Headline hogwash: Rosehip neurons

I was listening to the radio this morning, and heard some very strange coverage about something called “rosehip neurons.” The coverage was pushing this notion that these newly described neurons were somehow extra special and extra unusual and might be one of the things that make us human. I almost felt like rosehip neurons were being described the way I imagined René Descartes described the pineal gland.

I looked at some headlines, because headlines disproportionately influence what people believe about a story.

NPR, The Independent, Iran Daily, and India Today link these neurons to human “uniqueness.” News Medical and Biocompare flat out state rosehip neurons are unique to humans.

Facebook juggernaut I Fucking Love Science, Science Alert, Interesting Engineering, and News.com.au are more cautious, saying “possibly,” “looks like” or “may be” that rosehip neurons are only in humans.

Science, Science Daily, Wired (*), Forbes, and LiveScience carefully specify these neurons are found in people or humans. Yet media will almost never say when research is done in mice or some other animal.

The cumulative effect  of looking through these news headlines is that you get the impression that rosehip neurons are the first thing we have ever found that is unique to humans. Walter (2008) has a whole book of uniquely human traits.

And people are falling for this narrative already. I say “falling” because the reasoning trying to link these neurons to the uniqueness of humans is spurious.

The paper by Boldog and colleagues does not show rosehip neurons are “human specific.” The paper shows rosehip neurons are “not seen in mouse cortex”. That’s a big difference. It’s like calling whiskers “mouse specific” because you look at a mouse and a human, and you see that the mouse has whiskers and humans don’t. It sounds good until you look at a cat.

For all we know, cats might have rosehip neurons. Bats might have them. Elephants might have them. Chimps, gorillas, and whales might have them. Lions, and tigers, and bears might have them.

Different species are different. This is not a surprise. The idea that human brains are just very large mouse brains might be a great strawman to get money from medical funding agencies, but it’s not a position that anyone who understands evolution and animal diversity should take.

References

Boldog et al. Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type. Nature Neuroscience. https://doi.org/10.1038/s41593-018-0205-2 (Preprint available here.)

Walter C. Thumbs, Toes, and Tears (see also interview)

Related posts

New rule for medical research headlines

External links

What Makes A Human Brain Unique? A Newly Discovered Neuron May Be A Clue

Mysterious new brain cell found in people

Scientists identify a new kind of human brain cell

Meet the Rose Hip Cell, a New Kind of Neuron (* The Wired headline that appears in Google search results is, “Meet the Rosehip Cell, a New Kind of Human Neuron | WIRED”)

Scientists Discover A New Type Of Brain Cell In Humans

Neuroscientists identify new type of “rose hip” neurons unique to humans

Team Discovers New ‘Rosehip’ Neuronal Cells Found Only in Humans

Scientists Find a Strange New Cell in Human Brains: The 'Rosehip Neuron

International Team Discovers New Type Of Neuron That May Be Unique To Humans

New, and possibly unique, human brain cell discovered

Mysterious new type of cell could help reveal what makes human brain special

Scientists Discovered A New Type of Brain Cell That May Only Exist in Humans

How to present statistics: a gap in journals’ instructions to authors

I recently reviewed a couple of papers, and was reminded by how bad the presentation of statistics in many papers is. This is true even from veterans with lengthy publication records who you might think would know better. Here are a few tips on presenting statistics that I’ve gleaned over the years.

Averages

One paper wrote “(7.8 ± 0.8).” I guess this was supposed to be a mean and standard deviation. But I had to guess, because the paper didn’t say. But people often report other measures of dispersion around an average (standard errors, coefficient of variations) the exact same way.

Curran-Everett and Benos (2004) write, “The ± symbol is superfluous: a standard deviation is a single positive number.” When I tweeted this yesterday, a few wrote that this was silly, because Curran-Everett and Benos’s recommended format was a few characters longer and people worried about it being repetitive and hard to read. This reminds me of fiction writers who try to avoid repeating “He said,” usually with unreadable results. My concern is not about the ± symbol as the numbers having no description at all.

Regardless, my usual strategy is similar to Curran-Everett and Benos. I usually write something like, “(mean = 34.5, SD = 33.0, n = 49).” Yes, it’s longer, but it’s explicit.

That strategy isn’t the only way, of course. I have no problem with a line saying, “averages are reported as (mean ± S.D.) throughout.” That’s explicit, too.

Common statistical tests

Another manuscript repeatedly just said, “p < 0.05.” It didn’t tell me what test was used, nor any other information that could be used to check that it is correct.

For reporting statistical tests, I write something like, “(Kruskal-Wallis = 70.76, df = 2, p < 0.01).” That makes it explicit:

• What test I am using.
• The exact test statistic (i.e., the result of the statistical calculations).
• The degrees of freedom, or sample size, or any other values that is relevant to checking and interpreting the test’s calculated value.
• The exact p value, and never “greater than” or “lesser than” 0.05. Again, anyone who wants to confirm that the calculations have been done correctly needs an exact p value.  People’s interpretations of the data change depending on the reported p value. People don’t interpret a p value of 0.06 and 0.87 the same, even though both are “greater than 0.05.” Yes, I know that people probably should not put much stake in that exact value, and that p values are less reproducible than people expect, but there it is.

My understanding is that these values particularly matter for people doing meta-analyses.

Journals aren’t helping (much)

I wondered why I keep seeing stats presented in ways that are either uninterpretable or unverifiable. I checked the author’s instructions of PeerJ, PLOS ONE, The Journal of Neuroscience, and The Journal of Experimental Biology. As far as I could find, only The Journal of Neuroscience provided guidance on what their standards for reporting statistics is. The Journal of Experimental Biology’s checklist says, “For small sample sizes (n<5), descriptive statistics are not appropriate, and instead individual data points should be plotted.”

(Additional: PeerJ does have some guidelines. They are under “Policies and procedures” rather than “Instructions for authors,” so I missed them in my quick search.)

This stands in stark contrast to the notoriously detailed instructions practically every journal has for reference formatting. This is even true for PeerJ, which has a famously relaxed attitude towards reference formatting.

In the long haul, the proper reporting of statistical tests is probably more important to the long term value of a paper in the scientific record than the exact reference format.

Judging from how often I see minimal to inadequate presentation of statistics in manuscripts that I’m asked to review, authors need help. Sure, most authors should “know better,” but journals should provide reminders even for authors who should know this stuff.

How about it, editors?

Additional: One editor took me up on this challenge. Alejandro Montenegro gets it. Hooray!

More additional: And Joerg Heber gets it, too. Double hooray!

Update, 20 September 2019: PLOS ONE has now added guidelines for reporting statistics. This seems to have been prompted at least in part by this post.

References

Curran-Everett D, Benos DJ. 2004. Guidelines for reporting statistics in journals published by the American Physiological Society. American Journal of Physiology - Gastrointestinal and Liver Physiology 287(2): G307-G309. http://ajpgi.physiology.org/content/287/2/G307.short

Maybe we can’t fix “fake news” with facts

There’s been a few recent moves in the war on “fake news.” For instance, several platforms stopped hosting a certain conspiracy-laden podcast today. (You can still get all that conspiratorial stuff. The original website is untouched.) But the discussion about “fake news” seems to be focusing on one thing: its content.

Lately, I’ve been thinking about this diagram I made about communication, based on Daniel Kahneman’s work. Kahneman argues you need three things for successful communication:

1. Evidence
2. Likeability
3. Trust

I feel like most of the talking about “fake news” is very focused on “evidence.” This article, for instance, describes some very interesting research about how people view news articles. It’s concerned with how people are very prone to value opposing sources, but are very poor at evaluating the credibility of those sources.

All good as far as it goes. But, as I mentioned before, it feels a lot like science communicators who, for years and years, tried to beat creationists, flat Earthers, anti-vaccine folks, and climate change deniers by bringing forward evidence. They were using the deficit model: “People must think this because they don't know the facts. We must get the facts to them.”

That didn’t work.

I’m kind of seeing the same trend in fighting fake news. “Remove the falsehoods, and all will fix itself.”

But where I see the truly big gap between where we were and where we are isn’t about facts. It’s about trust.

When you bring evidence to a fight that isn’t about facts, you will lose. Every time. Facts mean nothing without trust. “Check the facts” means nothing when you are convinced everyone is lying to you. This is why conspiratorial thinking is so powerful and dangerous: it destroys trust.

You see the results in how someone who buys into one conspiracy theory often buys into several other conspiracy theories. If you believe Obama wasn’t born in the US because conspiracy (say), it’s not that big a leap to the moon landings were fake and the Earth is a flat square.

I have some hypotheses about how America in particular got to this point. I suspect the erosion of trust was slow, gradual, and – importantly – started long before social media. Maybe more like, I don’t know, let’s say 1996.

I don’t know how to reverse a long-term trend of distrust and paranoia. I’m not saying, “We need to understand and sympathize with fascists,” either. But you can’t cure a disease when you misdiagnose it. I just don’t see focusing on the factual content of social media getting very far.

Update, 29 August 2018: Jenny Rohn is discouraged, too.

(W)riters like me, who specialise in evidence-based communication, have been deluded as to the power of our pens in the face of this inexorable tide. ... I am now starting to think that none of this makes much difference. When does any of our evidence, no matter how carefully and widely presented, actually sway the opinion of someone whose viewpoint has been long since been seduced by the propagandists?

... I am starting to believe that the best way to affect the current state of affairs is by influencing those in power, using more private and targeted channels.

Related posts

The Zen of Presentations, Part 59: The Venn of Presentations
Post fact politics catches up to science communication

External links

Fake news exploits our obliviousness to proper sourcing
Looking for life on a flat Earth
How can I convince someone the Earth is round?
Why do people believe conspiracy theories?

Crayfish clothing contest conqueror!

You are looking at the winner of the International Association of Astacology T-shirt contest! By me!

• First place: “Astacus fluviatilis” by Zen Faulkes
• Second place: “Euastacus,” front and back design by Premek Hamr
• Third place: “Astacolic” by Alexa Ballinger (which you can see here)

I haven’t yet see the runner-up designs, which were shown at the last IAA meeting in Pitssburgh, but I look forward to seeing them! This started with the quote. I found it on page vi of Thomas Henry Huxley’s monograph on the crayfish (also Google Books edition). It took a little digging to find the author’s complete name and year of the quote. (Yes, my academic training is showing: obsession with complete and correct citations.)

While looking up the person who wrote the quote, I discovered that Rösel von Rosenhof was an amazing illustrator of the natural world. And he painted crayfish! So I was able to combine this wonderful quote about crayfish with this brilliant plate by the same person.

I cleaned up an image of one of Rösel von Rosenhof’s paintings, cleaning up page blemishes left over from the scan and making it a little brighter.

I kept some of the writing on the painting but repositioned it. The quote that started me off was not on the page, so I had to add it. I had just the thing: the Adorn font family evoked the style the old plate well. But the wonderful thing about a well made font family is that you can use a lot of different variations of text, and it still feels coherent.

Adorn has a lot of built in letter variants, and it was fun to play around with different swashes in CorelDraw! I am pleased people like this, but I’m sure that it won the contest is more a tribute to the artistry of Rösel von Rosenhof than my own graphic design skills. But this was not the only T-shirt design I submitted. Oh no. I was having fun with the shirt designs. This was actually the first concept I worked on:

The outline is a signal crayfish claw, if I remember right.The words inside the claw outline are the names of every genus of freshwater crayfish (according to Crandall and de Grave 2017). Originally, I played with the idea of using the name of every species of crayfish, but with over 600 and rising, there were too many and it was too likely to go out of date soon.

I like this design, but I was never able to get it to look exactly like it was in my head. I wanted the shape of the claw to be defined by the words alone. I like the big, bold shape of the claw and that it includes all the crayfish diversity within it, though.

I worried that the genus names might be too small and fussy for a T-shirt, but I liked that claw shape, so I made this variant:

It’s bold, though I worry that it’s a little simple.

To be honest, this was my favourite design:

I traced an image of a crayfish using in CorelDraw. I love Japanese and Chinese calligraphy, and modified the lines making up the trace to taper, giving it a sort of brush-like appearance. The font is Cherry Blossoms, which I wrapped around on an oval. This font, like Adorn, has a lot of options, and I had way too much fun trying out different swashes. (Discovering alternate glyphs and swashes has been a revelation.)

Initially, I only had “International Association of Astacology.” But the words traced out the oval so clearly on the top that the bottom looked broken and incomplete. I needed something to complete the shape, so I added in “the science of crayfish.” I loved this, because I feel like one of the big problems with being a member of the International Association of Astacology is explaining what “astacology” is!

I made variations of the three no-winning designs, too, changing the fonts and colours in different ways.The first version of the brushwork crayfish above had the colours flipped, with the crayfish in red, and the text above in black. But since ink was the inspiration, making the crayfish black made more sense.

Even though my favourite design didn’t win, I am completely thrilled to have won the T-shirt contest. I am mentioning this award this in my annual review folder!

And maybe a few more people will discover and appreciate the fine artwork of Rösel von Rosenhof.

References

Crandall KA, De Grave S. 2017. An updated classification of  the freshwater crayfishes (Decapoda: Astacidea) of  the world, with a complete species list. Journal of Crustacean Biology 37(5): 615-653. https://doi.org/10.1093/jcbiol/rux070

External links

August Johann Rösel von Rosenhof
How to swash: using a font’s alternate glyphs, text styles, and numbers
Critique: The Capricorn Experiment, plus: Font families

Tuesday Crustie: Crab emojis rated

It is, according to my social media, World Emoji Day. No sure why that needs a day, but I’m not here to judge. Well, not, today I am, because I am here to judge crab emojis!

Apple

I think this crab is cold. That would explain why it seems to be wearing mittens over its claws. 6 out of 10.

EmojiOne

Is this crab doing a shadow puppet play about warring sibling birds in the nest? The claws look like little bird beaks.The eyes seem way to big for its stalks. This is some sort of angsty, emo teenage crab with an art project. It might be nice when it grows out of its akward phase. 3 out of 10.

Facebook

Sure, this social media giant is contributing the decline and probable fall of democracies in several nations, but damn! They got someone who was paying attention in invertebrate biology and respects the crustacean to draw their emoji. The claws look like they could do serious damage. The lines on the carapace show more attention to detail than anyone else. I feel like I could almost key it out to the genus. 10 out of 10.

Google

The Google crab has seen your browser history and is shocked, shocked it says, by the websites you visit. It wants to push you away, which is why its claws are in some sort of weird backwards pose. 4 out of 10.

LG

An abyssal crab, judging from the teensy-weensy eyes. Kind of funky bulbous claws, but bonus points for its wickedly curved final pair of thoracopods. They look like kama. 7 out of 10.

Microsoft

I think this crab was produced by a game of telephone between artists. Someone once saw a crab, drew it, then showed their drawing to someone who copied the drawing, who showed it to another person who copied the drawing, and this went on maybe about ten to twenty times. As Magritte might say, “Ce n’est pas un crabe.” (This is not a crab.) 3 out of 10.

Samsung

Argh! Dude! What happened to your legs? And your claws can’t open! I’m so sorry. Is there a foundation we can donate for to support research into your condition? 1 out of 10.

Emojidex

Flashback to 1984 and the release of Romancing the Stone:

Gloria: [observing men in a bar]

Wimp. Wimp. Loser. Loser. Major loser. Too angry. Too vague. Too desperate. God, too happy.

This is the “God, too happy” crab. Seriously freaking me out how happy this guy is. I think this crab has had chemical stimulation. -2 out of 10.

Twitter

Another poor unfortunate victim of some sort of leg disfigurement. Those claws cannot work, the leg tips look unsuitable for grasping any benthic substratum. And yet I can feel somethings besides pity for this crab. Something about the dots on the carapace say to me, “This is a crab that has not stopped living. This is a crab happy to get a tramp stamp and put it out there.” 6 out of 10.

WhatsApp

Ooh, it’s a little baby crab! It’s so tiny! It looks like it lives in the water column, floating and hoping no fish eats it. It will be sad when it grows up and will turn into into the EmojiOne artsy emo teen crab. 8 out of 10.

What have we learned from all this? That all crabs in the Internet are red. Or orange-y red. Except for Samsung crab, whose brown colour is obviously some sort of symptom of whatever disease it has.

Inspiration from ant emoji ratings. Hat tip to Alex Wild and Melanie Ehrenkranz.

Come back for World Emoji Day 2019, when we’ll rate shrimp emoji!

External links

an entomologist rates ant emojis

Ego

Hypothesis:

Complaints about peer review are often made by people who believe that their work is so infallible and perfect that it cannot be made better by peer review.

It trickles through in complaints about how long peer review is taking (when the review time may be reasonable), It trickles through when asking what reviewers could possibly say about a manuscript. It trickles through when questioning the value of journals organizing peer review.

This is a dangerous habit of mind for a scientist. As David Brin likes to say, “Criticism is the only known antidote to error.”

Sure, most scientists are professionals who are trained to produce competent science. It’s not surprising that most papers pass peer review, and that the improvement is not always that large. But there shouldn’t be an expectation that everything a scientist does is going to be worth publishing as is. Everyone makes mistakes.

As Rose Eveleth said yesterday:

Sure, some editors are annoying, but you know what is worse? Literally any writer’s raw copy.

This is a message a lot of scientists need to hear.

External links

How long should peer review take?

Giving an article a DOI does not make it citable

With preprint servers and data repositories like Figshare gaining in popularity, a related myth is also gaining in popularity: “Giving this article / dataset a DOI makes it a citable academic product!”

Exposition for bystanders: DOI is short for “digital object identifier.” I usually describe it as “a serial number for a journal article.” You often seen them tucked at the top or bottom of academic papers,  a lengthy number beginning with 10. But as the name indicates, it’s mean to be usable for any kind of “digital object,” not just papers.

The beauty of a DOI is that if you have it, you can type in “https://doi.org/” followed by that number beginning with 10, and it will take you straight to the paper.No having to go to Google to find the journal, then drill down to the volume, then the issue, and so on.

A Twitter search shows people have been wrongly making the connection between “having a DOI” and “something that can be cited” for at least seven years. Here’s a tweet from 2011 (emphasis added):

#DataCite offers DOIs for making data sets citable and getting credits for its reuse.

A few example: here, here, and here. And also here, here, and here. And people have been pointing out this is wrong for the same amount of time.

What is “citable” is an editorial policy set by journals individually.

Most journals have long traditions of allowing you to cite things that are not part of the formal scientific literature. After all, journals existed well before links ever existed, never mind the DOI standard.

But not every journal will let you cite whatever. If a journal says, “We will only allow citations to peer-reviewed journal articles,” saying, “But this has a DOI!” is not going to make any editor change her or his mind.

I don’t quite understand why people think this. I suspect this myth arises because it plays into scientists’ obsession with formalism and simple “If this, then that” rules. Maybe people are confusing the DOI number itself with, “Anyone who goes to the bother of giving DOIs to things is probably an organization that is fairly large, stable, and has its act together.” But that exploitative journals regularly give their articles working DOIs shows that it can’t take that much to assign those number and get the links working.

It’s another example of the information vacuum around academic publishing: publishers make up new stuff and assume academics will figure out how it works.

While I’m here, Lyndon White pointed out another DOI myth: that the link “never breaks.” They can, although in practice I’ve found them to be far less susceptible to link rot than publisher links, which get rearranged every few years, it seems.

Related posts

Innovation must be accompanied by education

Why can’t I cite Mythbusters?

Not hot: the Rate My Professor chili pepper is done

The website Rate My Professors is getting rid of its “hotness” rating. Which means you won’t see stuff like this any more:

The idea of getting rid of the “chili pepper” has been floating around for a while, but fellow neuroscientist Beth Ann McLaughlin was able to hit a nerve on Twitter this week. Almost 3,000 retweets and many professors chimed in to say, “Get rid of this appearance rating.”

And to their credit, the website owners did.

This is a good thing for people in higher education. The Rate My Professors site is well known to people in higher education, both faculty and students. I’ve encouraged students to use Rate My Professors, because I have a record teaching, and people have a right to hear other students’ experiences. It matters when they tacitly suggest it’s okay to ogle professors.

It’s nice to have a little good news. And to be reminded that sometimes, faceless corporate websites – and the people behind them – do listen to reason, and can change.

External links

Why The Chili Pepper Needs To Go: Rape Culture And Rate My Professors (2016)
RateMyProfessors.com Is Dropping The "Hotness" Rating After Professors Called It Sexist
I Killed the Chili Pepper on Rate My Professor
RateMyProfessors.com Retires the Sexist and Uncomfortable “Chili Pepper” Rating After Academics Speak Out
RateMyProfessors Removes Hotness Rating

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.

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

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

https://www.theguardian.com/world/2018/jun/03/crayfish-becomes-online-hero-by-detaching-claw-to-escape-boiling-soup

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.

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.

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.

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.

Update, 3 December 2021: Lawrence Lessig’s free culture talk was originally presented as a Flash animation, which is mostly dead now.

Here it is, in parts, on YouTube: Part 1 • Part 2 • Part 3.

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

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

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

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. (Edit: Yes, this is admittedly a big gap in my education. I should have known.)

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 past, 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 opioids, 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 Sackler drug connection 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. 88% 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

Teaching online and inclusion

 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:

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

“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.