Minding the scientific skeleton in the closet

Categories: guest blogger
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Published on: October 22, 2013

Two weeks ago, Pamela Roland from UC Davis retracted a Science paper originally published in 2009. She gave her perspective on the events leading to the retraction in a Scientific American blog post. Here a post-doc in her lab gives his side of the story, emphasising the importance of teamwork, honesty, and willingness to speak up at every level of the academic hierarchy.

Benjamin Schwessinger obtained his PhD at The Sainsbury Laboratory, under GARNet Advisory Committee member Cyril Zipfel. He joined Pamela Roland’s UC Davis group in 2011. This post is an edited version of DO mind the scientific skeletons in the closet, originally published on the blog he co-hosts with Ksenia Krasileva, a postdoctoral fellow in Jorge Dubcovskey’s lab.

 

Yet another Science paper retracted today. Nothing much new unfortunately – except that for me and my colleagues this was not just another example of non-reproducible work. We planned our research projects around it. So here are my thoughts about this, and just in time for Halloween.

There has been much talk about the problem of reproducibility of data and the rise in retractions. The discourse is mostly centered around the perpetrators and the negative impact this sloppy or knowingly flawed science has on the industry and the perception of scientific endeavor in society: Who did this awful study? What reviewer did not catch this missing control, the sloppy stats? Why don’t they admit their mistake? What’s wrong with peer-review? Well, much is wrong with the industry, and many people have great ideas about how to tackle some of these issues.

What is usually missed from the discussion is the impact such dubious science can have on young, early career scientists. What do you do if you come to a famous (or not so famous) lab, you get a project, which is based on fantastic data and high impact publications, but you cannot reproduce it? How do you approach this issue? What does it mean for you and your career if your project goes to shreds because it’s based on bad data? Do you get another chance? Will you be forever associated with this flawed data and your reputation damaged? Will you get so disillusioned with science to the point that you leave academia? Do you try to fix the problem or silently move on? Do you tell the boss and explain your situation? Or is it you? Can you just not get it to work? Can it really be that this is all wrong? Why cannot I reproduce this data? And the questions go on and on … I think everyone can appreciate the complexity of the issue. Many people I talked to had their own experience to share.

Here is what’s frightening:  sloppy science and misconduct, I thought, is something you read about in journals and not something I would experience myself. This would never affect me or close friends in other labs, who are all great scientists in my eyes. I was wrong.

We young, early career scientists in our lab went through a very serious and fairly high profile example of this recently. In mid 2011 to beginning 2012 we joined the lab of Pamela Ronald during a huge turnover of people. Everyone of the ‘old crew’ of many years left or were about to leave around the time we came in. We were all super excited to get going and to push the borders and boundaries of science

However, no matter how hard we tried, our data did not add up and we could not make much sense of it in the view of the lab’s recent publications, which had appeared in Science and Plos One.

/// Here is a three sentence summary of the relevant research: The lab cloned an amazing immune receptor XA21 in rice that confers resistance to the most important pathogenic bacteria of rice (Xanthomonas oryzae pv. oryzae) in 1995. In 2009 they published the identification of the bacterial protein Ax21 as ligand of this immune receptor. In 2011 they reported the function of this bacterial protein Ax21 as a novel cell-cell communication factor (also referred to as quorum sensing factor) in X. oryxae pv. oryzae. ///

We, as a group of concerned early career scientists in the lab, brought this discrepancy regarding the 2009 and 2011 studies to the attention of our PI and explained to her what we thought was wrong. We began a long, intense, careful, multifaceted, repetitive and diligent truth-searching endeavour – I won’t bore you with the details. In short, we were not able to reproduce the core findings of either Ax21-related paper. Of course, this was very distressing for everyone involved, especially as other people had published similar work in relation to the Ax21. As an aside, I am not sure what this says about the current state of science. I find it very concerning.

Kudos to our PI Pamela Ronald, who reached the only scientifically correct decision and retracted both papers. She received much praise for this brave step. For sure, not every PI would have followed through in a similar situation. Pamela Ronald’s decision became the topic of the inaugural post in the new category ‘Doing the right thing’ on the famous ‘Retraction Watch’ blog. You can read her perspective on how this whole story unfolded in her guest post on the Scientific American blog. I can only applaud Pamela Ronald for making the right decision and retracting these two papers.

What I would like to highlight is the importance of clearing the scientific record once mistakes in publications are discovered. People should not fear speaking up, but rather be rewarded for doing so. I am sure every reader of this blog knows of multiple scientific skeletons in people’s closets. It takes much courage from the PI’s perspective to bring these mistakes out in the open. They potentially have much to lose, of course… but the PI will have the time to correct the situation.

On the other side, what’s going to happen to the early career scientists who just fell into one of these situations? Who is routing for them? What happens if the PI does not retract the paper(s) and disregards the concerns? I know of least of one person, a friend of mine, to whom this exact thing happened. Finally she left academia, because there was no support and no way out.

Young scientists can be treated like a dispensable commodity if they don’t play along. Of course, this is the worst-case scenario, but once you are trapped in the non-reproducibility hole you will lose a lot of time no matter what. You might be asked to repeat experiments multiple times, generate the same material anew, and spend a lot of time on research that is hardly publishable – no impact factor for retractions! No one can give you this time back, and many people will not understand why you aren’t moving forward.

Only once everything is cleared up will you be able to move on with your career, and hopefully without losing too much. This is the only way out, and it is important for PIs should be aware that they are not only dealing with their own careers – thanks again to Pamela Ronald for taking the courage.

In summary, it is not only the PI’s but also the early career scientists’ significant efforts and courage that leads to the clean-up of the scientific record. Be diligent in these situations. Talk critically with your co-workers in the lab. Verify your own stock and everything given to you. Perform the right controls. Ask for advise from other senior colleagues. Follow your understanding of science as a truth-finding endeavour. This journey won’t always be linear and sometimes mistakes happen. If they do, deconstruct them, correct them, learn from them and build something new. In my opinion, this is what truly makes a reputable scientist.

P.S. So let’s figure out what’s really going on with this amazing rice immune receptor XA21. For the love of wisdom.



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