Metagenomics bears upon all aspects of microbiology, including our understanding of mitochondrial and eukaryote origin. Recently, ribosomal protein phylogenies show the eukaryote host lineage – the archaeal lineage that acquired the mitochondrion – to branch within the archaea. Metagenomic studies are now uncovering new archaeal lineages that branch more closely to the host than any cultivated archaea do. But how do they grow? Carbon and energy metabolism as pieced together from metagenome assemblies of these new archaeal lineages, such as the (...) Deep Sea Archaeal Group (including Lokiarchaeota) and Bathyarchaeota, do not match the physiology of any cultivated microbes. Understanding how these new lineages live in their environment is important, and might hold clues about how mitochondria arose and how the eukaryotic lineage got started. Here we look at these exciting new metagenomic studies, what they say about archaeal physiology in modern environments, how they impact views on host‐mitochondrion physiological interactions at eukaryote origin. (shrink)

Known as the Darwin of the twenty-first century, the German biologist Ernst Walter Mayr (1904-2005) studied a great variety of subjects such as Ornithology, Genetics, Evolution, Classification, History, and Philosophy of Biology. This scientist was a giant of the previous century and an icon of Evolutionary Biology. He became famous for his Biological Species Concept and his conclusion that allopatry is the main cause for the origin of species. He provided a decisive contribution to the New Systematics and was the (...) pioneer of the punctuated equilibrium idea. Mayr was one of the main architects of the evolutionary synthesis as also of the Neo-Darwinian wave. Evaluated together, all of his works reveal several elements of his ambition – to organize a philosophical conception inherent for Biology. An assiduous defender of autonomous Biology, Mayr asserted that four sets of factors in Biology differ from those in the Exact Sciences: (I) refutation of essentialism, mechanism, vitalism, and teleology; (II) some physical principles cannot be applied to Biology; (III) absence of general laws in Biology; and (IV) basic principles of biology and their specific character cannot be applied to the inanimate world. The present study took as an axis a minor or even invisible theme from the Ernst Mayr literature and aims to analyze critically the theoretical and epistemological basis that subsidizes – or not– the affirmation that Biology is an autonomous Science. - O biólogo alemão Ernst Walter Mayr (1904-2005), conhecido como o Darwin do século XXI, trabalhou com uma grande variedade de temas: Ornitologia, Genética, Evolução, Classificação, História e Filosofia da Biologia. Esse cientista foi um dos gigantes do século XX e um ícone para a Biologia Evolutiva. Ficou famoso com o seu Conceito Biológico de Espécie e sua conclusão de que a alopatria era a principal causa da origem das espécies. Forneceu uma contribuição decisiva à Nova Sistemática, foi precursor da ideia de equilíbrio pontuado e um dos principais arquitetos da síntese evolutiva, bem como do movimento Neodarwinista. Quando avaliados em conjunto, seus trabalhos revelam os diversos elementos de sua ambição – organizar um corpo de concepções filosóficas próprias da Biologia. Defensor assíduo de uma Biologia autônoma, Mayr afirmou que há quatro conjuntos de fatores que diferenciam a Biologia do conjunto das Ciências Exatas: (I) refutação do essencialismo, do mecanicismo, do vitalismo e da teleologia; (II) convicção de que certos princípios da Física não podem ser aplicados à Biologia; (III) ausência de leis naturais universais em Biologia; e (IV) percepção do caráter único de certos princípios básicos da Biologia não aplicáveis ao mundo inanimado. O presente artigo tomou por eixo um tema aparentemente menor ou mesmo invisível na obra de Ernst Mayr e pretende realizar uma análise crítica acerca de suas bases teóricas e epistemológicas que subsidiaram – ou não – a afirmação da Biologia como uma Ciência autônoma. (shrink)

Controversy and activism have long been linked to the subject of primate research. Even in the midst of raging ethical debates surrounding fertility treatments, genetically modified foods and stem-cell research, there has been no reduction in the campaigns of activists worldwide. Plying their trade of intimidation aimed at ending biomedical experimentation in all animals, they have succeeded in creating an environment where research institutions, often painted as guilty until proven innocent, have avoided addressing the issue for fear of becoming targets. (...) One area of intense debate is the use of primates in stroke research. Despite the fact that stroke kills more people each year than AIDS and malaria, and less than 5% of patients are candidates for current therapies, there is significant opposition to primate stroke research. A balanced examination of the ethics of primate stroke research is thus of broad interest to all areas of biomedical research. (shrink)

Controversy and activism have long been linked to the subject of primate research. Even in the midst of raging ethical debates surrounding fertility treatments, genetically modified foods and stem-cell research, there has been no reduction in the campaigns of activists worldwide. Plying their trade of intimidation aimed at ending biomedical experimentation in all animals, they have succeeded in creating an environment where research institutions, often painted as guilty until proven innocent, have avoided addressing the issue for fear of becoming targets. (...) One area of intense debate is the use of primates in stroke research. Despite the fact that stroke kills more people each year than AIDS and malaria, and less than 5% of patients are candidates for current therapies, there is significant opposition to primate stroke research. A balanced examination of the ethics of primate stroke research is thus of broad interest to all areas of biomedical research. (shrink)

For a theory T, we study relationships among IΔ n +1 (T), LΔ n+1 (T) and B * Δ n+1 (T). These theories are obtained restricting the schemes of induction, minimization and (a version of) collection to Δ n+1 (T) formulas. We obtain conditions on T (T is an extension of B * Δ n+1 (T) or Δ n+1 (T) is closed (in T) under bounded quantification) under which IΔ n+1 (T) and LΔ n+1 (T) are equivalent. These conditions depend (...) on Th Πn +2 (T), the Π n+2 –consequences of T. The first condition is connected with descriptions of Th Πn +2 (T) as IΣ n plus a class of nondecreasing total Π n –functions, and the second one is related with the equivalence between Δ n+1 (T)–formulas and bounded formulas (of a language extending the language of Arithmetic). This last property is closely tied to a general version of a well known theorem of R. Parikh. Using what we call Π n –envelopes we give uniform descriptions of the previous classes of nondecreasing total Π n –functions. Π n –envelopes are a generalization of envelopes (see [10]) and are closely related to indicators (see [12]). Finally, we study the hierarchy of theories IΔ n+1 (IΣ m ), m≥n, and prove a hierarchy theorem. (shrink)

This project examined the ethical issues faced by academics and professionals in the Humanities. We conducted focus groups to gather information about the ethical concerns in these fields and used the qualitative data arising from the discussions to create a taxonomy that represents the structure of ethical issues in the Humanities. A key implication of our findings is that while the focus of ethics research and interventions has been primarily on the sciences and engineering, academics and professionals in other fields (...) also encounter some unique critical ethical dilemmas that require further research and methods of intervention. (shrink)

The passivity is for many the key of Michel Henry’s phenomenology. Ricoeur, ‘Soi-même comme un autre’, recognizes that, in Henry’s work, passivity is a witness to alterity taking this concept out of ties of the speculative speech. On the other side, Marion being, however, aware of it, as stated in his essay ‘La chair ou la donation de soi’ argues that essence ‘sentante’ is prior to ‘l’épreuve de soi’. I’ll try to disclose further in this work that essence ‘sentante’ is (...) the passivity itself. Thus more than witnessing (Ricoeur) or appropriating (Marion), the others and the limits are data of affective life in three passivity levels, ranging from sensations, feelings and affections. (shrink)

In this paper we continue the study of the theories IΔ n+1 (T), initiated in [7]. We focus on the quantifier complexity of these fragments and theirs (non)finite axiomatization. A characterization is obtained for the class of theories such that IΔ n+1 (T) is Π n+2 –axiomatizable. In particular, IΔ n+1 (IΔ n+1 ) gives an axiomatization of Th Π n+2 (IΔ n+1 ) and is not finitely axiomatizable. This fact relates the fragment IΔ n+1 (IΔ n+1 ) to induction (...) rule for Δ n+1 –formulas. Our arguments, involving a construction due to R. Kaye (see [9]), provide proofs of Parsons’ conservativeness theorem (see [16]) and (a weak version) of a result of L.D. Beklemishev on unnested applications of induction rules for Π n+2 and Δ n+1 formulas (see [2]). (shrink)

During the past decade, the Philosophy for Children Program has offered teacher-training workshops throughout the United States and elsewhere. The workshops frequently supported by grants, enable teachers to work with a professional philosopher in developing the skills required for teaching critical thinking to elementary and intermediate schools.

Current UK legislation is impacting upon the feasibility and cost-effectiveness of medical record-based research aimed at benefiting the NHS and the public heath. Whereas previous commentators have focused on the Data Protection Act 1998, the Health and Social Care Act 2001 is the key legislation for public health researchers wishing to access medical records without written consent. The Act requires researchers to apply to the Patient Information Advisory Group for permission to access medical records without written permission. We present a (...) case study of the work required to obtain the necessary permissions from PIAG in order to conduct a large scale public health research project. In our experience it took eight months to receive permission to access basic identifying information on individuals registered at general practices, and a decision on whether we could access clinical information in medical records without consent took 18 months. Such delays pose near insurmountable difficulties to grant funded research, and in our case £560 000 of public and charitable money was spent on research staff while a large part of their work was prohibited until the third year of a three year grant. We conclude by arguing that many of the current problems could be avoided by returning PIAG’s responsibilities to research ethics committees, and by allowing “opt-out” consent for many public health research projects. (shrink)

Collapse is a term that has attracted much attention in social science literature in recent years, but there remain substantial areas of disagreement about how it should be understood in historical contexts. More specifically, the use of the term collapse often merely serves to dramatize long-past events, to push human actors into the background, and to mystify the past intellectually. At the same time, since human societies are complex systems, the alternative involves grasping the challenges that a holistic analysis presents, (...) taking account of the many different levels and paces at which societies function, and developing appropriate methods that help to integrate science and history. Often neglected elements in considerations of collapse are the perceptions and beliefs of a historical society and how a given society deals with change; an important facet of this, almost entirely ignored in the discussion, is the understanding of time held by the individuals and social groups affected by change; and from this perspective ‘collapse’ depends very much on perception, including the perceptions of the modern commentator. With this in mind, this article challenges simplistic notions of ‘collapse’ in an effort to encourage a more nuanced understanding of the impact and process of both social and environmental change on past human societies. (shrink)

Current UK legislation is impacting upon the feasibility and cost-effectiveness of medical record-based research aimed at benefiting the NHS and the public heath. Whereas previous commentators have focused on the Data Protection Act 1998, the Health and Social Care Act 2001 is the key legislation for public health researchers wishing to access medical records without written consent. The Act requires researchers to apply to the Patient Information Advisory Group for permission to access medical records without written permission. We present a (...) case study of the work required to obtain the necessary permissions from PIAG in order to conduct a large scale public health research project. In our experience it took eight months to receive permission to access basic identifying information on individuals registered at general practices, and a decision on whether we could access clinical information in medical records without consent took 18 months. Such delays pose near insurmountable difficulties to grant funded research, and in our case £560 000 of public and charitable money was spent on research staff while a large part of their work was prohibited until the third year of a three year grant. We conclude by arguing that many of the current problems could be avoided by returning PIAG’s responsibilities to research ethics committees, and by allowing “opt-out” consent for many public health research projects. (shrink)

Members of the legal, medical and accounting professions are guided in their professional behavior by their respective codes of ethics. These codes of ethics are not static. They are ever evolving, responding to forces that are exogenous and endogenous to the professions. Specifically, changes in the ethical codes are often due to economic and social events, governmental influence, and growth and change within the professions. This paper presents an historical analysis of the major events leading to changes in the legal, (...) medical and accounting codes of ethics. (shrink)

BackgroundPreprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the reader’s ability to independently interpret data and reproduce findings.MethodsIn this observational study, we initially compared independent samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. After that, we performed paired comparisons (...) between preprints from bioRxiv to their own peer-reviewed versions in journals.ResultsPeer-reviewed articles had, on average, higher quality of reporting than preprints, although the difference was small, with absolute differences of 5.0% [95% CI 1.4, 8.6] and 4.7% [95% CI 2.4, 7.0] of reported items in the independent samples and paired sample comparison, respectively. There were larger differences favoring peer-reviewed articles in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Changes in reporting from preprints to peer-reviewed versions did not correlate with the impact factor of the publication venue or with the time lag from bioRxiv to journal publication.ConclusionsOur results suggest that, on average, publication in a peer-reviewed journal is associated with improvement in quality of reporting. They also show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions. (shrink)

Nanomedicine is yielding new and improved treatments and diagnostics for a range of diseases and disorders. Nanomedicine applications incorporate materials and components with nanoscale dimensions where novel physiochemical properties emerge as a result of size-dependent phenomena and high surface-to-mass ratio. Nanotherapeutics and in vivo nanodiagnostics are a subset of nanomedicine products that enter the human body. These include drugs, biological products, implantable medical devices, and combination products that are designed to function in the body in ways unachievable at larger scales. (...) Nanotherapeutics andin vivonanodiagnostics incorporate materials that are engineered at the nanoscale to express novel properties that are medicinally useful. These nanomedicine applications can also contain nanomaterials that are biologically active, producing interactions that depend on biological triggers. Examples include nanoscale formulations of insoluble drugs to improve bioavailability and pharmacokinetics, drugs encapsulated in hollow nanoparticles with the ability to target and cross cellular and tissue membranes and to release their payload at a specific time or location, imaging agents that demonstrate novel optical properties to aid in locating micrometastases, and antimicrobial and drug-eluting components or coatings of implantable medical devices such as stents. (shrink)

Synaesthesia is a condition in which one type of stimulation evokes the sensation of another, as when the hearing of a sound produces photisms, i.e. mental percepts of colours. R is a 20 year old colour blind subject who, in addition to the relatively common grapheme-colour synaesthesia, presents a rarely reported cross modal perception in which a variety of visual stimuli elicit aura-like percepts of colour. In R, photisms seem to be closely related to the affective valence of stimuli and (...) typically bring out a consistent pattern of emotional responses. The present case study suggests that colours might be an intrinsic category of the human brain. We developed an empirical methodology that allowed us to study the subject's otherwise inaccessible phenomenological experience. First, we found that R shows a Stroop effect elicited by photisms despite the fact that he does not show a regular Stroop with real colours. Secondly, by manipulating the colour context we confirmed that colours can alter R's emotional evaluation of the stimuli. Furthermore, we demonstrated that R's auras may actually lead to a partially inverted emotional spectrum where certain stimuli bring out emotional reactions opposite to the normal ones. These findings can only be accounted for by considering R's subjective colour experience or qualia. Therefore the present paper defends the view that qualia are a useful scientific concept that can be approached and studied by experimental methods. (shrink)

This study examines the outcomes of a four-year faculty learning community (FLC) that aimed to transform departmental ethics curriculum by supporting Earth Sciences faculty members as they ethically inquired into their teaching of ethics and refined existing courses in alignment with an Integrated Community-Engaged Learning and Ethical Reflection (ICELER) framework. We present ethnographic case studies that unpack processes through which three faculty members transformed undergraduate courses. We assembled case studies by triangulating interview data, course artifacts, and faculty reflections. We examine (...) how faculty (1) built awareness around teaching ethics, (2) took responsibility for and made judgments about teaching ethics, (3) experimented by designing and implementing ICELER-inspired courses, and (4) interrogated the outcomes of their ethics teaching, utilizing findings to enhance awareness and revise courses. The paper closes by introducing a model detailing how instructors inquire into ethics teaching and how model components might inspire future educational practice and research. (shrink)

Synaesthesia is a condition in which one type of stimulation evokes the sensation of another, as when the hearing of a sound produces photisms, i.e. mental percepts of colours. R is a 20 year old colour blind subject who, in addition to the relatively common grapheme-colour synaesthesia, presents a rarely reported cross modal perception in which a variety of visual stimuli elicit aura-like percepts of colour. In R, photisms seem to be closely related to the affective valence of stimuli and (...) typically bring out a consistent pattern of emotional responses. The present case study suggests that colours might be an intrinsic category of the human brain. We developed an empirical methodology that allowed us to study the subject's otherwise inaccessible phenomenological experience. First, we found that R shows a Stroop effect (delayed response due to interference) elicited by photisms despite the fact that he does not show a regular Stroop with real colours. Secondly, by manipulating the colour context we confirmed that colours can alter R's emotional evaluation of the stimuli. Furthermore, we demonstrated that R's auras may actually lead to a partially inverted emotional spectrum where certain stimuli bring out emotional reactions opposite to the normal ones. These findings can only be accounted for by considering R's subjective colour experience or qualia. Therefore the present paper defends the view that qualia are a useful scientific concept that can be approached and studied by experimental methods. (shrink)

We study the quantifier complexity and the relative strength of some fragments of arithmetic axiomatized by induction and minimization schemes for Δn+1 formulas.

We study the quantifier complexity and the relative strength of some fragments of arithmetic axiomatized by induction and minimization schemes for Δn+1 formulas.

This book highlights some of the most pressing safety, ethical, legal and societal issues related to the diverse contexts in which robotic technologies apply. Focusing on the essential concept of well-being, it addresses topics that are fundamental not only for research, but also for industry and end-users, discussing the challenges in a wide variety of applications, including domestic robots, autonomous manufacturing, personal care robots and drones.