Why Open Science is the Road to the Future

In this article, guest contributor and OSCU Faculty Ambassador Sander van der Laan gives his vision on why Open Science (including Open Scholarship) is essential for the progression of science. [This article appeared previously on the intranet of UMC Utrecht]  

Valentine’s Day
On Friday, February 14, 2020, scientists, educators and other interested parties came together for the Symposium “For the Love of Science” organized by YoungSiT (follow us on Twitter @SciTransitYoung). The participants appeared in large numbers and not just for free drinks afterwards. They all shared one passion: Science. An exciting program of talks and workshops guided the enthusiastic participants through concepts such as “Open Science”, “Outreach & Communication”, and “Career & Reward” (Figure 1). Professor Cecile Janssens concluded with her story about better science through “slow science”.

Looking back, we can be satisfied with what we achieved that day. The dean promised to dedicate himself to the three main themes and received a lasting memory of that day (a unique illustration created exclusively by Jeroen Krul, Figure 2).

It was a Friday filled with Love for Science, and a passion and urge to make the (scientific) world a little bit better. Valentine’s Day was an energizer for the rest of 2020.

Figure 1: On the participants of “For the Love of Science 2020”.

Figure 2: Unique illustration of Jeroen Krul presented to the dean by YoungSiT on February 14^th.

Contagion 2020
What bloomed those first weeks of 2020, was suddenly gagged when the cabinet announced an “intelligent lockdown” after a mutated version of the SARS virus spread. The world fell under the spell of #COVID19, “R0”, Philips’ ventilation equipment, “Frontline stories”, and the latest figures from RIVM and Johns Hopkins¹ – Jeroen Pauw led the conversation on NPO1 for one last time. Research and education at our institute was halted and all eyes were on the ever-dwindling number of IC beds available, while outside people applauded for their neighbor who kept the care going. Suddenly Contagion was no longer “just a movie” – it had become the harsh reality in 2020².

In all its misery, #COVID19 also turned out to be a blessing in disguise for science and #OpenScience. The gravity of the situation became apparent in a matter of weeks, and the world looked to science for solutions: a vaccine, treatments, rapid diagnostic tests, knowledge about the virus, an analysis of what was to come. Scientists around the world worked day and night to crack the genetic code of the SARS-Cov-2. Within a few weeks the first preprints appeared on bioRxiv and medRxiv³, and now almost 7 months later there are more than 8,500 submitted manuscripts on these preprint servers (± 34 per day since 1/1/2020). In no time, preprint servers became the scientific equivalent of cnn.com for the latest news about #COVID19 – every finding was shared openly with everyone as soon as possible.

In our own hospital, Marc Bonten and colleagues from Radboud UMC quickly set up a clinical study to investigate the effects of BCG vaccination against COVID19 placebo-controlled⁴, and Folkert Asselbergs and Marijke Linschoten started the CAPACITY COVID Register⁵ to study the effects in patients with cardiovascular disease⁶. Across the Atlantic, writer Carl Zimmer et al. tracks vaccine development for The New York Times⁷. It was unimaginable 6 months ago (to me at least) that there are now 9 potential vaccines in ‘phase 3 trials’^8,9 and that there are already 3 vaccines available (albeit on a small scale and with the caveat that at least the Russian vaccine has skipped a step)¹⁰. In Boston, scientists who normally decipher the human genome have teamed up to help the community test for #COVID19. In March they converted the genetic lab into a large #COVID19 test lab¹¹ and the BROAD Institute has now processed more than 1.4 million tests¹².

#OpenScience is #TeamScience
#COVID19 shattered communities, the economy and the budgets of countries and regions¹³, but the virus seems to have made the scientific world even closer. Scientists from all kinds of fields have come together to work together in the combat of the pandemic and to share knowledge: #TeamScience on a roll. #COVID19 shows that #OpenScience works, and with it #TeamScience too – not just now, but always.

#COVID19 shows that #OpenScience works, and with it #TeamScience too – not just now, but always.

A shining example of #TeamScience to me, but I am biased¹⁴, is the COVID19 Host Genetics Initiative (HGI) led by Andrea Ganna and Mark Daly¹⁵. More than 200 studies provide data to investigate the genetic causes of illness and death from #COVID19. In accordance with the #OpenScience principle, analysis protocols and the results are shared, while different teams of experts answer the main and sub questions. This summer, a genetic study from Germany, Italy and Spain was published¹⁶ showing a relationship with a region on the genome that codes for blood types (ABO, Figure 3). Commercial parties are also trying to collect and share knowledge about #COVID19 – 23andMe (a company that sells genetic tests), for example, conducted a study in more than 1 million people, confirming the previously found association with ABO¹⁷ (although the jury is not yet out, on the variation in ABO and susceptibility of #COVID19). Previously we wrote about the usefulness of such large-scale genetic studies¹⁸ and others showed that when genetics is taken into account during drug development, putative drug candidates are more likely to make it to the finish line¹⁹.

Figure 3:  This “Manhattan” plot visualizes the results of a genome-wide association study (GWAS) on COVID-19 with severe lung failure.

Each point is 1 genetic variation in the genome (a “single-nucleotide polymorphism”, SNP [pronounced “snip”]) of which approximately 9 million were measured and tested in this study¹⁶. The chromosomal location is on the x-axis and on the y-axis the –log10 of the p-value. So a p value of 10^-8 becomes 8 on the y-axis. The dashed gray line indicates the genome-wide significance level, calculated as -log10 (5.0 x 10^-8), which equates to approximately 7.3. The highest two ‘towers’ in this figure show a region with, among other things, the CXCR6 gene (which plays a role in HIV) and a region at ABO, the gene that codes for the blood types (adaptation of a figure and text published elsewhere¹⁶).

Outreach & Communication
The team behind #COVID19 HGI is also a good example when it comes to Outreach & Communication. The #OpenScience approach almost automatically leads to a wider reach of science. All layers of the scientific community are approached, but patients and policy makers are also involved. Andrea Ganna’s team previously did this when they studied the genetics of “same-sex behavior”²⁰. A loaded topic that sparked fierce discussions on Twitter and in other media, but also one where – again – The BROAD Institute facilitated the debate and devoted an extensive blog to it²¹. #OpenScience is good for healthy scientific debate. Andrea Ganna’s team did not shy away from the debate, and from the outset tried to involve all kinds of stakeholders (including outspoken critics), witness https://geneticsexbehavior.info/. Spoiler alert: a “gay gene” obviously does not exist.

#TeamScience also means that old ranking systems and tools to measure scientists really do not work anymore – if ever they did.

Career & Rewards
#TeamScience also means that old ranking systems and tools to measure scientists really do not work anymore – if ever they did. #TeamScience and #OpenScience are Science in Transition through and through. The days of Leonardo Da Vinci are over, the Homo universalis has not existed for the past 501 years. To solve the big issues (#COVID19!) you need the expertise of many. And so, valuing the individual on the basis of rankings, impact factors, H-indices or his position on a paper is no longer appropriate.

Fortunately, many scientists and policymakers also recognize this issue. In November 2019 a position paper from NWO, ZonMW, NFU, and VSNU described a new plan to recognize and value researchers, in which quality takes precedence over quantity, and #TeamScience is just as important as the individual²².

This was also the prelude to the digital Symposium on the theme Career & Rewards, which YoungSiT organized on September 3^rd. More than 70 visitors listened carefully to the forthcoming plans of Utrecht University through Paul Boselie: in the coming 12 months, UU will take all kinds of initiatives to put the vision of the aforementioned position paper into practice. For example, the MERIT system will be introduced; a scientist should not be a five-legged sheep, nor a one-trick pony²³. The assessment of the scientist should be done on the basis of core domains (Management, Education, Research, Impact, and Team player), taking into account the personal preferences of the individual, who is not having to do everything excellently. Annemijn Algra (YoungSiT, resident neurology) presented the success story of the New Recognition & Valuation of assessing young doctors and researchers in training²⁴ as conceived by her and two other YoungSiT team members, Inez Koopman and Rozemarijn Snoek. Kristine Steenbergh²⁵ came to share the Young Academy’s vision on this subject. Lucille Mattijssen, chair of PhD Network Netherlands²⁶, shared the first results of a survey²⁷ among PhD students in the Netherlands, showing that many PhDs have burnout symptoms, among other things, fueled by the Old Recognition & Valuation²⁸. Just like Annemijn, Inze and Rozemarijn, Rick Bonants, partnering with Chiel van Hal, tries to give a head and tail to the New Recognition & Valuation, but this time in the form of a start-up, InSci, which is developing an online platform with which the scientific can be followed and assessed based on this new vision. Did you miss the Symposium? Don’t worry: you can stream the full-feature action movie again for free here.

Road to the Science of the Future
In short, #ScienceMatters. Now, in these days of#COVID19, but it is timeless. Humans are curious to the core and this urge to know ourselves and the world around us has led to fantastic discoveries (gravity and chloroplasts) and brilliant applications (velcro and MRI). Many questions about #COVID19 remain open, and only #OpenScience and #TeamScience will be able to answer them. What if the Russian vaccine unexpectedly gives side effects²⁹? Will society then lose faith in vaccination? What are the psychological effects of working from home for a long time and little social (and physical) interaction? Do apparently healthy top athletes indeed have an inflamed heart muscle due to #COVID19³⁰? What does the correlation between a high BMI and a higher risk of dying from #COVID19 mean? What is the role of blood types and the risk of death from #COVID19?

Despite (or thanks to?) #COVID19, hundreds of scientists from different disciplines are now working together even more efficiently and purposefully to tackle the pandemic.

Despite (or thanks to?) #COVID19, hundreds of scientists from different disciplines are now working together even more efficiently and purposefully to tackle the pandemic. This often happens “remotely” and concepts such as “let’s zoom” are now commonplace. Ultimately, the begeisterung – this primal passion that drives and energizes a scientist – wins from the dreadful cuts³¹, the tremendous workload³², political stunts^33,34, populist demagoguery³⁵, and the pandemic. Post #COVID19 only a few remain in the Elfenbeinturm.

#COVID19 shows that #OpenScience and #TeamScience are the key to scientific success and a successful society – now, at the time of this pandemic, and in the future. Knowledge is power, and knowledge is freedom.

Sander W. van der Laan, @swvanderlaan

Faculteit Ambassadeur Open Science Community Utrecht, @OpenSciUtrecht

Member of Young Science in Transition, @SciTransitYoung

References

1.   University, J. H. COVID-19 map-Johns Hopkins Coronavirus Resource Center. (2020).

2.   Soderbergh, S. Contagion. (2011).

3.   COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxiv. https://connect.biorxiv.org/relate/content/181.

4.   Internationaal onderzoek met BCG-vaccin tegen COVID-19 bij zorgmedewerkers ook van start in Nederland – UMC Utrecht. https://www.umcutrecht.nl/nieuws/studie-naar-tuberculose-vaccin-tegen-covid-19.

5.   Studie naar relatie corona/hart- & vaatziekten. https://www.umcutrecht.nl/nieuws/studie-naar-relatie-corona-hart-vaatziekten.

6.   Linschoten, M. & Asselbergs, F. W. CAPACITY-COVID: a European Registry to determine the role of cardiovascular disease in the COVID-19 pandemic. Eur. Heart J. 41, 1795–1796 (2020).

7.   Corum, J., Grady, D., Wee, S.-L. & Zimmer, C. Coronavirus Vaccine Tracker. The New York Times (2020).

8.   Seladi-Schulman, J. Clinical Trial Phases: What Happens in Phase 0, I, II, III, and IV. https://www.healthline.com/health/clinical-trial-phases (2018).

9.   Wikipedia contributors. Phases of clinical research. Wikipedia, The Free Encyclopedia https://en.wikipedia.org/w/index.php?title=Phases_of_clinical_research&oldid=977553623 (2020).

10. Russia’s approval of a COVID-19 vaccine is less than meets the press release. https://www.sciencemag.org/news/2020/08/russia-s-approval-covid-19-vaccine-less-meets-press-release (2020).

11. How Broad Institute converted a clinical processing lab into a large-scale COVID-19 testing facility in a matter of days. https://www.broadinstitute.org/news/how-broad-institute-converted-clinical-processing-lab-large-scale-covid-19-testing-facility (2020).

12. Broad COVID-19 Testing Dashboard. https://covid19-testing.broadinstitute.org/.

13. COVID-19: the EU’s response to the economic fallout. https://www.consilium.europa.eu/en/policies/coronavirus/covid-19-economy/.

14. van der Laan, S. W. Van der Laan & Science. https://swvanderlaan.github.io/ (2018).

15. Home. https://www.covid19hg.org/.

16. Ellinghaus, D. et al. Genomewide Association Study of Severe Covid-19 with Respiratory Failure. N. Engl. J. Med. (2020) doi:10.1056/NEJMoa2020283.

17. Shelton, J. F. et al. Trans-ethnic analysis reveals genetic and non-genetic associations with COVID-19 susceptibility and severity. Infectious Diseases (except HIV/AIDS) (2020) doi:10.1101/2020.09.04.20188318.

18. Asselbergs, F. W., van der Laan, S. W. & de Bakker, P. I. W. Uitvoering en nut van genoombrede associatiestudies. Ned. Tijdschr. Geneeskd. 158, A5821 (2014).

19. Kamb, A., Harper, S. & Stefansson, K. Human genetics as a foundation for innovative drug development. Nat. Biotechnol. 31, 975–978 (2013).

20. Ganna, A. et al. Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior. Science 365, (2019).

21. Perspectives on the complex genetics of same-sex sexual behavior. https://www.broadinstitute.org/news/perspectives-complex-genetics-same-sex-sexual-behavior (2019).

22. Erkennen en waarderen in de wetenschap gaan drastisch veranderen. https://www.scienceguide.nl/2019/11/erkennen-en-waarderen-moet/ (2019).

23. Meer waardering voor de wetenschapper. https://www.uu.nl/opinie/meer-waardering-voor-de-wetenschapper.

24. 林琳, 何书金, 朱晓华 & 王岱. Nature Index 对科技创新评价的意义与思考. 中国科技期刊研究 26, 191–197 (2015).

25. Steenbergh, Dr. K. (Kristine) —. https://www.dejongeakademie.nl/nl/leden/leden/15242.

26. Anneveldt, K. Lucille Mattijssen new president of PhD Network Netherlands. https://hetpnn.nl/en/2019/09/24/lucille-mattijssen-nieuwe-voorzitter-promovendi-netwerk-nederland/.

27. PhD Survey 2020. https://hetpnn.nl/en/phdsurvey2020/.

28. Anneveldt, K. Press release: Nearly half of PhDs have increased risk of mental problems, 40% have considered quitting. https://hetpnn.nl/en/2020/08/26/persbericht-bijna-helft-promovendi-heeft-vergroot-risico-op-mentale-klachten-40-overweegt-te-stoppen/.

29. BBC News. Coronavirus: Russian vaccine shows signs of immune response. BBC (2020).

30. Penn State clarifies remark by doctor about myocarditis and covid-19 positive Big Ten athletes. The Washington Post (2020).

31. EU leaders slash science spending in €1.8 trillion deal. https://www.sciencemag.org/news/2020/07/eu-leaders-slash-science-spending-18-trillion-deal (2020).

32. Werkdruk in hoger onderwijs onverminderd hoog door corona. https://www.scienceguide.nl/2020/09/werkdruk-in-hoger-onderwijs-onverminderd-hoog-door-corona/ (2020).

33. Dennis Wiersma: ‘Ik heb het gevoel dat ik het nooit goed kan doen in het hoger onderwijs.’ – ScienceGuide. https://www.scienceguide.nl/2020/09/dennis-wiersma-ik-heb-het-gevoel-dat-ik-het-nooit-goed-kan-doen-in-het-hoger-onderwijs/ (2020).

34. Sigrid Kaag: ‘D66 heeft het wetenschappelijk onderwijs teleurgesteld’. https://www.scienceguide.nl/2020/08/sigrid-kaag-d66-heeft-het-wetenschappelijk-onderwijs-teleurgesteld/ (2020).

35. ‘Normaliter reageer ik niet op een politieke proefballon’ – ScienceGuide. https://www.scienceguide.nl/2019/04/vrijheid-in-het-onderwijs/ (2019).