We live in a world filled with viruses; they are everywhere that host species exist.
The Human Virome's Permanent Mark
The Human Virome's Permanent Mark
The virome doesn’t get as much love as its charismatic older brother, the microbiome. Studies of the bacteria that live inside us have caught the public imagination, showing that we contain a teeming diversity of critters whose populations affect everything from our diets to our immune systems. Thanks to cheap DNA sequencing, you can send samples of your microbiome to a lab and have a quick census taken; services like American Gut will even give you a colorful chart showing you which bacteria have been found and in what numbers. (Strictly the virome is part of the microbiome, which includes all the viruses, protozoa, and fungi living in one environment ― but bacteria are the stars of the show.)[more inside]
'Why People Oppose GMOs Even Though Science Says They Are Safe - Intuition can encourage opinions that are contrary to the facts' (SciAm)
Warren G. Harding is known for many things. Teapot Dome, dying in office (or maybe not), having the middle name "Gamaliel", and consistently being ranked one of the worst Presidents ever. His personal life was little better than his presidential one, with allegations of multiple affairs and even one claim of an illegitimate child born just a couple of years before he was elected to the White House. Which, according to DNA testing, is totally true. [more inside]
Since it folds in three dimensions, we could store all of the world’s current data—everyone’s photos, every Facebook status update, all of Wikipedia, everything—using less than an ounce of DNA. And, with its propensity to replicate given the right conditions, millions of copies of DNA can be made in the lab in just a few hours. Such favorable traits make DNA an ideal candidate for storing lots of informations, for a long time, in a small space.But how stable is DNA? The Reed-Solomon method, long used to error-check data transmission and duplication, is now being explored as an adjunct to the long-term archiving of information encoded in DNA. A post by Alex Riley at the PBS Science blog NOVA/NEXT.
In 2012 the genetics company 23andme gave web app developers the ability to create app mashups with DNA information. Most apps help users add genetics to their electronic health record, or connect with relatives, or explore risk factors for diseases. Two days ago a new webapp did something different: it showed how to only let white people in. [more inside]
You're arrested for murder. You didn't do it. But your DNA was found on the dead man's finger. How could that happen? The Surprisingly Imperfect Science of DNA Testing: How a proven tool may be anything but. A longform story by Katie Worth, produced by Frontline, Fusion, and The Marshall Project.
Kennewick Man - or the Ancient One - has a contentious history (previously and previouslier) that inspired a long legal and moral battle between scientists who said he probably wasn't Native American and wanted to study him, and local tribes who insisted that he was an ancestor and wanted to re-bury him. The scientists won in court in 2005, and a study has now determined from DNA evidence that Kennewick Man "was most closely related to DNA from the Confederated Tribes of the Colville Reservation, one of the five tribes who originally claimed Kennewick Man as an ancestor."
DNA carries traces of past events meaning poor lifestyle can affect future generations Between week two and week nine of an embryo’s development the genetic code is being rewritten to erase genetic alterations from the parents. However the researchers found that the processes does not clear all of the changes. Around 5 per cent of DNA appears resistant to reprogramming.
Carl Zimmer writes for The New York Times: How Simple Can Life Get? It's Complicated - "Scientists have long wondered how much further life can be stripped down and still remain alive. Is there a genetic essence of life? The answer seems to be that the true essence of life is not some handful of genes, but coexistence." [more inside]
... and linked an innocent man to a 20-year-old murder case. Analysis by the EFF of the case of Michael Usry, a New Orleans filmmaker whose father's DNA profile in a non-profit DNA database, which he had been assured would remain private, dragged him into a grisly unsolved murder case. [more inside]
The CRISPR Revolution [ungated: 1,2,3] - "Biologists continue to hone their tools for deleting, replacing or otherwise editing DNA and a strategy called CRISPR has quickly become one of the most popular ways to do genome engineering. Utilizing a modified bacterial protein and a RNA that guides it to a specific DNA sequence, the CRISPR system provides unprecedented control over genes in many species, including perhaps humans. This control has allowed many new types of experiments, but also raised questions about what CRISPR can enable." [more inside]
Doggie DNA test. You gotta do it!
Scientists are developing ways to edit the DNA of tomorrow’s children. Should they stop before it’s too late?
Using DNA to Build a Face, and a Case by Andrew Pollack [New York Times]
The growing capability to determine physical characteristics from genetics can help the police, but it also raises questions of rights and profiling.
Locals couldn’t understand why police hunting the murderer of a 13-year-old girl were taking DNA samples of elderly women. A high profile Italian murder investigation exposes the secrets of more than one family, with controversial collateral damage. [more inside]
"No one really wants to admit I exist," says co-discoverer of the DNA molecule, James Watson, who after years of shunning over controversial statements is auctioning his 1962 Nobel Prize medal this Thursday to help pay bills and buy some artwork. Online bidding is an option.
"Scientists have reconstructed the genome of a man who lived 45,000 years ago, by far the oldest genetic record ever obtained from modern humans. The research, published on Wednesday in the journal Nature, provided new clues to the expansion of modern humans from Africa about 60,000 years ago, when they moved into Europe and Asia. And the genome, extracted from a fossil thighbone found in Siberia, added strong support to a provocative hypothesis: Early humans interbred with Neanderthals."
In a book to be released Tuesday, an 'armchair detective' claims to have solved Jack the Ripper's identity using DNA.
Clones Are People Too: The Science and Science Fiction of BBC America’s Orphan Black. BBC America's science fiction series Orphan Black has returned for a second season, with Tatiana Maslany reprising her extraordinary performance playing half a dozen different clone characters. Meanwhile, in the real world, scientists have created cloned embryonic stem cells from the DNA of two adult humans. [Previously]
In February 2008, Yehia Gad sequenced Tutankhamun's genes in front of a documentary crew from the Discovery Channel. Jo Marchant writes about the previous work studying his tomb and remians and the unfortunate timing of the last study. (King Tut Previously) [more inside]
Much easier to put together custom DNA An interdisciplinary study led by Dr Ali Tavassoli, a Reader in chemical biology at the University of Southampton, has shown for the first time that 'click chemistry' can be used to assemble DNA that is functional in human cells, which paves the way for a purely chemical method for gene synthesis. Writing in Angewandte Chemie International Edition Dr Tavassoli's team and his collaborators, Dr Jeremy Blaydes and Professor Tom Brown, show that human cells can still read through strands of DNA correctly despite being stitched together using a linker not found in nature.
In the 1920s, two tons of pig parts were needed to produce eight ounces of purified insulin. In 1982 Humulin, human insulin produced by recombinant DNA, became the first such product approved by the United States Food and Drug Administration. Diabetes Forecast offers a look into modern insulin production.
"Read this carefully so that you understand it. When you come home we will show you the model. Lots of love, Daddy." In 1953 Francis Crick, sat down to write his twelve-year-old son Michael a letter explaining his brand-new discovery: the double-helix structure of DNA. Now you can read the original, seven-page hand-written letter, complete with an interactive feature that lets you click for details, context and explanations. Courtesy of the Smithsonian. [more inside]
Epigenetics (prev) is the study of changes in gene expression or cellular phenotype, caused by mechanisms other than changes in the underlying DNA sequence. David Epstein, a senior writer for Sports Illustrated has written about this topic for his book The Sports Gene (not as reductive as the title might suggest), but cut the chapter because the material he researched was so new as to require that he "caveat the writing rather heavily." Instead, he shared his chapter How an 1836 Famine Altered the Genes of Children Born Decades Later on IO9. You can read or hear more about the book in a half-hour segment from NPR's Fresh Air, opening with a story of Jennie Finch, a softball pitcher who "just whiff[ed] the best hitters in the world." (Related video clip: FSN Sport Science - Episode 7: Myths - Jennie Finch, on the force of fast baseball vs softball; ends with smarmy teaser for a "sex test")
For the first time in the United Kingdom, cat hair DNA has led to the conviction of a killer. [more inside]
They came from test tubes. They came pale as ghosts with eyes as blue-white as glacier ice. They came first out of Korea. N-Words - a science fiction short story by Ted Kosmatka. Audio version.
Full opinion (dissent at page 33): In what is arguably the most important criminal procedure case the Supreme Court has decided in decades, the Court today announced its 5-4 holding in Maryland v. King. The majority opinion, authored by Justice Kennedy, held that the 4th Amendment allows states to collect and analyze DNA from people arrested (but not convicted) of serious crimes.
Artist Heather Dewey-Hagborg uses the DNA found on things like discarded chewing gum and cigarette butts to recreate the faces of the people who left them behind.
Remember the Central Park jogger case from 1990? Here's a (lengthy, fascinating) New York Magazine article discussing the case just around the time of the 2002 exoneration of the initial five accused, four of whom had previously confessed to the crime. 24 years after the attack, a group of filmmakers, together with the five wrongly convicted men, have created a documentary telling the tale: The Central Park Five. Criminal reform activists everywhere are hoping the story might change a few minds. Previously
Celebrate the 60th anniversary of the discovery of DNA's structure with a pictorial story behind DNA's double helix and the Rosalind Franklin papers, including correspondences and lab notes that detail some of her crystallography research, findings that laid the groundwork for Watson and Crick's later publication.
Geneticists have proposed that if the evolution of life follows Moore's Law, then it predates the existence of planet Earth.
In Iceland, with a population of around a third of a million, the danger exists of that heady one-night stand ending up as an intimate encounter between near-relatives, as nearly happened to the friend of Elin Edda. No longer, due to the launch of an android app ("Bump the app before you bump in bed") which easily tells a budding couple how related they are. [more inside]
Have created "logic gates" they call “Boolean Integrase Logic,” or “BIL gates” for short. Original article in Science. This is same team that created DNA storage and what they are calling a "biological Internet" before.
The Hidden Life Of the Cell (57:24) There is a battle playing out inside your body right now. It started billions of years ago and it is still being fought in every one of us every minute of every day. It is the story of a viral infection - the battle for the cell. This film reveals the exquisite machinery of the human cell system from within the inner world of the cell itself - from the frenetic membrane surface that acts as a security system for everything passing in and out of the cell, the dynamic highways that transport cargo across the cell and the remarkable turbines that power the whole cellular world to the amazing nucleus housing DNA and the construction of thousands of different proteins all with unique tasks. The virus intends to commandeer this system to one selfish end: to make more viruses. And they will stop at nothing to achieve their goal. Exploring the very latest ideas about the evolution of life on earth and the bio-chemical processes at the heart of every one of us, and revealing a world smaller than it is possible to comprehend, in a story large enough to fill the biggest imaginations.
You may be familiar with molecular movies from my two previous megaposts collecting them, but this extended documentary uses original animation that is collected into a coherent educational narrative and is just so fucking gorgeous. Enjoy.[more inside]
November 24, 2012: analysis of extensive DNA sequencing of 'a novel hominin hybrid species, commonly called “Bigfoot” or “Sasquatch” ... suggests that the legendary Sasquatch is a human relative that arose approximately 15,000 years ago as a hybrid cross of modern Homo sapiens with an unknown primate species.' The press release claimed that the research was "currently under peer-review," except that no scientific journal would publish the research, until now: DeNovo, an open access scientific journal. But DeNovo isn't really open access, as it costs $30 to view the article, the paper itself is brand new, the domain was recently purchased, and the website features generic stock photos. Ars Technica digs deeper, summarizing some of the "open access" article, and providing a link to a particularly insightful clip on YouTube, with an odd water mark. [more inside]
"The researchers began with the computer files from some notable cultural highlights: an audio recording of MLK Jr.’s 1963 “I Have a Dream” speech, all 154 of Shakespeare’s sonnets, and, appropriately, a copy of Watson and Crick’s original research paper describing DNA’s double helix structure. On a hard drive, these files are stored as a series of zeros and ones. The researchers worked out a system to translate the binary code into one with four characters instead: A, C, G and T. They used this genetic code to synthesize actual strands of DNA with the content embedded in its very structure. The ouput was actually pretty unimpressive: just a smidgeon of stuff barely visible at the bottom of a test tube. The wow factor arose when they reversed the process. The researchers sequenced the genome of the data-laden DNA and translated it back into zeros and ones. The result was a re-creation of the original content without a single error, according to the results published in Nature on Wednesday."
"If the history of public health has until now been embodied by the map—as in British physician John Snow’s famous map, which allowed him to curb the London cholera outbreak of 1854 and to found, in doing so, the modern field of epidemiology—Snitkin was embarking on a new kind of epidemiology: one founded on the phylogenetic tree." Writing for Wired, Carl Zimmer describes how Evan Snitkin and Julie Segre used genome sequencing to halt a bacterial outbreak at the National Institute of Health's Clinical Center. (via The Feature)
Scientists at the European Bioinformatics Institute successfully encoded several different file formats onto strands of synthetic DNA, which were then sent to an American lab and sequenced to extract the data. Selections included Shakespeare, audio of Dr. Martin Luther King, and photos of their lab. If the idea sounds vaguely familiar, you've probably been reading Dresden Codak.
Just think about it for a moment: One gram of DNA can store 700 terabytes of data. That’s 14,000 50-gigabyte Blu-ray discs… in a droplet of DNA that would fit on the tip of your pinky. To store the same kind of data on hard drives — the densest storage medium in use today — you’d need 233 3TB drives, weighing a total of 151 kilos. In Church and Kosuri’s case, they have successfully stored around 700 kilobytes of data in DNA — Church’s latest book, in fact — and proceeded to make 70 billion copies (which they claim, jokingly, makes it the best-selling book of all time!) totaling 44 petabytes of data stored. [more inside]
"The Double Helix has more in common with Truman Capote's In Cold Blood than, say, The Decline and Fall of the Roman Empire."
"The Turn of the Screw: James Watson on The Double Helix and his changing view of Rosalind Franklin": Maggie Koerth-Baker's brief interview with Watson, co-discoverer of the structure of DNA, about his "infamous" treatment of Franklin in his book The Double Helix, on the occasion of the publication of an annotated and illustrated edition of the same.
Hacking the President’s DNA. "The U.S. government is surreptitiously collecting the DNA of world leaders, and is reportedly protecting that of Barack Obama. Decoded, these genetic blueprints could provide compromising information. In the not-too-distant future, they may provide something more as well—the basis for the creation of personalized bioweapons that could take down a president and leave no trace."
The Genome Compiler is an IDE for DNA projects for all you DIYbio enthusiasts. Previously. Previously.
With the possible exception of the Nobel awards, physicists seem to get all the press these days, whether they're doing quantum level work at the LHC, or cosmology via the latest satellite data. Biologists, not so much. It's too bad, because Richard Lenski is running one of the great evolutionary experiments of our time, and it's producing interesting results. [more inside]
Plurality... in 2023, the Grid knows who you are and where you go at all times. A short near future sci-fi movie (15 min).