MitoPedia: Gentle Science

From Bioblast


Bioenergetics Communications        
Tributes to pioneers in bioenergetics
       
Gnaiger 2020 BEC MitoPathways
       
Gnaiger Erich et al โ€• MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1.
        MitoPedia: BEC         MitoPedia: Gentle Science         MitoFit Preprints
Bioenergetics Communications is the Open Science journal on bioenergetics and mitochondrial physiology with Living Communications Open Access logo.png - ISSN 2791-4690

MitoPedia: Gentle Science

Bioenergetics Communications

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MitoPedia

MitoPedia: Gentle Science

TermAbbreviationDescription
ASAPbioScience only progresses as quickly and efficiently as it is shared. But even with all of the technological capabilities available today, the process of publishing scientific work is taking longer than ever. ASAPbio (Accelerating Science and Publication in biology) is a scientist-driven nonprofit working to address this problem by promoting innovation and transparency in life sciences communication. In 2015, ASAPbio founder Ron Vale published an analysis of the increasing time to first-author publication among graduate students at UCSF, and proposed a more widespread use of preprints in the life sciences as a potential solution.
Advantage of preprintsThe advantages of preprints, the excitement and concerns about the role that preprints can play in disseminating research findings in the life sciences are discussed by N Bhalla (2016).
Ambiguity crisis
Graphical ambiguity: Fliegende Blรคtter (1892-10-23): Perception versus interpretation (Ludwig Wittgenstein) or paradigm shift (Thomas Kuhn)
The ambiguity crisis is a contemporary crisis comparable to the credibility or reproducibility crisis in the biomedical sciences. The term 'crisis' is rooted etymologically in the Greek word krinein: meaning to 'separate, decide, judge'. In this sense, science and communication in general are a continuous crisis at the edge of separating clarity or certainty from confusing double meaning, or obscure 'alchemical' gibberish, or even fake-news. Reproducibility relates to the condition of repeating and confirming calculations or experiments presented in a published resource. While ambiguity is linked to relevant issues of reproducibility, it extends to the communications space of terminological and graphical representations of concepts. Type 1 ambiguities are the inevitable consequence of conceptual evolution, in the process of which ambiguities are replaced by experimentally and theoretically supported paradigm shifts to clear-cut theorems. In contrast, type 2 ambiguities are traced in publications that reflect merely a disregard and ignorance of established concepts without an attempt to justify the inherent deviations from high-quality science. There are many shades of grey between these types of ambiguity.
Bioenerg Commun
Bioenergetics Exhibition - Art meets Gentle Science
Ethics on publishingEthics on publishing follow COPE's guidelines (or equivalent). A journal's policy on publishing ethics should be clearly visible on its website, and should refer to: (1) Journal policies on authorship and contributorship; (2) How the journal will handle complaints and appeals; (3) Journal policies on conflicts of interest / competing interests; (4) Journal policies on data sharing and reproducibility; (5) Journal's policy on ethical oversight; (6) Journal's policy on intellectual property; and (7) Journal's options for post-publication discussions and corrections.
F1000ResearchF1000Research is an Open Research publishing platform for life scientists, offering immediate publication of articles and other research outputs without editorial bias. All articles benefit from transparent peer review and the inclusion of all source data. It is thus not a preprint server, but posters and slides can be published without author fees. Published posters and slides receive a DOI (digital object identifier) and become citable after a very basic check by our in-house editors.
Gentle Science
Living CommunicationsLCWith Living Communications, Bioenergetics Communications (BEC) takes the next step from pre-print to re-print. The concept of Living Communications pursues a novel culture of scientific communication, addressing the conflict between long-term elaboration and validation of results versus sharing without delay improved methods and preliminary findings. Following the preprint concept, updates may be posted on the BEC website of the resource publication. Updated versions of Living Communications are submitted for Open Peer Review with full traceability. In contrast to static papers, evolution of Living Communications is more resourceful and efficient than a โ€˜newโ€™ publication. Living Communications provide a pathway along the scientific culture of lively debate towards tested and trusted milestones of research, from pre-print to re-print, from initial steps to next steps.
MitoFit PreprintsMitoFit Prep
MitoFit Preprints.png
MitoFit Preprints is an Open Access preprint server for mitochondrial physiology and bioenergetics.
MitoPedia: BEC
Open AccessOA
Open Access logo.png
Open Access (OA) academic articles comprise all different forms of published research that are distributed online, free of charge and with an open license to facilitate the distribution and reuse. The open access repositories serve as the perfect vehicle to transmit free knowledge, including but not limited to peer-reviewed and non-peer-reviewed academic journal articles, conference papers, theses, book chapters and monographs. Driven by the problems of social inequality caused by restricting access to academic research, the Open Access movement changes the funding system of published literature allowing for more readers and thus increased access to scientific knowledge, as well as addressing the economic challenges and unsustainability of academic publishing. In addition to being free to read (gratis), open access articles may also be free to use (libre) where the copyright is held by the authors and not the publisher. Definition by the Directory of Open Access Journals (DOAJ): "We define these as journals where the copyright holder of a scholarly work grants usage rights to others using an open license (Creative Commons or equivalent) allowing for immediate free access to the work and permitting any user to read, download, copy, distribute, print, search, or link to the full texts of articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose."
Open ScienceOS
Open Access logo.png
Building on the essential principles of academic freedom, research integrity and scientific excellence, open science sets a new paradigm that integrates into the scientific enterprise practices for reproducibility, transparency, sharing and collaboration resulting from the increased opening of scientific contents, tools and processes. Open science is defined as an inclusive construct that combines various movements and practices aiming to make multilingual scientific knowledge openly available, accessible and reusable for everyone, to increase scientific collaborations and sharing of information for the benefits of science and society, and to open the processes of scientific knowledge creation, evaluation and communication to societal actors beyond the traditional scientific community. It comprises all scientific disciplines and aspects of scholarly practices, including basic and applied sciences, natural and social sciences and the humanities, and it builds on the following key pillars: open scientific knowledge, open science infrastructures, science communication, open engagement of societal actors and open dialogue with other knowledge systems.
PREreviewPREreview encourages scientists to post their scientific outputs as preprints. PREreview makes it easier to start and run a Preprint Journal Club, or integrate preprint review into conventional journal clubs. PREreview seeks to diversify peer review in the academic community by crowdsourcing pre-publication feedback to improve the quality of published scientific output, and to train early-career researchers (ECRs) in how to review others' scientific work. We want to facilitate a cultural shift in which every scientist posts, reads, and engages with preprints as standard practice in scholarly publishing. We see PREreview as a hub to support and nurture the growth of a community that openly exchanges timely, constructive feedback on emerging scientific outputs. We believe that by empowering ECRs through peer review training programs, thereby increasing the diversity of researchers involved in the peer review process, PREreview will help establish a healthier and more sustainable culture around research dissemination and evaluation. This project was born in April 2017 as a collaboration between Samantha Hindle and Daniela Saderi, scientists and ASAPbio Ambassadors, with help from Josh Nicholson, at the time working for Authorea.
PreprintA preprint is {Quote} a way in which a manuscript containing scientific results can be rapidly communicated from one scientist, or a group of scientists, to the entire scientific community {end of Quote}. Preprints are disseminated without peer review, e.g. in the preprint server MitoFit Preprints. In contrast, the journal Bioenergetics Communications publishes peer-reviewed articles, which preferentially are communicated in advance in MitoFit Preprints.
Quality Assurance
Reproducibility crisisThe reproducibility crisis is alarming.1 An experiment or study is reproducible or replicable when subsequent experiments confirm the results. This is re-search. However, we can define different types of reproducibility depending on the conditions that we use to replicate the previous work or in the information available. Our aim is to focus mostly on two different kinds2: 1. Direct: is when we obtaining the same results using the same experimental conditions, materials, and methods as described in the original experiment. This would be the ideal reproducibility of an experiment. However, it requires a very accurate description of how the original experiment was performed. Some journals are trying to resolve the reproducibility crisis improving the rigor and the excellence on the reported methods and results (e.g. STAR Methods in Cell Press). 2. Systematical: refers to obtaining the same results, but under different conditions; for example, using another cell line or mouse strain or humman study, or inhibiting a gene pharmacologically instead of genetically. This opens the door to subsequent studies to find the conditions under which an initial finding holds.
Science - the conceptScienceAs per the 2017 UNESCO Recommendation on Science and Scientific Researchers, the term โ€˜scienceโ€™ signifies the enterprise whereby humankind, acting individually or in small or large groups, makes an organized attempt, in cooperation and in competition, by means of the objective study of observed phenomena and its validation through sharing of findings and data and through peer review, to discover and master the chain of causalities, relations or interactions; brings together in a coordinated form subsystems of knowledge by means of systematic reflection and conceptualization; and thereby furnishes itself with the opportunity of using, to its own advantage, understanding of the processes and phenomena occurring in nature and society.


Gentle Science

References: Gentle Science

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