Do Students See the “Selection” in Organic Evolution? A Critical Review of the Causal Structure of Student Explanations

This paper critically reviews and characterizes the student's causal-explanatory understanding; this is done as a step toward explicating the problematic of evolution education as it concerns the cognitive difficulties in understanding Darwin's theory of natural selection. The review concludes that the student's understanding is fundamentally different from Darwin's, for the student understands evolutionary change as necessary individual transformation caused by the transformative action of various physical and behavioral factors. This is in complete contrast to Darwin's (and even the Darwinian's, for that matter) understanding of evolutionary change as a change caused by accumulative selection. Hence, to understand natural selection, the student has to learn to “see” how the accumulative selection causes evolutionary change.

The nature of developmental constraints and the difference-maker argument for externalism

One current version of the internalism/externalism debate in evolutionary theory focuses on the relative importance of developmental constraints in evolutionary explanation. The received view of developmental constraints sees them as an internalist concept that tend to be shared across related species as opposed to selective pressures that are not. Thus, to the extent that constraints can explain anything, they can better explain similarity across species, while natural selection is better able to explain their differences. I challenge both of these aspects of the received view and propose a hierarchical view of constraints.

Adaptationism and the adaptive landscape

Debates over adaptationism can be clarified and partially resolved by careful consideration of the ‘grain’ at which evolutionary processes are described. The framework of ‘adaptive landscapes’ can be used to illustrate and facilitate this investigation. We argue that natural selection may have special status at an intermediate grain of analysis of evolutionary processes. The cases of sickle-cell disease and genomic imprinting are used as case studies.

Optimality modeling in a suboptimal world

The fate of optimality modeling is typically linked to that of adaptationism: the two are thought to stand or fall together (Gould and Lewontin, Proc Relig Soc Lond 205:581–598, 1979; Orzack and Sober, Am Nat 143(3):361–380, 1994). I argue here that this is mistaken. The debate over adaptationism has tended to focus on one particular use of optimality models, which I refer to here as their strong use. The strong use of an optimality model involves the claim that selection is the only important influence on the evolutionary outcome in question and is thus linked to adaptationism. However, biologists seldom intend this strong use of optimality models. One common alternative that I term the weak use simply involves the claim that an optimality model accurately represents the role of selection in bringing about the outcome. This and other weaker uses of optimality models insulate the optimality approach from criticisms of adaptationism, and they account for the prominence of optimality modeling (broadly construed) in population biology. The centrality of these uses of optimality models ensures a continuing role for the optimality approach, regardless of the fate of adaptationism.

Engineering-approach accelerates computational understanding of V1–V2 neural properties

We present two computational models (i) long-range horizontal connections and the nonlinear effect in V1 and (ii) the filling-in process at the blind spot. Both models are obtained deductively from standard regularization theory to show that physiological evidence of V1 and V2 neural properties is essential for efficient image processing. We stress that the engineering approach should be imported to understand visual systems computationally, even though this approach usually ignores physiological evidence and the target is neither neurons nor the brain.

Sexual selection and mate choice in evolutionary psychology

The importance of mate choice and sexual selection has been emphasized by the majority of evolutionary psychologists. This paper assesses three cases of work on mate choice and sexual selection in evolutionary psychology: David Buss on cross-cultural human mate preferences, Randy Thornhill and Steve Gangestad on the link between mate preferences and fluctuating asymmetry, and Geoffrey Miller on the role of Fisher’s runaway process in human evolution. A mixture of conceptual and empirical problems in each case highlights the general weakness of work in evolutionary psychology on these issues.

Individual variability of behavioural responses by Wandering Albatrosses (Diomedea exulans) to human disturbance

Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.

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Productivity,relevance and natural selection

Recent papers by a number of philosophers have been concerned with the question of whether natural selection is a causal process, and if it is, whether the causes of selection are properties of individuals or properties of populations. I shall argue that much confusion in this debate arises because of a failure to distinguish between causal productivity and causal relevance. Causal productivity is a relation that holds between events connected via continuous causal processes, while causal relevance is a relationship that can hold between a variety of different kinds of facts and the events that counterfactually depend upon them. I shall argue that the productive character of natural selection derives from the aggregation of individual processes in which organisms live, reproduce and die. At the same time, a causal explanation of the distribution of traits will necessarily appeal both to causally relevant properties of individuals and to causally relevant properties that exist only at the level of the population.

Artificial Selection and Domestication: Modern Lessons from Darwin’s Enduring Analogy

It is clear from his published works that Charles Darwin considered domestication to be very useful in exploring and explaining mechanisms of evolutionary change. Not only did domestication occupy the introductory chapter of On the Origin of Species, but he revisited the topic in a two-volume treatise less than a decade later. In addition to drawing much of his information about heredity from studies of domesticated animals and plants, Darwin saw important parallels between the process of artificial selection by humans and natural selection by the environment. There was resistance to this analogy even among Darwin’s contemporary supporters when it was proposed, and there also has been disagreement among historians and philosophers regarding the role that the analogy with artificial selection actually played in the discovery of natural selection. Regardless of these issues, the analogy between artificial and natural selection remains important in both research and education in evolution. In particular, the present article reviews ten lessons about evolution that can be drawn from the modern understanding of domestication and artificial selection. In the process, a basic overview is provided of current approaches and knowledge in this rapidly advancing field.

The connectionist framework for gene regulation

I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability that can be learned by examining the generic features of connectionist networks.

Sophisticated selectionism as a general theory of knowledge

Human knowledge is a phenomenon whose roots extend from the cultural, through the neural and the biological and finally all the way down into the Precambrian “primordial soup.” The present paper reports an attempt at understanding this Greater System of Knowledge (GSK) as a hierarchical nested set of selection processes acting concurrently on several different scales of time and space. To this end, a general selection theory extending mainly from the work of Hull and Campbell is introduced. The perhaps most drastic change from previous similar theories is that replication is revealed as a composite function consisting of what is referred to as memory and synthesis. This move is argued to drastically improve the fit between theory and human-related knowledge systems. The introduced theory is then used to interpret the subsystems of the GSK and their interrelations. This is done to the end of demonstrating some of the new perspectives offered by this view.

Allomaternal Care among the Hadza of Tanzania

Cooperative child care among humans, where individuals other than the biological mother (allomothers) provide care, may increase a mother’s fertility and the survivorship of her children. Although the potential benefits to the mother are clear, the motivations for allomothers to provide care are less clear. Here, we evaluate the kin selection allomothering hypothesis using observations on Hadza hunter-gatherers collected in ten camps over 17 months. Our results indicate that related allomothers spend the largest percentage of time holding children. The higher the degree of relatedness among kin, the more time they spend holding, supporting the hypothesis of nepotism as the strongest motivation for providing allomaternal care. Unrelated helpers of all ages also provide a substantial amount of investment, which may be motivated by learning to mother, reciprocity, or coercion.

Hierarchical analysis of piecewise affine models of gene regulatory networks

A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions. In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns out to be quite relevant because of the strong discrete structure underlying these equations. Its biological relevance is shown on a 7-dimensional PWA system modeling the gene network responsible for the carbon starvation response in Escherichia coli.

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Biosemiotic Questions

This paper examines the biosemiotic approach to the study of life processes by fashioning a series of questions that any worthwhile semiotic study of life should ask. These questions can be understood simultaneously as: (1) questions that distinguish a semiotic biology from a non-semiotic (i.e., reductionist–physicalist) one; (2) questions that any student in biosemiotics should ask when doing a case study; and (3) still currently unanswered questions of biosemiotics. In addition, some examples of previously undertaken biosemiotic case studies are examined so as to suggest a broad picture of how such a biosemiotic approach to biology might be done.

Individual optimization efforts and population dynamics: a mathematical model for the evolution of resource allocation strategies, with applications to reproductive and mating systems

We develop a formal framework for the optimal allocation of limited resources that includes and clarifies the interplay between individual optimization and the resulting effects at the population level. As an example, in regard to the evolution of sexual recombination, the paradox of the twofold cost of sex is avoided by distinguishing between the evolution of recombination and the subsequent emergence and stability of different mating types as a result of individual optimization within a population that benefits from recombination.

Compositional reasoning of performance in component-based distributed systems

Rapid prototyping of distributed systems can be achieved by integrating commercial off-the-shelf (COTS) components. With components as the building blocks, it is important to predict the performance of the system based on the performance of individual components. In this paper, performance prediction of a system consisting of a small number of components is investigated under different inter-component communication patterns, and the number of threads provided by components. Based on the experimental results, it can be inferred that the proposed composition rules provide a reasonably accurate prediction of the performance of a system made out of these components.

The design of a novel context-aware policy model to support machine-based learning and reasoning

The purpose of autonomic networking is to manage the business and technical complexity of networked components and systems. However, the lack of a common lingua franca makes it impossible to use vendor-specific network management data to ascertain the state of the network at any given time. Furthermore, the tools used to analyze management data are all different, and hence require different data in different formats. This complicates the construction of context from diverse information sources. This paper describes a new version of the DEN-ng context-aware policy model, which is part of the FOCALE autonomic network architecture. This model has been built using three guiding principles: (1) both the context model and the policy model are rooted in information models, so that they can govern managed entities, (2) each model is expressly constructed to facilitate the generation of ontologies, so that reasoning about policies constructed from the model may be done, and (3) the model is expressly constructed so that a policy language that supports machine-based reasoning and learning can be developed from it.

Leitlinien zur molekulargenetischen Diagnostik: Fragiles-X und Fragiles-X assoziiertes Tremor/Ataxie Syndrom

Ohne Zusammenfassung

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Intelligent design and mathematical statistics: a troubled alliance

The explanatory filter is a proposed method to detect design in nature with the aim of refuting Darwinian evolution. The explanatory filter borrows its logical structure from the theory of statistical hypothesis testing but we argue that, when viewed within this context, the filter runs into serious trouble in any interesting biological application. Although the explanatory filter has been extensively criticized from many angles, we present the first rigorous criticism based on the theory of mathematical statistics.

Realistic threshold policy with hysteresis to control predator–prey continuous dynamics

This paper introduces a threshold policy with hysteresis (TPH) for the control of one-predator one-prey models. The models studied are the Lotka–Volterra and Rosenzweig–MacArthur two species density-dependent predator–prey models and the Arditi–Ginzburg nondimensional ratio-dependent model. The proposed policy (TPH) changes the dynamics of the system in such a way that a bounded oscillation is achieved confined to a region that does not allow extinction of either species. The policy can be designed by a suitable choice of so called virtual equilibrium points in a simple and intuitive manner.