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.