Scientific misconduct: more cops, more robbers?

Abandoning an earlier pretense that research misconduct is too rare to matter, the scientific community is trying to figure out how to minimize and police it. Could broadening the definition be the key?     

Fertility intentions: are the undecided more like those who want more or want no more children?

In fertility surveys often women (and sometimes men) are asked their fertility desires, i.e. whether they want a/nother birth or not. Some respond that they are undecided. This study examines whether these persons are more like those who say they want more births or like those who say they want no more births. Data on married men and women in 29 Demographic and Health Surveys with sample sizes ranging from 300 to 3000 are used. A logistic regression equation is estimated within each country for those with known desires and then used to classify each person who was undecided. In all sub-Saharan African countries (n=20) and for both sexes, 50% or more of the undecided persons are classified as wanting more children (with one exception of wives in Kenya). By contrast in all five Latin American countries for both sexes less than 50% of the undecided were classified in the 'want more' group (with an exception of husbands in the Dominican Republic). Generally, the undecided tend to be classified the same as the majority among those in the survey with stated desires.     

Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?

A computer simulation study has been made of the accuracy of estimates of Theta = 4Nemu from a sample from a single isolated population of finite size. The accuracies turn out to be well predicted by a formula developed by Fu and Li, who used optimistic assumptions. Their formulas are restated in terms of accuracy, defined here as the reciprocal of the squared coefficient of variation. This should be proportional to sample size when the entities sampled provide independent information. Using these formulas for accuracy, the sampling strategy for estimation of Theta can be investigated. Two models for cost have been used, a cost-per-base model and a cost-per-read model. The former would lead us to prefer to have a very large number of loci, each one base long. The latter, which is more realistic, causes us to prefer to have one read per locus and an optimum sample size which declines as costs of sampling organisms increase. For realistic values, the optimum sample size is 8 or fewer individuals. This is quite close to the results obtained by Pluzhnikov and Donnelly for a cost-per-base model, evaluating other estimators of Theta. It can be understood by considering that the resources spent collecting larger samples prevent us from considering more loci. An examination of the efficiency of Watterson's estimator of Theta was also made, and it was found to be reasonably efficient when the number of mutants per generation in the sequence in the whole population is less than 2.5.     

Are more diverse parts of the mammalian skull more?labile?

Morphological variation is unevenly distributed within the mammalian skull; some of its parts have diversified more than others. It is commonly thought that this pattern of variation is mainly the result of the structural organization of the skull, as defined by the pattern and magnitude of trait covariation. Patterns of trait covariation can facilitate morphological diversification if they are aligned in the direction of selection, or these patterns can constrain diversification if oriented in a different direction. Within this theoretical framework, it is thought that more variable parts possess patterns of trait covariation that made them more capable of evolutionary change, that is, are more labile. However, differences in the degree of morphological variation among skull traits could arise despite variation in trait lability if, for example, some traits have evolved at a different rate and/or undergone stabilizing selection. Here, we test these hypotheses in the mammalian skull using 2D geometric morphometrics to quantify skull shape and estimating constraint, rates of evolution, and lability. Contrary to the expectations, more variable parts of the skull across mammalian species are less capable of evolutionary change than are less variable skull parts. Our results suggest that patterns of morphological variation in the skull could result from differences in rate of evolution and stabilizing selection.     

Canonical antigen-binding loop structures in immunoglobulins: more structures, more canonical classes?

Grafting the antigen-binding loops onto a human antibody scaffold is a widely used technique to humanise murine antibodies. The success of this approach depends largely on the observation that the antigen-binding loops adopt only a limited number of canonical structures. Identification of the correct canonical structure is therefore essential. Algorithms that predict the main-chain conformation of the hypervariable loops using only the amino acid sequence often provide this information. Here, we describe new canonical loop conformations for the hypervariable regions H1 and H2 as found in single-domain antibody fragments of dromedaries or llama. Although the occurrence of these new loop conformations was not predicted by the algorithms used, it seems that they could occur in human or mouse antigen-binding loops. Their discovery indicates that the currently used set of canonical structures is incomplete and that the prediction algorithms should be extended to include these new structures.     

Phase-contrast versus off-axis illumination: is a more complex microscope always more powerful?

In this article, a practical demonstration suitable for any biology college classroom is presented. With the examples of a complex biological specimen (slug's radula) and a simple reference specimen (electron microscopical grid imprint in gelatin), both of which can be easily prepared, the capabilities of two imaging modes commonly used in optical microscopy are demonstrated. The results obtained under phase contrast (a rather sophisticated method, 1953 Nobel Prize to Zernike) and off-axis illumination (a very simple method) are compared. The off-axis illumination setup is capable of delivering noticeably better microscopic images of these two particular specimens, yet it can be easily assembled in a laboratory classroom. The outcome of such a demonstration is expected to be the realization on the part of the students that one needs to carefully choose the apparatus to address a given biological problem, with the "bottom line" being that a more complex one may not necessarily yield better results. An attempt to explain this "paradox" is presented, in the particular case presented here, partly from the physiology of vision perspective (the shape-from-shading problem). The overall aim of the present article is to induce in students critical thinking about the capabilities of a laboratory equipment in general and about data interpretation.     

Are sex-biased genes more dispensable?

Many genes show different expression levels in males and females, and these form the basis of sexually dimorphic phenotypes. Sex-biased genes experience accelerated rates of protein evolution, which has been attributed to sexual selection. However, it is possible that the increased rates of molecular evolution, and more importantly the sex-biased gene expression pattern itself, are due to decreased selective constraint. This notion may explain many of the patterns associated with sex-biased gene expression, and changes how we should view the role of natural and sexual selection in relation to these genes.     

Centrosomes: Central no more?

It has recently been found that the zygotic development of a morphologically normal fly can occur without properly functioning mitotic centrosomes. Does this mean that centrosomes are not required for cell division in animals at all?     

Are tropical butterflies more colorful?

There is a common and long-standing belief that tropical butterflies are more striking in their coloration than those of cooler climates. It has been suggested that this is due to more intense biotic selection or mate selection in the tropics. We tested whether there were differences in coloration by examining the dorsal surface color properties of male butterflies from three regions of the western hemisphere: the Jatun-Satcha Reserve in lowland Ecuador (tropical), the state of Florida, USA (subtropical) and the state of Maine, USA (cool temperate). We digitally photographed the dorsal wing and body surface of male butterfly specimens from Maine, Florida, and Ecuador. For each photograph, we analyzed the mean and variation for the color-parameters that are thought to be related to colorfulness; namely Hue, saturation and intensity. Overall, the Ecuadorian sample exhibited more varied intensity, saturation, and Hue compared to the other regions. These results suggest a more complex assemblage of colors and patterns regionally and on a butterfly-by-butterfly basis in the tropics. The greater complexity of colors within each butterfly in our Ecuadorian sample suggests that tropical butterflies are indeed more ‘colorful’, at least by some measures. Possible reasons for this include stronger predation pressure selecting for aposematism, greater species diversity selecting for camouflage or warning coloration against potential predators, and easier recognition of potential mates in a species rich environment.     

Is slow walking more stable?

Several efforts have been made to study gait stability using measures derived from nonlinear time-series analysis. The maximum finite time Lyapunov exponent (λ_max) quantifies how a system responds to an infinitesimally small perturbation. Recent studies suggested that slow walking leads to lower λ_max values, and thus is more stable than fast walking, but these studies suffer from methodological limitations. We studied the effects of walking speed on the amount of kinematic variability and stability in human walking. Trunk motions of 15 healthy volunteers were recorded in 3D during 2 min of treadmill walking at different speeds. From those time series, maximum Lyapunov exponents, indicating short-term and long-term divergence (λ_S-stride and λ_L-stride), and mean standard deviation (MeanSD) were calculated. λ_S-stride showed a linear decrease with increasing speed for forward–backward (AP) movements and quadratic effects (inverted U-shaped) for medio-lateral (ML) and up–down (VT) movements. λ_L-stride showed a quadratic effect (inverted U-shaped) of walking speed for AP movements, a linear decrease for ML movements, and a linear increase for VT movements. Moreover, positive correlations between λ_S and MeanSD were found for all directions, while λ_L-stride and MeanSD were correlated negatively in the AP direction. The different effects of walking speed on λ_S-stride and λ_L-stride for the different planes suggest that slow walking is not necessarily more stable than fast walking. The absence of a consistent pattern of correlations between λ_L-stride and MeanSD over the three directions suggests that variability and stability reflect, at least to a degree, different properties of the dynamics of walking.     

Glial cells more than support cells?

Glial cells are the most abundant cells in the human brain and have long been considered as passive supporting cells for neurons. In contrast to the extensive studies on various neuronal functions in the nervous system, we still have limited knowledge about glial cells. Recently a number of pioneering studies have provided convincing evidence that glia play active roles in development and function of the central nervous system. This review discusses recent advances in our understanding of the molecular mechanisms underlying glial cell differentiation. We then highlight some of the novel findings about glial function, i.e. the role of glia in synaptogenesis and the intricate relationship between astrocytes and adult neural stem cells. Finally, we summarize the emerging studies that implicate abnormalities in the formation or maintenance of glia leading to severe brain diseases, such as Alexander disease, glioblastoma and multiple sclerosis, and potential therapeutic strategies to tackle these diseases.     

Do men yawn more than women?

The aim of this study was to test the hypothesis that sex differences in primate yawning are related to size dimorphism in canine teeth. Data were collected on yawning by a primate species (Homo sapiens) in which the two sexes differ only slightly in canine size. Unlike more dimorphic primates, human males and females did not differ in the frequency of yawning, although uncovered yawns were more frequent in men than in women.     

Why don't birds lay more eggs?

Fifty years ago David Lack put forward a key hypothesis in life-history theory: that avian clutch is ultimately determined by the number of young that parents can provide with food. Since then, a plethora of brood manipulations has shown that birds can rear more young than the number of eggs they lay, and prompted a search for negative effects of increased effort on future reproduction. However, recent studies have shown that the demands of laying and incubating eggs generally omitted from experiments, could affect parental fitness. Lack's hypothesis, and the tests of its validity, need to be extended to encompass the full demands of producing and rearing the brood.     

Lysine: Is it worth more?

Lysine, an essential cationic amino acid, has a positively charged R group. The structure of lysine is given as (H₃N⁺-)CH(-COO^-)-CH₂-CH₂-CH₂-CH₂-N⁺H₃.While the anabolic role(s) of the molecule has been in focus for quite a few decades now, its biological properties, e.g. role in cellular proliferation in vitro (both anchorage dependent and anchorage independent) and in vivo, its ability to induce strong inflammatory and immune responses - both humoral and cell mediated, its role in augmented healing of all types of wounds in animal models as well as in human subjects (both acute and chronic), as well as its role in inducing extensive angiogenic responses, have never received reasonable attention so far. In the current brief and indicative review (rather than exhaustive reviews of each area), we intend to bring these biological properties of the molecule to focus while discussing a few other interesting aspects - lysine as a food preservative as well as its possible role(s) in immune therapy. While the areas look extremely divergent, we propose a common denominator in the form of a possible molecular mechanism of action of the molecule in all these diverse situations. This revised version was published online in July 2006 with corrections to the Cover Date.