Patching Science – amending the literature through version control | bioRxiv

Abstract:  The ideal of self-correction in science is not well served by the current culture and system surrounding amendments to published literature. Here we report on a survey (N = 132) that highlights academics’ dissatisfaction with the status quo and their support for an alternative approach. We then describe our view of how amendments could and should work by drawing on the idea of an author-led version control system. Here authors would include a link in their published manuscripts to an updatable website (e.g. a GitHub repository or similar) that could be disseminated in the event of any amendment. Such a system is already in place for computer code and, as such, requires nothing but buy-in from the scientific community – a community that is already evolving towards various open science frameworks. This would remove a number of frictions that discourage amendments thus leading to an improved scientific literature and a healthier academic climate.

A comment on “The big idea: should we get rid of the scientific paper?” | SciELO in Perspective

“In The big idea: should we get rid of the scientific paper?, published by the Guardian newspaper, Stuart Ritchie argues for a radical action: scientists should abandon the current format of the scientific paper, which is static and not interactive. Despite being currently published in electronic medium, they are still very similar to the printed version that dominated the scientific publishing landscape for more three centuries. In fact, the current scientific article is only an electronic version of “the physical black and white printed paper” in PDF (portable document format). This format is not friendly for reading on the screen of computers, tablets and mobile phones, which are dynamic and offer countless alternatives to interact with information. Reading a scientific article nowadays should be more than getting passive information about a subject matter, rather it should be an opportunity to think, check, review and reproduce the data and analysis presented in the article.

However, the standards of scientific publishing industry, and the rules of academic establishment as well, oppose any change in this static, passive and mostly non-transparent system of science dissemination. The Guardian newspaper article points out some alternatives to the PDF packaging of scientific articles, e.g., interactive “notebooks” that combine images, data, code, methods, and analysis into a single interactive and dynamic “article” that might be read, reviewed, reproduced, edited, and shared at any time. This format is known as “living article”.

But the problem does not lay solely on the “static scientific article”. There are the journals and the rules dictated (mostly) by the financial interests of the major commercial publishers. The predominant system for the communication of scientific results has not been developed by scientists, and they cannot freely decide what is the best “vehicle” or format to disseminate their research work. Actually, the publishers of scientific journals decide and control which format is accepted or not. A scientist today must follow the rules determined by journal editors, who are also dependent on the consensus and standards defined by the entire publishing industry.

By this reasoning, the problem is not the article itself, rather it is the vehicle that widespread the scientist’s message: the scientific journal and its rules! It is not possible to “get rid of the scientific article” without reforming the concept and practice of the “scientific journal”! ”

Aligning the Research Library to Organizational Strategy – Ithaka S+R

“Open access has matured significantly in recent years. The UK and EU countries have committed largely to a “gold” version of open access, driven largely by transformative agreements with the major incumbent publishing houses.[14] The US policy environment has been far more mixed, with a great deal of “green” open access incentivized by major scientific funders, although some individual universities pursued transformative agreements. Both Canadian and US libraries have benefitted from the expansion of free and open access in strengthening their position at the negotiating table with major publishers.[15]

Progress on open access has radically expanded public access to the research literature. It has also brought with it a number of second-order effects. Some of them are connected to the serious problems in research integrity and the growing crisis of trust in science.[16] Others can be seen in the impacts on the scholarly publishing marketplace and the platforms that support discovery and access.[17]

While open access has made scientific materials more widely available, it has not directly addressed the challenges in translating scholarship for public consumption. Looking ahead, it is likely that scholarly communication will experience further changes as a result of computers increasingly supplanting human readership. The form of the scientific output may decreasingly look like the traditional journal article as over time standardized data, methods, protocols, and other scientific artifacts become vital for computational consumption….”

Multimodal Publishing – First International Symposium, February 23-25, 2022 (in person & online)

The First International Symposium on Scholarly Multimodal Publishing will be held at the University of Victoria Legacy Art Gallery from February 23-25, 2022 in Victoria, BC. Publishing multimodal research (video, sound clips, graphic stories, etc.) can be challenging for scholarly journals. There is no standard for guiding the peer review processes of these multimedia texts. It is also unclear how Open Access platforms (i.e. OJS) can technically support multimodal publications. This symposium aims at reflecting on how non-standard innovative scholarly works can be published and disseminated in scholarly journals. 

During this two-day event, experts, scholars, librarians and graduate students will be invited to share their knowledge, expertise and ideas about how to develop standards to guide peer review processes of multimodal submissions, as well as to identify the technical challenges and opportunities afforded by Open Access production and publishing platforms. 

Make Way for the Metaverse – The Scholarly Kitchen

“Predicting where a new tool will take us is a fool’s errand, of course, but practitioners of scholarly communications may want to consider the Metaverse as a new medium, comparable in some respects to audio or video or the networked worlds of Twitter or Pinterest. When Twitter came along, the right question was, What can we do with it? Some people are dismissive about any medium for scholarly communications that is not as good as, or a substitute for, the formally published article. But the formal article is only one aspect of scholarly communications.”

The Value of Data and Other Non-traditional Scholarly Outputs in Academic Review, Promotion, and Tenure in Canada and the United States | The Open Handbook of Linguistic Data Management | Books Gateway | MIT Press

“This leaves us to ask: What role do activities and outputs beyond those that appear in traditional publication channels such as journals, books, and academic conferences play in review, promotion, and tenure processes? To investigate this topic, we focus on three related sub-questions:

1. What activities and outputs are mentioned in documents related to RPT?

2. How do the activities and outputs mentioned in documents related to RPT vary across institution types and disciplines?

Finally, and more specifically, given the topic of this handbook, we examine the following third sub-question:

3. To what extent and in which ways are data-related outputs mentioned in RPT documents? ”

The “Pre” in [my] “Preprint” is for Pre-figurative · Commonplace

“When you are a PhD student that just published your research, and you decided to publish it as a preprint, one of the most common questions you then get asked is “Where is it now?” At least this has been my experience. Well-meaning PIs or postdocs, colleagues, strangers, that all really enjoyed reading your research and findings but also really want to know “which journal have you submitted it to now?” It’s important for them to know, or maybe it’s just a conversation starter while queuing for the cafeteria. Who knows. Your answer of “Journal X” will be followed by an understanding nod, an approving “yep, that one is a nice one,” the sharing of a funny story about their own experience with that journal. Certainly, and generally unspoken, some sort of gauging of the value of the research. Did you send it to a journal that matches the value they thought your research had? It’s a fun game to play.

Except I have nothing to answer.

They do not warn us about this when submitting to preprint servers, this ethology of post-preprint-submission in the life sciences. Maybe it should be under the disclaimer about preprints not being certified by peer-review. “Please make sure you are sending this to a journal too, or be prepared for very awkward small talk from here on.” “Make sure you also publish it for real.” They do not warn us but there are many, many signs. It’s in the way submission guidelines are written. It’s in the way preprints are talked about.undefined It’s in the way preprints are talked about in the preprint server itself.undefined It’s in the many spinoffs, add-ons, “overlay services” and “integrated pipelines” that make it more and more seamless and easy to transfer your preprint to a journal. It is in the expectations of those around you. It’s in the awkwardness of you admitting that no, you did not submit it anywhere (else?)….

I published my research on a preprint server. Making it accessible to everyone and without having to pay my way out of paywalls. More importantly, I published my research on a preprint server without plans to send it to a journal. And this is what I encourage fellow PhD students to do too. I published it with no format constraints, no figure limits, no restriction on the length of my materials and method, no cut-offs to the length of my bibliography, no “STAR-methods,” no word counts. I published it — because why not? — with an anomalously long introduction that reads more like a review and that could well be a publication of its own. I published it in my voice and in my style. I published it with an open license and without transferring copyright. I published it in its most liberated form.

Well-meaning voices will remind you that without peer-review your preprint still needs to go through the “print” process. Services now exist for that too (I should here thank ReviewCommonsundefined), and allow you to submit your preprint for review by experts in the field without having to submit it to a journal. So I did exactly that and got my preprint peer-reviewed. Peer-reviewed for its content and not for its fit for a journal. Peer-reviewed journal-independently. I posted the peer review comments publicly, alongside my research and with them, my answers.undefined Answers that I wrote not only to the reviewers themselves, but to the future readers of those reviews. I wrote them conversationally, like a three-way-dialogue, in a way that was open to possibilities and to discussion and not in a way constrained by imposed timeframes for revision and resubmission. I recommend this to my fellow PhD students too. Peer-review in a liberated and liberating form, where critical evaluation of your research are just that, critical evaluation by a peer. A contextualising opinion. Not the yes or no on whether your research should even deserve to be seen by the world….”

eLife Latest: Including “Ideas and Speculation” in eLife papers | Inside eLife | eLife

“Speculating about the implications of data and results, both your own and that of other researchers is an essential part of the scientific process, and one of the joys of being a scientist. However, while not completely outlawed, pure speculation has been discouraged in all but its mildest forms.

There are, of course, good reasons to regulate how speculation enters the literature. The primary role of a scientific paper is to describe a set of experiments or observations – how they were conducted and what were their results – along with conclusions that the authors believe are well supported by these data. And one of the primary tasks assigned to reviewers and editors is to decide whether the conclusions reported by the authors are actually justified by their results.

As a result, the “Discussion” section of papers, which was once the home to much speculation, has over the years become a repository of only the most obvious and strongest conclusions, along with any accompanying caveats. And when authors try to include ideas that arise from, but which are not yet well supported by, the data, it is common for reviewers to demand that such speculation be removed.

While we agree that it makes sense to differentiate conclusions, we also feel something important is lost for both readers and authors by denying the people most familiar with the data the chance to freely speculate about its meaning and implications. Indeed it is one of the more common complaints of authors that current norms in peer review largely deny them this opportunity.

After discussing this matter with our editorial board, where opinions about the need for and wisdom of intervention were highly varied, we have decided to offer authors the opportunity to include an “Ideas and Speculation” subsection within their Discussion….”

Partnering with publishers to break down barriers to preserving new forms of scholarship – Digital Preservation Coalition

“NYU Libraries initiated a project, in partnership with Portico, CLOCKSS, and five university presses that aimed to better understand the limits of current preservation approaches when applied to new forms of scholarly publication. The project, which I described in a previous blog post, focused on a diverse selection of open access monograph-like publications with features that made them more complex to preserve than traditional text-and-image publications. …”

Taking the research journal in a new direction | Cambridge University Press & Assessment

“A new journal concept from Cambridge University Press will bring researchers from different fields together around the fundamental questions that cut across traditional disciplines.

By focussing research on finding answers to such questions, this unique approach will speed discovery by fostering collaboration and knowledge sharing between subject communities. It will also provide opportunities to publish research from areas that are not well served by traditional, discipline-specific journals.

Informed by feedback from hundreds of researchers, the first titles under the Research Directions banner will launch in 2022, with an initial set of questions and a publishing model that mirrors the research lifecycle, with results, analysis and impact reviews all published as separate, Open Access, peer-reviewed and citable outputs on the Press’s Cambridge Core platform.

In contrast to the traditional, self-contained research paper, researchers will be able to contribute at different stages in the process, sharing and building on each other’s work. They can submit results that address the questions posed, or analysis of others’ results, offering alternative insights and interpretations and using the findings to inform their own work. As the final part of the process, review articles will bring together the work done in response to particular questions, describing the context and the impact of what has been published….”

Taking the research journal ‘in a new direction’ | Research Information

“A new journal concept from Cambridge University Press will bring researchers from different fields together around the fundamental questions that cut across traditional disciplines.

The Press says that, by focussing research on finding answers to such questions, this  approach will speed discovery by fostering collaboration and knowledge sharing between subject communities. It is also aimed at providing opportunities to publish research from areas that are not well served by traditional, discipline-specific journals.

Informed by feedback from hundreds of researchers, the first titles under the Research Directions banner will launch in 2022, with an initial set of questions and a publishing model that mirrors the research lifecycle, with results, analysis and impact reviews all published as separate, open access, peer-reviewed and citable outputs on the Press’s Cambridge Core platform.

In contrast to the traditional, self-contained research paper, researchers will be able to contribute at different stages in the process, sharing and building on each other’s work. They can submit results that address the questions posed, or analysis of others’ results, offering alternative insights and interpretations and using the findings to inform their own work. As the final part of the process, review articles will bring together the work done in response to particular questions, describing the context and the impact of what has been published….”

‘New journals concept’ from CUP’s Research Directions | The Bookseller

“Cambridge University Press is launching an initiative it describes as a “new concept” for the journal, bringing researchers from different fields together to explore fundamental questions which cut across traditional disciplines.

Research Directions is the brainchild of Fiona Hutton, CUP executive publisher and its head of STM Open Access publishing. A former research scientist, Hutton wants to provide alternatives to traditional journal formats and bring communities together to frame research to problems that no one discipline would be able to tackle alone, said the publisher.

CUP said the approach would “speed discovery by fostering collaboration and knowledge sharing between subject communities” as well as provide “opportunities to publish research from areas not well served by traditional, discipline-specific journals”. 

The first titles under the Research Directions banner will be published in 2022, with an initial set of questions to answer, informed by feedback from hundreds of researchers. The publishing model will “mirror the research lifecycle”, with the results, analysis and impact reviews all published as separate, Open Access, peer-reviewed and citable outputs on CUP’s Cambridge Core platform….”

This week is ‘Peer Review Week’ – a time to ‘celebrate’ that aspect of scientific publishing that academia loves to hate. – Research

“Imagine if every statistical analysis was accompanied by comments from a professional statistician; if every method described had been critiqued by a methodological expert; if interpretations could be published of the same analysis from a wide variety of people with different training, backgrounds or experience. How much richer would the research record be? How much more useful than each of us only passing our own personal judgement on each article, bounded by our own inevitably narrow experience, and unshared with others?

This was all part of my thinking when coming up with Octopus, the platform that is designed to be the new, digital-first primary research record for scientific work….”

Credibility of scientific information on social media: Variation by platform, genre and presence of formal credibility cues | Quantitative Science Studies | MIT Press

Abstract:  Responding to calls to take a more active role in communicating their research findings, scientists are increasingly using open online platforms, such as Twitter, to engage in science communication or to publicize their work. Given the ease with which misinformation spreads on these platforms, it is important for scientists to present their findings in a manner that appears credible. To examine the extent to which the online presentation of science information relates to its perceived credibility, we designed and conducted two surveys on Amazon’s Mechanical Turk. In the first survey, participants rated the credibility of science information on Twitter compared with the same information in other media, and in the second, participants rated the credibility of tweets with modified characteristics: presence of an image, text sentiment, and the number of likes/retweets. We find that similar information about scientific findings is perceived as less credible when presented on Twitter compared to other platforms, and that perceived credibility increases when presented with recognizable features of a scientific article. On a platform as widely distrusted as Twitter, use of these features may allow researchers who regularly use Twitter for research-related networking and communication to present their findings in the most credible formats.