Gene clustering is a useful exploratory technique to group together genes with similar expression levels under distinct cell cycle phases or distinct conditions. It helps the biologist to identify potentially meaningful relationships between genes. In this study, we propose a clustering method based on multivariate normal mixture models, where the number of clusters is predicted via sequential hypothesis tests: at each step, the method considers a mixture model of m components (m = 2 in the first step) (...) and tests if in fact it should be m - 1. If the hypothesis is rejected, m is increased and a new test is carried out. The method continues (increasing m) until the hypothesis is accepted. The theoretical core of the method is the full Bayesian significance test, an intuitive Bayesian approach, which needs no model complexity penalization nor positive probabilities for sharp hypotheses. Numerical experiments were based on a cDNA microarray dataset consisting of expression levels of 205 genes belonging to four functional categories, for 10 distinct strains of Saccharomyces cerevisiae. To analyze the method’s sensitivity to data dimension, we performed principal components analysis on the original dataset and predicted the number of classes using 2 to 10 principal components. Compared to Mclust (model-based clustering), our method shows more consistent results. (shrink)

In the wake of the advent of genome editing technology CRISPR-Cas9 (clustered regularly interspaced palindromic repeat (CRISPR)-associated protein 9), there has been a global debate around the implications of manipulating the human genome. While CRISPR-based germline gene editing is new, the debate about the ethics of gene editing is not – for several decades now, scholars have debated the ethics of making heritable changes to the human genome. The arguments that have been raised both for and against the (...) use of genetic technologies in human reproduction reiterate much of the arguments made in the pre-CRISPR debate. As such, it is instructive for South Africa to reflect on these arguments now, in considering our position on the regulation of the use of this novel biotechnology. There are two dominant schools of thought in this area, bioliberalism and bioconservatism. Bioconservatives raise concerns about the risks of genetic manipulation, and argue that it ought to be limited or prohibited to avert these risks to human health and human nature. Bioliberal scholars are more open to the prospect of genetic manipulation, because of its potential utility. In this article, I conclude that in liberal democracies such as our own, bioliberal arguments ought to be seriously considered when formulating policy on human genome editing because of the extent to which they resonate with our Constitutional values and human rights. I further suggest that there is a need for an enquiry into the relevance of African perspectives on the ethical questions that arise concerning germline genome editing. (shrink)

Peter Winch famously critiqued Michael Oakeshott's view of human conduct. He argued that Oakeshott had missed the fact that truly human conduct is conduct that 'follows a rule.' This paper argues that, as is sometimes the case with Oakeshott, what seems, on the surface, to be a disagreement with another, somewhat compatible thinker about a matter of detail in some social theory in fact turns out to point to a deeper philosophical divide. In particular, I contend, Winch, as typical of (...) those who only picked up on Oakeshott's work in the 1940s and 1950s, when Oakeshott became known for his critique of rationalism, failed to understand the idealist metaphysics underlying that critique. (shrink)

A number of social theorists have contended that the essence of historical analysis is the employment of ideal types to comprehend past goings-on. But, while acknowledging that the study of history through ideal types can yield genuine insight, we may still ask if it represents the full emancipation of historical understanding from other modes of conceiving the past. This paper follows Michael Oakeshott's work on the philosophy of history in arguing that explaining the historical past by means of ideal types, (...) even though offering a coherent and fruitful enterprise, nevertheless falls short of fully embodying the characteristics that differentiate historical understanding. -/- This dispute involves fundamental issues regarding the nature of the social sciences. Furthermore, I suggest that it is of more than purely theoretical interest, in that social theorists who have accepted the Weberian view of historical inquiry will tend to be unaware of the defects inherent in all attempts to capture the nature of past events in a net of generalizations, and thus may be lead to ignore the inherent partiality of the understanding of historical happenings provided by ideal typification. (shrink)

The paper aims to explore what it means for something to be a social cycle, for a theory to be a social cycle theory, and to offer a suggestion for a simple, yet, we believe, fundamentally grounded schema for categorizing them. We show that a broad range of cycle theories can be described within the concept of disruption and adjustments. Further, many important cycle theories are true endogenous social cycle theories in which the theory provides a reason why the cycle (...) should recur. We find that many social cycle theories fit with a two-population disruption and adjustment model similar to the well-known predator-prey model. This implies that a general modeling framework could be established for creating agent-based models of many social cycle theories. (shrink)

The problem Plato sounds from the first lines of LAWS, his final dialogue, might be put in Jean-François Lyotard's term: it is the problem of the differend. Lyotard's position is briefly explained, shown to be applicable to the discussion in several ways (not the least of which is the three different gods appealed to as sources of the laws). We then see how Plato makes a chorus of the differend, resolving Lyotard's modern problem.

This reading of Plato's Ion shows that the philosophic action mimed and engendered by the dialogue thoroughly reverses its (and Plato's) often supposed philosophical point, revealing that poetry is just as defensible as philosophy, and only in the same way. It is by Plato's indirections we find true directions out: the war between philosophy and poetry is a hoax on Plato's part, and a mistake on the part of his literalist readers. The dilemma around which the dialogue moves is false, (...) and would have been recognized as such by Plato's contemporaries. Further, it is intrinsically related to a false, but popular, view of language. So the way out of the false dilemma of the dialogue is the way out of the war between philosophy and poetry, and also makes one see what is false about the view of language which makes such war plausible. (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)

As Shakespeare is closer in time and spirit to medieval psychology than to popular modern explanations of psyche, this article presents a fourfold analysis of ecstasy from Aquinas' Summa Theologiae to examine the characters of the play. I also suggest performance choices which make a variety of these ecstasies of soul more visible.

Discussion of partial grounds that aren't parts of full grounds; definition of full grounding in terms of partial grounding.

The usual interpretation of Republic 10 takes it as Socrates’ multilevel philosophical demonstration of the untruth and dangerousness of mimesis and its required excision from a well ordered polity. Such readings miss the play of the Platonic mimesis which has within it precisely ordered antistrophes which turn its oft remarked strophes perfectly around. First, this argument, famously concluding to the unreliability of image-makers for producing knowledge begins with two images—the mirror (596e) and the painter. I will show both undercut the (...) argument they introduce. Secondly, Socrates repeats the “three removes” argument three times. Each has its own object and philosophical axis. The “bed” argument (596a-598d) concerns the ontological status of images vis-à-vis human makers and the divine idea. The bit and bridle,” 601b-601d) emphasizes the epistemological status of image-making as beneath the human maker of bridles (having correct opinion) and the human user, who knows. This second takes away the ontological distinction which was the point of the first. Thus, any human being could be in any of the three positions—user, maker, imitator. This dance might bring one to doubt the conclusion that the imitator has “neither knowledge nor right opinion” (602a). Plato leads into his concluding psychological and moral argument (602c-605c) after a third variation of the 3 removes. This last gives us the image of the flute player (601d-602) as the one who knows and so can order the flute maker. We will conclude by considering what it is this flutist could know, and given that his art is itself a mimesis, who the imitator of this imitative artist could be. Thus attention to the differences among these examples opens a defense of the arts, which reverses many of the claims made against the arts within the ostensible “Platonic” argument. (shrink)

In a very literarily complicated setting, Frater Taciturnus sets a remark about Hamlet not being a Christian tragedy. After unpeeling that literary setting and noting that Taciturnus' remark aims more at Jacob Börne than at Shakespeare, the paper shows how Frater Taciturnus' remark calls into question the religious project of a certain danish author. For, Taciturnus' primary concern is to show that religious drama is not possible, or at least "ought not be." This general law applies to Hamlet as well, (...) and if Shakespeare was attempting a religious drama he a) shouldn't have because such a thing is essentially undramatizable, and b) failed because he did not begin (which would be possible) by showing the hero's religious presuppositions. Frater Taciturnus himself has given considerable thought to the extent and the manner in which the religious can be represented; in fact the letter to the reader is his proof of how perfectly his own narrative, "Guilty/Not Guilty," was constructed with precisely these problems in mind. The play is not the thing that Taciturnus is really interested in, nor is he interested in the playwright's intentions, he considers that the play's the thing that catches out Börne's misunderstanding of the religious, and it is this field—in particular, that area where the religious life and literary art intersect, that is the brother's interest and forte. But if Taciturnus is correct in his criticism of Börne, it should be impossible for S. Kierkegaard to produce a religious authorship as well. (shrink)

This paper aims at interpreting (primarily) the first six chapters of Aristotle’s Poetics in a way that dissolves many of the scholarly arguments conceming them. It shows that Aristotle frequently identifies the object of his inquiry by opposing it to what is other than it (in several different ways). As a result aporiai arise where there is only supposed to be illuminating exclusion of one sort or another. Two exemplary cases of this in chapters 1-6 are Aristotle’s account of mimesis (...) as other than enunciative speech (speech that makes truth claims, or representation) and his account of the final cause of tragedy in itself as plot, vis a vis its final cause as regards the audience, which is katharsis. Confusions arising from failure to see the otherness of representation and katharsis leads to an overly intellectualist understanding of the purpose of tragedy. (shrink)

ABSTRACT Clinicians, researchers and the informed public have come to view addiction as a brain disease. However, in nature even extreme events often reflect normal processes, for instance the principles of plate tectonics explain earthquakes as well as the gradual changes in the face of the earth. In the same way, excessive drug use is predicted by general principles of choice. One of the implications of this result is that drugs do not turn addicts into compulsive drug users; they retain (...) the capacity to say ?no?. In support of the logical implications of the choice theory approach to addiction, research reveals that most addicts quit using drugs by about age 30, that most quit without professional help, that the correlates of quitting are the correlates of decision making, and, according to the most recent epidemiological evidence, the probability of quitting remains constant over time and independent of the onset of dependence. This last result implies that, after an initial period of heavy drug use, remission is independent of any further exposure to drugs. In short, there is much empirical support for the claim that addiction emerges as a function of the rules of everyday choice. (shrink)

Kant admits that there are two kinds of human works that have something sublime about them, the work of the poet, e.g., tragedy, and the work of the politician, i.e., war. This paper will explore Kant's reasoning about the sublime element in these two human works.

In this book, author Gene Fendt shows how Plato's Republic provides a liturgical purification for the political and psychic delusions of democratic readers, even as Socrates provides the same for his interlocutors at the festival of Bendis. Each of the several characters is analyzed in accord with Book Eight's 6 geometrically possible kinds of character showing how their answers and failures in the dialogue exhibit the particular kind of movement and blindness predictable for the type.

Defense of an account of intrinsic properties in terms of (what is now called) grounding rather than naturalness.

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)

Talk of different types of cells is commonplace in the biological sciences. We know a great deal, for example, about human muscle cells by studying the same type of cells in mice. Information about cell type is apparently largely projectible across species boundaries. But what defines cell type? Do cells come pre-packaged into different natural kinds? Philosophical attention to these questions has been extremely limited [see e.g., Wilson (Species: New Interdisciplinary Essays, pp 187–207, 1999; Genes and the Agents of Life, (...) 2005; Wilson et al. Philos Top 35(1/2):189–215, 2007)]. On the face of it, the problems we face in individuating cellular kinds resemble those biologists and philosophers of biology encountered in thinking about species: there are apparently many different (and interconnected) bases on which we might legitimately classify cells. We could, for example, focus on their developmental history (a sort of analogue to a species’ evolutionary history); or we might divide on the basis of certain structural features, functional role, location within larger systems, and so on. In this paper, I sketch an approach to cellular kinds inspired by Boyd’s Homeostatic Property Cluster Theory, applying some lessons from this application back to general questions about the nature of natural kinds. (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)

Over the last two decades, there was an upsurge of research and innovation in biotechnology and related fields, leading to exciting new discoveries in areas such as the engineering of biological processes, gene editing, stem cell research, CRISPR-Cas9 technology, Synthetic Biology, recombinant DNA, LMOs and GMOs, to mention only a few. At the same time, these advances generated concerns about biosafety, biosecurity and adverse impacts on biodiversity and the environment, leading to the establishment of Research Ethics Committees (RECs) at (...) Higher Education and Research Institutions dedicated to reviewing research with implications for biosafety and the environment. -/- These Biosafety and Environment Research Ethics Committees, referred to as EBRECs, are in the early stages of their establishment and formalisation, and there is much uncertainty about their composition, scope, procedures of decision-making and the principles that should guide their deliberations and assessments. In many respects, EBRECs are venturing into uncharted territory, facing a very wide range of complex research fields, far-reaching research practices and deep concerns new to Review Boards, raising the question to what extent EBRECs can fall back on the fairly well-established principles and procedures of RECs focusing on Human, Health or Animal research, and to what extent they need new or adapted principles and procedures. -/- Against this background, I set out to answer the following three main research questions in this thesis: 1. What is the current state of ethical principles for ethics reviews in the field of environmental and biosafety research ethics? Which principles are currently used in this context, and how? 2. What are the shortcomings of the current principles used by EBRECs and how can they be overcome? 3. What ethical principles must be adopted by environmental and biosafety research ethics committees and guide them in their decision-making? -/- In order to prepare the ground and set the scene for my discussion of these questions, I also formulated four supporting research questions: i. What is environmental research ethics in action? ii. What is biosafety research ethics in action? iii. How are environmental and biosafety ethics related to one another? iv. How should the guidelines and ethical principles related to these two overlapping fields be implemented in the ethics review process? Following my introduction and problem statement in Chapter 1, I devoted Chapters 2 and 3 to an overview of my supporting questions to set the scene for Environmental and Biosafety Research Ethics. In Chapter 4, I turned to my main research question with a discussion of national and international declarations, frameworks and legislation and an investigation of principles in the different research areas to get a picture of applicable principles that can guide EBRECs. -/- The main finding of my thesis is that due to the complexity of EBR, different categories of principles could be the solution for EBRECs. I elaborate on this in Chapter 5, my concluding chapter, in which I also propose a list of core principles that can serve as an accessible and easy-to-use guide for EBRECs in their decision-making. In this proposal, I cluster different kinds of principles in terms of four categories: 1. Principles as a Moral Concept 2. Principles as a Social Concept 3. Principles as a Legal Concept 4. Principles as a Safety Concept . (shrink)

The gene's-eye view of evolution is an influential but contentious perspective on biology. It emerged in the aftermath of the Modern Synthesis and both proponents and detractors have stressed the link between the two. In particular, both the Modern Synthesis and the gene's-eye view have been criticized for overemphasizing the role genes at the expense of organisms in evolutionary explanations. In this chapter, I discuss the connection between the Modern Synthesis and the gene’s-eye view and evaluate the (...) status of genes and organisms in contemporary biology. I show that while the gene’s-eye view traces its origin back to the Modern Synthesis, it can most accurately be said to represent a specific – adaptationist and gene-centric – version of it. To assess the role of genes and organisms, I examine the intimate relationship between the gene’s-eye view and another post-Synthesis development, the concept of inclusive fitness. I argue that the popularity and influence of inclusive fitness theory demonstrate that the individual organism remains safe at the heart of modern evolutionary biology. (shrink)

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)

Noah Rosenberg et al.'s 2002 article “Genetic Structure of Human Populations” reported that multivariate genomic analysis of a large cell line panel yielded reproducible groupings (clusters) suggestive of individuals' geographical origins. The paper has been repeatedly cited as evidence that traditional notions of race have a biological basis, a claim its authors do not make. Critics of this misinterpretation have often suggested that it follows from interpreters' personal biases skewing the reception of an objective piece of scientific writing. I contend, (...) however, that the article itself to some degree facilitates this misrepresentation. I analyze in detail several verbal and visual features of the original article that may predispose aspects of its racial interpretation; and, tracing the arguments of one philosopher and one popular science writer, I show how these features are absorbed, transformed into arguments for a biological basis of race, and re-attributed to the original. The essay demonstrates how even slight ambiguities can enable the misappropriation of scientific writing, unintentionally undermining the authors' stated circumspection on the relationship between cluster and race. (shrink)

What is a gene? Does it represent a natural kind, or is it just a tool for genomics? A clear answer to these questions has been challenged by postgenomic discoveries. In response, I will argue that the gene can be deemed a natural kind as it satisfies some requirements for genuine kindhood. Specifically, natural kinds are projectible categories in our best scientific theories, and they represent nodes in the causal network of the world (as in Khalidi. Natural Categories (...) and Human Kinds: Classification in the Natural and Social Sciences. Cambridge University Press, Cambridge, 2013; Khalidi. Synthese 195: 1379–1396, 2018; Khalidi. Are Sexes Natural Kinds, In: Dasgupta S, Weslake B (eds) Current Controversies in Philoso-phy of Science. Routledge, New York, 2020; Khalidi. Philos Sci 88:1–21, 2021). In Sect. 2, I will present a brief history of the gene and the controversy over its status. In Sect. 3, I will introduce the account of natural kinds considered in this paper. In Sect. 4, I will first present the relevant definition of genes and how they can be classified. Then, I will argue that the gene can be considered a natural kind as it satisfies the criteria for natural kindhood. Section 5 concludes. (shrink)

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)

The cluster account, one of the best attempts at art classification, is guilty of ahistoricism. While cluster theorists may be happy to limit themselves to accounting for what art is now rather than how the term was understood in the past, they cannot ignore the fact that people seem to apply different clusters when judging art from different times. This paper shows that while allowing for this kind of historical relativity may be necessary to save the account, doing so could (...) result in incorporating an essentially institutional component or making the theory extremely complex and virtually impossible to use. (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)

Many arguments have been made against gene editing. This paper addresses the commonly invoked argument that gene editing violates human dignity and is ultimately a subversion of human nature. There are several drawbacks to this argument. Above all, the concept of what human dignity means is unclear. It is not possible to condemn a practice that violates human dignity if we do not know exactly what is being violated. The argument’s entire reasoning is thus undermined. Analyses of the (...) arguments involved in this discussion have often led to the conclusion that gene editing contravenes the principle of genetic identity (genetic immutability) thereby subverting a requisite of human dignity and ultimately threatening human nature. This paper refutes these arguments and shows that any opposition to gene editing cannot rely on the human dignity argument. (shrink)

Our prominent definitions of cognition are too vague and lack empirical grounding. They have not kept up with recent developments, and cannot bear the weight placed on them across many different debates. I here articulate and defend a more adequate theory. On this theory, behaviors under the control of cognition tend to display a cluster of characteristic properties, a cluster which tends to be absent from behaviors produced by non-cognitive processes. This cluster is reverse-engineered from the empirical tests that comparative (...) psychologists use to determine whether a behavior was generated by a cognitive or a non-cognitive process. Cognition should be understood as the natural kind of psychological process that non-accidentally exhibits the properties assessed by these tests (as well as others we have not yet discovered). Finally, I review two plausible neural accounts of cognition's underlying mechanisms?one based in localization of function to particular brain regions and another based in the more recent distributed networks approach to neuroscience?which would explain why these properties non-accidentally cluster. While this notion of cognition may be useful for a number of debates, I here focus on its application to a recent crisis over the distinction between cognition and association in comparative psychology. (shrink)

Although there once was a general consensus among race scholars that applying race categories to humans is biologically illegitimate, this consensus has been erased over the past decade. This is largely due to advances in population genetics that allow biologists to pick out genetic population clusters that approximate some of our common sense racial categories. In this paper, I argue that this new ability really ought not undermine our confidence in the biological illegitimacy of the human races. Unfortunately, the claim (...) that races are biologically legitimate is ambiguous—the sense I will be concerned with here holds that the human species can be divided into biological subspecies. Sesardic and Andreasen have both argued that the cluster results are evidence for subspecies within the human population. I show the cluster results are in fact evidentially inert relative to each author’s preferred subspecies concept. I then sketch the kinds of biological facts that could be used to adjudicate whether human subspecies have existed in the past. (shrink)

The unit of selection is the concept of that ‘something’ to which biologists refer when they speak of an adaptation as being ‘for the good of’ something. Darwin identified the organism as the unit of selection because for him the ‘struggle for existence’ was an issue among individuals. Later on it was suggested that, in order to understand the evolution of social behavior, it is necessary to argue that groups, and not individuals, are the units of selection. The last addition (...) to this debate was the formulation by Dawkins, in 1976, that the genes themselves are the units of selection while the organisms are merely the temporary receptacles and vehicles for such genes. Thus, the preposterous dissolution of the organism into genes and the proteins coded by such genes has been introduced in the evolutionary discourse by neglecting that the explanations for biological phenomena can be either synchronic or diachronic, depending on the phenomenon to be explained. Therefore explanations in molecular biology are synchronic while evolutionary biology needs diachronic explanations. Nevertheless, for ultra-Darwinians such as Dawkins, efficient replication is all that biology is about. Here I develop an argument in order to show that there is nothing in molecular and cell biology that might support such a contention and that the idea of the gene as the unit of selection is incompatible with the evident evolution of biological complexity. (shrink)

The unit of selection is the concept of that ‘something’ to which biologists refer when they speak of an adaptation as being ‘for the good of’ something. Darwin identified the organism as the unit of selection because for him the ‘struggle for existence’ was an issue among individuals. Later on it was suggested that, in order to understand the evolution of social behavior, it is necessary to argue that groups, and not individuals, are the units of selection. The last addition (...) to this debate was the formulation by Dawkins, in 1976, that the genes themselves are the units of selection while organisms are merely the temporary receptacles and vehicles for such genes. Thus, the preposterous dissolution of the organism into genes and the proteins coded by such genes has been introduced in the evolutionary discourse by neglecting that the explanations for biological phenomena can be either synchronic or diachronic, depending on the phenomenon to be explained. Therefore explanations in molecular biology are synchronic while evolutionary biology needs diachronic explanations. Nevertheless, for ultra-Darwinians such as Dawkins, efficient replication is all that biology is about. Here I develop an argument in order to show that there is nothing in molecular and cell biology that might support such a contention and that the idea of the gene as the unit of selection is incompatible with the evident evolution of biological complexity. (shrink)

We attempt to improve the understanding of the notion of agene being `for a phenotypic trait or traits. Considering theimplicit functional ascription of one thing being `for another,we submit a more restrictive version of `gene for talk.Accordingly, genes are only to be thought of as being forphenotypic traits when good evidence is available that thepresence or prevalence of the gene in a population is the resultof natural selection on that particular trait, and that theassociation between that trait and (...) the gene in question isdemonstrably causal. It is therefore necessary to gatherstatistical, biochemical, historical, as well as ecologicalinformation before properly claiming that a gene is for aphenotypic trait. Instead of hampering practical use of the `genefor talk, our approach aims at stimulating much needed researchinto the functional ecology and comparative evolutionary biologyof gene action. (shrink)

The homeostatic property cluster theory is widely influential for its ability to account for many natural-kind terms in the life sciences. However, the notion of homeostatic mechanism has never been fully explicated. In 2009, Carl Craver interpreted the notion in the sense articulated in discussions on mechanistic explanation and pointed out that the HPC account equipped with such notion invites interest-relativity. In this paper, we analyze two recent refinements on HPC: one that avoids any reference to the causes of the (...) clustering of properties and one that replaces homeostatic mechanisms with causal networks represented by causal graphs. We argue that the former is too slender to account for some inductive inference in science and the latter, thicker account invites interest-relativity, as the original HPC does. This suggests that human interest will be an un-eliminative part of a satisfactory account of natural kindness. We conclude by discussing the implication of interest-relativity to the naturalness, reality, or objectivity of kinds and indicating an overlooked aspect of natural kinds that requires further studies. (shrink)

A dominant strand of philosophical thought holds that natural kinds are clusters of objects with shared properties. Cluster theories of natural kinds are often taken to be a late twentieth-century development, prompted by dissatisfaction with essentialism in philosophy of biology. I will argue here, however, that a cluster theory of kinds had actually been formulated by William Whewell (1794-1866) more than a century earlier. Cluster theories of kinds can be characterized in terms of three central commitments, all of which are (...) present in Whewell’s work on classification. Like contemporary cluster theorists, Whewell claims that kinds are united by similarity, that many kinds do not have essences, and that there are “gaps” between kinds. Moreover, Whewell advises taxonomists to look for consilience (roughly, convergence) between different classificatory schemes, a recommendation that reinforces the identification of natural classes with property clusters. Thus Whewell was not only an early cluster theorist, but one with important insights into what a cluster theory of kinds means for the practice of classification. (shrink)

In accordance with Order No. 548 of the Ministry of Infrastructure dated December 21, 2015 “On measures for the development of road transport and the road economy for the period until 2020”, strategic directions and strategic development goals were developed. This is necessary to ensure the implementation of plans and the implementation of EU legislation in accordance with the Association Agreement. In accordance with the Order, the priorities were to reform the road sector and to ensure the development and maintenance (...) of the road network in good condition. It was also proposed to modify the existing road financing system. (shrink)

When we think about postmodernism we have to consider its implication in every aspect of society and none would doubt that homosexuality is one of these major implication especially for the contemporary church. The influence of relativism and the paradigm shift in humanity made homosexuality not just acceptable, but in many cases a norm. For a long time the church barricaded herself not only behind her Jewish-christian worldview and theological values, but also behind the absolutes of science that just has (...) to agree that in the beginning there were only male and female. For long time homosexuality has been viewed as a behavior option, but what about if science has come up with a new discovery so called Gay Gene? That is exactly what we want to discuss in this essay. (shrink)

The paper argues for a decompositionalist account of lexical concepts. In particular, it presents and argues for a cluster decompositionalism, a view that claims that the complexes a token of a word corresponds to on a given occasion are typically built out of a determinate set of basic concepts, most of which are present on most other occasions of use of the word. The first part of the paper discusses some explanatory virtues of decompositionalism in general. The second singles out (...) cluster decompositionalism as the best explanation of the variability of meaning. The third part is devoted to responding to some problems. (shrink)

Personalized genomics companies (PG; also called ‘direct-to-consumer genetics’) are businesses marketing genetic testing to consumers over the Internet. While much has been written about these new businesses, little attention has been given to their roles in science communication. This paper provides an analysis of the gene concept presented to customers and the relation between the information given and the science behind PG. Two quite different gene concepts are present in company rhetoric, but only one features in the science. (...) To explain this, we must appreciate the delicate tension between PG, academic science, public expectation, and market forces. (shrink)

I present and defend a novel version of the homeostatic property cluster account of natural kinds. The core of the proposal is a development of the notion of co-occurrence, central to the HPC account, along information-theoretic lines. The resulting theory retains all the appealing features of the original formulation, while increasing its explanatory power, and formal perspicuity. I showcase the theory by applying it to the problem of reconciling the thesis that biological species are natural kinds with the fact that (...) many such species are polymorphic. (shrink)

Despite myriad controversies about reasons, two theses are frequently taken for granted: (i) reasons are sources of normative support for actions, attitudes, etc; and (ii) reasons, at least in simple, paradigmatic cases, consist in atomic facts. Call this conjunction “the atomic view.” Against this, we advocate what we call “the cluster view,” on which even in the simplest cases, the normative support for an action or attitude is typically provided by a whole cluster of facts. Moreover, many of these facts (...) are on an explanatory par—they each play the same kind of role in explaining why there is normative support for the action or attitude in question. We show that presupposition of the atomic view generates unnecessary (psuedo-)puzzles⁠—about topics such as rationality, moral worth, and doxastic justification⁠—that can be largely (dis)solved with the cluster view in place. The cluster view’s ability to do this constitutes an argument in its favor, beyond intuitive considerations that we also adduce. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality (...) through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

This paper is trying to put together two different researches, from theology and from genetics, about a general and undetermined topic, death. It is undetermined because no one can say something demonstrable and unequivocal about it, since no person alive can cross over the edge of life and come back from the domain of death with information about it. But we can discuss nevertheless things that are obvious and possible to be reasonably inferred about death even by livings. In this (...) regard Theology will provide the mainline of what is to be known as death for religion in general, while Genetics will try to come with its research to sustain or contradict the general premise: death is not an ontological behavior of living matter, but an imposed attribute after the sin occurred into the world. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of (...) certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

In markets globalization and increasing competition context, governments of the world’s leading countries are forced to use complex organizational and economic instruments to support the countries’ economy. One of such instruments is creation of Free Economic Zones (FEZ) with favorable conditions for doing business. Over the last decade activation process of Free Economic Zones mechanism disposal for the economy of a particular country development has been possible to observe. If in 1995 there were approximately 500 zones in the world, now (...) there are more than 4,300 zones in more than 130 countries which employ more than 68 thousand workers. In addition, global practice has shown that FEZ activities effective organization is efficient not only in giving impetus to the country’s economy development, but in bringing it into the world leaders as well. (shrink)

It is widely accepted that the way information transfers across networks depends importantly on the structure of the network. Here, we show that the mechanism of information transfer is crucial: in many respects the effect of the specific transfer mechanism swamps network effects. Results are demonstrated in terms of three different types of transfer mechanism: germs, genes, and memes. With an emphasis on the specific case of transfer between sub-networks, we explore both the dynamics of each of these across networks (...) and a measure of their comparative fitness. Germ and meme transfer exhibit very different dynamics across linked networks. For germs, measured in terms of time to total infection, network type rather than degree of linkage between sub-networks is the primary factor. For memes or belief transfer, measured in terms of time to consensus, it is the opposite: degree of linkage trumps network type in importance. The dynamics of genetic information transfer is unlike either germs or memes. Transfer of genetic information is robust across network differences to which both germs and memes prove sensitive. We also consider function: how well germ, gene, and meme transfer mechanisms can meet their respective objectives of infecting the population, mixing and transferring genetic information, and spreading a message. A shared formal measure of fitness is introduced for purposes of comparison, again with an emphasis on linked sub-networks. Meme transfer proves superior to transfer by genetic reproduction on that measure, with both memes and genes superior to infection dynamics across all networks types. What kinds of network structure optimize fitness also differ among the three. Both germs and genes show fairly stable fitness with added links between sub-networks, but genes show greater sensitivity to the structure of sub-networks at issue. Belief transfer, in contrast to the other two, shows a clear decline in fitness with increasingly connected networks. When it comes to understanding how information moves on networks, our results indicate that questions of information dynamics on networks cannot be answered in terms of networks alone. A primary role is played by the specific mechanism of information transfer at issue. We must first ask about how a particular type of information moves. (shrink)

A discussion of plasticity genes and the genetic architecture of gene-environment interactions.

In this paper, I explore the “expressivist critique” of the use of prenatal testing to select against the birth of persons with impairments. I begin by setting out the expressivist critique and then highlighting, through an investigation of an influential objection to this critique, the ways in which both critics and proponents of the use of technologies of genetic selection negotiate a difficult set of dilemmas surrounding the relationship between genes and identity. I suggest that we may be able to (...) advance the debate about these technologies by becoming more aware of the ways in which this debate is itself in part a political contestation over this relationship. Ultimately, I will argue, the real force of the expressivist objection lies in its capacity to draw our attention to political questions about the role of the state and about relationships between different social groups rather than between parents and prospective children. That is to say, crucial issues, when evaluating the force of this criticism, turn out to be: the nature of the institutions which determine how decisions about prenatal selection are made; and how we think of each other, that is, what we take to be the defining characteristics of human beings. Paradoxically, arguments about the ethics of the “sorting society”, both supportive and critical, are an important arena in which these institutions and these ideas about identity are contested and shaped. An increased awareness of the reflexive nature of the process of debating these issues may assist us in better negotiating them. (shrink)

Molyneux’s question, whether the newly sighted might immediately recognize tactilely familiar shapes by sight alone, has produced an array of answers over three centuries of debate and discussion. I propose the first pluralist response: many different answers, both yes and no, are individually sufficient as an answer to the question as a whole. I argue that this is possible if we take the question to be cluster concept of sub-problems. This response opposes traditional answers that isolate specific perceptual features as (...) uniquely applicable to Molyneux’s question and grant viability to only one reply. Answering Molyneux’s question as a cluster concept may also serve as a methodology for resolving other philosophical problems. (shrink)