18 September 2017

A pre-print experiment, continued


Over a year ago, I uploaded a preprint into bioRxiv. When people upload preprints, bioRxiv sensible puts on a disclaimer that, “This article is a preprint and has not been peer-reviewed.”

A little over a week ago, the final, paginated version of the paper that arose from the preprint was published. Now, bioRxiv is supposed to update its notice automatically to say, “Now published in (journal name and DOI).”

Perhaps because the final paper was substantially different than the preprint – in particular, the title changed – bioRxiv didn’t catch it. I had to email bioRxiv’s moderators through the contact form asking them to make the update.

The preprint was making more work for me. Again. It wasn’t a lot of work, I admit, but people advocating preprints often talk about them as though they take effectively zero time. They don’t. You have to pay attention to them to ensure things are being done properly. I want people to cite the final paper when it’s available, not the preprint.

Some journals are talking about using bioRxiv as their submission platform. This would be a good step, because it would remove work duplication.

I’m glad I’ve been through the preprint experience. But I am still not sold on its benefits to me as a routine part of my workflow. It seems all the advantages that I might gain from preprints can be achieved by other methods, notably publishing in open access journals with a good history of good peer review and production time.

Related posts

A pre-print experiment: will anyone notice?

13 September 2017

A look back at the crystal ball

I wrote the bulk of this post this post five years ago, back in 2012. That week, a paper came out in Nature that claimed to predict... the future! At least, it claimed to predict one part of my academic future, namely, my h-index:


At the time the paper came out, there was an online calculator. It hasn’t succumbed to link rot: it’s still there! I entered in the following values then:

  • Current h-index: It was 8 in 2012 (according to Google Scholar).
  • Number of articles: 24 (I only counted my original technical articles).
  • Years since first article: 20 (then; my first paper was in 1992).
  • Number of distinct journals: 20.
  • Number in “top” journals (a.k.a. the glamour mags): 0.

The program predicted my h-index now, five years later, would be 13. Since I used my Google Scholar data, I went back and checked my Google Scholar profile.


How did the prediction fare? Zooming in...


Holy cow!


Perfect. The prediction was perfect.

It’s a bit spooky.

Now I’m having one of those existential crises of whether my fate is set and whether there is anything I can do about it. As Ahab said in Moby Dick:

Is it I, God, or who, that lifts this arm? But if the great sun move not of himself; but is as an errand-boy in heaven; nor one single star can revolve, but by some invisible power; how then can this one small heart beat; this one small brain think thoughts; unless God does that beating, does that thinking, does that living, and not I.

The 2012 prediction reaches ten years forward, predicting an h-index of 21 in 2022. Of course, my publishing profile has changed in five years. I entered my updated data, and experienced my second existential crisis of the day:


My predicted h-index for 2022 has gone down from five years ago! The new prediction drops my 2022 h-index by 3 points! Argh! It does kind of make you feel like you’re failing at science.

Next, to schedule a post with this graph for 2022. We’ll see how close it is.

Related posts

Gazing into the crystal ball of h-index
Academic astrology

11 September 2017

Chasing pidgeys


In the game Pokémon Go, pidgeys are pokémon that you see everywhere. They’re super common, super small. They are not very powerful. You’d be hard pressed to win any gym battle with them.

When I started playing the game, I quickly stopped collecting them because, well, I had them already. And they seemed useless.

But I was wrong. And now I chase after them all the time.

There are a lot of different resources in Pokémon Go, but one is experience. You “level up” as a player with a certain number of experience points. One of the ways to get experience points is to evolve pokémon, and you get quite a lot of experience for doing so. It turns out that pidgeys are cheap to evolve. A few other pokémon are just as cheap, but they are much less common, and harder to catch.


Thus, what looks like something trivial and boring turns out to be one of the most reliable ways to advance in the game.

It occurred to me that this is a good metaphor for careers, including academic careers. Much of your success comes from chasing pidgeys: the boring, mundane tasks that you have to do a lot of, and that earn little recognition individually. Grading assignments, getting reviews back to editors, going to meetings, consistently working on papers.

(This post inspired by a student in General Biology who asked me what level I was at in Pokémon Go and whether I’d caught Raikuo yet.)

Picture from here.

08 September 2017

The Voynich manuscript and academic writing


The Voynich manuscript is a potentially obsession creating item. It’s routinely described with phrases like, “the world’s most mysterious book.” For more than a century, nobody could read it or make heads nor tails about what it was about. Debate raged about whether it was coded or just an unreadable hoax.

Until recently.

The book has, apparently, finally yielded to insightful scholarship and has been decoded.

(I)t was more or less clear what the Voynich manuscript is: a reference book of selected remedies lifted from the standard treatises of the medieval period, an instruction manual for the health and wellbeing of the more well to do women in society, which was quite possibly tailored to a single individual.

But what I want to talk about is not the solution, but about writing style and communication.

Here we have a century old mystery, solved. Here’s how I learned about it. A tweet from Benito Cereno that read:

Holy shit holy shit holy shit holy shit

The Voynich manuscript, decoded

You can feel Benito’s excitement in that tweet! This is so exciting, there’s no time for punctuation marks!

Now read Nicholas Gibbs’s first hand account of solving this mystery. Here’s the opening paragraph, which does use a good narrative structure, the ABT (and, but therefore) template (championed by Randy Olson):

For medievalists or anyone with more than a passing interest, the most unusual element of the Voynich manuscript – Beinecke Ms. 408, known to many as “the most mysterious manuscript in the world” – is its handwritten text. (And) Although several of its symbols (especially the ligatures) are recognizable, adopted for the sake of economy by the medieval scribes, the words formed by its neatly grouped characters do not appear to correspond to any known language. (And) It was long believed that the text was a form of code – one which repeated attempts by crypt­o­graphers and linguists failed to penetrate. (And) As someone with long experience of interpreting the Latin inscriptions on classical monuments and the tombs and brasses in English parish churches, I recognized in the Voynich script tell-tale signs of an abbreviated Latin format. But interpretation of such abbreviations depends largely on the context in which they are used. (Therefore) I needed to understand the copious illustrations that accompany the text.

But even with that good narrative structure in place, the opening paragraph shows so many of the problems of this article. Like many academics, Gibbs overloads on facts, with “and, and, and...” before we get to the “but.”

It’s about as devoid of excitement as you can imagine. This is a very careful walk through of the process. To use another of Randy Olson’s ideas, the “four organs of communication” (pictured; more in Don’t Be Such a Scientist) this description is all head (intellect). There’s nothing from the heart (emotion) or gut (intuition, humour). No emotion, nothing personal.

It’s disappointing.

Gibbs completely bypasses the intensity of interest in the strange book, of how many people have tried to crack it. “Repeated attempts” is so weak to describe a century long set of efforts to crack this this. It is such a typically cautious, couched language that is used in academic writing all the time.

And having solved a problem that so many people have brought so much talent and effort to bear upon, you might expect Gibbs to describe opening a bottle of champagne in celebration. Or maybe a beer. Or a description of the satisfaction he had from his insights – the “Aha!” moments, as it were.
Instead, Gibbs treats it with about as much enthusiasm as a walk to from the living room couch to the bathroom. 

You want to hear about the feeling of triumph of solving the puzzle, not just the step by step solution to it.

If you want to connect with people, you need the passion. You need the guts. You need the emotions.

Update, 9 September 2017: I’m seeing tweets from people grumbling that the Voynich manuscript probably hasn’t been solved. Nobody that I’ve seen has said why they doubt that the problem is solved. (Update, 10 September 2017: Ah, see here.) Regardless, that doesn’t change the points made here.

Related posts

Connection: Hollywood Storytelling Meets Critical Thinking review
Review: Don’t Be Such a Scientist

External links

Voynich manuscript: the solution
So much for that Voynich manuscript “solution”

Picture from here.

02 September 2017

Thank you, New Hampshire


It’s been a week since Harvey changed everything for Houston, Texas.

And since then, I’ve been waiting. After Katrina hit new Orleans, my university (then The University of Texas Pan American) offered enrollment to students affected by the hurricane. Since Harvey was hitting Texas, I expected that and more.

I emailed our president’s office, reminding them of what happened back in 2005. I got an email back from our Office of Emergency Preparedness, saying:

(UTRGV) has been in communication with University of Texas System... since last week. There are system-wide plans in place in the event student relocation becomes necessary.

I waited to hear what those system-wide plans were. I waited all week. All that happened at my institution was that the Atheletics department teamed with a Texas grocery store to fundraise. Hardly an institution wide response or plan.

Finally, University of Texas System Chancellor William McRaven writes this, titled, “Texans stop for no storm.”

This annoys me to no end. It feels like McRaven is taking this moment to do say, “Look how tough we are,” posturing instead of actually offering concrete plans for help.

On Twitter, the UT System account tweeted a Storyify about how institutions were helping people affected by Harvey. And this is nice, but it’s things like student organizations doing fundraising, universities offering counseling services, not institutions offering anything like what a New Hampshire university has done.

Franklin Pierce University will provide free tuition, room and board to up to 20 students for the fall semester.

That’s what I was expecting UTRGV and other UT System universities to do. But no.

Thank you, Franklin Pierce University, for doing for Texas students what Texas universities didn’t.

Related posts

Credit where it’s due

External links

New Hampshire university to take in students after Harvey
Texans stop for no storm

Picture from here.

29 August 2017

Why a proposed UTRGV doctoral program will probably struggle

When I took my current job, one of the things that attracted me was that I was told the department would probably have a Ph.D. program, maybe in about five years. It’s been a lot more than five years, but a biology related Ph.D. is finally on the horizon for my university. This should make me happy. It does not.

Last week, the UT System tweeted:

.@utrgv Pres Bailey looks to create PhD in Cellular, Molecular & Biomedical Sciences and Doctor of Physical Therapy programs. #UTRegentsMeet

And yesterday, it was confirmed that the university has the go ahead for preliminary planning for this proposed doctoral degree.

I want to go on record as to why I think this is not a good idea. (You get tenure in part so you can make these kinds of analyses.) For context, I have been the graduate program coordinator for biology at this institution for over a decade. So yeah, I know the backstory here.

First and foremost, the primary issue I have with the proposal for this degree is that it is being driven by institutional wants. Not to meet clear needs in the community. Not students’ interests. Not faculty research strengths. The university is trying to get to ten doctoral programs as fast as it possibly can, so it can meet the criteria for an “emerging research university.” Getting to that number of Ph.D. by any means they can is more important than coming up with a program that has faculty support and that will ultimately serve the students.

Second, the proposed program – “Cellular, molecular, and biomedical sciences” – might as well say, “and the kitchen sink.” There is no theme or connection there. There is no department of “cell, molecular, and biomedical sciences.” It seems like the plan is to conscript any faculty member in any department that knows how to use a PCR machine. With no single department to house the program, there will be tremendous problems of organization and cohesion. It will be difficult to instill that intangible but critical sense of community.

Third, there are already four cell and molecular biology doctoral programs in Texas (not to mention broader general biology programs). They are at University of North Texas, UT Austin, UT Dallas, and one of our closest neighbours, UT San Antonio. There is an case to be made that the proposed degree would unnecessarily duplicate existing programs, which the Texas Higher Education Coordinating Board warns against.

Lastly, the graph that no administrator has an answer for is this one (from here):


The article has UTRGV president Guy Bailey talking about job growth projections from the Bureau of Labor Statistics. But knowing demand don’t tell you much unless you know the supply. Administrators will ignore the existing backlog in students being trained, and the growth of programs training them.

The Bureau of Labour Statistics lists one biology related occupation that requires a doctoral degree: “Biological science teachers, postsecondary” (i.e., professors). They project a total of 21,200 job openings from 2012-2022. Using 2011 data on doctoral production, the projected 10 year need can be met in less than three years at recent rates of doctorate creation at the national level.

The only other biology related occupation listed by the Bureau of Labor Statistics that requires a doctoral degree is animal scientists (1,200 job openings, 8.8% growth). Again, this need can be met by current levels of doctorate attainment in the United States.

There are not clear projections for how much demand there will be for biology doctoral recipients outside academia, because the Bureau of Labor Statistics does not separate “Life sciences” jobs on whether they require a B.S., M.S., or Ph.D.

I think the students and the region deserve a good doctoral program they can be proud of. Instead, we’re likely to get a rushed, rudderless, “me too” doctoral program that nobody asked for and nobody wanted.

External links

UTRGV gets green light to seek two new doctorate degrees

28 August 2017

A sense of community


Last week, Stephen Heard wrote a post about being paid for peer review that generated a lot of discussion on Twitter. A fair number of people were quite emphatic that they were not being paid, and a few seemed very grumpy about that.

Earlier in my career, I remember people complaining about the individual reviews they got, or how long reviews took. But I don’t remember people grumbling over doing reviews, or not being compensated for them. And I never heard complaints from editors about how many people were refusing to do reviews.

Now, I suspect part of this is just a shift in perspective. I hear more voices via social media than I did before, and hear more perspectives. I know people who are on editorial board on Twitter, which I didn’t before. Still, from my perspective, it feels like grumpiness over having to do peer review is a relatively recent thing.

It seemed to me that annoyance about doing reviews might be symptomatic of researchers having a degraded sense of community.

When you feel like you belong to a community, you just pitch in. You help. Not because you are paid to do so, but because it’s friends and neighbours and it’s just what you do to make your community a nice place to be.

I think people are refusing to do reviews in part because they don’t feel connected to the academic community. And I get why that would be: it’s a rough, competitive market for ideas now. The shortages in funds and jobs and everything else feels like it’s forcing people into a “me first, me only” mindset to try to survive.

People will complain about journals more when they don’t feel they those journals are part of their scientific community. Maybe this is why many academics have continued to support society journals, even as more and more of them get run by one of the big main “for profit” publishers.

I have been thinking a lot about community, too, because of things like university administration. This tweet went out last week, reading in part:

@utrgv President Bailey looks to create PhD in Cellular, Molecular & Biomedical Sciences.

Yeah, neither faculty nor students asked for that program. It certainly doesn’t make me feel part of a community in my own institution.

Same with graduate programs. I’ve seen some research that one of the biggest predictors of successful programs is that graduate students feel a sense of belonging. That is, of community. And while I tried to create that feeling in our graduate program, I have come to the conclusion I have failed.

This is one reason why science Twitter and the science online community has been important to me: because it truly does seem like a community. People offer ideas and support, for no reason, just because. Someone came up with the term “pocket friends,” which I think is a good phrasing. I’ve said to a lot of people that online conversations are real conversations. And online friends are real friends.

Update, 29 August 2017: This post was featured in today’s Daily Briefing in the Chronicle of Higher Education. Thanks to them!

Update, 30 August 2017
: Mike Taylor has a response.

External links

Can we stop saying reviewers are unpaid?

Picture from here.