The case for storing digital data in DNA

Using DNA to store digital data has been a classic forecast in infotech futurism for more than two decades. The basic concept is that you could synthesize strands of DNA encoded with digital information and then decode it with DNA sequencing techniques. While several amazing experiments have demonstrated that DNA data storage is possible, it's mostly been thought of as too expensive and impractical. But as researchers continue to make technical strides in the technology, and the price of synthesizing and sequencing DNA has dropped exponentially, systems for backing up to the double helix may actually be closer than you think. From IEEE Spectrum:

Even as our data storage needs surge, traditional mass-storage technologies are starting to approach their limits. With hard-disk drives, we’re encountering a limit of 1 terabyte—1,000 GB—per square inch. Past that point, temperature fluctuations can induce the magnetically charged material of the disk to flip, corrupting the data it holds. We could try to use a more heat-resistant material, but we would have to drastically alter the technology we use to read and write on hard-disk drives, which would require huge new investments. The storage industry needs to look elsewhere....

It still may not match other data storage options for cost, but DNA has advantages that other options can’t match. Not only is it easily replicated, it also has an ultrahigh storage density—as much as 100 trillion (1012) GB per gram. While the data representing a human genome, base pair by base pair, can be stored digitally on a CD with room to spare, a cell nucleus stores that same amount of data in a space about 1/24,000 as large.

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The astounding present and dizzying future of synthetic biology

George Church's Harvard lab is one of the most celebrated fonts of innovation in the world of life sciences. George's earliest work on the Human Genome Project arguably pre-dated the actual start of that project. Subsequently, he's been involved in the creation of almost a hundred companies - 22 of which he co-founded.

Much of George's most recent and celebrated work has been with a transformationally powerful gene-editing technique called CRISPR, which he co-invented. George and I discuss CRISPR and its jarring ramifications throughout this week's edition of the After on Podcast. You can listen to our interview by searching "After On" in your favorite podcast app, or by clicking right here:

Our conversation begins with a higher-level survey of the field -- one which cleanly and clearly defines CRISPR by placing it into a broader, and also a quite fascinating framework. We cover four topics, which I'll now define up-front for you, so as to make the interview more accessible.

We begin by discussing genetic sequencing. "Sequencing" is a fancy (and rather cool way) of saying, "reading." Your genome is about three billion characters long. It's written in a limited alphabet, of just four letters: A, G, C, and T. And if someone sequences your genome, it simply means they've read it. They haven't modified it in any way. They haven't have cloned you. They've just gotten a readout (kind of like determining your blood type -- only a few billions times more complicated).

George and I next discuss gene editing. Read the rest

The promise and peril of synthetic biology in 78 minutes

Below you’ll find an unhurried interview with Autodesk Distinguished Researcher Andy Hessel. Andy is a prime instigator behind GP-Write – which is, on some levels, heir to the Human Genome Project – and a co-founder of Humane Genomics, which is developing virus-based therapies for cancer.

It’s the fourth episode of my podcast series (co-hosted by Tom Merritt), which launched here on Boing Boing three weeks ago. The series goes deep into the science, tech, and sociological issues explored in my present-day science fiction novel After On – but no familiarity with the novel is necessary to listen to it.

The upside and the downside of synthetic biology are vast and Andy is deeply versed in both. He co-wrote a chilling fictive scenario about a bioterror plot for the Atlantic – but he tends toward relentless optimism when contemplating synthetic biology’s future.

Synbio newbies should find our wide-ranging discussion to be a robust introduction to the field. But Andy’s sophisticated commentary will give expert listeners plenty to chew on. After considering the astounding decades-long drop in the cost of reading DNA (which makes price/performance gains in computing look trivial), we discuss the sudden and accelerating plunge in the cost of writing DNA that does not exist in nature.

Andy explains how this is enabling the explosive rise of a market for metabolic circuits – clusters of genes designed to churn out industrial enzymes and other chemically complex output. This is a giant step down a path toward bioprinting an immense array of tissues (new skin for burn victims, cow-free steaks that could fool a cattleman, and much more), and then onward to boundless breeds of wholly synthetic critters. Read the rest

More thoughts on lab meat

Yesterday, Rob told you about the first public tasting of a burger that was grown in a laboratory, from strips of flesh built up from muscle stem cells. I found a couple of great links today that build on that news. First: The secret ingredient in lab-grown meat is fetal cow blood. (It's both a significant part of the high price of lab meat, and a reason why your vegan friend won't be eating lab meat anytime soon.) Also be sure to check out synthetic biologist Christina Agapakis' perspective — she tones down some of the hype while making it clear why lab meat is still pretty impressive. Read the rest

E. coli engineered into an analog computer

Synthetic biology researchers at MIT are creating simple analog computers in living cells, complete with fluorescent "displays." Rahul Sarpeshkar and Timothy K. Lu engineered genetic circuits in E. coli so that the bacteria glows with a brightness determined by the amount of certain chemicals surrounding it. From Science News:

By making bacteria glow more or less brightly depending on the number of different chemicals around, the new circuit can compute answers to math problems, Lu’s team reports May 15 in Nature. To add 1 plus 1, for example, the circuit would detect two chemicals and crank up the bacteria’s glow to “2.”

"Analog circuits boost power in living computers" (Science News)

"Cell-Based Computing Goes Analog" (The Scientist)

"Synthetic analog computation in living cells" (Nature) Read the rest

Westerfeld's Goliath: suitably thrilling conclusion to cracking steampunk WWI YA trilogy

Scott Westerfeld's Goliath ships today, concluding his fabulous steampunk YA trilogy that began with Leviathan and continued in Behemoth. This alternate history of WWI is set in a world divided into two technological camps. On the Darwinist side, scientists manipulate the "life threads" of animals to create useful synthetic animals ranging from little "message lizards" that can parrot brief phrases up to enormous organic zeppelins that are part whale, part hydrogen-breather. Clankers -- the Austro-Germanic camp, mostly -- create huge, steam-driven mecha and work-horses that do useful and deadly work. When Archduke Ferdinand is assassinated, his son, Aleks, is smuggled away to neutral Switzerland before his uncle can have him killed to get him out of the chain of succession. There, he ends up joining forces with the Leviathan, a British airship whose crew includes the intrepid Dylan, a plucky girl who has dressed as a boy in order to secure a spot in the ship's crew. Once Aleks and Dylan have joined forces, Westerfeld begins to retell the history of WWI with ingenious variations drawing on his notional Darwinist/Clanker split, a tale of air-battles, naval warfare, diplomacy, skullduggery and sneakery.

Goliath picks up where Behemoth let off, after a spot of bother and a revolution in Constantinople, and takes the Leviathan to Tunguska, Siberia, where Nikola Tesla is secretly investigating the progress of his death ray, which may end the war -- or life as we know it. Goliath hurdles on from there in the classic Westerfeld style, a cracking adventure story that revolves around science and engineering in equal measures with love, jealousy and honor. Read the rest