YouTube: https://youtube.com/watch?v=595Vd35Zqrw
Previous: Learning Mnemonics: Can You Really Hack Your Memory?
Next: A New Map of the Human Brain!

Categories

Statistics

View count:115,871
Likes:2,362
Dislikes:51
Comments:315
Duration:24:28
Uploaded:2016-07-28
Last sync:2017-03-21 00:10
Curious about genetics? Dig in a little deeper with this special SciShow Talk Show featuring science writer and 2016 Stephen Jay Gould prize winner Carl Zimmer talking about what he did after receiving himself on a hard drive.

Host: Hank Green
Guest: Carl Zimmer

Check out 'Game of Genomes' at: https://www.statnews.com/feature/game-of-genomes/season-one/
Check out the raw data at: https://zimmerome.gersteinlab.org/

Table of Contents

00:10 - Introductions
04:47 - How Carl Got His Genome and How He Got Help Deciphering It
07:53 - How Much Would This Cost?
09:42 - What Did He Find In His Genome?
11:56 - What's the Difference Between This and 23andMe?
14:00 - Why are People Getting Their Genomes Sequenced?
17:15 - Concerns About Sample Populations
19:32 - Genome Sequencing as a Tool to Study the History of Humanity
22:55 - Where You Can Learn More
----------
Support SciShow by becoming a patron on Patreon: https://www.patreon.com/scishow
----------
Dooblydoo thanks go to the following Patreon supporters -- we couldn't make SciShow without them! Shout out to Kathy & Tim Philip, Kevin Bealer, Andreas Heydeck, Thomas J., Accalia Elementia, Will and Sonja Marple. James Harshaw, Justin Lentz, Chris Peters, Bader AlGhamdi, Benny, Tim Curwick, Philippe von Bergen, Patrick Merrithew, Fatima Iqbal, Mark Terrio-Cameron, Patrick D. Ashmore, and charles george.
----------
Like SciShow? Want to help support us, and also get things to put on your walls, cover your torso and hold your liquids? Check out our awesome products over at DFTBA Records: http://dftba.com/scishow
----------
Looking for SciShow elsewhere on the internet?
Facebook: http://www.facebook.com/scishow
Twitter: http://www.twitter.com/scishow
Tumblr: http://scishow.tumblr.com
Instagram: http://instagram.com/thescishow

  (00:00) to (02:00)


Hank: Hello, this is Hank Green, for a special episode of SciShow where we're gonna be interviewing Carl Zimmer, who is a science writer of great renown. Uh, We're really excited to have him here. And he has been working on a project where he got his entire genome sequenced - which is different from what you might hear about with 23andMe where you spit into a tube. That is a more limited version of what Carl has done - not only getting his entire genome sequenced but also getting it delivered to him whole so that he could have it for himself, and he could have himself on his hard drive, and then working with a bunch of scientists to tell him exactly what it all means (well I mean not exactly) - some of what it all means. So I'm really pleased to have Carl Zimmer, winner of the 2016 Stephen J. Gould Prize, congratulations on that by the way. Hello Carl!


Carl: Hi.


Hank: Uh, What's it like to win the Stephen J. Gould Prize?


Carl: Oh, it's a, that's a very big honor. Yeah, I mean, I grew up reading Stephen J. Gould essays, so being able to get an award in his name means a lot to me as - now that I'm a science writer.


Hank: Yeah. That's fantastic. Congratulations. Um, what is it like to get you delivered to you on a hard drive?


Carl: Um, It's - it's pretty disconcerting. I mean, you know, I like literally have this thing on my desk, just - that's it. That is - that is me. That is my genome, and you know, it showed up one day, and plugged it into my computer and we were off to the races. So it's uh-  [words spoken over by Hank]


Hank: I mean, they delivered it to you on like a monogrammed, embossed, hard drive. That's a beautiful thing. It should have had your name on it.


  (02:00) to (04:00)


Carl: Yeah. It should have, it should have. But, uh, I stuck it, I stuck my name on it with a little label, I don't know if you can see it, and uh.


Hank: Okay, good.


Carl: Yeah, anyway. The reason they have to do this is it's like 70 gigabytes of data, so, uh, they couldn't just, you know, send me an e-mail or something like that.


Hank: Is a, is a genome about 70 gigabytes, or does that include some extra information?


Carl: Yeah, so this is actually a lot more than a, than a genome sequence itself. That's because the way that a company like Illumina, which sequenced my DNA, the way they get at your genome is they actually, um, make lots of copies of fragments of your DNA, so you know, thirty times over, really, and then, um, what you can then do with all those fragments is you can kind of stack them up and try to figure out from that what at each point your genome is. So your genome is only three - three and a half billion base pairs, which you could fit on a much smaller file, if you wanted. So this is really just a raw-


Hank: So they got you everything. And the reason they do that fragmentation is just so that they can do the smaller segments faster?


Carl: Yeah, I mean, this particular way of doing DNA is kind of like parallel processing, you know. You take, you know, billions of little fragments, each 300 bases long, and you can read each one all at the same time on a little slide. And so you can get it done pretty quickly. Um, you may make some mistakes along the way, but because you're making so many copies, there's sort of an error correction built into it. There are a lot of new methods coming online that, you know, try to read in longer fragments, and those may be more accurate and they may be able to read things that Illumina can't, but, you know, it's a work in progress.


 


Hank: Yeah, I mean, it's, it's remarkable that it's accessible at all.


  (04:00) to (06:00)


Hank: I mean, we're talking- how long ago was it that it cost- like, the first human genome was sequenced and it was in the billions of dollars.


Carl: That's right, yeah, so once upon a time there was just one human genome, and it took hundreds of people many years to read it, and it wasn't even a very good version; there were a lot of errors in it, and it cost maybe around 3 billion bucks.


Hank: (laughs)


Carl: Then a few years later, in the early 2000's, Craig Venter got his own genome sequenced, and I believe that was in the neighborhood of 100 million dollars? Which, you know, that's down a lot but that's still- a little steep. Uh, but now we're down to the few thousands of dollars, you know, in some cases maybe just a thousand dollars, some companies are saying. It's crashed.


Hank: So, how much did it cost to get- did you pay, by the way? Like how did you uh, how did you cash in on this opportunity?


Carl: So, the way that this came about was that this company Illumina runs meetings called "Understanding Your Genome". Which are really sort of scientific conferences, but um people who go to the meetings, if they wanna pay extra, can get their genome sequenced. Well, I went to my editor [???] and said, "Okay, here's an expense I'd like to file." (laughter) "You know, roughly 3 thousand dollars, I'll get my genome sequenced, and I'll write the hell out of it, and uh, it'll be worth your while. I promise." Um, but the thing was that, you know, what I knew was that I was gonna have to pay a little bit extra, not just to get it sequenced, but to then actually have them convert it onto a hard drive and send that to me. That was like an extra step, and actually not a step that was very easy at all to get done. So I don't know how many people can kinda wave around a genome on a hard drive, um, it definitely took me a lot of uh, a lot of shenanigans to get it.


Hank: (laughs) Uh, so, and then of course it's not just getting the genome.


  (06:00) to (08:00)


Hank: Uh, it's just a bunch of letters and numbers, I imagine, that don't mean a lot just to look at. At least at first, how did you go about getting help deciphering what has- what is going on inside of you?


Carl: Yeah, I mean the fact is that if I unlock that disk, and if I, you know, look at the raw data, with you know some browser tools, really it's like a horrible spreadsheet. I mean it's just, you know you have like a 300 letter long piece of gibberish and then a little note about where Illumina thinks it is in my genome. And then the next one, and the next and the next one, for like, over a billion lines. 


Hank: (laughs)


Carl: So, yeah. I mean, that's not really gonna say much to me. Um, so I started getting in touch with scientists and saying, "I'm working on this project and I would like to write about what it's like to study genomes and what you can learn from genomes by having you help me understand mine." And so I went to places like the Broad Institute, or Yale, or Cornell Weill Medical, and people would just show me what they do. They'd say "okay, let's take your data, here's what we do first. First we uh, we're gonna use our own methods to figure out where in the genome all these fragments belong. Then we're gonna look for special kinds of mistakes. Um, then we're going to- you know 'cause the problem is that we're all a little bit different. And so if you come across a particular fragment, then you don't necessarily know where it belongs in your genome. So, they use all sorts of really clever, almost cryptographic, cryptological techniques to uh, to figure this all out. And only then can they actually analyze it. So it's an amazing process.


Hank: And uh, first question here. Give a guess: so it's thirty-- three thousand dollars-ish, 3600 dollars to get your genome sequenced.


  (08:00) to (10:00)




  (10:00) to (12:00)




  (12:00) to (14:00)




  (14:00) to (16:00)




  (16:00) to (18:00)




  (18:00) to (20:00)




  (20:00) to (22:00)




  (22:00) to (24:00)




  (24:00) to (24:28)



Website Security Test