Thread by @MicrobiomDigest

Hi everyone! I am Elisabeth Bik, PhD, a science integrity consultant and volunteer.
In this thread for #YoungScientistNetworking (invited by @QuantumTessera), I will tell a bit about my somewhat unusual career.
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I was born in The Netherlands. My father was a family MD with home practice. My mother tutored in Greek and Latin.
In the morning, patients would line up for the walk-in hours, and in the afternoon my dad would drive around town to visit patients at their homes.
Our home:
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Sometimes I would sit in my dad's car doing homework, while he was driving around. Growing up in a doctor's practice, I was interested in biology and medicine, but I did not like the interactions with (demanding) patients. So I chose to study biology @UniUtrecht.
Me at 6y old:
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@UniUtrecht Microbiology and molecular biology were my favorite topics in college. This was in the mid-80s, so molecular biology was a bit different than nowadays. In fact, it was such a new topic, that it still fell under Chemical Biology.
I also had crazy 80s hair! Me at 23 years old.
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@UniUtrecht I did two different internships @UniUtrecht and @RIVM (Dutch NIH), working on in-vitro protein translation, plasmid cloning, Southern blotting, and radioactive sequencing. I loved it! I also enjoyed TA'ing students who where just one year younger.
#YoungScientistNetworking
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At the @rivm we worked on insertion elements in Mycobacteria. It was a lot of radioactive sequencing, with very long films, with each nt in a separate column. On a good day, we could read 200 nucleotides! We typed those manually into a text file.
en.wikipedia.org/wiki/Sanger_se…

One day (I was still an undergraduate) I saw a repetitive pattern on my long X-ray film. I thought I had made a dumb mistake. But it was a repetitive pattern indeed! 36 bp direct repeats with spacers.
We now know it was the Mycobacterium CRISPR region.
journals.asm.org/doi/abs/10.112…

I stayed at the @RIVM to do my PhD, working on characterizing epidemic Vibrio cholerae strains, and discovering that a new serotype O139, was a 'wolf in sheep's clothing'.
I drew that wolf for the cover of my thesis.
utrechtuniversity.on.worldcat.org/oclc/69010637

@rivm This is me (in the middle) on the day of my PhD defense in the beautiful Academy Building of @UniUtrecht.
On the left, Annelies, the awesome lab assistant who helped me in the lab, and on my right my brother @AartBik. They were my "paranimphs".
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@rivm @UniUtrecht @AartBik After my PhD, I found a job at @antoniuszkh, a clinical hospital, where set up molecular microbiology diagnostics and typing.
Very different than doing research. Short-term projects, but it was great to see a direct contribution to patient care. I loved the microbiology lab.

@rivm @UniUtrecht @AartBik @antoniuszkh Then, in 2001, my husband @gerard_harbers who worked at @lumileds in the Netherlands, was offered a job at the office in San Jose, CA. After some hesitation from my end (I had to leave my position), we moved to California in October 2001, just after 9/11.

@rivm @UniUtrecht @AartBik @antoniuszkh @gerard_harbers @lumileds Through a connection with my undergraduate lab, I was fortunate to find a position at @StanfordMed.
I stayed here 15 years, first as a postdoc, and later as a staff scientist.
This is me in the @DavidRelman lab, navigating the PCR quad machine.
#YoungScientistNetworking
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@rivm @UniUtrecht @AartBik @antoniuszkh @gerard_harbers @lumileds @StanfordMed @DavidRelman I first worked on the microbiome of humans. Over the years, we investigated the human gut, stomach, and mouth microbiome. It was a great combination of lab work, statistics, bioinformatics, and writing.


science.org/doi/full/10.11…
pnas.org/doi/abs/10.107…
academic.oup.com/ismej/article-…

Together with @fueledbyscience, we analyzed the development of the human infant gut microbiome. I must have seen baby poop in all forms and colors! We did part of the analysis using @Agilent microarrays and visiting their labs was fantastic.
journals.plos.org/plosbiology/ar…

@fueledbyscience @Agilent Another very cool project was to work on the oral/stomach/rectal microbiome of dolphins and sea lions, in a project together with the @USNavy Marine Mammal Program in San Diego.


cisac.fsi.stanford.edu/news/stanford-…
nature.com/articles/ncomm…
niwcpacific.navy.mil/About/Departme…

@fueledbyscience @Agilent @USNavy The position of research scientist at @Stanford was great. It was a staff position with a decent salary, benefits and a retirement plan (so nice after being a postdoc!). I did not have to teach and could completely focus on my research. We need more of these positions.

@fueledbyscience @Agilent @USNavy @Stanford During this time, around 2013, I started my blog MicrobiomeDigest, and started tweeting about microbiome papers and news articles. Here is my very first tweet:
#YoungScientistNetworking

https://twitter.com/MicrobiomDigest/status/395408532251475968

@fueledbyscience @Agilent @USNavy @Stanford I ran the blog by myself for three years, and then handed it over to a team of enthusiastic volunteers, such as @svetlana_up, @knstnr, @Itumeleng_M, @alifescientist, Xin Huang, @tyhsu389, @TinaSilovic, @Feargal_Ryan and many more. Thank you so much.
microbiomedigest.com

@fueledbyscience @Agilent @USNavy @Stanford @svetlana_up @knstnr @Itumeleng_M @alifescientist @tyhsu389 @TinaSilovic @Feargal_Ryan Some other things you can enjoy on :
* A list of Expert Women in Microbiology:
* Lab Stock Photo Fails:
* Bik's Brain - MicrobiomeDigest.com
microbiomedigest.com/sample-page/wo…
microbiomedigest.com/fun-stuff/lab-…
microbiomedigest.com/fun-stuff/i-co…

@fueledbyscience @Agilent @USNavy @Stanford @svetlana_up @knstnr @Itumeleng_M @alifescientist @tyhsu389 @TinaSilovic @Feargal_Ryan Some time in 2013, I read about plagiarism, and decided to test if someone had ever plagiarized a review article I had written a couple of years back. I grabbed a random sentence from my article, and found hits with an online Open Access book chapter and a newer article.
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@fueledbyscience @Agilent @USNavy @Stanford @svetlana_up @knstnr @Itumeleng_M @alifescientist @tyhsu389 @TinaSilovic @Feargal_Ryan Some other scientists had stolen two paragraphs I had written! I was very mad.
This accidental finding led me to a new hobby. In my free time I started searching for plagiarized sentences using Google Scholar. I found about 80 papers and PhD theses with over 50% copied text.
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@fueledbyscience @Agilent @USNavy @Stanford @svetlana_up @knstnr @Itumeleng_M @alifescientist @tyhsu389 @TinaSilovic @Feargal_Ryan Then, in another coincidence, I found reused Western blot images in a PhD thesis (later published articles) with plagiarized text. They'd been stretched or mirrored, to represent different experiments.
This made me angry again!
It looked like cheating.
#YoungScientistNetworking

I realized I have a strange talent to find patterns - I always found them in bathroom tiles or laminate floor planks.
I could also recognize EcoRI sites in sequence reads.
Perhaps I could use this weird 'gift' to find image duplications in scientific papers.
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To learn how often one would find inappropriate image duplications, I searched over 20,000 molecular biology papers and found duplications in ~800 (4%) articles. My co-authors @ACasadevall1 and @FangFerric had to both agree with my findings.

/ journals.asm.org/doi/pdf/10.112…

@ACasadevall1 @FangFerric About half of these might have been honest errors, but the other half (2% of the 20k papers) might have been done intentionally, suggestive for research misconduct. And this is just the tip of the iceberg. Many types of fraud are not detectable by looking at a paper.
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@ACasadevall1 @FangFerric Almost nobody believed our findings.
Our manuscript was rejected four times, by @elife, @PNASNews, @PLOSBiology, and @JCellBiol.
We finally published it on @biorxivpreprint and then in @mbiojournal.
It was also covered @RetractionWatch
retractionwatch.com/2016/04/19/one…

@ACasadevall1 @FangFerric @eLife @PNASNews @PLOSBiology @JCellBiol @biorxivpreprint @mbiojournal @RetractionWatch I reported the 800 papers with image problems to their respective journals in 2015. Five years later, only one-third had been corrected or retracted; as of now this number stands at ~50%.

@ACasadevall1 @FangFerric @eLife @PNASNews @PLOSBiology @JCellBiol @biorxivpreprint @mbiojournal @RetractionWatch Frustrated with the lack of response, I started posting my findings to @PubPeer, a site where you can leave anonymous or signed comments and concerns on scientific papers.
Here is one of my first posts (anonymously). This paper got retracted 3 years later.
pubpeer.com/publications/C…

@ACasadevall1 @FangFerric @eLife @PNASNews @PLOSBiology @JCellBiol @biorxivpreprint @mbiojournal @RetractionWatch @PubPeer I also realized that several others had been doing groundbreaking work before me. Scientists build on each other's work.
Already in 2004, @mike_rossner and Kenneth Yamada realized how easy it is to manipulate digital photos.


#YoungScientistNetworking
/ rupress.org/jcb/article/16…

@ACasadevall1 @FangFerric @eLife @PNASNews @PLOSBiology @JCellBiol @biorxivpreprint @mbiojournal @RetractionWatch @PubPeer @mike_rossner .@PSBROOKES posted 100s of image concerns on a website called .
Clare Francis sent 100s of concerns to journals before I started this work.

@Image_Integrity started in 2011 as the first image integrity analyst at @EMBOPressscience-fraud.org
en.wikipedia.org/wiki/Clare_Fra…

@ACasadevall1 @FangFerric @eLife @PNASNews @PLOSBiology @JCellBiol @biorxivpreprint @mbiojournal @RetractionWatch @PubPeer @mike_rossner @PSBROOKES @Image_Integrity @EMBOPress In 2016, I switched to industry. I started working at a company called uBiome, which sold kits to customers to determine which microorganisms were present in their gut, mouth, or vaginal samples. When I joined, there were only 25 people in the San Francisco office.

@ACasadevall1 @FangFerric @eLife @PNASNews @PLOSBiology @JCellBiol @biorxivpreprint @mbiojournal @RetractionWatch @PubPeer @mike_rossner @PSBROOKES @Image_Integrity @EMBOPress The first year was a fun time. Because it was a startup, you basically had to do all kinds of things, from unpacking boxes, moving lab centrifuges, to learning mySQL, electronic lab books, to writing scientific papers.

In the next year, the company grew, and leadership became less interested in science and more in making money. I started looking for another job, which took a bit longer than I had thought. I applied to ~20 jobs but got rejected or did not hear back.
#YoungScientistNetworking
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In 2018, I finally was hired at @AstarteMedical, where we worked on analyzing the microbiome of premature babies, to see if we could e.g. predict the development of NEC or prevent it with certain feeding regimes.

@AstarteMedical In my free time I was still working on finding concerns in scientific papers.
One night at a dinner party, I reliazed I was talking much more enthusiastically about my #ImageForensics work than my paid job. I wished Astarte all the best and gave my two week notice.

@AstarteMedical And so it started, my new career as a Science Integrity Consultant.
A risky step! We had some savings, but how were we going to make money for health insurance and groceries?
It is not a career step I would recommend to an early-career scientist.
#YoungScientistNetworking

But after a while, I got some consultancy jobs, working for some publishers and research institutions to investigate image problems and plagiarism allegations.
That gave me a lot of insight into how publishers and editors work.

I also get financial support through @Patreon.
Raising concerns about scientific papers is not work for which you can easily get a grant, so I am heavily dependent on my Patreon supporters and I am intensely grateful for this.
patreon.com/elisabethbik

Currently, my work has shifted from consulting to traveling to give invited talks about research integrity at department seminar series or at conferences.
It is great to visit a lot of places, but traveling can be stressful.

In April 2019, 5 months after I had left uBiome, the San Francisco office was raided by the FBI. The two founders were charged with health insurance fraud and money laundering. None of the employees was named in the indictment.


/cnbc.com/2019/04/26/the…
justice.gov/usao-ndca/pr/u…

My work is not always met with enthusiasm. No one likes their work to be criticized, and I completely understand! While most authors do not reply on @PubPeer, others will lash out and criticize my appearance, or calling me a fraud because the uBiome founders were charged.
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@PubPeer While this is not fun, authors who attack me without any scientific rebuttal of the concerns I raise, might have something to hide - so I might dig even deeper.
Lawsuit threats are much harder to deal with.
This work could financially ruin me.
It's a risk I am willing to take.

The problem of science misconduct is not just that of a rogue researcher or a big-ego-professor, it has turned into organized crime. Scam organizations such as #PaperMills and #PredatoryJournals are massively on the rise.
theguardian.com/science/2024/f…

Journals/publishers have been too late to realize this tsunami of fake papers that has been sent their way. Work to detect these has mainly relied on volunteers such as @SmutClyde @AbalkinaAnna @JAByrneSci @Image_Integrity @Thatsregrettab1 et al.

/scienceintegritydigest.com/2020/02/21/the…

@SmutClyde @AbalkinaAnna @JAByrneSci @Image_Integrity @Thatsregrettab1 And, of course, Artificial Intelligence will greatly enable paper mills to generate even more fake datasets, fake figures, and fake papers.
We need computer scientists to help us detect these.
#YoungScientistNetworking
wired.com/story/use-of-a…

@SmutClyde @AbalkinaAnna @JAByrneSci @Image_Integrity @Thatsregrettab1 Even better, we need to slow down science. Make it less about metrics (h-index, citations, impact factor) and more about quality, rigor, reproducibility. Publish smaller and open experiments and have other reproduce them. Reward this.
undark.org/2023/07/27/sci…

@SmutClyde @AbalkinaAnna @JAByrneSci @Image_Integrity @Thatsregrettab1 I will end by talking a bit about career options in the field of scientific integrity. I am often critical about publishers, editors, and institutions, and how they are slow to respond. But I have met some wonderful folks at these places as well. We need more of those.
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There are good career options at scientific publishers, research integrity officers at institutions or funding agencies, and computer scientists developing tools to detect scientific fraud.
I hope to see some of you choosing a career in this fast growing field.
Thank you!
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Small addendum: you can see in the unkind replies to tot s thread how fans/sockpuppets of authors whose work I criticized will continuously bombard me with their insults.