20 December 2024

Le Monde est à vous: Academic hoaxes in French newspaper article

The second article that arose from my posting of preprints is now available. The title is, “Why scientific hoaxes aren’t always useless.”

Translation of first paragraph by Google Translate:

Canadian biologist Zen Faulkes is not a naturalist, even if he likes to collect crayfish or sand crabs for his research. However, he has a taste for unexpected collections. For several years, he has been collecting, listing and classifying... scientific hoaxes. That is to say, parody, ironic or insane research articles that should never have been published. “Of course, if these texts disappeared, it would not be a great loss. But it is important to keep track of them and try to learn some lessons from their existence,” says the researcher, whose collection spans 432 pages, for forty-two examples.

While I have been very pleased in the last few weeks to have been quoted in a couple of fairly high profile venues, I am struck by the disconnect this week between good professional news and terrible personal news. (There have been a couple of deaths close to our family in the last week.)

External links

Pourquoi les canulars scientifiques ne sont pas toujours inutiles (Paywalled and in French)

Related blog posts

Clearing out the vault by posting preprints

09 December 2024

Bar graphs, how do they work?

I make a brief cameo appearance in a new article about data visualization. Bar graphs are about as simple and basic as you get in data visualization, but a couple of new preprints (one of which is mine) show that people struggle to get even those right. The major preprint by Lin and Landry finds all sorts of issues in bar graphs. Mine is much smaller, and I just want people to label their error bars.

By the way, this was the unexpected call I got after posting a preprint last month.

Related posts

Clearing out the vault by posting preprints

Reference

Heidt A. 2024. Bad bar charts are pervasive across biology. Nature. https://doi.org/10.1038/d41586-024-03996-w

04 December 2024

“Pay me now or pay me later” in reproducibility

“Reproducibility debt” is an interesting and useful take on the matter of reproducibility and replication. I stumbled across a discussion on a recent podcast.

What I like about this phrasing is that a lot of discussion around reproducibility focuses on bad practices. Things like p-hacking, HARKing, and the like. Framing issues around reproducibility as debt makes it more obvious that what we are talking about are trade-offs.

You might have a more reproducible result if you had a bigger sample size and wrote a perfect paper. But that takes time (opportunity costs), and often takes money (financial costs). And there are benefits to getting papers out - both personal (another thing to add to your annual evaluation) and to the community (puts new ideas out and generates leads for others).

In the short term, it can make sense to take on debt. But you will have to pay it back later.

The paper develops a preliminary list of the kinds of trade-offs that cause reproducibility debt. 

  • Data-centric issues (e.g., data storage)
  • Code-centric issues (e.g., code development)
  • Documentation issues (i.e., incomplete or unclear documentation)
  • Tools-centric issues (e.g., software infrastructure)
  • Versioning issues (e.g., code unavailable)
  • Human-centric issues (e.g., lack of funding)
  • Legal issues (e.g., intellectual property conflicts)

It’s very software focused, so I don’t think the list is comprehensive. For example, in biology, reproducibility might become an issue because a species becomes rare or extinct.

If we have reproducibility debt, maybe we can also conceive of reproducibility bankruptcy: a point where the accumulated shortcuts add up to a complete inability to move forward on knowledge.

References

Hassan Z, Treude C, Norrish M, Williams G, Potanin A. 2024. Characterising reproducibility debt in scientific software: A systematic literature review. http://dx.doi.org/10.2139/ssrn.4801433 

Hassan Z, Treude C, Norrish M, Williams G, Potanin A. 2024. Reproducibility debt: Challenges and future pathways. Companion Proceedings of the 32nd ACM International Conference on the Foundations of Software Engineering: 462-466. https://doi.org/10.1145/3663529.3663778

External links

To Be Reproducible or Not To Be Reproducible? That is so Not the Question

29 November 2024

A journal paying for reviews

The BMJ will start paying £50 for reviews.

The catch? It’s not for peer review, it’s for reviews from patients and the public. They still expect peer reviews to be done as part of service.

Their announcement post does not describe how they will address several of what I consider to be potential problems. While my previous post was about posting for reviews from academics, I think many of the issues will also apply to public and patient review.

I’m going to sign up as a public reviewer. Because why not? I could use 50 quid. And I’d like to see what this looks like from the inside.

Related posts

Potential problems of paying peer reviewers

External links

The BMJ will remunerate patient and public reviewers

25 November 2024

“Neurosurgery on Saturn” paper shows academics’ blind spots

The planet Saturn.
In the last few days, a bunch of people on Bluesky discovered a paper that has been out for a few months, “Practice of neurosurgery on Saturn.”

Looking through the social media posts about this paper, a lot of people played that favourite academic game, “How did this get published?” Many people suggested it’s a hoax. Academic hoaxes are a particular interest of mine, and I am always looking for the next entry in the Stinging the Predators collection of academic hoaxes.

I didn’t think this was a hoax? Hoaxers usually reveal the prank almost immediately, and this paper had been out for months.

My hunch seems to have been correct. The lead author has an extensive Google Scholar page and said on PubPeer: “it is clear that the document focuses on fictitious and hypothetical situations.” I am not clear about what the point of the article is, but never mind. It’s filed under “Letters to the editor,” which I think is an arena where researchers and journals can be allowed a little leeway.

But this is a good example of something that I think is decidedly lacking in many discussions about academic publishing and academic integrity. In none of the posts I read did anyone do any actual investigation.

Nobody looked to see if the authors were real.

Nobody emailed the authors. It seems to just be happenstance that the lead author saw the PubPeer comments and replied.

Nobody emailed the journal (although editors are often notoriously slow to reply to these sorts of things).

In collecting academic hoaxes, I’ve noticed a similar pattern. People create hoaxes to show that there are bad journals out there that accept anything for money. But by and large, that is where it stops

People know predatory journals are out there, but nobody is actively digging behind the scenes to see how they work. How do people decide to start running them? How much money do they make? Why would a scam artist only in it for the money do apparently counterintuitive things like waiving the article processing charges? (There are multiple instances of that in the Stinging the Predators collection.)

A recent paper came out that made a similar point about the lack of investigation about paper mills  (Byrne et al. 2024). 

Academics treat too many of these problems around dubious publishing as some sort of black box that cannot be opened. They only study the outputs. I think someone needs to approach these sorts of problems more like an investigative journalist or an undercover law enforcement officer might.

Go in and find the people who are doing all this dishonest stuff. Get them talking. I want hear what some of the people organizing predatory journals or paper mills or citations rings have to say. Why do they do what they do?

I don’t expect academics themselves to do this. This kind of investigative journalism is expensive and time consuming and being done less and less. But without this kind of insight, we will probably never be able to understand and curb these problems.

References

Byrne JA, Abalkina A, Akinduro-Aje O, Christopher J, Eaton SE, Joshi N, Scheffler U, Wise NH, Wright J. 2024. A call for research to address the threat of paper mills. PLoS Biology 22(11): e3002931. https://doi.org/10.1371/journal.pbio.3002931

Mostofi K, Peyravi M. 2024. Practice of neurosurgery on Saturn. International Journal of Surgery Case Reports 122: 110139. https://doi.org/10.1016/j.ijscr.2024.110139

External links

PubPeer commentary on “Practice of neurosurgery on Saturn”

Altmetric page for “Practice of neurosugery on Saturn”

Google Scholar page for Keyvan Mostofi

Photo by Steve Hill on Flickr, used under a Creative Commons licence. 

Generative AI: Two of of three is bad

There’s an old joke: “Fast, cheap, good: Pick two.”

Generative AI is fast and cheap. It will not be good.

I would like “good” to be a higher priority.

Edit, 1 December 2024: I think academics, under the intense pressure to be productive, prioritize those three characteristics in that order. The first two might switch (grad students are more likely to prioritize “cheap”), but I think “good” is regularly coming last.



22 November 2024

Clearing out the vault by posting preprints

Old books on a shelf
My last jobs didn’t have any expectations for research, so my publication rate slowed significantly. I wanted to do something about that.

A few months ago, I published a submitted but not completed article on paying peer reviewers here on the blog and on Figshare. This got me digging around in folders on my hard drive and I got thinking about other articles that I had written, submitted, but weren’t accepted. And at the time, I just ran out of steam to revise and resubmit them in ways that would satisfy an editor and a couple of reviewers. 

So in recent weeks, I have taken to submitting some of those manuscripts to a preprint server.

In the past, I was a little cool to the value of preprints. I always thought they had some uses, but I was skeptical that they would replace journals, which was the stated wish for some of the strongest preprint advocates. I was always worried about the Matthew effect: that famous labs would benefit from preprints and everyone else would just have more work to do.

But since I last wrote about preprints, the attention landscape has changed. More people in biology have started scanning through preprint servers part of their routine. I was surprised when a reporter emailed me about one of these preprints and wanted to chat for an interview. I don’t think that would have happened a few years ago.

Whether these will be “final” public version of these little projects, I can’t say. I have other projects that I want to get out that have not been written up at all yet that I want to try to get into a journal. But I am glad that every one of these received at least a little attention on Bluesky.

Here’s the list of my recent preprints, all on bioRxiv.

Update, 26 November 2024: I’ve now had two journalists reach out to me because of these preprints. I’ve never had that high a level of interest from the dozens of peer-reviewed journal articles I published.

Related posts

A pre-print experiment: will anyone notice?

A pre-print experiment, continued  

A pre-print experiment, part 3: Someone did notice  

Photo by umjadedoan on Flickr. Used under a Creative Commons license.

18 November 2024

The cat that fooled Google Scholar, the newest hoax in my collection

I finally got a chance to update my collection of academic hoaxes!

Stinging the Predators 23.0: Now with a cat! (The Internet loves cats, right?) http://bit.ly/StingPred

I am now up to 42 academic hoaxes, which is triple the number that I started with in version 1.0 in 2017.

The latest hoax targets not a predatory journal, but an academic search engine. While this is unusual, it is not the first hoax that was pulled to show how easy it is to manipulate Google Scholar. (One of the things that has been interesting to me as this project has continued is that many hoaxers feel compelled to make the same point again.)

And one other things that has been rewarding is that this collection, which I’ve only ever had on Figshare and promoted on my socials and personal websites, has been viewed tens of thousands of times and has been cited by scholars writing in proper journals a few time.

External links

Faulkes Z. 2024. Stinging the Predators: A Collection of Papers That Should Never Have Been Published (version 23). Figshare. https://doi.org/10.6084/m9.figshare.5248264