Getting rid of interventions

According to James Woodward’s influential interventionist account of causation, X is a cause of Y iff, roughly, there is a possible intervention on X that changes Y. Woodward requires that interventions be merely logically possible. I will argue for two claims against this modal character of interventions: First, merely logically possible interventions are dispensable for the semantic project of providing an account of the meaning of causal statements. If interventions are indeed dispensable, the interventionist theory collapses into (some sort of) a counterfactual theory of causation. Thus, the interventionist theory is not tenable as a theory of causation in its own right. Second, if one maintains that merely logically possible interventions are indispensable, then interventions with this modal character lead to the fatal result that interventionist counterfactuals are evaluated inadequately. Consequently, interventionists offer an inadequate theory of causation. I suggest that if we are concerned with explicating causal concepts and stating the truth-conditions of causal claims we best get rid of Woodwardian interventions.     

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.     

More on how and why: cause and effect in biology revisited

In 1961, Ernst Mayr published a highly influential article on the nature of causation in biology, in which he distinguished between proximate and ultimate causes. Mayr argued that proximate causes (e.g. physiological factors) and ultimate causes (e.g. natural selection) addressed distinct ‘how’ and ‘why’ questions and were not competing alternatives. That distinction retains explanatory value today. However, the adoption of Mayr’s heuristic led to the widespread belief that ontogenetic processes are irrelevant to evolutionary questions, a belief that has (1) hindered progress within evolutionary biology, (2) forged divisions between evolutionary biology and adjacent disciplines and (3) obstructed several contemporary debates in biology. Here we expand on our earlier (Laland et al. in Science 334:1512–1516, 2011) argument that Mayr’s dichotomous formulation has now run its useful course, and that evolutionary biology would be better served by a concept of reciprocal causation, in which causation is perceived to cycle through biological systems recursively. We further suggest that a newer evolutionary synthesis is unlikely to emerge without this change in thinking about causation.     

‘Do you have a mobile?’ Mobile phone practices and the refashioning of social relationships in Port Vila Town

Mobile phones have quickly become an important part of young people's social relationships in Port Vila Vanuatu. In particular, young people embrace the new technology's capacity to broaden the breadth of their sociality. They use the mobile phone to facilitate private and secretive communication, engage in unsanctioned relationships, pre‐marital sexual relationships, and also multiple concurrent intimate relationships. Literature on mobile phone use often either takes the approach that mobile phone technology becomes purely incorporated into pre‐existing social practices, or that it dramatically reshapes social ontologies. The present article argues for an alternative view, one that takes into account the nuances between these two analytical poles. This article suggests that young people use the mobile phone in practices informed by previous models of social relationships, yet the specific materiality of the mobile phone technology is influencing the direction in which models of social relationships are changing. In demonstrating this point, I pay particular attention to two material aspects of the mobile phone technology ‐ the mobile phone as a repository of a particular kind of information ‐ ‘evidence’, and the capacity of the mobile phone to ‘disconnect’ people from their relationships by switching off the mobile. This article argues that these practices are influencing the emergence of a radically altered kinship and gender landscape in the urban context.     

Charles Darwin,embryology, evolution and skeletal plasticity

Darwin provided us with the theory of evolutionary change through natural selection. Just as important to the science of biology was Darwin’s recognition that all organisms could be classified and were related to one another because they arose from a single common universal ancestor – what we know as the universal tree of life (UtoL). All the features of the skeletal biology of fish therefore can be explained, both in an evolutionary framework (ultimate causation) and in the framework of development, growth and physiology (proximate causation). Neither approach is complete without the other. I will outline the elements of Darwin’s theories on evolution and classification and, as importantly, discuss what was missing from Darwin’s theories. An important class of evidence for evolution used by Darwin came from embryology, both comparative embryology and the existence of vestiges and atavisms. After discussing this evidence I examine some fundamental features of skeletal development and evolution These include: the presence of four skeletal systems in all vertebrates; the existence of two skeletons, one based on cartilage, the other on bone and dentine; the modular nature of skeletal development and evolution; and the plasticity of the skeleton in response to either genetic or environmental changes.     

Adaptability in protein structures: structural dynamics and implications in ligand design

The basic framework of understanding the mechanisms of protein functions is achieved from the knowledge of their structures which can model the molecular recognition. Recent advancement in the structural biology has revealed that in spite of the availability of the structural data, it is nontrivial to predict the mechanism of the molecular recognition which progresses via situation-dependent structural adaptation. The mutual selectivity of protein–protein and protein–ligand interactions often depends on the modulations of conformations empowered by their inherent flexibility, which in turn regulates the function. The mechanism of a protein’s function, which used to be explained by the ideas of ‘lock and key’ has evolved today as the concept of ‘induced fit’ as well as the ‘population shift’ models. It is felt that the ‘dynamics’ is an essential feature to take into account for understanding the mechanism of protein’s function. The design principles of therapeutic molecules suffer from the problems of plasticity of the receptors whose binding conformations are accurately not predictable from the prior knowledge of a template structure. On the other hand, flexibility of the receptors provides the opportunity to improve the binding affinity of a ligand by suitable substitution that will maximize the binding by modulating the receptors surface. In this paper, we discuss with example how the protein’s flexibility is correlated with its functions in various systems, revealing the importance of its understanding and for making applications. We also highlight the methodological challenges to investigate it computationally and to account for the flexible nature of the molecules in drug design.     

Distribution of excitation energy among photosystem I and photosystem II in red algae. I. Action spectra of light reactions I and II

Action spectra of light reaction I and light reaction II from red algae (marine members of Florideae and Bangiales) were measured with 550 nm (light 2) or 699 nm (light 1) background light, using a Teflon-covered platinum electrode for O₂ measurement. Care was taken to ensure that maximum enhancement was reached by the background light.The action spectra of light reaction I, we found under these conditions, are very similar to the thallus absorption, whilst the action spectra of light reaction II show, besides strong bands of the phycobilins, only minor bands of chlorophyll a, which account for only 10–20% of the total chlorophyll.The spectra are discussed on the basis of two main types of models of energy distribution over both photosynthetic systems. If this distribution is considered to be invariable (models 1a and b), one has to assume that almost exactly half of the total chlorophyll is not involved in the supply of the non-cyclic electron transport with excitation energy. This part, however, has to be thought of as incorporated in the thylakoid membrane in a similar manner to the chlorophyll in photosystem I. However, if one supposes an almost complete equilibration in the energy distribution over both systems as long as the primary absorption in photosystem II prevails (models 2a and b), there is no need for the assumption of such photosynthetically ‘inactive’ or less active chlorophyll. Some evidence is shown that strongly supports model 2.     

Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces

We present the first study of patterns of genetic diversity of sorghum landraces at the local scale. Understanding landrace diversity aids in deciphering evolutionary forces under domestication, and has applications in the conservation of genetic resources and their use in breeding programs. Duupa farmers in a village in Northern Cameroon distinguished 59 named sorghum taxa, representing 46 landraces. In each field, seeds are sown as a mixture of landraces (mean of 12 landraces per field), giving the potential for extensive gene flow. What level of genetic diversity underlies the great morphological diversity observed among landraces? Given the potential for gene flow, how well defined genetically is each landrace? To answer these questions, we recorded spatial patterns of planting and farmers’ perceptions of landraces, and characterized 21 landraces using SSR markers. Analysis using distance and clustering methods grouped the 21 landraces studied into four clusters. These clusters correspond to functionally and ecologically distinct groups of landraces. Within-landrace genetic variation accounted for 30% of total variation. The average F _is over landraces was 0.68, suggesting high inbreeding within landraces. Differentiation among landraces was substantial and significant (F _st = 0.36). Historical factors, variation in breeding systems, and farmers’ practices all affected patterns of genetic variation. Farmers’ practices are key to the maintenance, despite gene flow, of landraces with different combinations of agronomically and ecologically pertinent traits. They must be taken into account in strategies of conservation and use of genetic resources.     

Study of water sorption on modified Agave fibres

Polymer composite materials are usually reinforced by synthetic matter such as carbon or glass fibres. However, owing to their good mechanical properties and low density, natural fibres are now increasingly being considered as reinforcement. With the aim of a new natural fibre based composite, various chemical treatments have been performed on Agave (Americana L.) fibres in order to improve their compatibility with the polymer matrix and to reduce their affinity for water. The effect of these treatments on the fibre water sorption power has been investigated by means of a micro-balance. Equilibrium water sorption isotherms have been deduced from weight variations of the fibres under water vapor pressure increments. Several specific physico-chemical models have been tested to describe the water sorption isotherms. The Park’s model was found to describe the experimental results accurately and over a wide activity range. The sorption kinetics was also exploited in order to evaluate the diffusivity of water in the fibres. The variation of the water diffusion coefficient with water concentration is in agreement with the triple sorption mode described by the Park’s model. These results show a global increase of moisture resistance of the fibres after chemical treatment. This effect is interpreted in terms of chemical and structural modifications of the cell-wall structure.     

Rethinking relevance: Repetition priming reveals the psychological reality of adaptive specializations for reasoning

Theories advanced to explain conditional reasoning range from those that invoke inference systems that evolved for specific domains (such as social exchange, precautions, or deontic regulations) to relevance theory, a relatively domain-general account that invokes conversational pragmatics. The present research utilized a novel extension of repetition priming, in conjunction with the Wason selection task (a widely known and used task to test people's conditional reasoning), to evaluate alternative theories of human reasoning. Across five experiments, testing over 600 participants, consistent priming across selection tasks was demonstrated. The pattern of priming effects supports models of human reasoning based on specific evolved reasoning abilities, and was inconsistent with general conditional reasoning models such as relevance theory. These results also converge with neurological and clinical evidence of divided psychological processes for reasoning about relatively specific domains, based on functionally distinct inference systems.     

The Science and Philosophy of a Method for Assessing Environmental Causes

When an environmental impairment has been identified, it becomes necessary to identify the cause so that an appropriate action can be planned. However, causation is difficult to establish—both conceptually and in practice. To ensure that the U.S. Environmental Protection Agency's (USEPA's) method for causal assessment is appropriate and defensible, we reviewed concepts of causation from philosophers, statisticians, epidemiologists, and others. This article summarizes the results of that review and explains how it relates to the USEPA's method. We include a five-step process: (1) identify alternative candidate causes; (2) logically eliminate when possible; (3) diagnose when possible; (4) analyze the strength of evidence for remaining candidate causes; and (5) identify the most likely cause. We also encourage three practices: (1) use a consistent process; (2) do not claim proof of causation; and (3) document the evidence and inferences. This approach allows assessors to identify the most likely cause or, failing that, to reduce the set of possible causes and identify information needs for another iteration of causal assessment.     

A harmony of illusions: clinical and experimental testing of Robert Koch’s tuberculin 1890–1900

One of Ludwik Fleck’s ideas about the development of scientific knowledge is that—once a system of interpretation is in place—the process that follows can be characterised as one of inertia: any new evidence comes under a strong pressure to be incorporated into the established frame. This can result in what Fleck called a harmony of illusions (Harmonie der Täuschungen) when contradictory evidence becomes almost invisible or is incorporated into the established frame only by huge efforts.The paper analyses early explanations of the tuberculin reaction as a case study of Fleck’s argument. For Robert Koch, who had presented tuberculin in 1890, the compound was supposed to be a diagnostic tool and a cure for tuberculosis. His conception of its effect was rather peculiar, but strictly in line with ideas on the pathogenesis of infectious diseases he had developed much earlier. After tuberculin was released in late 1890, whether Koch’s conception was convincing depended on the place that a given observer had in the medical world in late-nineteenth-century Germany. Inside Koch’s group, the status of the tuberculin reaction remained stable and tuberculin retained its value as a diagnostic and curative tool. On the other hand, observers from outside that thought collective, and in particular from clinical medicine, soon pointed to flaws in its conception. These critics developed a rather different picture of tuberculin as a mysterious and dangerous drug. No reconciliation followed and what we find instead in German medicine around the year 1900 is the presence of rather contradictory concepts and practices surrounding Koch’s wonder cure.     

Has winter body condition varied with population size in a long-distance migrant,the Bewick’s Swan (<Emphasis Type="Italic">Cygnus columbianus bewickii</Emphasis>)?

Assessments of body condition can provide useful information on changes in the state of individuals within a population, which may in turn help to inform conservation efforts. For example, decreases in body condition over time can indicate reduced food resources. Mass and skull length measures recorded for 195 adult and 467 first winter (cygnets) Bewick’s Swans (Cygnus columbianus bewickii) at wintering sites in the UK between winters 1966/1967 and 2017/2018 therefore were analysed to determine whether a ca. 40% decline in numbers in the Northwest European Bewick’s Swan population between 1995 and 2010 corresponded with poorer body condition from the mid-1990s onwards. Parents and siblings were known for all individuals, allowing us to account for shared genetic factors and rearing environment in our analysis. We used linear mixed-effects models and an information-theoretic approach to test different models of temporal variation in scaled body mass index (SBMI). Within our study population, although SBMI values varied both within and between years, we found no evidence of any directional trends in body condition. Of our competing time models of swan SBMI, a model in which age-specific body condition was constant over time received the greatest support in the data. Body condition was greater for adults than cygnets, but did not vary between sexes or wintering sites. Our findings suggest no connection between the recent declines in population size and body condition. Population decline is therefore unlikely to be caused by inadequate food supplies.     

A computable expression of closure to efficient causation

In this paper, we propose a mathematical expression of closure to efficient causation in terms of λ-calculus; we argue that this opens up the perspective of developing principled computer simulations of systems closed to efficient causation in an appropriate programming language. An important implication of our formulation is that, by exhibiting an expression in λ-calculus, which is a paradigmatic formalism for computability and programming, we show that there are no conceptual or principled problems in realizing a computer simulation or model of closure to efficient causation. We conclude with a brief discussion of the question whether closure to efficient causation captures all relevant properties of living systems. We suggest that it might not be the case, and that more complex definitions could indeed create crucial some obstacles to computability.     

On Monitoring Outcomes of Medical Providers

An issue of substantial importance is the monitoring and improvement of health care facilities such as hospitals, nursing homes, dialysis units or surgical wards. In addressing this, there is a need for appropriate methods for monitoring health outcomes. On the one hand, statistical tools are needed to aid centers in instituting and evaluating quality improvement programs and, on the other hand, to aid overseers and payers in identifying and addressing sub-standard performance. In the latter case, the aim is to identify situations where there is evidence that the facility’s outcomes are outside of normal expectations; such facilities would be flagged and perhaps audited for potential difficulties or censured in some way. Methods in use are based on models where the center effects are taken as fixed or random. We take a systematic approach to assessing the merits of these methods when the patient outcome of interest arises from a linear model. We argue that methods based on fixed effects are more appropriate for the task of identifying extreme outcomes by providing better accuracy when the true facility effect is far from that of the average facility and avoiding confounding issues that arise in the random effects models when the patient risks are correlated with facility effects. Finally, we consider approaches to flagging that are based on the Z-statistics arising from the fixed effects model, but which account in a robust way for the intrinsic variation between facilities as contemplated in the standard random effects model. We provide an illustration in monitoring survival outcomes of dialysis facilities in the US.     

Directional Persistence of Cell Migration Coincides with Stability of Asymmetric Intracellular Signaling

Photosynthetic chromatophore vesicles found in some purple bacteria constitute one of the simplest light-harvesting systems in nature. The overall architecture of chromatophore vesicles and the structural integration of vesicle function remain poorly understood despite structural information being available on individual constituent proteins. An all-atom structural model for an entire chromatophore vesicle is presented, which improves upon earlier models by taking into account the stoichiometry of core and antenna complexes determined by the absorption spectrum of intact vesicles in Rhodobacter sphaeroides, as well as the well-established curvature-inducing properties of the dimeric core complex. The absorption spectrum of low-light-adapted vesicles is shown to correspond to a light-harvesting-complex 2 to reaction center ratio of 3:1. A structural model for a vesicle consistent with this stoichiometry is developed and used in the computation of excitonic properties. Considered also is the packing density of antenna and core complexes that is high enough for efficient energy transfer and low enough for quinone diffusion from reaction centers to cytochrome bc₁ complexes.     

Temporal dynamics of leafy spurge (Euphorbia esula) and two species of flea beetles (Aphthona spp.) used as biological control agents

The goal of this study was to evaluate the biological control program of leafy spurge (Euphorbia esula) in a large natural area, Theodore Roosevelt National Park, western North Dakota, USA. Aphthona lacertosa and Aphthona nigriscutis have been released at more than 1800 points in the 18,600-ha South Unit of the park beginning in 1989; most releases have occurred since 1994. We established permanent vegetation plots throughout the infested area of the park and determined stem counts and biomass of leafy spurge and abundance of the two flea beetle species at these plots each year from 1999 to 2001. Both biomass and stem counts declined over the 3 years of the study. Both species of flea beetle are well established within the park and have expanded into areas where they were not released. A. nigriscutis was more abundant than A. lacertosa in the grassland areas we surveyed, but in all other habitats abundances were similar. Using structural equation models, only A. lacertosa could be shown to have a significant effect on counts of mature stems of leafy spurge. A. nigriscutis numbers were positively correlated with stem counts of mature stems. Previous year’s stem counts had the greatest influence on change in stem counts over each 2-year time step examined with structural equation models.