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.