How BitTorrent Can Teach Students DNA Sequencing
Written by Ernesto on December 08, 2008DNA sequencing is complex, and teaching students how it works can be quite a challenge. It often helps to use analogies, and give real life examples people are familiar with. At the University of Toronto they have found the perfect analogy to explain how DNA sequencing works: BitTorrent.
A growing number of Internet users know that BitTorrent is a great tool to download large files such as movies and music albums. While BitTorrent itself is based on economic principles, only a few know that it can also be used in biology class, since it’s a great analogy for DNA sequencing.
In a course on ‘Organisms in their Environment’ taught by Prof John Stinchcombe at the University of Toronto, this resemblance is used to help students to understand this complex matter. One of Stinchcombe’s students told TorrentFreak that he was “pleasantly surprised” when he saw BitTorrent being linked to his course material, and shared the slides with us.
Similar to BitTorrent, the first step is to chop the material into small pieces (with enzymes). After that, all the pieces are put back together again with computer algorithms, thereby reconstructing the DNA. Similarly, with BitTorrent the pieces are also put back together again, reassembling the file that’s being shared.
The whole analogy is of course a little oversimplified, but it did at least grab the attention of some of the more tech savvy students. The slide at the bottom of the post is the one that Prof John Stinchcombe used to compare DNA sequencing to an “everyday life” example, with The Pirate Bay as one of its applications.
Is this news? Hardly. But, perhaps more than anything, it shows how mainstream BitTorrent has become recently.
DNA sequencing vs. BitTorrent
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13 Responses
nice to see another use of BitTorrent
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
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.
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.
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!
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*
can someone please seed my dna? ive been waiting forever.
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.
Haha, this is quite a funny and interesting article, I must say.
@3
Speaking from experience or…?
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 -
Wow, BiTorrent can be used to educate! How about that!
jess
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