Living systems employ several mechanisms and behaviors to achieve robustness and maintain themselves under changing internal and external conditions. Regulation stands out from them as a specific form of higher-order control, exerted over the basic regime responsible for the production and maintenance of the organism, and provides the system with the capacity to act on its own constitutive dynamics. It consists in the capability to selectively shift between different available regimes of self-production and self-maintenance in response to specific signals and (...) perturbations, due to the action of a dedicated subsystem which is operationally distinct from the regulated ones. The role of regulation, however, is not exhausted by its contribution to maintain a living system’s viability. While enhancing robustness, regulatory mechanisms play a fundamental role in the realization of an autonomous biological organization. Specifically, they are at the basis of the remarkable integration of biological systems, insofar as they coordinate and modulate the activity of distinct functional subsystems. Moreover, by implementing complex and hierarchically organized control architectures, they allow for an increase in structural and organizational complexity while minimizing fragility. Finally, they endow living systems, from their most basic unicellular instances, with the capability to control their own internal dynamics to adaptively respond to specific features of their interaction with the environment, thus providing the basis for the emergence of minimal forms of cognition. (shrink)

Evolutionary Psychology is based on the idea that the mind is a set of special purpose thinking devices or modules whose domain-specific structure is an adaptation to ancestral environments. The modular view of the mind is an uncontroversial description of the periphery of the mind, the input-output sensorimotor and affective subsystems. The novelty of EP is the claim that higher order cognitive processes also exhibit a modular structure. Autism is a primary case study here, interpreted as a developmental failure (...) of a module devoted to social intelligence or Theory of Mind. In this article I reappraise the arguments for innate modularity of TOM and argue that they fail. TOM ability is a consequence of domain general development scaffolded by early, innately specified, sensorimotor abilities. The alleged Modularity of TOM results from interpreting the outcome of developmental failures characteristic of autism at too high a level of cognitive abstraction. (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)

Living systems employ several mechanisms and behaviors to achieve robustness and maintain themselves under changing internal and external conditions. Regulation stands out from them as a specific form of higher-order control, exerted over the basic regime responsible for the production and maintenance of the organism, and provides the system with the capacity to act on its own constitutive dynamics. It consists in the capability to selectively shift between different available regimes of self-production and self-maintenance in response to specific signals and (...) perturbations, due to the action of a dedicated subsystem which is operationally distinct from the regulated ones. The role of regulation, however, is not exhausted by its contribution to maintain a living system’s viability. While enhancing robustness, regulatory mechanisms play a fundamental role in the realization of an autonomous biological organization. Specifically, they are at the basis of the remarkable integration of biological systems, insofar as they coordinate and modulate the activity of distinct functional subsystems. Moreover, by implementing complex and hierarchically organized control architectures, they allow for an increase in structural and organizational complexity while minimizing fragility. Finally, they endow living systems, from their most basic unicellular instances, with the capability to control their own internal dynamics to adaptively respond to specific features of their interaction with the environment, thus providing the basis for the emergence of minimal forms of cognition. (shrink)

This article began as a review of a conference, organized by Gerhard Schlosser, entitled “Modularity in Development and Evolution.” The conference was held at, and sponsored by, the Hanse Wissenschaftskolleg in Delmenhorst, Germany in May, 2000. The article subsequently metamorphosed into a literature and concept review as well as an analysis of the differences in current perspectives on modularity. Consequently, I refer to general aspects of the conference but do not review particular presentations. I divide modules into three kinds: (...) structural, developmental, and physiological. Every module fulfills none, one, or multiple functional roles. Two further orthogonal distinctions are important in this context: module-kinds versus module-variants-of-a-kind and reproducer versus nonreproducer modules. I review criteria for individuation of modules and mechanisms for the phylogenetic origin of modularity. I discuss conceptual and methodological differences between developmental and evolutionary biologists, in particular the difference between integration and competition perspectives on individualization and modular behavior. The variety in views regarding modularity presents challenges that require resolution in order to attain a comprehensive, rather than a piecemeal and fragmentary, evolutionary developmental biology. (shrink)

Any problem is a problem until a solution is designed and implemented. This paper reports on a workshop that highlights preliminary work done by the working group on Gamification in the scope of European Network for Academic Integrity, which aims to explore the possibility of developing and testing a gamified learning module on academic integrity values. In this paper, the group aims to look at proposing steps we are currently using to develop storyboards of scenarios for the first phase (...) of the project, which were presented at the 6th International Conference Plagiarism Across Europe and Beyond 2020 held virtually in Dubai as a workshop. The study also presents updated findings and scenarios drawn from the workshop conducted and audience feedback, in the following sections that pave the way for the future stages of the gamification process. This serves as a guide to academics and researchers in academic integrity who may wish to study gamification and apply it to develop their own modules for their learning modules. (shrink)

Schizophrenics exhibit a deficit in theory of mind (ToM), but an intact theory of biology (ToB). One explanation is that ToM relies on an independent module that is selectively damaged. Phillips & Silverstein's analyses suggest an alternative: ToM requires the type of coordination that is impaired in schizophrenia, whereas ToB is spared because this type of coordination is not involved.

Doctoral programs at U.S. universities play a critical role in the development of human resources both in the United States and abroad. This volume reports the results of an extensive study of U.S. research-doctorate programs in five broad fields: physical sciences and mathematics, engineering, social and behavioral sciences, biological sciences, and the humanities. Research-Doctorate Programs in the United States documents changes that have taken place in the size, structure, and quality of doctoral education since the widely used 1982 editions. This (...) update provides selected information on nearly 4,000 doctoral programs in 41 subdisciplines at 274 doctorate-granting institutions. This volume also reports the results of the National Survey of Graduate Faculty, which polled a sample of faculty for their views on the scholarly quality of program faculty and the effectiveness of doctoral programs in preparing research scholars/scientists. This much-anticipated update of such an essential reference will be useful to education administrators, university faculty, and students seeking authoritative information on doctoral programs. (shrink)

The clonal evolution model and the cancer stem cell model are two independent models of cancers, yet recent data shows intersections between the two models. This article explores the impacts of the CSC model on the CE model. I show that CSC restriction, which depends on CSC frequency in cancer cell populations and on the probability of dedifferentiation of cancer non-stem cells into CSCs, can favor or impede some patterns of evolution and some processes of evolution. Taking CSC restriction into (...) account for the CE model thus has implications for the way in which we understand the patterns and processes of evolution, and can also provide new leads for therapeutic interventions. (shrink)

Carbon monoxide (CO), a product of organic oxidation processes, arises in vivo during cellular metabolism, most notably heme degradation. CO binds to the heme iron of most hemoproteins. Tissue hypoxia following hemoglobin saturation represents a principle cause of CO‐induced mortality in higher organisms, though cellular targets cannot be excluded. Despite extreme toxicity at high concentrations, low concentrations of CO can confer cytoprotection during ischemia/reperfusion or inflammation‐induced tissue injury. Likewise, heme oxygenase, an enzyme that produces CO, biliverdin and iron, as well (...) as a secondary increase in ferritin synthesis, from the oxidation of heme, can confer protection in vivo and in vitro. CO has been shown to affect several intracellular signaling pathways, including guanylate cyclase, which generates guanosine 3′:5′ cyclic monophosphate and the mitogen‐activated protein kinases (MAPK). Such pathways mediate, in part, the known vasoregulatory, anti‐inflammatory, anti‐apoptotic and anti‐proliferative effects of this gas. Exogenous CO delivered at low concentrations is showing therapeutic potential as an anti‐inflammatory agent and as such can modulate numerous pathophysiological states. This review will delve into the biological significance and medical applications of this gas molecule. BioEssays 26:270–280, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Gamification in education is still a very new concept in South Africa. Being a 21st-centuryinvention, it has already established itself in the world within the environs of the corporatemarket, marketing, training and the social world. This article will first discuss gamification(and all its other designations) and its applications in general; thereafter, the focus will be onthe application of gamification within the environment of education, and more specificallywith an emphasis on assessment. The burning question for South Africa is (...) whethergamification can enhance a module or course on the level of higher education so much that aneducational institution cannot do without it anymore, knowing that we are working withstudents belonging to the ‘Digital Wisdom generation’. This article would like to open theway for the implementation of gamification as a transformative online assessment tool inhigher education. (shrink)

Noam Chomsky has failed to provide a satisfactory explanation of the "creativity of language" that he maintains is an essential part of the mental representation that makes the acquisition of languages possible. I argue that Chomsky's problems in articulating an acceptable concept of creativity is symptomatic of greater problems embedded in his idea of an "innateness hypothesis." An examination of the historical development of Chomsky's views on the nature of language shows that conclusions with regard to the creativity of language (...) remain either quite speculative or else untenable. This result establishes some agreement with Chomsky on the idea that cognitive capacities are largely structure determined. However, I argue against his idea that creativity is itself a part of those structures. In conclusion, I argue that creativity is an aspect of autonomy. In view of the integrative role of autonomy with respect cognitive capacities in general, we must conclude that creativity does not belong to the biological domain that Chomsky has characterized. (shrink)

Evolutionary developmental biologists categorize many different kinds of things, from ontogenetic stages to modules of gene activity. The process of categorization—the establishment of “kinds”—is an implicit part of describing the natural world in consistent, useful ways, and has an essentially practical rather than philosophical basis. Kinds commonly serve one of three purposes: they may function (1) as practical tools for communication; (2) to support prediction and generalization; or (3) as a basis for theoretical discussions. Beyond the minimal requirement that (...) classifications reflect biological reality, what sorts of kinds or classification will be useful in advancing a research program depends on the epistemological context. Thus, the important meaning of “natural” in “natural kinds” is not “natural with respect to nature,” but “natural with respect to the question.” This conclusion arises from the recognition that the proper role of concepts (e.g. natural kind, module, homology, model) is not to answer biological questions, but rather to help frame them. From a scientist’s perspective, arguing about the wording (or existence) of a single definition of “natural” or “kind” is beside the point: we get more work done by letting the question at hand determine what kinds of kinds are natural, on the basis of their ability to help answer it. We should be content to let “natural kinds” remain vague, multivalent, and–therefore broadly useful. For a philosopher like Hacking, the diverse, disparate, and ultimately incommensurable uses of the term “natural kind” have diluted its value so far that it loses all meaning. For practicing scientists, however, defining useful kinds in the context of particular questions and systems remains a productive epistemological strategy. (shrink)

Phytomorphology — if concerned with development — often concentrates on correlative changes of form and neglects the aspects of age, time and clock, although the plant's spatial and temporal organisation are intimately interconnected. Common age as measured in physical time by a physical process is compared to biological age as measured by a biological clock based on a biological process. A typical example for a biological clock on the organ level is, for example, a shoot. Its biological age is measured (...) by the biological time unit of a plastochron, which itself is defined by the cyclic-periodic initiation of the leaves. In a controlled environment biological age may replace physical age. However, biological and physical age are not necessarily linearly convertible into each other. In stationary or steady state conditions the repetitive initiation of any organ, unit or module of an articulate plant or plant modular system may define the biological time unit. A linear — monotonous biological process, e.g. axis elongation, may also define a biological time unit as a certain amount of additional growth, e.g. of length. One may speak of periodical and of continuous plastochron or, perhaps, of plastochron and rheochron. A precise measure of biological age is the generalized plastochron index applying to any modular system and module respectively. However, one should be aware that it is based on two clocks, one of them referring to the periodic process of module initiation for counting the integer plastochrons and the other to the continuous plastochron of module growth for the determination of the fraction of one plastochron. The application of the concepts is restricted to phases of stationary or steady state growth and development. In certain cases of non-stationary or non-steady state conditions a normalized-age concept may apply. (shrink)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through (...) detailed studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

But as for most genes, they are not the units of interest once we get to the network level: it is the whole conspiracy we care about. Biologists, more precisely evolutionary biologists, and not only psychologists and philosophers also speak of modularity. However the way in which this theoretical construct functions in their discipline is relatively different from the role it obtains in evolutionary psychology and cognitive science. Rather than postulating modules to explain particular traits of organisms, such as (...) the specificity of input systems or limitations of human reasoning abilities, biologists originally simply assume that some form of modularity constitutes a precondition of evolution. They argue that, in order for natural selection to fine tune organisms to their environment, different traits must be able to evolve independently from one another. This implies modularity in one form or another. Organisms will only be able to adapt if they do not come all in one piece, so to speak. It must therefore be possible for changes to occur in one characteristic of an animal without those changes having repercussions throughout the whole organism. (shrink)

In this paper we present a new framework of idealization in biology. We characterize idealizations as a network of counterfactual and hypothetical conditionals that can exhibit different "degrees of contingency". We use this idea to say that, in departing more or less from the actual world, idealizations can serve numerous epistemic, methodological or heuristic purposes within scientific research. We defend that, in part, this structure explains why idealizations, despite being deformations of reality, are so successful in scientific practice. For (...) illustrative purposes, we provide an example from population genetics, the Wright-Fisher Model. (shrink)

In this paper we present a new framework of idealization in biology. We characterize idealizations as a network of counterfactual and hypothetical conditionals that can exhibit different “degrees of contingency”. We use this idea to say that, in departing more or less from the actual world, idealizations can serve numerous epistemic, methodological or heuristic purposes within scientific research. We defend that, in part, this structure explains why idealizations, despite being deformations of reality, are so successful in scientific practice. For (...) illustrative purposes, we provide an example from population genetics, the Wright-Fisher Model. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best (...) conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

Developmental biology is expanding into several new areas. One new area of study concerns the production of adult-onset phenotypes by exposure of the fetus or neonate to environmental agents. These agents include maternal nutrients, developmental modulators (endocrine disruptors), and maternal care. In all three cases, a major mechanism for the generation of the altered phenotype is chromatin modification. Nutrient conditions, developmental modulators, and even maternal care appear to alter DNA methylation and other associated changes in chromatin that regulate gene (...) expression. This brings a new, under-appreciated, dimension of gene regulation into developmental biology, and it also demonstrates the poverty of the nature versus nurture framework for discussing phenotype production. Moreover, while such epigenetic mechanisms undermine genetic determinism, they add a layer of probabilistic biological causality for the maintenance of social inequalities. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Convention for Protection of Human Rights and Dignity of the Human Being with Regard to the Application of Biology and Biomedicine: Convention on Human Rights and BiomedicineCouncil of EuropePreambleThe Member States of the Council of Europe, the other States and the European Community signatories hereto,Bearing in mind the Universal Declaration of Human Rights proclaimed by the General Assembly of the United Nations on 10 December 1948;Bearing in mind (...) the Convention for the Protection of Human Rights and Fundamental Freedoms of 4 November 1950;Bearing in mind the European Social Charter of 18 October 1961;Bearing in mind the International Covenant on Civil and Political Rights and the International Covenant on Economic, Social and Cultural Rights of 16 December 1966;Bearing in mind the Convention for the Protection of Individuals with Regard to Automatic Processing of Personal Data of 28 January 1981;Bearing also in mind the Convention on the Rights of the Child of 20 November 1989;Considering that the aim of the Council of Europe is the achievement of a greater unity between its members and that one of the methods by which that aim is to be pursued is the maintenance and further realisation of human rights and fundamental freedoms;Conscious of the accelerating developments in biology and medicine;Convinced of the need to respect the human being both as an individual and as a member of the human species and recognising the importance of ensuring the dignity of the human being; [End Page 277]Conscious that the misuse of biology and medicine may lead to acts endangering human dignity;Affirming that progress in biology and medicine should be used for the benefit of present and future generations;Stressing the need for international co-operation so that all humanity may enjoy the benefits of biology and medicine;Recognising the importance of promoting a public debate on the questions posed by the application of biology and medicine and the responses to be given thereto;Wishing to remind all members of society of their rights and responsibilities;Taking account of the work of the Parliamentary Assembly in this field, including Recommendation 1160 (1991) on the preparation of a Convention on bioethics;Resolving to take such measures as are necessary to safeguard human dignity and the fundamental rights and freedoms of the individual with regard to the application of biology and medicine;Have agreed as follows:Chapter IGeneral provisionsArticle 1. (Purpose and object)Parties to this Convention shall protect the dignity and identity of all human beings and guarantee everyone, without discrimination, respect for their integrity and other rights and fundamental freedoms with regard to the application of biology and medicine.Each Party shall take in its internal law the necessary measures to give effect to the provisions of this Convention.Article 2. (Primacy of the human being)The interests and welfare of the human being shall prevail over the sole interest of society or science.Article 3. (Equitable access to health care)Parties, taking into account health needs and available resources, shall take appropriate measures with a view to providing, within their jurisdiction, equitable access to health care of appropriate quality. [End Page 278]Article 4. (Professional standards)Any intervention in the health field, including research, must be carried out in accordance with relevant professional obligations and standards.Chapter IIConsentArticle 5. (General rule)An intervention in the health field may only be carried out after the person concerned has given free and informed consent to it.This person shall beforehand be given appropriate information as to the purpose and nature of the intervention as well as on its consequences and risks.The person concerned may freely withdraw consent at any time.Article 6. (Protection of persons not able to consent)1. Subject to Articles 17 and 20 below, an intervention may only be carried out on a person who does not have the capacity to consent, for his or her direct benefit.2. Where, according to law, a minor does not have the capacity to consent to an intervention, the intervention may only be carried out with the authorisation of his or her representative or an authority or a person or... (shrink)

We highlight the various domains of the flavivirus virulence factor NS1 and speculate on potential implications of the NS1 3D structure in understanding its role in flavivirus pathogenesis. Flavivirus non‐structural protein 1 (NS1) is a virulence factor with dual functions in genome replication and immune evasion. Crystal structures of NS1, combined with reconstructions from electron microscopy (EM), provide insight into the architecture of dimeric NS1 on cell membranes and the assembly of a secreted hexameric NS1‐lipid complex found in patient sera. (...) Three structural domains of NS1 likely have distinct roles in membrane association, replication complex assembly, and immune system avoidance. A conserved hydrophobic inner face is sequestered either on the membrane or in the interior of the secreted hexamer and contains regions implicated in viral replication. The exposed variable outer face is presented to cellular and secreted components of the immune system in infected patients and contains candidate regions for immune system modulation. We anticipate that knowledge of the distinct NS1 domains and assembly will lead to advances in elucidating virus‐host interactions mediated through NS1 and in dissecting the role of NS1 in viral genome replication. (shrink)

The concept of mechanism in biology has three distinct meanings. It may refer to a philosophical thesis about the nature of life and biology (‘mechanicism’), to the internal workings of a machine-like structure (‘machine mechanism’), or to the causal explanation of a particular phenomenon (‘causal mechanism’). In this paper I trace the conceptual evolution of ‘mechanism’ in the history of biology, and I examine how the three meanings of this term have come to be featured in the (...) philosophy of biology, situating the new ‘mechanismic program’ in this context. I argue that the leading advocates of the mechanismic program (i.e., Craver, Darden, Bechtel, etc.) inadvertently conflate the different senses of ‘mechanism’. Specifically, they all inappropriately endow causal mechanisms with the ontic status of machine mechanisms, and this invariably results in problematic accounts of the role played by mechanism-talk in scientific practice. I suggest that for effective analyses of the concept of mechanism, causal mechanisms need to be distinguished from machine mechanisms, and the new mechanismic program in the philosophy of biology needs to be demarcated from the traditional concerns of mechanistic biology. (shrink)

Until recently, the notions of function and multiple realization were supposed to save the autonomy of psychological explanations. Furthermore, the concept of supervenience presumably allows both dependence of mind on brain and non-reducibility of mind to brain, reconciling materialism with an independent explanatory role for mental and functional concepts and explanations. Eliminativism is often seen as the main or only alternative to such autonomy. It gladly accepts abandoning or thoroughly reconstructing the psychological level, and considers reduction if successful as equivalent (...) with elimination. In comparison with the philosophy of mind, the philosophy of biology has developed more subtle and complex ideas about functions, laws, and reductive explanation than the stark dichotomy of autonomy or elimination. It has been argued that biology is a patchwork of local laws, each with different explanatory interests and more or less limited scope. This points to a pluralistic, domain-specific and multi-level view of explanations in biology. Explanatory pluralism has been proposed as an alternative to eliminativism on the one hand and methodological dualism on the other hand. It holds that theories at different levels of description, like psychology and neuroscience, can co-evolve, and mutually influence each other, without the higher-level theory being replaced by, or reduced to, the lower-level one. Such ideas seem to tally with the pluralistic character of biological explanation. In biological psychology, explanatory pluralism would lead us to expect many local and non-reductive interactions between biological, neurophysiological, psychological and evolutionary explanations of mind and behavior. This idea is illustrated by an example from behavioral genetics, where genetics, physiology and psychology constitute distinct but interrelated levels of explanation. Accounting for such a complex patchwork of related explanations seems to require a more sophisticated and precise way of looking at levels than the existing ideas on (reductive and non-reductive) explanation in the philosophy of mind. (shrink)

Previous work has suggested that many stem cells can be found in microanatomic niches, where adjacent somatic cells of the niche control the differentiation and proliferation states of their resident stem cells. Recently published work examining intestinal stem cells (ISCs) in the adult Drosophila midgut suggests a new paradigm where some stem cells actively control the cell fate decisions of their daughters. Here, we review recent literature(1) demonstrating that, in the absence of a detectable stem cell niche, multipotent Drosophila ISCs (...) modulate the Notch signaling pathway in their adjacent daughter cells in order to specify the differentiated lineages of their descendants. These observations made in Drosophila are challenging and advancing our understanding of stem cell biology. BioEssays 30:107–109, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The question of whether cultural transmission is faithful has attracted significant debate over the last 30 years. The degree of fidelity with which an object is transmitted depends on 1) the features chosen to be relevant, and 2) the quantity of details given about those features. Once these choices have been made, an object is described at a particular grain. In the absence of conventions between different researchers and across different fields about which grain to use, transmission fidelity cannot be (...) evaluated because it is relative to the choice of grain. In biology, because a genotype-to-phenotype mapping exists and transmission occurs from genotype to genotype, a privileged grain of description exists that circumvents this ‘grain problem.’ In contrast, in cultural evolution, the genotype–phenotype distinction cannot be drawn, rendering claims about fidelity dependent upon researchers’ choices. Thus, due to a lack of unified conventions, claims about fidelity transmission are difficult to evaluate. (shrink)

Selected-effects theories provide the most popular account of biological teleology. According to these theories, the purpose of a trait is to do whatever it was selected for. The vast majority of selected-effects theories consider biological teleology to be introduced by natural selection. We want to argue, however, that natural selection is not the only relevant selective process in biology. In particular, our proposal is that biological regulation is a form of biological selection. So, those who accept selected-effects theories should (...) recognize biological regulation as a distinctive source of biological teleology. The purposes derived from biological regulation are of special interest for explaining and predicting the behavior of organisms, given that regulatory mechanisms directly modulate the behavior of the systems they regulate. This explanatory power, added to the fact that regulation is widespread in the biological world, makes the idea that regulation gives rise to its own form of teleology a substantial contribution to the debate on biological teleology. (shrink)

In the past 20 years, the concept of instinct has been discussed in respect to various disciplines such as evolutionary biology, evolutionary psychology, linguistics, ethics, aesthetics, and phenomenology, etc. However, the meaning of instinct still remains unclarified in many respects. In order to overcome this situation, it is necessary to elucidate the genuine meaning of instinct so that the discussion of instinct in these disciplines can be carried out systematically. The objective of this paper is to establish the genuine (...) concept of instinct on the basis of a phenomenological criticism of A. Gehlen’s theory of instinct-reduction. Moreover, it seeks to show that this concept is the genetic origin of the embodied consciousness. According to Gehlen, instinct is defined as Instinkthandlung. However, this definition of instinct is problematic in the formal logical sense, since the definiendum is already included in the definiens. Moreover, it faces different kinds of serious material problems. Criticizing Gehlen’s theory of instinct systematically, I will show that instinct should be redefined as “the innate living force that urges a species of living being to pursue a certain kind of object,” and I will attempt to clarify this definition of instinct in a more detailed manner by offering 11 points. Thereafter, I will argue that Gehlen’s theory of instinct-reduction has to be replaced by the theory of instinct-enlargement in human beings. Finally, I will point out that the genuine concept of instinct is nothing other than the genetic origin of the embodied consciousness. (shrink)

For over 20 years, the Schmid Training Course (STC) has offered unique opportunities for marine biology students from European universities to learn about marine model organisms. While the topics of the course have continuously changed over the years with the advent of new research techniques and discoveries, the pedagogical approach has remained largely the same – a combination of lectures, lab practicals, and field excursions. Several life science researchers, who have taught in the STC for many years, sought to (...) bring the course's pedagogical approach into the 21st century, and with the support of Erasmus+ Programme of the European Community funding, the Digital Marine project was developed. Digital Marine began in 2018 as an international partnership between the six research centers from which the STC instructors hail, and its main objective was to introduce a flipped, blended approach to learning and teaching with respect to established and emerging marine biological model systems. The Digital Marine platform, which covers 12 marine model organisms, is now publicly available. (shrink)

Much contemporary debate on the nature of mechanisms centers on the issue of modulating negative causes. One type of negative causability, which I refer to as “causation by absence,” appears difficult to incorporate into modern accounts of mechanistic explanation. This paper argues that a recent attempt to resolve this problem, proposed by Benjamin Barros, requires improvement as it overlooks the fact that not all absences qualify as sources of mechanism failure. I suggest that there are a number of additional types (...) of effects caused by absences that need to be incorporated to account for the diversity of causal connections in the biological sciences. Furthermore, it is argued that recognizing natural variability in mechanisms, such as attenuation, leads to some interesting line-drawing issues for contemporary philosophy of mechanisms. (shrink)

The use of informational terms is widespread in molecular and developmental biology. The usage dates back to Weismann. In both protein synthesis and in later development, genes are symbols, in that there is no necessary connection between their form (sequence) and their effects. The sequence of a gene has been determined, by past natural selection, because of the effects it produces. In biology, the use of informational terms implies intentionality, in that both the form of the signal, and (...) the response to it, have evolved by selection. Where an engineer sees design, a biologist sees natural selection. (shrink)

It is often argued that biological generalizations have a distinctive and special status by comparison with the generalizations of other natural sciences, such as that biological generalizations are riddled with exceptions defying systematic and simple treatment. This special status of biology is used as a premise in arguments that posit a deprived explanatory, nomological, or methodological status in the biological sciences. I will discuss the traditional and still almost universally held idea that the biological sciences cannot deal with exceptions (...) and application conditions of their generalizations with their own distinctive and proprietary explanantia, but need the help of lower-level sciences to carry out this task. The idea of lower-level explanations of exceptions is connected to the idea that the biological sciences need lower-level sciences to better themselves and to the idea that biological sciences cannot provide reliable and extrapolatable results or explanations by themselves. I present counterexamples to the idea of lower-level explanations of exceptions in biology. I also discuss and refute more general arguments why the idea of lower-level explanations of exceptions has been held to hold in the special sciences, such as the screening-off and openness arguments. This suggest that there might be nothing special about the biological sciences vis-à-vis the more fundamental natural sciences, such as physics insofar as explanations of exceptions are concerned, and that the biological sciences can provide reliable and extrapolatable results or explanations by themselves. (shrink)

Biological agency has received much attention in recent philosophy of biology. But what is the motivation for introducing talk of agency into biology and what is meant by “agent”? Two distinct motivations can be discerned. The first is that thinking of organisms as agents helps to articulate what is distinctive about organisms vis-à-vis other biological entities. The second is that treating organisms as agent-like is a useful heuristic for understanding their evolved behavior. The concept of agent itself may (...) be understood in at least four different ways: minimal agent, intelligent agent, rational agent, and intentional agent. Which understanding is most appropriate depends on which of the two motivations we are concerned with. (shrink)

Much contemporary debate on the nature of mechanisms centers on the issue of modulating negative causes. One type of negative causability, which I refer to as "causation by absence," appears difficult to incorporate into modern accounts of mechanistic explanation. This paper argues that a recent attempt to resolve this problem, proposed by Benjamin Barros, requires improvement as it overlooks the fact that not all absences qualify as sources of mechanism failure. I suggest that there are a number of additional types (...) of effects caused by absences that need to be incorporated to account for the diversity of causal connections in the biological sciences. Furthermore, it is argued that recognizing natural variability in mechanisms, such as attenuation, leads to some interesting line-drawing issues for contemporary philosophy of mechanisms. (shrink)

Explanation in biology has long been characterized as being very different from explanation in other scientific disciplines, very much so from explanation in physics. One of the reasons was the existence in biology of explanation types that were unheard of in the physical sciences: teleological explanations (e.g. Hull 1974), evolutionary explanations (e.g. Mayr 1988), or even functional explanations (e.g. Neander 1991). More recently, and owing much to the rise of molecular biology, biological explanations have been depicted as (...) mechanisms (e.g; Machamer, Darden and Craver 2000). The aim of this volume is to shed some new light on the diversity of explanation types in biology. What are the different types of explanation that occur in biology? Are these types of explanation specific to particular sub-disciplines of biology, or to particular types of problems across biology? How do they relate to each another? Do they compete with one another for answering the same questions? Or do they complement each other, providing insights to different questions? What are the reasons for such diversity? Can this diversity be overcome by a broader unifying model of explanation or is it more profound and irreducible? Why? This volume aims at making sense of this diversity of types of explanations that are found in biology, of their relationship with one another. After all, explanation in biology may prove not only different from explanation in the physical sciences, but also much more diverse than originally anticipated. (shrink)

Myosin self‐assembly is generally considered to be the major process in thick filament formation within striated muscles. The biological assembly of myosin into thick filaments is being analysed by genetic dissection as well as biochemical and morphological experiments in the nematode Caenorhabditis elegans. This work shows that the assembly of myosin is modulated by its biosynthesis and interaction with non‐myosin proteins. Assemblages which generate multiple nascent thick filaments may play a central role in a catalytic cycle of myosin assembly.

Richard Lewontin's (1970) early work on the units of selection initiated the conceptual and theoretical investigations that have led to the hierarchical perspective on selection that has reached near consensus status today. This paper explores other aspects of his work, work on what he termed continuity and quasi-independence, that connect to contemporary explorations of modularity in development and evolution. I characterize such modules and argue that they are the true units of selection in that they are what evolution by (...) natural selection individuates, selects among, and transforms. (shrink)

Besides mechanistic explanations of phenomena, which have been seriously investigated in the last decade, biology and ecology also include explanations that pinpoint specific mathematical properties as explanatory of the explanandum under focus. Among these structural explanations, one finds topological explanations, and recent science pervasively relies on them. This reliance is especially due to the necessity to model large sets of data with no practical possibility to track the proper activities of all the numerous entities. The paper first defines topological (...) explanations and then explains why topological explanations and mechanisms are different in principle. Then it shows that they are pervasive both in the study of networks—whose importance has been increasingly acknowledged at each level of the biological hierarchy—and in contexts where the notion of selective neutrality is crucial; this allows me to capture the difference between mechanisms and topological explanations in terms of practical modelling practices. The rest of the paper investigates how in practice mechanisms and topologies are combined. They may be articulated in theoretical structures and explanatory strategies, first through a relation of constraint, second in interlevel theories, or they may condition each other. Finally, I explore how a particular model can integrate mechanistic informations, by focusing on the recent practice of merging networks in ecology and its consequences upon multiscale modelling. (shrink)

Should the philosophy of biology deal with organismic, or with molecular aspects , or with both ? We are, of course, not the first to appreciate the ...

Kant's Critique of Teleological Judgment is read as a reflection on philosophical methodological problems that arose through the constitution of an independent science of life - biology. This work presents an example of the interconnections between philosophy and the history of science.

_Philosophy of Molecular Medicine: Foundational Issues in Theory and Practice_ aims at a systematic investigation of a number of foundational issues in the field of molecular medicine. The volume is organized around four broad modules focusing, respectively, on the following key aspects: What are the nature, scope, and limits of molecular medicine? How does it provide explanations? How does it represent and model phenomena of interest? How does it infer new knowledge from data and experiments? The essays collected here, (...) authored by prominent scientists and philosophers of science, focus on a handful of mainstream topics in the philosophical literature, such as _causation_, _explanation_, _modeling_, and _scientific inference_. These previously unpublished contributions shed new light on these traditional topics by integrating them with problems, methods, and results from three prominent areas of contemporary biomedical science: _basic research_, _translational_ and _clinical research_, and _clinical practice_. (shrink)

Eye movement desensitization and reprocessing therapy is a well-established therapeutic method to treat post-traumatic stress disorder. However, how EMDR exerts its therapeutic action has been studied in many types of research but still needs to be completely understood. This is in part due to limited knowledge of the neurobiological mechanisms underlying EMDR, and in part to our incomplete understanding of PTSD. In order to model PTSD, we used a biologically inspired computational model based on firing rate units, encompassing the cortex, (...) hippocampus, and amygdala. Through the modulation of its parameters, we fitted real data from patients treated with EMDR or classical exposure therapy. This allowed us to gain insights into PTSD mechanisms and to investigate how EMDR achieves trauma remission. (shrink)