31 August 2016

The IOT test

This is an excerpt of a data set from a manuscript I’ve been working on.

The box shows where half the data live, with a line dividing the boxes marking the median. The small black square in the mean, and the little crosses show highest and lowest data points.

When I submitted the manuscript, I didn’t do any statistical analysis of the data. One reviewer asked me to to a statistical analysis. It was a perfectly reasonable request that I should have anticipated. The reviewer didn’t see the same plot that I have above and didn’t know the data as well as I do.

But it got me thinking. John Vokey, one of my undergraduate professors at the University of Lethbridge,used to refer to some differences as “significant by the IOT test.” IOT was an acronym for “Inter Ocular Test.” In other words, the difference was so bloody obvious that it hit you right between the eyes.

“If the mean for one group is up here with only a little variation, and the mean for the other group is down here with this much variation, what do you need a test for? Why not just say they’re different?”

I didn’t do an analysis because I thought there was no point. In the data above, there is no overlap between the two sets at all. Do you need a statistical test to tell you that those two data sets are different?

It is easy enough to do a simple t-test on the data above.

But does adding the test and p value tell you anything more, or different, than the plot alone? Or is including the p value a statistical “fig leaf”?

Do your thoughts about analysis change when I plot the raw data next to the box plot?

Now you can see more clearly that the sample size is small. But even then, when there is no overlap in the data sets, is there any test or condition that will say those two are not statistically different?

30 August 2016

Show me what you value

My dad used to have an expression: “Don’t tell me what you value. Show me your budget, and I’ll tell you what you value.” - Joe Biden

Press releases, liked budgets, are often uncomfortably honest revelations into what institutions value. With that in mind, consider this tweet from UT System about UTRGV’s first year:

Philanthropy: Up 530%
Research expenditures: Up 56%
Student applications: Up 21%

Based on this, the UT System values money above all.

This is consistent with comments UTRGV president Guy Bailey made to faculty last year. He said he was often asked about what problems the new university was facing. He said, roughly (not a direct quote) that he told people, “I don’t have any problems that money can’t solve.” And indeed, the rest of his presentation talked about how UTRGV could get more money from the state by optimizing patterns of student enrollment. The main times I have seen our president in the news have been when he’s accepting money from donors.

The longer press release is a bit better. The first bullet in the list is student retention rate. That is indeed something to be proud of, considering that retention was something the legacy institutions struggled with. But the next two items on the list are about money.

Realted posts

What does an institution brag about?

External links

UTRGV off to a stellar start in historic first year
UTRGV receives largest donation in RGV higher education history, names business college in honor of Robert C. Vackar

26 August 2016

Broader impacts

I find it interesting that I can know I’ve crossed half a million views on a Q&A site, but still have no idea what having a journal’s “Top 10 paper” for a month means in terms of page views, downloads, and so on.

23 August 2016

Memory whiplash: “Baby eat that chicken slow...”

I’m far from the first to note how music locks us into times. You can’t control what songs are playing and popular in any year, and they become indelibly associated with that time in your life.

For me, I can’t think of The Tragically Hip without thinking of grad school. 100.3 The Q, the local Victoria rock radio station, declared The Hip to be their “house band,” so they were kind of ubiquitous on the airwaves when I was doing my doctorate.

When I moved out of the country, I didn’t hear their music any more. I’d heard about Gord Downie’s diagnosis of terminal cancer. But I happened to be in Canada this last weekend, and caught a bit of the Hip’s final show on CBC. I saw people’s reaction on Twitter. Even with my tiny little familiarity with the band and the music, I was awestruck by how they touched people last Saturday night.

I was never actually a big fan of the Tragically Hip’s music. But I always liked this one a lot.

Thank you, Gord.

11 August 2016

Master’s theses should be published

Mark Humphires has a nice post about the difference in research conducted at private organizations versus universities. His argument is that universities have screwed up scientific research because of those pesky wrong-headed incentives. (You know, the ones that scientists create for themselves.)

In the middle of a good article, I find this aside:

(Last semester, we even got a Faculty-wide email encouraging us to write up our Master’s students’ project work for publication. Because what science needs right now is more unfinished crap.)


It’s terrible to characterize master’s theses as “unfinished crap.” It shows how little regard you hold for master’s students and their work. What have master’s students done to warrant their research being treated with such contempt?

I wish I could say this was surprising, but I have seen over and over again this disinterest in master’s students, their work, and their degrees. Research universities view master’s degrees as the exit route for bad doctoral students. Funding agencies don’t want to support them, because they buy into the “failed doctoral student” narrative, and because master’s are not terminal degrees.

This is another one of those biases that works against the stated aim of many institutions to increase diversity in science. As Terry McGlynn has often noted, under-represented students come from under-represented institutions. Many of the under-represented students we say we want to recruit may not have immediate access to an institution with a doctoral program. They may want to gain research experience in a master’s that may not have be available to them as undergrads (but that undergrad students at the more swanky universities may have already had).

In my role as grad program coordinator, I have been the person sending those emails asking, “Why we are graduating so many master’s students with thesis, but we are not seeing papers being published based on that thesis research?” I send them because we have always had in our program’s guidelines that a master’s thesis should represent a publishable peer-reviewed journal. My rough and ready guide is that a master’s thesis represents one paper, and a doctoral dissertation represents about three papers.

If you think your students’ work is “unfinished crap,” let me suggest to you that it is not always the students’ fault. Maybe it’s the fault of professors who didn’t mentor the student, didn’t support the work, and can’t be bothered to do their job right.

Related posts

The cages we scientists make for ourselves

External links

How a happy moment for neuroscience is a sad moment for science
Disadvantaged students come from disadvantaged universities

10 August 2016

Emily through the aquarium glass: The Dragon Behind The Glass reviewed

Ahab had a great white whale.

Emily Voigt had a great red fish.

Then a great batik fish.

Then a great silver fish.

In every case, Voigt is pursuing the arowana. She first hears the name from a law enforcement who is talking to her about the exotic pet trade in New York. She learns that the arowana is a large fish prized by a certain kind of aquarium owner: usually Asian, male, and rich. The latter is the most necessary feature for many arowana owners, because single individual arowanas are fetching hundreds of thousands of American dollars.

That’s not a typo. It’s no surprise that you find arowana gracing the landing page of Aquarama, a trade show for the aquarium industry that Voigt visits early in the book.

Even by the time Voigt visits Aquarama, it’s clear that the arowana is the center of an unusual market, often shrouded in secrecy, and both threats and acts of violence. Again and again throughout the book, arowana are stolen, smuggled, and fought over, both in the professional and literal sense of the word.

The strangeness of it all is compelling for the reader and Voigt, who ends up pursuing this fish through multiple countries and jungles. She’s accompanied by a memorable set of other people, who I found myself constantly googling to see by the time I reached the second half of the book.

The Dragon Behind the Glass is not an academic work, but it almost could have been. Voigt’s research on the pet trade and the science is flawless. There is lots of solid biology and scientific history. For instance, we learn one species of arowana was collected and drawn by no less than the co-discoverer of natural selection, Alfred Russel Wallace, on an expedition to the Amazon that was ultimately doomed. (Sean Carroll’s Into the Jungle describes why in more detail than here. It’s about the only example in the book where I felt Voigt missed a good story.)

I came to this book because of my own research on the aquarium industry. But I was an armchair investigator. I was frustrated by my inability to get a handle on much of the supply chain for aquarium animals (crayfish in my case). Voigt provides that inside view of the production and wholesale end of the aquarium trade, and has many thoughtful asides about the pet trade. She considers the pros and cons of collecting from wild populations, CITES listings, and the paradox of the arowana being “a mass produced endangered species” (a term that applies perfectly to some crayfish in the pet trade, too).

While I was originally interested in this book because of its relevance to my own research, I kept reading because it was intertwined with the personal stuff, and her own jungle adventures, in such an entertaining way. Voigt is self aware enough to realize that her interest in this fish is... not normal. There’s a recurring theme of, “Why am I doing this and is it worth it?” that I think anyone deeply invested in a project will recognize.

The Dragon Behind the Glass is part exposé, part travelogue, part scholarship, and part descent into madness. It’s a combination as addictive as a skillfully made desert.

External links

Emily Voigt
The Dragon Behind the Glass (publisher page)
The Dragon Behind the Glass (Amazon page)
The deadly trade around exotic fish
Aquarama trade show
Early evolution pioneers’ artwork now online

Talks at Google:

09 August 2016

Tuesday Crustie: Enunciate

It’s trivia night at the pub! Because I am a non-imbiber, the most fun alcohol ever gets for me is enjoying the names and the bottle designs. I was tickled by this name when I saw it on the menu: “Evil crawfish.”

This was the art before all the brewer’s insignia got added.

Another version of the tells the story behind the name. The same company makes “Eagle Claw Fist.”

Once upon a time a man walked into a bar where a friend of our’s was tending the taps. He tried to order an Eagle Claw Fist, but got it wrong and asked for an Evil Crawfish. When we heard the story, after much laughter, we knew one day we’d make the beer. Finally, here it is, built off of ECF, but cleaner, meaner, less bitter, and dry hopped with Citra, El Dorado, and Mosaic.

Related posts

Building a winning trivia team

External links

Clow Shoes Beer: Meet the label artist

08 August 2016

Research is more than bench work and field work

I sometimes get emails from undergraduate student here asking if there are research opportunities with me. Partly because I have some bottlenecks in my lab (microscopes are a limiting factor), I can’t have a lot of students in my lab.

I’ve started offering them research opportunities to do data extraction or analysis, rather than data collection. I ask them to extracting data from websites or journal articles, and get them into an analyzable form. For example, getting latitude and longitude coordinates for species locations in the literature. Or compiling weather data.

I never heard from those students again.

I can only speculate as to why they never follow up. But, at a guess, I think they don’t consider working with spreadsheets “real” research. For them, “real” research means having a lab coat on and a pipette in hand, or getting a sunburn out in the field with a notebook in hand.

Students are shortchanging themselves.

First, I suspect that by the time you’re asking someone to compile and analyze data from some other source, it may be more likely to result in the student getting their name on a publication than bench or field work.

Second, extracting existing data and putting into a form that can be analyzed is far, far more likely to be a skill that these students will use throughout their professional career. Lots of professional level jobs require working with spreadsheets; very few require running gels.

01 August 2016

Campus carry day

August is rarely a happy month for academics. Summer is more than halfway gone, we haven’t done as much research or as much writing as we wanted, and classes are going to start gearing up again very soon.

At my university, and public universities across Texas, today marks the start of an even less happy month. Today, 1 August 2016, is the day Texas’s campus carry law goes into effect.

The sign above, on the door leading to the research labs, including mine, went up Friday. The law permits university administrators to set “reasonable rules” for “campus safety.” (Yes, the wording is vague, which caused no end of difficulties in drafting policy, I’m sure.) Consequently, there is a long list of exclusionary zones on UTRGV campus, including labs.

University administators, and many others, lobbied harder against this law than any other I have seen in my time here, but to no avail. It’s telling that private universities were given the option to opt out of the law, and 36 out of 37 did.

Not surprisingly, the #CampusCarry hashtag on Twitter shows the usual split of rote political talking points, just adding more fuel to me desire for blogging to be my main social media outlet for a while.

And because fiftieth anniversaries matter more than usual to me this year, I can’t go without mentioning that this law is going into effect 50 years to the day after the first major mass shooting in an American university at the University of Texas in Austin. <sarcasm> That was extra classy, Texas legislature. </sarcasm>

I don’t feel safer today. Quite the opposite.

External links

Campus carry goes into effect at UTRGV