Readers’ wildlife photos: Humorous titles of science papers

January 30, 2023 • 8:15 am

Well, there aren’t any photos today (I have about a week’s worth, but am conserving them), but we do have science—in the form of weird titles of scientific papers. Athayde Tonhasca Júnior sent this collection with a brief intro:

Perhaps your readers would be amused by scientists being witty or mischievous (sometimes unintentionally), with varied degrees of success.

Any notes are mine. Click titles to enlarge them.

Oy, the citation!

More citation humor:

I presume this acronym was deliberate:

 

Guardian retracts claim that Cornwall is infested with “venomous crabs”

August 8, 2022 • 11:15 am

Yesterday morning, thanks to Matthew, I pointed out that the Guardian had screwed up one of its biology stories, the one noted in this headline:

What apparently had happened is that somebody at a news service (see below) googled “crab spider” instead of “spider crab”, and concluded that spider crabs were venomous. Then the Guardian simply cut and pasted the false assertions about the spider crab—no crabs are venomous though some are toxic to eat—to create a clickbait story.

Pity, pity, because since the crabs aren’t venomous, the story loses a lot of its click-y allure.  A number of people pointed out to the Guardian that this story wasn’t exactly true (the swarming part was). Matthew also informed one of his friends who works at the Guardian (see below). Regardless, the complaints worked, and now there’s a new story sans venomous crabs. Click below to see the latest story, lacking the word “venomous”.

And kudos to the Guardian for noting that they changed the story. At the bottom of the new page you can read this:

 This article was amended on 8 August 2022. An earlier version incorrectly stated in the headline and text that the spider crabs massing at Cornish beaches were “venomous”; no species of crab is venomous. Also, their Latin species name is Maja brachydactyla, not “Hyas araneus” as we said.

Someone else must have corrected the species name. I took the paper at its word, for Hyas araneus is the “great spider crab”. Now we learn that these un-venomous crabs are actually Maja brachydactyla, in a completely different family. Now how did they screw that one up?  By copying from another source?

Well, all’s well that ends well, except, perhaps, for the would-be bathers who avoided the waters off Cornwall.

*********

Here’s Matthew’s email to the Guardian:

From: Matthew Cobb

Subject: Crab spiders

Date: 7 August 2022 at 22:11:22 BST

To: guardian.letters@guardian.co.uk” <guardian.letters@guardian.co.uk>

Over the weekend The Guardian website followed the rest of the UK press by printing a story about ‘venomous spider crabs’ moving into shallow waters off Cornwall to moult [https://www.theguardian.com/environment/2022/aug/06/spider-crabs-swarm-in-shallow-waters-on-cornish-beach].

Virtually all of these stories – including that in the Guardian –  claimed the crabs ‘have a venomous bite that is poisonous to their prey but harmless to humans’.

This is not true. No crab is venomous. Indeed, out of over 7.000 species of crustacean, only one is known to be venomous, and it is not a crab.

This error – which the Guardian has still not uncorrected, despite repeated alerts on social media – appears to have originated in some journalist googling ‘spider crab’  and not noticing that the pages they got back referred to ‘crab spider’. It was then simply copied by other journalists, including your own.

It is hard to know which is more disheartening: the original error, or your thoughtless repeating of it. This example does not particularly matter, but confidence in the press is a fragile thing.

Matthew Cobb

The Guardian responded by saying that the false claims about venom and species name were provided by a news agency based in south-west England, and noted that they’d changed the text and added a footnote. 

The Guardian has photo issues as well as evolution issues

June 30, 2022 • 1:45 pm

I just had to put up as a standalone this posted comment from reader Mike on yesterday’s Guardian article on why evolutionary theory is supposedly obsolete. There was a rather substantial boo-boo in one image, which was wonky in three ways: the species identification was wrong, and two parts were photoshopped in. This manipulation was not indicated.  It’s just one more sign that the Guardian needs some kind of science editor.

From Mike:

In case anyone is still checking in on this post and that crazy Grauniad article, turns out one of the feature images of the “spadefoot toad” was a photoshop nightmare: not a spadefoot toad; has a chameleon’s tongue; catching a dragonfly that’s photoshopped into the image; and perched on a toadstool.

Now that’s phenotypic plasticity!

The kicker is that the Guardian has stealth edited the image out of the version that’s up today on the website. The wayback machine shows the original article with that frankenimage.

The “frankenimage” from the wayback machine.

It’s gone now; no toad photo to be seen and no indication it was ever there.  And whoever Buddy Mays is, he should be roundly trounced (I think that this is him.)

Below: the tweet that corrects the species ID and the photoshopped tongue and dragonfly.

I have a big stupid grin on my face!

Bad academic writing of the year award

February 16, 2022 • 3:30 pm

Well, it’s only February, but I have a contender for the Worst Academic Writing Award already.  It’s not of Judith-Butler-level opacity, but it’s pretty convoluted, and in fact I have a hard time figuring out what the authors are trying to say.

The whole article is as badly written as the passage I quote below.  And pity me, as I had to read the whole article. Click on screenshot if you want the mental equivalent of a root canal:

This is just the opening passage, and is just a single paragraph:

It has been argued many times over the course of decades and across diverse paradigms that science, technology, engineering, and mathematics (STEM) education practices-as-usual (re)produce systems of dominance: be it patriarchy, heteronormativity, white supremacy, Eurocentrism, (neo-)colonialism, able-ism, classism, labor inequity, anthropocentrism, and/or others. Thankfully, there are many who are doing the critical and creative work of (re)opening STEM education to the possibility of eco-social justice to-come through a plurality of productive approaches, orientations, and stances: anti-oppressive, anti-racist and critical race-based, decolonizing and de/colonizing, queer, Indigenous, gender-equitable, post-colonial, community-based and participatory, critical place-based, inter-species, and many more. Further, there are many examples taking richly critical and complicit stances to work within and against logics of exclusion. Yet, in doing so, many of these engagements are oft depoliticized and atheoretical practices of inclusion in ways that continue othering those formerly excluded, albeit differently. As readers of the field, we note the ways in which efforts often center around questions of curriculum and pedagogy; as they should, these are central and major nodes within STEM education. How coming-to-know-nature, coming-to-know-number, and coming-to-know-technology are conceptualized and enacted matters deeply: in terms of the curricular destinations and the pedagogical pathways that might allow such learning, as well as for whom. For example, as Megan Bang and Ananda Marin (2015) remind, the curricular inclusion of Indigenous perspectives is differentially problematic if we cannot also attend to the taken-for-granted and naturalized epistemological, ontological, and axiological commitments and enactments of what we are including perspectives into. As Bang and Marin (2015) state, if science education continues to “focus on ‘settled’ phenomena as well as ‘settled’ perspectives and relations to phenomena” (p. 531), which rely on and reinforce recursive whiteness and settler privilege while simultaneously dismissing, diminishing, and denying Indigenous ways-of-living-with-nature, presence, and futurities, it will remain but a tokenistic inclusion which serves to distract from the more unsettling demands of this work and is often primarily an effort to reconceptualize and recenter the subject of dominance. Again, how curriculum, pedagogy, and its central nodes are conceptualized matters.

You could have a drinking game with this: a shot of tequila for every woke buzzword you read. The thing is, though, you’d be a goner before line ten.

Want more? Here’s the second paragraph:

Similarly, methodology is alsoFootnote1 an important site in which the movements of power occur, differentially (re)producing articulations of dominance. While these often manifest in much more subtle ways, we argue that it remains important to ask ourselves how the diverse methodologies we employ in and through our research practices as scholars of STEM education contribute or work to maintain and privilege the prevailing trajectory of STEM education. To this end, highlighting the ways in which the disciplines discipline what counts as knowledge and, more to the point, knowledge production processes, Linda Tuhiwei Smith and colleagues (2016) ask, “are methodologies simply new technologies of cultural assimilation?” (p. 133). For Smith and colleagues (2016), attending to methodology is to address lingering colonial referents which lurk within our methodological constellation of concepts (e.g., voice, identity, data, and reflexivity). To engage in critical goals yet engage in “conventional” methodologies, whose taken-for-grantedness does not and cannot identify which conventions inform them, sends a subtle yet insidious message: that alternative perspectives need to be validated in and through the norms of dominance in order to “count.”Footnote2 There is a need to actively de-center these taken-for-granted notions and to pull through alternative and multiple ways of assembling theory, practice, and ethics. However, disrupting and displacing methodologies is not strictly a call for methodological pluralism, a means of “losing the way — as losing any sense that just one ‘way’ could ever be prefixed and privileged by the definite article” (Gough 2006, p. 640, emphasis ours). It is also a call for “disrupting the hegemonic ways of seeing and how this relates to subjects making themselves dominant” (McKinley 2001, p. 76). We do not suggest that the critical and creative reworking of methodology is (wholly) a panacea to this poison. Nonetheless, there is purpose in critically engaging with the work of disrupting and displacing methodology: it is to at least dare to fail in new ways.

Do these people think they can write? This is the worst kind of obscurantist postmodernism in town, and Orwell would have a field day with it.  What are the sweating professors trying to say? (See p. 271 here, in one of the funniest and most scathing book reviews every published.)

I thought this kind of execrable and impenetrable postmodern prose went out of fashion two decades ago.

Jesse Singal fact-checks Science-Based Medicine again

July 18, 2021 • 9:30 am

The battle between Jesse Singal and the site Science-Based Medicine (SBM) continues. SBM originally hosted a positive review of Abigail Shrier’s book Irreversible Damage written by one of their editors, Harriet Hall, and then two other editors, David Gorski and Steven Novella (G&N), removed Hall’s review and replaced it with three pieces critical of Shrier’s thesis about the possible social origins of rapid onset gender dysphoria (ROGD) and the possible dangers of treating the syndrome with hormones and surgery when it starts in adolescence. (See the whole story in these posts.)

Although G&N claimed that they removed Hall’s review because it contained scientific errors and also glossed over Shrier’s own errors, I suspect it was also pushback from those who deemed Shrier’s book “transphobic” (it’s not).  Jesse Singal, who’s read a lot about gender dysphoria has published a critique of G&N’s stated reasons for the censorship, arguing that G&N played fast and loose with the literature themselves, mis-citing papers, engaging in confirmation bias, and so on.

Now, in four further tweets, Singal has accused A. J. Eckert (AJE), one of the people whose posts replaced Hall’s on SBM (Eckert wrote two of them), of fabricating quotes from Shrier’s book that don’t appear in it. Here are the four tweets. While these made-up quotes aren’t as potentially damaging to SBM’s reputation as is Singal’s long critique, it still shows a lack of care in SBM’s methods—something one doesn’t expect on the site, which has been careful and a valuable asset. Now, however, it may well be slanted by wokeness.

The first one deals with a phrase that, says Eckert, is used repeatedly by Shrier to characterize the social environment that, she says, pushes adolescent girls towards ROGD. Eckert says, among other things, “These [factors] are characterized as a ‘woke gender ideology,’ an oft-recited phrase that is never really defined.” In fact, Singal found that Shrier doesn’t use the phrase even once.

Singal’s second tweet notes that it was supposedly only one quote that was fabricated, but that AJE said it was “oft-recited.”

Then Singal discovers two things. First, Eckert attributes to Shrier the phrase “radical trans ideology” as characterizing what the Internet instills in some adolescent girls that get ROGD (third tweet). That phrase doesn’t appear in Shrier’s book, though AJE puts it in quotes.

Second, AJE apparently grossly mischaracterized the treatment of Lisa Littman’s study of the etiology and manifestation of ROGD published in PLoS ONe (underlined bit below).

No, Littman’s study wasn’t pulled; in fact, it’s still up at the PLoS ONE website. What happened was that the editors required some tweaks in the original version, which were made. What was pulled was a Brown University press release promoting Littman’s study. (Littman works at Brown.) And that retraction, as well as perhaps some of the changes suggested by PLoS’s editors, may have come from social-media pressure.

This last claim about pulling the study, combined with the fabricated quotations, show a lack of care of AJE and SBM, and perhaps the editors, in describing the work. I won’t call these lies or deliberate fabrications, but they do show a disturbing lack of care from a site that has spent much of its time debunking others for carelessness and duplicity.  And I’m not sure if it’s “potentially libelous”, though Eckert/G&N really should issue a couple of corrections for the site.

Judge it as you will; your mileage may vary. There will, of course, be more to come. In the meantime, Shrier’s book, now a year old, is still selling rapidly on Amazon because of all the attention that the ACLU and people like G&N give it. It’s the Streisand Effect.

h/t: cesar

A new podcast: Dawkins on how to write popular science

July 4, 2021 • 12:30 pm

This morning I was interviewed by Iona Italia on her “Two for Tea” podcast, designed to enlighten listeners as well as to support Areo Magazine, of which Iona is Editor-in-Chief. The podcast has featured guests with expertise on science, religion, humanism, philosophy, freedom of speech, and so on—much like the contents of Areo—and has been running for three years.

My interview should be out in a few weeks, but the last half of it will be for subscribers only. You can become a patron here; the $1/month memberships are sold out, so your minimum contribution is $5 a month, though I’m told that if you’re poor you can get a one-time $1 link. And, at any rate, the first half is free. I’ll post a link when it’s up.

While looking at who’s been interviewed, I saw that the latest episode (second link below), features Richard Dawkins, talking mostly about the themes of his new book on science writing (first link below). It’s Richard’s version of Pinker’s A Sense of Style, I guess, and I’m looking forward to seeing what he has to say on his philosophy of writing popular science. Some of his books, like The Blind Watchmaker, represent, to me, a near-perfect fusion of lyricism and science. And although I can’t aspire to write anywhere near as well as he, he’s been a role model of both clear and moving science exposition. You can order the book from Amazon by clicking on the link below.

I listened to the free 24 minutes of the podcast, and if you’re already very familiar with Dawkins you may not learn much that is new, but it’s a good way to spend an hour (or half hour) on a lazy Fourth of July. Here are the timestamps for Dawkins podcast, which unfortunately (if you don’t pay) stops right before the “literature and poetry” bit, which I’d much want to hear. I’d also like to know what his favorite book is.

At any rate, if you click on the screenshot below, you’ll go to the page where you can hear the first 24 minutes.

Timestamps

4:24 Why more non-scientists should take pleasure in science writing
6:15 Why it is important for scientists to write clearly
14:43 Continuously updated virtual reality
16:41 The genetic book of the dead
20:17 The extended phenotype
25:12 Literature and poetry
28:06 Misconceptions of the gene’s eye view
33:21 Misinterpretations of evolutionary biology and of Dawkins’ own work in particular
35:56 Defying our genes
36:16 Anti-Darwinian ethics
37:28 Threats to the understanding of science
39:20 Dawkins’ gift for satire
44:37 Dawkins’ own favourite work

While we’re at it, do note your favorite Dawkins book. If you’re into pure science, you might like The Selfish Gene or The Extended Phenotype, while if you favor popular science that’s a bit easier to read, you might like The Blind Watchmaker or Climbing Mount Improbable.

 

Donald McNeil, fired from the New York Times, finally defends himself

March 3, 2021 • 10:45 am

After leaving the New York Times for, among other things, uttering the full n-word while accompanying a group of students on a 2019 junket to Peru, Donald McNeil has finally told his part of the story—on the day after he left the paper. The story, in four parts on Medium, was vetted by two lawyers.  And it’s long. Printed out in 9-point type, single spaced, it still occupies 43 pages, and took me 70 minutes to read.

However, if you want to see how toxic things are at the Times, and read McNeil’s defense, you might want to take an hour to read it.  Here are the links to the four parts:

Part 1. “The Introduction

Part 2. “What happened on January 28?

Part 3. “What happened during the investigation?

Part 4. “What happened in Peru?

Now the n-word accusations, and several others by 13 students, had already been investigated by the NYT in 2019; McNeil was reprimanded, and a letter put in his folder, solely for using that n-word, but he wasn’t penalized beyond that. But when The Daily Beast published a story on the accusations on January 28 of this year, the merde hit the fan. The Times staffers, largely the black ones, met with executive editor Dean Baquet, and, well, there was a complicated process of negotiation, with Baquet finally telling McNeil that he should “consider” resigning. Somehow—and this part isn’t clear in the account—McNeil, who didn’t want to resign, finally wound up leaving the paper. I suspect a lawsuit is in the offing.

Here are McNeil’s defenses, written this year, against three of the most serious accusations against him. The first is that he used the n-word in a discussion with a student, the second that he supposedly said that there was no such thing as “white privilege” and also denied the existence of systemic racism, and the third that he suposedly justified the use of blackface. None of the students’ accusations hold water, save that he did use the n-word, but just in a question about whether the student had indeed used that specific word.

McNeil’s partial defense (he goes on at length later in the series):

1. Yes, I did use the word, in this context: A student asked me if I thought her high school’s administration was right to suspend a classmate of hers for using the word in a video she’d made in eighth grade. I said “Did she actually call someone a “(offending word”? Or was she singing a rap song or quoting a book title or something?” When the student explained that it was the student, who was white and Jewish, sitting with a black friend and the two were jokingly insulting each other by calling each other offensive names for a black person and a Jew, I said “She was suspended for that? Two years later? No, I don’t think suspension was warranted. Somebody should have talked to her, but any school administrator should know that 12-year-olds say dumb things. It’s part of growing up.”

2. I was never asked if I believed in white privilege. As someone who lived in South Africa in the 1990’s and has reported in Africa almost every year since, I have a clearer idea than most Americans of white privilege. I was asked if I believed in systemic racism. I answered words to the effect of: “Yeah, of course, but tell me which system we’re talking about. The U.S. military? The L.A.P.D.? The New York Times? They’re all different.”

3. The question about blackface was part of a discussion of cultural appropriation. The students felt that it was never, ever appropriate for any white person to adopt anything from another culture — not clothes, not music, not anything. I counter-argued that all cultures grow by adopting from others. I gave examples — gunpowder and paper. I said I was a San Franciscan, and we invented blue jeans. Did that mean they — East Coast private school students — couldn’t wear blue jeans? I said we were in Peru, and the tomato came from Peru. Did that mean that Italians had to stop using tomatoes? That they had to stop eating pizza? Then one of the students said: “Does that mean that blackface is OK?” I said “No, not normally — but is it OK for black people to wear blackface?” “The student, sounding outraged, said “Black people don’t wear blackface!” I said “In South Africa, they absolutely do. The so-called colored people in Cape Town have a festival every year called the Coon Carnival* where they wear blackface, play Dixieland music and wear striped jackets. It started when a minstrel show came to South Africa in the early 1900’s. Americans who visit South Africa tell them they’re offended they shouldn’t do it, and they answer ‘Buzz off. This is our culture now. Don’t come here from America and tell us what to do.’ So what do you say to them? Is it up to you, a white American, to tell black South Africans what is and isn’t their culture?”

He expands on these explanations in detail, but it’s pretty convincing that, although he is a bit of a curmudgeon (and admits it), he wasn’t guilty of the offenses of which the paper accused him. The n-word was used more or less didactically—certainly not as a racial slur—and the paper itself has used the word (printed in full) several times. Their claim, then that “intent is irrelevant” when you use the word also holds no water.
If you want the short version, the NYT itself has published a pretty straightforward summary of the story and McNeil’s defense. But you won’t get the full flavor of this incident unless you have a look at McNeil’s side. Why is this important? Because the New York Times is America’s best newspaper—or at least used to be. Right now it looks to be a slave to Wokeness and a paper run not by the editors, but by an easily outraged staff in combination with social media.

There are indications of how toxic the NYT atmosphere is throughout the long series, but I’ll let Greg Mayer put this in an addendum to this post, so come back here in a day or so. Of course McNeil’s defense is just that: his defense, and you can say that he’s covering up things or putting a favorable spin on what happened. But it doesn’t seem like that, and we already know about the toxicity of the New York Times from its treatment of other staffers like Bari Weiss and James Bennet.

What offends me most is that the paper already fully investigated the accusations detailed in the Daily Beast article two years ago, and nothing new arose since. But it was the publicity, and the new outrage of the staff in the newsroom, that made the paper revisit the accusations and finally decide to dump one of its best science reporters. 

Watch this space for the addendum by Greg. I’ve concentrated briefly on the accusations against McNeil, while Greg is outraged at how the whole incident bespeaks a ham-handedness and unfairness in how the paper deals with its employees.

Addendum by Greg Mayer; as promised, here are some further thoughts on the McNeil matter.

When I first spoke to Jerry about McNeil’s account, I referred to the New York Times as a “hellhole” for the people who work there. Jerry, who focused his attention on the veracity of the allegations against McNeil, later asked me what made me characterize it in that way, and I responded with an unrehearsed litany of woe, as recounted by McNeil. When Jerry suggested I add something here about this, I at first hesitated to use that word, but, reflecting on what I had just told him, hellhole it is.

McNeil had a decades-long career at the Times, and had long been stationed overseas. Returning from overseas, he became a union leader, negotiating with Times management over contracts. The Times, however much it professes to be so on its editorial page, is not a champion of workers’ rights when it comes to its own workers, either in their compensation or their workplace rights. McNeil engaged in some tough negotiations, and the Times‘ eagerness to squeeze its workers is unedifying.

In 2019, some prep school students, who participated in a Times-sponsored trip to South America, complained about McNeil. He was called before a veritable star chamber, where he was peppered with questions, given no opportunity to examine or even learn what ‘evidence’ was being used against him, and– the pièce de résistance— his interrogators were the very management negotiators with whom he had already tangled on behalf of his fellow workers. Surprisingly, his union gave him little or no assistance. Times editors and managers, including those who asked McNeil to go on the trip, proved to be either ineffectual or unwilling to aid in his time of need. This ended, as one might expect, badly and unfairly– McNeil was officially disciplined.

Earlier this year, an article in the Daily Beast publicized the 2019 event, and the Times came back at him for a second round of punishment. Once again, Times editors were helpless, hostile, or both, and the union did little or nothing. The added element now was that McNeil’s fate was also put to a sort of plebiscite of his fellow workers– or some selected set of them, anyway– and they don’t like him. Displaying their weakness as a badge of honor, they called for management to get rid of him. Whatever happened to worker solidarity! As Marx didn’t write,

Workers of the world divide! You have nothing to lose but your institutional safeguards against arbitrary dismissal!

McNeil was forced to resign. (This may be construed as constructive dismissal, and it might also violate the union contract to be disciplined twice for the same ‘offense’, so McNeil may have grounds to sue. However, he has indicated a disinclination to do so. I’d like to see him write for the NY Daily News!)

Executive editor Dean Baquet comes off especially badly in the whole affair. Appearing weak and ineffectual in 2019, in 2021 he feigns sympathy, and then stabs McNeil publicly in the back, issuing his transparently mendacious and now infamous “regardless of intent” statement. If Dean Baquet likes you (as McNeil thinks–or thought– he did), you’d better run!

What McNeil– and the Times— needed were discerning adults who knew what was going on, and had some sense of judgment; who knew how to weigh a few teenagers’ complaints against a decades-long career, which was just, in many ways, peaking, with much lauded coverage of the COVID pandemic. Instead, he got inquisitors who combined personal animus, management vendetta, ideological axe-grinding, and corporate CYA into a witches brew of poison, which has now ended his career, and further degraded the now sagging reputation of the Times.

McNeil expresses some fondness and respect for the Times— who wouldn’t, after having given more than 40 years of his life to it. And any institution as large as the NY Times must have good and bad aspects. But it’s beginning to seem a bit like East Germany– sure, you could live a decent life there if you kept your head down and went about your business, but woe betide he who runs afoul of the system.

(I’ll mention two things parenthetically here. First, I met McNeil several years ago when he visited UW-Parkside as part of a program the Times was running to encourage subscriptions and the use of newspapers at college campuses. I went to his presentation, and asked him a few questions afterward. I mention this not because I have any relationship to him, but because it shows that, good Timesman that he is– or was– he was out on the hustings, hustling for the Times– much as he was in Peru.

Second, disrespect for a shaman? You gotta be kidding me. Having taught a course called “Science and Pseudoscience” for many years, this really riled me. In a trip designed to educate students about rural public health, the teachers damn well better be able to distinguish between medicine and quackery, and to develop that skill in their students. While the distinction between cranks and charlatans is a useful one (the former to be granted some leeway for their sincerity), disdain and even ridicule is sometimes called for. As H.L. Mencken said, and Martin Gardner endorsed, “One horse-laugh is worth ten thousand syllogisms.”)

h/t: William, Greg

Shabby science reporting in the New York Times

January 10, 2021 • 11:00 am

I’ve noticed lately that the quality of science writing in newspapers has declined, even in The New York Times, which used to have some really good writing, especially by Carl Zimmer, who doesn’t seem to appear in its pages so often.

_____________________

CORRECTION:  Zimmer is still writing prolifically in the NYT, but covering a beat—vaccination—that I’d missed, (mis)leading me to believe that he was engaged in activities other than writing for the NYT. He’s asked me to correct this in a comment below, so I’ll just add his comment here:

If you had bothered to look at my author page at the Times, you’d see that I have been busier than ever there as I help cover the science of the pandemic. Over the past 10 months, I’ve written 93 stories about Covid-19, which comes to about two articles a week. Please correct your post. You are misleading your readers about my work. https://www.nytimes.com/by/carl-zimmer

I guess he was peeved. The misstatement was my fault, of course, and I’ve fixed it, but I have to say that this is a rather splenetic reply from someone whose work I’ve always praised.

_____________________

Rather, in place of long-form biology and physics, a variety of people now write for the Times‘s biological “Trilobite” column, and seem to take a more gee-whiz approach to science, producing short columns that are also short on information.

Part of the problem may be that many of these columns are written by freelancers who haven’t spent most of their writing career dealing with biology. My general impression is that the NYT is starting to reduce its coverage of science. That would be a damn shame since it was the only major paper to have a full science section (I don’t get the paper issues any longer, so I don’t know if they still have the Tuesday science section I’d read first).

The sloppy writing seems to be the case with this week’s column, a column reporting a new genome-sequencing study in Nature of monotremes: the platypus and the echidna (“spiny anteater”). I have only scanned the paper briefly, and will read it thoroughly, but on reading the NYT’s short summary I spotted two errors—not outright misstatements of fact, but statements that are incomplete descriptions of the truth, and where an extra word or two would have made the column not only more accurate, but more interesting.

Here’s the article (click on the screenshot):

 

Maybe I’m being petulant, but here are two quasi-misstatements in the piece. First, this one (emphases are mine):

When the British zoologist George Shaw first encountered a platypus specimen in 1799, he was so befuddled that he checked for stitches, thinking someone might be trying to trick him with a Frankencreature. It’s hard to blame him: What other animal has a rubbery bill, ankle spikes full of venom, luxurious fur that glows under black light and a tendency to lay eggs?

The facts: Only the males have ankle spurs, and of course only the males have venom. (This probably shows that the trait is used not for defense against predators, but for male-male competition during mating.) Females have no venom and have rudimentary spur nubs that drop off before maturing. Of course, females have the genes for producing ankle spurs and venom, as those genes don’t know which sex they’ll wind up in—just like human males have genes for vaginas and breasts and human females carry genes for penises. But the sex-development pathway prevents the expression of venom and spurs in females, just as it prevented me from developing a vagina.

The sex-limitation of the spurs isn’t mentioned in the Nature piece, but every biologist who knows their platypuses also knows that only the males have venom spurs. And, by the way, the echidna has some genes that used to produce venom, but they’re non-expressed “pseudogenes” that have become inactivated. That shows that the ancestral monotreme was almost certainly venomous (this isn’t mentioned in the NYT piece, either).

About those egg-yolk genes:

For instance, many birds and insects have multiple copies of a gene called vitellogenin, which is involved in the production of egg yolks.

Most mammals don’t have the vitellogenin gene, said Dr. Zhang. But the new genomes reveal that platypuses and echidnas have one copy of it, helping to explain their anomalous egg-laying — and suggesting that this gene (and perhaps the reproductive strategy itself) may have been something the rest of us lost, rather than an innovation of the monotremes. 

Well, yes, mammals do have the vitellogenin gene. In fact, our own species has three of them, but, as in other mammals they’re pseudogenes—genes that are there in the genome but are broken and not expressed. Humans and other placental mammals don’t require egg yolk because we’re nourished through the placenta, not yolks in shells. The platypus has two vitellogenin genes (described in the Nature paper as “genes”, so the statement that platypuses and echnidas have “one copy” is misleading)—they’re just not “functional” genes.

Now you may say this is quibbling, but it’s not. First of all, the statement that playtpuses have one copy of the egg yolk gene is wrong. They have two, but one doesn’t function. More important, the statement that there are nonfunctional yolk genes in all mammals says something powerful about evolution, something that I discuss in my book Why Evolution is True.  Those “vestigial” and nonfunctional genes are evolutionary remnants of our ancestors who did produce egg yolk. Why else would they be there in our genome, doing nothing? Chickens, who of course evolved from reptiles, as we did, have all three vitellogenin genes in working order.

Another error, then, is the statement “suggesting that this genes. . . may have been something the rest of us lost.” No, we didn’t lose it; it’s still there in our genomes. And there’s no “suggestion” about it: it’s sitting there in our DNA, has been sequenced, and has been shown to be nonfunctional. Finally, we KNOW that this gene is NOT an innovation of the monotremes, and have known that for a long time (e.g., see here). It was inherited from their reptilian ancestors.

This isn’t flat out erroneous science reporting, but it’s incomplete science reporting—the summary of a paper phoned in to the NYT. (I also find the Time’s summary curiously devoid of what’s really new in the paper; at least half of it reprises what we already knew.) More important, the reporter missed a good chance to give some powerful evidence for evolution, both in ourselves and in monotremes, whose genomes harbor some dead egg-yolk genes that are active in our avian and reptilian relatives. And yes, those echidnas have dead genes for venom.

h/t: Gregory

Superfluous article of the month

September 4, 2019 • 12:30 pm

Do we really need another article that telling us that evolution isn’t always “progressive”, going in a straight line towards traits that we consider “advanced”? (These are nearly always traits that humans have, like intelligence, high consciousness, and big brains.)

This form of evolution, often represented by the “straight line” diagram of human evolution shown in the new The Conversation article below, also called “orthogenesis,” is said to misrepresent evolution in several ways. It implies, for instance, that there’s an inherent directionality to evolution, which isn’t true (though in some cases, like arms races, it can approximate truth). It could be taken to imply that the directionality isn’t conferred by natural selection, but by some teleological force, like the “drive to consciousness” broached by computer scientist David Gelernter in a recent, dreadful, and grossly misleading critique of evolution. And it implies a scala naturae—a “scale of nature”—that could be (and was) taken as a ranking of how “evolved” something was. In the case of human races, the scale was used to imply that some races (invariably white ones) were more evolved than, and hence superior to, their pigmented brethren.

Click on the screenshot to read this short piece:

Perhaps I’m being too captious here. Perhaps misconceptions about evolution like this one need constant rebutting as each new generation becomes prey to scientific errors or the blandishments of creationists. Still, the three authors, all biologists, spend most of their time decrying the cartoon depiction of orthogenesis, like the one above, presenting lots of examples (easy to find), but neglecting some really interesting glosses on this idea. In fact, all they really say is that evolution doesn’t work this way, and pointing out three errors (an excerpt):

Originating with Plato and Aristotle, this view gets three main things wrong.

First, it holds that nature is organized hierarchically. It is not a random assortment of beings.

Secondly, it envisions two organizing criteria: things progress from simple to perfect and from primitive to modern.

And thirdly, it supposes there are no intermediary stages between levels in this hierarchy. Each level is a watertight compartment of similar complexity – a barnacle and a coral reef on the same rung are equally complex. No one is halfway between two steps.

Well, I’d argue that the first “error” is wrong, but is not necessarily implied by the figure, which shows straight-line evolution in a lineage, while the hierarchy comes from the branching of lineages, barely mentioned. And I’d argue as well that the progression doesn’t really imply that there are no intermediate stages. It just shows selected segments of an evolutionary lineage.

Had I written this, I would have added a few other points to flesh it out:

a). You can convert a branching bush into a straight line simply by following one line of ancestry. Here’s part of a slide I use to show that point in the evolution of the modern horse, which traces only the path to one twig on the luxuriant historical branching of equids:

The human “progression” above can be derived from picking out one lineage in the evolution from early australopithecines to modern H. sapiens, but hominin evolution was a branching bush, and many of the twigs went extinct. In fact, we are still ignorant of the exact lineage that took early hominins to modern ones.

b.) I would have added that sometimes evolution might take place in one direction, but it’s because natural selection, which could be reversed, drives it that way. No irreversible teleological forces are involved. I gave the example of predator-prey “arms races”, in which predators become ever faster, prompting the prey to also evolve fleetness. Or there might be an “open niche” in which mutations push evolution in a single direction. Brain size (and intelligence) in humans might be one example, although even here not all lineages got bigger and bigger brains: some died out and some, like H. floresiensis, might even have evolved reduced brain size as a consequence of smaller body size (the origin of this species is, of course, a mystery). Another example might be the ancestors of whales, which likely found an open niche in the sea, full of unexploited food. Ergo early whales became more and more amphibian and then fully marine. Natural selection made them that way: more marine whales presumably got more fish and experienced less competition.

c.) I would have pointed out examples in which evolution is regressive, losing features that evolved adaptively in other lineages. Fleas lost their wings, as did penguins. Tapeworms lost most of their sensory systems and their entire digestive system. Some Antarctic fish have lost their swim bladders, and the subgroup of icefish have also lost their hemoglobin, becoming the only vertebrates to lack that protein (dead hemoglobin genes still reside in their genomes, giving evidence of their ancestry). To compensate, they have also lost their scales, so that they can exchange oxygen through their skin. (By the way, I know of no good adaptive story for the loss of hemoglobin in this group).

At any rate, the misconceptions about orthogenesis give plenty of opportunity to impart lessons about and cool examples of evolution. What a pity that the three authors blew this chance (Conversation articles can be longer) to concentrate on example after example of straight-line evolution.

As I said, the article is not harmful to scientific education; in fact, it’s marginally useful. But it could have been much more useful.

h/t: Michael

Marianne Williamson’s vaccine woo

August 2, 2019 • 12:45 pm

I have to admit that when I first saw Marianne Williamson in the Democratic debates my jaw dropped. How did this woomeister, who doesn’t hold elective office and never did, manage to get on stage with credible candidates? I did know about her history of anti-vaccination efforts as well as denial of depression and other mental illnesses, as well as her attacks on “Big Pharma,” but I didn’t comport that with her being on the Big Stage with real candidates. And yet some people like her! One of them is the ever-cringeworthy David Brooks, who wrote this editorial in today’s New York Times (click on screenshot). The title alone is astounding!

How does she know how to beat Trump? With a moral uprising! By defeating the dark psychic force of collectivized hatred! Well, Ms. Williamson (and Mr. Brooks), that’s easier said than done. Where would you propose that we begin?

Here’s Brooks:

It is no accident that the Democratic candidate with the best grasp of this election is the one running a spiritual crusade, not an economic redistribution effort. Many of her ideas are wackadoodle, but Marianne Williamson is right about this: “This is part of the dark underbelly of American society: the racism, the bigotry and the entire conversation that we’re having here tonight. If you think any of this wonkiness is going to deal with this dark psychic force of the collectivized hatred that this president is bringing up in this country, then I’m afraid that the Democrats are going to see some very dark days.”

And she is right about this: “We’ve never dealt with a figure like this in American history before. This man, our president, is not just a politician; he’s a phenomenon. And an insider political game will not be able to defeat it. … The only thing that will defeat him is if we have a phenomenon of equal force, and that phenomenon is a moral uprising of the American people.”

A moral uprising of the American people might also include criticizing of those like Williamson whose anti-vaxer views would lead to the death of children.  And this is what the no-punch-pulling Orac (a surgeon) does in this new article at Respectful Insolence (click on screenshot):

In case you’re wondering about Orac’s title, first, he appears to have gotten her name wrong (I’ve made a comment on his site to that effect), though in the rest of the article he gets it right. More important, part of his article is a criticism of a somewhat exculpatory article about Williamson by science writer Faye Flam at Bloomberg.com (click on screenshot):

Faye is a friend of mine, so this hurts doubly, but I think Orac rightly rakes her over the coals for casting Williamson as a misunderstood “science skeptic” rather as a science denialist. Here’s how Faye gives Williamson a pass:

The accusation of being “anti-science” has become a popular and effective way to discredit people, at least in certain circles. Self-help guru turned presidential candidate Marianne Williamson is learning that after her debate performances.

People often end up accused of being “anti-science” when they question scientific dogma, but questioning dogma is what science is all about. Donald Trump could be more accurately labelled as anti-science for the blatant cutting of funds for important scientific studies – though even he may not be opposed to the scientific enterprise so much as he is trying to protect his friends in industry at the expense of science and people exposed to pollution.

A particularly scathing anti-Williamson critique appeared in the Daily Beast, though the author couldn’t seem to find much fault with anything said in this week’s debate, instead digging up past statements. Indeed, she has dealt with some new-age ideas that are unscientific or even antithetical to science, but not more so than much organized religion is.

Williamson seems likely to disappear from the national conversation soon, and critics are right to go after her lack of policy experience. Criticizing her, or any other candidate, on the basis of ideas and experience makes perfect sense. But trying to discredit skeptics with the label of “anti-science” is not very scientific.

Well, the response to this, especially if you know Williamson’s history as well as her weaving-and-bobbing views now that she’s been called out for her anti-vaxerism and wonky views on mental illness, is this:

Here’s the thing about science (and being “antiscience”). There’s a hierarchy, gradations, if you will, of how unscientific or antiscientific your beliefs are. Believing something for which there is no scientific evidence and, in fact, there is plenty of scientific evidence that refutes that belief is on the extreme end, as is believing such things based on conspiratorial thinking. That’s what Williamson has a long history of doing with respect to vaccines. Remember what she has said on more than one occasion?

And here’s one of MW’s tweets (and a response):

Orac also dismantles Wiliamson’s claim that chronic illnesses in children have risen to 54%, which is simply a lie. When pressed on this, or on her views that mental illness is just reified “sadness”, she tends to revert to her attacks on “Big Pharma”. Now Orac isn’t a huge fan of the pharmaceutical industry, but for Williamson it’s a displacement activity, designed to divert attention from her profoundly antiscientific views when she’s called out for lying:
Orac:

Yes, it must be conceded that there is a legitimate debate to be had over the treatment of mental health and the issue of regulatory capture in the regulation of pharmaceutical companies and their products, but Williamson’s dismissal of so much depression as “medicalizing normal grief” is a vast oversimplification and exaggeration. Of course, when Melber gets around to the issue of “skepticism” on vaccinations (a horrible horrible, horrible choice of a word for this) and tries to press her on it, we see her lay down this “I’m not antivaccine” antivaccine patter:

I think it’s an overstatement to say that I cast skepticism on vaccination. [Orac note: Actually, it’s an understatement.] On the issue of vaccinations I’m pro-vaccination, I’m pro-medicine, I’m pro-science. On all of these issues, what I’m bringing up that I think is very legitimate and should not be derided and should not be marginalized, particularly in a free society, is questions about the role of predatory Big Pharma.

I’ll take “I’m not antivaccine, I just question big pharma” for $800, Alex.

Orac has a lot to say, but even if you just skim his piece and just listen to Williamson’s flaky lucubrations, you’ll wonder why anyone takes her seriously. Is it because Americans don’t know how settled the question of vaccination safety and efficacy really is? I don’t know.

Here’s one more bit from Orac’s piece, but you should watch this video of her with Anderson Cooper first (this was posted yesterday):

Orac’s take on this:

In this segment, Anderson Cooper focused primarily on Williamson’s past statements about antidepressants and psychiatric drugs. Cooper pressed her on her past statements about antidepressants “numbing” people, pointing out quite reasonably that depression itself numbs people. In responses, Williamson goes full woo, denying that she’d ever said what she’s been documented saying and then going on:

What I’ve talked about is a normal spectrum of human despair, normal human despair, which traditionally was seen as the purview of spirituality and religion, that which gave people comfort. gave people hope and inspiration in their time of pain. And with the advent of modern psychotherapy, a lot of the baton passed from religion and spirituality to modern psychotherapy, which was an interesting transition. Then, over the last few years, very very quickly, the baton was passed again to psychopharmacology, and so a nuanced conversation was lost regarding the nature of human despair.

Holy hell. Marianne Williamson’s entire objection to modern psychopharmacology for depression is that it has pushed aside religion and spirituality as the primary means of dealing with “human despair.” Given that she’s a New Age grifter, one shouldn’t be surprised. She doesn’t like a disease-based model of clinical depression because it cuts into her grift. She even goes on to suggest that the treatment of depression is seeking to keep us from feeling normal sadness after, for instance, the death of a loved one, which is a complete mischaracterization of modern psychotherapy.

If that isn’t antiscience, I don’t know what is.

Williamson, of course, got her start by coddling religion, and has simply leveraged that into her non-goddy but still wooey spirituality.

In this case, I think that Faye’s piece is off the mark, for it does conflate healthy skepticism with bald-faced denialism. There’s a huge difference, and Faye’s conflation of these damages the public understanding of science.

And nobody should view Williamson as a viable Presidential candidate, much less a thoughtful human being.

 

 

h/t: Michael