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. The NCRO ontology is free and open to all users. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic (...) annotation of large amounts of ncRNA biological and clinical data. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Current knowledge of the RNA world indicates 2 different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share—as main characteristics—a non-repetitive syntax. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their (...) syntax structure are coherent with the differences of the functions they represent. Interestingly, these 2 genetic codes resemble the function of all natural languages, i.e., the repetitive non-coding sequences serve as appropriate tool for organization, coordination and regulation of group behavior, and the nonrepetitive coding sequences are for conservation of instrumental constructions, plans, blueprints for complex protein-body architecture. This differentiation may help to better understand RNA group behavioral motifs. (shrink)

The concepts of the origin of the genetic code and the definitions of life changed dramatically after the RNA world hypothesis. Main narratives in molecular biology and genetics such as the “central dogma,” “one gene one protein” and “non-coding DNA is junk” were falsified meanwhile. RNA moved from the transition intermediate molecule into centre stage. Additionally the abundance of empirical data concerning nonrandom genetic change operators such as the variety of mobile genetic elements, persistent viruses and defectives do not (...) fit with the dominant narrative of error replication events (mutations) as being the main driving forces creating genetic novelty and diversity. The reductionistic and mechanistic views on physico-chemical properties of the genetic code are no longer convincing as appropriate descriptions of the abundance of non-random genetic content operators which are active in natural genetic engineering and natural genome editing. (shrink)

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and non-coding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a re-examination. (...) In this review we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioural motifs of cooperative RNA consortia. In addition to molecular biological perspectives this may lead to a better understanding of genetic code evolution and dynamics. (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)

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)

Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops are the basic players. We thus redefine quasispecies as RNA quasispecies consortia (...) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competence-not error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs. (shrink)

Natural genome editing from a biocommunicative perspective is the competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing integrates both natural editing of genetic code and epigenetic marking that determines genetic reading patterns. As agents that edit genetic code and epigenetically mark genomic structures, viral and subviral agents have been suggested because they may be (...) evolutionarily older than cellular life. This hypothesis that viruses and viral-like agents edit genetic code is developed according to three well investigated examples that represent key evolutionary inventions in which non-lytic viral swarms act symbiotically in a persistent lifestyle within cellular host genomes: origin of eukaryotic nucleus, adaptive immunity, placental mammals. Additionally an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on the genetic code. Most of these RNA agents such as transposons, retroposons and small non-coding RNAs act consortially and are remnants of persistent viral infections that now act as co-opted adaptations in cellular key processes. (shrink)

Starting with the results of Li et al. in 1992 there is valuable interest in finding long range correlations in DNA sequences since it raises questions about the role of introns and intron-containing genes. In the present paper we studied two sequences that are the human T-cell receptor alpha/delta locus, Gen-Bank name HUMTCRADCV, a noncoding chromosomal fragment of M = 97630 bases (composed of less than 10% of coding regions), and the Escherichia Coli K12, Gen-Bank name ECO110K, a genomic (...) fragment with M = 111401 bases consisting of mostly coding regions and containing more that 80% of coding regions. We attributed the value (+1) to the purines and the value (-1) to the pirimidines and to such reconstructed random walk we applied the method of the Recurrence Quantification Analysis(RQA) that was introduced by Zbilut and Webber in 1994. By using dimension D=1 and Embedded Dimensions D=3 and D=5, we obtain some indicative results. Also by a simple eye examination of the reconstructed maps, the differences between coding and non coding regions are evident and impressive and consist in the presence in noncoding regions of long patches of the same colour that are absent in the coding sequence. At first sight this suggests a simple explanation to the concept of „long-range‟ correlation. On the quantitative plane, we used the %Rec., the %Det., the Ratio, the Entropy, the %Lam., and the Lmax that, as explained in detail in the text, represent the basic variables of RQA. The significant result that we have here is that both Lmax and Laminarity exhibit very large values in HUMTCRADCV and actually different in values respect to ECO110K where such variables assume more modest values. Therefore we suggest that there is the observed difference between HUMTCRADCV and ECO110K. The claimed higher long-range correlations of introns respect to exons from many authors may be explained here in reasonof such found higher values of Lmax and of Laminarity in HUMTCRADCV respect to ECO110K. (shrink)

The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a result, (...) the barrier seriously impedes the emergence of individuality, complex functionality and the transition to life. This barrier is analogous to the cooperation barrier that also impedes the emergence of complex cooperation at all levels of living organization. As has been shown at other levels of organization, the barrier can be overcome comprehensively by appropriate ‘management’. Management implements a system of evolvable constraints that can overcome the cooperation barrier by ensuring that beneficial co-operators are supported within the organization and by suppressing free-riders. In this way, management can control and manipulate the chemical processes of a collectively autocatalytic organization, producing novel processes that serve the interests of the organization as a whole and that could not arise and persist in an un-managed chemical organization. Management self-organizes because it is able to capture some of the benefits that are produced when its interventions promote cooperation, thereby enhancing productivity. Selection will therefore favour the emergence of managers that take over and manage chemical organizations so as to overcome the cooperation barrier. The managed-metabolism hypothesis demonstrates that if management is to overcome the cooperation barrier comprehensively, its interventions must be digitally coded. In this way, the hypothesis accounts for the two-tiered structure of all living cells in which a digitally-coded genetic apparatus manages an analogically-informed metabolism.GraphicalOpen image in new window. (shrink)

The Knower paradox purports to place surprising a priori limitations on what we can know. According to orthodoxy, it shows that we need to abandon one of three plausible and widely-held ideas: that knowledge is factive, that we can know that knowledge is factive, and that we can use logical/mathematical reasoning to extend our knowledge via very weak single-premise closure principles. I argue that classical logic, not any of these epistemic principles, is the culprit. I develop a consistent theory validating (...) all these principles by combining Hartry Field's theory of truth with a modal enrichment developed for a different purpose by Michael Caie. The only casualty is classical logic: the theory avoids paradox by using a weaker-than-classical K3 logic. I then assess the philosophical merits of this approach. I argue that, unlike the traditional semantic paradoxes involving extensional notions like truth, its plausibility depends on the way in which sentences are referred to--whether in natural languages via direct sentential reference, or in mathematical theories via indirect sentential reference by Gödel coding. In particular, I argue that from the perspective of natural language, my non-classical treatment of knowledge as a predicate is plausible, while from the perspective of mathematical theories, its plausibility depends on unresolved questions about the limits of our idealized deductive capacities. (shrink)

In this paper, I will argue that it is a moral obligation for companies, firstly, to accept their moral responsibility with respect to non-discrimination, and secondly, to address the issue with a full-fledged programme, including but not limited to the countering of microsocial discrimination processes through specific policies. On the basis of a broad sketch of how some discrimination mechanisms are actually influencing decisions, that is, causing intended as well as unintended bias in Human Resources Management, I will argue that (...) the well known tools of legislation and ethical codes are necessary although insufficient to cope with the problem. However, based on empirical evidence, we know which set of measures is likely to diminish discrimination. Taking non-discrimination seriously implies complex and longitudinal policies which include assigning responsibility for a non-discrimination policy within the firm, making managers conscious of implicit stereotypes and helping them to cope with prejudices that no one can totally overcome. Insofar as corporate responsibility with respect to non-discrimination is accepted and strategies that are not prohibitively expensive are known, companies are bound to implement them. Not implementing the best set of measures may be considered at least as a moral shortcoming or, depending on the size of the company, mere lip service to the non-discrimination principle. Although the paper refers to empirical material of diverse backgrounds, its intent is clearly normative. It wishes to spell out what companies ought to do if they are committed to responsible behaviour. The discussion of effective remedies against discrimination is based on a case study of a French company. The retailer Auchan was recently surprised to learn that it was discriminating against ethnic minorities despite strong ethical standards, an ethics committee and ethical leadership. The company dropped its naïve beliefs and set up an ambitious policy cope with the issue. The case illustrates what recent empirical research has revealed about the effectiveness of diversity policies: establishing responsibility for diversity results, firm ethical commitment and support from top management make diversity programs effective. (shrink)

While moral philosophers have paid significant attention to the concept of moral supererogation, far less attention has been paid to the possibility that supererogation may also exist in other areas of normativity. Recently, though, philosophers have begun to consider the possible existence of prudential, epistemic, aesthetic, and sporting supererogation. These discussions tend to focus on aspects of our practices in these areas of normativity that suggest an implicit acceptance of the existence of supererogation. In this chapter, I will offer a (...) different kind of defense of non-moral supererogation. I will begin by considering a particular kind of argument made in support of moral supererogation. According to this line of argument, we should accept the existence of moral supererogation because a moral code which makes room for supererogation is likely to be more effective at promoting morally desirable behavior than a moral code which leaves no room for the supererogatory. I will begin by outlining this argument. I will then develop a similar line of argument for prudential, epistemic, aesthetic, and sporting norms. (shrink)

Recent advances in neuroscience lead to a wider realm for philosophy to include the science of the Darwinian-evolved computational brain, our inner world producing organ, a non-recursive super- Turing machine combining 100B synapsing-neuron DNA-computers based on the genetic code. The whole system is a logos machine offering a world map for global context, essential for our intentional grasp of opportunities. We start from the observable contrast between the chaotic universe vs. our orderly inner world, the noumenal cosmos. So far, philosophy (...) has been rehearsing our thoughts, our human-internal world, a grand painting of the outer world, how we comprehend subjectively our experience, worked up by the logos machine, but now we seek a wider horizon, how humans understand the world thanks to Darwinian evolution to adapt in response to the metaphysical gap, the chasm between the human animal and its environment, shaping the organism so it can deal with its variable world. This new horizon embraces global context coded in neural structures that support the noumenal cosmos, our inner mental world, for us as denizens of the outer environment. Kant’s inner and outer senses are fundamental ingredients of scientific philosophy. Several sections devoted to Heidegger, his lizard debunked, but his version of the metaphysical gap & his doctrine of the logos praised. Rorty and others of the behaviorist school discussed also. (shrink)

Even if the “value-free ideal of science” (VFI) were an unattainable goal, one could ask: can it be a useful fiction, one that is beneficial for the research community and society? This question is particularly crucial for scholars and institutions concerned with research integrity (RI), as one cannot offer normative guidance to researchers without making some assumptions about what ideal scientific research looks like. Despite the insofar little interaction between scholars studying RI and those working on values in science, the (...) overlap of topics and interests make collaboration between the two fields promising for understanding research and its ethics. Here, we identify—for the use of RI scholars—the non-epistemic reasons (societal, political, professional) for and against the VFI considered in the literature. All of these are concerned with the beneficial or detrimental consequences that endorsing the VFI would have on society, policy-making, or the scientific community, with some authors appealing to the same principles to argue for opposite positions. Though most of the reviewed articles do not endorse the VFI, it is generally agreed that some constraints have to be put on the use of non-epistemic values. Disagreement on the utility of the VFI lies both on the different epistemic-descriptive positions taken by different authors, and on the scarcity of relevant empirical studies. Engaging critically with the reasons here identified and more in general with the values in science debate will help the RI community decide whether the VFI should be included in future codes of conduct. (shrink)

Together, the code and inferential models of communication are often thought to range over all cases of communication. However, their prevailing versions seem unable to fully explain what I call underdeterminacy without ostension. The latter is constituted by communication where stimuli that are not (nor appear to be) produced with communicative or informative intentions nevertheless communicate information underdetermined by the relevant codes. Though the prevailing accounts of communication cannot fully explain how communication works in such cases, I suggest that some (...) version of the inferential model can—if we allow it to extend to non‐ostensive, non‐intentional behaviors. (shrink)

Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence. However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural genome-editing competences of (...) viruses and RNA consortia that are able to insert or delete, combine and recombine genetic sequences more precisely than random-like into cellular host organisms according to adaptational needs or even generate sequences de novo. Increasing knowledge about natural genome editing questions the traditional narrative of mutations (error replications) as essential for generating genetic diversity and genetic content arrangements in biological systems. This may have far-reaching consequences for our understanding of artificial genome editing. (shrink)

Darwinian evolutionary theory has two key terms, variations and biological selection, which finally lead to survival of the fittest variant. With the rise of molecular genetics, variations were explained as results of error replications out of the genetic master templates. For more than half a century, it has been accepted that new genetic information is mostly derived from random error-based events. But the error replication narrative has problems explaining the sudden emergence of new species, new phenotypic traits, and genome innovations (...) as a sudden single event. Meanwhile, it is recognized that errors cannot explain the evolution of genetic information, genetic novelty, and complexity. Now, empirical evidence establishes the crucial role of non-random genetic content editors, such as viruses, diversity generating retroelements, and other RNA networks, to produce new genetic information, complex regulatory control, inheritance vectors, genetic identity, immunity, new sequence space, evolution of complex organisms, and evolutionary transitions. (shrink)

The idea that development is the expression of information accumulated during evolution and that heredity is the transmission of this information is surprisingly hard to cash out in strict, scientific terms. This paper seeks to do so using the sense of information introduced by Francis Crick in his sequence hypothesis and central dogma of molecular biology. It focuses on Crick's idea of precise determination. This is analysed using an information-theoretic measure of causal specificity. This allows us to reconstruct some of (...) Crick's claims about information in transcription and translation. Crick's approach to information has natural extensions to non-coding regions of DNA, to epigenetic marks, and to the genetic or environmental upstream causes of those epigenetic marks. Epigenetic information cannot be reduced to genetic information. The existence of biological information in epigenetic and exogenetic factors is relevant to evolution as well as to development. (shrink)

Applying mild methods of preparation, part of the ribosomes of rabbit reticulocytes are found in aggregates (later called polyribosomes) of up to six ribosomal units. Upon treatment with RNA-ase, they desintegrate into single ribosomes. The fast-sedimenting aggregates are found to be more active in protein synthesis in terms of incorporation of radioactive amino acids, whereas the single ribosomes are more receptive to stimulation by the artificial messenger RNA poly-U. The findings indicate that the linkage of ribosomes into aggregates is due (...) to the messenger RNA. They support a tape-reading mechanism of protein synthesis whereby growth of the peptide chain is accompanied by shifting the active site of the ribosome from one coding group of nucleotides of the messenger RNA to the next. (shrink)

Abstract The quasispecies theory is a helpful concept in the explanation of RNA virus evolution and behaviour, with a relevant impact on methods used to fight viral diseases. It has undergone some adaptations to integrate new empirical data, especially the non-deterministic nature of mutagenesis, and the variety of behavioural motifs in cooperation, competition, communication, innovation, integration, and exaptation. Also, the consortial structure of quasispecies with complementary roles of memory genomes of minority populations better fits the empirical data than did the (...) original concept of a master sequence and its mutant spectra. The high productivity of quasispecies variants generates unique sequences that never existed before and will never exist again. In the present essay, we underline that such sequences represent really new ontological entities, not just error copies of previous ones. Their primary unique property, the incredible variant production, is suggested here as quasispecies productivity, which replaces the error-replication narrative to better fit into a new relationship between mankind and living nature in the twenty-first century. (shrink)

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

The inconsistent relation between word frequency and free recall performance and the non-monotonic relation found between the two cannot all be explained by current theories. We propose a theoretical framework that can explain all extant results. Based on an ecological psychology analysis of the free recall situation in terms of environmental and informational resources available to the participants, we propose that because participants’ cognitive system has been shaped by their native language, free recall performance is best understood as the end (...) result of relational properties that preexist the experimental situation and of the way the words from the experimental list interact with those. In addition to this, we borrow from predictive coding theory the idea that the brain constantly predicts “what is coming next” so that it is mainly prediction errors that will propagate information forward. Our ecological psychology analysis indicates there will be “prediction errors” because the word frequency distribution in an experimental word list is inevitably different from the particular Zipf’s law distribution of the words in the language that shaped participants’ brains. We further propose the particular distributional discrepancies inherent to a given word list will trigger, as a function of the words that are included in the list, their order, and of the words that are absent from the list, a surprisal signal in the brain, something that is isomorphic to the concept of Bayesian surprise. The precise moment when Bayesian surprise is triggered will determine to what word of the list that Bayesian surprise will be associated with, and the word the Bayesian surprise will be associated with will benefit from it and become more memorable as a direct function of the magnitude of the surprisal. Two experiments are presented that show a proxy of Bayesian surprise explains the free recall performance and that no effect of word frequency is found above and beyond the effect of that proxy variable. We then discuss how our view can account for all data extant in the literature on the effect of word frequency on free recall. (shrink)

Non-commuting quantities and hidden parameters – Wave-corpuscular dualism and hidden parameters – Local or nonlocal hidden parameters – Phase space in quantum mechanics – Weyl, Wigner, and Moyal – Von Neumann’s theorem about the absence of hidden parameters in quantum mechanics and Hermann – Bell’s objection – Quantum-mechanical and mathematical incommeasurability – Kochen – Specker’s idea about their equivalence – The notion of partial algebra – Embeddability of a qubit into a bit – Quantum computer is not Turing machine – (...) Is continuality universal? – Diffeomorphism and velocity – Einstein’s general principle of relativity – „Mach’s principle“ – The Skolemian relativity of the discrete and the continuous – The counterexample in § 6 of their paper – About the classical tautology which is untrue being replaced by the statements about commeasurable quantum-mechanical quantities – Logical hidden parameters – The undecidability of the hypothesis about hidden parameters – Wigner’s work and и Weyl’s previous one – Lie groups, representations, and psi-function – From a qualitative to a quantitative expression of relativity − psi-function, or the discrete by the random – Bartlett’s approach − psi-function as the characteristic function of random quantity – Discrete and/ or continual description – Quantity and its “digitalized projection“ – The idea of „velocity−probability“ – The notion of probability and the light speed postulate – Generalized probability and its physical interpretation – A quantum description of macro-world – The period of the as-sociated de Broglie wave and the length of now – Causality equivalently replaced by chance – The philosophy of quantum information and religion – Einstein’s thesis about “the consubstantiality of inertia ant weight“ – Again about the interpretation of complex velocity – The speed of time – Newton’s law of inertia and Lagrange’s formulation of mechanics – Force and effect – The theory of tachyons and general relativity – Riesz’s representation theorem – The notion of covariant world line – Encoding a world line by psi-function – Spacetime and qubit − psi-function by qubits – About the physical interpretation of both the complex axes of a qubit – The interpretation of the self-adjoint operators components – The world line of an arbitrary quantity – The invariance of the physical laws towards quantum object and apparatus – Hilbert space and that of Minkowski – The relationship between the coefficients of -function and the qubits – World line = psi-function + self-adjoint operator – Reality and description – Does a „curved“ Hilbert space exist? – The axiom of choice, or when is possible a flattening of Hilbert space? – But why not to flatten also pseudo-Riemannian space? – The commutator of conjugate quantities – Relative mass – The strokes of self-movement and its philosophical interpretation – The self-perfection of the universe – The generalization of quantity in quantum physics – An analogy of the Feynman formalism – Feynman and many-world interpretation – The psi-function of various objects – Countable and uncountable basis – Generalized continuum and arithmetization – Field and entanglement – Function as coding – The idea of „curved“ Descartes product – The environment of a function – Another view to the notion of velocity-probability – Reality and description – Hilbert space as a model both of object and description – The notion of holistic logic – Physical quantity as the information about it – Cross-temporal correlations – The forecasting of future – Description in separable and inseparable Hilbert space – „Forces“ or „miracles“ – Velocity or time – The notion of non-finite set – Dasein or Dazeit – The trajectory of the whole – Ontological and onto-theological difference – An analogy of the Feynman and many-world interpretation − psi-function as physical quantity – Things in the world and instances in time – The generation of the physi-cal by mathematical – The generalized notion of observer – Subjective or objective probability – Energy as the change of probability per the unite of time – The generalized principle of least action from a new view-point – The exception of two dimensions and Fermat’s last theorem. (shrink)

T. M. Scanlon’s contractualism attempts to give an account of right and wrong in terms of the moral code that could not be reasonably rejected. Reasonable rejectability is then a function of what kind of consequences the general adoption of different moral codes has for different individuals. It has been shown that moral codes should be compared at a lower than 100% level of social acceptance. This leads to the counter-culture challenge. The problem is that the cultural background of the (...) individuals who have not internalized the majority code affects the consequences of the codes and furthermore there does not seem to be a non-arbitrary way of choosing the minority cultures. This chapter first surveys and critically evaluates different responses to this challenge. It then outlines a version of ‘Real World Contractualism’, which offers the best response to the counter-culture challenge. (shrink)

The challenge posed by legal indeterminacy to legal legitimacy has generally been considered from points of view internal to the law and its application. But what becomes of legal legitimacy when the legal status of a given norm is itself a matter of contestation? This article, the first extended scholarly treatment of the International Holocaust Remembrance Alliance (IHRA)’s new definition of antisemitism, pursues this question by examining recent applications of the IHRA definition within the UK following its adoption by the (...) British government in 2016. Instead of focusing on this definition’s substantive content, I show how the document reaches beyond its self-described status as a “non-legally binding working definition” and comes to function as what I call a quasi-law, in which capacity it exercises the de facto authority of the law, without having acquired legal legitimacy. Broadly, this work elucidates the role of speech codes in restricting freedom of expression within liberal states. (shrink)

The most recent work by Jürgen Habermas tries to revalue religion in today's society. For this he tries to find genealogical connections between secular content and the worldviews that emerged in the Axial Age, including Jewish monotheism. In this article we try to propose that a genealogical approach to monotheism from the perspective of those involved would have to start from the context of undetected origin that constitutes the ethical universalism of Judaism: the Noahide code. To do this, we analyze (...) narrative and conceptual elements of axial and non-axial cultures and show their parallels with the seven laws of the children of Noah as the moral core of humanity. (shrink)

This paper considers the question of whether the influential distinction between levels of explanation introduced by David Marr can be used as a general framework for contemplating levels of explanation in cognitive sciences. Marr introduced three levels at which we can explain cognitive processes: the computational, algorithmic, and implementational levels. Some argue that Marr’s levels of explanation can only be applied to modular cognitive systems. However, since many psychological processes are non-modular, it seems that Marr’s levels of explanation cannot explain (...) such psychological processes. To show that the latter claim is not convincing, the paper draws upon an influential paradigm from cognitive sciences that is based on the principle of free energy. Based on this paradigm, the paper argues that even non-modular psychological processes can be computationally analyzed and algorithmically implemented. The conclusion of the paper is that, at least under the assumption that the func- tion of the mind is to minimize free energy, Marr’s levels of explanation can be successfully used as a general framework for understanding psychological processes at different levels of description. (shrink)

Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein (...) complexes, epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution. (shrink)

This chapter conceptually analyzes the post-traumatic stress injuries called moral injury, moral fatigue or exhaustion, and broken spirit. It then identifies two puzzles. First, soldiers sometimes sustain moral injury even from doing right actions. Second, they experience moral exhaustion from making decisions even where the morally right choice is so obvious that it shouldn’t be stressful to make it; and even where rightness of decision is so murky that no decision could be morally faulted. The injuries result of mistaken moral (...) self-evaluation. Methods of preventing and treating these injuries are defended, including training in self-forgiveness, moral off-loading of actions and decisions to persons and devices less likely to feel inappropriate guilt, and the use of drugs to prevent such guilt. The foregoing has been about moral injury erroneously resulting from the non-violation of a correct moral code. But the chapter then introduces the concept of moral pseudo-injury—felt moral injury that has in reality resulted from violation of a false moral code, so that no one has really been morally injured. This can be used as a method in warfighting. And since the injuries it produces are illusory, this would be morally superior to physical violence. For it causes less injury to its victims, and should cause less guilt in those who must inflict it. Historical precedents are considered. Finally, our enemies often use moral pseudo-injury against us, in the form of terrorist violence against civilians. Terrorism causes comparatively few harms, yet we mistakenly see it as more morally horrific than conventional combat that causes much worse loss of life among armed forces members. Here we need the nuancing and clarifying power of philosophy to restore a sense of proportion, thence to prevent or therapize the moral pseudo-injury we may experience from these sorts of attacks. (This is a pre-penultimate version of the published version, available from OUP at the external link, which contains minor variances. The paper was earlier known as "PTSD Weaponized: A Theory of Moral Injury"; that now superseded version is archived under "past conferences" on the Center for Ethics and the Rule of Law website.). (shrink)

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

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)

Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular techniques and biotechnological innovation have proven to be of utmost importance for rapid developments in disease diagnostics and treatment, including DNA and RNA sequencing technology, treatment with drugs and natural products and vaccine development. The COVID-19 crisis, however, has also demonstrated the need for systemic thinking and transdisciplinarity and the limits (...) of MSM: the neglect of the bio-psycho-social systemic nature of humans and their context as the object of individual therapeutic and population-oriented interventions. COVID-19 illustrates how a medical problem requires a transdisciplinary approach in epidemiology, pathology, internal medicine, public health, environmental medicine, and socio-economic modeling. Regarding the need for conceptual integration of these different kinds of knowledge we suggest the application of general system theory (GST). This approach endorses an organism-centered view on health and disease, which according to Ludwig von Bertalanffy who was the founder of GST, we call Organismal Systems Medicine (OSM). We argue that systems science offers wider applications in the field of pathology and can contribute to an integrative systems medicine by (i) integration of evidence across functional and structural differentially scaled subsystems, (ii) conceptualization of complex multilevel systems, and (iii) suggesting mechanisms and non-linear relationships underlying the observed phenomena. We underline these points with a proposal on multi-level systems pathology including neurophysiology, endocrinology, immune system, genetics, and general metabolism. An integration of these areas is necessary to understand excess mortality rates and polypharmacological treatments. In the pandemic era this multi-level systems pathology is most important to assess potential vaccines, their effectiveness, short-, and long-time adverse effects. We further argue that these conceptual frameworks are not only valid in the COVID-19 era but also important to be integrated in a medicinal curriculum. (shrink)

This fifth volume on Advances and Applications of DSmT for Information Fusion collects theoretical and applied contributions of researchers working in different fields of applications and in mathematics, and is available in open-access. The collected contributions of this volume have either been published or presented after disseminating the fourth volume in 2015 in international conferences, seminars, workshops and journals, or they are new. The contributions of each part of this volume are chronologically ordered. First Part of this book presents some (...) theoretical advances on DSmT, dealing mainly with modified Proportional Conflict Redistribution Rules (PCR) of combination with degree of intersection, coarsening techniques, interval calculus for PCR thanks to set inversion via interval analysis (SIVIA), rough set classifiers, canonical decomposition of dichotomous belief functions, fast PCR fusion, fast inter-criteria analysis with PCR, and improved PCR5 and PCR6 rules preserving the (quasi-)neutrality of (quasi-)vacuous belief assignment in the fusion of sources of evidence with their Matlab codes. Because more applications of DSmT have emerged in the past years since the apparition of the fourth book of DSmT in 2015, the second part of this volume is about selected applications of DSmT mainly in building change detection, object recognition, quality of data association in tracking, perception in robotics, risk assessment for torrent protection and multi-criteria decision-making, multi-modal image fusion, coarsening techniques, recommender system, levee characterization and assessment, human heading perception, trust assessment, robotics, biometrics, failure detection, GPS systems, inter-criteria analysis, group decision, human activity recognition, storm prediction, data association for autonomous vehicles, identification of maritime vessels, fusion of support vector machines (SVM), Silx-Furtif RUST code library for information fusion including PCR rules, and network for ship classification. Finally, the third part presents interesting contributions related to belief functions in general published or presented along the years since 2015. These contributions are related with decision-making under uncertainty, belief approximations, probability transformations, new distances between belief functions, non-classical multi-criteria decision-making problems with belief functions, generalization of Bayes theorem, image processing, data association, entropy and cross-entropy measures, fuzzy evidence numbers, negator of belief mass, human activity recognition, information fusion for breast cancer therapy, imbalanced data classification, and hybrid techniques mixing deep learning with belief functions as well. (shrink)

Local reports from different international societies have considered the achievement of the successful Glocalized architecture model in line with the 2030 UN Sustainable Development Goals (SDGs). The Aga Khan Cultural Foundation’s International Program for Islamic Architecture has also prioritized the understanding of the success drivers in architectural projects. This study aimed to detect the potentials of the common global indicators to access qualitative design assessment through analyzing the Aga Khan Award’s reports. The selected methodology in the present study is a (...) quantitative approach using the systematic content analysis and coding techniques for qualitative data obtained from the technical. The physical, non-physical, modern, and traditional factors that have contributed to the success of the works as well as their combinations were extracted and analyzed using Sensible and Abstract international, national, and local indications. There is a relative superiority for Sensible indications (A combination of modern and physical factors). The hybrid data distribution provides the ground to assess the works, and this can be used to manage the globalization challenges in the contemporary architecture of Muslim societies. (shrink)

Within the United States, the most prominent justification for criminal punishment is retributivism. This retributivist justification for punishment maintains that punishment of a wrongdoer is justified for the reason that she deserves something bad to happen to her just because she has knowingly done wrong—this could include pain, deprivation, or death. For the retributivist, it is the basic desert attached to the criminal’s immoral action alone that provides the justification for punishment. This means that the retributivist position is not reducible (...) to consequentialist considerations nor in justifying punishment does it appeal to wider goods such as the safety of society or the moral improvement of those being punished. A number of sentencing guidelines in the U.S. have adopted desert as their distributive principle, and it is increasingly given deference in the “purposes” section of state criminal codes, where it can be the guiding principle in the interpretation and application of the code’s provisions. Indeed, the American Law Institute recently revised the Model Penal Code so as to set desert as the official dominate principle for sentencing. And courts have identified desert as the guiding principle in a variety of contexts, as with the Supreme Court’s enthroning retributivism as the “primary justification for the death penalty.” While retributivism provides one of the main sources of justification for punishment within the criminal justice system, there are good philosophical and practical reasons for rejecting it. One such reason is that it is unclear that agents truly deserve to suffer for the wrongs they have done in the sense required by retributivism. In the first section, I explore the retributivist justification of punishment and explain why it is inconsistent with free will skepticism. In the second section, I then argue that even if one is not convinced by the arguments for free will skepticism, there remains a strong epistemic argument against causing harm on retributivist grounds that undermines both libertarian and compatibilist attempts to justify it. I maintain that this argument provides sufficient reason for rejecting the retributive justification of criminal punishment. I conclude in the third section by briefly sketching my public health-quarantine model, a non-retributive alternative for addressing criminal behavior that draws on the public health framework and prioritizes prevention and social justice. I argue that the model is not only consistent with free will skepticism and the epistemic argument against retributivism, it also provides the most justified, humane, and effective way of dealing with criminal behavior. (shrink)

Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not (...) be comparable if the ontological commitments employed differ. Comparisons between different nomenclatures cannot assume that either the naming practices or the object to which these names are intended to apply identifies some universally agreed upon object of interest. Investigating this suite of philosophical problems, I explore the role grey nomenclatures play in classification. ‘Grey nomenclatures’ are defined as those that employ names that are either intentionally or accidentally non-Linnaean. The classification of the lichen thallus (a symbiont) has been classified outside the Linnaean system by botanists relying on the International Code of Nomenclature for algae, fungi, and plants (ICN). But, I argue, the use of grey names is not isolated and does not occur exclusively within institutionalized naming practices. I suggest, ‘grey names’ also aptly describe nomenclatures employed by indigenous communities such as the Samí of Northern Finmark, the Sherpa of Nepal, and the Okanagan First Nations. I pay particular attention to how naming practices are employed in these communities; what ontological commitments they hold; for what purposes are these names used; and what anchors the community’s nomenclatural practices. Exploring the history of lichen naming and early ethnolichenological research, I then investigate the stakes that must be considered for any attempt to preserve, retain, integrate, or compare the knowledge contained in both academically formalized grey names and indigenous nomenclatures in a way that preserves their source-specific informational content. (shrink)

The purpose of this paper is to show whether the two crucial dimensions used for assessing the quality of argumentation, argument-as-a-product (argument structure) and argument-as-a-process (relevance), are interrelated, and how they can be used to assess the effect of argumentative mode on students’ arguments. To this purpose, a twofold coding scheme will be developed, aimed at capturing: a) the argumentative function of evidence use and b) the dialogical relevance of evidence use. A study will be described in which students’ (...) use of evidence is elicited in two distinct argumentative modes (dialogical vs. non-dialogical). According to the results, in the dialogical mode students tended to use evidence in a more sophisticated way from both argument evaluation perspectives. (shrink)

In the exploratory study reported here, we tested the efficacy of an intervention designed to train teenagers with Möbius syndrome (MS) to increase the use of alternative communication strategies (e.g., gestures) to compensate for their lack of facial expressivity. Specifically, we expected the intervention to increase the level of rapport experienced in social interactions by our participants. In addition, we aimed to identify the mechanisms responsible for any such increase in rapport. In the study, five teenagers with MS interacted with (...) three naïve participants without MS before the intervention, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual non-verbal behavior was assessed via behavioral coders, whereas verbal behavior was automatically extracted from the sound files. Alignment was assessed using cross recurrence quantification analysis and mixed-effects models. The results showed that observer-coded rapport was greater after the intervention, whereas self-reported rapport did not change significantly. Observer-coded gesture and expressivity increased in participants with and without MS, whereas overall linguistic alignment decreased. Fidgeting and repetitiveness of verbal behavior also decreased in both groups. In sum, the intervention may impact non-verbal and verbal behavior in participants with and without MS, increasing rapport as well as overall gesturing, while decreasing alignment. (shrink)

Computational reproducibility possesses its own dynamics and narratives of crisis. Alongside the difficulties of computing as an ubiquitous yet complex scientific activity, computational reproducibility suffers from a naive expectancy of total reproducibility and a moral imperative to embrace the principles of free software as a non-negotiable epistemic virtue. We argue that the epistemic issues at stake in actual practices of computational reproducibility are best unveiled by focusing on software as a pivotal concept, one that is surprisingly often overlooked in accounts (...) of reproducibility issues. Software is not only about designing and coding but also about maintaining, supporting, distributing, licensing, and governance; it is not only about developers but also about users. We focus on openness debates among computational chemists involved in molecular modeling software packages as empirical grounding for our argument. We then identify and analyse four epistemic characteristics as key to the role of software in computational reproducibility. (shrink)

Metaphors can be used as crucial tools for reaching shared understanding, especially where an epistemic imbalance of knowledge is at stake. However, metaphors can also represent a risk in intercultural or cross-cultural interactions, namely in situations characterised by little or deficient common ground between interlocutors. In such cases, the use of metaphors can lead to misunderstandings and cause communicative breakdowns. The conditions defining when metaphors promote, and hinder understanding have not been analyzed in detail, especially in intracultural contexts. This study (...) proposes an analysis of metaphors identified within an Italian corpus of diabetes care interviews. Through a coding scheme capturing the types and the probative weights of the linguistic evidence that can be used to detect misunderstandings, the communicative effectiveness of metaphors is indirectly assessed. The quantitative and qualitative analyses show a positive correlation between metaphor use and problematic understanding. A more detailed scrutiny of the interlocutors’ roles and topics of the metaphors points out that most of the problematic metaphors are used by patients, while most of the problematic ones used by providers concern non-clinical matters. These results can be explained as resulting from incorrect presumptions of common ground between the interlocutors. (shrink)

Analysis of grip force signals tailored to hand and finger movement evolution and changes in grip force control during task execution provide unprecedented functional insight into somatosensory cognition. Somatosensory cognition is a basis of our ability to manipulate, move, and transform objects of the physical world around us, to recognize them on the basis of touch alone, and to grasp them with the right amount of force for lifting and manipulating them. Recent technology has permitted the wireless monitoring of grip (...) force signals recorded from biosensors in the palm of the human hand to track and trace human grip forces deployed in cognitive tasks executed under conditions of variable sensory (visual, auditory) input. Non-invasive multi-finger grip force sensor technology can be exploited to explore functional interactions between somatosensory brain mechanisms and motor control, in particular during learning a cognitive task where the planning and strategic execution of hand movements is essential. Sensorial and cognitive processes underlying manual skills and/or hand-specific (dominant versus non-dominant hand) behaviors can be studied in a variety of contexts by probing selected measurement loci in the fingers and palm of the human hand. Thousands of sensor data recorded from multiple spatial locations can be approached statistically to breathe functional sense into the forces measured under specific task constraints. Grip force patterns in individual performance profiling may reveal the evolution of grip force control as a direct result of cognitive changes during task learning. Grip forces can be functionally mapped to from-global-to-local coding principles in brain networks governing somatosensory processes for motor control in cognitive tasks leading to a specific task expertise or skill. Under the light of a comprehensive overview of recent discoveries into the functional significance of human grip force variations, perspectives for future studies in cognition, in particular the cognitive control of strategic and task relevant hand movements in complex real-world precision task, are pointed out. (shrink)

Modular approaches to the architecture of the mind claim that some mental mechanisms, such as sensory input processes, operate in special-purpose subsystems that are functionally independent from the rest of the mind. This assumption of modularity seems to be in tension with recent claims that the mind has a predictive architecture. Predictive approaches propose that both sensory processing and higher-level processing are part of the same Bayesian information-processing hierarchy, with no clear boundary between perception and cognition. Furthermore, it is not (...) clear how any part of the predictive architecture could be functionally independent, given that each level of the hierarchy is influenced by the level above. Both the assumption of continuity across the predictive architecture and the seeming non-isolability of parts of the predictive architecture seem to be at odds with the modular approach. I explore and ultimately reject the predictive approach’s apparent commitments to continuity and non-isolation. I argue that predictive architectures can be modular architectures, and that we should in fact expect predictive architectures to exhibit some form of modularity. (shrink)

Most contractualist ethical theories have a subjunctivist structure. This means that they attempt to make sense of right and wrong in terms of a set of principles which would be accepted in some idealized, non-actual circumstances. This makes these views vulnerable to the so-called conditional fallacy objection. The moral principles that are appropriate for the idealized circumstances fail to give a correct account of what is right and wrong in the ordinary situations. This chapter uses two versions of contractualism to (...) illustrate this problem: Nicholas Southwood’s and a standard contractualist theory inspired by T.M. Scanlon’s contractualism. It then develops a version of Scanlon’s view that can avoid the problem. This solution is based on the idea that we also need to compare different inculcation elements of moral codes in the contractualist framework. This idea also provides a new solution to the problem of at what level of social acceptance should principles be compared. (shrink)

Within the United States, the most prominent justification for criminal punishment is retributivism. This retributivist justification for punishment maintains that punishment of a wrongdoer is justified for the reason that she deserves something bad to happen to her just because she has knowingly done wrong—this could include pain, deprivation, or death. For the retributivist, it is the basic desert attached to the criminal’s immoral action alone that provides the justification for punishment. This means that the retributivist position is not reducible (...) to consequentialist considerations nor in justifying punishment does it appeal to wider goods such as the safety of society or the moral improvement of those being punished. A number of sentencing guidelines in the U.S. have adopted desert as their distributive principle, and it is increasingly given deference in the “purposes” section of state criminal codes, where it can be the guiding principle in the interpretation and application of the code’s provisions. Indeed, the American Law Institute recently revised the Model Penal Code so as to set desert as the official dominate principle for sentencing. And courts have identified desert as the guiding principle in a variety of contexts, as with the Supreme Court’s enthroning retributivism as the “primary justification for the death penalty.” While retributivism provides one of the main sources of justification for punishment within the criminal justice system, there are good philosophical and practical reasons for rejecting it. One such reason is that it is unclear that agents truly deserve to suffer for the wrongs they have done in the sense required by retributivism. In the first section, I explore the retributivist justification of punishment and explain why it is inconsistent with free will skepticism. In the second section, I then argue that even if one is not convinced by the arguments for free will skepticism, there remains a strong epistemic argument against causing harm on retributivist grounds that undermines both libertarian and compatibilist attempts to justify it. I maintain that this argument provides sufficient reason for rejecting the retributive justification of criminal punishment. I conclude in the third section by briefly sketching my public health-quarantine model, a non-retributive alternative for addressing criminal behavior that draws on the public health framework and prioritizes prevention and social justice. I argue that the model is not only consistent with free will skepticism and the epistemic argument against retributivism, it also provides the most justified, humane, and effective way of dealing with criminal behavior. (shrink)

The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...) the Foundry’s goal of consistent and non-redundant annotation if appropriate mappings of data annotated with their aid can be achieved. To construct such mappings in reliable fashion, however, it is necessary to analyze terminological resources from an ontologically realistic perspective in such a way as to identify the exact import of the ‘concepts’ and associated terms which they contain. We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research. (shrink)

While this article aims to explore the connections between citizenship and ‘race’, it is the first study to use fictional tools as a sociological resource in exemplifying the deviation between citizenship in principle and practice in an Austrian context. The study involves interviews with 73 Austrians from three ethnic/racial groups, which were subjected to a directed approach to qualitative content analysis and coded based on sentences from George Orwell’s fictional book, ‘Animal Farm’. By using fiction as a conceptual and analytical (...) device, this article goes beyond the orthodox particulars of citizenship to expose the compressed entitlements of some racial/ethnic minorities. In particular, data analysis revealed two related and intertwined central themes: (a) “all animals are not equal or comrades”; and (b) “some animals are more equal than others”. All ‘animals’ may be equal in principle, whereas, in practice, their ‘race’ serves as a critical source of social (dis)advantage in the ‘animal kingdom’. Thus, since citizenship is a precondition for possessing certain rights that non-citizens are not granted, I argue that citizenship cannot only be judged by whom it, in theory, excludes (i.e., non-citizens), but also by how it treats the included (i.e., citizens) on the basis of their ‘race’. I conclude that skin colour is a specific aspect of the hierarchy of citizenship in Austria, which reinforces that ‘some animals are more equal than others’. (shrink)

A mesure qu'ils avancent dans leur œuvre de prospection, les sémioticiens s'aperçoivent que tout est communication, la langue bien sûr, mais aussi les images, les sons, les objets, les gestes, et que tous ces phénomènes constituent des systèmes de signes qui doivent être étudiés en ramenant chaque message aux codes qui en régissent l'émission et la compréhension. Comprendre les systèmes de signes impose toutefois d'envisager les codes comme des structures, puis de recouvrir à des structures toujours plus vastes, dans un (...) mouvement de régression vers la matrice originelle de toute communication possible, vers un prétendu Code des Codes qui devrait représenter la détermination " naturelle " précédant toute culture. Mais si la sémiotique s'engageait dans cette voie, elle ne pourrait qu'aboutir à la " source " de toute structure possible, forcément non structurée, à ce qu'Umberto Ecco appelle la structure absente. Son livre, tout en refusant ce Code des Codes, essaie de montrer que tout acte communicatif est dominé par la présence massive de codes socialement et historiquement déterminés. La sémiotique découvre ainsi dans la dialectique entre code et message les rapports entre l'univers de signes et l'univers des idéologies, qui se reflètent dans les modes communicatifs préconstitués, et elle relie le monde des choses au monde de la culture, qui formalise les choses non pas pour les reconnaître comme elles sont mais afin de les transformer. Après avoir étudié dans L'œuvre ouverte (1965) les structures des langages expérimentaux de l'art contemporain, Umberto Ecco traite ici l'ensemble des problèmes sémiotiques et ce livre constitue à la fois sa contribution à la recherche en cours et le panorama actuellement le plus vaste et le plus complet sur les préalables constitutifs à toute sémiotique et sur l'état présent du structuralisme. (shrink)