DNA Now Stands For Data And Knowledge Accumulation

February 18, 2020 by Bob Baddeley 33 Comments

Technology frequently looks at nature to make improvements in efficiency, and we may be nearing a new breakthrough in copying how nature stores data. Maybe some day your thumb drive will be your actual thumb. The entire works of Shakespeare could be stored in an infinite number of monkeys. DNA could become a data storage mechanism! With all the sensationalism surrounding this frontier, it seems like a dose of reality is in order.

The Potential for Greatness

The human genome, with 3 billion base pairs can store up to 750MB of data. In reality every cell has two sets of chromosomes, so nearly every human cell has 1.5GB of data shoved inside. You could pack 165 billion cells into the volume of a microSD card, which equates to 165 exobytes, and that’s if you keep all the overhead of the rest of the cell and not just the DNA. That’s without any kind of optimizing for data storage, too.

This kind of data density is far beyond our current digital storage capabilities. Storing nearly infinite data onto extremely small cells could change everything. Beyond the volume, there’s also the promise of longevity and replication, maintaining a permanent record that can’t get lost and is easily transferred (like medical records), and even an element of subterfuge or data transportation, as well as the ability to design self-replicating machines whose purpose is to disseminate information broadly.

So, where is the state of the art in DNA data storage? There’s plenty of promise, but does it actually work?

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Enzymes From The Deep – The Polymerase

March 22, 2016 by Nava Whiteford 46 Comments

Our bodies rely on DNA to function, it’s often described as “the secret of life”. A computer program that describes how to make a man. However inaccurate these analogies might be, DNA is fundamental to life. In order for organisms to grown and replicate they therefore need to copy their DNA.

dna-replication — DNA structure and replication

Since the discovery of its structure in 1953, the approximate method used to copy DNA has been obvious. The information in DNA is encoded in 4 nucleotides (which in their short form we call A,T,G, and C). These couple with each other in pairs, forming 2 complimentary strands that mirror each other. This structure naturally lends itself to replication. The two strands can dissociate (under heat we call this melting), and new strands form around each single stranded template.

However, this replication process can’t happen all by itself, it requires assistance. And it wasn’t until we discovered an enzyme called the DNA polymerase that we understood how this worked. In conjunction with other enzymes, double stranded DNA is unwound into 2 single strands which are replicated by the polymerase.

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Hackaday’s 48-Hour Tokyo Speedrun

November 3, 2014 by Aleksandar Bradic 29 Comments

“The future is already here – it’s just not evenly distributed,” goes the clichéd [William Gibson] quote. Growing up on all the Cyberpunk literature and spending a more-than-healthy amount of time obsessing over [Fred Gallagher’s] Megatokyo series, I always imagined Japan to be at the very tail of this distribution. The place where the Future lives. Though it has been decades since the Bubble burst, and there’s no way this could still be the case, there was something romantic about believing it just might be. Thus, I opted for keeping the dream alive and never actually visited the place.

Not until a few weeks ago — [Bilke], one of our crazy sysadmin guys that keeps Hackaday.io alive, made me do it. He found these cheap tickets from LA, and the next thing you know – we were flying out for a 48-hours-in-Tokyo weekend. With no time to prepare, we reached out to [Akiba] from Freaklabs and [Emery] from Tokyo Hackerspace for some tips. By the time we landed, emails were waiting for us, with our full schedule completely worked out. It’s great to know that no matter where you are, there’s always a friendly local hacker willing to help.

Past the immigration, we took the JR Narita Express line into to the City that Friday evening. From there we grabbed a taxi because we couldn’t understand a word in katakana but then we hopped the JR Yamanote Metro line once we had figured things out. We checked out all the major places we had ever heard of (Shinjuku, Shibuya, Roppongi, Ginza…) because the jet lag was not letting us sleep anyway.

Sometime way past midnight, it hit me – Future Shock. But this was the kind I never expected…

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