What mechanisms can’t do: Explanatory frameworks and the function of the p53 gene in molecular oncology

What has been called the new mechanistic philosophy conceives of mechanisms as the main providers of biological explanation. We draw on the characterization of the p53 gene in molecular oncology, to show that explaining a biological phenomenon (cancer, in our case) implies instead a dynamic interaction between the mechanistic level—rendered at the appropriate degree of ontological resolution—and far more general explanatory tools that perform a fundamental epistemic role in the provision of biological explanations. We call such tools “explanatory frameworks”. They are called frameworks to stress their higher level of generality with respect to bare mechanisms; on the other hand, they are called explanatory because, as we show in this paper, their importance in explaining biological phenomena is not secondary with respect to mechanisms. We illustrate how explanatory frameworks establish selective and local criteria of causal relevance that drive the search for, characterisation and usage of biological mechanisms. Furthermore, we show that explanatory frameworks allow for changes of scientific perspective on the causal relevance of mechanisms going beyond the account provided by the new mechanistic philosophy.     

Highly impulsive rats: modelling an endophenotype to determine the neurobiological,genetic and environmental mechanisms of addiction

Impulsivity describes the tendency of an individual to act prematurely without foresight and is associated with a number of neuropsychiatric co-morbidities, including drug addiction. As such, there is increasing interest in the neurobiological mechanisms of impulsivity, as well as the genetic and environmental influences that govern the expression of this behaviour. Tests used on rodent models of impulsivity share strong parallels with tasks used to assess this trait in humans, and studies in both suggest a crucial role of monoaminergic corticostriatal systems in the expression of this behavioural trait. Furthermore, rodent models have enabled investigation of the causal relationship between drug abuse and impulsivity. Here, we review the use of rodent models of impulsivity for investigating the mechanisms involved in this trait, and how these mechanisms could contribute to the pathogenesis of addiction.     

The causal structure of mechanisms

Recently, a number of philosophers of science have claimed that much explanation in the sciences, especially in the biomedical and social sciences, is mechanistic explanation. I argue the account of mechanistic explanation provided in this tradition has not been entirely satisfactory, as it has neglected to describe in complete detail the crucial causal structure of mechanistic explanation. I show how the interventionist approach to causation, especially within a structural equations framework, provides a simple and elegant account of the causal structure of mechanisms. This account explains the many useful insights of traditional accounts of mechanism, such as Carl Craver’s account in his book Explaining the Brain (2007), but also helps to correct the omissions of such accounts. One of these omissions is the failure to provide an explicit formulation of a modularity constraint that plays a significant role in mechanistic explanation. One virtue of the interventionist/structural equations framework is that it allows for a simple formulation of a modularity constraint on mechanistic explanation. I illustrate the role of this constraint in the last section of the paper, which describes the form that mechanistic explanation takes in the computational, information-processing paradigm of cognitive psychology.     

The embryotoxicity of phenytoin: an update on possible mechanisms

PHT has multiple effects in adult humans and animals, and there is no reason to assume that it will not have multiple effects in embryos and fetuses. Although one of the first associations between anticonvulsant therapy and an adverse development effect in humans was noted in 1964 (104), the mechanism(s) whereby these adverse effects occur has thus far eluded research efforts. In this review, I have focused on three possible mechanisms. Overall, the evidence does not appear to implicate folate deficiency in PHT-induced embryotoxicity. A role for glucocorticoids or interaction between PHT and the glucocorticoid receptor has not been ruled out. However, a significant amount of work remains to be done to examine the involvement of the arachidonic acid cascade in PHT-induced embryotoxicity in vivo. The bulk of the experimental evidence would seem to favor a role for the generation of a reactive intermediate and its subsequent binding to embryonic macromolecules. This metabolite(s) has not been identified. Additionally, the association between covalent binding of metabolites and embryotoxicity remains simply an association; a causal relationship has not been established. Much work remains to be done to determine whether any of these possibilities, some other possibility, or a combination of several mechanisms will explain the adverse development effects of this very important, therapeutically useful anticonvulsant.     

Factors affecting the variability of the central mechanisms for maintaining bilingualism

The article discusses the probable role of many factors that determine the individual variety of the neurophysiological mechanisms that provide the opportunity to learn and use fluently two or more languages. The formation of the speech function is affected by both the general factors for bilinguals and monolinguals, as well as by the specific characteristic of bilingualism. General factors include genetic and environmental impacts explaining the diversity of individual options for the development of the morphofunctional organization of the speech function. Bilinguals, obviously, have an even wider variation of the central maintenance of speech ability, due to the combination of different conditions that influence the language environment, which include the age of second language acquisition, the language proficiency, the linguistic similarity of the languages, the method of their acquisition, intensity of use, and the area where each language is used. The influence of these factors can be mediated in different ways by the individual characteristics of the bilingual??s brain. Being exposed to two languages from the first days of life, the child uses for the development of speech skills the unique features of the brain that exist only at the initial stages of postnatal ontogenesis. At an older age, mastering a second language requires much more effort, when, in the course of maturation, the brain acquires new additional possibilities but permanently loses that special ??bonus?? that nature gives to a small child only in the first months of life. Large individual variability patterns of activation of the cortex during verbal activity in older bilinguals, compared with the younger ones, allows us to assume that the brain of the older bilingual mastering a new language is forced to manipulate a large number of backup mechanisms, and this is reflected in an increase in the variation of the cerebral processes responsible for speech functions. In addition, there is a serious reason to believe that learning a second language contributes to the expansion of the functional capabilities of the brain and creates the basis for successful cognitive activity.     

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

Cis-regulatory sequences, such as enhancers and promoters, control development and physiology by regulating gene expression. Mutations that affect the function of these sequences contribute to phenotypic diversity within and between species. With many case studies implicating divergent cis-regulatory activity in phenotypic evolution, researchers have recently begun to elucidate the genetic and molecular mechanisms that are responsible for cis-regulatory divergence. Approaches include detailed functional analysis of individual cis-regulatory elements and comparing mechanisms of gene regulation among species using the latest genomic tools. Despite the limited number of mechanistic studies published to date, this work shows how cis-regulatory activity can diverge and how studies of cis-regulatory divergence can address long-standing questions about the genetic mechanisms of phenotypic evolution.     

Protein Folding,Misfolding, Aggregation and Their Implications in Human Diseases: Discovering Therapeutic Ways to Amyloid-Associated Diseases

Protein folding is a very complex process, and recognition of the molecular mechanisms responsible for protein folding is one of the demanding queries in biochemistry. Protein molecules have a fixed propensity either to misfold or unable to sustain their precisely folded states, under assured conditions. Taking into account that the protein misfolding and aggregation are central in the pathogenesis of protein conformational disorders, a therapy focussed to the root of the disease should target to restrain and/or undo the conformational alterations that lead to the development of the pathological protein conformer. In future, an understanding of the causes of protein aggregation and genetic and environmental vulnerability features of an exact individual may offer an enhanced prospect for a successful therapeutic intrusion. Dealing with these and related problems not only provides great prospects for involvement with numerous, presently fatal diseases but will also ultimately disclose the basically essential association between proteostasis and prolonged existence.     

Host diversity drives parasite diversity: meta‐analytical insights into patterns and causal mechanisms

Statistical correlations of biodiversity patterns across multiple trophic levels have received considerable attention in various types of interacting assemblages, forging a universal understanding of patterns and processes in free‐living communities. Host–parasite interactions present an ideal model system for studying congruence of species richness among taxa as obligate parasites are strongly dependent upon the availability of their hosts for survival and reproduction while also having a tight coevolutionary relationship with their hosts. The present meta‐analysis examined 38 case studies on the relationship between species richness of hosts and parasites, and is the first attempt to provide insights into the patterns and causal mechanisms of parasite biodiversity at the community level using meta‐regression models. We tested the distinct role of resource (i.e. host) availability and evolutionary co‐variation on the association between biodiversity of hosts and parasites, while spatial scale of studies was expected to influence the extent of this association. Our results demonstrate that species richness of parasites is tightly correlated with that of their hosts with a strong average effect size (r= 0.55) through both host availability and evolutionary co‐variation. However, we found no effect of the spatial scale of studies, nor of any of the other predictor variables considered, on the correlation. Our findings highlight the tight ecological and evolutionary association between host and parasite species richness and reinforce the fact that host–parasite interactions provide an ideal system to explore congruence of biodiversity patterns across multiple trophic levels.     

How different types of pattern formation mechanisms affect the evolution of form and development

Here we investigate how development and evolution can affect each other by exploring what kind of phenotypic variation is produced by different types of developmental mechanisms. A limited number of developmental mechanisms are capable of pattern formation in development. Two main types have been identified. In morphodynamic mechanisms, induction events and morphogenetic processes, such as simple growth, act at the same time. In morphostatic mechanisms, induction events happen before morphogenetic mechanisms, and thus growth cannot influence the induction of a pattern. We present a study of the variational properties of these developmental mechanisms that can help to understand how and why a developmental mechanism may become involved in the evolution and development of a particular morphological structure. Using existing models of pattern formation in teeth, an extensive simulation analysis of the phenotypic variation produced by different types of developmental mechanisms is performed. The studied properties include the amount and diversity of the phenotypic variation produced, the complexity of the phenotypic variation produced, and the relationship between phenotype and genotype. These variational properties are so different between different types of mechanisms that the relative involvement of these types of mechanisms in evolutionary innovation and in different stages of development can be estimated. In addition, type of mechanism affects the tempo and mode of morphological evolution. These results suggest that the basic principles by which development is organized can influence the likelihood of morphological evolution.     

Organization of vertebrate annual cycles: implications for control mechanisms

The majority of vertebrates have a life span of greater than one year. Therefore individuals must be able to adapt to the annual cycle of changing conditions by adjusting morphology, physiology and behaviour. Phenotypic flexibility, in which an individual switches from one life history stage to another, is one way to maximize fitness in a changing environment. When environmental variation is low, few life history stages are needed. If environmental variation is large, there are more life history stages. Each life history stage has a characteristic set of sub-stages that can be expressed in various combinations and patterns to determine state at any point in the life of the individual. Thus individuals have a finite number of states that can be expressed over the spectrum of environmental conditions in their life spans. Life history stages have three phases-development, mature capability (when characteristic sub-stages can be expressed) and termination. Expression of a stage is time dependent (probably a minimum of one month), and termination of one stage overlaps development of the next stage. It follows that the more life history stages an individual expresses, the less flexibility it will have in timing those stages. Having fewer life history stages increases flexibility in timing, but less tolerance of variation in environmental conditions. To varying degrees it is possible to overlap mature capability of some life history stages to effectively reduce 'finite stage diversity' and maximize flexibility in timing. Theoretical ways by which this can be done, and the implications for neuroendocrine and endocrine control mechanisms are discussed. Twelve testable hypotheses are posed that relate directly to control mechanisms.     

Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory

Individual variation in ecologically important features of organisms is a crucial element in ecology and evolution, yet disentangling its underlying causes is difficult in natural populations. We applied a genomic scan approach using amplified fragment length polymorphism (AFLP) markers to quantify the genetic basis of long‐term individual differences in herbivory by mammals at a wild population of the violet Viola cazorlensis monitored for two decades. In addition, methylation‐sensitive amplified polymorphism (MSAP) analyses were used to investigate the association between browsing damage and epigenetic characteristics of individuals, an aspect that has been not previously explored for any wild plant. Structural equation modelling was used to identify likely causal structures linking genotypes, epigenotypes and herbivory. Individuals of V. cazorlensis differed widely in the incidence of browsing mammals over the 20‐year study period. Six AFLP markers (1.6% of total) were significantly related to herbivory, accounting altogether for 44% of population‐wide variance in herbivory levels. MSAP analyses revealed considerable epigenetic variation among individuals, and differential browsing damage was significantly related to variation in multilocus epigenotypes. In addition, variation across plants in epigenetic characteristics was related to variation in several herbivory‐related AFLP markers. Statistical comparison of alternative causal models suggested that individual differences in herbivory are the outcome of a complex causal structure where genotypes and epigenotypes are interconnected and have direct and indirect effects on herbivory. Insofar as methylation states of MSAP markers influential on herbivory are transgenerationally heritable, herbivore‐driven evolutionary changes at the study population will involve correlated changes in genotypic and epigenotypic distributions.     

Laboratory models,causal explanation and group selection

We develop an account of laboratory models, which have been central to the group selection controversy. We compare arguments for group selection in nature with Darwin's arguments for natural selection to argue that laboratory models provide important grounds for causal claims about selection. Biologists get information about causes and cause-effect relationships in the laboratory because of the special role their own causal agency plays there. They can also get information about patterns of effects and antecedent conditions in nature. But to argue that some cause is actually responsible in nature, they require an inference from knowledge of causes in the laboratory context and of effects in the natural context. This process, cause detection, forms the core of an analogical argument for group selection. We discuss the differing roles of mathematical and laboratory models in constructing selective explanations at the group level and apply our discussion to the units of selection controversy to distinguish between the related problems of cause determination and evaluation of evidence. Because laboratory models are at the intersection of the two problems, their study is crucial for framing a coherent theory of explanation for evolutionary biology.     

Primary and secondary causes and consequences of contemporary forest decline

Realization that forest decline (Waldsterben) has become an ecological crisis throughout the developed world has resulted in massive research efforts to determine the causes of declines. It is now recognized that no single causal factor is responsible, but that there are a variety of anthropogenic causal factor complexes interacting with natural events and processes that, together, induce stresses in forests that culminate in declines of individual plants and of ecosystems. It is the thesis of this article that forest declines involve all biotic and abiotic facets and parameters of forested ecosystems and that the declines are themselves new causal factor complexes that continue to affect the stability of forested ecosystems independently of the initial causal factor complexes. Lacking direct field or laboratory studies on these cascades of causes and effects, this article attempts to utilize the growing body of information on plant physiological ecology to provide a heuristic framework for evaluating long-term forest declines.     

Unravelling causal components of the Ordovician Radiation: the Builth Inlier (central Wales) as a case study

Hypotheses about the causes of biodiversification during the Ordovician have been focused in three main areas: tectonic activity and nutrient supply, palaeogeography, and ecological escalation. There is as yet no consensus on mechanisms, and it is unclear whether it is better to study the patterns at local or regional scales. By applying ecological knowledge to the available palaeontological information, it can be shown that neither tectonic nor palaeogeographic effects could account for the permanence of the diversity rise, in the absence of elements of ecological escalation. However, it may be possible to identify trigger mechanisms resulting in enhanced speciation or reduced extinction. Areas of local diversity increase should be distinguished from speciation centres. An ongoing study of the Middle Ordovician Builth-Llandrindod Inlier of central Wales, conducted over 10 years, has identified elements of all three of the above categories of causal mechanisms affecting local diversity. This implies that the patterns of causal relationship and diversification are complex even at very local scales, and at this stage we should not anticipate a clear correlation of global diversity with any single factor. More data are needed from small-scale but intensive studies before we can generalize about the causal mechanisms of the Ordovician Radiation.     

Closing the ‘phenotype gap’ in precision medicine: improving what we measure to understand complex disease mechanisms

The central concept underlying precision medicine is a mechanistic understanding of each disease and its response to therapy sufficient to direct a specific intervention. To execute on this vision requires parsing incompletely defined disease syndromes into discrete mechanistic subsets and developing interventions to precisely address each of these etiologically distinct entities. This will require substantial adjustment of traditional paradigms which have tended to aggregate high-level phenotypes with very different etiologies. In the current environment, where diagnoses are not mechanistic, drug development has become so expensive that it is now impractical to imagine the cost-effective creation of new interventions for many prevalent chronic conditions. The vision of precision medicine also argues for a much more seamless integration of research and development with clinical care, where shared taxonomies will enable every clinical interaction to inform our collective understanding of disease mechanisms and drug responses. Ideally, this would be executed in ways that drive real-time and real-world discovery, innovation, translation, and implementation. Only in oncology, where at least some of the biology is accessible through surgical excision of the diseased tissue or liquid biopsy, has “co-clinical” modeling proven feasible. In most common germline disorders, while genetics often reveal the causal mutations, there still remain substantial barriers to efficient disease modeling. Aggregation of similar disorders under single diagnostic labels has directly contributed to the paucity of etiologic and mechanistic understanding by directly reducing the resolution of any subsequent studies. Existing clinical phenotypes are typically anatomic, physiologic, or histologic, and result in a substantial mismatch in information content between the phenomes in humans or in animal ‘models’ and the variation in the genome. This lack of one-to-one mapping of discrete mechanisms between disease and animal models causes a failure of translation and is one form of ‘phenotype gap.’ In this review, we will focus on the origins of the phenotyping deficit and approaches that may be considered to bridge the gap, creating shared taxonomies between human diseases and relevant models, using cardiovascular examples.

     

More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms

Many different crop species were selected for a common suite of ‘domestication traits’, which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two independently evolved weed strains found in US rice fields, strawhull (S) and blackhull awned (B). Genotyping‐by‐sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6016 and 13 730 SNPs mapped in F₅ lines of the S and B populations, respectively. For some weediness traits (awn length, hull pigmentation and pericarp pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed that trait variation was largely attributable to individual loci. However, for more complex quantitative traits (including heading date, panicle length and seed shattering), we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Candidate gene sequencing revealed causal genetic bases for 8 of 27 total mapped QTL. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms.     

Neurobiological mechanisms involved in recognition of olfactory signature of the young in sheep

The following review focuses on neurobiological mechanisms responsible for the individual recognition of the olfactory signature of the young by the ewe at parturition. Steroids and vaginocervical stimulation are responsible for neurochemical and electrophysiological changes within the olfactory bulb that are part of the learning mechanisms of the individual lamb odour, thus allowing the establishment of a selective bond between the ewe and her lamb. There is an increase in the number of mitral cells, the principal cells of the olfactory bulb that respond to lamb odours, which is associated with increased release of glutamate and gamma-aminobutyric acid from the dendrodendritic synapses between the mitral and granule cells. The relation between the release of the two transmitters after birth suggests an increased efficacy of glutamate evoked gamma-aminobutyric acid release. Parturition is also accompanied by increased oxytocinergic, cholinergic and noradrenergic neurotransmitter release that are essential for selective recognition of lambs. These increases in transmitter release depend on maternal experience, so that greater amounts have been found in multiparous than primiparous ewes. Therefore maternal experience seems to induce a neural maturation process that facilitates effective transmitter release in the olfactory bulb.     

Fish shoal composition: mechanisms and constraints

Observations were made on three fish species (banded killifish (Fundulus diaphanus), golden shiner (Notemigonus crysoleucas) and white sucker (Catostomus commersoni)) in a temperate lake (New Brunswick, Canada) in order to investigate the relationship between shoal choice behaviour of individual fishes and shoal composition. Encounters between shoals were observed to take place every 1.1 min per shoal and an encounter lasted 3.7 s on average. The duration of shoal encounters was influenced by shoal size but not by differences between shoals in either body length or species. Conversely, the outcome of shoal encounters (i.e. ences between shoals in either body length or species. Conversely, the outcome of shoal encounters (i.e. whether or not an individual changes shoal) was influenced by body length and species differences but not by shoal size. Together, these results suggest that encounter duration itself is unlikely to have an important influence on encounter outcome. The collection of ten entire fish shoals showed that they were assorted by species and body length. A simulation model demonstrated that individual shoal choice behaviour alone could account for the generation and maintenance of the observed levels of size assortedness of shoals without invoking the existence of other sorting mechanisms such as differential swimming speeds. However, the generation of species assortedness was not predicted by the model. Furthermore, our data suggest that fish density acts as a constraint on shoal choice, influencing both shoal size and composition. This work has implications for studies on information transfer and reciprocal altruism within populations.     

Evaluating the role of income,state dependence and individual specific heterogeneity in the determination of subjective health assessments

This paper investigates the role of various determinants of an individual's subjective self-assessment of own health. While the economics literature has focused primarily on the role of income on these assessments, we include an examination of the role of state dependence and unobserved individual specific time invariant heterogeneity. We employ a dynamic fixed effects ordered choice model to examine the responses of Australian residents. We find no statistically significant relationship between transitory income and health responses. We also find that while there is evidence of state dependence, this does not appear to be responsible for the distribution of responses. Our results suggest that the variation in the individual specific effects, comprising both observed and unobserved time invariant factors, is primarily responsible for the variation across individuals’ responses.