Operationalising a real-time research ethics approach: supporting ethical mindfulness in agriculture-nutrition-health research in Malawi

Background There have been notable investments in large multi-partner research programmes across the agriculture-nutrition-health (ANH) nexus. These studies often involve human participants and commonly require research ethics review. These ANH studies are complex and can raise ethical issues that need pre-field work, ethical oversight and also need an embedded process that can identify, characterise and manage ethical issues as the research work develops, as such more embedded and dynamic ethics processes are needed. This work builds on notions of ‘ethics in practice’ by developing an approach to facilitate ethical reflection within large research programmes. This study explores the application of a novel ‘real-time research ethics approach’ (RTREA) and how this can support ethical mindfulness. This involves embedding ethical analysis and decision-making within research implementation, with a continuous dialogue between participants and researchers. The aim is to improve ethical responsiveness and participant experience, which in turn may ethically support adherence and retention. In this case study, a bioethics team (BT) was embedded in a community-based randomised, controlled trial conducted in rural Malawi, titled the ‘Addressing Hidden Hunger with Agronomy’. To identify ethical issues, the researchers conducted ten focus group discussions, fourteen in-depth interviews with key informants, two workshops, observed two sensitisation and three activity meetings conducted by the trial team, and analysed fifteen reports from pre-trial to trial implementation. Results The RTREA facilitated the identification of social and ethical concerns and made researchers aware of participants’ ‘lived research experience’. To address concerns and experiences, the BT worked with researchers to facilitate conversation spaces where social and ethical issues were discussed. Conversation spaces were designed to create partnerships and promote participatory methods to capture trial participants’ (TPs) perspectives and experiences. Conclusions The use of RTREA showed the value of real-time and continuous engagement between TPs and researchers. These real-time processes could be embedded to complement traditional ethical guidance and expert opinions. A deeper engagement appeared to support greater operationalising of principles of inclusion, empowerment, and participant autonomy and supported researchers ‘ethical mindfulness’ which in turn may support instrumental outcomes of high recruitment, retention, and adherence levels.

Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction

We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. The quality of library preparation was tested by constructing libraries from Escherichia coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex (recently renamed as Illumina DNA Prep) or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower G+C content, library construction methods were also tested on Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC 25923, respectively. We demonstrated that Hackflex can produce high-quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size-selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large-insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per-sample reagent cost for library prep of A$7.22 (Australian dollars) (US $5.60; UK £3.87, £1=A$1.87), which is 9.87 times lower than the standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programmes where sequencing large numbers of libraries is beneficial.

Degeneration and Entropy

Lakatos’s analysis of progress and degeneration in the Methodology of Scientific Research Programmes is well-known. Less known, however, are his thoughts on degeneration in Proofs and Refutations. I propose and motivate two new criteria for degeneration based on the discussion in Proofs and Refutations – superfluity and authoritarianism. I show how these criteria augment the account in Methodology of Scientific Research Programmes, providing a generalized Lakatosian account of progress and degeneration. I then apply this generalized account to a key transition point in the history of entropy – the transition to an information-theoretic interpretation of entropy – by assessing Jaynes’s 1957 paper on information theory and statistical mechanics.

Progressive and Degenerative Journals: On the Growth and Appraisal of Knowledge in Scholarly Publishing

Despite continued attention, finding adequate criteria for distinguishing “good” from “bad”scholarly journals remains an elusive goal. In this essay, I propose a solution informed by thework of Imre Lakatos and his methodology of scientific research programmes (MSRP). I beginby reviewing several notable attempts at appraising journal quality – focusing primarily on theimpact factor and development of journal blacklists and whitelists. In doing so, I note theirlimitations and link their overarching goals to those found within the philosophy of science. Iargue that Lakatos’s MSRP and specifically his classifications of “progressive” and“degenerative” research programmes can be analogized and repurposed for the evaluation ofscholarly journals. I argue that this alternative framework resolves some of the limitationsdiscussed above and offers a more considered evaluation of journal quality – one that helpsaccount for the historical evolution of journal-level publication practices and attendantcontributions to the growth (or stunting) of scholarly knowledge. By doing so, the seemingproblem of journal demarcation is diminished. In the process I utilize two novel tools (themistake index and scite index) to further operationalize aspects of the MSRP.

Kultura robotnicza – niedokończony projekt: od sceptycyzmu do kulturoznawstwa historycznego [Workers’ Culture – an Unfinished Project: From Scepticism to Historical Cultural Studies]

Workers’ Culture – an Unfinished Project: From Scepticism to Historical Cultural StudiesThe research on workers’ culture carried out in Poland from the 1960s to the late 1980s has been recognised in this article as a failure. The author discusses the numerous attempts to conceptualise research programmes and their actual implementation in the fields of sociology, anthropology and the emerging cultural studies. She looks for the sources of their failure, reflecting on its nature and possible causes. She asks whether the failure of the research on workers’ culture was not due to the scepticism of the researchers themselves, who might have overlooked important attempts at demonstrating self-awareness and pro-active attitude on the part of the workers, treating them as politically manipulated and therefore inauthentic. She raises the question about both ideological and methodological reasons behind this stance, the latter having to do with a clash between quantitative research and humanistic orientation. She calls for “preposterous” research (as proposed by Mieke Bal) to be undertaken, which would give a different interpretation of the workers’ various cultural initiatives from today’s perspective. Perhaps this would inspire the creation of a counter-history of workers’ culture.Kultura robotnicza – niedokończony projekt: od sceptycyzmu do kulturoznawstwa historycznegoBadania kultury robotniczej w Polsce od lat sześćdziesiątych do późnych osiemdziesiątych XX wieku diagnozowane są w tym artykule jako porażka. Autorka przypomina liczne próby konceptualizacji programów badawczych i konkretne ich realizacje w obszarze socjologii, antropologii i rodzącego się wówczas kulturoznawstwa. Szuka źródeł tej porażki, zastanawia się, na czym ona polegała i co mogło być jej przyczyną. Stawia pytanie: czy niepowodzenia badań nad kulturą robotniczą nie wynikały ze sceptycyzmu samych badaczy, którzy mogli przeoczyć ważne próby manifestacji samoświadomości i aktywnego uczestnictwa robotników, traktując je jako sterowane politycznie, a więc nieautentyczne. Pyta o przyczyny zarówno ideologiczne, jak i metodologiczne – ścieranie się badań ilościowych z orientacją humanistyczną. Proponuje, aby z dystansu czasowego podjąć badania preposteryjne, pozwalające dziś inaczej odczytywać różne robotnicze inicjatywy kulturalne. Być może byłoby to inspirujące dla budowania przeciw-historii kultury robotniczej.

How Well Does Evolution Explain Endogenous Retroviruses?—A Lakatosian Assessment

One of the most sophisticated philosophies of science is the methodology of scientific research programmes (MSRP), developed by Imre Lakatos. According to MSRP, scientists are working within so-called research programmes, consisting of a hard core of fixed convictions and a flexible protective belt of auxiliary hypotheses. Anomalies are accommodated by changes to the protective belt that do not affect the hard core. Under MSRP, research programmes are appraised as ‘progressive’ if they successfully predict novel facts but are judged as ‘degenerative’ if they merely offer ad hoc solutions to anomalies. This paper applies these criteria to the evolutionary research programme as it has performed during half a century of ERV research. It describes the early history of the field and the emergence of the endogenization-amplification theory on the origins of retroviral-like sequences. It then discusses various predictions and postdictions that were generated by the programme, regarding orthologous ERVs in different species, the presence of target site duplications and the divergence of long terminal repeats, and appraises how the programme has dealt with data that did not conform to initial expectations. It is concluded that the evolutionary research programme has been progressive with regard to the issues here examined.

تأسيس الشركات بين الجامعات السودانية و مؤسسات المجتمع خاصة الشركات الخاصة

تأسيس الشركات بين الجامعات السودانية و مؤسسات المجتمع خاصة الشركات الخاصة This research tackles the way in which Sudanese universities establish partnerships with community institutions especially private sector companies in order to spare universities needs materially and physically which helps in achieving the economical job of the universities by benefiting from Peculiarities Of knowledge economics. The research also handles how Sudanese universities translates their developing efforts in academic process and scientific research through encouraging and adopting innovations and Excellent Research Ideas. In addition, The research aimed at identifying the important role of Innovations and Excellent Research Ideas Centers in universities in transforming Excellent Research Ideas into successful projects which enables universities in developing their Learning Inputs in order to obtain developed outputs, then accordingly, universities will find the way paved to Establish successful partnerships with community institutions especially private sector companies, in doing so, universities will spare the needed finance for scientific programmes, training, academic, and research programmes. The research confirms that transforming Excellent Research Ideas into successful projects attains good beneficial income for universities in especial* and thereafter for the economy of the country in general

Applied History in the Netherlands and Flanders

This contribution shifts the debate on ‘applied history’ from the archetypal question abouts terminology and definition (‘what’s in a name’) to its current context and potential (‘why it is here again, and why it is most probably here to stay’). Those advocating ‘applied history’ in the Netherlands and Flanders by and large agree on a shared endeavour to apply both historical skills and insights to contemporary societal debates. They thereby tend to promote long-term, comparative and out-of-the-box thinking to confront today’s (wicked) problems. In these endeavours they offer an alternative to writing commissioned histories and commercial joint ventures, as well as to the 'public history' initiatives co-created by heritage institutions, museums or media outlets. Changing constellations of ideas and incentives in education, science, and society have certainly helped to create an incubation period for the development of applied history. History curricula now allow students to experience their added value in the workplace, research programmes ask to reflect upon the impact and valorisation of historical research, and most of all, younger generations are eager to merge postmodern approaches with clear societal achievements and are trying to do so on safe ethical and methodological grounds. This contribution argues that applied and fundamental research in the field of history could be mutually beneficial, rather than antithetical or antipathetic, and that both approaches can reinforce each other in future. Deze bijdrage verschuift het debat over ‘toegepaste geschiedenis’ van de archetypische vragen over terminologie en definities (‘what’s in a name?’) naar zijn huidige context en potentieel (‘waarom is het opnieuw hier en waarom zal het hoogstwaarschijnlijk blijven?’). In Nederland en Vlaanderen zijn voorstanders van toegepaste geschiedenis het grotendeels eens over een gezamenlijk streven om zowel historische vaardigheden als inzichten toe te passen op maatschappelijke debatten. Daarbij hebben ze de neiging om langetermijn-, vergelijkend en ‘out-of-the-box’ denken te bevorderen bij de aanpak van hedendaagse complexe problemen. Zo bieden ze niet alleen een alternatief voor commerciële samenwerkingsverbanden of het schrijven van geschiedenisboeken in opdracht, maar ook voor publiekshistorische initiatieven die mede zijn opgezet door erfgoedinstellingen, musea of mediakanalen. Veranderende opvattingen in onderwijs, wetenschap en samenleving hebben bijgedragen aan deze ontwikkeling van toegepaste geschiedenis. Geschiedeniscurricula laten studenten tegenwoordig hun toegevoegde waarde direct op de werkplek ervaren via stages, terwijl onderzoeksprogramma’s vragen om na te denken over de impact en valorisatie van historisch onderzoek. Vooral jongere historici combineren al een postmoderne benadering met concrete maatschappelijke verwezenlijkingen en proberen dat te doen op een ethische en methodologisch verantwoorde manier. Deze bijdrage stelt dat toegepast en fundamenteel historisch onderzoek voor beide deelgebieden voordelig zou kunnen zijn, in plaats van antithetisch of antipathiek, en dat beide benaderingen elkaar in de toekomst kunnen versterken.ActualiteitsparagraafToegepaste geschiedenisWaarom historici steeds meer over ‘vandaag’ spreken Kun je iets uit het verleden leren? Het is een stokoude vraag die steeds meer historici in Nederland en België zich opnieuw stellen. Onder invloed van maatschappelijke vraagstukken zoals corona, klimaatverandering, diversiteit en (geo)politieke instabiliteit, maar ook door veranderende eisen van studenten en onderzoeksfinanciers, vinden historici het in toenemende mate belangrijk om na te denken over de ‘toegepaste waarde’ van historische kennis en expertise. In hun bijdrage voor BMGN 136:4 bespreken Violet Soen en Bram De Ridder hoe dergelijke ‘toegepaste geschiedenis’ aan een opmars bezig is en benadrukken ze het veelzijdige karakter daarvan. Ze beargumenteren dat toegepaste geschiedenis niet iets radicaal nieuw is maar eigenlijk al langer ingebed zit in de praktijk van veel historici. Tegelijk is het van groot belang om deze activiteiten een nieuwe methodologische en ethische basis te geven en om een constructieve dialoog te houden met historici die ‘vroeger’ vooral vroeger willen laten zijn. Kan je iets leren uit het verleden? Soen en De Ridder menen van wel, maar enkel als historici en hun maatschappelijke partners voldoende hard nadenken over het hoe en wat van toegepaste geschiedenis.

Geomorphology and Earth System Science

This chapter surveys the history of geomorphology and Earth system science 1965-2000. With roots in Enlightenment thought from Hutton, Somerville, Humboldt and Darwin we see a preoccupation with a holistic form of Earth system science develop through the reductionist, mechanistic ideas of the 19th and 20th century to be re-awoken in the 1960 and 1970s environmental movements and the space age, culminating in the major research programmes set by NASA and others subsequently. At the same time the chapter charts the evolution in geomorphology to consider plate tectonics and the origins of mountain ranges, geochemistry and its links between surfaces systems and the atmosphere, to later ideas emphasising the interplay between landforms and life. This chapter surveys changing interconnected ideas within this field and draws parallels and contrasts between the holistic depictions of Earth system science in the early part of the subject's history and the fundamental challenges facing us today as we grapple to find science-led solutions to global environmental change.

Selective Learning: China, the CGIAR, and Global Agricultural Science in Flux

This article analyses the interaction between China and the CGIAR (formerly the Consultative Group on International Agricultural Research) since the 1970s, exploring the formation of China’s modern agricultural science capability and its approach towards learning. While China was previously regarded and treated as a recipient of international scientific expertise, it is now a more equal partner and contributor, with capacity to provide funds, support exchange programmes for scientists, and collaborate in building laboratories and joint research programmes. Some of these now extend beyond the CGIAR system and are creating new platforms for scientific collaboration and knowledge production in the South. By offering an illustration of China’s ‘selective learning’ approach, emphasising self-reliance and pragmatism in its engagement with the CGIAR, this article feeds into broader debates on how China contributes to global development knowledge and learning.