Over the last couple of days, you might have heard about the "duon" — a "second" genetic code that's being hyped as a radical new "breakthrough" in science.
Based solely on the number of words I've put in quotations here, you can probably guess that the actual news doesn't really match the hype.
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You can’t patent the building blocks of life, but you can patent a type of synthetic DNA that contains all the same information. Maggie Koerth-Baker explains how the Justices misunderstood the science and the effect that their verdict could have on future research.
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Back in February, a Texas forensic scientist announced that she'd identified a DNA sample from Bigfoot and had sequenced the creature's genome. Now the sequences have been released for wider scrutiny and Ars Technica's John Timmer had a chance to dig into the data
and speak with the discoverer of the possible Bigfoot genome. This is a story that, I think, everybody can enjoy — a skeptical analysis that's respectful to the Bigfoot researchers and genuinely interested in understanding where the DNA in question came from and what the genome sequences can tell us. — Maggie
Scientists at the University of Copenhagen sequenced the oldest genome yet — 700,000-year-old DNA
from an ancient ancestor of the horse. The Nature Podcast explains why doing this is valuable
(and, no, it's not about creating a cloned ancient horse park) and how you go about sequencing such elderly, and thus degraded, DNA. — Maggie
Nine people who have not recently made any sweeping judgements about biotechnology.
Last week, I told you about the US Supreme Court ruling that made it illegal to patent naturally occurring DNA. In that article, I talked briefly about the fact that the new ruling doesn't cover all DNA. It's still perfectly legal to patent synthetic DNA, and the court documents referred specifically to complementary DNA (aka cDNA).
This is where things get murky. Complementary DNA is a thing that can be both natural and synthetic. And, as a laboratory creation, it's an important step in a common method of replicating naturally occurring DNA. All of which leaves some holes in the idea that the Supreme Court ruling is a simple "win" for open-access science, patent activists, and patients. After all, if you can't patent a gene, but you can patent the laboratory copy of the gene, what's that mean? It's sort of like not being able to patent a novel, but being able to patent a copy of its contents that's had all the white space removed. It seems like everybody is a bit confused by this. So I wanted to take a moment to at least clarify what cDNA is and what some people, on different sides of the science/law/biotech divides, are thinking about it.
It starts with some stuff you learned back in junior high — how information from your DNA gets turned into actual working proteins.
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Before you get excited about the bones of Richard III being found under a parking lot
, consider this — the announcement included no mention of how common the DNA sequences that ostensibly identified the body as Richard really are. Those sequences might match Richard's descendants, but if the sequences are also really common, well, that's not saying much. — Maggie
Researchers have successfully stored information in synthetic DNA and then sequenced the DNA to read the data. Nick Goldman and his colleagues from the European Bioinformatics Institute (EBI) encoded all of Shakespeare's sonnets, an audio clip of Martin Luther King's "I have a dream" speech, Watson and Crick's paper on DNA's structure, a photo of the EBI, and an explanation of their data conversion technique. Last year, Harvard molecular geneticist George Church encoded a book he had written in DNA, but EBI's breakthroughs are in the way the data is encoded and its error-correction. From the abstract of their scientific paper published at Nature
We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information10 of 5.2 × 106 bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade.
"Synthetic double-helix faithfully stores Shakespeare's sonnets
" (Thanks, Mike Pescovitz!)
An interview with the co-discoverer of the structure of DNA.
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The Curiosity rover can do a lot of things, but nobody is expecting her to find direct evidence of life on Mars. In fact, the hunt for life on the Red Planet has been a pretty stunted one. The last time we really looked was during the Viking missions, which tried to find chemical "footprints" that would exist if there had once been life on Mars, but that could end up on that planet for other reasons, as well. What we got back was a less-than-enthralling "Outlook Hazy. Try Again Later."
Ever since, we've contented ourselves with searching for indirect evidence — assessing the planet for signs that it might once have had the conditions necessary for life to happen. That's important, and it will make direct evidence of life more believable if we ever do find it, but it's not quite the same thing.
But now, DNA sequencing tools have become portable enough (and drilling technology has become powerful enough) that some scientists and Craig Ventner think we could send a probe to Mars which could find buried traces of actual DNA protected in the dirt and sequence that DNA on site.
It's also possible that life hitched a ride between Earth and Mars in their early days. Asteroid impacts have sent about a billion tonnes of rock careering between the two planets, potentially carrying DNA or its building blocks. That could mean that any genetic material on Mars is similar enough to DNA that we have a chance of finding it using standard tests.
Even if we don't, we can set up future sequencers to look for molecules that use alternative sugars or chemical letters in the genetic code. "We're not there yet, but it's not a fundamental limitation," says Chris Carr of the Massachusetts Institute of Technology, who works on the NASA-backed Search for Extraterrestrial Genomes.
Read the rest of the story at New Scientist
A study at Nanjing University in China found that ingested "microRNA" (very small pieces of ribonucleic acid, or RNA) from plants were able to survive digestion and influence the function of human cells.
Food columnist Ari Levaux has a piece digging into the implications, in The Atlantic. The basic idea: if this research stands up to the rigors of scientific scrutiny, it could prove that when we eat food, we consume not just fuel and nutrients, but information that changes us on a cellular level, and influences health.
Monsanto's website states, "There is no need for, or value in testing the safety of GM foods in humans." This viewpoint, while good for business, is built on an understanding of genetics circa 1950. It follows what's called the "Central Dogma" (PDF) of genetics, which postulates a one-way chain of command between DNA and the cells DNA governs.
The Central Dogma resembles the process of ordering a pizza. The DNA knows what kind of pizza it wants, and orders it. The RNA is the order slip, which communicates the specifics of the pizza to the cook. The finished and delivered pizza is analogous to the protein that DNA codes for.
We've known for years that the Central Dogma, though basically correct, is overly simplistic. For example: Pieces of microRNA that don't code for anything, pizza or otherwise, can travel among cells and influence their activities in many other ways. So while the DNA is ordering pizza, it's also bombarding the pizzeria with unrelated RNA messages that can cancel a cheese delivery, pay the dishwasher nine million dollars, or email the secret sauce recipe to WikiLeaks.
Monsanto's claim that human toxicology tests are unwarranted is based on the doctrine of "substantial equivalence." This term is used around the world as the basis of regulations designed to facilitate the rapid commercialization of genetically engineered foods, by sparing them from extensive safety testing.
via The Very Real Danger of Genetically Modified Foods - The Atlantic. You'll also want to read the actual study, and make up your own mind.
Update: Here's a critical take on the linked-to Atlantic piece. Ari responds here.
The black-and-white spotted "Dalmatian" horses depicted in some prehistoric European cave art may have actually existed
. (Via Steve Silberman) — Maggie
Love these (sadly unattributed) Hitchhiker's Guide to the Galaxy tattoos. Illustrating the flowerpot/whale scene is particularly poignant, as it is perhaps the most humorously existential moment in one of the great existential comedies of all time.
Hitchhikers Guide to the Galaxy Tattoo
(via Forbidden Planet)
The condo association at Scarlett Place, a posh Baltimore building, have proposed to DNA-test all the dogs on the premises, and use DNA from errant dog-turds to identify feckless owners and fine them $500 per dog-pie.
Using all the dog swabs, BioPet would create a doggie database of sorts for the complex. It would compare all those samples to the mysterious doggie-doo. When BioPet identifies the guilty pooch, the owner would pay a $500 fine.
DNA Could Solve Doggie-Doo Caper
"We pay all this money, and we're walking around stepping in dog poop," resident Steven Frans told The Sun. "We bring guests over and this is what they're greeted by."
Frans is the board member who proposed the plan, calling it a reasonable and objective way to find the culprit.
(via Freakonomics Blog
(Image: A New Way to Complain About Dog Poop, a Creative Commons Attribution (2.0) image from aoifecitywomanchile's photostream)
Aaron sez, "This piece from the LA Times includes a stunning description of how an undercover cop lifted a DNA sample from Stephanie Lazarus, a police woman was under investigation for murdering her romantic rival."
An undercover officer surreptitiously trailed Lazarus, 49, as she ran errands, waiting until she discarded a plastic utensil or other object with her saliva on it. The DNA in her saliva was compared with evidence collected from the murder scene. The genetic code in the samples matched conclusively, police and prosecutors have said.
And this is one of the main reasons that biometric identifiers are so very risky... You can protect the PIN for your debit card by shielding the keypad when you enter it, but how do you keep counterfeiters from getting your DNA for authenticating the debit-card of the future? We throw off fingerprints, DNA, hand-geometry impressions, gaits and other biometrics at a titanic rate, and there's no way to stop, short of spending all your time in a hazmat suit.
Bail is set at $10 million for LAPD detective accused of murder
(Image: DNA Molecule display, Oxford University, a Creative Commons Attribution photo from net_efekt's photostream)
Britain's cops have the largest DNA database in the world, and it's full of innocent people who were arrested but not charged, or charged but not convicted (the EU's Court of Human Rights have ordered this practice to stop, but the cops refuse to comply with the law -- their latest dodge is to keep innocents' DNA for six years
). Now an inquiry that begins today claims that police are "routinely arresting people" that they know they can't convict of any crime, simply to get their DNA into the database.
The highly critical report from the government's advisory body on the development of human genetics is published as the number of innocent people on the database is disclosed to be far higher than previously thought â€‘ nearing 1 million.
Police routinely arresting people to get DNA, inquiry claims
The commission says the policy of routinely adding the DNA profiles of all those arrested has led to a highly disproportionate impact on different ethnic groups and the stigmatisation of young black men, with the danger of their being seen as "an 'alien wedge' of criminality"...
The chairman of the commission, Prof Jonathan Montgomery, said: "It's now become pretty routine to take DNA samples on arrest. So large numbers of people on the DNA database will be there not because they have been convicted, but because they've been arrested."
He said the commission had received evidence from a former police superintendent that it was now the norm to arrest offenders for everything possible. "It is apparently understood by serving police officers that one of the reasons, if not the reason, for the change in practice is so that the DNA of the offender can be obtained," said Montgomery, adding that it would be a matter of very great concern if this was now a widespread practice.
(Image: DNA Molecule display, Oxford University, a Creative Commons Attribution photo from net_efekt's Flickr stream