WEBVTT

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Okay, so I'm here with John Doyle. We're still both at the KITP for the workshop

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on network architecture.

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This is Paul Fouchure, the Convergence Science Network.

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Work and john you you presented your work on on architectures as a control engineer,

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you looked at at architectures in

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particular focusing on single cellular organisms right

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so so and that seems a bit of counterintuitive move

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for a control engineer but why why did

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you move to the to biology well i

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got interested in biology you know around 10 years ago or

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10 or 15 years ago um i'd been

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working initially motivated i'm pretty much

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a very much at the theoretical end my phd is in math but i

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was early mostly motivated by aerospace control problems because they were doing

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in you know the 80s the most cutting edge things but then in the 90s networks

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started coming you know we we the internet really grew to prominence um didn't

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really have a theory so i got interested more in networks and uh just kind of gravitated towards,

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um bacteria because i had uh colleagues at caltech who worked on it it was kind

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of a convenient um but also um i've found that they have in nature one of the most remarkable.

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And evolvable architectures the architecture of

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the bacterial biosphere um for one thing it evolved into us but it also continues

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to have tremendous evolvability and robustness and so i want to understand what

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gave that biosphere that robustness and i think we've now found.

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Deep principles that are very consistent with what we're learning about how

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to build technology networks so it was examples in addition to the internet

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of really sophisticated

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evolvable networks that we

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could compare but now before you go to internet and talk about robustness,

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What's what are these principles of robustness that?

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That you see these biological systems. Well so one thing is they are.

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They get robustness by having a plug-and-play, sort of what we in technology

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call a plug-and-play architecture.

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That is, on almost every timescale you look, they can quickly adjust to,

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say, changing environments.

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And so on very short timescales, they can very quickly rearrange their protein

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networks to respond as they needed. But on longer time scales,

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they can change their genomes very rapidly.

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They can swap genes.

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So the bacterial biosphere as a whole almost acts as one large gene pool.

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So on long time scales, they can very quickly evolve their genome.

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And on short time scales, they're very quick in responding to the environment.

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And what's interesting is I think their architecture makes both of those better.

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And that's one of the things that I think has surprised the biologists a bit

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is that the proper architecture can facilitate both rapid robustness on short

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time scales and rapid evolvability on long time scales.

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Else but now in your so

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this is a bit the phenomena right these are

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the phenomena we want to understand but not in in terms of principles you you

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talked about layering you talked about constraints um and you talk about let's

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say feedback so so how does this now relate to these phenomena that we're trying

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to look at right well the way we the way in engineering Engineering,

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we think about, and mathematics,

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the way we think about describing architecture is in terms of constraints.

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And the IEEE Transactions paper on architecture takes that point of view,

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as does the recent PNAS paper aimed at neuroscientists, and it tries to explain

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how we think about constraints.

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And one of the place constraints come from is the behavior of the system as

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whole is constrained by the environment it must act in and if it's going to survive and persist.

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And then there's usually constraints on the components which come up from the bottom.

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What can you build? What are the resources? What can you build it out of?

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And then additionally, there are constraints that come out of theory in some sense.

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I mean, theory reflects reality. But the idea is that much of engineering theory

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is about the additional hard limits that come either out of limitations on computing,

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which is Turing, limitations on communication, which is Shannon.

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And what I talked about in this KTP lectures is the Bode limits on robustness and feedback systems.

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These aren't well known in the scientific community.

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And they're a little bit fragmented even within engineering.

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But we're trying to build unified theories now.

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But the final constraint then is the design choices that are made,

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either through evolution or through deliberate design.

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And Gerhardt and Kirshner, who are biologists, have a very nice phrase for what

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a good architecture is, is constraints that deconstrain.

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And you choose a few constraints, and it might be, for example,

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the use of ATP as an energy carrier, the use of NADH as a redox carrier, the codons.

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In the internet, it would be the packet formats and the TCPIP protocol.

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Those are chosen wisely. Then they free you up to use that as a platform.

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For both very robust networks and very evolvable networks and that's

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where layering comes in is because layering is seems to

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be the strategy that both engineers and biology have adopted to make flexible

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uh robust evolvable systems and what layering is is a particular way of structuring

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the chosen constraints and so that's what we talked a lot about it's not a simple topic

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but um it's familiar enough

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to people from neuroscience and from cell biology and

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from engineering that there is becoming

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i'm hoping a common language which is what i'm trying to promote about

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what is layering but then how do

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layers map to modules right because also in

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your analysis you you stress the notion of

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modules quite a bit yeah so how should i see this

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is related to layers and modules so layering is

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i think the the highest level view of what modularity is and i think it's the

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most uh important aspect of modularity um i think there's been a lot written

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in the scientific community lately about modularity that is i think

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naive and not wrong so much as not the most important aspects of Larry.

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And so the thing that people are probably most familiar with modularity is the laptop that they have.

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And they can, or they download this podcast and it just runs immediately.

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And so the idea is that the kind of modularity it has is that you can download

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new software, you can download new podcasts and they immediately work largely

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independent of which computer you happen to have.

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Um, and you can, you can go to the store, uh, order online, uh,

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hardware that you just plug in.

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And what makes that possible is what's hidden,

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what you don't see, which is the operating systems and that,

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that they sit between all these applications and the hardware and,

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uh, and allow you the modularity.

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And the idea is that the modularity looks so simple and so easy when it works.

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It usually either works perfectly or not at all.

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But it's the layered structure that allows that to happen.

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And we believe that's the same thing in biology. It's what allows for horizontal

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gene transfer as a mechanism for bacteria to evolve rapidly, for example.

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And that so they have the same sort of

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plug and play modularity that our technologies

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have when they're good but now does modularity always

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imply let's say a static organization of

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of a structure or can you

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have let's say virtual modules that change if

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you want their boundaries and their interfaces to other modules so

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how could i think about this well i think i think

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the constraints a deconstraint way of looking at

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this is that there's always different time

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scales for different aspects of the architecture there's there's usually

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things that are persistent on very long time scale so an example of something

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that is persistent on very long time scales in biology would be the use of atp

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as an energy carrier it's both universal across all of biology and probably

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has been there for billions of years um the the uh the codon usage is nearly universal and has

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probably been there for also similar long times.

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So those are constraints that really persist for a long, long time.

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What they facilitate, however, is tremendously dynamic responses.

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And so by having a common energy carrier throughout the cell.

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Individual modules don't have to worry about an energy source.

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Core metabolism make sure that that

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the atp charge is maintained as constant as

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possible and an enormous amount

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of sophisticated control goes on inside the cell or inside our bodies to maintain

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that energy charge um and then what that allows you to do is on again on every

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time scale adapt very dynamically to the challenges so what you see is the combination of a

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permanent constraint that's fixed forever.

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But that choice, if done wisely, enables very, very much dynamics.

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Now what happens is on fast time scales, even what's a module is changing very rapidly.

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So for example, just in say in metabolism, you'll the depending on what,

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what biosynthetic pathways are needed, we may come and go on demand.

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Um and and what

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what and depending again on what's in the environment what

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was a food source may go away

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and now all of a sudden there that's a say an amino acid that

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you have to start manufacturing again this is bacteria are the

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most plastic in this regard we're not very flexible right but

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at the same time we can eat all sorts of things um and so we're

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omnivores and our ability to do that is

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again because we have a

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sort of front-end process that turns

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whatever we eat into a few basic building blocks from

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which we synthesize all of our tissues okay but now if you

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if you describe it like this coming from engineering you

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seem to be implying that actually engineering also

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works according to these principles yeah is it actually true

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for for sort of the larger systems

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that we have put together as humans well one.

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Of the problems is the larger systems we put together as humans

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are not sustainable and so they

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have design flaws and one of the ironies is uh

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when i first started getting interested in biology the biologists

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would tell me oh you know you're going to see biology's kludgy it's

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an accident it's a tinker evolution's the tinkerer um that's

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very true but in fact you don't

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you don't tend to see uh the gross

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design flaws in biology that are all over in engineering and the reason for

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that is that that much of the core uh these core protocols in biology have had

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millions to billions of years to evolve um and And sure,

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we have some funny aspects of because we were built out of fish parts.

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And so building a human out of fish parts is going to have some problems.

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But the the biochemical layer.

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It seems to be spectacularly uh well designed from an engineering point of view,

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so i think and so what the what you what's hard to do with any of these systems

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is to sort out what is a hard necessary constraint and trade-off and and what is a,

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an accidental design flaw either of evolution or of engineering and then you

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see both um so the problem with engineering though is in our at the big scale

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we're profoundly unsustainable,

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In our energy, transportation, waste, water, food, almost everything.

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And the more you learn about it, the more disturbing it is.

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The more I understand ecosystems and their interactions with our technologies,

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the more frightened I am.

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I think I'm, funny, I'm kind of a global warming skeptic. I think it's much

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worse than the scientists are telling us.

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I don't think they have the tools yet to do the sort of worst case scenario

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analysis that we do in engineering.

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And we take for granted that our planes rarely crash, and that's because engineers

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do that kind of worst-case analysis.

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So we do certain things very, very well in engineering. We've gotten to the

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point where we can build platforms like airplanes and vehicles that are very

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sophisticated and very robust, but we're not so good at the networks yet.

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And the internet was a spectacular innovation, but it now has a lot of recognizable design flaws,

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but we've built so much on top of it

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that it's hard to now change

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those if you make a if you make a mistake in

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a core protocol and then you build a

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lot on top of it it can be very hard to now change that right so if atp wasn't

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a good energy carrier biology would have very little choice but to just stick

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with it yeah exactly so but now so so what but this seems to be also a conundrum

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a bit in your, well, these ladies are getting a bit noisy, right?

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So maybe we should change location.

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Because I have to filter all this stuff out later again. Keep on going.

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Because what I want to bring up now is that in your, so the one that now we

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see, if you want, a bit of a contrast here, right, between your analysis of

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life, of biology, biological systems, Thank you.

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And the success of this framework you see in nature, in actual development of

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these large integrated systems like internet, right?

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Because like you said earlier, if you look at how internet has been put together,

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it's one big kludge, right? It's not really.

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But it was based on a few very profound and visionary insights.

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And it's not necessarily from from control engineering

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in any way no no in fact it was operating systems

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uh and engineers right and um and

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they now they knew elementary

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control theory and made quite a bit of use of

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it at a time and they did it at a

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time when uh communication theory was almost

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entirely dominated by information theory and

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so decades ago there was a major battle between sort of the information theorists

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and the operating systems people over how to build these networks and and for

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almost accidental reasons in the u.s.

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The OS system people won and they built the internet and now what's happened

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in the last 10 to 15 years as we really now have a much more integrated theory

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that includes information and control theory and And greatly explains both the

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successes and the flaws in the current Internet architecture.

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And one of the big challenges now is to use those insights to build a next generation.

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But the Internet's a good example of a situation where the really brilliant

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engineers are always way out ahead of any of the theoretical understanding.

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And so we're always playing catch up with the best.

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It's the same way, I think, in medicine. And I think the best doctors are always

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making leaps way out ahead of any scientific basis.

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And then, and I think the scientific community in some ways quit doing this,

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is trying to come back and help the doctors flesh out the details.

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I think the doctors have, for a few decades, really been on their own as the

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scientific community pursued genomics as the answer to everything.

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Thing right but the only problem is of course that with respect

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to internet we might be already so much committed into

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one certain way of structuring the system that we have no chance ever to to

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re-engineer or redeploy anything that's a big worry yeah that's a big worry

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and so um i'm a little less concerned about that than i was from a technical

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point of view in the sense that i think.

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The architectures that I think are the most appealing that are being proposed

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actually have the internet as kind of a lousy special case.

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So I think it could be organically grown around a new architecture and then

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it's a little bit like a city.

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You could sort of leave the old parts as a kind of scruffy old neighborhood.

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I think that's possible. I think the challenge is going to be probably in these

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big systems, not technological, but the interplay between technology, markets, and policy.

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And I think if there's a system that we understand most poorly,

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it's the interplay between technology and policy and markets.

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And right now, extremely ideologically driven, not the least bit rigorous.

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And I would say of the fields that I've looked at, I think the area of economics,

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and finance and markets in that world is among the most ideological driven of any.

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And so the problems ultimately there may not be just purely technological. Right.

00:18:56.856 --> 00:19:01.036
But now to get back to the first architecture, right?

00:19:01.096 --> 00:19:06.476
So in some of those Also in the discussions here in this workshop.

00:19:07.456 --> 00:19:10.916
We want to get to some notion of, let's say, brain architecture.

00:19:11.456 --> 00:19:15.536
But then let's first try to understand what we mean with architecture.

00:19:15.856 --> 00:19:22.276
And you have used this analogy with, let's say, a garment to illustrate how

00:19:22.276 --> 00:19:23.256
you think about architecture.

00:19:23.736 --> 00:19:30.056
Could you maybe explain? Yeah, I've been trying to look for an example of an

00:19:30.056 --> 00:19:37.696
architecture that would be so simple you could explain it to a school child, right?

00:19:38.876 --> 00:19:42.816
Because I think we need these concrete metaphors. And of course,

00:19:42.836 --> 00:19:47.596
anything that simple is dangerous because it can't have many of the important

00:19:47.596 --> 00:19:51.956
features that we care about. But the reason I picked on clothing is everybody knows about clothing.

00:19:52.396 --> 00:19:57.096
And the thing about clothing is that it shows two very different kind of layers.

00:19:57.996 --> 00:20:04.136
And the PNAS paper that's now online and soon to be in print discusses that.

00:20:04.136 --> 00:20:08.356
And the idea is that the most familiar one is sort of inner to outer wear.

00:20:08.496 --> 00:20:09.876
So you have an inner layer that's

00:20:09.876 --> 00:20:13.836
close to the skin. And I'm imagining clothing in a cold environment.

00:20:14.016 --> 00:20:20.016
We're naturally adapted to live in a very hot environment and don't really even

00:20:20.016 --> 00:20:21.356
need clothing in a hot environment.

00:20:21.456 --> 00:20:24.776
But where we really need clothing is harsh, cold environments.

00:20:25.216 --> 00:20:29.676
And so in those environments, we often have an inner layer that's close to the skin. Right.

00:20:30.522 --> 00:20:34.562
And then you have an outer layer that protects you against the weather from

00:20:34.562 --> 00:20:36.582
the outside, wet, cold, wind.

00:20:36.982 --> 00:20:41.042
And then a middle layer that provides warmth. And what's interesting about this

00:20:41.042 --> 00:20:43.882
view of layering is it's so simple anybody can understand it.

00:20:44.042 --> 00:20:49.642
What you have is three very different kinds of layers that combine synergistically

00:20:49.642 --> 00:20:54.902
to create a whole that feels good to the skin, protective of the outside,

00:20:55.062 --> 00:20:56.102
and as warm as necessary.

00:20:56.102 --> 00:20:59.262
And tremendous plug

00:20:59.262 --> 00:21:02.962
and play modularity you can swap in different parts

00:21:02.962 --> 00:21:06.002
of the garments but it also shows another

00:21:06.002 --> 00:21:09.022
point which is enormously confusing within

00:21:09.022 --> 00:21:12.202
the scientific community not in engineering but most

00:21:12.202 --> 00:21:15.402
combinations of garments do not produce functional outfits

00:21:15.402 --> 00:21:18.502
they really while there's enormous variability

00:21:18.502 --> 00:21:21.222
in what you can do there's still

00:21:21.222 --> 00:21:24.282
pretty strict strict rules in what can go where or they don't

00:21:24.282 --> 00:21:27.762
work at all so you can't you can't make underwear

00:21:27.762 --> 00:21:30.922
outerwear you can't make socks into hats

00:21:30.922 --> 00:21:34.142
you can't you know for the most part so that's one

00:21:34.142 --> 00:21:42.662
way of looking at the layering and but another is the composition of fiber which

00:21:42.662 --> 00:21:49.542
is then um spun into yarn which is then knit or woven into cloth which is then

00:21:49.542 --> 00:21:53.262
sewn into garments A whole other dimension of layering.

00:21:53.562 --> 00:22:00.782
Very different than the first, but again, illustrates properties both of biology and technology.

00:22:01.062 --> 00:22:07.362
And so, in that PNS paper, I try to flesh out that example as one that I think would help.

00:22:08.449 --> 00:22:13.189
Both engineers and neuroscientists talk to each other because it's a,

00:22:13.229 --> 00:22:14.469
it's such a simple example.

00:22:14.549 --> 00:22:18.629
Now the danger is it's too simple. It doesn't have dynamics.

00:22:19.869 --> 00:22:23.489
The, the, these compositional forms are very, very simple.

00:22:23.569 --> 00:22:27.889
The way clothing just sits on top of, you know, one layer of clothing sits on

00:22:27.889 --> 00:22:33.309
top of another doesn't really, doesn't really lock in like you would in a,

00:22:33.309 --> 00:22:35.829
in, in many other systems. There's a lot of things that are wrong with the thing,

00:22:35.909 --> 00:22:37.029
but it gets a starting point.

00:22:37.469 --> 00:22:41.169
Okay, that's good. So if we have layers, we also have different,

00:22:41.229 --> 00:22:44.969
let's say, processes that give rise to the key properties of these layers.

00:22:45.409 --> 00:22:49.109
But now, if I would like to have, let's say, a more parametric description of

00:22:49.109 --> 00:22:54.409
such an architecture, what are the key, let's say, parameters that I should worry about?

00:22:55.249 --> 00:22:59.529
Well, in this, I mean, again, using this, stretching this probably to the point where we'll break,

00:22:59.529 --> 00:23:10.429
um there is there is the rules by which the constraints by which you can assemble

00:23:10.429 --> 00:23:17.729
so like i said most most combinations of garments do not produce a functional outfit,

00:23:19.149 --> 00:23:27.469
and there's a few rules that you can write down in principle anyway and we certainly

00:23:27.469 --> 00:23:32.769
learn them And children learn them as to what make a functional garment.

00:23:32.929 --> 00:23:37.369
But the interesting thing is, once the garments are selected...