Science
Antibiotics wreak havoc on the gut. Can we kill the bad bugs and spare the good ones?
Inside every human is a thriving zoo of bacteria, fungi, viruses and other microscopic organisms collectively known as the microbiome. Trillions of microbes live in the digestive tract alone, a menagerie estimated to contain more than 1,000 species.
This ecosystem of tiny stuff affects our health in ways science is only beginning to understand, facilitating digestion, metabolism, the immune response and more. But when serious infection sets in, the most powerful antibiotics take a merciless approach, wiping out colonies of beneficial bacteria in the digestive tract and often prompting secondary health problems.
“Increasingly, researchers are recognizing the benefits of protecting the human gut microbiome, particularly because its integrity and diversity is linked to metabolic influences on mental health and physical health conditions,” said Dr. Oladele A. Ogunseitan, a professor of population health and disease prevention at UC Irvine.
Drug-resistant bugs are evolving faster than new medicines are being developed, rendering the current arsenal of medicines increasingly ineffective. But the more we understand about the microbiome, the clearer it is that we need antibiotics that are discerning in their targets.
With that goal in mind, a chemistry team at the University of Illinois Urbana-Champaign is experimenting with a compound that attempts to address both problems. The antibiotic, lolamicin, both successfully vanquished several drug-resistant pathogens in mice while sparing the animals’ microbiome. The results were published in the journal Nature.
“Only recently has it been recognized that killing these [beneficial] bacteria is having many deleterious effects on patients,” said Paul J. Hergenrother, a chemistry professor at the University of Illinois Urbana-Champaign who co-led the study. “We have been interested for some time in finding antibiotics that would be effective without killing the good bacteria.”
The team set out to create an antibiotic that would both preserve the gut microbiome while targeting gram-negative bacteria, a particularly hardy category of superbugs. Encased in both an inner and outer membrane that antibiotics struggle to cross, gram-negative bacteria are resistant to most currently available therapies. They are responsible for the majority of the estimated 35,000 deaths in the U.S. each year from drug-resistant infections, according to the U.S. Centers for Disease Control and Prevention.
Worldwide, antimicrobial resistance kills an estimated 1.27 million people directly every year and contributes to the deaths of millions more.
Not all gram-negative bugs make us sick. Bacteria populations in the average human gut are roughly split between gram-negative and gram-positive types, said Kristen Munoz, a former doctoral student at the University of Illinois who co-led the study.
Broad spectrum antibiotics can’t tell which bugs to spare, she said. As a result, anything strong enough to treat a bad infection “is going to wipe out a good amount of your gut microbiome,” she said, even though they “aren’t doing anything wrong.”
The team focused its search for a new drug on compounds that suppress the Lol system, which shuttles lipoproteins between the inner and outer membranes in gram-negative bacteria.
The Lol system’s genetic code looks different in harmful bacteria than it does in beneficial ones, which suggested to researchers that medicines that targeted the Lol system would be able to distinguish good bugs from bad ones.
The team designed multiple versions of these Lol-inhibiting compounds. When tested against 130 drug-resistant strains of Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae, one in particular proved especially potent.
They tested this antibiotic, which they named lolamicin, on mice that had been infected with drug-resistant strains of septicemia or pneumonia. All of the mice with septicemia survived after receiving lolamicin, as did 70% of the mice with pneumonia.
To measure the effect on gut bacteria, the researchers gave healthy mice either lolamicin, a placebo or one of two common antibiotics, amoxicillin and clindamycin. After collecting baseline stool samples, they sampled the animals’ poop seven, 10 and 31 days after treatment.
Mice treated with amoxicillin or clindamycin had lower beneficial bacteria counts and less diversity of gut bacteria. In contrast, the guts of lolamicin-treated mice appeared largely the same.
“It was exciting to see that lolamicin did not really cause any changes in the microbiome, whereas the other clinically used antibiotics did,” Munoz said.
A disrupted microbiome can have immediate consequences for people battling infection. When beneficial microbes are decimated, dangerous bugs have fewer competitors and secondary infections can take hold.
Clostridium difficile is a notorious opportunistic pathogen, so the researchers did an experiment where they exposed mice treated with lolamicin, amoxicillin or clindamycin to C. difficile. The mice who took standard antibiotics were soon crawling with C. difficile. The lolamicin mice showed little to no infection.
The lab hopes to one day take lolamicin or a version of it to clinical trials, Hergenrother said. (Munoz received her doctorate last year and now works as a scientific analyst in Los Angeles.) Yet these are still early days for the drug. While the concept of a discerning antibiotic is a welcome development, it must clear significant barriers before it could make a difference for patients.
“Distinguishing a quote-unquote ‘bad bug’ from a quote-unquote ‘good bug’ is not always as straightforward as it may seem,” said Dr. Sean Spencer, a Stanford University gastroenterologist and physician scientist who was not involved with the research.
Some beneficial bugs in the gut bear a striking genetic resemblance to harmful pathogens, he said. Others are benign in some contexts and dangerous in others: “In a critically ill individual, a good bug can do bad things.”
Years can pass between a new antibiotic’s proof of concept and its entry to the market, and the vast majority never make it to the end of that pipeline. It’s also not clear how easily or how quickly bacteria will develop resistance, which is perhaps the most formidable obstacle that lolamicin or any new antibiotic faces.
“One of the biggest problems is that bacteria are so smart. You can tackle one particular protein system or protein target in bacteria, but they will quickly find a resistance mechanism,” Munoz said. “They just have so many inherent mechanisms to overcome antibiotics.”
Science
5 Great Stargazing Trains
Stargazing, it turns out, doesn’t have to be a stationary activity.
On railway lines around the world, from the Arctic Circle to New Zealand, a select set of evening train excursions take riders deep into dark-sky territory — some en route to remote station stops decked out with telescopes, others featuring onboard astronomers.
These five rail journeys (all of which are accessible) range from two- to three-hour desert outings to a hunt for the northern lights. One route even has a planetarium on rails. All promise a renewed appreciation of train travel — and of our pale blue dot’s improbable place in the cosmos.
Nevada
The Great Basin Star Train
Any stargazing train worth its salt requires one thing: a dark sky. The Star Train resoundingly checks that box, traveling through a part of eastern Nevada that is one of the least-populated places in the lower 48.
Run by the Nevada Northern Railway in partnership with nearby Great Basin National Park, the train departs the historic East Ely Depot, in Ely, Nev., early enough in the evening to catch the sunset over the Steptoe Valley, and then cruises through darkening skies to its destination: a remote corner of the desert appropriately called Star Flat, where a stargazing platform outfitted with telescopes awaits. There, riders disembark (equipped with red-light necklaces to help preserve their night vision) and take turns viewing the cosmos, guided by professional astronomers. (Last year’s onboard stargazing guides came from Caltech; in previous seasons, the National Park Service’s Dark Rangers, who specialize in night-sky activities, accompanied trips.)
The Star Train makes its two-and-a-half-hour round-trip journey most Friday evenings between mid-May and mid-September, and tickets ($65 for adults) can sell out almost a year in advance — though members of the Nevada Northern Railway Museum get early access. Alternatively, the railroad’s more frequent Sunset, Stars and Champagne excursions trade telescopes for desert sundowners but feature the same expert stargazers and the same Nevada night sky, which is often dark enough to see the Milky Way with the naked eye.
New Mexico
The Stargazer
While plenty of heritage railroads across the United States offer twilight rides and nighttime excursions, at the moment there’s only one other dedicated, regularly scheduled stargazing train in North America besides the Star Train: the Stargazer, operated by Sky Railway, in Santa Fe, N.M.
Much like its Nevada counterpart, the Stargazer makes a two-and-a-half-hour round trip through dark-sky country, though in this case, the journey really is the destination, because it doesn’t make any stops. More of a rolling night-sky revue, the Stargazer features live music and professional astronomers who share their celestial knowledge and stories as the train rumbles into the vast Galisteo Basin south of Santa Fe. Sky Railway’s colorfully painted trains feature heated, enclosed passenger cars to stave off the evening chill and flatbed cars open to the night sky.
Departing from the Santa Fe Depot downtown, the train normally runs once a month (adult tickets from $139, including a champagne welcome toast). Sky Railway also occasionally schedules excursions for special celestial events.
New Zealand
Matariki Rail Experience
With its alpine landscapes and rugged coastline, New Zealand’s South Island is practically tailor-made for scenic daytime train journeys. But when night falls, the sparsely populated island — home to the Southern Hemisphere’s largest International Dark Sky Reserve — is heaven for stargazers, too.
This year, Great Journeys New Zealand, which operates the country’s tourist-centric long-distance trains, is offering a special nighttime run of the Coastal Pacific, whose route skirts the South Island’s northeastern coast. Timed to Matariki, the Maori new year, which is heralded by the first rising of the Pleiades star cluster, the eight-hour round trip from Christchurch is a cultural and astronomical celebration.
After the first half of a four-course onboard dinner, the train arrives in Kaikoura, in dark-sky country, for a guided stargazing stop with a range of telescopes — and fire pits and a night market. (The rain plan involves a virtual stargazing session at the local museum using virtual reality headsets.) Dinner resumes back on the train as it returns to Christchurch. This is a strictly limited engagement, on the rails for one night only: July 11, for 499 New Zealand dollars, about $295, per person.
In the far northern reaches of Norway, inside the Arctic Circle, you can ride a train that chases another wonder of the night sky: the aurora borealis. Twice a week from October to March, the Northern Lights Train takes its riders into the dark polar night in pursuit of the aurora’s celestial light show.
From the remote town of Narvik, the train travels along the Ofoten Railway, the northernmost passenger rail line in Western Europe. The destination on this three-hour round-trip excursion (1,495 kroner, or about $160) is Katterat, a mountain village accessible only by rail and free of light pollution, making it an ideal place to spot the aurora. At the Katterat station, local guides and a campfire cookout await, as does a lavvu, the traditional tent used by the Sami people of northern Scandinavia, offering a respite from the cold (as well as hot drinks and an open fire for roasting sausages).
And aboard the train, the lights stay off, which means that on a clear night, you might even catch the northern lights on the way there and back.
Leave it to Japan to take the stargazing train to another level.
The High Rail 1375 train — so named because it runs along Japan’s highest-elevation railway line (the high point is 1,375 meters, or roughly 4,500 feet, above sea level) — is one of JR East’s deliberately unhurried Joyful Trains, which the railway company describes as “not only a means of transportation, but also a package of various pleasures.” This astronomy-themed train certainly packs plenty of joy into its two cars, with seat upholstery inspired by constellations, a snack bar, a souvenir shop and a planetarium car with a library of astronomy books and images of the night sky projected onto its domed ceiling.
The train makes two daytime runs along the mountainous Koumi Line, taking a little over two hours to travel between Kobuchizawa (accessible by express train from Tokyo) and Komoro. But the main event is the High Rail Hoshizora (“Starry Sky”) evening trip, which includes an extended stop at Nobeyama Station (the highest in the country) for a guided stargazing session. A one-way ride on High Rail 1375, which runs on weekends and occasional weekdays, requires a seat reservation if you’re traveling on a Japan Rail pass, or a stand-alone ticket plus seat reservation (2,440 yen, or about $15). And remember to preorder a special “Starry Sky” bento box.
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Science
A Physicist Who Thinks in Poetry from the Cosmic Edge
Much of the praise for Chanda Prescod-Weinstein’s debut book in 2021, “The Disordered Cosmos: A Journey Into Dark Matter, Spacetime, and Dreams Deferred,” lauded the way she used personal experiences in physics to discuss the social and political inequities that exist alongside scientific breakthroughs.
“It contains the narrative of dreams deferred,” Dr. Prescod-Weinstein, a physicist at the University of New Hampshire, explained in April at a bookstore in Chicago. But its very existence, she said, also “represented a dream deferred, because that was not the dream of what my first book was going to be.”
Her second book reclaims that dream. Released on April 7, “The Edge of Space-Time: Particles, Poetry, and the Cosmic Dream Boogie” is less pain and more play, a homage to the big questions that made Dr. Prescod-Weinstein want to become a physicist in the first place. She begins the book by asserting that it is humanity’s duty to uncover and share the story of our universe. Her latest offering toward that duty is a journey through physics that is tightly bound to her own cultural roots.
In the midst of a multicity book tour, Dr. Prescod-Weinstein spoke with The New York Times about guiding readers through the cosmos from her own point of view and about some of the art, poetry and literature she drew on to shape that journey. This conversation has been edited for brevity and clarity.
Why include so many references to poetry in a book about physics?
I knew poetry before I knew physics. It was part of my upbringing. I loved A.A. Milne’s “Now We Are Six” and Edward Lear’s “Nonsense Limericks.” Both of my books draw their subtitles from Langston Hughes’s “Montage of a Dream Deferred.”
Adrienne Rich’s poem “The Burning of Paper Instead of Children” became a guiding light for how my work would move in the world. It also opened up for me that I need language. That’s true among physicists. Even an equation is a sentence; even an equation is telling a story.
As physicists, we’re always working in language to connect what we learn with what we know. Poetry is one of the first places that my brain goes to draw those links. Language, as it moves in my brain, is often in Hughes and Rich and Shakespeare. Those are the lines that flicker up for me.
What if we got away from the argument that doing cosmology and particle physics is practical or materially valuable? Then we have to accept that we’re like the poets. What we do is important culturally in the same way poetry is. A piece of this book is me saying there is value in banding with the poets, and fighting for the value of being curious and trying to articulate the world with whatever tools are available to us. Not for the purposes of selling something, but for the purpose of fulfilling our humanity.
Another theme throughout the book is the story of Lewis Carroll’s Alice and her adventures in Wonderland.
Being a science adviser on future installments in The Legendborn Cycle, a fantasy series written by Tracy Deonn, is one reason Alice is in my book. It has allowed me to be open to the playful side that physics, as a Black queer person, can take from you. I wanted the book to be whimsical, because that’s who I was when I first arrived in physics, and that’s who I want to be when I die.
Part of the call of quantum physics is to change what our sense and sensibility are. When you look at the world through this framework — like the idea that particles have spin but don’t really spin — it sounds like nonsense. Except that’s literally how the universe works. Physics is our “through the looking glass.” It’s real.
Your first chapter invites readers to reflect on the metaphors used to describe the universe, like the “fabric” of space-time or electromagnetic “fields.” Why open in this way?
A lot of books about quantum physics start with its history. I wanted as much as possible not to just do that. I had actually planned to start it with the Stern-Gerlach experiment of 1922. But then I read an essay by the poet Natasha Trethewey about abiding metaphors and started to ask myself what the abiding metaphors of my physics training were.
We don’t ever take time in our classes to ask, “What do we mean when we say ‘space’? What do we mean when we say ‘space-time’?” There are these metaphysical questions that I often told myself were for the philosophers. This book was me letting myself think of them as physics.
One metaphor you invoke is the “edge” — not only the edge of the universe and of scientists’ understanding, but also existing at the edge of certain identities.
In “Disordered Cosmos,” I talked a lot about being at the margin and looking toward the center. With “The Edge of Space-Time,” I’m choosing to make the margin the center of the story. Part of that was me fully embracing what makes me the physicist I am. I’m an L.A. Dodgers fan. I love “Alice in Wonderland.” I love “Star Trek.” There’s lots of all of that in the book.
Picking a metaphor is a culturally situated decision. I wrote a line that says black holes are the best laid edges in the universe. I did, at some point, think that only some people were going to get this. But for people who don’t understand the reference to Black hairstyles, the sentence is still legible. And for those who do, it will feel like we just had an in-group moment. Anyone who thinks about laying their edges deserves to have an in-group moment in a physics book. Because we are physics, too.
Black students are often told that if you want to be a physicist, then you will make yourself as close to such-and-such mold as possible. At a young age, we have this understanding that whiteness and science are associated with each other, but we are also witnessing in ourselves that this can’t be entirely correct. There’s this narration of, “Well, sure, you can be Black in physics, but that means you have to acclimate to the ‘in physics’ part, and never that physics has to acclimate to the Black part.”
I use the example of rapper Big K.R.I.T.’s song “My Sub Pt. 3 (Big Bang),” in which someone tries to wire up subwoofers in his car but fries the wires because he doesn’t ground them properly. I don’t know if Big K.R.I.T. would think of this as a science story, but I think we should learn to read it as one. Not to contain it in science, but to say it overlaps there. This can be a rap song. It can be about the cultural significance of subwoofers and the Big Bang as a metaphor for the beat. And it can also be about cosmology and about how everybody who wires up cars or does this kind of work is a scientist, too.
How do you want readers to approach this book?
There is this feeling that you’re supposed to read a book like this and walk away an expert. That’s actually not the point of this book at all. The point is to wander through physics. Even if math terrifies you, you are entitled to spend some time with it.
And so here, I have made you a book with a bunch of tidbits on the oddities of the universe. The universe is stranger and more queer and more wonderful and more full of possibility than whatever limitations you might be experiencing right now. Physics challenges what we are told are social norms. For example, non-trinary neutrinos are fundamental to our standard model of physics.
“Non-trinary,” as in they shift between three different forms.
Non-trinary is natural. It’s such a challenge to the current anti-trans rhetoric that says people can only ever be one thing.
I don’t need my book to be the most important thing that someone reads. But I want it to be a source of hope. If it reminds you that, as my mom says, the universe is bigger than the bad things that are happening to us, then that’s all you need to remember. I’m good with that.
Science
Footage shows Central Valley dairy workers kicking young calves, pulling them with pliers
In late February, animal rights activists flew a drone over a calf ranch in the Central Valley and watched as workers kicked and punched the animals.
For the record:
7:15 p.m. May 12, 2026This article has been updated to reflect that no calves from Agresti Calf Ranch have ever gone on to be used for Clover Sonoma milk supplies, and the calf ranch opened only in 2025. In additional comments, Clover Sonoma also said in the future, no animals from Agresti Calf Ranch will be part of its supply.
Footage reviewed by The Times shows a worker pulling a calf by the nose with pliers.
It shows two workers removing the budding horns of a calf with a hot iron. While one held the frightened animal’s head, the other — wearing a sweatshirt with an image of the Virgin Mary — applied the iron to a horn. After a puff of smoke, the calf fell to its side, appearing motionless.
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Both male and female calves produce horns. To prevent injury to the animals and their handlers, these are commonly removed. Humane guidelines require anesthesia.
The footage was collected by the group Direct Action Everywhere, known for tactics including releasing beagles from medical breeding facilities and abused calves from farms. It was shot at the Agresti Calf Ranch in Ceres, near Modesto, which is certified by the American Humane Society for its ethical treatment of animals. The workers could not be reached for comment. One was subsequently terminated, the Humane Society said.
The Agresti Calf Ranch opened in 2025 and is operated by the owners of Double D Dairy, just up the road. Double D Dairy owns more than 10,000 cows across several operations.
The owner of Double D, Dominic Assali, declined to answer questions in person. A phone number for the dairy online is disconnected. In response to an email to his personal account, Assali said, “Animal welfare and safety are incredibly important to us, and we have a zero-tolerance policy for any mistreatment.
“We’ll always take immediate, thorough action to address any operational issues, as we have in this instance,” the email said.
The American Humane Society is a 150-year-old nonprofit focused on animal welfare. Among other things, it certifies animal safety on farms as well as on movie sets. In a statement, it said only 10% of animals raised on farms in the U.S. are certified as humanely treated.
Assali is the grandson of the farm’s founders, Harold and Marlene Agresti. He is a board member of Western United Dairies, the largest dairy trade group in California.
The mistreatment captured on video has also created a headache for a prominent California sustainable milk brand, Clover Sonoma, based in Sonoma County.
It gets 10% to 15% of its milk from Double D, and Assali and his family are featured on Clover Sonoma’s website. No calves from Agresti Calf Ranch have ever gone on to be used in Clover Sonoma milk supplies, the company said in a statement. It’s unclear whether the abused calves were being raised for beef or dairy.
A Clover Sonoma sign hung outside the main dairy complex on a recent visit.
Clover Sonoma markets its milk, yogurt and cheese products as humanely sourced and environmentally sound. It was the first dairy company to receive a cruelty-free certification from the American Humane Society in 2000. The website also features a “Our Promise” page, which states the company demands “the humane treatment of animals.”
“We were deeply concerned by the reported mistreatment of some cows captured on video at Agresti Calf Ranch during a separate cow operation,” the company said in an email.
“The rough handling shown at Agresti Calf Ranch is contrary and inconsistent with the humane practices we have fostered for decades and which we demand of all our suppliers.”
Clover Sonoma said it suspended business with Double D as soon as it became aware of the incidents and began “a rigorous audit,” which just ended.
“Clover and the American Humane Society have concluded that the mistreatment was an isolated issue, not systemic or reflective of Agresti Calf Ranch’s personnel. Corrections have been made, including the termination of the employee in the video. As such, we are comfortable reinstating the milk from Double D Dairy.”
After this story published, Clover went further and said a condition of Double D’s reinstatement will be that no animals from Agresti Calf Ranch will be part of Clover’s dairy supply.
A statement from the Humane Society said Clover Sonoma is working with Double D to strengthen its whistleblower policy and training, and has “reiterated its commitment to ongoing independent, third-party audits,” with both announced and unannounced visits.
Clover Sonoma mainly buys and processes milk from dairies in verdant Sonoma County, as the company’s marketing suggests. Double D Dairy is one of its few suppliers in the Central Valley, which is associated more with industrial-scale agriculture.
On a recent weekday, the calf ranch and dairy farm were visible from a public road. Holstein calves, a popular dairy breed, could be seen in cages through small trees in front of the enclosures. The sound of mooing and a pressure washer could be heard. The smell of manure and dirt wafted in the humid air.
Most dairy companies remove calves from their mothers after birth, raising them separately so they don’t take the mother’s commercially valuable milk. Some dairy farms send calves out to third-party calf ranches for rearing. Others raise them on-site. Female calves are typically raised to become milk cows. Male calves are sent away to become beef or other meat-based products, such as pet food.
A 2025 State Water Board document shows the farm houses an average of 700 calves at any one time, with a maximum 1,400.
The Direct Action Everywhere activists were recently on a public road near Double D’s main farm, flying a drone over the property. Within 30 minutes of their arrival, seven Stanislaus County sheriff’s vehicles arrived and surrounded the activists.
A heavily armed officer asked to see the drone pilot’s Federal Aviation Administration license, which he provided. After confirming it was valid, a sheriff’s deputy — one of nine at the scene — told the activists they could remain on the road but could not trespass.
Asked about the heavy response, a deputy said there had been several recent violent incidents from animal rights groups at the site, and mentioned the groups had sent in “busloads” of activists.
The Times reached out to the Sheriff’s Office to get more details about those events but did not get a response.
Temple Grandin, author and professor of livestock medicine at Colorado State University, said that punching and kicking livestock is considered abusive.
An expert in livestock welfare, she said that handlers can tap, push and nudge animals. But if the level of force goes beyond what could bend the side of a cardboard box, “it’s abuse. Period.”
She said the calves’ reaction to the hot iron indicates that pain medication, such as lidocaine, was not applied before the procedure. Double D did not respond to a question about whether medication was given before the procedure.
A pickup truck rolls by the barns at Agresti Calf Ranch at sunrise in Ceres.
(Tomas Ovalle/For The Times)
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