Origin of life in a digital microcosm

While all organisms on Earth descend from a common ancestor, there is no consensus on whether the origin of this ancestral self-replicator was a one-off event or whether it was only the final survivor of multiple origins. Here we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry). We generated the exhaustive set of minimal-genome self-replicators and analyzed the network structure of this fitness landscape. We further examined the evolvability of these self-replicators and found that the evolvability of a self-replicator is dependent on its genomic architecture. We studied the differential ability of replicators to take over the population when competed against each other (akin to a primordial-soup model of biogenesis) and found that the probability of a self-replicator out-competing the others is not uniform. Instead, progenitor (most-recent common ancestor) genotypes are clustered in a small region of the replicator space. Our results demonstrate how computational systems can be used as test systems for hypotheses concerning the origin of life.Comment: 20 pages, 7 figures. To appear in special issue of Philosophical Transactions of the Royal Society A: Re-Conceptualizing the Origins of Life from a Physical Sciences Perspectiv

Paul\u27s Process of Preaching the Gospel to the Gentiles

This thesis will be concerned with the spoken or preached Gospel in contrast to the other ways of presenting the Gospel

Watching others in a positive state does not induce optimism bias in common marmosets (Callithrix jacchus), but leads to behaviour indicative of competition

Emotional contagion is suggested to facilitate group life by enhancing synchronized responses to the environment. Cooperative breeders are an example of a social system that requires such intricate coordination between individuals. Therefore, we studied emotional contagion in common marmosets by means of a judgement bias test. Demonstrators were exposed to an emotion manipulation (i.e., positive, negative, control), and observers perceived only the demonstrator’s behaviour. We predicted that the positive or negative states of the demonstrator would induce matching states in the observer, indicating emotional contagion. All subjects’ emotional states were assessed through behaviour and cognition, the latter by means of a judgement bias test. Behavioural results showed a successful emotion manipulation of demonstrators, with manipulation-congruent expressions (i.e., positive calls in the positive condition, and negative calls and pilo-erect tail in the negative condition). Observers showed no manipulation-congruent expressions, but showed more scratching and arousal after the positive manipulation. Concerning the judgement bias test, we predicted that subjects in a positive state should increase their response to ambiguous cues (i.e., optimism bias), and subjects in a negative state should decrease their response (i.e., pessimism bias). This prediction was not supported as neither demonstrators nor observers showed such bias in either manipulation. Yet, demonstrators showed an increased response to the near-positive cue, and additional analyses showed unexpected responses to the reference cues, as well as a researcher identity effect. We discuss all results combined, including recently raised validation concerns of the judgement bias test, and inherent challenges to empirically studying emotional contagion

FY 2017 Center Innovation Fund Annual Report - Highlights/Abstract section

This project evaluated the feasibility of low pressure cold plasma (CP) for two applications: disinfection of produce grown in space and sterilization of medical equipment in space. Currently there is no ISS capability for disinfecting pick and eat crops, food utensils, food production areas, or medical devices. This deficit is extended to projected long duration missions. Small, portable, cold plasma devices would provide an enhanced benefit to crew health and address issues concerning microbial cross contamination. The technology would contribute to the reduction of solid waste since currently crews utilize benzalkonium chloride wet wipes for cleaning surfaces and might use PRO-SAN wipes for cleaning vegetables. CP cleaning/disinfection/sterilization can work on many surfaces, including all metals, most polymers, and this project evaluated produce. Therefore CP provides a simple system that has many different cleaning application in space: produce, medical equipment, cutlery, miscellaneous tools

Degradation of Organics in a Glow Discharge Under Martian Conditions

The primary objective of this project is to understand the consequences of glow electrical discharges on the chemistry and biology of Mars. The possibility was raised some time ago that the absence of organic material and carbonaceous matter in the Martian soil samples studied by the VikinG Landers might be due in part to an intrinsic atmospheric mechanism such as glow discharge. The high probability for dust interactions during Martian dust storms and dust devils, combined with the cold, dry climate of Mars most likely results in airborne dust that is highly charged. Such high electrostatic potentials generated during dust storms on Earth are not permitted in the low-pressure CO2 environment on Mars; therefore electrostatic energy released in the form of glow discharges is a highly likely phenomenon. Since glow discharge methods are used for cleaning and sterilizing surfaces throughout industry, the idea that dust in the Martian atmosphere undergoes a cleaning action many times over geologic time scales appears to be a plausible one

Left ventricular assist device implantation augments nitric oxide dependent control of mitochondrial respiration in failing human hearts

AbstractOBJECTIVESThe objective of the study was to evaluate nitric oxide (NO) mediated regulation of mitochondrial respiration after implantation of a mechanical assist device in end-stage heart failure.BACKGROUNDVentricular unloading using a left ventricular assist device (LVAD) can improve mitochondrial function in end-stage heart failure. Nitric oxide modulates the activity of the mitochondrial electron transport chain to regulate myocardial oxygen consumption (MVO2).METHODSMyocardial oxygen consumption was measured polarographically using a Clark-type oxygen electrode in isolated left ventricular myocardium from 26 explanted failing human hearts obtained at the time of heart transplantation.RESULTSThe rate of decrease in oxygen concentration was expressed as a percentage of baseline. Results of the highest dose of drug are shown. Decrease in MVO2 was greater in LVAD hearts (n = 8) compared with heart failure controls (n = 18) in response to the following drugs: bradykinin (−34 ± 3% vs. −24 ± 5%), enalaprilat (−37 ± 5% vs. −23 ± 5%) and amlodipine (−43 ± 13% vs. −16 ± 5%; p < 0.05 from controls). The decrease in MVO2 in LVAD hearts was not significantly different from controls in response to diltiazem (−22 ± 5% in both groups) and exogenous NO donor, nitroglycerin (−33 ± 7% vs. −30 ± 3%). Nw-nitro-L-arginine methyl ester, inhibitor of NO synthase, attenuated the response to bradykinin, enalaprilat and amlodipine. Reductions in MVO2 in response to diltiazem and nitroglycerin were not altered by inhibiting NO.CONCLUSIONSChronic LVAD support potentiates endogenous NO-mediated regulation of mitochondrial respiration. Use of medical or surgical interventions that augment NO bioavailability may promote myocardial recovery in end-stage heart failure

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an increasingly large practical barrier. Here we introduce a memory-efficient graph representation with which we can analyze the k-mer connectivity of metagenomic samples. The graph representation is based on a probabilistic data structure, a Bloom filter, that allows us to efficiently store assembly graphs in as little as 4 bits per k-mer, albeit inexactly. We show that this data structure accurately represents DNA assembly graphs in low memory. We apply this data structure to the problem of partitioning assembly graphs into components as a prelude to assembly, and show that this reduces the overall memory requirements for {\em de novo} assembly of metagenomes. On one soil metagenome assembly, this approach achieves a nearly 40-fold decrease in the maximum memory requirements for assembly. This probabilistic graph representation is a significant theoretical advance in storing assembly graphs and also yields immediate leverage on metagenomic assembly