AI teaching atomic simulations from 150+ years of data

55:50it can tell me how I would actually construct it. The this and I don't need to keep bringing up our past stories, but the other thing this reminds me of is when we did the deep seek story at the beginning of the year uh around their new architecture of how they was I can't quite remember the concept name. Manifold uh uh constrained >> Yeah, hyper parameters. >> Yeah, correct. W- where in that process where you're going back the the the highways were small initially and they created figured out a way to create more lanes in the highway. Yeah, and they had a trick. W- so when you're going back in this back propagation concept you're talking about, you you just have more that you're working with uh to get a

56:30better outcome. And so And you're and you're and the main thing is you're constraining that function to be smooth. >> Yes. >> So that if I do a step in one way or the other, it's not like drastically changing >> Yes. what the function is. Yes. I'm just trying to prove the point that our episodes do build on each other. So if you haven't watched the library, there's a lot of great stuff >> of good stuff, guys. in both season 1 and the first half of season 2. >> Mhm. Yep. >> Fas- fascinating. Th- that that that's actually super cool. >> is out of the This is um a paper that's in Nature Communications >> Yes. out of the University of Michigan engineering. Yes. >> Friend of the show, Blackbird Physics. Shout out to Blackbird Physics. He's a

57:11He's He's a great science communicator out of the University of Michigan. Um >> I I see that you left out the the left out the French university on that one. Oh, okay. Yeah, there was also a French university, Université Paris-Saclay. Well, you told me to uh told me to talk about them. That's how I I don't know how say it. That's how you say it. A great great first story uh on material science. Yep. Our story number two in the rundown um is about DNA. And so every person of non-African ancestry so people who are not me

57:54alive today carry Neanderthal DNA. Yeah, so I do. Yeah. Yeah, unfortunately. Unfortunately. All right. And it turns out the story of how it got there has a very specific direction. Yeah, this one was this one was pretty funny. So for decades we've all wondered why modern human X chromosomes are completely devoid of Neanderthal DNA. We can sequence uh human DNA and then we can sequence Neanderthal DNA. We've Svante Pääbo very famously, I think maybe two or three years ago, won the Nobel Prize in Medicine for actually doing that, for sequencing ancient genomes that were human-adjacent. And

58:36um from that we can figure out that the human X chromosome is almost completely devoid of Neanderthal DNA. Okay? But Neanderthal DNA exists everywhere else. So how come the X chromosome, which is a giant chromosome with, you know, millions of base pairs, how come that has almost none of it? And this new study that uses computer modeling is suggesting that it's not because of bio-incompatibility, but it's because of mating habits. Oh, interesting. >> in our ancient past. >> Interesting. Here's what they did. They compared genomes and they actually found that the Neanderthals carried far more human DNA

59:19in their X chromosomes. So what does that tell us? >> Yes. Let's do a A bit of review of basic genetics okay? Um the female gender has XX and then the male has an XY, right? So, when females are born, you get an X chromosome from the dad and an X chromosome from the mom. But when males are born, you get a Y chromosome from your dad and an X chromosome from your mom okay? Now, the fact that X chromosomes in Neanderthals have a lot of human DNA, but X chromosomes in humans don't have a lot of don't have a lot of Neanderthal DNA, that suggests one thing, which is that

1:00:02the specific inheritance pattern points to a long-term bias where Neanderthal males were mating with human females and it was this one-way asymmetric mating. Do you see what I'm saying? It's the only way to explain this discrepancy between why the X chromosome is only one way. The Neanderthals have the humans but the humans don't have the Neanderthals because the humans were only inheriting the Y chromosome from the Neanderthals, not the X. But the the Neanderthals were inheriting the the X chromosome because they were they were

1:00:42getting the human female. >> Yes, yes, yes. The idea is human males exclusively mated with human women. Yeah. It's obviously not exclusively, but like by and large is the idea. By and large. That's a good correction. No, no, that's a good correction. By and large. Whereas Neanderthals were regularly fraternizing with the enemy. The men The men were The men were They were Neanderthal men, dude. >> It's always the men. It's always the men that are just like going at it. But but but this but what's interesting is we're we're sort of describing like the sociological and psychological uh decision-making

1:01:24>> Mhm. is what has is driving this observation we have in the genetic record. >> Yeah, yeah. And it's I mean it it opens up a lot of cool genetic studies about like population dynamics and things like that. I just I just find it really cool that we can actually trace back and look at mating patterns like that and be like, "Oh, it's actually sex-specific, specific right? >> Neanderthal males like the human females were fine going for Neanderthal males. >> Yeah. But somehow the human males >> Yeah, they're not about that life. >> They were not about the life of the Neanderthal. Like human males were not going for Neanderthal females, you know? Yeah. I don't know, for whatever reason.

1:02:04There's a there's a this makes me think of the the channel HO Math, which I will not pronounce because this is a family-friendly show, but this channel talks about dating dynamic stuff and and a and a graphical way like in a great like drawing graphics and and like kind of creating a formula. >> I'm not going to opine on the accuracy or lack of accuracy of HO Math. However, if any of you have participated in consuming that media, please feel free to add your comments below. >> Yeah. This study was out of the University of Pennsylvania and it was in science and it was covered by Archaeology magazine.

1:02:44Our third story in the rundown is something biology teachers have been constantly getting wrong for decades and it just got a serious reality check and it took, of all things, transparent fish embryos >> Yes. to catch it. So, what was my teacher in high school wrong about? Well, she was wrong about um mitosis. Why was it Why is it got to be a she? Why that's that's why I like Why >> My my my biology teacher, Miss Saeed. She was She was an amazing biology teacher. Um she taught me AP biology and she really got me into um like thinking about biology from like the ground up. She was an amazing

1:03:26>> maybe an inciting incident to why you became a biophysics teacher. >> Yeah, yeah, totally. She was She was awesome. Um AP bio She was wrong about mitosis. Not she apparently every textbook including the AP textbook by the way by the college board which is a racket but that's for another day. Um here's the idea. Have you heard of mitosis? Yes. Right? It's the idea of like cell splitting into two. They um they replicate their DNA, they split into two and then they split into two. This happens a lot during embryonic development, right? Because you start from a single cell, you make like about blastula, all the DNA has to be exact.

1:04:07Um giant embryonic stem cells, sorry, giant embryonic cells like animals in zebra fish, sharks, and birds, they don't divide the way that we think they should divide. And here's what I mean. So here's what what we think is how mitosis happens. You've got a cell. The DNA, the chromosomes line up in the middle and there's this kind of purse string. So there's a bunch of cytoskeleton with actin and myosin filaments that grab the DNA and sort of surround it in a ring and then you pull it and as you pull it that purse string sort of like Yep. tightens up >> Yep. and then and then that causes

1:04:47cytokinesis. The the cells come together and split into two. The The analogy I'm thinking of is imagine you have a bubble in the middle and you have a string over the top and a string over the bottom and you put your fingers to pinch the strings on both ends and then you pull those strings. The The string will pinch Yeah. >> and then ultimately split the bubble. >> Yeah, exactly. And this is the the like telophase part of um mitosis where at the end it pinches and it goes through. >> Mhm. Now, that works for like smaller cells, but cells from zebrafish, sharks, and birds have extremely large size and very large yolk. And these cells it physically doesn't make sense.

1:05:29>> Mhm. Like if you calculate the amount of noise and the amount of physics that's required to coordinate this giant ring to come together, it's just not actually going to work. And so the reason why this this particular paper actually worked and figured it out