26 February 2016

Open access paper, closed data

A new paper in Science Advances by Kicheli-Katz and Regev (2016) is interesting in several ways. It’s a very interesting look at gender bias using eBay auction data.

I’ve used data from eBay myself (Faulkes 2015), and it was hard going. I visited the website roughly daily and pulled auction data into a spreadsheet by hand for each listing. Nothing was automated.

Kicheli-Katz and Rege, however, got data directly from eBay. And they got over one million transactions to analyze. That’s an awesome sample that gives them a lot of statistical power. I was curious to know more, but found this text in several places in the paper.

According to our agreement with eBay, we cannot use, reproduce, or access the data.

I raised my eyebrows at that a bit. All sorts of questions bubbled into my mind. The acknowledgements section provided more detail, however:

eBay has provided written assurance that researchers wishing to replicate the work would be afforded access to the data under the same conditions as the authors.

Okay. That’s more helpful information, and I wish it was in the main body of the text, rather than buried at the end of the acknowledgements. On the Science Advances webpage, it is the second to last thing on the page (the last is the copyright notice).

Clearly, social media companies realize that their data is scientifically valuable and want to use that for their own gain. OKCupid used to write amazing blog posts based on their data that give you a hint of how rich the kinds of questions and answers you can tackle are using large social media datasets. (Although OKCupid also got flak for running unregulated experiments on its users, and rightfully so.)

The eBay disclaimer runs counter to the major trends we are seeing in scientific publication: more transparency, more access to raw data. I am not sure how confident I am with eBay’s promise to share the data with other researchers. From the point of view of reading this paper, eBay is mostly a big black box.


Kricheli-Katz T, Regev T. 2016. How many cents on the dollar? Women and men in product markets. Science Advances 2(2): e1500599. http://dx.doi.org/10.1126/sciadv.1500599

Faulkes Z. 2015. 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

Picture from here.

25 February 2016

Mission creep in scientific publishing

Sometimes, it feels like every proposed reform of scientific publishing involves me doing more work.

There’s significant mission creep in the checklist of disseminating scientific information. While “publish” is necessary to avoid “perish,” it is no longer sufficient. It’s “Be visible, or vanish.” And visibility requires work.

When I was in grad school, I had to write a paper and publish it.

Now, people are suggesting that I also pre-register my experiments; curate and upload all my raw data (which may be in non-standard or proprietary formats); deposit pre-prints; publish the actual paper in a peer-reviewed journal (because that’s not going away); promote it through social media; upload it into sites like Academia.edu or ResearchGate; update my publication information in databases like ORCID, ImpactStory, and institutional measures; and watch for comments on post-publication peer review sites like PubPeer and engage with them as necessary.

Now, don’t get me wrong. Those are good things to do. Individually, each one has a solid rationale. But I don’t have an army of students, or post-docs, or administrative assistants to help with any of that. It’s all me. The cumulative effect could be draining.

My approach has been to do these things when the time cost is expected to be fairly minimal. I’ve put data up for many of my papers on Figshare... usually based on whether it was already in a spreadsheet. Converting a megabytes, if not gigabytes, of physiological recordings to some sort of interoperable standard? Nope.

Similarly, after the #ASAPbio meeting, I voted “No” to a Twitter poll asking if I would commit to posting my “best” science as pre-prints. I’ll do it if it makes sense for the project (timeliness of information is important, say).

External links

Are you an  ‘academic superhero’?

23 February 2016

Things that are 50

Celebrating their golden anniversary this year:

Star Trek. I think it’s safe to say this show had an effect on me, though we’ve drifted apart over the years.

Batman. A TV series that is often mocked by comic fans but that left a mark on pop culture. People remember it.

The Green Hornet. Underappreciated today, I think.

Both a force in TV and music.

The Stones’ classic album.

You can’t have a 1960s retrospective without the Beatles.

All of Generation X.

This guy.

Related posts


External links

Fans celebrate the 50th anniversary of Batman, Star Trek and the Monkees

Tuesday Crustie: Beer

“It’s okay, we can regrow the claw!”

Hat tip to John Wares on Twitter.

19 February 2016

Steampunk open access

Consider a world much like our own. Scientists do research, and publish their findings in academic journals, made of paper and ink and glue and leather.

Except... that the concept of open access took hold in the early days of academic publishing. Authors paid article processing fees to pay for printing costs. The resulting print journals and books were sent to libraries and to archive free of charge. People who wanted copies merely had to ask.

This system continues until the late twentieth century, when the Internet becomes readily available to researchers and the public alike. Now, all those centuries of research (still freely available, mind you) are in an antiquated, inconvenient format. People want get digital copies of research papers that interest them.

Who would put in all the hours of work to digitize those open access articles? Who would pay the costs? Who would create the websites? Who would assign the DOIs?

There used to be a complaint that younger scientists’ reference lists rarely went back before the 1990s because papers weren’t online. Imagine how much worse the problem would be in the steampunk open access scenario.

In our world, a lot of the world’s scientific back catalog got digitized by those bad guys, commercial publishers.

It is short-sighted to think that electronic text, and particular PDFs, are the final form of academic communication. When the next transition of formats occurs, how will open access papers make the jump?

Photo by Don Shall on Flickr; used under a Creative Commons license.

16 February 2016

Science Blogging: The Essential Guide companion website up!


We’re exactly two weeks out from the launch of Science Blogging: The Essential Guide. When I got my review copy, one of the first things I did was to look for the online resource mentioned in the book, and was a bit nervous not to find it. But that is now remedied, and it is up for you to check out today at The Open Notebook!

Among the goodies is a Q&A with the editors here, with some good thoughts on the past and future of blogging.

Scicurious put together a Twitter list of all the authors and editors for your following pleasure.

Meanwhile, I noticed that Amazon will be offering a Kindle edition of the book for those of you who already have enough physical stuff lining your bookshelves. It’s also up for sale at other vendors, such as Barnes and Noble, although they don’t seem to have an ebook version available yet.

Update, 23 March 2016: Joanne Manaster interviewed the editors, Bethany, Christie, and Jason on her Read Science hangout series.

Update, 24 March 2016: Editor Jason Goldman is interviewed on Science Writing Radio, Episode 31!

Related posts

Incoming: The Complete Guide to Science Blogging
Incoming: Science Blogging
Science blogging book: now with blurbs!
Science Blogging: The Essential Guide book cover reveal
The unenveloping* of Science Blogging!
Science Blogging: The Essential Guide already making waves!

External links

The twain shall meet
Science Blogging on Yale University Press
Science Blogging page of Facebook
Science Blogging on Amazon

Tuesday Crustie: Lobsterworthy

We can thank Queen B for the latest crustacean meme.

External links

After BeyoncĂ© Shout Out, Red Lobster Makes “Lobsterworthy” Shirts For Valentine’s Day

15 February 2016

Another UTRGV teachable moment

UTRGV tweeted this image from our Brownsville campus:

I’ve walked through this lobby a few times, but it never clicked that the spiral is supposed to represent DNA, the molecule of life. It is in the lobby of the Life and Health Sciences Building.

I realized there’s a problem.

The spiral is going the wrong way.

It’s twisting to the left (counterclockwise). DNA twists right.

It’s not the only problem with the image. The two strands of DNA are not evenly spaced, for one, but I am willing to let that one slide because of limitations of the medium (bricks and tile). But it would have been as easy to build it twisting the other way. Indeed, this seems to be such a common mistake that I wonder if there are more incorrect depictions than correct ones out there.

I knew that DNA strands have a particular direction. Pretty much all biological molecules are “handed” in some way. But I am not a molecular biologist, and was never able to remember which was the right way around. Thanks to this pillar, I’ll probably never forget now. Even it that knowledge is tinged with a little embarrassment that a new research university is displaying something factually wrong.

External links

DNA's twist to the right is not to be meddled with, so let's lose the lefties

12 February 2016

Editors are responsible when you get a bad review, too

Jon Tennant, writing at Science Open, has me thinking about the ongoing issue of anonymity in science again, particularly in peer review. My thinking on this matter has changed a lot. I sign my reviews, but I’m much more sympathetic to those who don’t sign their reviews than I used to be.

Jacquelyn Gill recently provided a useful reminder of how unhelpful and downright crappy some reviews can be:

I recently had an NSF proposal reviewer say outright that I was only on a proposal to check the gender diversity box, and that I am a “competent palynologist” (sic) and don’t need “pity support” from male colleagues. ... the implication that I wasn’t deeply involved in the conception and writing of the proposal was insulting to me and my colleagues, and there was zero evidence of that in the proposal.

When you get a bad review, the first thing you’re tempted to do is lay blame on the reviewers. After all, the words originated there. This carries through to most of the writing and research on peer review: most arguments center on anonymity of the reviewers, and to some degree, the authors.

If an author gets such a bad, biased review, it is not solely the fault of the reviewer. An editor passed that along. An editor decided that stupid review was worth conveying to the author.

An editor who did that should have her or his feet put to the fire. Part of the job of an editor is to provide oversight. An editor who blindly forwards all reviews regardless of their content, regardless of how blindingly unhelpful or even blatantly sexist they are, is incompetent.

While most journals allow anonymous peer review, they don’t allow anonymous editors. Until scientific culture changes to make reviews more open (and it may not), editors should be pressure points of accountability. We need to publicize cases where editors pass on the dumbass reviews.

This can work. There’s been at least one case of an associate editor being relieved of duties after passing on a bad review.

External links

Peer review: open sesame?
Over-proved, but fantastic flavor: The Great British Baking Show as a model for writing reviews

10 February 2016

Science Blogging: The Essential Guide already making waves!

We’re still more than two weeks away from the official release of Science Blogging: The Essential Guide, but the book has already racked up its first citation, in the New York Times Sunday Book Review.

It’s kind of a throwaway reference at the end of a longer book review (on atheism and religion, by James Jones, but it’s exciting. Early references to the book bode well for its reception.

Harker’s book, though of interest to anyone looking for a guide to such controversies, is aimed at college students in an introductory philosophy of science course. Should he ever decide to communicate these views more broadly — which is to say, to blog about them — he might consider picking up a copy of SCIENCE BLOGGING: The Essential Guide (Yale University, paper, $24), edited by Christie Wilcox, Bethany Brookshire and Jason G. Goldman, which offers practical advice on such matters as “blogging about controversial topics” and “persuading the unpersuadable.” For example: Always link to the relevant research, avoid “muppet flailing” (excessive fervor, I gather) and “don’t let the trolls get you down.” Words not just to blog but to live by.

“Words not just to blog but to live by.” That’s not a bad pull quote for a book blurb!

Additional, 8 March 2016: I guess I’ll use this post to compile reviews and features of the anthology. This article just in from Times Higher Education! It also has a very brief cameo at the end of this Canadian Science Press post, Science Blogging 101.

Additional, 17 March 2016: Andrew David Thaler, himself no slouch at blogging, reviews the book in Science magazine.

Related posts

Incoming: The Complete Guide to Science Blogging
Incoming: Science Blogging
Science blogging book: now with blurbs!
Science Blogging: The Essential Guide book cover reveal
The unenveloping* of Science Blogging!

External links

The twain shall meet (New York Times)
How to set up a blog about science (Time Higher Education)
Science Blogging 101
Blogging for beginners (Science, paywalled)

Sales links

Science Blogging on Yale University Press
Science Blogging page of Facebook
Science Blogging on Amazon

09 February 2016

Tuesday Crustie: Colour your own crustacean!

Colouring books for adults are popular now, so I applaud the BioDiversity Library for making this outreach tool! They have a whole big big available here.

Hat tip to Ely Wallis.

08 February 2016

The unenveloping* of Science Blogging!

It’s here!

It’s been a long time in writing and editorializing and proofing and printing (I first announced it in fall 2014), but the book is finally here! I can read Science Blogging: The Essential Guide! And you can’t yet, nyah nyah nyah!

Honestly, I’m excited not only as one of the chapter authors (first publication of 2016, I get to have some Canadian chocolate today!), but as a reader. I certainly didn’t know the complete list of chapter authors when I started writing. Looking at the other contributors to this volume is, frankly, terrifying. They are such great writers. I feel like:

I started working on my chapter on the plane to Science Online 2013. It’s almost exactly three years ago. I got 422 words written (less than many of my blog posts), which are still on my iPad. Here’s a snippet of the very start of the very first draft:

Ronin blogging
I have three science related blogs. I started what became NeuroDojo in 2002, followed by Marmorkrebs in 2007 and Better Posters in 2008,

There are advantages to belonging to a network, but they may not be as great as you think. Being on a network in and of itself does not guarantee readership.

While you are an independent blogger, you still need to develop a community.

And it goes on from there. Looking back at that first draft, it’s interesting to see how many of those first sketchy ideas survived into the final chapter.

I do have one disappointment in my chapter, though. Because this chapter references “ronin” as a metaphor extensively, I had wanted to pay tribute to Legend of the Five Rings and use this John Wick quote from one of the very first L5R promo cards, Dairya, to open the chapter:

“You call me a masterless man. You are wrong. I am my own master.”

Alas, that lead-in quote did not survive the edit, but I was able to get some L5R references in the main body of the text.

And the references to me being at The University of Texas-Pan American are also obviously out of date.

But I am so happy that this book is now out! I’m very happy with some of the turns of phrase in m contribution, and I cannot wait to work through everyone else’s chapters.

And, for the first time, something about this book has moved faster than expected! Previously, I announced it would be out 22 March, but Amazon is now showing it for sale on 1 March!

* Normally, the reveal of a fresh new something is called “unboxing,” but since this didn’t come in a box...

Bird picture from here.

External links

Science Blogging on Yale University Press
Science Blogging page of Facebook
Science Blogging on Amazon

Related posts

Incoming: The Complete Guide to Science Blogging
Incoming: Science Blogging
Science blogging book: now with blurbs!
Science Blogging: The Essential Guide book cover reveal

03 February 2016

Setting an agenda

Despite the title, committee chairs don’t have all that much power, particularly in academia. The whole point of having committees is that committees vote, and responsibility is diffused.

Committee chairs do have one actual power: to set an agenda.

I’m only a few days into my term as chair of the Student and Post-doc affairs committee at SICB, but I just want it to be known publicly that preventing sexual harassment of students and trainees has jumped to the top of the agenda.

This went to the top this morning when I opened my Twitter feed and saw, over and over, people discussing this article in the New York Times about an individual who harassed students at multiple institutions. This comes on the heels of other examples in recent months. This blog post could easily turn into a litany of harassment, so let’s just say this: there’s too much of that crap going on.

I don’t know whether harassment has been a topic of conversation for the committee before, but I look forward to finding out. If it hasn’t, it’ll be new. If it has, I plan to keep it front and center.

And I’m blogging this because I want to be accountable. I want people to know that this is what I want to try to do, so they can see if I succeed or not.

Related posts

Okay, SICB students and post-docs, I’m your guy

External links

Chicago professor resigns amid sexual misconduct investigation
Here’s how Geoff Marcy’s sexual harassment went on for decades
Work in progress: changing academic culture
You are worthy.

Photo by A Syn on Flickr; used under a Creative Commons license

02 February 2016

Who is Jingmai O’Connor, and why is she saying nasty things about science blogggers?

We’re less than two months away from an entire book about science blogging dropping from a major university press (disclaimer: which I have a chapter in), and here we have a reminder that many believe blogs are not a legitimate form of academic writing:

What’s your view on social media and science? For example, the role of science blogs in critiquing published papers? Those who can, publish. Those who can’t, blog. I understand that blogs can be useful in affording the general public insights into current science, but it often seems those who criticize or spend large amounts of time blogging are also those who don’t generate much publications themselves. If there were any valid criticisms to be made, the correct venue for these comments would be in a similar, peer-reviewed and citable published form. The internet is unchecked and the public often forgets that. They forget or are unaware that a published paper passed rigorous review by experts, which carries more validity than the opinion of some disgruntled scientist or amateur on the internet. Thus, I find that criticism in social media is damaging to science, as it is to most aspects of our culture.

This quote is from an interview with Jingmai O’Connor, a paleontologist currently in China.

Let’s break down the problems here.

Those who can, publish. Those who can’t, blog.” There are many researchers who do both, productively.

I understand that blogs can be useful in affording the general public insights into current science...” It’s nice that we bloggers got tossed a bone (no pun intended). But science blogs do not just help the general public; there are many technical comments on papers that help provide needed context for other scientists, whose own research is tangential to published research: close enough to see the relevance, but without the deep expertise needed to pick out specific problems.

(I)t often seems those who criticize or spend large amounts of time blogging are also those who don’t generate much publications themselves.” O’Connor is hypothesizing that there is an inverse correlation between blogging and primary literature. This an interesting empirical question. It’s true that time spent blogging is time that cannot be spent writing primary peer-reviewed journal articles, so prima facie, there might be truth to this. But as far as I know, there is no actual peer-reviewed literature on this. Will update this post if I find any.

If there were any valid criticisms to be made, the correct venue for these comments would be in a similar, peer-reviewed and citable published form.” The venue a claim is published in does not determine the validity of the claims. She is correct that certain journals are averse to citing non-peer reviewed material, and that putting material in the literature helps to assure the long-term findability of the critique. But these matters are not central to the main issue: is the criticism valid? Then it does not matter where it was published.

The internet is unchecked and the public often forgets that. They forget or are unaware that a published paper passed rigorous review by experts, which carries more validity than the opinion of some disgruntled scientist or amateur on the internet.” Some things on the Internet are unchecked. Some things on the Internet are rigoruously checked. It should also be noted that some journals that call themselves peer reviewed provide checks that are, at best, cursory (see here and here, for instance). Even “top” journals have published papers that made pro scientists ask, “How did this get published?” Has Dr. O’Connor not heard of arsenic life or STAP cells?

I find that criticism in social media is damaging to science, as it is to most aspects of our culture.” I’ve written a whole article (Faulkes 2014) about why I find that criticism in social media generally valuable. To name just two: it is rapid, and provides a way to bypass powerful gatekeepers with vested interests.

I have no idea what damaging effects of social media on culture she is referring to. It’s off topic, in any case.

Not surprisingly, as soon as someone on social media found this, this quote began spreading like wildfire. But there is apparently a backstory that is not spreading as fast. Jon Tennant wrote:

In this situation, she’s actually right. There's a core of semi-pro bloggers who attack her work/never formally publish anything.

I went digging. And I was surprised, because my first impressions are that Dr. O’Connor is not a stereotypical stick in the mud, conservative older scientist that is sort of the stereotype for critiques of blogging and social media. Honestly, she seems... kind of... awesome.

I went through the first ten pages of Google results, and found tons of positive stuff about her, including tons of stuff on blogs. She’s had lots of high profile papers. She’s done some science outreach. She strikes me as smart, outspoken, and a little unconventional. Jingmai O’Connor seems like exactly the sort of person I’d use a counter-example to the “scientists are old white dudes” stereotype.

I did a Google search for her name plus “blog.” Went through multiple pages and still found nothing negative about her, or controversies around her work. Tried her name plus “controversy.” Still nothing.

Maybe the blogging criticism is behind the Great Firewall of China.

Even when intentionally looking for the backstory that might have motivated her comment, I can’t find it. Whoever the bloggers are who have criticized her, they didn’t appear to make a big dent in her online reputation to an outsider like me. Which makes me all the more puzzled why she would paint all bloggers with such a broad brush.

It’s unfortunate. I hope that the criticism of her ill-advised comments don’t cement her “The Internet is bad” opinions. If she had a blog, I would be reading it.

Additional: Lengthened the blog post with a line by line fisking of the quote.


Faulkes Z. 2014. The vacuum shouts back: post-publication peer-review on social media. Neuron 82(2): 258-260. http://dx.doi.org/10.1016/j.neuron.2014.03.032

O’Connor J. 2016. Jingmai O’Connor. Current Biology 26(1): R11–R12. http://dx.doi.org/10.1016/j.cub.2015.11.046

External links

Jingmai O’Connor home page
Interview with Dr. O’Connor
A teacher can never tell where his influence stops
Fashionista: Jurassic Jingmai
Jingmai Kathleen O'Connor: Badass archeologist (sic)
Society for Vertebrate Paleontology 2014

Blogging is wonderful for science. More scientists should blog and tweet.
Chill out about Jingmai O’Connor’s criticism of bloggers

01 February 2016

DoctorZen.net moved

My home page, DoctorZen.net, has migrated over to a new institutional server. The old site will be up for a while until I get a redirect notice up, but it will eventually close as website support for my previous institution (The University of Texas-Pan American) transitions to my new one (The University of Texas Rio Grande Valley).

If you visit the site by a directly typing in the URL into a browser, you should see no difference.

If you bookmarked the homepage, take a moment to check that it links to the new URL:

You can let me know if there are any problems by emailing me at zen.faulkes@utrgv.edu.

Okay, SICB students and post-docs, I’m your guy

I knew this was coming, but I just got the official email.

I am writing to appoint you as Chair of the Student & Postdoctoral Affairs Committee within the Society for Integrative and Comparative Biology. Your appointment will be for three years, starting immediately and running until the end of the annual meeting in January of 2019.

I had been approached about this back before the last SICB meeting in Portland. I thought a very, very long time before stepping up and accepting this.

I was extremely hesitant about being another old white guy in a leadership position of a scientific society. This is especially true of a leadership position that is about engagement of young researchers, the place where our diversity in the sciences is the greatest.

I also paused when I considered that I’m at an institution with no doctoral programs or post-docs. Yes, I’m a graduate program coordinator for my department, but it’s a master’s program. Would I be in touch enough with the realities of the more advanced training programs that would make up the bulk of the constituents?

Finally, I had a truly selfish reason: committee work will cut into research time. And the research had been going well, and I don’t want that to stop.

Ultimately, one of the main reasons I agreed to do this was that the hint was dropped that if I didn’t do the student committee, the Executive Committee would keep after me to do something for the society. The judgement had been rendered, and it was all a question of how sentence would be carried out. I picked the devil I knew versus the one I didn’t.