And that is the crux of today's blog: the inherent conflict-of-interest (COI) that special issues present. You see, while MDPI journals offer some of the most absurd examples of how a special issue editor can abuse the system to publish their own works, the entire model of special issue publishing is rife with COIs; I can say that with confidence, as I experienced this firsthand. And I experienced such ethics concerns while guest-editing a special issue for the oldest extant academic publisher, a not-for-profit society journal with a centuries-long history and a rigorous selection process for what article collections get approved - yikes.

While I think there is a place for special issue publishing in the academic landscape, it really REALLY has to receive more oversight. And I'm not just talking about the groups like MDPI that are clearly abusing the definition of "special issue", but I'm even extending this to well-meaning and rigorous groups like Phil Trans B. The model of special issue publishing has some glaring COI problems, and as a former editor, this really should be considered and corrected moving forward. Let's dive in.
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Please reach out ([email protected]), or through the website's "Contact" web form, and we can grab a tea/coffee in person or over Zoom.

Immune genes evolve faster than almost any other gene in the genome. My work on antimicrobial peptides revealed how these host defence genes contribute to killing pathogens. What I found defied assumptions about immune defences that had held for decades, and blew the field of host peptide-pathogen evolutionary interactions wide open. These are still early days, but my work in the model fruit fly Drosophila melanogaster suggested that single peptides were immensely important for defence against specific microbes. What was striking was how you could delete entire groups of other defence peptides with no effect on survival outcome. In Hanson et al. (2023; Science, pdf here), I took this a step further, describing why these highly specific host effector-pathogen interactions exist: they're a product of millions of years of host evolution to ecological microbiome compositions. So these things I was seeing in the lab weren't just artefacts of our infection system, they reflected something ancient and meaningful.

To date, my own work and the broader field of Drosophila immunity has described numerous highly-specific host peptide-microbe interactions. Yet the causative mechanisms remain poorly understood. It's also unclear how far beyond D. melanogaster one can trust a host-pathogen interaction to play by the same rules. And if different species do play by different rules, what are those rules? Are there signals we can look for to tell us when something is expected to behave the same or different from our classic model organism that we know so well? As the first line of defence against infection, and the core effectors that actually do the killing, antimicrobial peptides and other effector mechanisms (e.g. melanisation) are key arenas of host-pathogen evolution. There are so many observations to follow up on, and even genetic tools in the lab just waiting for a motivated student to use. Please reach out if you'd like to reveal some of the core principles of host-pathogen interactions using a powerful genetic model system.

A short but sweet post: join us!

I have a funded PhD studentship opportunity to for 3.5 years to characterise aphid immune evolution. Details can be found at the link below:
www.exeter.ac.uk/study/funding/award/?id=5191

The project is co-supervised by myelf (lead supervisor), Bartek Troczka, and Chris Bass.

Feel free to drop me an email at [email protected] for more information. You can also use the Contact form on the website here.

Cheers,
​Mark

Reading time: 13 minutes
TLDR: "Watercooler" and "Frankenstein" Special Issues are very different things. We should really be distinguishing them from each other. It's publishers that profit off of free guest editor work that want us to view all things called "Special Issues" as similar products. They aren't, and we need terms that define a spectrum for what goes into editing a "Special Issue."

Figure: Special Issue (red) and Regular Issue (blue) articles by publisher from The strain on scientific publishing.

So you may have read a preprint recently: "The strain on scientific publishing." I found the topic fascinating; heck, I was lead author. In that preprint, we highlighted two mechanisms of publisher growth that generates strain, one of which was the use of "Special Issues" (emphasis on the air quotes). Some publishers have adopted Special Issues as an outlet for publishing guest-edited articles en masse. Now, our preprint took off across the globe, being covered in English, Spanish, Arabic, and Swahili... just to name a few. Somewhat as a result, we've even been attacked by Frontiers Media for somehow being "anti-special issue," which is the topic of today's post: am I anti-special issue? I don't think so. After all, I just finished editing one.

Before I get to Special Issues, I think it's important to discuss where they're published. Even more important to understanding their value, I think it's also worth talking about "when."

Reading time: 8-10 minutes
This blog has been critical of MDPI in the past. That came about honestly: in 2021 I looked at how inflated a journal's Clarivate Journal Impact Factor was relative to a metric that has built-in rank normalizers, the SciMago Journal rank. In that analysis, MDPI was far and away the most severe in terms of Impact Factor Inflation, having significantly different citation behaviour compared to all not-for-profit publishers, but also compared to for-profit Open Access publishers like BioMed Central (BMC) and even Frontiers Media ("Frontiers in ____").

​I followed that analysis with a simple poll asking Twitter users what their opinions were of various publishers. I repeated that poll in 2023 on both Twitter and Mastodon getting basically the same result (if anything, more settled into camps): nearly everyone labelled MDPI a somewhat or outright "predatory" publisher.

Around the same time, Paolo Crosetto wrote a fantastic piece on MDPI's anomolous growth of Special Issues. Year-after-year growth of Special Issues exploded between 2020 and 2021, going from 6,756 in 2020 to 39,587 in 2021. The journal Sustainability has been publishing ~10 special issues per day: and keep in mind a special issue is often comprised of ~10 articles. As Crosetto put it: "If each special issue plans to host six to 10 papers, this is 60 to 100 papers per day. At some point, you are bound to touch a limit – there possibly aren’t that many papers around... That’s not to talk about quality, because even if you manage to attract 60 papers a day, how good can they be?”

Reading time: 10-12 minutes
In this article:

• "Predatory publishing" is an overly-vague term
• Poll 2023: What is a predatory publisher anyways?
• Moving past the word "predatory"
  • Vampire press (similar to "vanity press")
  • Rent-seeker / Rent-extractor
  • Scam

​Edit Feb 15th 2023: added term "vanity press" to Vampire press section to highlight similarities and distinctions in use between the two terms.
Edit Mar 25th 2023: moved Twitter vs. Mastodon tangent to "p.s." section

A year ago I wrote a blogpost called "What is a predatory publisher anyways?" In that post I looked at the origin of the term in 2012, and what it meant at its inception. I held a Twitter poll, gathering ~175 respondents from across the spectrum that asked people's opinions on whether various publishing groups were "predatory."

​SPOILERS: I just redid the poll in Jan 2023 on both Twitter and Mastodon.

The aim of that poll was not only to get a sense of publisher reputations, but to look at what are the behaviours of publishers that people associate with "predatory publishing." What did I learn in 2021? Well... not exactly what I expected (fun!).