Talk to Open Science conference

The Dutch government has been very active to push the Open Science agenda, both on a national and European level. Their newest initiative is the “National Plan Open Science”, which has been cosigned by several different national science organisations (funding, educations, academia, library, SURFnet etc). You can find it here.

On Monday May 29th, scientists who are interested in Open Science gathered. It was a very fruitful and energetic meeting. I noticed that there is a real Open Science community in the Netherlands, but it is rather patchy, scattered over many different fields. This means that when you are interested in Open Science, the chances are not very high that your closest colleagues share your interest, which complicates it. However, my experience sofar has been very positive (see talk below) and many people in my field were enthusiastic or at least curious to hear more. I was honored to speak at the conference, find my talk below.  It contains several of my ideas about peer review (the silver standard), but also scooping/replicating (the gold standard). There is overlap with previous talks.

(Update 15/06/2017: I have made some grammar and spelling changes and gave intermediate headings for structure. I also uploaded it to FigShare.)

I want to start off by thanking and congratulating our secretary Sander Dekker and his team for his achievements in pushing the open science agenda both here as well as on the European front. I realize that there are many interests you could have been pushing and you chose the topic of open science thereby accelerating the enormous change the scientific communities has to go through. In this talk I would like to give you an insight on my own plans and ideas about open science.

Ladies and gentlemen,

Last year, when I left my postdoc project in the USA, was the first time since in my adult life that I was outside of academia. No longer did I have an .edu account that provided access to literature, no students around, no . I hated every part of it. And I realized that when you leave academia, you’re really out, There is no fluent transition, you’re in or you’re out. You don’t know how high the walls of the academic bubble really are, until you found yourself outside.

I studied here in Delft and in Leiden, did a PhD in Amsterdam and then I continued as a postdoc at Washington University in St Louis Missouri, where I worked on vaginal microbes, lactobacilli but also other bugs. I also write a weekly column in NRC Handelsblad and I worked on a book. That is finally here. It’s called Ode aan de E-nummers, it’s on a hobby of mine, a side project, food technology, and I spend the past weeks promoting it.

The funny thing is that all the written output I create in those different jobs, both as a writer for a newspaper, as a writer of a book and as a scientist, you have to pay in order to read my stuff. The big difference is that when you purchase one of my articles for the newspaper NRC Handelsblad you indirectly pay me, the author. When you purchase one of the articles from a scientific journal, you don’t pay me, you don’t pay the people who reviewed it, you pay Elsevier, or Springer or another publisher. This is problematic, even fraud if you ask me. Furthermore, the public is higher educated than ever. More people are going to colleges where they are exposed to basic scientific ideas, having to read and even write research articles. The saddest outcome of this system is when you end up having to send journal articles to the family of severely sick patients because you are the only access they have. I believe the open access train is well underway, partially thanks to the open science iniative pushed by the Netherlands.

My book is doing well, I can make a living as a writer and entrepreneur. Still my heart breaks with the idea to no be involved with science any longer. The big question for me was how I was going to continue after having left my postdoc.

The push factor in science

There are pull and a push factors in science. The pull-factor is clear. I love science. I love the excitement of understanding how the chemistry of life works. This is the best job in the world. But there are also push factors. I love how free I am as a freelance writer, to just say whatever the hell I want, to communicate freely, on my own, just push the send button, without first having to consult 7 co-authors, and three anonymous peers. As a scientist you’re not free like that. Publishing in the right journals is essential for success. In the academic monetary system, high impact peer-reviewed publication are currency. And those papers need to be shiny, solid filled with good news. Scientists are therefore keeping their cards to their chest. Often you hear people say: “you don’t want to give full openness, because what if somebody takes your research and uses it?”. Then I ask: “isn’t that the whole purpose of science?”

There are some steps taken to open up in academia, but the biggest advances you see on the education front, not the scientific front. In higher education people are slowly breaking down the walls of academia. I was able to follow a Massive Online Open Course on Computer science and bio-informatics from home. I believe real progress is being made on that aspect. On the other side of academia, the research part, we’re far behind. We are still waiting for the digital revolution in scientific communication. The only way you’re able to follow science when you are outside academia, is through peer reviewed articles in journals. That means that from outside the bubble, you can only follow your field with a few years of delay, because that is how long it generally takes for research to make it into a paper.

Luckily papers are not the only way we communicate. In biology, we also show parts of ongoing projects at conferences. There you see rows and rows of carefully crafted A0-sized posters full of information, some people are taking pictures with their phone, because you never see digital versions of those posters, they’re never published. they are only meant for the handful of lucky ones who happened to be present at that conference. Why don’t we publish them? Is it because publishing one of those posters online, on social media or a blog or Researchgate doesn’t result in an impactful publication, with an impact factor? That would sad, right?

I follow many scientists on Twitter. I know what their children look like, I know what music they love or where they go on vacation, but I rarely here what they are doing in the lab. Sometimes they ask each other questions, mostly around scientific trivia or funny side projects in their lab: what is this bug? Why does it look weird? Or they ask: what is the best software to study this problem? Rarely do they say: look what I found. Here is some fresh knowledge, straight from the lab. It is very disappointing how much openness social media has brought to science. It is still a very closed system. Rigid, institutionalized and behind very high walls. That should change.

Open Kitchen Science

So I decided to go back to science, but on my own terms. I want to work from the deep conviction that the purpose of science is to increase our collective knowledge and by doing that make the world a better place. If I manage to increase our general knowledge, or if my work facilitates others to do the same, I achieve my goal. So therefore I chose to share as much possible.

Not only open access, not only sharing raw data and materials. But “real-time open science”. Compare it to vloggers. Those people that share hour-long footage on the regular, banal activities like how they put on their make-up or drive their car or cook their food, eat their food. We have an abbreviation for it: TMI, too much information. That is exactly how I want to do science. I want to publish ALL my findings. The whole process. Every method, everything that works or doesn’t work. Every assay I am trying to develop. Every question I have, every experiment, no, every thought of an experiment and just write it down and put it online, by myself, without having to consult with anyone. I want my work to be open and free for everyone. Any social media or blog is fine, I am now working on crafting my own WordPress-blog, I don’t want it to be too shiny, I don’t care about the form. I care about the content. It just needs has a proper comment section and a clear indication what results have been reviewed, or what results have independently been validated, reproduced.

I am calling this project RebLab, and the type of science I call radical transparent science or OpenKitchenScience. It is not entirely new, a few scientists are choosing to work this way, some call it Open Notebook Science. One great example is labscribbles, where you can follow the work on the Huntingtin protein by dr. Rachel Harding in real time.

Peer review

The biggest science rule I am breaking by doing this is by not having everything peer reviewed. Don’t get me wrong: I believe peer review is very important to maintain a high standard of scientific quality. At the same time I believe we’re overdoing it. Peer review is starting to hold us back. It places a huge hurdle in between scientists because it means everyone is only communicating with a delay. Peer review is probably also the most important reason why results that don’t make it to a paper are never shared,. We are sharing shiny positive nice stories with each other, while so much of our knowledge, ugly practical things, negative results, stays in the lab. Why are we not sharing that? Why don’t we throw it on a blog, send around a newsletter, throw it on Facebook for all I care. Communication in science takes too much effort, time and money, and an important reason is because we want to have everything peer reviewed.

Reproducibility crisis

We are currently facing a reproducibility crisis. Our current system of science, of increasing our knowledge is not working properly. More than one third of the high impact prestigious cancer studies were found to be irreproducible. It was the pharmaceutical industry that pointed to this problem. “Hey guys”, they said “I don’t know what you’re doing. These might be superfancyschmanzy Cell Nature Science results but they are not working for us. They don’t hold up when we are trying to do the same things as you tried”. In social psychology it was apparently even worse and over half of the studies cannot be independently reproduced.

Dutch funding organization NWO is now spending 3 million euros specifically on replication studies. Great! But here is a question: aren’t we already replicating each other’s work all the time? We call it different and we’re normally not very excited when it happens, we call it scooping. In my view peer review is the silver standard. Getting scooped is the gold standard.

Here is an assumption: in the cancer field where one third of those studies could not be replicated, they already knew. This is a highly competitive field. There must be at least 20 labs worldwide working on that same problem. There must have been already awareness in the field that these same results were not found across the board. Perhaps, in a scientific world where the default is to share, and the gold standard is to reproduce and not to review, we would have already known.

First steps towards Open Kitchen Science

In February I went to Prof. Remco Kort, both working at TNO and the Free University of Amsterdam, and I proposed to him to do a project on carbohydrate metabolism of vaginal microbes. I basically want to know what the lactic acid bacteria that colonize the human vagina, what carbohydrates they metabolize. What material they use to convert into lactic acid and acidify the vagina. That’s my research question. That question has been haunting me for a few years now. Luckily that question also has his interest.

And then I said: “it’s not a normal research project. It has to be radically transparent, it has to be open kitchen science”. And he said: “sure”.

Sure? I expected to run into a plethora of problems. This was radical right? Suddenly I doubted the rebellious nature of this endeavor. Hello? I want to publish science on a blog, I want to publish my posters unreviewed. Where are all those walls I need to break down. He said: “fine”.

Then I asked a few scientific journals, the ASM (American Society for Microbiology) journals that we, microbiologists often publish in. I asked: “what if I prepublish my experiments, would you still consider it for your journal?” This is important because any collaborations or students who want to work with me, might still need papers for their CV. And at some point I do want to have stuff reviewed by colleagues. And you know what the journals said? “Fine”.

Then we went to the safety officer to ask if we could do open kitchen science and she said “fine”. Then we went to the communication department to ask if we could do Open Kitchen Science and they said “great”. And then we went to the head of the department to ask if we could do Open Kitchen Science, and he said “awesome”.

It went surprisingly smooth. No big hurdles yet. My blog is not up and running yet, but I hope to make some advances in the lab this summer. What I learned sofar is that it really looks like this whole system of holding your cards close to your chest, this system is mostly cultural. I learned, that there are no rules that stop you from sharing. We humans are herd animals, and we do what the other people do. Scientists are no exception to that rule. We have strong culture and social norms about how you behave in this academic setting. It’s both good news and bad news. A lot of the hurdles for openness are in our minds, the barriers are mostly imagined but they are holding us back. I believe we should change this culture because it is not good enough. It should be standard procedure to overshare. After all, there is no such thing as Too Much Information in science.

Negative Results Week

As a last remark: I am very excited about the National Plan for Open Science. I feel that there is currently true momentum here in the Netherlands but also elsewhere in the scientific community to change the way we communicate in science. I also understand not everyone in the academic world is going to radically open up and throw everything they know and have online, like I plan to do. I believe people need a bit of a nudge to dip their toes in the open science waters and see how it feels. To help them I want to propose to, as part of the Dutch Open Science community, to invite other scientists to engage in a challenge. I believe we should organize a negative results week. we invite scientists to share a short paper, unreviewed, on some platform, that is unowned, independent, Wikipedia-like, open source, with a negative result. Once. Just to see if they like it. If you are interested in organizing something like this, with me, let me know.

Thank your for your attention.

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