08 August 2022

Lessons from megapodes: You can waste a lot of time trying to save time

Tanimbar megapode nest, much bigger than person standing to the left of it.
In his book Last Chance to See (co-authored with Mark Carwadine), Douglas Adams describes nesting by megapode birds. Megapodes don’t build a typical next out of sticks and feathers and mud and the like. Instead, they build these enormous mounds, stacked with decaying vegetable matter.  Compost, basically. As the compost decays, it generates enough heat to incubate the megapode’s eggs.

In his often imitated but never equalled style, Adams wrote:

So all the megapode has to do to incubate its eggs is to dig three cubic yards of earth out of the ground, fill it with three cubic yards of rotting vegetation, collect a further six cubic yards of vegetation, build it into a mound, and then continually monitor the heat it is producing and run about adding bits or taking bits away.

And thus it saves itself all the bother of sitting on its eggs from time to time.

Put like that, it doesn’t seem like that much of a time saver.

To get those numbers of megapode nest size to put into his book, Adams had to do some calculating. Two facts about Adams are relevant here.

  1. He was an early Apple fanboy.
  2. He was a notorious procrastinator.

Not satisfied with pen and paper or a spreadsheet, Adams wrote a complete program in HyperCard to calculate the volume of megapode nests on his Mac. It is a rather beautiful little app for the time.

Adams was naturally aware of the parallel between himself and the megapode.

I’ve just spent a cheerful hour of my time writing a program on my computer that will tell me instantly what the volume of the mound was. It’s a very neat and sexy program with all sorts of pop-up menus and things, and the advantage of doing it the way I have is that on any future occasion on which I need to know the volume of a megapode nest, given its basic dimensions, my computer will give me the answer in less than a second, which is a wonderful saving of time. The downside, I suppose, is that I cannot conceive of any future occasion that I am likely to need to know the volume of a megapode nest(.)

I see a tendency in a lot of scientists (myself included) to build megapode nests. Because some existing solution fails in one way, we will create elaborate schemes and software to do something that is ostensibly “better” in that one way. 

The amount of time spent can be large.

The potential re-use of that solution for yourself, never mind others, can be tiny.

And the moral of the story is: Before you start some project because you don’t like the existing solutions, ask if you’re acting like a megapode parent.

External links

Douglas Adams’s megapode next volume calculator

 Picture from here.

02 August 2022

The Last Days of the Dinosaurs reviewed

The Last Days of the Dinosaurs cover

Some say the world will end in fire. Some say in ice.” – Robert Frost

We got both at the end of the Cretaceous. Heat pulse. Impact winter. It didn’t end the world, but it came closer than anything before or since.

Look back at old books about dinosaurs, and you might see something like, “We may never know why they went extinct.” It’s amazing how much we can learn in one lifetime. We learned about Chixulub impact, the presumptive “smoking gun” meteor strike that killed the dinosaurs, decades ago.

But no account that I have ever read before The Last Days of the Dinosaurs delivered such a clear and compelling explanation for why dinosaurs went extinct, but birds, mammals, and a few other lineages didn’t.

The answer seems to be down in the underground.

Black paints a vivid picture of a world on fire after the meteor struck. The air temperature with like an oven and forests lit up like matches. Unlike forest fires today, animals could not hope to outrun the flames by crossing a lake or fiver. The only way out was down, into the ground. An ankylosaur or ceratopsian or tyrannosaur couldn’t do that, but small mammals and birds could. Just a few inches of soil coverage made the difference between life and extinction.

Black’s description of the impact and its immediate aftermath are the highlight of the book, but not the bulk of the book. Despite the title, most of the book is the first days of the mammals (in an ecological sense rather than an origin sense). 

In that sense, the book has a problem: the best material is right up front, and the extended “what happened next” doesn’t have the same built-in drama. 

This is not to say the rest of the book is boring – far from it. I appreciated the personal last chapter, which Black draws parallels between the devastation of regrowth of, well, the planet, with her own personal journey.

But the book doesn’t stop with the last chapter. For the scientifically minded who want some of evidence behind Black’s descriptions, the endnotes for each chapter are little mines of information. 

My only quibbles are not about the fossils or rocks, where Black is as knowledgeable as anyone. There is a tiny passing comment about the low level sense of smell in birds, which is a common myth that I believed, too. I might not have caught it if it hadn’t been for listening to an interview about birds’ smelling ability. Black also refers to “the numbers game” a couple of times without explanation, and I don’t know if every reader will understand it’s a reference to a reproductive strategy (r selection: make a lot of low cost offspring with a high chance of dying).

And, putting on my graphic design hat for a moment, the cover is just so smart. I love it.

This is my favourite of Black’s books (so far). I know there will be more good stuff coming from her.

External links

The Last Days of the Dinosaurs publisher site

01 August 2022

An Immense World reviewed

Cover of "An Immense World"

Dear Mr. Yong,

I wish to make a complaint.

Your book, An Immense World, covers ground with which I am well familiar. I teach the concept of Umwelt – the “sensory world” of animals – frequently in my university classes, and have made my own modest contributions to the field of sensory biology. That confession might lead you to think that my complaint is that I was not among one of the many researchers interviewed for your work, as you have clearly done substantial and thorough investigation of the material presented in this volume. Indeed, the interviews sprinkled liberally throughout the book are informative and often delightful. I assure you, sire, I have a clear-eyed understanding of my stature in the scientific community and I am not so vain as to think my trifling work on crustacean nociception warranted inclusion in this volume.

Indeed, this book is so close to my interests in teaching that one might suspect that my complaint is that I wished to write this book. But this is not the nature of my complaint, since I have many other works to complete already, and I surely could not have completed the task with your admirable skills. This work does not “scoop,” as we academics say, any current or aspiring projects of mine.

I enjoyed the book’s straightforward structure. Most chapters cover a single sensory system, replete with fascinating examples from many species, often interspersed with conversations from the scientists who discovered the abilities of these animals. What reader will not delight is the description of pyrophilic nettles that seek out distant first fires? Or that the skill of echolocation, perfected by bats, is one that humans can also learn? You have often said, Mr. Yong, that you “cover the ‘Wow’ beat” in your journalism, and this surely rings true here. Indeed: wow.

No, the reason for my displeasure is that you have written a book that is not only laudable and will surely be lauded, much as your previous work has been. I note with pleasure that it has already appeared on the bestseller lists of a prominent American newspaper of record. It is surely one of the most accessible and widely read introductions to the field of neuroethology as has ever been written.

And that, good sir, is the nature of my complaint. You have composed a veritable paean to neuroethology, and interviewed many members of the International Society for Neuroethology (of which I am, alas, not presently a member due to my current position asking that I be solely focused on instruction of students), yet nowhere in this estimable book does the word “neuroethology” appear.

This is a grave sin of omission. An Immense World is so clearly and delightfully written that it shall doubtless be read my many a curious and impressionable student, who might well wonder, “How might I, in my studies, eventually become a person who contributes to this field?” And such a wayward learner would have no guides, no indication at all that there is an entire discipline devoted to answering these and related questions, and that its name is neuroethology.

I realize that this is, to a degree, a parochial concern. Yet because this book is so good, and will no doubt be more widely read than many university textbooks on neuroscience or animal behaviour, that I cannot help but lament a missed opportunity to share the wonders of the academic discipline that has been my main scientific “home,” as it were, for many years.

Nevertheless,  this book has already inspired my to make sensory biology the focus of a seminar class that I am scheduled to teach this fall.  Further, I will recommend this book widely to any who might show an interest in zoology.

Yours in blogging, etc., etc.

P.S.—I confess to having no idea why I chose to author this review in the style of an open letter in the dense prose style favoured in Victorian England, other from it seemed apt.

External links

An Immense World publisher site

30 June 2022

Is using AI to write a paper academic misconduct?

We’ve come a long way from ELIZA. Or the ridiculous duelling chatbots.

Natural language artificial intelligence has recently gotten far better than I think many people realize, and today’s article in Scientific American points that out.

A researcher asked an open source artificial intelligence program, GPT-3, to write an academic paper. It did such a good job that the preprint is out and the paper is now under review at a technical journal.

Publicity stunt? It smells a little like that, but then again, this is an area that needs some publicity.

As natural language program like  GPT-3 get more widely available and more widely known, of course university students are going to do what these researchers did. They are going to get the programs to write their papers.

How is that going to shape up in our thinking about teaching?

It using an artificial intelligence to write a term paper cheating? I suspect a lot of my colleagues would say, “Yes,” for the same reason that asking an actual person to write a paper for you is cheating.

But how would you detect that?

The new article suggests that these papers are not going to be obviously defective. If anything, the clue for a professor might be that the paper is too good.

Every one would be a unique output of the artificial intelligence, so that it might skirt plagiarism detectors. I don’t know enough about how GPT-3 generates text to know if it has a “tell”: predictable quirks in expression that might indicate it was an artificial intelligence rather than a person.

I don’t think many university professors are thinking at all about what this means for student assessment. We professors have traditionally wanted to build towards using writing as the preferred assessment. We ask grad students to write theses, after all. But writing as a form of assessment keeps getting compromised and harder to validate.

For another look at what GPT-3 can do, check out this video of someone who used it to recreate a childhood imaginary friend - which turned evil and tried to kill him.

Disclaimer: The story in the video is so wild that I can’t help but wonder if some of it is staged.

External links

We asked GPT-3 to write an academic paper about itself. Then we tried to get it published

26 June 2022

Prediction: American creationists will try again to get evolution out of schools

On Friday, the United States Supreme Court repealed Roe v. Wade, which was precedent for the nation-wide legal right to an abortion.

That sucks. 

I won’t pretend for an instant that I have anything particularly insightful to say about that particular case. But I do want to post something here about something this signals that are relevant to my own particular interests, namely science education.

It is clear that the US Supreme Court repealed Roe v. Wade because they could. Far right conservatives have been wanting this and threatening this for years. It was always clear that as soon as there was conservative majority on the court, Roe v. Wade would be under threat. And now it’s done.

There was not a reasoned legal decision. This was a partisan power play to give far right conservatives what they wanted.

There is every reason to think that far right conservatives are going send a host of cases going to the Supreme Court. Andy Kim reported hearing, “Let’s keep this going now” on the floor of the House of Representatives. 

Judge Clarence Thomas (who will not bury a hatchet) practically invited it when he laid out three cases that he thinks the court should revisit. They are all high on the conservative wish list to repeal and all concern people’s sex lives. (Which is, by the way, super creepy.)

But Edwards v. Aguillard has to on the far right conservative hit list. 

That’s the ruling that said it was unconstitutional to teach creationism (or “creation science” as it was called for a while) in science classes in US K-12 public schools because it violated the Establishment Clause of the First Amendment. That said, “states can’t get promote one particular religion over the others.”

No, Edwards v. Aguillard hasn’t been mentioned by name by Thomas or others. I haven’t seen anyone else bring this up yet. But I would bet that creationists are already looking to line up court cases in hope of getting the issue on the docket of the Supreme Court. 

Given that Kitzmiller v. Dover never got to the national stage, it wouldn’t surprise me if the Discovery Institute or some other entity decided to make another run at making “intelligent design” legal in schoolrooms.

Creationism is important to the same far right, religious fundamentalist conservatives who have been spearheading the assault on Roe v. Wade. Mike the Mad Biologist has often written about “Nothing in movement conservatism makes sense except in the light of creationism.” (2012, 2019, to give a couple of examples.) My take is similar. The tactics used by creationists for decades were eventually adopted by the wider US conservative political machine as their default mode of operation.

The teaching of creationism will be come up, and soon, if the court continues the way it’s been acting.

This week, the national meeting of the Society for the Study of Evolution has been happening and I’ve asked a couple of times if anyone is even talking about Edwards v. Aguillard. No answer yet. This makes me worry that my colleagues are going to be shocked and appalled if this goes to court and they lose, because they won’t have taken any action or prepared for such an eventuality.

This is small potatoes compare to the big ticket fantasies that conservatives have (i.e., terrorize people who are not white conservative Christian fundamentalists). An enormous amount of damage could be done well before the courts get to repealing a science education case.

But it’s not nothing, either. 

Attacks on education undercut the future you can even imagine, never mind the future you can build.

Edit: On reflection, it might not be creationism that goes up for a court challenge. It might be Engel v. Vitals, which ruled against prayer in schools. Or something else about Christianity (disguised as generic “religion”) in public schools. Because it’s one of their big bugbears. They know the power of public education in shaping culture and they want to influence it.

Update, 27 June 2022: Well, this morning’s ruling on Kennedy v. Bremerton School District seems relevant to this post. In particular, the Supreme Court rejects the so-called “Lemon test” that I have seen cited consistently in cases regarding the teaching of creationism.

This is getting out of my knowledge base very fast, but here is one early reaction:

(T)he Supreme Court effectively grants special, heightened First Amendment rights to religious speech, allowing public school teachers to pray on the job while denying most other public employees basic free speech rights.

And from David Shiffman:

I went to public school in a very blue part of a purple state.

As a Jew, I requested that our music class “holiday concert” include at least one song that’s not a Christmas song.

A Christian classmate threatened to murder me.

Today the Supreme Court sided with him, not me.

This seems to be a very clear move towards more religion in public schools. And that would include science classes.

Update 2, 27 June 2022: Something that puzzled me in the decision was verbiage that the Supreme Court had long ago abandoned the Lemon test or words to that effect. Steve Vladek disputes this.

As Leah notes, the conservative majority in Kennedy overrules SCOTUS’s major prior Establishment Clause precedent in Lemon, but tries to pretend that the Court had already overruled it in prior cases (spoiler alert: it hadn’t [Emphasis added.]). This is sketchy even if you think it's correct.

And other people seem to agree. This isn’t ye olde coute rulyngs, but the first time the Supreme Court has explicitly rejected the Lemon test. Tweets here and here, for instance.

14 June 2022

End abstract sponsorship for the Neuroscience meeting

Logo for Neuroscience 2022 meeting
Tomorrow is the deadline to submit abstracts for the Neuroscience meeting (the biggest academic meeting in the world).

This meeting does something that I have never seen at any other meeting. Every presentation and poster needs a society member to “sponsor” the abstract. And a member can only sponsor one scientific and one “metascience” presentation.

“So just become a member.” Not that easy, because membership also requires you to be sponsored by two active existing members. So if you are in a smaller campus, there may be no existing member who can sponsor you.

If you are in a lab with three society members but want to present four posters, you’re stuck.

The problem is so obvious that the Society’s Twitter account has taken to trying to help people rustle up a member to sponsor abstracts by retweeting requests. Like this.

Desperate last minute request from a @UniLeiden postdoc! Would anybody mind sharing their @SfNtweets membership ID for me to be able to use as a sponsor? Much appreciated 🙃

Or this or this. Not to mention this and this.

This is a failure on a couple of levels. First, it’s a stressful waste of time for people who want to present at the meeting. Second, it’s clear that people are willing to sponsor presentations they had nothing to do with.

I suspect that this policy could also cause problems with around representation, which occur pretty much any time you create an obstacle that has anything to do with money.

And it shouldn’t be up to a social media account to try to fix a conference admission problem.

I can see three possible reasons for this policy – two okay and one bad.
  1. Keeps out cranks, kooks, and quacks who want to present crackpot ideas. I think there are better ways of achieving this.
  2. Limits the size of the meeting. Sorry, but that ship has sailed.
  3. Drives membership. This is the bad reason. Look, either make membership worth having or increase the registration fee for non-members to compensate for lost revenue.

The meeting has done this for a long time. I ran into the problem the very first time I submitted an abstract. And that was, as they say, a while ago now. It feels like the kind of policy that sticks around because “We’ve always done it this way” instead of serving any valuable purpose.

It is time for the Society to publicly say why they limit submissions this way, or get rid of the policy altogether.

External links

Neuroscience call for abstracts

06 June 2022

New podcast epiode for ABT Time

ABT Time podcast. The world never has to be boring.
My newest podcast interview is the ABT Time podcast, episode 39, hosted by Randy Olson.

Randy has featured on the blog a few times before, so long time readers may recognize that “ABT” in ABT Time is an abbreviation for “And, but, therefore” – the key words for making a concise narrative.

The ABT structure features prominently in the Better Posters book because it is an powerful tool for encapsulating a project in a sentence. 

The podcast mostly talks about narrative and posters, but because I’ve crossed paths with Randy a few times, our chat is more conversational than formal interview.

The ABT Time podcast should be available wherever you get your podcasts (Apple, Spotify, YouTube, etc.).

External Links

ABT Time #39 on ABT Agenda