15 November 2022

Does anyone read German?

A paper I helped with on the Czech aquarium trade (Novák et al. 2022) has gotten a little write-up in the German aquarium magazine, Aquaristik.

Magazine article in German

At least. I think it’s this article? I don’t read German, and my cut and paste from the PDF into Google Translate wasn’t copying text correctly.

Update: Aha! A screenshot of the article and a little optical character recognition solved my problem. Loosely translated with Google, the article reads:

Researchers investigate the "Czech Aquatics Phenomenon"

An international research group led by the Czech scientist Jindřich Novák introduces the term “Czech aquarium phenomenon” to describe the considerable economic and scientific importance of the Czech Republic in ornamental fish aquaculture. A large part of ornamental fish farming is carried out by private individuals and companies in tropical countries because many species come from the tropics, however, the Czech Republic is an exception and suppliers there have dominated the global market for decades influenced. The study goes into the history of aquaristics in the Czech Republic and discusses the associated risks. It lists the most traded and exported species, including species that rarely reproduce in captivity. Given the tremendous diversity and scale of species traded, “we propose to take this phenomenon into account when designing aquaculture policies, including management of invasive alien species and ex situ conservation programs for threatened species.”

This is a cool thing about research. You never know who takes notice and where it will pop next.

References

Novák J, Magalhães ALB, Faulkes Z, Yonvitner, Maceda-Veiga A, Dahanukar N, Kawai T, Kalous L, Patoka J. 2022. Ornamental aquaculture significantly affected by the “Czech aquarium phenomenon”. Aquaculture 555: 738259. https://doi.org/10.1016/j.aquaculture.2022.738259

External links

Aquaristik Volume 2022, Issue 4

24 October 2022

eLife chooses not to decide (but still has made a choice)

eLife logo
Last week, science Twitter was abuzz with an announcement from the journal eLife that they don’t “accept” papers any more.

Lots of people had opinions, and of course I do too.

I think this tweet from editor Michael Eisen is informative (emphasis added):

The future of science publishing is author directed publishing (preprints) combined with multifaceted, ongoing, public post-publication peer review. There is no other way. And I'm glad we're finally getting into the nitty gritty of how to do it right.

This statement has the zeal of a missionary, which I appreciate. But saying that “This is the future of scholarly communication” and “There is no other way” does not make it so. It’s an assertion, not a fact. Karl Marx was convinced that bloody revolutions would lead to more perfect collective societies. But that didn’t work out the way he envisioned.

A bit of background. Eisen was involved in the Public Library of Science, and particularly PLOS ONE. PLOS ONE was revolutionary because it said, “We are not reviewing for importance.” eLife’s new policy is another attempt to get people to not assess whether something is “important” because it appears in a particular journal.

Why does that matter? As far as I can see, this is mostly about career progression. 

Over the last couple of decades, more and more decisions about hiring, tenure, promotion, merit raises, and grant funding have become highly influenced by what journal the work appears in. A lot of people believe that careers are won or lost on the basis of whether you can get a paper in Nature or Science. (Data don’t bear that out – you can have a career without those papers in glamour magazines – but their influence looms large.)

Indeed, these concerns about assessment were the entire impetus for the creation of eLife.

eLife’s new policies feel like an attempt to “fix” committees doing that decision making, in a highly circuitous, roundabout way. This is not an attempt to fix publishing, it’s an attempt to change assessment culture.

Those assessing committees are under no obligation to pay attention to what eLife does. Committees could simply decide that eLife manuscripts don’t “count” for assessment purposes. More likely is that committees will try to force reviews into a binary: to use topline review summaries in the same way that they use “accepted for publication” now.

The “Everyone should just read the paper and assess the science themselves” is understandable. We all want out work to be assessed on its own merits, and with deep reading with attention paid to the nuances. But it runs counter to a world of bestseller lists, boxoffice lists, and online ratings. Lots of people are looking for quick ways of deciding, “Is this any good or not?” I don’t see how science can be immune from that.

I can’t help but think that everyone is all crazy about publication and how it affects careers and assessments because we are so busy fighting for crumbs. The number of people with the desire, training, and skill who want to have scientific careers exceeds the number of career opportunities out there. If we could address that, maybe things like eLife’s new direction in becoming “not a journal” would just be seen as an interesting experiment by a single player in the publishing landscape, rather than a harbinger of doom or salvation.

Update, 26 October 2022: I will be watching the results of this Twitter poll with interest.

Do you think it is sound career advice to encourage a postdoc looking for a TT job or assistant professor hoping for tenure to submit their work to eLife 2.0?

Currently very close.


External links

eLife’s new model: Changing the way you share your research

06 October 2022

Schlimmbesserung: A German word that academics need to add to their vocabulary

I have a new entry in my list of German words I like:

“Schlimmbesserung.”

According to Holly Tuten,  it means, “Something that was meant to be an improvement, but actually makes things worse.”

How useful is that? Especially to academics, who often believe that every suggestion reviewers make for a manuscript is a Schlimmbesserung.

It could also be a useful word in biocontrol efforts. What was the introduction of can toads into Australia if not Schlimmbesserung? In fact, I had found people talking about “cane toading” years ago to describe this phenomenon. But it’s nice to have

It is not my favourite German word, though. My favourite German word is “Backpfeifengesicht.” Roughly, a face in need of a punch.  

Related posts

Definition of the moment

Picture from here

20 September 2022

Supreme Court of the US (SCOTUS) decision clears way for new science education battles

I did not want this to be a blog post. 

Below is an article I first wrote back at the end of June. I thought this was important, and I submitted it over and over again (six times, I think?), trying to find a bigger venue than my blog to publish it in. No takers.

None of the editors disliked what I had written. Some even agreed it was timely. In a couple of cases, the sticking point seemed to be that I was not a lawyer. (How dare a mere biologist comment on a matter of law?!) But nobody said the analysis below is wrong.

Alton Lemon
I was reminded of this because Nature published an article on the Supreme Court’s “war on science.” (I did not submit this piece to Nature, thinking a UK based journal might not be the best home for a comment / analysis piece on US law. Oh well. Maybe I gave up too soon.) I admit I am surprised the Nature article does not mention the Kennedy ruling or the Lemon test, which has been key to court cases about the teaching of evolution. (Pictured: Alton Lemon, whose 1971 Supreme Court case gave us the “Lemon test.”)

My impression from trying to get this piece published? I feel like both the biological research communities and the science teaching communities are sleepwalking into disaster. The court did a rug pull on teaching evolution. Scientific communities are like cartoon characters after the rug has been pulled out from under them: suspended in mid-air, not realizing that in a moment they are going to come crashing down very hard, very fast.

Anyway, here’s the last version of the article I submitted before accepting its fate was just to be a blog post.

Unless there’s an editor reading this who is interested? (Hope springs eternal, I guess.)

 • • • • •

Abstract

For decades, teaching creationism in the United States was ruled unconstitutional because it violated the First Amendment of the US constitution. A recent US Supreme Court decision rejects the legal test that prevented teaching creationism in public classrooms. Educators should expect renewed efforts to insert creationism into public schools.

Keywords: evolution • creationism • Supreme Court of the United States • constitutional law • lawsuits

There is a long history of legal battles over teaching evolution in America. While many might have thought this settled after the Scopes “monkey trial” in 1925 (stirringly – if not always accurately – shown in the play Inherit the Wind and movie adaptations), there have been many legal challenges seeking either to limit instruction of science or to introduce religious concepts into science classrooms. Court rulings have consistently rejected arguments against teaching religion.

But a recent Supreme Court decision opens the path for new legal challenges that might allow the teaching of creationism, intelligent design, young Earth geology, or any number of other religious claims about the natural world.

The Supreme Court case Kennedy v. Bremerton School District (2022) did not concern science education. The issue was a football coach who prayed before his players. The court ruled in favor of the coach. But more important than whether the ruling favors religion is the justification the ruling. In its ruling for the praying coach, the Supreme Court explicitly rejected the so-called “Lemon test,” which had provided the legal footing for rejecting religious instruction in science classes.

The “Lemon test” refers to Lemon v. Kurtzman (1971), a First Amendment case before the Supreme Court. The ruling established a three-part test for whether the state had violated the Establishment Clause of the First Amendment that forbids government from establishing a religion. Actions concerning religion were legal if (1) the rule had a secular purpose, (2) the main effect did not advance any particular religion, and (3) the actions did not excessively entangle the government with religion. All three of these considerations needed to be met for the action to be constitutional.

The Lemon test had been an important consideration three court cases concerning teaching of evolution. Arkansas tried to pass legislation that required evolution and “creation science” get equal time in schools. Maclean v. Arkansas Board of Education (1982) ruled that the law failed the Lemon test and was unconstitutional. That same decade, Louisiana tried to prohibit the teaching of evolution unless it was accompanied by “creation science.” Edwards v. Aguillard (1987) also ruled this as unconstitutional. Most recently, the Lemon test was used again in Kitzmiller v. Dover (2005), the only major court case on “intelligent design” (creationism with references to God stripped away in hopes that it could pass a court case). Intelligent design advocates lost this case resoundingly. The presiding judge described the board’s actions as “breathtaking inanity.” The ruling was so decisively opposed to the Dover School Board’s efforts to introduce intelligent design that it effectively killed all further efforts to introduce intelligent design into schools – until now.

In the Kennedy decision (2022), Judge Neil Gorsuch surprised court observers by claiming that the Supreme Court had “long ago abandoned” the Lemon test. Gorsuch called the Lemon test “abstract, and ahistorical.” Instead, his opinion argues that the Supreme Court should interpret the Establishment clause by “reference to historical practices and understandings.”

The move away from the Lemon test and towards history in the Kennedy decision is consistent with other recent decisions. The Kennedy decision came days after Dobbs v. Jackson (2022), in which the Supreme Court overturned Roe v. Wade, which assured a right to an abortion. Both Kennedy and Dobbs concerned with religious issues, and both were justified by arguments about history and tradition. Critics pointed out that the court’s description of both history and current facts were selective.

The loss of the Lemon test is a precarious moment for science education. Despite a Supreme Court ruling that teaching creationism was unconstitutional, many parents and teachers have tried to insert some creationism into classrooms. People often make no pretense about their efforts: they want their religion taught in public schools. While such efforts were usually not fought in court, science educators were usually confident if they did, they were likely to win. Decades of precedent supported the idea that schools should teach science in science classes.

Science educators should be prepared for a legal system that no longer has their back.

These recent decisions by the Supreme Court confirm that the court is far further to the political right than it has been in decades and seeks to undo civil rights victories of the left. Judge Clarence Thomas wrote a supporting opinion for Dobbs that said that the Supreme Court should revisit cases like availability of contraception and marriage equality.

Conclusion

While the Kennedy decision was not specifically about science education, the loss of the Lemon test should be the writing on the wall for professional scientific and educational societies. Conservative parents, local school boards, and state boards of education have showed time and time again that they are determined and persistent in their efforts to have their religious beliefs taught in public schools alongside, or in place of, established science. Supporters for science education must be prepared for renewed legal battles to push creationism and other religious ideas into classrooms.

References

Kennedy v. Bremerton School District. 2022. https://www.supremecourt.gov/opinions/21pdf/21-418_i425.pdf

Lemon v. Kutzman. 1971. https://tile.loc.gov/storage-services/service/ll/usrep/usrep403/usrep403602/usrep403602.pdf

Maclean v. Arkansas Board of Education. 1982. https://law.justia.com/cases/federal/district-courts/FSupp/529/1255/2354824/

Edwards v. Aguillard. 1987. https://www.loc.gov/item/usrep482578/

Kitzmiller v. Dover. 2005. https://www.documentcloud.org/documents/2426499-kitzmiller-v-dover-decision

Dobbs v. Jackson. 2022. https://www.supremecourt.gov/opinions/21pdf/19-1392_6j37.pdf

13 September 2022

A second look back in the crystal ball

I wrote the bulk of this post this post five years ago, back in 2017. Ten years ago, a paper came out in Nature that claimed to predict... the future! At least, it claimed to predict one part of my academic future, namely, my h-index:


At the time the paper came out, there was an online calculator. It hasn’t succumbed to link rot: it’s still there! (Remember, the preceding sentence was written in 2017.) I entered in the following values then:

  • Current h-index: It was 8 in 2012 (according to Google Scholar).
  • Number of articles: 24 (I only counted my original technical articles).
  • Years since first article: 20 (then; my first paper was in 1992).
  • Number of distinct journals: 20.
  • Number in “top” journals (a.k.a. the glamour mags): 0.

The program predicted my h-index now, five years later, would be 13. It got it exactly right, which I mentioned in a 2017 post.

Next, to schedule a post with this graph for 2022. We’ll see how close it is.

Five years later

[Wakes up in 2022, sees post, checks Google Scholar]

PI predictor said in 2012 that my H-index this year would be 21. Google Scholar says it’s...

Zen Faulkes' 2022 publication stats in Google Scholar. Alt-time citations 1237, h-index 22, i10-index 36.

22!

I exceed expectations, woohoo! And it’s even better than the 2017 prediction, which said I would only have an h-index of 18.

It’s a good thing I checked back in 2017, because the online PI Predictor page seems to have finally succumbed to link rot.

Related posts

Gazing into the crystal ball of h-index

A look back in the crystal ball

References

Acuna D, Allesina S, Kording K. 2012. Predicting scientific success. Nature 489: 201-202. https://doi.org/10.1038/489201a

06 September 2022

Students: Write shorter emails

Mail coming out of computer screen, obscuring the person at the screen.
The fall semester is underway at almost all universities now, so this is as good a time as any to give some advice to students. 

Write shorter emails.I gave that away in the post title, so why am I still writing? Because I want to try to explain why I give this advice.

Friends, your profs get a emails. A lot of emails. A great heaping buttload of emails. We get them from chairs, we get them from deans, we get emails from chair who are forwarding the dean’s emails, we get them from funding agencies that we have never applied to a grant from, we get them from almost every administrative office on campus, we get them from journals, and we get them from students.

I don’t think it’s easy to understand how much of a professor’s life revolves around emails. It is the default mode of communication for universities.

I think for many students, their typical mode of communication is through their phone, either by text or social media. Email? That’s for old people. 

But a lot of professors are old people. And even for new professors who might prefer to communicate with their phones, they are more or less forced to work with emails.

To make things worse, we profs are usually forced into using byzantine forms of email because of “security.” There’s a huge difference between using my personal Gmail account (say) and my university *.edu email account. 

I can open up my Gmail app on my phone and just... read my emails. 

My institutional account, my email might take over my phone login and force me to use a “more secure” method (using a PIN instead of an unlock pattern, say), force me to use two factor authentication every time I want to read an email, or force me to install an “Authenticator” app that requires entering my PIN, approving a request, entering my PIN again before I can read my emails.

So, students, trust me when I say this.

Writing shorter emails is one of the simplest things you can do to make your professor’s life easier. 

Look, I get that you, as a student, don’t want to seem rude. You might think that anything less than three carefully composed paragraphs is some sort of slight or that you won’t be taken seriously. 

Just tell us what you want. Need an extension? Just say, “Can I have an extension for this assignment.” You don’t need to detail that you need an extension because you were out with a friend and ordered coffee but it was way hotter than you expected and you burnt your tongue and went to an emergency room to see if there was anything they could do. If we need more information, we’ll ask for it.

Also? This is why, when you write one of those three paragraph emails to a professor, you might only get a “Sure. - ZF” or a sentence back.

04 September 2022

Nociceptors are not pain receptors

From time to time, I see people say that some group of animals have nociceptirs or "pain receptors" amd then use to to say this prooves those animals feel pain.

There is a lot of subtle misuse of definitions going on there.

Nociceptors are neurons tuned to tissue damage. Pain is not tissue damage. The two are related but they are not the same.

Calling nociceptors “pain receptors” is like calling auditory sensory neurons “music receptors.” And then use that animals can hear to claim that animals appreciate music. Well, no. There is a difference between sensory neurons and a higher order perception or psychological state arising from those sensory signals.

31 August 2022

The only real work

"Worthy" next to picture of Thor in Avengers: Endgame.
A lot of arguments about science, and particularly scientific publication, seem based around an underlying difference of opinion about what work is worthy. 

I get the strong sense that for some researchers, running experiments is the only work that matters.

Anything else is just a nuisance, a distraction, a thing that no “real scientist” would do if they weren’t forced to do so by career necessity.

On search committees, it was job candidates who kept asking about how they could get out of teaching.

Online, I think this attitude informs a lot of discussion around publishing and peer review. 

Submitting to journals? Nuisance. For some people, science paradise would be a website that automatically pushes out protocols and data and protocols, so anyone who wanted could use the data. But no time wasted on pesky explaining work to other people. Just pure flow in data collection.

Peer reviewing? That takes me away from data collection, so you better pay me to make it worth my time. 

Proofreading and editing? Not even real work. This may partly explain why some people keep asking, “Why aren’t all scientific article free?” Because they just can’t imagine that managing articles is real work that deserves fair compensation.

To be clear, I have no problem with anyone saying, “Running experiments is what I value and how I want to spend my time.” But other people should get to value other things.

Maybe we are doing a better job now of recognizing the labour that goes into scientific research. More people are rightfully insisting that doing research should be treated as work, not a vocation or calling or passion (you know, things that don’t get you paid). But I feel like we not doing such a great job of recognizing that what other people do that supports research is also worthwhile work.

16 August 2022

Why do you want to switch your name with your co-author?

A perennial academic question resurfaced on Twitter yesterday:

“If I’m a co-author with an ‘equal contribution’ statement, is it okay to switch the place of my name and my co-author name on my CV?”

Usually, the discussion is about how swapped names might be interpreted by a potential CV reader. 

The general mood in responses is usually, “Don’t do it, because some readers will see this as shenanigans.” Everyone who has read a lot of CVs from students or early career researchers knows that some people try to “puff up” their credentials.* Readers do not appreciate that. 

It’s not even whether this counts as “lying.” Readers of CVs usually have a lot of CVs to assess, and it’s reasonable to be annoyed by CVs that make readers put in more mental effort recalibrating those inflated claims of accomplishments.

What I want to do, though, is flip the script. I don’t want to talk about how the reader might interpret re-arranging the order of names on a paper listed in a CV.  I want to ask why the author of the CV wants to switch the order of names.

It seems authors want to swap names because they think there is an advantage to doing so. They seem to think that putting their name first will be more assessed more positively.

If authors truly believed in that “equal contribution” statement, what is the point to changing the order of names? 

“Well, they are interchangeable” is not a good enough answer, because it’s easier to leave it than it is to change it. 

The desire to swap names shows that “equal contribution” or “co-first” footnotes are nearly meaningless in practice. Wanting to swap name order later indicates that you should have advocated for yourself harder before the paper was submitted to a journal.

Maybe I am wrong. Maybe there are some other reasons that people want to swap name order on CVs.  

Maybe people think there is no way to show “equal contribution” on a CV? Sure there are. Here’s one.

Taffe M*, Faulkes Z*. 2022. Journal article title. Journal 3: 34-35.
* Equal contribution

Maybe people worry that their name will get lost in a long list of names? There are other ways to emphasize names beside order. Here’s one.

Taffe M, Faulkes Z. 2022. Journal article title. Journal 3: 34-35.

If we have a better handle on why people want to swap names, we might have better advice on how to create a CV that meets the author’s goal without annoying any readers.

* Like listing articles as “in preparation for Nature.” Sure, friend, we all have articles that we plan to submit to Nature.  Except we know there’s no way to verify it and most things that are submitted to Nature get rejected.

External links 

Co-first authorship is a lie and a sham and an embarrassment to our profession

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