This looks like a fascinating webinar on Open Access and more, with a nice lineup of speakers: https://events.unesco.org/event?id=192545367531&lang=1033
I quite liked this webinar and it addressed a few points of open science that I hadn’t thought about much before. The recording is now on YouTube, but I thought I’d also post some notes on what I thought were the key points.
Two-word Summary: Epistemic (in)justice
This comment by the UNESCO host got to the heart of what that means at the moment:
The public must have the right to receive opportune, accurate and factual information on the developments of COVID-19 and its threats to their lives. The proactive publication of data and information relevant to the pandemic supports and protects the public from disinformation and the disease itself.
The UNESCO advisory committee on Open Science has proposed the core values of: collective benefits, equity and fairness, quality and integrity, diversity, and inclusiveness.
On several occasions, Jean-Claude Guédon brought up the point that while open access was important for open science, it wasn’t sufficient for epistemic justice. This also requires more global equality in the opportunities to practice science and publish scientific articles, and that this starts with having equality in setting the goals and priorities of research programs I.e. ideally people from a developing country should be setting the priorities for research that is done for their country’s benefit, rather than having them set by foreign funders and universities. (I suspect that [percieved?] differences in expertise and ethics often makes this hard to realize in practice.)
The above point was elaborated on by Samia Kaddor from the Tunisian government, who pointed out that international collaborations Tunisia had participated intended to focus on addressing Western issues in a Western/Northern context. She viewed the most successful research for Tunisia’s response to COVID as having been done by funding local researchers to find local solutions. (This makes me wonder if there are any collaboration between Southern countries do more successful research by focusing on regional problems and solutions)
Rob Terry from the WHO TDR said that they viewed open science as being important for the input, output and impact of research, as shown in this diagram:
In response to a question about the importance of pre-prints for COVID research, Rob Terry replied:
Pre-prints have a role to share early results between mainly between experts - the same researchers that are the peer reviewers in published papers. Many pre-prints are now able to go one and become traditional papers - in some cases on the same platform e.g. F1000. However, for guidelines and technical guidance the key is the aggregation of many studies (systematic reviews) which have been peer reviewed and an assessment of their quality e.g. GRADE in order to form evidence based policy. So pre-prints are timely and needed but require the reader to interpret the quality. NB the hydroxychloroquine peer reviewed papers in Lancet and NEJM would have been unlikely to go further if they had been published first as pre-prints.
Latin American is considered to have the best Open Science environment in the world, with infrastructure like Scilo and many non-profit publishers (indexed on Redalyc). Indeed, the post-war/1960’s Western publication system led by national scientific agencies was viewed much more favourably than the current system led by commercial publishers, and Latin America was commended for having its current system retain many of the merits of the old Western one. (This was somewhat surprising to me, I live in Brazil and know a few researchers in Sao Pãulo - they mostly seem to try to publish in American or European journals)
Glenn Hampson from the Open Scholarship Initiative had this excellent slide about an Open Renaissance. Interestingly, although his organization has a clear view of current problems and grand vision for the future, he explained that they were very focused on working towards that by pursuing goals that were realizable within 10 years (their Plan A). This appeared to be in contrast to the approach used by Coalition S, which seems to advocate for a larger scale systemic change toward Open Science.
Quite a bit of progress has been made on open-access in the last 20 years. All new journals are OA, and subscription-based journals are viewed as being in decline (or adapting to OA). More broadly, journals are now basically an artefact of printing and re-evaluation of the entire publication system can be done for open science in the digital age.
Open access is important but won’t solve everything. Not all open science is reliable and high integrity, and likewise, not all reliable and high integrity science is open. Work should focus on promoting the intersection of these areas, and better assessment of the quality individual research items is the next hurdle.
Following on from the above point the assessment of research output needs to move away from journal metrics (i.e. impact factor) and focus on the value of individual publications. This doesn’t need to be based on peer review or defined by where it is published (top-down assessment), something can be published and then evaluated by the community before value is assigned (bottom-up assessment). Interestingly, there was a general consensus on the need for the qualitative assessment of research value, not just the need for different, but still quantitative, article-level metrics.
The current publication system encourages competition between researchers for scarce resources (i.e. space in top-tier journals. Also, grants). Open science should move forward to encourage sharing and collaboration. There is also the need for inclusiveness, diversity, and a global/international context. The later can be hard as scientific funding agencies are usually nationally constrained.
Creating better open science platforms and infrastructure are important and should be considered a public good. As an example, Rob Terry said that a platform that could link across research projects (at all their stages) and across languages could provide real value for the WHO.
@Gavin thank you so much for writing this.
I agree this was a insightful webinar providing much food for thought. Like I was telling in this thread, I started talking about the importance of representation last year in 2019, when I kind of chose (for myself) to never advocate for Open Science without being able, at the same time, to listen to the voices we have neglected for so long. This is the keynote I gave at the OS Fair Porto 2019, which really coincides with this realization/decision of mine. This is why, since then, I have tried to communicate that there cannot be Open Science without Inclusive Science. This blog post of @rebecca made me think about how all these terms can somehow be confusing and that perhaps this diversification of goals/issues does not help the cause (the ultimate goal being, for me at least, to enable a much wider participatory science that does not leave anybody behind in the world).
I don’t know if you have looked at these slides yet (from my recent webinar) - I would love to hear your thoughts!
well we are discussing this from a wider viewpoint tomorrow…
Topic: WABAH & ILMU PENGETAHUAN Time: Oct 8, 2020 20:00 Jakarta
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From the latest Open Science Newsletter.
UNESCO has released its preliminary report on the first draft of the Recommendation on Open Science. Among the draft recommendations, this appears to be a good summary: “Ensuring that public research funders require Open Science practices and that all scientific outputs from publicly funded research are as open as possible, and only as closed as necessary.” Another important theme in the document, in my opinion, is the global, equitable access to research infrastructure and facilities.
check out some of my comments and their responses to unesco asia pacific open science recommendation webinar:
"From Surya Dalimunthe to Everyone: 01:47 PM @richard: i have emailed james. could you send an email to email@example.com so i could forward you my email to him? this is an issue i hold very dear to my heart, as tou could see in this igdore forum thread:
From Dasapta Erwin Irawan / ITB / Indonesia to Everyone: 01:48 PM richard: thank you for the link. good news from malaysia. however, i can still see the majority of scientific community in malaysia (and also Indonesia) is still favoring for quantitative measurement (eg: university rank, etc). we can see this every year after the QS and THES publish their report.
From Surya Dalimunthe to Everyone: 01:51 PM 2 more issues/information i think still missing from the asia pacific open science document:
- modern monetary theory
- green new deal for 1, countries which create their own currencies such as indonesia (rupiah) could actually increase its scientific/education funding by a lot, perhaps even 10 to 100 times, depending on political agreement, so it could compete and collaborate with other countries on an equal footing… nowadays, we are tired of hearing the WORLD-CLASS rhetoric in every other sentence that our bureaucrats utte4, but never WORLD-CLASS funding! reason given, no budget! i’m sorry, with the knowledge of mmt, this is a lot of bull!
From Surya Dalimunthe to Everyone: 01:53 PM 2. green new deal open science efforts should be connected to green new deal efforts… one framing:(tbc)
From Miguel Ramirez/UK/IDN to Everyone: 01:55 PM Mr. Surya, that’s indonesia for you, very agree with that.
Question From Surya Dalimunthe to Everyone: 02:05 PM @fitrie:is unesco jakarta actually in contact with indonesian scientific/education bureaucrats? if yes, why do none of these bureaucrats mention open science? our constitution actually mandates an even higher level openness, that is open knowledge. see constitution’s preamble (mencerdaskan kehidupan bangsa) and rights-related article (e.g. article 28, which most clauses are adapted from undhr)…
Answer From Rae Sita Pratiwi to Everyone: 02:18 PM Dear Pak @surya dalimunthe: LIPI actually has been doing a kind of open science practices. I would suggest to have a discussion with them."
A good discussion on how the pandemic is effecting open data practices.
Given the intense interest in his open repository platform since the virus outbreak, Mahé is hopeful that the pandemic will have had a positive impact on open data. ‘A lot of researchers have now had access to free and open data that would not have been accessible without the Covid-19 crisis,’ he says. ‘I hope that collectively we become more conscious on how open data and open access publishing can help researchers and their colleagues to work more productively.’
Baynes is also certain that researchers need to clearly understand why good practice is worth their time; and believes Covid-19 may have helped. “One of the hardest areas to share data is medical and clinical research, often because it has sensitive data,” she says. “However, the ways in which this data can be managed and shared will now be more obvious to researchers that hadn’t had to think about data-sharing before Covid-19
Lowenberg asserts that publishers should no longer accept data as supplementary files to the article, as these simply aren’t re-usable, citable or accessible. ‘I believe that all publishers must require researchers to put data in either a discipline-specific or general repository – this would change a lot of what we’re seeing,’ she says. ‘And then we need to have quality data curation across the board, involving institutional libraries and data curators.’
The pandemic brings home the real need for putting in place a structured and shared approach to research data… to ensure that data is as open and discoverable as possible,’ she adds. ‘And I’m really looking forward to the times when research data really starts to catch up with where we are on open access publications.’
I thought this interview about clinical testing of convalescent plasma therapy offered some insights into the considerations of clinical research during the pandemic. It also implicitly highlights the importance of open and replicable methods.
the line of defense, science‚ was actually pretty stressed before this began, you know, with funding cuts in most places, problems […] with employment and all that. Yet it is amazing when you think over 100 vaccines are in development.
We can always do things better, but we also have to celebrate the tremendous amount of work that has gone on and the options that are available in October as a result of having a vibrant worldwide scientific enterprise
I urge the [readers] and I urge anyone who’s interested to approach the data carefully […] [and] ask the question: Did they give [convalescent plasma] early, did they give enough, and what were the conditions of the [trial]?
And you can often find that information [in the studies]. And certainly, even when [convalescent plasma] is given late, we’re not getting [conclusive] results or side effects. But [in terms of establishing] the efficacy — it’s early [days].
And for those of you who are planning clinical trials, please incorporate this information into [the study papers], because it’s very important to have conclusions
Sadly this is not the case in indonesia…
Six Entities Developing Merah Putih COVID-19 Vaccine: Minister Translator: Antara Editor: Petir Garda Bhwana
28 October 2020 06:35 WIB
TEMPO.CO, Jakarta - Minister of Research and Technology Bambang PS Brodjonegoro has said six research entities are currently developing Indonesia’s indigenous vaccine against COVID-19, the Merah Putih, hence, several versions of the vaccine would eventually be released.
“Since they (the research teams) are using different platforms, the result would also be some six versions of the vaccine," Brodjonegoro said during an online press conference held at the National Agency of Disaster Management (BNPB) building in Jakarta on Tuesday.
“They are now working on the vaccine in each manner, but they would have eventually resulted (in developing their own version of the) COVID-19 vaccine, and we will be facilitating the production," he added.
The six entities working on the vaccine are the Eijkman Institute for Molecular Biology, the Indonesian Institute of Sciences (LIPI), Gadjah Mada University, University of Indonesia, Airlangga University, and Bandung Institute of Technology.
The Eijkman is currently leading vaccine development. Work on its vaccine, which is based on a recombinant sub-unit protein platform, has progressed more than 50 per cent on the laboratory scale, and the vaccine is expected to enter the stage of pre-clinical testing on animals by November, 2020.
LIPI, on the other hand, is using recombinant fusion proteins as its vaccine platform, while Gadjah Mada University is developing a recombinant protein platform.
University of Indonesia is using DNA, mRNA, and virus-like particles for its COVID-19 vaccine.
Bandung Institute of Technology is working on an adenoviral platform, while Airlangga University is using both adenoviral and adeno-associated viral (AAV) platforms to develop its vaccine.
Brodjonegoro has tasked the research institutions as well as his ministry with developing the vaccine prototype. The vaccine’s further development, including clinical trials and production, will be undertaken by state-owned pharmacy company Bio Farma.
Bio Farma, the minister said, plans to establish a consortium with Indonesian private-run companies to produce the Merah Putih vaccine at a higher capacity in the near future.
Wait, six research institutions are working on what was intended to be a single vaccine development project? Or did they actually intended to try six different things?
To be honest, I feel the whole framing of global vaccine development as a ‘race’ to be ‘won’ (Pfizer #1) has been a bit counter-productive. It would be good if this could be framed as collaborative progress towards a goal - vaccines #2+ will probably still get developed and some may better than vaccine #1, either generally or in specific situations. And groups that try to a vaccine approach that doesn’t end working aren’t ‘losers’, they are just crossing off part of the search space so nobody else has to look there. Sadly, the world does approach problems in this way.
six different things…
also, here we have someone who claimed to have started the whole thing…
Interesting article on the challenges evidence-based medicine has faced during Covid.
How COVID broke the evidence pipeline https://www.nature.com/articles/d41586-021-01246-x
As cases of COVID-19 climbed in February, Carley thought that clinicians were suddenly abandoning evidence and reaching for drugs just because they sounded biologically plausible. Early studies Carley saw being published often lacked control groups or enrolled too few people to draw firm conclusions. “We were starting to treat patients with these drugs initially just on what seemed like a good idea,” he says. He understood the desire to do whatever is possible for someone gravely ill, but he also knew how dangerous it is to assume a drug works when so many promising treatments prove to be ineffective — or even harmful — in trials. “The COVID-19 pandemic has arguably been one of the greatest challenges to evidence-based medicine since the term was coined in the last century,” Carley and his colleagues wrote of the problems they were seeing.
Carley compares the time before and after COVID-19 to a choice of meals. Before the pandemic, physicians wanted their evidence like a gourmet plate from a Michelin-starred restaurant: of exceptional quality, beautifully presented and with the provenance of all the ingredients — the clinical trials — perfectly clear. But after COVID-19 hit, standards slipped. It was, he says, as if doctors were staggering home from a club after ten pints of lager and would swallow any old evidence from the dodgy burger van on the street. “They didn’t know where it came from or what the ingredients were, they weren’t entirely sure whether it was meat or vegetarian, they would just eat anything,” he says. “And it just felt like you’ve gone from one to the other overnight.”
Even when rigorous clinical trials are too slow or difficult to run, the pandemic served as a reminder that it’s still possible to recommend what to do. In the United Kingdom, Trish Greenhalgh, a health researcher and doctor at the University of Oxford, expressed frustration at those who wanted bullet-proof evidence from randomized controlled trials before recommending the widespread use of face masks, even though there was a wealth of other evidence that masks could be effective and, unlike an experimental drug, that they posed little potential harm. (The United Kingdom mandated face masks on public transport in June 2020, long after some other countries.) “I think that was just a blast of common sense,” says David Tovey, co-editor in chief of the Journal of Clinical Epidemiology and an adviser to COVID-END, based in London. “People have focused too much on randomized trials as being the one source of truth.”
At the same time, there’s a thrill in seeing the enormous difference that evidence — that science — can make. “When results come out and you see that dexamethasone is going to save literally hundreds of thousands of lives worldwide,” he says, “you think — ‘that’s amazing’.”
A white-knuckle ride of open COVID drug discovery
In early 2020, a spontaneous global collaboration came together to design a new, urgent antiviral treatment. There are lessons in what happened next.
Nice article about Open Science research challenging the accepted timeline for drug development.
This experiment pulled together a spontaneous, open, global, Twitter-fuelled collaboration called the COVID Moonshot. Urgency and a commitment to working openly recruited more than 150 active participants, spanning a huge range of expertise and technology across academia, biotechnology, pharmaceuticals and more, all working without claiming intellectual property. Open drug-discovery efforts are invariably super slow — ours has been an express train on tracks we have laid down as we go. It is a way of working that none of us realized was possible.