29 April 2014

Tuesday Crustie: Plush

It’s return of Kiwa hirsuta, the yeti crab. How much do I love yeti crabs? Have you seen them dancing? But this time, it’s in huggable soft toy form!

You can find the pattern and instructions here.

External links

Meet Tasty, the stuffed Kiwa hirsuta

28 April 2014

Reverse empathy

“But what if they’re different?”

Empathy is the ability to realize what someone else experiences, because it would be what you would experience in that situation. Philip K. Dick used empathy as the standard for being human in Do Androids Dream of Electric Sheep? (dramatized as Blade Runner).

Another thing that can be important is reverse empathy: the ability to realize that what someone else experiences may be dramatically different from your experience in that situation.

This is something that comes into play all the time as a neurobiologist. Jakob von Uexküll was on that track when he coined the concept of Umwelt, or “sensory world.” von Uexküll realized that animals’ sensory abilities may be dramatically different to our own, and we can’t assume that something invisible to us is invisible to other species... or that what we can perceive, every other species can perceive.

It’s important in academia and mentoring, too. A common pattern is that someone says, “This is what I went through,” and someone else jumps in to nay say it. “I can’t believe that would happen.” “That’s not been my experience at all.” “Are you sure you didn’t misunderstand?” This is particularly prone to happen if the person describing their experience is female, minority, or otherwise seen as not very powerful.

We’re told to be empathetic, but maybe we should also practice asking ourselves, “But what if their experience isn’t like mine?”

24 April 2014

Cost of Elsevier journals by university enrolment

Tim Gowers has a long post on the cost of Elsevier journals. My contribution to the discussion is to plot data he showed in tables relating Elsevier subscription costs (bundles of journals) to university enrolment.

Whether university enrollment is the right predictor for subscription costs is a good question, but one that should be directed at Gowers, not me! I just plotted the data.

Here are the data for American universities (dashed line in linear regression, dotted lines are 95% confidence intervals, and a couple of outliers labeled). You can click to enlarge:

And here are data for UK universities:

I’m interested in the differences in slope of these two lines.

Update: Due to a request, here’s both countries plotted on the same graph. I converted pounds to American dollars using the current exchange rate on XE.com.

Now we can see that despite huge differences in enrolment, the price being paid by Cambridge and Arizona for the bundle of Elsevier journals are... not that different.

And for the truly geeky, here’s the linear regression for each.

United States: Y = 326185.525 + 33.96366 × X, r = 0.93621, n = 23, p < 0.0001

United Kingdom: Y = 363131.99382 + 36.07912 × X, r = 0.46124, n = 19, p = 0.04684

More updates: And because Richard Van Noorden posted more data on university income in the UK, I get to  make another graph:

“Because I was asked” update: Erika Saloman asked for this graph, showing cost as a function of university income per student:

Update, 28 April 2014
: The Scholastica blog makes an infographic out of Gowers’s data. It’s not terrible looking, but I like my graphs better than theirs.

22 April 2014

Top down hiring decision

Faculty searches at universities are usually driven by the faculty. Even if a dean or other administrator usually makes the offer, the search is usually run by faculty, who vote and make very strong recommendations for who to extend the offer to.

Which is why this is a surprise.

The University of Texas Board of Regents has, apparently, hired Dr. Abdullah (Faiz) Rahman as faculty member to join our department. It’s on page 355 in the meeting minutes.

And they’ve awarded him tenure, at the full professor level, up front.

And at a salary 66% higher than any other full professor in the department; about double the average for our tenured full professors (budget data here).

Dr. Rahman interviewed as part of the Valley STARS program, described here:

The ValleySTARs program will permit UTB and UTPA to request funding to cover faculty salary and benefits for no more than three years in support of their recruitment efforts for new “star” faculty to teach in STEM fields. Recruited faculty will be appointed to full-time, tenured positions. It is essential that the quantity and quality of teaching and learning in STEM fields is enhanced by state of the art teaching concepts and technology employed by scholar teachers.

The thing is: the faculty in our department never voted on this. We never voted on whether he met our tenure requirements. Apparently, neither did our equivalent department at University of Texas at Brownsville, who will also be part of the UTRGV in a little over a year.

It’s a very unusual move. And perhaps not one that will build bridges and engender the most good will.

External links

Faiz Rahman

Tuesday Crustie: “Wait... that’s no coconut!”

It would be quite a shock to be walking along in a forest, then look up...

Not a coconut, but a coconut crab, which is featured in this Wired piece a few months back.

External links

21 April 2014

Alternative metrics, but mainstream happiness

Because I am starved for attention, I have been obsessively watching the altmetric score for my article on post publication peer review in Neuron last week. It’s performed well from day one. But I’m screen grabbing this today:

“Other articles of a similar age in Neuron: Ranks 1st.”

Thanks to all who read the piece, tweeted, and shared it. I am grateful for your attention.

18 April 2014

The varieties of peer review

I’ve been very pleased with the response to my Neuron article on post-publication peer review. (Read more about the backstory here). The commentary on PubPeer got me thinking some more about the different kinds of peer review. In particular, the topic of pre-print servers like arXiv came up. I noted that arXiv is “moderated by experts”... which sounds kind of like peer review.

This lead me to thinking about the continuum from traditional pre-publication peer review to post-publication peer review, from “sanity test” to predicting “impact” or “importance.” Before you know it, I made this (click to enlarge):

Everyone wants peer review to be thorough and rigorous, so that’s the horizontal X axis. Because my last article was on post-publication peer review, the time relative to widespread distribution is the vertical Y axis.

Some points (like the two points for “Conference” and “Peer review”) are separated in the vertical Y axis to make the text legible, not because one always happens before the other. Likewise, each point should be a smear indicating a range, not a point. But this is just a first pass. Maybe this can help characterize the different kinds of peer review and commentary.

Additional: To answer a question posed by Jason Goldman, by “blog posts,” I had in mind blog posts by scientists.

Related posts

Kabuki theatre versus the mosh pit: notes from my Neuron article on post-publication peer review

16 April 2014

Kabuki theatre versus the mosh pit: notes from my Neuron article on post-publication peer review

I have a new article in Neuron! This is a pleasant surprise to me, because I never thought I would ever get anything in that journal.

One of the Neuron editors emailed me out of the blue in December, asking if I would be interested in doing an opinion piece for them about social media. (In this journal, opinion pieces are called “NeuronView.”) After a follow-up phone call, it became clear that she was interested not just in social media, but particularly how people are using it for post-publication peer review.

I wanted to do it, because it’s nice to be asked. As I said... Neuron!? Neuron! Being asked to write this article is an example of what is one of the most important points in it:

One of the most profound things about social media is that it has lowered the barrier to creating and spreading conversations.

Without social media, I don’t think someone like me would have had a shot at being asked to write a feature like this. There would be too many obstacles for me to start conversations: there are geographic barriers (physical isolation), disciplinary barriers (I’d never published in Neuron), and so on.

Even so, I was initially a little reluctant. I was in the middle of writing my Manuscript of Desperation (more on that one later). I was in the thick of prepping for the parasite symposium I was co-organizing with Kelly Weinersmith, and I knew manuscripts from that would be due early in the new year. I asked when it would be due. “End of February.” I decided I could probably make that happen.

I managed to get the article submitted a little early and exactly on length. From there, the editorial and proofing process was very fast and completed in early April.

My last task was to create an image for the Neuron home page (shown above). The production team decided they didn’t want to use an image with the Creative Commons credit text on it, but used it as a template to create a new image:

The problem with writing an article like this is that no matter how fast you write it, and how quickly it’s published, there will be things coming out after you sent in the article that you wish you could have talked about.

For instance, the day after I sent back the checked page proofs, I read this article about how blogging about a research paper leads to increased corrections.

I thought of adding in at the eleventh hour was a mention of the current STAP stem cell kerfuffle. When I submitted the article, this story hadn’t really taken off, but during the intervening time of reviewing, production, and proofreading, it just got bigger by the day. Bigger by the hour, almost. But I decided that the STAP case didn’t yet have any clear lessons for post-publication peer review that wasn’t shown by examples already in the paper.

Then, I learned of this story by Haier and colleagues concerning the editorial process at Neuron, the journal I had just written for (my piece was in press by then). The short version is that authors had been asked to write a preview piece. Haier and company submitted a critical article, and the journal pulled the plug on it. Commentary on the Neuroskeptic blog ensues (Haier et al. link to the blog, but not the specific article, which is here), which includes remarks from someone who had knowledge of the typically anonymous review process.

This is an excellent example of one of the issues I talk about in my Neuron article: the difficulty of getting critical commentary published. Haier and colleagues started this process in the second half of 2012, and only more a year later, in April 2014, are they able to detail their concerns about the editorial process.

I could have talked about the importance of sites like ScienceSeeker, Faculty of 1000, and Researchblogging in providing portals for post-publication peer review. ResearchBlogging was certainly critical to my own development as a science blogger.

But despite all that, I’m pretty happy about this piece. Sometimes, when you keep having to re-read something you wrote, you get a little sick of it. I’ve had to re-read this one quite a lot, and there are some turns of phrase in it that I still quite like.

Now, I’m looking forward to the post-publication peer review of my own paper! Whether you think I had anything interesting to say or whether you think I was wrong, wrong, wrongity wrong, please comment here on the blog, tweet your thoughts to me (@DoctorZen), write your own blog post, or whatever form of social media turns your crank.

Meanwhile, I’m going to enjoy seeing this on the home page of Neuron for the next two weeks:

Additional: The cycle begins... my article gets post-publication peer review on PubPeer. And thanks to those who have tweeted so far!

Update, 17 April 2014:  My article is open access at the Neuron home page here, but, weirdly, paywalled at Science Direct.

After a little after one day, I’m also very happy to see this article’s Altmetric score:

(T)his article has done particularly well and is in the 98th percentile: it’s in the top 5% of all articles ever tracked by Altmetric.

It is not surprising that an article about social media does particularly well on social media. But, as I said, it is nice nevertheless.

I’ve also created a Storify of some of the responses so far.


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

External links

The new dilemma of online peer review: too many places to post?
Online exposure ‘leads to higher research paper correction rate’
What can we do about junk science?
How intelligent is IQ?
Stick to Your Ribs: The Problems With Calling Comments “Post-Publication Peer-Review”
A guide to post publication peer review

Comments for first half of April 2014

Impact Story looks at what people consider to be obstacles publishing in “megajournals” like PLOS ONE. Their list is good, but it doesn’t have the number one reason I’ve heard for people not submitting there: $$$

Excusion Set looks at cranks and the deficit model of science communication. In other words, how can you communicate with someone who thinks you’re wrong?

I make a cameo appearance in this post at The Molecular Ecologist on why people sign their reviews of research papers.

ImpactStory looks at ORCIDs and why they should become as common as DOIs. Poster session organizers should ask for them, too!

15 April 2014

If I’m to be skeptical of open access publishing, I’d like to have good reasons

A.A. Agrawal (whose alliterative name I envy) has penned a letter saying the people should be skeptical of open access publishing. In brief, his reasons are:

1. “Some are for profit!” Just like most traditional scientific publishers. While Agrawal says this creates a conflict of interest, the profit incentive can also move journals to provide more and better services for authors at lower prices; see this interview with open access publisher Ahmed Hindawi.

Hindawi’s argument seems to be that in a subscription market librarians have no choice but to buy access to an entire journal in order to provide their institution’s researchers with access to any single article in it — since no other journal can substitute for the one in which the desired article has been published.

In an OA world, by contrast, authors will have the choice of taking their papers to a number of different publishers (i.e. shop around). And since the paper will be freely available to all once it is publisher, there can be no monopoly on access. This, says Hindawi, will drive prices down.

2. “Most don’t copy edit.” Data or citation needed.

3. “There isn’t a citation advantage.” This is the point that is most annoying, because it shows poor scholarship. Agrawal cites one study that finds no citation for advantage, but there have been many others. It’s worth having a look through this summary of many projects testing this hypothesis. Not all of them show an open access advantage, but many do. Picking one study alone, even if it’s a good one, smacks of confirmation bias.

4. “People care about journal prestige,” Alas, the “prestige” argument this is probably one of the main reasons that people will not consider particular open access journals. However, it ignores the prospects for article level metrics. And I am not impressed with an argument that can be rephrased as, “Your peers are lazy.”

Hat tip to Prof-like Substance.


Agrawal AA. 2014. Four more reasons to be skeptical of open-access publishing. Trends in Plant Science 19(3): 133.

Reposted at Always Researching, with a link here but not credit (yet). Hat tip to Ross Mounce for noticing.

Tuesday Crustie: Hello, world!

World, meet Gramastacus lacus. Gramastacus lacus, world.

This is an interesting new burrowing crayfish species. For one, it’s only the second in its genus. Second, it has an unusual way of walking on land. (I started my scientific career doing locomotion, so this fascinates me.)

There is a unique forward movement via a series of rhythmic plunges. The crayfish raises the cephalothorax and both claws up with its legs and then moves forward overbalancing and plunges down and forward then repeats the movement. This up and forward movement is unusual, but the crayfish easily moves up, forward and down without “missing a beat”.

I would love to see a video of this!I emailed the author, Robert McCormack, and he doesn’t have any yet. He tells me he’s put recording it, and putting it up on YouTube, onto his research agenda.

Not surprisingly, the headlines are focusing on things that don’t seem so notable. They are not really that small. The technical paper calls them “robust and strong” compared to the other species in their genus. The description on NBC news referring the “cannibal” nature of the crayfish is weird, given that pretty much every crayfish will make a meal out of another if the opportunity arises.

Hat tip to David Shiffman.


McCormack R. 2014. The eastern swamp crayfish Gramastacus lacus sp. n. (Decapoda, Parastacidae) a new species of freshwater crayfish from coastal New South Wales, Australia. ZooKeys 398:53-67. http://dx.doi.org/10.3897/zookeys.398.7544

External links

08 April 2014

Tueday Crustie: Eat my ride

From the Aquatilis Expedition (on Twitter here):

Hyperia galba is a small crustacean which uses jellyfish as its home and a source of food simultaneously.

Hat tip to Miss Mola Mola.

04 April 2014

Publishing may be a button, but publishing isn’t all we need

I’m hearing a lot of people say, “Publishing is a button” as a simple argument against scientific publishers and, to a lesser extent, journals: some scientists argue that both are completely unnecessary and have outlived their usefulness. This is a paraphrase of Clay Shirky; what he actually wrote was:

Publishing is going away. Because the word “publishing” means a cadre of professionals who are taking on the incredible difficulty and complexity and expense of making something public. That’s not a job anymore. That’s a button. There’s a button that says “publish,” and when you press it, it’s done.

Much like Stuart Brand’s quote “Information wants to be free” is often thrown out without acknowledging that the next line is “Information also wants to be expensive,” the Shirky sound bite overlooks something in his following paragraphs (my emphasis).

The question is, what are the parent professions needed around writing? Publishing isn’t one of them. Editing, we need, desperately. Fact-checking, we need. For some kinds of long-form texts, we need designers.

For scientific publishing, there are are least three things that are not just “buttons.” They need to be done by humans.

Quality control. Shirky alluded to this in his paragraph above. For academics, the major aspect of quality control means peer review. Some argue that pre-publication peer review doesn’t improve papers, but I think that’s a rare opinion. Most researchers who’ve been to this rodeo a few times will admit, however grudgingly, that reviewers have improved papers. For various reasons, I am not a fan of only post-publication review doing the job; more on this in an article that I will have out in Neuron in a couple of weeks. (Update, 21 April 2014: That article is here.)

Archiving. This is one of my biggest concerns with the “just stick it all on the web” approach, as I’ve mentioned before. I find so much link rot in my own blog. We need institutions that will outlast individual researchers, and currently, journals do that. Anyone who wants to get rid of scientific journals needs to pay attention to what institutions will take their place in curation and archiving. Björn Brembs has identified university libraries as a possible alternative for archiving, but we are a long way from that point yet.

Publicity and public relations. Some might argue that this wouldn’t be necessary in an ideal world. But even in this age of “help yourself to information” via search engines, lots of folks recognize that you can benefit a lot by thinking and working on “search engine optimization” (SEO). Putting something on the web does not guarantee people can find it. Publicizing research findings can be valuable. Some new research might have health or policy implications. Some we want to publicize because it’s cool, and it can help increase public understanding of science. And then there are the more limited but pragmatic considerations of individual scientists who want to enhance their reputation.

5 April 2014: In thinking about this a little more, I think Shirky’s idea might have been better expressed as, “Distribution is a button.” Printing things on paper and physically hauling it around the country, that’s largely been supplanted. But when you say “publishing” to most people, they are thinking about the things that Shirky still says are necessary: editors, designers, etc.

Related posts

Self archiving science is not the solution
Taxonomists as science survivalists
Scientific publishing and tree-shaped frosted sugar cookies

External links

How We Will Read: Clay Shirky
Publishing is a button: what Clay Shirky didn’t say 

01 April 2014

Tuesday Crustie: Taxi!

This is a Cape River crab (Potamonautes perlatus)... with passengers. A new paper by Badets and Du Preez (2014) shows how these crabs act as taxis for leeches (seen in the inset). While we often think of leeches as bloodsuckers, in this case, they are not harming the crab at all. They are simply using the crab as a way to be spread around in hope of finding their preferred host, the clawed frog (Xenopus laevis).


Badets M, Du Preez L. 2014. Phoretic interaction between the kangaroo leech Marsupiobdella africana (Hirudinea: Glossiphoniidae) and the cape river crab Potamonautes perlatus (Decapoda: Potamonautidae). International Journal for Parasitology: Parasites and Wildlife 3(1): 6–11. http://dx.doi.org/10.1016/j.ijppaw.2013.10.001

External links

ScienceShot: Kangaroo Leeches Use Horny Male Crabs as Taxicabs

Comments for second half of March 2014

Retraction Watch covers the graphical abstracts train wreck at Journal of Proteomics, which I wrote about here.

Terry McGlynn says scientists know how to communicate with the public.

I make a cameo in Mike Taylor’s post about putting more information in citations.