The neutral theory often is presented as a theory of "noise" or silent changes at an isolated "molecular level", relevant to marking the steady pace of divergence, but not to the origin of biological structure, function, or complexity. Nevertheless, precisely these issues can be addressed in neutral models, such as those elaborated here in regard to scrambled ciliate genes, gRNA-mediated RNA editing, the transition from self-splicing to spliceosomal splicing, and the retention of duplicate genes. All of these are (...) instances of a more general scheme of "constructive neutral evolution" that invokes biased variation, epistatic interactions, and excess capacities to account for a complex series of steps giving rise to novel structures or operations. The directional and constructive outcomes of these models are not due to neutral allele fixations per se, but to these other factors. Neutral models of this type may help to clarify the poorly understood role of non-selective factors in evolutionary innovation and directionality. (shrink)

This paper aims to clarify the relationship between consciousness and attention through theoretical considerations about evolution. Specifically, we will argue that the empirical findings on attention and the basic considerations concerning the evolution of the different forms of attention demonstrate that consciousness and attention must be dissociated regardless of which definition of these terms one uses. To the best of our knowledge, no extant view on the relationship between consciousness and attention has this advantage. Because of this characteristic, (...) this paper presents a principled and neutral way to settle debates concerning the relationship between consciousness and attention, without falling into disputes about the meaning of these terms. A decisive conclusion of this approach is that extreme views on the relationship between consciousness and attention must be rejected, including identity and full dissociation views. There is an overlap between the two within conscious attention, but developing a full understanding of this mechanism requires further empirical investigations. (shrink)

The neutral and nearly neutral theories of molecular evolution are sometimes characterized as theories about drift alone, where drift is described solely as an outcome, rather than a process. We argue, however, that both selection and drift, as causal processes, are integral parts of both theories. However, the nearly neutral theory explicitly recognizes alleles and/or molecular substitutions that, while engaging in weakly selected causal processes, exhibit outcomes thought to be characteristic of random drift. A narrow focus (...) on outcomes obscures the significant role of weakly selected causal processes in the nearly neutral theory. (shrink)

The text examines methodological consequences of anti-metaphysical turn of British empiricism in the field of anthropology. I argue that this shift reinforces anthropology in its descriptive and interdisciplinary form, because destruction of metaphysically grounded subjectivity carried out in the course of evolution of empiricism provides epistemological legitimization of the idea of anthropological research as morally neutral and religiously indifferent procedure. In the final part of the article the difficulties caused by application of this new methodology are emphasized.

As British and American idealism waned, new realisms displaced them. The common background of these new realisms emphasized the problem of the external world and the mind-body problem, as bequeathed by Reid, Hamilton, and Mill. During this same period, academics on both sides of the Atlantic recognized that the natural sciences were making great strides. Responses varied. In the United States, philosophical response focused particularly on functional psychology and Darwinian adaptedness. This article examines differing versions of that response in William (...) James and Roy Wood Sellars. James viewed the mind as a “fighter for ends.” His neutral monism, by taming the mind-body problem and the problem of the external world, provided a secure metaphysics of mind as functional activity. In contrast, Sellars ’s scientific realism endorsed physical reality but was not mechanistic or reductionist. His critical realism and evolutionary naturalism offered novel metaphysical and epistemological positions in comparison with other American and British realisms. James and Sellars are distinguished from British philosophy in 1890–1918 in the types of realism they endorsed and in their success at introducing Darwinian evolutionary considerations and functional psychology into mainstream philosophy. (shrink)

In 1968, Motoo Kimura submitted a note to Nature entitled “Evolutionary Rate at the Molecular Level,” in which he proposed what has since become known as the neutral theory of molecular evolution. This is the view that the majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral or nearly neutral alleles. Kimura was not proposing that random drift explains all evolutionary change. He does not challenge the view that natural (...) selection explains adaptive evolution, or, that the vertebrate eye or the tetrapod limb are products of natural selection. Rather, his objection is to “panselectionism’s intrusion into the realm of molecular evolutionary studies”. According to Kimura, most changes at the molecular level from one generation to the next do not affect the fitness of organisms possessing them. King and Jukes (1969) published an article defending the same view in Science, with the radical title, “Non- Darwinian Evolution,” at which point, “the fat was in the fire” (Crow, 1985b). The neutral theory was one of the most controversial theories in biology in the late twentieth century. This chapter will review the debate over the netural theory subsequent to Kimura. (shrink)

The thesis investigates the implications for moral philosophy of research in psychology. In addition to an introduction and concluding remarks, the thesis consists of four chapters, each exploring various more specific challenges or inputs to moral philosophy from cognitive, social, personality, developmental, and evolutionary psychology. Chapter 1 explores and clarifies the issue of whether or not morality is innate. The chapter’s general conclusion is that evolution has equipped us with a basic suite of emotions that shape our moral judgments (...) in important ways. Chapter 2 presents and investigates the challenge presented to deontological ethics by Joshua Greene’s so-called dual process theory. The chapter partly agrees with his conclusion that the dual process view neutralizes some common criticisms against utilitarianism founded on deontological intuitions, but also points to avenues left to explore for deontologists. Chapter 3 focuses on Katarzyna de Lazari-Radek and Peter Singer’s suggestion that utilitarianism is less vulnerable to so-called evolutionary debunking than other moral theories. The chapter is by and large critical of their attempt. In the final chapter 4, attention is directed at the issue of whether or not social psychology has shown that people lack stable character traits, and hence that the virtue ethical view is premised on false or tenuous assumptions. Though this so-called situationist challenge at one time seemed like a serious threat to virtue ethics, the chapter argues for a moderate position, pointing to the fragility of much of the empirical research invoked to substantiate this challenge while also suggesting revisions to the virtue-ethical view as such. (shrink)

In a first part I present the results of the philosophy of scientific explanation with an attempt to apply them to the case of the theory of evolution. Then I observe that the requirements of modelization of phenomena with the help of inductive logic do not capture efficiently the pertinent factors and fail just as much to exclude those which end up being neutral as explanatory premises. I then query in the direction of confirmation theory, and show that (...) probabilistic reasoning does not possess the syntactic means of testing evolutionary hypotheses in a way that would rely on a valid mode of inference. In a second part, I try to show how biology has oscillated between two privileged modes of explanation, the first one being through form of which I suggest here that it has never been replaced and that it has known a forgotten vitality in the middle and latter part of the 19th Century, and the second one being through function here evaluated critically alongside that of tinkering. Finally, some limits are seen to hold against the pretence to epistemological exclusivism of those two outlooks on the biological object. (shrink)

The theory of evolution of complex and comprising of human systems and algorithm for its constructing are the synthesis of evolutionary epistemology, philosophical anthropology and concrete scientific empirical basis in modern (transdisciplinary) science. «Trans-disciplinary» in the context is interpreted as a completely new epistemological situation, which is fraught with the initiation of a civilizational crisis. Philosophy and ideology of technogenic civilization is based on the possibility of unambiguous demarcation of public value and descriptive scientific discourses (1), and the object (...) and subject of the cognitive process (2). Both of these attributes are no longer valid. For mass, everyday consciousness and institutional philosophical tradition it is intuitively obvious that having the ability to control the evolutionary process, Homo sapiens came close to the borders of their own biological and cultural identity. The spontaneous coevolutionary process of interaction between the «subject» (rational living organisms) and the «object» (material world), is the teleological trend of the movement towards the complete rationalization of the World as It Is, its merger with the World of Due. The stratification of the global evolutionary process into selective and semantic (teleological) coevolutionary and therefore ontologically inseparable components follows. With the entry of anthropogenic civilization into the stage of the information society, firsty, the post-academic phase of the historical evolution of scientific rationality began, the attributes of which are the specific methodology of scientific knowledge, scientific ethos and ontology. Bioethics as a phenomenon of intellectual culture represents a natural philosophical core of modern post- academic (human-dimensional) science, in which the ethical neutrality of scientific theory principle is inapplicable, and elements of public-axiological and scientific-descriptive discourses are integrated into a single logic construction. As result, hermeneutics precedes epistemology not only methodologically, but also meaningfully, and natural philosophy is regaining the status of the backbone of the theory of evolution – in an explicit form. (shrink)

We are fallible creatures, prone to making all sorts of mistakes. So, we should be open to evidence of error. But what constitutes such evidence? And what is it to rationally accommodate it? I approach these questions by considering an evolutionary debunking argument according to which (a) we have good, scientific, reason to think our moral beliefs are mistaken, and (b) rationally accommodating this requires revising our confidence in, or altogether abandoning the suspect beliefs. I present a dilemma for such (...) debunkers, which shows that either we have no reason to worry about our moral beliefs, or we do but we can self-correct. Either way, moral skepticism doesn’t follow. That the evolutionary debunking argument fails is important; also important, however, is what its failure reveals about rational belief revision. Specifically, it suggests that getting evidence of error is a non-trivial endeavor and that we cannot learn that we are likely to be mistaken about some matter from a neutral stance on that matter. (shrink)

This paper explores the relationship between technological and human intelligence through ‘The New Natural’, a term which at once accepts the nature of technological intelligence as real instead of forever ‘artificial’. It supports an evolutionary, reciprocal relationship between humans and technology that culminates in technological singularity and rejects the primacy of human perception known to popular human access theories, before seriously considering the ‘decentered’ implications of posthuman access. In conversation with western-centric sci-fi film of the late twentieth century, then, this (...) philosophical study explores how the concept of a technology-only intelligence entity can: (1) help us dispose of the core problems often associated with human-only access, (2) neutral-ize our fears of human annihilation at the hands of technological intelligence, and (3) establish strong grounds for why we may have to push back against early conceptions of nature’s opposition to technology, if only so we may resist falling into the great, and most human-centered traps known to the Anthropocene. (shrink)

The idea that mind and body are distinct entities that interact is often claimed to be incompatible with physics. The aim of this paper is to disprove this claim. To this end, we construct a broad mathematical framework that describes theories with mind-body interaction (MBI) as an extension of current physical theories. We employ histories theory, i.e., a formulation of physical theories in which a physical system is described in terms of (i) a set of propositions about possible evolutions of (...) the system and (ii) a probability assignment to such propositions. The notion of dynamics is incorporated into the probability rule. As this formulation emphasises logical and probabilistic concepts, it is ontologically neutral. It can be used to describe mental `degrees of freedom' in addition to physical ones. This results into a mathematical framework for psycho-physical interaction (ΨΦI formalism). Interestingly, a class of ΨΦI theories turns out to be compatible with energy conservation. (shrink)

Most philosophical accounts on scientific theories are affected by three dogmas or ingrained attitudes. These dogmas have led philosophers to choose between analyzing the internal structure of theories or their historical evolution. In this paper, I turn these three dogmas upside down. I argue (i) that mathematical practices are not epistemically neutral, (ii) that the morphology of theories can be very complex, and (iii) that one should view theoretical knowledge as the combination of internal factors and their intrinsic (...) historicity. (shrink)

Through Heidegger’s re-reading of Descartes, this article explores a fundamental issue in the contemporary conception of worldliness. In a restricted sense, the human being is the maker of the world in that he appropriates what composes it, i.e., the worldly beings or things. Greatly influenced by the Cartesian notion of extensio, this tendency no longer entails the world as a thing in itself, but as a set of measurable things, thus available and open to activity. This article articulates the threat (...) relative to the idea of the forming, by the human being, of the essence of the world. Every being, be it an object, an animal or even a human being, seems to be considered as a producer of energy and a structure that could be possessed. For example, such natural space is not campaign or land, but automatically field, that is to say, an agricultural deposit that is symbolically exploited and empirically exploitable. This ontological device prevents us from grasping the world in any other way than in terms of use and productivity. As a result, the ontology of the thing becomes an aesthetic issue in its own right. This issue does not involve here the capture of the object as a bearer of Beauty, but an aesthetic relation in the fundamentally etymological sense (αἰσθητικός) of what is felt, of what is sensible and perceptible. The need for an aesthetic rereading of the world and the things that stand in it presupposes, therefore, the evolution of the human gaze and a metaphysical approach to worldliness, detached from the instrumentalization of the beings and focused on their presence or their proximity. This article aims at demonstrating the necessity of a real human aesthetic responsibility, which can be concretized in the metaphysical thought of the thing that the human being unfolds, by considering it as the persistence in the world of an object whose ontological disposition could never be neutral. (shrink)

The Upanishads reveal that in the beginning, nothing existed: “This was but non-existence in the beginning. That became existence. That became ready to be manifest”. (Chandogya Upanishad 3.15.1) The creation began from this state of non-existence or nonduality, a state comparable to (0). One can add any number of zeros to (0), but there will be nothing except a big (0) because (0) is a neutral number. If we take (0) as Nirguna Brahman (God without any form and attributes), (...) then from where and how did the universe come into existence? -/- The neutral power (0) cannot produce anything without having an element of duality in it. Although Nirguna Brahman is neutral, it has a positive, negative, and neutral pole, constituting its Prakriti or nature. Prakriti has three latent Gunas (modes or qualities): Satva, Rajas, and Tamas. They are related to Gyana Shakti (the power of knowledge) Sankalpa Shakti (the power of ideation), and Kriya Shakti (the power of action). Science says that Atom is the basic element from which the universe evolved. The Atom has three nuclei- electron, pluton, and neutron. The Satva, Rajas, and Tamas in Indian spirituality are nothing but the mystical names for the nuclei of an atom. -/- According to Bhagavata Purana, Prakriti is also constituted of the elements of Time, Karma (action/destiny) and Swabhava (innate nature). Time disturbs the equilibrium of Gunas. From the aspect of Karma is produced an entity called Mahat, in the form of intelligence. Mahat is dominated by Satva and Rajas. From Mahat manifests the next evolute dominated by Tamas with three predominant qualities – Dravya (substance), Kriya (action), as well as intelligence. It forms to become the Ego principle (Ahamkara). -/- Ahamkara has three modes – Satvic, Rajasic and Tamasic. Satvic is Jnana oriented, Rajasic action-oriented and Tamasic Dravya (substance) oriented. From the Tamasic Ahankara, five gross elements are produced (ether, air, fire, water, and earth - Akash, Vayu, Agni, Jal and Prithvi). From the Satvic Ahamkara, guardian deities (the sun and moon, deities of sense organs, and organs of action) and from Rajasic Ahamkara, ten senses (Indriyas), five senses of perception, five organs of action, the faculties of intellect and Prana (life breath) are produced. -/- Bhagavata says that since these energies, elements, and faculties remained disassociated, they were combined to form a Cosmic Egg. The egg floats in the primal waters for a thousand years. Then God enters this Cosmic Egg and manifests himself as the Cosmic Purusha. He is the first nucleus, the God particle equivalent to the number (1) which is the embodiment of everything in the universe. The concept of creation and dissolution in Hinduism can be compared to the waves in an ocean that appear and disappear incessantly. The Manvantaras are such successive episodes of creation emerging from the Cosmic Person, the Manu who is embodied God-Consciousness, God himself. These episodes of creation are measured in Hinduism in terms of Manvantaras, the epochs of Manus. -/- Manu is the ‘First-Born’ (1) of God, the Cosmic Purusha from whom the world has originated. This Cosmic Person (Purusha) has been described as having fourteen biospheres (heavens) that are inhabited by various life forms in the order of evolution of consciousness. If we begin from the human biosphere (Bhuloka), there are ten astral biospheres that a man must transcend to attain liberation or Mukti from the cycle of births and deaths. -/- The number (1) produces the primary numbers up to (9) through the transmutation of the creational energies and qualities. The process can be related to the descent and cyclical evolution of (1) through ten spiritual stages, finally merging with the nondual (0). The number (10) marks the merger of (1) with (0). The Hindu worldview is that all life forms in an episode of creation must evolve to become one with the non-dual state (0) to attain liberation from the cycle of births and deaths in a cyclical process. -/- . (shrink)

Central conceptual terms, such as ‘culture’, ‘environment’, ‘nature’ and‘landscape’, are far from being neutral scientific objects. They are academic constructions which need to be understood in their emergence across their historic contexts. -/- Moral it is a cultural expression determined by social dominance and historical context, who gives them a sectary character. We need a moral theory that can be universal, trans-temporal and available to light human individual conduct and the human science and their political ideologies, but not considering (...) the man in the zenith of the Life. The Life, with their biodiversity it is in the pinnacle of the complex cosmos evolution but we don’t know if our specie, born in the Earth, is the end of cosmos evolution. For demanding that answer, was born a new ethical perspective, theory built with the meta-ethics principles and applicable to all human activities. -/- Environmental ethics supported by the two principles_ the critical against anthropocentrism and the critical against ethnocentrism, gives a universal answer to the macro moral problems of our era_ environmental, social, economical and political crises, war and mass destructive weapons…and contributes to rebuilt the human activities in all domains of individual and social life; that’s is the cultural landscape, for instance. (shrink)

Menas is a term that has attracted a great deal of attention on the political scene in Spain at present. Although the term had a neutral usage originally, being an acronym for unaccompanied foreign minors, it has recently evolved into a term with clear negative connotations. This article explores what kind of term menas is today. Specifically, we will examine whether menas is a slur or an ESTI, an ethnic/social term used as an insult. First, we point out the (...) most defining characteristics of both types of terms. Then, using analyses on linguistic corpora, we show that menas exhibits the most defining characteristics of ESTIs. We end by discussing the possible evolution of the term, pointing out that, although the term presents the features related to ESTIs, there are two possible scenarios. On the one hand, the term may retain its neutral uses and thus remain an ESTI. On the other hand, the neutral uses may disappear, and thus the term may become a slur. (shrink)

The body is a highly complex, coordinated system engaged in coping with many environmental problems. It can be considered as some sort of opportunity or obstacle, with which internal processing must deal. Internal processing must take into account the possibilities and limitations of the particular body. In other words, even if the body is not involved in the realization of some cognitive explicit task, it is not a neutral factor of our understanding of why a system solves a task (...) in one way or another. Therefore, when conducting research on embodiment and the body’s cognitive system we should not neglect internal, cognitive processing. I appeal to Goldman’s research on embodied cognition to sketch the broader framework for internal processing in embodied cognition. I believe that even if we don’t accept Goldman’s approach as the viable proposal for embodied cognition in general, it’s a quite natural starting point for our analysis. Goldman (2012; 2014, and with de Vignemont 2009) argue for the essential role of the bodily formats or bodily codes (respectively: B-formats and B-codes) in embodied cognition. B-codes are here described as the processing of regions or sub-regions of the central nervous system. They are primarily employed for body control or monitoring, and reused for cognitive tasks. Beyond doubt, this conception provides an excellent starting point for analyzing the internal (mostly neural) processing in cases of embodied cognition. At the end of this paper, I will argue that the embodiment of cognition needs a conceptual twist. Following Keijzer’s (2015) interest in the evolution of the nervous system, and the minimal forms of cognition, I argue that in investigating embodied cognition, we should investigate the role played by cognitive processing for specific kinds of organisms, meaning organisms with a body of a particular morphology (size, shape, kinds, and distribution of sensors and effectors). Doing that, I refer to some conceptual and empirical considerations. I will also try to show that research on embodied cognition is still not sufficiently anchored in evolutionary and comparative studies on cognition, nor on the nervous system and body morphology. Bigger reliance on these kinds of studies, will make it make possible to gain a deeper understanding of internal processing in embodied cognition. (shrink)

Neutrosophic Genetics is the study of genetics using neutrosophic logic, set, probability, statistics, measure and other neutrosophic tools and procedures. In this paper, based on the Neutrosophic Theory of Evolution (that includes degrees of Evolution, Neutrality (or Indeterminacy), and Involution) – as extension of Darwin’s Theory of Evolution, we show the applicability of neutrosophy in genetics, and we present within the frame of neutrosophic genetics the following concepts: neutrosophic mutation, neutrosophic speciation, and neutrosophic coevolution.

Three distinct turning points (“bottleneck breakings”) in universal evolution are discussed at some length in terms of “self-reference” and (corresponding) “Reality Principles.” The first (origin and evolution of animate Nature) and second (human consciousness) are shown to necessarily precede a third one, that of Marxist philosophy. It is pointed out that while the previous two could occupy a natural (so in a sense neutral) place as parts of human science, the self-reference of Marxism, as a _social_ human (...) phenomenon, through its direct bearings on the _practice_ of society, did have a stormy history. I conclude that the fall of Bolshevism was unavoidable, and still, we might uphold our hope for a truly free society of humankind, just on the very basis of what we have learned of the fate of Marxist philosophy as such, as a _recursively evolving_ social _practice_: the freedom of humankind of its own ideological burdens (constraints). (shrink)

The new phase of science evolution is characterized by totality of subject and object of cognition and technology (high-hume). As a result, forming of network structure in a disciplinary matrix modern are «human dimensional» natural sciences and two paradigmal «nuclei» (attraktors). As a result, the complication of structure of disciplinary matrix and forming a few paradigm nuclei in modern «human dimensional» natural sciences are observed. In the process of social verification integration of scientific theories into the existent system of (...) mental and valued options of spiritual culture takes place. The attribute of classical science – ethics neutrality of scientific knowledge becomes an unattainable ideal. One of the trends in the evolution of theoretical epistemology is the study of migration mechanisms of generation of scientific knowledge from the sphere of its own logic and methodology of science in the field of sociology - the consideration of this process, as the resulting system of interactions of social structures and institutions. Ensuing ideas and settings become the dominant worldview of philosophical and technological civilization. -/- . (shrink)

The new phase of science evolution is characterized by totality of subject and object of cognition and technology (high-hume). As a result, forming of network structure in a disciplinary matrix modern are «human dimensional» natural sciences and two paradigmal «nuclei» (attraktors). As a result, the complication of structure of disciplinary matrix and forming a few paradigm nuclei in modern «human dimensional» natural sciences are observed. In the process of social verification integration of scientific theories into the existent system of (...) mental and valued options of spiritual culture takes place. The attribute of classical science – ethics neutrality of scientific knowledge becomes an unattainable ideal. One of the trends in the evolution of theoretical epistemology is the study of migration mechanisms of generation of scientific knowledge from the sphere of its own logic and methodology of science in the field of sociology - the consideration of this process, as the resulting system of interactions of social structures and institutions. Ensuing ideas and settings become the dominant worldview of philosophical and technological civilization. -/- . (shrink)

The appearance of consciousness in the universe remains one of the major mysteries unsolved by science or philosophy. Absent an agreed-upon definition of consciousness or even a convenient system to test theories of consciousness, a confusing heterogeneity of theories proliferate. In pursuit of clarifying this complicated discourse, we here interpret various frameworks for the scientific and philosophical study of consciousness through the lens of social insect evolutionary biology. To do so, we first discuss the notion of a forward test versus (...) a reverse test, analogous to the normal and revolutionary phases of the scientific process. Contemporary theories of consciousness are forward tests for consciousness, in that they strive to become a means to classify the level of consciousness of arbitrary states and systems. Yet no such theory of consciousness has earned sufficient confidence such that it might be actually used as a forward test in ambiguous settings. What is needed now is thus a legitimate reverse test for theories of consciousness, to provide internal and external calibration of different frameworks. A reverse test for consciousness would ideally look like a method for referencing theories of consciousness to a tractable model system. We introduce the Ant Colony Test as a rigorous reverse test for consciousness. We show that social insect colonies, though disaggregated collectives, fulfill many of the prerequisites for conscious awareness met by humans and honey bee workers. A long lineage of philosophically-neutral neurobehavioral, evolutionary, and ecological studies on social insect colonies can thus be redeployed for the study of consciousness in general. We suggest that the ACT can provide insight into the nature of consciousness, and highlight the ant colony as a model system for ethically performing clarifying experiments about consciousness. (shrink)

Contemporary biology has inherited two key assumptions from the Modern Synthesis about the nature of population lineages: sexual reproduction is the exemplar for how individuals in population lineages inherit traits from their parents, and random mating is the exemplar for reproductive interaction. While these assumptions have been extremely fruitful for a number of fields, such as population genetics and phylogenetics, they are increasingly unviable for studying the full diversity and evolution of life. I introduce the “mixture” account of population (...) lineages that escapes these assumptions by dissolving the Modern Synthesis’s sharp line separating reproduction and development and characterizing reproductive integration in population lineages by the ephemerality of isolated subgroups rather than random mating. The mixture account provides a single criterion for reproductive integration that accommodates both sexual and asexual reproduction, unifying their treatment under Kevin de Queiroz’s generalized lineage concept of species. The account also provides a new basis for empirically assessing the effect of random mating as an idealization on the empirical adequacy of population genetic models. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a (...) post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

L’humanité est devenue facteur d’évolution au niveau planétaire. En complexifiant toujours plus les modalités de ses relations avec l’environnement, elle pense trouver dans la science l’outil principal de son développement et en définitive de sa survie. La science, en effet, est un système d’acquisition de connaissances qui génère une interprétation systématique et rationnelle du monde naturel ethumain, jamais définitive et en renouvellement continu. En tant qu’explication rationnelle des phénomènes naturels et sociaux, elle nous permet de raffiner sans cesse la compréhension (...) de notre place et notre rôle dans le monde. Au vu des enjeux inhérents à l’exploitation des acquis scientifiques et de leurs conséquences sur la vie des populations humaines et sur les équilibres biosphériques, continuer à imaginer que les scientifiques vivent isolés dans une sorte de tour d’ivoire de la connaissance, éloignée de l’agitationde la πόλις, signifie ignorer que la responsabilité sociale est consubstantielle à l’activité de la science. Un scientifique ne vit pas dans un vacuum social, il est porteur de valeurs sociales dans la sphère scientifique. En même temps, il véhicule dans la sphère sociale des valeurs qui découlent de son activité. Si, d’une part, son rôle est celui de développer des connaissances qui soient à la fin du processus d’enquête scientifique exemptes de la marque de la subjectivité, d’autre part, pendant ce processus les valeurs s’affrontent en laissant le dernier mot aux tests expérimentaux et observationnels propres à la méthode scientifique. En dernière analyse, ce sera la réalité phénoménologique qui tranchera vis-à-vis des multiples modèles et constructions épistémiques, plus ou moins imprégnés de valeurs, soumis par l’ensemble de la communauté scientifique. La Conférence générale de l’Organisation des Nations-Unies pour l’éducation, la science et la culture (UNESCO), réunie à Paris en 1974, a adopté la Recommandation concernant la condition des chercheurs scientifiques, où ont été définis normes et principes pouvant servir de guide pour optimiser l’activité de recherche et les conditions de sa mise en place. Au vu de la complexité toujours croissante des relations entre la science et la société, la Commission nationale française pour l’UNESCO (CNFU) a été consultée sur la mise à jour de la Recommandation en focalisant son attention sur la question de la responsabilité morale des scientifiques dans l’exercice de leur profession. (shrink)

Neutral monism is a position in metaphysics defended by Mach, James, and Russell in the early twentieth century. It holds that minds and physical objects are essentially two different orderings of the same underlying neutral elements of nature. This paper sets out some of the central concepts, theses and the historical background of ideas that inform this doctrine of elements. The discussion begins with the classic neutral monism of Mach, James, and Russell in the first part of (...) the paper, then considers recent neo-Russellian versions in the second half. The chances for a revival of neutral monism are probably slight; its key ideas and starting points lie far from those in contemporary philosophy of mind. A better route might be through the philosophy of science and a deeper understanding of causation. (shrink)

Some philosophers think that life is worth living not merely because of the goods and the bads within it, but also because life itself is good. I explain how this idea can be formalized by associating each version of such of a view with a function from length of life to the value generated by life itself. Then I argue that every version of the view that life itself is good faces some version of the following dilemma: either (1) good (...) human lives are worse than very long lives wholly devoid of pleasure, desire-satisfaction, knowledge, or any other goods, or (2) very short lives containing nothing but suffering are worth living. Since neither result is plausible, we ought to reject the view that life itself is good. On the view I favor, any given life may be worth living because of the goods that it contains, but life itself is neutral. (shrink)

According to the “Textbook View,” there is an extensional dispute between consequentialists and deontologists, in virtue of the fact that only the latter defend “agent-relative” principles—principles that require an agent to have a special concern with making sure that she does not perform certain types of action. I argue that, contra the Textbook View, there are agent-neutral versions of deontology. I also argue that there need be no extensional disagreement between the deontologist and consequentialist, as characterized by the Textbook (...) View. (shrink)

(Winner of The Res Publica Essay Prize) This article defends a moderate version of state perfectionism by using Gerald Gaus’s argument for liberal neutrality as a starting point of discussion. Many liberal neutralists reject perfectionism on the grounds of respect for persons, but Gaus has explained more clearly than most neutralists how respect for persons justifies neutrality. Against neutralists, I first argue that the state may promote the good life by appealing to what can be called “the qualified judgments about (...) the good life,” which have not been considered by liberal perfectionists including Joseph Chan and Steven Wall. Then I clear up several possible misunderstandings of these judgments, and argue that: (a) moderate perfectionism does not rely on controversial rankings of values and is committed to promoting different valuable ways of life by pluralistic promotion; and (b) moderate perfectionism requires only an indirect form of coercion in using tax money to support certain moderate perfectionist measures, which is justifiable on the grounds of citizens’ welfare. Thus, I maintain that moderate perfectionism does not disrespect citizens, and is not necessarily unfair to any particular group of people. It is, in fact, plausible and morally important. The defence of moderate perfectionism has practical implications for the state’s policies regarding art development, drug abuse, public education, and so on. (shrink)

I defend the idea that a liberal commitment to value neutrality is best honoured by maintaining a pure cardinality component in our rankings of opportunity or liberty sets. I consider two challenges to this idea. The first holds that cardinality rankings are unnecessary for neutrality, because what is valuable about a set of liberties from a liberal point of view is not its size but rather its variety. The second holds that pure cardinality metrics are insufficient for neutrality, because liberties (...) cannot be individuated into countable entities without presupposing some relevantly partisan evaluative perspective. I argue that a clear understanding of the liberal basis for valuing liberty shows the way to satisfying responses to both challenges. (shrink)

Recent pragmatic accounts of slurs argue that the offensiveness of slurs is generated by a speaker's free choice to use a slur opposed to a more appropriate and semantically equivalent neutral counterpart. I argue that the theoretical role of neutral counterparts on such views is overstated. I consider two recent pragmatic analyses, Bolinger (Noûs, 51, 2017, 439) and Nunberg (New work on speech acts, Oxford University Press, 2018), which rely heavily upon the optionality of slurs, namely, that a (...) speaker exercises a deliberate lexical choice to use a slur when they could have easily used a neutral counterpart instead. Against such views, I argue that across a range of different offensive uses of slurs, a speaker's choice to use a slur opposed to a neutral counterpart plays little to no role in accounting for why the slur generates offence. Such cases cast serious doubt upon the explanatory depth of these pragmatic analyses, and raise more general concerns for views which draw upon the relationship between a slur and its neutral counterpart. The main upshot is this: theorists should exercise caution in assuming that neutral counterparts play any fundamental or systemic role in explaining why slurs are offensive. (shrink)

Epistemologists often claim that in addition to belief and disbelief there is a third, neutral, doxastic attitude. Various terms are used: ‘suspending judgment’, ‘withholding’, ‘agnosticism’. It is also common to claim that the factors relevant to the justification of these attitudes are epistemic in the narrow sense of being factors that bear on the strength or weakness of one’s epistemic position with respect to the target proposition. This paper addresses two challenges to such traditionalism about doxastic attitudes. The first (...) concerns the relevance of non-epistemic factors we might call "future-comparative" – e.g., that you’ll have more decisive evidence on whether p tomorrow – to the justification of suspending judgment. The second, from Jane Friedman, is to explain the point of the neutral attitude without appealing to inquiry and thus taking goal-related factors, which are not epistemic, such as the value of the goal or the prospects for finding means to achieve it, to bear on the justification of the neutral attitude. My defense of traditionalism relies on distinguishing three ways of being neutral on a question: agnosticism, inquiry and suspension of judgment. Traditionalism is saved because, of these, agnosticism alone is a genuine doxastic attitude. (shrink)

According to the Value-Neutrality Thesis, technology is morally and politically neutral, neither good nor bad. A knife may be put to bad use to murder an innocent person or to good use to peel an apple for a starving person, but the knife itself is a mere instrument, not a proper subject for moral or political evaluation. While contemporary philosophers of technology widely reject the VNT, it remains unclear whether claims about values in technology are just a figure of (...) speech or nontrivial empirical claims with genuine factual content and real-world implications. This paper provides the missing argument. I argue that by virtue of their material properties, technological artifacts are part of the normative order rather than external to it. I illustrate how values can be empirically identified in technology. The reason why value-talk is not trivial or metaphorical is that due to the endurance and longevity of technological artifacts, values embedded in them have long-term implications that surpass their designers and builders. I further argue that taking sides in this debate has real-world implications in the form of moral constraints on the development of technology. (shrink)

Despite the widespread presence of public arts funding in liberal societies, some liberals find it unjustified. According to the Neutrality Objection, arts funding preferences some ways of life. One way to motivate this challenge is to say that a public goods-styled justification, although it could relieve arts funding of these worries of partiality, cannot be argued for coherently or is, in the end, too susceptible to impressions of partiality. I argue that diversity-based arts funding can overcome this challenge, because it (...) invests in non-excludable infrastructure that fosters cultural literacy. We all have some interest as citizens in living in a society which fosters cultural literacy, seeing as this helps others to understand us, supports us to understand ourselves, and helps alleviate confusion and alienation we feel toward social difference. While some of these benefits can be enjoyed by those who make and consume art, they are also gained by those who don’t, because arts funding affects the makeup of public spaces and the communicative practices we all use to make sense of the world. (shrink)

It is commonly held that all deontological moral theories are agent-relative in the sense that they give each agent a special concern that she does not perform acts of a certain type rather than a general concern with the actions of all agents. Recently, Tom Dougherty has challenged this orthodoxy by arguing that agent-neutral deontology is possible. In this article I counter Dougherty's arguments and show that agent-neutral deontology is not possible.

The study of cultural evolution has taken on an increasingly interdisciplinary and diverse approach in explicating phenomena of cultural transmission and adoptions. Inspired by this computational movement, this study uses Bayesian networks analysis, combining both the frequentist and the Hamiltonian Markov chain Monte Carlo (MCMC) approach, to investigate the highly representative elements in the cultural evolution of a Vietnamese city’s architecture in the early 20th century. With a focus on the façade design of 68 old houses in Hanoi’s (...) Old Quarter (based on 78 data lines extracted from 248 photos), the study argues that it is plausible to look at the aesthetics, architecture, and designs of the house façade to find traces of cultural evolution in Vietnam, which went through more than six decades of French colonization and centuries of sociocultural influence from China. The in-depth technical analysis, though refuting the presumed model on the probabilistic dependency among the variables, yields several results, the most notable of which is the strong influence of Buddhism over the decorations of the house façade. Particularly, in the top 5 networks with the best Bayesian Information Criterion (BIC) scores and p<0.05, the variable for decorations (DC) always has a direct probabilistic dependency on the variable B for Buddhism. The paper then checks the robustness of these models using Hamiltonian MCMC method and find the posterior distributions of the models’ coefficients all satisfy the technical requirement. Finally, this study suggests integrating Bayesian statistics in the social sciences in general and for the study of cultural evolution and architectural transformation in particular. (shrink)

In Beyond Neutrality, George Sher criticises the idea that state neutrality between competing conceptions of the good helps protect society from oppression. While he is correct that some governments are non-neutral without being oppressive, I argue that those governments may be neutral at the core of their foundations. The possibility of non-neutrality leading to oppression is further explored; some conceptions of the good would favour oppression while others would not. While it is possible that a non-neutral state (...) may avoid oppression, it is argued that the risks are so great that it is better to bet on government being neutral, thereby minimizing the possibility of oppression. (shrink)

Ecological neutral theory has been controversial as an alternative to niche theory for explaining community structure. Neutral theory, which explains community structure in terms of ecological drift, is frequently charged with being unrealistic, but commentators have usually not provided an account of theory or model realism. In this paper, I propose a framework for comparing the “realism” or accuracy of alternative theories within a domain with respect to the extent to which the theories abstract and idealize. Using this (...) framework I argue, contrary to most previous commentators, that neutral and niche theories are similarly realistic. Realism cannot provide a basis for accepting or rejecting either type of theory; instead, community ecologists should continue working with a plurality of models. While theoretical unification may become possible, we should treat a plurality of complementary, partial models as the expected situation within community ecology. (shrink)

An idea that has attracted a lot of attention lately is the thought that consequentialism is a theory characterized basically by its agent neutrality.1 The idea, however, has also met with skepticism. In particular, it has been argued that agent neutrality cannot be what separates consequentialism from other types of theories of reasons for action, since there can be agent-neutral non-consequentialist theories as well as agent-relative consequentialist theories. I will argue in this paper that this last claim is false. (...) The paper is divided into four sections. Section one specifies two senses in which consequentialism is agent-neutral. Section two and three examine and reject, respectively, the claim that there are agent-relative consequentialist views as well as agent-neutral non-consequentialist views. I end the paper with some remarks on the plausibility, or better, the implausibility of characterizing consequentialism in terms other than agent neutrality. (shrink)

Abstract. The neutral monism suggested by Constantin Rădulescu-Motru was a theoretical frame intended to match the general idea of Kant’s apriorism with the results reached by physics and psychology at the beginning of the 20th Key words: transcendental aesthetic; consciousness in general; empirical consciousness; psychophysical parallelism; phenomenal ontology; scientistic ontology.

The creation-evolution “controversy” has been with us for more than a century. Here I argue that merely teaching more science will probably not improve the situation; we need to understand the controversy as part of a broader problem with public acceptance of pseudoscience, and respond by teaching how science works as a method. Critical thinking is difficult to teach, but educators can rely on increasing evidence from neurobiology about how the brain learns, or fails to.

The ecologist today finds scarce ground safe from controversy. Decisions must be made about what combination of data, goals, methods, and theories offers them the foundations and tools they need to construct and defend their research. When push comes to shove, ecologists often turn to philosophy to justify why it is their approach that is scientific. Karl Popper’s image of science as bold conjectures and heroic refutations is routinely enlisted to justify testing hypotheses over merely confirming them. One of the (...) most controversial theories in contemporary science is the Neutral Theory of Ecology. Its chief developer and proponent, Stephen Hubbell, presents the neutral theory as a bold conjecture that has so far escaped refutation. Critics of the neutral theory claim that it already stands refuted, despite what the dogmatic neutralists say. We see the controversy through a Popperian lens. But Popper’s is an impoverished philosophy of science that distorts contemporary ecology. -/- The controversy surrounding the neutral theory actually rests on a methodological fault. There is a strong but messy historical link between the concepts of being neutral and being null in biology, and Hubbell perpetuates this when he claims that the neutral theory is supplies the appropriate null for testing alternative theories. What method is being followed here? There are three contenders: -/- Null hypothesis testing tests for whether a there is a pattern to be explained. Null modeling tests for whether a process is causally relevant to a pattern. Baseline modeling apportions relative responsibility to multiple processes each relevant to a pattern. -/- Whether the neutral theory supplies an appropriate “null” depends upon whether null hypothesis, null modeling, or baseline model is intended. These methods prescribe distinct inference patterns. If they are null hypothesis testing or null modeling, the neutralists’s reasoning is invalid. If they are baseline modeling, the justification of a crucial assumption remains opaque. Either way, the neutral-null connection is being exploited rhetorically to privilege the neutral theory over its rivals. Clarifying the reasoning immunizes us against the rhetoric and foregrounds the underlying virtues of the neutralist approach to ecology. -/- The Popperian lens distorts theoretical development as dogmatism. Lakatos’s view of science as the development of research programmes clarifies the epistemology of the neutral theory. Focusing philosophical attention on the neutralist research programme illuminates (1) the synchronic uses of the neutral theory to make predictions and give descriptions and explanations; (2) its diachronic development in response to theoretical innovation and confrontation with data; (3) its complex relationships to alternative theories. For example, baseline modeling is now seen to be its primary explanatory heuristic. The justification for baseline modeling with the neutral theory, previously hidden from view, is seen in the logic of in the neutralist research programme. (shrink)

Algorithms wield increasing control over our lives—over the jobs we get, the loans we're granted, the information we see online. Algorithms can and often do wield their power in a biased way, and much work has been devoted to algorithmic bias. In contrast, algorithmic neutrality has been largely neglected. I investigate algorithmic neutrality, tackling three questions: What is algorithmic neutrality? Is it possible? And when we have it in mind, what can we learn about algorithmic bias?

I argue that traditional views on which beliefs are subject only to purely epistemic assessment can reject demographic profiling, even when based on seemingly robust evidence. This is because the moral failures involved in demographic profiling can be located in the decision not to suspend judgment, rather than supposing that beliefs themselves are a locus of moral evaluation. A key moral reason to suspend judgment when faced with adverse demographic evidence is to promote social equality—this explains why positive profiling is (...) dubious, along with more familiar cases of negative profiling, and why profiling is suspect even when no particular action is at stake. My suspension-based view, while compatible with revisionary normative positions, does not presuppose them. Philosophers of all stripes can reject demographic profiling both in thought and deed. (shrink)

Die Beziehung der Entwicklung des Lebens im Weltall - von den einfachsten Formen bis zu Leben mit Geist und Bewusstsein – zu der Physik, wie wir sie aus der unbelebten Natur kennen, ist Thema dieses Essays. Ist die Entstehung des Lebens Zufall, ist es Folge einer physikalischen Logik, die noch zu entdecken ist, oder ist „Lebensfreundlichkeit“ ein eigenes Prinzip des Naturgeschehens, das zum Beispiel offene Naturkonstanten der physikalischen Gesetze festlegt, zu denen die geheimnisvollen Grossen Zahlen der Kosmologie gehören – „The (...) Lore of Large Numbers…“? Wissenschaftlich bleibt diese Frage nicht eindeutig zu klären; intuitiv wird das „Prinzip lebensfreundlich“ der menschlichen Evolution wohl am ehesten gerecht. Dabei ist „lebensfreundlich“ in diesem Artikel nicht psychologisch im Sinne menschlicher Beziehungen gemeint, sondern eine Art Kurzbezeichnung für eine Physik, die im Kosmos irgendwann und irgendwo Leben, auch menschliches Leben mit Geist und Bewusstsein ermöglicht. Der Artikel ergänzt auch Texte des Autors über Physik und Bewusstsein, um physikalische und anthropologische Aspekte der Kosmologie (unter philpapers im Volltext). (shrink)

The extent to which normal (nonmalignant) cells of the body can evolve through mutation and selection during the lifetime of the organism has been a major unresolved issue in evolutionary and developmental studies. On the one hand, stable multicellular individuality seems to depend on genetic homogeneity and suppression of evolutionary conflicts at the cellular level. On the other hand, the example of clonal selection of lymphocytes indicates that certain forms of somatic mutation and selection are concordant with the organism-level fitness. (...) Recent DNA sequencing and tissue physiology studies suggest that in addition to adaptive immune cells also neurons, epithelial cells, epidermal cells, hematopoietic stem cells and functional cells in solid bodily organs are subject to evolutionary forces during the lifetime of an organism. Here we refer to these recent studies and suggest that the expanding list of somatically evolving cells modifies idealized views of biological individuals as radically different from collectives. (shrink)

Discussion of whether values and norms are neutral or not has mainly appeared in works on the nature of prudential rationality and morality. Little systematic has yet appeared in the up and coming field of the meaning of life. What are the respects in which the value of meaningfulness is neutral or, in contrast, partial, relational, or ‘biased’? In this article, I focus strictly on answering this question. First, I aim to identify the salient, and perhaps exhaustive, respects (...) in which issues of neutrality arise in the contexts of life’s meaning. In addition to providing a taxonomy of the key points of contention, a second aim is to advance reflection about them by considering the most important arguments that have been marshalled in favour of one side or the other, particularly as they appear in recent neutral positions. I conclude that meaning in life is neutral with respect to time but not any other conditions such as agents and patients, with a third aim being to point out that this makes the value of meaning different from the kinds of non/neutrality encountered in some salient conceptions of prudence and morality. (shrink)

DARWIN’s (1859, 1871) discoveries have profound ethical implications that continue to be misrepresented and/or ignored. In contrast to socialdarwinistic misuses of his theory, Darwin was a great humanitarian who paved the way for an integrated scientific and ethical world view. As an ethical doctrine, socialdarwinism is long dead ever since its defeat by E. G. Moore although the socialdarwinistic thought is a hard-die in the biological community. The accusations of sociobiology for being socialdarwinistic are unfounded and stem from the moralistic (...) fallacy that is, a false assumption that morality is good by definition. Both social and developmental psychology demonstrate that the moral agency is a motivational device for executing reciprocity that remains at the core of any morality across all studied societies and throughout the ontogeny of moral judgment. The level of true universalizing ethical reflection (KOHLBERG’s postconvential stages or GIBBS’s existential phase) is achieved by a small minority of humans, thus showing that Homo sapiens is a moral but not an ethical animal. While the origin of reciprocity has been perfectly explained by sociobiology, the evolutionary assembly of affective and cognitive elements that make up the moral agency is being successfully studied by the social/personality/developmental psychology as extended to non-human primates. As DARWIN (1871) expected, the key innovation for the evolution of moral agency was the emergence of empathy that evolved independently at least three times: in elephants, dolphins and primates. Empathy has a motivational power of its own; it is also necessary for moral agency that requires two cognitive abilities: reflective self-consciousness and understanding of causality; the two make possible the attribution of responsibility. All these requirements are met by the chimpanzees whose moral agency operates in dyads. In contrast, the human moral agency allows for a third party intervention that opens up vast opportunities for ideologies, especially religions, to use and misuse the moral agency to enforce a reciprocation that may be harmful to both individuals and the entire group. Also, the moral agency is known to enforce enhanced intragroup cohesion and loyalty in response to conflict and war, which suggests that the two prima facie opposed human universals, morality and warfare, may have coevolved. The most important ethical consequence that follows from the increasing understanding of the primate moral agency is that every received morality is ethically flawed, none can be taken as a paragon of goodness, and each needs corrections by science-informed ethics. In fact, Darwin pioneered the integration of science and ethics, an approach that has come to be appreciated only recently under the heading of consilience. (shrink)

Slurs have been standardly assumed to bear a very direct, very distinctive semantic relationship to what philosophers have called “neutral counterpart” terms. I argue that this is mistaken: the general relationship between paradigmatic slurs and their “neutral counterparts” should be assumed to be the same one that obtains between ‘chick flick’ and ‘romantic comedy’, as well a huge number of other more prosaic pairs of derogatory and “less derogatory” expressions. The most plausible general relationship between these latter expressions (...) — and thus, I argue, between paradigmatic slurs and “neutral counterpart” terms — is one of overlap in presumed extension, grounded in overlap in associated stereotypes. The resulting framework has the advantages of being simple, unified, and, unlike its orthodox rivals, neatly accommodating of a much wider range of data than has previously been considered. More importantly, it positions us to better understand, identify, and confront the insidious mechanisms of ordinary bigotry. (shrink)