Are stone-age genes created out of whole cloth? Evaluating claims about the evolution of behavior

This paper provides an overview of historical and current standard scientific practices for investigating the evolution of behavior. I argue that Evolutionary Psychology (EP) ignores its historical precedents—ethology and the instinct critics—and while acknowledging current perspectives—epigenetics and developmental systems theories—does so only in terms of lip service. In particular, EP does not investigate the dynamic interplay between genes and context that is essential for understanding the development and evolution of behavior. Thus, EP does not conform to the rigorous standards of biology or psychology, is often unresponsive to methodological critiques, skirts theoretical controversies, and is disconnected from a large body of scholarship on issues surrounding the evolution of behavior.     

A module is a module is a module: evolution of modularity in Evolutionary Psychology

The concept of modularity has been central in behavioral and neural sciences since the publication of Fodor’s The Modularity of Mind (1983). Fodor strived to explain the functional architecture of the mind based on the distinction between modular and central systems. Modular systems were deemed to have certain architectural features, such as automaticity, encapsulation, and domain specificity. Evolutionary psychologists have adopted the concept to characterize purportedly evolved human adaptations. In an influential paper, Barrett and Kurzban (Psychol Rev 113(3):628–647, 2006) proposed a definition of modules purely in terms of functional specialization. It is here argued that such strategy marks a shift in Evolutionary Psychology’s theoretical emphasis, as it trivializes the investigation of proximate causes in evolutionary theorizing; furthermore, it leaves the door open to too much flexibility on what counts as evidence for purportedly evolved modules.     

Evolutionary thinking among biology students in a third world country

Background

Evolutionary thinking is traditionally directly related to education and inversely to religiosity. Accordingly, biology students are naturally expected to be more prone to naturalist evolution due to their close contact with this theory and high scientific literacy. To test this, we performed a cross-national study surveying biology students’ evolutionary opinions in Brazil, contrasting the proportions of creationism (Cr), divinely guided evolution (DGE) and naturalist evolution (NaE).

Results

We found that NaE comprised 44.4%, DGE 43.3%, and Cr 12.3% of students’ opinions. NaE was higher among postgraduate than undergraduate students. There were marked geographic differences, with NaE peaking in the most socioeconomically developed regions and Cr in the less. Opinions related to divine influence as a whole (Cr + DGE) became more likely as the score of students’ institutions decreased (i.e. institutions with lower-quality standards).

Conclusions

Most biology students paradoxically do not have NaE as an explanation (55.6%), a high proportion given their presumed contact with the theory. We demonstrate that socioeconomic and institution quality factors are apparently important in determining the evolutionary thinking patterns. NaE paucity among biology students may also be influenced by low scientific literacy and the extreme religiosity of the population, which incorporates divine influence in students’ opinions long before they have any contact with evolutionary theory.

     

Scientific reasoning ability does not predict scientific views on evolution among religious individuals

Background

Acceptance of evolutionary theory varies widely and is often associated with religious background. Some have suggested there exists an additional relationship between scientific reasoning ability and the acceptance of evolutionary theory. In this study, we used structural equation modeling to test whether scientific reasoning ability predicts religiosity, acceptance of creationist views, or acceptance of evolution. We administered internet-based surveys to 724 individuals nationwide who self-describe as being religious and built a structural-equation model to test predictive abilities.

Results

We found that while religiosity positively predicts the acceptance of creationist views and negatively predicts the acceptance of evolution, scientific reasoning ability does not predict religiosity, acceptance of creationist views, or acceptance of evolutionary theory.

Conclusions

With a lack of any relationship between scientific reasoning ability and acceptance, an approach to evolution education that focuses on appealing to scientific reasoning may prove fruitless in changing student attitudes toward evolution; alternative teaching approaches regarding evolution are warranted.

     

The Use and Abuse of Sir Karl Popper

Karl Popper has been one of the few philosophers of sciences who has influenced scientists. I evaluate Popper's influence on our understanding of evolutionary theory from his earliest publications to the present. Popper concluded that three sorts of statements in evolutionary biology are not genuine laws of nature. I take him to be right on this score. Popper's later distinction between evolutionary theory as a metaphysical research program and as a scientific theory led more than one scientist to misunderstand his position on evolutionary theory as a scientific theory. In his later work Popper also introduced what he took to be improvements of evolutionary theory. Thus far these improvements have had almost no influence on evolutionary biology. I conclude by examining the influence of Popper on the reception of cladistic analysis.     

How to Rethink Evolutionary Theory: A Plurality of Evolutionary Patterns

Nature has recently depicted the empirical advancements of the theory of evolution as a confrontation between “reformists”, that claim for an urgent rethinking of the standard neo-Darwinian approach including so far neglected factors and processes, and “conservatives” who reply “all is well” about the current evolutionary research programme based on genetic variation and natural selection. The fight is mainly around genetic reductionism, but it seems inconclusive. Reformists stress very important factors, but they are still missing a coherent proposal about the architecture of the future extended evolutionary theory. Conservative react defensively, relying just on non-essential add-ons to the old and stable neo-Darwinian core. We analyze the debate and we propose an interpretation. Evolutionary biology is a rapidly expanding field. The bone of contention is how to update and extend the central core of the Darwinian legacy. We propose here the idea that what is happening in the field today is a development of the evolutionary research programme, whose structure is composed of a set of compatible and integrated evolutionary patterns. Evolutionary biology has been extended over its history by the inclusion of more and more patterns, rather than by revision to core theory. Niles Eldredge’s “Hierarchy Theory” is an example of global structure (meta-theory) aiming at incorporating and unifying the currently observed evolutionary patterns.     

A Philosophical Evaluation of Adaptationism as a Heuristic Strategy

Adaptationism has prompted many a debate in philosophy of biology but the focus is usually on empirical and explanatory issues rather than methodological adaptationism (MA). Likewise, the context of evolutionary biology has provided the grounding for most discussions of the heuristic role of adaptationism. This paper extends the debate by drawing on case studies from physiology and systems biology to discuss the productive and problematic aspects of adaptationism in functional as well as evolutionary studies at different levels of biological organization. Gould and Lewontin’s Spandrels-paper famously criticized adaptationist methodology for implying a risk of generating ‘blind spots’ with respect to non-selective effects on evolution. Some have claimed that this bias can be accommodated through the testing of evolutionary hypotheses. Although this is an important aspect of overcoming the pitfalls of adaptationism, I argue that the issue of methodological biases is broader than the question of testability. I demonstrate the productivity of adaptationist heuristics but also discuss the deeper problematic aspects associated with the imperialistic tendencies of the strong account of MA.     

Evolutionary fallacies of Nazi psychiatry. Implications for current research

Evolutionary theory has had a major impact on psychiatry since the middle of the 19th century. During the Nazi regime psychiatry supported compulsory sterilization and euthanasia of physically and mentally ill and subsequently the killing of "inferior" races by borrowing scientifically invalid conclusions from evolutionary biology. The present paper deals with some of the flaws and shortcomings of the scientific paradigms of evolutionary theory adopted by psychiatry during the Nazi regime and discusses possible implications for modern research in evolutionary psychology and psychiatry.     

On mechanistic reasoning in unexpected places: the case of population genetics

A strong case has been made for the role and value of mechanistic reasoning in process-oriented sciences, such as molecular biology and neuroscience. This paper shifts focus to assess the role of mechanistic reasoning in an area where it is neither obvious nor expected: population genetics. Population geneticists abstract away from the causal-mechanical details of individual organisms and, instead, use mathematics to describe population-level, statistical phenomena. This paper, first, develops a framework for the identification of mechanistic reasoning where it is not obvious: mathematical and mechanistic styles of scientific reasoning. Second, it applies this framework to demonstrate that both styles are integrated in modern investigations of evolutionary biology. Characteristic of the former, applied population genetic techniques provide statistical evidence for associations between genotype, phenotype, and fitness. Characteristic of the latter, experimental interventions provide causal-mechanical evidence for associations between the very same relationships, often in the same model organisms. The upshot is a richer perspective of how evolutionary biologists build evidence for hypotheses regarding adaptive evolution and a general framework for assessing the scope of mechanistic reasoning across the sciences.     

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges,Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology.     

Evolutionary theory and systematics: relationships between process and patterns

The relevance of the Modern Evolutionary Synthesis to the foundations of taxonomy (the construction of groups, both taxa and phyla) is reexamined. The nondimensional biological species concept, and not the multidimensional, taxonomic, species notion which is based on it, represents a culmination of an evolutionary understanding. It demonstrates how established evolutionary mechanisms acting on populations of sexually reproducing organisms provide the testable ontological basis of the species category. We question the ontology and epistemology of the phylogenetic or evolutionary species concept, and find it to be a fundamentally untenable one. We argue that at best, the phylogenetic species is a taxonomic species notion which is not a theoretical concept, and therefore should not serve as foundation for taxonomic theory in general, phylogenetics, and macroevolutionary reconstruction in particular. Although both evolutionary systematists and cladists are phylogeneticists, the reconstruction of the history of life is fundamentally different in these two approaches. We maintain that all method, including taxonomic ones, must fall out of well corroborated theory. In the case of taxonomic methodology the theoretical base must be evolutionary. The axiomatic assumptions that all phena, living and fossil, must be holophyletic taxa (species, and above), resulting from splitting events, and subsequently that evaluation of evolutionary change must be based on a taxic perspective codified by the Hennig ian taxonomic species notion, are not testable premises. We discuss the relationship between some biologically, and therefore taxonomically, significant patterns in nature, and the process dependence of these patterns. Process-free establishment of deductively tested “genealogies” is a contradiction in terms; it is impossible to “recover” phylogenetic patterns without the investment of causal and processual explanations of characters to establish well tested taxonomic properties of these (such as homologies, apomorphies, synapomorphies, or transformation series). Phylogenies of either characters or of taxa are historical-narrative explanations (H-N Es), based on both inductively formulated hypotheses and tested against objective, empirical evidence. We further discuss why construction of a “genealogy”, the alleged framework for “evolutionary reconstruction”, based on a taxic, cladistic outgroup comparison and a posteriori weighting of characters is circular. We define how the procedure called null-group comparison leads to the noncircular testing of the taxonomic properties of characters against which the group phylogenies must be tested. This is the only valid rooting procedure for either character or taxon evolution. While the Hennig -principle is obviously a sound deduction from the theory of descent, cladistic reconstruction of evolutionary history itself lacks a valid methodology for testing transformation hypotheses of both characters and species. We discuss why the paleontological method is part of comparative biology with a critical time dimension ana why we believe that an “ontogenetic method” is not valid. In our view, a merger of exclusive (causal and interactive, but best described as levels of organization) and inclusive (classificatory) hierarchies has not been accomplished by a taxic scheme of evolution advocated by some. Transformational change by its very nature is not classifiable in an inclusive hierarchy, and therefore no classification can fully reflect the causal and interactive chains of events constituting phylogeny, without ignoring and contradicting large areas of corroborated evolutionary theory. Attempts to equate progressive evolutionary change with taxic schemes by Haeckel were fundamentally flawed. His ideas found 19th century expression in a taxic perception of the evolutionary process (“phylogenesis”), a merger of typology, hierarchic and taxic notions of progress, all rooted in an ontogenetic view of phylogeny. The modern schemes of genealogical hierarchies, based on punctuation and a notion of “species” individuality, have yet to demonstrate that they hold promise beyond the Haeckel ian view of progressive evolution.     

Oyun: A New, Free Program for Iterated Prisoner's Dilemma Tournaments in the Classroom

Evolutionary applications of game theory present one of the most pedagogically accessible varieties of genuine, contemporary theoretical biology. We present here Oyun (oy-oon, http://charlespence.net/oyun), a program designed to run iterated prisoner's dilemma tournaments, competitions between prisoner's dilemma strategies developed by the students themselves. Using this software, students are able to readily design and tweak their own strategies, and to see how they fare both in round-robin tournaments and in ??evolutionary?? tournaments, where the scores in a given ??generation?? directly determine contribution to the population in the next generation. Oyun is freely available, runs on Windows, Mac, and Linux computers, and the process of creating new prisoner's dilemma strategies is both easy to teach and easy for students to grasp. We illustrate with two interesting examples taken from actual use of Oyun in the classroom.     

Methodological problems in evolutionary biology VI. The force of evolutionary epistemology

Evolutionary epistemology takes various forms. As a philosophical discipline, it may use analogies by borrowing concepts from evolutionary biology to establish new foundations. This is not a very successful enterprise because the analogies involved are so weak that they hardly have explanatory force. It may also veil itself with the garbs of biology. Proponents of this strategy have only produced irrelevant theories by transforming epistemology's concepts beyond recognition. Sensible theories about knowledge and biology should presuppose that various long-standing problems concerning relations between the mental and the physical are solved. Such problems are wrongly disregarded by evolutionary epistemologists.     

The phylogeny fallacy and the ontogeny fallacy

In 1990 Robert Lickliter and Thomas Berry identified the phylogeny fallacy, an empirically untenable dichotomy between proximate and evolutionary causation, which locates proximate causes in the decoding of ‘genetic programs’, and evolutionary causes in the historical events that shaped these programs. More recently, Lickliter and Hunter Honeycutt (Psychol Bull 129:819–835, 2003a) argued that Evolutionary Psychologists commit this fallacy, and they proposed an alternative research program for evolutionary psychology. For these authors the phylogeny fallacy is the proximate/evolutionary distinction itself, which they argue constitutes a misunderstanding of development, and its role in the evolutionary process. In this article I argue that the phylogeny fallacy should be relocated to an error of reasoning that this causal framework sustains: the conflation of proximate and evolutionary explanation. Having identified this empirically neutral form of the phylogeny fallacy, I identify its mirror image, the ontogeny fallacy. Through the lens of these fallacies I attempt to solve several outstanding problems in the debate that ensued from Lickliter and Honeycutt’s provocative article.     

On predictions and laws in biological evolution: Is biology able to formulate general laws and develop inductive predictions as in physics or chemistry?

Biology has so far had difficulties formulating general laws akin to physics and chemistry. Evolution and its propensity to reduce entropy could become a start for such laws in biology. Subject Categories: Evolution & Ecology, History & Philosophy of Science

Science uses evidence‐based inductive reasoning to build theories, principles, and laws. A common type of inductive reasoning is generalization, that is, projecting conclusions drawn from one or a few case studies onto a broader context. The reliability of generalizations depends upon the representativeness and the formal validation of the selected case studies, which is usually performed by hypothesis testing. Another usual type of inductive reasoning is prediction, which uses observations to develop general principles and laws that can predict or anticipate future outcomes. The reliability of these predictions is confirmed by the accomplishment of the anticipated situation. It is interesting to note that generalizations are based on the analysis of empirical evidence, whereas predictions are formulated before the desired empirical evidence, which is actually the target of the prediction, is available.

… generalizations are based on the analysis of empirical evidence, whereas predictions are formulated before the desired empirical evidence, which is actually the target of the prediction, is available.

The American philosopher of science Peter Lipton (2005) commented that we are commonly more impressed by predictions than by accommodations, as he called hypothesis testing. To illustrate this, Lipton used the discovery of Halley''s Comet. In 1705, the British astronomer Edmond Halley proposed that the comets observed in 1531, 1607, and 1682 were actually the same comet with a periodic elliptical orbit. Back then, his hypothesis did not have much impact within the scientific community. However, when Halley''s prediction was confirmed in 1758 by the return of the comet, the intellectual world in Europe widely accepted the existence of a single comet, which was subsequently named Halley''s Comet. Halley''s prediction may seem straightforward, even trivial, considering the characteristic periodicity of 75 years in previous observations. Yet, it was the predictive success, rather than prior observations, that convinced the scientific community of his conclusion.Physics is considered one of the strongest branches of science—along with chemistry and mathematics—in regard to the generality and accuracy of its predictions. Biology seems still to be in its infancy, and the search for regularities that could lend to potential generalizations is the most common approach (Dodds, 2009). This is due in part to the high level of complexity of the living world, its evolutionary change over time, and its relationships with the environment. As emphasized by the German evolutionary biologist Ernst Mayr (2004), these intrinsic and unique features of living beings, which are intimately associated with the genetic code, clearly differentiate biology from other natural sciences and make the fundamental laws of physics and chemistry insufficient to understand the living world.The main aim of this essay is to discuss whether biological research is able to develop inductive predictions similar to physics or chemistry. First, I present some classical examples of physical and chemical discoveries based on inductive predictions, such as the Higgs boson, interstellar dark matter, and the periodic table of elements. As all these advances are based on the previous existence of fundamental laws, the question arises whether similar laws exist in biology to support physics‐like inductive predictions. I suggest that, if these laws exist, they should emerge from the evolutionary process, which is the main biological singularity. Thus, it should be possible to make inductive predictions based on the fossil record, which is the fundamental evolutionary evidence. Indeed, it seems that the lack of evolutionary laws is the main drawback for inductive prediction in studying evolution, which cannot escape to Lipton’s accommodation procedures, that is, hypothesis testing and generalization.

Physics is considered one of the strongest branches of science – along with chemistry and mathematics – in regard to the generality and accuracy of its predictions.

     

Multiple Explanations in Darwinian Evolutionary Theory

Variational evolutionary theory as advocated by Darwin is not a single theory, but a bundle of related but independent theories, namely: (a) variational evolution; (b) gradualism rather than large leaps; (c) processes of phyletic evolution and of speciation; (d) causes for the formation of varying individuals in populations and for the action of selective agents; and (e) all organisms evolved from a common ancestor. The first four are nomological-deductive explanations and the fifth is historical-narrative. Therefore evolutionary theory must be divided into nomological and historical theories which are both testable against objective empirical observations. To be scientific, historical evolutionary theories must be based on well corroborated nomological theories, both evolutionary and functional. Nomological and general historical evolutionary theories are well tested and must be considered as strongly corroborated scientific theories. Opponents of evolutionary theory are concerned only with historical evolutionary theories, having little interest in nomological theory. Yet given a well corroborated nomological evolutionary theory, historical evolutionary theories follow automatically. If understood correctly, both forms of evolutionary theories stand on their own as corroborated scientific theories and should not be labeled as facts.     

Methodological problems in evolutionary biology

One of the major criticisms of optimal foraging theory (OFT) is that it is not testable. In discussions of this criticism opposing parties have confused methodological concepts and used meaningless biological concepts. In this paper we discuss such misunderstandings and show that OFr has an empirically testable, and even well-confirmed, general core theory. One of our main conclusions is that specific model testing should not be aimed at proving optimality, but rather at identifying the context in which certain types of behaviour are optimal. To do this, it is necessary to be aware of the assumptions made in testing a model. The assumptions that are explicitly stated in the literature up to now do not completely cover the actual assumptions made in testing OFT models in practice. We present a more comprehensive set of assumptions. Although all the assumptions play a role in testing models, they are not of equal status. Crucial assumptions concern constraints and the relation between fitness and currency. Therefore, it is essential to make such assumptions testable in practice. We show that a more explicit relationship between OFT modelling and evolutionary theory can help with this. Specifically, phylogeny reconstruction and population dynamic modelling can and should be used to formulate assumptions concerning constraints and currencies.     

进化发育生物学--发育、进化和遗传的再联合

发育生物学和进化生物学,以及遗传学历史上曾一度是彼此不分的统一体,后来由于各自研究重点的不同和相应研究手段的独立发展彼此分道扬镳了。如今,由于分子遗传学研究手段的革新使得基因序列测定成为分析发育机理、区分物种和评估种间亲缘关系的常规手段,三者又在基因水平上再度统一起来了,并形成一门被称为进化发育生物学（ｅｖｏｌｕｔｉｏｎａｒｙ ｄｅｖｅｌｏｐｍｅｎｔａｌ ｂｉｏｌｏｇｙ）的新学科。     

Teleology and its constitutive role for biology as the science of organized systems in nature

'Nothing in biology makes sense, except in the light of teleology'. This could be the first sentence in a textbook about the methodology of biology. The fundamental concepts in biology, e.g. 'organism' and 'ecosystem', are only intelligible given a teleological framework. Since early modern times, teleology has often been considered methodologically unscientific. With the acceptance of evolutionary theory, one popular strategy for accommodating teleological reasoning was to explain it by reference to selection in the past: functions were reconstructed as 'selected effects'. But the theory of evolution obviously presupposes the existence of organisms as organized and regulated, i.e. functional systems. Therefore, evolutionary theory cannot provide the foundation for teleology. The underlying reason for the central methodological role of teleology in biology is not its potential to offer particular forms of (evolutionary) explanations for the presence of parts, but rather an ontological one: organisms and other basic biological entities do not exist as physical bodies do, as amounts of matter with a definite form. Rather, they are dynamic systems in stable equilibrium; despite changes of their matter and form (in metabolism and metamorphosis) they maintain their identity. What remains constant in these kinds of systems is their 'organization', i.e. the causal pattern of interdependence of parts with certain effects of each part being relevant for the working of the system. Teleological analysis consists in the identification of these system-relevant effects and at the same time of the system as a whole. Therefore, the identity of biological systems cannot be specified without teleological reasoning.