A far-reaching and influential view in evolutionary biology claims that species are cohesive units held together by gene flow. Biologists have recognized empirical problems facing this view; after sharpening the expression of the view, we present novel conceptual problems for it. At the heart of these problems is a distinction between two importantly different concepts of cohesion, what we call integrative and response cohesion. Acknowledging the distinction problematizes both the explanandum of species cohesion (...) and the explanans of gene flow that are central to the view we discuss. We conclude by tracing four broader implications for the study and conceptualization of species. (shrink)

We defend a realistic attitude towards biological species. We argue that two species are not different species because they differ in intrinsic features, be they phenotypic or genomic, but because they are separated with regard to gene flow. There are no intrinsic species essences. However, there are relational ones. We argue that bearing a gene flow relation to conspecifics may serve as the essence of a species. Our view of the (...) class='Hi'>species as a Gene-Flow Community differs from Mayr’s definition of the species as a reproductive community. In a reproductive community, each organism is able to successfully reproduce with each other. However, there are species in which geographically distant organisms lost their ability to successfully reproduce, due to strong genetic adaptations to the respective local environmental conditions. Despite this loss of the ability to mutually reproduce, they are still bound by gene flow via continuous intermediate populations. This replacement of Mayr’s notion of an interbreeding potential as a criterion for species membership has important implications for the treatment of populations in allopatry and sympatry. (shrink)

Evolutionary theory usually neglects two variables: the changes induced in the environment by the evolving organism, and individual uniqueness in sexually reproducing species. In order to fuel its maintenance and reproduction, an organism must average a positive net energy balance vis-a-v}s its environment. It achieves this via aptations, which consist of information (i.e., the internalization of all that is predictable about the environment, including the machinery to take advantage of this information) and stored energy (to operate the machinery, including (...) a safety margin to deal with events that are unpredictable in principle). Taking advantage of a prediction, however, interferes with what has been predicted; each adaptation by the organism therefore changes its environmental target. Today's organism is adapted to yesterday's environment, and today's predator inherits yesterday's prey image. This paper attempts to show that, over evolutionary time, the persistence of this asymmetric, time-lagged relationship is owed increasingly to genetically unique individuals. Individual uniqueness as resulting from sexual reproduction is janusfaced. It endows an evolving population with both a forward-looking (promethean) and backward-looking (protean) feature. A population made up of genetically unique individuals is promethean (creative) in its ability to exploit non-homogeneous resources and respond serendipitously to environmental change via new genotypes; it is protean (elusive) in presenting a pursuer (predator or parasite) with a scattered target. Furthermore, because of the asymmetry between the winnowing of the target gene pool by the pursuer, and the genetic fixation in the pursuer of an outdated target image, the target keeps evolving away from the pursuer at a speed and in a direction that are a function of the pursuer's success. This mechanism ensures an evolutionary time lag be102 W. Sterrer tween pursuer and target, which explains escalation, the stability of asymmetric coevolutionary systems such as the life/dinner principle, and the pervasiveness of the Red Queen effect. Individuality thus both promotes and retards the speed of evolution. Having probably originated simultaneously with predation, sex-generated individuality is a self-accelerating evolutionary process that may account for much of today's organismic and environmental complexity. (shrink)

Genes and the Agents of Life undertakes to rethink the place of the individual in the biological sciences, drawing parallels with the cognitive and social sciences. Genes, organisms, and species are all agents of life but how are each of these conceptualized within genetics, developmental biology, evolutionary biology, and systematics? The 2005 book includes highly accessible discussions of genetic encoding, species and natural kinds, and pluralism above the levels of selection, drawing on work from across the biological sciences. (...) The book is a companion to the author's Boundaries of the Mind (2004), also available from Cambridge, where the focus is the cognitive sciences. The book will appeal to a broad range of professionals and students in philosophy, biology, and the history of science. You can download the table of contents and the first chapter here. (shrink)

Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program, and several of these have been called “Darwinian principles.” Here, we suggest that caution should be taken in calling these principles Darwinian because of the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and hybridization. (...) Because the “Darwinian principles” are brought about by both vertical and reticulate evolutionary mechanisms and processes, they should be understood as foundational for a more pluralistic theory of evolution, one that surpasses the classic scope of the Modern and the Neo-Darwinian Synthesis. Reticulate evolution moreover demonstrates that what conventional (Neo-)Darwinian theories treat as intra-species features of evolution frequently involve reticulate interactions between organisms from very different taxonomic categories. Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction therefore cannot be understood as “traits” or “properties” of genes, organisms, species, or ecosystems because the phenomena are irreducible to specific units and levels of an evolutionary hierarchy. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals. (shrink)

The so-called ‘‘species problem’’ has plagued evolution- ary biology since before Darwin’s publication of the aptly titled Origin of Species. Many biologists think the problem is just a matter of semantics; others complain that it will not be solved until we have more empirical data. Yet, we don’t seem to be able to escape discussing it and teaching seminars about it. In this paper, I briefly examine the main themes of the biological and philosophical liter- atures on the (...) species problem, focusing on identifying common threads as well as relevant differences. I then argue two fundamental points. First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require—but cannot be settled by—empirical evidence. Second, the (dis-)solution lies in explicitly adopting Wittgenstein’s idea of ‘‘family resemblance’’ or cluster concepts, and to consider spe- cies as an example of such concepts. This solution has several attractive features, including bringing together apparently diverging themes of discussion among bio- logists and philosophers. The current proposal is con- ceptually independent (though not incompatible) with the pluralist approach to the species problem advocated by Mishler, Donoghue, Kitcher and Dupre ́, which implies that distinct aspects of the species question need to be emphasized depending on the goals of the researcher. From the biological literature, the concept of species that most closely matches the philosophical discussion pre- sented here is Templeton’s cohesion idea. (shrink)

Most current techniques to deal with invasive species are ineffective or have highly damaging side effects. To this end suppression-drives based on clustered regularly inter-spaced short palindromic repeats (CRISPR/Cas9) have been touted as a potential silver bullet for the problem, allowing for a highly focused, humane and cost-effective means of removing a target species from an environment. Suppression-drives come with serious risks, however, such that the precautionary principle seems to warrant us not deploying this technology. The focus of (...) this paper is on one such risk – the danger of a suppression-drive escaping containment and wiping out the target species globally. Here, I argue that in most cases this risk is significant enough to warrant not using a gene-drive. In some cases, however, we can bypass the precautionary principle by using an approach that hinges on what I term the ‘Worst-Case Clause’. This clause, in turn, provides us with a litmus test that can be fruitfully used to determine what species are viable targets for suppression-drives in the wild. Using this metric in concert with other considerations, I suggest that only three species are currently possible viable targets – the European rabbit, ship rat and Caribbean Tree Frog. (shrink)

Two major clarifications have greatly abetted the understanding and fruitful expansion of the theory of natural selection in recent years: the acknowledgment that interactors, not replicators, constitute the causal unit of selection; and the recognition that interactors are Darwinian individuals, and that such individuals exist with potency at several levels of organization (genes, organisms, demes, and species in particular), thus engendering a rich hierarchical theory of selection in contrast with Darwin’s own emphasis on the organismic level. But a piece (...) of the argument has been missing, and individuals at levels distinct from organisms have been denied potency (although granted existence within the undeniable logic of the theory), because they do not achieve individuality with the same devices used by organisms and therefore seem weak by comparison. We show here that different features define Darwinian individuality across scales of size and time. In particular, species-individuals may develop few emergent features as direct adaptations. The interactor approach works with emergent fitnesses, not with emergent features; and species, as a consequence of their different mechanism for achieving individuality (reproductive exclusivity among subparts, that is, among organisms), express many effects from other levels. Organisms, by contrast, suppress upwardly cascading effects, because the organismic style of individuality (by functional integration of subparts) does not permit much competition or differential reproduction of parts from within. Species do not suppress the operation of lower levels; such effects therefore become available as exaptations conferring emergent fitness—a primary source of the different strength that species achieve as effective Darwinian individuals in evolution. (shrink)

Species concepts aim to define the species category. Many of these rely on defining species in terms of natural lineages and groupings. A dominant gene-centred metaconception has shaped notions of what constitutes both a natural lineage and a natural grouping. I suggest that relying on this metaconception provides an incomplete understanding of what constitute natural lineages and groupings. If we take seriously the role of epigenetic, behavioural, cultural, and ecological inheritance systems, rather than exclusively genetic inheritance, (...) a broader notion of what constitutes a natural grouping or lineage may be required. I conclude by outlining an alternative metaconception that is a de-centred metaschema for species. (shrink)

Mosquito-borne diseases represent a significant global disease burden, and recent outbreaks of such diseases have led to calls to reduce mosquito populations. Furthermore, advances in ‘gene-drive’ technology have raised the prospect of eradicating certain species of mosquito via genetic modification. This technology has attracted a great deal of media attention, and the idea of using gene-drive technology to eradicate mosquitoes has been met with criticism in the public domain. In this paper, I shall dispel two moral objections (...) that have been raised in the public domain against the use of gene-drive technologies to eradicate mosquitoes. The first objection invokes the concept of the ‘sanctity of life’ in order to claim that we should not drive an animal to extinction. In response, I follow Peter Singer in raising doubts about general appeals to the sanctity of life, and argue that neither individual mosquitoes nor mosquitoes species considered holistically are appropriately described as bearing a significant degree of moral status. The second objection claims that seeking to eradicate mosquitoes amounts to displaying unacceptable degrees of hubris. Although I argue that this objection also fails, I conclude by claiming that it raises the important point that we need to acquire more empirical data about, inter alia, the likely effects of mosquito eradication on the ecosystem, and the likelihood of gene-drive technology successfully eradicating the intended mosquito species, in order to adequately inform our moral analysis of gene-drive technologies in this context. (shrink)

Never was dogmatic reductionism helpful in conceiving the phenomenon of life. The post-genomic era has made it clear that genes alone cannot explain the functioning of whole organisms. Already each cell represents a unique, non-recurring individual. Recent progress in developmental biology has conveyed new perspectives both on the makings of individual organisms (ontogeny), as on evolutionary change (Evo-Devo). The genome (the entirety of all genes) of an animal remains constant from fertilization onwards in each cell. The realization of genes requires (...) molecular environments, in particular pertinent to the cytoplasm of the unfertilized egg. Individuality of an organism therefore is not only determined by its genome, but is shaped through developmental processes (it needs time!). Organisms can only exist through mutual interplays with their respective (molecular and cellular) environments at all levels of organization. Thus, life can be conceived of as endless networks of communication, e.g. as a mutual continuum, connecting all individuals, all species and all generations within their given environments. Evolutionarily, nature does not select fitting genes, but rather viable traits. The presented concepts render it unlikely that it was genes that founded our living world, but rather that distinct environments shaped “genes” (of whatever chemical nature) which proved to be “life-suitable”. (shrink)

This paper isolates a hard, long-standing species problem: developing a comprehensive and exacting theory about the constitutive conditions of the species category, one that is accurate for most of the living world, and which vindicates the widespread view that the species category is of more theoretical import than categories such as genus, sub-species, paradivision, and stirp. The paper then uncovers flaws in several views that imply we have either already solved that hard species problem or (...) dissolved it altogether – so-called We Are Done views. In doing so the paper offers new criticisms of the general lineage species concept (GLSC), evolutionary species concept (EvSC), biological species concept (BSC), other similar concepts, Ereshefsky’s eliminative pluralism about the species category, and both Mishler’s pessimism and Wilkins’ phenomenalism about that category. Opposed to We Are Done views, the paper argues for a Revving Up view, on which we are nearly ready to begin the hard species problem in earnest. To help work towards these conclusions, the paper begins with an outline of a new kind of view of species (Barker 2019a), which proposes they are feedback systems of a mathematically specifiable and empirically testable sort. (shrink)

The potential to collect brain data more directly, with higher resolution, and in greater amounts has heightened worries about mental and brain privacy. In order to manage the risks to individuals posed by these privacy challenges, some have suggested codifying new privacy rights, including a right to “mental privacy.” In this paper, we consider these arguments and conclude that while neurotechnologies do raise significant privacy concerns, such concerns are—at least for now—no different from those raised by other well-understood data collection (...) technologies, such as gene sequencing tools and online surveillance. To better understand the privacy stakes of brain data, we suggest the use of a conceptual framework from information ethics, Helen Nissenbaum’s “contextual integrity” theory. To illustrate the importance of context, we examine neurotechnologies and the information flows they produce in three familiar contexts—healthcare and medical research, criminal justice, and consumer marketing. We argue that by emphasizing what is distinct about brain privacy issues, rather than what they share with other data privacy concerns, risks weakening broader efforts to enact more robust privacy law and policy. (shrink)

A systematic survey of Rapti River was conducted once in a month for a period of one year from August 2018 to July 2019 from ten collection sites of Shravasti and Balrampur districts. Its main aim was to find out ichthyofaunal diversity and their conservation status. The results of the present study revealed the occurrence of 46 species belonging to 30 genera 19 families and 9 orders. The family Cyprinidae were dominated by 13 species followed by Bagridae (6 (...) species); Ophiocephalidae (4 species); Siluridae (3 species); Schileidae, Clariidae, Gobiidae, Notopteridae and Mastacembeleidae each with two species; Saccobranchidae, Chacidae, Ophiocephalidae, Gobiidae, Anabantidae, Nandidae, Osphronemidae, Ambassidae, Clupeidae, Eugraulidae, Belonidae and Tetradontidae each with one species. The fishes in these areas are under threat due to anthropogenic activities such as overfishing and pollution hence authors strongly recommend practical conservation action plan to prevent the species from extinction. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project (...) also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

As the international genomic research community moves from the tool-making efforts of the Human Genome Project into biomedical applications of those tools, new metaphors are being suggested as useful to understanding how our genes work – and for understanding who we are as biological organisms. In this essay we focus on the Human Microbiome Project as one such translational initiative. The HMP is a new ‘metagenomic’ research effort to sequence the genomes of human microbiological flora, in order to pursue the (...) interesting hypothesis that our ‘microbiome’ plays a vital and interactive role with our human genome in normal human physiology. Rather than describing the human genome as the ‘blueprint’ for human nature, the promoters of the HMP stress the ways in which our primate lineage DNA is interdependent with the genomes of our microbiological flora. They argue that the human body should be understood as an ecosystem with multiple ecological niches and habitats in which a variety of cellular species collaborate and compete, and that human beings should be understood as ‘superorganisms’ that incorporate multiple symbiotic cell species into a single individual with very blurry boundaries. These metaphors carry interesting philosophical messages, but their inspiration is not entirely ideological. Instead, part of their cachet within genome science stems from the ways in which they are rooted in genomic research techniques, in what philosophers of science have called a ‘tools-to-theory’ heuristic. Their emergence within genome science illustrates the complexity of conceptual change in translational research, by showing how it reflects both aspirational and methodological influences. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in (...) the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has (...) been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or significant). (...) Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate--namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. (shrink)

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: (...) We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (shrink)

Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique (...) of phylogenetic bacterial species, arguing that phylogenetic bacterial classification requires a questionable metaphysical commitment to the existence of essential genes. I conclude by considering how microbiologists have dealt with these biological complexities by using more pragmatic and not exclusively evolutionary accounts of species. I argue that this pragmatism is not borne of laziness but rather of the substantial conceptual problems in classifying bacteria based on any evolutionary standard. (shrink)

One of the reasons why GMOs have met public resistance in the past is that they are perceived as “unnatural”. The basis for this claim has, in part, to do with crossing species boundaries, which is considered morally objectionable. The emergence of CRISPR is sometimes argued to be an ethical game-changer in this regard since it does not require the insertion of foreign genes. Based on an empirical bioethics study including individual interviews and focus groups with laypeople and other (...) stakeholders, this article analyses the normative role of appeals to naturalness in discussions about the moral acceptability of using CRISPR in salmon farming. It discusses two dimensions of naturalness found in the material– living by species-specific nature and being unaffected by humans– and argues that these dimensions put down criteria for the application of CRISPR that lead to a conflict between our moral duties towards the farmed salmon and those we hold towards the wild salmon as a threatened species. It also points to a paradox which is likely to gain traction with further climate change and biodiversity loss, namely that while nature, understood as that which is unaffected by humans, is presented as an ideal, conserving nature in its pristine state may rely on technology and human intervention. (shrink)

In The Future of Human Nature, Jürgen Habermas raises the question of whether the embryonic genetic diagnosis and genetic modification threatens the foundations of the species ethics that underlies current understandings of morality. While morality, in the normative sense, is based on moral interactions enabling communicative action, justification, and reciprocal respect, the reification involved in the new technologies may preclude individuals to uphold a sense of the undisposability of human life and the inviolability of human beings that is necessary (...) for their own identity as well as for reciprocal relations. Engaging with liberal bioethics and Catholic approaches to bioethics, the article clarifies how Habermas’ position offers a radical critique of liberal autonomy while maintaining its postmetaphysical stance. The essay argues that Habermas’ approach may guide the question of rights of future generations regarding germline gene editing. But it calls for a different turn in the conversation between philosophy and theology, namely one that emphasizes the necessary attention to rights violations and injustices as a common, postmetaphysical starting point for critical theory and critical theology alike. In 2001, Jürgen Habermas published a short book on questions of biomedicine that took many by surprise.[1] To some of his students, the turn to a substantive position invoking the need to comment on a species ethics rather than outlining a public moral framework was seen as the departure from the “path of deontological virtue,”[2] and at the same time a departure from postmetaphysical reason. Habermas’ motivation to address the developments in biomedicine had certainly been sparked by the intense debate in Germany, the European Union, and internationally on human cloning, pre-implantation genetic diagnosis, embryonic stem cell research, and human enhancement. He turned to a strand of critical theory that had been pushed to the background by the younger Frankfurt School in favor of cultural theory and social critique, even though it had been an important element of its initial working programs. The relationship of instrumental reason and critical theory, examined, among others, by Max Horkheimer, Theodor W. Adorno, and Herbert Marcuse and taken up in Habermas’ own Knowledge and Interest and Theory of Communicative Action became ever-more actual with the development of the life sciences, human genome analysis, and genetic engineering of human offspring. Today, some of the fictional scenarios discussed at the end of the last century as “science fiction” have become reality: in 2018, the first “germline gene-edited” children were born in China.[3] Furthermore, the UK’s permission to create so-called “three-parent” children may create a legal and political pathway to hereditary germline interventions summarized under the name of “gene editing.”In this article, I want to explore Habermas’ “substantial” argument in the hope that philosophy and theology become allies in their struggle against an ever-more reifying lifeworld, which may create a “moral void” that would, at least from today’s perspective, be “unbearable”, and for upholding the conditions of human dignity, freedom, and justice. I will contextualize Habermas’ concerns in the broader discourse of bioethics, because only by doing this, his concerns are rescued from some misinterpretations.[1] Jürgen Habermas, The Future of Human Nature.[2] Ibid., 125, fn. 58. 8[3] Up to the present, no scientific publication of the exact procedure exists, but it is known that the scientist, Jiankui He, circumvented the existing national regulatory framework and may have misled the prospective parents about existing alternatives and the unprecedented nature of his conduct. Yuanwu Ma, Lianfeng Zhang, and Chuan Qin, "The First Genetically Gene‐Edited Babies: It's “Irresponsible and Too Early”," Animal Models and Experimental Medicine ; Matthias Braun, Meacham, Darian, "The Trust Game: Crispr for Human Germline Editing Unsettles Scientists and Society," EMBO reports 20, no. 2. (shrink)

Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants (...) during stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general. (shrink)

Attempts to ‘naturalize’ phenomenology challenge both traditional phenomenology and traditional approaches to cognitive science. They challenge Edmund Husserl’s rejection of naturalism and his attempt to establish phenomenology as a foundational transcendental discipline, and they challenge efforts to explain cognition through mainstream science. While appearing to be a retreat from the bold claims made for phenomenology, it is really its triumph. Naturalized phenomenology is spearheading a successful challenge to the heritage of Cartesian dualism. This converges with the reaction against Cartesian thought (...) within science itself. Descartes divided the universe between res cogitans, thinking substances, and res extensa, the mechanical world. The latter won with Newton and we have, in most of objective science since, literally lost our mind, hence our humanity. Despite Darwin, biologists remain children of Newton, and dream of a grand theory that is epistemologically complete and would allow lawful entailment of the evolution of the biosphere. This dream is no longer tenable. We now have to recognize that science and scientists are within and part of the world we are striving to comprehend, as proponents of endophysics have argued, and that physics, biology and mathematics have to be reconceived accordingly. Interpreting quantum mechanics from this perspective is shown to both illuminate conscious experience and reveal new paths for its further development. In biology we must now justify the use of the word “function”. As we shall see, we cannot prestate the ever new biological functions that arise and constitute the very phase space of evolution. Hence, we cannot mathematize the detailed becoming of the biosphere, nor write differential equations for functional variables we do not know ahead of time, nor integrate those equations, so no laws “entail” evolution. The dream of a grand theory fails. In place of entailing laws, a post-entailing law explanatory framework is proposed in which Actuals arise in evolution that constitute new boundary conditions that are enabling constraints that create new, typically unprestatable, Adjacent Possible opportunities for further evolution, in which new Actuals arise, in a persistent becoming. Evolution flows into a typically unprestatable succession of Adjacent Possibles. Given the concept of function, the concept of functional closure of an organism making a living in its world, becomes central. Implications for patterns in evolution include historical reconstruction, and statistical laws such as the distribution of extinction events, or species per genus, and the use of formal cause, not efficient cause, laws. (shrink)

Are the methods of synthetic biology capable of recreating authentic living members of an extinct species? An analogy with the restoration of destroyed natural landscapes suggests not. The restored version of a natural landscape will typically lack much of the aesthetic value of the original landscape because of the different historical processes that created it—processes that involved human intentions and actions, rather than natural forces acting over millennia. By the same token, it would appear that synthetically recreated versions of (...) extinct natural organisms will also be less aesthetically valuable than the originals; that they will be, in some strong sense, ‘inauthentic’, because of their peculiar history and mode of origin. I call this the ‘genesis argument’ against de-extinction. In this article I critically evaluate the genesis argument. I highlight an important disanalogy between living organisms and natural landscapes: viz., it is of the essence of the former, but not of the latter, to regularly reproduce and die. The process of iterated natural reproduction that sustains the continued existence of a species through time obviously does not undermine the authenticity of the species. I argue that the authenticity of a species will likewise be left intact by the kind of artificial copying of genes and traits that a de-extinction project entails. I conclude on this basis that the genesis argument is unsound. (shrink)

As a species, we are on the cusp of being able to alter that which makes us uniquely human, our genome. Two new genetic technologies, embryo selection and germline engineering, are either in use today or may be developed in the future. Embryo selection acts to alter the human gene pool, reducing genetic diversity, while germline engineering will have the ability to alter directly the genomes of engineered individuals. Our genome has come to be what it is through (...) an evolutionary process extending over millions of years, a process that has involved exceedingly complex and unpredictable interactions between ourselves or our ancestors and myriad other life forms within Earth's biosphere. In this paper, the ecological imperative, which states that we must not alter the human genome or the collective human genetic inheritance, will be introduced. It will be argued based on ecological principles that embryo selection and germline engineering are unethical and unwise because they will diminish our survivability as a species, will disrupt our relationship with the natural world, and will destroy the very basis of that which makes us human. (shrink)

continent. 1.1 : 3-13. / 0/ – Introduction I want to propose, as a trajectory into the philosophically weird, an absurd theoretical claim and pursue it, or perhaps more accurately, construct it as I point to it, collecting the ground work behind me like the Perpetual Train from China Mieville's Iron Council which puts down track as it moves reclaiming it along the way. The strange trajectory is the following: Kant's critical philosophy and much of continental philosophy which has followed, (...) has been a defense against horror and madness. Kant's prohibition on speculative metaphysics such as dogmatic metaphysics and transcendental realism, on thinking beyond the imposition of transcendental and moral constraints, has been challenged by numerous figures proceeding him. One of the more interesting critiques of Kant comes from the mad black Deleuzianism of Nick Land stating, “Kant’s critical philosophy is the most elaborate fit of panic in the history of the Earth.” And while Alain Badiou would certainly be opposed to the libidinal investments of Land's Deleuzo-Guattarian thought, he is likewise critical of Kant's normative thought-bureaucracies: Kant is the one author for whom I cannot feel any kinship. Everything in him exasperates me, above all his legalism—always asking Quid Juris? Or ‘Haven’t you crossed the limit?’—combined, as in today’s United States, with a religiosity that is all the more dismal in that it is both omnipresent and vague. The critical machinery he set up has enduringly poisoned philosophy, while giving great succour to the academy, which loves nothing more than to rap the knuckles of the overambitious [….] That is how I understand the truth of Monique David-Menard’s reflections on the properly psychotic origins of Kantianism. I am persuaded that the whole of the critical enterprise is set up to to shield against the tempting symptom represented by the seer Swedenborg, or against ‘diseases of the head’, as Kant puts it. An entire nexus of the limits of reason and philosophy are set up here, namely that the critical philosophy not only defends thought from madness, philosophy from madness, and philosophy from itself, but that philosophy following the advent of the critical enterprise philosophy becomes auto-vampiric; feeding on itself to support the academy. Following Francois Laruelle's non-philosophical indictment of philosophy, we could go one step further and say that philosophy operates on the material of what is philosophizable and not the material of the external world. [1] Beyond this, the Kantian scheme of nestling human thinking between our limited empirical powers and transcendental guarantees of categorical coherence, forms of thinking which stretch beyond either appear illegitimate, thereby liquefying both pre-critical metaphysics and the ravings of the mad in the same critical acid. In rejecting the Kantian apparatus we are left with two entities – an unsure relation of thought to reality where thought is susceptible to internal and external breakdown and a reality with an uncertain sense of stability. These two strands will be pursued, against the sane-seal of post-Kantian philosophy by engaging the work of weird fiction authors H.P. Lovecraft and Thomas Ligotti. The absolute inhumanism of the formers universe will be used to describe a Shoggothic Materialism while the dream worlds of the latter will articulate the mad speculation of a Ventriloquil Idealism. But first we must address the relation of philosophy to madness as well as philosophy to weird fiction. /1/ – Philosophy and Madness There is nothing that the madness of men invents which is not either nature made manifest or nature restored. Michel Foucault. Madness and Civilization. The moment I doubt whether an event that I recall actually took place, I bring the suspicion of madness upon myself: unless I am uncertain as to whether it was not a mere dream. Arthur Schopenhauer. The World as Will and Idea, Vol. 3. Madness is commonly thought of as moving through several well known cultural-historical shifts from madness as a demonic or otherwise theological force, to rationalization, to medicalization psychiatric and otherwise. Foucault's Madness and Civilization is well known for orientating madness as a form of exclusionary social control which operated by demarcating madness from reason. Yet Foucault points to the possibility of madness as the necessity of nature at least prior to the crushing weight of the church. Kant’s philosophy as a response to madness is grounded by his humanizing of madness itself. As Adrian Johnston points out in the early pages of Time Driven pre-Kantian madness meant humans were seized by demonic or angelic forces whereas Kantian madness became one of being too human. Madness becomes internalized, the external demonic forces become flaws of the individual mind. Foucault argues that, while madness is de-demonized it is also dehumanized during the Renaissance, as madmen become creatures neither diabolic nor totally human reduced to the zero degree of humanity. It is immediately clear why for Kant, speculative metaphysics must be curbed – with the problem of internal madness and without the external safeguards of transcendental conditions, there is nothing to formally separate the speculative capacities for metaphysical diagnosis from the mad ramblings of the insane mind – both equally fall outside the realm of practicality and quotidian experience. David-Menard's work is particularly useful in diagnosing the relation of thought and madness in Kant's texts. David-Menard argues that in Kant's relatively unknown “An Essay on the Maladies of the Mind” as well as his later discussion of the Seer of Swedenborg, that Kant formulates madness primarily in terms of sensory upheaval or other hallucinatory theaters. She writes: “madness is an organization of thought. It is made possible by the ambiguity of the normal relation between the imaginary and the perceived, whether this pertains to the order of sensation or to the relations between our ideas” Kant's fascination with the Seer forces Kant between the pincers of “aesthetic reconciliation” – namely melancholic withdrawal – and “a philosophical invention” – namely the critical project. Deleuze and Guattari's schizoanalysis is a combination and reversal of Kant's split, where an aesthetic over engagement with the world entails prolific conceptual invention. Their embrace of madness, however, is of course itself conceptual despite all their rhizomatic maneuvers. Though they move with the energy of madness, Deleuze and Guattari save the capacity of thought from the fangs of insanity by imbuing materiality itself with the capacity for thought. Or, as Ray Brassier puts it, “Deleuze insists, it is necessary to absolutize the immanence of this world in such a way as to dissolve the transcendent disjunction between things as we know them and as they are in themselves”. That is, whereas Kant relied on the faculty of judgment to divide representation from objectivity Deleuze attempts to flatten the whole economy beneath the juggernaut of ontological univocity. Speculation, as a particularly useful form of madness, might fall close to Deleuze and Guattari’s shaping of philosophy into a concept producing machine but is different in that it is potentially self destructive – less reliant on the stability of its own concepts and more adherent to exposing a particular horrifying swath of reality. Speculative madness is always a potential disaster in that it acknowledges little more than its own speculative power with the hope that the gibbering of at least a handful of hysterical brains will be useful. Pre-critical metaphysics amounts to madness, though this may be because the world itself is mad while new attempts at speculative metaphysics, at post-Kantian pre-critical metaphysics, are well aware of our own madness. Without the sobriety of the principle of sufficient reason we have a world of neon madness: “we would have to conceive what our life would be if all the movements of the earth, all the noises of the earth, all the smells, the tastes, all the light – of the earth and elsewhere, came to us in a moment, in an instant – like an atrocious screaming tumult of things”. Speculative thought may be participatory in the screaming tumult of the world or, worse yet, may produce its spectral double. Against theology or reason or simply commonsense, the speculative becomes heretical. Speculation, as the cognitive extension of the horrorific sublime should be met with melancholic detachment. Whereas Kant's theoretical invention, or productivity of thought, is self -sabotaging, since the advent of the critical project is a productivity of thought which then delimits the engine of thought at large either in dogmatic gestures or non-systematizable empirical wondrousness. The former is celebrated by the fiction of Thomas Ligotti whereas the latter is espoused by the tales of H.P. Lovecraft. /2/ – Weird Fiction and Philosophy. Supernatural horror, in all its eerie constructions, enables a reader to taste treats inconsistent with his personal welfare. Thomas Ligotti Songs of a Dead Dreamer. I choose weird stories because they suit my inclination best—one of my strongest and most persistent wishes being to achieve,momentarily, the illusion of some strange suspension or violation of the galling limitations of time, space, and natural law which forever imprison us and frustrate our curiosity about the infinite cosmic spaces beyond the radius of our sight and analysis H.P. Lovecraft. “Notes on Writing Weird Fiction” Lovecraft states that his creation of a story is to suspend natural law yet, at the same time, he indexes the tenuousness of such laws, suggesting the vast possibilities of the cosmic. The tension that Lovecraft sets up between his own fictions and the universe or nature is reproduced within his fictions in the common theme of the unreliable narrator; unreliable precisely because they are either mad or what they have witnessed questions the bounds of material reality. In “The Call of Cthulhu” Lovecraft writes: The most merciful thing in the world, I think, is the inability of the human mind to correlate all its contents. We live on a placid island of ignorance in the midst of black seas of infinity, and it was not meant that we should voyage far. The sciences, each straining in its own direction, have hitherto harmed us little; but some day the piecing together of dissociated knowledge will open up such terrifying vistas of reality, and of our frightful position therein, that we shall either go mad from the revelation or flee from the deadly light into the peace and safety of a new dark age. Despite Lovecraft's invocations of illusion, he is not claiming that his fantastic creations such as the Old Ones are supernatural but, following Joshi, are only ever supernormal. One can immediately see that instead of nullifying realism Lovecraft in fact opens up the real to an unbearable degree. In various letters and non-fictional statements Lovecraft espoused strictly materialist tenets, ones which he borrowed from Hugh Elliot namely the uniformity of law, the denial of teleology and the denial of non-material existence. Lovecraft seeks to explore the possibilities of such a universe by piling horror upon horror until the fragile brain which attempts to grasp it fractures. This may be why philosophy has largely ignored weird fiction – while Deleuze and Guattari mark the turn towards weird fiction and Lovecraft in particular, with the precursors to speculative realism as well as contemporary related thinkers have begun to view Lovecraft as making philosophical contributions. Lovecraft's own relation to philosophy is largely critical while celebrating Nietzsche and Schopenhauer. This relationship of Lovecraft to philosophy and philosophy to Lovecraft is coupled with Lovecraft's habit of mercilessly destroying the philosopher and the figure of the academic more generally in his work, a destruction which is both an epistemological destruction and an ontological destruction. Thomas Ligotti's weird fiction which he has designated as a kind of “confrontational escapism” might be best described in the following quote from one of his shortstories, “The human phenomenon is but the sum of densely coiled layers of illusion each of which winds itself on the supreme insanity. That there are persons of any kind when all there can be is mindless mirrors laughing and screaming as they parade about in an endless dream”. Whereas Lovecraft's weirdness draws predominantly from the abyssal depths of the uncharted universe, Ligotti's existential horror focuses on the awful proliferation of meaningless surfaces that is, the banal and every day function of representation. In an interview, Ligotti states: We don't even know what the world is like except through our sense organs, which are provably inadequate. It's no less the case with our brains. Our whole lives are motored along by forces we cannot know and perceptions that are faulty. We sometimes hear people say that they're not feeling themselves. Well, who or what do they feel like then? This is not to say that Ligotti sees nothing beneath the surface but that there is only darkness or blackness behind it, whether that surface is on the cosmological level or the personal. By addressing the implicit and explicit philosophical issues in Ligotti's work we will see that his nightmarish take on reality is a form of malevolent idealism, an idealism which is grounded in a real, albeit dark and obscure materiality. If Ligotti's horrors ultimately circle around mad perceptions which degrade the subject, it takes aim at the vast majority of the focus of continental philosophy. While Lovecraft's acidic materialism clearly assaults any romantic concept of being from the outside, Ligotti attacks consciousness from the inside: Just a little doubt slipped into the mind, a little trickle of suspicion in the bloodstream, and all those eyes of ours, one by one, open up to the world and see its horror [...] Not even the solar brilliance of a summer day will harbor you from horror. For horror eats the light and digests it into darkness. Clearly, the weird fiction of Lovecraft and Ligotti amount to a anti-anthrocentric onslaught against the ramparts of correlationist continental philosophy. /3/ – Shoggothic Materialism or the Formless Formless protoplasm able to mock and reflect all forms and organs and processes—viscous agglutinations of bubbling cells—rubbery fifteen-foot spheroids infinitely plastic and ductile—slaves of suggestion, builders of cities—more and more sullen, more and more intelligent, more and more amphibious, more and more imitative—Great God! What madness made even those blasphemous Old Ones willing to use and to carve such things? H.P. Lovecraft. “At the Mountains of Madness” On the other hand, affirming that the universe resembles nothing and is only formless amounts to saying that the universe is something like a spider or spit. Georges Bataille. “Formless”. The Shoggoths feature most prominently in H.P. Lovecraft's shortstory “At the Mountains of Madness” where they are described in the following manner: It was a terrible, indescribable thing vaster than any subway train – a shapeless congeries of protoplasmic bubbles, faintly self -luminous, and with myriads of temporary eyes forming and un-forming as pustules of greenish light all over the tunnel-filling front that bore down upon us, crushing the frantic penguins and slithering over the glistening floor that it and its kind had swept so evilly free of all litter. The term is a litmus test for materialism itself as the Shoggoth is an amorphous creature. The Shoggoths were living digging machines bio engineered by the Elder Things, and their protoplasmic bodies being formed into various tools by their hypnotic powers. The Shoggoths eventually became self aware and rose up against their masters in an ultimately failed rebellion. After the Elder Ones retreated into the oceans leaving the Shoggoths to roam the frozen wastes of the Antarctic. The onto-genesis of the Shoggoths and their gross materiality, index the horrifyingly deep time of the earth a concept near and dear to Lovecraft's formulation of horror as well as the fear of intelligences far beyond, and far before, the ascent of humankind on earth and elsewhere. The sickly amorphous nature of the Shoggoths invade materialism at large, where while materiality is unmistakably real ie not discursive, psychological, or otherwise overly subjectivist, it questions the relation of materialism to life. As Eugene Thacker writes: The Shoggoths or Elder Things do not even share the same reality with the human beings who encounter them—and yet this encounter takes place, though in a strange no-place that is neither quite that of the phenomenal world of the human subject or the noumenal world of an external reality. Amorphous yet definitively material beings are a constant in Lovecraft's tales. In his tale “The Dream-Quest of Unknown Kadatth” Lovecraft describes Azathoth as, “that shocking final peril which gibbers unmentionably outside the ordered universe,” that, “last amorphous blight of nethermost confusion which blashphemes and bubbles at the centre of all infinity,” who, “gnaws hungrily in inconceivable, unlighted chambers beyond time”. Azathoth's name may have multiple origins but the most striking is the alchemy term azoth which is both a cohesive agent and a acidic creation pointing back to the generative and the decayed. The indistinction of generation and degradation materially mirrors the blur between the natural and the unnatural as well as life and non-life. Lovecraft speaks of the tension between the natural and the unnatural is his short story “The Unnameable.” He writes, “if the psychic emanations of human creatures be grotesque distortions, what coherent representation could express or portray so gibbous and infamous a nebulousity as the spectre of a malign, chaotic perversion, itself a morbid blasphemy against Nature?”. Lovecraft explores exactly the tension outlined at the beginning of this chapter, between life and thought. At the end of his short tale Lovecraft compounds the problem as the unnameable is described as “a gelatin—a slime—yet it had shapes, a thousand shapes of horror beyond all memory”. Deleuze suggests that becoming-animal is operative throughout Lovecraft's work, where narrators feel themselves reeling at their becoming non-human or of being the anomalous or of becoming atomized. Following Eugene Thacker however, it may be far more accurate to say that Lovecraft's tales exhibit not a becoming-animal but a becoming-creature. Where the monstrous breaks the purportedly fixed laws of nature, the creature is far more ontologically ambiguous. The nameless thing is an altogether different horizon for thought. The creature is either less than animal or more than animal – its becoming is too strange for animal categories and indexes the slow march of thought towards the bizarre. This strangeness is, as aways, some indefinite swirling in the category of immanence and becoming. Bataille begins “The Labyrinth” with the assertion that being, to continue to be, is becoming. More becoming means more being hence the assertion that Bataille's barking dog is more than the sponge. This would mean that the Shoggotth is altogether too much being, too much material in the materialism. Bataille suggests that there is an immanence between the eater and the eaten, across the species and never within them. That is, despite the chaotic storm of immanence there must remain some capacity to distinguish the gradients of becoming without reliance upon, or at least total dependence upon, the powers of intellection to parse the universe into recognizable bits, properly digestible factoids. That is, if we undo Deleuze's aforementioned valorization of sense which, for his variation of materialism, performed the work of the transcendental, but refuse to reinstate Kant's transcendental disjunction between thing and appearance, then it must be a quality of becoming-as-being itself which can account for the discernible nature of things by sense. In an interview with Peter Gratton, Jane Bennett formulates the problem thusly: What is this strange systematicity proper to a world of Becoming? What, for example, initiates this congealing that will undo itself? Is it possible to identify phases within this formativity, plateaus of differentiation? If so, do the phases/plateaus follow a temporal sequence? Or, does the process of formation inside Becoming require us to theorize a non-chronological kind of time? I think that your student’s question: “How can we account for something like iterable structures in an assemblage theory?” is exactly the right question. Philosophy has erred too far on the side of the subject in the subject-object relation and has furthermore, lost the very weirdness of the non-human. Beyond this, the madness of thought need not override. /4/ - Ventriloquial Idealism or the Externality of Thought My aim is the opposite of Lovecraft's. He had an appreciation for natural scenery on earth and wanted to reach beyond the visible in the universe. I have no appreciation for natural scenery and want the objective universe to be a reflection of a character. Thomas Ligotti. “Devotees of Decay and Desolation.” Unless life is a dream, nothing makes sense. For as a reality, it is a rank failure [….] Horror is more real than we are. Thomas Ligotti. “Professor Nobody's Little Lectures on Supernatural Horror”. Thomas Ligotti's tales are rife with mannequins, puppets, and other brainless entities which of replace the valorized subject of philosophy – that of the free thinking human being. His tales such as “The Dream of the Manikin” aim to destroy the rootedness of consciousness. James Trafford has connected the anti-egoism of Ligotti to Thomas Metzinger – where the self is at best an illusion and we plead desperately for someone else to acknowledge that we are real. Trafford has stated it thus, “Life is played out as an inescapable puppet show, an endless dream in which the puppets are generally unaware that they are trapped within a mesmeric dance of whose mechanisms they know nothing and over which they have no control”. An absolute materialism, for Ligotti, implies an alienation of the idea which leads to a ventriloquil idealism. As Ligotti notes in an interview, “the fiasco and nightmare of existence, the particular fiasco and nightmare of human existence, the sense that people are puppets of powers they cannot comprehend, etc.” And then further elaborates that,“[a]ssuming that anything has to exist, my perfect world would be one in which everyone has experienced the annulment of his or her ego. That is, our consciousness of ourselves as unique individuals would entirely disappear”. The externality of the idea leads to the unfortunate consequence of consciousness eating at itself through horror which, for Ligotti, is more real than reality and goes beyond horror-as-affect. Beyond this, taking together with the unreality of life and the ventriloquizing of subjectivity, Ligotti's thought becomes an idealism in which thought itself is alien and ultimately horrifying. The role of human thought and the relation of non-relation of horror to thought is not completely clear in Ligotti's The Conspiracy Against the Human Race. Ligotti argues in his The Conspiracy Against the Human Race,that the advent of thought is a mistake of nature and that horror is being in the sense that horror results from knowing too much. Yet, at the same time, Ligotti seems to suggest that thought separates us from nature whereas, for Lovecraft, thought is far less privileged – mind is just another manifestation of the vital principal, it is just another materialization of energy. In his brilliant “Prospects for Post-Copernican Dogmatism” Iain Grant rallies against the negative definition of dogmatism and the transcendental, and suggests that negatively defining both over-focuses on conditions of access and subjectivism at the expense of the real or nature. With Schelling, who is Grant's champion against the subjectivist bastions of both Fichte and Kant, Ligotti's idealism could be taken as a transcendental realism following from an ontological realism. Yet the transcendental status of Ligotti's thought move towards a treatment of the transcendental which may threaten to leave beyond its realist ground. Ligotti states: Belief in the supernatural is only superstition. That said, a sense of the supernatural, as Conrad evidenced in Heart of Darkness, must be admitted if one's inclination is to go to the limits of horror. It is the sense of what should not be- the sense of being ravaged by the impossible. Phenomenally speaking, the super-natural may be regarded as the metaphysical counterpart of insanity, a transcendental correlative of a mind that has been driven mad. Again, Ligotti equates madness with thought, qualifying both as supernatural while remaining less emphatic about the metaphysical dimensions of horror. The question becomes one of how exactly the hallucinatory realm of the ideal relates to the black churning matter of Lovecraft's chaos of elementary particles. In his tale “I Have a Special Plan for This World” Ligotti formulates thus: A: There is no grand scheme of things. B: If there were a grand scheme of things, the fact – the fact – that we are not equipped to perceive it, either by natural or supernatural means, is a nightmarish obscenity. C: The very notion of a grand scheme of things is a nightmarish obscenity. Here Ligotti is not discounting metaphysics but implying that if it does exist the fact that we are phenomenologically ill-equipped to perceive that it is nightmarish. For Ligotti, nightmare and horror occur within the circuit of consciousness whereas for Lovecraft the relation between reality and mind is less productive on the side of mind. It is easier to ascertain how the Kantian philosophy is a defense against the diseases of the head as Kant armors his critical enterprise from too much of the world and too much of the mind. The weird fiction of both Lovecraft and Ligotti demonstrates that there is too much of both feeding into one another in a way that corrodes the Kantian schema throughly, breaking it down into a dead but still ontologically potentiated nigredo. The haunting, terrifying fact of Ligotti's idealism is that the transcendental motion which brought thought to matter, while throughly material and naturalized, brings with it the horror that thought cannot be undone without ending the material that bears it either locally or completely. Thought comes from an elsewhere and an elsewhen being-in-thought. The unthinkable outside thought is as maddening as the unthought engine of thought itself within thought which doesn't exist except for the mind, the rotting décor of the brain. /5/ - Hyperstitional Transcendental Paranoia or Self -Expelled Thought Weird fiction has been given some direct treatment in philosophy in the mad black Deleuzianism of Nick Land. Nick Land along with others in the 1990s created the Cyber Culture Research Unit as well as the research group Hyperstition. The now defunct hyperstitional website, an outgrowth of the Cyber Culture Research Unit, defined hyperstition in the following fourfold: 1-Element of effective culture that makes itself real. 2-Fictional quantity functional as a time-traveling device. 3-Coincidence intensifier. 4-Call to the Old Ones. The distinctively Lovecraftian character of hyperstition is hard to miss as is its Deleuzo-Guattarian roots. In the opening pages of A Thousand Plateaus Deleuze and Guattari write, “We have been criticized for over-quoting literary authors. But when one writes, the only question is which other machine the literary machine can be plugged into”. The indisinction of literature and philosophy mirrors the mess of being and knowing as post-correlationist philosophy, where philosophy tries to make itself real where literature, especially the weird, aims itself at the brain-circuit of horror. The texts of both Lovecraft and Ligotti work through horror as epistemological plasticity meeting with proximity as well as the deep time of Lovecraft and the glacially slow time of paranoia in Ligotti. Against Deleuze, and following Brassier, we cannot allow the time of consciousness, the Bergsonian time of the duree, to override natural time, but instead acknowledge that it is an unfortunate fact of existence as a thinking being. Horror-time, the time of consciousness, with all its punctuated moments and drawn out terrors, cannot compare to the deep time of non-existence both in the unreachable past and the unknown future. The crystalline cogs of Kant's account of experience as the leading light for the possibility of metaphysics must be throughly obliterated. His gloss of experience in Prolegomena to any Future Metaphysics could not be more sterile: Experience consists of intuitions, which belong to the sensibility, and of judgments, which are entirely a work of the understanding. But the judgments which the understanding makes entirely out of sensuous intuitions are far from being judgments of experience. For in the one case the judgment connects only the perceptions as they are given in sensuous intuition [....] Experience consists in the synthetic connection of appearances in consciousness, so far as this connection is necessary. Here it is difficult to dismiss the queasiness that Kant's legalism induces upon sight for both Badiou and David-Menard. Kant's thought becomes, as Foucault says when reflecting on Sade's text in relation to nature, “the savage abolition of itself”. For Badiou, Kant's philosophy simply closes off too much of the outside, freezing the world of thought in an all too limited formalism. Critical philosophy is simply the systematized quarantine on future thinking, on thinking which would threaten the formalism which artificially grants thought its own coherency in the face of madness. Even the becoming-mad of Deleuze, while escaping the rumbling ground, makes grounds for itself, mad grounds but grounds which are thinkable in their affect. The field of effects allows for Deleuze's aesthetic and radical empiricism, in which effects and/or occasions make up the material of the world to be thought as a chaosmosis of simulacra. Given a critique of an empiricism of aesthetics, of the image, it may be difficult to justify an attack on Kantian formalism with the madness of literature, which does not aim to make itself real but which we may attempt to make real. That is, how do Lovecraft's and Ligotti's materials, as materials for philosophy to work on, differ from either the operative formalisms of Kant or the implicitly formalized images of Deleuzian empiricism? It is simply that such texts do not aim to make themselves real, and make claims to the real which are more alien to us than familiar, which is why their horror is immediately more trustworthy. This is the madness which Blanchot discusses in The Infinite Conversation through Cervantes and his knight – the madness of book-life, of the perverse unity of literature and life a discussion which culminates in the discussion of one of the weird's masters, that of Kafka. The text is the knowing of madness, since madness, in its moment of becoming-more-mad, cannot be frozen in place but by the solidifications of externalizing production. This is why Foucault ends his famous study with works of art. Furthermore extilligence, the ability to export the products of our maligned brains, is the companion of the attempts to export, or discover the possibility of intelligences outside of our heads, in order for philosophy to survive the solar catastrophe. To borrow again from Deleuze, writing is inseparable from becoming. The mistake is to believe that madness is reabsorbed by extilligence, by great works, or that it could be exorcised by the expelling of thought into the inorganic or differently organic. Going out of our heads does not guarantee we will no longer mean we cannot still go out of our minds. This is simply because of the outside, of matter, or force, or energy, or thing-in-itself, or Schopenhauerian Will. In Lovecraft’s “The Music of Erich Zahn” an “impoverished student of metaphysics” becomes intrigued by strange viol music coming from above his room. After meeting the musician the student discovers that each night he plays frantic music at a window in order to keep some horridness at bay, some “impenetrable darkness with chaos and pandemonium”. The aesthetic defenses provided by the well trained brain can bear the hex of matter for so long, the specter of unalterability within it which too many minds obliterate, collapsing everything before the thought of thought as thinkable or at least noetically mutable on our own terms. Transcendental paranoia is the concurrent nightmare and promise of Paul Humphrey's work, of being literally out of our minds. It is the gothic counterpart of thinking non-conceptually but also of thinking never belonging to any instance of purportedly solid being. As Bataille stated, “At the boundary of that which escapes cohesion, he who reflects within cohesion realizes there is no longer any room for him” Thought is immaterial only to the degree that it is inhuman, it is a power that tries, always with failure, to ascertain its own genesis. Philosophy, if it can truly return to the great outdoors, if it can leave behind the dead loop of the human skull, must recognize not only the non-priority of human thought, but that thought never belongs to the brain that thinks it, thought comes from somewhere else. To return to the train image from the beginning “a locomotive rolling on the surface of the earth is the image of continuous metamorphosis” this is the problem of thought, and of thinking thought, of being no longer able to isolate thought, with only a thought-formed structure. [1] One of the central tenets of Francois Laruelle's non-philosophy is that philosophy has traditionally operated on material already presupposed as thinkable instead of trying to think the real in itself. Philosophy, according to Laruelle, remains fixated on transcendental synthesis which shatters immanence into an empirical datum and an a prori factum which are then fused by a third thing such as the ego. For a critical account of Laruelle's non-philosophy see Ray Brassier's Nihil Unbound. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a (...) framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

As a continuation of this author’s previous cosmological neuroscience papers on the hypothesized Soul of Multiverse and its possible laws, the present work examined the social aspects of four of these laws. The following key aspects were recognized: (1) Knowing about the cosmic Law of Coexistence in Diversity can let our mind respect not only the endless diversity of human beings but also the cohesive force of space-time in which all are connected. This may help realizing the superiority of cooperation (...) for shared goals over competition for gaining by harming others. (2) Knowing about the cosmic Law of Truth in Complexity can ready our mind to confront the problems of societies with the understanding that these problems are much more complex than generally thought. This may help initiating the needed intellectual renaissance of the 21st century. (3) Knowing about the cosmic Law of Divine - Evil Asymmetry can make our mind appreciate the slight yet sufficient supremacy of divine over evil. This may help restoring faith in the eventual creation of a just society, where social justice is defined as an administrative mechanism providing the right conditions for every human being to accomplish his or her Conscience-led Mission throughout life, while allowing each of these accomplishments to be reciprocated with the gratitude it induced in the involved social systems, small or large, to let equal opportunities in life coexist with due diversity in welcomed, not abused, social recognitions. And (4) knowing about the cosmic Law of Lives to Transcend can empower our mind to build on these advances. This may help moving evolution towards the human species worthy of its origin and destination. (shrink)

The file on this site provides the slides for a lecture given in Hangzhou in May 2018, and the lecture itself is available at the URL beginning 'sms' in the set of links provided in connection with this item. -/- It is commonly assumed that regular physics underpins biology. Here it is proposed, in a synthesis of ideas by various authors, that in reality structures and mechanisms of a biological character underpin the world studied by physicists, in principle supplying detail (...) in the domain that according to regular physics is of an indeterminate character. In regular physics mathematical equations are primary, but this constraint leads to problems with reconciling theory and reality. Biology on the other hand typically does not characterise nature in quantitative terms, instead investigating in detail important complex interrelationships between parts, leading to an understanding of the systems concerned that is in some respects beyond that which prevails in regular physics. It makes contact with quantum physics in various ways, for example in that both involve interactions between observer and observed, an insight that explains what is special about processes involving observation, justifying in the quantum physics context the replacement of the unphysical many-worlds picture by one involving collapse. The link with biology furthermore clarifies Wheeler’s suggestion that a multiplicity of observations can lead to the ‘fabrication of form’, including the insight that this process depends on very specific ‘structures with power’ related to the 'semiotic scaffolding' of the application of sign theory to biology known as biosemiotics. -/- The observer-observed 'circle' of Wheeler and Yardley is a special case of a more general phenomenon, oppositional dynamics, related to the 'intra-action' of Barad's Agential Realism, involving cooperating systems such as mind and matter, abstract and concrete, observer and observed, that preserve their identities while interacting with one another in such a way as to act as a unit. A third system may also be involved, the mediating system of Peirce linking the two together. Such a situation of changing connections and separations may plausibly lead in the future to an understanding of how complex systems are able to evolve to produce 'life, the universe and everything'. -/- (Added 1 July 2018) The general structure proposed here as an alternative to a mathematics-based physics can be usefully characterised by relating it to different disciplines and the specialised concepts utilised therein. In theoretical physics, the test for the correctness of a theory typically involves numerical predictions, corresponding to which theories are expressed in terms of equations, that is to say assertions that two quantities have identical values. Equations have a lesser significance in biology which typically talks in terms of functional mechanisms, dependent for example on details of chemistry and concepts such as genes, natural selection, signals and geometrical or topologically motivated concepts such as the interconnections between systems and the unfolding of DNA. Biosemiotics adds to this the concept of signs and their interpretation, implying novel concepts such as semiotic scaffolding and the semiosphere, code duality, and appreciation of the different types of signs, including symbols and their capacity for abstraction and use in language systems. Circular Theory adds to this picture, as do the ideas of Barad, considerations such as the idea of oppositional dynamics. The proposals in this lecture can be regarded as the idea that concepts such as those deriving from biosemiotics have more general applicability than just conventional biology and may apply, in some circumstances, to nonlinear systems generally, including the domain new to science hypothesised to underlie the phenomena of present-day physics. -/- The task then has to be to restore the mathematical aspect presumed, in this picture, not to be fundamental as it is in conventional theory. Deacon has invoked a complex sequence of evolutionary steps to account for the emergence over time of human language systems, and correspondingly mathematical behaviour can be subsumed under the general evolutionary mechanisms of biosemiotics (cf. also the proposals of Davis and Hersh regarding the nature of mathematics), so that the mathematical behaviour of physical systems is consistent with the proposed scheme. In conclusion, it is suggested that theoretical physicists should cease expecting to find some universal mathematical ‘theory of everything’, and focus instead on understanding in more detail complex systems exhibiting behaviour of a biological character, extending existing understanding. This may in time provide a more fruitful understanding of the natural world than does the regular approach. The essential concepts have an observational basis from both biology and the little-known discipline of cymatics (a discipline concerned with the remarkable patterns that specific waveforms can give rise to), while again computer simulations also offer promise in providing insight into the complex behaviours involved in the above proposals. -/- References -/- Jesper Hoffmeyer, Semiotic Scaffolding of Living Systems. Commens, a Digital Companion to C. S. Peirce (on Commens web site). Terrence Deacon, The Symbolic Species, W.W. Norton & Co. Karen Barad, Meeting the Universe Halfway: Quantum Physics and the Entanglement of Matter and Meaning, Duke University Press. Philip Davis and Reuben Hersh, The Mathematical Experience, Penguin. Ilexa Yardley, Circular Theory. (shrink)

Biological diversity or biodiversity refers to the variety of life on Earth, comprising millions of plants, animals, microorganisms and the genes they contain. It simply means the existence of a wide variety of plant and animal species in their natural environments or the diversity of plant and animal life in a particular habitat. Environmental ethics is a branch of ethics and a form of philosophy which deals with the studies of relation of human beings and the environment. It includes (...) a moral consideration of human approach to natural resources and believes that human as well as other living creatures as parts of society. Biggest environmental ethic for human is to care for creation. (shrink)

The genomics “revolution” is spreading. Originating in the molecular life sciences, it initially affected a number of biomedical research fields such as cancer genomics and clinical genetics. Now, however, a new “wave” of genomic bioinformation is transforming a widening array of disciplines, including those that address the social, historical and cultural dimensions of human life. Increasingly, bioinformation is affecting “human sciences” such as psychiatry, psychology, brain research, behavioural research (“behavioural genomics”), but also anthropology and archaeology (“bioarchaeology”). Thus, bioinformatics is having (...) an impact on how we define and understand ourselves, how identities are formed and constituted, and, finally, on how we (on the basis of these redefined identities) assess and address some of the more concrete societal issues involved in genomics governance in various settings. This article explores how genomics and bioinformation, by influencing research agendas in the human sciences and the humanities, are affecting our self-image, our identity, the way we see ourselves. The impact of bioinformation on self-understanding will be assessed on three levels: (1) the collective level (the impact of comparative genomics on our understanding of human beings as a species), (2) the individual level (the impact of behavioural genomics on our understanding of ourselves as individuals), and (3) the genealogical level (the impact of population genomics on our understanding of human history, notably early human history). This threefold impact will be assessed from two seemingly incompatible philosophical perspectives, namely a “humanistic” perspective (represented in this article by Francis Fukuyama) and a “post-humanistic” one (represented by Peter Sloterdijk). On the basis of this analysis it will be concluded that, rather than focussing on human “enhancement” by adding or deleting genes, genome-oriented practices of the Self will focus on using genomics information in the context of identity-formation. Genomic bioinformation will increasingly be built into our self-images and used in order to tailor and adapt our practices of Self to our “personalised” genome. We will keep working on ourselves, no doubt, not by modifying our genomes, but rather by fine-tuning our behaviour. What we are experiencing is a bioinformatisation of the life-world. Genomics-based technologies will increasingly pervade our daily lives, our autobiographies and narratives, as well as our anthropologies, rather than our genomes as such. (shrink)

In the future, human destiny may depend on our ethics. In particular, biotechnology and expansion in space can transform life, raising profound questions. Guidance may be found in Life-centered ethics, as biotic ethics that value the basic patterns of organic gene/protein life, and as panbiotic ethics that always seek to expand life. These life-centered principles can be based on scientific insights into the unique place of life in nature, and the biological unity of all life. Belonging to life then (...) implies a human purpose: to safeguard and propagate life. Expansion in space will advance this purpose but will also raise basic questions. Should we expand all life or only intelligent life? Should we aim to create populations of trillions? Should we seed other solar systems? How far can we change but still preserve the human species, and life itself? The future of all life may be in our hands, and it can depend on our guiding ethics whether life will fulfil its full potentials. Given such profound powers, life-centered ethics can best secure future generations. Our descendants may then understand nature more deeply, and seek to extend life indefinitely. In that future, our human existence can find a cosmic purpose. (shrink)

This essay moves along broad lines from molecular biology to evolutionary biology and ecology to theology. Its objectives are to: 1) present some recent scientific findings in the emerging field of epigenetics that indicate that it is “the genome in context,” not genes per se, that are important in biological development and evolution; 2) show that this weakens the gene-centric neo-Darwinist explanation of evolution which, in fact, shares a certain preformationist orientation with intelligent design theory; 3) argue that the (...) evidence against a gene-centric view in no way negates Darwin’s central idea of “descent with modification”; 4) argue that an embrace of the evolutionary story, with all of its contingency and apparent lack of directionality, is not only consistent with Christianity, but actually resonates with the notion of the self-emptying love of God in Jesus Christ; and finally 5) suggest that we are called through an ecological imperative to embrace our evolutionary story, to listen to our “genetic coding,” and to reclaim our grounding as a species in the natural world. Corrigendum (published in later issue of journal): There was an error in the paragraph describing the mode of action of the small temporally-expressed RNAs (stRNAs) lin-4 and let-7 from Caenorhabditis elegans. Instead of reading "These two stRNAs act by binding to the tails of their target messenger RNAs (mRNAs); this results in destruction of the target and an overall drop in the level of production of protein from agouti mRNA" [note that agouti mRNA is not a target of these stRNAs], the sentence should have read, "These two stRNAs act by binding to the tails of target messenger RNAs (mRNAs); this leads to inhibition of translation of the mRNAs into protein and a consequent drop in the levels of the corresponding target protein.". (shrink)

About death, grief, mourning, life after death and immortality. Why should we die like humans to survive as a species. -/- "No one wants to die. Even people who want to go to heaven don't want to die to get there. And yet death is the destination we all share. No one has ever escaped it. And that is as it should be, because Death is very likely the single best invention of Life. It is Life's change agent. It (...) clears out the old to make way for the new." (Steve Jobs) -/- CONTENTS: -/- Death - Philosophy of death - Religions - - Animism - - Atheism - - Buddhism - - Christianity - - Hinduism - - Islam - - Jainism - - Jehovah's Witnesses - - Judaism - - Latter-day Saints - - Spiritism - Symbolism - Personification of Death - - Notable personifications - - In mythologies - - - Hindu mythology - - - In Japan - - - Slavic paganism - - - Lithuanian paganism - - In the three monotheistic religions - - - Judaism - - - Christianity - - - In Mexico - - - Islam - Axiochos - - The characters of dialogue - - Dialogue - - Prologue - - Arguments - - Citations - Paradise - - Greco-Roman mythology - - Mesopotamian mythology and influences - - According to Judaism - - According to Christianity - - - According to Catholicism - - - According to Protestantism - - - According to the Church of Jesus Christ of Latter-day Saints - - According to Islam - - According to Hinduism - - According to modern spiritualities - - - According to the esoteric - Hell - - Mesopotamian origins - - According to Christianity - - - Names appearing in the biblical texts - - - Medieval artistic representations - - - Concepts according to Christian movements - - According to Judaism - - According to Islam - - According to Buddhism - - According to Hinduism - - According to modern esotericism - - - According to Aïvanhov - - - According to Allan Kardec - - Philosophy - - - Jewish Kabbalah - - - Sartre - - - Popular wisdom Funerals - The funeral ritual: a rite of passage - Prehistory - Ancient death customs - - The family bereavement - - Mummification - - Sarcophagi - - Funerals - - Ancient Greece - - Ancient Rome - - Celts, Germans and Scandinavians - Religious funeral rites - - Buddhism - - Judaism - Christianity - - Protestantism - - Islam - Funeral rites by continent - - In Africa - - In Europe - The contemporary era - Mourning (Grief) - - Steps - - - Death of a close - - Loss events without mourning value (white factors) - - Duration and manifestations - - Risks - - Colors - Graveyards (Cemeteries) - - First cemeteries - - Cemeteries today - Funerary art - Dolmens - - Types of dolmens - - Function - - Location - Passage graves - Cenotaphs - - Famous cenotaphs - Lanterns of the Dead Afterlife - History - Questions about death and immortality - Testimonials - - Spiritualistic experiences - - Popular literature on the afterlife - - "Memories" and reminiscences - - Early studies of the science of the 19th century and early 20th century - Types of scenarios - Some religious and philosophical concepts - - Afterlife in Buddhism - - Afterlife in Christianity - - According to Hinduism - - According to Islam - - According to Judaism - - According to Mormonism - - According to the ancient philosophies - - According to Spiritism - - According to Native American traditions - - According to Vedism - - According to Esotericism - In science - Near-death experiences - - Clinical death - - NDE frequency - - Effects of depth of NDE on survival - - Near-death experiences and shared-death experience - - - The first contemporary testimonials - - - Experience according to Moody - - - The concept of "shared death" - - - The NDE scales - - The study of Pim van Lommel - - Spiritual and patient point of view - - - Survivalists studies - - - The religious understanding of the phenomenon - - Scientific views - - - Physiological explanation - - - Psychological explanation - Reincarnation - - Religions - - - In Hinduism - - - In Jainism - - - In Buddhism - - - In Judaism - - - In Christianity - - - In Islam - - In contemporary times - - - Esotericism - - - Works of the psychiatrist Ian Stevenson - - - Radical increase in life expectancy and artificial reincarnation - - Criticism - - - Arthur Schopenhauer - - - Ramana Maharshi - - - Rene Guenon - - - Ananda Kentish Coomaraswamy - Metempsychosis - - Theories - - Ideas - Maschalismos Immortality - Immortality of the soul and religious traditions - - Buddhism - - Christianity - - Islam - - Mormonism - Contemporary perception of the immortality of the body - - Observation in the animal kingdom - - Perspectives for mankind - Immortality in science - - Alexis Carrel - - Jean Rostand - - Hayflick limit - - Étienne-Émile Baulieu and DHEA - - Aubrey de Grey - - Professor Skulachev - - Regenerative medicine - - Professor Christopher Jaeger - Eternal Return - - According to the Mesopotamians - - According to Heraclitus and the Stoics - Fountain of Youth - - History of myth and relatives myths - - - In Roman mythology, Germanic, Celtic and Irish - - - In the Middle-East - - - In Spain - - - In the Bible - - The fountain in art and literature - - Painting - - - Literature and cinema - - Persistent of the myth until today - Senescence - - Why do we age? - - Gene regulation - - Cellular senescence Undead - Ghoul - Lich - Mummy - Skeleton - Vampire - Zombie - Other legendary creatures - Creatures specific to a particular universe - Spiritism - - Point out - - Origins of spiritism - - - The traditions through the ages - - - Advent of Christianity in Europe - - - The survival of necromancy - - - The precursors - - - Relations of spiritualism to science - Mediumship - - History - - Skeptical point of view - - Favorable doctor's viewpoint - Ghosts - - Appearance - - Belief in ghosts - - Origin - - - Duality and return dead - - - Ancient roots - - Typology - - - Poltergeists - - - Revenants - - - Ghosts - - - Banshees - - - Apparitions of crisis - - - Phantasms of the living - - - Vision of his own double - - - Ghost armies - - - Ghosts of animals - - - Means of transport - - Science perspective - - - Hallucinations - - - Sleep paralysis - - - Induced ghosts - - - Aches and infrasounds - - - Magnetic fields - Vampires - - Characteristics - - - Vampire transformation - - - Identification - - - Faculties - - Protection against the vampires - - - Precautions at death and burial - - - Apotropaic objects and places - - Destruction of vampires - Zombie - - The concept - - Africa and voodoo - - - West Africa - - - South Africa - - - In Haiti (and the Caribbean) - - - Scientific research - - The "revenants" in the Western imaginary Death in art - Memento mori - - History - - - Antiquity - - - Christianity - - - Mexican syncretism - - Performing arts - - - In painting - - - In literature - - - In movies - - - In video games - - - In Japanese animation - - - In music - The iconography of Weighing of souls (Particular judgment) - - Origin - - Written sources - - Weighing in Romanesque art - - Weighing in Gothic art - - Weighing in the late Middle Ages: to a new iconography - - Weighing of souls or actions? - Poems - - Charlotte Brontë, “On the Death of Anne Brontë” - - Edgar Allan Poe, “Annabel Lee” - - Edna St. Vincent Millay, “And you as well must die” - - Emily Dickinson, “Because I could not stop for Death” - - Emily Dickinson, “If I Should Die” - - Lord Byron, “Epitaph to a Dog” - - Pablo Neruda, “Only Death” - - Stephen Crane, “God Lay Dead in Heaven” - - W. B. Yeats, “He Wishes His Beloved Were Dead” - - Rainer Maria Rilke, “Death” - Paintings - - The Three Dead Kings - - The Death of Nelson - - Beata Beatrix - Sculptures - - The Kiss of Death - - Background - - Imagery - - Angel of Grief - - Fallen Astronaut - Quotes References About the author - Nicolae Sfetcu - - By the same author - - Contact Publishing House - MultiMedia Publishing -/- DOI: 10.58679/TW44411. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to (...) develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

CONTENT 1. Misconceptions of Darwin's Theory of Evolution 2. Darwinism against Essentialism and the Concept of Species 3. Function and Biological Explanation 4. The Gene 목차 1. 다윈의 진화론에 대한 오해들 2. 본질주의에 대한 진화론의 반대와 종(Species)의 개념 3. 기능(function)과 생명과학적 설명 4. 유전자 맺음말.

Microbial biofilm created huge burden in treatment of both community and hospital infections. A biofilm is complex communities of bacteria attached to a surface or interface enclosed in an exopolysaccharide matrix and protected from unfavorable conditions such as presence of antibiotics, host defense or oxidative stresses. Biofilms are often considered hot spot for horizontal gene transfer among same or different bacterial species. Furthermore, bacteria with increased hydrophobicity facilitate biofilm formation by reducing repulsion between the extracellular matrix and the (...) bacterium. There is a marked increase in the rate of persons nonresponsive to antibiotic therapy for infections of the Urinary Tract (UTIs), burns and upper respiratory tract due to biofilm formations. It is estimated that 90% of nosocomial infections are mediated by biofilm. The role of biofilm in infections has become so great that the treatment of such antibiotic resistance infections is proving difficult and costly to health care systems. The biofilm related infections varied from dental plaque, destruction of prosthetic valve to death of cystic fibrosis patients. This review aims to provide a summary of role of bacterial biofilm and its clinical implications for the patients. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

What is a race? Ernst Mayr (1904–2005) distinguishes between species in which biological change is continuous in space, and species in which groups of populations with different character combinations are separated by borders. In the latter species, the entities separated by borders are geographic races or subspecies. Many anthropology textbooks describe human races as discrete (or nearly discrete) clusters of individuals, geographically localized, each of which shares a set of ancestors, and hence can be distinguished from other (...) races by their common gene pool or by different alleles fixed in each. (shrink)

While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other hand, matters (...) are more complex. We provide a brief overview of recent proposals concerning the ontology of species, dealing with species as sets, classes and as collections, the views of Ernst Meyr, and mereological views. (shrink)

This week, the Royal Swedish Academy of Sciences announced the names of Nobel laureates in different fields. This year, the Nobel Prize in Biomedical Sciences was awarded to Swedish geneticist Svante Paabo for his discoveries concerning the DNA sequence of apes and human evolution. His work is especially meaningful as the question of human origin has long been a major concern to mankind. Modern-day wise humans belong to the genus Homo sapiens, along with seven ancient human races that existed millions (...) of years ago. Over time, many species became extinct and Professor Paabo discovered the gene transfer of these extinct species to Homo sapiens. With this discovery, he laid the foundation for other scientists to continue to search for the origin of modern humans. (shrink)

Rohwer & Marris claim that “many conservation biologists” believe that there is a prima facie duty to preserve the genetic integrity of species. (A prima facie duty is a necessary pro tanto moral reason.) They describe three possible arguments for that belief and reject them all. They conclude that the biologists they cite are mistaken, and that there is no such duty: duties to preserve genetic integrity are merely instrumental: we ought act to preserve genetic integrity only because doing (...) so is required by some other duty, such as the duty to preserve taxonomic biodiversity, or the duty to preserve the reproductive fitness of existing species. In permitting for instance the introgression of cattle genes into the genome of Bison bison we therefore do not necessarily fail in any respect ethically. I criticize the paper on three fronts. (shrink)

The purpose of this paper is to show the agreement of Camus and Aristotle on the cultural function of the art community, in particular their criticism of what should be called barbarian or nihilistic practices of art. Camus' art and criticism have been frequent targets of modern critics, but his point is and would be that such critics have the wrong idea of the purpose of art. His answer to such critics and the parallelism of his ideas with Aristotle's criticism (...) of barbarian culture, show that the real issue between Camus and his critics is cultural. (shrink)

The flow construct has been influential within positive psychology, sport psychology, the science of consciousness, the philosophy of agency, and popular culture. In spite of its longstanding influence, it remains unclear [a] how the constituents of the flow state ‘hang together’—how they relate to each other causally and functionally—[b] in what sense flow is an ‘optimal experience,’ and [c] how best to describe the unique phenomenology of the flow state. As a result, difficulties persist for a (...) clear understanding of the flow state’s structure and function. After explicating the standard view of the flow construct, I articulate several basic questions regarding its nature and functional roles, and I argue that these questions are best answered by integrating flow within broader streams of research on the dynamics of thought, on cognitive control resource allocation, and on creative thought. (shrink)

Let us start by some general definitions of the concept of complexity. We take a complex system to be one composed by a large number of parts, and whose properties are not fully explained by an understanding of its components parts. Studies of complex systems recognized the importance of “wholeness”, defined as problems of organization (and of regulation), phenomena non resolvable into local events, dynamics interactions in the difference of behaviour of parts when isolated or in higher configuration, etc., in (...) short, systems of various orders (or levels) not understandable by investigation of their respective parts in isolation. In a complex system it is essential to distinguish between ‘global’ and ‘local’ properties. Theoretical physicists in the last two decades have discovered that the collective behaviour of a macro-system, i.e. a system composed of many objects, does not change qualitatively when the behaviour of single components are modified slightly. Conversely, it has been also found that the behaviour of single components does change when the overall behaviour of the system is modified. There are many universal classes which describe the collective behaviour of the system, and each class has its own characteristics; the universal classes do not change when we perturb the system. The most interesting and rewarding work consists in finding these universal classes and in spelling out their properties. This conception has been followed in studies done in the last twenty years on second order phase transitions. The objective, which has been mostly achieved, was to classify all possible types of phase transitions in different universality classes and to compute the parameters that control the behaviour of the system near the transition (or critical or bifurcation) point as a function of the universality class. This point of view is not very different from the one expressed by Thom in the introduction of Structural Stability and Morphogenesis (1975). It differs from Thom’s program because there is no a priori idea of the mathematical framework which should be used. Indeed Thom considers only a restricted class of models (ordinary differential equations in low dimensional spaces) while we do not have any prejudice regarding which models should be accepted. One of the most interesting and surprising results obtained by studying complex systems is the possibility of classifying the configurations of the system taxonomically. It is well-known that a well founded taxonomy is possible only if the objects we want to classify have some unique properties, i.e. species may be introduced in an objective way only if it is impossible to go continuously from one specie to another; in a more mathematical language, we say that objects must have the property of ultrametricity. More precisely, it was discovered that there are conditions under which a class of complex systems may only exist in configurations that have the ultrametricity property and consequently they can be classified in a hierarchical way. Indeed, it has been found that only this ultrametricity property is shared by the near-optimal solutions of many optimization problems of complex functions, i.e. corrugated landscapes in Kauffman’s language. These results are derived from the study of spin glass model, but they have wider implications. It is possible that the kind of structures that arise in these cases is present in many other apparently unrelated problems. Before to go on with our considerations, we have to pick in mind two main complementary ideas about complexity. (i) According to the prevalent and usual point of view, the essence of complex systems lies in the emergence of complex structures from the non-linear interaction of many simple elements that obey simple rules. Typically, these rules consist of 0–1 alternatives selected in response to the input received, as in many prototypes like cellular automata, Boolean networks, spin systems, etc. Quite intricate patterns and structures can occur in such systems. However, what can be also said is that these are toy systems, and the systems occurring in reality rather consist of elements that individually are quite complex themselves. (ii) So, this bring a new aspect that seems essential and indispensable to the emergence and functioning of complex systems, namely the coordination of individual agents or elements that themselves are complex at their own scale of operation. This coordination dramatically reduces the degree of freedom of those participating agents. Even the constituents of molecules, i.e. the atoms, are rather complicated conglomerations of subatomic particles, perhaps ultimately excitations of patterns of superstrings. Genes, the elementary biochemical coding units, are very complex macromolecular strings, as are the metabolic units, the proteins. Neurons, the basic elements of cognitive networks, themselves are cells. In those mentioned and in other complex systems, it is an important feature that the potential complexity of the behaviour of the individual agents gets dramatically simplified through the global interactions within the system. The individual degrees of freedom are drastically reduced, or, in a more formal terminology, the factual space of the system is much smaller than the product of the state space of the individual elements. That is one key aspect. The other one is that on this basis, that is utilizing the coordination between the activities of its members, the system then becomes able to develop and express a coherent structure at a higher level, that is, an emergent behaviour (and emergent properties) that transcends what each element is individually capable of. (shrink)

This chapter contains sections titled: The Key: Losing Oneself Windsurfing Performance, Psychology, and Embedded Cognition Windsurfing and Flow.

Cooperation is rife in the microbial world, yet our best current theories of the evolution of cooperation were developed with multicellular animals in mind. Hamilton’s theory of inclusive fitness is an important case in point: applying the theory in a microbial setting is far from straightforward, as social evolution in microbes has a number of distinctive features that the theory was never intended to capture. In this article, I focus on the conceptual challenges posed by the project of extending Hamilton’s (...) theory to accommodate the effects of gene mobility. I begin by outlining the basics of the theory of inclusive fitness, emphasizing the role that the concept of relatedness is intended to play. I then provide a brief history of this concept, showing how, over the past fifty years, it has departed from the intuitive notion of genealogical kinship to encompass a range of generalized measures of genetic similarity. I proceed to argue that gene mobility forces a further revision of the concept. The reason in short is that, when the genes implicated in producing social behaviour are mobile, we cannot talk of an organism’s genotype simpliciter; we can talk only of an organism’s genotype at a particular stage in its life cycle. We must therefore ask: with respect to which stage(s) in the life cycle should relatedness be evaluated? For instance: is it genetic similarity at the time of social interaction that matters to the evolution of social behaviour, or is it genetic similarity at the time of reproduction? I argue that, strictly speaking, it is neither of these: what really matters to the evolution of social behaviour is diachronic genetic similarity between the producers of fitness benefits at the time they produce them and the recipients of those benefits at the end of their life-cycle. I close by discussing the implications of this result. The main payoff is that it makes room for a possible new mechanism for the evolution of altruism in microbes that does not require correlated interaction among bearers of the genes for altruism. The importance of this mechanism in nature remains an open empirical question. (shrink)