Harvard cracks DNA storage, crams 700 terabytes of data into a single gram • Hacker News Board

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#51

Post by gibybo » Fri, Aug 17, 2012, 6:40 PM UTC

wbizzle wrote: post #44

This article is incredibly misleading. First of all there is an inconsistency. The headline says they stored 700 terrabytes (4.4 petabytes). It then later says that they actually stored 700 kilobytes (Their book) and that they did made 70 billion copies (44 petabytes?). The main thing is that storing 700 kilobytes and then making 700 billion copies is considerably less useful than storing 70 billion terabytes outrigh…

It says they stored 44 petabytes total (70 billion * 700 kilobytes), and 700 terabytes in a single gram (which is 5.5 petabits, not 4.4 petabytes).

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#52

Post by will_work4tears » Fri, Aug 17, 2012, 6:45 PM UTC

dontblink wrote: post #40

acomar wrote: post #32

Earlier quoted context omitted.

But you can also embed interesting information into an image without distorting the image itself (much). Similarly, the DNA of most organisms have a ton of garbage space that could be used to encode information without hurting the organism. Not saying it's practical or desirable, just that it is possible.

Leads me to wonder if the current "garbage" sequences in our own DNA could be encoded information that we were meant to decode - and by that I mean that that information may not just be entirely genetic code.

It's the memories of all of our ancestors.

I must not fear, fear is the mind killer...

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#53

Post by dsirijus » Fri, Aug 17, 2012, 6:46 PM UTC

Why binary if DNA naturally has 4 bits?

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#54

Post by UnFleshedOne » Fri, Aug 17, 2012, 6:57 PM UTC

dontblink wrote: post #40

acomar wrote: post #32

Earlier quoted context omitted.

But you can also embed interesting information into an image without distorting the image itself (much). Similarly, the DNA of most organisms have a ton of garbage space that could be used to encode information without hurting the organism. Not saying it's practical or desirable, just that it is possible.

Leads me to wonder if the current "garbage" sequences in our own DNA could be encoded information that we were meant to decode - and by that I mean that that information may not just be entirely genetic code.

They are not garbage sequences iirc, they control gene expression. DNA is a string that is coiled tight several times over itself (can't explain better than that, see the video below :)). So the garbage sequence is like padding that pushes genes in and out of areas that can be read. Changing amount or composition(?) of the garbage can turn a gene on or off just because it becomes inaccessible to RNA replication mechanism.

https://www.youtube.com/watch?v=bW5JnYZImJA

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#55

Post by whatgoodisaroad » Fri, Aug 17, 2012, 7:04 PM UTC

jwr wrote: post #42

Does anybody know how to escape their horrible "mobile" version that they force onto ipad users? It can't even be zoomed :-( More and more often I find myself not reading articles because someone thought it would be a great idea to create a non-scrolling, non-obvious, paginated "iPad format" with additional misleading and unintuitive buttons looking like native ones but doing something different. Sorry for the rant.…

Use the chrome browser for iPad and request the desktop version.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#56

Post by Jun8 » Fri, Aug 17, 2012, 7:06 PM UTC

And, of course, this brings us to the question: Do we already have messages in our DNA? Here's a post (from 2007) on this: http://blog.sciencefictionbiology.com/2007/07/messages-in-ou.... Actually, if it's from the aliens who seeded life on Earth, it would probably be in a prokaryotic DNA perhaps?

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#57

Post by whatgoodisaroad » Fri, Aug 17, 2012, 7:06 PM UTC

dsirijus wrote: post #53

Why binary if DNA naturally has 4 bits?

Bases can only pair with one other base. Adenine can only pair with thymine. Guanine can only pair with cytosine. Knowing one base implies the other, so there are only two possible pairs.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#58

Post by InclinedPlane » Fri, Aug 17, 2012, 7:07 PM UTC

tocomment wrote: post #13

I don't understand how this density could be so much better than something like flash drives. Aren't they also on the same scale of nanometers?

State of the art flash drive feature density is 19nm, however an actual flash memory cell is larger than that. In contrast, a DNA base pair is about 2nm in diameter by about 3nm tall.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#59

Post by InclinedPlane » Fri, Aug 17, 2012, 7:09 PM UTC

conanite wrote: post #2

They're using T and G for a 1, and A and C for a 0; why not double the density and get two bits from each letter? T = 00 G = 01 A = 10 C = 11 for example.

I'm not sure exactly why they decided on that encoding, I suspect there is some technical reason such as error tolerance.

Re: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

#60

Post by epistasis » Fri, Aug 17, 2012, 7:10 PM UTC

tarice wrote: post #34

I notice that the article fails to mention how long it would take to extract all 700 terabytes of data... Assuming 5.5 petabits stored with 1 base pair representing 1 bit, we can extrapolate the time required to extract the data based off the time taken to sequence the human genome (3 billion base pairs). 5.5 petabits / 3 billion bits ~= 2 million, so theoretically it should take 2 million times longer to sequence th…

I think that DNA, if ever used in practice, will be primarily used for long-term, archival storage of data that's rarely accessed, if ever. However there are a couple of things that alleviate the problems with reading the DNA.

1) DNA sequencing technology is currently advancing much faster than silicon technology, so give it time and it's likely that it will catch up with current hard disk reading speed at comparable sizes and volumes. 2) DNA's self-hybridizing nature makes it easy to pull out blocks with specific addresses (if you wait for the hybridization). So if you include address labels in the DNA as you write it out, you can probably pull it out in chunks of kilobase to megabase at a time. 3) As the other commenter pointed out, this is extremely easy to parallelize. So if you want to go twice as fast, divide the sample in half put half in each machine. Dilute and pipette as necessary.