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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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      A New Search for Ripples in Space From the Beginning of Time

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      The universe burst into existence 13.8 billion years ago. What happened in that earliest moment is of intense interest to anyone trying to understand why everything is the way it is today.“I think this question of what happens at the beginning of the universe is a profound one,” said David Spergel, president of the Simons Foundation, a nonprofit organization that supports research at the frontiers of mathematics and science. “And what is remarkably exciting to me is the fact that we can do observations that can give us insight into this.”A new $110 million observatory in the high desert of northern Chile, $90 million financed by the foundation, could uncover key clues about what happened after the Big Bang by looking at particles of light that have traveled across the universe since almost the beginning of time.The data could finally provide compelling corroboration for a fantastical idea known as cosmic inflation. It holds that in the first sliver of time after the universe’s birth, the fabric of space-time accelerated outward to speeds far faster than the speed of light.Alternatively, the observatory’s measurements could undercut this hypothesis, a pillar in the current understanding of cosmology.The observatory is named after the foundation and its founders: Jim Simons, the hedge fund billionaire and philanthropist who died on May 10, and his wife, Marilyn, a trained economist. Two of the four telescopes began taking measurements in April, in time for Dr. Simons’s 86th birthday on April 25.Traces of Ancient LightAn illustration shows how light from the early universe might have been polarized by the push and pull of gravitational waves as the universe expanded. The Simons Observatory will search for evidence of this polarization. More

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      The Doomsday Clock Keeps Ticking

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      Year
      Minutes to Midnight

      2023
      1.5

      2020
      1.67

      2018
      2

      2017
      2.5

      2015
      3

      2012
      5

      2010
      6

      2007
      5

      2002
      7

      1998
      9

      1995
      14

      1991
      17

      1990
      10

      1988
      6

      1984
      3

      1981
      4

      1980
      7

      1974
      9

      1972
      12

      1969
      10

      1968
      7

      1963
      12

      1960
      7

      1953
      2

      1949
      3

      1947
      7

      The Bomb and I go way back. In Seattle, where I grew up in the 1950s and ’60s, it was common wisdom that in the event of nuclear war, we were No. 2 on the target list because Seattle was the home of Boeing, maker of B-52 bombers and Minuteman missiles.In school we had various drills for various catastrophes, and we had to remember which was which. Earthquake? Run outside. The Bomb? Run inside, to an inner corridor that had no windows. In the summer, my high-school friends and I would disappear for a couple of weeks into the backcountry of the Cascades or the Olympic Mountains. I always wondered whether we would emerge to find the world in ashes.Once, in Santa Monica in 1971, I thought it was finally happening. I woke up on the floor, having been bounced out of my bed early one February morning. There was a huge roar. Everything was shaking. I crept to my one window and pulled aside the curtain, expecting to see a mushroom cloud rising over the Los Angeles basin. I saw nothing. When the radio came back, I learned there had been a deadly earthquake in the San Fernando Valley.I was sent on this trip down memory lane by the announcement on Jan. 23 from the Bulletin of the Atomic Scientists that it had decided not to change the setting of the Doomsday Clock, a metaphorical timepiece invented in 1947 as a way to dramatize the threat of nuclear Armageddon. The clock was originally designed with a 15-minute range, counting down to midnight — the stroke of doom — and the Bulletin’s members move it from time to time in response to current events, which now include threats like climate change and pandemics.In a burst of optimism in 1991, after the Soviet Union broke up and the first Strategic Arms Reduction Treaty was signed, the clock was turned way back to 17 minutes to midnight. “The Cold War is over,” the Bulletin’s editors wrote. “The 40-year-long East-West nuclear arms race has ended.”A year ago, after Russia invaded Ukraine and brandished the threat of using nuclear weapons, the clock was set to 90 seconds to midnight, the closest it has yet come to The End. The threat of nuclear weapons in Ukraine has diminished since then, but the clock remains poised at 90 seconds before zero.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