22 May 2017

A short conversation on the beach

Last week, I was out on the beach at South Padre Island, collecting sand crabs for my research. This involved lots of shoveling. When I do this, I often have people come up and ask me what I’m doing. A common guess is clams (none worth digging for on South Padre). Jokingly, people ask if I'm looking for buried treasure.

Normally, I try to cut the conversation short. I’m working. If you’re trying to get something done, it’s not always the time you want to chat with others.

Last week, I had just found an Emerita benedicti and was walking up to deposit it in my bucket. A woman came up while I was doing so and said, “Tortugas?”

Guessing she did not speak English, I searched my brain for the tiny amount of Spanish I knew. I held out my hand to show the little beast, and replied, “Cangrejos.”

“Ah, cangrejos!”

I guess my pronunciation was at least understandable. I was weirdly proud of that.

16 May 2017

Broader impacts, part 2


Hooray for arbitrary large round numbers! My answers on Quora have tallied one million views on Quora.


And yesterday saw my most views ever. Not sure what answer is getting all that traffic.

Related posts

Broader impacts

09 May 2017

Tuesday Crustie: Say a prayer

Australian crayfish are often like the country itself. Big, brash, and often highly charismatic. This newly discovered crayfish is a fine example of that.


Meet Euastacus vesper.As the Australians say, “She’s a beauty.”


Sadly, the authors expect this species is already criticially endangered. Like many crayfish species, it has a tiny distribution. But in slightly more cheerful news,the authors note they are working on describing even more new species in this genus.

Reference

McCormack RB, Ahyong ST. 2017. Euastacus vesper sp. nov., a new giant spiny crayfish (Crustacea, Decapoda, Parastacidae) from the Great Dividing Range, New South Wales, Australia. Zootaxa 4244(4): 556–567. https://doi.org/10.11646/zootaxa.4244.4.6

External links

Euastacus vesper, a new Euastacus for NSW
Eustacus vesper – a NEW Euastacus for NSW

 



08 May 2017

Perfecting the wheel instead of reinventing it

Back in grad school I read a lot about movement analysis and dance notation, and that was when I came across this dedication of the book Choreo-graphics, by Ann Hutchinson Guest:

This book is also dedicated to those who come after and who, instead of contemplating inventing a new dance notation system, discover what has already been achieved and contribute to the art of dance by directing their energies and talents to the perfection of the best one available.

I haven’t read this book in decades, but this quote stuck with me. I think the book said something like there had been a new dance notation system proposed every four years. I could sense her mild frustration that there were so many different systems out there, and people weren’t building on previous work. They were blowing things up and starting from scratch, every. Single. Time.

I think of this quote when people suggest that we should have new scientific journals. Or new programs. Or new administrative structures. So often our reaction to finding something that we think is not performing to our expectations is to walk away from it and start over again. But I like Guest’s approach: direct energies and talents to perfecting the best ones available.

References

Guest AH. 1989. Choreo-graphics: A Comparison of Dance Notation Systems from the Fifteenth Century to the Present. Routledge.

01 May 2017

We do not need new journals for negative results

Experiments are intended to show one thing effects another. However, not everything affects something else. Many experiments that show “no effect,” or “p > 0.05” are often called negative results.

The general wisdom is that negative results are harder to publish than one that show an experimental manipulation did have an statistically significant effect (“p < 0.05”). Anecdotally, the paper of mine that had the longest, toughest slog to publication was one with negative results.

Is the solution to this problem to create another journal? No.

First, we already have journals in biology that specifically say in their titles that they exist to publish negative results. We have the Journal of Negative Results in BioMedicine (started 2002) and Journal of Negative Results - Ecology & Evolutionary Biology (started 2004).

Second, we have journals that, while not specifically created to accept negative results, specifically include publication of negative results in their editorial mandate. Usually, this is phrased as “reviewed only for technical soundness, not perceived importance,” and these have become known as “megajournals” (regardless of how many papers they actually publish). This format, pioneered by PLOS ONE, is still quite new. Several megajournals are less than five years old (click to enlarge pic below).


The age of these journals is important to consider when talking about publishing negative results. In my experience, many academics take a long time to realize when the publishing landscape has changed. For example, I have been in many discussions with scientists who are actively publishing, active on social media, who mistakenly believe that “open access” is synonymous with “article processing charge” (APC). This is incorrect.

It takes time to change academics’ publishing habits. Five years is not enough to see how the creation of these journals affects the publication of negative results.

And more journals are on the way. The Society for the Study of Evolution has Evolution Letters coming, and Society for Integrative and Comparative Biology has an open access journal coming (though it seems likely these will review for “impact,” not only for technical soundness).

I do realize that some journals are better at upholding this editorial standard than others. For example, sometimes PLOS ONE reviewers have sent back reviews considering “importance” of the findings, even though the journal tells them not to do that.

In biology, you probably have at least six perfectly respectable journals that happily publish negative results. This is why I contend that we do not need to create new journals for negative results. We need to use the ones we have.

I think the underlying problem with discussions of negative results is that we talk about “negative results” as though they were all the same, scientifically: “no effect.” All negative results are not equivalent; some are more interesting than others. Below is a crude first attempt to rank them.

  1. Negative results that refute strongly held hypotheses. Physicists hypothesized that space contained an aether. Nope. Harry Whittington though the Burgess Shale fossil, Opabinia, was an arthropod. Nope. That was just a big old bunch of negative results. But they were clearly recognized as important in getting us off the wrong path.
  2. Negative results that fail to replicate an effect. These are tricky. We all recognize that replication is important, but how we react to them differs. Sometimes, failure to replicate is seen as important is demonstrating incorrect claims (like Rosie Redfield and others showing that GFAJ-1 bacteria, sometimes referred to as “arsenic life”, did indeed have phosphorus in its DNA rather than arsenic as initially claimed). Sometimes, failure to replicate can be dismissed as technical incompetence. (The “Tiger Woods” explanation.)
  3. “Hey, I wonder if...” (HIWI*) negative results. These are negative results that have no strong hypotheses driving the experimental outcome. Like asking, “What is the effect of gamma rays on man-in-the-moon marigolds?” Well, do you have any reason to believe that gamma rays would affect the marigolds differently than other organisms? If you don’t, negative results are deeply uninteresting.

In other words, that results are negative has very little bearing on how people view their importance. The importance of the hypothesis that underlies those negative results play a much bigger role in whether people are liable to think those negative results are interesting.

That is, even if you have another journal specifically for negative results, people are still going to think some results are more interesting and publishable than others. People whose negative results fall into the HIWI category (which may be a lot of those experiments) are still going to have a rough ride in publication, even for journals that consider negative results.

External links

Garraway L. 2017. Remember why we work on cancer. Nature 543(7647): 613–615. http://dx.doi.org/10.1038/543613a (Source of the “Tiger Woods” metaphor)

* In my head, “HIWI” rhymes with “Wi-Fi.”

This post prompted by Twitter discussion with Anthony Caravaggi.

26 April 2017

You think you deserved authorship, but didn’t get it. Now what?

You’re involved in a research project. You do a lot of work. And then your name appears nowhere on the manuscript or paper in the journal.

Pop quiz, hotshot!


What do you do?

While you think about that, let me talk about practices in another field: screenwriting. I’ve argued that movie credits provide a better model for contemporary science than current authorship practices. How do you determine who wrote a movie? (What follows is based on practices in Hollywood filmmaking, as far as I know. I don’t know if practices differ in, say, Bollywood.)

Like authorship of scientific papers, screenwriting credit is not simple and somewhat cryptic to outsiders. For instance:


“Screenplay by Jeffrey Boam and Jeffrey Boam & Robert Mark Kamen. Story by Jeffrey Boam.” Why is Boam in there twice? Why are the names joined with the word “and” and an ampersand? And how is that different from “Story by”? If you haven’t looked it up, it’s baffling. Research papers play similar games with things like authorship position.

Like research teams, you can have large numbers of people who work on a movie script. Over thirty writers were involved writing in The Flintsones live action movie. But only three names appeared on the screen.

And, just like scientific papers, you can have disputes over credit. And here’s where academic authorship and screenwriting diverge.

Credit for movie scripts can go to arbitration. Usually, the Writer’s Guild of America is the final arbiter. And they have rules for determining who gets credit, although there is wiggle room for interpretation, like what “substantial” means.

In a dispute over an authorship credit for a scientific paper, there is effectively nobody to turn to for help in resolving it. On Twitter, I asked people on journal editorial boards the “Pop quiz, hotshot” question at the start of this post. Someone says they were should have gotten authorship, but didn’t. Or possibly higher placement in authorship. What do you do?

So far, I’ve had more retweets than answers.

To make matters worse, there’s no widely accepted criteria for what constitutes authorship. Yes, there are the Vancouver Guidelines for paper authorship in biomedicine, but almost every time I mention them, I hear grumbling about how poor they are. Researchers either don’t known about, don’t care about, or disagree with those guidelines.

The ideal option to resolve authorship disputes, as far as I am concerned, is for the authors to talk to each other and try to resolve their differences on their own. But I suspect that once disputes raise to the point of withholding authorship, it’s going to be hard to resolve that on your own.

A trainee might try to inform the department chair of faculty involved in the project. But increasingly, there are multiple faculty and it may not be who is the relevant person overseeing the faculty. It also seems unlikely than many chairs are willing to step into an authorship dispute, or, even if they are, what they can do about it.

Some institutions might have a research compliance office. But because the standards for authorship are so vague, the question becomes, “What are you supposed to be complying with?” You can have a valid authorship dispute that involves no misconduct. Are compliance offices supposed to resolve differences of opinion about who deserves first author placement versus second author placement?

About the only logical step left is to appeal to the journals themselves. And the Committee on Publication Ethics has a procedure for adding authors (PDF). But if the authors don’t agree, the guidelines are to toss the ball back into the court of the institution, which is, as we just saw, problematic. And it isn’t clear if the recommendations for journals to add authors also apply to, say, changing author order or some other kind of authorship dispute.

Out of 3,000 or so Retraction Watch posts, 177 are tagged with “Authorship issues.” For instance, here are papers published without knowledge of “the bosses.” And here is one case where a student contacted a journal. And here’s one where authors couldn’t agree on author placement.

While I haven’t gone through every entry at Retraction Watch, I am willing to bet that more retractions arise from omitted senior scientists than omitted trainees.

And that’s a big part of the problem. There is a huge power differential between trainees and senior scientists. There seem to be few places more ripe for abuses of that power than in doling out authorship credit.

Regardless, it seems unfair and unwise to expect journals to resolve authorship disputes. There are too few standards across the community (see discontent over Vancouver Guidelines). Journals probably have no resources to investigate the facts of a dispute thoroughly. This probably means that in most cases, they will favour the senior scientist (see power differential).

I don’t know what the solution is. But I think this is a problem that is not given enough discussion. It seems likely that in many cases, trainees in disputes will be left twisting in the wind.

The moral of the story, if you are a trainee of any sort, is: Extensively discuss your expectations for authorship at the very start of any project. Be prepared to negotiate.

Hat tip to Amy Criss for COPE guidelines.

Related posts

Badges for scientific paper contributors

External links

The myth of screenwriting credits
Who gets credit for a screenplay?
A Graduate Student’s Guide to Determining Authorship Credit and Authorship Order (PDF; hat tip to Carolyn O’Meara)
Case studies in coauthorship: what would you do and why?

24 April 2017

Time is the difference between superficiality and scholarship

Many science questions emerge from a place similar to what Penn Jillette describes in this quote about people’s attitudes to video games. (Emphasis added.)

You know, when I was 15, 16, 17-years-old, I spent five hours a day juggling, and I probably spent six hours a day seriously listening to music. And if I were 16 now, I would put that time into playing video games.

The thing that old people don’t understand is – you know if you’ve never heard Bob Dylan, and someone listened to him for 15 minutes, you’re not going to get it. You are just not going to understand. You have to put in hours and hours to start to understand the form, and the same thing is true for gaming. You’re not going to just look at a first-person shooter where you are killing zombies and understand the nuances. There is this tremendous amount of arrogance and hubris, where somebody can look at something for five minutes and dismiss it. Whether you talk about gaming or 20th century classical music, you can’t do it in five minutes. You can’t listen to The Rite of Spring once and understand what Stravinsky was all about. It seems like you should at least have the grace to say you don’t know, instead of saying that what other people are doing is wrong.

The cliché of the nerdy kid who doesn’t go outside and just plays games is completely untrue. And it’s also true for the nerdy kid who studies comic books and turns into this genius, and it is also true for the nerdy kid who listens to every nerdy thing that Led Zeppelin put out. That kind of obsession in a 16-year-old is not ugly. It’s beautiful. That kind of obsession is going to lead to a sophisticated 30-year-old who has a background in that artform.

I think about this quote a lot.

It seems to me that many people who ask questions about science are working from that background of “They listened to Dylan for 15 minutes.”. They’ve been exposed to a few basic ideas. They’ve maybe had one or two lectures in high school about evolution. They get reproduction is important. They get that natural selection leads to adaptation. They get “survival of the fittest.”


But they haven’t mastered the art. So they ask why human evolution has stopped (it hasn’t) or why some trait is so obviously bad (lots of reasons). They can’t get those nuances without having spent that time on task.

Same with people who think that half an hour Googling an answer constitutes “independent research” on climate change or vaccines or what have you. Sorry, that’s the equivalent of listening to The Rite of Spring once.

It’s similar to what I talked about recently: you need time to live with ideas to understand the subtleties.

Related posts

Some “light bulb moments” are controlled by dimmers, not switches

External links

Penn Jillette Is Tired Of The Video Game Bulls***

19 April 2017

My game is coming back. L5R is coming back!


Forgive me a fanboy moment as I react to the announcement of the new Legend of the Five Rings card game!

At first glance, it looked like the game I knew. Two decks, provinces, events, two main stats on the characters. Then, as I read deeper, I realized that the mechanics of the game were going to be almost entirely different. That will take getting used to.

But one of the things I always loved about L5R was the art. It was literally what made me pick up the game. And I have to say, I like the art direction. They’ve managed to keep the aesthetic, particularly for the characters and the clans.

I can’t wait to play my game again. I’ve missed Rokugan.

External links

A Peek Into The World of Legend of the Five Rings
Reddit AMA, 20 April 2017

Stop pussyfooting around the problem of biases in awards

At the Sociobiology blog, Joan Strassman tackles inequality in scientific awards. This topic has been making the round lately because of the National Science Foundation’s Waterman award, which this year went to two men. Again. It looks like the last time the award went to a woman was in 2004, to Kristi Anseth. Weirdly, it looks like the Waterman did a pretty good job of splitting between men and women in the first few years, and then it’s been all men since 2005.

Partially in response to community input, the NSF changed the eligibility criteria for the award. It is basically extending the time frame for eligibility since a person received their Ph.D. (And I will pause to take note that you are still considered a “young” scientist in your late 30s.)

I’m betting you right now that’s not going to fix the problem. And I doubt the measures Strassman suggests, like “Let’s be active in nominating women!” will do it, either. But here’s what will fix the problem. Guaranteed.

You get the award organizers to say, in public, “We’re going to give half these awards to women. Agender individuals are eligible for either.”

And that’s it. Dust off your hands. You’re done.

The NSF gave two awards this year and in 2012. Give two awards every year, one to a man and one to a woman. Or alternate years. It doesn’t matter.

Yes, I know people will jump in and say, “But merit...”,  but I don’t care. This is not a job. Nobody’s livelihood is harmed because they did not receive an award. The question is, “Are you serious about fixing inequality or not? If you are, this fixes it immediately. Everything else just allows the problem to linger.”

I’ve had discussions with people about why the Oscars split their acting into two categories, one for men, one for women. But one good thing about it is that every year, women win awards.

External links

Can we fix inequity in awards for women scientists?
When a series of entirely reasonable decisions leads to biased outcomes: thoughts on the Waterman Award
Let’s nominate folks for NSF’s Waterman award, including womenNSF’s Water Man awardNational Science Foundation modifies Alan T. Waterman Award eligibility criteria

18 April 2017

This better not have anything to do with crayfish

So apparently this happened a couple of hours ago.


I have no idea what “Project C.R.A.W.F.I.S.H.” might be about, despite being the only researcher on this university who actually publishes research about crayfish. It is a little reminiscent of a neuroscience announcement a while back.

Maybe there are no crayfish at all in this thing, whatever it is.

Far too much effort has been put into that acronym, though. Someone is priming themselves for a role in the federal government with that, I reckon. 

Tuesday Crustie: The Pink Floyd shrimp

Last week saw the announcement of a shrimp that kills with sound and was named after Pink Floyd.


That is Synalpheus pinkfloydi. This newspaper article says the reason it was named for the band is because of a legend that the band once played so loud that it killed fish in a nearby lake. Plus, one of the authors is a rock and roll fans, previously naming a shrimp after Mick Jagger.

The article missed a damn good bit of the paper, though:

Distribution: Presently only known from the type locality on the Pacific side of Panama; likely more widespread in the tropical eastern Pacific, but unlikely to occur on the Dark Side of the Moon due to lack of suitable habitat.

Hat tips to GrrlScientist, Miss Mola Mola, and Mark Carnall.

Reference

Anker A, Hultgren KM, De Grave S. 2017. Synalpheus pinkfloydi sp. nov., a new pistol shrimp from the tropical eastern Pacific (Decapoda: Alpheidae). Zootaxa 4251(1): 102–110. http://www.mapress.com/j/zt/article/view/zootaxa.4254.1.7/10782

16 April 2017

Superhero art exhibition does disservice to comic artists

I saw the opening of “My Hero” exhibition at IMAS McAllen yesterday (originally curated by the Bedford Gallery in California). I enjoyed it a lot. But it continued a long simmering problem with “fine art” exploiting “comic art” without credit.

Here’s artist Russ Heath’s desciption of what it was liked to have his work ripped off by Roy Lichtenstein, for instance.


Almost nowhere in the exhibit do you see acknowledgements of some of the original creators. (One, a lovely pastiche Captain America in the style of Norman Rockwell, includes the names of Cap’s creators, Joe Simon and Jack Kirby, in the art.) But most don’t, even when a piece is directly referencing a specific classic image. For instance, one piece references this specific panel from The Amazing Spider-Man #50:


The piece in the exhibition is clever, and I liked it. The descriptive text accompanying the piece mentions the issue, but not the name of the original artist, John Romita, Sr.

Superhero iconography is treated as if it were created by artists lost to time, instead of people who are often still alive today, and struggling to make ends meet.

External links

Russ Heath’s Comic About Being Ripped Off By Lichtenstein
IMAS exhibits
Bedford Gallery Travelling exhibits

14 April 2017

Can’t wait to see this in an “Acknowledgements” section

Making the rounds today is a new story that an adult entertainment website has provided a $25,000 research scholarship to Natalie Nevárez, a neurobiologist, to study monogamy. (Not mentioning the name of said website to try to prevent blog from being overridden with bots and spam.)

Congratulations to Natalie!

I would like to point out that in the last two months, adult entertainment websites have provided:


These are small, token gestures, sure. But at this point, adult entertainment websites are showing a better understanding of civic responsibility than many elected politicians are. All of these used to be services that we expected to be provided largely by governments.

Update, 15 April 2017: A couple of people on Twitter noted that these sites do have problematic aspects to them, such as stolen content. I certainly don’t want to let these businesses off the hook for their bad practices. Ultimately, issues like “fair compensation of workers” matters more than a scholarship here or there.

But that they have made some of the gestures above kind of makes me wonder if they might smarten up.

These sites have also taken the lead on Internet security.

External links

A neurobiologist studying monogamy wins scholarship from porn site
Utah rejects sex education bill, so porn site redirects to instructional videos
Porn site says it will plow snow in Boston for free

 

13 April 2017

From predator to mutualist, or: What if predatory journals published reviews?


Earlier this week, I argued that we could kill predatory junk journals with a single stroke if regular scientific journals would publish the text of the pre-publication reviews along with the paper. This way, junk journals couldn’t hide behind the claim that they are peer-reviewed.

I argued that junk journals wouldn’t want to take the time and effort to create reviews in any way. But a couple of people on Twitter responded that the junk journals could (and apparently sometimes do) ask for reviews, but ignore them.

This makes things interesting.

Even for a regular journal, soliciting reviews but ignoring them is not out of the question. The buck stops with editors. The editor makes the decision about what to publish, and in some cases this means overriding recommendations of one or all reviewers. We just don’t expect it to happen intentionally and systemically.

When viewed from the traditional norms of pre-publication review, consistently asking for reviews but ignoring them is a massive waste of effort. But the traditional norm is that reviews only exist in the files of the reviewers, editor, and author.

What happens under the suggested new norm, that the reviews are published along with the paper?

Suddenly, the difference between a traditional journal and a predatory journal gets very blurry, very fast.

Presumably, the scam publisher would ignore the reviews and publish the paper immediately alongside the reviews. The paper would not get the benefit of revision in light of the reviews. But that would put the paper at the same level of editorial vetting as a pre-print. Let’s take a second to note that many have found great value in pre-prints (though my experience has been underwhelming). Even stodgy old biologists are using them more and more.

But let’s not forget that it is now a verifiable fact that the paper has indeed been peer-reviewed. The review is available for all to see to help form a judgement about that paper. And we can also judge how detailed the review is. In this scenario, we can think of pre-publication reviews as a rating instead of as a publication decision maker.

Essentially, by publishing the pre-publication reviews, the predatory journal has suddenly moved to a format that is very similar to what some scientists have been advocating for years: the “publish, then filter” model of publishing, rather than “filter, then publish.” If there are verifiable pre-publication peer reviews done, can we even still call it a “predatory” journal?

What the predatory journal no longer provides is any judgement of the importance of their submissions, which many readers badly want. Readers want guidance as to what is more likely to be a breakthrough. But then, the rise of open access megajournals has shown that journals can be successful without rating “importance.” Articles in megajournals can still be found and cited and used by people in the field.

If “publish review content” became standard practice across the board, predatory journals might start to serve a useful purpose instead of being the bane of science.

Related posts

One weird trick that would kill predatory journals
Pic from here.

12 April 2017

Some “light bulb moments” are controlled by dimmers, not switches


Understanding something for the first time is often shown in comics and cartoons as a light bulb appearing over someone’s head. It’s off. Then suddenly it lights up. People use the phrase “light bulb moments” to describe insight all the time. Or even just “light bulb” alone, like Grue does in the Despicable Me movies.

There are few more rewarding moments for an educator than when you see someone having that “light bulb moment” right in front of you. It happens sometimes.

But we might expect too many of those light bulb moments: where there is a clear line between, “I don’t get it” and “Oh! I get it!”

Thinking about my own education, there are lots of concepts that I teach to students now that I remember trying to learn. For many of them, there was no light bulb moment. Instead, there was just an ever increasing familiarity, and in some cases, skill in carrying out tasks related to it.

The way I put it to people is, “I got used to the idea.”

I think at some level we know that learning can be a slow, gradual thing. You might follow an explanation while it’s given, but mostly forget it by the next day. You make mistakes about something you ostensibly “know.”

I think this is particularly important to keep in mind because so much of formal education is timed. We go by weeks, by semesters, and if students can’t learn something in the allotted time, the student is deemed not to have learned the material. I think it biases us to think that students who don’t get it in that prescribed amount of time won’t get it.

Professors get frustrated when students ask about concepts and materials that were covered in previous classes. The student should just know it, and they get badmouthed for not remembering. Instead of seeing this as indicating a bad student, we should see it as an opportunity to let the students get more used to the ideas.

One of the differences between between an entering university student and a graduating one is not their raw intelligence, or study skills, but the number of repeated exposures they have had to core ideas.

A light bulb moment might be a second long, but it can be years long, too.

10 April 2017

Grad student stops meeting supervisor, who doesn’t notice

Two years ago, Eleftherios Diamandis wrote a horrible piece in Science Careers that glorified overwork. This was widely criticized. And for this, he now gets... a platform at Nature?

Yes, Diamandis just published a new piece in a glamour magazine, in which he freely confesses to being a negligent grad student mentor. He writes (my emphasis):

I remember remarking on the slow progress of one PhD student's research project at our second review meeting (typically held six months after their project launch). Three months later, I repeated my concerns, which were mainly about how slowly the student was learning essential techniques such as mass spectrometry, the workhorse of our lab. But instead of addressing those concerns, the student stopped scheduling meetings. I was too busy to notice for another six months.

I should be surprised by Diamandis’s lack of self-awareness, but he’s already amply demonstrated his obliviousness. I guess I’m surprised that when he boasted about all the time he spent away from his family and the hours and hours and hours of working, I somehow thought that he might actually care enough about his work to be competent at it.

Grad students are not loose change that you can lose in a couch cushion, for crying out loud.

When Diamandis suggests the student do a master’s degree:

I was horrified when my suggestion elicited tears. The student and I decided to give the programme another try, with the proviso that we would hold mandatory monthly meetings. I also ensured that the student could get technical support from my lab manager. After three years, the student published in a good journal, and 18 months and two research papers later, was ready to write a thesis.

This guy is surprised that a student cries after literally forgetting that the student did not meet with him. And why is technical support not available to grad students all the time?

He may publish a lot of papers (and he does), but this event marks him as an incompetent supervisor. Diamandis cares only about one person: Diamandis.

Hat tip to Justin Kiggins and Meghan Duffy.

Additional: I’d forgotten than Diamandis had another Nature piece last year, pontificating about when he would retire. I think one of the more revealing moments in that piece is when he talks about how much he loves the h-index as a measure of productivity. It explains why he can take the time to write all these career opinion pieces but forget his student.

He measures his importance by his publication record, his h-index, and the Impact Factor of the journals he publishes in. Those are things he values. His trainees, not so much.

Given what he’s written, particularly the newest piece, a lot of people might suggest he move the clock on his retirement up quite a bit. Like, “You can retire any time now. Here’s your hat, what’s your hurry?”

Update, 11 April 2017. Edge for Scholars has summarized  some of the reaction from social media to Diamandis’s article.

More update, 11 April 2017: I changed the title of this post. It was originally, “Grad student goes missing and supervisor doesn’t notice.” That was not a correct characterization of the situation. It is not like the student vanished, nobody knew where he was, and a missing persons report should have been filed. The student was there, just not making progress.

A couple of other issues raised by Diamandis’s post that have come up.

First, I noted that this article shows how disrespected master’s degrees are. It is seen as a failure, not an achievement. This is a bit of a slap to the many faculty and students who work hard at master’s degrees, whether they do not want, or are not able, to do doctoral work.

Second, Kevin Wright noted that this is a sign of the inefficiency of large labs. Someone making no progress would not escape notice in a small lab. A small lab could not afford to have a student doing very little for half a year.

Related posts

Glorifying overworking: another self-inflicted crisis in Science Careers

External links

A growing phobia
The question I hate the most
Glam Journals Whiff Again: Nature Shares Advice from Neglectful Mentor

One weird trick that would kill predatory journals

Another obviously bogus paper accepted got accepted by a junk journal. This is hardly news; barely a year goes by without someone demonstrating that some journals will publish any old crap. This one made the round because it had a lot of Seinfeld references. Marginally wittier than usual.

People continue to be (in my mind) disproportionately upset about junk journals. The Ottawa Citizen has been paying a surprising amount of attention to them for a city newspaper. One recent article argued that Canadian universities are tacitly permitting their faculty to publish in junk journals with no consequences:

In a study published in the current issue of the Journal of Scholarly Publishing, I find that the majority of research faculty in the business school at one Canadian university have publications in predatory journals. Well before the study was published, I made the dean, provost and others aware of this result. It did create friction with the dean, who did not appreciate my emails and other communications about the problem. However, the truly surprising reaction was that there was absolutely no attempt to discuss my findings, verify the problem or otherwise address the issue.  Indeed, the business school is currently preparing a performance metric that will count publications in predatory and legitimate journals equally. 

The main reason that junk journals can fool people (even some in relatively sophisticated academic environments in an industrialized nation) is that they can claim to be peer-reviewed. There is no simple way to know if a journal is peer reviewed, because those critical pre-publication reviews are normally confidential.

My “not at all novel” solution for how we could kill off junk journals is:

Publish the reviews.

Just the content of the review, not necessarily the identity of the reviewers. I don’t want to wade into the “signed” versus “anonymous” peer reviews right now. The goal is to demonstrate that the paper received substantive review, not who did it.

Real journals have the reviews to publish. Junk journals will have no reviews they can publish. The effort spent generating plausible fake reviews seems to be far too high for a junk journal to keep up the charade for long.

With that one change, whether a journal is truly peer reviewed (or not) is easily verifiable.

There have been many other people who have called for publishing reviews to be a more normal part of the publication process. There are many reasons to do this, but possibly shooting a poison dart in the direction of junk journals would be a nice side benefit.

External links

Hello…Newman: Yet another sting pranks a predatory journal, Seinfeld-style

‘Study about nothing’ highlights the perils of predatory publishing
Are universities complicit in predatory publishing?
How can we know if the journal is peer-reviewed?

05 April 2017

When academic success is news

Pretty regularly, American news media runs a story with some version of this headline:

Accepted into every Ivy League school

That’s obviously a big achievement for a high school student. But I have noticed this:


The students making the headlines are almost always minorities.

News coverage focuses on the unexpected. That news coverage so consistently focuses on minority students means that their success was not expected. Success is not normalized for them. Their success is some sort of bizarre, noteworthy exception.

Even while I appreciate the importance of visibility of success for minorities, the underlying message being sent – “We didn’t expect this kind of success from you” – is kind of crappy.

28 March 2017

Pay your interns

Matt Shipman pointed to a crowdfunding campaign for a student who wants to do an internship at NASA.

That’s horrible.

Internships should be work that give entry level experience. But the key word is “work.” If you don’t pay interns, you’re just exploiting them. And that’s wrong.

Spotting this on top of a university getting ready to destroy millions of museum specimens, and a new professor being criticized publicly for caring too much about teaching and outreach, make me feel like this about science culture, particularly academic science:


The University of Loisiana at Monroe is run by vandals

This is shocking.

From the University of Louisiana at Monroe Museum of Natural History’s Facebook page:


Dear Friends,

It is my sad duty to report to you that the ULM administration has decided to divest the research collections in the Museum of Natural History. This includes the 6 million fish specimens in the Neil Douglas fish collection and the nearly 500,000 plant specimens in the R. Dale Thomas plant collection. They find no value in the collections and no value of the collections to the university. The College was given 48 hours to suggest an alternate location for the collections so that Brown Stadium can be renovated for the track team. With only about 20 hours left, we have found no magic solution yet. To add insult to injury on what was a very hard day, we were told that if the collections are not relocated to other institutions, the collections will be destroyed at the end of July.

While we weep that our own institution would turn its back on 50+ years of hard work and dedication, we will not abandon the collections to the dumpsters. They did not have the courage to inform us face-to-face, but we have the courage to persevere through these dark times.

Oh, in other sad news, we were informed that there will not be any expansion of the public displays in Hanna Hall.

I understand that sometimes universities need to change what they do. And I’ll say that it’s not reasonable that universities support athletics and student athletes. But come on. Giving 48 hours notice over the fate of millions of specimens is ludicrous.

This is the exact opposite of what universities are supposed to do. Universities are supposed to be institutions that preserve knowledge for future generations, not chuck it in dumpsters.

Shame on you, ULM. Shame on you. You’re acting like vandals, not scholars.

I think the only hope for this collection is that enough people draw attention to its plight on social media that the university administration will change its course.

Hat tip to Terry McGlynn.

Update, 29 March 2017: The original Facebook post is gone. Now there’s this one:

Press Release: ULM to donate two collections from Museum of Natural History

By mid-July the fish and plant collections of the University of Louisiana Monroe Museum of Natural History will hopefully have a new home, according to Dr. Eric Pani, Vice President for Academic Affairs.

Several factors led to the decision to donate the collections, which have been stored in Brown Stadium since the museum was moved to Hanna Hall last year. Many of the specimens are preserved in flammable liquid and must be kept in a facility with a fire sprinkler system.

“Unfortunately, the fiscal situation facing the university over the years requires us to make choices like this. We can no longer afford to store the collections and provide all of the public services we have in the past,” Pani said.

Last week Pani told leaders of the College of Arts, Education and Sciences, which manages the museum, of the decision. He met with them again this week. He said the collections, except for some of the teaching specimens, will be donated and relocated by mid-July. The CAES people asked for 48 hours to determine if space on campus could be found and the entire collection retained.

Tuesday posts on social media could have been interpreted that the collection would be destroyed in a few hours.

Pani addressed other statements on social media, including that there would be no expansion of the museum. He clarified that expansion will be postponed for about two years while another project is underway.

The collections in Hanna Hall are open for public viewing; the specimens in Brown Stadium are for research.

Pani said renovations and improvements to the track at Brown Stadium are slated to begin in the summer. The work will raise the track to sanctioned status, allowing meets to be held there and other schools to host track and field competitions. Thus, it will provide an economic development boost for the region.

“It would be an honor for the university to donate the collection to an organization with the space to preserve and display it, and we fully expect to find such a facility as soon as possible,” Pani said.

I’m still kind of gobsmacked that a provost would argue that a stadium should take precedence over a museum because money. A museum represents a university’s primary mission. Sports does not.

This press release is nowhere to be found on the university’s news center.

More additional: Gizmodo features the story and has more comments from the VP for academic affairs, Eric Pani.

Because state appropriations have been cut more than 50% since 2008, we have struggled to provide public services. The collections have not been used for research by our students and faculty much in the last few years but are being used in class. Research use has largely been done by others from loans we have made to them.

Given that, I asked that Biology pare the collection down to something that would fit into a space typical of a classroom and would meet their teaching needs. The rest of the collection needed to be moved.

I asked that they begin to seek other institutions willing to accept our donation and transport it to their new home. As I further explained to them, this work needed to be done by mid-July because of the construction timeline involved in the renovation of the space. The 48-hr period mentioned in the Facebook post was based on their request to locate other space on our campus where the whole collection could be moved. Given what I know about campus space, I doubt they will find anything, so it would be better for them to spend the time looking for someone to accept the donation. However, I am willing to listen if they can find oncamous space. I just don’t want the search dragging on.

Christopher Dick shares an email from Pani. It’s basically the same as the Gizmodo statement.

As the Gizmodo article notes:

You can’t spell Pani without pain.

Still more additional: Andy Farke lays out the problems of trying to find a home for abandoned museum collections.

Without $$$, it's asking the impossible. It costs a lot to transfer even a well curated collection from one place to the next, even under the best of circumstances. ... Space, cabinets, databasing, archival materials, staff time, etc. It adds up fast! This is also the reason why museums are often very picky about what we take as donations or accessions.

External links

ULM Museum of Natural History Facebook post

08 March 2017

Why people with university degrees still can’t name a scientist

I was thinking about the “Most people can’t name a living scientist” factoid again. Something that often puzzled me was that the fraction of people who can name a living scientist is often reported as being so much lower than the fraction of people with a university degree.

Why, if so many people have university experience, do they not know scientists at those universities? Even non-science majors usually have to take some introductory science classes to meet breadth requirements.

I had an hypothesis about that, so I ran this poll:


The results were consistent with my hypothesis. Maybe one of the reasons people wouldn’t name a professor as a “living scientist” was because they mainly associate the occupation of “professor” with the role of teaching more than research.

But I realize now that I was probably operating under a false premise. My question was premised on the idea that science classes were taught by people with doctorates. That is, tenured and tenure-track faculty.

I saw some data a few years back showing that my university bucked a lot of national trends for a long time. The proportion of tenured and tenure-track instructors had increased in the 2000s. But this is not the case for most institutions. This article forcibly makes the point that most higher education instructors across the United States do not have a doctorate and were not tenured or tenure-track.

Consequently, even people who go through a full university degree may not have very much contact with instructors who have ever had an active research program. That might be another contributing factor to why so few people can name a living scientist.

External links

The decline of faculty tenure

02 March 2017

Traditional lands

Katherine Crocker suggested that scientists should acknowledge when their work was carried was carried out on First Nations / native American territories. Karen James found an excellent (though still in progress) mapping tool that shows what locations in the United States and Canada were the territory of what tribes, nations, and bands.

It’s too late to put any acknowledgement in my existing papers, but hey, this one of the things academic blogs are for.



The collection of sand crab in my doctoral work was carried out in the traditional land of the Costanoan Rumsen Carmel Tribe.
 
One of my next papers, to be published in Journal of Coastal Research, had two locations.

 
My #SciFund funded field work took place in traditional Seminole land.

The last was the most interesting, and most affecting:


My local field site, which has been where I have collected animals for many of my papers, sits in a region of native Americans that have been collectively referred to as Coahuiltecan. They were not considered so much a unified tribe as bands.

Unlike the tribes listed above, which are still active, the Coahuiltecans were wiped out by European contact. It made me realize why I had never heard about local native groups, unlike other places I’ve lived. I knew about the Blackfoot in Southern Alberta, I heard much discussion about aboriginals in Australia, I saw Seminole buildings when I was collecting in Florida.

Thank you, Katherine Crocker. I learned something.

Update, 20 March 2017: My colleague Frank Dirrigl informs me that much of the lower Rio Grande Valley was Lipan Apache land.

External links

Native land

01 March 2017

The value of editors

There is a line of thought among some scientists – and it is not a short line among a small fraction of scientists – that pre-publication peer review is useless, reviewers are useless, and editors are useless. Thus, journals are useless.

Albrecht Schulte-Hostedde was brave enough to post one of his old rejection letters this on Twitter (text follows images). Albrecht prefaced this saying, “Lessons learned as a young and arrogant graduate student.”



Canadian Journal of Zoology
17 April 1997
File Number: Y1150

Mr. A.I. Schulte-Hostedde

Department of Zoology
Umversity of Guelph
Guelph. Ontario NlG 2W1

Dear Mr. Schulte-Hostedde:

Subject: Patterns of Association in a Temperate Rodent Community

We have sent your paper out for re-review. Neither reviewer has been convinced by your rebuttal and as a consequence we have decided to reject your paper. We are returning the paper to you.

Neither reviewer has provided comments for transmission to the authors. Let me, however, add some comments of my own, since I detect that you may not understand the nature of the review process. We try to select reviewers who are knowledgeable and objective and who understand the role of the Canadian Journal of Zoology as a generalist journal. They are volunteers who support the discipline by committing some of their time to helping authors get their work into an acceptable form. In your case both reviewers had a number of substantive suggestions for improvement. We indicated that the paper was unlikely to be accepted without major revisions.

Your revisions were anything but major. So far as I can determine, they consisted of changing the title and adding a short section on predation. Under such circumstances we sometimes return the manuscript directly to the authors, asking them to try again. But in this case, there was an extensive rebuttal, and we thought that the reviewers should see that. The reviewers have, as I say, not been convinced, and they are both deeply disappointed by the nature and tone of your response. To quote one of them “if the authors do not respect the reviews I do not know why they would want to publish their research in the Canadian Journal of Zoology nor do I understand why the editors would accept it.”

You are just beginning your career. Let me take off my editorial hat and, as a person who has been publishing in the field for more than 40 years, offer some advice. Of the approximately 200 papers which I have published, only two were accepted without change. Of the remainder, I have invariably benefited from the advice of the reviewers. I think that you would be wise to regard the reviewers not so much as gate-keepers, but as persons who volunteer helpful advice.

Yours sincerely,

K.G. Davey/A.S.M. Saleuddin
Editors

You know what? This was written by people who care both about the scientific enterprise, and the professional development of the author. This is mentoring. This is humane. You are far less likely to get this sort of interaction from posting draft manuscripts on pre-print servers and hoping people click “Like” bottons afterwards.

I know that this is an unusual, dare I say, exceptional bit of editorial advice. But if more editors worked like this, fewer people who would question the value of journals.

How to talk to professors in their offices

I see an amazing number of questions on social media and Quora and the like from students of all sorts where my answer is, “You have to talk to faculty.”

“How do I approach a professor about my class?”

“Should I include this information on my application?”

“Should I get authorship on this journal article?”

“How can I get more time with my professor?”

Dear students, program applicants, and the like: There’s no way to talk to faculty that guarantees you get what you want. There is no risk free, fool proof conversation outline. Professors are people, and at some point, you have to learn how to talk to people. You’re an adult. The professor is an adult. Have adult conversations.

You may be shy; I get that. I was, too. But trust me, your life will get so much better and less complicated when you ask questions to the person you want an answer from, not random people on social media. Embarrassment is momentary, knowledge you gain lasts.

And a good way to ensure you don’t get what you want is not to ask, or to ask the wrong person.

Talk to professors, not about them.

28 February 2017

Tuesday Crustie: Space crabs



Man, I love vintage science fiction covers. The cover may be the best thing about the book, since the author’s work is described thus:

(T)wo sf novels remarkable for their clumsiness and their apparent ignorance of the basic laws of Physics.

Hat tip to Pulp Librarian and Miriam Goldstein.

18 February 2017

“Explain it like you would to...”


People like to tell scientists what sort of explanation counts as “clear.”

So you get clichéd advice like, “You don’t really understand something unless you can explain it to a six year old child.” (Maybe this is why doing a Google Image search for “explainer” gives me the results above: the top results are all simplistic, almost child-like, cartoon images.)

Well, I’m sorry, but there are some things that a young kid is just not ready to understand. Differential equations? Quantum mechanics? Tesseracts? There are tons of perfectly fine scientific concepts that are no less legitimate because kids won’t get them.

Meanwhile, at the AAAS meeting in Boston, Mike Taylor tweeted another “explainer” cliché:

Claudia Dreifus: “If you can’t explain it to your grandmother, don’t bring it to a reporter.”

The “Explain it to your grandmother” cliché makes me even grumpier than “Explain it to a child.” Why is “grandmother” become a synonym for “uninformed person”? And it’s always, and I mean always, a “grandmother.” Never a “grandfather” or a “grandparent.” So there’s an assumption that women are the uninformed ones that need to have things explained.

Then there’s the age issue. Plenty of older people are perfectly clever. Indeed, some of them are called, “professors.” Other examples:

All three of my children’s grandmothers have college degrees, including graduate degrees and a law degree. - Keith Bertelsen

My kids’ grandmother was one of first women to enter IT in the 1980s, and she does not appreciate condescension. - Miriam Goldstein

My grandmother is one of the sharpest and most well-informed people I know, so def seems like an odd use of “grandmother” to me - Rachel Fritts

Friend of the blog Al Dove raised one good point in defense of the “grandmother” advice:

I’m 99.9% certain grandma was picked to mean “be RESPECTFUL,” not because she’s old and dumb.

Being respectful is a good goal in communication, but given the baggage that “Explain it to your grandmother” has, I think it’s best to look for a new metaphor. The desiderata might be someone who is:

  • An adult with some education, although not an expert.
  • Someone you should treat with respect.
  • Someone whose time is limited and valuable.

My suggestion for an imaginary target audience is:

“Explain is like you would to a world leader.”

A prime minister, president, and the like are all people that any scientist should aspire to be able to coherently and concisely explain what they do and why. Justin Kiggins arrived at similar advice to me independently. But while he was being facetious, I am being sincere.

But even that will have it’s limitations. Politicians are people who often think very short-term (new cycles and next elections), which can be tough for a scientist. This reinforces a lesson I have seen many writers: “There is no ‘general public.’”

Update, 23 May 2017:  Ed Yong suggests, “Explain it like you would to an airport security agent.”

Airport security lines, it turns out, are a fantastic venue for scientists to try their hand at outreach. Various scientists are said to have claimed that you don’t really understand something if you can’t explain it to your grandmother, a barmaid, a six-year-old, and other such sexist or ageist variants. But how about this: can you successfully explain it to an TSA official—someone who not only might have no background in science, but also strongly suspects that you might be a national security threat? Can you justify your research in the face of questions like “What are you doing?” or “Why are you doing it?” or “Why are you taking that onto a plane?”

Hat tip to Megan Duffy.

14 February 2017

More March for Science thoughts

A while back, I noted that the planned March for Science had gotten a lot of flak, much of which seemed... unhelpful.

I want to be clear, though: this is not to say that March for Science should be immune from criticism.

I reckon it’s fair to say they are not making everyone feel welcome to the march. They’ve also made other communication missteps, like tweeting outdated news articles and misleading science facts. That said, I have not been following everything the March organizers have been doing or saying super closely (though I’ve collected a lot of links in this post).

I think the March for Science is important. It has excited a lot of people, but soured some. I hope that the organizers do better. Sometimes, even reviewer two has a fair point.

Update and correction, 16 February 2017: The claim that Science March had tweeted out an out of date news article was incorrect (strikethrough above). It may have come from supporter of the March, but not March organizers themselves.

Related posts

March for Science and Reviewer Two
An outsider’s perspective on protest

External links

March for Science

12 February 2017

Bilingual university plans; more program woes

The Texas observer has a profile on UTRGV focusing on plans to make the university a bilingual institution.

When this has been brought up on campus within faculty, I had heard that there was a law somewhere that said the language of instruction for public universities had to be English. I could not find it, so maybe this was just a rumour. It used to be that the state’s K-12 schools were English only... but that was over 40 years ago.

While I’m here, on top of our institution’s issues with accreditation, the nursing program is under warning.

External links

Inside the Nation’s First Bilingual University
Bilingual education
UTRGV nursing program under warning

10 February 2017

My heart beats true


It’s only the second round, and I am absolutely hooked on the AFL’s women’s competition.

Why am I hooked? Check out the 8 February edition of the Outer Sanctum podcast. Listen to how people flooded out to the first round of games because they recognized it was something historic. Listen to people admitting they were moved to tears, particularly a lot of women who never had a chance to play in a top competitions. Listen to the presenters talk about the diversity in the league, and how different the players’ stories are from the men’s competition: the men footballers had a pretty straight line into professional sports. The women have day jobs of all sorts (one Demons player is a dairy farmer), and many excel at several sports.

And what other sporting league – particularly football of any code – would have an openly gay couple playing for two different teams and competing against each other? The bigger, longer running men’s competition has never had a single out gay player, never mind a couple.

I am so enthralled that I decided to become club member, even though I will never get to a game in person this year. I barracked for the Demons since I lived in Melbourne years ago, and I’m continuing that in the AFLW. Go the Dees!

Related posts

The best ad during a football game was in AFL Women’s, not the SuperBowl

External links

Outer Sanctum podcast
First openly gay AFL player couple: "We're proud, and proud of each other"
Melbourne Demons

Staying active in the lab and/or field when you’re the boss

For many scientists, there comes a point in their careers where they are not collecting their own data. They supervise students, and the students collect the data, leaving the senior scientist (or, to use grant-speak I hate, the principle investigator or “PI”) to write grant proposals and help draft papers.

I’m a beleiver that senior scientists should have at least one project of their own. One project where they collecting their own data and write it up themselves as first author. I know that this is overly optimistic, and not a lot of people can do this. But even if you don’t have your own project, it’s still valuable to be in the field or in the lab doing something.

I’ve been thinking about this a lot this week. I’ve been spending quite a bit of time in the lab collecting data. I’m quite excited by the small amount of data I have so fa.

But the project I’m collecting data for started as an incidental observation last summer. I was helping one of my students on a project, and noticed something interesting. Just happenstance while we were looking at something mostly unrelated.

That incidental observation last summer is probably going yield at least one paper.

No matter how good and dedicated students are, the likelihood that any of them would have noticed what I noticed, and recognized it as interesting, is low.

There are benefits to having experienced observers, and that’s almost always the PI. You transition from lab bench to office desk at your own peril of missing some cool stuff.

09 February 2017

The name game and fame

 
There have been several “Scientists need to do more outreach!” editorial lately. Some have reminded people that most Americans can’t name a living scientist.

The “Do more outreach” editorials got some justified pushback from science Twitter. People listed the many, many things that scientists have been doing for outreach, not least of which was the #ActualLivingScientist hashtag on Twitter. Teachers in K-12 schools started printing out their favourites and stuck them to boards for students to see (above).

But while I love this stuff to death, I don’t think that it will make a big dent in the ability of people in polls to name a living scientist.

If you were asked in a poll to name a living lawyer, would you name a local attorney whose billboard you pass every day on your commute?

If you were asked to name a living football player, would you name your kid’s friend who plays on the high school team?

Probably not, because when you are thinking about answering a poll, you tend to think have to think fast. The names that pop to people’s heads are probably people who have some national fame. So no matter how much grassroots stuff scientists do, in a poll, people are still going to answer with names like Bill Nye or Neil Tyson or Bill Gates or Albert Einstein.

Related posts

Do you know this man?
Who gets to be a scientist?
I want to be Carl Sagan, but can’t

External links

A lot of Americans don’t know a single scientist. We need to fix that
Meet some #actuallivingscientists on Twitter
Picture from here.