(Roughly) Daily

Posts Tagged ‘genetics

“It is sad to go to pieces like this but we all have to do it”*…

Still, some species “do it” differently than others…

It is well known that somatic mutations — mutations in our body’s genetic code that accumulate over time — can cause cancer, but their broader role in ageing is less clear.

Now a team of researchers have measured the somatic mutation rates of a range of mammals and discovered a striking correlation between mutation rate and lifespan. Lending evidence to the theory that somatic mutations are a cause of ageing rather than a result of it…

Ageing is linked to accumulated mutations: “The lifespan secret: why giraffes live longer than ferrets,” from @Nature.

* Mark Twain, on aging

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As we grow old gracefully, we might send carefully-deduced birthday greetings to William Ian Beardmore (WIB) Beveridge; he was born on this date in 1908.  A veterinarian who served as  director of the Institute of Animal Pathology at Cambridge, he identified the origin of the Great Influenza (the Spanish Flu pandemic, 1918-19)– a strain of swine flu.

WIB Beveridge

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Happy Shakespeare’s Birthday!

“The world is bound in secret knots”*…

Everyone knows what a knot is. But knots have special significance in math and science because their properties can help unlock secrets hidden within topics ranging as widely as the biochemistry of DNA, the synthesis of new materials, and the geometry of three-dimensional spaces. In his podcast, The Joy of Wh(Y), the sensational Steven Strogatz explores the mysteries of knots with his fellow mathematicians Colin Adams and Lisa Piccirillo

How do mathematicians distinguish different types of knots? How many different kinds of knots are there? And why do mathematicians and scientists care about knots anyway? Turns out, there’s lots of real-world applications for this branch of math, now called knot theory. It started out with the mystery of the chemical elements about 150 years ago, which were, at the time, thought to be different kinds of knots tied in the ether. Nowadays, knot theory is helping us understand how enzymes can disentangle strands of linked DNA. And also, knot theory has potential in basic research to create new kinds of medicines, including some chemotherapy drugs. But in math itself, knot theory is helping mathematicians work out the riddles of higher-dimensional spaces…

The study of knots unites the interests of researchers in fields from molecular biology to theoretical physics: “Untangling Why Knots Are Important,” from @stevenstrogatz in @QuantaMagazine. Listen here; read the transcript here.

Athanasius Kircher

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As we take stock of tangles, we might might send nicely-tied birthday greetings to a beneficiary and user of knot theory, Francis Collins; he was born on this date in 1950. A physician and geneticist, he discovered the genes associated with a number of diseases, led the Human Genome Project, and served as the director of the National Institutes of Health.

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“How is it that you keep mutating and can still be the same virus?”*…

Thale cress (Arabidopsis thaliana)

A common plant has yielded insights that question a fundamental assumption in biology– more specifically, an assumption about the mechanism of natural selection…

A simple roadside weed may hold the key to understanding and predicting DNA mutation, according to new research from University of California, Davis, and the Max Planck Institute for Developmental Biology in Germany.

The findings, published today in the journal Nature, radically change our understanding of evolution and could one day help researchers breed better crops or even help humans fight cancer.

Mutations occur when DNA is damaged and left unrepaired, creating a new variation. The scientists wanted to know if mutation was purely random or something deeper. What they found was unexpected.

“We always thought of mutation as basically random across the genome,” said Grey Monroe, an assistant professor in the UC Davis Department of Plant Sciences who is lead author on the paper. “It turns out that mutation is very non-random and it’s non-random in a way that benefits the plant. It’s a totally new way of thinking about mutation.”

Knowing why some regions of the genome mutate more than others could help breeders who rely on genetic variation to develop better crops. Scientists could also use the information to better predict or develop new treatments for diseases like cancer that are caused by mutation.

“Our discoveries yield a more complete account of the forces driving patterns of natural variation; they should inspire new avenues of theoretical and practical research on the role of mutation in evolution,” the paper concludes.

Evolutionary theory revised? A new study challenges the received wisdom that that DNA mutations are random. Read the underlying paper here.

* Chuck Palahniuk, Invisible Monsters

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As we contemplate change, we might send micro-biological birthday greetings to Ruth Sager; she was born on this date in 1918. A geneticist, she had two careers in science.

In the 1950s and 1960s, she pioneered the field of cytoplasmic genetics by discovering transmission of genetic traits through chloroplast DNA, the first known example of genetics not involving the cell nucleus. The academic community did not acknowledge the significance of her contribution until after the second wave of feminism in the 1970s.

Then, in the early 1970s, she moved into cancer genetics (with a specific focus on breast cancer); she proposed and investigated the roles of tumor suppressor genes.

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“I like it when a flower or a little tuft of grass grows through a crack in the concrete. It’s so f#@kin’ heroic.”*…

From dilapidated power plants, abandoned medical facilities, and amusement parks left in rusted ruin, the compelling scenes that French photographer Jonathan Jimenez, aka Jonk (previously), captures are evidence of nature’s endurance and power to reclaim spaces transformed by people. Now compiled in a new book titled Naturalia II, 221 images shot across 17 countries frame the thriving vegetation that crawls across chipped concrete and architecture in unruly masses.

This succeeding volume is a follow-up to Jonk’s first book by the same name and focuses on the ways the ecological crisis has evolved during the last three years. He explains the impetus for the book in a statement:

On the one hand, the situation has deteriorated even further with yet another species becoming extinct every single day. Global warming continues and has caused repeated natural catastrophes: floods, fires, droughts, etc. On the other hand, our collective awareness has widely increased. We are still a long way from the commitment needed to really change things, but we are heading in the right direction. Millions of initiatives have already emerged, and I hope that my photos and the message contained within them can play a small part in the collective challenge facing us all…

More at “Nature Resurges to Overtake Abandoned Architecture in a New Book of Photos by Jonk” and at his site.

On an apposite note: “Forest the size of France regrown worldwide over 20 years, study finds.”

* George Carlin

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As we inspect the inexorable, we might spare a thought for Hugo Marie de Vries; he died on this date in 1935. A botanist, he introduced the experimental study of organic evolution– and was, thus, was one of the first geneticists. His rediscovery in 1900 (simultaneously with the botanists Carl Correns and Erich Tschermak von Seysenegg) of Gregor Mendel’s principles of heredity and his theory of biological mutation, though considerably different from a modern understanding of the phenomenon, resolved ambiguous concepts concerning the nature of variation of species that, until then, had precluded the universal acceptance and active investigation of Charles Darwin’s system of organic evolution.

He suggested the concept of genes and introduced the term “mutation”, and developed a mutation theory of evolution.

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“If Ancestry or its businesses are acquired… we will share your Personal Information with the acquiring or receiving entity”*…

If you’ve never before considered how valuable an asset your DNA might be, you are far behind. Some of the biggest direct-to-consumer DNA sequencing companies are busy monetizing their large-scale genomics databases, with hopes to shape the burgeoning DNA economy and reap its rewards. And if you spit in a cup for one of these companies, your DNA might already be under the corporate control of some of the richest firms on Wall Street.

With their purchase of Ancestry.com late last year, the private equity firm Blackstone now owns the DNA data of 18 million people. And Blackstone is currently ramping up efforts to monetize the data amassed among the companies it owns. But experts say Wall Street firms’ interest in genomics poses new and unforeseen threats, and risks sowing distrust among DNA donors. Without trust, could we miss out on the genome’s real value?

Since the global financial crisis of 2008, private equity firms—which buy up and reshape diverse private companies—have quietly overtaken traditional investment banks like Goldman Sachs as the “dominant players in the financial world,” according to the Financial Times. It’s been a rough tenure so far. While private equity mega-deal hits have made billions for investors, often the companies acquired pay the price, as with high-profile flops including mismanaged music group EMI and bankrupt retailer Toys R Us. The industry has become “the poster child for financial firms that suck value out of the economy,” said U.S. Senator Elizabeth Warren, while introducing an act to Congress aimed at reining in private equity “vampires.

In December the biggest, most dominant private equity company of them all, the Blackstone Group, Inc., which boasts half a trillion dollars in assets under management, made a dramatic entry into the genomics space when it bought a controlling stake in Ancestry.com as part of the deal that valued the genealogy and gene testing company at $4.7 billion. And with that one stroke of the pen, the firm acquired the largest trove of DNA data assembled by any consumer gene tester. If your own DNA sequence is included in this collection, it exists on servers somewhere along with the genomes of 18 million people from at least 30 countries.

Announcing the deal, David Kestnbaum, a senior managing director at Blackstone said he foresees Ancestry growing by “investing behind further data, functionality, and product development.” At the same time, many privacy-concerned watchers had the same question: How does Blackstone aim to monetize Ancestry’s massive database, which includes users’ most sensitive genomic data and family histories?

Those lingering worries were ignited in the final days of 2020 by revelations buried in U.S. Securities and Exchange Commission (SEC) filings, and unearthed by Bloomberg, that showed Blackstone will begin to “package and sell data” from the companies it acquires as a fresh revenue stream. 

For any entrepreneur or investor in the genomics space who knows the industry needs investment to realize its dramatic potential, the question is vexed. Are deals that bring sensitive data under the control of private equity mega-funds a much-needed path to realizing the industry’s goals? Or do they threaten to derail the rapid progress that consumer gene science is making?…

A Wall Street giant’s big bet on Ancestry.com drives home the financial realities– and the privacy challenges– facing the consumer genomic revolution: “Is Your DNA Data Safe in Blackstone’s Hands?

* from Ancestry.com’s EULA, September 23, 2020 (between Blackstone announcing its plan to buy and the deal completing)

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As we appraise the personal, we might send carefully-deduced birthday greetings to Samuel “Sam” Loyd; he was born on this date in 1841. A chess player, chess composer, puzzle author, and recreational mathematician, he was a member of the Chess Hall of Fame (for both his play and for his exercises, or “problems”). He gained broader posthumous fame when his son published a collection of his mathematical and logic puzzles, Cyclopedia of 5000 Puzzles after his father’s death.  As readers can see here and here, his puzzles still delight.

Loyd’s most famous puzzle was the 14-15 Puzzle, which he produced in 1878. His original authorship is debated; but in any case, his version created a craze that swept America to such an extent that employers put up notices prohibiting playing the puzzle during office hours.

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Written by (Roughly) Daily

January 31, 2021 at 1:01 am

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