Wednesday, November 16, 2022

20 years of open science or how we haven't radically changed the way we do science online

Around 20 years ago I was a starting PhD student and it was an exciting time for the internet. It was the time of blogs, wikis and a large increase in public participation with more user generated content in what is commonly known as the start of Web 2.0.  These were the times of web based online communities such as the now defunct Kuro5hin or the great survivor I started this blog 19 years ago and I was also "hanging out" in an online community called Nodalpoint. Nodalpoint no longer exists but it was a discussion forum/wiki for bioinformatics with some of these discussions still preserved thanks to the magic of the way back machine. 

Around the time of 2002-2006 all of the excitement around Web 2.0 was also infecting academia with many discussions around open science. I know that open science is a vague term that can mean many different things including open access, citizen science, open source and many others. One specific aspect that I want to focus on is the idea of organizing research in a way that is not based on local group structures. In 2005 I wrote a Nodalpoint post on "Virtual collaborative research" which is similar in spirit to open source software development but with a focus on discovery not tool development. Part of this would mean surfacing more of our ongoing research and taking part in research projects that are not organized by traditional research group structures. The idea of being extremely open about ongoing research activities was advocated by others under the term of "open notebook science".

Over the following years I made a few attempts at starting such open research projects with blog posts where I tried to set up tools and ideas where others could take part in (see posts from 2007, 2008 and 2010).  The last project idea I tried to propose in such way ended up being one of the major projects from my postdoc and basically one of research lines I am still working on. In the end, none of these attempts really took off as open collaborative research projects. In hindsight, I am not surprised it didn't work. Even within local structures of research institutes and university departments there is so much discussion on incentives for local collaborations. While I think the traditional structures for organizing research do work, as a PhD student and postdoc I was very frustrated by the apparent difficulty of making the most of everyone's expertise. As a group leader I have more capacity to establish collaborations but I still think we aren't using the internet to its full capacity. 

So what happened in the decade from 2010 to 2020 ? Blogs and online communities mostly died out and Web2.0 was swallowed by corporations. One major change was the rise of large social networks and the standardization of the stream as way for people to share information and interact. Academia started participating in social networks around the time of Friendfeed (2007-2015) and such participation become mainstream with the popularization of Twitter. I honestly would never have predicted the rise of academic twitter and it is truly a sign of how the geeks have inherited the earth. 

The reason I am even thinking about open science these days is that over the past couple of years we have been involved in projects that have illustrated this potential of large collaborations empowered by the internet. I wanted to write this down also to have something to come back to in the future. The first project was a study of phosphorylation changes during SARS-CoV-2 infection. Like many others, when the pandemic sent our research group home, I though about what we could do to help and sent emails to a few people that could be working on the topic. Nevan Krogan, my former postdoc supervisor, was very keen to involve us which lead to several projects including this study of protein phosphorylation. This was probably one of the most exciting projects I have been involved with and included a very spontaneous collaboration among a large international team coordinated by a few people through slack. In this case the network of interactions was provided by Nevan and it was possible because everyone was pushing in the same direction triggered by a catastrophe. I wish everyone could feel the sense of power that I think we felt during this project. There was so much scientific capacity at the disposal of this single project and we could iterate through experiments and data analysis at an incredible pace. It is even hard to express how it felt to be able to just get things done when you had the world experts for what was required to do at every step. 

A second even more interesting example was a community effort to study the value of AlphaFold2 in a series of applications. When AlphaFold2 was released, several scientists started sharing their early observations of how AlphaFold2 and predicted structures could be used for different applications. I though all of these examples were really exciting and that we could structure this output into a manuscript. So I just contacted people that were doing this and also asked on social media if anyone else wanted to participate. In the end every contribution to this was quite modular and it was easy to integrate this into a manuscript with a few meetings and a google doc to put things together. Perhaps the less usual thing that happened was receiving actual results through Twitter chat. 

I think both of these examples required a trigger - the pandemic and the release of AlphaFold2 - that led to many scientists moving in the same direction.  In both of these cases I think we achieved in a few months what would take a single group potentially one to several years to do. Yet, these interactions remain difficult to make. Perhaps simply because we are just too busy with our own research questions or more likely because of the importance of credit and evaluation systems in academia.  These days I am actually less in favor of radical sharing of ongoing research, in the spirit of open notebook science.  I don't think we have the attention span for it. It would be too difficult to navigate and may lead to more "group think" instead of divergent thinking and ideas. Maybe the simple existence of social networks like twitter are already a good step forward. I certainly get to know more people and what they may be up to via this. Lets see what the next 20 years bring.