Metabolic theory or metabolic models?

The metabolic theory of ecology (MTE) claims to derive ecological relationships from the structure of resource distribution networks, which is assumed to determine the scaling of metabolism with body mass, and from the effect of temperature on the rate of biological processes. MTE is controversial. I propose that some of the controversy stems from the implicit adoption of different views of science by the proponents and critics of MTE. The perspective of proponents is consistent with the theory-centric view of science called the received view, whereas many of the critics implicitly adopt an alternative view consistent with a model-centric view of science. I propose that adopting the model-centric view can help to settle some of the differences among proponents and critics of MTE.     

Mathematical theory for plant—herbivore systems

The interactions of host plants with herbivores can be mediated by factors other than population sizes or biomass alone. Recent evidence indicates that features of the vegetation (loosely termed plant quality) may change in response to herbivory and may, in turn, influence the performance of herbivores (i.e. by affecting survivorship, fecundity, or growth rates). A model which incorporates the effect of plant quality is presented. First it is shown that the frequency distribution of plant quality in the vegetation (p(q, t)) satisfies an equation of conservation. Then, qualitative aspects of the system are discussed in three situations: (1) mobile herbivores interacting with all plants; (2) sessile herbivores feeding exclusively on single plants; (3) intermediate situations in which mobility is moderate to low.I show that depending on the plant quality response, f(q, h), and the herbivore response, g(q, h), it is possible to obtain stable equilibria as well as stable periodic oscillations. In the former case the populations tend to lose their heterogeneity. In the latter case, oscillations are accompanied by alternate narrowing and broadening of the distribution. Empirical testing and further research are suggested.     

The derivation of D’Arcy Thompson’s theory of transformations from the theory of optimal design

It is shown informally that Cohn’s theory of Optimal Forms can be construed as a comparative theory, and that when this is done the celebrated theory of transformations of D’Arcy Thompson follows as a consequence. The implications of this type of theoretical foundation for the Thompson theory with regard to problems of comparative morphology are discussed, and some suggestions for the further implementation of the theory are described. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Contract No. AF 49(638)-917.     

What remains of the Cholodny-Went theory? Introduction

The Cholodny-Went theory, which states that plant tropisms in roots and shoots are due to the unequal distribution of the growth regulator auxin in reponse to light or gravity, presented a simple and direct explanation of these phenomena. This was significant in the 1930s when simple explanations were lacking, and much research into this theory has been performed since that time. From the 1980s forward, there has been much questioning and controversy surrounding the theory. In this introduction to 15 brief articles, the author describes how leading scientists in the field were asked to air their opinions of the theory and formulate questions for each other. The resulting articles are presented in an attempt to stimulate discussion and give insights into the state of the Cholodny-Went theory in the 1990s.     

Tetz’s theory and law of longevity

Here, we present new theory and law of longevity intended to evaluate fundamental factors that control lifespan. This theory is based on the fact that genes affecting host organism longevity are represented by subpopulations: genes of host eukaryotic cells, commensal microbiota, and non-living genetic elements. Based on Tetz’s theory of longevity, we propose that lifespan and aging are defined by the accumulation of alterations over all genes of macroorganism and microbiome and the non-living genetic elements associated with them. Tetz’s law of longevity states that longevity is limited by the accumulation of alterations to the limiting value that is not compatible with life. Based on theory and law, we also propose a novel model to calculate several parameters, including the rate of aging and the remaining lifespan of individuals. We suggest that this theory and model have explanatory and predictive potential to eukaryotic organisms, allowing the influence of diseases, medication, and medical procedures to be re-examined in relation to longevity. Such estimates also provide a framework to evaluate new fundamental aspects that control aging and lifespan.     

Can the theory of evolution be falsified?

In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called the theory of common descent), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.     

Small-angle x-ray scattering from lipid bilayers is well described by modified Caillé theory but not by paracrystalline theory.

X-ray scattering data at high instrumental resolution are reported for multilamellar vesicles of L alpha phase lipid bilayers of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine at 50 degrees C under varying osmotic pressure. The data are fitted to two theories that account for noncrystalline disorder, paracrystalline theory (PT) and modified Caillé theory (MCT). The MCT provides good fits to the data, much better than the PT fits. The particularly important characteristic of MCT is the long power law tails in the scattering. PT fits (as well as ordinary integration with no attempt to account for the noncrystalline disorder) increasingly underestimate this scattering intensity as the order h increases, thereby underestimating the form factors used to obtain electron density profiles.     

The heat dissipation limit theory and evolution of life histories in endotherms--time to dispose of the disposable soma theory?

A major factor influencing life-history strategies of endotherms is body size. Larger endotherms live longer, develop more slowly, breed later and less frequently, and have fewer offspring per attempt at breeding. The classical evolutionary explanation for this pattern is that smaller animals experience greater extrinsic mortality, which favors early reproduction at high intensity. This leads to a short lifespan and early senescence by three suggested mechanisms. First, detrimental late-acting mutations cannot be removed because of the low force of selection upon older animals (mutation accumulation). Second, genes that promote early reproduction will be favored in small animals, even if they have later detrimental effects (antagonistic pleiotropy). Third, small animals may be forced to reduce their investment in longevity assurance mechanisms (LAMs) in favor of investment in reproduction (the disposable soma theory, DST). The DST hinges on three premises: that LAMs exist, that such LAMs are energetically expensive and that the supply of energy is limited. By contrast, the heat dissipation limit (HDL) theory provides a different conceptual perspective on the evolution of life histories in relation to body size. We suggest that rather than being limited, energy supplies in the environment are often unlimited, particularly when animals are breeding, and that animals are instead constrained by their maximum capacity to dissipate body heat, generated as a by-product of their metabolism. Because heat loss is fundamentally a surface-based phenomenon, the low surface-to-volume ratio of larger animals generates significant problems for dissipating the body heat associated with reproductive effort, which then limits their current reproductive investment. We suggest that this is the primary reason why fecundity declines as animal size increases. Because large animals are constrained by their capacity for heat dissipation, they have low reproductive rates. Consequently, only those large animals living in habitats with low extrinsic mortality could survive leading to the familiar patterns of life-history trade-offs and their links to extrinsic mortality rates. The HDL theory provides a novel mechanism underpinning the evolution of life history and ageing in endotherms, and makes a number of testable predictions that directly contrast with the predictions arising from the DST.     

Cytokinesis: an emerging unified theory for eukaryotes?

In animal and fungal cells, cytokinesis involves an actomyosin ring that forms and contracts at the division plane. Important new details have emerged concerning the composition, assembly, and dynamics of these contractile rings. In addition, recent advances suggest that targeted membrane addition is a central feature of cytokinesis in animal cells - as it is in fungi and plants - and the coordination of actomyosin ring function with targeted exocytosis at the cleavage plane is being explored. Important new information has also emerged about the spatial and temporal regulation of cytokinesis, especially in relation to the function of the spindle midzone in animal cells and the control of cytokinesis by GTPase systems.     

Contributions to the mathematical theory of epidemics—I

(1) A mathematical investigation has been made of the progress of an epidemic in a homogeneous population. It has been assumed that complete immunity is conferred by a single attack, and that an individual is not infective at the moment at which he receives infection. With these reservations the problem has been investigated in its most general aspects, and the following conclusions have been arrived at. (2) In general a threshold density of population is found to exist, which depends upon the infectivity, recovery and death rates peculiar to the epidemic. No epidemic can occur if the population density is below this threshold value. (3) Small increases of the infectivity rate may lead to large epidemics; also, if the population density slightly exceeds its threshold value the effect of an epidemic will be to reduce the density as far below the threshold value as initially it was above it. (4) An epidemic, in general, comes to an end, before the susceptible population has been exhausted. (5) Similar results are indicated for the case in which transmission is through an intermediate host.     

π-π stacking tackled with density functional theory

Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing pi-pi stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound pi-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the pi-pi stacking potential energy surface.     

Mechanism of meiotic recombination in eukaryotes—A theory

It is proposed that in meiotic chromosomes single strand breaks of DNA originate either in the delayed regions of replicons or as a result of the excision activity of DNA polymerase during zygotene DNA synthesis. Rejoining of the break points belonging to non-sister chromatids takes place by switching over of the polymerase from one strand of DNA to another non-sister strand of the same polarity and gives rise to recombination intermediates (half-chromatid chiasmata). Strand migration in a recombination intermediate or copying of the same parental strand twice during zygotene as a consequence of a delay in copying the homologous strand would lead to gene conversion. Nicking of the cross strands (parental strands) in any recombination intermediate and subsequent repair leads to recombination for flanking markers. A possible way in which three-strand double crossovers occur and the process of recombination are discussed.     

Canalization in evolutionary genetics: a stabilizing theory?

Canalization is an elusive concept. The notion that biological systems ought to evolve to a state of higher stability against mutational and environmental perturbations seems simple enough, but has been exceedingly difficult to prove. Part of the problem has been the lack of a definition of canalization that incorporates an evolutionary genetic perspective and provides a framework for both mathematical and empirical study. After briefly reviewing the importance of canalization in studies of evolution and development, we aim, with this essay, to outline a research program that builds upon the definition of canalization as the reduction in variability of a trait, and uses molecular genetic approaches to shed light on the problems of canalization.     

Is the oxidative stress theory of aging dead?

Currently, the oxidative stress (or free radical) theory of aging is the most popular explanation of how aging occurs at the molecular level. While data from studies in invertebrates (e.g., C. elegans and Drosophila) and rodents show a correlation between increased lifespan and resistance to oxidative stress (and in some cases reduced oxidative damage to macromolecules), direct evidence showing that alterations in oxidative damage/stress play a role in aging are limited to a few studies with transgenic Drosophila that overexpress antioxidant enzymes. Over the past eight years, our laboratory has conducted an exhaustive study on the effect of under- or overexpressing a large number and wide variety of genes coding for antioxidant enzymes. In this review, we present the survival data from these studies together. Because only one (the deletion of the Sod1 gene) of the 18 genetic manipulations we studied had an effect on lifespan, our data calls into serious question the hypothesis that alterations in oxidative damage/stress play a role in the longevity of mice.