Chance as an explanatory factor in evolutionary biology.

Darwinian evolutionary biology has often been criticized for appealing to the notion of 'chance' in its explanations. According to some critics, such appeals exhibit the explanatory poverty of evolutionary theory. In response, defenders of Darwinism sometimes downplay the importance of 'chance' in evolution. I believe that both of these approaches are mistaken. The main thesis of this paper is that the term 'chance' encompasses a number of distinct concepts, and that at least some of these concepts serve essential explanatory functions in evolutionary biology. This claim is defended by way of an historical survey of the major concepts of 'chance' in the history of evolutionary biology, especially the concepts used by Jean Baptiste Lamarck, Charles Darwin, and Sewall Wright. An examination of their biologies shows how the concepts of 'chance' used cohere with their major scientific objectives and methods. These concepts survive and continue to function as important explanatory factors in contemporary evolutionary biology. Examples of such usage are given, and the explanatory status of 'chance' assessed.     

Porphyrin‐Based Bulk Heterojunction Organic Photovoltaics: The Rise of the Colors of Life

Organic photovoltaics (OPV) represent a thin‐film PV technology that offers attractive prospects for low‐cost and aesthetically appealing (colored, flexible, uniform, semitransparent) solar cells that are printable on large surfaces. In bulk heterojunction (BHJ) OPV devices, organic electron donor and acceptor molecules are intimately mixed within the photoactive layer. Since 2005, the power conversion efficiency of said devices has increased substantially due to insights in the underlying physical processes, device optimization, and chemical engineering of a vast number of novel light‐harvesting organic materials, either small molecules or conjugated polymers. As Nature itself has developed porphyrin chromophores for solar light to energy conversion, it seems reasonable to pursue artificial systems based on the same types of molecules. Porphyrins and their analogues have already been successfully implemented in certain device types, notably in dye‐sensitized solar cells, but they have remained largely unexplored in BHJ organic solar cells. Very recent successes do show, however, the strong (latent) prospects of porphyrinoid semiconductors as light‐harvesting and charge transporting materials in such devices. Here, an overview on the state‐of‐the‐art of porphyrin‐based solution‐processed BHJ OPV is provided and insights are given into the pathways to follow and hurdles to overcome toward further improvements of porphyrinic materials and devices.     

EWOD silicon biosensor for multiple nucleic acids analysis

In this paper, a miniaturized biosensor containing 96 silicon microchambers electroloaded with nano-volumes of liquid (EW-chip) is presented. The liquid electroloading is achieved by the appropriate modulation of interface properties. The surface chemistries have been studied to guarantee effective interface properties for both electrowetting on dielectric actuation and biocompatibility versus biochemical reactions. The silicon microchambers are 200 nl in volume and are connected to a specific system of electrodes able to deliver liquid sample on each well. The device also integrates temperature sensors and heaters to perform biochemical reactions. On that, the effectiveness of this device has been successfully proven towards the nucleic acids detection via real-time polymerase chain reaction amplification. Hepatitis B virus genome target has been used to assess the device performance. Results show very uniform amplification over the 96 microchambers without any cross-contamination process. These features make this system a very appealing potential solution for genetic point-of-care devices where a high level of parallelism of analysis is required.     

Imidazolium‐Substituted Polythiophenes as Efficient Electron Transport Materials Improving Photovoltaic Performance

In the field of polymer solar cells, improving photovoltaic performance has been the main driver over the past decade. To achieve high power conversion efficiencies, a plethora of new photoactive donor polymers and fullerene derivatives have been developed and blended together in bulk heterojunction active layers. Simultaneously, further optimization of the device architecture is also of major importance. In this respect, we report on the use of specific types of electron transport layers to boost the inherent I–V properties of polymer solar cell devices, resulting in a considerable gain in overall photovoltaic output. Imidazolium‐substituted polythiophenes are introduced as appealing electron transport materials, outperforming the currently available analogous conjugated polyelectrolytes, mainly by an increase in short‐circuit current. The molecular weight of the ionic polythiophenes has been identified as a crucial parameter influencing performance.     

Neurostimulation and the minimally conscious state

Neurostimulation to restore cognitive and physical functions is an innovative and promising technique for treating patients with severe brain injury that has resulted in a minimally conscious state (MCS). The technique may involve electrical stimulation of the central thalamus, which has extensive projections to the cerebral cortex. Yet it is unclear whether an improvement in neurological functions would result in a net benefit for these patients. Quality-of-life measurements would be necessary to determine whether any benefit of neurostimulation outweighed any harm in their response to different degrees of cognitive and physical disability. These measures could also indicate whether the technique could be ethically justified and whether surrogates could give proxy consent to its use on brain-injured patients.     

On the Function of Wall Sculpturing in Xylem Conduits

The water-conducting network of capillaries in vascular plants has evolved over hundreds of millions of years in order to beable to cope with bubble clogging,a problem which also affects modern microfluidic devices.Decades of anatomical studieshave revealed that plants growing in habitats in which the formation of bubbles,or emboli,is likely to be a frequent occurrenceoften have various forms of geometrical sculpturing on the internal surfaces of the xylem conduits.The possible function of suchwall sculpturing has long been the subject of speculation.We have investigated the hypothesis that wall sculpturing is a functionaladaptation designed to increase the wettability of the walls of xylem conduits,an effect which could be described as theinverse of the well-known lotus-effect.Our results show that wall sculpturing does enhance wettability.Importantly,theoreticalcalculations reveal that the geometric parameters of various types of wall sculpturing are such that the resulting surfaces aresufficiently rough to enhance wettability,but not significantly rougher.The results provide an appealing answer to thelong-standing debate on the function of wall sculpturing in xylem conduits,and may provide biomimetic clues for new approachesto the removal of bubbles in microfluidic channels.     

The equivalence of two phylogenetic biodiversity measures: the Shapley value and Fair Proportion index

Most biodiversity conservation programs are forced to prioritise species in order to allocate their funding. This paper contains a mathematical proof that provides biological support for one common approach based on phylogenetic indices. Phylogenetic trees describe the evolutionary relationships between a group of taxa. Two indices for computing the distinctiveness of each taxon in a phylogenetic tree are considered here—the Shapley value and the Fair Proportion index. These indices provide a measure of the importance of each taxon for overall biodiversity and have been used to prioritise taxa for conservation. The Shapley value is the biodiversity contribution a taxon is expected to make if all taxa are equally likely to become extinct. This interpretation makes it appealing to use the Shapley value in biodiversity conservation applications. The Fair Proportion index lacks a convenient interpretation, however it is significantly easier to calculate and understand. It has been empirically observed that there is a high correlation between the two indices. This paper shows the mathematical basis for this correlation and proves that as the number of taxa increases, the indices become equivalent. Consequently in biodiversity prioritisation the simpler Fair Proportion index can be used whilst retaining the appealing interpretation of the Shapley value.     

The age‐cause proxy relationship in infant mortality

Abstract

Data presented in this brief note show that one of the consequences of recent gains in the control of neonatal mortality has been an increase in the frequency of endogenous causes of death in the postneonatal period. This in turn has greatly diminished the validity of using the postneonatal death rate as a proxy for the level of exogenous mortality in infancy. Moreover, although there continues to be a very strong correlation between neonatal and endogenous mortality, the increasing dominance of the latter causes throughout infancy also weakens the value of the age‐cause proxy relationship during the first month of life.     

Problems associated with the study of cellular oscillations

Data from the article by Brodsky et al. (2000) have been examined in order to confirm that the fluctuations they report are not random but have a rhythmic basis, thereby verifying their conclusions regarding the existence of periodicity in protein synthesis. Reasons are outlined why oscillations should be expected in all cellular biochemical studies. Associated practical problems are briefly discussed together with comments on the validity and value of less rigorous methods of analysis. The subject of aliasing is raised as justification for doubting the validity of much published data, especially where periodicity has not been suspected. The existence of oscillations indicates the need for a thorough re-evaluation of our understanding of cell biochemistry.     

Hemocompatibility and hemodynamic comparison of two centrifugal LVADs: HVAD and HeartMate3

Mechanical circulatory support using ventricular assist devices is a common technique for treating patients suffering from advanced heart failure. The latest generation of devices is characterized by centrifugal turbopumps which employ magnetic levitation bearings to ensure a gap clearance between moving and static parts. Despite the increasing use of these devices as a destination therapy, several long-term complications still exist regarding their hemocompatibility. The blood damage associated with different pump designs has been investigated profoundly in the literature, while the hemodynamic performance has been hardly considered. This work presents a novel comparison between the two main devices of the latest generation–HVAD and HM3–from both perspectives, hemodynamic performance and blood damage. Computational fluid dynamics simulations are performed to model the considered LVADs, and computational results are compared to experimental measurements of pressure head to validate the model. Enhanced performance and hemocompatibility are detected for HM3 owing to its design incorporating more conventional blades and larger gap clearances.

     

Structural and organisational conditions for being a machine

Although the analogy between macroscopic machines and biological molecular devices plays an important role in the conceptual framework of both neo-mechanistic accounts and nanotechnology, it has recently been claimed that certain complex molecular devices (consisting of biological or synthetic macromolecular aggregates) cannot be considered machines since they are subject to physicochemical forces that are different from those of macroscopic machines. However, the structural and physicochemical conditions that allow both macroscopic machines and microscopic devices to work and perform new functions, through a combination of elemental functional parts, have not yet been examined. In order to fill this void, this paper has a threefold aim: first, to clarify the structural and organisational conditions of macroscopic machines and microscopic devices; second, to determine whether the machine-like analogy fits nanoscale devices; and third, to assess whether the machine-like analogy is appropriate for describing the behaviour of some biological macromolecules. Finally, the paper gives an account of ‘machine’ which, while acknowledging the physicochemical and organisational differences between man-made machines and biological microscopic devices, nevertheless identifies a common conceptual core that allows us to consider the latter ‘machines’.     

Are responses of herbivores to environmental variability spatially consistent in alpine ecosystems?

Animal responses to global climate variation might be spatially inconsistent. This may arise from spatial variation in factors limiting populations' growth or from differences in the links between global climate patterns and ecologically relevant local climate variation. For example, the North Atlantic Oscillation (NAO) has a spatially consistent relation to temperature, but inconsistent spatial relation to snow depth in Scandinavia. Furthermore, there are multiple mechanistic ways by which climate may limit animal populations, involving both direct effects through thermoregulation and indirect pathways through trophic interactions. It is conceptually appealing to directly model the predicted mechanistic links. This includes the use of climate variables mimicking such interactions, for example, to use growing degree days (GDD) as a proxy for plant growth rather than average monthly temperature. Using a unique database of autumn body mass of 83331 domestic lambs from the period 1992–2007 in four alpine ranges in Norway, we demonstrate the utility of hierarchical, mechanistic path models fitted using a Bayesian approach to analyse explicitly predicted relationships among environmental variables and between lamb body mass and the environmental variables. We found large spatial variation in strength of responses of autumn lamb body mass to the NAO, to a proxy for plant growth in spring (the Normalized Difference Vegetation Index, NDVI) and effects even differed in direction to local summer climate. Average local temperature outperformed GDD as a predictor of the NDVI, whereas the NAO index in two areas outperformed local weather variables as a predictor of lamb body mass, despite the weaker mechanistic link. Our study highlights that spatial variation in strength of herbivore responses may arise from several processes. Furthermore, mechanistically more appealing measures do not always increase predictive power due to scale of measurement and since global measures may provide more relevant “weather packages” for larger scales.     

Developments in craniomaxillofacial surgery: use of self-reinforced bioabsorbable osteofixation devices.

Because of the problems associated with the conventional osteofixation devices used in craniomaxillofacial surgery, absorbable devices present an appealing alternative. Devices made of the polymers polylactide, polyglycolide, and their copolymers (PLGA and P[L/DL]LA) are currently the most commonly used. Ultrahigh-strength implants can be manufactured from these polymers with the self-reinforcing technique. Over the authors' almost two decades of study, both in experimental and clinical settings, self-reinforced devices have proved to be biocompatible, easy to handle, and mechanically strong, even for the fixation of femoral neck fractures. In craniomaxillofacial surgery, the authors have used self-reinforced devices for over 8 years without complications. Because of the more favored degradation characteristics, currently the copolymeric self-reinforced devices (P[L/DL]LA, Biosorb FX and PLGA, Biosorb PDX; Elite Performance Technologies, Solana Beach, Calif.) represent the advancing front in the application of absorbable devices in craniomaxillofacial surgery. The authors' share their experience and their studies of self-reinforced devices, which possess the highest strength and ductility of all bioabsorbable products.     

P. falciparum in vitro killing rates allow to discriminate between different antimalarial mode-of-action

Chemotherapy is still the cornerstone for malaria control. Developing drugs against Plasmodium parasites and monitoring their efficacy requires methods to accurately determine the parasite killing rate in response to treatment. Commonly used techniques essentially measure metabolic activity as a proxy for parasite viability. However, these approaches are susceptible to artefacts, as viability and metabolism are two parameters that are coupled during the parasite life cycle but can be differentially affected in response to drug actions. Moreover, traditional techniques do not allow to measure the speed-of-action of compounds on parasite viability, which is an essential efficacy determinant. We present here a comprehensive methodology to measure in vitro the direct effect of antimalarial compounds over the parasite viability, which is based on limiting serial dilution of treated parasites and re-growth monitoring. This methodology allows to precisely determine the killing rate of antimalarial compounds, which can be quantified by the parasite reduction ratio and parasite clearance time, which are key mode-of-action parameters. Importantly, we demonstrate that this technique readily permits to determine compound killing activities that might be otherwise missed by traditional, metabolism-based techniques. The analysis of a large set of antimalarial drugs reveals that this viability-based assay allows to discriminate compounds based on their antimalarial mode-of-action. This approach has been adapted to perform medium throughput screening, facilitating the identification of fast-acting antimalarial compounds, which are crucially needed for the control and possibly the eradication of malaria.     

Methods in sustainable monitoring: plot sampling versus interviews

Biodiversity monitoring in developing countries has long been haunted by problems with sustaining monitoring programs, especially after funding stops. Current programs are developed to fulfill strict scientific demands, which often results in high priced programs, with little local participation and attention. Thus, to enhance sustainability of the biodiversity programs, there is a great need to reconcile scientific rigor with local involvement. In this paper, we analyze the cost-effectiveness and usefulness of a standard and a participatory monitoring method, in their ability to monitor biodiversity, while rising local participation. As a standard method we used a forest characteristic with tree basal area and Shannon index as proxy for biodiversity. Interviews were used as a participatory approach, with hunters’ catch-effort as proxy. The analysis showed that the interviews reached a better precision with fewer work hours spent and at the same time involved local populations and stake holders. As a tradeoff, the interviews lacked the scientific rigor from forest characteristic. In order to sustain monitoring programs, we conclude that conservation biologists needs to compromise between scientific rigor and public participation.     

Inferring maximum lifespan from maximum recorded longevity in the wild carries substantial risk of estimation bias

When comparing lifespan (longevity) between species, it is common practice to take the maximum recorded longevity value within each species as a proxy of maximum lifespan. Whether maximum recorded longevity is a reliable proxy of species' maximum longevity remains unclear. Some researchers correct for previously documented life history correlates of maximum recorded longevity before analysing new predictors of lifespan across species in the context of their current, specific hypotheses. At present there is no certainty that all relevant statistical, phenotypic, or ecological biases are accounted for by such corrective measures. Here, we employ Monte Carlo simulation to investigate the effect of differences in recapture numbers, recapture types (the point in life at which individuals are initially captured or recaptured), and actuarial population decay structure of simulated species on their maximum recorded longevities. We show that maximum recorded longevities differ in response to all three of these variables, as well as all of their two‐ and three‐way interactions. We then investigate empirical avian band‐recapture data for evidence of biases caused by recapture number and recapture type, predicted by the Monte Carlo analysis, and confirm the predicted biases as major sources of variance. Finally, we investigate the relationship between recapture type, recapture number, and a selection of ecological and life‐history variables previously documented to correlate with maximum recorded longevity, and find significant correlations between the biasing variables and those published correlates. Our results call into question the validity of using maximum recorded longevity as a proxy for different species' maximum longevities in comparative studies investigating the evolution of lifespan.     

Training to vasodilate in a cooling environment: a valid treatment for Raynaud's phenomenon?

While many reports indicate that voluntary modification of skin temperature is possible and may be useful in the treatment of Raynaud's phenomenon, little attention has been paid to the ecological validity of training skin temperature increases when a considerable amount of vasodilation of digital vessels may already exist (room temperature, 22-24 degrees C). Patients with Raynaud's vasospastic attacks may benefit from learning to avoid attacks when they are impending by voluntarily vasodilating the vessels of their digits under conditions when vasoconstriction has begun. The results in 14 patients with primary and secondary Raynaud's phenomenon indicated that (a) patients learned to voluntarily increase digital skin temperatures in a "cooling" environment during documented vasoconstriction, and (b) there was a 31% decrease in the occurrence of vasospastic attacks following such learning. These data suggest that a new methodology may be useful in the biofeedback treatment of Raynaud's phenomenon, but further research is needed to determine the specific mechanism(s) involved, and the limits to its usefulness.     

Body mass is less important than bird order in determining the molecular rate for bird mitochondrial DNA

A negative relationship between body mass and molecular evolution rates has been suggested, and recently a correlation equation has been published based on mitochondrial genomic data of 475 bird species and their body masses. Here, we re‐analysed these data and show that the bird order as a proxy of monophyletic groups was a stronger predictor of the molecular rate than the body mass. We provide order‐specific molecular substitution rates. Only three orders (Galliformes, Gruiformes, Pelecaniformes) showed a very clear negative correlation, and specific correlation equations are given for these. The molecular rates of bird orders differed strongly at similar mean body masses, and we suggest that the previously described trend across all birds may arise as smaller species also tend to have characteristic life histories, namely faster turnover of generations, higher fecundity and shorter lifespans.     

Theodosius Dobzhansky and the genetic race concept

The use of ‘race’ as a proxy for population structure in the genetic mapping of complex traits has provoked controversy about its legitimacy as a category for biomedical research, given its social and political connotations. The controversy has reignited debates among scientists and philosophers of science about whether there is a legitimate biological concept of race. This paper examines the genetic race concept as it developed historically in the work of Theodosius Dobzhansky from the 1930s to 1950s. Dobzhansky’s definitions of race changed over this time from races as ‘arrays of forms’ or ‘clusters’ in 1933–1939, to races as genetically distinct geographical populations in 1940–1946, to races as genetically distinct ‘Mendelian populations’ in 1947–1955. Dobzhansky responded to nominalist challenges by appealing to the biological reality of race as a process. This response came into tension with the object ontology of race that was implied by Dobzhansky’s increasingly holistic treatment of Mendelian populations, a tension, the paper argues, he failed to appreciate or resolve.     

Detecting Positioning Errors and Estimating Correct Positions by Moving Window

In recent times, improvements in smart mobile devices have led to new functionalities related to their embedded positioning abilities. Many related applications that use positioning data have been introduced and are widely being used. However, the positioning data acquired by such devices are prone to erroneous values caused by environmental factors. In this research, a detection algorithm is implemented to detect erroneous data over a continuous positioning data set with several options. Our algorithm is based on a moving window for speed values derived by consecutive positioning data. Both the moving average of the speed and standard deviation in a moving window compose a moving significant interval at a given time, which is utilized to detect erroneous positioning data along with other parameters by checking the newly obtained speed value. In order to fulfill the designated operation, we need to examine the physical parameters and also determine the parameters for the moving windows. Along with the detection of erroneous speed data, estimations of correct positioning are presented. The proposed algorithm first estimates the speed, and then the correct positions. In addition, it removes the effect of errors on the moving window statistics in order to maintain accuracy. Experimental verifications based on our algorithm are presented in various ways. We hope that our approach can help other researchers with regard to positioning applications and human mobility research.