Category: Science

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.”)

Medical Research Focuses More on Antibiotics Than on Phages Partly Because Antibiotics Are Easier to Patent

(p. 13) While recent events have provided a painful reminder of the very bad viruses that prey on us, Tom Ireland’s “The Good Virus” is a colorful redemption story for the oft-neglected yet incredibly abundant phage, and its potential for quelling the existential threat of antibiotic resistance, which scientists estimate might cause up to 10 million deaths per year by 2050. Ireland, an award-winning science journalist, approaches the subject of his first book with curiosity and passion, delivering a deft narrative that is rich and approachable.

In the hands of d’Herelle and others, the phage became a potent tool in the fight against cholera. But, in the 1940s, when the discovery of the methods to produce penicillin at an industrial scale led to the “antibiotic era,” phage therapy came to be seen as quackery in Europe and America, in part, Ireland suggests, because antibiotics, unlike phages, fit the mold of capitalist society.

Capitalists love patents. A funny quirk of the patent system is that you cannot patent entire natural things, but you can sometimes patent the way you extract their byproducts. The first antibiotics, being the secretions of fungi, were easier to patent in the United States than phages, which were whole viruses.

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:

Ireland, Tom. The Good Virus: The Amazing Story and Forgotten Promise of the Phage. New York: W. W. Norton & Company, 2023.

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.”)

“Unexpected” New Evidence of the Ubiquity and Resilience of Life on Earth

(p. D3) Off the western shores of Central and South America, there is a Lovecraftian, lava-licked realm thousands of feet beneath the ocean. There, on the seafloor, volcanically powered exhaust ports known as hydrothermal vents fire off jets of water that reach temperatures of up to 700 degrees Fahrenheit. While the surfaces and peripheries of these vents have long been known to host a diverse mosaic of life, scientists had never known animals to find a home beneath these hellish geysers.

But that changed in July [2023] when a diving robot overturned volcanic bedrock pockmarked with hydrothermal vents and revealed an explosion of animal life — including an abundance of tubeworms, bizarre creatures that resemble sentient spaghetti.

“This is the first time that animal life was found below the surface” of hydrothermal vents, said Monika Bright, an ecologist at the University of Vienna and lead scientist on the expedition.

. . .

Much about these unusual habitats is a mystery. But, like many revelations found at the bottom of the sea, this discovery once again pushes the boundaries of what scientists consider possible — perhaps even normal — for life on Earth.

Hydrothermal vents, first discovered off the Galápagos Islands, are Dalí-esque chimneys and chasms that often grow atop or close to midoceanic ridges — vast volcanic fissures in the seafloor made by the divergence of two tectonic plates. Deep below, the magmatic heat roasts percolating seawater, which jets back out into the water column as superheated, mineral-rich soups.

Despite their extreme natures, these vents are metropolises of strange critters. Common among them are tubeworms, which start life as free-swimming larvae before becoming immobile adults that grow to several feet in length and that are fed by sulfur-eating bacteria living in their guts.

Dr. Bright suspected that these wiggly weirdos could also be found beneath the vents. “It’s kind of a really crazy idea I had,” she said.

. . .

. . . for Dr. Bright, Earth is all that matters. “I’m not thinking of other planets and moons — I’m thinking that there’s so much mystery to be discovered in our Earth,” she said. “I feel like I know this place. I’ve studied this place for 30 years. And still, you can find something unexpected.”

For the full story, see:

Robin George Andrews. “Odd Creatures Found Under Oceanic Vents.” The New York Times (Tuesday, August 15, 2023): D3.

(Note: ellipses, and bracketed years, added.)

(Note: the online version of the story has the date Aug. 8, 2023, and has the title “Under a Hellish Ocean Habitat, Bizarre Animals Are Lurking.”)

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.)

As Worms Return to Arctic, Some Life Forms Will Thrive and Others Will Not

(p. A1) Worms are on the move, and people are nervous.

That’s because they’re taking over territory in the Far North that’s been wormless since the last ice age.

. . .

Because of changes in the chemistry and physics of the ground, grasses and shrubby plants tend to thrive, taking over from tundra mosses and lichens. That’s good news for the lemmings and voles that favor such plants, according to Hanna Jonsson, an ecology researcher at Umea University. But probably not good for other herbivores that might not adapt easily to a change in available food.

For the full story, see:

Sofia Quaglia. “Worms Haven’t Lived in the Arctic Since the Last Ice Age. But Now, They’re Back.” The New York Times (Saturday, July 15, 2023): A10.

(Note: ellipsis added.)

(Note: the online version of the story has the date July 14, 2023, and has the title “Some Squirmy Stowaways Got to the Arctic. And They Like It There.”)

Seaweed Blob Disappears as Unpredictably as It First Appeared

(p. 19) For months, Florida’s usually picturesque coast was plagued by a rotting tangle of seaweed, known as sargassum. Then, as quickly as the stinking mass arrived, it began to disappear.

. . .

Last month, the amount of sargassum in the Gulf of Mexico dropped by a staggering 75 percent, Dr. Hu and colleagues at the University of South Florida Optical Oceanography Lab noted in a bulletin published [June 30, 2023].

. . .

But scientists don’t know why the decline was so rapid. One theory is that strong winds caused by recent tropical storms could have dissipated the sargassum into smaller clumps, or sunk it to the ocean floor, Dr. Hu said, making it hard to see from a satellite. “There could be other reasons, we just don’t know,” he added.

For the full story, see:

Livia Albeck-Ripka. “The Blob That Threatened Florida . . . Is Disappearing.” The New York Times, First Section (Sunday, July 9, 2023): 19.

(note: ellipses in story added; ellipsis in title in original.)

(Note: the online version of the story has the date July 7, 2023, and has the title “Good News, Florida. The Giant Seaweed Blob Has Shrunk.” The bracketed date was in the print, but not the online, 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.

Mice on Taurine Lived 10% Longer and Looked Healthier

(p. A3) Scientists are exploring a new biological link to longer life.

Boosting levels of an amino acid called taurine made mice and worms live longer, according to research published Thursday [June 7, 2023] in the journal Science. Middle-aged monkeys given taurine supplements became healthier, researchers said. In humans, lower levels of taurine were associated with age-related problems.

“This is a very promising molecule,” said Vijay Yadav, an assistant professor of genetics and development at Columbia University, who co-wrote the paper.

People have been searching for life-extending substances for millennia. Other recent studies have explored antiaging properties of compounds including resveratrol, found in red wine, and the immunosuppressive drug rapamycin. Yadav said he first suspected taurine’s connection with aging over a decade ago when his lab compared the contents of blood drawn from people of different ages.

. . .

Researchers gave daily doses of taurine to hundreds of 14-month-old mice, considered middle-aged, and compared their average lifespans to mice that didn’t get extra taurine. The female mice given taurine lived 12% longer on average and male mice that got taurine lived 10% longer, researchers said.

Mice that received taurine also appeared to be healthier.

For the full story, see:

Dominique Mosbergen. “Amino Acid Found To Slow Down Aging.” The Wall Street Journal (Friday, June 9, 2023): A3.

(Note: ellipsis, and bracketed date, added. The online version is longer, but the passages quoted above appear in both versions.)

(Note: the online version of the story was updated June 9, 2023, and has the title “Is Taurine the Key to Longer Life? It Made Monkeys Healthier.”)

The Science paper on taurine mentioned above is:

Singh, Parminder, Kishore Gollapalli, Stefano Mangiola, Daniela Schranner, Mohd Aslam Yusuf, Manish Chamoli, Sting L. Shi, Bruno Lopes Bastos, Tripti Nair, Annett Riermeier, Elena M. Vayndorf, Judy Z. Wu, Aishwarya Nilakhe, Christina Q. Nguyen, Michael Muir, Michael G. Kiflezghi, Anna Foulger, Alex Junker, Jack Devine, Kunal Sharan, Shankar J. Chinta, Swati Rajput, Anand Rane, Philipp Baumert, Martin Schönfelder, Francescopaolo Iavarone, Giorgia di Lorenzo, Swati Kumari, Alka Gupta, Rajesh Sarkar, Costerwell Khyriem, Amanpreet S. Chawla, Ankur Sharma, Nazan Sarper, Naibedya Chattopadhyay, Bichitra K. Biswal, Carmine Settembre, Perumal Nagarajan, Kimara L. Targoff, Martin Picard, Sarika Gupta, Vidya Velagapudi, Anthony T. Papenfuss, Alaattin Kaya, Miguel Godinho Ferreira, Brian K. Kennedy, Julie K. Andersen, Gordon J. Lithgow, Abdullah Mahmood Ali, Arnab Mukhopadhyay, Aarno Palotie, Gabi Kastenmüller, Matt Kaeberlein, Henning Wackerhage, Bhupinder Pal, and Vijay K. Yadav. “Taurine Deficiency as a Driver of Aging.” Science 380, no. 6649 (June 9, 2023): eabn9257.