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10 petabytes - visualized

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Re: 10 petabytes - visualized

#11

Post by jacquesm »

melpo wrote: post #10
jacquesm wrote: post #6

I'll give you a much more compact way to envision 10 Pb: 10 Petabytes is 10,000,000,000,000,000 bytes or 80,000,000,000,000,000 bits, divided by 8,000,000,000 bits per full human genome (2 bits per base-pair) that's about 10,000,000 cells (not red blood cells because they don't contain DNA), or about 5 milliliters! (10 um diameter on average so about 500 cubic um, so 2 million or so per ml), and that includes all the…

First off, I didn't downvote you. However, the comparison is wrong imho because disk storage is not simply about storing information. Disks also need fast read/write access, which DNA certainly doesn't have for us (for now?).

We are envisioning storage, a bunch of disconnected drives piled on top of each other is also not accessible for read/write access.

Re: 10 petabytes - visualized

#12

Post by ramchip »

jacquesm wrote: post #6

I'll give you a much more compact way to envision 10 Pb: 10 Petabytes is 10,000,000,000,000,000 bytes or 80,000,000,000,000,000 bits, divided by 8,000,000,000 bits per full human genome (2 bits per base-pair) that's about 10,000,000 cells (not red blood cells because they don't contain DNA), or about 5 milliliters! (10 um diameter on average so about 500 cubic um, so 2 million or so per ml), and that includes all the…

I see many debatable points:

- Blood is far from being that dense, but I'll assume you mean to calculate a theoretical limit.

- If you use the whole of a cell's DNA to encode information, the cell will die. It can't be used to freely encode information like a hard disk.

- There is no way to retrieve information in this system. This is a bit like packing a large amount of extremely high-density magnetic platters in a box and calling this a storage system, which is very different from using actual hard drives with all the complex reading/writing system (heads, space between the platters, magnets...). Even if they're not connected, it still takes room.

- Reliability of hard disks is far, far better than this. Encoding information as a single copy in a single cell is wildly unsafe. Even using multiple copies, it's likely to degrade with mutations.

Edit: I was under the impression that a base pair could only encode one bit of information, since only T-C and A-G are valid combinations. Wikipedia appears to disagree with me but I see no source; does anyone know why Wiki says a base pair could encode 2 bits?

Re: 10 petabytes - visualized

#13

Post by die_sekte »

ramchip wrote: post #12
jacquesm wrote: post #6

I'll give you a much more compact way to envision 10 Pb: 10 Petabytes is 10,000,000,000,000,000 bytes or 80,000,000,000,000,000 bits, divided by 8,000,000,000 bits per full human genome (2 bits per base-pair) that's about 10,000,000 cells (not red blood cells because they don't contain DNA), or about 5 milliliters! (10 um diameter on average so about 500 cubic um, so 2 million or so per ml), and that includes all the…

I see many debatable points: - Blood is far from being that dense, but I'll assume you mean to calculate a theoretical limit. - If you use the whole of a cell's DNA to encode information, the cell will die. It can't be used to freely encode information like a hard disk. - There is no way to retrieve information in this system. This is a bit like packing a large amount of extremely high-density magnetic platters in a…

Re: Number of bits per pair: TC, AG, CT and GA? I.e. composition (1 bit) and direction (1 bit)? Not sure, but that seems to be the most logical way.

Re: 10 petabytes - visualized

#14

Post by incomethax »

ramchip wrote: post #12
jacquesm wrote: post #6

I'll give you a much more compact way to envision 10 Pb: 10 Petabytes is 10,000,000,000,000,000 bytes or 80,000,000,000,000,000 bits, divided by 8,000,000,000 bits per full human genome (2 bits per base-pair) that's about 10,000,000 cells (not red blood cells because they don't contain DNA), or about 5 milliliters! (10 um diameter on average so about 500 cubic um, so 2 million or so per ml), and that includes all the…

I see many debatable points: - Blood is far from being that dense, but I'll assume you mean to calculate a theoretical limit. - If you use the whole of a cell's DNA to encode information, the cell will die. It can't be used to freely encode information like a hard disk. - There is no way to retrieve information in this system. This is a bit like packing a large amount of extremely high-density magnetic platters in a…

The reason one base pair can encode 2 bits is that T-C and C-T are different valid base pairs. The same is true for A-G and G-A as well. A "single" strand (the famous double helix) of DNA actually contains 2 copies of genetic information.

Re: 10 petabytes - visualized

#15

Post by stevenbedrick »

ramchip wrote: post #12
jacquesm wrote: post #6

I'll give you a much more compact way to envision 10 Pb: 10 Petabytes is 10,000,000,000,000,000 bytes or 80,000,000,000,000,000 bits, divided by 8,000,000,000 bits per full human genome (2 bits per base-pair) that's about 10,000,000 cells (not red blood cells because they don't contain DNA), or about 5 milliliters! (10 um diameter on average so about 500 cubic um, so 2 million or so per ml), and that includes all the…

I see many debatable points: - Blood is far from being that dense, but I'll assume you mean to calculate a theoretical limit. - If you use the whole of a cell's DNA to encode information, the cell will die. It can't be used to freely encode information like a hard disk. - There is no way to retrieve information in this system. This is a bit like packing a large amount of extremely high-density magnetic platters in a…

If I had to guess, it's because the way you read DNA is only along one of the strands (starting at the 5' end, IIRC), in which case you've still got four possible "characters" to use in your representation- A-G is different from G-A, etc. People have thought up all sorts of clever ways to think of how one might encode data using DNA base pairs, but it's been too long since I did any bioinformatics for me to be able to remember exactly how they calculated it all out.

Re: 10 petabytes - visualized

#16

Post by jacquesm »

ramchip wrote: post #12
jacquesm wrote: post #6

I'll give you a much more compact way to envision 10 Pb: 10 Petabytes is 10,000,000,000,000,000 bytes or 80,000,000,000,000,000 bits, divided by 8,000,000,000 bits per full human genome (2 bits per base-pair) that's about 10,000,000 cells (not red blood cells because they don't contain DNA), or about 5 milliliters! (10 um diameter on average so about 500 cubic um, so 2 million or so per ml), and that includes all the…

I see many debatable points: - Blood is far from being that dense, but I'll assume you mean to calculate a theoretical limit. - If you use the whole of a cell's DNA to encode information, the cell will die. It can't be used to freely encode information like a hard disk. - There is no way to retrieve information in this system. This is a bit like packing a large amount of extremely high-density magnetic platters in a…

> - Blood is far from being that dense, but I'll assume you mean to calculate a theoretical limit.

There are more ways of having cells arranged, I explicitly mentioned red blood cells because they are exceptional in not containing any DNA, but any chunk of tissue with that volume would do.

> If you use the whole of a cell's DNA to encode information, the cell will die. It can't be used to freely encode information like a hard disk.

Yes, that's obvious, but a cell's DNA does hold that much information, it's just not our information.

> - There is no way to retrieve information in this system.

There actually is, the information retrieval mechanism that is used to 'express' the DNA (actually, the RNA, an 'unzipped' strand of DNA, but who's counting) is a wonderful little nano machine called a ribosome, it's probably the most amazing structure that I know of outside of the DNA itself.

They're in the volume quoted, the DNA only occupies about 25% of that volume iirc.

> Reliability of hard disks is far, far better than this.

The error correction mechanism that allows your cells to be copied through very large numbers of generations is actually pretty good, most 'mutations' are lethal and only very few actually result in viable copies passing their changes on to newer generations. Mutations are also pretty rare on the whole.

You are right that only TC and AG are valid, but those combinations can be attached 'in reverse' as well (CT / GA) so that makes for four possible combinations in all.

If it weren't for that the movie 'GATTACA' would have been unpronouncable :)

Re: 10 petabytes - visualized

#17

Post by shadowpwner »

quinndupont wrote: post #7

My 350GB of music is backed up on Backblaze (a wonderful service), but seeing those visualizations reminded me of the environmental impact of my digital packratting. That's a sizable data center keeping my data happy and backed up.

Off topic, but what do you listen to that takes up 350GB? Is everything in FLAC?

Re: 10 petabytes - visualized

#19

Post by rphlx »

quinndupont wrote: post #7

My 350GB of music is backed up on Backblaze (a wonderful service), but seeing those visualizations reminded me of the environmental impact of my digital packratting. That's a sizable data center keeping my data happy and backed up.

I wonder how many thousands of people are paying them to back up stuff they could easily redownload. Great business model if they de-dupe internally.

Re: 10 petabytes - visualized

#20

Post by skeltoac »

If you took all of those drives apart and put the spindles in a pile you'd have a big pile of motors. The Petabox consumes 6kW so let's be generous and call it 60kW of servo motors.

60kW is roughly 80hp. (I know this is a specious comparison in several ways but bear with me.) 80hp is enough power a small but highway-capable motorcycle. A single 60kW brushless DC motor weighs over 100kg. That's heavier than a good many of us HN readers.

Imagine a motor like that bolted to one long spindle of large platters--say the 99cm platters from a 1961 hard drive.

If these platters were remade with the data density of modern 2TB drives, how tall would the spindle be if this giant hard drive had a 10PB capacity? How over- or under-sized would our motor be?

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