Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges, Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology

Franck-Condon Effect in Central Spin System

We study the quantum transitions of a central spin surrounded by a collective-spin environment. It is found that the influence of the environmental spins on the absorption spectrum of the central spin can be explained with the analog of the Franck-Condon (FC) effect in conventional electron-phonon interaction system. Here, the collective spins of the environment behave as the vibrational mode, which makes the electron to be transitioned mainly with the so-called "vertical transitions" in the conventional FC effect. The "vertical transition" for the central spin in the spin environment manifests as, the certain collective spin states of the environment is favored, which corresponds to the minimal change in the average of the total spin angular momentum.Comment: 8 pages, 8 figure

TGA2 signaling in response to reactive electrophile species is not dependent on cysteine modification of TGA2

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Reactive electrophile species (RES), including prostaglandins, phytoprostanes and 12-oxo phytodienoic acid (OPDA), activate detoxification responses in plants and animals. However, the pathways leading to the activation of defense reactions related to abiotic or biotic stress as a function of RES formation, accumulation or treatment are poorly understood in plants. Here, the thiol-modification of proteins, including the RES-activated basic region/leucine zipper transcription factor TGA2, was studied. TGA2 contains a single cysteine residue (Cys186) that was covalently modified by reactive cyclopentenones but not required for induction of detoxification genes in response to OPDA or prostaglandin A1. Activation of the glutathione-S-transferase 6 (GST6) promoter was responsive to cyclopentenones but not to unreactive cyclopentanones, including jasmonic acid suggesting that thiol reactivity of RES is important to activate the TGA2-dependent signaling pathway resulting in GST6 activation We show that RES modify thiols in numerous proteins in vivo, however, thiol reactivity alone appears not to be sufficient for biological activity as demonstrated by the failure of several membrane permeable thiol reactive reagents to activate the GST6 promoter.Peer reviewedFinal Published versio

Effect of early vasopressin vs norepinephrine on kidney failure in patients with septic shock. The VANISH Randomized Clinical Trial

IMPORTANCE: Norepinephrine is currently recommended as the first-line vasopressor in septic shock; however, early vasopressin use has been proposed as an alternative. OBJECTIVE: To compare the effect of early vasopressin vs norepinephrine on kidney failure in patients with septic shock. DESIGN, SETTING, AND PARTICIPANTS: A factorial (2×2), double-blind, randomized clinical trial conducted in 18 general adult intensive care units in the United Kingdom between February 2013 and May 2015, enrolling adult patients who had septic shock requiring vasopressors despite fluid resuscitation within a maximum of 6 hours after the onset of shock. INTERVENTIONS: Patients were randomly allocated to vasopressin (titrated up to 0.06 U/min) and hydrocortisone (n = 101), vasopressin and placebo (n = 104), norepinephrine and hydrocortisone (n = 101), or norepinephrine and placebo (n = 103). MAIN OUTCOMES AND MEASURES: The primary outcome was kidney failure-free days during the 28-day period after randomization, measured as (1) the proportion of patients who never developed kidney failure and (2) median number of days alive and free of kidney failure for patients who did not survive, who experienced kidney failure, or both. Rates of renal replacement therapy, mortality, and serious adverse events were secondary outcomes. RESULTS: A total of 409 patients (median age, 66 years; men, 58.2%) were included in the study, with a median time to study drug administration of 3.5 hours after diagnosis of shock. The number of survivors who never developed kidney failure was 94 of 165 patients (57.0%) in the vasopressin group and 93 of 157 patients (59.2%) in the norepinephrine group (difference, -2.3% [95% CI, -13.0% to 8.5%]). The median number of kidney failure-free days for patients who did not survive, who experienced kidney failure, or both was 9 days (interquartile range [IQR], 1 to -24) in the vasopressin group and 13 days (IQR, 1 to -25) in the norepinephrine group (difference, -4 days [95% CI, -11 to 5]). There was less use of renal replacement therapy in the vasopressin group than in the norepinephrine group (25.4% for vasopressin vs 35.3% for norepinephrine; difference, -9.9% [95% CI, -19.3% to -0.6%]). There was no significant difference in mortality rates between groups. In total, 22 of 205 patients (10.7%) had a serious adverse event in the vasopressin group vs 17 of 204 patients (8.3%) in the norepinephrine group (difference, 2.5% [95% CI, -3.3% to 8.2%]). CONCLUSIONS AND RELEVANCE: Among adults with septic shock, the early use of vasopressin compared with norepinephrine did not improve the number of kidney failure-free days. Although these findings do not support the use of vasopressin to replace norepinephrine as initial treatment in this situation, the confidence interval included a potential clinically important benefit for vasopressin, and larger trials may be warranted to assess this further. TRIAL REGISTRATION: clinicaltrials.gov Identifier: ISRCTN 20769191

Transcriptional Profiling Uncovers a Network of Cholesterol-Responsive Atherosclerosis Target Genes

Despite the well-documented effects of plasma lipid lowering regimes halting atherosclerosis lesion development and reducing morbidity and mortality of coronary artery disease and stroke, the transcriptional response in the atherosclerotic lesion mediating these beneficial effects has not yet been carefully investigated. We performed transcriptional profiling at 10-week intervals in atherosclerosis-prone mice with human-like hypercholesterolemia and a genetic switch to lower plasma lipoproteins (Ldlr−/−Apo100/100 Mttpflox/flox Mx1-Cre). Atherosclerotic lesions progressed slowly at first, then expanded rapidly, and plateaued after advanced lesions formed. Analysis of lesion expression profiles indicated that accumulation of lipid-poor macrophages reached a point that led to the rapid expansion phase with accelerated foam-cell formation and inflammation, an interpretation supported by lesion histology. Genetic lowering of plasma cholesterol (e.g., lipoproteins) at this point all together prevented the formation of advanced plaques and parallel transcriptional profiling of the atherosclerotic arterial wall identified 37 cholesterol-responsive genes mediating this effect. Validation by siRNA-inhibition in macrophages incubated with acetylated-LDL revealed a network of eight cholesterol-responsive atherosclerosis genes regulating cholesterol-ester accumulation. Taken together, we have identified a network of atherosclerosis genes that in response to plasma cholesterol-lowering prevents the formation of advanced plaques. This network should be of interest for the development of novel atherosclerosis therapies

Electrons surfing on a sound wave as a platform for quantum optics with flying electrons

Electrons in a metal are indistinguishable particles that strongly interact with other electrons and their environment. Isolating and detecting a single flying electron after propagation to perform quantum optics like experiments at the single electron level is therefore a challenging task. Up to date, only few experiments have been performed in a high mobility two-dimensional electron gas where the electron propagates almost ballistically. Flying electrons were detected via the current generated by an ensemble of electrons and electron correlations were encrypted in the current noise. Here we demonstrate the experimental realisation of high efficiency single electron source and single electron detector for a quantum medium where a single electron is propagating isolated from the other electrons through a one-dimensional channel. The moving potential is excited by a surface acoustic wave, which carries the single electron along the 1D-channel at a speed of 3\mum/ns. When such a quantum channel is placed between two quantum dots, a single electron can be transported from one quantum dot to the other, which is several micrometres apart, with a quantum efficiency of emission and detection of 96% and 92%, respectively. Furthermore, the transfer of the electron can be triggered on a timescale shorter than the coherence time T2* of GaAs spin qubits6. Our work opens new avenues to study the teleportation of a single electron spin and the distant interaction between spatially separated qubits in a condensed matter system.Comment: Total 25 pages. 12 pages main text, 4 figures, 5 pages supplementary materia

Effects of a penthiopyrad and picoxystrobin fungicide mixtureon phoma stem canker (Leptosphaeria spp.) on UK winteroilseed rape

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2016. This is a pre-copyedited, author-produced PDF of an article accepted for publication in European Journal of Plant Pathology following peer review. The final publication [Sewell, T.R., Moloney, S., Ashworth, M. et al., European Journal of Plant Pathology (2016) 145: 675-685, first published online April 5, 2016] is available at Springer via doi: http://dx.doi.org/10.1007/s10658-016-0916-8In the UK, fungicides are often used to controlphoma stem canker on winter oilseed rape. Field trialswere established near Boxworth, Cambridgeshire for fourcropping seasons (2011/2012, 2012/2013, 2013/2014 and2014/15) to test the efficacy of a new fungicide mixtureRefinzar® (penthiopyrad + picoxystrobin) by comparisonto an existing fungicide Proline 275® (prothioconazole)against phoma stem canker (Leptosphaeria spp.) andthe effect on winter oilseed rape (cv. Catana) yield. Ineach season, weather data were collected from a weatherstation at Boxworth and the release of ascospores wasmonitored using a nearby Burkard spore sampler. Thepatterns of ascospore release differed between seasonsand related to weather conditions. Fungicidespenthiopyrad + picoxystrobin and prothioconazole wereapplied in October/November when 10 % of plants hadphoma leaf spotting (T1, early), 4/8 weeks after T1 (T2,late) or at both T1 and T2 (combined). When phoma leafspot symptoms were assessed in autumn/winter,penthiopyrad + picoxystrobin and prothioconazole bothdecreased numbers of phoma leaf spots caused byL. maculans; there were few leaf spots caused byL. biglobosa. Penthiopyrad + picoxystrobin andprothioconazole both reduced phoma stem canker severitybefore harvest compared to the untreated control butdid not increase yield in these seasons when epidemicswere not severe. In 2013/2014, the presence ofL. maculans and L. biglobosa in upper stem lesions orstem base cankers was determined by species-specificPCR. The proportions of stems with L. maculans DNAwere much greater than those with L. biglobosa DNA forboth upper stem lesions and basal stem cankers. Theseresults suggest that both penthiopyrad + picoxystrobinand prothioconazole can decrease phoma stem cankerseverity on winter oilseed rape in severe disease seasons.Peer reviewe

Not a melting pot: Plant species aggregate in their non-native range

Aim: Plant species continue to be moved outside of their native range by human activities. Here, we aim to determine whether, once introduced, plants assimilate into native communities or whether they aggregate, thus forming mosaics of native- and alien-rich communities. Alien species might aggregate in their non-native range owing to shared habitat preferences, such as their tendency to establish in high-biomass, species-poor areas. Location: Twenty-two herbaceous grasslands in 14 countries, mainly in the temperate zone. Time period: 2012–2016. Major taxa studied: Plants. Methods: We used a globally coordinated survey. Within this survey, we found 46 plant species, predominantly from Eurasia, for which we had co-occurrence data in their native and non-native ranges. We tested for differences in co-occurrence patterns of 46 species between their native (home) and non-native (away) range. We also tested whether species had similar habitat preferences, by testing for differences in total biomass and species richness of the patches that species occupy in their native and non-native ranges. Results: We found the same species to show different patterns of association depending on whether they were in their native or non-native range. Alien species were negatively associated with native species; instead, they aggregated with other alien species in species-poor, high-biomass communities in their non-native range compared with their native range. Main conclusions: The strong differences between the native (home) and non-native (away) range in species co-occurrence patterns are evidence that the way in which species associate with resident communities in their non-native range is not species dependent, but is instead a property of being away from their native range. These results thus highlight that species might undergo important ecological changes when introduced away from their native range. Overall, we show origin-dependent associations that result in novel communities, in which alien-rich patches exist within a mosaic of native-dominated communities

Shifting Attention From Theory to Practice in Philosophy of Biology

Traditional approaches in philosophy of biology focus attention on biological concepts, explanations, and theories, on evidential support and inter-theoretical relations. Newer approaches shift attention from concepts to conceptual practices, from theories to practices of theorizing, and from theoretical reduction to reductive retooling. In this article, I describe the shift from theory-focused to practice-centered philosophy of science and explain how it is leading philosophers to abandon fundamentalist assumptions associated with traditional approaches in philosophy of science and to embrace scientific pluralism. This article comes in three parts, each illustrating the shift from theory-focused to practice-centered epistemology. The first illustration shows how shifting philosophical attention to conceptual practice reveals how molecular biologists succeed in identifying coherent causal strands within systems of bewildering complexity. The second illustration suggests that analyzing how a multiplicity of alternative models function in practice provides an illuminating approach for understanding the nature of theoretical knowledge in evolutionary biology. The third illustration demonstrates how framing reductionism in terms of the reductive retooling of practice offers an informative perspective for understanding why putting DNA at the center of biological research has been incredibly productive throughout much of biology. Each illustration begins by describing how traditional theory-focused philosophical approaches are laden with fundamentalist assumptions and then proceeds to show that shifting attention to practice undermines these assumptions and motivates a philosophy of scientific pluralism

Nasal Chemosensory-Stimulation Evoked Activity Patterns in the Rat Trigeminal Ganglion Visualized by In Vivo Voltage-Sensitive Dye Imaging

Mammalian nasal chemosensation is predominantly mediated by two independent neuronal pathways, the olfactory and the trigeminal system. Within the early olfactory system, spatiotemporal responses of the olfactory bulb to various odorants have been mapped in great detail. In contrast, far less is known about the representation of volatile chemical stimuli at an early stage in the trigeminal system, the trigeminal ganglion (TG), which contains neurons directly projecting to the nasal cavity. We have established an in vivo preparation that allows high-resolution imaging of neuronal population activity from a large region of the rat TG using voltage-sensitive dyes (VSDs). Application of different chemical stimuli to the nasal cavity elicited distinct, stimulus-category specific, spatiotemporal activation patterns that comprised activated as well as suppressed areas. Thus, our results provide the first direct insights into the spatial representation of nasal chemosensory information within the trigeminal ganglion imaged at high temporal resolution