WEBVTT

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So Paul Voucher and Tony Prescott. And Partha was describing to us an amazing

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project where you have this sort of massive automated data collection on a very

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detailed anatomical level that can lay a foundation for new insights in the brain.

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So Partha, why don't you try to give us a short summary how you ended up doing this?

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I was really shocked to find out how little we know about how the brain is wired.

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That's what got me started.

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I trained as a theoretical physicist, and when I came into biology,

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I'm slowly coming to grips with the knowledge that we are very much limited by lack of information.

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And we have this paradox that we are data rich and data poor at the same time.

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We have lots of data, but sometimes critical pieces are missing.

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And once I realized that even in the most thoroughly studied model organism, which is the rat,

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the wiring diagram of the brain at a scale that neuroanatomists have studied

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has large empirical gaps in it, I thought I would set out to try to rectify that situation.

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But in some sense, it's very counterintuitive because often in neuroscience,

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also when you talk with other neuroscientists, it's this feeling like,

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well, we're drowning in data.

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We have so much data, different scales, different species, physiology, anatomy, etc.

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So how do you position that with respect to this data richness?

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So how do you now deal with this paradox?

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I think the way I think about it is that we are data rich.

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You're quite right. there's more than half a million articles being

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published on abstracts being published on PubMed every year so there's a tremendous

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amount of information out there I think this information is very heterogeneous

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and not really integrated there

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is no super brain that really has all the information and so does you,

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so yes we are data rich in this very heterogeneous sense lots of bits of data.

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We're data poor in the sense in neuroscience compared with, let us say,

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in genomics, where we have comprehensive information about a certain scale of organization.

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Let's say the genome. We've got the full genome of multiple species,

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but we can't say the same at any scale really of any organism for the nervous

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system, that we have the full set of information with the exception of C.

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Elegans, which has been kind of the you know example that people have put out um so for me the,

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Reconciliation is that on the one hand, we do have a lot of heterogeneous,

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unintegrated information, sometimes partial, because people have focused,

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over-specialized on certain areas of the system.

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A lot of studies have been attempted, a lot of studies of the visual system.

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So if one takes an integrated perspective and does a project where you map out,

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as in our in our case, the whole brain circuit at some level of resolution.

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Yes, that's generating a significant data set.

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But at the same time, it's not even at the scale of this large heterogeneous data that's out there.

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But given how you summarize this argument, you're facing two challenges in some sense, no?

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Because on the one hand, isn't one implication that you say,

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well, yes, we have all this data, But you might as well have not collected it

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because it's not organized in the right way.

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Is that really the consequence of what you're saying? Would you agree?

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Yeah, I mean, I think that that's one way of putting it. I think a good analogy

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that is certainly not new at this point is thinking about Google Earth.

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We probably have a lot of information about geography, about,

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you know, restaurants in a particular city and so on and so forth.

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But until there was a framework on which to hang all these pieces of information,

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they remained disparate. it.

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So perhaps this project that we've initiated, one thing that it will do is to

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provide a framework in which to collect this heterogeneous information.

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If that succeeds, then, you know, we will resolve the paradox to some extent.

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Underlying your argument, though, is another assumption, which is really interesting,

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because sometimes you're saying, well, the human genome project was actually

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a great success, and I want to follow this paradigm now from neuroscience.

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But is that really a reasonable assumption? I wouldn't quite put it in those terms.

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I would say that, yes, it was a success, but success as defined in certain ways.

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I think one way in which it succeeded is providing this integrated framework

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for pulling information together.

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Another way in which it succeeded was it helped us gain understanding of the evolution of genomes.

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We've also gained information about human history.

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So, we haven't solved certain problems which were promised and maybe we will

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still solve those problems in the future, but in certain ways it has been successful.

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And I think in those ways is where I would want to borrow from the success or hope for the success.

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Looking ahead to when you've built this new huge data set, what's your idea

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about how people are going to use it?

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I mean, I can see sort of neuroanatomists looking at the raw data and say,

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yeah, this fills the gap.

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I don't any longer need to do that experiment because I can just look at your database.

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But for those people that want to draw something out of it to condense it down

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into some more compact understanding of the brain, what kind of tools do you

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think they will be able to use on this database?

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Well, we will try to provide integrated versions of the data at lower resolutions.

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So in the ideal world, what we should be able to provide is a probabilistic

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math saying that if you start from point A in a reference brain and you were

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a neuron with a cell body near point A,

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what's the probability that you had a projection or an arbor at point B?

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So, that sort of information integrated across the injections,

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we will be able to provide.

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That will then presumably help people who are trying to gain an understanding

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of the architecture of the whole brain circuit.

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I mean, I know that this is a

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nascent field in the sense that not a lot of people are trying to do that.

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There's more interested in understanding the microcircuits in a particular region of the brain.

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But we do hope to provide some integrated pieces of information apart from guiding,

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thinking about how the system is organized and how it works.

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My hope is that we will also get multiple species, so we will be able to address

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evolutionary questions.

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Previously, brain evolution has been studied largely in the context of shapes and sizes.

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So cortex has grown in size, the olfactory bulb has shrunk its size, and so on.

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But we haven't really studied it at the level of what circuits are and how they

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have changed, with exceptions.

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But it has been very much driven by non-circuit considerations,

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the evolution. I don't know if you agree with,

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Well, what I was wondering in that in that respect is also the incredible individual

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variability you might try to get.

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So how are you going to handle that? Right. So you might take,

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let's say, a mouse or a rat or or a monkey from which you get your anatomical data.

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But now you know that over individuals, there'll be an incredible dispersion

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of these kinds of projections.

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So how do you see yourself extracting the rules from that kind of variability?

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I do have a premise that the variability will not be so large that we cannot

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extract these regularities.

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So going back to a comment you made during my presentation, is that I do have

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a hypothesis, in some sense a weak hypothesis,

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that there is something to be learned from these experiments because there is

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some underlying organization that is relatively concerned from individual to

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individual in this mouse strain,

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we will do multiple injections and multiple repeats of the same injections in the same brain region.

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So empirically, we will hope to answer this question. I don't think it's a theoretical question.

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So I do have a theoretical hypothesis that the variation will be controlled

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enough that there is a meaningful mesocircuit, but we will try to prove it empirically.

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And how many different...

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Since the brain is continuously changing also ontogenetically,

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so how many measurement points do you think you would need in a single species?

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We are doing it in the mouse at a single age.

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We have not yet even started thinking about a developmental version of this.

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One thing that I'm hoping is that yes,

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we are running this particular experimental project in my lab but we are hoping

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to demonstrate that this kind of project can be done quite economically in multiple laboratories.

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So once that comes about, I think people should be able to fill in multiple ontogenetic steps.

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What we are hoping to do is to take one age and then look at different mouse

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strains, so different genetic constructs, and see how the circuit changed at

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a given age. Right. So how,

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There's something interesting about the trajectory that you went through.

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As you said earlier, you started as a theoretical physicist and then sort of

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discovering the brain, if you want, and in some sense now becoming much more

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an experimentalist in some sense.

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But then, let's say, a large-scale anatomist or industrial-scale anatomist.

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And if I look at the way you present the argument, it seems also interesting

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that along the way, you've been shedding more and more of your theoretical skin,

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right? I do it at night privately.

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Is that fair to say? No, my bedtime reading recently has been,

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you know, formal logic and models of real computation.

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I mean, I haven't shed my theoretical interests. It's just that I have become

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much more conservative than when I started in making theoretical models because

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I've come to realize how difficult the problems really are that we are trying to describe.

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What happened to me when I was a theoretical physicist is I developed a great admiration of theory.

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So I don't want to take the name lightly, so to speak.

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It's very interesting. So in some sense, what you're saying is that in this

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move from, let's say, the naive but maybe very ambitious theoretical person

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into now, let's say, the anatomist at the bench,

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you have acquired more humility towards the problem. Absolutely. Absolutely.

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That's the point. Absolutely, yeah. I think that these are very hard problems,

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and I still hope to make some theoretical contributions, but I would like them

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to be solid contributions.

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So where do you think we are in terms of theories of the brain?

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What aspects of the brain do we understand well, and where do we need to pay attention to?

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I think single-neuron biophysics is a clear success story,

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to the extent that there's a well-developed theoretical framework,

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and that it's got an attached experimental framework, and there's a close feedback

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loop between the theory and the experiment.

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Some other parts, I think it's piecemeal. I think certain systems in the brain

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are well-developed theoretically.

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I'm not saying that they are fully developed, but the sensory systems are relatively

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well-developed in that way.

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We have a good, at least, approach to the visual system or the auditory system.

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Also, to a lesser extent, but also to motor systems.

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At the peripheral levels, I think we've got good models. models,

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what I feel is lacking is a more systems-level understanding of the whole system.

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I think that the theoretical work that has been done there is non-mathematical,

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but still legitimate theorizing,

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and people who have done that are perhaps not thought of as theorists because

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they've really thought about the system, they've articulated their thoughts.

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I would still call that theory. I mean, Darwin didn't have a single equation, right?

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So what is the status?

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I think that there is a lot of work to be done.

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Progress seems to me to be pragmatically occurring in fields which are tied into robotics.

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Insect locomotion is one area that I've followed to some extent,

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and it seems to me to be working quite well.

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Of course, that's limited in the sense of understanding the brain.

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One lesson that I've drawn from there is really to think about engineering theories

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and to think about what the system does,

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what's the logic that one would employ in constructing systems like that,

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and then trying to understand whether the evolutionary processes are compatible with such thinking?

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Is there a role for convergent evolution?

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So if I were to say in a single sentence where I see the future of theory,

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I would say take engineering much more seriously.

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I think that it's certainly been a theme that has been explored since the times of cybernetics.

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It has perhaps been sidelined in some areas of neuroscientific theorizing,

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but I think it needs to be brought more to the fore and more training is necessary

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in engineering disciplines of the,

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some of the neuroscientific theorists.

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Are you saying that we should give up this more physics-based dream of,

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let's say, closed-form solutions of the phenomena that we're trying to study and go more towards,

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let's say, open solutions or descriptions of these systems? Is that a key step there?

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Yeah, I think that there has been a certain limitation in the theory community,

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at least those of us who came from a physics background to take a point of view

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that resembled too closely the successes of theoretical physics and simply hoping

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that the same trick will work again.

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I think that that's not working, is really the evidence.

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There are some isolated examples like the Hauss-Gnostic equation,

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a partial differential equation describing how the action potential works,

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might lead us to believe that in general, ordinary and partial differential

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equations are what we are looking for in terms of theoretical constructs.

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Again, looking in a forward modeling perspective, observing some physical phenomena

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in the brain and then modeling with ordinary or partial differential equations,

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seems to me that that approach in spite of being very successful in one domain has not generalized.

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It seems to me one needs a multiplicity of theoretical framework.

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So I have coined this motto, I say ontological monism and epistemological pluralism.

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So there is only one reality out there.

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We all agree. You always win at Scrabble, I understand.

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I don't think there's a disembodied soul that is driving my brain.

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But at the same time, I think there are multiple legitimate descriptions,

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epistemologies, ways of theorizing,

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modes of theorizing. They may use different mathematical tools.

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And it is not true that one reduces to the other. I think this is an assumption people have made.

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So when people talk about reductionism, the discussion is a bit confused because

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it's not whether they're talking about physical phenomena reducing to each other.

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That doesn't make any sense to me because there's only one phenomenon.

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The question is whether theories reduce to each other.

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And sometimes they do, sometimes they don't. And I think one has to be a little

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more Catholic. So you take a very Kuhnian approach here.

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I would like to, yeah, take a more Catholic approach to theorizing.

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And that is definitely new for me.

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I mean, I did not come from a tradition where that is done, although having

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trained as a condensed matter theorist, I was perhaps more open to it than if

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I were, let's say, trained in particle physics.

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Why do you think the mesoscopic scale is such an important scale to understand

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the brain at, as opposed to other scales?

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Or is it just that we haven't done enough work on that level?

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Yeah, I think that it is a scale at which the brain needs to be understood and

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a scale in which understanding is comparatively lacking.

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I'm also inspired to study this scale because it seems to be developmentally

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patterned. So it is in the genetic code, so to speak.

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Given that there is a juggernaut out there, which is kind of genome biology,

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and we have learned, certainly human knowledge has progressed in that domain.

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It would be great if we could link up neuroscience with that progress.

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One scale where I see that link occurring quite distinctly is at this mesoscale,

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because the mesoscale is developmentally patterned out of the genome,

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or at least that would be the quote-unquote hypothesis.

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So the heterogeneity at the mesoscopic scale,

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within elements at that scale, there might be Bohr-Humann homogeneity and the

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potential for using learning algorithms or developmental algorithms to wire up systems.

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Right, so the hypothesis would be that, let's say the genome patterns this mesoscale

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with environmental input, but let's say the genome, that's understood in modern

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day discussions, right?

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But without making those caveats, let us just say the genome patterns the mesoscale.

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Then variations in the mesoscale are, related to genomic variations,

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then one should be able to relate those two things, if one looks across species

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or if one looks across individuals.

00:19:04.173 --> 00:19:08.173
There could be also environmental perturbations that cause fluctuations at the

00:19:08.173 --> 00:19:12.133
mesoscale, but the idea is that it's genomically sculpted.

00:19:12.253 --> 00:19:19.553
And then variations at a more micro scale, certainly some of that patterning is also due to rules.

00:19:19.913 --> 00:19:24.033
Let's say one neuron has to connect to another neuron. So kind of self-organization,

00:19:24.133 --> 00:19:27.753
would you hope that that would give us leverage at the smaller scale?

00:19:27.953 --> 00:19:31.933
Right. One would expect that self-organization is playing a more important role at the smaller scale.

00:19:32.033 --> 00:19:36.113
So this would be a way of separating where the developmental program is more

00:19:36.113 --> 00:19:40.673
important from where the learning self-organization rules are more important.

00:19:41.033 --> 00:19:43.953
But what's the metric of this mesoscopic scale exactly?

00:19:44.653 --> 00:19:50.973
I don't think there is a fixed length scale that I would associate because if

00:19:50.973 --> 00:19:53.593
you look in different parts of the brain, there are different sizes.

00:19:54.173 --> 00:19:58.013
But I would simply point to classical neuroanatomical atlases,

00:19:58.353 --> 00:20:07.633
where the sizes of regions of nuclei vary if you look across the brain.

00:20:08.433 --> 00:20:11.833
They could get down to, depending on what brain you're looking at,

00:20:12.173 --> 00:20:15.353
in the mouse brain, they could get down to hundreds of microns,

00:20:15.533 --> 00:20:18.953
but they could also be larger, you know, millimeters.

00:20:18.953 --> 00:20:26.753
Meters so we have to we have to refine or improve this definition certainly

00:20:26.753 --> 00:20:33.093
if we want to do a comparative anatomy yeah i think it has to be data-driven i don't think there is a.

00:20:34.293 --> 00:20:37.173
Definition i can give today in advance of having

00:20:37.173 --> 00:20:41.453
gathered the data set what i hope is after we have data sets like this and we

00:20:41.453 --> 00:20:45.133
already have some existence proof from the gene expression data set from the

00:20:45.133 --> 00:20:52.433
allen institute that one can maybe empirically extract these correlation lengths

00:20:52.433 --> 00:20:54.833
or scales directly by looking at the data.

00:20:54.973 --> 00:21:00.693
What we can hypothesize based on neuroanatomical literature is that such scales exist.

00:21:02.319 --> 00:21:05.739
And, you know, good guesses as to what those scales are in specific brain regions.

00:21:06.099 --> 00:21:12.559
One thing you said earlier is that you felt that, let's say,

00:21:12.579 --> 00:21:17.639
the genome would be controlling development at just one of these scales.

00:21:17.779 --> 00:21:22.339
Well, let's say these lower levels would be more self-organizing.

00:21:22.859 --> 00:21:23.959
Why are you saying that?

00:21:25.319 --> 00:21:31.939
Well, it's a guess. Yes, I cannot articulate all my previous knowledge that

00:21:31.939 --> 00:21:37.119
leads to the guess, but one reason is you look at different mice,

00:21:37.419 --> 00:21:40.359
you get the same atlas.

00:21:40.559 --> 00:21:44.599
This is just a statement about how the community is organized in this research.

00:21:45.059 --> 00:21:49.739
If it was the case that there was tremendous environmental influence on the

00:21:49.739 --> 00:21:53.459
scale at which classical neuroanatomical atlases are organized,

00:21:53.819 --> 00:21:59.899
we would probably not be able to use atlases, So the very fact that we can use these atlases, to me,

00:22:00.039 --> 00:22:10.379
is some indication that these are not specifically environmentally sculpted.

00:22:10.379 --> 00:22:13.699
But this could also be a bias of how we treat these phenomena.

00:22:13.919 --> 00:22:17.579
Like in psychology, it's a typical problem that, okay, we move into statistics

00:22:17.579 --> 00:22:20.739
because we cannot understand humans from an individual level.

00:22:20.979 --> 00:22:25.219
On the other hand, now in psychology, people are bumping into this limitation

00:22:25.219 --> 00:22:29.579
statistical approach because actually there is not this normative person.

00:22:30.159 --> 00:22:33.779
So maybe for your emphasis, you're facing a similar kind of problem.

00:22:34.499 --> 00:22:39.879
I would certainly agree that there is not a normative mouse brain, the platonic brain.

00:22:40.379 --> 00:22:44.599
But what I do believe is that there's a low-dimensional manifold of brains,

00:22:44.719 --> 00:22:50.919
that it's not as high-dimensional a space as, let's say, the number of neurons

00:22:50.919 --> 00:22:52.539
in the brain would lead us to believe.

00:22:55.359 --> 00:23:01.239
So even though there is variability, and that variability could well be developmental

00:23:01.239 --> 00:23:05.939
plasticity that has environmental impact on it, in the same way that we would

00:23:05.939 --> 00:23:08.439
expect it in psychology.

00:23:10.739 --> 00:23:19.839
But I at least have a strong hypothesis that this pace of variation.

00:23:21.520 --> 00:23:27.840
Is quite constrained. It's quite small. And I would also say it differs from

00:23:27.840 --> 00:23:30.740
region to region in the brain, and we will probably find that out.

00:23:30.960 --> 00:23:34.800
This is an empirical question. We will be doing these studies in multiple mice,

00:23:35.000 --> 00:23:40.900
so we will be able to look across individuals and really ask the question empirically.

00:23:41.100 --> 00:23:42.000
I think that's the way to ask it.

00:23:42.300 --> 00:23:45.180
What's your feeling about this low-dimensional manifold? And certainly,

00:23:45.180 --> 00:23:49.600
if you look also across species or even including species that do not exist anymore.

00:23:50.020 --> 00:23:53.880
I mean, what's this common template there? What's your feeling about this?

00:23:54.180 --> 00:24:01.080
Are you expecting to converge to, say, a common design template for all vertebrates, for instance?

00:24:02.240 --> 00:24:05.960
It's a very intriguing thought, right?

00:24:06.040 --> 00:24:13.260
That there are, whether due to common ancestry or due to convergent evolution,

00:24:13.260 --> 00:24:15.380
solution, in some sense,

00:24:15.540 --> 00:24:21.540
selecting for the same circuit because the same function has to be subserved.

00:24:21.920 --> 00:24:27.740
It's a very intriguing hypothesis, which I hope is right, that there are these

00:24:27.740 --> 00:24:31.980
common design rules or templates that we will find.

00:24:32.680 --> 00:24:38.100
It may not turn out to be true, but that would be the interesting hypothesis in my mind.

00:24:38.240 --> 00:24:42.660
And it's an empirical hypothesis. this is, I would say that I hope it is true

00:24:42.660 --> 00:24:47.260
because there is certainly some theoretical biases I have that are pushing me

00:24:47.260 --> 00:24:49.580
in that direction. I think the system wouldn't work otherwise.

00:24:49.960 --> 00:24:52.480
Well, it gives them the finite set of genes building the brain.

00:24:54.271 --> 00:24:59.031
There you go. I mean, there is certainly some developmental rules, and I think that.

00:25:02.711 --> 00:25:08.771
We have other examples like our musculoskeletal system that are also patterned

00:25:08.771 --> 00:25:10.471
about which we don't ask these questions.

00:25:10.991 --> 00:25:14.931
So is the brain really that different from all the other organs in the body

00:25:14.931 --> 00:25:19.311
at the level, let's say, of this mesocircuit?

00:25:20.731 --> 00:25:23.751
So your idea is to do a lot of the work in

00:25:23.751 --> 00:25:26.911
your own laboratory at Cold Harbor but you're

00:25:26.911 --> 00:25:29.831
trying to get other people on board this project because

00:25:29.831 --> 00:25:35.911
by the sounds of it it expands to include many other species also to include

00:25:35.911 --> 00:25:41.651
animals at different ages there's a huge work program here why do you think

00:25:41.651 --> 00:25:45.411
people should prioritize this as opposed to all the other things that we might

00:25:45.411 --> 00:25:49.451
be doing in the neuroscience well I guess you you know, it's a free world.

00:25:50.691 --> 00:25:56.051
I have to choose from that side. No, no, no.

00:25:56.091 --> 00:26:02.411
But more seriously, I think that, I don't know, talking about humility,

00:26:02.671 --> 00:26:04.991
I've just come to realize that the problems are extremely hard.

00:26:05.131 --> 00:26:10.531
So I would like to work on areas where clearly progress can be made.

00:26:10.611 --> 00:26:11.671
Now that can be very dangerous.

00:26:11.871 --> 00:26:14.371
One can get into instrumental fallacy, right? Right.

00:26:15.231 --> 00:26:22.231
But I have tried to articulate some of the arguments in the position paper that

00:26:22.231 --> 00:26:24.651
we put together that I would draw people's attention to,

00:26:24.711 --> 00:26:31.891
plus computational biology that came out last year with the first author,

00:26:32.071 --> 00:26:34.191
Jay Boland, and the last author being myself.

00:26:34.191 --> 00:26:37.931
Self um but just to

00:26:37.931 --> 00:26:41.591
you know try to lay out some motivations

00:26:41.591 --> 00:26:44.411
uh one great

00:26:44.411 --> 00:26:47.531
motivation is that we are at the technological cost where

00:26:47.531 --> 00:26:52.971
this has just become doable within the funding constraints of individual laboratory

00:26:52.971 --> 00:26:58.071
i think that's for me a great motivation and that was not true a few years ago

00:26:58.071 --> 00:27:02.591
simply due to memory costs today it is doable yeah but this is the because we

00:27:02.591 --> 00:27:04.931
can't argument so Because we can't argue with that.

00:27:04.971 --> 00:27:06.191
I think it's an important argument

00:27:06.191 --> 00:27:08.551
because there are many… You can win elections with that, you know.

00:27:11.871 --> 00:27:16.651
That's it. No, I mean, I think it's an important argument.

00:27:17.711 --> 00:27:21.811
But the second argument, I think, is that….

00:27:24.609 --> 00:27:26.289
The scope of discovery, I think,

00:27:26.289 --> 00:27:37.809
is large. We simply don't have these circuits at a very simple level.

00:27:37.889 --> 00:27:41.169
How are we going to understand how the brain works? The brain is a circuit.

00:27:41.589 --> 00:27:45.089
We don't have the circuit. People could argue we know certain bits and pieces

00:27:45.089 --> 00:27:47.449
of it, but that's a very simple argument.

00:27:48.669 --> 00:27:51.229
One can try to refine the argument, but that's one argument.

00:27:51.229 --> 00:27:55.129
And then there's a third argument, which is this information integration that

00:27:55.129 --> 00:28:00.709
we were talking about, that we are battling this huge deluge of data and information.

00:28:00.849 --> 00:28:03.789
How to tie it together? Well, here's a way we could.

00:28:05.269 --> 00:28:11.909
And it's clearly a project that is much bigger than something that I could handle in my laboratory.

00:28:12.169 --> 00:28:14.889
So I'm definitely hoping that other people will want to join in.

00:28:14.889 --> 00:28:19.409
And we are very open, by the way, with our data set, even before publication,

00:28:19.629 --> 00:28:24.209
when the data will officially be made public, if people would like to collaborate

00:28:24.209 --> 00:28:28.149
with us at the level of data analysis, we're happy to do that.

00:28:28.189 --> 00:28:31.609
If people would like to learn how to do these experiments, or if they're interested

00:28:31.609 --> 00:28:36.569
in setting up their own pipelines, we're also very happy to actually provide

00:28:36.569 --> 00:28:37.569
that input and expertise.

00:28:38.009 --> 00:28:41.569
Because I think that the reality is that we'll publish a two,

00:28:41.689 --> 00:28:45.429
three-page paper, let us say, but that won't summarize what's going on.

00:28:45.669 --> 00:28:49.449
Things are changing in that way. However, one thing I was wondering about now

00:28:49.449 --> 00:28:55.349
is whether you're not stepping a bit too easily over this challenge that also Tony put in front of you.

00:28:55.409 --> 00:29:01.849
Imagine now we have this whole federation of laboratories contributing to this

00:29:01.849 --> 00:29:04.429
pipeline, and they all have their own species to work on or whatever.

00:29:06.046 --> 00:29:09.406
You have a huge problem integrating all this data because at some point people

00:29:09.406 --> 00:29:13.426
would like to bring in other kinds of data, physiological data, behavioral data.

00:29:13.666 --> 00:29:20.306
Do you really have a taxonomy in place to bring all that information together in an integrated form?

00:29:20.566 --> 00:29:25.106
Or do you think that's just going to self-organize? It's a work in progress.

00:29:25.846 --> 00:29:28.366
Some people are working on it.

00:29:29.366 --> 00:29:32.526
I do think it has to be, to some extent, data-driven.

00:29:32.686 --> 00:29:38.466
And talking about theory, here is one place I think theorists really need to pitch in.

00:29:39.286 --> 00:29:43.406
Because taxonomy is really a theory about the system.

00:29:43.526 --> 00:29:47.766
Once you start dividing what the parts are and naming them, you've kind of made

00:29:47.766 --> 00:29:50.726
your mind up about how to divide the system and how to name them.

00:29:51.146 --> 00:29:54.806
But isn't it a scary thought to actually now open the floodgates,

00:29:54.946 --> 00:29:57.506
but you don't have the buckets ready yet to catch the water?

00:29:57.506 --> 00:30:04.266
I think that there are some starting efforts.

00:30:05.126 --> 00:30:10.926
So it's not as bad as it could be in other fields. Because in anatomy,

00:30:11.066 --> 00:30:12.226
there has been a scholarly tradition.

00:30:13.606 --> 00:30:18.486
And so there is certainly a good head start, I would say.

00:30:19.586 --> 00:30:23.206
But you're right. I mean, it is a challenge.

00:30:24.826 --> 00:30:31.166
I think that we will be helped simply by having unified datasets.

00:30:31.466 --> 00:30:38.546
This taxonomy problem, what we want to call a region will be less important

00:30:38.546 --> 00:30:44.086
than having a coordinate where you can really say that, well, I call it A, you call it B,

00:30:44.286 --> 00:30:46.646
but we are all referring to the same objective,

00:30:47.925 --> 00:30:50.865
artifact and that's what will help that taxonomy problem

00:30:50.865 --> 00:30:53.965
so what was amazing in the human genome project is

00:30:53.965 --> 00:30:57.205
that there was this expectation that would take quite some

00:30:57.205 --> 00:31:02.025
time to sequence human genome and then actually some people really industrialize

00:31:02.025 --> 00:31:05.665
this whole process and it turned out could be done just in a few years which

00:31:05.665 --> 00:31:09.365
was astonishing even though it's still debatable how informative all this data

00:31:09.365 --> 00:31:14.925
is now how many many years is it going to take you to to get the data for,

00:31:15.225 --> 00:31:18.025
let's say, a single mouse species?

00:31:18.625 --> 00:31:20.305
How many men years are we talking about?

00:31:21.125 --> 00:31:24.305
Well, we are hoping to release a draft next fall.

00:31:24.885 --> 00:31:29.225
And there's about... Now, what I mean by... But I meant complete, right? Everything.

00:31:31.325 --> 00:31:36.885
Everything will take infinitely long, by definition. The whole brain.

00:31:37.045 --> 00:31:42.265
But I think on the scale of two to three years,

00:31:43.305 --> 00:31:53.725
we will have given existing projects we will have a quote unquote mesocircuit even next year we will,

00:31:54.605 --> 00:32:01.185
you know in every laboratory order 10 people maybe so you have 30 man years

00:32:01.185 --> 00:32:05.765
you said 30 man years to get one mesocircuit of one species done.

00:32:05.925 --> 00:32:11.185
I think that's reasonable but we have defined mesocircuit in a particular way

00:32:11.185 --> 00:32:13.825
People are going to challenge that and have arguments about it.

00:32:15.845 --> 00:32:18.665
Yeah, I think it's a doable project on a short time scale.

00:32:19.065 --> 00:32:22.325
And for yourself, I mean, is there going to come a point where you say,

00:32:22.405 --> 00:32:26.245
okay, I've got enough data of a sufficient quality.

00:32:26.965 --> 00:32:30.385
I'll go back and be a theorist about this data.

00:32:31.985 --> 00:32:37.505
It's happening already. Okay. You know, in the sense that even when trying to

00:32:37.505 --> 00:32:41.085
interpret our very first data sets or in trying to analyze them,

00:32:41.185 --> 00:32:44.645
the problems that come up are definitely of a conceptual theoretical nature.

00:32:44.805 --> 00:32:45.625
I'll give you an example.

00:32:47.925 --> 00:32:51.365
This question came up about quantifying connection strength.

00:32:52.565 --> 00:32:58.225
You often see isolated neurons in different parts of the brain showing up.

00:33:00.285 --> 00:33:05.445
If you have hundreds of thousands or tens of thousands of neurons in a particular,

00:33:05.445 --> 00:33:09.885
or let's say region of the brain that you have injected, and if one neuron shows

00:33:09.885 --> 00:33:11.965
up in some other part of the brain,

00:33:12.745 --> 00:33:18.185
in some sense, the circuit is, or doesn't have this clean organization that

00:33:18.185 --> 00:33:19.505
we theoretically started out.

00:33:20.891 --> 00:33:22.091
That it has got these tails.

00:33:24.331 --> 00:33:27.351
How do you even think theoretically about a circuit like that?

00:33:27.391 --> 00:33:29.471
What are those individual neurons doing?

00:33:29.591 --> 00:33:33.791
Are they artifacts of the fact that biology is not a clean engineer?

00:33:34.611 --> 00:33:37.031
Or was it a reason? Is it a feature or a bug?

00:33:38.191 --> 00:33:44.571
But now in this endeavor, which also your project got supported to go after

00:33:44.571 --> 00:33:45.791
this connecto of the brain,

00:33:46.491 --> 00:33:50.191
there are also other initiatives underway where people would look more at,

00:33:50.191 --> 00:33:54.471
Let's say what we call the effective connectivity of the brain based on data

00:33:54.471 --> 00:33:59.771
sets that are of a very different nature, using different kinds of imaging techniques and so on.

00:33:59.971 --> 00:34:03.291
Do you expect a convergence among these different approaches,

00:34:03.451 --> 00:34:06.051
or do you think that's just too far in the future?

00:34:06.391 --> 00:34:10.131
I have a theoretical disagreement with, and I'll be very frank about this,

00:34:10.271 --> 00:34:17.331
about the term functional connectivity being used to describe what are temporal correlations.

00:34:17.331 --> 00:34:24.071
So, simply because two time series are correlated, and this we have known for

00:34:24.071 --> 00:34:29.471
a long time, does not mean that there is a, let's say, anatomical connection

00:34:29.471 --> 00:34:32.171
between those two points.

00:34:33.491 --> 00:34:37.491
So, I don't see any reason why there should be a quote-unquote convergence.

00:34:37.811 --> 00:34:43.371
It's certainly true that the anatomical connectivity is going to drive correlations,

00:34:43.691 --> 00:34:46.631
but I don't see the reverse rub.

00:34:47.331 --> 00:34:50.631
So the correlations are a necessary condition of the causal structure, right?

00:34:50.911 --> 00:34:56.791
Of the anatomical structure. And I strongly advocate calling correlations correlations.

00:34:56.931 --> 00:35:03.811
I think it is misleading and perhaps even distracting to call it connectivity.

00:35:04.591 --> 00:35:07.091
Your database will be monosynaptic.

00:35:08.217 --> 00:35:12.077
Our database is really of neuronal morphology. We don't really have synapse.

00:35:12.257 --> 00:35:16.237
Oh, okay. But you'll be just looking along a single fiber.

00:35:17.817 --> 00:35:22.517
So it'll still be a problem for me if I want to know if there's a connection

00:35:22.517 --> 00:35:25.397
between A and B that might go via C.

00:35:26.617 --> 00:35:31.097
I can tell there's a projection that goes into C, a projection from C into B,

00:35:31.197 --> 00:35:35.257
but I can't know from your database that those two things meet up. Correct.

00:35:35.537 --> 00:35:39.977
And there are other limitations to this project. Namely, we are not being cell-type specific.

00:35:40.597 --> 00:35:44.797
There are other projects which are coming about which will try to be more cell-type

00:35:44.797 --> 00:35:48.217
specific and yet get neuro-anthropomical connectivity in place.

00:35:49.117 --> 00:35:56.317
I regard this particular mesocircuit that we are mapping out as operationally defined.

00:35:56.597 --> 00:36:00.237
Operationally because it's defined in terms of retrograde and anterograde injections

00:36:00.237 --> 00:36:06.417
and whole-brain imaging object. object, but there will be missing pieces of

00:36:06.417 --> 00:36:11.037
information that will then have to be layered onto this thing, more projects.

00:36:12.197 --> 00:36:16.957
Now, also in your presentation, also in your work, you have been spending quite

00:36:16.957 --> 00:36:19.577
some time to look at gene expression patterns in the brain. Yeah.

00:36:19.977 --> 00:36:25.857
And do you see that as giving you leverage in understanding these anatomical

00:36:25.857 --> 00:36:30.477
pathways that you're trying to reveal right now, or do you see this really as

00:36:30.477 --> 00:36:32.457
separate databases as well?

00:36:33.017 --> 00:36:38.317
No, I see the connection that they are both indicating a meso-structure, so to speak.

00:36:38.517 --> 00:36:41.917
You know, they are getting us objectively at this intermediate length scale

00:36:41.917 --> 00:36:43.657
that is there in neuroanatomy.

00:36:43.997 --> 00:36:47.897
The gene expression data sets are probably giving us indirectly information about cell types.

00:36:48.517 --> 00:36:50.637
I don't think they are directly telling us about connections.

00:36:52.481 --> 00:36:57.441
But yes, they are definitely connected. So within this gene expression data

00:36:57.441 --> 00:37:00.221
you showed, there was something very puzzling because anatomically,

00:37:00.481 --> 00:37:03.381
at least if I listen to an anatomist, I'm not an anatomist myself,

00:37:03.581 --> 00:37:06.501
they would always tell you, look, cortex is relatively uniform,

00:37:07.041 --> 00:37:09.141
well-structured, modular, etc.

00:37:09.881 --> 00:37:15.181
And if you go to subcortical areas, things get more messy. It's more variable,

00:37:15.481 --> 00:37:17.081
heterogeneous, and so on.

00:37:17.961 --> 00:37:21.321
And if I look at your gene expression data, you made the point.

00:37:21.861 --> 00:37:25.521
Actually, you have less genes expressed at the subcortical levels than at the cortical levels.

00:37:25.921 --> 00:37:29.881
So what do you make of this apparent contradiction?

00:37:30.621 --> 00:37:33.841
I actually think it's the other way around. I think the subcortical structures

00:37:33.841 --> 00:37:38.921
are more homogeneously structured and more carefully sculpted.

00:37:39.701 --> 00:37:44.101
You have much more interspersion of cell populations, also the kind of transmitter

00:37:44.101 --> 00:37:47.221
systems. Correct. So they are more... Yeah, I see what you're saying.

00:37:48.021 --> 00:37:52.181
It's more messy in the sense that the modules are not well separated,

00:37:52.361 --> 00:37:54.821
but it may be less variable.

00:37:58.321 --> 00:38:03.061
So, yes, it is messy. It will be messy for us to disentangle,

00:38:03.241 --> 00:38:07.421
but it will be less variable, I think, from animal to animal.

00:38:07.721 --> 00:38:11.901
So sometimes what you're saying is maybe cortex is so neatly organized because

00:38:11.901 --> 00:38:16.001
there are just more genes being expressed there to keep that clean structure in place.

00:38:16.761 --> 00:38:20.401
While you would have less genes expressed subcortically, leading to more of

00:38:20.401 --> 00:38:24.461
a dispersion of how these cells actually anchor themselves in the substrate and so on.

00:38:24.521 --> 00:38:27.361
Is that how I interpret what you're saying? That's an interesting hypothesis.

00:38:29.721 --> 00:38:35.161
I guess the cortex is not translationally homogeneous, as we know from Brodmann.

00:38:35.421 --> 00:38:39.501
Areas in the gene expression pattern certainly show that there are different...

00:38:41.129 --> 00:38:46.629
Vertical structures. Cool. So look, I have two questions to finish up.

00:38:48.129 --> 00:38:49.649
If we had to,

00:38:51.809 --> 00:38:58.509
define the Partha law of science, our attempts on the brain,

00:38:58.789 --> 00:39:02.809
what would be this Partha-Mitra law of investigation and understanding?

00:39:03.069 --> 00:39:04.609
What's the law we should adhere to?

00:39:05.109 --> 00:39:08.469
Law? Well, I made my aphorism, right?

00:39:08.969 --> 00:39:14.069
There's one reality about multiple theoretical approaches, I think we have to

00:39:14.069 --> 00:39:19.169
be open-minded about disciplines.

00:39:19.469 --> 00:39:27.689
And this sounds like a truism, and it sounds really something that people say as a slogan,

00:39:27.849 --> 00:39:32.689
but I really think that we need to educate ourselves in different disciplines

00:39:32.689 --> 00:39:36.829
like engineering disciplines or neuroscientists need to learn more about population

00:39:36.829 --> 00:39:38.669
biology and evolution and so on and so forth.

00:39:38.669 --> 00:39:42.149
Perfect and then so so if i

00:39:42.149 --> 00:39:45.229
go visit you again in cold spring harbor five

00:39:45.229 --> 00:39:48.229
years from now i'm gonna say okay there's this

00:39:48.229 --> 00:39:50.789
one prediction you gave to me today and today i'm going

00:39:50.789 --> 00:39:53.529
to check whether it's true or not what's this one

00:39:53.529 --> 00:39:57.129
prediction you're willing to stick your neck out today well that's

00:39:57.129 --> 00:40:03.249
a very tough one come on you're a tough guy um i

00:40:03.249 --> 00:40:10.029
guess this notion that the meso circuit is genetically wired and that genetic

00:40:10.029 --> 00:40:16.449
polymorphisms will cause alterations in the mesocircuitry that may be correlated

00:40:16.449 --> 00:40:17.989
with neuropsychiatric disorders,

00:40:18.329 --> 00:40:21.369
which also have genetic predispositions.

00:40:21.669 --> 00:40:27.229
That's for me, especially the affective systems that are related to emotional behaviors.

00:40:27.749 --> 00:40:33.169
That for me is sort of the, I don't know if it's a prediction,

00:40:33.329 --> 00:40:41.489
but that's a story that I hope in five years to really understand and gain insight into our behaviors.

00:40:41.849 --> 00:40:44.789
Wonderful. Parthamitra, thank you very much. Thank you.