The anticancer drug bleomycin investigated by density functional theory

Activated bleomycin (ABLM) is an oxygenated iron drug complex which embodies the drug's DNA-cleaving activity. This activity is exercised on DNA, if present, but if DNA is absent, the drug itself is inactivated. We have employed quantum density functional theory (DFT)-based methods to investigate (i) the structure of the Fe(II)BLM complex that is first formed in the human body after drug's administration, and (ii) the activation mechanism of the O–O bond present in the ABLM. We have identified the controversial second axial ligand as the endogenous oxygen atom of the carbamoyl group. Our first principles molecular dynamics (MD) simulations indicate a homolytic cleavage as the mechanism of the O–O bond activation in the ABLM complex.     

Can natural selection favour altruism between species?

Darwin suggested that the discovery of altruism between species would annihilate his theory of natural selection. However, it has not been formally shown whether between‐species altruism can evolve by natural selection, or why this could never happen. Here, we develop a spatial population genetic model of two interacting species, showing that indiscriminate between species helping can be favoured by natural selection. We then ask if this helping behaviour constitutes altruism between species, using a linear‐regression analysis to separate the total action of natural selection into its direct and indirect (kin selected) components. We show that our model can be interpreted in two ways, as either altruism within species, or altruism between species. This ambiguity arises depending on whether or not we treat genes in the other species as predictors of an individual's fitness, which is equivalent to treating these individuals as agents (actors or recipients). Our formal analysis, which focuses upon evolutionary dynamics rather than agents and their agendas, cannot resolve which is the better approach. Nonetheless, because a within‐species altruism interpretation is always possible, our analysis supports Darwin's suggestion that natural selection does not favour traits that provide benefits exclusively to individuals of other species.     

Fluxes theory in experiments with random distributed channels on vesicles

When channels are randomly distributed in a population of vesicles, disregarding the number of channels per vesicle, these channels follow a Poisson distribution. This has been verified in many cases, determining the average of channels per vesicle. However, to determine kinetic parameters in population studies, a mathematical expression for the mean flux of solute through channels per vesicle is necessary. Hence, here, this mean flux is calculated, assuming Poisson distributed channels in a population of vesicle. Moreover, this result has been generalized to any number of different kinds of channels (i.e., channels with different permeabilities). These results, useful for in vitro experiments with mixed both channels and vesicles, can be supplemented with those from other techniques, in order to understanding how the nature of the lipid membrane affects kinetic parameters of channel.     

Integrating the Rabinowitz rarity framework with a National Plant Inventory in South Korea

Increasingly large presence‐only survey datasets are becoming available for use in conservation assessments. Potentially, these records could be used to determine spatial patterns of plant species rarity and endemism. We test the integration of a large South Korean species record database with Rabinowitz rarity classes. Rabinowitz proposed seven classes of species rarity using three variables: geographic range, habitat specificity, and local population size. We estimated the range size and local abundance of 2,215 plant species from species occurrence records and habitat specificity as the number of landcover types each species’ records were found in. We classified each species into a rarity class or as common, compared species composition by class to national lists, and mapped the spatial pattern of species richness for each rarity class. Species were classed to narrow or wide geographic ranges using 315 km, the average from a range size index of all species (D_max), based on maximum distance between observations. There were four classes each within the narrow and wide range groups, sorted using cutoffs of local abundance and habitat specificity. Nationally listed endangered species only appeared in the narrow‐range classes, while nationally listed endemic species appeared in almost all classes. Species richness in most rarity classes was high in northeastern South Korea especially for species with narrow ranges. Policy implications. Large presence‐only surveys may be able to estimate some classes of rarity better than others, but modification to include estimates of local abundance and habitat types, could greatly increase their utility. Application of the Rabinowitz rarity framework to such surveys can extend their utility beyond species distribution models and can identify areas that need further surveys and for conservation priority. Future studies should be aware of the subjectivity of the rarity classification and that regional scale implementations of the framework may differ.     

Recent Progress in First Principles O(N) Methods

Abstract

We describe recent progress in developing practical first principles methods for which the computer effort is proportional to the number of atoms: linear scaling or O(N) methods. It is shown that the locality property of the density matrix gives a general framework for constructing such methods. We then outline some of the main technical problems which must be solved in order to develop a practical O(N) method based on density functional theory and the pseudopotential method. Recent progress in solving these problems is presented, and we show that the spatial cut-off distances needed to achieve good accuracy are small enough to make the calculations feasible. Parallel implementation of the O(N) methods in the CONQUEST code is outlined, and it is shown that the code exhibits excellent linear-scaling behaviour on test systems of several thousand atoms. It is pointed out that the most important remaining problem concerns the optimal strategy for seeking the ground state. It is argued that there are three different mechanisms of ill-conditioning which cause present search methods to be inefficient, and some partial solutions are suggested.     

Superorganismality and caste differentiation as points of no return: how the major evolutionary transitions were lost in translation

More than a century ago, William Morton Wheeler proposed that social insect colonies can be regarded as superorganisms when they have morphologically differentiated reproductive and nursing castes that are analogous to the metazoan germ‐line and soma. Following the rise of sociobiology in the 1970s, Wheeler's insights were largely neglected, and we were left with multiple new superorganism concepts that are mutually inconsistent and uninformative on how superorganismality originated. These difficulties can be traced to the broadened sociobiological concept of eusociality, which denies that physical queen–worker caste differentiation is a universal hallmark of superorganismal colonies. Unlike early evolutionary naturalists and geneticists such as Weismann, Huxley, Fisher and Haldane, who set out to explain the acquisition of an unmated worker caste, the goal of sociobiology was to understand the evolution of eusociality, a broad‐brush convenience category that covers most forms of cooperative breeding. By lumping a diverse spectrum of social systems into a single category, and drawing attention away from the evolution of distinct quantifiable traits, the sociobiological tradition has impeded straightforward connections between inclusive fitness theory and the major evolutionary transitions paradigm for understanding irreversible shifts to higher organizational complexity. We evaluate the history by which these inconsistencies accumulated, develop a common‐cause approach for understanding the origins of all major transitions in eukaryote hierarchical complexity, and use Hamilton's rule to argue that they are directly comparable. We show that only Wheeler's original definition of superorganismality can be unambiguously linked to irreversible evolutionary transitions from context‐dependent reproductive altruism to unconditional differentiation of permanently unmated castes in the ants, corbiculate bees, vespine wasps and higher termites. We argue that strictly monogamous parents were a necessary, albeit not sufficient condition for all transitions to superorganismality, analogous to single‐zygote bottlenecking being a necessary but not sufficient condition for the convergent origins of complex soma across multicellular eukaryotes. We infer that conflict reduction was not a necessary condition for the origin of any of these major transitions, and conclude that controversies over the status of inclusive fitness theory primarily emanate from the arbitrarily defined sociobiological concepts of superorganismality and eusociality, not from the theory itself.     

Evolutionary Psychology, Human Universals, and the Standard Social Science Model

Proponents of evolutionary psychology take the existence of humanuniversals to constitute decisive evidence in favor of their view. Ifthe same social norms are found in culture after culture, we have goodreason to believe that they are innate, they argue. In this paper Ipropose an alternative explanation for the existence of humanuniversals, which does not depend on them being the product of inbuiltpsychological adaptations. Following the work of Brian Skyrms, I suggestthat if a particular convention possesses even a very small advantageover competitors, whatever the reason for that advantage, we shouldexpect it to become the norm almost everywhere. Tiny advantages aretranslated into very large basins of attraction, in the language of gametheory. If this is so, universal norms are not evidence for innatepsychological adaptations at all. Having shown that the existence ofuniversals is consistent with the so-called Standard Social ScienceModel, I turn to a consideration of the evidence, to show that thisstyle of explanation is preferable to the evolutionary explanation, atleast with regard to patterns of gender inequality.     

Assessing Allowable Take of Migratory Birds

ABSTRACT Legal removal of migratory birds from the wild occurs for several reasons, including subsistence, sport harvest, damage control, and the pet trade. We argue that harvest theory provides the basis for assessing the impact of authorized take, advance a simplified rendering of harvest theory known as potential biological removal as a useful starting point for assessing take, and demonstrate this approach with a case study of depredation control of black vultures (Coragyps atratus) in Virginia, USA. Based on data from the North American Breeding Bird Survey and other sources, we estimated that the black vulture population in Virginia was 91,190 (95% credible interval = 44,520-212,100) in 2006. Using a simple population model and available estimates of life-history parameters, we estimated the intrinsic rate of growth (r_max) to be in the range 7–14%, with 10.6% a plausible point estimate. For a take program to seek an equilibrium population size on the conservative side of the yield curve, the rate of take needs to be less than that which achieves a maximum sustained yield (0.5 × r_max). Based on the point estimate for r_max and using the lower 60% credible interval for population size to account for uncertainty, these conditions would be met if the take of black vultures in Virginia in 2006 was <3,533 birds. Based on regular monitoring data, allowable harvest should be adjusted annually to reflect changes in population size. To initiate discussion about how this assessment framework could be related to the laws and regulations that govern authorization of such take, we suggest that the Migratory Bird Treaty Act requires only that take of native migratory birds be sustainable in the long-term, that is, sustained harvest rate should be <r_max. Further, the ratio of desired harvest rate to 0.5 X r_max may be a useful metric for ascertaining the applicability of specific requirements of the National Environmental Protection Act.