14 June 2018

Another preprint complication

While I knew some journals won’t publish papers that had previously been posted as preprints, I didn’t know that some journals are picky.

Jens Joschinski wrote:

Some journals (well, @ASNAmNat) will not accept papers posted at @PeerJPreprints or other commercial services.

This makes no sense to me. What does the business model of the preprint server have to do with anything regarding later publication?

There’s a list of journal policies. Thanks to Jessica Polka.

But frankly, every little bit of legwork just makes me less inclined to post preprints. I’ll still do it if I think I have some compelling reasons to do so, but doing this routinely as part of my regular publication practices? Maybe not.

11 June 2018

Does biorXiv have different rules for different scientists?

Last year, I submitted a preprint to biorXiv. I was underwhelmed by the experience.

But I am a great believer in the saying, “Never try something once and say, ‘It did not work.’” (Sometimes attributed to Thomas Edison, I think.) I submitted another manuscript over the weekend which I thought might be a little more suited to preprinting, so after I submitted it to the journal, I went and uploaded it to biorXiv. It was the weekend, so it sat until Monday. Today, I received a reply. My preprint was rejected.

bioRxiv is intended for the posting of research papers, not commentaries(.)

How interesting.

I like that this demonstrates that preprint servers are not a “dumping ground” where anyone can slap up any old thing.

My paper is not a research paper. I don’t deny that. Following that rule, biorXiv made a perfectly understandable decision.

But the whole reason I thought this new paper might be appropriate to send to biorXiv was I had seen papers like “Transparency in authors’ contributions and responsibilities to promote integrity in scientific publication” on the site before. I opened up that PDF and looked at it again. There’s no “Methods” section. There’s no graphs of data. There’s no data that I can find at all.

How is that a research paper? And how is that not a commentary? Maybe I’m missing something.

But although the paper above doesn’t have data, what it does have is a lead author who was the former editor-in-chief of Science and current current president of the National Academy of Science of the US, Marcia McNutt. The paper was submitted in May 2017, some time after McNutt became president of the National Academy in 2016.

And while she is the only one to have “National Academy of Sciences” listed in the authors’ affiliations, the rest of the author list is nothing to sneeze at. It boasts other people with “famous scientist” credentials, like Nobel laureate and eLife editor Randy Schekman. Most of the authors are involved in big science journals.

One of my criticisms of preprints is that they would make the Matthew Effect for publication worse. People who are in well-known labs at well-known institutions would receive the lion’s share of attention. People who are not would have just another expectation with minimal benefits.

But this feels even worse. This feels like there’s one set of rules for the rank and file scientists (“No commentaries!”) and another set of rules for scientists with name recognition (“Why yes, we’d love to have your commentary.”).

I like the idea of preprints, but this is leaving a sour taste in my mouth.

Update, 12 June 2018: The manuscript found a home at a different preprint server, Peer Preprints.

Related posts

A pre-print experiment: will anyone notice?
A pre-print experiment, continued

External links

Twitter thread
Transparency in authors' contributions and responsibilities to promote integrity in scientific publication

04 June 2018

Viral video verdict: Crayfish claw cutting complicated

Making the rounds in international news in the last couple of days is a viral video that is normally described in the headlines this way:

"Heroic crayfish cuts off own claws to escape the pot!"

Crayfish behavior, heat, pain, claws... This is right on target with some of my research. But so far, nobody has called me to break down what is going on in this video. 

What the crayfish is doing probably autotomy, not desperate self-mutilation. A crayfish dropping a claw is not like a person ripping off an arm. But the narrative is so good that nobody cares about the science.

I'm away from my desktop, so it's too hard to write a detailed blog post like I normally would. Instead, I wrote a Twitter thread about it: https://mobile.twitter.com/doctorzen/status/1003645638213623808 

External links

03 June 2018

Theory and practice

Years ago, while listening to CBC's Morningside, I heard this description:

"Canada is a country that works in practice, but not in theory. The United States is a country that works in in theory, but not in practice."

I was reminded of this over the weekend reading a thread about data sharing (https://twitter.com/danirabaiotti/status/1002824181145317376). Universal a data sharing between scientists is one of those ideas that sounds great in theory. So great that people tend to undervalue how it will work in practice.

Another example that I was thinking about recently was post publication peer review. In theory, it might be nice to have a single cenatralized site that included all post publication comments. In practice, blogs have a pretty good track record of bringing important critical comments to a broader audience.

I see this over and over again with people putting forward ideas about how we should do science? The meta science, so to speak. Around publication, peer review, career incentives, statistical analysis. I've been guilty of this. There's old posts on this blog about open peer review that I still think were fine in theory, but not grounded in practice. 

I think we scientists often get very enamoured of those solutions that work in theory, and undervalue things that work in practice.

22 May 2018

Tuesday Crustie: Mollie

Never heard of the US Digital Services agency? Now you have. Meet Mollie, their mascot:


Yes, those are light sabers. Slate has the story behind this adorable creation.

Hat tip to Miriam Goldstein.

18 May 2018

All scholarship is hard

Nicholas Evans wrote:

The solution levied by synthetic biologists is to get more biologists doing ethics. That this is always the suggestion tells me a) you think it’s easier to think about ethics than synbio; b) you want to keep the analysis in house. Neither are good.

Seconded, confirmed, and oh my God yes. I’ve been through several iterations of this in biology curriculum meetings, where I or others have suggested incorporating some non-biology class into a degree program, or even just an elective students funded by a training grant have to take. And the reaction is just what Nicholas describes:

“Why don’t we just do it ourselves?”

The single exception seemed to be chemistry. Maybe there was less suspicion because of the blurry line between molecular biology and biochemistry. Or maybe it was because their department was right above ours and we knew the people better. But when it was ethics or writing or statistics: nope, we’ll develop out own class taught by our own faculty in our own department.

I get a lot of variations of “Is is easier to do this or that in academia?” questions on Quora, too.

In an institution, this attitude of “We know best” is made worse by administrative measurements. Departments are evaluated by how many credit hours they generate. So when I suggest students might take a course taught by the Philosophy or Math or Communications or Psychology department, the response is, “We’re just giving credit hours away.” Since credit hours are one thing that are looked at to determine resources, it’s an understandable reaction. It’s Goodheart’s law in action. The measure becomes a target and changes what the measure does.

Nicholas notes:

The vast majority of people talking synbio ethics have almost no training in ethics. You wouldn’t accept that in the technical side of synbio, so don’t accept it in ethics.

Exactly. We often complain about how people don’t respect expertise on many controversial subjects, like evolution, climate change, or vaccination. But we see the same disrespect within universities for scholarship in different fields. Scholarship in every field is hard, and “My field is better than your field” is a shitty game.

Hat tip to Janet Stemwedel.

16 May 2018

The Zen of Presentations, Part 71: Slides per minute

In grad school, I was introduced to a nice, simple rule for giving a talk.

One slide per minute.

I used this rule for a long time. It seemed to work well. In particular, any slide with data seemed to take at least a minute to digest. You had to orient yourself to the axis labels, the units, there is reader an interpretation to do, and that takes a little time.

I did know it was a rule of thumb, not an ironclad rule. I would estimate a slide would be up for a little less than a minute when it was a picture of an animal or something else that had no data or nothing to read

But then I saw Lawrence Lessig’s presentation, “Free culture” (via Garr Reynolds’s blog). His talk had 243 slides, but it was not 243 minutes. Lessig used his slides in a way I’d never seen before. They weren’t illustrations to be described or explained. His slides were his rhythm section, laying out a beat and emphasizing what he said. Even though his slides were up for such a short time, I never felt confused or lost or thinking, “Wait, wait, go back!”

I was blown away. I showed me how limited my views about what a “good presentation” were.

Then I learned about formats like pecha kucha and Ignite talks. Like Lessig, they emphasized quick pacing, running through slides at 3 to 4 per minutes. And those talks often rocked.

The key to such rapid fire delivery was planning and practice. The automatic slide advance rule for pecha kucha and Ignite talks forced to you plan and practice relentlessly. Practice never leads you wrong.

There are some images and slides that probably do warrant a full minute. But the audience can often pick up on points faster than you’d think

There isn’t any magic number of slides in a talk. Your talk can have hundreds of slides. Your talk can have no slides. Or your talk can even have one slide per minute.

Related posts

The Zen of Presentations, Part 40: Lighting a fire under speakers
How Gilmore Girls change my teaching

External links

Free culture presentation
The “Lessig method” of presentation