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

11 May 2018

The Zen of Presentations, Part 70: Giving away the plot

Mike Nitenbach wrote:

Huge mistake to design scientific presentation like fucken Sherlock Holmes story.

Becca replied:

If you set things up and present your logic at every step, the audience can tell where things are headed without being explicitly told in advance.

Over on Better Posters, I’ve talked a lot about the Columbo principle. Columbo taught us that even when the audience knows the answer, the fun can be in learning how you prove it. I think that advice works well for titles, but it still implies a sort of “mystery” aspect that Nitenbach is criticizing.

But you can structure a talk where you tell the audience what’s going to happen, but not leave them disappointed.

When making Star Trek II: The Wrath of Khan, writer Nicholas Meyer (who also directed) was faced with a problem: Spock, the show’s most popular character, was going to die.


Actor Leonard Nimoy was bored with the part, not interested in doing another movie, and was sort of lured back in by the prospect of killing off the character. Fans learned about this, and were upset. Meyer got death threats. So what did Meyer do?

He killed Spock in the opening scene.

Of course, Spock doesn’t actually die at that point. He pretends to die as part of the Kobayushi Maru training scenario. So when the film is winding up for the actual, powerful death scene of Spock, people were not thinking about, “This is the one where Spock dies!”

Meyer said he learned on this movie that you can show an audience anything in the first ten minutes of a movie, and they will forget about it by the end of the movie.

You can do the same thing in a talk. You can tell people right at the start of a talk what you found. If you involve them, and make the narrative of that process well told, you can bring people through to the end, and they will think, “Oh yeah, I already knew that!”


Meyer said in the film’s Blu-ray commentary:

The question is not whether you kill him. It’s whether you kill him well. If it’s perceived as a working out of a clause in a star’s contract, then they’re gonna hate it. If it’s organic, if it’s really part of the story, then no one’s gonna object.

Or, to paraphrase Anton Chekov, if you want fire a gun in the third act, load it in the first act. The audience will forget the gun was even loaded until that final climactic shot.

External links

Detective stories: “Whodunnit?” versus “How’s he gonna prove it?”
38 Things We Learned from the ‘Star Trek II’ Commentary

04 May 2018

Rhodes Trust is academia’s equivalent to Confederate statues and flags

Bree Newsome taking down South Carolina Confederate flag

In the last few years in the United States, there’s been debate about the presence of Confederate flags and statues in public places. I credit Bree Newsome for getting this ball rolling. The Confederacy was built on the notion that slavery was right and just.

Continuing to display the symbols of that failed government on public grounds is tacit endorsement of the ideals of white supremacy. Put those statues and flags that are on government property in museums.

This morning, I was given a link to a fellowship and was asked to promote it. I had two problems with that, and the first was that the fellowship had a lot of ties to the Rhodes Trust.

As a student, I learned about Cecil Rhodes because of his association with Oxford’s Rhodes Scholarships (supported by the Rhodes Trust). That name had a positive association for me.

It was only later that I learned, “Man, this dude was racist as fuck.” In Born a Crime, Trevor Noah says if many Africans had a time machine, they wouldn’t go back in time to stop Adolf Hitler, they’d be packing heat for Cecil Rhodes.


I wish I had learned about Rhodes’s colonial racism first, not years after hearing about the scholarships. The misery Rhodes caused in life seems more important to me than the money he left behind after death.

The second problem I had with this fellowship was that it was for “leading academic institutions.” I’m pretty sure that means American Ivy League institutions and English Oxbridge universities, and not the sort of public, regional institutions where most students in the world get their university educations. (The sort of place I work.)

Racist and elitist was not a winning combination for me. I did not push out notification of the fellowship. Admittedly, this was made easier because the deadline was post, but I wouldn’t have done it regardless.

Is Rhodes the only example? When I mentioned this on Twitter, “Sackler” came up. Like Rhodes, I first heard that name in a positive light: the Sackler symposium on science communication, which I’ve blogged about several times (here in 2012, here in 2013). But the Sackler family is problematic: they made a lot of money from opiods, which is now a major public health problem. And that name is on museums and medical schools.

Like Rhodes, I should have known about the drugs before I knew about the symposium. That’s not good.

Turning money isn’t as easy as taking down a flag on a pole, or a statue in a park. But the principle is the same. Academia needs to look harder at how to stop giving these unspoken endorsements to people who caused a lot of suffering.

Update, 14 May 2018: Poll results from Twitter. 84% of people surveyed said they’d take money with the Rhodes name,


Picture from here.

Rethinking the graduate admissions process

Warning: The following post is a piece of devil’s advocacy. I’m not sure I believe myself.

The process for selecting graduate students is mostly deeply flawed and should be revamped from the ground up. Almost everything in the admission process works against increasing diversity in academia.

Let’s take the elements apart piece by piece.

Application fee: Many program charge an application fee. This works against students who are good, but economically disadvantaged. There is no way that those fees are paying the bills of the graduate office, Friction can be a useful thing in preventing spurious applications, but generally the cost is so high that multiple applications quickly add up and remove options from students who can’t pay them all.

GRE scores: The cost of writing and submitting scores is another economic barrier. Many have written about the low predictive power of the test (also here).

Undergraduate GPA: Grade inflation is making it difficult to distinguish student performance. Plus, they are not exactly comparable from institution to institution, both in calculation (is the top score 4 or 4.3?), a situation that gets even more complex when student cross national borders. And it’s highly likely that the same grade point average will be interpreted differently depending on the issuing institution.

Recommendation letters: So much room for bias here. People write different recommendations for men and women. Like, twice the men get glowing letters than women. People are influenced by university of the letter writer and the seniority of the recommender and probably other factors that have nothing to do with the candidate. Recommendation letters are the primary tool for old boy’s networks to reinforce themselves.

CVs: Recently, we learned that a large number of graduate fellowship applicants were told they didn’t get the award because they didn’t have a publication yet. These are supposed to be people at the start of their academic careers, so it is not reasonable to expect them to have a lot on a CV. And given that so many places have not cracked down on unpaid internships, experience on paper will tend to favour people in well off families. Again.

Personal statement: This one might be okay, as long as applicants gave no indication of their gender. Because just the name alone works against increasing diversity.

If grad review is so messed up, what can we do?

One idea is to stop the tedious review by committee and just let individual faculty pick students they want to supervise. It doesn’t eliminate all the biases, but at least it’s less work.

In research grant applications, there’s occasionally serious suggestions crop up that the peer review process is kind of ineffective and that we’d be better off assigning funding by lottery. Maybe we should consider admitting grad students by lottery, too.

On Twitter, I asked students what they would like to see in the application process. Zachary Eldredge brings up the idea of a lottery, and Olivia mentions a face-to-face interview. Will Lykins says it would be good to normalize non-academic work on the forms, which again many students increasingly have to do to make ends meet instead of doing those unpaid enrichment activities.

Related posts

I come to bury the GRE, not to praise it
How do you test persistance?
Why grade inflation is good for the GRE
Does grad school have a mismatch problem?
The “Texas transcript” is a good idea, but won’t solve grade inflation

18 April 2018

Teaching online and inclusion

"Do you expect me to talk, Goldfinger?" "No Mr. Bond, I expect you to make this online course ADA compliant!"

 I’ve been teaching a completely online class this semester. I’ve done partly online classes, and practically live online anyway, so I thought this would be a fairly simple thing for me to do.

It has not. It has been a real eye-opener for thinking about student needs.

One of the biggest challenges I’ve been working with is making the class compliant with the rules for students with disabilities. The rules are that whether there are students in the class who have declared disabilities or not, you must make every item in the class as readily available and accessible as if there were students with disabilities.

This means video lectures need closed captioning. There is voice recognition software that does closed captioning automatically, which is great, but it never does it perfectly. Every time I say, “Doctor Zen,” the software puts in, “doctors in.” This means you have to go in, listen to the entire lecture, and proofread the captioning for entire lecture.

Similarly, every image needs a description so that someone who is blind or otherwise visually impaired can understand the material. And many scientific diagrams are complex and challenging. Today, I was forced with trying to write a complete description of this:

Human genome influences traits. Human genome has 2 copies in every cell. 1 copy is made of 3 billion base pairs. Cell makes up tissue. In cell, genome divided into nuclear genome and mitochondrial genome. Cells manifest traits. Tissues make up organs. Tissues manifest traits. Organs make up body. Body manifests traits. Traits leads back to Lesson 1. Mitochondrial genome has 1 circular chromosome. Mitochondrial genome is many per cell. Circular chromosome is many per cell. Circular chromosome made of nucleic acid and histone proteins. Nuclear genome is one per cell. Nuclear genome is 23 pairs of linear chromosomes. 23 pairs of linear chromosomes has 22 pairs called autosomes. 23 pairs of linear chromosomes has 1 pair called sex chromosomes. Sex chromosomes are XX for female. Sex chromosomes are XY for male. 23 pairs of linear chromosomes are made of nucleic acid and histone proteins. Nucleic acid wraps around histone proteins. Nucleic acid has two types, DNA and RNA. RNA leads to lesson 3. DNA is composed on deoxynucleotides. DNA is double stranded. DNA composed of deoxynucleotides. Double stranded leads to helical shape. Double stranded by base pairs. Deoxynucleotides are 4 types of nitrogenous bases. Nitrogenous bases can form base pairs. Nitrogenous base connects to A, T, C, G. A base pairs with T and vice versa. G base pairs with C and vice versa.

Here’s what I came up with for the concept map above:

Human genome influences traits. Human genome has 2 copies in every cell. 1 copy is made of 3 billion base pairs. Cell makes up tissue. In cell, genome divided into nuclear genome and mitochondrial genome. Cells manifest traits. Tissues make up organs. Tissues manifest traits. Organs make up body. Body manifests traits. Traits leads back to Lesson 1. Mitochondrial genome has 1 circular chromosome. Mitochondrial genome is many per cell. Circular chromosome is many per cell. Circular chromosome made of nucleic acid and histone proteins. Nuclear genome is one per cell. Nuclear genome is 23 pairs of linear chromosomes. 23 pairs of linear chromosomes has 22 pairs called autosomes. 23 pairs of linear chromosomes has 1 pair called sex chromosomes. Sex chromosomes are XX for female. Sex chromosomes are XY for male. 23 pairs of linear chromosomes are made of nucleic acid and histone proteins. Nucleic acid wraps around histone proteins. Nucleic acid has two types, DNA and RNA. RNA leads to lesson 3. DNA is composed on deoxynucleotides. DNA is double stranded. DNA composed of deoxynucleotides. Double stranded leads to helical shape. Double stranded by base pairs. Deoxynucleotides are 4 types of nitrogenous bases. Nitrogenous bases can form base pairs. Nitrogenous base connects to A, T, C, G. A base pairs with T and vice versa. G base pairs with C and vice versa.

Writing that description... took time.

Anyone who think that online teaching is going to be some sort of big time saver that will allow instructors to reach a lot more students has never prepared an online class. It’s long. It’s hard. It’s often bordering on tortuous (hence the “No Mr. Bond” gag at the top of the post).

These things take time, but I don’t begrudge the time spent. It’s the right thing to do. It’s forced me to think more deeply about how I can provide more resources that are more helpful to more students. It’s not just deaf students who can benefit from closed captions, for instance. Someone who can hear could benefit from seeing words spelled out, or maybe use them when they are listening in a noisy environment, or one where sound would be distracting.

And I keep thinking that if I think it takes a lot of work to put these it, it’s nothing compared to students who need these materials who have to navigate through courses every day.

External links

Flowcharts and concept maps

16 April 2018

“It makes no sense!” versus history

There’s no channel 1 on televisions in North America.

It makes no sense.

That is, it makes no sense from the point of view of an engineer that had to design a channel system today, starting from scratch.

It makes sense from the point of view of a historian examining how broadcasting developed in North America.

Sometimes, discussions about academic systems of various sorts feel like people complaining mightily about how stupid it is that there is no channel 1, and proposing fix after fix after fix to correct it. And they do so in an environment where lots of people aren’t bothered by the lack of channel 1. And they do so even if the proposed fixes will mean some people’s televisions won’t work any more.

“Sure, but they’ll be better televisions!” Maybe, but it misses that a consistent channel numbering system is not what most people want out of a television.

03 April 2018

The NSF GRFP problem continues

This morning, a fine scientist congratulated two undergraduates in her lab about winning National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) awards. I thought, “Huh. They’re out? And two seems like a lot from one lab.”

A few years ago, Terry McGlynn wrote an important blog post about how tilted the playing field is for the NSF GRFP awards. He compared awards to Harvard students (with about 7,000 undergraduates) to the more than 20 campuses in the California State University system (over 400,000, according to a check of Wikipedia).

The NSF is good about making it easy to find a list of all 2,000 awards in this program. I went looking for the same comparison of one Ivy League university to an entire state’s system. Embarrassingly, I screwed up the calculation on the first pass, not realizing that several California State universities don’t say “California State” in their name, unlike the University of Texas institutions.

Harvard got 43, and all of California State get 50 (thanks to Terry for counting here and here).

Cal Poly Pomona 4
Cal Poly SLO 5
CSUCI 1
CSUDH 1
CSU Fresno 1
CSU Fullerton 8
CSULB 2
CSULA 1
Sac State 1
CSUSB 1
CSUN 5
CSUSM 3
SDSU 6
SFSU 6
SJSU 3
Humboldt State 2

So one lab in Harvard alone equaled the entire combined output of eight different California State universities (separately, not combined).

If this sort of pattern intrigues you, you must for to Natalie Telis’s post where she digs down into the numbers. Not just this year’s, but over 28,000 awardees worth of data, from 2011 to 2017. It’s bloody brilliant. One of her first points is, “The most expensive undergraduate schools have an extreme excess of (NSF GRFP) recipients.” She also makes some comments on Twitter about this.

I can’t wait to see what she finds for 2018 data.

Matt Cover did some similar things the previous year, and found no relationship between institutional enrollment and number of grants.

External links

NSF Graduate Fellowships are a part of the problem
The price of a GRFP, part 1
Matt Cover thread from 2017