Biological Information, Causality and Specificity - an Intimate Relationship

In this chapter we examine the relationship between biological information, the key biological concept of specificity, and recent philosophical work on causation. We begin by showing how talk of information in the molecular biosciences grew out of efforts to understand the sources of biological specificity. We then introduce the idea of ‘causal specificity’ from recent work on causation in philosophy, and our own, information theoretic measure of causal specificity. Biological specificity, we argue, is simple the causal specificity of certain biological processes. This, we suggest, means that causal relationships in biology are ‘informational’ relationships simply when they are highly specific relationships. Biological information can be identified with the storage, transmission and exercise of biological specificity. It has been argued that causal relationships should not be regarded as informational relationship unless they are ‘arbitrary’. We argue that, whilst arbitrariness is an important feature of many causal relationships in living systems, it should not be used in this way to delimit biological information. Finally, we argue that biological specificity, and hence biological information, is not confined to nucleic acids but distributed among a wide range of entities and processes

Gene

The historian Raphael Falk has described the gene as a ‘concept in tension’ (Falk 2000) – an idea pulled this way and that by the differing demands of different kinds of biological work. Several authors have suggested that in the light of contemporary molecular biology ‘gene’ is no more than a handy term which acquires a specific meaning only in a specific scientific context in which it occurs. Hence the best way to answer the question ‘what is a gene’, and the only way to provide a truly philosophical answer to that question is to outline the diversity of conceptions of the gene and the reasons for this diversity. In this essay we draw on the extensive literature in the history of biology to explain how the concept has changed over time in response to the changing demands of the biosciences . Finally, we outline some of the conceptions of the gene current today. The seeds of change are implicit in many of those current conceptions and the future of the gene concept looks set to be at as turbulent as the past

Muscimol acts in dorsomedial but not paraventricular hypothalamic nucleus to suppress cardiovascular effects of stress

Both the dorsomedial hypothalamic nucleus (DMH) and the paraventricular hypothalamic nucleus (PVN) have been implicated in the neural control of the cardiovascular response to stress. We used the GABAA agonist muscimol to inhibit neuronal activation and attempted to identify hypothalamic nuclei required for the cardiovascular response to air stress. Chronically instrumented rats received bilateral injections of either 80 pmol of muscimol or 100 nl of saline vehicle into the DMH, the PVN, or an intermediate area (including the rostral edge of the DMH and the region between the two nuclei) and were placed immediately in a restraining tube and subjected to 20 min of air stress. In all rats, air stress after vehicle injections caused marked increases in heart rate (137 +/- 6 beats/min) and blood pressure (26 +/- 2 mmHg). Microinjection of muscimol into the DMH suppressed the heart rate and blood pressure response by 85 and 68%, respectively. Identical microinjection of muscimol into the intermediate area between the DMH and the PVN attenuated the increases in heart rate by only 46% and in blood pressure by 52%. In contrast, similar injections into the vicinity of the PVN failed to alter the cardiovascular response to air stress. These findings demonstrate that muscimol-induced inhibition of neuronal activity in the region of the DMH blocks air stress-induced increases in heart rate and arterial pressure, whereas similar treatment in the area of the PVN has no effect

An Enu Mutagenesis Screen For Dominant Genetic Modifiers Of Thrombosis In The Factor 5 Leiden Mouse

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106055/1/jth03031.pd

Genes in the postgenomic era

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype

In situ electrochemical cells to study the oxygen evolution reaction by near ambient pressure x-ray photoelectron spectroscopy

In this contribution, we report the development of in situ electrochemical cells based on proton exchange membranes suitable for studying interfacial structural dynamics of energy materials under operation by near ambient pressure X-ray photoelectron spectroscopy. We will present both the first design of a batch-type two-electrode cell prototype and the improvements attained with a continuous flow three-electrode cell. Examples of both sputtered metal films and carbon-supported metal nanostructures are included demonstrating the high flexibility of the cells to study energy materials. Our immediate focus was on the study of the oxygen evolution reaction, however, the methods described herein can be broadly applied to reactions relevant in energy conversion and storage devices

Graphene-Capped Liquid Thin Films for Electrochemical Operando X-ray Spectroscopy and Scanning Electron Microscopy

Electrochemistry is a promising building block for the global transition to a sustainable energy market. Particularly the electroreduction of CO2 and the electrolysis of water might be strategic elements for chemical energy conversion. The reactions of interest are inner-sphere reactions, which occur on the surface of the electrode, and the biased interface between the electrode surface and the electrolyte is of central importance to the reactivity of an electrode. However, a potential-dependent observation of this buried interface is challenging, which slows the development of catalyst materials. Here we describe a sample architecture using a graphene blanket that allows surface sensitive studies of biased electrochemical interfaces. At the examples of near ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) and environmental scanning electron microscopy (ESEM), we show that the combination of a graphene blanket and a permeable membrane leads to the formation of a liquid thin film between them. This liquid thin film is stable against a water partial pressure below 1 mbar. These properties of the sample assembly extend the study of solid–liquid interfaces to highly surface sensitive techniques, such as electron spectroscopy/microscopy. In fact, photoelectrons with an effective attenuation length of only 10 Å can be detected, which is close to the absolute minimum possible in aqueous solutions. The in-situ cells and the sample preparation necessary to employ our method are comparatively simple. Transferring this approach to other surface sensitive measurement techniques should therefore be straightforward. We see our approach as a starting point for more studies on electrochemical interfaces and surface processes under applied potential. Such studies would be of high value for the rational design of electrocatalysts

Avalanche amplification of a single exciton in a semiconductor nanowire

Interfacing single photons and electrons is a crucial ingredient for sharing quantum information between remote solid-state qubits. Semiconductor nanowires offer the unique possibility to combine optical quantum dots with avalanche photodiodes, thus enabling the conversion of an incoming single photon into a macroscopic current for efficient electrical detection. Currently, millions of excitation events are required to perform electrical read-out of an exciton qubit state. Here we demonstrate multiplication of carriers from only a single exciton generated in a quantum dot after tunneling into a nanowire avalanche photodiode. Due to the large amplification of both electrons and holes (> 10^4), we reduce by four orders of magnitude the number of excitation events required to electrically detect a single exciton generated in a quantum dot. This work represents a significant step towards single-shot electrical read-out and offers a new functionality for on-chip quantum information circuits

Teaching undergraduate students gynecological and obstetrical examination skills: the patient's opinion

Introduction Our study assesses the patients’ opinion about gynecological examination performed by undergraduate students (UgSts). This assessment will be used in improving our undergraduate training program. A positive opinion would mean a lower chance of a patient refusing to be examined by a tutor or student, taking into account vaginal examination (VE). Materials and methods We performed a prospective cross-sectional survey on 1194 patients, consisting of outpatient and inpatient at the departments of obstetrics and gynecology from November 2015 to May 2016. The questionnaire consisted of 46 questions. Besides demographic data, we assessed the mindset of patients regarding the involvement of undergradu ate student (UgSt) in gynecological and obstetrical examinations. We used SPSS version 23 for the statistical analysis. For reporting the data, we followed the STROBE statement of reporting observational studies. Results The median age was 38 years having a median of one child. 34% presented due to obstetrical problems, 38% due to gynecological complaints, and 19% due to known gynecological malignancies. Generally, we retrieved a positive opinion of patients towards the involvement of students in gynecological and obstetrical examination under supervision in 2/3 of the cases. Conclusions There is no reason to exclude medical UgSts from gynecological and obstetrical examinations after obtaining a written or oral consent