27 June 2017

Being scared: academics getting death threats for having an opinion

Kate Clancy is someone who I admire. She is someone who says stuff the needed saying. Like pointing out the high incidence of sexual harassment in field work.

For the second time today, I am compiling a Twitter thread about something important. Lightly edited.

My local paper, the News-Gazette, ran an editorial yesterday. That editorial, written by their staff, was half about me. I am the “ideologue” who got a James Watson talk cancelled. The thing is, date hadn’t been set yet, and Watson has a history of being implored to give science-focused talks then just saying racist shit. Perhaps I was the only one who publicly denounced the Woese Institute for Genomic Biology talk. But I wasn’t the only one who spoke against it.

Here’s what happened next: Julie Wurth of the News-Gazette called and asked to interview me about my tweets, and I said yes. So the News-Gazette was the first, and for a while only, story about the Watson cancellation. After that, the story got picked up by conservative websites and blogs. This is when I started getting hate mail. It turns out the smartest thing most conservative trolls can zing at me is that I’m a “fucking cunt.”

Unfortunately days went by and the story didn’t go away. For this reason, I eventually started getting more serious hate mail, threats. I involved campus police. One officer has been sympathetic. But the most I got was a form to fill out for a domestic violence safety plan.

So far, neither the University of Illinois nor Institute for Genomic Biology have corrected the record on my being the sole person against the Watson talk. Nor have they done anything to defend my academic freedom, nor support my personal safety. I’m 36 weeks pregnant by the way.

Today, the day after that editorial, I found a sticky note on the front door of my home asking me to check my email.

I want to say, very clearly, that I hold News-Gazette, the University of Illinois, and the Woese Institute for Genomic Biology responsible for this loss of my personal safety.

In response to another thread about science blogging and activism, Kate wrote:

Honestly, with the experience I’ve recently had and how the conservative trolls are getting worse, I’d advocate against speaking up.

This is how a lot of people lose. Kate loses, for obvious reasons. Academics lose, because they see someone who was a strong voice saying that it’s a mistake to be outspoken. News organizations and universities lose, because people lose trust in those institutions.

Intimidation is how fascism wins.

Update: Kate has asked for the following:

For those of you offering to help: first steps are to write News-Gazette and Institute for Genomic Biology for their lack of control/protection. Contact info for News-Gazette: http://www.news-gazette.com/contact. For head of Institute for Genomic Biology: generobi@illinois.edu.

The problem is scientists, not publishers

Because I hate people who just retweet something interesting and say, “Thread,” I’m compiling Jason Hoyt’s series of tweets about the state of scientific publishing into a blog post. Jason’s thread was initiated by this article in The Guardian, “Is the staggeringly profitable business of scientific publishing bad for science?”

For context, Jason is founder and CEO of PeerJ, which I have published in, and will do so again. I have lightly edited the tweets for clarity and emphasis.

This will be controversial, but the problem is scientists, not publishers. While the article may get the history of the problem accurate, it is going to perpetuate several myths about the current root of the issue. Scientists continuing to blame publishers, rather than the root, is pretty damn unscientific.

Plenty of cheap or even free publishing solutions exist. PeerJ even provides lifetime publishing open access for almost nothing, but very few scientists care about price when deciding where to publish. Scientists care about impressing grant and tenure and hiring committees, made up by other scientists, and the committees care about Impact Factor as a vanity metric for quality. It is the tenure/hiring, NIH, NSF, grant committees, not publishers, that are the ones in power and need to make the changes. Demanding publishers do so will do little.

So why aren’t the pitchforks out against the committees? There is only one group that can lead that charge, and it isn’t the publishers. Why aren’t committees looking at the merits of the article rather than the journal it is published in? Why aren’t committees more proactive in saying publish in cheaper open access alternatives like PeerJ?

PeerJ started out at $99 for lifetime publishing. That would have saved governments and funders $9 billion a year. Yet zero funders and committees have yet to approach PeerJ since it was launched five years ago with any support, acknowledgement or promotion. Instead, Nobel laureates and funders launch an elitist journal (I believe Jason is referring to eLife. - ZF), perpetuate the Impact Factor, whilst hypocritically blaming Cell, Nature, and Science journals. Instead, they fund elitist “non-profit” journals that charge $2,000 an article yet still only cover half their costs. This makes no sense.

Then scientists wonder why PeerJ had the gall to raise lifetime open access publishing from $99 to $399. The world doesn’t want nice things.

One of the myths is that academics do all the work. And daily I see an academic complain about journals and propose starting their own. Well – I am one of those academics who started their own. And let me say a peer-reviewed journal does not run itself. At best you’d get a few pubs out per year with only volunteers. And the quality would be shite.

For starters – authors demand peer review to be timely. Counter to that, the reviewers don’t want to be rushed and get angry. Without anyone chasing reviewers, the world would never see reviews hit the light of day. That’s fine then, the world doesn’t need millions of papers, just the ones people want to actually review without chasing. The problem with that is the literature is full of papers now highly cited that were rejected many times. So who is going to chase the reviewers for a million manuscripts? Volunteers? Nope. You have paid staff. So how do you pay the staff? Either through grants, subscriptions, or open access fees. So now the journal you started in protest of commercial publishers is in the same boat.

“But certainly you could do it cheaper!” you say. Cheaper than $99 for lifetime publishing like PeerJ? Don’t forget long-term archiving storage, a stupid typeset PDF, because that’s what readers demand, etcetera, etcetera.

“Well, screw it,” they say. “We’ll do preprints and have ‘overlay’ journals for post-pub peer review.” Except preprints aren’t free either. Arxiv costs more than $1 million a year to operate as a non-profit. And again, who is going to chase the reviewers for the preprint post-pub reviews? Volunteers? Volunteers for over 1 million preprints?

So again, when I see people complain about high cost of publishing, I have to laugh. More like cry. We have the solutions already, but little uptake. Who is to blame then? When I read tweets from academics that they won’t bother reading low Impact Factor journals, who is to blame? (By the way, how unscientific is skipping a literature review just because the journal has a lower Impact Factor, for fuck’s sake?)

The world doesn’t want nice things. We built a quid pro quo system of cheap open access with PeerJ. We asked $99 lifetime members, if invited, to do a peer review to support the community. People complained about the quid pro quo. The world could still have cheap publishing – if it is willing.

Elsevier and others are more than happy to keep taking the blame for the system. It’s a misdirection. As long as scientists don’t start protesting tenure and hiring committees, then Elsevier’s profit margins are safe. Every time there is a new Elsevier boycott, it lasts a week, and then everyone forgets. They know this. And they’re just cogs in the system like everyone else.

Related posts

The cages we scientists make for ourselves
 

24 June 2017

Texas losing academic opportunities from its dicriminatory agenda

Yesterday, I learned that the Society for the Study of Evolution will not hold meetings in Texas for the foreseeable future. And they were in Austin just last year.

Yesterday, I learned that public employees of California cannot come to Texas using state funds. This includes professors from the University of California system and the California State University system, such as Janet Stemwedel, who visited our campus back when it was UTPA.

The reason is that Texas is one of several states that has been actively pushing legislation that allows for discrimination against LGBTQI individuals (e.g., with so called “bathroom bills”) and against certain religious views.

I doubt that these will be the last academic and scientific organizations that will be taking public stands against Texas and other states with this agenda. I’m deeply disappointed that these actions should be necessary, but they are. These are the right decisions on the part of those organizations. Sadly, I doubt legislators will pay attention. But one can hope.

19 June 2017

Beware simple narratives in academic publishing

NeuroLogica blog has an article examining the loss of Jeffrey Beall’s list of dubious publishers. This post presents a nice, clean narrative: a good guys versus bad guys story. Jeffrey Beall is the good guy and predatory publishers are the bad guys. You can practically here the movie trailer voiceover. “In a world where lawless predatory journals abound, one librarian has the courage to name and shame them. Fighting strongarm tactics from the publishers and spineless university administration, he fights to save the world from ever more dodgy science.”

But the reality is more complicated, I’ll argue.

The NeuroLogica post says:

Traditional journals earn their money from subscriptions and advertising.

This suggests that libraries – the main customers for traditional commercial publishers – are going in and making journal subscription decisions on a case by case basis (like you would with magazine subscriptions). But many libraries don’t have that option. Instead, most libraries get journals through “big deals” from publishers, where large numbers of journals bundled together in a single indivisible package. These “big deals” don’t have a standard price (plotted graphically here) and librarians are bound by confidentiality agreements not to discuss them.

Subscription publishers have incentives to create more journals to justify increasing the price tag on their “big deals.” It’s not clear that incentives to create more journals has substantially different results than incentives to accept more papers.

Many journals do not run ads at all. Some do, but don’t run many.

And, as one commenter noted, this description overlooks page charges entirely.

NeuroLogica continues:

In 2013 Science magazine published the results of a sting in which a fake and terrible paper was submitted to over 300 open access journals. Sixty percent of the journals published the bogus paper, which should not have made it past even the flimsiest peer-review.

The implication here is that zero percent of subscription journals would have accepted the fake paper. But we don’t know, because no subscription journals were sent the fake paper. But some of the journals that accepted the fake paper were listed in Web of Science, which is supposed to be a vetted database of “best of the best” scientific journals. This suggests more subscription journals might have fallen for this fake paper than we would like to think.

The game of “How did this get published?” is one that scientists played long before the phrase “open access” was coined.

Predatory journal contribute to a blurring of the lines between science and pseudoscience, essentially flooding the world with low quality and bogus studies and promoting the borderline academics who produce them.

One of the biggest academic publishers in the world, Elsevier, publishes a subscription journal called Homeopathy. It doesn’t get much more pseudoscientific than that.

Beall was providing an invaluable service by pointing out practices among some journals that violated the spirit and the process of quality control in science.

Granted, but we should not overlook that “Beall’s list” was written and maintained by one person. His decisions were based on criteria that were not objective or transparent. For example, Beall once included then new publisher Hindawi on his list of predatory publishers, then later removed it for no readily apparent reasons.

This seems like an opportune moment to note that there is a new service from a Texas company called Cabell’s that will attempt to provide both a journal blacklist and a journal whitelist. This is an established company (founded 1978), but their lists are new. I think this is a very interesting development worth watching.

External links

Open Access Predatory Journals

Cabell’s: ‘Our journal Blacklist differs from Jeffrey Beall’s’

Related posts
 
Open access of vanity press, the Science “sting” edition
How much harm is done by predatory journals? 
Time for a new list of junk journals

12 June 2017

First in the family


I was the first in my family to go to university. My mom finished high school. My dad didn’t get that far. (People attended university less often then.)

What strikes me now is that I don’t know how that affected me.

In my institution, much is made that most of our students are “first generation” students. There’s a lot of talk about how hard it can be for them to transition to university, how they don’t know how to navigate university systems, and that we should try to provide more support mechanisms for them.

I don’t know if that was even a conversation faculty at my undergraduate university were having at the time. In any case, I never felt like I needed any of that.

Maybe it was because I was graduating high school from a small town with no university that I had no idea which adults had university degrees and which didn’t. It seemed to me that the cohort of students from my high school were all just in the same boat. I never felt like people from families with university experience had any sort of “inside information” coming from their parents.

Maybe it was because I was a white middle class guy. I wasn’t faced with some of the socio-economic hurdles that are often associated with “first generation” students in some places. Particularly here.

Maybe it was because I was academically inclined, and a nerd, and universities were just a good fit for me that I didn’t feel the culture shock that others felt. After all, I liked universities so much that I’ve basically spent my entire adult life in them.

But I think this is something I need to mention to my students more often. It might help some of them see that university degrees are not inherited feudal titles. And maybe it can help my “first in family” students see the possibilities for themselves. “You can’t be it if you can’t see it,” as the saying goes.

Just because you are the first to travel a pathway in your family doesn’t mean you’re the first ever.

Hat tip to TatooedDevil on Twitter for the hashtag, #FollowFirstGenerationAcademics.

10 June 2017

A blog quinceaƱera

I’ve been very excited by the way this graph has been coming along:

You don’t get many graphs like that in my business where the difference between the groups is so clear!

I get one, maybe two, points on that graph most weekdays, so that’s a few months of steady work there.

I’ve been so distracted by the awesome data above that I neglected to mention that this blog clocked past the 15 year mark. Fifteen years is one of those anniversary years that feels... almost not worth celebrating. But I was reminded because I was tweeting about what I do as part of the #NDTMeetScienceTwitter hashtag, and I mentioned the blog’s age.

It’s now been so long that sometimes even I forget how long this project has been running. I recently re-read a forthcoming piece I wrote about blogging, where I said I started this blog in 2003, not 2002. Whoops. That’s going to drive me crazy if I see that in print now.

While much of science online has moved to other media platforms (and to some degree, I have followed that trend), the longer I have done this, the more the value of this blog has risen for me. “Tweetstorms” and Twitter threads are okay, but I still like sentences and paragraphs for some things. Blog posts are easier for me to find. I refer back to old posts constantly for one reason or another. Lots of topics are practically evergreen in science and academia, so a blog post can have a very long tail.

01 June 2017

New snail species is hard to find, in more ways than one

Last year, I tweeted:

One of today's highlights: helping a colleague photograph the holotype of an undescribed species!

I’m pleased that this species description is now out. The species in question was a little snail, now named Praticolella salina! The discovery is highlighted on the university’s home page! But the university’s article doesn’t tell you where to find the paper. Putting the name into Google Scholar didn’t help either. I finally found it because someone posted a shot of the article on Instagram:


Once I knew the journal, I went looking for its home page. I found it is still a print-only affair, with PDFs of the journal lagging three years behind the publication date.

Just remember that the next time anyone says of scientific publishing, “Everything is all online now.” No. No it is not.

External links

UTRGV professor and student researchers discover, name new species of South Texas snail
The Nautilus (journal)

29 May 2017

Ireland vs. the pet trade


My newest paper is part of my own Pirates of the Caribbean franchise. It’s the fifth in a series, “pet crayfish on the internet.” 

The first (Faulkes 2010) used surveys; the second, Google alerts (Faulkes 2013); the third, online auctions, and (Faulkes 2015a); the fourth (Faulkes 2015b), classified ads. The fourth one was short, but I pushed it out because I thought documenting the illegal sale of marbled crayfish in Ireland would be useful for policy makers.

But there was an obvious question: if I blundered across ads for illegal crayfish in Ireland without looking, how many illegal crayfish would I find if I went looking?

While doing this paper, I was reminded was how useful it is to start writing the paper as soon as possible. This paper has a year of data from the Republic of Ireland, but only about half a year of data from the UK. Thats because I started writing the manuscript halfway through the year. I thought, “Hey, I’ve got half the data, I know what this paper is going to look like in broad strokes, so I can start putting this together.”

As soon as I started writing, I started thinking, “Uh oh.” I realized that there were gaps in what I was collecting (sigh), but that I might still have time to address (whew!). Writing forced me to articulate what I was doing, and I started imagining what the reviewers might say if I didn’t have certain things.

An advantage of having a scientific franchise is that some things get easier. I learned that it was useful to have a project run one calendar year. It’s a time frame that people get, and is manageable. You have a clearly defined end date, so you know how far along you are at all times. Data collection finished 1 January, 2016. Because I had done quite a bit of the leg work up front, I was able to finish writing and submit the paper less than two weeks later.

Where to submit the paper was tricky. Some articles have obvious homes, but there wasn’t for this one. There is no Journal of Pet Trade Studies. I looked at a lot of journals before settling on Biology and Environment. I had never published there before, but I couldn’t get a better fit than a regional Irish journal with a broad editorial mandate.

There was a cost to that good fit, though. The journal had no open access options. I’ve been trying to publish my papers open access when possible, and this is one of the first papers in a while (besides book contributions) that isn’t. In this case, I thought the fit was so good, this journal was the best chance for my paper to find its target audience, and that was worth the sacrifice.

Once the paper was submitted, I waited. I sent an email after two months, asking if I could post a pre-print while waiting for a decision. I was politely asked not to, so I didn’t. I waited some more. And waited. After six months, I sent an email making sure nobody had forgotten my manuscript. (Because that’s happened to me before.) I was assured it hadn’t been. I waited some more.

I checked in again around the nine month mark to make sure the manuscript was still a live concern for the journal. The editors really wanted a particular person to review this paper, and was just waiting on the one review to come in. So, yes, this is one of those frustrating cases where the editorial decision making was slowed by reviewers not promptly returning reviews. I was a bit miffed, since the paper was neither long nor complex, and I didn’t think it needed the many months it took to review. But I was pleased that I had learned to be more persistent in checking with the journal.

That said, once the reviews were back, I was pleased with the rest of the journal’s service. The typesetting and copy editing process was thorough and responsive, and it felt like they genuinely wanted to get everything right.

It’s funny to think that when I started my academic career as an undergraduate, I didn’t have an email address. The Internet existed, but practically nobody knew about it. The web was about a decade away. And now, I can publish papers about Ireland from my desk in Texas just by watching what people do the Internet.

Like any good franchise, I am already working on the sequel.

Update, 1 June 2017: I received a hard copy of the journal in the post today (cover above). It’s been a while since that happened! And I must say, the production is top notch. The colour pictures look bright and beautiful. The paper feels good in your hands. And there is an editor’s introduction to each article. The one to mine reads, in part:

Ain’t no barricade high (or wide) enough

Enforcing any restriction on the movement of goods or organisms is beset by problems even when physical barriers are used. We have been lucky in Ireland that the movement of many unwanted organisms has been prevented because we are separated from both the UK and continental Europe by natural water barriers. Whilst natural barriers are important these can still be circumvented often through trade-related, human assisted transportation. ...

Perhaps there is a message here–that the implementation of any barrier to the movement of an unwanted species is always likely to be too later–and that such a move has to be combined with an appropriate follow-up management plan?

This relates to a point I made on Twitter last week. It’s not fair to compare the delay in posting a pre-print to the delay in publication in a journal, as Leslie Vosshall did.

I say that knowing that I myself have complained about editors have never helped papers become more readable. But I think that was a little unfair. For one, I’m a native English speaker, and though I say it myself, a pretty good writer. My writing probably doesn’t need dramatic revision to be readable.

Since I wrote that blog post, I’ve worked with more journals. Several of them actively made my paper better after acceptance. Like this one, the improvement came in the copy editing and proofing stages. Lots of little details got detected and corrected before the final version was produced that would appear in the journal, and be the version of public record. I greatly appreciated that intense, detailed, checking of the text. That care showed up in the production of figures and tables, too.

Sometimes, it seems that some scientists are so confident of their abilities that they think their uncorrected, unreviewed manuscript cannot possibly be improved. Reviewing and editing are just unnecessary delays in getting their brilliant science out to the world .

I think that such manuscripts are extraordinarily rare.

Related posts

Can civil servants defuse a bomb? An Irish crayfish problem
Academic publishers need better defenders
The editor’s influence

References


Faulkes Z. 2010. The spread of the parthenogenetic marbled crayfish, Marmorkrebs (Procambarus sp.), in the North American pet trade. Aquatic Invasions 5(4): 447-450. http://dx.doi.org/10.3391/ai.2010.5.4.16

Faulkes Z. 2013. How much is that crayfish in the window? Online monitoring of Marmorkrebs, Procambarus fallax f. virginalis (Hagen, 1870) in the North American pet trade. Freshwater Crayfish 19(1): 39-44. http://dx.doi.org/10.5869/fc.2013.v19.039

Faulkes Z. 2015a. Marmorkrebs (Procambarus fallax f. virginalis) are the most popular crayfish in the North American pet trade. Knowledge and Management of Aquatic Ecosystems 416: 20. http://dx.doi.org/10.1051/kmae/2015016

Faulkes Z. 2015b. A bomb set to drop: parthenogenetic Marmorkrebs for sale in Ireland, a European location without non-indigenous crayfish. Management of Biological Invasions 6(1): 111-114. http://dx.doi.org/10.3391/mbi.2015.6.1.09

Faulkes Z. 2017. Slipping past the barricades: the illegal trade of pet crayfish in Ireland. Biology and Environment: Proceedings of the Royal Irish Academy 117(1): 15-23. http://dx.doi.org/10.3318/BIOE.2017.02