Category: Methodology

In His Bathysphere Beebe “Maintained a Sense of Childlike Optimism”

(p. 28) Beautifully written and beautifully made, “The Bathysphere Book” is a piece of poetic nonfiction that strives to conjure up the crushing blackness of the midnight zone. Full color, overflowing with stunning illustrations of the uncanny creatures that live beyond the sun, it raises questions of exploration and wonder, of nature and humanity, and lets readers find answers on their own.

. . .

As he slipped deeper and deeper beneath the waves, Beebe bore witness to “a black so black it called his very existence into question,” and saw creatures that could be recorded only by describing them to Else Bostelmann, a painter who worked like a police sketch artist to render animals she would never see in colors like “bittersweet orange, metallic opaline green, orange rufous and orange chrome.”

. . .

. . . he maintained a sense of childlike optimism that pervades the book, cutting through the limitless cold of the sea: “Having traveled the world from the depths of the sea to the highest mountains, tramped through jungles and flown across continents, Beebe was more and more adamant that wonder was not produced by swashbuckling adventures — it was a way of seeing, an attitude toward experience that was always available. At every turn, the world’s marvels were right before our eyes.”

For the full review, see:

W. M. Akers. “Under the Sea.” The New York Times Book Review (Sunday, June 4, 2023): 28-29.

(Note: ellipses added.)

(Note: the online version of the review was updated May 31, 2023, and has the title “Deep-Sea Creatures of Bittersweet Orange and Metallic Opaline Green.”)

The book under review is:

Fox, Brad. The Bathysphere Book: Effects of the Luminous Ocean Depths. New York: Astra Publishing House, 2023.

Organisms Differ Based on How DNA’s Fluid Instructions Are Implemented by Different Cells

(p. 13) Martinez Arias, a developmental biologist, has lived and breathed the cell’s struggle to be heard over a career spanning 40-odd years. His story is one of DNA elites against hardworking, blue-collar cells. Cells, not DNA, Martinez Arias points out, determine the ripples of our fingerprints and the texture of our irises.

Martinez Arias builds his argument against the supremacy of DNA around Frankenstein-like experiments that involve borrowing a gene from one organism and dropping it into another. Take, for instance, the fruit fly PAX6 gene. When this gene is mutated, flies develop without eyes. Yet when a human version of PAX6 is swapped in for the fly gene, it makes a fly with fly eyes, not a fly with human eyes.

This is because fly cells are doing the work. Living things are much more fluid, Martinez Arias argues, than the concept of a DNA instruction manual would have us believe. An organism is less like a car, built according to a precise blueprint, he suggests, than a hobbyist’s renovation project, where the cells who live there build a deck or replace a light fixture based on the tools that happen to be lying around in the garage and whatever lumber is on sale at the store. Many of the differences between you and me are the result of accidents in time, enacted by our cells.

For the full review, see:

Alex Johnson. “Going Viral.” The New York Times Book Review (Sunday, September 17, 2023): 13.

(Note: the online version of the review has the date Aug. 15, 2023, and has the title “A Reason to Cheer for Cells and the Viruses That Feed on Them.”)

The book under review is:

Arias, Alfonso Martinez. The Master Builder: How the New Science of the Cell Is Rewriting the Story of Life. New York: Basic Books, 2023.

European Farmers Want Climate Protected by More Innovation, Not by Less Agriculture

(p. 4) To meet climate goals, some European countries are asking farmers to reduce livestock, relocate or shut down — and an angry backlash has begun reshaping the political landscape before national elections in the fall.

. . .

Those like Helma Breunissen, who runs a dairy farm in the Netherlands with her husband, say that too much of the burden is falling on them, threatening both their livelihoods and their way of life.

For almost 20 years, Ms. Breunissen has provided the Dutch with a staple product, cow’s milk, and she felt that her work was valued by society, she said. The dairy sector in the Netherlands, which also produces cheeses like Gouda and Edam, is celebrated as a cornerstone of national pride.

But the sector also produces almost half the Netherlands’ emissions of nitrogen, a surplus of which is bad for biodiversity. Ms. Breunissen and thousands of other farmers bridle that they are now labeled peak emitters.

“I was confused, sad and angry,” said Ms. Breunissen, who manages a farm of 100 cows in the middle of the country. “We are doing our best. We try to follow the rules. And suddenly, it’s like you are a criminal.”

. . .

In the Netherlands, the government has asked thousands of farmers to scale back, move or close. The authorities set aside about 24 billion euros, about $26 billion, to help farmers put in place more sustainable solutions — or to buy them out.

. . .

For Ms. Breunissen, who is 48 and works as a veterinarian in addition to her duties on the farm, none of the government-proposed options seem feasible. She is too young to quit and too old to uproot her life, she said, and the authorities have not provided enough support and information on how to change what she now does.

“There are so many questions,” she said. “The trust in the government is completely gone.”

. . .

A host of new groups are vying to displace traditional parties. They include the Farmer Citizen Movement, known by its Dutch acronym BBB, which was established four years ago.

. . .

Caroline van der Plas, the party’s co-founder, used to be a journalist in The Hague covering the meat industry, and she has never worked in farming. But she grew up in a small city in a rural area, and she said in an interview that she wanted to be “the voice of the people in rural regions who are not seen or heard” by policymakers.

She and her party have talked down the need for drastic steps to cut emissions, saying the reductions can be achieved through technological innovation. Policies should be based on “common sense,” she said, while offering no concrete solutions.

“It’s not like science says this or that,” Ms. van der Plas said, referring to how theories can change. “Science is always asking questions.”

For the full story, see:

Monika Pronczuk and Claire Moses. “New Climate Standards Have Farmers in Europe Bristling.” The New York Times, First Section (Sunday, Aug. 27, 2023): 4.

(Note: ellipses added.)

(Note: the online version of the story was updated Aug. 28, 2023, and has the title “Labeled Climate Culprits, European Farmers Rebel Over New Standards.”)

The “Woke-Mind” Is “Anti-Science, Anti-Merit and Anti-Human”

(p. 9) At various moments in “Elon Musk,” Walter Isaacson’s new biography of the world’s richest person, the author tries to make sense of the billionaire entrepreneur he has shadowed for two years — sitting in on meetings, getting a peek at emails and texts, engaging in “scores of interviews and late-night conversations.” Musk is a mercurial “man-child,” Isaacson writes, who was bullied relentlessly as a kid in South Africa until he grew big enough to beat up his bullies. Musk talks about having Asperger’s, which makes him “bad at picking up social cues.”

. . .

At one point, Isaacson asks why Musk is so offended by anything he deems politically correct, and Musk, as usual, has to dial it up to 11. “Unless the woke-mind virus, which is fundamentally anti-science, anti-merit and anti-human in general, is stopped,” he declares, “civilization will never become multiplanetary.”

. . .

The musician Grimes, the mother of three of Musk’s children (. . .), calls his roiling anger “demon mode” — a mind-set that “causes a lot of chaos.” She also insists that it allows him to get stuff done.

. . .

He is mostly preoccupied with his businesses, where he expects his staff to abide by “the algorithm,” his workplace creed, which commands them to “question every requirement” from a department, including “the legal department” and “the safety department”; and to “delete any part or process” they can. “Comradery is dangerous,” is one of the corollaries. So is this: “The only rules are the ones dictated by the laws of physics. Everything else is a recommendation.”

Still, Musk has accrued enough power to dictate his own rules. In one of the book’s biggest scoops, Isaacson describes Musk secretly instructing his engineers to “turn off” Starlink satellite internet coverage to prevent Ukraine from launching a surprise drone attack on Russian forces in Crimea. (Isaacson has since posted on X that contrary to what he writes in the book, Musk didn’t shut down coverage but denied a request to extend the network’s range.)

. . .

Isaacson believes that Musk wanted to buy Twitter because he had been so bullied as a kid and “now he could own the playground.”  . . .  Owning a playground won’t stop you from getting bullied.

For the full review, see:

Jennifer Szalai. “Self-Driving Czar.” The New York Times Book Review (Sunday, September 24, 2023): 9.

(Note: ellipses added.)

(Note: the online version of the review was updated Sept. 11, 2023, and has the title “Elon Musk Wants to Save Humanity. The Only Problem: People.”)

The book under review is:

Isaacson, Walter. Elon Musk. New York: Simon & Schuster, 2023.

Weight Loss Drugs Discovered Through “Tedious Trial and Error”

The first sentence quoted below implies that weight loss drugs are an exception in being discovered through trial and error rather than “through a logical process.” But I believe that drug discoveries in recent decades for cancer, heart disease, and Alzheimer’s also owe a lot to trial and error processes.

(p. A1) While other drugs discovered in recent decades for diseases like cancer, heart disease and Alzheimer’s were found through a logical process that led to clear targets for drug designers, the path that led to the obesity drugs was not like that. In fact, much about the drugs remains shrouded in mystery. Researchers discovered by accident that exposing the brain to a natural hormone at levels never seen in nature elicited weight loss. They really don’t know why, or if the drugs may have any long-term side effects.

“Everyone would like to say there must be some logical explanation or order in this that would allow predictions about what will work,” said Dr. David D’Alessio, chief of endocrinology at Duke, who consults for Eli Lilly among others. “So far there is not.”

. . .

(p. A16) . . . results from a clinical trial reported last week indicate that Wegovy can do more than help people lose weight — it also can protect against cardiac complications, like heart attacks and strokes.

But why that happens remains poorly understood.

“Companies don’t like the term trial and error,” said Dr. Daniel Drucker, who studies diabetes and obesity at the Lunenfeld-Tanenbaum Research Institute in Toronto and who consults for Novo Nordisk and other companies. “They like to say, ‘We were extremely clever in the way we designed the molecule,” Dr. Drucker said.

But, he said, “They did get lucky.”

. . .

After tedious trial and error, Novo Nordisk produced liraglutide, a GLP-1 drug that lasted long enough for daily injections. They named it Victoza, and the F.D.A. approved it as a treatment for diabetes in 2010.

It had an unexpected side effect: slight weight loss.

. . .

Finally, after liraglutide was approved in 2010 for diabetes, Dr. Knudsen’s proposal to study the drug for weight loss moved forward. After clinical trials, the F.D.A. approved it as Saxenda for obesity in 2014. The dose was about twice the diabetes dose. Patients lost about 5 percent of their weight, a modest amount.

. . .

Despite the progress on weight loss, Novo Nordisk continued to focus on diabetes, trying to find ways to make a longer-lasting GLP-1 so patients would not have to inject themselves every day.

The result was a different GLP-1 drug, semaglutide, that lasted long enough that patients had to inject themselves only once a week. It was approved in 2017 and is now marketed as Ozempic.

It also caused weight loss — 15 percent, which is three times the loss with Saxenda, the once-a-day drug, although there was no obvious reason for that. Suddenly, the company had what looked like a revolutionary treatment for obesity.

. . .

Researchers continue to marvel at these biochemical mysteries. But doctors and patients have their own takeaway: The drugs work. People lose weight.

For the full story, see:

Gina Kolata. “Medical Mystery Shrouds Drugs for Weight Loss.” The New York Times (Friday, August 18, 2023): A1 & A16.

(Note: ellipses added.)

(Note: the online version of the story has the date Aug. 17, 2023, and has the title “We Know Where New Weight Loss Drugs Came From, but Not Why They Work.”)

Improved AI Models Do Worse at Identifying Prime Numbers

(p. A2) . . . new research released this week reveals a fundamental challenge of developing artificial intelligence: ChatGPT has become worse at performing certain basic math operations.

The researchers at Stanford University and the University of California, Berkeley said the deterioration is an example of a phenomenon known to AI developers as drift, where attempts to improve one part of the enormously complex AI models make other parts of the models perform worse.

“Changing it in one direction can worsen it in other directions,” said James Zou, a Stanford professor who is affiliated with the school’s AI lab and is one of the authors of the new research. “It makes it very challenging to consistently improve.”

. . .

The goal of the team of researchers, consisting of Lingjiao Chen, a computer-science Ph.D. student at Stanford, along with Zou and Berkeley’s Matei Zaharia, is to systematically and repeatedly see how the models perform over time at a range of tasks.

Thus far, they have tested two versions of ChatGPT: version 3.5, available free online to anyone, and version 4.0, available via a premium subscription.

The results aren’t entirely promising. They gave the chatbot a basic task: identify whether a particular number is a prime number. This is the sort of math problem that is complicated for people but simple for computers.

Is 17,077 prime? Is 17,947 prime? Unless you are a savant you can’t work this out in your head, but it is easy for computers to evaluate. A computer can just brute force the problem—try dividing by two, three, five, etc., and see if anything works.

To track performance, the researchers fed ChatGPT 1,000 different numbers. In March, the premium GPT-4, correctly identified whether 84% of the numbers were prime or not. (Pretty mediocre performance for a computer, frankly.) By June its success rate had dropped to 51%.

. . .

The phenomenon of unpredictable drift is known to researchers who study machine learning and AI, Zou said. “We had the suspicion it could happen here, but we were very surprised at how fast the drift is happening.”

For the full commentary, see:

Josh Zumbrun. “THE NUMBERS; AI Surprise: It’s Unlearning Basic Math.” The Wall Street Journal (Saturday, Aug. 5, 2023): A2.

(Note: ellipses added.)

(Note: the online version of the commentary has the date August 4, 2023, and has the title “THE NUMBERS; Why ChatGPT Is Getting Dumber at Basic Math.”)

Bullshit Is Worse Than a Lie

(p. A17) Professor Frankfurt became best known for a single, irreverent paper largely unrelated to his life’s main work.

The paper, written in the mid-1980s under the same title as his eventual book, discussed what to his mind was a pervasive but underanalyzed feature of our culture: a form of dishonesty akin to lying but even less considerate of reality. Whereas the liar is at least mindful of the truth (if only to avoid it), the “bullshitter,” Professor Frankfurt wrote, is distinguished by his complete indifference to how things are.

Whether its purveyor is an advertiser, a political spin doctor or a cocktail-party blowhard, he argued, this form of dishonesty is rooted in a desire to make an impression on the listener, with no real interest in the underlying facts. “By virtue of this,” Professor Frankfurt concluded, “bullshit is the greater enemy of truth than lies are.”

. . .

For all this sang-froid, Professor Frankfurt was heartfelt in his philosophical pursuits. Throughout his career, he was drawn to lines of inquiry — about freedom, love, selfhood and purpose — that he said appealed to him not only as an academic but also “as a human being trying to cope in a modestly systematic manner with the ordinary difficulties of a thoughtful life.”

For the full obituary, see:

James Ryerson. “Harry G. Frankfurt, a Philosopher Eager to Cut the Bull, Dies at 94.” The New York Times (Tuesday, July 18, 2023): A17.

(Note: ellipsis added.)

(Note: the online version of the obituary has the date July 17, 2023, and has the title “Harry G. Frankfurt, Philosopher With a Surprise Best Seller, Dies at 94.”)

Frankfurt’s best-known book is:

Frankfurt, Harry G. On Bullshit. Princeton, NJ: Princeton University Press, 2005.

Scientists Had Political Motives for Dismissing Wuhan Lab-Based Covid Origin

(p. A17) On March 17, 2020, the journal Nature Medicine published a paper by five scientists, “The Proximal Origin of SARS-CoV-2,” that dismissed “any type of laboratory based scenario” for the origin of the pandemic. It was cited by thousands of news outlets to claim that the virus emerged naturally. But Slack messages and emails subpoenaed and released by the House Oversight Select Subcommittee on the Coronavirus Pandemic suggest that some of the authors didn’t believe their own conclusions. Before, during and even after the publication of their paper, they worried privately that Covid-19 was caused by a laboratory escape, perhaps even of a genetically engineered virus.

. . .

On April 16, a month after publication, Mr. Andersen wrote that “I’m still not fully convinced that no culture was involved” and “we also can’t fully rule out engineering”—i.e., that the virus not only was released from the lab but had been genetically manipulated there. He worried about the Wuhan lab’s research on live SARS-like viruses from bats at low biosafety levels: “it’s definitely concerning work, no question about it.”

So why did they publish a paper denying that laboratory origin was plausible? The answer may lie in their messages. In early February 2020, Mr. Rambaut wrote: “Given the s— show that would happen if anyone serious accused the Chinese of even accidental release, my feeling is we should say that given there is no evidence of a specifically engineered virus, we cannot possibly distinguish between natural evolution and escape so we are content to ascribing it to natural processes.”

Mr. Andersen replied: “I totally agree that that’s a very reasonable conclusion. Although I hate when politics is injected into science—but it’s impossible not to.”

. . .

To adjust the conclusions in a scientific paper for political reasons isn’t part of the scientific process. The world was misled with serious consequences.

For the full commentary, see:

Matt Ridley and Alina Chan. “The Covid Lab-Leak Deception.” The Wall Street Journal (Thursday, July 27, 2023): A17.

(Note: ellipses added.)

(Note: the online version of the commentary has the date July 26, 2023, and has the same title as the print version.)

Scientist Latta Knows, but Cannot Prove, That Ivory-Billed Woodpecker Is Not Extinct

I respect and admire Dr. Latta for having the courage to affirm what he saw with his own two eyes. Other scientists should not be so quick to ‘give him the bird’ (so to speak ;).

(p. A19) If there’s new hope, it’s blurry. What’s certain: The roller coaster tale of the ivory-billed woodpecker, a majestic bird whose presumed extinction has been punctuated by a series of contested rediscoveries, is going strong.

The latest twist is a peer-reviewed study Thursday [May 18, 2023] in the journal Ecology and Evolution presenting sighting reports, audio recordings, trail camera images and drone video. Collected over the last decade in a Louisiana swamp forest, the precise location omitted for the birds’ protection, the authors write that the evidence suggests the “intermittent but repeated presence” of birds that look and behave like ivory-billed woodpeckers.

But are they?

“It’s this cumulative evidence from our multiyear search that leaves us very confident that this iconic species exists, and it persists in Louisiana and probably other places as well,” said Steven C. Latta, one of the study’s authors and director of conservation and field research at the National Aviary, a nonprofit bird zoo in Pittsburgh that helps lead a program that searches for the species.

But Dr. Latta acknowledges that no single piece of evidence is definitive, and the study is carefully tempered with words like “putative” and “possible.”

. . .

. . . Dr. Latta, the study co-author, insisted that he had seen one clearly with his own eyes. He was in the field in 2019 to set up recording units, and he figures he spooked the bird. As it flew up and away, he got a close, unimpeded view of its signature markings.

“I couldn’t sleep for, like, three days,” Dr. Latta said. “It was because I had this opportunity and I felt this responsibility to establish for the rest of the world, or at least the conservation world, that this bird actually does exist.”

For the full story, see:

Catrin Einhorn. “Experts Strive to Prove ‘This Bird Actually Does Exist’.” The New York Times (Friday, May 19, 2023): A19.

(Note: ellipses, and bracketed date, added. The online version of the article says that the print version appears on p. 21. My national edition of the print version appeared on p. 19.)

(Note: the online version of the story was updated May 18, 2023, and has the title “A Vanished Bird Might Live On, or Not. The Video Is Grainy.”)

The peer-reviewed paper, co-authored by Latta and mentioned above, is:

Latta, Steven C., Mark A. Michaels, Thomas C. Michot, Peggy L. Shrum, Patricia Johnson, Jay Tischendorf, Michael Weeks, John Trochet, Don Scheifler, and Bob Ford. “Multiple Lines of Evidence Suggest the Persistence of the Ivory-Billed Woodpecker (Campephilus Principalis) in Louisiana.” Ecology and Evolution 13, no. 5 (2023): e10017 https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.10017.

Data Set Too Small to Support Claim of 250,000 Annual ER Deaths Due to Misdiagnosis

(p. A17) A shocking headline recently claimed that every year 250,000 people in the U.S. die after misdiagnosis in the emergency room. Even more shocking, the statistic was extrapolated from the death of one man—in a Canadian emergency room more than a decade ago.

. . .

The statistical methods used to arrive at the report’s estimate of 250,000 deaths are very bad, resulting in inaccurate findings that exaggerate potential harm in ERs. The estimate was derived from a single study that included only 503 patients discharged from two Canadian emergency rooms from August to December 2004. Researchers found that among the 503 patients, one person unexpectedly died related to a delay in diagnosis by an ER physician. The patient had signs of an aortic dissection—a tear in the major vessel that carries blood from the heart. For reasons we don’t know, the diagnosis was delayed for seven hours.

The goal of the Canadian study was to measure all kinds of medical errors, not to estimate the death rate from erroneous or late diagnoses. The sample size wasn’t big enough for that. Had nobody in the study sample died, would that mean that ERs never make fatal errors? Obviously not.

The AHRQ report misused this single death to estimate a death rate across the entire U.S. Dividing one death by 503 patients, the researchers estimate a death rate of 0.2%. They then multiply 0.2% by total annual ER visits in the U.S.—130 million—and come up with 250,000 deaths.

For the full commentary, see:

Kristen Panthagani. “A Study Sounds a False Alarm About America’s Emergency Rooms.” The Wall Street Journal (Friday, Dec. 30, 2022): A17.

(Note: ellipsis added.)

(Note: the online version of the commentary has the date December 29, 2022, and has the same title as the print version.)

China Still Seeks to Censor International Journals and Databases on Covid

(p. A1) Early in 2020, on the same day that a frightening new illness officially got the name Covid-19, a team of scientists from the United States and China released critical data showing how quickly the virus was spreading, and who was dying.

The study was cited in health warnings around the world and appeared to be a model of international collaboration in a moment of crisis.

Within days, though, the researchers quietly withdrew the paper, which was replaced online by a message telling scientists not to cite it. A few observers took note of the peculiar move, but the whole episode quickly faded amid the frenzy of the coronavirus pandemic.

What is now clear is that the study was not removed because of faulty research. Instead, it was withdrawn at the direction of Chinese health officials amid a crackdown on science. That effort kicked up a cloud of dust around the dates of early Covid cases, like those reported in the study.

“It was so hard to get any information out of China,” said one of the authors, Ira Longini, of the University of Florida, who described the back story of the removal publicly for the first time in a recent interview. “There was so much covered up, and so much hidden.”

That the Chinese government muzzled scientists, hindered international investigations and censored online discussion of the pandemic is well documented. But Beijing’s stranglehold on information goes far deeper than even many pandemic researchers are aware of. Its censorship campaign has targeted international journals and scientific databases, shaking the foundations of shared scientific knowledge, a New York Times investigation found.

Under pressure from their government, Chinese scientists have withheld data, withdrawn genetic sequences from public databases and altered crucial details in journal submissions. Western journal editors enabled those efforts by agreeing to those edits or withdrawing papers for murky reasons, a review by The Times of over a dozen retracted papers found.

Groups including the World Health Organization have given credence to muddled data and inaccurate timelines.

For the full story, see:

Mara Hvistendahl and Benjamin Mueller. “China Censors Are Thwarting Covid Science.” The New York Times (Monday, April 24, 2023): A1 & A9.

(Note: the online version of the story has the date April 23, 2023, and has the title “Chinese Censorship Is Quietly Rewriting the Covid-19 Story.”)