Archive for The language of science

35%, 3%, whatever…

"Straight talk on the FDA’s tumultuous weekend — and new questions about its independence", Stat 8/24/2020:

Matt Herper: So for those just back from a tour of Jupiter’s moons, last night the FDA granted emergency use authorization of convalescent plasma to treat patients with Covid-19. Trump characterized the decision as a major breakthrough. FDA Commissioner Stephen Hahn, who joined him at a news conference to announce the decision, backed him up — but he also misspoke, claiming that giving plasma would help 35 out of 100 people treated.

Adam Feuerstein: Misspoke is being kind. Hahn grossly mischaracterized the benefit of convalescent plasma on Sunday night. I’ll just quote him here: “A 35% improvement in survival is a pretty substantial clinical benefit. What that means is — and if the data continue to pan out — 100 people who are sick with Covid-19, 35 would have been saved because of the administration of plasma.” […]

Matt: That number should be at best 5 out of 100 people. To my eye, it’s more like 3 out of 100 people. And all that is from subgroups of an observational study, so it should be taken with a grain of salt.

Researchers didn’t compare patients who got plasma to a control group. They compared those who got the drug early to those who got it late, and between high levels of antibodies in the plasma and low ones. For the main subset in the study, which was led by the Mayo Clinic, mortality at seven days was 11% for those who got lots of antibodies, versus 14% for those who got few. That’s three out of 100 — again, with a grain of salt.

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Translating "phenotypically diverse"

Michael Marshall, "The hidden links between mental disorders", Nature 5/5/2020:

Perhaps there are several dimensions of mental illness — so, depending on how a person scores on each dimension, they might be more prone to some disorders than to others. An alternative, more radical idea is that there is a single factor that makes people prone to mental illness in general: which disorder they develop is then determined by other factors. Both ideas are being taken seriously, although the concept of multiple dimensions is more widely accepted by researchers.

The details are still fuzzy, but most psychiatrists agree that one thing is clear: the old system of categorizing mental disorders into neat boxes does not work.

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Conceptual zombies and vampires

Lisa Feldman Barrett, "Zombie ideas", Observer 10/2019:

It’s October, a month auspicious for All Hallow’s Eve and everything spooky. Accordingly, our topic for this month is … zombies. Not the charmingly decayed corpses you encounter in movies and books, but zombie ideas. According to the economist Paul Krugman (2013), a zombie idea is a view that’s been thoroughly refuted by a mountain of empirical evidence but nonetheless refuses to die, being continually reanimated by our deeply held beliefs. […]

If you think that formal science training will zombie-proof your mind, you’re out of luck, my friend. Hordes of zombie ideas flourish in science (Brockman, 2015). They also fester in our own field, quietly biding their time in peer-reviewed papers and textbooks, waiting to infect another generation of unsuspecting psychological scientists.

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Quantum Bullshit Detector

Twitter is a good medium for this:

 

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The life cycle of unicorns

Maybe the tide is turning against "Gene for X" thinking — Ed Yong, "A Waste of 1,000 Research Papers", 5/17/2019:

Decades of early research on the genetics of depression were built on nonexistent foundations. How did that happen?

In 1996, a group of European researchers found that a certain gene, called SLC6A4, might influence a person’s risk of depression.

[…]

But a new study—the biggest and most comprehensive of its kind yet—shows that this seemingly sturdy mountain of research is actually a house of cards, built on nonexistent foundations.

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"Instant replay" and intellectual referees

The title of a post at MedPage Today echoes the widely negative reaction to obviously blown calls in the recent NFL conference title games — "Is Journal Peer-Review Now Just a Game? Milton Packer wonders if the time has come for instant replay":

Many believe that there is something sacred about the process by which manuscripts undergo peer-review by journals. A rigorous study described in a thoughtful paper is sent out to leading experts, who read it carefully and provide unbiased feedback. The process is conducted with honor and in a timely manner.

It sounds nice, but most of the time, it does not happen that way.

For some comments about the process from the perspective of editors, reviewers, and authors, see the rest of Packer's post. His experience is in the biomedical field, but the situation is similar in other fields. Amazingly bad stuff is often published in respectable and even eminent journals, and genuinely insightful work can be delayed for years by painfully slow interactions with inattentive and dubiously competent reviewers.

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Group differences

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Language machinery

Xavier Marquez, "Stalin as Reviewer #2", Abandoned Footnotes 117/2018:

Most people reading this blog probably know about Trofim Lysenko, who, with Stalin’s help, set back Soviet genetics in the late 1940s, preventing any discussion of Mendelian inheritance. Yet Stalin’s influence on Soviet scholarship after WWII was much more far reaching. He intervened in disputes concerning philosophy, physics, physiology, linguistics, and political economy; in fact one of the epithets by which he was sometimes referred in the press was “the coryphaeus of science”, i.e., the leader of the chorus of Soviet science. (Lysenko himself used the term in his eulogy for Stalin in 1953, though it was first used in 1939).

Most of these interventions were editorial in character. He edited pre-publication drafts of articles and books, often in close consultation with their authors and at great length (he was actually a decent editor), and occasionally provided feedback on published and unpublished work. And he did this despite the fact that he was the undisputed ruler of one of the victors of World War II, a country that was facing the gigantic task of reconstruction after one of the most destructive conflicts in human history. In short, he was the editor and reviewer from hell.

The story of Stalin’s intervention into Soviet linguistics is particularly funny, at least in the morbid way that anything from that time can be funny. And it also brings out some interesting points about how official ideological commitments both constrained and enabled Stalin and Stalinism.

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Replicate vs. reproduce (or vice versa?)

Lorena Barba, "Terminologies for Reproducible Research", arXiv.org 2/9/2018:

Reproducible research—by its many names—has come to be regarded as a key concern across disciplines and stakeholder groups. Funding agencies and journals, professional societies and even mass media are paying attention, often focusing on the so-called "crisis" of reproducibility. One big problem keeps coming up among those seeking to tackle the issue: different groups are using terminologies in utter contradiction with each other. Looking at a broad sample of publications in different fields, we can classify their terminology via decision tree: they either, A—make no distinction between the words reproduce and replicate, or B—use them distinctly. If B, then they are commonly divided in two camps. In a spectrum of concerns that starts at a minimum standard of "same data+same methods=same results," to "new data and/or new methods in an independent study=same findings," group 1 calls the minimum standard reproduce, while group 2 calls it replicate. This direct swap of the two terms aggravates an already weighty issue. By attempting to inventory the terminologies across disciplines, I hope that some patterns will emerge to help us resolve the contradictions.

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Belles infidèles in the neuroscience of bilingualism

Following up on "Citation crimes and misdemeanors" (9/9/2017), Breffni O'Rourke sent in a link to Michel Paradis, "More belles infidèles — or why do so many bilingual studies speak with forked tongue?", Journal of Neurolinguistics 2006:

This note reports misquotations, misinterpretations, misrepresentations, inaccuracies and plain falsehoods found in the literature on the neuroscience of bilingualism. They are astounding in both number and kind. Authors cite papers that do not exist, or that exist but are absolutely irrelevant to, or even occasionally argue against, the point they are cited to support; or they attribute a statement to the wrong source, sometimes to a person who has vehemently and persistently argued against it. Obvious errors are quoted for years by numerous authors who have not read the original paper, until somebody blows the whistle — and even then, some persevere. As Darwin [Darwin, C. (1872). The origin of species. 6th edition. New York: A. L. Burt.] put it: ‘great is the power of steady misrepresentation’.

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Citation crimes and misdemeanors

Terry Provost wrote to express interest in the topic of "citation plagiarism", linking to a couple of Bill Poser's LLOG posts ("Citation plagiarism", 6/15/2007; "Citation Plagiarism Once Again", 4/23/2008), and noting that "yours was one of very few mentions of the topic I found". Provost points to a somewhat more recent article on a related topic (Charlie Tyson, "Academic Urban Legends", Inside Higher Ed 8/6/2014), and added "Bottom line, I think the subject is quite important, as concerns things like the Jick letter, NEJM".

That's a reference to a letter reporting only four cases of addiction in 11,882 hospital patients who were given narcotics: Jane Porter and Hershel Jick, "Addiction rare in patients treated with narcotics", New England Journal of Medicine 1980. The idea seems to be that a harmful conclusion was spread by people who cited the letter without considering its content — see Taylor Haney, "Doctor Who Wrote 1980 Letter On Painkillers Regrets That It Fed The Opioid Crisis", NPR 6/16/2017.

I'm following up on this note because Bill Poser's old LLOG post no longer accepts comments, and so Terry Provost added his remarks as a comment on a randomly selected recent article, which is something we discourage. This new post gives Mr. Provost a chance to say his piece. (The reason for closing comments on old articles is that we were logging about 10,000 spam comments per day, before we closed comments on posts more than a couple of weeks old. We still get plenty of spam comments, but the number is more manageable, since there are fewer targets. )

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Unintended consequences: What is a "clinical trial"?

More than 2,400 researchers have now signed an "Open Letter to NIH Director Francis Collins" that starts like this:

We are writing to request that NIH delay implementation of its policy that sweeps basic science into a clinical trials framework until adequate feedback about its impact is obtained from the affected scientific community. We wholeheartedly agree with NIH’s goals of increasing scientific transparency and rigor, but we ask that you consider alternative mechanisms to accomplish those goals that would have fewer adverse effects on basic research.

The background is a new definition of what counts as a "clinical trial", to be enforced starting 1/1/2018 ("NIH's Definition of a Clinical Trial"):

A research study in which one or more human subjects are prospectively assigned to one or more interventions (which may include placebo or other control) to evaluate the effects of those interventions on health-related biomedical or behavioral outcomes.

Interpreted literally, this means that a study of priming effects on speech perception in healthy undergraduate students might count as a "clinical trial", since "human subjects are prospectively assigned to one or more interventions" (the priming part), and speech perception is a "health-related biomedical or behavioral outcome". Or maybe not. NIH has given some bizarrely irregular examples of how to interpret this rather general definition — thus vision and memory in adults are apparently "health-related outcomes" but learning in children is not.

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Death by french fries

The Daily Telegraph did not do much for its reputation, at least in my eyes, when it confused the defense with the prosecution after a celebrity sexual assault mistrial. Nor when it recently consulted me about whether there were grammar mistakes on a banknote, learned that there clearly were not, but went ahead and published the claim that there were anyway. Now for a sample of the Telegraph's science reporting, written by Adam Boult, who I suspect didn't complete his statistics course:

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