ATG Interviews Elizabeth Bik

Science Integrity Consultant, Harbers Bik LLC

Interview conducted by Michael Upshall (ConsultMU)

Transcript edited by Leah Hinds (Executive Director, Charleston Hub)

The following is a lightly edited transcript of an excerpt from ATG the Podcast. The video for this episode can be found at https://youtu.be/uEYsqTKHits?feature=shared.

This episode features guest host, Michael Upshall, Community and Outreach Manager at Core, who talks with Dr. Elisabeth Bik, Microbiologist and Science Integrity Consultant. Elisabeth is a prominent microbiologist and renowned investigator into scientific misconduct, particularly the manipulation and falsification of research data. She has uncovered issues in over 8,000 scientific papers, resulting in more than 1,400 retractions. Her work has gained international attention, earning her the 2021 John Maddox Prize and the 2024 Einstein Foundation Award for her work. This conversation explores Elisabeth’s career trajectory, her work on identifying scientific malpractice, and her thoughts on the systemic issues and potential reforms within the research and publishing ecosystem.

MU: Okay, well, welcome to ATG the Podcast, and I’m very pleased to have today the chance to talk to Elisabeth Bik, who’s one of the best known investigators into scientific malpractice. Elisabeth is a PhD microbiologist, but is better known today for identifying issues with more than 7,000 scientific papers and with over 1,000 retractions. She’s been featured in national newspapers, such as the New York Times and The Guardian, and she was awarded the 2021 John Maddox Prize for her work in science communication for exposing research misconduct. So good to talk to you, Elisabeth.

EB: Great to be here, Michael. Lovely. Good morning from California. It’s quite a time difference.

MU: Yeah, absolutely. Tell me, how did you become a scientist in the first place?

EB: Well, I guess I always wanted to be a biologist. When I was, I think, I don’t know, ten years old or so in elementary school, the teacher asked, what do you want to become? And you know, the boys wanted to become firemen or pilots, and the girls maybe wanted to become, we’re talking about the 1970s here, pretty stereotypical, maybe a nurse. But I wanted to become a biologist. So, I was already the weird one out. And I stuck to my plan and studied biology. Initially, I wanted, I liked birds, so that was what I thought I was going to do for the rest of my life. But then I really liked bacteria, and I liked my microbiology teacher very much and I liked the classes. And I, yeah, I just stayed, I loved lab work. I did internships in labs, really loved that. And then stuck in one of the labs at the Dutch National Institute for Health and did my PhD there.

MU: Your PhD was on, I believe, cholera. Which doesn’t sound the most enticing of subjects to spend years of your life studying.

EB: No, it’s a haunting topic. If you read about cholera and what it can cause and how horrible the disease is, it’s quite something that will stay with you for the rest of your life. If you read those descriptions of patients dying. And cholera also is not a disease that is really present in the Netherlands where I was at that time. But it was a topic, a research project that the person who became then my mentor, my PhD supervisor, wrote and it was approved. And he said, I think you’re the perfect person for it. Do you want to do your PhD on that? And it was about developing a vaccine for cholera, which we thought was a good thing, because we were working at the Institute that made all the vaccines for the Netherlands. So, but it turned out, of course, a little bit different. My topic, the vaccine part of my PhD thesis, didn’t work out. That was, I could not reproduce somebody else’s results. And that was quite frustrating. But luckily, another topic related to cholera came along, and I had much more success there and finished my PhD in that topic.

MU: That’s very interesting. So, you found lack of reproducibility actually made quite a difference to you.

EB: Absolutely. It was very frustrating; you see somebody else’s results, and I did exactly what that person before me did. And one day it worked, and this next day didn’t work, but I had to do ten replicates or so. It was just all over the map. And I said, I’m not quite sure what I do wrong, because I did exactly the same thing. So, there must be something very finicky that, you know, maybe it works on a Tuesday, but not on a Monday. You’re just starting to believe in all kinds of voodoo, of course. But yeah, it didn’t work out, I could not reproduce it. That was one of those points in your PhD, where you’re just ready to give up everything because it didn’t work.

MU: I can imagine. So, you then worked with microbiomes. And for the benefit of non-technical people like myself, can you tell me what a microbiome is?

EB: Yes, that was when I moved to the U.S. and started working at Stanford. A microbiome is a group of organisms, like an ecosystem, that lives at a particular place. So usually we refer to it, to the human microbiome. The bacteria that live in our bodies, in our mouths, on our skin, in our stomachs, in our guts, that’s where most of them live. They help you digest your food and they do some wonderful things. They can also, if there’s a bad bacteria or bad virus in there, they can make you sick. But it’s like a forest. It’s an ecosystem of different species. And we still know very little about them because it’s not just one species that lives in our guts. There are probably thousands of them. Each of us has a unique collection of these bacteria and viruses and archaea and some yeasts in there. It’s a very complex situation. And each of these species has their own little biochemical factories in them. They can convert certain molecules into others. So, depending on which bacteria you carry, you might be able to convert, let’s say, a particular drug into a drug that is actually more active or less active. the microbiome that we carry and its uniqueness might be partially explaining why certain drugs don’t work in a person, but work in the other person, or why certain foods are maybe not going down well. And we’re still learning lots about it. It’s a fascinating topic.

MU: You spent 15 years at Stanford, and this is working with microbiomes. So why leave after that time?

EB: Because I saw a job advertisement for a scientific editor at a very new startup company called uBiome. And it didn’t end well, uBiome. But at that time, it was a nice startup. After working 15 years at a particular place, I just felt I couldn’t grow anymore there at Stanford, or at any university, I guess. In the U.S., you have a professor, and then you have the people working in their group. I felt I wasn’t learning anything more. And also, the topic changed a little bit more from less lab work and more bioinformatics work, which I just was never trained in, so I felt very uncomfortable trying. I was trying to learn it, but I just felt I didn’t have enough background to really enjoy using it. I wasn’t a Unix guru. You run into all these issues where your computer just says, nope, error. And I just couldn’t do that. I really liked doing the lab work, but that was less and less of it. I saw this job advertisement, and I really had started to enjoy scientific writing, peer review. I also was looking already at shoddy, bad papers. And so, the whole process about scientific editing and publishing became a little bit more interesting. And it was a job at a microbiome startup. There was a nice salary involved, much better than what I earned at Stanford, and what was not to like, and I got the job. I really liked the first year. The second year, the company was starting to do some shady stuff with insurances and prescriptions, so I left. And at some months after I left, the company got raided by the FBI, quite something, they confiscated all the computers, and of course, never recovered from that. And the founders fled to Europe, apparently, and from the U.S., this was in San Francisco. They were charged with, or at least indicted, and I, you know, I’m not a lawyer, so I don’t know the difference, but they were indicted with all kinds of insurance fraud, and money embezzlement, so all kinds of bad things.

MU: You already had exposure to research, and I don’t know if you can call it research misconduct, but non non-replicability. Was that something that started to develop during your time at Stanford, or when?

EB: Yeah, it was during my 15 years at Stanford, that I came across a paper that had plagiarized one of my papers. I’d written this review article on the human microbiome, my topic of interest. I’d heard about plagiarism, and I had a vague concept of what it was. But I thought, let’s just take a sentence from my review article, and put it in between quotes in Google Scholar, and probably nothing will come up, right? But something else came up, something that was not my paper, but somebody else’s paper that turned out that these authors had stolen several sentences from me, but also from other scientists, and made this patchwork of this Frankenstein monster of different paragraphs. That made me so mad that I started to work on plagiarism as a hobby. I started to find other plagiarized articles. Now, this was 2013. I’m finding all these articles from 2006 or so, before most journals and publishers were starting to screen for plagiarism. I was finding all these old, plagiarized articles. But then one day, another coincidence, I found a PhD thesis with not only plagiarized text, but also an image that had been duplicated. I recognized that, and it was a western blot, a bit of a technical term. But it had basically looked like horizontal stripes, four horizontal stripes with a little dot in the top right corner. And then a couple of pages later, I’m like, hey, there’s that same photo again, except now, it’s, it’s a mirror image. Now the dot is on the top left, but it’s the same photo. It was used to represent a different experiment, so that was bad. And then I switched, because I switched from plagiarism searching to searching for these duplicated images.

MU: Tell us a bit more about the wonderfully named western blot, because that seems to be quite a central part of your work on image manipulation. What is a western blot?

EB: What is a western blot? Well, how long do we have? It’s a way to determine how much of a particular protein is present in a biological sample. Let’s say you’re testing mice, and you’re treating them with your drug, and you have your placebo group. So, you have two groups of mice, one that was treated and one that was not treated. But you want to see how the treatment of the drug affects the expression, or let’s say, roughly the quantity of a particular protein. That’s when you use a western blot. In a western blot, you run first your soup of proteins, let’s say it’s a serum sample or a liver sample from these mice, and you homogenize that. You run it in an electrical field. All the proteins will separate like a barcode, according to their weight or the height or the length of the molecule. First, you separate them like that. So, it looks then sort of like a barcode with different proteins all in a row. Then you transfer that gel to a membrane and you incubate it with a particular antibody to just search for your one protein that you’re interested in, in that big soup. Now, of that whole barcode, you only visualize one of the bands. The outcome is a film, and it starts to look like horizontal stripes, dark horizontal stripes on a white or light gray background. It will become a photo, and the photo of that western blot will show your five treated mice and your five untreated mice. Just that one stripe, that one little horizontal band, that is the protein of interest. And so, it’s a photo in a scientific article. Very often I find that there’s problems with these photos. Sometimes photos are reused to represent another experiment, like the one I initially found, or they are rotated, mirrored, stretched and representing different experiments. Or they’re even photoshopped where one band, one of those horizontal stripes, is photoshopped a couple of times. It basically looks like a photo of a dinner party to me, where you see the same people, you know, Uncle John is sitting both on the left side of the table, but you also see his face on the right side of the table of your photo of your dinner party. And that just doesn’t look right. It looks like the same, in this case, the same protein band visible twice in a photo. So that is what I’m looking for.

MU: It seems incredible to me that as an outsider, that anyone can even contemplate doing this kind of image manipulation. Why do you think, I know this is a tough question, but why do you think it takes place?

EB: I assume that people do it because then the results look better. Scientists might do an experiment, they might have a very firm hypothesis, they think they have an idea how a particular molecular pathway works, or whatever, and they do their experiments. And now the outcome is not as nice, or maybe it looks okay, but the blot looks smudged, or there’s a crack or a hair, and maybe they just try to Photoshop the crack or the hair away. They try to beautify it, or they might try to make the experiment look a little bit better than it actually was. Because if an experiment looks good, it’s easier to publish it. And if it’s easier, if it looks really good, you can even publish it in a high impact factor journal. And that is very good for one’s career. So Photoshopping in the end will enhance your career and just to make some shortcuts there. It’s tempting to do it, because it is possible within the digital age, you can actually easily Photoshop your experiments. You know, in the olden days, you brought your blots to the photographer in the basement, like I did, but now you can just take a photo with your cell phone and Photoshop at home and it’s very easy. Who will ever find out? Well, sometimes, I will find out about it.

Editor’s Note: Thank you very much to Michael Upshall for hosting this interview, and to Elisabeth Bik for speaking with us. Please tune into the podcast at https://www.charleston-hub.com/ podcast/atgthepodcast-266-a conversation-with-dr-elizabethbik-science-integrity-consultant-and-microbiologist/ to listen to the entire conversation, or watch the video at https://youtu.be/uEYsqTKHits?feature=shared