Blog: the Road to Open Science

Open Science Symposium – Starting off with the Natural Sciences

On February 6, the Open Science Community Utrecht (OSCU) organized a symposium on Open Science at the Faculty of Science of Utrecht University. Guest blogger Max Bautista Perpinyà, student member of OSCU, visited this symposium to get an impression of the latest developments in Open Science for the natural sciences. Together with OSCU resident science journalist Stefan Gaillard he wrote an impression of the event, covering some but not all of the lectures. [This article appeared simultaneously on]  

The first ever symposium on Open Science at the Faculty of Science of Utrecht University achieved what these symposiums are for. They set the mood for new ways of doing science, and build community by providing not just an ethos, but also very specific tools for researchers of different domains. 

As Open Science symposia go, they tend to be filled by an optimistic crowd, mostly researchers sharing their knowledge and teaching others how to share theirs. It was therefore refreshing to see not only researchers, but other important stakeholders of science. Library staff and faculty administrators are crucial in the process of making Open Science a reality, and their presence was much appreciated.

As Open Science symposia go, they tend to be filled by an optimistic crowd.

From the Faculty, Dean Isabel Arends encouraged the community to keep pushing forward the ideals of openness, and made the commitment of doing what is in the administration’s power to ‘facilitate’ them. And while ideals are inspiring and necessary, this symposium was overall informative and offered a variety of tools for us researchers to use. 

The keynote address was by Erik van Sebille, oceanographer and chair of the ‘University and Society’ study group of the 2020-2024 UU Strategic Plan. Van Sebille showed his efforts concerning making the ‘workflow of scientific knowledge more open’. In the field of computational physics, GitHub is an extremely useful tool to work with the global research community. For example, his team’s code Parcels analyses the movement of particles (like the ‘plastic soup’) throughout the oceans, and is openly accessible (anyone can contribute by reporting bugs, improving it, using it…). 

After the plastic soup in our oceans, physicist Sanli Faez provided the audience with another recipe. This time it was the ingredients for a healthy and tasty open community. With ‘the need of belonging’ as a principle of Open Science, Faez suggested that in order to move from a egocentric to a networked structure of science, we could look up to other successful communities, like Mozilla (check their extensive list of resources), and the Global Village Construction Set, with their grand vision of reconstructing civilisation with open source industrial machinery. In thinking about the recurring debates on recognition and reward in the new Open Science era, Faez recommended the work of second-wave feminist Jo Freeman in ‘The tyranny of Structurelessnes’, which gives specific suggestions for how necesary it is to establish a structure within a community, ensuring a fair and democratic allocation of responsability, power, and yes: credit. An important aspect in scientific practice, and which Open Science aims, first of all – to have conversations explicitly and transparently. 

While in the computational world and physics departments sharing code is a well-established tradition, in the field of structural biology things look slightly different. Tzviya Zeev-Ben-Mordehai is working in a very competitive field and acknowledges that the fear of getting “scooped” prevents scientists from sharing their advances in the long process of decoding proteins’ molecular structures. In this field of biology, non-fair play seems to have itself a long tradition. Mordehai cited the widely-known case of Francis Crick and James Watson, who in the early 1950s got (somehow) hold of Rosalind Franklin’s ‘photo 51’, which helped them decisively in deciphering DNA’s structure in 1953. However, not all is bad news in the world of proteins and genes. Since early 1971 the WorldWide Protein Data Bank (wwPDB) has hosted the results of scientists throughout the globe working on establishing the 3D structures of proteins and nucleic acids. Moreover, Mordehai says, the wwPDB is curated , which ensures quality information. Important also is the fact that it is a requirement for the majority of journals that scientists first deposit their results in the database before heading for the press, which ensures proper recognition and open accessibility to the information. 

Then, it was the turn of PhD student in molecular plant physiology Laura Dijkhuizen, who shared the progress of making their ongoing research more open. For their bioinformatic study of plant meta-genomics, Dijkhuizen uses tools such as e-labjournal, and GitHub to make code openly available, but also to help them in project management tasks. 

The Open Science Symposium at the Faculty of Science at Utrecht University was a strong kick off to the series of symposia that the Open Science Community Utrecht (OSCU) will be hosting this year. The organisation, location and speakers were all excellent – a promising indication of how the next six symposia might look like. Besides the speakers mentioned in this article, fantastic talks were provided by Wouter van Joolingen on ‘How to make research accessible for practitioners?’, by Enrico Mastrobattista on ‘The Reproducibility Crisis in the Life and Pharmaceutical sciences’ and by Armel Lefebvre on ‘Computational Reproducibility and Lab Forensics’. Hopefully OSCU can continue to find a way to bring something interesting for researchers from all disciplines, while at the same time preventing too much overlap between the symposia. Regardless, bottom-up Open Science seems to have made a large breakthrough at Utrecht University.  

Thank your for reading this blog entry. If you want to stay updated, do keep an eye on this website, the Open Science Community Utrecht newsletter and follow us on Twitter.

'No Fee Science' – interview with Christopher Stevens

In this installment of the Road to Open Science, we interview Christopher James Stevens, initiator of the No Fee Science movement – a campaign for more profound Open Science. Christopher is a PhD candidate in France and the No Fee Science manifesto was the first grassroots francophone Open Science initiative of its kind. We interviewed him to get his perspective on why Open Science should be completely free, both for scientists seeking to publish and for potential readers. [Open Science, when used in this article, is meant in the sense of Open Science and Scholarship, so including all the academic disciplines. Views expressed by Stevens do no necessarily reflect those of the Open Science Community Utrecht.]

Christopher, can you shortly describe your academic background?
My serious academic studies began late, at 28 – after wandering around for 10 years variously dressed in a suit or Megadeth t-shirt. At the height of the 2008 economic crisis, I moved to Paris to study political philosophy. During my degree I lost some faith in the capacity of politics to effect profound lasting change, except in education. This led me to a master’s degree in Philosophy of Science and the Mind at the Université Paris-Sorbonne, where I began directing my research towards cognitive dissonance and pluralism.

Over those two years I lost faith again, this time in philosophy’s obsession with pontificating on science it knew very little about. I realized I had no practical knowledge of what doing science involved. So, at that point, I threw myself into the study of biology, talked my way into a two year master’s degree in neuroscience and ended up being awarded a PhD grant at the end of it.

What are you currently working on?
With my own funding to do a PhD, I was able to propose a project of my own, conducted in collaboration with the great Marighetto and Marsicano teams at the Neurocentre Magendie in Bordeaux. Though I see myself as a bit of a philosophical mole working in science, and in fact I’m simultaneously working on a philosophy PhD under the supervision of Barbara Stiegler at the Université Bordeaux-Montaigne.

My neuroscience research explores the neurobiology of confirmation bias. People seem to think confirmation bias is too complex to be found in ‘lower’ mammals. However, I didn’t see any reason to believe that naturally curious animals capable of rule-learning wouldn’t also display confirmation bias given the right circumstances. And they do! I’ve designed and validated the first animal model of this phenomenon.

In philosophy, my focus is still (science) education, closely tied to my work in neuroscience. The strength of confirmation bias that manifests in the activities of researchers themselves can be seen as a function of dogmatic thought habits, something which should be combated since the earliest school introductions to science. Critical thinking, of course, is key, but also what I call cognitive pluralism, which is the idea of holding more than one theoretical explanation for a set of phenomena in your mind/brain at the same time.

Critical thinking, of course, is key, but also what I call cognitive pluralism.

According to you, what are the structural problems underlying the current situation in academia? You seem to, for example, take issue with the economic structures surrounding science publishing?
I think I have learned more about these structural problems since publishing the #NoFeeScience manifesto than I knew when we first wrote it! I state this openly, because the original intention of the manifesto was to really highlight the moral problems with how science is currently communicated and evaluated. If we take science as having some kind of purpose or goal, then some actions will be apt for moving towards that goal, while other actions will cause movement away from it. Since I believe the goal of science should be to enrich the human experience of, in a nutshell, life, the universe, and everything, then anything that moves science away from that end becomes morally problematic.

I believe the goal of science should be to enrich the human experience of life, the universe, and everything.

The fact that the results of scientific research are not freely available to all curious individuals moves us away from the aforementioned goal of science. The fact that, with regards to publications, the scientific community values surface prestige (legacy journals, impact factor, etc.) over careful examination of content also moves us away from that goal. Institutionalized prestige seeking, which those who view themselves as winners (or potential winners!) are not willing to let go of, is both the foundation upon which the current publishing model was built and the carrot that is used to keep selling it to the community. If there’s a central structural problem, it’s this last one.

So what’s the primary purpose of the #NoFeeScience movement?
The primary purpose of #NoFeeScience can be found in the second slogan we use in our material; #MarchForBetterScience. Like the manifesto states, scientific knowledge should be made ‘fully and freely accessible to one and all’. When I moved into science, I very quickly saw how petty, ego-centered and very unedifying much of accepted scientific activity actually is. I had come into science from philosophy, armed with these grand ideas for revolutionizing scientific education with the aim of provoking a revolution of the human mind. Instead of fertile ground for progress, I found a scientific enterprise that was willfully entangled in a system of knowledge communication and evaluation whose intellectual immaturity beggared belief. Yet this very enterprise was parading around asking the wider public to entrust the welfare of the entire planet to it!

I had come into science from philosophy, armed with these grand ideas for revolutionizing scientific education…

Once I started seeing movements like #MarchForScience and #NoFakeScience insisting that the public needed to place more trust in scientists, it seemed an obvious time for a voice to shout back that this trust needed to be earned. The #NoFeeScience manifesto aimed to ‘raise the alarm on the availability of scientific information in the public sphere’. If science genuinely wants the nations and powers of the world to behave better, so to speak, then it needs to lead by practical, visible example! In that sense, the overriding aim was to hold a mirror up to science, to reveal how deeply undemocratic its internal values have become and how far it had departed from any genuine societal or indeed species-wide concerns. Plus, this undemocratic and ego-elevating structure actually multiplies the probability that bad science gets done.

What challenges have you encountered since you’ve started the #NoFeeScience movement?
Well, as you may have gathered by now, the views expressed in the manifesto were not designed with diplomacy in mind. We did go to pains to underline our understanding of the fact that many researchers, especially young ones, are trapped by this prestige system – wherein publishing in a prestigious journal is the best way to advance your career and the most prestigious journals are not open access. However, this concession to the pressure weighing upon individual researchers’ publishing choices was, I think, lost beneath the weight of the overall punch.

…the views expressed in the manifesto were not designed with diplomacy in mind…

As a result, despite great support from those who signed the manifesto, it didn’t spread very fast, because every researcher who felt themselves a target thereby became a wall of resistance to it. I highlighted this point recently when a petition against certain comments by the president of the CNRS (Centre National de Recherche Scientifique) went viral within the French research community, gaining over 5,000 signatures in a matter of days. Ultimately, that petition and our manifesto were decrying some very similar things, with the essential difference that one was pointing the finger only at an external big bad wolf whereas the other was pointing the finger inward at internal complicity, and indeed complacency.

In short, it’s very easy to sign a petition and make noise about a cause that implies no changes in one’s own actions! In science, we should be able to speak plainly, not feel obliged to cushion hard truths, and that’s the road we went down. This also meant that we got little to no support from much of the ‘official’ diplomatic open science movement in France, which was quite disheartening. Thankfully, Bernard Rentier, former rector of the Université de Liège and author of the excellent Open Science, the Challenge of Transparency, found and signed the manifesto. This showed us that there were others in the francophone open science movement who were willing to openly articulate plain truths. No one can read the #NoFeeScience manifesto without being obliged to take a good hard look at their own practices towards genuine improvement of science.

Finally, and I think most unfortunately, we also lost out on signatures from young researchers who were worried about what their non-open science practicing supervisors and lab heads would think.

Were you surprised by some of the challenges – like worried young researchers – or were they something you saw coming from the start?
Naively, I thought the manifesto would reach critical mass and spread a lot faster than it did. Initially, we had worried only that it was perhaps too long. Since we wanted it to be as comprehensive as possible, it kept getting longer as we went from draft to draft, but at least it now serves as a complete summary of the current situation in scientific publishing, something which in French there aren’t many examples of.

I also thought we would get more support from open science advocates in France, but it seemed that they had become content at this point to simply allow Plan S and the French ‘Comité pour la science ouverte’ to take over the work. However, both movements consist of simply pushing new obligations onto how scientists publish. Obliging someone to do something can never replace attempts to make that person understand why they should wish the change themselves! If a scientist doesn’t understand that open science is just science done right, then there is something missing from their understanding of what science is, and merely obliging them to act otherwise will not wake them up to that. As for young researchers who felt too intimidated by their superiors to sign, this is something we had anticipated.

What drew you to Open Science in the first place?
Paywalls! The first paywalls I encountered were on papers in the humanities – philosophy, history, etc. I couldn’t believe it. They just instantly struck me as profoundly wrong. Science, historically, has liked to distinguish itself from religion, but the state of science today has often reminded me of the story of Jesus going into the temple and casting out the money-changers in righteous anger. Paywalls cheapen what should be the greatest collective intellectual achievement of humanity, and in that sense I think science, just like religion, has strayed too far from its initial ideals. Just another stall in the marketplace. So yeah, let’s get paywalls (and exorbitant pay-to-publish fees along with them!) the hell out of our research temple!

Would you say that Open Science is more of an ideological movement, or a practical solution to specific problems?
I certainly don’t think it’s black and white in that sense. Open access leans more towards being an ideological movement whereas open science (data sharing, methodological transparency, etc.) is a practical solution to problems such as replicability, and so on. However, it’s generally accepted that you can’t have genuine open science without open access. This intertwining of ideology and practicality is, from my perspective, the pragmatic beauty of the movement; open science is the right thing to do, but it’s also the best thing to do for science. Those who tend to be more ideological need to keep this practical side in mind, and vice versa.

Those who tend to be more ideological need to keep this practical side in mind, and vice versa.

What do you think of top-down implementations of Open Science, for instance through the EU, like Plan S?
I was very excited when Plan S was first announced in September 2018. Then, after the first round of feedback, they announced the revised version in May 2019 and they seemed to have rolled back on a lot of what had made it seem great. Hybrid journals (some articles paywalled, others OA) were back in on the grounds of ‘academic freedom’ (ha!), the whole timeframe had been delayed by a year, and so on and so forth.

Around August 2019, I started looking into the various kinds of feedback that had been returned by different collectives of researchers. Some thought it a scandal, complaining about an attack on their ‘academic freedom’ to choose to publish in limited access journals (apparently the irony escaped them), while others thought Plan S didn’t go far enough into promoting full open science practices. Plan S seemed to encourage gold open access (author pays an article processing charge to publish an article, thus financing the journal) more than what is referred to as platinum open access (author pays nothing to publish, journal is funded through other channels).

How best to publish scientific results is a question that should be looked at scientifically, not managerially. The scientific community needs to decide what the most democratic, fertile, and transparent publishing model is and then look at how this can be financed. ‘Ten Hot Topics Around Scholarly Publishing‘ is a great paper that attempts this kind of approach. Currently there are too many managerial minds involved and they’ve been spoiling the broth for long enough. The scientific community needs to take back control of how science is done and funded.

How do you try to incorporate Open Science best practices into your own work?
Since I’m still working on my PhDs, I only have a couple of papers to speak of so far. To this point, incorporating open science best practices in my own work has sometimes involved stepping away from publications which I didn’t believe in. To be frank, if the worst came to the worst, I’d prefer to work a normal 9 to 5 rather than succeed at the science game through science I can’t in good conscience be proud of and communicate openly. Fortunately, now with open data upload platforms and pre-print sites such as Biorxiv, it is possible to complement the ‘official’ published version with all the work, including both positive and negative results, which led to it. And, of course, it’s out of the question that any of my first author papers will appear behind a paywall.

I’d prefer to work a normal 9 to 5 rather than succeed at the science game through science I can’t in good conscience be proud of and communicate openly.

Besides your own project, could you tell us about a development or project within Open Science that caught your eye and that you admire?
I’ll give two brief examples. One is the Open Science MOOC, an online training course in best open science practices. When first approaching open science through the literature, it can seem a bit of a jungle, so a video training course like this, with certificates of accomplishment included, is an excellent way to ease things in.

Open access to bad science will be nothing to celebrate!

The other is the work of Björn Brembs, who has authored many papers and blog entries on the subject. He has an innovative take on the open access question: we should already start taking open access as a given and now shift our attention to the deeper improvements of science that are also needed; more rigorous evaluation, better replication processes, etc. As he quite correctly puts it, open access to bad science will be nothing to celebrate! This take can seem like a slap in the face at first, since we all still work so hard to attain open access, but there is a deeper insight there which cannot be ignored; open science goes far beyond open access to science, and that’s why we need our vision of the scientific enterprise to go far beyond open access too.

Thank your for reading this blog entry. If you want to stay updated, do keep an eye on this website, the Open Science Community Utrecht newsletter and follow us on Twitter.

The Road to Open Science Continues…

Welcome to the sequel to the Road to Open Science! You might know the Road to Open Science as  the podcast first presented by Sanli Faez and later by Bianca Kramer and Jeroen Bosman. You can find the first few episodes here and I would highly recommend that you give them a listen as these episodes touch upon the foundations of Open Science and are now perhaps more relevant than ever. In the meantime I, Stefan Gaillard, will continue the Road to Open Science project with some help from Bianca and Jeroen, albeit in a slightly new format. In addition to podcasts, I will also work on written texts, vlogs and whatever else might seem like an interesting format. Below you can find a textual interview with myself.   

What is your scientific background?
‘I come from a diverse scientific background: I have expertise in history, philosophy and psychology. Right now, I mostly work on history and philosophy of science. Combining these multidisciplinary interests into a transdisciplinary framework hasn’t always been easy. I took part in the Graduate Honours Interdisciplinary Seminars, which really helped me to unify multiple aspects of various fields and taught me how to apply interdisciplinary theory and methodology to scientific challenges.

Having completed this honors program, I am currently investigating the psychological aspects of susceptibility to fake news – together with an interdisciplinary team of multiple students and professor Michael Burke. I believe we need interdisciplinarity to properly understand and contribute to Open Science, while at the same time Open Science enables interdisciplinary research. I was already interested in Open Science before really exploring interdisciplinarity, though.’        

What motivates you?
‘What always drives me is a probably somewhat naïve optimism. An optimism related to a more open, free society. In my opinion, it’s impossible to separate science from things like government, the private sector, and culture. For example, independent science (an unreachable ideal that we must continuously strive for) is only possible under conditions that are dependent on the role of government and companies in society. This role in turn depends on cultural attitudes among the citizens of the countries in which these governments and companies operate.

I truly believe that in the complex system that the modern world has become, decentralization, bottom-up initiatives, and diversity of all kinds enable us to adequately address contemporary challenges. The Open Science Community Utrecht is precisely such a bottom-up initiative, and I am incredibly excited to work with them.’  

How else does this motivation relate to Open Science and Scholarship?
‘What I find most attractive about Open Science and Scholarship (sometimes used interchangeably with Open Science) is the idea that it enables forms of citizen science, citizen medicine and citizen journalism; in essence, open science and scholarship provides critical civilians of all stripes with the tools necessary to hold scientists and politicians accountable. This might be an unpopular opinion in the age of widespread fake news coverage and increased polarization with regards to manmade climate change, but I wholeheartedly believe in a healthy symbiosis between laypeople and professionals.

I wholeheartedly believe in a healthy symbiosis between laypeople and professionals.

A nice example of this at our own university is the Nieuwe Utrechtse School (New Utrecht School), a medical humanities initiative that brings medical professionals, patients and humanities scholars together. While the theories and methods are grounded in academic medical, narrative and phenomenological theories, the viewpoint of the patient is continuously taken into account. The input of the layperson is crucial for the professional, who in turn helps the layperson with their healing or coping process.’        

What can we expect on this science blog?
‘As I wrote earlier, you can expect many different formats on this blog, ranging from written texts to podcasts and vlogs. I will cover global trends in Open Science, but my primary focus will remain on open manners in the Netherlands and Utrecht specifically.

A sample of the next few posts hopefully illustrates this diversity. These coming months, you can enjoy an interview with Christopher James Stevens, initiator of the #NoFeeScience; a roadmap by data visual computing scientist Victor Schetinger; and interviews with the Open Science ambassadors at Utrecht University.

However, there is still room for much more! I hope to engage with academics from all fields with regards to open manners. I encourage you all to leave comments with your critical thoughts or questions on this website and/or on Twitter. If you would like to see an entry on a particular subject, would like to be interviewed or if you want to provide a guest post, please mail me.

Thank your for reading this blog entry. If you want to stay updated, do keep an eye on this website, the Open Science Community Utrecht newsletter and follow us on Twitter.