Explanation and Falsification in Phylogenetic Inference: Exercises in Popperian Philosophy

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction (the classes defined in terms of similarity relations) into a thing (such as an historical individual). The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs.     

Hugo de Vries and the reception of the “mutation theory”

Conclusion De Vries' mutation theory has not stood the test of time. The supposed mutations of Oenothera were in reality complex recombination phenomena, ultimately explicable in Mendelian terms, while instances of large-scale mutations were found wanting in other species. By 1915 the mutation theory had begun to lose its grip on the biological community; by de Vries' death in 1935 it was almost completely abandoned. Yet, as we have seen, during the first decade of the present century it achieved an enormous popularity. As this paper has tried to suggest, one of the principal reasons for this was that de Vries' theory served as a banner around which a whole crowd of disaffected Darwinians or anti-Darwinians could rally. However, not all of those who favored de Vries did so for quite the same reasons. Underlying the multitude of views ran several common threads: a dissatisfaction with current Darwinian theory born out of misunderstanding natural selection, a general misunderstanding of the nature of species, and a prejudice against speculative, nontestable theories in biology.Supporters of de Vries were not the only opponents of Darwinism, nor was the mutation theory the only alternative to natural selection. In the early twentieth century a number of theories had been proposed to explain away the problems which Darwin had left unsolved. There was the idea of orthogenesis, championed by the American paleontologists Cope, Osborn and others; organic selection (or orthoplasy) was championed by M. M. Baldwin and C. Lloyd Morgan; there were the concepts of convergent evolution proposed by Hermann Friedmann, the theory of physiological selection by John George Romanes, and the concepts of reproductive divergence by H. M. Vernon. Virtually none of these men either accepted or were strong supporters of the de Vriesian theory, for each had his own particular ism to advocate as the major factor in evolution. The existence of a large number of such theories, each purporting to be the explanation, was characteristic of evolutionary theory at the turn of the century. It is to a large extent the emphasis on such fragmentary concepts that retarded development of the comprehensive theory of evolution which emerged in the 1920's and 1930's. For the historian, however, a study of these alternative theories is instructive in trying to understand the inherent difficulties which Dawwinian theory posed to biologists at the time. De Vries' mutation theory serves historically as a mirror to reflect the critical mood of a generation hostile to the theory of natural selection.It has often been claimed that it was impossible to understand the mechanism of natural selection until it could be placed in genetic and mathematical terms. It is certainly true that great strides have been made in population genetics and the treatment of evolutionary concepts with mathematical tools in the last forty years. But the very people who developed the genetical and mathematical approach to evolution were already convinced of the essential correctness of Darwinian theory before they started. Advances in an understanding of Mendelian heredity aided greatly in solving one important issue for evolutionists: the origin of variations. And the rigor with which selection acted could best be studied by observing changes in gene frequencies (calculated mathematically) over a number of generations. But as this paper has shown, two of the basic problems which biologists faced in evaluating Darwinian theory at the turn of the century-the nature of species, and the criteria of what constituted an acceptable explanation in biological science-could not be answered directly by mathematics. What mathematical and genetical theory did do was to help convince the skeptics of the validity of the Darwinian proposition.The change in explanatory criteria which many hailed as de Vries' most important contribution to evolutionary theory seems to have been part of a general emergence of twentieth-century biology from the domination of theorizers in the nineteenth. It also marked the emergence of America from the domination of biological, and particularly evolutionary, influence of Europeans. The change occurred in three areas: in the kinds of questions asked: testable versus non-testable; in the kind of data sought: quantitative versus qualitative; and in the kinds of theories proposed: analytical and reductive—the attempt to see complex processes in terms of simpler components-as opposed to synthetic and speculative. Although ultimately wrong in his idea, de Vries and his theories rode high on the wave of experimentalism which was the harbinger of a new era in evolutionary theory.Preparation of this paper has been aided by a grant from National Science Foundation (GS 1832).     

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.     

ON THE INDEPENDENCE OF SYSTEMATICS

Abstract— Before the publication of On the Origin of Species the standing patterns of natural history—common plan, homology, ontogenetic parallelism, and the hierarchy of groups — were taken as indications of a biological order that had not yet been understood. Darwin covered all of these in chapter 13 of the Origin , arguing that his theory was the first to provide a reasonable explanation for the existence of such patterns. Since Darwin took these relations to be established by previous biology, and used them as evidence for the explanatory power of his theory, he was clearly of the opinion that they were independent of that theory. Although several modern figures have argued to the contrary, it seems that Darwin was right. The patterns listed above are recoverable from observation without reference to evolutionary theory, which theory may then be applied to provide an account of the processes by which they may have come about. That aspect of systematics concerned with the identification of the empirical patterns evidently constitutes a study prior to and independent of theories of process.     

Explaining consumer choice: coming to terms with intentionality

Any attempt to understand the nature of behaviorism as a philosophy of science, to depict the essence of its distinctive explanatory system, or to delimit the scope of its capacity to explicate behavior, requires an appreciation of how its practitioners use language. Three behaviorist theories that are especially relevant to the explanation of economic behavior - radical behaviorism, teleological behaviorism, and picoeconomics - provide a necessary array of theoretical perspectives in that each contributes uniquely to understanding consumer choice. Despite the differences that separate them at a methodological level, and the internecine disputes in which their adherents sometimes address one another, these three perspectives play complementary roles in the depiction of everyday consumer behavior. Moreover, this combination of behavior theories owes much to the way in which each has responded to the challenge of intentional explanation. In order to demonstrate this, the paper proposes a framework of analysis which portrays the essential differences between intentional explanation and the extensional approach towards which many behaviorists have striven, and argues that while radical behaviorism scrupulously avoids intentional terms, teleological behaviorism and picoeconomics have in differing ways come to terms with the necessity of combining a behaviorist perspective with the explanatory value of intentional terminology. This continuum of explanations is applied to recent findings of consumer behavior analysis on consumer choice in natural environments.     

Explanations in search of observations

The paper explores how, in economics and biology, theoretical models are used as explanatory devices. It focuses on a modelling strategy by which, instead of starting with an unexplained regularity in the world, the modeller begins by creating a credible model world. The model world exhibits a regularity, induced by a mechanism in that world. The modeller concludes that there may be a part of the real world in which a similar regularity occurs and that, were that the case, the model would offer an explanation. Little concrete guidance is given about where such a regularity might be found. Three modelling exercises in evolutionary game theory—one from economics and two from biology—are used as case studies. Two of these (one from each discipline) exemplify ‘explanation in search of observation’. The third goes a step further, analysing a regularity in a model world and treating it as informative about the real world, but without saying anything about real phenomena. The paper argues that if the relation between the model and real worlds is understood in terms of similarity, and if modelling is understood as an ongoing discovery process rather than as the demonstration of empirical truths, there can be value in creating explanations before finding the regularities that are to be explained.     

Group behaviour in physical,chemical and biological systems

Groups exhibit properties that either are not perceived to exist, or perhaps cannot exist, at the individual level. Such ‘emergent’ properties depend on how individuals interact, both among themselves and with their surroundings. The world of everyday objects consists of material entities. These are, ultimately, groups of elementary particles that organize themselves into atoms and molecules, occupy space, and so on. It turns out that an explanation of even the most commonplace features of this world requires relativistic quantum field theory and the fact that Planck’s constant is discrete, not zero. Groups of molecules in solution, in particular polymers (‘sols’), can form viscous clusters that behave like elastic solids (‘gels’). Sol-gel transitions are examples of cooperative phenomena. Their occurrence is explained by modelling the statistics of inter-unit interactions: the likelihood of either state varies sharply as a critical parameter crosses a threshold value. Group behaviour among cells or organisms is often heritable and therefore can evolve. This permits an additional, typically biological, explanation for it in terms of reproductive advantage, whether of the individual or of the group. There is no general agreement on the appropriate explanatory framework for understanding group-level phenomena in biology.     

Population thinking and natural selection in dual-inheritance theory

A deflationary perspective on theories of cultural evolution, in particular dual-inheritance theory, has recently been proposed by Lewens. On this ‘pop-culture’ analysis, dual-inheritance theorists apply population thinking to cultural phenomena, without claiming that cultural items evolve by natural selection. This paper argues against this pop-culture analysis of dual-inheritance theory. First, it focuses on recent dual-inheritance models of specific patterns of cultural change. These models exemplify population thinking without a commitment to natural selection of cultural items. There are grounds, however, for doubting the added explanatory value of the models in their disciplinary context—and thus grounds for engaging in other potentially explanatory projects based on dual-inheritance theory. One such project is suggested by advocates of the theory. Some of the motivational narratives that they offer can be interpreted as setting up an adaptationist project with regard to cumulative change in cultural items. We develop this interpretation here. On it, dual-inheritance theory features two interrelated selection processes, one on the level of genetically inherited learning mechanisms, another on the level of the cultural items transmitted through these mechanisms. This interpretation identifies a need for further modelling efforts, but also offers scope for enhancing the explanatory power of dual-inheritance theory.     

Sporadic sustained nonperiodic oscillations in the activities of organismic sets

In combining the author's theories of organismic sets (Rashevsky,Bull. Math. Biophysics,31, 159–198, 1969a) and Robert Rosen's theory of (M, R)-systems (Bull. Math. Biophysics,20, 245–265, 1958), a conclusion is reached that the number of either normal or pathological phenomena in organismic sets may occur. Those phenomena are characterized by occurring spontaneously once in a while but are not exactly periodic. Some epilepsies are an example of such pathological phenomena in the brain.     

Darwin's concept of final cause: neither new nor trivial

Darwin'suse of final cause accords with the Aristotelian idea of finalcauses as explanatory types – as opposed to mechanical causes, which arealways particulars. In Wright's consequence etiology, anadaptation is explained by particular events, namely, its past consequences;hence, that etiology is mechanistic at bottom. This justifies Ghiselin'scharge that such versions of teleology trivialize the subject, But a purelymechanistic explanation of an adaptation allows it to appear coincidental.Patterns of outcome, whether biological or thermodynamic, cannot be explainedbytracing causal chains, even were that possible. They are explicanda of aspecialkind. The form of their explanation, in statistical mechanics or by naturalselection, is not captured by statistical variants of the covering-law model orrelated models of explanation. In them as in classical teleology, types ofoutcome are cited to explain why there are outcomes of those types. But onlywhen types are explanatory by being selected for, as inexplanations of animal and human behavior as well as in Darwin's theory ofnatural selection, but not in statistical mechanics, is the explanationteleological. Darwin's theory is nontrivially teleological.     

A succession of theories: purging redundancy from disturbance theory

The topics of succession and post‐disturbance ecosystem recovery have a long and convoluted history. There is extensive redundancy within this body of theory, which has resulted in confusion, and the links among theories have not been adequately drawn. This review aims to distil the unique ideas from the array of theory related to ecosystem change in response to disturbance. This will help to reduce redundancy, and improve communication and understanding between researchers. We first outline the broad range of concepts that have developed over the past century to describe community change in response to disturbance. The body of work spans overlapping succession concepts presented by Clements in 1916, Egler in 1954, and Connell and Slatyer in 1977. Other theories describing community change include state and transition models, biological legacy theory, and the application of functional traits to predict responses to disturbance. Second, we identify areas of overlap of these theories, in addition to highlighting the conceptual and taxonomic limitations of each. In aligning each of these theories with one another, the limited scope and relative inflexibility of some theories becomes apparent, and redundancy becomes explicit. We identify a set of unique concepts to describe the range of mechanisms driving ecosystem responses to disturbance. We present a schematic model of our proposed synthesis which brings together the range of unique mechanisms that were identified in our review. The model describes five main mechanisms of transition away from a post‐disturbance community: (i) pulse events with rapid state shifts; (ii) stochastic community drift; (iii) facilitation; (iv) competition; and (v) the influence of the initial composition of a post‐disturbance community. In addition, stabilising processes such as biological legacies, inhibition or continuing disturbance may prevent a transition between community types. Integrating these six mechanisms with the functional trait approach is likely to improve the predictive capacity of disturbance theory. Finally, we complement our discussion of theory with a case study which emphasises that many post‐disturbance theories apply simultaneously to the same ecosystem. Using the well‐studied mountain ash (Eucalyptus regnans) forests of south‐eastern Australia, we illustrate phenomena that align with six of the theories described in our model of rationalised disturbance theory. We encourage further work to improve our schematic model, increase coverage of disturbance‐related theory, and to show how the model may link to, or integrate with, other domains of ecological theory.     

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.     

The effect of microstructure on the rheological properties of blood

The micromorphic theory of Eringen is applied to study the tube flow of blood. The blood is considered to be a deformable suspension, with constitutive relations of the form of those of simple microfluids. By means of energy consideration, a relation is established between the local concentration parameter and the measure of rotationality involving both macro-and micromotions. The tube flow problem is then solved with some analyses on viscosity coefficients and boundary conditions. The results obtained indicate an integrated explanation of various important physical phenomena associated with blood flow, such as the tube size dependence of the apparent viscosity and the non-uniform concentration distribution over a tube cross section.     

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.     

Energy transfer and molecular switching. I. The nerve action potential

In previous papers (Barrett, 1977b, 1980), the concept of chemical paramemetric excitation was applied to a number of diverse chemical phenomena and contrasted with the concept of chemical resonance, which is a special case of parametric excitation. In the present paper, its status as the fundamental concept of energy transfer and molecular switching is indicated, providing a mechanically sound explanation of nerve excitation at a basic level.The mechanism addressed by the parametric excitation concept is intermediate between macroscopic models of membrane assymetry and molecular models. No assumptions are made concerning the related macroscopic processes, but a systematic approach to organizational aspects of the processes involved in energy transfer is proposed.The chemical analog of the Manley-Rowe relations, which are the power conservation relations for parametrically excited electrical networks, is also derived. The demonstration of such Manley-Rowe relations for chemical systems indicates, for the first time, an explanation for the directionality of flow of power, and thus designates a pumping role. The generalized Manley-Rowe relations translated into flow, reaction, as well as oscillatory system terms, are suggested to be a universal law. Non-linearity is due to the coupling of three systems—each separately describable by Onsager linear relations—by the generalized Manley-Rowe conditions relating flows/reactions/oscillations.All phenomena considered are treated in accordance with a principle of power transfer optimization (Odum & Pinkerton, 1955). Parametric excitation involves three-body interaction, with one system as energy donor, the pump, another as energy receiving, the idler, and a third as mediator of this energy flow, the signal. A conservation law is mandatory for flows/reactions/oscillations, ω_i so that ω_pump= ω_idler±ω_signal. The macroscopic structure, which sets up the conditions for this law to be in operation, may be of diverse kinds, e.g. membrane-bounded compartments, macromolecules capable of multiple conformations and bound cations, etc. All are non-linear.     

Beyond explanation and understanding: Anthropology and hermeneutics

Conclusion The fact that Ricoeur's influential essay on the model of the text was published twenty years ago has not in any way reduced its significance for addressing critical issues of interpretation in the human sciences. However, Ricoeur's suggestion that we turn to structural linguistics as a basis from which to develop a critical interpretive theory rooted in the logic of the human sciences has since been challenged, but not superseded, by the post-structuralist assertion that text, or human action as a text, lacks coherence. Jacques Derrida and his followers have argued that the objective of their method is to deconstruct a text which means to discover what it excludes through its representation. It is, therefore, a fiction, Derrida maintains, to presuppose that one can unveil the meaning or truth of a text, as the reading of a text must necessarily take place in its margins.Whatever may be the practical implications, or implications for praxis, in the assertion that a text lacks a unity or truth, I contend that the key question raised by Ricoeur, and not to my knowledge resolved by post-structuralism, is how to maintain a sense of action as meaningful while being able to grasp it critically. This question establishes a point of tension between human agency and the objective structural constraints to which it is subject, thus, as I have asserted, connecting the formal properties of a text to the conditions of its generation. Although I have argued that Ricoeur's moment of structural or semiotic mediation is faulted in that it locates oppositions or contradictions in the avowed worldlessness of the text's interior rather than in the historical process of humanity's self-formation, this weakness does not altogether eclipse the merit of his analogy between the interpretation of texts and human actions. To the contrary, Ricoeur has shown how it is possible through rejecting the methodological implications of an explanation and understanding dichotomy — or how emics and etics have come to be used in contemporary anthropology to distinguish types of theoretical constructs — to develop an interpretation theory with critical implications based on the logic of the human sciences. Anthropologists who resort to an exclusive explanation or etic position, through the drawing of nomological hypotheses, fail to recognize that cultural phenomena are intentional in that they owe their generation and identity to a historically constituted intersubjectivity. On the other hand, anthropologists who privilege the understanding position, which is highly prevalent in contemporary symbolic and interpretive anthropology, conceptualize this process as the logical reconstruction of the subjective intentions of actors, or in a more complex sense, the identification of meaning with context. Ricoeur has argued that the pursuit of an exclusive explanation or understanding theory is based upon an epistemological reduction. The privileging of theories based upon natural science explanation reduced the intersubjectivity of meaning to the classification and verification of facts, while theories based upon understanding reduce the dialectical movement of meaning to the ostensive reference of context. From either the exclusive explanation or understanding trajectories, the critical potentialities of anthropology are vitiated because the reflexive dimension of the interpretive process is absent. As Ricoeur has repeatedly emphasized, knowledge of remote historical periods, texts, or other cultures not only produces a comprehension of these phenomena as radically other, but also casts light onto our own life situation.Ricoeur's theory is important, therefore, for anthropologists and other students of the human sciences, because it combines an emphasis on mediation, or the critique of naive consciousness, with the conceptualization of human actions as intentional, communicative events. It therefore goes a long way towards bridging some of the deepest objections raised by the scientistic outlook against the method of versteben, while retaining the latter's emphasis on a hermeneutic understanding of social life. This bridge has been built without resorting to the objectivism of the natural sciences and by pursuing the logic of a method that is in concert with the unique object-subject of the human sciences.

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Pyrogeography,historical ecology,and the human dimensions of fire regimes

In our 2011 synthesis (Bowman et al., Journal of Biogeography, 2011, 38 , 2223–2236), we argued for a holistic approach to human issues in fire science that we term ‘pyrogeography’. Coughlan & Petty (Journal of Biogeography, 2013, 40 , 1010–1012) critiqued our paper on the grounds that our ‘pyric phase’ model was built on outdated views of cultural development, claiming we developed it to be the unifying explanatory framework for all human–fire sciences. Rather, they suggest that ‘historical ecology’ could provide such a framework. We used the ‘pyric transition’ for multiple purposes but did not offer it as an exclusive explanatory framework for pyrogeography. Although ‘historical ecology’ is one of many useful approaches to studying human–fire relationships, scholars should also look to political and evolutionary ecology, ecosystems and complexity theories, as well as empirical generalizations to build an interdisciplinary fire science that incorporates human, ecological and biophysical dimensions of fire regimes.     

Reply to Lawler: feeding competition, cooperation, and the causes of primate sociality

This is a reply to Richard Lawler's commentary on our previous work [Lawler, 2011; this issue] in which he develops a set of operational models to test socioecological theories of the evolutionary importance of feeding competition. We strongly agree that we need to critically re-evaluate the basic assumptions of all models of primate sociality, and to verify the explanatory power of alternative models. We also feel Lawler's commentary provides an important opportunity to broaden the debate concerning the fundamental roles of cooperation, competition, and aggression in understanding primate social systems. Lawler provides a number of suggestions as to how models developed in primate socioecology might be tested. We agree with these suggestions, make further suggestions, and call for specific operational definitions so that researchers might begin to develop and test various methodologies. However, we also call for testing alternative theories. Current socioecological theory is based on the assumption that competition and positive selection is always in operation and has driven the evolution of living organisms. We believe that this "explanation of choice" often is treated as an assumed truth to which data are forced to fit, rather than being seen as a theory to be tested. Furthermore, we agree with Weiss and Buchanan [2009. The Mermaid's Tale: Four Billion Years of Cooperation in the Making of Living Things] that on ecological and developmental scales, where organisms actually live out their lives, cooperation may play a more fundamental role than competition.