31 December 2015

So what happened this year?

In this, the mid-point of the second decade of the twenty-first century (which is still awkward because it doesn't really have a name... nobody calls it the “teens” or anything), what happened for me professionally?

When the year started, I was an associate professor at The University of Texas Pan American. When the year ended, I was a professor at The University of Texas Rio Grande Valley.

I made up a word. And, shockingly, people noticed it. Make you cite this post when you add “kiloauthors”, Oxford English Dictionary!

I saw a rock fall out of the sky!

My name was on the cover of a time travelling book that arrived in print this year, even though every place in the book says it was published in 2016.

My little presentation ebook I self-published got reviewed by the awesome Natalie Morales (who’s the best reason to watch The Grinder) and was translated into Russian.

I wrote or contributed to some review articles.

But I was happiest about publishing three reasonably big data-driven papers this year (plus a note): one with the most direct test of the “lobster in the pot” problem yet, one on beautiful giant neurons in shrimp, and one the crayfish pet trade. And two of them were all me. I’m happy that I still collect my own data, and not just write grants and supervise other people’s research. I want more like those in 2016, please!

But it’ll be tricky. Currently, the only thing I have in press is a chapter in the forthcoming Science Blogging book. Data collection on two projects is officially complete today, but there are, of course, lots of other teaching and service tasks to do.

Note to self:


28 December 2015

Time policing

Are you reading the blog post from your home or your office?

It’s the start of the week between Christmas and New Year’s. There is a lot of discussion on my social media feed today about academic work, I think prompted by this tweet:

Quick test to see if you're going to “make it” in academia: Are you working this week?

As advice, it’s dumb. Whether you’re working this week is no test of whether you will be a successful academic. Lots of people might work this week, but work on the wrong things. Like writing a blog post instead of that NSF pre-proposal... but I digress.

As a joke, it’s mean. It suggests overwork is the norm in academia, and that if you’re not working now, you are obviously inferior.

Academia has a deep and sometimes oppressive culture of overwork. There are many examples on this blog. There was Scott Kern saying colleagues lacked passion because research labs were empty on evenings and weekends. More recently, Eletftherios Diamandis wrote about how he worked sixteen hours a day, left childcare to his wife, and had his kids playing in the lobby and eating food from the microwave – and this was in a career advice column as an exemplar of success.

Put that attitude together in a person whose position gives them a fair amount of power and minimal oversight – like someone in charge of a grad student or post-doc – and you have the potential for stressful, terrible situations where people work like dogs because they think there is no alternative.

That said... I am a bit concerned by the potential for time policing that’s hinted at in the reactions to this tweet, and in similar situations.

First, a lot of people outside of academia have to work the week between Christmas and New Year’s. For most people, suggesting that you work this week is not something that only a Dickensian factory owner would say. That is is even an argument could contribute to the perception among non-academics that academics are overpaid, lazy fat cats.

Second, we should be careful about criticizing academics who do choose to work this week. There are many reasons to do so.

I have animals that need feeding and looking after. It’s my job to look after them. I don’t like the implication that I’m contributing to a workaholic culture because I’m doing animal care.

There are also externalities that work against taking this week off for many people. For instance, for biologists, the Society for Integrative and Comparative Biology meeting is held in early January. The deadline for many National Science Foundation pre-proposals is in January. Yes, in theory, people are well organized to have completed all those proposal and presentations and posters before Christmas, but in actuality, for real people, this is a good time to do that work.

And that sort of leads into my biggest point. Is it so bad to like what you do? SciCurious wrote:

Well, I mean...it doesn't help that I...enjoy work. A lot. Part of academic conditioning?

I’m reluctant to admit that I am in the office writing this post, and that I’m happy about working this week. I like the quiet. I like that I don’t have meetings or deadlines. Yet if you’re an academic who likes working more than 40 hours a week, you can be tagged as part of the problem and a victim of mindwashing. For instance:

Nobody dies wishing they published one more paper.

We’re expected to resent work. Mike Rowe talks about this, based in part on his experience on the TV show Dirty Jobs (emphasis added):

We’ve declared war on work, as a society, all of us. It’s a civil war. It’s a cold war, really. We didn’t set out to do it and we didn’t twist our mustache in some Machiavellian way, but we’ve done it. ... We’ve waged this war on Madison Avenue. I mean, so many of the commercials that come out there – in the way of a message, what’s really being said? Your life would be better if you could work a little less, if you didn’t have to work so hard, if you could get home a little earlier, if you could retire a little faster, if you could punch out a little sooner – it’s all in there, over and over, again and again.

A job well done is rewarding. It’s rewarding to be able to look back and see that you have created a body of work. Some people might die wishing they had created more, or done more professionally, or solved an unanswered question. Why should regrets about unfinished things be confined to the personal, non-work realm?

We do have to be careful not to let that desire to work become a macho bullshit test of endurance. In academia, feeling guilt over not working is almost infinitely more common that feeling shame about working when others are not. The expectation that research academics should work long hours, including evenings, weekends, and holidays, is the bigger problem.

But you shouldn’t be made to feel embarrassed if you’re working this week and you’re happy about it. While we’re pushing back against a very real culture of overwork, let’s not forget how great it is to have work that is fulfilling.

Update: I’m tempted to characterize this as another example of work shaming:

Maybe the most relevant answer to academic productivity discussions on Dec 29th is “Nobody cares, go get a life.”

More additional: Post edited for emphasis and clarity, prompted by Julie Brommaert.

Related posts

My new work week
Why cure disease?Why cure disease?
Glorifying overworking: another self-inflicted crisis in Science Careers

21 December 2015

Beta testing UTRGV

Grades were due today, marking the official end of UTRGV’s first semester.  How did we do?

Well, we kept the wheels on the bus. The university did not grind to a screeching halt, and students took their classes.

But it’s been a rough semester.

After all the “We are one” pep talks at the start of the semester about the distributed campuses in Edinburg, Brownsville, and so on, I saw a whole lot of people who didn’t get that memo. There didn’t seem to be a lot of work into building bridges between the campuses. Quite the opposite: I saw efforts that seemed designed to insulate people at one campus or another.

When UTRGV was pitched, one of the selling points to the politicians and state administrators would be that UTRGV would be less expensive than UTB and UTPA because the number of administrators would be halved. Instead of a president, provost, and college deans at two universities, there would only be one of each.

Instead of streamlining administration, there are clear signs of huge administrative bloat. While it is true that there is only one dean for each college (for example), what wasn’t factored into the discussion was the rapid proliferation of vice provosts, assistant deans, deputy administrators, and sub-vice deputy positions. So far, I haven’t seen any cases of these administrative positions adding any value to the tasks I need to complete. So far, the only power these individuals seem to have is the power to call meetings.

The first semester was like the beta release of UTRGV. Functional, but buggy and glitchy. I think Beta testing will be continuing for at least one more semester.

Picture from here.

18 December 2015

Today is the day and I just can’t wait!

Today is the day I will finish grading this last assignment I gave my neurobiology students! Just five left! I cannot remember the last time grading has taken so long and taken so much out of me. It’s been tough this semester.

Oh yeah, there’s also a sequel out to a movie that rocked my world some thirty odd years ago.


But apart from this blog post, I am staying off social media for a few days* until I can submit my final grades and avoid all the trolls posting Star Wars spoilers!

* Except maybe Google Plus. Because not much ever happens there, right?

15 December 2015

Tuesday Crustie: Dream house

I’ve shown custom hermit crab shells on the blog before, but artist Aki Inomata has made the more beautiful I've seen.



More here.

Hat tip to Amy Freitang and Liz Neeley.

External links

Why not hand over a shelter to hermit crabs?

14 December 2015

Bad design used to make a good point

Michael Eisen recently took all the journal titles off descriptions of his papers on his lab website. This upset some people, which Eisen chalked it up to “the cult of the journal title.”

Alternate hypothesis: maybe it upset people because it was a bad design decision.

I’ve explored design a lot over at the Better Posters blog, and one of the most powerful lessons I’ve learned has been that good design is about empathy. Good designers empathize with their users, anticipate their needs, and fulfill their needs.

One of the things a person going to a lab publication list wants to do is to be able to find articles that interest them. Removing journal titles makes it harder for users to find articles. And while many (but, importantly, not all) articles have DOIs and links, they are not necessarily things that people relate to as much as a journal title. If you need to scribble a reference on a piece of paper, a journal, volume, and first page number is easier than a DOI link.

The argument that you don’t need journal titles because everything is on the Internet overlooks that the Internet doesn’t need journal articles. People do. People have to work with imperfect memories (some of us more than others) before starting a search on Google Scholar or PubMed. There are many papers that I look at, and I will never commit the DOI or link to memory. I remember the journal that papers were published in quite regularly, though. I don’t remember journals because of their Impact Factors, but because of the content of the journal, the layout and formatting, and other features. A PLOS ONE paper looks different than a PeerJ paper.

By removing a piece of information that users expect and want, Eisen is not meeting the user’s needs. Quite the opposite, he’s explicitly criticizing users who want this information. But good design is not about the designer. It’s about the experience of the end user.

That said, running in the opposite direction is no better:


This was a joke from Yoav Gilad (archived by Claus Wilke; it doesn’t look like that now). But for the sake of argument, let’s analyze it anyway. Here, the changes in text size for the journals (related to Impact Factor) is, for those outside of academia, pointless, and therefore confusing. For those in academia, it looks like an ego trip. (“Oooh, look at the fancy journal I published in!”)

Again: design is not about you.

Now, there is more to life than good design. Removing journal titles from a publication list is a successful act of advocacy against evaluation by “prestige,” which is a much-needed discussion to have. But it may be that users are upset not (only?) because of a cultish belief that journal titles are important signifiers of quality, but because they realize that the design effectively gives them the finger by leaving out something they want.

Update, 15 December 2015: Expanded the post with Gilad’s joke and more discussion.

External links

What’s in a journal name?
Picture from here.

11 December 2015

A strange attack on tenure from Science

Science’s latest editorial is a strange attack on tenure that seems to have originated from some non-academic think-tank rather than anyone associated with academia. But it’s penned by editor Marcia McNutt.

McNutt opens with a strange argument that tenure is preventing women from succeeding in academia.

(Women) are still underrepresented among tenured faculty as compared to, for example, the number of women in similar positions that do not require tenure... A major reason is that young academics must concentrate on their careers to earn tenure at the same time as they would be starting their families, and this issue affects women disproportionately more. ... Whether women see the tenure hurdle and opt out for family instead, or just never opted in to begin with, the result is that there are too few women for a diverse academic enterprise, and if this process does not evolve, how can the highest institutes of learning promote academic freedom and progress?

So let me get this straight. The institution of tenure is the problem for women, and not, say, unrealistic expectations of tenure decision makers, who, by pretty much every set of summary statistics out there, are over-represented by men?

I am willing to bet not one woman working in academic who would feel that their prospects of continued employment would be enhanced by the removal of tenure.

McNutt then argues that, darn it, professors are just old dogs who can’t learn new tricks.

(N)ot all tenured faculty are motivated to stay abreast of new developments. What might have been a booming job market 20 years ago when a faculty member earned tenure may be entirely moribund now. ... Today, tenured professors can continue to hold their positions 40 to 50 years past the date when they received tenure.

Fortunately, I only had to wait a day before this profile of active, engaged researchers who are past traditional retirement age but still doing good science. McNutt’s argument is discriminatory and ageist.

Revising the tenure system to a more flexible form of employment is not going to be easy. ... Those hurt by the system are powerless.

It’s not clear to me who is hurt by the tenure system. I think McNutt is trying to argue that young academics, particularly women, are hurt, because they are more likely to take non-tenured positions. That is not a problem with tenure. This is a problem with adminstrators trying to cut costs.

McNutt’s suggests basically that universities should just give the finger to their tenure faculty and ideals of shared governance.

But it's time for universities to discuss unilateral action and institute some other mechanism.

The editorial comes just a day before this news of faculty – including tenured faculty – being cut from College of Saint Rose. So... yeah. Tenure provides tissue-thin job protection already.

For example, promotion to associate professor could be rewarded with a longer-term contract (10 years), followed by a series of renewable 10-year contracts (or in rare cases, longer contracts) as a full professor. The contracts would be nonbinding, giving the faculty member flexibility to consider opportunities at other institutions.

Oh! How generous! We have to get rid of tenure to make it easier for people to find new work! Because that’s what people want, to have less stability in their lives!

An appeals process (through a national university association) could adjudicate contract disputes or cases of dismissal on grounds of intellectual disagreements.

I’d be more encouraged is I had ever heard of a case of such a mechanism working. In the United States at least, universities are largely under the regulation of the states, so it’s not clear how any national organization could have any teeth.

For goodness’ sake, tenure is not the problem here. The problem is administrators have been cheap, and have tended to exploit their non-tenured faculty with heavy responsibilities and few benefits because they could. Instead of tearing down tenure and turning everyone into contingent faculty and wondering nomads, why can’t we do the opposite?

Why can we not give women on the tenure clock with reasonable performance expectations, not those determined by workaholics with no other responsibilities?

Why can we not provide adjunct and contingent faculty with some of the job security and resources that tenure people enjoy?

Why can we not have strong post-tenure review that ensures that people continue to be competent at their job?

Tenure is not supposed to be a guarantee of a job for life. It’s supposed to provide security against arbitrary dismissal. That long-term security is valuable for research, and I suspect provides a strong incentive for people to work at universities. It certainly did for me.

Pay at universities is often lower than similar positions in the private sector. Would universities who got rid of tenure be willing to bring their pay in line with what people could get in industry? My guess is, “No.”

When McNutt became editor of Science, lots said, “Hey, it’s great to have a woman in charge of Science!” But this editorial is just the latest in a repeated set of regressive articles getting by Science’s editorial team, which have regularly seemed to involve gender issues, and McNutt’s presence as editor doesn’t seem to be slowing things down. I just don’t get it.

Hat tip to Terry McGlynn and Bashir3000.

Additional: In an unrelated but somehow in the same vein of deeply problematic: AAAS, the publisher of Science, elected Patrick Harran a fellow of the society. Harran was charged with four counts of felony following the death of an undergraduate student in a lab accident. More at the Curious Wavefunction and Chemjobber.

Related posts

Breaking brand: Science magazine’s latest self-inflicted crisis

External links

Whither (wither?) tenure?
Saint Rose faculty informed of cuts Friday

“Hey, did anyone win a Nobel?”

Earlier this week, I got one of those emails that had been forwarded through the administrative chain (Provost’s office to dean to associate dean to department chair to faculty).

“Our Strategic Analysis office need to know what awards our faculty have won!”

I keep wondering why individual faculty are being asked to for this information through email when our institution subscribes to a service called Digital Measures that tracks this stuff. Faculty enter their achievements in the system, and people can pull reports from it at any time. I also wonder why this information can’t be pulled from the annual reports faculty have to submit every year.

Although I hadn’t won any awards, I opened up the spreadsheet to see what they were looking for. First line of the spreadsheet:

Nobel prize.

Eyebrow raise.


I keep looking down the list. Pulitzer prize. McArthur award. Awards that get international coverage.

If a faculty member won a Nobel prize, most universities would have press releases sent to every major news outlet and announcements up on their website out before the first morning coffee break.

The thought that adminstration has to ask, “By the way, did anyone on our campus win a Nobel while we weren’t looking?” makes adminstrators look like they’re isolated in some alternate universe bubble that only rarely connects to our own, and they occasionally manage to break through for a brief peek at what’s happening in the reality of faculty, staff, students, and major media outlets.


08 December 2015

Tuesday Crustie: Down deep

This crustacean isn’t big, but space is in short supply when you’re 1.4 kilometers under the surface of the earth.


This little animal may be a copepod - Borgonie and colleagues (2015) list it as Amphiascoides with a question mark behind it, but provide no more details.

This picture has been contrast enhanced from the original in the journal article.

Reference


Borgonie G, Linage-Alvarez B, Ojo AO, Mundle SOC, Freese LB, Van Rooyen C, Kuloyo O, Albertyn J, Pohl C, Cason ED, Vermeulen J, Pienaar C, Litthauer D, Van Niekerk H, Van Eeden J, Sherwood. Lollar B, Onstott TC, Van Heerden E. 2015. Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa. Nature Communications 6: 8952. http://dx.doi.org/doi:10.1038/ncomms9952

External link 

Animals found living in rock deep, deep underground

02 December 2015

Ideas are cheap

In tooling around Quora, I see a lot of questions from non-scientists that sort of run like this:

“I have an idea! How do I proclaim it to science?”

I’ve heard that authors get similar things all the time. Someone will approach them and say, “I have this great idea for a book. Why don’t I tell you the idea, you write it, and we’ll split the profits?” To which the writer says, “So... you want me to do all the work, and you take half of the money? Thank you, but no.”

To top it off, when people tell the author their brilliant idea for a book, the idea is usually hackneyed and trite. “A man and a woman in a space ship crash land on a deserted alien planet. Their names are.... wait for it... Adam and Eve. Brilliant, huh?”

The cold reality is scientists will probably think your idea is not worthy of their time or talents. Scientists have ideas of their own that they want to test. They don’t lack for ideas.

This is not a knock against non-scientists having ideas. Scientists have much the same reaction to ideas from other scientists. Most of them are not going to influence the research questions that we already want to solve.

Ideas are cheap and plentiful. Testing them is hard.

That’s not to say that scientists don’t need to have ideas. Far from it. One of the reasons why first authorship of papers is so critical for early career scientists is that middle authorship is associated with being a data collector, not the intellectual driver of the project.

To be a scientist, you need ideas plus willingness to put in the grunt work.

External links

The efficient research hypothesis

01 December 2015

Tuesday Crustie: Funding a familiar face


Ah, Emerita analoga. It’s been a while. What have you been up to?

Emerita analoga is one of the sand crabs species I studied for my doctoral work. I found this picture in the usual roundabout way. I was reading an article on science crowdfunding (a topic with which I have substantial experience, though I say it myself) at UT Austin. I went to check out the UT Austin crowdfunding site, Hornraiser, and stumbled across the familiar face above. It’s a project I’m happy to support!

The project is on Emerita analoga’s distribution, which is pretty interesting (shown in green in the map below, from here):


They have these two disconnected places they live: the west coast of North America, from Alaska down to California. They stop through Central America, and pick up again along the coast of Peru and Chile. Are those two different populations connected at all? Are they really the same species, or are they two different species genetically?

I’m happy to support this project! And, of course, you can, too! Because sand crabs are super cute crusties and are awesome!

But where were you when I was doing this kind of crowdfunding stuff years ago, Texas Tribune? Huh?

External links

With Federal Funding Elusive, Professors Crowdfund ResearchAssessing Retention in Sand Crab Populations

25 November 2015

Academic boycotts

Mark Carrigan’s website poses this question as part of a lead-up to a roundtable in early December:

Why have researchers been so ready to campaign against for-profit academic publishers such as Elsevier, Springer, Wiley-Blackwell, and Taylor & Francis/Informa, but not against for-profit platforms such as Academia.edu, ResearchGate, and Google Scholar?

Because “someone’s making money” isn’t what bugs researchers. What bugs researchers is being impeded from the business of doing their research.

Paywalls and subscription fees obstruct academics trying to do research.

Platforms like Google Scholar facilitate research. I could not do my job half as effectively if Google Scholar didn’t exist. Academia and ResearchGate haven’t been as useful yet, but I have never felt the frustration in using them like I have when I’ve hit the “pay now” screen for that article I want to read..

It’s also worth noting that the original question contains an assumption: that campaigns against for-profit publishers are major academic movements. But those calls for boycotts have...well... not exactly left those business struggling. They are still highly profitable, and show no visible signs of worrying that academics are going to stop submitting papers to their journals.

External links

As Academia.edu Grows, Some Scholars Voice Concerns

24 November 2015

Tuesday Crustie: Flat footed

I’m such a sucker for digging crustaceans...


One of the matutid digging crabs, Ashtoret lunaris. Look at those lovely digging feet!

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

23 November 2015

Getting what’s paid for, scientific publishing edition


I like open access, but I think for profit publishers can continue to have a role in the scientific publishing ecosystem. But boy oh boy, some academic publishers do make it hard for a body to support them.

Recently, two independent blog posts from two separate scientists described the same problem from two separate publishers: both were downloading a lot of papers from their academic library for research purposes, and libraries were threatened by the publishers.

In both cases, the libraries had fully paid subscriptions to these journals.

Case one from Chris Hartgerink:

I started ‘bulk’ downloading research papers from, for instance, Sciencedirect. I was doing this for scholarly purposes and took into account potential server load by limiting the amount of papers I downloaded per minute to 9. I had no intention to redistribute the downloaded materials, had legal access to them because my university pays a subscription, and I only wanted to extract facts from these papers. ...

Elsevier notified my university that this was a violation of the access contract, that this could be considered stealing of content, and that they wanted it to stop.

Case two:

I was frequently obstructed by BioOne. My IP address kept getting blocked, stopping me from downloading any further papers from this publisher. I should note here that my institution (NHMUK) pays BioOne to provide access to all their papers – my access is both legitimate and paid-for. ...

I swiftly found out that downloading more that 100 full text articles in a single session is automatically deemed “excessive” and “a violation of permissible activity”.

My reaction is to give these publishers some high level side eye.

This is mind boggling. It’s so completely at odds with people’s understanding of what you should get from paying a subscription to an online resource. If your institution’s subscription fees are paid up, you should be able to access the resource. End of story.

Additional: Nature News picked up the first half of this story and covered Elsevier’s actions. Meanwhile, Elsevier has attempted to fix the situation, but Chris Hartgerink says Elsevier’s solution is not a very good one. It imposes several restrictions on the license, and doesn’t include images, which are necessary for the research.

External links

Traditional Publishers: please stop blocking research
Elsevier stopped me doing my research

20 November 2015

From spreadsheet to synthesis: my last paper from UTPA


My latest paper started as a spreadsheet.

During the writing of my last paper on the crayfish pet trade (described here), I was kind of surprised that I kept finding new papers about pet crayfish. I cited these in my paper, but mainly for the total numbers of species sold in different countries. I realized that I didn’t have a clear picture in my head of what the common species might be across all the places that had been examined.

So I made a great big spreadsheet compiling all the crayfish species sold as pets in all the countries from all the papers I could find. And I started to get a sense of the patterns. Here’s a visual (click to enlarge):


Germany was the hotspot for pet crayfish, by a long, long way. But as you can see from the map, the places that have been examined are patchy. I thought if I didn’t have a clear picture in my head, maybe others didn’t either.

So I wrote a review article.

Academics sometimes tend to view review articles as “make work” projects. Reviews are the things you write because you’ve hit a dry spell and can’t publish a data-driven experimental paper. You know, a real paper.

I get that. I’m proud of my data-driven papers. But there are a factors that can make a review very valuable.

First, when the literature is scattered, or in hard to get journals, a review provides people with a key to finding that literature. That was definitely the case here. These papers were published in were often obscure (thank goodness for Google Scholar and alerts), at least to me. There were many key papers in journals I’d never heard of before.

Second, when the literature is new, a review can draw attention to an emerging research topic. All the literature was pretty recent: 2010 and onwards. There wasn’t archival research that I could find on aquarium keeping in the twentieth century.

Third, when the research field is new, the literature is likely to be disconnected. A review of a new research topic can show where the empty spaces in knowledge are, and point ways forward. For instance, in this paper, I think one of the things that hasn’t been talked about explicitly in other papers is the supply chain from crayfish harvest to owner.

This was a fairly quick project compared to many of my papers. In some ways, I almost wish I had waited a little bit longer to submit. I didn’t think of including a couple of figures, like the map above, until it was too late. A new article about crayfish as pets in Japan appeared in the International Association of Astacology newsletter just before this article appeared.

On the other hand, I did sneak in some new data. It was data should have been in an earlier paper, but I hadn’t bothered to do the calculations until I had to give a presentation.

The journal, Crustacean Research, is a well-established society journal in Japan, but a new one to me. When I heard about it earlier this year, I kept it in mind for my papers. I like publishing in different journals, rather than going back to the same ones over and over. I like the challenge of having articles scrutinized by different sets of people, rather than going back to the same journal over and over again because you think the editor likes your work.

I liked that the journal is open access, and had moderate article charges. I had not submitted to them before, partly because their PDF production was slightly lower quality than other journals. But they just changed their production this year, and their new PDFs are as sharp as any other journal.

This paper has some personal significance for me, because it was the last I created under the auspices of The University of Texas Pan American. I completed it and submitted it two weeks before the university ceased to exist and I became a professor at The University of Texas Rio Grande Valley. The one trace of how close it was to the transition was that while I listed UTPA as my institutional affiliation, I gave UTRGV as my email. I listed my new email because I knew my UTPA email account would be dead in a few months.

And, as has been the tradition this year, I celebrated the publication of this review by dipping into my stash of Canadian chocolate:


Update, 21 November 2015: I just uploaded the spreadsheet that started this all to figshare. And I added in that newsletter article I mentioned, just for extra usefulness.

Related posts

A clone and two dwarfs
Can civil servants defuse a bomb? An Irish crayfish problem
How much is that crayfish in the window?
Tracking Crayfish Zero: The threat of pet crayfish

Throwing out the pennies

On not publishing results because they won’t end up in glam journals:

Refusing to release findings that you have already worked on, just because their most likely outlet has low standards, is like throwing all pennies out of your house because having them around make you look cheap.

Giner-Sorolla R. 2012. Science or art? How aesthetic standards grease the way through the publication bottleneck but undermine science. Perspectives on Psychological Science 7(6): 562-571. http://dxd.oi.org/10.1177/1745691612457576

Image from here.

18 November 2015

Presentation Tips for people in a hurry

Batman: [reads the second riddle] What people are always in a hurry?

Robin: Rushing people... Russians!

I’m very excited to announce that my itty-bitty ebook, Presentation Tips, is now available in Russian!


You can download the Russian language PDF here.

This translation is courtesy of Maksim, who took advantage of the book’s Creative Commons license. I’m so pleased someone found this resource useful enough to translate, and I thank Maksim to no end.

This arrives on the heels of yesterday’s post (about a citation of my paper published as blog post). Both the blogged paper and this ebook were released about the same time. Both were experiments in bypassing the traditional publishing route, just to see if you could make an impact. It took a few years, but it feels vindicating to see that these projects have made ripples, and didn’t vanish without a trace.

I never thought I would see my name in Cyrillic, never mind an entire work of mine in a language other than English.

External links

Подсказки докладчикам (Зен Фолкс, 2012)

Related posts

Presentation tips compiled
Presentation Tips for Kindle
Upload the universe: validating self-publishing
2012: waiting and DIY
Fanboying

17 November 2015

Science Blogging: The Essential Guide book cover reveal


I like it. Subdued and understated.

Related posts

Science blogging book: now with blurbs!

External links

Sci Blogging Guide Facebook Page
Yale University Press page
Amazon page

Paper published on this blog is cited because it’s a paper published on a blog

A few years ago, I published an original, data driven research paper here on this blog. As I wrote in a companion post:

I thought, “Let’s try something new.” ... I’ve also been paying attention to the people who say that scientific publishing is broken, and we should blow it up and start over. Lots of those people are basically advocating what I just did yesterday: “just blog the paper.” ...

Could blogging research work?

The acid test for whether blogging research could work is the same acid test for any academic product: do other people find it useful enough to re-use it? Usually, they show this by citing it. Admittedly, some journals are very narrow minded in what they allow you to cite, so that’s a big barrier for showing that others are using non-traditional online resources like pre-prints, blog posts, etc.

But I’m pleased to report that my crazy “self-published on a blog” paper has just got its first citation in an academic journal (Kooy, in press)!

As I expected, though, it’s being cited not because of the biology, but because it’s a paper on a blog.

Some scholars even post their research data and findings to their blogs.32

32 See for example, Zen Faulkes, “The Distal Leg Motor Neurons of Slipper Lobsters, Ibacus Spp. (Decapoda, Scyllaridae)," NeuroDojo, September 6, 2012, accessed January 3, 2015, http://neurodojo.blogspot.com/2012/09/Ibacus.html.

I expected this. The paper has been viewed 3,947 times, according to Blogger. The companion post explaining why I published the paper on this blog has been viewed 11,832 times. Publishing a paper is barely worth a mention, except to the authors and a few colleagues in the field. But publishing a paper on a blog is still remarkable. In fact, more than three years on, I can’t think of (m)any other examples where people have published entire original papers on their blogs.

Instead, biology is coming around to the concept of pre-prints. I think many people think of a pre-print server as a strange sort of journal: both serve to bundle traditional research articles in a single one-stop location. Plus, pre-print servers have been long running enough in areas like physics that depositing a paper on a pre-print server is a conservative move. Blogging a paper is still a radical act.

I am very happy that my publishing experiment has been cited by others. It’s a win for the discussion of alternate ways of publishing.

But I still crave complete victory: to see the paper cited by others because of the science, not just because it’s a paper on a blog.

Reference

Faulkes Z. 2012. The distal leg motor neurons of slipper lobsters, Ibacus spp. (Decapoda, Scyllaridae). NeuroDojo (blog): http://neurodojo.blogspot.com/2012/09/Ibacus.html [PDF version for printing]

Kooy BK. Building virtually free subject area expertise through social media: an exploratory study. College & Research Libraries: in press. http://crl.acrl.org/content/early/2015/08/11/crl15-759.abstract


Related posts

Why I published a paper on my blog instead of a journal
Why can’t I cite Mythbusters?

External links

Pre-print power

12 November 2015

Science blogging book: now with blurbs!

Science Blogging: The Essential Guide is now available for pre-order on Amazon!

The fun thing about the Amazon page, in comparison to the publisher’s page for the book, are a series of juicy blurbs. Here’s a couple:

“The word ‘essential’ is often overused but in this case, it suits perfectly.” — Deborah Blum, Director of Knight Science Journalism Program at MIT

“This is the guidebook science blogging deserves, and that every science blogger needs to read.” — Thomas Hayden, coeditor of The Science Writers’ Handbook: Everything You Need to Know to Pitch, Publish, and Prosper in the Digital Age

There you have it. You need a copy of this book! Make sure to order yours!

10 November 2015

Tuesday Crustie: Old hermit

And I mean really old... like, the Cretaceous.

Hermit crabs have a lot of flexibility in the shells they use, and different kinds of species have made shells over the millennia. So it’s surprising that we find hermits in shells of species that no longer exist, like ammonites:


Here’s a reconstruction of what that might have looked like:


The shells looks a little bigger in proportion to the crab that modern snail shells. But any ol’ port in a storm.

Reference

Fraaije RHB. 2003. The oldest in situ hermit crab from the Lower Cretaceous of Speeton, UK. Palaeontology 46(1): 53–57. http://dx.doi.org/10.1111/1475-4983.00286

Hat tip to Tim Ziegler (here) and Louise Johnson on Twitter.

05 November 2015

When you can say “There’s a lot we don’t know” (and when you can’t)

I’ve been digging Larry Wilmore’s The Nightly Show. Last night’s panel had this wonderful little exchange that was cut from broadcast, so I wanted to give it a little more visibility:

Larry Wilmore: But do you think dinosaurs were chasing Jesus?

Carl Lentz: (Laughs) Oh, man, that’s, uh… there’s a, there’s a lot we don’t know.

Neil DeGrasse Tyson: No no no we know… if… we know, if Jesus existed, if Jesus coexisted with other human beings on earth, he was not riding the back of any dinosaur. So we know that. You can’t say, “There’s a lot we don’t know” after someone says, “Was Jesus around hanging with the dinosaurs?”

Video below the fold.

03 November 2015

Tusday Crustie: Cutie

Great new crustacean species keep appearing! And this is a new genus, too!


Meet Aletheiana tenella, a new species from Indonesia. Lovely little guy!

Reference

Ng PKL, Lukhaup C. 2015. Aletheiana tenella, a new genus and new species of freshwater hymenosomatid crab (Crustacea: Decapoda: Brachyura) from Central Sulawesi, Indonesia. Zootaxa 4039(1): 118-128. http://dx.doi.org/10.11646/zootaxa.4039.1.4

28 October 2015

Putting on the cleaning gloves

“I have to clean the tub today.”


The tub’s been dirty for a while, but you finally have a quiet Sunday morning. So you pull on the cleaning gloves, get out a scrubber or rag for one hand, and put a bottle of cleaner in the other. You fully intend just to get rid of the soap scum in your tub.

But then you think, “I’ve already got the gloves on, and I’ve got the rag and cleaner, so I might as well do the bathroom sink.”

By the time the gloves come off, you’ve done the tub, bathroom sink, toilet, and kitchen sinks and counters.

For that reason, anytime you start a scientific project, open up your writing program and save a file. Even if it’s just a title, a few headings, your address, and maybe a few lines of introduction. If you have enough of an to start collecting data, you have enough of an idea to know, in broad strokes, some of the stuff you need to say in the introduction.

It’s easier to continue projects than it is to start them.

26 October 2015

Dubious journals from major scientific publishers: Homeopathy

Consumer Reports recently looked into homeopathic remedies. It was pretty timid repudiation, but did contain this critical line:

That makes no scientific sense, our experts say.

In this regard, Consumer Reports seems to be ahead of the giant science publisher Elsevier. Elsevier publishes an entire journal titled Homeopathy.


I was reminded of Homeopathy when Jane Hu commented that Elsevier’s journal Medical Hypotheses is “The X-Files division of Elsevier.”

Medical Hypotheses was intended to be a journal that would let people put out ideas that would be hard to publish in more conservative journals. This mostly meant ditching peer review, and a lot of crazy stuff got into its pages. I have never heard anyone praise a paper from Medical Hypotheses as demonstrably advancing a field. But I am at least sympathetic to the idea that maybe some speculative ideas need a home.

But if Medical Hypotheses is Elsevier’s X-Files, Homeopathy is its Area 51.

I hate to be blunt, and expect someone call me names, but... Homeopathy is crazy. Homeopathy is pseudoscience. It has no theoretical mechanism for action. It has failed test after test after test. It does not work.

Not only is this journal published by Elsevier, it is indexed in the Thomson Reuters Web of Knowledge and has an Impact Factor.


The Web of Knowledge is vetted, and claims:

Our rigorous selection process for Web of Science guarantees that the best, most relevant journals contribute to all of our data and evaluation solutions.

When a closely inspected scientific database can’t weed out the most obvious junk science, you have to wonder how serious they are about identifying “best, more relevant journals”.

Perhaps the most disturbing this is that it gets cited by other journals. They are mostly “alternative medicine” types of journals, but certainly not all.


As I have written before, I do not consider for profit scientific publishing an inherently evil idea. Burying traditional publishers is not a goal for me.

But whenever anyone talks about the importance of gatekeepers and reputation and the value of traditional publishers... ask if a major scientific publisher should have a journal like Homeopathy on its roster. Any publisher that claims to value scientific rigor should not only be embarrassed by a journal like this, they should shut it down.

Scientific publishers should be judged not only on their highest quality products, but by what crap they keep around and can’t be bothered to get rid of.

Additional, 27 October 2015: This journal is, of course, yesterday’s news. Librarian Jeffrey Beall (he of the dodgy publishers list) tweeted about this journal earlier this year. It elicited this disappointing response from Elsevier representative Tom Reller:

So for every topic that someone thinks is pseudoscience on wikipedia, STM pubs aren’t allowed to publish studies on it? What?

Sure, cast doubt on Wikipedia rather than addressing the question. Say it’s just “someone” on Wikipedia, as though it’s the work of a lone troublemaker instead of a page with (as of this count) 2,299 different users. Ignore that the Wikipedia article has 297 references, many of which go to peer reviewed journal articles. Ignore that homeopathy does not have credibility in the scientific community.

If I had time, I would love to create list of all the articles in Elsevier journals that have titles like, “Homeopathy cannot even be used to replace placebo”. Or maybe this article in the Elsevier journal The Lancet, which concludes in the abstract, “This finding is compatible with the notion that the clinical effects of homeopathy are placebo effects.”

I’m not arguing that academic publishers shouldn’t outlaw papers on a topic. The point is that having a dedicated journal to bunk looks bad, and provides an easy outlet for bunk.

Indeed, Homeopathy may be one of the best arguments for keeping research articles bundled in journals: it provides a quick signpost that reads, “You can ignore this.”

Hat tip to Björn Brembs for pointing out this journal to me. Further hat tip to Richard Poynder for pointing me to Reller’s response.

20 October 2015

Kiloauthor still gaining traction

Apparently this appears in the November issue of Wired:


I’m seriously wondering how far this word will go now. Oxford English Dictionary, are you listening?

Hat tip to Eric Topol.

Related posts

When does authorship stop meaning anything useful?
Living the Matthew effect with kiloauthors

Tuesday Crustie: Climbing purple tree crab leader

Ooh, this new land crab is a beauty...


Not only does Arachnothelphusa merarapensis have a pretty shade of purple going for it, it has some darned interesting habits, too:


All three individuals collected by the authors were all found in trees, often quite high off the ground. Three is obviously not a huge number, but the team looked for any burrows on the ground, and didn’t see them, suggesting this species is a climber by nature.


Because this seems to be a tree dweller, it could easily be affected by logging. The good news is that this animal was found at Merarap Hot Spring Resort (which gives it its name), so its habitat seems safe right now. But that the team could only find three individuals suggests it might be a rare species.

Additional: Loved Rachel Feltman’s comment about this species:

If a crab lives in a tree, then it’s basically just a pinchy spider.

Reference

Grinang J, Min PY, Ng PKL. 2015. A new species of tree-hole dwelling freshwater crab of the genus Arachnothelphusa Ng, 1991 (Crustacea: Decapoda: Brachyura: Gecarcinucidae) from northern Sarawak, Malaysia, Borneo. Raffles Bulletin of Zoology 63: 454-460. http://zoobank.org/urn:lsid:zoobank.org:pub:4CC4DC84-8F6E-4524-9D3F-BAA3C2DAF588

19 October 2015

Getting too old for this

“We at the Society for Neuroscience would like to take this moment to remind you...



“That you are old. I mean, seriously old. I mean, you think that wizard in Lord of the Rings is old...




“But he hasn’t been a member of the Society for a quarter century now, has he? No he has not.”

18 October 2015

#SfN15 bingo

By popular demand!

(Okay, one person asked. And there went a half hour of productivity...)


Update, 19 October 2015: Enough material came in for a second bingo card!


Update, 20 October 2015: I can’t stop myself!



Related posts

Neuroethology bingo
SfN 2013 bingo

15 October 2015

Mitochondrial misconceptions

A Google image search for mitochondria reveals this:


All the images show mitochondria a the shape of a short bean, more or less.

Now check out this fluorescent stain of mitochondria:


Instead of a bunch of short little football shapes, we see long, stringy networks of mitochondria within cells.

I’m embarrassed by how many times I’ve shown the artistic representations of the mitochondria in my classes. They’ve been mostly provided by textbook suppliers, but they are far from alone in getting it wrong, as the Google search shows. My colleague down the hall, Robert Gilkerson, works on mitochondria, tells me that researchers have known that mitochondria form these long, connected networks since the 1990s.

Weirdly, Wikipedia shows no less that four of the wrong “bean-like” pictures, then goes on to say:

Although commonly depicted as bean-like structures they form a highly dynamic network in the majority of cells where they constantly undergo fission and fusion.

Why do we keep perpetuating the wrong image? The artist’s renditions are very helpful in showing the double membrane structure of mitochondria, which is very relevant to function. But that could be shown in a more realistic representation of the structure, instead of copying from other textbooks.

I say “copy” deliberately, because there is clear evidence that undergrad biology textbook creators do copy from existing texts, sometimes for generations (Gould, 1991).

References

Gould SJ. 1991. The Case of the Creeping Fox Terrier Clone. Bully for Brontosaurus: Reflections in Natural History. W.W. Norton & Co.: New York. 


External links

Enhanced Yellow Fluorescent Protein (EYFP) Mitochondria Localization

06 October 2015

Tuesday Crustie: All hail the king!

When something makes normally conservative scientists put “remarkable” in the title of a paper, and name a species “king,” you stop and you open the paper.


This lovely hermit crab is Patagurus rex. This was a new genus, named after a legend in the world of crustaceans, Pat McLaughlin.

The species name is not given because it is particularly regal (sadly), but for “the extraordinary albeit superficial resemblance of this new species to some king crabs.”

This picture shows this hermit carrying not the curved snail shell you usually associate with hermit crabs, but a clam shell.

My only regret is that I didn’t stumble upon this lovely little hermit crab description when it was published a couple of years ago.

Reference

Aanker A, Paulay G. 2013. A remarkable new crab-like hermit crab (Decapoda: Paguridae) from French Polynesia, with comments on carcinization in the Anomura. Zootaxa 3722(2): 283-300. http://dx.doi.org/10.11646/zootaxa.3722.2.9

01 October 2015

Badges for scientific paper contributors


A news article in Nature examines the latest bid to reform scientific authorship: badges.

I completely agree that the problem the badges are trying to address is one that needs addressing: clarifying author contributions. The article describes efforts to come up with a standardized list of tasks that people might perform in a scientific study. I’ve done similar exercises in my biological writing classes. Usually, we end up with about five categories, something like this:

  • Concept 
  • Experimental design
  • Data collection
  • Statistical analyses
  • Writing

The taxonomy the badges are working from is more elaborate, with 14 categories, although the article mentions another group that recorded over 500 reasons (!) someone might be an author on a paper.

The Nature article links out to four papers with badges, each badge signifying an author’s contribution. The badges are standardized, appearing with the same design in both journals.

In neither journal do the badges appear in the PDF of the papers. To me, this immediately limits the usefulness of badges. I save papers as PDFs, and I consider that to be the most “official” version of the paper. If the goal is to clarify authorship, it needs to as integral a part of the paper as author affiliations or contact information.

Turning these contribution categories into badges seems like needless gamification. The article notes that software firms have used badges. This is probably why I have only heard our online learning center talk about badges. That’s been about it.

I’m hesitant about adopting trendy things from software companies. I think too often, you run the risk of investing a lot of time and effort into something nobody uses, and is quickly abandoned a few years later. For example, see this article about how universities bought into Second Life, and where that effort stands now:

I decided to travel through several of the campuses, to see what’s happening in Second Life college-world in 2015.

First, I didn’t see a single other user during my tour. They are all truly abandoned.

Second, the college islands are bizarre. They mostly are laid out in a way to evoke stereotypes of how college campuses should look, but mixed in is a streak of absurd choices, like classrooms in tree houses and pirate ships. These decisions might have seemed whimsical at the time, but with the dated graphics, they just look weird.

The work on standardizing the contributions seems very valuable to me. It moves us closer to to the movie credit model, which I think scientific authorship will ultimate evolve towards, particularly with kiloauthored papers. But I am trying to imagine having “writing,” “acting” and “special effect” badges go by at the end of movie. It wouldn’t deepen my understanding of who did what.

I do not understand how contribution badges add value that you don’t get by simply writing out the contributions in words.

Related posts

Letter in Science!
How common is “co-first” authorship?
When does authorship stop meaning anything useful?
Everybody gets to be corresponding author! 

References

Chawla DS. 2015. Digital badges aim to clear up politics of authorship. Nature 526: 145–146. http://dx.doi.org/10.1038/526145a

Photo by hyperdashery badges on Flickr; used under a Creative Commons license.

Comments for second half of September 2015

DrugMonkey asks how much it costs to generate a publication in something like Science or Nature or Cell. This was probably prompted by Steve Ramirez’s estimate that it took $3 million to generate one of his papers.

30 September 2015

Journals, tired of complaining about blogs, complain about PubPeer

Well, it had been a while since a journal complained about how the Internet is ruining science.

Fortunately, Michael Blatt,  Plant Physiology stepped up to the plate with an editorial re-hashing tired arguments about post-publication peer review.

How tired are they? The editorial pretty much checks off every box of arguments against post-publication peer review that I listed in my article on the subject over a year ago. It’s so familiar, Blatt could have used mine article as a template for his. “Hm. Have I complained about anonymity yet? I have. Oooh, but I haven’t said anything about the tone.”

The only wrinkle is that this time, it’s directed at PubPeer rather than blogs. Blatt goes so far as to say:

Until then, I urge scientists publishing in Plant Physiology and other reputable scientific journals not to respond to comments or allegations on PubPeer(.)

Weirdly, a very similar sentiment was expressed about the blog Retraction Watch just days before:

Mr. (Ariel) Fernández never filed the lawsuit he threatened against Retraction Watch in 2013. But he has not retracted his disdain for the blog.

“I thought about suing RW,” he told The Chronicle in an email this month, “then I quickly realized that nobody with scientific credentials takes RW seriously.”

It’s a slightly sad and desperate ploy. “Don’t look at them!”

I would do a deeper analysis of this editorial, but Paul Brookes and DrugMonkey have already done it. Go read.

Related posts

Back room science


External links

Punching down; In defense of PubPeer
Throwing punches about PubPeer

References

Blatt MR. 2015. Vigilante science. Plant Physiology 169(2): 907-909. http:/​/​dx.​doi.​org/​10.​1104/​pp.​15.​01443

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