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      A Mammoth DNA Discovery Helps Map an Ancient Genome in 3-D

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      In 2018 an international team of scientists — from labs in Houston, Copenhagen, Barcelona and beyond — got their hands on a remarkable biological specimen: a skin sample from a 52,000-year-old woolly mammoth that had been recovered from the permafrost in Siberia. They probed the sample with an innovative experimental technique that revealed the three-dimensional architecture of the mammoth’s genome. The resulting paper was published on Thursday in the journal Cell.Hendrik Poinar, an evolutionary geneticist at McMaster University in Canada, was “floored” — the technique had successfully captured the original geometry of long stretches of DNA, a feat never before accomplished with an ancient DNA sample. “It’s absolutely beautiful,” said Dr. Poinar, who reviewed the paper for the journal.The typical method for extracting ancient DNA from fossils, Dr. Poinar said, is still “kind of cave man.” It produces short fragments of code composed of a four-letter molecular alphabet: A (adenine), G (guanine), C (cytosine), T (thymine). An organism’s full genome resides in cell nuclei, in long, unfragmented DNA strands called chromosomes. And, vitally, the genome is three-dimensional; as it dynamically folds with fractal complexity, its looping points of contact help dictate gene activity.“To have the actual architectural structure of the genome, which suggests gene expression patterns, that’s a whole other level,” Dr. Poinar said.“It’s a new kind of fossil, a fossil chromosome,” said Erez Lieberman Aiden, a team member who is an applied mathematician, a biophysicist and a geneticist and directs the Center for Genome Architecture at Baylor College of Medicine in Houston. Technically, he noted, it is a non-mineralized fossil, or subfossil, since it has not turned to stone.Erez Lieberman Aiden, director of the Center for Genome Architecture at Baylor College of Medicine in Houston.Brandon Thibodeaux for The New York TimesThe trunk of a 39,000-year-old woolly mammoth nicknamed Yuka that also yielded fossil chromosomes in the study.Love Dalén/Stockholm UniversityWe are having trouble retrieving the article content.Please enable JavaScript in your browser settings.Thank you for your patience while we verify access. If you are in Reader mode please exit and log into your Times account, or subscribe for all of The Times.Thank you for your patience while we verify access.Already a subscriber? Log in.Want all of The Times? Subscribe. More

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      SpaceX’s Assault on a Fragile Habitat: Four Takeaways From Our Investigation

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      The development of Elon Musk’s facility in South Texas did not play out as local officials were originally told it would.When Elon Musk first eyed South Texas for a new base of space operations, he promised that SpaceX would have a small, eco-friendly footprint and that the surrounding area would be “left untouched.”A decade later, the reality is far different. An investigation by The New York Times shows how SpaceX’s ferocious growth in the area has dramatically changed the fragile landscape and has threatened the habitat that the U.S. government is charged with protecting there.More repercussions are likely coming, in South Texas and in other places where SpaceX is expanding. Mr. Musk has said he hopes to one day launch his Starships — the largest rocket ever manufactured — a thousand times a year.Executives from SpaceX declined repeated requests to comment. But Gary Henry, who until this year served as a SpaceX adviser on Pentagon launch programs, said the company was aware of concerns about SpaceX’s environmental impact and was committed to addressing them.Here are four takeaways from our investigation:Musk used preserved lands as a buffer for SpaceX operationsRocket launch sites in the U.S., such as Vandenberg Space Force Base in California and Kennedy Space Center in Florida, typically are enormous, secure facilities with tens of thousands of acres within their confines.Mr. Musk didn’t intend to buy up anything like that amount of land when he was looking at the area near Brownsville, Texas. Instead, he wanted to buy a tiny piece of property in the middle of public lands — what the team involved referred to as a “doughnut hole.” He figured the surrounding state parks and federal wildlife preserves would serve as natural buffers.We are having trouble retrieving the article content.Please enable JavaScript in your browser settings.Thank you for your patience while we verify access. If you are in Reader mode please exit and log into your Times account, or subscribe for all of The Times.Thank you for your patience while we verify access.Already a subscriber? Log in.Want all of The Times? Subscribe. More

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      Wildlife Protections Take a Back Seat to Elon Musk’s Ambitions

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      As Elon Musk’s Starship — the largest rocket ever manufactured — successfully blasted toward the sky last month, the launch was hailed as a giant leap for SpaceX and the United States’ civilian space program.Two hours later, once conditions were deemed safe, a team from SpaceX, the U.S. Fish and Wildlife Service and a conservation group began canvassing the fragile migratory bird habitat surrounding the launch site.The impact was obvious.The launch had unleashed an enormous burst of mud, stones and fiery debris across the public lands encircling Mr. Musk’s $3 billion space compound. Chunks of sheet metal and insulation were strewn across the sand flats on one side of a state park. Elsewhere, a small fire had ignited, leaving a charred patch of park grasslands — remnants from the blastoff that burned 7.5 million pounds of fuel.Most disturbing to one member of the entourage was the yellow smear on the soil in the same spot that a bird’s nest lay the day before. None of the nine nests recorded by the nonprofit Coastal Bend Bays & Estuaries Program before the launch had survived intact.Egg yolk now stained the ground.“The nests have all been messed up or have eggs missing,” Justin LeClaire, a Coastal Bend wildlife biologist, told a Fish and Wildlife inspector as a New York Times reporter observed nearby.The outcome was part of a well-documented pattern.On at least 19 occasions since 2019, SpaceX operations have caused fires, leaks, explosions or other problems associated with the rapid growth of Mr. Musk’s complex in Boca Chica. These incidents have caused environmental damage and reflect a broader debate over how to balance technological and economic progress against protections of delicate ecosystems and local communities. More

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      44-Foot Whale Found Dead on Bow of Cruise Ship Coming Into New York

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      The endangered sei whale, usually found in deep waters, was discovered on the bow of a cruise ship as it arrived at the Brooklyn Cruise Terminal, marine authorities said.As the cruise ship approached New York on Saturday, it was found to be carrying a grim, and unexpected, catch: The corpse of a 44-foot-long endangered whale, draped across its bow.The whale, which marine authorities described as a sei whale, is known for its rapid swimming and preference for deep waters, far from the coast. Its body was discovered as the ship neared the Brooklyn Cruise Terminal, and the authorities were “immediately notified,” said MSC Cruises, which owns the ship.A spokeswoman for the company said in an email that it had “comprehensive measures” in place to avoid such collisions, including training deck officers and altering itineraries in certain areas to avoid them. “We will continue to evaluate and update our procedures with our partners and the authorities,” she said.Marine authorities said that they had towed the animal, estimated to weigh some 50,000 pounds, from the bow, and transferred it by boat to a beach in Sandy Hook, N.J., where they conducted a necropsy on Tuesday.The investigation is continuing, but preliminary results — broken bones in the whale’s right flipper; tissue trauma along its right shoulder blade; a full stomach and decent layer of blubber — all pointed toward the animal having been in otherwise good health when it was likely struck and killed by the ship, said Robert A. DiGiovanni, the chief scientist of the Atlantic Marine Conservation Society, which is leading the investigation.The whale was already “pretty decomposed” by the time scientists began the necropsy, he added, so they worked quickly to collect samples that could be tested for contaminants and other biotoxins that would indicate any other relevant health issues. “It looks like the animal was alive and it was hit by a vessel,” he said, noting that investigators had not ruled out other factors.Mr. Giovanni said that his conservation group, which is federally authorized to respond to marine mammal strandings in New York, had dealt with around 100 whales over the past several years, many of which had been entangled in nets or struck by vessels. Most of those whales were humpback and North Atlantic right whales, he added, noting that it was more uncommon to come across a sei whale.We are having trouble retrieving the article content.Please enable JavaScript in your browser settings.Thank you for your patience while we verify access. If you are in Reader mode please exit and log into your Times account, or subscribe for all of The Times.Thank you for your patience while we verify access.Already a subscriber? Log in.Want all of The Times? Subscribe. More

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      ‘Dune’-like Sandworm Existed Millions of Years Longer Than Thought

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      Researchers examined fossils of the predatory worm and found a new species that persisted for 25 million years after it was believed to have become extinct.With a head covered in rows of curved spines, ancient Selkirkia worms could easily be confused with the razor-toothed sandworms that inhabit the deserts of Arrakis in “Dune: Part Two.”During the Cambrian Explosion more than 500 million years ago, these weird worms — which lived inside long, cone-shaped tubes — were some of the most common predators on the seafloor.“If you were a small invertebrate coming across them, it would have been your worst nightmare,” said Karma Nanglu, a paleontologist at Harvard. “It’s like being engulfed by a conveyor belt of fangs and teeth.”Thankfully for would-be spice harvesters, these ravenous worms disappeared hundreds of million years ago. But a trove of recently analyzed fossils from Morocco reveals that these formidable predators measuring only an inch or two in length, persisted much longer than previously thought.In a paper published today in the journal Biology Letters, Dr. Nanglu’s team described a new species of Selkirkia worm that lived 25 million years after this group of tube-dwellers was thought to have gone extinct.The newly described tubular worms were discovered when Dr. Nanglu and his colleagues sifted through fossils stored in the collection of Harvard’s Museum of Comparative Zoology. The fossils hail from Morocco’s Fezouata Formation, a deposit dating back to the Early Ordovician period, which began around 488 million years ago and spanned nearly 45 million years. This was a dynamic era when holdovers from the Cambrian rubbed shoulders with evolutionary newcomers like sea scorpions and horseshoe crabs.We are having trouble retrieving the article content.Please enable JavaScript in your browser settings.Thank you for your patience while we verify access. If you are in Reader mode please exit and log into your Times account, or subscribe for all of The Times.Thank you for your patience while we verify access.Already a subscriber? Log in.Want all of The Times? Subscribe. More

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      More Than 100 Animals Seized From Long Island Home

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      Animal welfare authorities say the animals were being illegally held and included a South American ostrich, a giant African snail, two prairie dogs and an endangered tiger salamander.Animal welfare authorities seized more than 100 animals from a Long Island home this week — including a South American ostrich, a giant African snail, two prairie dogs and an endangered tiger salamander — after a tip they received about exotic animals led them to their owner’s doorstep.“He was running a pop-up circus,” said Detective Matt Roper, director of law enforcement for the Nassau County SPCA. “Bringing these animals out in public and letting children play with these animals.”Detective Roper said the animals’ owner was given court summonses for several state and local violations, including endangering the public and housing and possessing endangered species. Federal authorities are also investigating, he said.Detective Roper emphasized that there were no signs that the animals had been abused or neglected.“They were all cared for,” Detective Roper said. “They were just in violation of being held or kept as either pets or for exhibition purposes.”Detective Roper, who declined to name the animals’ owner because the investigation is continuing, said that on Tuesday the authorities took 104 animals from the basement and backyard of the house, which is in North Bellmore.Humane Long Island, an animal advocacy organization that took custody of dozens of the animals that were seized, identified their owner as Matthew Spohrer, 32. He was issued 30 violations relating to illegal possession of animals, the group said in a news release.We are having trouble retrieving the article content.Please enable JavaScript in your browser settings.Thank you for your patience while we verify access. If you are in Reader mode please exit and log into your Times account, or subscribe for all of The Times.Thank you for your patience while we verify access.Already a subscriber?  More

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      What’s In (and Not In) the $1.7 Trillion Spending Bill

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      A big boost for the military, more aid for Ukraine, a preference for the lobster industry over whales and an overhaul of the Electoral Count Act are among the provisions in the 4,155-page bill lawmakers expect to pass this week.WASHINGTON — Billions of dollars in emergency aid to war-torn Ukraine and communities ravaged by natural disasters. A bipartisan proposal to overhaul the archaic law at the heart of former President Donald J. Trump’s effort to overturn the 2020 election. And a divisive oceanic policy that will change federal protections for whales in an effort to protect the lobster industry in Maine.In compiling the roughly $1.7 trillion catchall spending package that will keep the government open through September, lawmakers inserted several new funding and legislative proposals to ensure their priorities and policies become law before the end of the year.It includes funding that will guarantee the enactment of policies first authorized in bipartisan legislation approved earlier in this Congress, including money for innovation hubs established in the semiconductor manufacturing law and projects in the infrastructure law. The package also includes a round of earmarks, rebranded as community project funding, that allow lawmakers to redirect funds to specific projects in their states and districts.Here is a look at some of the provisions that would go into effect if enacted.Military spending is the big winner.The Defense Department would see an extraordinary surge in spending when adding its regular 2023 fiscal year budget together with additional funds being allocated to help respond to the war in Ukraine.All together, half of the $1.7 trillion in funding included in the package goes to defense, or a total of $858 billion. It comes after lawmakers bucked a request from President Biden and approved a substantial increase in the annual defense policy bill passed this month.The 2023 budget just for the Defense Department would total $797.6 billion in discretionary spending — a 10 percent increase over last year’s budget — representing an extra $69.3 billion in funds for the Pentagon, which is $36.1 billion above the president’s budget request.Sprinkled throughout the spending bill are hundreds of high-ticket add-ons that Congress wants to make to the president’s original Defense Department budget, such as an additional $17.2 billion for procurement that the Pentagon can largely distribute to military contractors to buy new ships, airplanes, missile systems and other equipment. The overall Pentagon procurement budget with these additional funds would be $162 billion.One of the biggest chunks of that extra money is for shipbuilding — an extra $4 billion that brings the Navy’s overall shipbuilding budget to $31.96 billion. That will allow it to buy 11 new ships, including three guided missile destroyers and two attack submarines.But that is just the start. There is $8.5 billion to buy 61 F-35 fighter jets made by Lockheed Martin and another $2.5 billion to buy 15 of Boeing’s new aerial refueling planes known as KC-46 tankers.There is also an extra $27.9 billion to help cover Defense Department costs associated with the war in Ukraine, as part of an emergency aid package to the country. That includes an extra $11.88 billion to replenish U.S. stocks of equipment sent to Ukraine — money that again will largely be used to purchase products from military contractors. That supplemental appropriation also includes $9 billion to assist Ukraine with training, equipment and weapons, as well as an extra $6.98 billion to cover U.S. military operations in Europe.— Eric Lipton and John IsmayMaking it easier (for some) to save for retirement.The package also includes a collection of new rules aimed at helping Americans save for retirement. The bill would require employers to automatically enroll eligible employees in their 401(k) and 403(b) plans, setting aside at least 3 percent, but no more than 10 percent, of their paychecks. Contributions would be increased by one percentage point each year thereafter, until it reaches at least 10 percent (but not more than 15 percent). But this applies only to new employer-provided plans that are started in 2025 and later — existing plans are exempt.Another provision would help lower- and middle-income earners saving for retirement by making changes to an existing tax credit, called the saver’s credit, now available only to those who owe taxes. In its new form, it would amount to a matching contribution, from the federal government, deposited into taxpayers’ retirement accounts.People struggling with student debt would also receive a new perk: Employees making student debt payments would qualify for employer matching contributions in their workplace retirement plan, even if they were not making plan contributions of their own.What to Know About Congress’s Lame-Duck SessionCard 1 of 5A productive stretch. More