An explanatory model for food-web structure and evolution

Food webs are networks describing who is eating whom in an ecological community. By now it is clear that many aspects of food-web structure are reproducible across diverse habitats, yet little is known about the driving force behind this structure. Evolutionary and population dynamical mechanisms have been considered. We propose a model for the evolutionary dynamics of food-web topology and show that it accurately reproduces observed food-web characteristics in the steady state. It is based on the observation that most consumers are larger than their resource species and the hypothesis that speciation and extinction rates decrease with increasing body mass. Results give strong support to the evolutionary hypothesis.     

Reappraising a decade old explanatory model for pharmacognosy

It has been a decade since a tripod model of pharmacognosy – organism, biological activity, chemical structure – was proposed. Since then advances in all disciplines have taken science into the 21st century. What are the implications for pharmacognosy? In this paper we expand the previous model, adding a new module with focus on informatics to encompass results of new technical and theoretical advancements for drug discovery.     

Formation of evolutionary approach as an explanatory principle for ecology

Although the connection of ecology with evolutionary idea and specifically with Darwinism was proclaimed for a long time it seems that Herbert Spencer's approach with its emphasize on natural equilibrium was much more often used as its real theoretical base. Elements of Darwinian approach appeared only in 1920-30s in works of those few researchers who studying the distribution and population dynamics of different species tried to understand general mechanisms providing their continuing existence. Later, in the middle of 1950s the first attempts were undertaken to consider the population life history (primarily the age specific schedule of death and reproduction) as a result of natural selection aimed to maintain the necessary level of fitness. A special attention in these studies that burgeoned in 1980-90s was paid to looking for various trade-offs between particular parameters of life history, e.g., between the survival of juveniles and fecundity of adults. The problem of life history optimization became central for the whole branch of science named "evolutionary ecology". Though traditionally this branch is connected with Darwinism, it is rooted rather in Spencer's ideas on moving equilibrium and deals more with static than dynamic. Disproportionately less attention was paid to the evolution of communities since these formations could be hardly interpreted as units of Darwinian selection. Moreover, the ecologists dealing with biosphere as a unified biogeochemical system began insist on "nondarwinian" nature of its evolution. The author considers this opinion as not sufficiently grounded. Darwin's ideas about unavoidable exponential growth, intrinsic for any population, consequent deficiency of resources, and differential survival and reproduction of individuals are still useful while studying the evolution of living organisms (phylogenetics) or the development of biosphere as a global ecosystem.     

Parsimony and explanatory power

Parsimony can be related to explanatory power, either by noting that each additional requirement for a separate origin of a feature reduces the number of observed similarities that can be explained as inheritance from a common ancestor; or else by applying Popper’s formula for explanatory power together with the fact that parsimony yields maximum likelihood trees under No Common Mechanism (NCM). Despite deceptive claims made by some likelihoodists, most maximum likelihood methods cannot be justified in this way because they rely on unrealistic background assumptions. These facts have been disputed on the various grounds that ad hoc hypotheses of homoplasy are explanatory, that they are not explanatory, that character states are ontological individuals, that character data do not comprise evidence, that unrealistic theories can be used as background knowledge, that NCM is unrealistic, and that likelihoods cannot be used to evaluate explanatory power. None of these objections is even remotely well founded, and indeed most of them do not even seem to have been meant seriously, having instead been put forward merely to obstruct the development of phylogenetic methods. © The Willi Hennig Society 2008.     

Descriptive and explanatory markedness

The wide empirical coverage of two number features, [??singular] and [??augmented], is used to show that (Greenbergian) category-internal markedness, (geometric) feature markedness, and value markedness are, respectively, epiphenomenal, untenable, and too simplistically formulated to be currently evaluated.     

Percent body fat estimations in college men using field and laboratory methods: A three-compartment model approach

Background

Methods used to estimate percent body fat can be classified as a laboratory or field technique. However, the validity of these methods compared to multiple-compartment models has not been fully established. The purpose of this study was to determine the validity of field and laboratory methods for estimating percent fat (%fat) in healthy college-age men compared to the Siri three-compartment model (3C).

Methods

Thirty-one Caucasian men (22.5 ± 2.7 yrs; 175.6 ± 6.3 cm; 76.4 ± 10.3 kg) had their %fat estimated by bioelectrical impedance analysis (BIA) using the BodyGram? computer program (BIA-AK) and population-specific equation (BIA-Lohman), near-infrared interactance (NIR) (Futrex^® 6100/XL), four circumference-based military equations [Marine Corps (MC), Navy and Air Force (NAF), Army (A), and Friedl], air-displacement plethysmography (BP), and hydrostatic weighing (HW).

Results

All circumference-based military equations (MC = 4.7% fat, NAF = 5.2% fat, A = 4.7% fat, Friedl = 4.7% fat) along with NIR (NIR = 5.1% fat) produced an unacceptable total error (TE). Both laboratory methods produced acceptable TE values (HW = 2.5% fat; BP = 2.7% fat). The BIA-AK, and BIA-Lohman field methods produced acceptable TE values (2.1% fat). A significant difference was observed for the MC and NAF equations compared to both the 3C model and HW (p < 0.006).

Conclusion

Results indicate that the BP and HW are valid laboratory methods when compared to the 3C model to estimate %fat in college-age Caucasian men. When the use of a laboratory method is not feasible, BIA-AK, and BIA-Lohman are acceptable field methods to estimate %fat in this population.

     

Why one model is never enough: a defense of explanatory holism

Traditionally, a scientific model is thought to provide a good scientific explanation to the extent that it satisfies certain scientific goals that are thought to be constitutive of explanation (e.g. generating understanding, identifying mechanisms, making predictions, identifying high-level patterns, allowing us to control and manipulate phenomena). Problems arise when we realize that individual scientific models cannot simultaneously satisfy all the scientific goals typically associated with explanation. A given model’s ability to satisfy some goals must always come at the expense of satisfying others. This has resulted in philosophical disputes regarding which of these goals are in fact necessary for explanation, and as such which types of models can and cannot provide explanations (e.g. dynamical models, optimality models, topological models, etc.). Explanatory monists argue that one goal will be explanatory in all contexts, while explanatory pluralists argue that the goal will vary based on pragmatic considerations. In this paper, I argue that such debates are misguided, and that both monists and pluralists are incorrect. Instead of any goal being given explanatory priority over others in a given context, the different goals are all deeply dependent on one another for their explanatory power. Any model that sacrifices some explanatory goals to attain others will always necessarily undermine its own explanatory power in the process. And so when forced to choose between individual scientific models, there can be no explanatory victors. Given that no model can satisfy all the goals typically associated with explanation, no one model in isolation can provide a good scientific explanation. Instead we must appeal to collections of models. Collections of models provide an explanation when they satisfy the web of interconnected goals that justify the explanatory power of one another.     

A resynthesis of the primordial and circumstantial approaches to ethnic group solidarity: Towards an explanatory model

Social scientists who have attempted to explain ethnic group solidarity have tended to use either the primordial or the circumstantial approach. The first approach accounts for strong ethnic attachments on the basis of their ineffable affective significance. Moreover, this affective significance most often surrounds images of the group's distinctive past, thus giving a historical dimension to the concept of primordialism. The second approach views ethnic group solidarity as resulting from certain social circumstances, both internal and external, under which the members of the group exist. It is argued that neither approach alone offers a sufficient explanation ‐ i.e., that the primordial approach cannot readily account for fluctuating ethnic group solidarity and that the circumstantial approach tends to ignore the affective significance of ethnic ties ‐ and that previous attempts to synthesize them have been inadequate as explanatory models. Such a synthetic model is offered, which is based on the oppositional approach originated by Edward Spicer and which maintains that fluctuating ethnicity, along with fluctuating primordial sentiments, can be best explained on the basis of the circumstance of fluctuating opposition.     

The role and meaning of susto in Mexican Americans' explanatory model of type 2 diabetes

This article examines the role and meaning of susto (fright) in Mexican Americans' explanatory model (EM) of type 2 diabetes. This analysis is based on a study of the health beliefs about type 2 diabetes mellitus among Mexican Americans living in El Paso County, Texas, on the U.S.-Mexico border. Susto was described as an event that could change the bodily state, causing a susceptible person to be more vulnerable to the onset of type 2 diabetes after some unspecified time. The study results illustrate the integration of multiple etiologies into Mexican Americans' EMs of diabetes and illustrate how the environment affects the way in which these explanations are manifested. Acculturation of biomedical system beliefs into the traditional Mexican health belief system has resulted in a synthesis of both systems and a blending of the participants' explanation of type 2 diabetes.     

Truth and explanatory power in biology

Responses

Truth and explanatory power in biology     

Probabilistic causation and the explanatory role of natural selection

The explanatory role of natural selection is one of the long-term debates in evolutionary biology. Nevertheless, the consensus has been slippery because conceptual confusions and the absence of a unified, formal causal model that integrates different explanatory scopes of natural selection. In this study we attempt to examine two questions: (i) What can the theory of natural selection explain? and (ii) Is there a causal or explanatory model that integrates all natural selection explananda? For the first question, we argue that five explananda have been assigned to the theory of natural selection and that four of them may be actually considered explananda of natural selection. For the second question, we claim that a probabilistic conception of causality and the statistical relevance concept of explanation are both good models for understanding the explanatory role of natural selection. We review the biological and philosophical disputes about the explanatory role of natural selection and formalize some explananda in probabilistic terms using classical results from population genetics. Most of these explananda have been discussed in philosophical terms but some of them have been mixed up and confused. We analyze and set the limits of these problems.     

Rational pH-engineering of the thermostable xylanase based on computational model

Locating sites of amino acids related to enzyme properties is still a challenge for rational engineering. Based on the strategy that sites of amino acids can be located by dipeptides, a computational model was made for pH-related dipeptides of xylanase. According to the dipeptide model, pH of a thermostable xylanase B from Thermotoga maritima was rationally designed by locating pH-related amino acids in its sequence and structure. In agreement with expectation, the optimum pH (pH_opt) of the xylanase was improved by five amino acids substitutions: E70Q, E74Q, E77Q, G85Q and T87Q. In parallel assay reactions, at 90 °C, its pH_opt increases to 5.5 from 5.1, and its whole pH profile also shifts 0.5 units towards alkaline area; at 80 °C, the relative activity decreases very little over a wide pH range from 5.25 to 6.0. This result demonstrated that the bioinformatics model is useful for pH rational design and engineering of xylanase, a model molecular of a large family of ～10% proteins with (β/α)₈-barrel structure.     

Contraception for men: a breakthrough new approach

There has not been a new reversible contraceptive for men since the development of the condom, centuries ago. Matzuk et?al. describe a new molecular approach using administration of a small molecule to directly and reversibly inhibit spermatogenesis in mice by blocking the function of a testicular bromodomain without apparent adverse effect on the organism or offspring.