The next software revolution: programming biological cells | Sara-Jane Dunn

The next software revolution: programming biological cells | Sara-Jane Dunn

The second half of the last century
was completely defined by a technological revolution: the software revolution. The ability to program electrons
on a material called silicon made possible technologies,
companies and industries that were at one point
unimaginable to many of us, but which have now fundamentally changed
the way the world works. The first half of this century, though, is going to be transformed
by a new software revolution: the living software revolution. And this will be powered by the ability
to program biochemistry on a material called biology. And doing so will enable us to harness
the properties of biology to generate new kinds of therapies, to repair damaged tissue, to reprogram faulty cells or even build programmable
operating systems out of biochemistry. If we can realize this —
and we do need to realize it — its impact will be so enormous that it will make the first
software revolution pale in comparison. And that’s because living software
would transform the entirety of medicine, agriculture and energy, and these are sectors that dwarf
those dominated by IT. Imagine programmable plants
that fix nitrogen more effectively or resist emerging fungal pathogens, or even programming crops
to be perennial rather than annual so you could double
your crop yields each year. That would transform agriculture and how we’ll keep our growing
and global population fed. Or imagine programmable immunity, designing and harnessing molecular devices
that guide your immune system to detect, eradicate
or even prevent disease. This would transform medicine and how we’ll keep our growing
and aging population healthy. We already have many of the tools
that will make living software a reality. We can precisely edit genes with CRISPR. We can rewrite the genetic code
one base at a time. We can even build functioning
synthetic circuits out of DNA. But figuring out how and when
to wield these tools is still a process of trial and error. It needs deep expertise,
years of specialization. And experimental protocols
are difficult to discover and all too often, difficult to reproduce. And, you know, we have a tendency
in biology to focus a lot on the parts, but we all know that something like flying
wouldn’t be understood by only studying feathers. So programming biology is not yet
as simple as programming your computer. And then to make matters worse, living systems largely bear no resemblance
to the engineered systems that you and I program every day. In contrast to engineered systems,
living systems self-generate, they self-organize, they operate at molecular scales. And these molecular-level interactions lead generally to robust
macro-scale output. They can even self-repair. Consider, for example,
the humble household plant, like that one sat
on your mantelpiece at home that you keep forgetting to water. Every day, despite your neglect,
that plant has to wake up and figure out how
to allocate its resources. Will it grow, photosynthesize,
produce seeds, or flower? And that’s a decision that has to be made
at the level of the whole organism. But a plant doesn’t have a brain
to figure all of that out. It has to make do
with the cells on its leaves. They have to respond to the environment and make the decisions
that affect the whole plant. So somehow there must be a program
running inside these cells, a program that responds
to input signals and cues and shapes what that cell will do. And then those programs must operate
in a distributed way across individual cells, so that they can coordinate
and that plant can grow and flourish. If we could understand
these biological programs, if we could understand
biological computation, it would transform our ability
to understand how and why cells do what they do. Because, if we understood these programs, we could debug them when things go wrong. Or we could learn from them how to design
the kind of synthetic circuits that truly exploit
the computational power of biochemistry. My passion about this idea
led me to a career in research at the interface of maths,
computer science and biology. And in my work, I focus on the concept
of biology as computation. And that means asking
what do cells compute, and how can we uncover
these biological programs? And I started to ask these questions
together with some brilliant collaborators at Microsoft Research
and the University of Cambridge, where together we wanted to understand the biological program
running inside a unique type of cell: an embryonic stem cell. These cells are unique
because they’re totally naïve. They can become anything they want: a brain cell, a heart cell,
a bone cell, a lung cell, any adult cell type. This naïvety, it sets them apart, but it also ignited the imagination
of the scientific community, who realized, if we could
tap into that potential, we would have a powerful
tool for medicine. If we could figure out
how these cells make the decision to become one cell type or another, we might be able to harness them to generate cells that we need
to repair diseased or damaged tissue. But realizing that vision
is not without its challenges, not least because these particular cells, they emerge just six days
after conception. And then within a day or so, they’re gone. They have set off down the different paths that form all the structures
and organs of your adult body. But it turns out that cell fates
are a lot more plastic than we might have imagined. About 13 years ago, some scientists
showed something truly revolutionary. By inserting just a handful of genes
into an adult cell, like one of your skin cells, you can transform that cell
back to the naïve state. And it’s a process that’s actually
known as “reprogramming,” and it allows us to imagine
a kind of stem cell utopia, the ability to take a sample
of a patient’s own cells, transform them back to the naïve state and use those cells to make
whatever that patient might need, whether it’s brain cells or heart cells. But over the last decade or so, figuring out how to change cell fate, it’s still a process of trial and error. Even in cases where we’ve uncovered
successful experimental protocols, they’re still inefficient, and we lack a fundamental understanding
of how and why they work. If you figured out how to change
a stem cell into a heart cell, that hasn’t got any way of telling you
how to change a stem cell into a brain cell. So we wanted to understand
the biological program running inside an embryonic stem cell, and understanding the computation
performed by a living system starts with asking
a devastatingly simple question: What is it that system actually has to do? Now, computer science actually
has a set of strategies for dealing with what it is the software
and hardware are meant to do. When you write a program,
you code a piece of software, you want that software to run correctly. You want performance, functionality. You want to prevent bugs. They can cost you a lot. So when a developer writes a program, they could write down
a set of specifications. These are what your program should do. Maybe it should compare
the size of two numbers or order numbers by increasing size. Technology exists that allows us
automatically to check whether our specifications are satisfied, whether that program
does what it should do. And so our idea was that in the same way, experimental observations,
things we measure in the lab, they correspond to specifications
of what the biological program should do. So we just needed to figure out a way to encode this new type of specification. So let’s say you’ve been busy in the lab
and you’ve been measuring your genes and you’ve found that if Gene A is active, then Gene B or Gene C seems to be active. We can write that observation down
as a mathematical expression if we can use the language of logic: If A, then B or C. Now, this is a very simple example, OK. It’s just to illustrate the point. We can encode truly rich expressions that actually capture the behavior
of multiple genes or proteins over time across multiple different experiments. And so by translating our observations into mathematical expression in this way, it becomes possible to test whether
or not those observations can emerge from a program of genetic interactions. And we developed a tool to do just this. We were able to use this tool
to encode observations as mathematical expressions, and then that tool would allow us
to uncover the genetic program that could explain them all. And we then apply this approach to uncover the genetic program
running inside embryonic stem cells to see if we could understand
how to induce that naïve state. And this tool was actually built on a solver that’s deployed
routinely around the world for conventional software verification. So we started with a set
of nearly 50 different specifications that we generated from experimental
observations of embryonic stem cells. And by encoding these
observations in this tool, we were able to uncover
the first molecular program that could explain all of them. Now, that’s kind of a feat
in and of itself, right? Being able to reconcile
all of these different observations is not the kind of thing
you can do on the back of an envelope, even if you have a really big envelope. Because we’ve got
this kind of understanding, we could go one step further. We could use this program to predict
what this cell might do in conditions we hadn’t yet tested. We could probe the program in silico. And so we did just that: we generated predictions
that we tested in the lab, and we found that this program
was highly predictive. It told us how we could
accelerate progress back to the naïve state
quickly and efficiently. It told us which genes
to target to do that, which genes might even
hinder that process. We even found the program predicted
the order in which genes would switch on. So this approach really allowed us
to uncover the dynamics of what the cells are doing. What we’ve developed, it’s not a method
that’s specific to stem cell biology. Rather, it allows us to make sense
of the computation being carried out by the cell in the context of genetic interactions. So really, it’s just one building block. The field urgently needs
to develop new approaches to understand biological
computation more broadly and at different levels, from DNA right through
to the flow of information between cells. Only this kind of
transformative understanding will enable us to harness biology
in ways that are predictable and reliable. But to program biology,
we will also need to develop the kinds of tools and languages that allow both experimentalists
and computational scientists to design biological function and have those designs compile down
to the machine code of the cell, its biochemistry, so that we could then
build those structures. Now, that’s something akin
to a living software compiler, and I’m proud to be
part of a team at Microsoft that’s working to develop one. Though to say it’s a grand challenge
is kind of an understatement, but if it’s realized, it would be the final bridge
between software and wetware. More broadly, though, programming biology
is only going to be possible if we can transform the field
into being truly interdisciplinary. It needs us to bridge
the physical and the life sciences, and scientists from
each of these disciplines need to be able to work together
with common languages and to have shared scientific questions. In the long term, it’s worth remembering
that many of the giant software companies and the technology
that you and I work with every day could hardly have been imagined at the time we first started
programming on silicon microchips. And if we start now to think about
the potential for technology enabled by computational biology, we’ll see some of the steps
that we need to take along the way to make that a reality. Now, there is the sobering thought
that this kind of technology could be open to misuse. If we’re willing to talk
about the potential for programming immune cells, we should also be thinking
about the potential of bacteria engineered to evade them. There might be people willing to do that. Now, one reassuring thought in this is that — well, less so
for the scientists — is that biology is
a fragile thing to work with. So programming biology
is not going to be something you’ll be doing in your garden shed. But because we’re at the outset of this, we can move forward
with our eyes wide open. We can ask the difficult
questions up front, we can put in place
the necessary safeguards and, as part of that,
we’ll have to think about our ethics. We’ll have to think about putting bounds
on the implementation of biological function. So as part of this, research in bioethics
will have to be a priority. It can’t be relegated to second place in the excitement
of scientific innovation. But the ultimate prize,
the ultimate destination on this journey, would be breakthrough applications
and breakthrough industries in areas from agriculture and medicine
to energy and materials and even computing itself. Imagine, one day we could be powering
the planet sustainably on the ultimate green energy if we could mimic something
that plants figured out millennia ago: how to harness the sun’s energy
with an efficiency that is unparalleled by our current solar cells. If we understood that program
of quantum interactions that allow plants to absorb
sunlight so efficiently, we might be able to translate that
into building synthetic DNA circuits that offer the material
for better solar cells. There are teams and scientists working
on the fundamentals of this right now, so perhaps if it got the right attention
and the right investment, it could be realized in 10 or 15 years. So we are at the beginning
of a technological revolution. Understanding this ancient type
of biological computation is the critical first step. And if we can realize this, we would enter in the era
of an operating system that runs living software. Thank you very much. (Applause)

100 thoughts on “The next software revolution: programming biological cells | Sara-Jane Dunn

  1. Imagine how the cognitive capitalism of tech giants will shape our future. And with the growing threat of mass surveillance and cyberwarfare, who is left to defend our human rights?

  2. Imagine that crazy billionaire who wants to reduce his carbon foot print… But not change his great life. Solution: reduce the carbon produced by a million people(kill them). Hollywood- Are you listening?

  3. I think inorder to recreate cellular programming you will require quantum level computing power….. two sides of the same coin

  4. "programming biology is not going to be something you are going to be doing in your garden shed".. doubt this quote stands the test of time. Recall a recent Netflix series… dude in shed with crisper. Not same techniques, but still.

  5. It’s all good if it’s in the right hands! There is a good chance it will be used to destroy humans!!

  6. Seems like a bit of mumbo jumbo… you took a bunch of rules derived directly from genetics and created a program to express those rules and then ran the program to discover what those rules are? What happens when you made a mistake? You pretend the program is perfect and that it's predictions are perfect? What actually has this program been used to do that can said to be a "breakthrough"? Everything works "in theory"….

  7. I'm sorry. TED is garbage. Unless you enjoy their pro pédôphilé videos, or genderfluid children videos. Not intelligent, just disgusting.

  8. "Programming biological cells." What could go wrong there? I assume 'Big Pharma,' so I would expect extremely bad things to occur. It's what they do.

  9. Jeez, why is everybody down here flipping out ? Am I the only one actually looking forward to what they'll be able to do ? Just because it's Microsoft doesn't make it automatically bad, just as an university research lab doing the same isn't automatically good.

  10. No one should live past their natural life cycle. What she is actually talking about is programming human beings. This should be outlawed now. The evils far outweight the benefits!

  11. Why is everything so focused on maintaining a growing population? Lack of resources aside, it's literally lowering the general quality of life. No one enjoys living on top of one another dude.

  12. Scientific reduction-ism does not explain biology, but neither is theology adequate. Some sort of chaos theory applicable to biology will have to be developed, but we will have to deal with our own species sense of entitlement to the Earth.

  13. A child licking a light switch may think it's interesting, they may be amazed by their ability to light a room and then make it dark again, they may feel like master of that room.
    But it's not the lack of understanding that makes this situation dangerous, it's being smart enough to think there are no consequences in nature.
    Human nature is to lose respect for all things we 'understand'.

  14. More then 50 years ago I read a book named "The biological bomb" that described how biological science was advancing sooo fast that in 50 years the world would have totally changed. Well here I am more then 50 years later and today many of us has lost our faith in artificial medicine/biology. (I did not watch the video to the end…)

  15. The problem is that computer codes are running on system that operates at the speed of light while biological codes will have to run on biological/chemical processes that operates at the speed of a snail. You write your "Hello World" codes and sit there for hours or days to know if you got it right. Your code-run-debug cycle takes too long. This will make "biological programmers" productivity a lot lower than computer programmers.

  16. The absolute WORST thing we could do with all this CRISPR-type stuff is rush into it. Humanity isn't ready for it, but unfortunately it does exist so lets not repeat the mistakes made during the software/internet revolution

  17. Great, now we're planning to play God with biology itself. Something tells me this going to go very badly for us. All these big companies care about is profits, and they're the ones calling the shots.

    Get ready for scientists to mess up the natural world as they "learn" more about how it actually works. Thanks science. 😒

  18. 1) Re-listen this delegant speech replacing ''programming biological cells'' with ''producing nuclear power''. Same arguments about energy, benefits in any account, scientific elegance and potential dangers. The only difference is that the second case is reality and we all are dominated from the fear of a nuclear holocaut.
    2)How come that people one hand show so much care about a unique or a batch of cells and on the other hand we just slaughter a brand new not even born whole organism inside his mother 's belly, with his mother's approval and scientific process. Is this political correct? And by the way, how come we want to produce life in any way ( cells, artificial insemination, humanlike artificial inteligence etc) and prevent physiological produce of life by any means (abortions, pills, etc). Aren't these contradictine? Aren't these implying for some kind of ''contemporary humankind schizophrenia''? Forgive me for the terms, I m just trying to be logical concequent.
    3)So far, technological improvements benefit all our lives, of course, but also made the rich less and richer and the poor more and poorer. It 's not only a matter of trying and qualifications, it 's also a matter of reduced job vacancies. And we all Know where too much power in too little hands inevitably lead us: ultimate domination. Emperors of Rome didn 't just want to rule their empire, they wanted to be worship like God…
    My best wishes to all of you.

  19. The stem cells are not the only ones in a naive state…
    You look like a doctor from the 16th century promoting bloodletting.
    And plz don't forget to make this technology easy and accessible to everyone!
    What could possibly go wrong…
    Plz at least try to understand the whole system before you "program" it.
    This will be the new crisis if we are able to fix climate change.

  20. So we're renaming GM to biological programming in the hopes the idiots who hate GM from ignorance don't notice what we did? Might work.

  21. Had me hooked right up until she mentioned Microsoft. Now Ive missed the rest of the talk as I was laughing to much. Then she was talking about resetting a cell … Isnt that CTRL-ALT-DEL? The implications for humanity are diabolical. My biggest question is who would do the tech support? Wait Ive just been hacked by a Russian teenager. Cant hit reset cos my arm just fell off … Oh look at the pretty wall paper … I cant hear you cos my audio driver is not compatible. USB-f what … let me see if I can find an adapter.

  22. In the various wisdom traditions of the world huge emphasis is placed on ethics and conduct. Goodwill for others is encouraged while greed is discouraged. Patience is always a virtue. Through applying these principles we come to see the utter beauty and perfection of things as-they-are. Musicians of profundity, especially classical but of all traditions express these things through their music for those with the patience to listen.
    There is a natural balance but it has no place for excessive greed.
    Note there is no awe or amazement expressed here about how biology is operating just as it is. How is has served and is serving us.
    Like Francis Bacon who spoke of stretching out mother nature on a rack and forcing her ro reveal her secrets the only concern here is how to squeeze out more, how to build human created things bigger and better. No concern is expressed at all about any form of limits or constraints.
    We just go our greedy way ahead and program biology to serve us with no appreciation whatsoever for what is since it's all godless anyway.
    There's another way and many know it. It's called love, gratitude and appreciation. Meet you there!

  23. Tyrants make money from genocide, do you know what they call people who have no moral compass Narcissists. They are the people who make you think evil is a good idea so that you stand up in front of the world not having given any of this a single thought beyond money.

  24. We mistakingly believe human freewill exists outside of the Biological Imperative. We assume we are directing our own evolution but, all we've ever been doing is setting up the next phase of human evolution. To Evolve – truly means to be 'mutated' into another species…

  25. I love how none of these tech folks bother discussing the horrible ways all of this stuff can and will be used for terrible reasons. They are already shoving things like "Alexa" down our throats and the sheep willingly buy, for some reason wishing to have a device in their home that is constantly listening. Who needs privacy? Sure, is nothing wrong with that…👀 BTW I never forget to water my houseplants. 😛

  26. So what you're saying is the groups of human beings that have destroyed the entire planet with technology will be in charge of reek programming all of life which they still don't understand absolute insanity

  27. Some take-aways : 1 Math is the language to uncover and understand patterns; 2. Everything can ultimately be reduced to physics; 3 System dynamics is far more useful than its typical application in engineering.

  28. I was thinking: maybe a group will split off from society and say "We will live in our own communities without adopting this new technology." And this made me think of the Amish.

  29. Great talk, but why the incorrect information about biomass solar efficiency? Plants collect sunlight at 2 – 6% efficiency. The current record for human-made solar cells is 46%. Lot's of great applications but learning from high-efficiency plant photosynthesis is not among them… =

  30. Between the computational power of Quantum Computing, the threat of AI, and now Biological Programing it's very clear that the world is about to be more divided that ever. Get wealthy! Lol.

  31. Microsoft please focus on creating public education and genetic protective systems. I removed my other comments. I still think this video should be removed. I presented very negatively towards the risks of this exposure. I do believe wholeheartedly this tech is necessary for an incredibly awesome future, though until then, things are going to get incredibly volatile.

  32. Fascinating and a bit scary too but as with any frontier of knowledge it’s well worth pursuing – we must be very aware of the risks tho’.

  33. Seems like a technology with more negative outcomes than positive ones ( new bio weapons , engineered babies with unknown outcomes) .

  34. ~~~ sturdy knowledge of Osiris is beyond human sight but able to be felt and trained by the third eye questionnaire of parabola timeline for UR DREAM LIFE in workouts and job apply creative force is frozen in your sin simulation tumbler angel investors are molecular mechanisms THE COURSEWORK OR COURSE IS ALL AROUND U REAP EXACTLY HOW AND WHAT N WHY ~~~

  35. Insight : Biology is like kids, you have to dominate it carefully with care, nurture it, guide it without being harsh. Plus, you and your intentions have to be very pure, like parents approach towards kids. Then only Biology will work in your favour, otherwise adversely. Domination should be enchanting, not brutal. Also, Biology works as a team, this should be considered too. One literally has to use emotions to program Biology.
    Edit: scope of Biology could be beyond cell level to global level, like a global consciousness or emergence. This is because of millions of years of evolution and connections at quantum level. This needs to be considered too. As of now it behaves like grumpy kid locally.

  36. This is how women in science get recognition. By being amazing at their job and presentation. Not through SJW bullshit.

  37. If you have a belly, you shouldn't put yellow trousers over it. Common sense is not that common?…I'm scared of her programming anything.

  38. Give me photosynthesis gene my cell can activate it and my cell can assimilate any gene as my own specially plant genes. I don't want the poisonous one.

  39. She's naming all these positive things when in all reality it's all lies because they will never use this for the good of the people. They want population control and this would literally put it right in their hands. The crap they spray in the air is already changing our DNA wait till 5G rolls out completely that's going to mutate our DNA not to mention all the other harmful crap it does. Don't get me started on their vaccines. God programmed me just fine and my DNA is what it's meant to be

  40. I am a software engineer by profession such project will lead to the degradation of human and make us vulnerable to man 👨

  41. I like to think of the genome, or dna, as a long ribbon, with codes along the ribbon being utilized from birth (start of genome, start of code) to death (end of genome, end of code)…. 2,500,000,000 genes is approximately 1 gene being executed each second.

  42. A beautiful aspiration that will unfortunately be disfigured by profits and greed and technological suppression………..prove me wrong?

  43. Its amazing that every cell in you is replaced and only your conscious stays the same.
    This could be that through water somehow it transfers the information or might actually be on the quantum level.

  44. You know I am waiting for biological evolution from 2010. It has been 9 years now but no groundbreaking evolution in biology 😣😥😢.

  45. Dare I say, what a beautiful (extraordinary) explanation, and presentation.
    It's been long since having the pleasure of experiencing such intellect, and expert articulation. And that, in parallel. Inspiring. Thank you for sharing Sarah-Jane.

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