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Posts Tagged ‘DNA

“‘Life’ is of course a misnomer, since viruses, lacking the ability to eat or respire, are officially dead”*…

The human genome contains billions of pieces of information and around 22,000 genes, but not all of it is, strictly speaking, human. Eight percent of our DNA consists of remnants of ancient viruses, and another 40 percent is made up of repetitive strings of genetic letters that is also thought to have a viral origin. Those extensive viral regions are much more than evolutionary relics: They may be deeply involved with a wide range of diseases including multiple sclerosis, hemophilia, and amyotrophic lateral sclerosis (ALS), along with certain types of dementia and cancer.

For many years, biologists had little understanding of how that connection worked—so little that they came to refer to the viral part of our DNA as dark matter within the genome. “They just meant they didn’t know what it was or what it did,” explains Molly Gale Hammell, an associate professor at Cold Spring Harbor Laboratory. It became evident that the virus-related sections of the genetic code do not participate in the normal construction and regulation of the body. But in that case, how do they contribute to disease?

An early clue came from the pioneering geneticist Barbara McClintock, who spent much of her career at CSHL. In the 1940s, long before the decoding of the human genome, she realized that some stretches of our DNA behave like infectious invaders. These DNA chunks can move around through the genome, copying and pasting themselves wherever they see fit, which inspired McClintock to call them “jumping genes.” Her once-controversial idea earned her a Nobel Prize in 1983.

Geneticists have since determined that jumping genes originate in the viral portion of the genome. Many of these genes turn out to be benign or even helpful. “But some of the things are full-on parasites,” Hammell says, like infections embedded within our own DNA. All it takes to set these bad actors loose, she is finding, is a slip-up in the body’s mechanisms that normally prevent the genes from jumping around and causing harm…

Half of your genome started out as an infection; if left unchecked, some parts of it can turn deadly all over again: “The Non-Human Living Inside of You.”

See also: “The Wisdom of Pandemics– viruses are active agents, existing within rich lifeworlds. A safe future depends on understanding this evolutionary story.”

* “‘Life’ is of course a misnomer, since viruses, lacking the ability to eat or respire, are officially dead, which is in itself intriguing, showing as it does that the habit of predation can be taken up by clusters of molecules that are in no way alive.” – Barbara Ehrenreich, Living with a Wild God: A Nonbeliever’s Search for the Truth about Everything

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As we check our baggage, we might send reforming birthday greetings to Abraham Flexner; he was born on this date in 1866.  The founding director of Princeton’s Institute for Advanced Studies, Flexner is best remembered for his pioneering work as a reformer of American higher education, especially medical education.  On the heels of his 1908 study, The American College, in which he effectively critiqued the university lecture as a method of instruction, he published the Flexner Report, which examined the state of American medical education and led to far-reaching reform in the training of doctors.  The report called on American medical schools to enact higher admission and graduation standards, and to adhere strictly to the protocols of mainstream science in their teaching and research.  While one unintended consequence of Flexner’s impactful advocacy was the reversion of American universities to male-only admittance programs to accommodate a smaller admission pool (female admissions picked up again only later the century), most historians agree with his biographer, Thomas Bonner, that Flexner was “the severest critic and the best friend American medicine ever had.”

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“Last time I checked, the digital universe was expanding at the rate of five trillion bits per second in storage”*…

 

Oz in DNA

 

… and rising.  Happily, technologists are keeping up:

The intricate arrangement of base pairs in our DNA encodes just about everything about us. Now, DNA contains the entirety of “The Wonderful Wizard of Oz” as well.

A team of University of Texas Austin scientists just vastly improved the storage capacity of DNA and managed to encode the entire novel — translated into the geek-friendly language of Esperanto — in a double strand of DNA far more efficiently than has been done before. DNA storage isn’t new, but this work could help finally make it practical…

The full story at “Scientists Stored “The Wizard of Oz” on a Strand of DNA.”  The UT release, here.

* George Dyson

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As we reconsider Kondo, we might send carefully-stowed birthday greetings to Jay Wright Forrester; he was born on this date in 1914.  A pioneering computer engineer and systems scientist, he was one of the inventors of magnetic core memory, the predominant form of random-access computer memory during the most explosive years of digital computer development (between 1955 and 1975).  It was part of a family of related technologies which bridged the gap between vacuum tubes and semiconductors by exploiting the magnetic properties of materials to perform switching and amplification.

And close to your correspondent’s heart, Forrester is also believed to have created the first animation in the history of computer graphics, a “jumping ball” on an oscilloscope.

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“Thinking within strict limits is stifling”*…

 

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Affectionately nicknamed “Conan the Bacterium,” Deinococcus radiodurans, a so-called polyextremophile, has an uncanny ability to rapidly repair damage to its genome. As a result, it can resist the most hostile conditions, from drought to radiation to acid baths to a Martian atmosphere. And if Canadian conceptual poet Christian Bök has his way, it will compose verse that will outlive our Sun.

Bök has earned a reputation for conducting extremely difficult poetic experiments and executing them with technical wizardry. In his award-winning 2001 bestseller Eunoia , for example, he uses only a single vowel in each chapter, a constraint that produces a form known as a univocalic . The first section is composed of words that include no vowels other than a , the second includes no vowels other than e , and so on. To build an appropriate lexicon for this demanding work, Bök read through Webster’s Third International Unabridged Dictionary five times and spent six years writing. His latest poetic challenge takes him into trickier and more technically specialized territory. Taking on the very perishability of text, Bök has devised a novel solution: In composing his verse, he is employing the medium of life itself.

The Xenotext: Book 1 represents the first phase of Bök’s wildly ambitious project—nearly 15 years in the making and still ongoing—of encoding poetry into the genome of the bacterium D. radiodurans . Using a substitution cipher, Bök “translates” his poetry into what he calls a “chemical alphabet” representing a genetic sequence. After simulating the resulting protein’s folding pattern, which is essential for its functioning, Bök sends his specifications to a biotechnical lab that engineers the gene accordingly. Finally, Bök’s team of biologists transplants a plasmid carrying the gene into the bacterium.

But why introduce such complexity into the process of poetic composition? The Xenotext provocatively wagers that—in the face of global catastrophe, whether in the form of ecological collapse, drug-resistant pandemic, or nuclear war—D. radiodurans can preserve at least a bit of humanity’s poetic heritage after the apocalypse. DNA, with its remarkable storage capacity and stability, is perhaps the “natural element,” the worthy vessel for the mind’s substance that Wordsworth expresses longing for in the epigraph above…

Writing an eternal poem, one that will survive in the DNA of extremophile bacteria when all other life on the planet is extinguished: “Poetry of the Apocalypse.”

For more on exactly how Bök “writes,” see: “The Making of a Xenotext.”

* Christian Bök

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As we ponder posterity, we might send straight-forward birthday greetings to Joseph Addison; he was born on this date in 1672.  A poet, playwright, and politician, Addison is probably best remembered for The Spectator, a daily publication– a “paper” as it was then called, and as it successors have been known ever since– which he founded in London with his partner Richard Steele.

The Spectator was widely read in London; indeed Jürgen Habermas suggests that the paper was instrumental in the emergence of the public sphere in 18th century England.  It also had North American readers (including Benjamin Franklin and James Madison).

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Written by LW

May 1, 2020 at 1:01 am

“Life is a DNA software system”*…

 

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DNA from discarded cigarette butts and chewed up gum has been used to create a series of life-sized 3D printed portraits for a new exhibition at the Wellcome Collection.

American artist Heather Dewey-Hagborg walked the streets of New York picking up cigarettes and hair for her project called Stranger Visions.

She then analysed the DNA to work out the gender and ethnicity of the people involved as well as their likely eye colour and other traits including the size of their nose, before using face-generating software and a 3D printer to create a series of speculative portraits

More– and more photos– at “3D printed portraits made with DNA from cigarette butts to feature in new Wellcome Collection display.”

See also the analogically-related “Artificial Intelligence Generates Humans’ Faces Based on Their Voices.”

* Craig Venter

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As we noodle on nature and nurture, we might recall that it was on this date in 1981 that the USDA announced the first genetically-engineered vaccine for any animal or human disease: an immunization against Hoof and Mouth Disease (also known as Foot and Mouth Disease, or FMD), created using gene splicing.

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“It is not the strongest or the most intelligent who will survive but those who can best manage change”*…

 

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In the near future, we will be in possession of genetic engineering technology which allows us to move genes precisely and massively from one species to another. Careless or commercially driven use of this technology could make the concept of species meaningless, mixing up populations and mating systems so that much of the individuality of species would be lost. Cultural evolution gave us the power to do this. To preserve our wildlife as nature evolved it, the machinery of biological evolution must be protected from the homogenizing effects of cultural evolution.

Unfortunately, the first of our two tasks, the nurture of a brotherhood of man, has been made possible only by the dominant role of cultural evolution in recent centuries. The cultural evolution that damages and endangers natural diversity is the same force that drives human brotherhood through the mutual understanding of diverse societies. Wells’s vision of human history as an accumulation of cultures, Dawkins’s vision of memes bringing us together by sharing our arts and sciences, Pääbo’s vision of our cousins in the cave sharing our language and our genes, show us how cultural evolution has made us what we are. Cultural evolution will be the main force driving our future…

An important essay by Freeman Dyson, emeritus professor of physics at the Institute for Advanced Study in Princeton: “Biological and Cultural Evolution– Six Characters in Search of an Author.”

* Leon C. Megginson (often misattributed to Darwin, on whose observations Megginson based his own)

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As we agonize over the anthropocene, we might recall that it was on this date in 1968 that James Watson’s The Double Helix was published.  A memoir, it describes– with manifest hubris– “perhaps the most famous event in biology since Darwin’s book,” the 1953 discovery, published by Watson and Francis Crick, of the now-famous double helix structure of the DNA molecule.

Crick, however, viewed Watson’s book as “far too much gossip,” and believed it gave short shrift to Rosalind Franklin’s vital contribution via clues from her X-ray crystallography results.  It was originally slated to be published by Harvard University Press, Watson’s home university,  Harvard dropped the arrangement after protests from Francis Crick and Maurice Wilkins (their supervisor, who shared the Nobel Prize);  it was published instead by Atheneum in the United States and Weidenfeld & Nicolson in the UK.

In any case, the book opens a window into the competitiveness, struggles, doubts, and human foibles that were baked into this landmark in science.

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