12 August 2022

There are invasive crayfish in South Texas and I have nothing to do with it

Australian red-clawed crayfish, Cherax quadricarinatus
Yesterday, Texas Parks and Wildlife released a press release about Australian red-clawed crayfish (Cherax quadricaratus) in South Texas.

What is kind of weird is that it the press release mentions “Researchers from the University of Texas Rio Grande Valley” (UTRGV) but didn’t say which researchers or even which department.

This morning, I get emails from people thinking I was involved, because I was the only crayfish researcher at UTRGV for a long time. Never mind that I haven’t worked there for while. I don’t know who from UTRGV had a hand in this.

Dan Johnson, who knows Texas crayfish better than I do, says that this is not a new discovery. He stated that red-clawed crayfish were found in one pond nine years ago. (I am a little annoyed that I was around at the time and nobody saw fit to mention this to me. I could think of a bunch of ways I could have used that information.) 

Edit: This might be a reference to this record of red-claws on iNaturalist.

They have now spread to one more location a few mile away. That’s... not much of an invasion?

Red-clawed crayfish were imported into Mexico years ago for aquaculture and the food market. They escaped, because crayfish are good at that, and now they are very widespread in Mexico. I don’t think there is any interest in trying to contain them in Mexico. One researcher joked, “They’ve been given their Mexican passports.”

Worth noting that there were people in Texas aquaculturing redclawed crayfish. But either spread from Mexico or release of pets seems the most likely source of these crayfish. That one of the ponds is right next to an apartment building suggests aquarium dumping to me .

External links

Invasive Australian Redclaw Crayfish Present in Texas

Photo from here.

Instructors with accents and students with complaints

From time to time, I hear students ask questions like, “Why don’t universities hire instructors who can speak English?” It’s usually a complaint about professors who have “foreign accents.”

Hereˆs one from Quora, with some more at the bottom of the post: “Does it make sense to hire Chinese professors in US universities when they can’t even speak basic English?” The “basic English” comments sounds contemptuous.

Okay, let’s acknowledge that everyone has an accent. And that it’s very difficult to separate complaints about accents from racist attitudes.

That said, there can be obstacles to communication between a professor and students. 

I once saw video of Stephen Hawking teaching – after his motor disease was fairly advanced but before he got his voice synthesizer. He could speak, but not loudly and not with full fluency. 

Hawking had an assistant (maybe a graduate student?) who was familiar with how Hawking spoke who relayed what he said. Some students did not need this. You could tell because some students would laugh at a joke before Hawkins’s assistant spoke.

You can hear Hawking in 1977 – when he was still able to talk – in this YouTube clip. It’s is comparable to the clip I saw.

I think the answer is universal design.

Instructors should think about how to design their course so anyone could take it. Like, say, a deaf student. What would you do? Use close captioning, video recordings with subtitles, transcripts, detailed notes.

Similarly, there are many reasons a student might not comprehend speech. If you couldn’t hear because of an ear infection, you probably wouldn’t start by complaining that the university made a hiring mistake. You would ask for repetition and clarification.

As usual, these would not just make the course accessible to people with hearing impairments, but would make things better for everyone. It gives everyone ore opportunities to interact with the course material.

These design and communication decisions also addresses issues around accent mismatch. Any student still complaining is probably just being a jerk.

External links

Does it make sense to hire Chinese professors in US universities when they can't even speak basic English?

Why do colleges hire professors who are extremely difficult to understand and sometimes are unintelligible?

Why do colleges hire so many professors with such heavy accents you cannot comprehend them?

How can students cope with professors that lecture in thick accents?

11 August 2022

“Listen”: Audio for journal articles is here!

I was looking at a new article and noticed an icon I had never seen before. 

“Listen.”

Listen icon

I’m a sucker for new things, so I clicked. And I am... quite impressed.

The audio is being read by a machine, not a person, but the tone is not horribly mechanical. There are subtle things like emphasis on emphasizing words like “widespread.” It says “For example” when the actual text reads, “e.g.”

By default, the program automatically scrolls through the text and highlights what it is reading. You can turn it off, though. As you can see, you can adjust the volume and reading speed. But once you adjust the speed, it goes back to the start of the article, which is frustrating.

Journal article with "listen" controls, showing highlighted text being read aloud.

The experience is not seamless. In this article, it skipped over the authors – but it read the tabs at the top (“Full Article (pause) Figures and data (pause) References (pause) Citations,” and so on). 

Another frustrating element of the experience is that the software says “parenthesis” and “end parenthesis.”  Worse, it does it completely inconsistently. It sometimes mentions the opening parenthesis but not the closing, or vice versa. And sometimes it passes over parentheses without comment.

The program continues to reads all the references. Including DOI hyperlinks. (“H, T, T, P, S, divided by, divided by...”) This is terrible to listen to and nearly useless, in my view.

Not as good as a person reading the text, but not bad. Not bad at all.

The dropdown menu reveals one more key feature:

Web reader dropdown menu showing "Settings" and "Download mp3" options.

You can download an mp3 of the audio file. Which means you can put it on your phone or other audio device to listen while you’re walking the dog, working out at the gym, or commuting.

The idea of being able to listen to journal articles like audiobooks has been floated on Twitter multiple times, so I will be curious to see how this is received.

This is a good – possibly great – addition to journals. It increases the accessibility of the literature to people with vision problems. It increases the portability of papers, making them more like podcasts.

Kudos to Taylor and Francis. Hopefully, other publishers will roll out this soon.

Here is an open access article that you can use to try the feature. https://www.tandfonline.com/doi/full/10.1080/15563650.2022.2105710

Update, 12 August 2022: The “Listen” feature is not on every Taylor and Francis article. This article on citation bias appears not to have it, even though it was published within the last week. But maybe that it because it is an authors’ preprint and not the final version of record.

Related posts

Audiopapers


09 August 2022

What happened to Matters?

Logo for journal Matters
A few years ago, a journal launched called Matters. The interesting thing about this journal was that it was devoted to single observations. Science magazine saw fit to write about Matters, so it’s not like it was hidden in a dark hole under the stairs somewhere.

The journal homepage is now offline.

The journal’s Twitter account hasn’t sent tweeted since 2019. The person behind the journal, Lawrence Rajendran, is still active on Twitter, however.

Worst of all, I can’t find articles published in Matters using the DOI. They seem to have completely vanished into the ether. (There was a cool one about hermit crabs.)

I’d noticed that Matters vanished a while ago, but couldn’t tell you when. But I was reminded because I learned of MicroPublication Biology. It seems to be trying the exact same thing Matters did: offer per reviewed publication for single short papers that don’t fit into some larger narrative.

I’m skeptical of MicroPublication Biology because nobody’s name appears anywhere in the journal’s website that I can find. Who is the editor? Are there associate editors? 

But I’m also skeptical because, well, we had Matters. And it tanked. It would be nice to know the full backstory of the journal, but even without that, I think it’s fair to say Matters didn’t take the academic publishing world by storm. It may be that this is a service that people say they want, but when push comes to shove, their actions don’t back up their words. Maybe researcher would rather publish “complete stories” – with all the ambiguity and frustration of what that phrase means.

External links

Got just a single observation? New journal will publish it

Matters description on PubLons

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