A dialogue in which Freya argues that conspiracy theories are illogical, but Orin is not so sure!

“I will show you fear in a handful of dust” (T. S. Eliot: The Wasteland) -/- How can dust and water become a conscious living person capable of fear? The way these elements are transformed into life is sketched out, but it's our conscious minds, our intensity of being in a flood of emotions; this is the big problem that science has so far failed to explain. Freya, a biologist, is dissatisfied with the way evolution has no explanation for her (...) own self. Instead, science treats people as robots with any self-awareness considered an illusion. In this way, it destroys our humanity. Max explains that given the chemical basis of life, this is the only possible conclusion. On the brink of accepting this unpalatable fact, she meets with Orin. Together they explore the unthinkable, that the basis of consciousness and self is present in the underlying operations of the universe. These skilfully constructed dialogues explain how the process philosophy of Alfred North Whitehead and panpsychism (primordial universal consciousness) can explain the evolution of not only bodies but also of life, self and consciousness. (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 dialogue arguing that morality has an objective basis in the mathematical object describing the "tit for tat" game theory. To play the game, a contractual obligation is freely made to cooperate and to fairly distribute the gains. Failure to meet these obligations results in social punishment.

It is widely affirmed that human beings have irreplaceable valuable, and that we owe it to them to treat them accordingly. Many theorists have been drawn to Kantianism because they think that it alone can capture this intuition. One aim of this paper is to show that this is a mistake, and that Kantianism cannot provide an independent rational vindication, nor even a fully illuminating articulation, of irreplaceability. A further aim is to outline a broadly Aristotelian view that provides a (...) more fitting theoretical framework for this appealing conception of human value. This critique of Kantianism extends to contemporary theorists with a broadly Kantian orientation, including Christine Korsgaard, Stephen Darwall and John Rawls. The problem with these views, at heart, is that they attempt to ground morality in respect alone. Yet it is love, not respect, that brings irreplaceability into view. The paper closes with a sketch of a virtue-theoretic theory that follows Aquinas in taking love to be a master virtue that refines the other virtues so as to ensure a continuous and practically efficacious sensitivity to the irreplaceable value of fellow human beings. (shrink)

IntroductionAssociative theories of political obligation offer a fresh alternative to approaches such as social contract theory, fair play, and the natural duty of justice. Few suggestions in ethics are more intuitive than the idea that we have special obligations to our family and friends, just in virtue of our relationships with them, and it is reasonable that obligations to political society are also grounded through association.A basic question for associative theories is to explain how associations give rise to obligation, but (...) here there is a common error. Many associative theorists and their critics take this question to be equivalent to the question: what distinguishes associations that are morally acceptable from those that are not? The assumption is that associations which are morally acceptable are those that give rise to obligations. However, this assumption is wrong in two ways. Associations that have some unacceptable features may still give rise to obl .. (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)

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.

A dialogue in which Freya nan Max are determined to argue abut free will.

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)

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)

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)

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.

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)

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 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)

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)

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)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (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)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

I argue that four of the fundamental claims of those calling themselves `genic pluralists'Philip Kitcher, Kim Sterelny, and Ken Watersare defective. First, they claim that once genic selectionism is recognized, the units of selection problems will be dissolved. Second, Sterelny and Kitcher claim that there are no targets of selection. Third, Sterelny, Kitcher, and Waters claim that they have a concept of genic causation that allows them to give independent genic causal accounts of all selection processes. I argue that each (...) one of these claims is either false or misleading. Moreover, the challenge that arises from the availability of genic causal accounts, namely, the inability to choose on rational grounds among genic and higher-level accounts, is unsupported. (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)

A number of debates in philosophy of biology and psychology, as well as in their respective sciences, hinge on particular views about the relationship between genotypes and phenotypes. One such view is that the genotype-phenotype relationship is relatively straightforward, in the sense that a genome contains the ?genes for? the various traits that an organism exhibits. This leads to the assumption that if a particular set of traits is posited to be present in an organism, there must be a corresponding (...) number of genes in that organism's genome to account for those traits. This assumption underlies what can be called the ?counting argument,? in which empirical estimates of the number of genes in a genome are used to support or refute particular hypotheses in philosophical debates about biology and psychology. In this paper, we assess the counting argument as it is used in discussions of the alleged massive modularity of the brain, and conclude that this argument cannot be upheld in light of recent philosophical work on gene concepts and empirical work on genome complexity. In doing so, we illustrate that there are those on both sides of the debate about massive modularity who rely on an incorrect view of gene concepts and the nature of the genotype-phenotype relationship. (shrink)

Concerns around Generative Artificial Intelligence (GenAI) in higher education have so far largely centred on assessment integrity, resulting in fundamental questions about students’ broader engagement with these tools remaining underexplored. This paper reports on the findings of a survey that forms part of a wider study, comprising the first empirical investigation of GenAI use by university students as a method of engaging with their academic readings. Our survey of 101 students shows that over half of all students surveyed used GenAI (...) to some degree as a method of engaging with their unit readings. Our findings suggest that students turn to these tools in response to time constraints and conceptual difficulties, while maintaining complex attitudes toward their use: most welcome their availability, yet few report trusting or relying on GenAI-generated interpretations or summaries of texts. Importantly, our data reveals substantial demographic variations in usage patterns, with international students and those taking subjects as electives showing significantly higher rates of AI use to assist with reading. This suggests GenAI tools may be serving as important mediators for attempting to overcome epistemic barriers to learning, particularly for students who face additional linguistic or disciplinary challenges. (shrink)

Heyes presents a compelling account of how cultural evolutionary processes shape and create “rules,” or norms, of social behavior. She suggested that normativity depends on implicit, genetically inherited, domain-general processes and explicit, culturally inherited, domain-specific processes. Her approach challenges the nativist point of view and provides supporting evidence that shows how social interactions are responsible for creating mental processes that assist in understanding and behaving according to rules or norms. We agree. In our commentary, we suggest that it is not (...) only that mental processes for grasping norms are recreated in each generation but also that social interactions shape the kinds of social groups that are recognized (for a more extensive discussion, see Kish Bar-On & Lamm, 2023). We highlight evidence showing that accounts of norm psychology thus require a richer notion of human groups. (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)

This paper points to some problems for the position that D.M. Walsh calls "alternative individualism," and argues that in defending this view Walsh has omitted an important part of what separates individualists and externalists in psychology. Walsh's example of Hox gene complexes is discussed in detail to show why some sort of externalism about scientific taxonomy more generally is a more plausible view than any extant version of individualism.

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (...) (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (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)

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)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO (...) relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Where does the mind begin and end? Most philosophers and cognitive scientists take the view that the mind is bounded by the skull or skin of the individual. Robert Wilson, in this provocative and challenging 2004 book, provides the foundations for the view that the mind extends beyond the boundary of the individual. The approach adopted offers a unique blend of traditional philosophical analysis, cognitive science, and the history of psychology and the human sciences. The companion volume, Genes and the (...) Agents of Life, explores the theme in the biological sciences. Written with verve and clarity, this ambitious book will appeal to a broad swathe of professionals and students in philosophy, psychology, cognitive science, and the history of the behavioural and human sciences. You can download the table of contents here. (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)

Intermediary metabolism molecules are orchestrated into logical pathways stemming from history (L-amino acids, D-sugars) and dynamic constraints (hydrolysis of pyrophosphate or amide groups is the driving force of anabolism). Beside essential metabolites, numerous variants derive from programmed or accidental changes. Broken down, variants enter standard pathways, producing further variants. Macromolecule modification alters enzyme reactions specificity. Metabolism conform thermodynamic laws, precluding strict accuracy. Hence, for each regular pathway, a wealth of variants inputs and produces metabolites that are similar to but not (...) the exact replicas of core metabolites. As corollary, a shadow, paralogous metabolism, is associated to standard metabolism. We focus on a logic of paralogous metabolism based on diversion of the core metabolic mimics into pathways where they are modified to minimize their input in the core pathways where they create havoc. We propose that a significant proportion of paralogues of well-characterized enzymes have evolved as the natural way to cope with paralogous metabolites. A second type of denouement uses a process where protecting/deprotecting unwanted metabolites - conceptually similar to the procedure used in the laboratory of an organic chemist - is used to enter a completely new catabolic pathway. (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 automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring (...) the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The Deaf culture in the United States is a unique culture that is not widely understood. To members of the Deaf community in the United States, deafness is not viewed as a disease or pathology to be treated or cured; instead it is seen as a difference in human experience. Members of this community do not hide their deafness; instead they take great pride in their Deaf identity. The Deaf culture in the United States is very communitarian not individualistic. Mary (...) Beth and Dominic are a married couple in their late 20s who are genetically deaf. They are active members in the Deaf community and work as advocates for individuals who are deaf, family members of Deaf people and sign language interpreters who identify with the Deaf culture. Mary Beth and Dominic approach the fertility clinic with a request that they only want a child with the genetic gene for deafness. They would want the embryos that do not have the gene to be destroyed. This would entail creating a child who would have the gene for deafness. Medically and ethically, should the fertility clinic agree to the couple’s request? The authors argue that the couple's request should be denied and provide reasons for it from the perspectives of foundational and clinical ethics. (shrink)

O valor nutritivo do leite de ovelha é superior quando comparado aos leites caprino e bovino, apresentando maior teor proteico, lipídico, minerais e vitaminas. Os humanos evoluíram em estreito contato com a natureza, sendo o leite a primeira fonte de alimento desta espécie ao nascer. Durante milhares de anos, o leite rico em nutrientes, como fonte de alimento, era unicamente materno e só veio a ser consumido pelo homem após idade de amamentação com a domesticação dos animais, primeiramente às ovelhas (...) e as cabras há aproximadamente 13 mil anos, seguido da domesticação das vacas quatro mil anos depois. Desde então o leite tornou-se um alimento indispensável para o homem. O valor nutritivo do leite de ovelha é superior quando comparado aos leites caprino e bovino, apresentando maior teor proteico, lipídico, minerais e vitaminas essenciais para a saúde humana. Este leite apresenta três vezes mais proteínas em relação ao leite de cabra e de vaca, sendo aquelas consideradas proteínas de alto valor biológico contribuindo para uma melhor digestibilidade. Outra característica é a conformação estrutural e a quantidade de micelas de caseína e suas subunidades, que são assim como o leite caprino, menores que as do leite bovino, proporcionando menor sensibilização às pessoas alérgicas. Estudos sugerem que o leite de ovelha pode ser considerado o substituto ideal do leite bovino para pessoas alérgicas ao leite bovino devido ao elevado teor dos principais componentes do leite e minerais. Entretanto, foi verificado que anticorpos IgE de pessoas alérgicas reconhecem as αS1-caseína, αS2-caseína e β-caseína de leite ovino e caprino, mas caseínas do leite bovino são raramente ou não reconhecidas. Além disso, os polimorfismos genéticos das proteínas do leite estão associados com os parâmetros quantitativos e qualitativos e desempenham um papel importante na indução de diferentes graus de reação alérgica. A coloração do leite de ovelha é intensamente branca e homogênea, o que o difere do leite de vaca, pois essa característica está associada à ausência de β-caroteno pigmento precursor do retinol (vitamina A) impedindo que o leite tenha coloração amarelada como no caso do leite bovino. No leite ovino, o β-caroteno apresenta-se na forma convertida da vitamina A que não possui coloração amarelada e essa característica possibilita a produção de diferentes variedades de queijo. A caseína no leite de ovelha compõe 80% do total de proteínas do leite dos ruminantes, enquanto que está presente em 50% da composição proteica do leite equino e em menor porcentagem no leite humano. A caseína do leite de ruminantes difere com relação às características de tamanho, hidratação e mineralização. As micelas de caseína do leite de ovelha possuem maior mineralização e menor hidratação, sendo mais estáveis ao aquecimento quando comparadas à micela de caseína do leite de vaca. Outra importante característica refere-se à conformação molecular e sequencial de aminoácidos com impacto sobre sua digestibilidade, qualidade nutricional e termoestabilidade proteica. As proteínas do leite de ovelha consistem em elevada quantidade de caseínas (resistente ao calor) e proteínas do soro (sensível ao calor) responsáveis pela textura e viscosidade de iogurtes. Tecnologicamente, elas têm propriedades únicas que permitem a fácil conversão do leite em iogurte e queijos, não sendo necessária a adição de sólidos na produção do iogurte, como leite em pó, ou concentração dos sólidos do leite por tecnologia de membrana. Estudos com variantes da caseína do leite ovino representam uma abordagem eficaz para identificar a associação de características de importância econômica e melhorar raças para a produção de proteína do leite específica. As características da caseína no leite de ovelha são particularmente interessantes devido ao número elevado de polimorfismo, alterando a expressão de genes e influenciando o processamento de queijos. Em adição, enzimas presente no leite de ovelha possui atividade proteolítica e lipolítica (quebra de proteínas e lipídios). Elas auxiliam na maturação de queijos - resultando em compostos de aroma e sabor típicos, tornando-os únicos em suas características. O sabor e o aroma do leite de ovelha são suaves e adocicados além de possuir uma textura cremosa devido aos pequenos glóbulos de gordura que apresentam tamanhos menores que 3,5 µm. Esta peculiaridade no tamanho dos glóbulos gordurosos do leite ovino propicia que esse seja digerido mais facilmente. O leite ovino apresenta também altas concentrações de ácidos graxos poli-insaturados com benefícios à saúde como isômeros de ácido linoleico conjugado (CLA) presentes em maior concentração nesta matriz comparado ao leite bovino que são o cis-9 trans-11 e o trans-10 cis-12, responsáveis por ações anticarcinogênica, antiaterogênico e antiobesidade. Ainda com relação aos lipídios do leite de ovelha, as lipases têm um papel importante na produção de leite na glândula mamária. As lipases naturais do leite catalisam e hidrolisam os triglicerídeos, produzindo ácidos graxos livres (AGL). A atividade das lipases, em leite ovino, é cerca de um décimo das do leite bovino. Além disso, o padrão de hidrólise da gordura de leite por ovinos apresenta maior taxa em relação aos triglicerídeos - contendo ácidos graxos de cadeia média em relação aos ácidos graxos de cadeia longa. Os níveis de AGL em queijos de leite ovino são o resultado do processo lipolítico que ocorre durante o período de maturação. Alguns produtos lácteos derivados usando como matéria-prima o leite de ovelha - como iogurte grego e queijos - foram descritos como possuindo peptídeos inibidores da enzima conversora da angiotensina (ECA), sendo a maioria derivada da subunidade β-caseína. Também, alguns peptídeos derivados da κ-caseína, resultante da hidrólise de leite ovino pela pepsina, tripsina e quimotripsina, exercem atividade antioxidante. Em queijos tradicionais derivados de ovelha, como o Scamorza, foram verificados diversos peptídeos com ação inibidora da ECA e ação antibacteriana. Nesse contexto, o leite de ovelha é uma rica fonte de nutrientes e seu principal uso é na produção de queijos devido ao elevado conteúdo de extrato seco total, que contribui com alto rendimento da massa. Todavia, esta matéria-prima permanece inexplorada pela indústria de laticínios com uma visão de alimento funcional, visto que o leite e seus derivados são reconhecidamente ótimos carreadores de fibras prebióticas e bactérias probióticas - que trazem benefícios ao consumidor favorecendo saúde e bem-estar. Nesse contexto, o leite de ovelha apresenta-se como um alimento de grande potencial e uma valiosa alternativa para a indústria de laticínios - que pode aumentar a diversidade de produtos oferecidos ao consumidor. (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)

Estudo comparado sobre o tratamento dado à reprodução humana assistida no direito do Brasil, Estados Unidos, Portugal, Espanha e Itália.

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 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)

"The Uneasy Heirs of Acquaintance" is my first-round contribution to a 4-way exchange with Bill Brewer, Anil Gupta, and John McDowell. In the first round, each of us writes a commentary on the other three, and in the second round we reply to each other's first-round contributions. This is my second-round contribution.

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...) multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

This paper addresses the cultural impact of genomics and the Human Genome Project on human self-understanding. Notably, it addresses the claim made by Francis Collins that the genome is the language of God and the claim made by Max Delbrück that Aristotle must be credited with having predicted DNA as the soul that organises bio-matter. From a continental philosophical perspective I will argue that human existence results from a dialectical interaction between two types of texts: the language of molecular biology (...) and the language of civilisation; the language of the genome and the language of our socio-cultural, symbolic ambiance. Whereas the former ultimately builds on the alphabets of genes and nucleotides, the latter is informed by primordial texts such as the Bible and the Quran. In applied bioethics deliberations on genomics, science is easily framed as liberating and progressive, religious world-views as conservative an... (shrink)

Projects of human improvement take both individual and intergenerational forms. The biosciences provide many technologies, including prenatal screening and the latest gene editing techniques, such as CRISPR, that have been viewed as providing the means to human improvement across generations. But who is fit to furnish the next generation? Historically, eugenics epitomizes the science-based attempt to improve human society through distinguishing kinds of people and then implementing social policies—from immigration restriction to sexual sterilization and euthanasia—that influence and even direct (...) what sorts of people populate our future. Despite recognition of the horrors of the eugenic extremes of the past and of the subhumanizing of those sufficiently below appearance or ability norms to be viewed as “defective” or “unfit”, many people continue to be drawn to strands of eugenic thinking. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use (...) statistical methods and formal ontological principles as a first step towards finding answers to this question. (shrink)

A Troublesome Inheritance, by Nicholas Wade, should be read by anyone interested in race and recent human evolution. Wade deserves credit for challenging the popular dog­ma that biological differences between groups either don't exist or cannot ex­plain the relative success of different groups at different tasks. Wade's work should be read alongside another re­cent book, The 10,000 Year Explosion: How Civilization Accelerated Human Evolution, by Gregory Cochran and Henry Harpending. Together, these books represent a ma­jor turning point in the public (...) debate about the speed with which relatively isolated groups can evolve: both books suggest that small genetic differences between members of different groups can have large impacts on their abilities and propensities, which in turn affect the outcomes of the societies in which they live. (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)