Printing the human genome on punched tape | Hacker News Reader

Printing the human genome on punched tape

blog.mattbierner.com

22 pointsmattbierner14 comments

If you have questions about the technical details of the project, I'd be happy to try answering them. It's been fun to use this retro tech in a really impractical way, and being able to see individual bits of data is neat.

I'll also be live streaming the printing off and on: http://twitch.tv/mattbierner

I'm really interested in the amount of paper this art project will use, and how much it'll weigh. He says " a cumulative length of some 5000 miles" but doesn't specify the paper so I can't calculate how many trees went into this. I'm not an extreme ecological conservationist, but this does come across as a huge waste for no real purpose.

I don't understand why he's not encoding information into the odd labelled columns. It really takes away from the project.

And using 8 bits to encode 2 is also a very strange choice.

Sure but keep in mind that there is no objective, this is just free expression, or, an art project.

That's not entirely true. There are also bits associated with ambiguous combinations of single base pairs, so there is actually 4 bits of information if all ambiguous combinations are possible. But it'd be much closer to 2 if you took into account how rare these are. Still, had he done exactly the same encoding without those column gaps between I wouldn't have criticized.

He wants it to be one base pair per row, and also to express the multi-possibility rows in the source data. So he needs 4 bits per row for that, and he spreads them out rather than bunch up on one side.

This is unbelievably wasteful and uninteresting.

Well, it is wasteful, everyone needs to be cutting down to 2kW of energy, from 4 in EU and 6 in N.America. Even then we'll need 70 times more nuclear power stations than we have today, and that's only for 50% of our energy needs, other 50% from renewables.

Seeing the piles of accumulated paper tape does actually illustrate an interesting question: How exactly is 3.2 billion base pairs of DNA folded up in a human cell?

From https://en.wikipedia.org/wiki/Chromatin:

> Chromatin is a complex of DNA, RNA, and protein found in eukaryotic cells. Its primary function is packaging very long DNA molecules into a more compact, denser shape, which prevents the strands from becoming tangled and plays important roles in reinforcing the DNA during cell division, preventing DNA damage, and regulating gene expression and DNA replication.

I wonder if it's possible to visualize how Chromatin works from the DNA paper tape?

Yes, it’s quite amazing, no less that the whole thing is constantly copied and repackaged, and remember there are 2 versions of your genome (one from mum one from dad) so it’s actually 6 billion base pairs. The 3 dimensional organisation of the genome is very important, it’s an active area of research.