On July 2, 2022, we retracted a paper we published last year in Evolution https://onlinelibrary.wiley.com/doi/10.1111/evo.14551. The reason I wanted to write this post is to explain what happened and how we dealt with it and thereby to help normalize honest retractions which should probably be more common. I’ll give a little detail on the experiment and then focus on the human side.
The experiment was an exciting one. We took several clones of the social amoeba we study, Dictyostelium discoideum, cured them of the bacteria that they carried symbiotically, and then let them proliferate through many generations isolated from their bacteria. We also took those same bacteria and let them proliferate on their own for many generations. If you evolve to make your partner worse when reintroduced, you would originally have been adapted to cooperate with them. And if you evolve to harm your partner less when reintroduced, you would originally have been adapted to exploit them. We feel it is a new approach using lab evolution to understand what originally happened in the wild.
We got a clear experimental response and published the paper. It was only later when we decided to sequence the lines to see what changed that we discovered the problem. Sequences from lines that should have been Paraburkholderia. hayleyella turned out to match P. agricolaris. There had been cross contamination. This was not a rare event but impacted all the P. hayleyella lines. By the time we did the final experiment mixing host and bacteria, all the bacterial lines were predominantly P. agricolaris. This might be an almost predictable problem because P. hayleyella has a very slow growth rate away from its Dictyostelium host and also has other signs of being well on its way to being an obligate symbiont. P. agricolaris, by contrast, grows fine on its own so a tiny amount of contamination could overwhelm P. hayleyella.
Here are some reflections from the very honest and brave graduate student who discovered the problem and shared it with us.
Retraction has a stigma about it. We’ve developed science with self-correcting mechanisms that are robust to misconception. Part of that means being honest about our errors. When I discovered the contamination, I could have quietly moved on and likely nobody would have ever known. Some selfish, anxious part of me wanted to do that. But I believe in the importance of intellectual honesty and owning my mistakes and never seriously flirted with the idea of burying them.
That is not to say it was easy. First, discovering the problem was a gradual process, in part because it did not even occur to me that something I had spent so much of my time and self-esteem on could have gone so awry. Early clues that something was wrong troubled me but were easy to explain away as some lesser error, particularly because the sequencing analyses that ultimately revealed the contamination were new to me. The first few results that did not turn out as I expected I assumed were because I had made some mistake in my code, had failed to set some needed argument, or failed to understand one of the multitude of assumptions inherent to doing bioinformatics. Each would send me off on some tangent trying to understand some new aspect of the program I was using.
Eventually, though, the simpler, uglier explanation occurred to me: I had messed up. I had messed up bigtime. Not with a few lines of code that could be fixed with some careful Google research. I had messed up the experiment itself, many months and dollars ago. Once that possibility had occurred to me all of my recent weird results made sense, and it was easy to confirm the worst. We would have to retract the paper.
Naturally I felt like a failure. I knew that I had done the research in good faith, and I believed that the ideas behind it had genuine merit, but I could not shake the idea that I had let down people who had invested in me. I’ve had to deliver the news to laymen and scientists alike – professors, post docs, fellow grad students, family members, the editors of the journal where we published the contaminated results. The response has been uniformly supportive. Nobody (but me) has scolded me for poor technique or for wasting time or money. Instead people have made excuses for me (“was it because of COVID?” was a popular one.) Nonetheless, the feeling that I had sinned was a hard one to dispel.
Here is the silver lining: I learned something, which is what science is about. I learned that the stigma I perceived was predominantly coming from my own ego. I learned how kind people could be about an honest mistake. I did the right thing, and none of the awful consequences I imagined following came to pass. I insisted on eating at least some crow (No, it wasn’t because of COVID), but in the end what really matters is the science and getting it as right as possible. Avoid mistakes with careful science. Correct them with honesty and humility. Have some faith that your fellow scientists will understand. And then get back to the lab.
What is the moral of the story? Do your best. Think hard about all the ways you can verify that your experiment does what you think it does. When problems are discovered after publication, retract the paper and do the experiment over if it is a good one. Treasure and support students that show their honesty and conviction when they point out their own mistakes. There should be no shame in an honest retraction, though there will always be regret.