Comments on: How BitTorrent Can Teach Students DNA Sequencing

By: Anonymous

Anonymous — Wed, 10 Dec 2008 13:42:31 +0000

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By: John Jones

John Jones — Tue, 09 Dec 2008 12:43:59 +0000

Wow, BiTorrent can be used to educate! How about that!

jess
http://www.online-privacy.cz.tc

By: TorrentHub

TorrentHub — Tue, 09 Dec 2008 07:07:21 +0000

Probably another simple analogy, but perhaps DNA sequencing could be compared to downloading from the internet in general. After all, one side has to split the data into packets and the other side reconstructs, right?

Also, way to go for a professor being (sort of) with the times. *thumbs up*

My 2c -

By: You

You — Tue, 09 Dec 2008 00:29:29 +0000

@3
Speaking from experience or…?

By: John Smith

John Smith — Mon, 08 Dec 2008 22:39:21 +0000

Haha, this is quite a funny and interesting article, I must say.

By: wilk0x

wilk0x — Mon, 08 Dec 2008 22:13:21 +0000

I’m not sure this is a very good analogy. Unless I totally misunderstand the BitTorrent protocol, each ‘fragment’ is downloaded only once, and its position within the complete file is known. With shotgun sequencing, there may be many overlapping fragments covering a given bit of sequence, and the position of the sequence within the final genome has to be figured out through some pretty intense analysis.
Two of the researchers in my lab write software for piecing together these fragments for metagenomic sequencing, which is the sequencing of a large number of different species at once where there’s no way of telling which species a particular fragment comes from. I’m constantly awed by the difficulty of their work: it’s a lot harder than simply linking together overlapping fragments, since genomes often contain large repeated regions. Shotgun sequencing often results in poor or no coverage of certain areas, and many segments (”contigs”) are riddled with errors. I think the BitTorrent analogy could give the false impression that sequencing and assembly are much more precise then in reality.

By: Norm

Norm — Mon, 08 Dec 2008 20:57:17 +0000

can someone please seed my dna? ive been waiting forever.

By: Shizuka

Shizuka — Mon, 08 Dec 2008 20:06:33 +0000

Also, way to go for a professor being (sort of) with the times. *thumbs up*

By: DakE_FeatH

DakE_FeatH — Mon, 08 Dec 2008 20:03:21 +0000

It was indeed a pretty good analogy in the way he approached it. He went to the very base of the digital system, by calling the bits that make up the file being downloaded digital fragments. 0 and 1’s being transmitted and forming music and movies in the end, after being put together. Same for DNA, only that DNA has 4 choices to choose from, A T C and G. Then you download these 0s and 1s from all over the world, and the program on the computer puts together these 2 options into one continuous string, resulting in the movie and music being played.

He went on to say that just as it is not illegal (well, not in Canada) to download these fragments because essentially they are just numbers (0’s and 1’s) and thus alone, they are not a song/movie. (So the individuals are not giving you the song or movie, they just give you 0 and 1’s that are useless by themselves)
When one does shotgun sequence DNA, each individual fragment is also not enough to be the full DNA material of an individual or a species. Without going into too much detail, with enough fragments, you stitch them together (using the computer algorithm) and you get the DNA.

What I found more interesting about this though, was that the lecturer knew about bit torrent, knew the concept behind it and knew it should be legal and free :D

Cheers guys!

By: BOO

BOO — Mon, 08 Dec 2008 19:16:11 +0000

At lest it a analogy better then none. More then likely the prof doesnt know much about bit torrent anyway so it would be how he thinks it works. But I wouldn’t know.

By: www.eZee.se

www.eZee.se — Mon, 08 Dec 2008 18:49:25 +0000

Would be nice to try it another way: catch Cary Sherman and Dan Glickman, cut them up into little pieces… then try putting them back together, if you fail… no big deal, they are a waste of flesh and bone anyway.

By: www.10ch.org

www.10ch.org — Mon, 08 Dec 2008 18:47:44 +0000

It feels like a limited analogy. It may be true that DNA sequencing divides it up, and allows everything to form back together. However, the rest of it seems to be a little… off.

However, even though I do not know much about DNA sequencing other than basic stuff taught to all high-school students, I do doubt that there are any entities that distribute these little bits to each other. After all, I thought that in DNA sequencing, all the pieces float around, and when it is the correct piece, it attaches.

In file-sharing, it does not quite seem like the pieces are floating around, waiting to be “attached” to the right piece – unless, of course, you are considering the “swarm” to be the vat – but then, nothing is sending any DNA pieces/information to each other.

Such is the case with this oversimplified analogy.

(By the way… did “oversimplified analogy” mean that the explanation of the analogy was oversimplified, or that the analogy itself was oversimplified, because it could be disambiguated as either when you said “[t]he whole analogy is of course a little oversimplified.”)

Roze

By: Anonymous

Anonymous — Mon, 08 Dec 2008 18:05:26 +0000

nice to see another use of BitTorrent