Can patents prohibit research? On the social epistemology of patenting and licensing in science

A topic of growing importance within philosophy of science is the epistemic implications of the organization of research. This paper identifies a promising approach to social epistemology—nonideal systems design—and uses it to examine one important aspect of the organization of research, namely the system of patenting and licensing and its role in structuring the production and dissemination of knowledge. The primary justification of patenting in science and technology is consequentialist in nature. Patenting should incentivize research and thereby promote the development of knowledge, which in turn facilitates social progress. Some have disputed this argument, maintaining that patenting actually inhibits knowledge production. In this paper, I make a stronger argument; in some areas of research in the US—in particular, research on GM seeds—patents and patent licenses can be, and are in fact being, used to prohibit some research. I discuss three potential solutions to this problem: voluntary agreements, eliminating patents, and a research exemption. I argue against eliminating patents, and I show that while voluntary agreements and a research exemption could be helpful, they do not sufficiently address the problems of access that are discussed here. More extensive changes in the organization of research are necessary.     

Long-term evolution and transmission dynamics of swine influenza A virus

Swine influenza A viruses (SwIV) cause significant economic losses in animal husbandry as well as instances of human disease and occasionally give rise to human pandemics, including that caused by the H1N1/2009 virus. The lack of systematic and longitudinal influenza surveillance in pigs has hampered attempts to reconstruct the origins of this pandemic. Most existing swine data were derived from opportunistic samples collected from diseased pigs in disparate geographical regions, not from prospective studies in defined locations, hence the evolutionary and transmission dynamics of SwIV are poorly understood. Here we quantify the epidemiological, genetic and antigenic dynamics of SwIV in Hong Kong using a data set of more than 650 SwIV isolates and more than 800 swine sera from 12?years of systematic surveillance in this region, supplemented with data stretching back 34?years. Intercontinental virus movement has led to reassortment and lineage replacement, creating an antigenically and genetically diverse virus population whose dynamics are quantitatively different from those previously observed for human influenza viruses. Our findings indicate that increased antigenic drift is associated with reassortment events and offer insights into the emergence of influenza viruses with epidemic potential in swine and humans.     

Modulation of Rab GTPase function by a protein phosphocholine transferase

The intracellular pathogen Legionella pneumophila modulates the activity of host GTPases to direct the transport and assembly of the membrane-bound compartment in which it resides. In vitro studies have indicated that the Legionella protein DrrA post-translationally modifies the GTPase Rab1 by a process called AMPylation. Here we used mass spectrometry to investigate post-translational modifications to Rab1 that occur during infection of host cells by Legionella. Consistent with in vitro studies, DrrA-mediated AMPylation of a conserved tyrosine residue in the switch II region of Rab1 was detected during infection. In addition, a modification to an adjacent serine residue in Rab1 was discovered, which was independent of DrrA. The Legionella effector protein AnkX was required for this modification. Biochemical studies determined that AnkX directly mediates the covalent attachment of a phosphocholine moiety to Rab1. This phosphocholine transferase activity used CDP-choline as a substrate and required a conserved histidine residue located in the FIC domain of the AnkX protein. During infection, AnkX modified both Rab1 and Rab35, which explains how this protein modulates membrane transport through both the endocytic and exocytic pathways of the host cell. Thus, phosphocholination of Rab GTPases represents a mechanism by which bacterial FIC-domain-containing proteins can alter host-cell functions.     

Optically healable supramolecular polymers

Polymers with the ability to repair themselves after sustaining damage could extend the lifetimes of materials used in many applications. Most approaches to healable materials require heating the damaged area. Here we present metallosupramolecular polymers that can be mended through exposure to light. They consist of telechelic, rubbery, low-molecular-mass polymers with ligand end groups that are non-covalently linked through metal-ion binding. On exposure to ultraviolet light, the metal-ligand motifs are electronically excited and the absorbed energy is converted into heat. This causes temporary disengagement of the metal-ligand motifs and a concomitant reversible decrease in the polymers' molecular mass and viscosity, thereby allowing quick and efficient defect healing. Light can be applied locally to a damage site, so objects can in principle be healed under load. We anticipate that this approach to healable materials, based on supramolecular polymers and a light-heat conversion step, can be applied to a wide range of supramolecular materials that use different chemistries.     

Long-term effects of tebuthiuron on Bromus tectorum

Use of herbicides to thin dense stands of Artemisia spp. (sagebrush) can free up resources for herbaceous plants and increase forage production, but may also facilitate weed invasion. We revisited a sagebrush thinning experiment in a north central Wyoming big sagebrush–grassland 11 years after application of tebuthiuron (N-[5-(1,1- dimethylethyl)-1,3,4-thiadiazol-2-yl]-N-N′-dimethylurea) to determine the long-term responses of shrubs, available soil resources, perennial grasses, and Bromus tectorum L. (downy brome). Tebuthiuron reduced shrub cover by more than half, from 31% in untreated plots to 15% in treated plots ( P = 0.002), and increased downy brome cover approximately 4-fold, from 0.9% in untreated plots to 3.5% in treated plots ( P = 0.02). Treatment with tebuthiuron also resulted in marginally significant increases in cover of perennial grasses (from 9% to 12.3%; P = 0.07) and bare ground (from 39.1% to 43.9%; P = 0.08). In comparisons of resource availability among microsites, available NO 3 was higher under dead sagebrush than under live sagebrush ( P = 0.03). No significant differences in soil water content were detected. The relatively recent expansion of downy brome populations at this site and the high NO 3 –N levels observed under dead sagebrush suggest that conditions facilitating downy brome invasion may persist for many years following sagebrush thinning. We demonstrate that sagebrush thinning can cause increases in downy brome populations years after initial treatment and suggest that managers should use caution when considering thinning sagebrush if downy brome is present, even if initial populations are small.     

Extracellular wildtype and mutant SOD1 induces ER–Golgi pathology characteristic of amyotrophic lateral sclerosis in neuronal cells

Amyotrophic lateral sclerosis (ALS) is a fatal and rapidly progressing neurodegenerative disorder and the majority of ALS is sporadic, where misfolding and aggregation of Cu/Zn-superoxide dismutase (SOD1) is a feature shared with familial mutant-SOD1 cases. ALS is characterized by progressive neurospatial spread of pathology among motor neurons, and recently the transfer of extracellular, aggregated mutant SOD1 between cells was demonstrated in culture. However, there is currently no evidence that uptake of SOD1 into cells initiates neurodegenerative pathways reminiscent of ALS pathology. Similarly, whilst dysfunction to the ER–Golgi compartments is increasingly implicated in the pathogenesis of both sporadic and familial ALS, it remains unclear whether misfolded, wildtype SOD1 triggers ER–Golgi dysfunction. In this study we show that both extracellular, native wildtype and mutant SOD1 are taken up by macropinocytosis into neuronal cells. Hence uptake does not depend on SOD1 mutation or misfolding. We also demonstrate that purified mutant SOD1 added exogenously to neuronal cells inhibits protein transport between the ER–Golgi apparatus, leading to Golgi fragmentation, induction of ER stress and apoptotic cell death. Furthermore, we show that extracellular, aggregated, wildtype SOD1 also induces ER–Golgi pathology similar to mutant SOD1, leading to apoptotic cell death. Hence extracellular misfolded wildtype or mutant SOD1 induce dysfunction to ER–Golgi compartments characteristic of ALS in neuronal cells, implicating extracellular SOD1 in the spread of pathology among motor neurons in both sporadic and familial ALS.     

Putting pragmatism to work in the Cold War: Science, technology, and politics in the writings of James B. Conant

This paper examines James Conant’s pragmatic theory of science—a theory that has been neglected by most commentators on the history of 20^th-century philosophy of science—and it argues that this theory occupied an important place in Conant’s strategic thinking about the Cold War. Conant drew upon his wartime science policy work, the history of science, and Quine’s epistemological holism to argue that there is no strict distinction between science and technology, that there is no such thing as “the scientific method,” and that theories are better interpreted as policies rather than creeds. An important consequence that he drew from these arguments is that science is both a thoroughly value-laden, and an intrinsically social, enterprise. These results led him to develop novel proposals for reorganizing scientific and technological research—proposals that he believed could help to win the Cold War. Interestingly, the Cold War had a different impact upon Conant’s thinking than it did upon many other theorists of science in postwar America. Instead of leading him to “the icy slopes of logic,” it led him to develop a socially- and politically-engaged theory that was explicitly in the service of the American Cold War effort.