A main thread of the debate over mathematical realism has come down to whether mathematics does explanatory work of its own in some of our best scientific explanations of empirical facts. Realists argue that it does; anti-realists argue that it doesn't. Part of this debate depends on how mathematics might be able to do explanatory work in an explanation. Everyone agrees that it's not enough that there merely be some mathematics in the explanation. Anti-realists claim there is nothing mathematics can (...) do to make an explanation mathematical ; realists think something can be done, but they are not clear about what that something is. I argue that many of the examples of mathematical explanations of empirical facts in the literature can be accounted for in terms of Jackson and Pettit's [1990] notion of program explanation, and that mathematical realists can use the notion of program explanation to support their realism. This is exactly what has happened in a recent thread of the debate over moral realism. I explain how the two debates are analogous and how moves that have been made in the moral realism debate can be made in the mathematical realism debate. However, I conclude that one can be a mathematical realist without having to be a moral realist. (shrink)

In the period 1875-1920, a debate about the generality and applicability of evolutionary theory to all organisms was motivated by work on unicellular ciliates like Paramecium because of their peculiar nuclear dualism and life cycles. The French cytologist Emile Maupas and the German zoologist August Weismann argued in the 1880s about the evolutionary origins and functions of sex (which in the ciliates is not linked to reproduction), and death (which appeared to be the inevitable fate of lineages denied sexual conjugation), (...) an argument rooted in the question of whether the ciliates and their processes where homologous to other cellular organisms. In the beginning of the twentieth century, this question of homology came to be less important as the ciliates were used by the British protozoologist Clifford Dobell and the American zoologist Herbert Spencer Jennings to study evolutionary processes in general rather than problems of development and cytology. For them, homology mattered less than analogy. This story illustrates two partially distinct problems in evolutionary biology: first, the question of whether all living things have common features and origins; and second, whether their history and current nature can be described by identical mechanisms. Where Maupas (contra Weismann) made the ciliates qualitatively the same as all other organisms in order to create a cohesive evolutionary theory for biology, Jennings and Dobell made them qualitatively different in order to achieve the same end. (shrink)

When natural selection theory was presented, much active philosophical debate, in which Darwin himself participated, centered on its hypothetical nature, its explanatory power, and Darwin's methodology. Upon first examination, Darwin's support of his theory seems to consist of a set of claims pertaining to various aspects of explanatory success. I analyze the support of his method and theory given in the Origin of Species and private correspondence, and conclude that an interpretation focusing on the explanatory strengths of natural selection theory (...) accurately reflects neither Darwin's own self-consciously held views, nor the nature of his support. Darwin's methodological and philosophical arguments were at once consistently empiricist and more sophisticated than such interpretations credit to him. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...) species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

In this paper I distinguish various ways in which empirical claims about evolutionary and ecological models can be supported by data. I describe three basic factors bearing on confirmation of empirical claims: fit of the model to data; independent testing of various aspects of the model, and variety of evident. A brief description of the kinds of confirmation is followed by examples of each kind, drawn from a range of evolutionary and ecological theories. I conclude that the greater complexity and (...) precision of my approach, as compared to, for instance, a Popperian approach, can facilitate detailed analysis and comparison of empirical claims. (shrink)

Comparison of the six editions of the Origin of Species reveals a definite change in Darwin's propounded theory.Although the tone of the statements seems to become more positive in later editions, the change of thought indicates a certain inability of the original theory to stand up to criticism.

Neural circuits linking local operations in the cortex and the basal ganglia confer reiterative capacities, expressed in seemingly unrelated human traits such as speech, syntax, adaptive actions to changing circumstances, dancing, and music. Reiteration allows the formation of a potentially unbounded number of sentences from a finite set of syntactic processes, obviating the need for the hypothetical.

In the title chapter of Did Darwin Write the Origin Backwards?, Sober argues for an asymmetry between facts about genealogy and facts about natural selection, which has the result that evidentially Darwin's book is the wrong way round. Here I make three points about Sober's argument in that chapter. First, it is not clear that Darwin employs what Sober calls 'tree thinking' as frequently as Sober himself suggests. Second, I argue that Darwin's reason for structuring the Origin as he did (...) can be understood if we think of the Origin's argument as an inference to the best explanation. Third, I show circumstances where, even if selection is the only important evolutionary force, we would still be able to infer common ancestry. (shrink)

The view that species are individuals, as developed by Ghiselinand Hull, has been touted as explaining the role of type specimens intaxonomy. The kinship of this explanation with the Kripke-Putnam theoryof names has long been recognized. In light of this kinship, however,Hull's account of type specimens can be seen to entail two relatedinscrutability problems – unreasonable limits placed on the natureand extent of biological knowledge. An appreciation for these problemsinvites us to consider the proper relation between metaphysical andepistemological inquires in (...) the philosophy of science. (shrink)

A. M. Turing has bequeathed us a conceptulary including 'Turing, or Turing-Church, thesis', 'Turing machine', 'universal Turing machine', 'Turing test' and 'Turing structures', plus other unnamed achievements. These include a proof that any formal language adequate to express arithmetic contains undecidable formulas, as well as achievements in computer science, artificial intelligence, mathematics, biology, and cognitive science. Here it is argued that these achievements hang together and have prospered well in the 50 years since Turing's death.

In this study, we investigate, both theoretically and empirically, the impact of language gender marking on gender wage inequality and country income inequality. We find that nations with a higher level of gender marking in their dominant language have a higher wage gap between genders. Using an instrumental variable approach, we also find that gender marking has an indirect impact on country income inequality via gender wage inequality. Furthermore, we find evidence that the income inequality of a society as a (...) whole is affected by gender wage inequality. Finally, we document that linguistic gender marking outperforms survey-based cultural gender dimensions as a predictor of both gender wage inequality and country income inequality. (shrink)

Theologian Benedikt Paul Göcke claimed that ‘as long as we do not have a sound argument entailing the necessity of the world, panentheism is not an attractive alternative to classical theism’ :75). As much of my research considers the alternatives to classical theism, I published a damning reply essay : 389–395). I comprehensively noted the many problems with his notion of ‘panentheism’, finding that it differed greatly from mainstream and earlier Eastern and Western interpretations, had little to do with the (...) etymology of the term and differed only from his concept of theism in that the world is necessary instead of contingent. It is the latter point that led to Göcke’s ‘unattractive’ conclusion, though he had not demonstrated whether the world is contingent or necessary. Göcke responded to my essay : 397–400), and this is my further response, which explains that—and why—my criticisms still stand. (shrink)

In this article I will analyze whether the so-called Extended Evolutionary Synthesis represents a synthesis and an extension with respect to its predecessor, Modern Synthesis. It will be argued that the MS proposes an externalist approach to evolution while the EES considers it necessary to overcome the internalism/externalism dichotomy by proposing more integrative approaches. It will be concluded that the EES cannot be considered an extension of MS and that the appeal to that extension is related to sociological aspects and (...) the epistemic value of theoretical unification that was always present in biological evolutionary thinking. (shrink)

Systems evolve in order to adjust and survive. The paper’s contribution is that this evolvement is inadequate without an evolutionary telos. It is argued that without the presence of self-destruction in multiple levels of our existence and surroundings, our survival would have been impossible. This paper recognises an appreciation of auto-catastrophe at the cell level, in human attitudes (both as an individual and in societies), and extended to Earth and out to galaxies. Auto-Catastrophic Theory combines evolution with auto-catastrophic behaviours and (...) innovative machinery by offering new themes of understanding their merging such as (a) protogenic and deuterogenic auto-catastrophic processes, (b) protogenic and deuterogenic survival processes, and (c) ‘alive’, partially ‘alive’, and non-‘alive’ systems. The value of self-destruction relies on a numerical stability within a system and correlational relationships between systems. Auto-Catastrophic Theory provides novel justifications why artificial intelligence: (a) is crucial to overcome the extinction of humanity (via H+), (b) is crucial to offer indirect survival of humanity (by saving its history), and (c) is at the same time a threat for humanity. These novel justifications and themes, developed by combining evolution with catastrophe as well as innovative machinery, expand our knowledge of how best to handle fresh challenges ahead. (shrink)

Theories of epistemology make reference—via the perspective of an observer—to the structure of information transfer, which generates reality, of which the observer himself forms a part. It can be shown that any epistemological approach which implies the participation of tautological structural elements in the information transfer necessarily leads to an antinomy. Nevertheless, since the time of Aristotle the paradigm of mathematics—and thus tautological structure—has always been a hidden ingredient in the various concepts of knowledge acquisition or general theories of information (...) transfer. We hold that Darwin's Evolutionary Theory is the first scientific theory which consistently presupposes a non-tautological structure for the information transfer and, at the same time, keeps it strictly distinct from the tautological metric of scientific observation. The consequences of this technique—namely the dissociation of information from intentionality—have not yet been fully drawn. Erkenntnistheorien beziehen sich über die Perspektive eines Beobachters auf die Struktur des Informationstransfers, der die Realität erzeugt, von der der Beobachter selbst ein Element ist. Man kann zeigen, dass jeder erkenntnistheoretische Ansatz, der an diesem Transfer von Information tautologische Strukturelemente teilnehmen lässt, zu einer Antinomie führt. Dennoch bilden das Paradigma der Mathematik—und damit tautologische Strukturen—seit Aristoteles einen festen Bestandteil von Erkenntnistheorien und generell von Theorien des Informationstransfers. Unserer These zufolge ist Darwins Evolutionstheorie die erste wissenschaftliche Theorie, die den Informations-transfer ausschließlich als nicht-tautologische Struktur auffasst und diese zugleich strikt von der tautologischen Struktur der Beobachtungsmetrik getrennt hält. Die Konsequenzen für die Erkenntnistheorie—namentlich die Trennung von Information und Intentionalitätsind bisher nicht gezogen worden. (shrink)

The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point (...) for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, “altruistic” shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools. (shrink)

Creatures living under the rule of domestication form a communicative union based on shared morphological, behavioural, cognitive, and immunologicalresemblances. Domestic animals live under particular conditions that substantially differ from the original (natural) settings of their wild relatives. Here we focus on the fact that many parallel characters have appeared in various domestic forms that had been selected for different purposes. These characters are often unique for domestic animals and do not exist in wild forms. We argue that parallel similarities appear (...) in different groups in response to their interaction with theumwelt of a particular host. In zoosemiotic sense, the process of domestication represents a kind of interaction in which both sides are affected and eventuallytransformed in such a way that one is more integrated with the other than in the time of initial encounter. (shrink)

Defining and measuring biodiversity is an important research area in biology, with very interesting theoretical and applied aspects. Numerous definitions have been proposed, and these definitions of biodiversity influence how it is measured. From the still commonly used measure of species diversity, through higher taxon diversity, molecular measures, ecological measures and indicator taxa, these measures have as their fundamental shortcoming the lack of an explicit consideration of the evolutionary context represented by phylogenies. Attempts have been made to incorporate phylogenetic considerations (...) into measuring biodiversity, but more hypothesis‐driven research needs to be done. A specific case study is presented of how this added emphasis on phylogeny‐based biodiversity measurement can influence the way in which research is directed and hypotheses are generated. The elucidation of the relationship of biodiversity to ecosystem functioning is a very timely concern with the unarguable loss of biodiversity this planet is experiencing, whichever way biodiversity is measured. (shrink)

This article describes the phenomenon of knowledge building in online environments. Knowledge building is a process within a community, which leads to the development of knowledge. In order to analyze this process, we will look into the ways in which individuals interact with the collective as a whole. For this purpose, the psychic and social systems, which are involved here are regarded as meaning-based systems in the sense of Luhmann’s systems theory—open to the environment, but operatively closed. The respective modes (...) of operation of psychic and social systems will be examined, and “structural coupling” between these systems described. Another characteristic of knowledge-building communities is self-organization, which is described here in the sense of autopoiesis. A pivotal task, which knowledge-building communities have to tackle, is to handle complexity and reach common understanding. These aspects will also be described using conceptualizations of Luhmann’s systems theory, illustrated by many examples. (shrink)

Catholic evolutionists have proposed to reconcile evolutionary anthropogenesis with Catholic doctrine by suggesting that a created soul could be infused into a body produced by evolution from an animal body. Could such an infusion yield not just a Platonic composite but a being with the unity of substance required by a Thomistic philosophy of nature? How could such a soul be the form of the body into which it was infused? This paper suggests that animals seem to have sense-powers with (...) a level of complexity, if not sufficient to underlie the abstraction of concepts in a being that also has a rational soul, then at least nearly so. The burden of proof lies rather on those who think that evolutionary development of such powers is not possible. In its final section, the paper argues that the existence of Eve as a second, and the only additional, initial rational being does not create special problems for the view here articulated. (shrink)

Are attributions of content and function determinate, or is there no fact of the matter to be fixed? Daniel Dennett has argued in favor of indeterminacy and concludes that, in practice, content and function cannot be fixed. The discovery of an electrical modality in vertebrates offers one concrete instance where attributions of function and content are supported by a strong scientific consensus. A century ago, electroreception was unimagined, whereas today it is widely believed that many species of bony fish, amphibians, (...) sharks, skates, and rays possess this non-human sensory modality. A look at the history of science related to this discovery reveals a highly interdisciplinary endeavor, encompassing ethology, behavioral analysis, neuroscience, and evolutionary biology. While each area provides important evidence, none is sufficient on its own to fix content and function. Instead, I argue that an interdisciplinary, neuroethological approach is required to carry out such determinations. Further, a detailed consideration of biological research suggests that while content and function claims are empirically underdetermined and uncertain, there is insufficient reason to believe in an additional problem of indeterminism. In particular, Dennett's indeterminism arises from a research methodology -- logical adaptationism -- that generates evidence from only one of the areas of neuroethology. However, logical adaptationism does not reflect adaptationism as it is practiced in contemporary biology. I conclude that Dennett is faced with a dilemma: On the one hand, he can hold to logical adaptationism and the indeterminism that results from it, while giving up the relevance of his arguments to biological practice. On the other, he can embrace a more accurate version of adaptationism -- one which plays a role in a larger neuroethological framework -- but from which no strong indeterminacy claims follow. (shrink)

In this article, we extend the Bayesian nonparametric regression method Gaussian Process Regression to the analysis of longitudinal panel data. We call this new approach Gaussian Process Panel Modeling (GPPM). GPPM provides great flexibility because of the large number of models it can represent. It allows classical statistical inference as well as machine learning inspired predictive modeling. GPPM offers frequentist and Bayesian inference without the need to resort to Markov chain Monte Carlo-based approximations, which makes the approach exact and fast. (...) GPPMs are defined using the kernel-language, which can express many traditional modeling approaches for longitudinal data, such as linear structural equation models, multilevel models, or state-space models but also various commonly used machine learning approaches. As a result, GPPM is uniquely able to represent hybrid models combining traditional parametric longitudinal models and nonparametric machine learning models. In the present paper, we introduce GPPM and illustrate its utility through theoretical arguments as well as simulated and empirical data. (shrink)

In view of the confusion about the use of the term ‘population’ in biology, an analysis has been made of the use of the concept of population in biology. Origin and development, logic and epistemology of the population-concept have been investigated for that purpose. It appears that several concepts of population coexist in biology. The term ‘population’ is used for all these concepts, so it is not amazing that confusion has arisen. This confusion is the more dangerous, since ‘population’ plays (...) an important part in the theory of evolution. A modus has been suggested to diminish this confusion by defining ‘population’ in a very wide sense of the term and by proposing a ‘deme’—terminology to specify the various special concepts of population. (shrink)

This paper analyzes the notion of possibility in biology and demonstrates how synthetic biology can provide understanding on the modal dimension of biological systems. Among modal concepts, biological possibility has received surprisingly little explicit treatment in the philosophy of science. The aim of this paper is to argue for the importance of the notion of biological possibility by showing how it provides both a philosophically and biologically fruitful category as well as introducing a new practically grounded way for its assessment. (...) More precisely, we argue that synthetic biology can provide tools to scientifically anchor reasoning about biological possibilities. Two prominent strategies for this are identified and analyzed: the design of functionally new-to-nature systems and the redesign of naturally occurring systems and their parts. These approaches allow synthetic biologists to explore systems that are not normally evolutionarily accessible and draw modal inferences that extend in scope beyond their token realizations. Subsequently, these results in synthetic biology can also be relevant for discussions on evolutionary contingency, providing new methods and insight to the study of various sources of unactualized possibilities in biology. (shrink)

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

Terminology within the biological sciences gets its import not just from semantic meaning, but also from the way it functions within the rhetorics of the various disciplinary practices. The ‘sociobiology’ of human behavior inherits three distinct rhetorics from the genetic disciplines. Sociobiologists use population genetic, biometrical genetic, and molecular genetic rhetorics, without acknowledging the conceptual and experimental constraints that are assumed by geneticists. The eclectic blending of these three rhetorics obscures important differences of context and meaning. Sociobiologists use foundational terms (...) in genetics, such as ‘gene’, ‘fitness’, ‘evolution’, ‘heritability’, ‘trait’ and ‘polygenic inheritance’, in starkly different ways from geneticists, while basing their analysis of human behavior on the implied authority of genetics. As a free‐floating ‘gene talk’ moves across different disciplinary contexts, and before different audiences, it takes the form of an over‐simplified and misleading arch‐determinism. The result is widespread application of vague, incomplete, and distorted biological theory. If most sociobiologists, do not deliberately promote biological determinism, still less a political agenda, there is ample evidence that they misconstrue the implications of the genetic language that they borrow. (shrink)

During the mid-nineteenth century, the eminent British zoologist Alfred Newton recognized that some of the ideas embedded in Origin of Species provided new scientific rationales for the preservation of endangered species. He then embarked on a twenty-five-year-long campaign for law reforms and successfully lobbied Parliament to enact three new statutes for the preservation of endangered wild birds that gave priority to the scientific value of rare species. The account of Newton’s campaign presented in this article helps to locate Newton in (...) the nineteenth century conservation movement, while also shining a side light on the relationship between conservation science and policy-making more generally, including the variety of voices and approaches taken to conservation in the UK and US. Today, as we pursue new regulatory responses to critical environmental issues, such as biodiversity loss and climate change, the history of Newton’s campaign offers an early example of a successful approach to science-based law reform. It also shows how some of the issues that Newton and his contemporaries confronted at the science-policy interface in the nineteenth century are enduring and remain relevant today, including debates about; the role of scientist-advocates in policy-making, the criteria that make science advice effective, and whether the “democratization” of science leads to better policy decisions. (shrink)

Skipper and Millstein analyze natural selection and mechanism, concluding that natural selection is not a mechanism in the sense of the new mechanistic philosophy. Barros disagrees and provides his own account of natural selection as a mechanism. This discussion identifies a missing piece of Barros's account, attempts to fill in that piece, and reconsiders the revised account. Two principal objections are developed: one, the account does not characterize natural selection; two, the account is not mechanistic. Extensive and persistent variability causes (...) both of these difficulties, so further attempts to describe natural selection as a mechanism are also unlikely to succeed. (shrink)

Science is as much defined by the local “instrumentarium,” the equipment available to an experimenter at a particular time and place, as by its discoveries and theories. Instruments are devices for detecting and measuring natural phenomena, linked causally to those aspects of nature they are used to record. Some are inorganic, made of glass and metal, while others are organic, the bodies and body parts of living or once living plants and animals. In contrast, pieces of apparatus are quite different (...) in the ways in which they work. They too can be organic or inorganic, but their role is to model things, process, structures, and so on in the natural world. They are used to study natural processes by simulating them in a user-friendly way. Keeping the distinction between instruments and apparatus in mind is crucial to understanding the power of the experimental method. (shrink)