dry mass were recorded in the laboratory—for 138 species ranging widely in body size and for 20 plants ranging widely in body size within each of 10 focal species. Dry mass and fresh mass were highly correlated (r² > .95) and isometric, suggesting that for some studies, between‐species (or between‐plant) variation in water content may be unimportant and fresh mass can therefore substitute for dry mass. However, several relationships between dry mass and other S–O body size metrics showed allometry—that is, plants with smaller S–O body size had disproportionately less dry mass. In other words, they have higher “body mass density” (BMD) — more dry mass per unit S–O body size. These results have practical importance for experimental design and methodology as well as implications for the interpretation of “reproductive economy”—the capacity to produce offspring at small body sizes—because fecundity and dry mass (produced in the same growing season) typically have a positive, isometric relationship. Accordingly, the allometry between dry mass and S–O body size reported here suggests that plants with smaller S–O body size—because of higher BMD—may produce fewer offspring, but less than proportionately so; in other words, they may produce more offspring per unit of body size space occupancy.     

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.     

Survivin study: An update of “What is the next wave?”

Studies on survivin over the past 2-3 years have shown that survivin possesses multiple subcellular localizations and is a multifunctional molecule involved in many aspects of cellular processes and/or behaviors. The subcellular localization and function of the survivin splice variants, however, have not yet been well elucidated. We have, therefore, provided additional observations on several survivin splice variants for further exploration. This review article will update the role of survivin, and its splice variants in the mitosis/cell cycle, apoptosis, tumorigenesis, chemoprevention, drug/radiation resistance, and cancer therapeutics.     

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.     

What are the dielectric “constants” of proteins and how to validate electrostatic models?

Implicit models for evaluation of electrostatic energies in proteins include dielectric constants that represent effect of the protein environment. Unfortunately, the results obtained by such models are very sensitive to the value used for the dielectric constant. Furthermore, the factors that determine the optimal value of these constants are far from being obvious. This review considers the meaning of the protein dielectric constants and the ways to determine their optimal values. It is pointed out that typical benchmarks for validation of electrostatic models cannot discriminate between consistent and inconsistent models. In particular, the observed pK(a) values of surface groups can be reproduced correctly by models with entirely incorrect physical features. Thus, we introduce a discriminative benchmark that only includes residues whose pK(a) values are shifted significantly from their values in water. We also use the semimacroscopic version of the protein dipole Langevin dipole (PDLD/S) formulation to generate a series of models that move gradually from microscopic to fully macroscopic models. These include the linear response version of the PDLD/S models, Poisson Boltzmann (PB)-type models, and Tanford Kirkwwod (TK)-type models. Using our different models and the discriminative benchmark, we show that the protein dielectric constant, epsilon(p), is not a universal constant but simply a parameter that depends on the model used. It is also shown in agreement with our previous works that epsilon(p) represents the factors that are not considered explicitly. The use of a discriminative benchmark appears to help not only in identifying nonphysical models but also in analyzing effects that are not reproduced in an accurate way by consistent models. These include the effect of water penetration and the effect of the protein reorganization. Finally, we show that the optimal dielectric constant for self-energies is not the optimal constant for charge-charge interactions.     

Is cyclin Zeuthen's “division protein”?

Biochemical evidence is presented for the presence of cyclin in Tetrahymena. Zeuthen previously postulated the existence of a heat-labile “division protein” to explain heat-shock-induced division synchrony in Tetrahymena [(1964) Synchrony in Cell Division and Growth (Zeuthen, E., Ed.), pp. 99–158, Interscience, New York]. We show that cyclin is heat-labile in Tetrahymena and suggest that cyclin may be Zeuthen's division protein. Cyclin and cell cycle control is of interest in Tetrahymena because the division mechanism drives macronuclear amitosis, closed and acentric micronuclear mitosis, and cortical differentiation in this cell type.     

Do “heavy” eaters live longer?

A new hypothesis is put forward, linking cellular endurance with dietary consumption of stable heavy isotopes. Due to the isotope effect, biomolecules that incorporate heavier isotopes give rise to more stable molecular structures with increased resistance to damages associated with aging and age-related disease. The inclusion of heavy isotopes might be either active (selection for heavier isotopes) or passive (incorporation reflecting the existing abundance). The hypothesis links consumption of foods relatively rich in heavy isotopes (such as (13)C and D, derived from C4-plants), especially at the early stages of the organism's development, with enhanced longevity. Implications of diets and intestinal microflora are also discussed.