Miniaturized biosignature analysis reveals implications for the formation of cold seep carbonates at Hydrate Ridge (off Oregon, USA)

Methane-related carbonates from Hydrate Ridge typically show several macroscopically distinguishable mineral phases, namely whitish aragonite, lucent aragonite, and gray micrite. The relationship of these phases to particular microorganisms or biogeochemical processes is as yet unclear. We used a miniaturized biomarker technique on mg samples, combined with factor analysis and subsequent electron microprobe analysis, to study lipid biomarkers and chemical compositions of the individual phases. This allows us to identify particular mechanisms involved in the formation of the different carbonate precipitates. Our combined analysis of biomarkers and petrographic traits shows that most of the lipids related to the anaerobic oxidation of methane (>90% by weight) are concentrated within only a minor compartment (~20% by volume) of the Hydrate Ridge carbonates, the whitish aragonite. The patterns indicate that the whitish aragonite represents fossilized biofilms of methanotrophic consortia containing mainly archaea of the ANME-2 group and sulfate reducing bacteria, whereas the precipitation of the lucent aragonite may have lacked the immediate proximity of microorganisms during formation. By contrast, the gray micrite formed by incorporation of allochthonous organic and inorganic matter during carbonate precipitation induced by the anaerobic oxidation of methane involving ANME-1 archaea

Probing molecular tracers in geobiological systems using imaging mass spectrometry

In this thesis ToF-SIMS was applied to the study of geobiological samples. Except for a few pioneering studies, ToF-SIMS has rarely been used in the field of geobiology and thus only a limited number of SIMS reference spectra for biogeochemical relevant compounds has as yet been published. One major goal of this thesis was to extend the spectral library by compounds particularly used as molecular markers in the analysis of geobiological systems. Consequently in the first study reference spectra of eight different glycerolipids functioning as important membrane constituents in eukaryotes, bacteria, and archaea, were presented and their detection in an extract and cryosections of microbial mats demonstrated. The analyses of the standard compounds showed that the detection of fragment ions, in particular from headgroups and alkyl chains, is particularly important for the reliable identification of glycerolipids in complex, environmental samples. As a follow-up study, ten cyclic lipid standards were analyzed by ToF-SIMS. These cyclic lipids are known as important membrane constituents or fulfill a protective function from oxidative stress in eukaryotes, bacteria, or archea. The results obtained showed that most of the compounds can reliably be analyzed in only one of the two polarity modes. In addition the study demonstrated, that not all fragment ions detected in the analyses of the standard compounds can be expected to be detectable in environmental samples containing this compound in complex mixtures with other organic molecules. The knowledge gained in the analysis of standard compounds was used to study a phototrophic microbial mat in detail for their lipid biomarker content by a combining ToF-SIMS, optical microscopy and GC-MS analyses. ToF-SIMS analyses of a cryosection of the microbial mat showed, that a wide range of lipids and pigments, e.g. acylglycerols, carotenoids and chlorophyll a, were present in the microbial mat. Testing the limits of the lateral resolution of the ToF-SIMS instrument, the burst alignment mode was used, to probe single cells for their biomarker content. By subsequent optical microscopy these cells were identified as the diatom species Planothidium lanceolatum and as a major source of lipids and pigments in the microbial mat. The results of the Tof-SIMS analyses were consistent with the diatom specific fatty acid pattern obtained from GC-MS analyses of the bulk microbial mat. This study demonstrated a potential future application of ToF-SIMS in biomarker related research, namely as a tool for the rapid, clear-cut assignment of biomarkers to specific microbial sources in complex environmental samples. This technique could be particularly useful for biomarker studies on the majority of microorganisms, which can as yet not be grown in pure cultures. However, it should be noted that most prokaryotic cells are by an order of magnitude smaller than the diatom cells analyzed in this study and thus more effort has to be spent on increasing the useful lateral resolution of ToF-SIMS imaging. In the last study ToF-SIMS was applied in combination with SEM to the analysis of thin organic films, i.e. conditioning films, forming on solid surfaces exposed to aquifer water prior to the attachment of microorganisms. The results showed that the initial conditioning film forming after a few minutes of exposure to aquifer water was inhomogenous and composed of amino acids, carbohydrates, and fatty acids. With increasing time, the film became more homogenous and microorganism had attached to the surface after a few hours. After 90 days biofilm like accumulations of cells enclosed in extracellular polymeric substances had formed on the wafer surface. This study gave an insight into the chemistry and growth rates of conditioning films and biofilms forming in aquifers in the subsurface and demonstrated the applicability of ToF-SIMS for the analysis of very low amounts of organic material in environmental samples. The studies comprised in this thesis showed that ToF-SIMS can offer unique analytical capabilities for the analyses of large organic ions in environmental samples

Knowledge from Scientific Expert Testimony without Epistemic Trust

In this paper we address the question of how it can be possible for a non-expert to acquire justified true belief from expert testimony. We discuss reductionism and epistemic trust as theoretical approaches to answer this question and present a novel solution that avoids major problems of both theoretical options: Performative Expert Testimony (PET). PET draws on a functional account of expertise insofar as it takes the expert’s visibility as a good informant capable to satisfy informational needs as equally important as her specific skills and knowledge. We explain how PET generates justification for testimonial belief, which is at once assessable for non-experts and maintains the division of epistemic labor between them and the experts. Thereafter we defend PET against two objections. First, we point out that the non-expert’s interest in acquiring widely assertable true beliefs and the expert’s interest in maintaining her status as a good informant counterbalances the relativist account of justification at work in PET. Second, we show that with regard to the interests at work in testimonial exchanges between experts and non-experts, PET yields a better explanation of knowledge-acquisition from expert testimony than externalist accounts of justification such as reliabilism. As our arguments ground in a conception of knowledge, which conceives of belief-justification as a declarative speech act, throughout the rearmost sections of this paper we also indicate to how such a conception is operationalized in PET

Social Exclusion, Epistemic Injustice and Intellectual Self-Trust

This commentary offers a coherent reading of the papers presented in the special issue ‘Exclusion, Engagement, and Empathy: Reflections on Public Participation in Medicine and Technology’. Focusing on intellectual self-trust it adds a further perspective on the harmful epistemic consequences of social exclusion for individual agents in healthcare contexts. In addition to some clarifications regarding the concepts of ‘intellectual self-trust’ and ‘social exclusion’ the commentary also examines in what ways empathy, engagement and participatory sense-making could help to avoid threats to intellectual self-trust that arise form being excluded from participation in communicative practices in the context of healthcare

How to Assess the Epistemic Wrongness of Sponsorship Bias? The Case of Manufactured Certainty

Although the impact of so-called “sponsorship bias” has been the subject of increased attention in the philosophy of science, what exactly constitutes its epistemic wrongness is still debated. In this paper, I will argue that neither evidential accounts nor social–epistemological accounts can fully account for the epistemic wrongness of sponsorship bias, but there are good reasons to prefer social–epistemological to evidential accounts. I will defend this claim by examining how both accounts deal with a paradigm case from medical epistemology, recently discussed in a paper by Bennett Holman. I will argue that evidential accounts cannot adequately capture cases of sponsorship bias that involve the manufacturing of certainty because of their neutrality with respect to the role of non-epistemic values in scientific practice. If my argument holds, it further highlights the importance of integrating social and ethical concerns into epistemological analysis, especially in applied contexts. One can only properly grasp sponsorship bias as an epistemological problem if one resists the methodological tendency to analyze social, ethical, and epistemological issues in isolation from each other

Knowledge from Scientific Expert Testimony without Epistemic Trust

This is a pre-print of an article published in Synthese. The final authenticated version is available online at: https://doi.org/10.1007/s11229-018-01908-w In this paper we address the question of how it can be possible for a non-expert to acquire justified true belief from expert testimony. We discuss reductionism and epistemic trust as theoretical approaches to answer this question and present a novel solution that avoids major problems of both theoretical options: Performative Expert Testimony (PET). PET draws on a functional account of expertise insofar as it takes the expert’s visibility as a good informant capable to satisfy informational needs as equally important as her specific skills and knowledge. We explain how PET generates justification for testimonial belief, which is at once assessable for non-experts and maintains the division of epistemic labor between them and the experts. Thereafter we defend PET against two objections. First, we point out that the non-expert’s interest in acquiring widely assertable true beliefs and the expert’s interest in maintaining her status as a good informant counterbalances the relativist account of justification at work in PET. Second, we show that with regard to the interests at work in testimonial exchanges between experts and non-experts, PET yields a better explanation of knowledge-acquisition from expert testimony than externalist accounts of justification such as reliabilism. As our arguments ground in a conception of knowledge, which conceives of belief-justification as a declarative speech act, throughout the rearmost sections of this paper we also indicate to how such a conception is operationalized in PET

Quantification, extractability and stability of dissolved domoic acid within marine dissolved organic matter

The widespread diatom Pseudo-nitzschia can produce domoic acid (DA). DA is a compound with well described neurotoxic effects on vertebrates including humans known as amnesic shellfish poisoning (ASP) syndrome. It has also been suggested to serve as an organic ligand that binds to iron and copper. By binding these trace elements, DA may increase their solubility and bioavailability. In order to serve this function, DA has to be excreted and reabsorbed by the cells. Only few records of dissolved domoic acid (dDA) concentrations in the ocean exist. To accomplish quantification by ultra performance liquid chromatography (UPLC), samples have to be pre-concentrated and desalted using solid-phase extraction, a procedure commonly applied for dissolved organic matter. Our major goals were to quantify dDA in a basin-wide assessment in the East Atlantic Ocean, to determine extraction efficiencies for complexed and uncomplexed dDA, and to assess whether domoic acid is represented by its molecular formula in direct-infusion high resolution mass spectrometry. Our results showed that dDA was extracted almost quantitatively and occurred ubiquitously in the ocean surface but also in deeper (and older) water, indicating surprisingly high stability in seawater. The maximum concentration measured was 173 pmol L−1 and the average molar dDA carbon yield was 7.7 ppm. Both carbon yield and dDA concentration decreased with increasing water depth. Providing quantification of dDA in the water column, we seek to improve our understanding of toxic bloom dynamics and the mechanistic understanding of DA production

Knowledge from Scientific Expert Testimony without Epistemic Trust

In this paper we address the question of how it can be possible for a non-expert to acquire justified true belief from expert testimony. We discuss reductionism and epistemic trust as theoretical approaches to answer this question and present a novel solution that avoids major problems of both theoretical options: Performative Expert Testimony (PET). PET draws on a functional account of expertise insofar as it takes the expert’s visibility as a good informant capable to satisfy informational needs as equally important as her specific skills and knowledge. We explain how PET generates justification for testimonial belief, which is at once assessable for non-experts and maintains the division of epistemic labor between them and the experts. Thereafter we defend PET against two objections. First, we point out that the non-expert’s interest in acquiring widely assertable true beliefs and the expert’s interest in maintaining her status as a good informant counterbalances the relativist account of justification at work in PET. Second, we show that with regard to the interests at work in testimonial exchanges between experts and non-experts, PET yields a better explanation of knowledge-acquisition from expert testimony than externalist accounts of justification such as reliabilism. As our arguments ground in a conception of knowledge, which conceives of belief-justification as a declarative speech act, throughout the rearmost sections of this paper we also indicate to how such a conception is operationalized in PET

UltraMassExplorer - a browser-based application for the evaluation of high-resolution mass spectrometric data

Rational: High-resolution mass spectrometry (HRMS) with high sample throughput has become an important analytical tool for the analysis of highly complex samples and data processing has become a major challenge for the user community. Evaluating direct-infusion HRMS data without automated tools for batch processing can be a time consuming step in the analytical pipeline. Therefore, we developed a new browser-based software tool for processing HRMS data. Methods: The software named UltraMassExplorer (UME) was written in the R programming language using the shiny library to build the graphical user interface. The performance of the integrated formula library search algorithm was tested using HRMS data derived from analyses of up to 50 extracts of marine dissolved organic matter. Results: The software supports the processing of lists of calibrated masses of neutral, protonated, or deprotonated molecules, respectively, with masses of up to 700 Da and a mass accuracy < 3 ppm. In the performance test, the number of assigned peaks per second increased with number of submitted peaks and reached a maximum rate 4,745 assigned peaks per second. Conclusions: UME offers a complete data evaluation pipeline comprising a fast molecular formula assignment algorithm allowing for the swift reanalysis of complete datasets, advanced filter functions, and the export of data, metadata, and publication-quality graphics. Unique to UME is a fast and interactive connection between data and its visual representation. UME provides a new platform enabling an increased transparency, customization, documentation and comparability of datasets

The Concept of “Genetic Responsibility” and Its Meanings: A Systematic Review of Qualitative Medical Sociology Literature

The acquisition of genetic information (GI) confronts both the affected individuals and healthcare providers with difficult, ambivalent decisions. Genetic responsibility (GR) has become a key concept in both ethical and socioempirical literature addressing how and by whom decision-making with respect to the morality of GI is approached. However, despite its prominence, the precise meaning of the concept of GR remains vague. Therefore, we conducted a systematic literature review on the usage of the concept of GR in qualitative, socioempirical studies, to identify the main interpretations and to provide conceptual clarification. The review identified 75 studies with primarily an Anglo-American setting. The studies focused on several agents: the individual, the family, the parent, the healthcare professional, and the institution and refer to the concept of GR on the basis of either a rational/principle-oriented approach or an affective/relational approach. A subtype of the rational/principle-oriented approach is the reactive approach. The review shows how the concept of GR is useful for analyzing and theorizing about socioempirical findings within qualitative socioempirical studies and also reveals conceptual deficits in terms of insufficient theoretical accuracy and heterogeneity, and in the rarity of reflection on cultural variance. The vagueness and multiplicity of meanings for GR in socioempirical studies can be avoided by more normative-theoretical explication of the underlying premises. This would provide a higher degree of differentiation of empirical findings. Thereby, the complex findings associated with the individual and social implications of genetic testing in empirical studies can be better addressed from a theoretical point of view and can subsequently have a stronger impact on normative and policy debates