SciShow Talk Show: Carl Zimmer & Genetics


Subtitles by Jan H, Zach W.
[Other creators please add your name here] Hello, this is Hank Green out for a special
episode of Scishow where we’re going to be interviewing Carl Zimmer, who is a
science writer of great renown. I’m 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 like 23andme, where you spit into a
tube. That is 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 can have it for himself, he
can have himself on his hard drive and and then working with a bunch of
scientists to tell him exactly what it all means. Well maybe not exactly… Some of what it all means. So I’m really pleased to have Carl Zimmer, winner of the 2016 Stephen Jay Gould prize, congratulations on that by the way, Hello Carl! ~ Hi! Ah, what’s it like to win the Stephen Jay Gould prize? ~ Oh it’s that… that’s a very big honor,
yeah. ~ I mean I grew up reading Stephen Jay Gould essays, ~ so being able to get an award
in his name means a lot to me, ~ now that I’m a science writer. Yeah. That’s.. that’s fantastic.
Congratulations. Ahm.. what is it like to get you delivered to you on a hard drive? ~ Ah.. It’s.. it’s pretty… Pretty disconcerting. ~ I mean you know I literally like have this thing on my desk. ~ Just.. that’s it. ~ I mean that is all.. That is my
genome and you know, it showed up one day and ~ I plugged it into my computer and we were off to the races ~ So it’s.. it’s a… I mean they delivered it
to you on.. like on an… On an monogrammed, embossed hard drive… That’s a beautiful thing. It should’ve had your name on it… ~ Yeah, it should have, it should have… ~ But, ah, I stuck it… I stuck my name on it with a little label. ~ I don’t know if you can see it. ~ Yeah anyway. They said the reason they
have to do this is: ~ It’s like 70GB of data, so… They couldn’t just, you know, send me an email or something like that. Is a genome about 70GB, or does that includes some extra information? ~ Yeah, so this is actually a lot more
than the the 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, uh… ~ they make lots of copies of fragments of your DNA, ~ so, you know, 30 times over really. ~ And then.. what you can then do with all those fragments is, ~ you can kind of stack them up and try
to figure out, ah, ~ you know, from that, what at each point
your genome is.. So your genome is only ~ three-and-a-half billion base pairs..
Which you could fit on a much smaller file, if you wanted. ~ So this is.. this is really just the raw.. They got.. They got you everything. And the reason that they do that
fragmentation is just so that they can do the smaller snippets faster? ~ Yeah, I mean this particular way of doing DNA is.. it’s kind of like ~ parallel processing. You know, you take a, you know..
Billions of a 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. ~ Ahm, you may make some mistakes along the way, but, you know, because you’re making ~ so many copies, you.. There’s sort of an error correction built into it. ~ There are a lot of new methods coming online, ahm that, you know, try to read in longer fragments, ~ and those may be more accurate, they may be able to read things that Illumina can’t, ~ but, you know, it’s a work in progress. Yeah, I mean it’s.. it’s remarkable that
it’s accessible at all. I mean we’re talking, how long ago was it
that it costs, you know, that like, the first human genome was
sequenced and it was in the billions of dollars. ~ That’s right, yeah, so, 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 costs maybe around three billion bucks. ~ And 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 a hundred million dollars, ~ which is, you know, that’s down a
lot, but that’s still a little steep. Yeah. Uh-huh. ~ 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. So how.. how much.. how much did it cost to get… Did you pay it, by the way? Like how did.. how did you cash in
on this opportunity? ~ So the way that this came about was that, uh.. 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 want to pay extra, ~ can get their genome sequenced. So I went to my editor’s staff and said: “Okay, here’s an expense, ~ I’d like to file. You know, roughly
three thousand dollars, ~ I’ll get my genome sequenced and I’ll
write the hell out of it, ~ and it’ll be worth your while, I promise.” ~ 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. And that was
like an extra step and actually not a ~ step that is very easy at all to get
done. So i don’t know how… ~ I don’t know how many people can kind of wave around their genome on a hard drive, ~ and it definitely took me a lot of.. a lot of shenanigans to get it. Uhh.. So.. And then, of course, it’s not just
getting the genome, that’s just a bunch of letters and numbers, I imagine. That don’t mean a lot, to just look at.. ~ No. At least at first… How did you go about getting help,
deciphering what has… what has… ahh, What is going going on inside of you? ~ Yeah, I mean the fact is that like.. like
if.. if I unlock that.. that ah.. that disk and ~ if I, you know, look at.. at the raw data
with, you know, some browser tools ~ really it’s like a.. it’s like a horrible
spreadsheet. ~ I mean it’s just, you know, you have like
a 300 letter long piece of garbage… ~ gibberish, and then a little note about
where Illumina thinks it is in my genome ~ and then the next one, and the next one, and the next one.. for like over a billion lines. ~ Yeah I mean, that… that’s not really going to say much to me. So I started getting ~ in touch with scientists and saying: “You know, I’m working on this project and I’d ~ 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’m.. I went to places like ~ the Broad Institute or Yale or Cornell medical and people would just show me ~ what they do, they say: “Okay let’s take
your data, ~ here’s what we do first, you know, first
we.. we’re going to, like.. you know, use our ~ own methods to figure out where the
genome the.. all these fragments belong, ~ then we’re gonna look for special
kinds of mistakes, then we’re going to ..” ~ ..because the problem is that, you know,
we’re all a little bit different.. ~ and so, you know, if you come across a particular fragment, like… ~ That you don’t necessarily know where it belongs in your genome.. So they use all sorts of really clever, ~ almost cryptographic.. cryptological techniques to.. to.. to figure this all out. ~ And only then can they actually analyze it. ~ So it’s an amazing process. And, uhh.. First question here: Give a guess. So it’s 30.. It’s $3,000-ish… 3600 dollars to get your genome sequenced. But give a guest if you had to
have paid all of the scientists, all of the
people who put time into this, their market rate,
~ Oh yeah! their billable hours that went into this project.. how much do you think this level of analysis would
cost, if it was just a rich person trying to to learn everything about their
genome? well i would hope that the scientists
would would charge an arm and a leg for this sort of stuff because it’s you know
this is a these are amazing insights that they were able to provide and they
were using tools that they just invented you know like you know they’ll say like
here’s some software I just put together recently let’s use it on your genome so I you
know I who knows that’s it I haven’t done the math but you know maybe a
hundred thousand I guess I don’t know I mean i know that like i ended up like
with a couple dozen scientists say hey this is cool yeah i’ll definitely help
you with that couple of them a lot of times what that meant was that you know
we got them that the data on their computer they fired up their programs
and they said okay let’s talk in two weeks because their computer was just
going to grind away it for two weeks yeah and you know and then and then they
could say like ah ha here is your list of Neanderthal genes
ah ha here is the list of pieces of DNA that are duplicated in a genome or ah ha here are the like 50 genes that in your
in your genome that have broken that just don’t workiright it takes a long time to grind
through all that data what are the weird fascinating things
you found out about yourself one you know one thing that’s
interesting is that we’re always really nervous about genome sequencing it’s
supposed to be this great horrible terror you know because we’re going to
find out something awful um and I’m not denying that there you
know people can have some pretty scary mutations it’s not about it on but it’s
easy to forget that a lot of the you know most high-profile mutations are
diseases like Huntington’s disease they’re are not that common mhm and so chances
are if you if you go in and you know ask to to find out if you
have say Huntington’s disease you will not have Huntington’s disease that’s
just the nature of the beast so on the other hand you may actually
find that you have a mutation that actually protects you from diseases and
this is actually a new area of research where scientists are trying to
find examples of mutations that actually are you know good for you ah and so you know we don’t
necessarily well have them but I turned out to have
one and that was really interesting I mutation on a gene for a protein that
sits on immune cells and it actually makes me much less likely to get crohn’s
disease or some other and autoimmune Immune disorders and so you know I I was it was
interesting to sort of learn about what how does that work and so it turns out that this mutation
means that I sort of i started dial down my immune system so that I don’t get
into kind of runaway feedback loops and get a lot of inflammation and little did
I know that you know this has all been worked out a few years ago and then some
drug companies took that basic biology and turned it into a drug for conditions
like psoriasis and which are now just coming out on the market and are making
lots of money I didn’t get any of that money but
that’s okay I didn’t even know I had this protection
and you will you know last month basically that’s great so so
that you know those sorts of unexpected surprises come come up left and right so
what’s the deal what’s the difference between like if i was going to pay to
get my genome you know take to get a little bit of information about my
genome for with 23andme versus what you did what yeah this is very different
process but you talk a little bit about that sure yeah so 23andme what they will do is
they will take your spit that they get in the mail and they will pull out the
DNA and and they will actually just put together
a file for you with information about certain genetic markers so in other
words on they’ll kind of take us a sort of a
survey across your genome they’re not going to give you your whole genome but
they can zero in on say a million different locations and say okay you
have this particular letter in your genome here and so you know the the
human genome which our genomes is over 3 billion base pairs long this is where I think they’re up to a
million or so of these markers so you’re talking about you know a fraction of a
tenth of one percent of the genome what you’re getting from 20 to me you can still learn a whole lot from
that you can learn about you know potentially if your carrier for certain
diseases you can use some of that variation to get an idea about your
ancestry there’s a lot that you can do with that
and then I don’t mean to diminish that at all thing is of that there is there’s you
know literally hundreds or thousands of times more information if you get your
whole genome sequence and that takes that’s a totally different process and
the way you handle that data is a totally different process and so you and
then you can address big questions that you can’t you just get a 23andme done
you can you can see you have gigantic chunks of DNA missing from your genome yeah right 23andme won’t be able to tell you
that so is this something that is happening now I mean obviously
something’s happening more what why are people like what are the
circumstances under which people are getting their whole genome sequence
right now so most of the time people are getting
whole genome sequencing just purely for research do this like reach out to a
bunch of people in there like we want to pull from a bunch of different
populations or is it people who have specific diseases or people who like
asked to be a part of the of the process or there are a lot of programs going on
right now where where people are basically donating their DNA to
scientific research group of researchers so Craig Venter for example has a company
called human longevity and they just published a paper where they did whole
genome sequencing on 10,000 people at once like it’s a amazing study huge
amounts of data very high quality and see what they want to do is they just
wanted to like compare 10,000 people genomes and see what kind of patterns
they could find like you know where the genome do people tend to like have more
mutations and others it’s much rarer for people to get their
genome sequence just for some sort of medical reason I mean it it’s still kind
of an extreme kind of thing to do and you know this is so really like people
will only get their genome sequence once they’ve exhausted every other avenue yeah because it’s still expensive and it
still takes a lot of work to understand all that data you know you get 3 billion base pairs
and then you’re left to figure out which one of these mutations that I have
actually matters you know which one is making me sick that is hard to do so I
my guess would be like it’s still in the thousands of in terms of people who have
had their whole genome sequenced for some sort of medical
question and and and then the rest of it is just like pulling from the population
to just increase our overall knowledge of of where we’re at up overall
knowledge of what our bodies are made of and and like you know the variation and
where mutations happen and another thing that people will do is they will they
will get a whole bunch of people to volunteer to have their genome sequence
and then they will look at medical information sometimes people you can start tie
peoples genomes to their medical records and
then you can start to ask questions like well you know to the group of
people like you know do these Ten thousand people all of whom have
diabetes I mean are they is there anything that
they share a common in their genome that you don’t find in 10,000 people who
never developed diabetes and if you can look at the whole genome and all those
people and if you can get that many people it’s incredibly powerful and you can
start to discover a mutation that you’re rolling we just didn’t know about before so i
have a weird concern I and it’s that we’re going to get a lot
of good data on the genomes of people who live in the developed world in
america and europe and australia and we will be left thinking that this is a
representative sample when in fact we’ve only sampled kind of like ten percent of
the world is that is that like legitimate thought to have it’s definitely something that needs to
be avoided at all costs because if you just have a bunch of genomes white
people and maybe just a bunch of genomes of rich white people then you have a
really fun representative sample of human diversity and you’re not going to
get to the bottom of a lot of disease I you know there’s a there’s a lot of
genetic variation all over the world and you’re not going to understand it unless
you really are sampling lots and lots of people and you know it’s it’s really kind
of shocking that even just a few years ago something like ninety-five percent
of ninety-six percent of all these what are called genome-wide Association
studies they’re trying to to look at the genome and tie mutations uses we’re done
on people of European descent proof that’s just ridiculous and so I’m so
there’s been a big move among a number of scientists to up get a real global
representation of of human genomes know and they’re there are places like for
example in New Guinea we’re scientists have been particularly
interested in going there and and just going from village to village and try to
sequence genomes because people into any they they showed up there maybe forty
fifty thousand years ago and have been there ever since oof and so they have a kind of genetic
variation there that you don’t find anywhere else and if you find for
example that you have some really unusual mutation that is linked with
particular disease that could tell you a lot about the disease general right so the more more genomes
from people not like me that better and it can tell us more than medical
information to we’re also starting to use and have been using you know genome
studies to learn more about the history of humanity about where we’ve been what
we’ve done how much sex we had with Neanderthals
all these wonderful things did you find out anything about your not
just like recent heritage but you’re sort of historical heritage yeah yeah I mean I’m really fascinated
with human history and you know our genomes carry lots of information about
that passed and and we’ve sort of accumulated in our ancestors accumulated
over literally millions of years so you know you can see for example of things
that you care in common chimpanzees because we have a I’m an
ancestor that live seven million years ago or so I’m you know neanderthal DNA is really fascinating
because it looks as if you know maybe between a hundred thousand fifty
thousand years ago something like that humans and Neanderthals interbred
numerous times and some of their DNA ended up in our genome so so this seems
to have happened after he was expanded out of africa and that means that
non-africans all have maybe a couple percent you know how DNA a place like 23
me will actually tell you like here’s your precise percentage of DNA which is fascinating on but I
would you know I would wonder well what part is an adopted by my name . genes
are probably different than yours because they’ve just been lost over tens
of thousands of years and each of us hold on to a different set so i was able
to go to some scientists who said like well here you go hear hear your Neanderthal genes 613 of
them a lot of them we don’t know what they do but some of them have actually
been tied to medical conditions so I’m actually protected slightly from
depression mind the indigenes I’m also slightly at risk of getting nosebleeds doesn’t any and all James sometimes
things are just you just sort of think like what does that really mean I but but for scientists like they
actually like that there are really deep evolutionary insights that you get you
can for example a lot of my Neanderthal genes turn out to be like other people
having to do with the immune system so it may be that the answer calls had
immune systems that were equipped to deal with all of the infections that
they faced out in europe and asia and and when you know our African when our
ancestors came out of Africa um they just didn’t have that equipment
so if there are these animal genes floating around the human gene pool that
give you protection to these pathogens that’s going to be in you’re more likely
to survive through those genes may be going around and allow the other ones
did last name so cool so you are writing a whole series on
your experience with your genome and parsing it and the scientists he worked
with and figuring out you know health you know recent ancestry historical ancestry tell me more about how this is going
down where it’s going to be because I’ve read a bit of it and I’m excited to see
more oh so i wrote this first at which is a
publication about medicine and life sciences and it appears in a three-part
series and it’s called game genome and so if you go to stand and look for game
of genomes you’ll be able to find this three-part series and for people who are
real data junkie some scientists and I actually set up a
parallel website where they put all of their analysis and all their data to my
genome up there it’s all there for people that to plow
into they want to really kind of see how scientists actually take a genome and
make sense of it came of genomes thank you so much Carl Zimmer for
joining us here on scishow as fascinating conversation and a great
work really cool and glad that you are not dying of any horrible genetic
diseases that not yet all right thank you thanks a lot thanks
for having me yeah we have the new host of crashcourse physics dr. Sidney samara
excited to have you here do you like this couch right

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