(Roughly) Daily

Posts Tagged ‘DNA

“I have all these great genes, but they’re recessive. That’s the problem here.”*…

DNA Sequence chromatograms produced by automated sequencing machines

When the Human Genome Initiative published its first findings in 2002, the world was shocked. Genetic biologists, however, had long ago come to realize that DNA sequences are only part of the story of how organisms develop…

Fueled by the expectation that knowing the sequence of our DNA would tell us who we are, US funding agencies launched one of the most ambitious scientific efforts of all time in 1990. I refer, of course, to the Human Genome Initiative. Since then, the pace of that effort has been furious:even before the decade was over, the finishing line was clearly in view. When in February 2001, two rival teams announced the results of their first analysis of this invaluable information, their report made front-page headlines around the world. Humans, it seems, have far fewer genes than had been expected — in fact, only a third more than the lowly roundworm. How can this be? And what does it mean? Are we really so similar to, and so little more than, mere worms? News of the extent of our commonality with all living species is as stunning as it is humbling. But at the same time, it invites a certain incredulity — and that not merely because of human pride. Simple observation of the manifest diversity of life also makes us resist, for it is impossible not to wonder: what is it, if not the number (and in many cases, even the structure) of the ‘genes’ encoded in our DNA that accounts for the extraordinary differences among living organisms? For the answer to this question, it seems that we will have to look to the regulatory dynamics that determine how the sequence information of the DNA is to be used by the cell. Here, in the complex regulation of genetic transcription, of translation, of protein structure and function, is where we will find what makes us human beings rather than worms, flies or mice. Knowledge of the sequence of our DNA can tell us an enormous amount, but it can almost certainly not tell us who we are.

But not everyone was taken aback by this news. While readers of the popular press may have been stunned, few biologists working at the frontiers of research in molecular genetics were astonished. True, they had expected a larger number of human ‘genes’, but they had long ago come to realise that DNA sequences are only part of the story of how organisms develop, and even of what we mean by a ‘gene’. They recognise, for example, that the spatial and temporal patterns of expression of a gene are even more crucial to the specification of an organism than the structure of that ‘gene’ is. They also know that no single definition of this word ‘gene’ can suffice. Of the many different definitions that are required to make sense of current usage, two stand out with particular clarity: one referring to a particular region of the DNA, and another to the unit of messenger RNA that is used in the synthesis of a particular protein. The number of genes of the second kind is in fact very much larger than that of the first kind (current estimates suggest more than ten times as many), for the fact is that many different ‘genes’ can be constructed out of a single specified region of the DNA. Because the particular context in which they use the word makes its meaning quite clear, ambiguities in usage rarely create problems for practising biologists. Not so, however, for most readers. Outside the laboratory, such linguistic uncertainties can lead to both confusion and misunderstanding — not only around the question of how many genes we have, but also of what genes are made of, where they reside, what they do and, perhaps most important, what genes are for.

The good news is that research in genetics has never been more exciting, and over the last few decades both the depth and the breadth of our understanding of the nature of genetic activity have grown spectacularly. With each advance, the picture of the role of genes in development that biologists learn to draw grows ever more complex and sophisticated, and in ever more conspicuous defiance of the simple mantra with which they began. The word ‘gene’ does not begin to do justice to the ingenuity of the mechanisms required to put biological organisms together — no more than the concept of the neuron does to the ingenuity and dynamic complexity of neural organisation, and no more than talk of individual minds to the complexities of language and cognition…

Unpacking the genome hasn’t turned out to be the master key to understanding life that many thought it would be– but that’s no reason not to celebrate what it does illuminate: “The century of the gene,” from Evelyn Fox Keller in @EngelsbergIdeas.

* Calvin, in Calvin and Hobbes (Bill Watterson)

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As we investigate inheritance, we might spare a thought for D’Arcy Wentworth Thompson; he died on this date in 1948.  A classics scholar who was also an accomplished biologist and mathematician, Thompson is best remembered for On Growth and Form (1917, new ed. 1942), a profound consideration of the shapes of living things, starting from the simple premise that “everything is the way it is because it got that way.”  Thus one must study not only finished forms, but also the forces that molded them: “the form of an object is a ‘diagram of forces’, in this sense, at least, that from it we can judge of or deduce the forces that are acting or have acted upon it.”

The book paved the way for the scientific explanation of morphogenesis, the process by which patterns are formed in plants and animals.  Thompson’s description of the mathematical beauty of nature inspired thinkers as diverse as Alan Turing and Claude Levi-Strauss, and artists including Henry Moore, Salvador Dali, and Jackson Pollock.  Peter Medawar, the 1960 Nobel Laureate in Medicine, called On Growth and Form “the finest work of literature in all the annals of science that have been recorded in the English tongue.”

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Written by (Roughly) Daily

June 21, 2022 at 1:00 am

“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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“A mind that is stretched by a new idea can never go back to its original dimensions”*…

Alex Berezow observes (in an appreciation of Peter AtkinsGalileo’s Finger: The Ten Great Ideas of Science) that, while scientific theories are always being tested, scrutinized for flaws, and revised, there are ten concepts so durable that it is difficult to imagine them ever being replaced with something better…

In his book The Structure of Scientific Revolutions, Thomas Kuhn argued that science, instead of progressing gradually in small steps as is commonly believed, actually moves forward in awkward leaps and bounds. The reason for this is that established theories are difficult to overturn, and contradictory data is often dismissed as merely anomalous. However, at some point, the evidence against the theory becomes so overwhelming that it is forcefully displaced by a better one in a process that Kuhn refers to as a “paradigm shift.” And in science, even the most widely accepted ideas could, someday, be considered yesterday’s dogma.

Yet, there are some concepts which are considered so rock solid, that it is difficult to imagine them ever being replaced with something better. What’s more, these concepts have fundamentally altered their fields, unifying and illuminating them in a way that no previous theory had done before…

The bedrock of modern biology, chemistry, and physics: “The ten greatest ideas in the history of science,” from @AlexBerezow in @bigthink.

* Oliver Wendell Holmes

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As we forage for first principles, we might send carefully-calcuated birthday greetings to Georgiy Antonovich Gamov; he was born on this date in 1904. Better known by the name he adopted on immigrating to the U.S., George Gamow, he was a physicist and cosmologist whose early work was instrumental in developing the Big Bang theory of the universe; he also developed the first mathematical model of the atomic nucleus. In 1954, he expanded his interests into biochemistry and his work on deoxyribonucleic acid (DNA) made a basic contribution to modern genetic theory.

But mid-career Gamow began to shift his energy to teaching and to writing popular books on science… one of which, One Two Three… Infinity, inspired legions of young scientists-to-be and kindled a life-long interest in science in an even larger number of other youngsters (including your correspondent).

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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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“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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