Scientist Phillippy Co-Led DNA Completion Because Gaps “Were Just Really Bugging Me”

People with different ways of thinking are better at doing different kinds of work. For instance those who are obsessive/compulsive or have some types of Asperger’s, may be better at careful detailed work that requires perfectionism. (I do not know anything about Phillippy beyond the article quoted below, so I am in no way suggesting that he is an examplar of either of these ways of thinking.)

(p. A10) Two decades after the draft sequence of the human genome was unveiled to great fanfare, a team of 99 scientists has finally deciphered the entire thing. They have filled in vast gaps and corrected a long list of errors in previous versions, giving us a new view of our DNA.

. . .

In 2019, two scientists — Adam Phillippy, a computational biologist at the National Human Genome Research Institute, and Karen Miga, a geneticist at the University of California, Santa Cruz — founded the Telomere-to-Telomere Consortium to complete the genome.

Dr. Phillippy admitted that part of his motivation for such an audacious project was that the missing gaps annoyed him. “They were just really bugging me,” he said. “You take a beautiful landscape puzzle, pull out a hundred pieces, and look at it — that’s very bothersome to a perfectionist.”

Dr. Phillippy and Dr. Miga put out a call for scientists to join them to finish the puzzle. They ended up with 99 scientists working directly on sequencing the human genome, and dozens more pitching in to make sense of the data. The researchers worked remotely through the pandemic, coordinating their efforts over Slack, a messaging app.

. . .

Dr. Altemose plans on using the complete genome to explore a particularly mysterious region in each chromosome known as the centromere. Instead of storing genes, centromeres anchor proteins that move chromosomes around a cell as it divides. The centromere region contains thousands of repeated segments of DNA.

In their first look, Dr. Altemose and his colleagues were struck by how different centromere regions can be from one person to another. That observation suggests that centromeres have been evolving rapidly, as mutations insert new pieces of repeating DNA into the regions or cut other pieces out.

While some of this repeating DNA may play a role in pulling chromosomes apart, the researchers have also found new segments — some of them millions of bases long — that don’t appear to be involved. “We don’t know what they’re doing,” Dr. Altemose said.

But now that the empty zones of the genome are filled in, Dr. Altemose and his colleagues can study them up close. “I’m really excited moving forward to see all the things we can discover,” he said.

For the full story, see:

Carl Zimmer. “Scientists Have Finally Filled in All the Gaps in the Human Genome.” The New York Times (Saturday, July 24, 2021): A17.

(Note: ellipses added.)

(Note: the online version of the story was updated July 26, 2021, and has the title “Scientists Finish the Human Genome at Last.”)

Entrepreneurs Hold “Business Showers” for Their Startups

(p. B1) Sid Singh, 36, was joking recently with a friend that everyone he knew seemed to be having their third baby while he was bringing something entirely different into the world. He had just quit his consulting job to build a financial coaching company. It dawned on him that he could have a baby shower for his new endeavor.

. . .

Across the United States, especially in New York City, entrepreneurs are appropriating the baby shower, an event previously reserved for expectant parents, usually mothers. The idea is that if building a business is just as compre-(p. B5)hensive (and expensive!) as having a baby, why not build in the same kind of communal support?

. . .

“I remember when I first started telling people I was pregnant, I had never been congratulated like this for anything in my life,” she said. “I know people were coming from a place of love and excitement, but for me, launching the business was that for me.”

. . .

Mr. Singh received some confused responses. “Some people thought I was hosting a baby shower for someone,” he said. “Others thought I was having a baby with someone.”

He laughed it off, but he did explain to his friends why he was doing this. “People need to understand I am basically committing my entire life to this,” he said. “I am taking the biggest risk I can.”

For the full story, see:

Alyson Krueger. “Congratulations! It’s a Start-Up.” The New York Times (Saturday, July 24, 2021): B1 & B5.

(Note: ellipses added.)

(Note: the online version of the story has the date July 19, 2021, and has the same title as the print version.)

Founding Entrepreneurs Have Similar Brain Patterns for Their Children and Their Startups

(p. R6) A study published in the Journal of Business Venturing in March 2019 looked at the brain patterns of 21 entrepreneurs and 21 parents who weren’t entrepreneurs. The goal was to investigate why and how company founders bond with their ventures.

The result: When entrepreneurs think about their businesses, their brain patterns are very similar to the brain patterns of parents thinking about their children. Those findings shed light on why entrepreneurs run companies the way they do—and how they ought to.

. . .

In the experiment, researchers used a technique called functional magnetic resonance imaging to see which parts of the participants’ brains were activated by a series of pictures. Entrepreneurs were shown photos of their business—such as the logo and product or service—as well as of other companies. The parents saw images of their own children, and other people’s.

The results were very similar for both test groups. When looking at the images of their own businesses or children, they experienced significantly more activity in the caudate nuclei, regions of the brain associated with parenting, as well as pleasant sensations and rewards, according to Tom Lahti, an associate professor at the Hanken School of Economics, in Helsinki, who co-wrote the study.

Meanwhile, when the test subjects viewed the images of the other companies or children, parts of the brain associated with negative emotional experiences, the bilateral insula, were much more active.

. . .

. . ., the emotional ties help explain why so many entrepreneurs are prepared to delay monetary gratification and stick with a venture in hopes of long-term success, Dr. Lahti says. That’s akin to parents making years of sacrifices on behalf of their children.

. . .

“The lead entrepreneur needs to share the responsibilities and ownership with the co-founders,” Dr. Lahti says, adding, “In some entrepreneurial teams, the lead entrepreneur may perceive [himself or herself as] owning the venture, while the other members of the entrepreneurial team do not. This could ultimately be a recipe for disaster, because the other members may not persist in the face of difficulty and setback.”

For the full story, see:

Cheryl Winokur Munk. “My Company, My Child.” The Wall Street Journal (Thursday, June 3, 2021): R6.

(Note: ellipses added.)

(Note: the online version of the story has the date June 2, 2021, and has the title “Why Many Entrepreneurs Treat Their Businesses Like Their Children.”)

The research discussed above was published in:

Lahti, Tom, Marja-Liisa Halko, Necmi Karagozoglu, and Joakim Wincent. “Why and How Do Founding Entrepreneurs Bond with Their Ventures? Neural Correlates of Entrepreneurial and Parental Bonding.” Journal of Business Venturing 34, no. 2 (March 2019): 368-88.

Serendipitous Water Cooler Collaboration “Is More Fairy Tale Than Reality”

(p. B1) When Yahoo banned working from home in 2013, the reason was one often cited in corporate America: Being in the office is essential for spontaneous collaboration and innovation.

. . .

Yet people who study the issue say there is no evidence that working in person is essential for creativity and collaboration. It may even hurt innovation, they say, because the demand for doing office work at a prescribed time and place is a big reason the American workplace has been inhospitable for many people.

“That’s led to a lot of the outcomes we see in the modern office environment — long hours, burnout, the lack of representation — because that office culture is set up for the advantage of the few, not the many,” said Dan Spaulding, chief people officer at Zillow, the real estate market-(p. B7)place.

“The idea you can only be collaborative face-to-face is a bias,” he said. “And I’d ask, how much creativity and innovation have been driven out of the office because you weren’t in the insider group, you weren’t listened to, you didn’t go to the same places as the people in positions of power were gathering?”

“All of this suggests to me that the idea of random serendipity being productive is more fairy tale than reality,” he said.

. . .

“There’s credibility behind the argument that if you put people in spaces where they are likely to collide with one another, they are likely to have a conversation,” said Ethan S. Bernstein, who teaches at Harvard Business School and studies the topic. “But is that conversation likely to be helpful for innovation, creativity, useful at all for what an organization hopes people would talk about? There, there is almost no data whatsoever.”

“All of this suggests to me that the idea of random serendipity being productive is more fairy tale than reality,” he said.

. . .

. . . Professor Bernstein found that contemporary open offices led to 70 percent fewer face-to-face interactions. People didn’t find it helpful to have so many spontaneous conversations, so they wore headphones and avoided one another.

. . .

. . . some creative professionals, like architects and designers, have been surprised at how effective remote work has been during the pandemic, while scientists and academic researchers have long worked on projects with colleagues in other places.

Requiring people to be in the office can drive out innovation, some researchers and executives said, because for many people, in-person office jobs were never a great fit. They include many women, racial minorities and people with caregiving responsibilities or disabilities. Also, people who are shy; who need to live far from the office; who are productive at odd hours; or who were excluded from golf games or happy hours.

For the full commentary, see:

Claire Cain Miller. “THE UPSHOT;Returning to the Office? The Myth of Serendipity.” The New York Times, SundayBusiness Section (Sunday, July 2, 2021): B1 & B7.

(Note: the online version of the commentary was updated July 1, 2021, and has the title “THE UPSHOT; Do Chance Meetings at the Office Boost Innovation? There’s No Evidence of It.”)

The Bernstein research mentioned above is:

Bernstein, Ethan, and Ben Waber. “The Truth About Open Offices.” Harvard Business Review 97, no. 6 (Nov./Dec. 2019): 82-91.

Government Cover Ups

(p. 230) It’s hard enough to find out about the things the universe prefers to keep hidden without our government, which somebody you know must have voted for, covering up what has already been found. Sometimes, of course, it hides things to save its own neck and sometimes seemingly just for the hell of it.

Norman Maclean’s musings, quoted above, are from his wonderful prize-winning account of the Mann Gulch fire in which Wag Dodge spontaneously invented a way to save his life from the wall of fire speeding toward him:

Maclean, Norman. Young Men and Fire. Chicago: University of Chicago Press, 2017 [first edition 1992].

Labrador Noses May Be Cheaper and More Accurate Than Rapid Antigen Test at Detecting Covid-19

(p. A1) . . . three Labradors, operating out of a university clinic in Bangkok, are part of a global corps of dogs being trained to sniff out Covid-19 in people. Preliminary studies, conducted in multiple countries, suggest that their detection rate may surpass that of the rapid antigen testing often used in airports and other public places.

. . .

(p. A6) . . . as a group, the dogs being trained in Thailand — Angel, Bobby, Bravo and three others, Apollo, Tiger and Nasa — accurately detected the virus 96.2 percent of the time in controlled settings, according to university researchers. Studies in Germany and the United Arab Emirates had lower but still impressive results.

Sniffer dogs work faster and far more cheaply than polymerase chain reaction, or P.C.R., testing, their proponents say. An intake of air through their sensitive snouts is enough to identify within a second the volatile organic compound or cocktail of compounds that are produced when a person with Covid-19 sheds damaged cells, researchers say.

“P.C.R. tests are not immediate, and there are false negative results, while we know that dogs can detect Covid in its incubation phase,” said Dr. Anne-Lise Chaber, an interdisciplinary health expert at the School of Animal and Veterinary Sciences at the University of Adelaide in Australia who has been working for six months with 15 Covid-sniffing dogs.

Some methods of detection, like temperature screening, can’t identify infected people who have no symptoms. But dogs can, because the infected lungs and trachea produce a trademark scent. And dogs need fewer molecules to nose out Covid than are required for P.C.R. testing, Thai researchers said.

The Thai Labradors are part of a research project run jointly by Chulalongkorn University and Chevron. The oil company had previously used dogs to test its offshore employees for illegal drug use, and a Thai manager wondered whether the animals could do the same with the coronavirus.

. . .

Dogs, whose wet snouts have up to 300 million olfactory receptors compared with roughly six million for humans, can be trained to memorize about 10 smell patterns for a specific compound, Dr. Kaywalee said. Dogs can also smell through another organ nestled between their noses and mouths.

Some research has suggested that dogs of various breeds may be able to detect diabetes, Parkinson’s disease, malaria and certain cancers — that is, the volatile organic compounds or bodily fluids associated with them.

Labradors are among the smartest breeds, said Lertchai Chaumrattanakul, who leads Chevron’s part of the dog project. They are affable, too, making them the ideal doggy detector: engaged and eager.

Mr. Lertchai noted that Labradors are expensive, about $2,000 each in Thailand. But the cotton swabs and other basic equipment for canine testing work out to about 75 cents per sample. That is much cheaper than what’s needed for other types of rapid screening.

For the full commentary, see:

Hannah Beech. “The Best Rapid Covid-19 Test Adores Treats and Belly Rubs.” The New York Times (Tuesday, June 1, 2021): A1 & A6.

(Note: ellipses added.)

(Note: the online version of the commentary has the date May 31, 2021, and has the title “On the Covid Front Lines, When Not Getting Belly Rubs.”)

Some Tech Startups, and Big Tech Firms, Want Workers Back in Office

(p. A1) For a tech guy, Mike de Vere, chief executive of fintech software startup Zest AI, has a contrarian return-to-work plan for his 100 employees: he wants them in the office full time.

Mr. de Vere said having employees together in the Burbank, Calif., headquarters improves communication, builds trust and allows for them to absorb knowledge from more experienced colleagues.

“We believe that we will be our best selves the more that we are together,” he said.

As more tech companies leverage the promise of flexible work arrangements as a competitive advantage, some are going the opposite route, betting that a strong office culture is what will help them recruit and retain the best talent.

Proponents of fully in-office work cite a range of benefits, from the collaboration that can result from happenstance interactions to easier communication. Plus, they add, plenty of people enjoy working in offices, especially after months spent, for some, in makeshift arrangements. Given the tech industry’s status as a bellwether for workplace trends, professionals in many industries are watching to see where it lands.

. . .

(p. A4) Dan Kaplan, a partner with organizational consulting firm KornFerry International, said the pandemic has permanently changed the equation for employees. The days of being in the office just to show your face are over: “People aren’t willing to do it anymore,” he said.

Though people early in their careers crave mentorship and the ability to build their social circles on the job, Mr. Kaplan said he’s started seeing flexibility as a point of negotiation between job seekers and employers. Candidates are trying to broker fewer days a week in the office and CEOs prefer more time in person, he said.

“There is going to be tension in the system,” he said. What tech companies do will have impacts across industries, he added.

. . .

An Amazon spokesman said the company plans to gradually return to an office-centric workweek because it “enables us to invent, collaborate, and learn together most effectively.”

For the full story, see:

Katherine Bindley. “Tech Startups Eye a World, Post-Covid, Back in the Office.” The Wall Street Journal (Monday, April 26, 2021): A1 & A4.

(Note: ellipses added.)

(Note: the online version of the story has the date April 25, 2021, and has the title “Five Days in the Office? For These Startups, the Future of Work Is Old School.” The online edition says that the title of the print edition was: “Tech Startups Eye a World, Post-Virus, Back in the Office Some Tech Firms View Office As Place to Lure, Hold Talent.” My copy of the print edition had the title in the citation above.)

As “Neotenous Apes,” Humans Retain Their “Wandering, Exploratory Inner Child”

(p. C4) Cephalopods are having a moment. An octopus stars in a documentary nominated for an Academy Award (“My Octopus Teacher”). Octos, as scuba-diving philosopher Peter Godfrey Smith calls them, also play a leading role in his marvelous new book “Metazoa,” alongside a supporting cast of corals, sponges, sharks and crabs.

. . .

Smart birds and mammals also keep their neurons in one place—their brains. But octos split them up. They have over 500 million neurons altogether, about as many as dogs. But there are as many neurons altogether in their eight arms as in their heads. The arms seem able to act as independent agents, waving and wandering, exploring and sensing the world around them—even reaching out to the occasional diving philosopher or filmmaker. Mr. Godfrey-Smith’s book has a fascinating discussion of how it must feel to have this sort of split consciousness, nine selves all inhabiting the same body.

I think there might be a link between these two strange facts of octopus life. I’ve previously argued that childhood and intelligence are correlated because of what computer scientists call the “explore-exploit” trade-off: It’s very difficult to design a single system that’s curious and imaginative—that is, good at exploring—and at the same time, efficient and effective—or good at exploiting. Childhood gives animals a chance to explore and learn first; then when they grow up, they can exploit what they’ve learned to get things done.

. . .

Human adults are “neotenous apes,” which means we retain more childhood characteristics than our primate relatives do. We keep our brains in our heads, but neuroscience and everyday experience suggest that we too have divided selves. My grown-up, efficient prefrontal cortex keeps my wandering, exploratory inner child in line. Or tries to, anyway.

For the full commentary, see:

Alison Gopnik. “MIND AND MATTER; The Many Minds of the Octopus.” The Wall Street Journal (Saturday, April 17, 2021): C4.

(Note: ellipses added.)

(Note: the online version of the commentary has the date April 15, 2021, and has the same title as the print version.)

The book discussed in Gopnik’s commentary is:

Godfrey-Smith, Peter. Metazoa: Animal Life and the Birth of the Mind. New York: Farrar, Straus and Giroux, 2020.

British Entrepreneur Shattered French Wine Pretension

(p. A23) The world was paying little attention on May 24, 1976, when a small wine tasting was held in Paris at the Intercontinental Hotel. But the echoes of that tasting, later called the Judgment of Paris, have resounded for decades.

The instigator, Steven Spurrier, an Englishman who owned a wine shop and wine school in Paris, had set up a blind tasting of 20 wines — 10 white and 10 red — for nine French judges, including some of the top names in the French wine and food establishment.

. . .

It was hardly thought to be a fair fight. As has been recounted countless times, the judges were thoroughly convinced that California wines were inferior.

“Ah, back to France,” one judge sighed after tasting a Napa Valley chardonnay. Another, sniffing a Bâtard-Montrachet, declared: “This is definitely California. It has no nose.”

When all was done, a shocking consensus revealed the favorite wines to be a 1973 chardonnay from Chateau Montelena and a 1973 cabernet sauvignon from Stag’s Leap Cellars, both in Napa Valley.

The Americans celebrated, the French shrank in consternation, and everlasting fame awaited Mr. Spurrier, who went on to a long career as a wine entrepreneur.

. . .

The Paris tasting might have swiftly been forgotten had not a single reporter, George M. Taber of Time magazine, been on hand to witness the events. His article, “Judgment of Paris,” gave the California wine industry a much-needed boost, lending its vintners international credibility at a time when they were searching for critical approval and public acceptance.

. . .

Mr. Taber, the reporter, in 2005 published a book, “Judgment of Paris: California vs. France and the Historic 1976 Paris Tasting That Revolutionized Wine.” A 2008 film, “Bottle Shock,” with Alan Rickman playing Mr. Spurrier, depicted the tasting as the climax of a triumph-of-the-underdog story.

. . .

As for Mr. Spurrier, he leveraged the tasting into different careers in wine, with both triumphs and failures.

. . .

In 1987, the Spurriers bought a farm in Dorset near the south coast of England, and he decided that the chalk soil, similar to what can be found in Champagne and Chablis, was a perfect place for vines.

They did not start planting until 2009, by which time a burgeoning sparkling wine industry had taken root in southern England. Their sparkling wine, Bride Valley, had its first release in 2014.

For the full obituary, see:

Eric Asimov. “Steven Spurrier, 79, a Merchant Who Upended the Wine World With a Taste Test.” The New York Times (Thursday, March 18, 2021): A23.

(Note: ellipses added.)

(Note: the online version of the obituary was updated March 18, 2021, and has the title “Steven Spurrier, Who Upended Wine World With a Tasting, Dies at 79.”)

The Tabar book mentioned above is:

Taber, George M. Judgment of Paris: California Vs. France and the Historic 1976 Paris Tasting That Revolutionized Wine. New York: Scribner, 2005.

Journals Publish Positive Results So Scientists “File-Drawer” Negative Results

(p. A15) In “The Quick Fix: Why Fad Psychology Can’t Cure Our Social Ills,” Jesse Singal, a contributing writer at New York magazine, chronicles several dubious enthusiasms that permeate our culture. Along the way, he tries to show why they are so widespread. His focus is on “the allure of fad psychology,” as he puts it, and on the ways in which “both individuals and institutions can do a better job of resisting it.”

. . .

Academic journals, too, are keen to publish supposedly newsworthy findings. Under such conditions, it’s easy to see why a psychologist would be reluctant to re-examine her too-good-to-be-true results when doubts—her own and those of colleagues—begin to nag.

Each chapter of “The Quick Fix” presents accessible explanations of the research that was eventually shown to be “half-baked,” as Mr. Singal puts it. The problems, he shows, often derive from dodgy statistical analysis or faulty experimental design. Researchers, for instance, might use various statistical tests until one shows a sought-for result, or they might submit only positive results to a journal for publication, holding the negative ones back, a practice known as “file-drawering.” Mr. Singal also traces the social and political currents that helped propel certain trends.

Mr. Singal’s analysis is thus a quick fix for readers who want to be more enlightened and thoughtful consumers of psychological science.

For the full review, see:

Sally Satel. “BOOKSHELF; A Bias Toward Easy Answers.” The Wall Street Journal (Monday, April 12, 2021): A15.

(Note: ellipsis added.)

(Note: the online version of the review has the date April 11, 2021, and has the title “BOOKSHELF; ‘The Quick Fix’ Review: A Bias Toward Easy Answers.”)

The book under review is:

Singal, Jesse. The Quick Fix: Why Fad Psychology Can’t Cure Our Social Ills. New York: Farrar, Straus and Giroux, 2021.