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.
You are real-life heroes. If there was an Olympic for the sciences, you’d be lighting the flame. Everyone should read and learn from you.
Kudos! Sorry that it had to happen but it’s great to see science working as it should.
Kudos to you! 🙂
This is very nice, Joan. Science is a collective and inherently social activity wherein we strive to understand how nature works a bit better, using protocols that often deliver verifiable evidence that reduces our collective ignorance. But it’s a PROCESS and, because it’s a human activity, an imperfect one. That means that we are sometimes simply wrong, usually because of some flawed (tacit!) assumption(s). There are two inevitable consequences of this imperfection. First, what we think we have learned today may prove errant tomorrow when somebody else finds a different result and, ideally, reveals the overlooked assumption. We should be gracious when that happens, just as we hope they’ll be gracious when we correct one of their mistakes. Second, we should remind ourselves that ALL scientific inferences are at least formally provisional, so when we are fortunate enough to uncover our own mistakes, we should own up to that — as you have done — and save everyone some time and trouble.
Something like this happened to me long ago. Initially I planned a five-chapter (five paper) Ph.D. thesis that included an analysis of “graded’ vs. ‘discrete’ heron/egret displays. That particular chapter won the very first AOU Best Student Paper award at the 1975 national meeting. But when I actually WROTE up that manuscript, I decided that I didn’t really think the argument was sound, so I simply left it out of the dissertation (after discussing the pros and cons with my major professor). This was not a public embarrassment (and thus not heroic) as your retraction must feel, but it was a conscious decision to raise my personal standards. I have never regretted it for a minute. To have continued with the process and reaping one more publication at an early career stage, I would have betrayed the collective trust. What would be the point of devoting my professional life to science if I had done otherwise?
HI Doug, Interesting story. We all have arguments that fail on closer inspection. Science is hard. I don’t think our actions were particularly heroic. For me it is part of my ongoing theme of revealing how science is done and what the academy is like. I figure if I make a mistake, others probably make similar ones sometime in their career, so I wanted to share how we dealt with it. Dave felt the same. Our grad student viewed it as a chance to tell the story. And really this is so much better than having a retraction someone stumbles on and wonders what the story was. So it was hard and embarrassing but better for us, better for science, and better for scientists.
Congratulations! only a scientist with a real-life science sense could retract a paper with honor.
Thanks for sharing your teaching with us.
I really appreciate reading this, it gives me hope for humanity.
Thank you. And well done.
Joan, you are a true scientist! I wish there were more like you.
Joan, this was an excellent post, and a tribute to your team and especially to your grad student. Hard? Yes. Honest? Yes. A boost to science, yes. And I’m pleased about the response received. It’s important to recognize efforts like this, to correct the record.
Science, probing the truth, is an ever changing process. Finding a result based on the current accepted phenomenon may change when new phenomenon arises. Observing the flaw in our own findings shows our continuous and concrete proceedings of the same work. It is the real research one should probe to find new phenomenon in depth. As you did, you set a record that every researcher in future will come forward to present their progressive work with constructive modifications, which is a healthy move in the scientific community. Hearty congratulations.
Inspirational. This person’s future research findings will be all the more credible and valuable for knowing they come from someone who is intellectually rigorous and honest.
Congrats for the humility.Way to go for scientists most of whom prefer to hope against hope that someone smart who tries to stand on the result in the future will discover ,much to their casyernation,its clay feet, or an attentive peer reviewer wont poke holes in our hypotheses. Infact trust some of us to come up with undignified reactions when our methods or results are somehow or authoritively questioned!
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As my campus’ IRB Chair, I send my congratulations – we should have awards for this responsible research. Do share this with RetractionWatch, a blog that highlights the opposite behavior…
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Joan writes: “I figure if I make a mistake, others probably make similar ones sometime in their career.”
I agree, we all make mistakes sometimes, even the most rigorous and clear-thinking scientists. The problem is: too many scientists think they need to hide their mistakes, and too many scientists try to bury mistakes, shortcoming, and outright f-ups while writing up research for publications. This was not the case here, and retracting the publication is no blemish.
I wish more resarchers were like this. I know a long list of researchers who would benefit from readig this post.
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Are we saying this is not happening all the time? Oh dear.
We’ve two influences to consider here, and stigma is the external one, a social force, a sanction imposed by others. The corresponding internal force is psychological, guilt. Ideally, guilt makes us confess when we’re shamed, or even beforehand, in anticipation of facing shame if we’re caught. But a problem follows in that shame is lifted once the appropriate guilt is shown, while stigma may be imposed permanently. And that’s without the unjust stigmas put on people for circumstances beyond their control, e.g., schizophrenia.
Unfortunately, sloppy work and outright scientific fraud have become more frequent, or at least more frequently discovered and publicized. So there’s a lot of suspicion, and even an honest practitioner admitting a mistake isn’t guaranteed forgiveness. Careers can end in our rampant cancel culture. This creates pressure to hide mistakes, and I think it took real courage to admit the mistake made here.
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Thank you for standing true to TRUTH.
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