Solve for X: Omri Amirav-Drory on synthetic life toolkits

Uploaded by wesolveforx on 07.02.2012

is quite an act to follow.
So I'll do my best. So let's talk about huge problems. Our
civilization is totally dependent on finite resources
of coal, oil, and natural gas.
We burn them.
We flow them through chemical refineries and factories.
And they produce almost everything that we use.
This is unsustainable.
And this is very dangerous.
A radical solution will be to harness the power of biology.
Because living things can use renewable resources, such as
sugars, sunlight, and CO2.
And they are versatile enough and can produce almost
everything we currently get from fossil fuels.
And the best thing about living things is that they can
scale to meet our global challenges.

And we can design living things.
We can program them.
Because biology is just another information
So take computers for example.
Computer understand code, binary ones and zero.
But you don't write computer software by
typing ones and zero.
You use abstraction layers.
You use tool to design, debug, and compile your code into
executables that runs on computers.
Living things also understand code.
They understand the a, c, t, and g of DNA.
The executables are chromosomes and genomes that
runs inside of biological computers inside of cells.
But genetic designers still write with ones and zero.
People in my lab still write with a, t, g, and c.
They don't have the design tool.
They don't have the compile and debug tool
that we have in software.
They don't a genome compiler.
So we believe that the breakthrough technology is to
create those tools that will enable the design and creation
of useful living things to solve our global challenges.
And we can do that because there is two underlying
technologies that power this new field
of synthetic biology--
reading DNA and writing DNA.
In both of those technologies the price performance has been
going down faster than most lower for the past 10 years.
So when I talk about reading DNA, where the price has been
falling down from $3 billion to read one human genome to
this year, 2012, $1000.
So as the price has been falling down so rapidly, our
databases exploded with genetic information, with
genes and genomes, nature's own software designs.
But the really cool thing, the really cool technology is
being able to write DNA.
Because now we can write our own software using whatever
genetic code that we want.
And we can turn our code into life by injecting it into
living cells, and then use the cell machinery, their
self-assembled nanomachine that was developed in four
wheels of evolution to read our code as you can see here
on the left alimade polymerize running all the genome,
transcribing the gene into the yellow RNA molecule, and then
on the right, using different cell machinery, the ribosome,
to read this RNA molecule three letters at a time and
translating it into protein, into flesh and blood.
So those are amazing machine that we could
never develop by ourself.
I think that it's just like giving iPads to cavemans.
You can maybe play Angry Birds.
But you could never build the chips behind it.
It's amazing technology.
And this is not science fiction.
At 2002, scientist has created the first synthetic creature.
It was a polio virus, 7500 letters.
That's it.
But think about it.
You can now go to the internet, download the whole
viral genome, and boot it up.
That's very interesting.
And then a year and a half ago, as Juan mentioned, the
Craig Venter Institute has chemically synthesized a
million base pair bacterial genome and boot it up-- so the
first living cell.
And then just a few months ago, scientists from the Johns
Hopkins University have synthesized the first
eukariotic chromosome, 2.3 million base pair of a yeast
Our capability is just increasing.
And if this trend continues who knows what we'll be able
to produce in the near future.
And I believe we should be able to construct any genome
that we like.
It's obvious to me.
So how do you go about designing living things?
Well we believe it should be as easy as just
logging into a website.
So this is what we are building right now.
If you want to look for a genome, it should be as easy
as searching for it or just browsing through genomes of
bacteria and viruses.
For example I want to open this ecoli.
Just press on the icon.
Download it directly from the databases.
And then if I want to manipulate it, just drag it
into the canvas.
And that's it.
Now this is just an icon, just a layer of abstraction.
But we can present real genetic information, for
example the genome properties, the number of genes, the
length of the genome, and what this genome knows to do, the
metabolic pathway.
Now this diagram might look complex.
But it's pretty simple.
Every circle is a molecule that this bacteria knows how
to produce, break down, or get from the environment.
And every line is an enzyme that turns one of these
circles, one of those molecules, to the next.
And once we read the whole genome and populate this kind
of diagram, then just like GoogleMap, we could start
asking for direction.
So let's say I want to go from glucose, simple sugar, and
produce biofuel, methanol for example.
So I'm just asking, well what's the shortest route?

So in this case the shortest route contains eight genes.
In white are the genes that are native in the genome.
They are already there.
But to close the circle from glucose to methanol, I need to
add the genes in red and orange.
They are not there.
But we can give you candidates.
And all you need to do is just select
from the list of creatures.
And you can select by closest evolutionary partners or three
other criteria and just export them and compile them.
Now this is the hardest thing that we are doing.
How do you run program from one creature in another?
You need to optimize a code.
You need to change the regulatory elements.
So we started to build that.
And as computer gets better, as we know more basic science,
our algorithm will get better.
Another thing that Juan showed is how you can start building
complex systems starting with small elements.
So that should be as easy as starting a new project, going
back to the material box, and searching for those element
like a promoter that tells you start reading this gene from
here, ribosome binding site, a gene, a terminator saying stop
reading this gene.
So in a few click, I created a whole genetic circuit, the
whole small genetic circuit.
If I want to learn more, just go to the tool panel and hey.
What does this gene does?
So here, I get the gene properties.
If this gene, if this protein, has experimentally solid
structure, I can zoom into the structure.
And if I know what I'm doing--
in this case it's a DNA binding protein--
I can zoom into the structure, select amino acid, delete
them, mutate them, change them, do some very cool
structural-based changes.

Now everything I showed you so far is just icons.
It's just layer of abstractions.
So how do you go about moving from one layer to the next?
Well we believe it should be as easy as zooming in.
So now we moved from this layer to the amino acid layer.
And in the background you can see the source code, the DNA.
And in each layer, we can do different things.
For example in this layer, if you want to change the
protein, just press on amino acid.
Get the code.
Change the code.
That's it.
You can save it.

You can save. You'll be prompt to give your
username and password.
Because we keep track of your previous designs.
And if you pay attention, your previous
designs are just icons.
It could be a very complicated design which will represent in
the simple icons.
And you can share this icon with your friends.
You can put it in our biological app store, so other
people can use and install your designs.
If you want to get the DNA, just drag it to the cart.
And we'll ship it to you.
And then minimize it.
And here is your new app.
If you want to install your f in this bacteria, just search
for a specific location.
And zoom in through the layer of abstraction until you find
what you are looking for.

And then once you find the gene you were looking for, it
should be as easy as dragging into the trash, getting your
new app and putting it in--
that simple.
Save, order.

And that's it.
Now as you can see, ordering the whole genome, even at
$0.25 a base pair, is pretty expensive.
But the price of small genetic elements is
reasonable right now.
And it's going down very fast. So it's as easy as that.
Press and order.

Now everything I showed you so far is how a person like
myself, a trained biologist in a research laboratory, can do
some very accurate and powerful genetic engineering
using tools like that.
But part of our vision is to get the tinkerers involved, to
democratize the tools of creation, get the do it
yourself biologists involved.
And what about the future of sustainability?
Some people think that this might be the future--
electric cars or solar powered LED lamps.
But we think that you can mash those together.
And maybe in the future, one of you can search for any life
form that you like.
I like trees.
I like oak trees very much.
So let me go to the biological app store.
Let me take the luminescence program from fireflies and
just compile it into my app.
And here I get renewable, self-assembled, solar powered,
sustainable street lamp for my home and the community.
And just order it.
So you might think this is science fiction.
But let me remind you we can build cells today.
This is not science fiction, right?
And a tree started with a cell.
You and I started with one cell.
And this is beautiful.
This is complex.
But this is just software.
It's software that drives its own hardware.
But it's just software.
And as the price of reading this software goes down, is
when we'll understand more and more about this software.
With tools like ours and with the constant ability to create
more and more complex structures, we believe that
anything will be possible moving forward.
We live in this beautiful living world.
Our world have huge problem.
Our current way of manufacturing is
Living things can help us if you can just design them, and
compile them, and create them.
And then in the future, we might have a future of
abundance, of sustainable abundance in our designed,
engineered living world.
Thank you.

MALE SPEAKER: Let us define x.
X is a solution, a solution to a seemingly insurmountable
problem, like climate change or cancer, one
that affects the world.
But what if we redefine x as a challenge, an opportunity for
radical thinking, a chance to light up the world with
breakthrough ideas and cutting-edge technology, the
stuff of science fiction that just might fly after all.
Solving for x requires wonder and imagination and a vision
to build seemingly impossible solutions to the world's
biggest problems. Solve For X, Moonshot Thinking.