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

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.

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

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.<sup>32

32</sup> 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

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!

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.

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.

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

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.

Tuesday Crustie: One little letter

From I Can Haz Cheezburger.

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 should outlaw papers on a topic. The point is that having a journal dedicated 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.

Additional, 13 June 2018: The journal Homeopathy is also indexed in PubMed.

This story notes that the journal had been delisted from Web of Science journal rankings in 2016. Since then, however, Web of Science has changed ownership, and the journal is still indexed in the service.

There is a tiny side note saying, “Suppressed in 2015,” with no explanation of what that means. It looks like it got back on the list the next year.

Update, 7 August 2019: The journal Homeopathy is no longer published by Elsevier! But if you think that means it is out of business, think again. It’s changed hands and is now published by Thieme. Thieme is a long established academic publisher (over 125 years), so I’m just as shocked to see them pick up this journal as I was surprised when I saw it in Elsevier’s stable.

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

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.”

#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

Comments for first half of October 2015

Dynamic Ecology rediscovers Up-goer Five. Been there, done that. It’s fun, but don’t confuse it with a path to clarity, as Carl Zimmer notes.

Prof-Like Substance talks about what he’s seeing in National Science Foundation grant proposals.

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

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

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.

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

“Ideas you shall have...”

The other day, someone said to me (roughly), “You made your research career by scratching it out with your fingernails.”

Which reminded me of this classic Sandman comic (#17):

All the pictures in my head. I had to get them down, but I didn’t have any paper, or ink. So I used the wall.

And my fingertips.

Sounds about right.

Meteor

I saw a meteor last night!

I was lucky. I was outside for just a few minutes, and turned around at just the right time.

Now, I’ve seen meteors before. Shooting stars, like the Perseid meteor shower. But this was a big ol’ bright fireball.

At first, I thought it was a firework or something man-made. It was bright, and moving slower than I’d seen shooting stars move. It had a long trail that changed colour as it fell, although it was mostly green.

And it looked like it was headed straight for the ground. I seriously wondered if it might have landed and made an impact.

Idiot that I am, I didn’t look at my watch to get the exact time. It was too fast for video. It lasted just a few seconds.

Of course, I did what anyone would do today when they want to catch up with real-time information: I hopped on Twitter. Sure enough, there were tweets about seeing a meteor at about the same time I did. Most people didn’t have where they lived, but the timing and description matched what I saw, so I was pretty sure this was real.

I tweeted if anyone knew where I could report this, since the trajectory led me to think it might, just might, have landed. Bad Astronomer and one-time UTPA presenter Phil Plait came through and told me about the American Meteor Society’s reporting website. It’s a very cool process; very easy to give a lot of information. If you ever see a meteor, report it! For science!

The phrase “once in a lifetime” gets overused a lot, but this probably was a true once in a lifetime event.

Additional: Here’s the report page of the American Meteor Society of last night’s fireball. Quite surprised by spread out the observers were!

Do you take science to where the people are, even if they’re at a vile cesspool?

I saw this question from a Reddit “Ask me anything” (known as AMA for short) science session on Twitter:

The gist of the question is, “female Neanderthal... do you bang or do you pass?”

Eww.

The answer is pretty funny, but the question comes close to encapsulating why I, personally, am less and less inclined to try to do an AMA on Reddit.

Lots has been written about Reddit’s culture of sexism (here’s one, two, three, four for starters). And yes, there is good stuff on Reddit. I have an account and post there from time to time. Some women report having never experienced sexism on Reddit. I get that.

Nevertheless, there are enough examples of problems that I ask myself: “Is this a forum I feel comfortable appearing in?”

Increasingly,  my answer to Reddit is no. Because from a distance, I’m kind of getting the impression the place is mostly a cesspool.

But I say this realizing that... there are a lot of people on Reddit. If you only go to where there are like-minded people, you can consign yourself to irrelevance.

For my fellow scientists, have you done outreach on places that are opposite to your views? Would you? Why or why not? Would you do a spot on Fox News in the U.S.? (Or, if you happen to be a politically conservative scientist, MSNBC?

Additional, 10 August 2016: The Science and Everything Science sub Reddits won’t let you post research from a journal article unless the journal has an Impact Factor of 1.5 or more. Another reason to avoid the place.

External links

Why Reddit is sexist
Sexist, racist – the web hounding of Ellen Pao shows the trolls are winning
Why Reddit Tends Towards Sexism In 1 Chart
Reddit’s woman problem

Everybody gets to be corresponding author!

Spotted in the comments section of DrugMonkey’s blog:

(C)an someone explain to me how a paper in this week’s Science is able to have 4 freaking corresponding authors?

It’s worse than that. In this week’s Science, there is one paper with two corresponding authors, one with three, and one with four corresponding authors, as mentioned above.

And that paper with four corresponding authors? It only has four authors! As Oprah might put it:

On top of that, the paper with four corresponding authors also has a note that two of the authors “contributed equally.”

DrugMonkey’s reply is on the ball:

It is because the Corresponding Author marker has now become a tick mark of academic contribution and credit instead of a mere convenience for getting in touch with the research team. So much like we’ve seen metastasis of “co-equal” first (and now last) authors, we’re seeing expansion of corresponding author credits.

We now have at least three “indicators” of relative contributions to a paper:

1. First author: this is usually assumed to be the person who did most of the “boots on the ground” work, a grad student or post-doc.
2. Last author: This is usually assumed to be the boss, the principle investigator, the person who came up with the idea and got the grant.
3. Corresponding author: Um... to me, I would take this as a signal that this person is the boss. That is, it’s the exact same assumption I make for “last author.”

If I saw a paper with different last author and corresponding author, I’d be confused. Add in multiple corresponding authors and multiple “co-last” authors and equal contribution notes, and I have no idea who’s to credit (or, if it’s bad, who’s to blame).

This is not an idle exercise for me. My new university is in the middle of trying to develop new promotion and tenure guidelines. I’m on a departmental tenure and promotion committee. Figuring out how people interpret authorship (particularly upper administration) has real implications for people’s careers. A couple of years ago, one administrator was complaining that our tenure-track faculty didn’t have enough first authored papers, apparently not realizing that in biology, the norm is that they would be last author on papers.

This is yet another indication of the phenomenon I’ve been talking about for a while. The concept of “authorship” for scientific papers isn’t the right model for assigning credit in large collaborative research projects.

Additional, 25 September 2015: Scott Edmunds on Twitter notes that “corresponsing author” has monetary value:

Chinese authors get paid (and also pay) to be corresponding, first and last author

He gave links out to China's Publication Bazaar and The outflow of academic papers from China: why is it happening and can it be stemmed?.

Related posts

When does authorship stop meaning anything useful?
Letter in Science

Overly honest recruitment ad

I spotted this recruiting ad for an undergraduate research position yesterday:

“You’re Only Limited by Your Imagination!

“and funding”

I’m not sure that this level of candor is attractive, helpful, or necessary for undergraduates.

Quote of the day: Career long shots

Applies to scientific careers as well. Emphasis added:

When first starting out, did making a career of fiction writing seem possible?

Sure, it was an awfully long shot, but also I was in my 20s, and that’s the time to take your long shots — when you don’t have a mortgage, don’t have kids, don’t have anybody else who’s depending on you. Yes, of course it was a long shot, but so is being a professional athlete, being a professional actor, being a professional musician. But the world would be devoid of arts and culture (and science - ZF) if everybody said, “Ah, it’s not easy, I’d better give up now.” - Robert J Sawyer

External links

Writers on Writing: Robert J. Sawyer
Hat tip to Robert J. Sawyer on his Facebook page. 

Ancient legacies promoting ancient legacies

In all the excitement about the discovery of the new fossils of Homo naledi, many of my friends in the science community have remarked on this discovery being published in the journal eLife, a new open access journal, rather than Science or Nature.

“Look, this shows that you don’t have to publish short articles in those closed access journals to get lots of attention!”

What I haven’t heard many people point out is that the discovery of Homo naledi had the advantage of being publicized by a well-oiled, well established, recognized print brand: National Geographic.

The style of coverage for Homo naledi was almost exactly what you would see for Science or Nature: simultaneous press releases, probably embargoes, cover of a magazine,and so on. The only difference is that National Geographic isn’t a peer reviewed journal, but I’m not sure that difference is one that a lot of the non-scientist crowd (maybe even including many in journalism) would recognize. I would wager that for many, National Geographic is viewed as having the same authority as Science or Nature.

Don’t get me wrong: it’s great that this kind scientific research is in an open access journal with an unlimited page count. See this post by team member John Hawks which shows how this publication compares to the scientific arguments over other fossils: short papers, long waits for descriptions, etc. And the scans of the fossils that people can print on 3-D printers are something pretty new to scientific publication. All of that is important for the science, but I’m asking more about the outreach.

If this same amount of attention had been garnered by the eLife articles alone – or, to head into complete fantasy, a bioRxiv or PeerJ pre-print (say) – then it will be safer to say the landscape for scientific publicity, news, and outreach has changed significantly. Right now, it’s just showing how much muscle the established media brands still have.

External links

New species of human relative discovered in South African cave
Is Homo naledi just a primitive version of Homo erectus?
Cover image from here.

Inspirational

I don’t think it matters what age they are: some people wonder if they can contribute. Young people wonder if they’ll get their shot. Mid-career people wonder if they’re making an impact. Older people wonder if they’ve still got it.

Some people do their best work early. Einstein’s “miracle year” was when he was about 26. As Tom Lehrer once said of another musician:

It is a sobering thought, for example, that when Mozart was my age, he had been dead for two years.

Then you have slow burners like Charles Darwin, who published the On the Origin of Species when he was 50.

I think you look for those examples of people who have success at different ages to convince yourself that there’s still a shot for you to stay creative and productive and vital.

So I was amazed and pleased to learn that last night, the Polaris music prize for independent Canadian music was won by a 74 year old. It was Buffy Sainte-Marie, whose music career started before I was even born.

Holy crap.

Frankly, I was never familiar with her music from when I was younger. I was never a fan. But I defy anyone to listen to “Power in the Blood” and tell me that they’d have guessed that song came from a septuagenarian. It’s got as much punch, nerve, and energy as songs by artists a third her age. It freakin’ rocks.

Huge congratulations to Buffy!

Update, 7 March 2025: The Polaris Prize has been rescinded from Buffy Sainte-Marie after she returned her Order of Canada and descibed herself as American. This is the latest in a long series of moves that arose from investigations into her claimed but falsified First Nations heritage.

Tuesday Crustie: Speedster

This animal has a superpower:

Speed.

Undinula vulgaris has one of the fastest reaction times in the the animal kingdom: 1.5-3 milliseconds. Most animals can barely get a message from one neuron to another in that amount time, never mind detect a stimulus, process it, send a signal to muscles, and make them contract.

How do they do it? Part of the answer is that they have myelinated neurons, which is unusual for an invertebrate (Lenz et al. 2000, Wetherby et al. 2000).

Reference

Lenz PH, Hartline DK. 1999. Reaction times and force production during escape behavior of a calanoid copepod, Undinula vulgaris. Marine Biology 133(2): 249-258. http://dx.doi.org/10.1007/s002270050464

Lenz PH, Hartline DK, Davis AD. 2000. The need for speed. I. Fast reactions and myelinated axons in copepods. Journal of Comparative Physiology A 186: 337-345. http://dx.doi.org/10.1007/s003590050434

Weatherby TM, Davis AD, Hartline DK, Lenz PH. 2000. The need for speed. II. Myelin in calanoid copepods. Journal of Comparative Physiology A 186: 347-357. http://dx.doi.org/10.1007/s003590050435

External links

What animal has the fastest reaction time?

Photo from here.

Prophetic paragraphs

Bradley Voytek wanted to read the last paragraphs of people’s doctoral dissertations. I dug up mine. It was in a section titled, “What next?”

Fourth, the brachyuran superfamily Raninoidea de Haan, 1841 are true crabs that, like hippoid sand crabs, are specialised for digging in sand and mud. Their gross morphology is reminiscent of albuneids: unlike the thorax of most brachyurans, the thorax of ranid crabs is not rostro-caudally compressed, and their legs have very flat, paddle-shaped dactyls. Comparing the convergent digging behaviours in the ranid crabs with the hippoid sand crabs could be illuminating in understanding the biomechanics of digging.

It’s, um, not a ringing last paragraph. No eternal verities or a big “What does it all mean?!” conclusion.

But what is cool is that of the four things I listed in my “What next?” conclusion, this was the only one I got to do. I did get to study those ranid crabs! And publish a paper about it!

Faulkes Z. 2006. The locomotor toolbox of spanner crabs, Ranina ranina (brachyura, Raninidae). Crustaceana 79(2): 143-155. http://dx.doi.org/10.1163/156854006776952874

That makes up a tiny little bit for not even coming close to doing any of the other three things I listed as possible avenues since then. That makes it a nice last paragraph.

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

Incoming: Science Blogging

After being listed as “in press” on my home page for some months now, Yale University Press has moved a step closer to publication of Science Blogging: The Essential Guide.

It now has a publication date (22 March 2016), an ISBN (9780300197556 – accept no substitutes), and a price (an affordable “buy one for yourself and one for a gift” price of $24.00).

Along the way, the book has gotten a slight title makeover from The Complete Guide to Science Blogging to Science Blogging: The Essential Guide. The change is probably a good one, as it puts the book’s subject matter right up front.

The cover is not up yet, but I’ll be sure to preview it when it’s available!

External links

Science Blogging on Yale University Press
Science Blogging page of Facebook

The book chapter you’ll never get to read

A while ago, I wrote about the importance of talking about failures. I thought I’d share this failure, because the release of the newest series of Doctor Who this weekend makes it kind of timely.

I submitted this proposal for a planned academic book titled Doctor Who & History. Even though I keep swearing off writing book chapters, I submitted it because I thought this might feel more like fun than work.

They wanted fifteen chapters, and got 50 proposals. This was one of them. It wasn’t selected. I have to commend the editors, who gave me one of the nicer rejection letters I’ve gotten.

The history of science in Doctor Who

The character of The Doctor is a scientist. Doctor Who was originally created with the goal of teaching history and science, but the show rarely mixed the two in its plotlines. This chapter will examine how the scientific history is treated in, and reflected by, Doctor Who. When set in the past, the show usually features social and cultural leaders than scientific ones. For example, Queen Victoria and Charles Dickens have both appeared in Doctor Who, but Charles Darwin, their contemporary, has not. The real history of science has rarely warranted more than The Doctor dropping the name of a famous scientist into a conversation. The show’s portrayal of its fictional scientists (other than The Doctor) is often suspicious and critical, with several stories centering on ambitious scientists overreaching, with disastrous consequences. But in their search for new plot material, writers often looked to emerging scientific ideas and worked them into their scripts. The most famous example of this was the creation of the Cybermen, which was inspired by research on organ replacement. Sometimes, the show’s scientific and technological elements would be familiar to any contemporary viewer. The many 1960s stories that incorporated crewed spaceflight would be completely familiar to people living in the middle of the space race. Less often, but more interestingly, Doctor Who sometimes used scientific ideas before they were well incorporated into popular culture. The supercomputer WOTAN threatened the world by joining a network of computers long before most people had even seen a pocket calculator let alone a computer, or that computers would eventually be connected by the Internet. “Earthshock” featured the dinosaurs being wiped out by a crashing spaceship just two years after the suggestion that an extraterrestrial impact first appeared in scientific journals. Since the show’s revival, living scientists, like physicist Brian Cox, have appeared with The Doctor. Therefore, Doctor Who provides insights into the history of science over the last half century and how those scientific discoveries percolate into popular awareness.

Update, 21 July 2017: The book is out now!

Related posts

Low points

External links

Doctor Who and history 
Publisher’s site 

Comments for first half of September 2015

Dynamic Ecology looks at the current scientific publishing field.

Texas A&M expected to announce local campus

With the formation of UTRGV this month, it is a little surprising to see that Texas A&M seems poised to announce plans for another university in the Lower Rio Grande Valley.

I wonder if this region has the population (and maybe the infrastructure) to support two major universities.

I was planning on abandoning the “new Texas university” label for posts, but I guess I can keep it going for a while yet.

Update: Confirmed!

External links

Texas A&M University plans to open McAllen campus
Texas A&M to open campus in McAllen