Finding virtue in open science? Biological scientists' constructions of openness in historical, advocacy and policy contexts

Science has a special relationship with the term “open” and its connotations. A traditional story about scientific openness goes as follows: if scientists share their findings, scientific communities can collectively build upon these findings and a progressive corpus of knowledge emerges. But since the turn of the twenty-first century, a distinctive, online “open science” has rapidly gained global salience, incorporating practices from open access publishing and open research data, to open preprints, open peer review, and open notebook science. Movements towards such practices have often been led from within scientific communities – by scientist-activists and entrepreneurs. Such actors see the Internet as an unprecedented opportunity to “open” science, and fix seemingly broken aspects of the scientific system: inaccessibility, opacity, irreproducibility. More recently, the “open” imperative is also top-down, as funding and research organisations increasingly treat open practices as desirable or mandatory. This work focuses on academic, biological scientists in the UK and Australia whose professional and epistemic worlds are undergoing transformation in this open science “revolution” – in whose communities openness may have long-standing meaning, but wherein “open science” may have risen from obscurity to salience in the space of only 15 or 20 years. While some scientists are the leaders of open movements, many are said to be ambivalent and slow to adopt open practices, forming a “cultural” barrier to openness that is rarely explored in systematic empirical studies. This disparity has a moral dimension, as openness is positioned a quality of good science and scientists. My research questions consider how scientists’ constructions sit in relation to historical, advocacy and policy framings; why scientists may be disengaged from contemporary open science movements; and the extent to which they construct and internalise openness as an epistemic virtue: a moralised truth-making quality. The thesis begins with an analysis of openness in science as a concept and practice with historical depth as well as contemporary salience; I then explore its contemporary framing in advocacy and policy contexts through document analysis. In both I consider how “open” (or “openness”) is being constructed, and the significance of its flexibility and expansiveness. These analyses set the scene for the empirical core of the work: 40 in-depth, semi-structured interviews with biologists, purposively sampled for disciplinary, generational, gender, and attitudinal diversity. For context and counterpoint, I conducted 14 similar interviews with open science advocates and policymakers. Through these interviews, I attend to how a broad population of scientists, as well as advocates and policymakers, construct “open” in science. My findings focus on the three most common categories of scientific openness emerging from interviews with biologists: open access, data openness, and interpersonal openness. The first two of these have close connections with policy and advocacy movements, whereas the third appears to be anchored only in scientists’ experiences and implicit conceptualisations. Nonetheless, interpersonal openness is constructed in consistent ways and with conviction: it refers to the practice and principle of “talking freely” about unpublished ideas and data in small-scale interpersonal situations, or the contextual withholding of such information. I characterise scientists’ constructions of each of these three categories as indicators of how scientists encounter and enact top-down and bottom-up forms of scientific openness. In my discussion and conclusion, I bring these three categories of scientific openness into conversation, using them to theorise the variety of relationships that scientists form with scientific openness under the contemporary open science “revolution” - including whether and how different forms of openness are internalised as epistemic virtues. In turn, this allows commentary about: the apparent disconnectedness of scientists from certain agendas of openness; the significance of generational differences; and interactions between openness, privilege and inequality in pressured scientific systems

Expression of the neuropeptides RFamide and LWamide during development of the coral Acropora millepora in relation to settlement and metamorphosis

Neuropeptides play critical roles in cnidarian development. However, although they are known to play key roles in settlement and metamorphosis, their temporal and spatial developmental expression has not previously been characterized in any coral. We here describe Acropora millepora LWamide and RFamide and their developmental expression from the time of their first appearance, using in situ hybridization and FMRFamide immunohistochemistry. AmRFamide transcripts first appear in the ectoderm toward the oral end of the planula larva following blastopore closure. This oral bias becomes less apparent as the planula develops. The cell bodies of AmRFamide-expressing cells are centrally located in the ectoderm, with narrow projections to the mesoglea and to the cell surface. As the planula approaches settlement, AmRFamide expression disappears and is undetectable in the newly settled polyp. Expressing cells then gradually reappear as the polyp develops, becoming particularly abundant on the tentacles. AmLWamide transcripts first appear in ectodermal cells of the developing planula, with minimal expression at its two ends. The cell bodies of expressing cells lie just above the mesoglea, in a position distinct from those of AmRFamide-expressing cells, and have a narrow projection extending across the ectoderm to its surface. AmLWamide-expressing cells persist for most of the planula stage, disappearing shortly before settlement, but later than AmRFamide-expressing cells. As is the case with AmRFamide, expressing cells are absent from the polyp immediately after settlement, reappearing later on its oral side. AmLWamide expression lags that of AmRFamide in both its disappearance and reappearance. Antibodies to FMRFamide stain cells in a pattern similar to that of the transcripts, but also cells in areas where there is no expression revealed by in situ hybridization, most notably at the aboral end of the planula and in the adult polyp. Adult polyps have numerous staining cells on the tentacles and oral discs, as well as an immunoreactive nerve ring around the mouth. There are scattered staining cells in the coenosarc between polyps and staining cells are abundant in the mesenterial filaments. The above results are discussed in the context of our knowledge of the behavior of coral planulae at the time of their settlement and metamorphosis. Corals are facing multiple environmental threats, and these results both highlight the need for, and bring us a step closer to, a mechanistic understanding of a process that is critical to their survival.This work was supported by the Australian Research Council through the Centre for Molecular Genetics of Development, the Centre of Excellence for Coral Reef Studies and Discovery Grants DP0209460, DP0344483, and DP1095343

Stories from the open science "revolution”: how (some)scientists talk about openness

Scientific openness is both very old and very new. For centuries, the communal sharing of findings has been valued, even if not practised, in the cultural sphere of academic science. But as we know, in recent decades new “open science” movements have practices have gained salience: from open access publishing and open archiving of research data, to open peer review and open notebook science. Movement towards such practices has often been led from within scientific communities – by scientist-activists and entrepreneurs who see the Internet an opportunity to “open up” and fix seemingly broken aspects of the scientific system. Increasingly, the “open” imperative is also top-down, as funding regimes and institutions increasingly treat open practices as desirable or mandatory. My work focuses on academic scientists whose professional and epistemic worlds are undergoing transformation in this open science “revolution”. While some scientists are the leaders of open movements, the majority are more ambivalent and slow to adopt open practices, forming a “cultural” barrier to openness that is rarely explored in systematic empirical studies. Based on my in-progress PhD data collection and analysis – qualitative interviews with (biological) scientists, and open science advocates and policymakers – I will explore the diverse meanings of scientific openness that scientists construct outside, within, and in tension with open advocacy and policy agendas. I ask questions such as: are scientists internalising openness as a quality that makes “good science”

Interindividual variation in epigenomic phenomena in humans

Our knowledge of regulatory mechanisms of gene expression and other chromosomal processes related to DNA methylation and chromatin state is continuing to grow at a rapid pace. Understanding how these epigenomic phenomena vary between individuals will have an impact on understanding their broader role in determining variation in gene expression and biochemical, physiological, and behavioural phenotypes. In this review we survey recent progress in this area, focusing on data available from humans. We highlight the role of obligatory (sequence-dependent) epigenomic variation as an important mechanism for generating interindividual variation that could impact our understanding of the mechanistic basis of complex trait architecture

A ''Neural'' Enzyme in Nonbilaterian Animals and Algae: Preneural Origins for Peptidylglycine a-Amidating Monooxygenase

Secreted peptides, produced by enzymatic processing of larger precursor molecules, are found throughout the animal kingdom and play important regulatory roles as neurotransmitters and hormones. Many require a carboxy-terminal modification, involving the conversion of a glycine residue into an α-amide, for their biological activity. Two sequential enzymatic activities catalyze this conversion: a monooxygenase (peptidylglycine α-hydroxylating monooxygenase or PHM) and an amidating lyase (peptidyl-α-hydroxyglycine α-amidating lyase or PAL). In vertebrates, these activities reside in a single polypeptide known as peptidylglycine α-amidating monooxygenase (PAM), which has been extensively studied in the context of neuropeptide modification. Bifunctional PAMs have been reported from some invertebrates, but the phylogenetic distribution of PAMs and their evolutionary relationship to PALs and PHMs is unclear. Here, we report sequence and expression data for two PAMs from the coral Acropora millepora (Anthozoa, Cnidaria), as well as providing a comprehensive survey of the available sequence data from other organisms. These analyses indicate that bifunctional PAMs predate the origins of the nervous and endocrine systems, consistent with the idea that within the Metazoa their ancestral function may have been to amidate epitheliopeptides. More surprisingly, the phylogenomic survey also revealed the presence of PAMs in green algae (but not in higher plants or fungi), implying that the bifunctional enzyme either predates the plant/animal divergence and has subsequently been lost in a number of lineages or perhaps that convergent evolution or lateral gene transfer has occurred. This finding is consistent with recent discoveries that other molecules once thought of as neural predate nervous systems

A "neural" enzyme in nonbilaterian animals and algae: preneural origins for peptidylglycine α-amidating monooxygenase

Secreted peptides, produced by enzymatic processing of larger precursor molecules, are found throughout the animal kingdom and play important regulatory roles as neurotransmitters and hormones. Many require a carboxy-terminal modification, involving the conversion of a glycine residue into an alpha-amide, for their biological activity. Two sequential enzymatic activities catalyze this conversion: a monooxygenase (peptidylglycine α-hydroxylating monooxygenase or PHM) and an amidating lyase (peptidyl-α-hydroxyglycine α-amidating lyase or PAL). In vertebrates, these activities reside in a single polypeptide known as peptidylglycine α-amidating monooxygenase (PAM), which has been extensively studied in the context of neuropeptide modification. Bifunctional PAMs have been reported from some invertebrates, but the phylogenetic distribution of PAMs and their evolutionary relationship to PALs and PHMs is unclear. Here, we report sequence and expression data for two PAMs from the coral Acropora millepora (Anthozoa, Cnidaria), as well as providing a comprehensive survey of the available sequence data from other organisms. These analyses indicate that bifunctional PAMs predate the origins of the nervous and endocrine systems, consistent with the idea that within the Metazoa their ancestral function may have been to amidate epitheliopeptides. More surprisingly, the phylogenomic survey also revealed the presence of PAMs in green algae (but not in higher plants or fungi), implying that the bifunctional enzyme either predates the plant/animal divergence and has subsequently been lost in a number of lineages or perhaps that convergent evolution or lateral gene transfer has occurred. This finding is consistent with recent discoveries that other molecules once thought of as "neural" predate nervous systems