Recent advances in genetics and neurobiology have greatly increased the degree of variation that one finds in what is taken to provide the biological foundations of our species-specific linguistic capacities. In particular, this variation seems to cast doubt on the purportedly homogeneous nature of the language faculty traditionally captured by the concept of “Universal Grammar.” In this article we discuss what this new source of diversity reveals about the biological reality underlying Universal Grammar. Our discussion (...) leads us to support (1) certain hypotheses advanced in evolutionary developmental biology that argue for the existence of robust biological mechanisms capable of canalizing variation at different levels, and (2) a bottom-up perspective on comparative cognition. We conclude by sketching future directions for what we call “comparative biolinguistics,” specifying which experimental directions may help us succeed in this new research avenue. (shrink)

Natural selection is commonly interpreted as the fundamental mechanism of evolution. Questions about how selection theory can claim to be the all-sufficient explanation of evolution often go unanswered by today's neo-Darwinists, perhaps for fear that any criticism of the evolutionary paradigm will encourage creationists and proponents of intelligent design.In Biological Emergences, Robert Reid argues that natural selection is not the cause of evolution. He writes that the causes of variations, which he refers to as natural experiments, (...) are independent of natural selection; indeed, he suggests, natural selection may get in the way of evolution. Reid proposes an alternative theory to explain how emergent novelties are generated and under what conditions they can overcome the resistance of natural selection. He suggests that what causes innovative variation causes evolution, and that these phenomena are environmental as well as organismal.After an extended critique of selectionism, Reid constructs an emergence theory of evolution, first examining the evidence in three causal arenas of emergent evolution: symbiosis/association, evolutionary physiology/behavior, and developmental evolution. Based on this evidence of causation, he proposes some working hypotheses, examining mechanisms and processes common to all three arenas, and arrives at a theoretical framework that accounts for generative mechanisms and emergent qualities. Without selectionism, Reid argues, evolutionary innovation can more easily be integrated into a general thesis. Finally, Reid proposes a biological synthesis of rapid emergent evolutionary phases and the prolonged, dynamically stable, non-evolutionary phases imposed by natural selection. (shrink)

There is an argument that has recently been deployed in favor of thinking that the mind is mostly (or even exclusively) composed of cognitive modules; an argument that draws from some ideas and concepts of evolutionary and of developmental biology. In a nutshell, the argument concludes that a mind that is massively composed of cognitive mechanisms that are cognitively modular (henceforth, c-modular) is more evolvable than a mind that is not c-modular (or (...) that is scarcely c-modular), since a cognitive mechanism that is c-modular is likely to be biologically modular (henceforth, b-modular), and b-modular characters are more evolvable (e.g., Sperber 2002, Carruthers 2005). In evolutionary biology, the evolvability of a character in an organism is understood as the “organism’s capacity to facilitate the generation of non-lethal selectable phenotypic variation from random mutation” with respect to that character. Here I will argue that the notion of cognitive modularity needed to make this argument plausible will have to be understood in terms of the biological notion of variational independence; that is, it will have to be understood in such a way that a cognitive feature is c-modular only if few or no other morphological changes (cognitive and not) are significantly correlated with variations of that feature arising in members of the relevant population. I will also argue that all –except for (possibly) one—of the connotations contained in a cluster of notions of cognitive modularity widely accepted in some of the mainstream currents of thought in classical cognitive science, are simply irrelevant to the argument. In order to argue for this, I will have to examine the question as to whether there are any strong theoretical connections between (1) those connotations and (2) notions of modularity accepted in biology, specially in evolutionary and in developmental biology, that are thought to be most relevant to arguments to the effect that biological modularity enhances evolvability. (shrink)

In a recent paper, Keith Hutchison has advanced the thesis that the Mechanical Philosophy represents a shift towards supernaturalism in our conception of the physical world. This paper concentrates on one of the great problems of seventeenth-century biological theory — animal generation — to illustrate (and modify) Hutchison's thesis, thereby also serving to locate one role of the life sciences in the Scientific Revolution. This choice of focus enables us to draw heavily on Jacques Roger's seminal work on (...) animal generation to illuminate the change that occurs, within the Mechanical Philosophy, between Descartes and Malebranche. Once the necessary distinctions have been drawn, it is argued, it will be seen that (in one important sense) this is a shift from naturalism to supernaturalism, brought about largely by problems native to the life sciences. (shrink)

Chance has been a focus of attention ever since the beginning of population genetics, but neutrality has not, as natural selection once appeared to be the only worthwhile issue. Neutral change became a major source of interest during the neutralist–selectionist debate, 1970–1980. It retained interest beyond this period for two reasons that contributed to its becoming foundational for evolutionary reasoning. On the one hand, neutral evolution was the first mathematical prediction to emerge from Mendelian inheritance: until then evolution by (...) natural selection was considered the alternative to the fixity of species; now it appears to be the alternative to continuous change. Second, neutral change generated a set of clear predictions on standing variation. These could be used as a reference for detecting more elusive alternative mechanisms of evolution including natural selection. In the wake of the transition from Mendelism to genomics, the combination of coalescent theory, DNA sequence variation, and numerical analysis made it possible to integrate contingent aspects of the history of species into a new null model, thus opening a new dimension in the concept of population that the Modern Synthesis formerly considered as a mere gene pool. (shrink)

In this paper I address an important question in Aristotle’s biology, What are the causal mechanisms behind the transmission of biological form? Aristotle’s answer to this question, I argue, is found in Generation of Animals Book 4 in connection with his investigation into the phenomenon of inheritance. There we are told that an organism’s reproductive material contains a set of "movements" which are derived from the various "potentials" of its nature (the internal principle of change that (...) initiates and controls development). These movements, I suggest, function as specialized vehicles for communicating the parts of the parent’s heritable form during the act of reproduction. After exploring the details of this mechanism, I then take up Aristotle’s theory of inheritance proper. At the heart of the theory are three general principles (or 'laws') that govern the interactions between the maternal and paternal movements, the outcome of which determines the pattern of inheritance for the offspring. Although this paper is primarily aimed at providing a detailed analysis of Aristotle’s account of inheritance, the results of that analysis have implications for other areas of Aristotle’s biology. One of the most interesting of these is the question of whether Aristotle’s biology is anti-evolutionary (as traditionally assumed) or whether (as I argue) it leaves room for a theory of evolution by natural selection, even if Aristotle himself never took that step. (shrink)

Philosophers of science have developed an account of causal-mechanical explanation that captures regularity, but this account neglects variation. In this article I amend the philosophy of mechanisms to capture variation. The task is to explicate the relationship between regular causal mechanisms responsible for individual development and causes of variation responsible for variation in populations. As it turns out, disputes over this relationship have rested at the heart of the nature–nurture debate. Thus, an explication (...) of the relationship between regular causal mechanisms and causes of variation and between individual development and variation offers both the necessary amendment to the philosophy of mechanisms and the resources to mediate the dispute. (shrink)

The last two centuries have been the centuries of the discovery of the cell evolution: in the XIX century of the germinal cells and in the XX century of two groups of somatic cells, namely those of the brain-mind and of the immune systems. Since most cells do not behave in this way, the evolutionary character of the brain-mind and of the immune systems renders human beings formed by two different groups of somatic cells, one with a deterministic and another (...) with an indeterministic (say Darwinian) behavior. An inherent consequence is that of the generation, during ontogenesis, of a dual biological identity. The concept of the dual biological identity may be used to explain the Kantian concept of the two metaphysical worlds, namely of the causal necessity and of the free will (Azzone, 2001). Two concepts, namely those of complex adaptive systems (CAS) and of emergence (Holland, 2002), are useful tools for understanding the mechanisms of adaptation and of evolution. The concept of complex adaptive systems indicates that living organisms contain series of stratified components, denoted as building blocks, forming stratified layers of increasing complexity. The concept of emergence implies the use of repeating patterns and of building blocks for the generation of structures of increasing levels of complexity, structures capable of exchanging communications both in the top-down and in the bottom-up direction. Against the concept of emergence it has been argued that nothing can produce something which is really new and endowed of causal efficacy. The defence of the concept of emergence is based on two arguments. The first is the interpretation of the variation-selection mechanism as a process of generation of information and of optimization of free energy dissipation in accord with the second principle of thermodynamics. The second is the objective evidence of the cosmological evolution from the Big Bang to the human mind and its products. Darwin has defended the concept of the continuity of evolution. However evolution should be considered as continuous when there is no increase of information and as discontinuous when there is generation of new information. Examples of such generation of information are the acquisition of the innate structures for language and the transition from absence to presence of morality. There are several discontinuity thresholds during both phylogenesis and ontogenesis. Morality is a relational property dependent on the interactions of human beings with the environment. Piaget and Kohlberg have shown that the generation of morality during childhood occurs through several stages and is accompanied by reorganization of the child mental organization. The children respect the conventions in the first stage and gradually generate their autonomous morality. The transition from absence to presence of morality, a major adaptive process, then, not only has occurred during phylogenesis but it occurs again in every human being during ontogenesis. The religious faith does not provide a logical justification of the moral rules (Ayala, 1987) but rather a psychological and anthropological justification of two fundamental needs of human beings: that of rendering Nature an understandable entity, and that of increasing the cooperation among members of the human societies. The positive effects of the altruistic genes in the animal societies are in accord with the positive effects of morality for the survival and development of the human societies. (shrink)

Evolutionary epistemology has experienced a continuous rise over the last decades. Important new theoretical considerations and novel empirical findings have been integrated into the existing framework. In this paper, I would like to suggest three lines of research that I believe will significantly contribute to further advance EE: ontogenetic considerations, key ideas from cognitive biology, and the framework of the Extended Evolutionary Synthesis. EE, in particular the program of the evolution of epistemological mechanisms, seeks to provide a phylogenetic (...) account of the generation of cognitive processes underlying knowledge creation. Traditionally, EE and EEM have been oriented towards an account of evolutionary theory that mainly drew from the tenets of the Modern Synthesis. The Modern Synthesis largely dismisses ontogenetic processes and considers them irrelevant for evolutionary explanations. If anything, the role of development in evolution is believed to be that of a constraint. There is, however, ample evidence for a tight intertwinement of developmental and evolutionary processes. Organisms employ their cognitive apparatus to interact with the environment in order to achieve a fully functioning perceptual and cognitive nervous system. Also, ontogeny provides generative potentials to enable variations that natural selection can act upon. EEM’s agenda may, therefore, strongly benefit from bringing together ontogenetic and phylogenetic approaches. To grapple with this challenge, an alternative vision of the evolutionary theory termed Extended Evolutionary Synthesis could be used. This extended evolutionary theory explores relationships between the processes of individual development and phenotypic change during evolution and can provide a more suitable framework for EEM to draw from. In recent years, cognitive biology has gained momentum as an independent research field. Cognitive biology builds on the concepts of EEM and understands knowledge as a biogenic phenomenon. Its main objective is also the formulation of substantiated interrelations between cognition and evolution but it focuses on cognitive functionality at all levels of biological organization. It thus employs a “vertical” approach that encompasses nested hierarchies which span from single molecules, cells, and tissues to the organismal level, communities, and societies. In contrast to cognitive biology, EEM is here understood to adopt a “horizontal” approach that focuses on phylogenetic explanations of cognition and knowledge acquisition. Linking EEM with the key ideas of cognitive biology could make EEM’s research program stronger as it can more easily accommodate phylogenetic and ontogenetic questions within a hierarchical, multilevel perspective. This is of particular importance for a more comprehensive account of cognition since living systems are subject to context-dependent causal influences from different organizational levels. In addition to EEM, there is a second program of EE. This program has been labeled evolutionary epistemology of theories and understands the increase in human knowledge, such as scientific theories, as naturalistic accounts of evolution. Both, EEM and EET initially drew from the core concepts of the Modern Synthesis. Several scholars have severely criticized the analogies made between EET and the Neo-Darwinian key processes of evolution. In particular processes of random mutation, the rate of variation, natural selection as the unique driving force, and the adaptationist agenda are believed to reveal disanalogies. In contrast to the Modern Synthesis, the Extended Evolutionary Synthesis not only recognizes developmental processes but also ecological interactions and systems dynamics as well as social and cultural evolutionary reciprocity as important evolutionary processes. Concepts of the Extended Evolutionary Synthesis are therefore expected to be more fruitful for re-conceptualizing parallels between scientific theorizing and biological evolution. (shrink)

In many fields of biology, both the phenomena to be explained and the mechanisms proposed to explain them are commonly presented in diagrams. Our interest is in how scientists construct such diagrams. Researchers begin with evidence, typically developed experimentally and presented in data graphs. To arrive at a robust diagram of the phenomenon or the mechanism, they must integrate a variety of data to construct a single, coherent representation. This process often begins as the researchers create a first sketch, (...) and it continues over an extended period as they revise the sketch until they arrive at a diagram they find acceptable. We illustrate this process by examining the sketches developed in the course of two research projects directed at understanding the generation of circadian rhythms in cyanobacteria. One identified a new aspect of the phenomenon itself, whereas the other aimed to develop a new mechanistic account. In both cases, the research resulted in a paper in which the conclusion was presented in a diagram that the authors deemed adequate to convey it. These diagrams violate some of the normative “cognitive design principles” advanced by cognitive scientists as constraints on successful visual communication. We suggest that scientists’ sketching is instead governed by norms of success that are broadly explanatory: conveying the phenomenon or mechanism. (shrink)

We develop a conceptual framework that connects biological heredity and organization. We refer to heredity as the cross-generation conservation of functional elements, defined as constraints subject to organizational closure. While hereditary objects are functional constituents of biological systems, any other entity that is stable across generations—and possibly involved in the recurrence of phenotypes—belongs to their environment. The central outcome of the organizational perspective consists in extending the scope of heredity beyond the genetic domain without merging it (...) with the broad category of cross-generation stability. After discussing some implications, we conclude with a reflection on the relationship between stability and variation. 1Introduction2From Extended Heredity to Cross-generation Stability 2.1Extending the scope of heredity: A brief state of the art2.2Rethinking heredity: Conceptual challenges3Biological Heredity in Light of Organization 3.1Biological organization within organisms and beyond3.2Extending organization in time3.3What is biological heredity?4Implications and Objections 4.1Heredity as a specific kind of cross-generation stability4.2Heredity at various levels of description4.3Non-functional and dysfunctional objects5Conclusions: From Conservation to Variation. (shrink)

The issue of the relationship between predictive processing (PP) and the free energy principle (FEP) remains a subject of debate and controversy within the research community. Many researchers have expressed doubts regarding the actual integration of PP with the FEP, questioning whether the FEP can truly contribute significantly to the mechanistic understanding of PP or even undermine such integration altogether. In this paper, I present an alternative perspective. I argue that, from the viewpoint of the constraint-based mechanisms approach, (...) the FEP imposes an important constraint, namely variational free energy, on the mechanistic architecture proposed by PP. According to the constraint-based mechanisms approach, high-level cognitive mechanisms are integral parts of extensive heterarchical networks that govern the physiology and behavior of agents. Consequently, mechanistic explanations of cognitive phenomena should incorporate constraints and flows of free energy as relevant components, given that the implemented constraints operate as long as free energy is available. Within this framework, I contend that the FEP provides a relevant constraint for explaining at least some biological cognitive mechanisms described in terms of Bayesian generative models that minimize prediction errors. (shrink)

While many different mechanisms contribute to the generation of spatial order in biological development, the formation of morphogenetic fields which in turn direct cell responses giving rise to pattern and form are of major importance and essential for embryogenesis and regeneration. Most likely the fields represent concentration patterns of substances produced by molecular kinetics. Short range autocatalytic activation in conjunction with longer range “lateral” inhibition or depletion effects is capable of generating such patterns (Gierer and Meinhardt, 1972). Non-linear (...) reactions are required, and mathematical criteria were derived to design molecular models capable of pattern generation. The classical embryological feature of proportion regulation can be incorporated into the models. The conditions are mathematically necessary for the simplest two-factor case, and are likely to be a fair approximation in multi-component systems in which activation and inhibition are systems parameters subsuming the action of several agents. Gradients, symmetric and periodic patterns, in one or two dimensions, stable or pulsing in time, can be generated on this basis. Our basic concept of autocatalysis in conjunction with lateral inhibition accounts for self-regulatory biological features, including the reproducible formation of structures from near-uniform initial conditions as required by the logic of the generation cycle. Real tissue form, for instance that of budding Hydra, may often be traced back to local curvature arising within an initially relatively flat cell sheet, the position of evagination being determined by morphogenetic fields. Shell theory developed for architecture may also be applied to such biological processes. (shrink)

How Darwin's “endless forms most beautiful” have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging (...) field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating “evolutionary thinking” into bacterial cell biology in the genomic era. (shrink)

The rise of the mechanistic worldview in the seventeenth century had a major impact on views of biological generation. Many seventeenth century naturalists rejected the old animist thesis. However, the alternative view of gradual mechanistic formation in embryology didn’t convince either. How to articulate the peculiarity of life? Researchers in the seventeenth century proposed both “animist” and mechanistic theories of life. In the eighteenth century again a controversy in biology arose regarding the explanation of generation. Some adhered to the (...) view that life is a physical property of matter (e.g. Buffon), others saw living entities as the result of the development of pre-existing germs (e.g. Bonnet). Naturalists, lacked a convincing account that could guide their research. In interaction with leading naturalists of his time Immanuel Kant articulated an approach to explaining generation. Kant’s account, delineated in his Kritik der Urteilskraft (Critique of the power of judgment) (1790), is a combination of Newtonian non-reductionist mechanism in explanation, and a concept of natural end comparable to Stahl’s formal conception of organic bodies. It consists of two claims: a) in biology only mechanical explanation is explanatory, and b) living entities contain some original organisation, which is mechanically unexplainable. In the nineteenth century this approach influenced naturalists as Müller, Virchow, and Von Baer, in their physiological research. Dissatisfied with a sheer mechanistic or, on the other hand, a sheer teleological approach, they appreciated the Kantian account of mechanical explanation of natural ends. In Germany, in the second halve of the nineteenth century, Ernst Haeckel reopened the debate about abiogenesis, which still continuous. (shrink)

Synthetic biology offers a powerful method to design and construct biological devices for human purposes. Two prominent design methodologies are currently used. Rational design adapts the design methodology of traditional engineering sciences, such as mechanical engineering. Directed evolution, in contrast, models its design principles after natural evolution, as it attempts to design and improve systems by guiding them to evolve in a certain direction. Previous work has argued that the primary difference between these two is the way they (...) treat variation: rational design attempts to suppress it, whilst direct evolution utilizes variation. I argue that this contrast is too simplistic, as it fails to distinguish different types of variation and different phases of design in synthetic biology. I outline three types of variation and show how they influence the construction of synthetic biological systems during the design process. Viewing the two design approaches with these more fine-grained distinctions provides a better understanding of the methodological differences and respective benefits of rational design and directed evolution, and clarifies the constraints and choices that the different design approaches must deal with. (shrink)

Explaining the complex dynamics exhibited in many biological mechanisms requires extending the recent philosophical treatment of mechanisms that emphasizes sequences of operations. To understand how nonsequentially organized mechanisms will behave, scientists often advance what we call dynamic mechanistic explanations. These begin with a decomposition of the mechanism into component parts and operations, using a variety of laboratory-based strategies. Crucially, the mechanism is then recomposed by means of computational models in which variables or terms in differential (...) equations correspond to properties of its parts and operations. We provide two illustrations drawn from research on circadian rhythms. Once biologists identified some of the components of the molecular mechanism thought to be responsible for circadian rhythms, computational models were used to determine whether the proposed mechanisms could generate sustained oscillations. Modeling has become even more important as researchers have recognized that the oscillations generated in individual neurons are synchronized within networks; we describe models being employed to assess how different possible network architectures could produce the observed synchronized activity. (shrink)

Developing models of biological mechanisms, such as those involved in respiration in cells, often requires collaborative effort drawing upon techniques developed and information generated in different disciplines. Biochemists in the early decades of the 20th century uncovered all but the most elusive chemical operations involved in cellular respiration, but were unable to align the reaction pathways with particular structures in the cell. During the period 1940-1965 cell biology was emerging as a new discipline and made distinctive contributions to (...) understanding the role of the mitochondrion and its component parts in cellular respiration. In particular, by developing techniques for localizing enzymes or enzyme systems in specific cellular components, cell biologists provided crucial information about the organized structures in which the biochemical reactions occurred. Although the idea that biochemical operations are intimately related to and depend on cell structures was at odds with the then-dominant emphasis on systems of soluble enzymes in biochemistry, a reconceptualization of energetic processes in the 1960s and 1970s made it clear why cell structure was critical to the biochemical account. This paper examines how numerous excursions between biochemistry and cell biology contributed a new understanding of the mechanism of cellular respiration. (shrink)

Recent research in philosophy of science has shown that scientists rely on a plurality of strategies to develop successful explanations of different types of phenomena. In the case of biology, most of these strategies go far beyond the traditional and reductionistic models of scientific explanation that have proven so successful in the fundamental sciences. Concretely, in the last two decades, philosophers of science have discovered the existence of at least two different types of scientific explanation at work in (...) the biological sciences, namely: mechanistic and structural explanations. Despite the growing evidence about the radically different nature of these two types of explanation, no inquiry has been conducted to date to determine the ontological reasons that might underlie these differences, nor the way in which these types of explanations can be systematically related with each other. Here, we aim to cover this gap by connecting this plurality of research strategies with the existence of emergent levels of reality. We argue that the existence of these different—and apparently incompatible—explanatory strategies to account for biological phenomena derives from the existence of “ontological jumps” in nature, which generate different regimes of causation that in turn demand the development of different explanatory frameworks. We identify two of these strategies—mechanistic modelling and network modelling—and connect them to the existence of two ontological regimes of causation. Finally, we relate them with each other in a systematic way. In this vein, our paper provides an ontological justification for the plurality of explanatory strategies that we see in the life sciences. (shrink)

What role does non-genetic inheritance play in evolution? In recent work we have independently and collectively argued that the existence and scope of non-genetic inheritance systems, including epigenetic inheritance, niche construction/ecological inheritance, and cultural inheritance—alongside certain other theory revisions—necessitates an extension to the neo-Darwinian Modern Synthesis (MS) in the form of an Extended Evolutionary Synthesis (EES). However, this argument has been challenged on the grounds that non-genetic inheritance systems are exclusively proximate mechanisms that serve the ultimate (...) function of calibrating organisms to stochastic environments. In this paper we defend our claims, pointing out that critics of the EES (1) conflate non-genetic inheritance with early 20th-century notions of soft inheritance; (2) misunderstand the nature of the EES in relation to the MS; (3) confuse individual phenotypic plasticity with trans-generational non-genetic inheritance; (4) fail to address the extensive theoretical and empirical literature which shows that non-genetic inheritance can generate novel targets for selection, create new genetic equilibria that would not exist in the absence of non-genetic inheritance, and generate phenotypic variation that is independent of genetic variation; (5) artificially limit ultimate explanations for traits to gene-based selection, which is unsatisfactory for phenotypic traits that originate and spread via non-genetic inheritance systems; and (6) fail to provide an explanation for biological organization. We conclude by noting ways in which we feel that an overly gene-centric theory of evolution is hindering progress in biology and other sciences. (shrink)

We contend that Ramsey et al.'s definition of animal innovation sensu process may be partially misleading when investigating mechanisms underlying animal innovation. By excluding social learning from the of innovation, they may be reproducing a dichotomous schema that does not accurately correspond to our knowledge of the acquisition of novel behavioral variants. This gives us some reason to doubt the functional specification of the defined process of innovation.

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, (...) such as life, reproduction, and agency. There has been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality. (shrink)

The ArgumentEugenics, in whatever form it may be articulated, is based on the idea that phenotypic characteristics of particular individuals can be predicted in advance. This paper argues that biology's capacity to predict many of the characteristics exhibited by an individual, especially behavioral or cognitive attributes, will always be very limited. This stems from intrinsic limitations to the methodology for relating genotypes to phenotypes, and from the nature of developmental processes which intervene between genotypes and phenotypes. While genetic (...) studies may generate valid population predictions for conditions which impact human health, neither genetics nor developmental biology are likely to generate useful individual predictions about variation in non-disease-related human behavioral and cognitive phenotypes in the foreseeable future. (shrink)

Diverse cultural norms governing economic behavior might emerge from a dynamic interaction of universal but flexible predispositions that get calibrated to biologically meaningful features of the local social and physical ecology. This impressive cross-cultural effort could better elucidate such gene-culture interactions by incorporating theory-driven experimental manipulations (e.g., comparing kin and non-kin exchanges), as well as analyses of mediating cognitive processes.

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the (...) properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields. (shrink)

It is a matter of contention whether or not a general explanatory framework for the biological sciences would be of scientific value, or whether it is even achievable. In this paper we suggest that both are the case, and we outline proposals for a framework capable of generating new scientific questions. Starting with one clear characteristic of biological systems – that they all have the potential to make mistakes - we aim to describe the nature of (...) this potential and the common processes that lie behind it. Given that under most circumstances biological systems function effectively, an examination of different kinds of mistake-making provides pointers to mechanisms that must exist to make failure uncommon. This in turn informs a framework for systematic enquiry, which in this paper we apply to the haemostatic system, but which we believe could be applied to any system across biology. (shrink)

The origin of novel traits is what draws many to evolutionary biology, yet our understanding of the mechanisms that underlie the genesis of novelty remains limited. Here I review definitions of novelty including its relationship to homology. I then discuss how ontogenetic perspectives may allow us to move beyond current roadblocks in our understanding of the mechanics of innovation. Specifically, I explore the roles of canalization, plasticity and threshold responses during development in generating a reservoir of cryptic genetic (...) variation free to drift and accumulate in natural populations. Environmental or genetic perturbations that exceed the buffering capacity of development can then release this variation, and, through evolution by genetic accommodation, result in rapid diversification, recurrence of lost phenotypes as well as the origins of novel features. I conclude that, in our quest to understand the nature of innovation, the nature of development deserves to take center stage. BioEssays 30:432–447, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The biogenesis of RNAs and proteins is a threat to the cell. Indeed, the act of transcription and nascent RNAs challenge DNA stability. Both RNAs and nascent proteins can also initiate the formation of toxic aggregates because of their physicochemical properties. In reviewing the literature, I show that co-transcriptional and co-translational biophysical constraints can trigger DNA instability that in turn increases the likelihood that sequences that alleviate the constraints emerge over evolutionary time. These directed genetic variations (...) rely on the biogenesis of small RNAs that are transcribed directly from challenged DNA regions or processed from the transcripts that directly or indirectly generate constraints or aggregates. These small RNAs can then target the genomic regions from which they initially originate and increase the local mutation rate of the targeted loci. This mechanism is based on molecular pathways involved in anti-parasite genome defence systems, and implies that gene expression-related biophysical constraints represent a driving force of genome evolution. Are randomly generated mutations the only source of genetic variation during evolution? This paper describes the molecular mechanisms by which co-transcriptional and co-translational biophysical constraints trigger genetic variations in targeted-genomic sequences in an RNA-depending manner. This directed-mutational process that drives genome evolution is related to antiparasite genome defence systems. (shrink)

Biological processes are often explained by identifying the underlying mechanisms that generate a phenomenon of interest. I characterize a basic account of mechanistic explanation and then present three challenges to this account, illustrated with examples from molecular biology. The basic mechanistic account is insufficient for explaining nonsequential and nonlinear dynamic processes, is insufficient for explaining the inherently stochastic nature of many biological mechanisms, and fails to give a proper framework for analyzing organization. I suggest (...) that biological processes are best approached as a multidimensional gradient—with some processes being paradigmatic cases of mechanisms and some being marginal cases. (shrink)

Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, (...) and then defines individual organisms as essentially possessing some mechanisms that play this role. (shrink)

The remodeling of biological membranes is crucial for a vast number of cellular activities and is an inherently multiscale process in both time and space. Seminal work has provided important insights into nanometer‐scale membrane deformations, and highlighted the remarkable variation and complexity in the underlying molecular machineries and mechanisms. However, how membranes are remodeled at the micron‐scale, particularly in vivo, remains poorly understood. Here, we discuss how using regulated exocytosis of large (1.5–2.0 μm) membrane‐bound secretory granules in (...) the salivary gland of live mice as a model system, has provided evidence for the importance of the actomyosin cytoskeleton in micron‐scale membrane remodeling in physiological conditions. We highlight some of these advances, and present mechanistic hypotheses for how the various biochemical and biophysical properties of distinct actomyosin networks may drive this process. (shrink)

Introduction: working together on individuality / Lynn K. Nyhart and Scott Lidgard -- The work of biological individuality: concepts and contexts / Scott Lidgard and Lynn K. Nyhart -- Cells, colonies, and clones: individuality in the volvocine algae / Matthew D. Herron -- Individuality and the control of life cycles / Beckett Sterner -- Discovering the ties that bind: cell-cell communication and the development of cell sociology / Andrew S. Reynolds -- Alternation of generations and individuality, 1851 / (...) Lynn K. Nyhart and Scott Lidgard -- Spencer's evolutionary entanglement: from liminal individuals to implicit collectivities / Snait Gissis -- Biological individuality and enkapsis: from Martin Heidenhain's synthesiology to the völkisch national community / Olivier Rieppel -- Parasitology, zoology, and society in France, ca. 1880-1920 / Michael A. Osborne -- Metabolism, autonomy, and individuality / Hannah Landecker -- Bodily parts in the structure-function dialectic / Ingo Brigandt -- Commentaries: historical, biological, and philosophical perspectives -- Distrust that particular intuition: resilient essentialisms and empirical challenges in the history of biological individuality / James Elwick -- Biological individuality: a relational reading / Scott F. Gilbert -- Philosophical dimensions of individuality / Alan C. Love and Ingo Brigandt. (shrink)

Contemporary psychologists seem to pull in two theoretical directions, namely the reduction of mind to brain and the dissolution of mind in society. Against these dominant trends, this article employs the tools of critical realism to argue for the resuscitation in the discipline, psychology, of an ontologically distinct, psychological concept of mind. This ‘mind’ is conceived here as a real, ontologically emergent property. Its distinctive property is consciousness, generated in the first instance by unconscious, non-conscious and conscious psychological mechanisms. (...) Nonetheless, it is emergent not only from psychological mechanisms, but also biological and social mechanisms, all of which act together in open systems. The article builds on various accounts of the hierarchy of the sciences and their objects to suggest that there is such a real psychological object. It seeks to refute trends in psychological theory that reduce mind either to neuro-physiological and neurobiological properties on the one hand or to social relational and discursive properties on the other. (shrink)

Young songbirds draw the source material for their learned songs from parents, peers, and unrelated adults, as well as from innovation. These learned songs are used for intraspecific communication, and have well-documented roles for such functions as territory maintenance and mate attraction. The songs of wild populations differ, forming local “dialects” that may shift over time, suggesting that cultural evolution is at work. Recent work has focused on the mechanisms responsible for the cultural evolution of bird songs (...) within a population, including drift, learning biases, and selection. In many songs or song repertoires, variability is partitioned, with some songs or song segments being stable and consistent, while others vary within the population and across time, and still others undergo population-wide transitions over time. This review explores the different mechanisms that shape the cultural evolution of songs in wild populations, with specific reference to a long-term investigation of a single population of philopatric Savannah sparrows. Males learn a single four-segment song during their 1st year and sing the same song thereafter. Within this song, the buzz segment is a population marker, and may be stable for decades – variant forms occur but eventually disappear. In contrast, the middle segment is highly variable both within the population and over time; changes in relative prevalence of different forms may be due to cultural drift or a rare-form learning bias. Within the introductory segment, a high note cluster was replaced by a click train between 1982 and 2010, following an S-shaped trajectory characteristic of both selective sweeps in population genetics and the replacement of one form by another in human language. In the case of the Savannah sparrows, this replacement may have been due to sexual selection. In subsequent generations, the number of clicks within trains increased, a form of cultural directional selection. In contrast to the narrowing of a trait's range during directional selection in genetic systems, variation in the number of clicks in a train increased as the mean value shifted because improvisation during song learning allowed the range of the trait to expand. Thus, in the single short song of the Savannah sparrow, at least four different mechanisms appear to contribute to three different types of cultural evolutionary outcomes. In the future, it will be import to explore the conditions that favor the application of specific learning rules, and studies such as the ongoing song seeding experiment in the Kent Island Savannah sparrow population will help in understanding the mechanisms that promote or repress changes in a population's song. (shrink)

Darwin's ideas on variation, heredity, and development differ significantly from twentieth-century views. First, Darwin held that environmental changes, acting either on the reproductive organs or the body, were necessary to generate variation. Second, heredity was a developmental, not a transmissional, process; variation was a change in the developmental process of change. An analysis of Darwin's elaboration and modification of these two positions from his early notebooks (1836-1844) to the last edition of the /Variation of (...) Animals and Plants Under Domestication/ (1875) complements previous Darwin scholarship on these issues. Included in this analysis is a description of the way Darwin employed the distinction between transmission and development, as well as the conceptual relationship he saw between heredity and variation. This paper is part of a larger project comparing commitments regarding variation during the latter half of the nineteenth century. (shrink)

Drawing from the gender wage gap literature, we explore four possible causes of sexual minority earnings gaps: variation in human capital and labor force participation, occupational and industrial sorting, differences in the institutional organization of the public and private sector, and different returns to marriage and parenthood. Using the 2006 Census of Canada, we find that heterosexual men earn more than gay men, followed by lesbians and heterosexual women. Oaxaca-Blinder decompositions show that industry of employment, rather than (...) occupation, disadvantages gay men, lesbians, and heterosexual women. High levels of educational attainment lead to employment in lucrative occupations, but sexual minorities earn significantly less than heterosexual men within these occupations. Wage gaps are reduced in the public sector for heterosexual women, gay men, and lesbians. Finally, we find that heterosexual women experience a motherhood penalty, heterosexual men experience a fatherhood premium, and both receive a premium for marriage; however, the presence of children and marriage have no effect on the earnings of either gay men or lesbians in conjugal relationships. (shrink)

This paper considers a central objection to evolutionary epistemology. The objection is that biological and epistemic development are not analogous, since while biological variation is blind, epistemic variation is not. The generation of hypotheses, unlike the generation of genotypes, is not random. We argue that this objection is misguided and show how the central analogy of evolutionary epistemology can be preserved. The core of our reply is that much epistemic variation is indeed (...) directed by heuristics, but these heuristics are analogous to biological preadaptations which account for the evolution of complex organs. We also argue that many of these heuristics or epistemic preadaptations are not innate but were themselves generatedby a process of blind variation and selective retention. (shrink)

Natural selection is the populational process whereby, for instance, the relative number of a variant better suited to a given environment’s attributes increases over generations. In other words, a population’s makeup is altered, over generations, to suit the requirements of a particular environment. Niche construction is the process whereby an environment’s attributes can be stably modified by organisms, over generations, to suit requirements of those organisms. Should the latter process, when it occurs, be considered as significant for the complementary fit (...) between organism and environment as the former? According to mainstream evolutionary theory, random genetic mutation is the only source of novel, unlearned, trans-generationally persistent behavior. A growing number of biologists and philosophers of science, however, maintain that organisms are capable of generating such behavior, in response to, for instance, trans-generationally persistent environmental change, by way of phenotype-mediated, developmentally plastic mechanisms that do not require mutation. Should mechanisms of this sort be more generally recognized as the source of the selectable variation that selection operates on? Niche construction theory answers “yes” to both these questions, and the result is a debate over the comprehensiveness of mainstream evolutionary theory. (shrink)

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the (...) need for a broadened philosophical conception of mechanisms and mechanistic explanation. Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation. (shrink)

Mechanisms, in the prominent biological sense of the term, are historical entities. That is, whether or not something is a mechanism for something depends on its history. Put differently, while your spontaneously-generated molecule-for-molecule double has a heart, and its heart pumps blood around its body, its heart does not have a mechanism for pumping, since it does not have the right history. My argument for this claim is that mechanisms have proper functions; proper functions are (...) historical entities; so, mechanisms are historical entities, too. This thesis runs against the mainstream new mechanist way of thinking about mechanisms, where mechanisms are generally thought of in an ahistorical way. After arguing for this thesis, I draw out some consequences for philosophy of science and metaphysics. (shrink)

Aravind Joshi famously hypothesized that natural language syntax was characterized (in part) by mildly context-sensitive generative power. Subsequent work in mathematical linguistics over the past three decades has revealed surprising convergences among a wide variety of grammatical formalisms, all of which can be said to be mildly context-sensitive. But this convergence is not absolute. Not all mildly context-sensitive formalisms can generate exactly the same stringsets (i.e. they are not all weakly equivalent), and even when two formalisms can both (...) generate a certain stringset, there might be differences in the structural descriptions they use to do so. It has generally been difficult to find cases where such differences in structural descriptions can be pinpointed in a way that allows linguistic considerations to be brought to bear on choices between formalisms, but in this paper we present one such case. The empirical pattern of interest involves wh-movement dependencies in languages that do not enforce the wh-island constraint. This pattern draws attention to two related dimensions of variation among formalisms: whether structures grow monotonically from one end to another, and whether structure-building operations are conditioned by only a finite amount of derivational state. From this perspective, we show that one class of formalisms generates the crucial empirical pattern using structures that align with mainstream syntactic analysis, and another class can only generate that same string pattern in a linguistically unnatural way. This is particularly interesting given that (i) the structurally-inadequate formalisms are strictly more powerful than the structurally-adequate ones from the perspective of weak generative capacity, and (ii) the formalism based on derivational operations that appear on the surface to align most closely with the mechanisms adopted in contemporary work in syntactic theory (merge and move) are the formalisms that fail to align with the analyses proposed in that work when the phenomenon is considered in full generality. (shrink)

It is widely accepted that stressful conditions can facilitate evolutionary change. The mechanisms elucidated thus far accomplish this with a generic increase in heritable variation that facilitates more rapid adaptive evolution, often via plastic modifications of existing characters. Through scrutiny of different meanings of stress in biological research, and an explicit recognition that stressors must be characterized relative to their effect on capacities for maintaining functional integrity, we distinguish between: (1) previously identified stress-responsive (...) class='Hi'>mechanisms that facilitate evolution by maintaining an adaptive fit with the environment, and (2) the co-option of stress-responsive mechanisms that are specific to stressors leading to the origin of novelties via compensation. Unlike standard accounts of gene co-option that identify component sources of evolutionary change, our model documents the cost-benefit trade-offs and thereby explains how one mechanism—an immediate response to acute stress—is transformed evolutionarily into another—routine protection from recurring stressors. We illustrate our argument with examples from cell type origination as well as processes and structures at higher levels of organization. These examples suggest a general principle of evolutionary origination based on the capacity to switch between regulatory states related to reproduction and proliferation versus survival and differentiation. (shrink)

The comparison between biological and social macroevolution is a very important (though insufficiently studied) subject whose analysis renders new significant possibilities to comprehend the processes, trends, mechanisms, and peculiarities of each of the two types of macroevolution. Of course, there are a few rather important (and very understandable) differences between them; however, it appears possible to identify a number of fundamental similarities. One may single out at least three fundamental sets of factors determining those similarities. First of all, (...) those similarities stem from the fact that in both cases we are dealing with very complex non-equilibrium (but rather stable) systems whose principles of functioning and evolution are described by the General Systems' Theory, as well as by a number of cybernetic principles and laws. -/- Secondly, in both cases we do not deal with isolated systems; in both cases we deal with a complex interaction between systems of organic systems and external environment, whereas the reaction of systems to external challenges can be described in terms of certain general principles (that, however, express themselves rather differently within the biological reality, on the one hand, and within the social reality, on the other). -/- Thirdly, it is necessary to mention a direct ‘genetic’ link between the two types of macroevolution and their mutual influence. -/- It is important to emphasize that the very similarity of the principles and regularities of the two types of macroevolution does not imply their identity. Rather significant similarities are frequently accompanied by enormous differences. For example, genomes of the chimpanzees and the humans are very similar – with differences constituting just a few per cent; however, there are enormous differences with respect to intellectual and social differences of the chimpanzees and the humans hidden behind the apparently ‘insignificant’ difference between the two genomes. Thus, in certain respects it appears reasonable to consider the biological and social macroevolution as a single macroevolutionary process. This implies the necessity to comprehend the general laws and regularities that describe this process, though their manifestations may display significant variations depending on properties of a concrete evolving entity (biological, or social one). An important notion that may contribute to the improvement of the operationalization level as regards the comparison between the two types of macroevolution is the one that we suggested some time ago – the social aromorphosis (that was developed as a counterpart to the notion of biological aromorphosis well established within Russian evolutionary biology). We regard social aromorphosis as a rare qualitative macrochange that increases in a very significant way complexity, adaptability, and mutual influence of the social systems, that opens new possibilities for social macrodevelopment. In our paper we discuss a number of regularities that describe biological and social macroevolution and that employ the notions of social and biological aromorphosis such as ones of the module evolution (or the evolutionary ‘block assemblage’), ‘payment for arogenic progress’ etc. (shrink)

Mechanisms consist of component parts and processes organized in a specific way to produce changes that may give rise to one or more phenomena. I aim to examine the generative mechanism of generative material models in the production of new material models. A generative material model in biology is a living material model that is capable of generating new material models. I contend that generative mechanisms of a generative material model are not to be conflated (...) with biological mechanisms: the former is a mechanism manipulated and altered by the modeler while the latter is a naturally occurring mechanism. I examine the ways in which idealization may contribute to the generative mechanism in generating new model organisms. I articulate that the component parts and activities in a generative mechanism are to a large extent shaped by idealization in generative material modeling. Although biological mechanisms do have a role to play in the generation of model organisms, I propose that we shall view the generative mechanism as a hybrid of biological mechanisms and modeling activities. I shall argue that the notion of generative mechanisms as hybrid mechanisms is different from the extant conceptions of mechanisms in various aspects. (shrink)

I examine an argument that has recently appeared in the cognitive science literature in favor of thinking that the mind is mostly composed of Fodorian-type cognitive modules; an argument that concludes that a mind that is massively composed of classical cognitive mechanisms that are cognitively modular is more evolvable than a mind that is not cognitively modular, since a cognitive mechanism that is cognitively modular is likely to be biologically modular, and (...) biologically modular characters are more evolvable. I argue that the notion of cognitive modularity needed to make this argument plausible will have to be understood in terms of the biological notion of variational independence, as follows: a cognitive feature is cognitively modular only if few or no other morphological changes are significantly correlated with variations of that feature arising in members of the relevant population as a result of ontogeny. I also argue that most of the connotations contained in a cluster of notions of classical cognitive modularity are, as far as we know, irrelevant to the argument, and that only the presence of selective impairments—also known as cognitive dissociations—can be considered as strong indicators of the type of modularity that genuinely enhances evolvability. (shrink)

The rise of molecular epigenetics over the last few years promises to bring the discourse about the sociality and susceptibility to environmental influences of the brain to an entirely new level. Epigenetics deals with molecular mechanisms such as gene expression, which may embed in the organism “memories” of social experiences and environmental exposures. These changes in gene expression may be transmitted across generations without changes in the DNA sequence. Epigenetics is the most advanced example of the new postgenomic and (...) context-dependent view of the gene that is making its way into contemporary biology. In my article I will use the current emergence of epigenetics and its link with neuroscience research as an example of the new, and in a way unprecedented sociality of contemporary biology. After a review of the most important developments of epigenetic research, and some of its links with neuroscience, in the second part I reflect on the novel challenges that epigenetics presents for the social sciences for a re-conceptualization of the link between the biological and the social in a postgenomic age. Although epigenetics remains a contested, hyped, and often uncritical terrain, I claim that especially when conceptualized in broader non-genecentric frameworks,. (shrink)

This paper seeks to characterize how the study of nutrition processes contributed to revisit the problem of vital organization in the late eighteenth century. It argues that focusing on nutrition leads to reformulate the problem of the relation between life and organization in terms of processes, rather than static or given structures. This nutrition-centered approach to life amounts to acknowledge the specific strategic role nutrition played in the development of a materialist approach to the generation of vital organization. The (...) paper proposes a clarification of the multiple meanings of the concept of organization in the context of Enlightenment physiology and nascent biology, before focusing on the century long analogy between nutrition and generation. It shows how, by contrasting different uses of this analogy, nutrition was employed as a key vital phenomenon in the development of epigenetic theories of generation, i.e. how a nutritive modeling of generation was used in the undermining of preformationism. To this purpose I contrast two seemingly opposite theories of generation, Buffon’s and Bonnet’s, and show that despite the obvious metaphysical discontent, their views of generation share a common mechanical conceptual frame in which nutrition is conflated with growth and repair. I then turn to the role nutrition played in the epigenetic conception of generation in C. F. Wolff’s embryology and analyze this rival understanding of nutrition as an organizing process. (shrink)

This article is the first one to offer an investigation, from a biological perspective, of “natural philia” or “kin-based” philia in Aristotle’s practical philosophy. After some preliminary considerations about its place in Aristotle’s ethical treatises, the discussion focuses on Aristotle’s biology. Here we learn that natural philia, couched in terms of a biological praxis rather than a trait of character, is widespread in the animal kingdom, although in different ways and to varying degrees. To account for such (...) differences, Aristotle establishes a Scala Philiae in two different biological texts—Historia Animalium and Generation of Animals—where natural bonds in animals are classified in view of their strength and duration. Each level of Aristotle’s Scala is examined. Finally, the argument returns to Aristotle’s ethical and political texts, drawing greater attention to the biological mechanisms that underlie natural philia in human beings. I conclude that natural philia provides one fundamental biological building-block of Aristotle’s ethics and politics. (shrink)

The theoretical status of ‘niche construction’ in evolution is intensely debated. Here we substantiate the reasons for different interpretations. We consider two concepts of niche construction brought to bear on evolutionary theory; one that emphasizes how niche construction contributes to selection and another that emphasizes how it contributes to development and inheritance. We explain the rationale for claims that selective and developmental niche construction motivate conceptual change in evolutionary biology and the logic of those who reject these (...) claims. Our analysis shows how the contention arises from alternative assumptions regarding the causal independence of the processes that generate variation, differential fitness and inheritance. (shrink)

The elliptical orbits resulting from Newtonian gravitation are generated with a multifaceted symmetry, mainly resulting from their conservation of both angular momentum and a vector fixing their orientation in space—the Laplace or Runge-Lenz vector. From the ancient formalisms of celestial mechanics, I show a rather counterintuitive behavior of the classical hydrogen atom, whose orbits respond in a direction perpendicular to a weak externally-applied electric field. I then show how the same results can be obtained more easily and directly from the (...) intrinsic symmetry of the Kepler problem. If the atom is subjected to an oscillating electric field, it enjoys symmetry in the time domain as well, which is manifest by quasi-energy states defined only modulo ħω. Using the Runge-Lenz vector in place of the radius vector leads to an exactly-solvable model Hamiltonian for an atom in an oscillating electric field—embodying one of the few meaningful exact solutions in quantum mechanics, and a member of an even more exclusive set of exact solutions having a time-dependent Hamiltonian. I further show that, as long as the atom suffers no change in principal quantum number, incident radiation will produce harmonic radiation with polarization perpendicular to the incident radiation. This unusual polarization results from the perpendicular response of the wavefunction, and is distinguished from most usual harmonic radiation resulting from a scalar nonlinear susceptibility. Finally, I speculate on how this radiation might be observed. (shrink)