SIO531: Your Brain Is Actually Two Separate Organs, According to a New Stanford Study

Transcript

This transcript was generated automatically and may contain errors — the audio is the record.

0:00:13 Thomas: Hello and welcome to Serious Inquiries Only, this is episode 531, I'm Thomas, that over there is Dr. Eric Jaffe, how you doing?

0:00:19 Eric: I'm doing well as always we're kind of in the middle of the school year RP1 is somehow already wrapping up next week so yeah we're gonna get into, oh, report period one so we have four report periods we're already a quarter of the way through

0:00:25 Thomas: The hell's RP1? Ah. That seems crazy, never that ceases to amaze me as no longer a kid in school but have kids in school where I'm like, Alright, just dropped him off for the first day, ah, it's Christmas.

0:00:43 Eric: As someone that just turned 38 last Friday, I have officially reached that point where time has become just accelerated it's crazy but luckily we've got another thing about time in this paper because we're going to be kind of using the evolutionary conservation of how we get our brain. So we're going to take a little bit of a molecular time machine today.

0:00:49 Thomas: Weird well that's so interesting I is one I'm excited about because I actually found this I found this uh study somewhere might have been reddit I don't know and I was like this seems really interesting and then it actually was for once a lot of times I send it and it's like it's just nothing but uh I sent it over and it'S like not only is this inspiring this episode episode I think it might even inspire a Jenessa episode because this seems really cool what are we going to be talking about today wait

0:01:28 Eric: So what we're talking about today is cell fate, right, and how cells become kind of the cells that they're going to become after they've left embryonic development and into adult tissue. And in particular, we're going be talking about the brain. And the reason why that's pretty exciting for me is oftentimes I often talk about how expertise is kind of a nested hierarchy, and like I'm not a dinosaur expert, I'm not a cancer expert. This is actually getting very close to the thing I actually am an expert in. So what I studied back when I was a researcher was how the non-neural ectoderm, the tissue that's right next to the cells we're going to be talking about, become cells during a process called neural tube closure. We're going be zooming in on the cells that are the next door neighbors of the cells I used to study, but with many of the same types of studies, experiments, and kind of mechanisms for how they become different parts of the brain right after this process called gastrulation so it's a really cool study and I don't want to quite give away the punch line yet but

0:02:27 Thomas: I was going to say, I was just about to say boo nerd. Here's the actual thing that's exciting, but I guess if you want to, we're probably going to assume it in an episode title.

0:02:38 Eric: If we spoil project hail mary I guess we can but uh this so basically what we're going to learn is that the brain isn't one organ that developed over time it's actually two parallel organs or tissues that developed in tandem together to build both the forebrain kind of the seat of conscious thinking and then the hindbrain which is much more of like your autonomous homeostatic um right like the things that you don't really think about that your brain has to do to keep you alive and we always thought that those used to be kind of same thing that evolved over time time and now we're gonna be talking about how we learned that these are actually two things so you can kind of think of our brain as like two kids in a trench coat as opposed to one person oh

0:03:20 Thomas: This totally makes sense to me because I feel like there's a ton of stuff in our evolutionary history that's, like, two kids had a fight and then they got together. It's, like, entities two had a fighting and then we got together and then there's, like, why don't we just team up? And then that's our cell or whatever. Is that DNA and RNA? I don't know. There's something in our cell that did that where it was like two different things, right? And possibly, yeah,

0:03:41 Eric: Although even that's slightly different because like DNA and RNA are probably derivatives from each other where like DNA probably came from an RNA modified sugar. Right. Where you lose one of those extra oxygen or you go from ribose to deoxyribose. Right? That's kind of what I thought this would do. So like, for instance, in the thing I used to study, right, there's three tissues that are kind of formed at the developing neural plate. Right, the neural plate is what will become your brain, which is what we're talking about today. And there's three tissues. One will become the skin, your non -neural ectoderm. One will become your brain. And then one tissue will be your neural crest cells, which makes a lot of like your craniofacial features. But only vertebrates have those neural crest cell. Older organisms that have brains and skin don't have that. But they do have the ectoderm and the non - neural and neural ectaderm with the neural crest being clearly derived from that already pre -existing tissue. And I I thought that the brain would kind of from evolve a similar structure to that where you get the different regions of the brain stemming from like an ancestral tissue that then duplicates and differentiates during development. Right. We're really seeing is truly two different tissues that form the hindbrain and the forebrain, and they really get their start from the start of patterning in the process we call gastrulation, which we can go through in a second. But really

0:05:07 Eric: From the very beginning yeah basically the way you want to think about is like I thought it would work more like the way we got spanish and french from latin and it's more like the way got yiddish from german and hebrew if that kind of makes sense

0:05:06 Thomas: This is so deep for the pre -break.

0:05:21 Thomas: That does not compute for me, but it sounds really interesting. I'm actually very curious to learn what that comparison means.

0:05:26 Eric: And spanish radiated out from the original latin as dialects got separated kind of like speciation right we formed those romance languages from kind of the bones and skeleton of latin Whereas Yiddish, which is the Jewish language that my family spoke back in Europe, it's really like a true mix of German and Hebrew, where a lot of German terms got localized and kind of incorporated into the Hebrew tongue. But the German and the Hebrew didn't come from the same space in the way that French and Spanish both come from Latin. Does that kind of make a little more sense?

0:06:00 Thomas: Interesting. Yeah. Well, this is really exciting. I can't wait to talk about this. We got to get to our first break. This is still in the preview. You so we'll go ahead and take a quick break and then we're going to dig even more into this we'll see if we can all keep up uh have the study up if that helps you know is there's picture are there pictures awesome

0:06:15 Eric: Does, because we're going to go figure by figure.

0:06:17 Thomas: Well I'm really excited so uh we'll take a break uh the ad support the show patreon.com/seriouspod and we'll be right back okay do we want to start how are we going to help me and everyone understand this how

0:06:41 Eric: So if you start at figure 1a, right, we'll just start at the beginning. This shows a branching diagram similar to like trees of life, right? Where the way cell differentiation works is obviously we all come from only one cell in the very beginning of embryonic development, right.

0:06:59 Thomas: Hell is that that possible I am already confused yeah

0:07:01 Eric: Well, sperm meets egg, right. And you've got your diploid genome. Genome. But from there, we have to make every single type of cell, which are going to look very, very different from each other, right? Even though every single cell has the exact same DNA. So what we're really talking about is how you use that DNA differently in something we call gene expression. The real start of that differentiation of tissues comes in a process called gastrulation. In gastruation, three major, what we call pluripotent stem cell populations, um, develop and they're called pluripotent because they can turn into a lot of different cells, but they can't turn into every cell anymore, right? They're not totipotant like those initial embryonic stem cells, totipoten meaning that they can turned into every self because they've already kind of differentiated just a little bit, right. So you have three major layers. You have the ectoderm. The ecto derm is what will eventually become your nervous system in your skin. You have your endoderm. This will be like the lining of a lot of your internal organs, your gastrointestinal system, your liver, things like that. And then you have your mesoderm, which will be a lot OF your skeletal system, your hematopoietic system, right? Your musculature, your connective tissues. And those three, what we call germ lines, get their start from a process called gastrulation, right? That's like that initial sorting that commits cells to a certain fate by having them produce different proteins. And where it gets interesting is before this study really kind of brought it home, a lot of people thought that that first step in gastrulation where you have ectoderm, right, ectODERM will either become neural ectODERM or non -neural ectoDERM. And non - neural eCTODERm will become your skin. Neural eCTODERm will be your brain and spinal cord. We didn't really know that differentiation would happen this early, and we thought that your neural ectoderm was a general stem cell that could become any part of your brain, if that makes sense. What we're finding is that even right at gastrulation, when we first get those three layers, there's already differences between cells that will become your forebrain and your midbrain, and cells that become your highbrain. The parts that will be like your conscious thinking and the parts that we'll just maintain. Do you know what I mean by homeostasis? Those basic kind of self regulatory events in your body that kind of keep you alive that are largely autonomous. Right. And that's the real key to the study is it's not just that your forebrain and your midbrain are a derived feature from that more primitive kind of lizard brain, for lack of a better word. Right? It's that they truly are a separate thing that was then combined together with those autonomous brain in your hindbrain. And that's what's really cool because what it means is that already before you even start developing your brain, your cells already know what part of the brain they're going to become.

0:09:54 Thomas: How just looking at the brain right I mean how there's are there a bunch of this kind of thing in our our body or is it the brain just more specifically a thing that need okay sorry

0:10:04 Eric: Does this throughout development, right? Every cell, you can kind of of think of it, there's this famous picture called like the hill of differentiation, right? Or the slope of differentiation. Once you roll downhill and commit to something, you lock in that path and you exclude everything else, right. Once I become ectoderm, I can become either skin or nervous tissue, but I can't become anything in the mesoderm or the endoderm. Once I become a ectaderm, I can become anything related to neural cells, well not actually anymore as we're We're about to find out, but I can't become non -neural ectoderm, right? I can'T become skin. So every time you make a decision to differentiate, you close off other paths in the same way you're like playing for keeps and career choice.

0:10:46 Thomas: When you say I'm making a decision what What is that process? So as they're like just dividing very early on, they're kind of all like, all right, let's see. I'll go this way. You go that way.

0:10:50 Eric: Your cell is making a decision. Exactly. Not only is location important, but do you remember when we talked about like Sonic Hedgehog and a couple of those other morphogens, right, they're going to get different cues.

0:11:05 Thomas: For anyone who didn't hear that, that's

0:11:07 Eric: Use?

0:11:07 Thomas: Going to be so confusing. Remember when we talked about Sonic the Hedgehog?

0:11:10 Eric: Sonic hedgehog is a very important gene in embryonic development.

0:11:13 Thomas: He's got the rings and stuff and he can run real fast.

0:11:17 Eric: Once Mario comes in, no, I'm kidding. Sonic hedge hog tells, and we actually will talk about Sonic hedgehog in a little bit, but right. Um, morphogens tell the cells to produce certain proteins, turn on different genes and alter the DNA's structure in, um. Chromosomes, right. Right, in something called histone modifications that start closing off certain abilities and start giving them different forms and functions. And what we thought was that the neural ectoderm was kind of the base layer of brain development, right? And if you took any neural eectoderm cell, you could turn it into any other part of the brain by giving it the right developmental cues. What this study is saying is that already by the time you get neural eictoderm, so by the the time you've already made that distinction between neural and non -neural ectoderm, and even by the time You've made that description between ecto derm and meso derm, you already know what cells are going to become your forebrain and your midbrain, and which cells are gonna become your hindbrain. Again, what that shows us is that the brain didn't evolve from like a hindbrained that kept getting more and more complex. Instead, it was two separate organs that were evolutionarily for it in parallel and then interface together in development?

0:12:34 Thomas: So does that mean, and I'm sure I'm going to be asking tons of really stupid questions. Does that mean at some point back in evolutionary history there's like two different animals of or what a being something whatever that had one just had the one brain and one had the other at some point if you go back far enough hmm mostly

0:12:51 Eric: A really good question. And my guess would be no. And the reason why is because we have a pretty good kind of phylogeny with extant animals of different layers of complexity of neuronal development, from single -celled organisms that just do basic voltage gating and ion channels that are like the precursors for those synapses and those propagation of signals that you need in neurons, we even have your planarians, your flatworms that have just simple nerve -like cells to our invertebrates like flies that are bilateral and have peripheral nervous system but no central nervous system to things like our hemichordates, things with half a nascent spinal cord but no true spinal cord. And through all those steps of development, you don't really see like one set without forebrains and a midbrain. And once it with a hind brain, what you see is you see a primitive brain and a spinal cord. Don't actually know and I don' think this author will tell you exactly where the two lineages come from. The only thing that this study points to is that it wasn't like we had a hindbrain and then a mutation happened in cells in the hindbraIN and that gave rise the forebrain. Instead, it's more that there was an early cell that was already present before gastrulation that decided to become the forebrain as opposed to neural ectoderm cells that were going to form the hindbrain that then became the forebrain. Probably sounded like gibberish, right?

0:14:18 Thomas: Yeah no I think someday this will be a netflix documentary when it turns out you're entirely a con man just using as many silly words as you can and he really thought sonic hedgehog yeah like thomas kept having me on I said sonic the hedgehog and he wouldn't believe that that so no but um I don't know if I get I I I kind of get what you're saying but well

0:14:29 Eric: With me, Nathan Felder and Elizabeth Holmes. Let me try one more time with the neural crest because I think that got a little interrupted.

0:14:46 Thomas: To clarify so you're saying because my question is about like you know there are things in evolution just to to clarify way back in evolution where it is like that right where it's like one if you go back far enough there's one had one kind of thing and another had another kind of things and eventually they combine in a way isn't that I mean that's like way back when right but not for this

0:15:05 Eric: I'll give a good example, actually. This going to go into the same basic time and place, right, right before the neural tube closes, before you really have neural ectoderm, which is what's going to become your your brain, and before you have non -neural ectoderm, where you have just skin cells, cells, you have justectoderma cells. And that's that first set of cells that migrate gastrulation, during right? And they form like a flat plate, right above the notochord.

0:15:32 Eric: Following so far? The notochorde is like the primitive, primitive spinal cord. Like before things had spines they had notochords yes

0:15:32 Thomas: What's the note kind of what's okay it's like putting your head on a platter oh

0:15:41 Eric: So think of like a flat plate around the middle of the embryo right because our embryo isn't three -dimensional really yet it's still just kind of a flat sheet of cells because our neural tube hasn't rolled up and formed that hollow tube right

0:15:52 Thomas: This is all fucking impossible but anyway yeah go ahead until

0:15:58 Eric: So in the middle you'll get a high amount of um signaling but a low amount amount of BMP signaling, and that will form the neural ectoderm, right? In the sides of that plate, you'll have high amounts of BNP, which is another one of those sonic hedgehog -like proteins, and that Will make it the non -neural ectодerm. And both us and flies have that, right. Flies don't have noses and ears and cartilage and bone. Those come from, right, yes, but a lot of that stuff, right, comes from neural crest cells, which is a third type of tissue that only exists in vertebrates. And the way you get neural crest cell is from the border between the neural and non -neural ectoderm. An intermediate amount of that BMP signaling will force them to become neural crests cells. But notice you can't make those neural crest cells without first having those primitive tissues of the neural non neural ectederm, right? They can only develop later on after those two things are already established. Does that kind of make sense?

0:16:24 Thomas: Jeff Goldblum goes in the machine setting that aside okay maybe I uh kind

0:17:03 Eric: Because without that border between neural and non -neural ectoderm, you wouldn't have those neural crests to begin with.

0:17:03 Thomas: Of right I I think I get that I'm still trying to place this in what the the conversation we're having before but go on

0:17:13 Eric: So all of them stem from that ectoderimal derivative, right? All of them come from the same population of cells that gets different cues from those morphogens that BMP, Wnt, and other things like Sonic Hedgehog that turns them into different cells, but they start off as one uniform tissue, right?

0:17:30 Thomas: And so that would tell you something about the evolutionary history like okay

0:17:33 Eric: That tells you that neural crest evolved after the neural and non -neural ectoderm and comes from that population, right, because you get them by deriving the less specified version. The forebrain and the midbrain don't come from more specialized and derived hindbrain cells. They come from a completely different population of ectoder. So it's not like it becomes neural ectoderm, and then it determines whether it's going to become hindbrain, midbrain or forebrain. By the time you have neural eczoderm. The hindbraIN is already the hindbraIn and the midbraIN IS already the mid brain and the forebraIN already the fore brain, which tells you that that development that evolution of those structures happen before the development of that neural ektoderm as a continuous sheet of tissue throughout your body to form the brain. Does that make a little more sense? Right.

0:18:23 Thomas: And so it kind of does

0:18:25 Eric: Because you're getting the differentiation before the basal cell layer.

0:18:25 Thomas: So then right but then so then what does that tell us in terms of I don't know like the timeline of that like does that put us

0:18:35 Eric: Tells us that both of them have probably been evolving for a long, long time. And it also tells usthat neuronal tissue can probably evolve in different ways at different times. It wasn't one singular event that gave us cognition. Right. So it does have some profound effects for what it means for the evolution of sentience, sapience, consciousness, nervous systems and things like that. It might be easier than we think to develop these structures. Right. Because it wasn't one thing that kept getting mutated.

0:19:07 Thomas: So be that if we take a chat gpt and a clod and put them together together, then we could make consciousness.

0:19:14 Eric: That's actually a really good analogy. Right? It's of AI coming from the large language models from each other and building into ChatGPT 3.0, 4.0, 5.0 where it keeps getting more and more complex, it's like Like if you took Claude and the internet, and that's how you get it, right? Whereas where cognition our is not just the AI, it's the AI interfacing with the more normal internet tissue, right, as opposed to AI creating itself from that initial internet. Do you want to talk about how they found this out?

0:19:50 Thomas: Yeah, sure. And just give us an idea. I mean, is this something like, why did it take so long? It's just truly because no one understands all these freaking words you're using. And then one guy's like, okay, I got all of them finally. Now I can study this.

0:20:02 Eric: I can't fully speak to why it would take so long. What I will say, when I studied kind of neural stem cells, right, back in my neural tube closure lab, by then there's already proteins that are common throughout all of the neural tissue that will eventually become your brain. So it was easy to assume that they weren't differentiated and specified yet. And that specification comes later, right? Right. Because if they're giving identical what we call transcriptional profiles, if they'RE producing very similar proteins that we use as markers as kind of like ways to signpost what type of cell they are, then it would make sense to kind of assume that they were from the same tissue. In the same way, right, we can assume that French and Spanish both come from Latin because they have similar verb conjugations. So what these people did is they just went earlier. Now, here's where it's interesting. There was some studies that suggested that this was true already, because we can actually track the movement of cells in zebrafish, which are translucent. We've actually done studies where we track zebrafish development and flatworm development, and we can follow every single cell as it develops. And so we knew that the hindbrain and forebrain came from a different spot and migrated from a different spot than the hind brain. Because that's already in a kind of complex tissue architecture, we didn't know whether the difference was because they're migrating to different spots, they were becoming different things, or whether they were kind of locked into that from the beginning. Does that kind of make sense?

0:21:32 Thomas: So it could be, they go over here. That's why they become a different thing or they're a different things. That they went over there in the first place kind of okay geez

0:21:39 Eric: Am but how much of this is the context how much was the intrinsic property of the cell and what this paper does is show pretty definitively that this is an intrinsic property of the cell

0:21:50 Thomas: So what shares this then this you said not flies is it all I was thinking it was like oh

0:21:56 Eric: Flies do share this, what flies don't share is the neural crest breasts the thing that will become like noses and ears and all that stuff this is 500 to 800 years of conserved evolution pretty much everything that it has bilateral symmetry right that has the same left side is right side this

0:21:58 Thomas: Is oh okay oh so like this is like all animals then or like a lot of them

0:22:18 Eric: All animals right because we have sponges we have um starfish

0:22:22 Thomas: Yeah you've mentioned there are ones that don't

0:22:23 Eric: Jellyfish cnidarians so we do have other things that aren't there. But we're getting pretty close to the part where it's not super wrong to say all animals, right? And gastrulation is part of all animals. All animals, do have those three germ layers of mesoderm, ectoderm and endoderm. Actually some don't have mesoderma, but they do have that gastrullation and that differentiation into the different germ layers.

0:22:48 Thomas: I was gonna call you on that but I did I

0:22:49 Eric: And so we really are talking highly, highly conserved processes. That shows because this differentiation happens super early in development. This is somewhat oversimplified, but there's a saying that ontology recapitulated phylongeny, which

0:23:01 Thomas: Say that all the time to my kids right

0:23:04 Eric: What it basically means is you can trace the history of your evolution through embryonic development. That's not totally true, but it does kind of to hold true that the

0:23:09 Thomas: But it's kind of true we get that like layer of monkey fur in there and we got like a tail and crap yeah

0:23:15 Eric: What it's basically saying is that the earlier you are in development the more foundational the processes are and the more conserved they are because it's easier to end up with a whole embryo termination right so gastrulation is one of those that's super super conserved and what this study did was instead of looking at the neural ectoderm at the very start of neurulation which is around e7 on the seventh embryonic day in mice they went slightly earlier earlier before we have that neural non neural ectoderm border. What they did find is even in that ectодerm tissue before it becomes a neural plate that turns into neural and non neural ectaderm, you still had differences in transcription factors, when you would expect all of them to still be showing the same stuff, because they haven't differentiated into that stuff yet. That kind of makes sense.

0:24:05 Eric: So what they're saying is, at this point, we already already know what's going to become forebrain, what's going to be hindbrain and midbrain. Our spinal cord and other things haven't fully formed yet because there's these other things that happen when our embryo gets longer a process called convergent extension. But we don't have to really talk about that other set of tissues that form our spine because that'll just make it even more complicated. So if you look at figure 1b, I think it'll make clear what I'm trying to say.

0:24:04 Thomas: Kind of okay was gonna say I'm not clear if you've gotten through the whole paper or if this is like the preamble to the first figure.

0:24:37 Eric: Is the preamble, but we will be able to start moving with a little little bit more speed now, right?

0:24:40 Thomas: I'm trying. All right.

0:24:42 Eric: So if you look at figure 1B, and 1A is what we were just sketching through, right, how there are these fate decisions that lock you into different things. And if you notice, right. Surface ectoderm and border ectaderm are those neural crest and non neural ectiderm, the skin cell I was talking about, the PNE is the posterior neural ectederm, and the A &E is the anterior. And what they're showing is that you can already see that there's a difference in colors in figure 1b in the types of proteins that they express depending on the location within that very very primitive mouse embryo and it's also very clear in 1d

0:25:17 Thomas: So that this is the figure that you told me just to describe for listeners. It's like HPS cells is like that top thing. And then definitive ectoderm is like the second thing. And then it's like branches off to four different things. That's the A &E, P &E border ectaderm, surface ectiderm. And Importantly, it seems like the A and E then branches to the forebrain and midbrain and the P and E branches tothe hindbrain. And those never the twain shall meet. It's like those are separate.

0:25:46 Eric: Whereas what we used to think was it would go ne border ectoderm surface ectiderm and then a and e p and e but that they shared a common neural ectaderm or ancestry it's

0:25:58 Thomas: It's such a slight difference, but it sounds so important and interesting.

0:26:02 Eric: Super interesting it it is a little in the weeds, but it does make that profound difference of you would expect if the four in the midbrain were kind of an offshoot of the hindbrain, that you would have that first neural ectoderm and then differentiation, right? Whereas here they're already different. Does that figure make it make a little more sense?

0:26:20 Thomas: No, I'm just trying to describe it for listeners and we'll try it in terms that aren't those technical terms as much as you can, you know, but I think we're getting there. So what the B one, Joe?

0:26:30 Eric: You can see in the picture, 1B, right, you can See that there's three different colors. And what they're doing here here's an assay called immunofluorescence. What they basically do is they make antibodies to different proteins that are expressed in cell or on the cell membrane. And then they label those antibodies with a fluorescent probe, right? That way, when you look under a microscope, depending on which antibody is binding to which proteins, you'll be able to label each cell with a different color, right, because the antibody will bind to the protein that exists on that cell. And depending on what antibody is bonding will tell you which proteins are on that self. And each antibody has a different color.

0:27:07 Thomas: Like they literally, this comes down to like, let's put some dye on some different things and see where it changes.

0:27:13 Eric: Was 90% of my research. Yes. You can see now that have these two populations and you can probably see in the picture, it just looks like a little ball, right? We don't have anything that looks like it's about to be a brain, spine, hindbrain, any of that stuff yet.

0:27:31 Thomas: Wasn't even sure if I thought we were looking at it like a graph, like a, that's an actual, Oh, okay. Thought it was like a scatterplot, not a scatter plot. I though it was one of those things where it's a, yeah.

0:27:35 Eric: That's the actual embryo. What happens when we get our spine and we make the rest of what will become a neural tube is you have this process called convergent extension where you literally build cells on top of each other. Like like Iceman building his ISA slide, right? The body will literally expand out from that place and make new cells. We haven't done that yet.

0:28:00 Thomas: Frozone after he finds his super supersuit okay there we go gotcha glad I could help

0:28:05 Eric: We haven't done that Yet. So we just have that little ball. What they keep showing in figure one is that this is a true difference in protein. So they do this thing where they analyze the RNA of each of of these cells in a really cool process called single cell RNA -seq, right? They take each individual cell from those layers and they analyze what proteins are being produced by looking at the RNA. Because if you remember, DNA makes RNA, which makes protein, so, so far, what they show is that by proteins, each of them have their own set program and they've already differentiated. But as I just mentioned, we don't know yet whether that's an intrinsic property of these cells, or whether it's the context within the embryo.

0:28:49 Thomas: So we're still building that case in these figures so

0:28:52 Eric: And so in order to do that, they actually take this in vitro into a plate of cells where you remove that context, right? And they take pluripotent stem cells that can become any ectodermal tissue, and they start trying to differentiate them, right. And what they find is that things Things that became anterior neuroectoderm cannot become hindbrain, and things that became posterior neuroectодerm cannot becomes forebrain or midbrain. No matter what signals, what kind of things you put into the media that you're growing the cell in. Whereas if this was a question of location and context, you would expect to be able to change their fate by changing the chemicals you give them.

0:29:37 Thomas: I would guess that you can do this with like the a anything you could make it forebrain and midbrain or something okay so

0:29:43 Eric: Exactly. That is exactly what they show in the very next figure yep

0:29:47 Thomas: Cool there you go there's I could have been able to read that I can't I still don't understand it was easier for me to think of that than to read the diagram that's how complicated this stuff is uh you're saying you put stuff in a little I don't know whatever a plate or something you're doing and the key is you're separating it from that context in order to answer that question of like were they just doing this because of like physically kind of where they were or the signals they're getting or both or either and

0:30:16 Eric: Like for instance was it the hox genes that set the body plan um head to toe was those giving them signals that were telling them to differentiate from the base ectoderm into anterior and posterior neural ectaderm right or

0:30:28 Thomas: So they're trying everything everything they can think of to recreate that but it can only get the hindbrain or the or the other thing okay I

0:30:37 Eric: Right they know which signals the body produces is exactly right and so they feed those into the plates of cells to try and induce it but they can only induce forebrain into forebraIN and midbrain or anterior into fore brain and mid brain and

0:30:51 Thomas: Cannot fucking believe that there's people doing this that we can't even it is a struggle for you to explain the first couple sentences of this thing and then our public health is run by a guy who thinks that there're demons in your blood and you can get autism from vaccines and all it's like the difference between how much scientists know and can do is incredible to me with the difference entre what the public knows and who guides our policy like what a depressing sorry I know it's not the time for it but like this is so freaking complicated

0:31:23 Eric: It but it it also does make sense right because right this is me trying to simplify this as much as possible but because it's so complex there's only so much you can without bordering on misinformation

0:31:35 Thomas: Then so in the end you're like I don't know man the rna vaccines are fine just they're fucking fine you know because at the end it's like how can I'm not gonna get rfk jr you can't even get me to understand it's not going to get that guy to understand

0:31:48 Eric: But you scroll down to figure two it might make a little more sense and

0:31:51 Thomas: We get to finally we could skip all this stuff thank god

0:31:53 Eric: Figure two starts looking a little bit like a mouse now right you can see in red right what they did was they made a transgenic mouse not a trans mouse a transgeneric mouse just you know apropos of rfk oh

0:32:05 Thomas: I'm actually not sure where figure two is because I see letters it's

0:32:08 Eric: It's right underneath figure two right the one that looks like a mouse with a red tail I

0:32:15 Thomas: Wish I had any idea what that one was is it page page five

0:32:19 Eric: Believe so do you see a bunch of like um red staining and then like graphs yes

0:32:23 Thomas: Where does it say figure two it's just so much information like

0:32:25 Eric: Figure two is right above it actually a really I don't know if this is ai assisted this reads really well for a science paper, to be honest. Like the writing is pretty flowy.

0:32:32 Thomas: Well okay so so you say I still don't see it but

0:32:41 Eric: You look at figure 2A, you'll the mouse, right, in blue OTX2 staining. So that's the protein they're using to mark that anterior part of the neural tissue. The red is using GBX2, which is another other protein, but this one is specific to the hindbrain and the spinal cord.

0:32:43 Thomas: I see an a okay okay yeah so So we got a little tiny embryo in there. It's cute. It looks like a human, even though I know it's not. But like that's how similar stuff is at the scale, right?

0:33:07 Eric: Is. These are very adorable, yes. Notice that the brain hasn't closed yet, right? So this is prior to neural tube closure beginning.

0:33:15 Thomas: Or closed. Now, how can you tell the brain hasn't close? I know that's obvious to you, but to me.

0:33:19 Eric: You see the two little folds that makes it look like a canal at the top?

0:33:22 Thomas: Sorry, in which particular one? I see E2A.

0:33:25 Eric: Where you see like the red tail flipping up, and then you see blue crest, like a dilophosaurus yep exactly yes so if you look in the box at e8 .5 you can see that the brain hasn't actually closed there's a gap between those two folds it's

0:33:28 Thomas: I got that. Oh, actually, yeah, that does help. But I see like E8 .5, E11 .5. Like what? Which one? All of them? Okay. Oh, okay. So there's two blue things are like the brain. So almost like the hemispheres are like apart and then they like, someone's like, all right, stick those together eventually.

0:33:55 Eric: That's pretty close to right at some point we do have to do neural tube closure as an episode but

0:33:59 Thomas: So that's what you keep talking about when you say neural tube closure. Okay? All

0:34:02 Eric: Yes but you Can see that though midbrain in the forebrain is producing an entirely different different protein than the hindbrain, right?

0:34:09 Thomas: Because dyed them using that thing you said. And so one, these ones are blue the other ones are red

0:34:15 Eric: Because we labeled it with OTX and GBX2. So that's marking the two different lineages, right. We know that they're on different programs because of that. But what we don't know is whether that's because of where they're at in the embryo, right, and if we move the blue cells further down, would they be able to turn red? And if we moved the red cells further up, would be able turn blue? That's what we're trying to figure out in the next thing.

0:34:18 Thomas: This is so crazy is okay okay that helps so like oh man this is a hard one to do for listeners so so picture a little embryo like you were saying and the part that's like the brain stem if you zoom in it's like it's not finished it's not quite closed it's like the two hemispheres are kind of separated but the that that part is blue and then the other like stuff coming off of that is red and you're saying we don't know if like if we took some cells from the blue and put it somewhere and gave it the red type of signals kind of could it do that stuff and we already know the punch line which is no right because of the difference that we're talking about here okay

0:35:14 Eric: We are now exactly on the same page.

0:35:16 Thomas: I wouldn't say that but okay I

0:35:20 Eric: Why they went into cell culture. So if you look at the B for that figure, it'll show you what they're doing. They take those anterior and posterior neuro ectoderm cells, and they give it the different signals that would be present in those locations in the embryo in a plate of cells.

0:35:36 Thomas: Okay. Makes sense, and we can kind of hopefully all agree that that happened.

0:35:55 Eric: So what you can see in C through F is a graph of the protein data, right?

0:36:01 Thomas: Hmm.

0:36:01 Eric: How much of each protein is, or really how much of each RNA is being made, right. And what you can see is that for the anterior neural ectoderm that's marked by orange, they produce a lot of those forebrain and midbrain lineages. But when you give the posterior neural ectoderm that same thing, they don't produce any versions of those proteins, right? You can see it in the staining right next to that, where the anterior neural ectoderm derived cells still light up with the proteins that you would expect with antibody staining, but the posterior ones do not.

0:36:35 Thomas: Okay, dear.

0:36:36 Eric: Whereas when you switch the experiment, right, and now you're giving them signals to turn into hindbrain, your posterior neural ectoderm cells perfectly form those proteins, right? But your anterior ones don't really at all. Here's the real kicker. When you culture them together, they don't overlap in their profiles. And when you merge the pictures of those fluorescent proteins that you're labeling, they don't what you call co-localize, right? The yellow and the pink aren't turning into a merged like orange color. The pink is staying pink and the yellow is staying yellow, which shows that they are staying and maintaining their identity, even though they're in the presence of other cells that would theoretically try to flip their switch. So that's really, really good evidence that these truly are two different cells from two completely different lineages. So the next thing they do, and we're going to scroll down two pages now, the next time they do is try and figure out why. The answer is what we call chromatin remodeling, right?

0:37:41 Thomas: God. What is that?

0:37:43 Eric: What that means is you can think of DNA as like beads on a string, right? The DNA wraps around these proteins called histones. Now, if I need to read DNA and turn it into RNA and then protein, what do you think is going to be easier for the proteins that make the RNA to read and produce from? The part that's not wrapped around the histone or the part that is wrapped around the histone?

0:38:08 Thomas: You lost me already. What's

0:38:10 Eric: Okay, picture like spool, right, with yarn. I need to knit something.

0:38:14 Thomas: Gotcha.

0:38:14 Eric: Am I going to knit from the yarn that's open or the yarn that's wrapped around the spool, right?

0:38:19 Thomas: Okay I see. So yeah, whatever's kind of coming off of it already you mean?

0:38:24 Eric: Exactly, right. That's what's open to be read and accessed by the proteins that will turn into RNA. So they do an experiment called ATAC-seq. What they basically do is they take transposons, things that shuttle DNA from one place to another, and they make it hyperactive. And then they see where that stuff inserts into the DNA with the logic being that if chromosomal DNA is wrapped around the histone, they won't be able to get access. But if it's open, they will be able to. And they use that to see kind of what parts of the DNA are open in each of their cells. And what they find is that different parts ofthe DNA is open in the posterior neural ectoderm and the anterior. And that's what lets those different transcription factors, those different proteins that turn on other proteins, to be differentially regulated in the two tissues, right? To have one turn on one program and one turn on another. Because if you look at C and E of figure three, you'll see those letters next to the pictures with green squares.

0:39:26 Eric: Those green squares are showing you what is open according to the chromatin, and then what sequences the transcription factors bind. And what you can see is that the anterior ectoderm cells that become forebrain and midbrain are open to be accessed, those transcription factors are open in the anterior neural ectoderm but they're completely absent from being accessed in the posterior and the opposite is

0:39:25 Thomas: Gattaca yeah okay for the listeners I'm looking at chica chica boom boom uh pretty much exactly for anyone who has kids it's a bunch of letters that a told b and b told c to meet you at the top of the coconut tree and they're all different colors and some are bigger and taller right

0:40:02 Eric: Those are are the sequences that those transcription vectors that turn on other proteins recognize right because transcription factors bind dna and then turn on a set of genes to make the cell it's programmed

0:40:09 Thomas: All right I think at this point we're going to take your word for it that this is because this is getting too much that we can I think so there's another way to test I think I kind of get what you're saying though it's like it's it's being able to test which of these gattaca letters are open or whatever and they're different for the two things that we've been establishing are different the four right

0:40:31 Eric: And it's why you can't just take one and turn it into the other because they're insensitive to those transcription factors

0:40:35 Thomas: It's trying to combine chicka chicka boom boom and numbers boom boom they're two different books all

0:40:43 Eric: Like like before it's we figured out programming and trying to run Mac on a PC um

0:40:47 Thomas: Proven well we will say that's proven we got it you

0:40:51 Eric: Can somewhat quickly go through the hedgehog and wind signaling part what they showed is that there's also a top and a bottom once the neural tube closes right once we become three -dimensional and those two folds work across to make the hollow tube, something will become the top part of your body, the dorsal part of Your body, and something will become the ventral, the bottom part of your body the belly side, right?

0:41:13 Thomas: What do you mean your body just are aren't we just talking about the brain or are we talking

0:41:15 Eric: But your brain has a has and a tummy side also, right. They're showing is that you can make any part of the dorsal or ventral midbrain or forebrain from the anterior neural ectoderm, but you can't make any of the posterior neural ectoderm and vice versa. So again, what it's showing is that it's not like they're locked into something and it's a kind of mistake in the way they're culturing these cells, right? It's not a mistake in their experimental protocol because they're able to show that things that aren't locked out of differentiation, right, because both dorsal and ventral comes from both of those populations later on in development. It's showing that they're still competent to differentiate, but that they really have already chosen their fate by the time gastrulation begins, right? It was a problem with the experimental protocol or something, you wouldn't be able to make both dorsal and ventral because they wouldn't be able further differentiate, for instance. That kind of make sense?

0:42:11 Thomas: I think I think this for most people this is going to go further in the category of okay these two things are different we've established that is there more we can um talk about the because there's a lot more paper to go so

0:42:23 Eric: We're all the way down to figure six. And so figure six, you'll see a picture of a worm, a fish, a chicken, a mouse, and a primate.

0:42:27 Thomas: The funniest thing is that I still have no idea where you're seeing the number of of the figure. I don't see it.

0:42:38 Eric: This one's underneath the pictures this time. It's right before the references.

0:42:42 Thomas: The pictures. Oh, there we go. It's all the way down on a different page. Okay. That would be why I didn't see him. Gotcha.

0:42:47 Eric: So here you can see that they actually tested this in other animal models and it is conserved all the way through these very primitive, what we call hemichordates, right?

0:42:59 Thomas: Oh.

0:42:59 Eric: Like worms.

0:43:00 Thomas: Like I was asking you about with the, with the, it was like, so we got a little chart here. We've got acorn worm, zebrafish, chicken, mouse, primate. And you're saying that applies to all of them.

0:43:09 Eric: Because deuterostomes basically means I make a tube with a mouth and a butt, basically anything that makes a tube with a mouse in the butt has this posterior and anterior neural ectoderm division from gastrulation, right

0:43:13 Thomas: Okay, yeah. Okay what are we really, but just a mere tube with the mouth and a butt. That's okay.

0:43:26 Eric: Where this gets interesting is what we were talking about though, is the very next step going back in evolution is basically like jellyfish and things like that with like Like, just no brain at all. And so this is really from the very first start of brain development, we already have these two lineages. There wasn't a brain that specialized into two things. This was always the case for brain development.

0:43:51 Thomas: Huh. I'm trying to understand the implications of that I still don't quite get it in terms of like evolutionary okay

0:43:56 Eric: Will be honest, I'm still wrapping my mind around the implications of it, right?

0:44:00 Thomas: It's not like it's like oh it's animals and like freaking plants or something where you could really understand it'slike animals and so stuff that wait did you say it's just stuff that doesn't have a brain no there's

0:44:09 Eric: Just right before. This is like anything pretty much what neurons will show this up at the start of when you start having like a primitive brain, right. Anything that has something that will turn into the central nervous system.

0:44:22 Thomas: Sorry I think I'm just to make sure I might be misunderstanding are are animals or whatever there are uh forms that have brains that don't have this thing we're talking about right or or no okay

0:44:32 Eric: Don't have brains. They have bundles of nerves, right?

0:44:36 Thomas: So it is something that's core to like any like brain development okay

0:44:41 Eric: That's what's key, is that this differentiation happened from the start of brainness, right. Whereas what I would have expected is you would start with something like a hindbrain that does primitive stuff, and then you would slowly add complexity that would become your foreign midbrain. That was my initial.

0:44:58 Thomas: Well wait sorry another stupid question this you're talking About just the tree of life as exists today but like the thing you just said wouldn't that apply in like evolutionary history couldn't there been something that has yeah

0:45:09 Eric: In mind that a lot of the tree in life and evolutionary history has representatives or things that are close to it in extant life, right? So we're using that extant Life that matches what we think those precursors look like, right. We probably didn't have something that different from a flatworm giving rise to bilateral symmetry, we probably didn't have something That different from like a lobe like worm giving rise the central nervous systems, right? So we're using them as proxies because obviously brains don't fossilize.

0:45:42 Thomas: Interesting I've never thought about that before so it's like for most things you're saying because you know whenever I think about evolution it's really interesting to think like oh this this time things had these features and then this feature developed and you're seeing we can pretty much always find like a modern thing that at least descended from that so it still has that split that we can kind of look at um

0:46:01 Eric: Exactly. And what animal choose to study is based on the evolutionary conservation of the thing you're studying with some experimental stuff. So like the reason why I'm still wrapping my mind around this, right, is we use a bunch of different animals to study neural tube closure, right? We study them in mice because mice are most similar to humans. And mice have multiple points where the neural tube starts to close. There's a closure point right at the boundary between the hindbrain and the spinal cord that works in both directions, up and down. And then there's another couple in the mid and forebrain, right? So those are separate closure points that would suggest different lineages, right. But if you go all the way back to a frog, they actually roll up the entire neural tube from forebrain to spinal cord at the exact same time, which would suggest that they come from the same tissue. And that's why I'm still wrapping my mind around this, right? They do their whole thing in one concerted process, whereas fish, for the most part, hollow out the neural tube through a process that we call secondary neurulation. So you can retrace the history of evolution of the neural tubal closure based on the animal model you're using, right, even all the way back to these things called ascidians, which just have a very basic kind of primitive spinal cord.

0:47:20 Eric: Takeaway there is you would think based on those differences in closure points that we would get one primitive brain because the further back you go in evolutionary time, the less amount of closure points you have, right? You don't have a difference between when the forebrain starts closing and when the hindbrain start closing. They close at the exact same time. Whereas in our brains, our hindbrains start closing first, or actually it starts closing at around the same time, but at different locations. And our forebrain has a completely different closure event.

0:47:50 Thomas: So like the more complicated a brain gets it has to have more closure points because it's like being built in development rather than like all right this is a brain that's got like three like like rfk junior's brain like that one just like slap it together

0:48:03 Eric: And honestly, that's what this study points to, right? Is that the reason you get those extra closure points is because of the actual mechanical movements of those brain tissues closing, as opposed to much more simple animals where you can just kind of roll it up. Really interesting study. I'm sure Jenessa will have a ton about the implications for like cognition and stuff, that would be a little outside my skis. I'm much more of the molecular markers and differentiation part.

0:48:40 Thomas: I mean this seems like kind of a big deal right or off how many people can understand it secondly for those people are they freaking out right now sure

0:48:47 Eric: Has implications. I am not sure it is like a new unique thing that like this, like I am pretty sure there are other organs that have these parallel tissue evolutions that then stitch together like you were talking about. What it does have implication for is things like ALS, right? Because ALS we now know how to culture and specify hindbrain cells much better as a result of this study, which could help with like problems with swallowing and breathing, right? Which your hindbrain is largely in control of.

0:49:15 Thomas: We should have started with that what is your hindbrain did you start with that what does the hindbraIN do oh I think you quickly went over it but I I might not have hmm

0:49:21 Eric: So yes. Your hindbrain does a lot more of those like autonomous things, right. The things you don't think about doing, but do. Whereas your forebrain and your midbrain do a lot more of the complex cognition, which is why you would think that like your forebrain and midbrain came from like the more simple hindbrain. And I think that was the model that was in place.

0:49:42 Eric: And this is now saying, no, those are actually two things that are stitched together. What I would be interested in seeing is the midbrain, which also does some of that autonomous stuff. Does that work as kind of like a adapter in the same way, like you need to plug into a European outlet

0:49:55 Thomas: But it's an adapter that would have been more from the

0:50:02 Eric: From the forebrain? Right, because the forebrain saying I need to connect to the hindbraIN. I'm going to make an adapter in between. Between

0:50:08 Thomas: That's interesting so does that though when you talk about it that way in terms of the function does that kind of almost answer my evolutionary question where it's like okay we'll go back to when there was stuff that could swallow and do whatever but couldn't do any of the other stuff isn't

0:50:21 Eric: But I'm not sure you would find that thing they did apparently evolve in parallel together right the prediction you would make if forebrain and midbrain came from hindbrain tissue that there would have been a hindbrain tissue first that then derived and specialized into mid and forebrain in a certain region

0:50:39 Thomas: Hmm well the the freak thing where it's like somehow they combine like two independent things I guess that's just like really really impossible though right or okay

0:50:48 Eric: There's no mitochondria to swallow in this case right

0:50:50 Thomas: So we're at too far because because that was true about like cellular evolution right like the weird all that the powerhouse of the cell you got all that stuff some of that was like oh we think it's two different lines that like just like ate each other and somehow formed one thing

0:51:05 Eric: But it's apparently more like building an arch where you need both of them to come from the opposite sides and connect together

0:51:09 Thomas: And connect oh but they are that's an interesting image so it's like okay that's really interesting that might help quite a bit where it's like they so you're saying it is like an arch where they are two independent it's an arch but like two different like people are building the arch and we know they're different building materials and they can't combine like you can't move them like they're totally separate like you can't use the materials from the right side for the left side but they come together and that's when you form an arch and so I'm over here saying like which one came first but but it doesn't really make sense because half an arch doesn't do anything.

0:51:44 Eric: Right each one would do something but apparently they do work together right but right it isn't is I have half a staircase and I need to get to the second floor the next level of cognition and I'm building my next set of staircases on top of what I already built right instead it's I have a bridge across a river and I need to build from both sides as opposed to building from one side and continuing to build until I get across that river to consciousness yeah

0:52:15 Thomas: Interesting. Still trying to grasp on how that applies to evolution, but I, you know, I thought I got there, but maybe not.

0:52:17 Eric: Basically what it's saying is that both parts of the brain didn't evolve sequentially they both came from that ancestral population of definitive ectoderm and were in parallel as they evolve together from that very first bit of nervous tissue right

0:52:37 Thomas: This might be dumb, but does that mean instead of like building the arch halves and then meeting, is it more like they've independent things. We know that they're like different things, but maybe they were like smaller so you just have a little arch and then they're like growing together in a way I'm just trying to visualize how this happens evolutionarily to still be two separate things but one didn't come from the other but they but it's not like one animal ate another and then you got a brain you know it's like I'm trying how does that work put

0:53:04 Eric: What you would have is you'd have ectoderm right and that ectодerm

0:53:09 Thomas: In arch terms that's not helping but

0:53:12 Eric: Would be like you have two people both trying to build across the river at the same time and they realize that it's easier to work together than to each build their own arch

0:53:23 Thomas: They're on opposite sides but is it like it started as such a tiny any river, they could like high five and they're like, okay, we're good. And then the river gets bigger and you're like oh shit. Okay, let's let's keep the river gets bigger. Let's keep building out what our side is. That's kind of what I was trying to say a second ago. That is a better image though.

0:53:38 Eric: It's both kind of like that and kind of, like, as, yeah, you're right, it's as the river gets bigger, right? Because the initial brains and initial nervous tissue wasn't very complex, right, so you didn't need sapience from your forebrain and midbrain at that point. You just needed like reaction to stimuli and stuff, right? And then as you get more and more complex, one of them specialized in more of that base homeostatic functions, and the other one specialized in signal propagation and solving problems, connecting and becoming more that emergent property of consciousness. Business um

0:54:16 Thomas: Okay. I think we got there with that image. Well, this is really cool. Anything else we should know about this or you know, any other implications?

0:54:24 Eric: I think for now like it's still new and to be honest again I'm still wrapping my head around a lot of it but I thought it was just really good science and to be honest I just wanted an excuse to look at confocal imaging and self-aid again oh

0:54:36 Thomas: Yeah, this really cool wait who did this? Did we even say maybe you did what

0:54:40 Eric: We should shout out the authors yes hold is from uh kai at all with uh dr low is the corresponding author and it's largely from Stanford University stanford does a lot of really good stuff

0:54:50 Thomas: Nice man that's really cool so despite maga's best efforts good science is still happening in america that's nice or maybe this is the last of it yeah

0:55:01 Eric: Does go to show you right like when people talk about science they don't really think through this level of complexity right like This actually, full disclosure to pull back the hood, this whole email chain came from me having a random thought about James Tallarico and the non-binariness of God, right? And what I really want to ask people, I think that's ridiculous, is are you saying God has differentiated cells? Are you saying he produces sperm? Are you say, right, like actually thinking through the mechanisms is how you do science. And to get to your point, that involves this level of complexity because that's the level of knowledge we have. So when you hear pithy things on cable news or from rfk just remember they are talking out of their ass unless they're able to describe things at this level

0:55:44 Thomas: You know they're just a tube with a mouth and a butt and they're talking out of the wrong part of it yeah yeah that's fucking deuterostomes all right well this was my yeah I think my brain stem came apart out of this I gotta go re-put it together but that was a lot of fun uh as always thanks so much dr eric jaffe uh cool stuff and yeah like there might be follow -ups on this like we're saying so really interesting thanks for thanks

0:55:47 Eric: They are deuterostomes more like doucherostomes yeah now time to go watch the yankees hopefully even up the series I

0:56:12 Thomas: Thanks for trying to help us understand this I think pretty successfully Hopefully, we'll see.

0:56:17 Eric: Towards the end we we landed the plane it had a rickety takeoff but I think we got there in the end take

0:56:22 Thomas: Alrighty, well, until next time.

0:56:24 Eric: Care Yeah. Make a tube with a mouth and a butt,