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: "Think piece" 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!).

Reading time: 6-8 minutes

The announcement by eLife to do away with formal accept/reject decisions has caused quite a stir. One of the major claims of the eLife announcement was:

“By relinquishing the traditional journal role of gatekeeper and focusing instead on producing public peer reviews and assessments, eLife is restoring control of publishing to authors, recovering the immense value that is lost when peer reviews are reduced to binary publishing decisions, and promoting the evaluation of scientists based on what, rather than where, they publish.”

I've underlined a couple key points in that statement. If you haven't already, I'd recommend reading my 5 minute take on the eLife announcement for full context. But I'll just dissect these two points here:

1. "eLife is restoring control of publishing to authors"

"Restoring" is a weird word isn't it? Since when have authors had control over publishing? I would argue that, even in the era before modern peer review (pre-1970ish) authors still didn't have control over where they published. In my last article, I made a point about how this is, in part, because experts need to be accountable to other experts (authors, reviewers, or editors). But even ignoring that, strictly from a marketing standpoint, there's no point in human history where an author could effectively disseminate their work - fiction, academic, or other - without the aid of a publishing house. Darwin didn't print, bind, and distribute all his own copies of "On the Origin of Species" any more than Harper Lee ran the printing press to produce every copy of "To Kill a Mockingbird." And neither of them saw to all the intricacies of marketing their work, distributing it, or filling orders.

"But we're in the internet age. We have social media for dissemination and we can even use LaTEX or rely on algorithms (e.g. bioRxiv web versions) to typeset our work." That's true. It's a fair point. But social media is only really effective if you start with a following. There are tons of stupid cat videos on the internet, but the ones you're most likely to see are coming from just a few famous channels. Don't forget survivor bias: for all the social media success stories out there, there are tens of thousands that completely failed. And the ones that succeeded are often propped up by shout-outs from existing prominent users. Take it from me, fun fact: I used to run a skateboarding trick tips YouTube channel back from 2007-2011: the early days of YouTube. I was even successful enough that my "How To Ollie" video came up before Tony Hawk's. But I was only successful because I produced videos that were half-decent at a time when YouTube was devoid of content. Were I to start my channel today, I'd be lucky to reach even a level of fame best described as "obscure."

So why do scientists think disseminating their work by social media is any different? Why do scientists think that they can start a Twitter, reddit, Facebook, post a link to their few hundred followers and "boom!" their work is out in the world! Sure, some preprints take off like wildfire. But that brings me to my second point...