04 May 2021

Type of scientific papers, very specific niche edition

Last week, Randall Munroe started a whole thing with one of his xkcd cartoons, “Types of scientific papers.”

People were inspired to make different versions for their field, then sub-field, then sub-sub-field, so I took the meme to it’s logical conclusion.

Types of scientific paper that Zen Faulkes has co-authored

07 April 2021

Gratitude



I’m grateful that:

  1. I had a book in me that I thought was worth writing.
  2. Pelagic Publishing gave me a chance to write it.
  3. I made it through a pandemic to see it in print.

I hope people find it helpful.

03 April 2021

Why “descriptive” science is downplayed

On Twitter, Rejji Kuruvilla asked:

I’m sorry, but WHY are descriptive studies a problem in grant or ms review? If you don’t provide the 1st description or visualization of a biological process, how do you provide the basis for hypothesis or mechanism-driven science?

Oh, I feel this. I complained about this since my grad school days. One of the biggest scientific endeavors that closed out the twentieth century, the human genome project, was pure description. I love this from Niko Tinbergen, in his most famous paper (1963):

Contempt for simple observation is a lethal trait in any science(.)

Here’s what I think is going on.

First, I suspect “descriptive” as a critique might mean any one of three things.

  1. Not hypothesis driven.
  2. Not investigated by controlled experiment.
  3. Studies only a single level of organization.

The bias against description is a symptom of the fact that basic biological research is has been supported by medical agencies. In the United States, the budget for the National Institutes of Health dwarfs that of the National Science Foundation. (Interestingly, this isn’t the case in Canada.)

Medical agencies aren’t funding science for science’s sake. They are not interested in making discoveries that broaden our understanding of the natural world. They have sick people they want to make better. They want treatments. They want results.

To their credit, most medical funding agencies recognize that investing in basic science pays dividends. That’s why they support it at all. But their priorities are not those of curiosity-driven science.

So it is no surprise that such agencies would strongly favour hypothesis-driven research. Because as much as I love basic description and serendipitous discoveries, I absolutely recognize that hypothesis-driven research –  particularly strong inference of pitting competing hypotheses against each other – is ferociously efficient at generating new knowledge.

I don’t think hypothesis-driven research is enough. But even I have to say that I don’t think any other approach generates knowledge as quickly or as consistently.

If you get the “too descriptive” critique, you can’t fix it just by working in the word “hypothesis” into your proposal at every opportunity. The “descriptive” critique is not necessarily about whether you have a hypothesis at all, but whether you address a hypothesis that is actively investigated by your research community. 

You can have a perfectly hypothesis driven project, but is the hypothesis doesn’t addresses what the community cares about, it will still get called “descriptive.”

Another aspect of the critique is that “descriptive” studies are contrasted against “mechanistic” studies. Again, I think this is a symptom of the “medicalization” of research funding.

This semester, I was unexpected assigned to teach part of a course in human pathophysiology. This is way outside my expertise, and I’ve been forced to learn about medical topics more than I ever have before in my life. And after a few months of digging into bone, muscle, and hormonal disorders, it’s surprised me how often developing treatments drill down to understanding molecular interactions. 

A description like “There’s too much hormone” is necessary. But treatments are often based in, “This drug blocks the receptor to this hormone” and “This drug blocks synthesis of this hormone.” In other words, the research spans multiple levels of analysis. When people talk about “mechanism,” they usually mean that they are looking for a level of analysis that is at more finely grained, by at least one step. 

If you are studying an organism, they want an explanation at the level of organs. 

If you’re studying organs, they want an explanation at the level of tissue.

If you’re studying cells, they want an explanation at the level of molecules.

(At least in biology, we usually stop there and don’t require explanations at the quantum level. Thank goodness.)

So seeing the challenges of the problems and the successes gained from these these molecular approaches helps me see why funding agencies like them. They have a proven track record.

I’ve also found that many students struggle to articulate hypotheses. I wonder if early career researchers writing their grants might also be struggling with this.


References

Tinbergen, N. 1963. On aims and methods in ethology. Ethology 20(4): 410-433.

24 March 2021

NSF GRFP award skew in 2021

Matthew Cover pulled numbers I was going to look for on this year’s graduate research fellowships from the National Science Foundation (NSF):

Congrats to the 13 current Cal State University students who were awarded NSF GRFPs!! For context, that is fewer awards to the largest 4-year system in the country (0.5million) than Stanford- 81, MIT- 76, Princeton- 34, Northwestern- 30, Yale- 26, Chicago- 22, Rice- 22, Duke- 20

I’ve been talking this a few years now, so why stop?

You know, there are some problems in academia that you recognize are going to be slow to fix because they rely on cultural changes.

This is not one of them. 

The NSF could dictate how awards are going to be distributed. But the agency seems unwilling to have that conversation.

Update, 5 April 2021: Megan Barkdull ran some numbers for this year’s awards. She focused on institutional “prestige” and found, unsurprisingly, that the Ivy league universities and their peers gobble up most of the awards. Her full analysis is here.

Related posts

The NSF GRFP problem, 2020 edition
Fewer shots, more diversity?
The NSF GRFP problem continues

External links

NSF Graduate Fellowships are a part of the problem

 

 



23 March 2021

Tuesday Crustie: Cinnamon Toast Crustie

The scandal of the day on Twitter: Jensen Karp asking why there appear to be bits of shrimp in his cereal.

Cinnamon Toast Cruch with apparent shrimp tails

The company claims they couldn’t possibly be shrimp, but those sure look like a telson and uropods to me.

28 February 2021

Australia’s CSIRO expends welfare guidelines to include decapod crustaceans

The Crustacean Compassion website is reporting that Australia’s major government research agency, CSIRO, will now be requiring ethics approval for research on decapod crustaceans.

I’m searching the CSIRO website, but can’t find the specific policy.

External links

Professor Culum Brown on protecting decapods in scientific research

24 February 2021

Austin bats: A case study in successful science communication

Bike rack in the shape of a bat from Austin, Texas
Check out the bike rack on the right. It’s a picture I took in Austin, Texas. People in Austin love bats now.

They didn’t always.

The podcast 99 Percent Invisible just dropped a great episode that looks at how the bats under an Austin bridge went from being viewed as terrors that needed to be eradicated to a major tourist attraction.

Lessons for science communication?

The key advocate for bats, Merlin Tuttle, was no carpetbagger. He moved to Austin and became part of the community he wanted to change.

He built a team. It wasn’t just Merlin – he had started a whole conservation group.

He got the right visuals. He didn’t photograph bats while echolocating because their mouth was open and they were showing their sharp teeth. He photographed them so they looked like they smiling.

Perhaps most important, he was patient and never called people stupid.

This is an incredible success story for conservation. It should be a case study in classes on science communication.

External links

The batman and the bridge builder

23 February 2021

It’s my birthday but you get the gift

Yes, I have successfully completed another trip around the sun. Rather than a birthday present, you can do me a favour: pre-order my book!

Better Posters book cover

The Better Posters book is currently scheduled for release in mid-April, 2021. The exact date is hard to say, because the COVID-19 pandemic is still creating delays and uncertainty in the production and shipping process. It’s been a long journey, to say the least. 

30% off
Pre-orders help books tremendously, and I would like to sell enough copies to have to write a second edition. You can pre-order from the publisher here and get a big 30% discount by using the code “POSTERS30” at check-out.

You could also recommend your university librarian purchase this!

Thank you for your support!

External links

Pelagic Publishing site for Better Posters

19 February 2021

Author jitters

I finished reading the latest proofs of the Better Posters book this week. Having just done that a couple of days ago, I appreciate this quote from Charles Darwin.

Charles Darwin

When I think of the many cases of men who have studied one subject for years, and have persuaded themselves of the truth of the foolishest doctrines, I feel sometimes a little frightened, whether I may not be one of these monomaniacs.

This was in a letter to one Dr. W.B. Carpenter in 1859, about none other than Darwin’s most famous work, On the Origin of Species. Darwin wrote the letter the same month the book was released and sold out in a day. I found the quote mentioned in this article

Re-reading my own book more than a year after finishing the manuscript and that nobody else has seen yet (besides the publisher’s staff) brings up “Did I just write something that nobody else will want to read?” thoughts.

Also: I love Darwin’s hat and think there should be a new version that evolutionary biologists can buy.


13 February 2021

Eagles and Falcon

 I’ve mentioned before that the Eagle from Space: 1999 is my favourite spaceship.

What I didn’t know what its role in my favourite space move, the first Star Wars

I knew the Milleneum Falcon went through several redesigns. The shots inside of the Falcon don’t always make sense relative to the exterior, because the Falcon was originally the ship that became the rebel blackade runner.

What I didn’t know was that a good part of the reason the design changed was that it looked just a little too much like the Eagle transporter.

Early Millenium  Falcon model next to Eage transporter model.

Which, side by side, I can see.

External links

FAB Facts: Star Wars’ Millenium Falcon almost looked like a Space:1999 Eagle

The complete history of the Millenium Falcon

11 February 2021

The worm lizard that’s rather like a whale

May I introduce Bipes biporus, also known as the Mexican mole lizard or Belding’s mole lizard.

Mexican worm lizard (Bipes biporus).

It’s an odd and fascinating beast, because it has arms (forelimbs) but no legs (hindlimbs). You can see its front legs very well in the picture above. They even look pretty chunky relative to the head.

Head and forelimbs of Mexican worm lizard (Bipes biporus).

But there are no obvious rear legs.

Mexican worm lizard (Bipes biporus).

There are tiny remnants of leg bones in the back of the animal, but they are not visible just by looking at the animal.

Pelvic skeleton from Mexican worm lizard (Bipes biporus).

Above is Figure 8 from Zangerl (1945).

A more recent paper (Kearney and Stuart 2004) says Blanus (another worm lizard genus) has forelimb skeletal elements but only vestiges of rear limbs. But pictures of Blanus don’t show obvious limbs like Bipes does.

Why do I say this worm lizard is like a whale? Because like whales, only the forelimbs are visible. The hindlimbs are all but lost. In some ways, the worm lizard is a more impressive specimen of evolution because its forelimbs are still obviously arms, unlike the flipper of a whale, which is so heavily modified that its relationship to out own arms is obscured.

References

Kearney M,  Stuart BL. 2004. Repeated evolution of limblessness and digging heads in worm lizards revealed by DNA from old bones. Proc. R. Soc. Lond. B. 271: 1677–1683. http://doi.org/10.1098/rspb.2004.2771

Zangerl R. 1945. Contributions to the Osteology of the Post-Cranial Skeleton of the Amphisbaenidae. American Midland Naturalist 33: 764–780.

22 January 2021

Classes taught by the dead and copyright

I feel like this should be a bigger story.

HI EXCUSE ME, I just found out the the prof for this online course I’m taking died in 2019 and he’s technically still giving classes since he’s literally my prof for this course and I’m learning from lectures recorded before his passing

..........it’s a great class but WHAT

IDK SOMETHING ABOUT IT IS WEIRD

I mean, I guess I technically read texts written by people who’ve passed all the time, but it’s the fact that I looked up his email to send him a question and PULLED UP HIS MEMORIAM INSTEAD that just THREW ME OFF A LITTLE

...that feeling when a tenured professor is still giving classes from beyond the grave

There’s job security, then there’s this lmfao.

Also like, all dystopian “you can retire when you’re dead” jabs @ the institution aside—this is actually really sad and somebody should have realized that.

This prof is this sweet old French guy who’s just absolutely thrilled to talk paintings of snow and horses, and somehow he always manages to make it interesting, making you care about something you truly thought could not possibly be that interesting.

It’s fucking sad man wtf

Why would you not tell someone that? Do you think students just don’t give a shit about the people they spend months learning from?


And like, it’s shitty that won’t get to thank him for making all of this information so engaging and accessible

I tend to you know...actually talk to my teachers a lot?

Idk man it’s just a weird thing to find out when you’re looking for an email address.

I’m getting a little tired of people comparing teachers to reusable objects so I’m going to go ahead and mute this lmao.

It’s weird to romanticize labor the way some of you do, and it’s weird to act like it’s normal to just not tell students that their teachers dead, goodnight!

Emphasis added.

The last time I was in the faculty senate at UTRGV, a recurring argument was about who owned courses that were created for online teaching. At the time, I thought there was far too much time spent discussing the matter.

But this example shows exactly why that question of who controls course materials matters. It is a sharp and sad reminder that as far as many institutions are concerned, teaching does not require personal interaction if pure Skinner boxing will do. Professors do not even rise to the level of interchangeable cogs. Professors are a mere convenience once they have created content.

External links

Dead man teaching (Added 26 January 2021; The Chronicle of Higher Education caught up)



02 January 2021

I’m in Abominable Science! (No, not like that)

Abominable Science book cover

A friend of mine sent me a screenshot of a page from Abominable Science: Origins of the Yeti, Nessie, and Other Famous Cryptids by Daniel Loxton and Donald Prothero.

It reads:

Invertebrate neuroethologist Zen Faulkes noted further that DeNovo lists no editor, no editorial board, no physical address—not even a telephone number: “The whole thing looks completely dodgy, with the lack of any identifiable names being the one screaming warning to stay away from this journal. Far, far away.”

The excerpt is from this blog post about the claim of sasquatch DNA being sequenced back in 2013. (Most scientists were deeply unconvinced by this.)

I’ve published enough stuff that getting cited is usually not worth a blog post. But having blog posts cited in real physical books still tickles me and is something a little unusual and wonderful.

And I think it speaks to something that makes the rounds now and then: the role of blogging in the 2020s. People occasionally pronounce blogs “dead.” While blogging isn’t a “scene” like it was in the late 2000s, a blog has a lifespan that social media just does not. Being cited in this book is one tiny little piece of evidence of that.

Related posts

Sasquatch DNA: new journal or vanity press?

External links

Abominable Science