New Rules For Heredity (Non-Mendelian Inheritance of Epigenetics) (EP 44)

Hosted by Lester Nare and Krishna Choudhary, this episode marks Krishna’s return to the studio after paternity leave — and the timing could not be more fitting. Today’s deep dive is about inheritance: not just the classic Mendelian rules most of us learned in biology class, but the stranger, more dynamic world of non-Mendelian epigenetic inheritance. Starting from Gregor Mendel and his pea plants, Lester and Krishna rebuild the foundations of genetics from first principles: dominant and recessive alleles, Punnett squares, chromosomes, fruit flies, DNA, and the physical mechanism behind inherited traits. Then they move into the “software layer” of biology: epigenetics, DNA methylation, chromatin packaging, RNA interference, and paramutation — cases where the genetic code is present, but the cell’s machinery silences or rewrites how that code is used. The episode centers on a new Nature Genetics paper, “Non-Mendelian inheritance of DNA methylation patterns in mice,” which suggests that non-Mendelian epigenetic inheritance may be more widespread in mammals than previously understood. The conversation also covers why Oxford Nanopore sequencing made this kind of analysis possible, why methylation patterns can be hard to trace across generations, and what all of this could mean for disease risk, drug response, sex differences, evolution, and the long-running nature-versus-nurture debate. Summary Mendel’s rules — how pea plants, true-breeding lines, dominant and recessive traits, and Punnett squares gave us the first mathematical laws of inheritance. The first cracks in Mendel — how chromosomes, fruit flies, sex-linked traits, and linked genes showed that inheritance is more complicated than independent assortment. DNA as hardware, epigenetics as software — why having a gene is not the same thing as expressing it, and how methylation and chromatin packaging can silence parts of the genome. Paramutation — how one allele can change the expression state of another allele across generations, creating inheritance patterns that do not follow standard Mendelian expectations. Oxford Nanopore and the technology shift — why long-read sequencing and direct methylation detection make it possible to trace epigenetic marks back to the parent they came from. The mouse methylation paper — how researchers used collaborative cross mice to show that most methylation inheritance looks Mendelian, but a meaningful fraction appears to follow stranger non-Mendelian rules. Why it matters — potential implications for clinical genetics, disease risk, drug efficacy, sex-specific biology, and the relationship between nature and nurture. Support the show Donate: FFPod.com/donate Follow: @FFPod on X / Instagram / TikTok / Facebook

Speaker names marked ? are inferred from speaking time and the show’s known hosts — they are not voice-verified.

• 0:00Lester Nare?

  And not everything is about genetics, meaning not everything is about the hardware of the DNA. It's also about the sort of software, which is the epigenetics part of it. They've done a thorough analysis of the genome and found that up to 7% of the DNA obeys these kinds of different weird rules. 7%, that's 1 in 14. So 1 in 14 genes, that's not a joke. Hello, internet. This is your captain speaking, Lester Nare. And breaking news, the Candyman is home. Ooh, ow, ooh. What is that? Someone call the dentist. Is that a cavity? We are back here in studio by popular demand after months

• 0:44Lester Nare?

  with just me and my back with our resident PhD, Krishna Choudhary. Welcome back, good sir. How are you?

• 0:53Krishna Choudhary?

  How's it going, man? I have barely had any sleep over the past two months. But you've been doing a great job with all of your content. And now we are back in the studio. It's been, it's been crazy. It's, it's been really crazy. And I remember like, the baby came, you know, for, for, for our viewers, the baby came two weeks early. And the day that it happened, we were supposed to record two additional episodes in preparation for my paternity break. And I texted you from the hospital like, hey, it's today, abort mission.

• 1:27Lester Nare?

  Abort mission.

• 1:28Krishna Choudhary?

  We're gonna, we're gonna just roll with it. But I'm glad to be back. Seems I've missed quite a bit. Quite a bit has happened in the world. The most important thing that happened is probably Lewis Hamilton won his first race with Ferrari. Finally, the promise of Lewis Hamilton has paid off for Ferrari. So I'm wearing my Ferrari gear for that.

• 1:52Lester Nare?

  We are very grateful to have Krishna back here in the promised land at FFP Nation. And in honor of you entering fatherhood, today's deep dive is going to be about non-Mendelian epigenetic inheritance. And so we're going to learn about the science from the ground up today, because this is from First Principles.

• 2:31Krishna Choudhary?

  So I was recently blessed with my first child and questions of inheritance are very forward in my mind, right? Questions that every person of color asks like, "How dark is the baby gonna be?" You know, among other things, like what color are his eyes gonna be? Is he gonna be an athlete? But you know, that's one of the big ones. If anyone's out there who's brown, they know, they know what I'm talking about. And so for most of the traits that are out there, you can use rules that were established 160 years ago by this guy called Gregor Mendel. And these traits follow Mendelian laws of inheritance. This is the stuff that you learn in like AP Bio, if you ever took AP Bio in high school. The rules are pretty simple and we're gonna go over them.

• 3:16Krishna Choudhary?

  There's like these dominant genes, recessive genes, some... And by and large, those rules work. But as with all things in biology, there are always exceptions. And genetics is something that has a bunch of exceptions because you're, you know, down to the molecular level and there's always weird stuff happening. And not everything is about genetics, meaning not everything is about the hardware of the DNA. It's also about the sort of software, which is the epigenetics part of things. This is a very dynamic package. This is how the DNA is wrapped around inside the cell, how much the DNA has access to protein-making machinery, things like that.

• 4:00Krishna Choudhary?

  And those things can change much more quickly than the actual genetic sequence itself. And we're only just starting to get into studying that higher level of genetic machinery, right? And... It turns out that those traits can also be inherited. Like this software package on top of the hardware is something that is also passed down. And we're just starting to understand that. There's exceptions for how it gets passed down. Most of the time, again, it follows Mendelian rules, but sometimes it doesn't. And that's what this story is about. There's a new paper out of Johns Hopkins University and Texas A and M that is documenting a new type of non-Mendelian inheritance of epigenetics in mammals.

• 4:45Krishna Choudhary?

  And it's showing that this genetics is far stranger and far more dynamic and far more interesting than I think Mendel could ever have imagined 160 years ago. And so like, why, why is this a big deal, right? Obviously, anything related to genetics is a big deal because genetics is like the blueprint of life, is the blueprint for who we are. But it touches on everything from like, why identical twins can have different disease outcomes, right? Identical twins have the same exact DNA, but sometimes one twin is going to have one disease and the other twin is going to be just fine. That's because the software package on top is different, right? Diseases can skip generations. That's something that happens to do with epigenetics.

• 5:29Krishna Choudhary?

  And sometimes the same gene variant can be benign in one person. If you do the genetic sequencing of two individuals, they'll have the same gene variant, but one individual will get the disease and the other one won't. Again, that has to do with the software on top. So this paper marks like a major shift in how we think about epigenetic inheritance, especially in mammals. And it shows that this is not actually an exception. That's the big part, okay? They've done a thorough analysis of the genome and found that up to 7% of the DNA obeys these kinds of different weird rules. 7%, that's 1 in 14. So 1 in 14 genes, that's not a joke.

• 6:11Lester Nare?

  That's pretty statistically significant, as we like to say.

• 6:14Krishna Choudhary?

  Yes, exactly. Like, that's something that you do have to worry about if we want to like, get a really comprehensive idea of how genetics affects outcomes and all that stuff. So, we're living through kind of a quiet revolution in the understanding of heredity. And in this episode, what I want to do is go through how it all started 200 years ago. We're gonna start with Mendel, then I'm gonna take you through some of the history of the field, and then why this particular paper is happening now and not 10 years ago or 20 years ago. There's some key technological advancements that have happened in recent years that is enabling this kind of analysis, and it's very, very cool.

• 6:50Lester Nare?

  There's an interesting, there's a mutual friend that we have that had been doing work around some of this epigenetic stuff, you know, through grant funding through the NHS. And it, what is, I think this is very timely because there's been a lot of chatter in social media around, you know, this idea of generational trauma.

• 7:10Krishna Choudhary?

  Yeah.

• 7:10Lester Nare?

  That's sort of a non-scientific term.

• 7:13Krishna Choudhary?

  Yeah.

• 7:13Lester Nare?

  And this, the idea that there is an impact on outcomes that are related to these concepts of like generational trauma.

• 7:21Krishna Choudhary?

  Yeah.

• 7:21Lester Nare?

  And I think this is gonna start to brush up against some of these social conversations that have been happening. And I'm super curious to understand, you know, particularly your point about why now?

• 7:32Krishna Choudhary?

  Yeah.

• 7:32Lester Nare?

  Are we able to start to get a better idea of what's going on on the epigenetic layer?

• 7:36Krishna Choudhary?

  Yes, that, that part is really, really cool. The technology, the biotechnology there is really, really cool. And what you're alluding to is the fact that, you know, trauma is something that is not going to affect the genetic layer, but it is going to affect the epigenetic layer. Because the epigenetic layer is the one that is dynamic and changes throughout the life of an organism. We, by and large, have the DNA that we were born with, okay? Unless, you know, if you look at tumors, there's a lot of mutations there. And tumor cells have very different DNA compared to normal benign cells, right? But epigenetically, the reason why this cell is a skin cell, and this cell is an eye cell, and the, the cells inside my brain are neurons,

• 8:20Krishna Choudhary?

  that has to do with epigenetics, right? Because- The cell is making a choice, what part of the gene to read out from and what part to ignore. That's the software level that I'm talking about. So it's extremely important for us to understand, right? So we're gonna start as always on this podcast. Guys, I'm, I might be a little rusty. It's been two months of, as I said, barely any sleep. So just bear with me if I'm a little slow, but we're gonna start as always with the history.

• 8:48Lester Nare?

  Yes.

• 8:49Krishna Choudhary?

  We're gonna go back. The story of genetics probably begins in the 160 years ago, improbably in a monastery. Okay, Gregor Johann Mendel.

• 9:02Lester Nare?

  Johann.

• 9:03Krishna Choudhary?

  He was an Augustinian monk who spent eight years cross breeding pea plants. And the, the green circle, you see the guy in the green circle in the back row? That's Mendel, along with all of his other monks in, in his monastery. He was cross breeding pea plants for like eight years. He tracked 29,000 plants across multiple generations.

• 9:25Lester Nare?

  That's huge.

• 9:26Krishna Choudhary?

  It's huge. This was, this was his hobby and he took it very seriously. He's the first guy to really do large scale statistical analysis of gardening effectively.

• 9:39Lester Nare?

  Okay, he was the first green thumb.

• 9:41Krishna Choudhary?

  Yeah, yeah, yeah, yeah. He, before Zach Galifianakis had the Netflix show about gardening, which by the way, a good friend of ours, Trevor, is the editor on that show. So go check it out on Netflix. It's a really good show, actually. So you can see his garden today, actually, the Mendel's garden. You can see it in Brno, which is currently in the Czech Republic, or I think now it's called Čečia. If, if I'm watching the World Cup correctly.

• 10:08Lester Nare?

  I've heard it Čečia.

• 10:09Krishna Choudhary?

  Čečia, yeah. So. But it used to be called the Czech Republic. That's what I'm comfortable with, but Čečia, Čečia, one of those. You can actually go see the, the garden and see the, the beds where he was planting the pea plants, which I think is really cool. One day, when FFP Pod goes on a field trip, that is definitely a place we're gonna visit. It's the birthplace, that garden is the birthplace of genetics, right? I think that's so cool. So why peas, first of all? Okay, this is something that we talk about a lot on this podcast and is a staple for the biomedical research community, which is model organisms, right? You have to choose the organism that you want to, that you want to study as a system.

• 10:52Krishna Choudhary?

  And you have to make that choice very deliberately for very specific reasons. Mendel is one of the first guys to do this. He chose peas because the one, the garden pea is actually pretty easy to grow. You don't have to worry about it too much.

• 11:05Lester Nare?

  Yep.

• 11:06Krishna Choudhary?

  It's has easily observable contrasting traits. These are the traits that he was studying. For example, is the pea round or wrinkled? That's a binary. You can look at the thing and there's no middle ground. It's either round or it's wrinkled, right? When you cut up the pea, is it yellow or green inside? The flower, is it white or is it purple? Like, these are all binary things that there's no, you know, when you, when you're trying to do statistical analysis by hand, right? You don't, you don't have like computer vision nonsense, right? And you, you just got a notebook. You're, you're, you're just making tally marks. So you need really easily identifiable traits that are in binary. The pea plant has seven of these, which is really nice. Okay?

• 11:50Lester Nare?

  So the, the idea of what you're saying is you want to have the fewest amount of variables to sort of control for. One, from at least in this time period from a management, it's like a management challenge.

• 11:59Krishna Choudhary?

  Exactly.

• 12:00Lester Nare?

  Uh, but two, there, there's less to deal with in terms of judging outcomes.

• 12:04Krishna Choudhary?

  Yes, exactly. There's no like, um, subjectivity in what the offspring of this and this was, right? You can just be like, okay, I bred round and wrinkled and I got this many wrinkled, this many round. And I can just make the tally marks, right? The other big thing about pea plants is they self fertilize. So that means that Mendel can really easily control crosses by, you can manually just transfer pollen. You can like, take like a Q tip or I, I, I think he used a paintbrush at the time. He would take the pollen from one paintbrush and, and put it in the stigma of the other one to like crossbreed manually. And I think we've got a, we've got a photo of that in the next photo, photo five.

• 12:45Krishna Choudhary?

  This is, this is how he did it. He would cut the, the stamen, which is the male part. Or am I, no, no, the pollen is the male part. So he would cut the pollen part and then he would use a brush to take the, the sperm effectively and put it in the female part of the. of the flower.

• 13:02Lester Nare?

  So this was it was a controlled breeding.

• 13:04Krishna Choudhary?

  Yes.

• 13:05Lester Nare?

  Because the also again, the the surface, the surface area of how you would do so was was very discreet.

• 13:11Krishna Choudhary?

  Yeah, exactly. It's super easy to control, right? And the first thing he does is he develops true breeding lines. What that means is he's going to self pollinate a bunch of pea plants, which pea plants are totally chill with. They don't care about like, oh, lack of genetic diversity, all that. They're actually, that's one of the reasons why it's a good thing to use pea plants. And you keep self pollinating until all of the offspring are something called true breeding. Meaning they always produce the same offspring identical to the parent. It's like you're making clones.

• 13:41Lester Nare?

  Yep.

• 13:41Krishna Choudhary?

  Over and over. So now what you do is you you're starting out with a clean slate.

• 13:45Lester Nare?

  Yes.

• 13:45Krishna Choudhary?

  Right? There's there's no genetic variability in this plant. And it's gametes and it's sperm and the the egg, right? It's like if you if I were to take the sperm and the egg of this and combine it, I would just get the same thing again. So it's like a a feedback cycle and completely clean, right? For example, offspring of purple flower times purple flower, always going to give me purple flower at this point. That's why it's called true breeding. Okay?

• 14:11Lester Nare?

  So the idea is we we have everyone is effectively genetically.

• 14:15Krishna Choudhary?

  Mm hmm.

• 14:15Lester Nare?

  The same.

• 14:15Krishna Choudhary?

  Yeah, and there's no nonsense in the in the like from one generation to the next. I'm not getting weird like effects.

• 14:24Lester Nare?

  It it's it's not just that this line of the generation is the same. It's that subsequent and prior to some number of generations forward and back.

• 14:33Krishna Choudhary?

  Mm hmm.

• 14:34Lester Nare?

  Are consistently.

• 14:35Krishna Choudhary?

  Yes.

• 14:35Lester Nare?

  Coming in as the same. So you're also removing the idea that, oh, this one was, but the next one might not.

• 14:39Krishna Choudhary?

  Yeah, yeah, exactly. So now when I do crosses in, I take the parent generation, the pea, and I do a cross. Let's say from a purple and a white, I'm going to get some weird effects, right?

• 14:49Lester Nare?

  Yeah.

• 14:49Krishna Choudhary?

  But I know that's not from the purple.

• 14:52Lester Nare?

  Yes.

• 14:52Krishna Choudhary?

  Doing its own thing or the white doing its own thing. I know it's because of the interaction of these two. Does that make sense?

• 14:58Lester Nare?

  Hundred percent.

• 14:58Krishna Choudhary?

  That's why you got to start with that true breeding.

• 15:00Lester Nare?

  This is a good, this is a really important point, which is we're we're creating the canvas. From which we're going to test in a way that removes any prior. A muddying of the water.

• 15:11Krishna Choudhary?

  Yes.

• 15:12Lester Nare?

  Uh, so that we can look downstream and say we had a clean foundation with which we're building from.

• 15:17Krishna Choudhary?

  Exactly, yeah. And now I can isolate the effect to an interaction between two individuals that have different genetics.

• 15:24Lester Nare?

  That makes sense.

• 15:25Krishna Choudhary?

  Okay. Here's what he observed. Okay, so he takes the parent generation. Let's, let's, let's just talk about the flower color right now. There's seven other traits that he could look at, but they all actually obeyed these rules. But it's nice to talk about flower color because it looks good on TV. Okay? So I'm gonna take a true breeding purple and a true breeding white plant. I'm gonna breed those two. The first generation, that's the F1, the first filial generation is, is how, how he put it. That one has all purple. Immediately you notice something weird. You're not getting a mix. Right? You're not getting, um, like lighter purple, like pink.

• 16:02Lester Nare?

  It's not a blend.

• 16:03Krishna Choudhary?

  It's not a blend.

• 16:03Lester Nare?

  It's not a mix of half and half.

• 16:05Krishna Choudhary?

  It's not even half and half. It's fully all purple. Okay? First thing that's kinda weird. Okay? It's almost as if the, the first generation is also true breeding. Right? So you're like, hey, so is the first, is the white just like doing nothing?

• 16:21Lester Nare?

  Right. Is everything coming from one?

• 16:23Krishna Choudhary?

  Is everything just coming from one? What's going on? That's when you take, do the second cross. So you do a second filial F2 generation where you take two of the first generation ones and you cross them. And now you get something weird. You get the white back, but the ratio of purple to white is always, and I mean always, three to one. In his notebooks.

• 16:45Lester Nare?

  Okay.

• 16:46Krishna Choudhary?

  He's got 29,000 plants that he's doing this with, and it's almost always three to one. Like statistically, that's the ratio that he's getting. Okay?

• 16:55Lester Nare?

  I think I see it. This is.

• 16:57Krishna Choudhary?

  Very weird.

• 16:57Lester Nare?

  It's very, so and with no context and no.

• 16:59Krishna Choudhary?

  Yeah, yeah, yeah. Now it's like trivial.

• 17:01Lester Nare?

  Right, but it's, it's, why did we, we had two different, the first generation, all only similar to one of the two parents, but the second generation that was bred from that F1 generation where everything was the same as one parent, is a three to one ratio of one parent to another.

• 17:17Krishna Choudhary?

  Yeah.

• 17:18Lester Nare?

  Almost all of the time.

• 17:19Krishna Choudhary?

  Almost all of the time. Okay? So let's try to figure out what, how this would happen. Okay?

• 17:26Krishna Choudhary?

  Mendel doesn't know.

• 17:27Lester Nare?

  Right.

• 17:27Krishna Choudhary?

  Okay. Mendel doesn't know anything about genes. He doesn't know anything about chromosomes. He just knows plants are doing this. Okay? So he takes a purely sort of empirical approach, which is I'm just gonna describe the mathematics as I see it. Okay, I wanna make up some rules that are just math rules, okay, about what happens. First thing he figures out, and what we've already seen, is the principle of dominance. There's two traits. One of them is going to dominate over the other.

• 17:53Lester Nare?

  Yeah.

• 17:53Krishna Choudhary?

  Okay, in this case that we saw, it was the purple.

• 17:57Lester Nare?

  Yes.

• 17:57Krishna Choudhary?

  The purple trait, which now we call an allele. There's two different types of alleles, the purple and the white. And the purple allele is going to dominate over the white allele, which we'll call recessive. So there's dominant and recessive. That's the first thing you establish. Second is something that he establishes called the law of segregation. This is the segregation of traits, okay? What he says is, there's actually two copies of an allele that every individual has. And if I have a true breeding plant, let's say, let's say the, the, the, the trait that we're looking for is the color of the flower. And we're gonna denote the type of allele by a capital A if it's dominant,

• 18:42Krishna Choudhary?

  and a lowercase a if it's recessive, okay? Now, if I have something that's true breeding, that means that I have two copies of the same dominant allele. Capital A, capital A. That's the one on the left up. And then the white true breeding is gonna be lowercase a, lowercase a, or recessive, recessive, okay? Now, when I cross them, there's gonna be four different ways to choose the A and the A, right? I can choose the first capital A and either of the two lower cases, or the second capital A and all. That's four total, but every single time, I'm gonna get a capital A and a lowercase a. So that first generation is gonna have at least one dominant. Copy, capital A, all the time. Every single one is gonna have a capital A and a lowercase a.

• 19:27Krishna Choudhary?

  And because the capital A is present, the dominant is present, I'm gonna get the dominant phenotype, and the thing is gonna be purple. But now, let's take the first generation, that capital A lowercase a, which we're gonna call heterozygous, because there's hetero, there's two different copies.

• 19:44Lester Nare?

  Right, one of each one.

• 19:45Krishna Choudhary?

  One of each, yeah, yeah. Compared to homozygous, which is what we had in the parent generation, that true breeding is now what we call homozygous. So if we take two heterozygous parents, and we cross them, now, combinatorically, I'm gonna get three offspring that have at least a capital A. There's actually gonna be one that's kinda like the true breeding parent.

• 20:08Lester Nare?

  Yes.

• 20:09Krishna Choudhary?

  In the beginning, the capital A, capital A, right?

• 20:10Lester Nare?

  That's the one we have in this top left.

• 20:12Krishna Choudhary?

  Yeah, in the, in the, in the square, those are called Punnett squares now. But the top left, that's capital A, capital A, that's gonna be purple. The two on the off diagonal, that's gonna have a capital A and a lowercase a. But because there's at least one, I'm still gonna get purple. And only one out of the four is gonna have homozygous recessive, lowercase a, lowercase a, and that's what's gonna be white.

• 20:37Lester Nare?

  This, this is interesting, and I think a key point here is, is we had the pure, the, the pure breed generation at first, two dominants from one, the purple, two recessives from the white. The first generation, because you always are gonna have that dominant from the purple, from the one side, you're always ever gonna get this dominant recessive combo.

• 20:56Krishna Choudhary?

  Yeah.

• 20:56Lester Nare?

  And so the reason why that first gen, first gen always had a dominant.

• 20:59Krishna Choudhary?

  Always has dominant, and so that's why you, you don't ever see the white.

• 21:03Lester Nare?

  Right, because it's always being basically overrun by, the recessive white is being overrun by the, the dominant. The thing that, the, where you get the diversity of color, begins to arise.

• 21:17Lester Nare?

  When you'd have two dominant recessive as the parent.

• 21:21Krishna Choudhary?

  Yeah, the heterozygous.

• 21:22Lester Nare?

  The heterozygous pair. And that's finally when you start to see from the original P1.

• 21:28Krishna Choudhary?

  Mm hmm.

• 21:28Lester Nare?

  The recessive begin to appear, but also from the the math you brought up earlier. It makes sense that only one, it's always gonna be three to one.

• 21:37Krishna Choudhary?

  Yeah.

• 21:37Lester Nare?

  Because of the way that it's this dynamic pair from each.

• 21:40Krishna Choudhary?

  Yes, exactly. It's always gonna be three to one. So this is an empirical rule that he comes up with. It makes sense. And the other nice thing about this kind of mathematics is it explains something else, which is the law of independent assortment. What he did, and this is something that we're seeing actually in fruit flies, because the particular visual that I found was for fruit flies, but he also did this for pea plants as well. Okay? What you can do is you can take two true breeding, you can you can take a true breeding parent generation with different traits.

• 22:21Krishna Choudhary?

  In a pea plant, you could say it's always purple and it's always tall. And I'm gonna cross that with always white, always short. Okay? So now I have homozygous for two traits in my parent. I'm gonna get some offspring that are, again, always purple, always tall, because the tall part is gonna work the same way as the purple part. And so everyone's gonna be the same. But now I do a cross between those guys. Now, if you just do the mathematics, there's gonna be 16 different choices instead of four, because you're doing four by four across. And the mathematics is gonna be such that I'm gonna get a ratio of nine to three to three to one. Okay?

• 23:02Krishna Choudhary?

  Nine being I'm gonna get the dominant parts of both. Three being I'm gonna get the dominant of one, the recessive of the other. The other three being I'm gonna get the dominant of the second one, recessive of the first one. And only one out of 16, I'm gonna recover that first generation of like recessive recessive. Okay?

• 23:22Lester Nare?

  It's basically, it scales as you as you get to more traits here, the the the ratio of distribution effectively scales.

• 23:29Krishna Choudhary?

  Exactly.

• 23:29Lester Nare?

  Accordingly.

• 23:30Krishna Choudhary?

  Yeah. And in this particular one, we're looking at fruit flies where we're seeing eye color and body color. Okay? And eye color, red is dominant, and body color, brown is dominant. Black. For both is recessive.

• 23:46Lester Nare?

  Eye color and body color.

• 23:47Krishna Choudhary?

  And so we're seeing nine to three to three to one. And you can go through the the Punnett square there and figure out how each of the alleles was matched. And you can convince yourself that this is the case.

• 23:56Lester Nare?

  That makes total sense.

• 23:57Krishna Choudhary?

  Okay, this is called the independent assortment law, meaning that the two different traits independently do combinatorics. They're not like related to one another. It's not like the eye color goes with body color is like correlated in some way. So that that was his thing. Okay, but these are Mendel's laws. He presented these findings in 1865, published in 1866, experiments on plant hybrids. The response complete silence. Papers ignored. It's cited a handful of times over the next 35 years. He died in 1884, unknown as a scientist.

• 24:36Lester Nare?

  Terrible.

• 24:37Krishna Choudhary?

  And his discoveries were buried in some obscure journal.

• 24:41Lester Nare?

  Terrible.

• 24:42Krishna Choudhary?

  Okay, 35 years later, we've got three botanists who start doing the same thing. Okay. Hugo de Vries in the Netherlands, Karl Korrens in Germany, and Eric von Schermark in Austria. And they independently figure all of this out. And then as they're deep diving into the literature, because the first thing you do is has someone else done it? You know, in the modern day, there's a joke in academia. There's always like a Zhang at all that's done it, that's done it before. So back then they're doing the same thing. They're trying to find like, has someone else done it? And all three of them actually find Mendel's old paper in the literature. And they realize, so these are the three, and they rediscover Mendel's work in 1900. And they're like, well, somebody beat us to the punch. And this, this is now colloquially known as the rediscovery of Mendel.

• 25:28Krishna Choudhary?

  And it launched modern genetics because now they're like, okay, so there is some kind of level of understanding that we can figure out. Right? Now, the next focus.

• 25:39Krishna Choudhary?

  Is always, how do we go from empirical math rules to some kind of mechanistic understanding?

• 25:44Lester Nare?

  Right.

• 25:45Krishna Choudhary?

  Right? What is actually happening?

• 25:46Lester Nare?

  Right.

• 25:47Krishna Choudhary?

  In the organism that is doing this?

• 25:49Lester Nare?

  Right, so we can predict, but we don't know how it works.

• 25:51Krishna Choudhary?

  Yeah, exactly. Okay, so first, first question, natural question, where are the alleles?

• 25:58Lester Nare?

  Yeah.

• 25:58Krishna Choudhary?

  Right? You're saying there's these two types of alleles. Well, and it seems like there's like actual stuff, right? That's like moving, like, and like, there's like physically two thingies that like get independently, that come out and then they recombine and stuff like that. But if that's the case, there should be something I can find inside organisms that is an allele, right? So Walter Sutton, he's a graduate student at Columbia University at the time, and he proposes in 1902, 1903, that these alleles are located on chromosomes, okay? He was actually working on grasshoppers at the time. And in grasshoppers, he could stain the chromosomes.

• 26:39Krishna Choudhary?

  And what he figured was that there's these threadlight structures called chromosomes, and they come in pairs. So that's interesting.

• 26:47Lester Nare?

  That's interesting.

• 26:48Krishna Choudhary?

  Because the alleles come in pairs. And they separate during cell division. And if you, if you look at the gametes, which are the sperm and the egg, they each get half and half. So he's like, coincidence? I think not.

• 27:01Lester Nare?

  Where there's smoke, there's fire.

• 27:02Krishna Choudhary?

  Yes, he's like, he's like, this could be the physical basis for Mendelian law of heredity. People are still doubting it, because it's, it's coincidence, okay? You could be missing something that also goes half and half.

• 27:16Lester Nare?

  Just because it has similar behavior

• 27:19Krishna Choudhary?

  Yeah.

• 27:19Lester Nare?

  does not mean it's not a causal link.

• 27:21Krishna Choudhary?

  Yeah, it's not a causal link. There's, there's a, there's a correlation, but in order to establish causation, you gotta dig deeper, right? And this is where our guy, Thomas Hunt Morgan, comes in, also at Columbia University. Early 1900s, Columbia was doing

• 27:33Lester Nare?

  On the board.

• 27:34Krishna Choudhary?

  amazing with, um, just like early biology, like even before DNA, before, you know, molecular biology, just like this kind of, this kind of early rudimentary work. So Thomas Hunt Morgan at Columbia University, he starts using the Drosophila. Fruit fly. He's the one who actually establishes the fruit fly as the model organism. Nowadays, the fruit fly is used in neuroscience, research, development, genetics, all sorts of things. He's the first guy to be like, let's do, let's, let's go to town with the fruit fly.

• 28:05Lester Nare?

  So, so Mendel was the pea plant. And then Morgan now moved us into a more complex biological organism that is a better model organism.

• 28:13Krishna Choudhary?

  Yeah, that's an animal so it can like learn and stuff.

• 28:16Lester Nare?

  Right.

• 28:16Krishna Choudhary?

  Like, like it sleeps, so you can do, like, there's so many more things you can do with a drosophila, right? And Morgan's team discovers that there's some traits that are sex-linked, like red eye color. Here's what I mean by that. So, um, what he does is he finds a female with red eyes, and then a male with white eyes, and when they have offspring, all of the kids have red eyes. So you could just be like, oh, red eyes, like this, like, uh, you know, um, homozygous type dominant trait or whatever. Now, let's take the female again that has red eyes. So in this case, you're gonna, this is gonna be a heterozygous female, right? Cause the male had a white eye.

• 28:59Krishna Choudhary?

  So this female is gonna have, um, one red eye allele and one white eye allele. And now I'm gonna cross that with a red-eyed male. Okay?

• 29:09Lester Nare?

  Mm-hmm.

• 29:10Krishna Choudhary?

  So the male, and, and we've done a true breeding with the male to make sure that the, the male is fully red. When we cross it, most of the offspring, in fact, every single one of the female offsprings has red eyes. But the males are half and half. They're not even doing three to one.

• 29:31Lester Nare?

  Right.

• 29:32Krishna Choudhary?

  Now they're doing half and half.

• 29:33Lester Nare?

  Right.

• 29:34Krishna Choudhary?

  And he identifies that the red eye allele is actually on the sex chromosome. And the way sex chromosomes work is, we only get one if we're male, right? The Y chromosome isn't really a chromosome, if I'm completely honest, right? We have X and Y, the Y, like, if you look at the two side by side, the X chromosome is this big and has a bunch of extremely important genes. The Y chromosome has absolutely like, nothing, right? It's like, it's, it's in, it's really tiny. And it's, in fact, it's so tiny that there's, it's like, the way the chromosome is like tied up, um, there's a, there's a little centromere that like holds the two strands together. And the, the Y chromosome is so tiny that there's very little room for-

• 30:19Krishna Choudhary?

  Genetic recombination. And so that's why like the Y chromosome, like your Y chromosome is identical to your dad's Y chromosome, to his dad's, to his dad's for like 10 generations. Because it's so small that physically you can't like mix things. Anyways, so the, the point is he identified a, a particular chromosome with that trait.

• 30:41Lester Nare?

  Right.

• 30:42Krishna Choudhary?

  And the reason why males are coming up 50 50 is because they only get one X chromosome from the mom. Right? So either you're going to get the red one or you're going to get the, the white one. Right?

• 30:52Lester Nare?

  And that's it.

• 30:53Krishna Choudhary?

  The females, on the other hand, they're getting one from the mom and one from the dad. And the dad is guaranteed to be red. So even if I get the white one from the mom, the dad is guaranteed to be red. So all of the female offspring are going to have red eye color.

• 31:05Lester Nare?

  That's fascinating. Yeah. Yeah. And so we've added another layer here.

• 31:09Krishna Choudhary?

  Yes.

• 31:09Lester Nare?

  To, because before we were saying the traits were not correlated.

• 31:13Krishna Choudhary?

  Yeah.

• 31:13Lester Nare?

  Uh, you know, color, size.

• 31:15Krishna Choudhary?

  Yeah.

• 31:16Lester Nare?

  But now with sex chromosomes.

• 31:18Krishna Choudhary?

  Yeah. Now it's like if they're on the sex chromosome, then the math is a bit different. And actually the correlated part is the second thing that Thomas Hunt Morgan did, which is he showed that some of the traits happened to be inherited together. Okay. So, you know, before I was, I was showing you about how body color and eye color on the drosophila.

• 31:37Lester Nare?

  Yes.

• 31:38Krishna Choudhary?

  They were independently assorted.

• 31:39Lester Nare?

  Yes.

• 31:39Krishna Choudhary?

  But there's some that if I have red and some other trait, those are going to go together. Okay. Why would they go together? Well, now it's obvious because if they're on the chromosome, if they're on the same chromosome, then they're coming in a package. Right? And so if, if, if they're coming in a package, you're going to have this correlation and that violates Mendel's law of independent assortment.

• 32:02Lester Nare?

  If I order something from Amazon, we thought it was going to come in two separate packages, which could have two different delivery days.

• 32:09Krishna Choudhary?

  Yeah. Yeah.

• 32:09Lester Nare?

  But it actually came in a big box.

• 32:11Krishna Choudhary?

  Yeah.

• 32:11Lester Nare?

  Two little boxes in it.

• 32:12Krishna Choudhary?

  Yeah.

• 32:12Lester Nare?

  And they were shipped at the same time.

• 32:14Krishna Choudhary?

  Yeah.

• 32:14Lester Nare?

  Very bad crude analogy.

• 32:15Krishna Choudhary?

  Yeah, but no, but that's exactly, that's exactly what's happening. Right? And this, this is actually the first major empirical crack to Mendel's.

• 32:24Krishna Choudhary?

  Laws. Okay, this is the first time where it's like, no, Mendel was actually wrong. But also, he did, it's fine. He had no idea what, you know.

• 32:32Lester Nare?

  He did it in a cave with a box of grass.

• 32:34Krishna Choudhary?

  Yeah, exactly. Yeah, yeah, yeah. So it's, it's fine. Uh, Morgan actually won the Nobel Prize in Physiology. He's one of the first, um, Americans to win the Nobel Prize in Physiology and Medicine. And side note about, um, Thomas Morgan, he's quite a character. So he's the nephew of Confederate General John Hunt Morgan, who, who got his butt kicked somewhere in the north. And then, um, the great grandson of Francis Scott Key, who is the, um, author of the Star Spangled Banner.

• 33:00Lester Nare?

  No way.

• 33:01Krishna Choudhary?

  Yeah, this guy's quite interesting. So he established something called the Fly Room in Columbia that became kind of this legendary place where scientists from all over the world would come and hang out and learn about how to take care of fruit flies, how to make sure that, you know, the crossing is the same. Because for Mendel, it's like pretty easy. You just cut the thing, you take a paintbrush. Here, you gotta like make the flies mate and stuff, right? So it's a bit more of a process, but there's a lot more room to, to work with scientifically. He became, he became this legendary place, um, established the fruit fly as a model organism. And, you know, the lineage of that is seen in every single university

• 33:45Krishna Choudhary?

  that does serious biomedical research. They have a fly lab somewhere doing something.

• 33:50Lester Nare?

  Isn't it incredible, something that people in there in their house are trying to look for ways to make these things go away?

• 33:55Krishna Choudhary?

  Yeah.

• 33:55Lester Nare?

  Not specifically the fruit fly, but just a fly in general.

• 33:57Krishna Choudhary?

  Yeah, fruit flies are a bit, you know, they're big.

• 33:59Lester Nare?

  And, and it is a cornerstone of us getting a greater understanding, not only of our, our own lives as humans, but the lives of all animals on the planet. It's just.

• 34:10Krishna Choudhary?

  And it's still going.

• 34:11Lester Nare?

  And it's right, it's still happening.

• 34:12Krishna Choudhary?

  It's still happening. There's still so much we can learn from the fruit, fruit fly. It's pretty insane. Another cool thing about Thomas Hunt Morgan is he went on to found the Department of Biology at Caltech when Caltech started in the 1920s. Caltech was this insane place because like, they, so they hired like the all-stars. Like they just poached all of the big, because they just got a bunch of money. Um, I believe from the, um, the Rockefeller Foundation.

• 34:43Krishna Choudhary?

  Either them or Carnegie, they're whatever, whatever, they're dead, but like if they were alive, they'd be pissed that I was mixing them up. But one of them gave a lot of money and they just, so George Hale, who was kind of the founder at the time, he, he took this Pasadena Community College type thing and was like, all right, we're just gonna hire the biggest names. It's kind of like when you start like a new team or something, you just like hire the best coach. If you, if you got the money, right? You hire the best coach, you hire like Erling Haaland or whatever.

• 35:10Lester Nare?

  The, the perfect analogy for this in, in soccer and football is PSG a couple of years ago.

• 35:16Krishna Choudhary?

  Oh, really?

• 35:16Lester Nare?

  The French league has been viewed for a while as being sort of like Farmer's League. They got Neymar, they got Messi, uh, uh, they got Mbappe, Donnarumma, a bunch of other players. They just got like literally all the best players in the world.

• 35:27Krishna Choudhary?

  Yeah, at the same time, right?

• 35:29Lester Nare?

  At the same time, yeah.

• 35:29Krishna Choudhary?

  And that's what Caltech did.

• 35:30Lester Nare?

  That's what they did.

• 35:31Krishna Choudhary?

  In, in the 1920s, they got Milliken for physics, they got, um, Thomas Hunt Morgan for biology. It was just an insane place to like start out like that, you know?

• 35:41Lester Nare?

  I will note, it's sometime, it doesn't always work because it did not work for PSG. They had that, they couldn't win the Champions League.

• 35:48Krishna Choudhary?

  Oh, they couldn't?

• 35:49Lester Nare?

  And then Messi and Mbappe left and, uh, Neymar left and then they won the Champions League.

• 35:54Krishna Choudhary?

  Oh, that's hilarious.

• 35:55Lester Nare?

  So it, it can work.

• 35:57Krishna Choudhary?

  It can work, yeah.

• 35:58Lester Nare?

  It worked in Caltech's case.

• 35:59Krishna Choudhary?

  Yeah, yeah, certainly, because they just, they, they became like a top institution immediately, which usually it takes years of work to do that, right? Um, and his students have won the Nobel Prize too, like, uh, John Howard Northrop, he's a Berkeley professor, 1946 Chemistry Nobel for Isolation and Crystallization of Enzymes and Hermann Miller won the 1946 Nobel Prize in Medicine for X-rays to make mutations. So the big lineage from Thomas Hunt Morgan.

• 36:26Lester Nare?

  Huge legacy.

• 36:26Krishna Choudhary?

  Anyways, after Morgan, then you have the modern synthesis of genetics. So this is, we've covered this in a previous episode, um, with James Watson and his discovery of DNA, but, um, Avery, McLeod and McCarty, they showed in 1944 that genes are from DNA and then Watson and Crick together crucially with.

• 36:46Krishna Choudhary?

  Evidence from Rosalind Franklin discovered the helical structure of DNA and how the sequence of base pairs is really how genes work.

• 36:55Lester Nare?

  We had a huge deep dive on this, particularly the work of Rosalind Franklin, which in part was not included in a lot of the accolades that came afterwards, has since been rectified, at least slightly.

• 37:07Krishna Choudhary?

  At least slightly.

• 37:08Lester Nare?

  At least slightly in the modern era. It's a great deep dive if you haven't watched it already, because that also has a great, the science is great, but the palace intrigue in how the university ecosystem worked and was being established, not only in the UK but in the US at the time, was really, really fascinating.

• 37:26Krishna Choudhary?

  Yeah, and just how many shenanigans.

• 37:29Lester Nare?

  So much, so much.

• 37:31Krishna Choudhary?

  So much shenanigans. So now we've got kind of a more complete picture of how genes work and how Mendel's laws come from genes. So I just want to go over all of that, okay? So first we know now from, you know, all of the work is DNA stores the data of these alleles and genes, and what an allele really is, is one version of the ATGC sequence, okay? The different allele will be a different version of that ATGC sequence, right? And the two alleles are different in only a few base pairs, because that's going to code for a different protein, and that protein is going to make the different trait.

• 38:06Lester Nare?

  For folks who might not know when you say ATCG sequence, can you clarify?

• 38:09Krishna Choudhary?

  Yeah, yeah, yeah, good point. The ATCGs are the nucleotides that make up DNA. So DNA is a molecule that's kind of a twisted ladder, and the rungs of the ladder come in four different types, A, T, G, and C. The sequence of those letters in that ladder tell you what kind of protein to make, okay?

• 38:29Lester Nare?

  So it's like the rungs on the ladder, they can be in different order, and so you can do different things based on the order that they're in. And each chromosome comes in with a different rungs on the ladder order from each of the parents in this context.

• 38:40Krishna Choudhary?

  Yes, exactly. And when we say that there are two alleles, what we really mean is there's two distinct sequences of ATGCs, right, that will code for the protein. And that DNA is stored in the chromosome. So when we see the chromosome, like the two strands. Each strand is a giant molecule, a single molecule of DNA that if you were to unravel would be like this big, literally. Like that fits inside every single one of our cells, but it's like, it's like several inches long.

• 39:07Lester Nare?

  That's so.

• 39:07Krishna Choudhary?

  Right. It's a, a single molecule of just ATGC strung together, right? And it's wrapped around a bunch of stuff to create the chromosomes. So that's what a chromosome is. All right. Now we know what a chromosome is. Now each chromosome, as we said, has two chromatids. Those are the two different sequences of DNA. And each allele is located on the different chromatids. So now, when we look at the laws of independent assortment and things like that, and how to create gametes. Well, during meiosis, the two chromatids, they replicate and then they physically separate into different cells. So the sperm cells all get half, one chromatid each. And that's now making sense, right? With the whole Punnett squares and all that stuff. How's that working? Well, when the egg and the sperm come together, you get half and half to create a whole. Right?

• 39:52Lester Nare?

  Right.

• 39:52Krishna Choudhary?

  So, so now that, that's making sense. Now the independent assortment works, the whole correlated genes also works because if you're on the same chromatid, then you're going to get the same package. And then finally, how does the dominant and recessive work? Right? Well, a lot of times the dominant version just codes for the protein that works. And the recessive version codes for the protein that doesn't work. So if you get two dominants, you just get maybe a little bit more of the protein. There can be some gene regulation stuff to like downplay one of the chromatids so that I don't like have too much of the same protein. There's actually stuff that goes on there, which is very interesting. But if I have like the heterozygous, meaning one functional type and one dysfunctional type, I still have a working copy. So I can create that gene.

• 40:37Krishna Choudhary?

  But if I have two dysfunctional types, then I've got no way to create the gene. Eye color is a very good example of this. The OCA2 allele combinations, so there's a.

• 40:49Krishna Choudhary?

  There's a gene for melanosome, melanosome. That's the protein that gives brown eye color. Okay. And if you've got two versions of that protein, then you're going to create melanosome and you're going to have brown eyes. If you've got a single version of the protein, body can still create melanosome. But if you've got no functional melanosome, then it's kind of like the naked retina, or not retina, iris is the color that you're going to see. It's a bit more complicated, obviously, because you have like green and hazel. And so there's different versions of even melanosome. And there's other little things that go in. But by and large, this is how dominant versus recessive works.

• 41:28Lester Nare?

  And this is why people have to wear sunglasses if they have like colored eyes, because they don't have that melanosome. That provides that additional protection for the eyes. As one example.

• 41:38Krishna Choudhary?

  Exactly. So, and so far, what we've been covering is effectively, it's still been Mendelian. Even like Thomas Hunt Morgan talking about the packages coming together. It's still Mendelian in some sense, right? I mean, you're kind of proving his point that they come in these packages. It's just that some of them are correlated. There are now a growing, there is now a growing body of work that there are a lot of exceptions. And so that's where we're going to get to next. But before we do that, we've got some housekeeping.

• 42:05Lester Nare?

  Some housekeeping here. So we are super excited, everybody, to have our resident PhD Krishna Choudhary back in the studio. We, I'm so excited for our upcoming episodes. We are working through a studio redesign. You might notice that our dock behind us is in a different location. We have some neon signs coming in shortly. And we are adding the FFP bookshelf that will be behind us. And we are going to have a collection of some of our favorite books. We would love to get some suggestions for what you think should go into the FFP library. So over the next couple of episodes, you'll start to see things begin to take place and a little bit of changing of scenery.

• 42:48Lester Nare?

  If you enjoy the show, if you are happy to see us back doing these deep dives, not only on the frontier of science research. But the context with how we got there, you can always support the show by sharing clips or your favorite episodes with your friends, family and colleagues. You can watch the show. We always encourage you to watch the show on YouTube and Spotify. The full video podcast is available there. You can listen wherever you get your podcasts. And for clips, we're across our socials, TikTok, Instagram, X. Some of the best key moments from the show, easy to send that DM to slide into the DMs. Getting more eyes on the show is super helpful for us.

• 43:31Lester Nare?

  If you can support the show directly, we have a donation portal on the website, ffpod.com backslash donate. And if you haven't been to the website, you can watch full episodes. We have chaptering. We link out to all of our research papers that we cover, connected to each episode. And I will note, there have been some of you that have been asking for an RSS feed for the website. We are working on that as well, so keep an eye out for that over the next couple of weeks. So be sure to comment what books you want to see on the bookshelf. I hope we didn't order neon signs that are too big. They're going to be quite large.

• 44:09Krishna Choudhary?

  Yeah.

• 44:10Lester Nare?

  So hopefully it works out here, but we are super grateful for all of you in FFP Nation and the audience who have been super supportive of the show. We are super excited to get back on the hopper here. We have some great, great episodes lined up. But before we get to those great episodes, we need to finish up because I'm very curious about how we now talk about epigenetics.

• 44:33Krishna Choudhary?

  Yeah.

• 44:33Lester Nare?

  As it relates to this background we've just talked about on Mendelian genetics.

• 44:37Krishna Choudhary?

  Right. So what we've talked about so far is just the genetic part of things. And even then, we've only talked about Mendel's rules. And from our understanding now, it's been 160 years of study. It is a gross oversimplification of what is actually happening. Now, the goal here is to predict from genetic input, what the offspring's genotype is going to be, what the offspring's genetic makeup is going to be, and then how the offspring is going to look on the outside, right? By, by look, I mean like what are the traits that it has, okay? Even if it's on the inside, right? But that's what we call a phenotype compared to the genotype, which is just the actual genetic makeup. Now, as people worked on this over many, many years, anomalies started piling up.

• 45:22Krishna Choudhary?

  Okay, there are several, several, we are going to focus on just one, okay?

• 45:28Krishna Choudhary?

  The anomaly is called paramutation. It starts with maize. It was first documented in the 1950s by geneticist Alexander Brink, when he was studying the red one locus in maize, location of the red one gene in maize. Maize is just corn, but biologists always say maize for some reason. Okay, maybe someone can tell me why in the comments, but I've never seen someone just say corn. But then I look at the photos and it's just corn. Okay, anyways, so the red one location in this organism controls for the anthocyanin pigment. Okay, and that's the pigment that is responsible for the dark coloring of corn kernels. You've seen like those like exotic corn, like it's like purple. That's what this is, okay?

• 46:13Krishna Choudhary?

  So that's the trait that we're gonna look at.

• 46:14Lester Nare?

  In Zim, we have this dish called sadza, which is cornmeal. And you can have sort of, you know, different color styles. You usually don't use when you have that red pigment style. You'll usually just cook it straight. You won't make that into cornmeal. It'll usually be either yellow or white, but that's it's in. Yeah, we call it maize back home.

• 46:31Krishna Choudhary?

  Yeah.

• 46:32Lester Nare?

  Which is interesting.

• 46:33Krishna Choudhary?

  Yeah, but like, but these are Americans that are working on it. So that's why I just want to know what's going on. Okay, like even like Dorothy, no, it's Barbara McClintock with the jumping genes. She discovered those in maize. It's maize.

• 46:47Lester Nare?

  It's maize.

• 46:48Krishna Choudhary?

  Okay, whatever. Anyways, so let's, let's talk about this red one location. Okay, the anthocyanin pigment pathway. Here is what he observed. Okay, what I'm gonna do is do kind of the same thing that Mendel used to do, which is I'm gonna get two true breeding plants, one that has the purple pigment thingy and then one that doesn't. I'm gonna cross those. Weirdly, I get all recessive, even though the purple is the pigment, right? Like, so that should be dominant because that's the working pigment. According to like what I told you about what is dominant and recessive.

• 47:23Lester Nare?

  Yes.

• 47:23Krishna Choudhary?

  It's not just arbitrary. It's just like one is the protein is actually working. The other one, the protein's not working. Here, if I have a true breeding purple and a true breeding green, I'm actually getting no working pigment. I'm getting all green. It's like the opposite of the F1 generation, right? This isn't even getting to F2. This is like in the F1 generation, it's as if Mendel did purple cross white and got all white.

• 47:47Lester Nare?

  That's okay, that's fascinating, which which would not make sense, given that

• 47:50Krishna Choudhary?

  Given that it was all purple.

• 47:51Lester Nare?

  It had the dominance across, it should have the dominance in all four of the offspring.

• 47:55Krishna Choudhary?

  Yeah, okay, so again, what the hell?

• 47:58Lester Nare?

  What's going on there?

• 47:58Krishna Choudhary?

  What's going on there? So so now, next thing to do is now, I mean, usually what you do is you take that and then you crossbreed with itself. So you do a self fertilization, but now things are weird. So now let's let's cross it with a true breeding purple again, right? Because let's say something weird happened and I got like recessive recessive here. Um, and then the purple? Or maybe I got like one bit of purple, but like it's not showing up. In the in the F2 generation, I should get some purple. I cross it, I get all green. No purple. It's almost as if the green, whatever it is, has like completely nixed the advantage of the purple gene. And silenced it. This is called a paramutation, okay?

• 48:43Krishna Choudhary?

  And it's also, it's as if there's the newly altered silent allele that that's there, right? Because I know I have the purple allele, but that purple allele has somehow been silenced. And now that purple allele, you would assume if it if it made it with another purple allele, I would get I would get purple, but this purple allele has turned to the dark side somehow. And and started nixing all of its other compatriots with the purple allele.

• 49:10Lester Nare?

  We'll call it the Anakin allele.

• 49:12Krishna Choudhary?

  Yeah, yeah, yeah, yeah, something like that, right? It's like you've got like a weird corrupted computer file that now goes and infects every other computer.

• 49:19Lester Nare?

  And so what this brings up is that there's not this 100% all of the time sort of viewpoint.

• 49:24Krishna Choudhary?

  That's the first thing, yeah.

• 49:26Lester Nare?

  Because this should be dominant.

• 49:28Krishna Choudhary?

  Yeah, first of all, it's not dominant, but okay, fine, but now it's it's making everything else recessive somehow. It has an ability.

• 49:35Lester Nare?

  Right, yeah, cross generation downstream.

• 49:37Krishna Choudhary?

  Yeah, yeah.

• 49:37Lester Nare?

  It's not just a one off outlier.

• 49:39Krishna Choudhary?

  Exactly, yeah, this is very strange, okay? This was in 1950s, it was a very big deal when it when when it was discovered. Okay, and so now to understand, now we've got a better understanding of what's going on. So in order to understand this, we've got to understand two things, okay? First thing is gene regulation. That is the um, that is some of the software on top of the genetics, okay? So we've got two types of gene regulation pathways. You've got enhancers and promoters. We've talked about this a lot on the podcast, right? When you've got a gene, the gene is a recipe for creating a protein, right? But there is an on button that is telling the machinery to come make the protein. And then there is a volume control button that is saying how much protein to make.

• 50:23Krishna Choudhary?

  That is the promoter and the enhancer respectively. The promoter is the on button, the enhancer is the volume control.

• 50:29Lester Nare?

  I loved that episode where we talked about this.

• 50:31Krishna Choudhary?

  Yeah, we we we've talked about this a lot, right? And frequently what happens is the promoter is right next to the gene. Because like basically what happens is you've got the gene on this part. This is the part that has the recipe. The promoter is right next to it. So what it's gonna do is take something called RNA polymerase, which is the thing that makes it into RNA that then goes into making proteins. The promoter is gonna be like, yo RNA polymerase, come over here, attach to me and then go this way. And it's gonna be like da da da da and it goes that way. The enhancer can be way far apart from where the from where the gene is. And the the genetic code can literally fold such that the enhancer gets close to the promoter. The enhancer recruits the RNA polymerase to come. And it's it's very essential for creating that two step sort of regulation.

• 51:16Lester Nare?

  Yes.

• 51:16Krishna Choudhary?

  Right, so this is genetic regulation. That's the first thing we got to understand. Second thing we got to understand is epigenetics, okay? Epigenetics is the software and the modifying of the structure of DNA and chromatin. Chromatin is the thread that the DNA is, right?

• 51:33Krishna Choudhary?

  There's two levels to doing this that are by and large, these are the two level levels of epigenetics. The first one is something called methylation. Effectively, as I told you, DNA is made up of four distinct nucleotides, A, T, G and C. Now, the C, the cytosine. Can sometimes be modified by attaching a methyl group. A methyl group is, I think, just CH3. You just take a CH3 part of a molecule and you attach it to the cytosine. When you do that, if you've got a bunch of cytosine and a segment of DNA that has these methyl groups, the RNA polymerase can't really get to it because you've altered the look. And the RNA polymerase comes in and is like, I don't know what I'm looking at.

• 52:18Krishna Choudhary?

  I'm gonna go somewhere else.

• 52:19Lester Nare?

  I'm gonna go somewhere else.

• 52:20Krishna Choudhary?

  Right? So this is one way to silence parts of the dean, parts of the genetic sequence, by just like adding a little chemical tag. And those are the little tiny, like, red pins that you're seeing, okay? And they only attach crucially to the C, the cytosine. Okay, so the A's, T's, and G's are always left alone, okay?

• 52:40Lester Nare?

  The part of what we're sort of speaking to here is there's, in the practice of your body generating the proteins that your genetics sort of has the instructions for, that's a whole functional process.

• 52:57Krishna Choudhary?

  Yeah.

• 52:57Lester Nare?

  In and of itself. And much like all functional processes, there are opportunities for it to break down in multiple different places.

• 53:07Krishna Choudhary?

  Yeah.

• 53:07Lester Nare?

  And that's where you begin to get the impacts on outcomes. Because you might have the instructions, but when you go to the factory to build it, the power goes off, the doors are locked, you offshore it to China, whatever.

• 53:24Krishna Choudhary?

  Yeah, exactly, yeah, exactly, exactly. And so that's the first part, the methylation, okay? The second step is, in order to actually create the chromatin, which is the stuff that makes chromosomes, it's like a thicker sort of wool compared to stringy. The DNA is like a string, and then the chromatin is like wool. You have to like sort of bunch up a bunch of string together to create the thicker part, right? And in order to do that, if you bring that photo back, you wrap it around these nucleosomes, which are made up of histones, okay? So they're like little proteins that you wrap it around, and then those sort of get packaged together, right? Now, if you wrap it around that part of DNA that's wrapped around the nucleosome, the RNA polymerase can't get to.

• 54:08Lester Nare?

  Right.

• 54:08Krishna Choudhary?

  Right? So this is another level of silencing certain parts of the DNA. If you don't ever want this part of DNA, To to be expressed in a cell, like, let's say you're an eye cell. I don't want the proteins that neurons want. Package it up. And, you know, put it in a warehouse, put it in your garage effectively. Right? Only read the part that tells me how to be an eye.

• 54:32Lester Nare?

  And this is how it's able to control for if all cells all have the same instruction list. How it only focuses on a certain portion, a certain portion of it in order to build out the complex different parts of us where it's not just reading everything and

• 54:45Krishna Choudhary?

  Yeah, yeah, yeah.

• 54:46Lester Nare?

  Not really having any idea.

• 54:47Krishna Choudhary?

  You know, we don't have like a bunch of mini like Krishnas, right? It's like, no, there's like skin Krishna, hair Krishna and all that, all that other kind of stuff. So that is epigenetics. Okay, these two sort of layers, that's that's effectively what we want to focus on. How do we, how does this explain the maze paramutation that we observed? Well, it's a combination of the genetic regulation with the epigenetic silencing. Okay, right, here's what's happening. There's something called RNA interference. What that is, is tiny little bits of RNA that act like mobile

• 55:31Krishna Choudhary?

  silencers. A part of the DNA makes this RNA interference thingy. It's a little piece of RNA that goes and like attaches to DNA elsewhere. And because this thing is small enough, it can just move around the nucleus. Okay, and what it does is recruit DNA methylation machinery to come in and put those methyl groups in the Cs. Okay, so now what's going to happen? What's going to happen is I've got my purple. I've got my purple trait and I've got the green trait. They both actually have the gene for purple.

• 56:12Krishna Choudhary?

  What's different is that the green one has a mechanism to create this small tiny thingy of RNA to go and silence that purple gene.

• 56:21Lester Nare?

  Right.

• 56:22Krishna Choudhary?

  Okay, right, the purple one doesn't have that. But now when I cross it. I'm gonna get, one of the chromatins is gonna have that thing that makes the little tiny RNA, the RNA interference, but that RNA interference is gonna go do it for both.

• 56:36Lester Nare?

  Right.

• 56:36Krishna Choudhary?

  Right?

• 56:37Lester Nare?

  Because it's not, it's not, um, it is not limited by, it is free, is able to free flow through the nucleus and do what it did previously to get the green.

• 56:46Krishna Choudhary?

  Yeah.

• 56:46Lester Nare?

  And so regardless of the fact that both have this dominant purple, uh, this sort of secondary

• 56:51Krishna Choudhary?

  Yeah.

• 56:52Lester Nare?

  functional process is free to move despite the genetic code and instruction.

• 56:57Krishna Choudhary?

  Exactly, yeah. And because now the RNA interference is on both the chromatins, now when I take that and, and I subsequently breed it with another true breeding purple, again, all the offspring are

• 57:09Lester Nare?

  That makes a lot of sense, right.

• 57:10Krishna Choudhary?

  Because the RNA interference is kinda like this little mini molecular virus type thing, right?

• 57:15Lester Nare?

  Just because you have the instructions doesn't mean your body is going to execute on them.

• 57:19Krishna Choudhary?

  Yeah, yeah. If you've got an agent that's just like, like erasing it.

• 57:24Lester Nare?

  Right.

• 57:24Krishna Choudhary?

  Or like, you know, putting like a paper on top of the instructions or whatever.

• 57:28Lester Nare?

  That's a really interesting note. It, again, going back to this idea that there is, there is sort of a, a few layers between the instruction and the completed production of the protein.

• 57:39Krishna Choudhary?

  Yeah.

• 57:40Lester Nare?

  And there are mechanisms that can go and silence component parts

• 57:44Krishna Choudhary?

  Mm-hmm.

• 57:45Lester Nare?

  uh, in that production process.

• 57:48Krishna Choudhary?

  Yeah.

• 57:49Lester Nare?

  And in the case we just brought up, that was happening, even though it was a purple dominant on the green, that's what was happening. And so, when, if you just looked purely at the genetic

• 57:58Krishna Choudhary?

  At the genetic thing, you'd be like, this should be, the green should also be purple. It's got the purple gene on it.

• 58:03Lester Nare?

  And now this epigenetic layer around the silencing on the C, uh,

• 58:08Krishna Choudhary?

  Yeah, getting methylated.

• 58:09Lester Nare?

  Getting methylated is what is causing the different phenotypic outcome?

• 58:15Krishna Choudhary?

  Yes, very good. Exactly. And this is non-Mendelian, because it's doing all this weird shenanigans, and it's the epigenetics that's doing it, okay? So this is, this is already an example of non-Mendelian epigenetic inheritance. But for the longest time, this has been ubiquitously reported in plants, insects like Drosophila, because we're so good that prosophila genome that like it's like easy to find, okay? But proving their prevalence in higher order mammals was next to impossible. And we're going to get into why. That's where the technological revolution comes in that enables this paper. Okay, and just a side note, in 2006, there was a paper that showed that mice can have RNA mediated

• 58:57Krishna Choudhary?

  non Mendelian inheritance, but there was a lot of dismissal of the findings because

• 59:05Krishna Choudhary?

  they were like, oh, this is just something that happens in strange transgenic mice. Because the mouse model that was used here was transgenic. And I think it's totally fair.

• 59:14Lester Nare?

  I just wanna, this is the funding issue.

• 59:16Krishna Choudhary?

  Oh, this is the funding issue thing.

• 59:17Lester Nare?

  Yeah, we don't, we don't have to get into it. We don't have to get into it.

• 59:19Krishna Choudhary?

  The trans mice, yes, trans genetic mice, right? Please do not cut our funding. We're not, we're not making mice trans. But in any case, it was an interesting little finding. I mean, it got published in Nature, so it was a big deal. But again, it's in transgenic mice. It's easier to do analysis in transgenic mice because you've got a very nice blueprint of what the genetics is. It's not a naturally like sort of super diverse genetic population, right? So you know exactly what to look for. But perhaps it's not so general, right? And if it's an RNA mediated thing, maybe it's just special. And it's not as general as like DNA methylation. This RNA mediated mechanism was not through DNA methylation. It was through something else. There's a bunch of other stuff that can happen, right?

• 1:00:02Lester Nare?

  So the, the point was they were looking at this mice population is not necessarily representative of the natural world in a way that we can extrapolate the results.

• 1:00:09Krishna Choudhary?

  Exactly, yeah. And it's like, at the end of the day, I want to see like, is this something I can apply to humans?

• 1:00:13Lester Nare?

  Right.

• 1:00:13Krishna Choudhary?

  Right? So still, some scientists suspected that param mutation is probably happening in mammals. I mean, it's happening in plants so ubiquitously, it should prob, there, there shouldn't be, there's no like first principles reason why it shouldn't be happening in mammals, right? But you need to, you need to actually get, get the evidence. And for, for a long time, the, it was largely at the level of theory. Now, why is that the case? Why is it so hard to prove? So it has to do with.

• 1:00:43Krishna Choudhary?

  Measuring DNA methylation.

• 1:00:45Lester Nare?

  Okay.

• 1:00:46Krishna Choudhary?

  Okay, how does one? If I get a strand of DNA, it's actually very easy to sequence DNA. Okay, there's ever since the days of the 1960s and 70s, I mean, we've sequenced the entire human genome. Now we've sequenced tens of thousands of human genomes. I think it's up to the even might be millions now. So, you know, the sequencing DNA is not a big deal because it's distinct. A, T, G, C, right? There's ways that I can make the A like combine with a T that has a little like, you know, a little GFP tag that like lights up a certain color. So then like every time it's red, I know it's an A. Every time it's a G, I know it's it's green, it's a G, right? And like, there's so many cool sequencing technologies.

• 1:01:30Krishna Choudhary?

  But those sequencing technologies aren't good with methylation. Okay, one way to do it that a lot of people use is bisulfide sequencing. Okay, here's how you do it. You take your, you take your DNA. Okay, you take your DNA. Now your DNA is going to have AT, ATGCs all over. Some of the Cs, some of the cytosines is going to have that methyl group.

• 1:01:55Lester Nare?

  Okay. Those little red.

• 1:01:56Krishna Choudhary?

  Those, yeah, those little red pointies here, here as well. They're little like red tags on the Cs, right? There's some Cs that are that are like blue. And then there's other Cs you can tell that are not. And those are like normal cytosines that aren't methylated. Right? What you're going to do is you're going to treat it with a detergent effectively. Okay, a chemical treatment that is going to convert unmethylated cytosines into uracils. U is the letter that is used in RNA. Okay, so it's going to leave the the cytosines with the methyl alone, but it's going to change the Cs into U's. Okay, and then I just sequence like normal.

• 1:02:32Lester Nare?

  Right.

• 1:02:33Krishna Choudhary?

  Like, like I used to.

• 1:02:34Lester Nare?

  Right.

• 1:02:34Krishna Choudhary?

  Okay.

• 1:02:35Lester Nare?

  Right.

• 1:02:35Krishna Choudhary?

  Because I'm good at sequencing. I'm not good at the, the, like, finding where the methyl is. But this is one way, right? Because I've just, I've taken all the ones that don't have the methyl groups. I've turned them into another letter. And then now I just sequence like normal. And I'm like, oh, this is a U. The DNA shouldn't have a U. That's. Probably where the the sea was, right? Or I can like, I can, I can sequence the original gene. And then I can sequence the gene after treating it with this detergent. And wherever the difference is, that's where the Cs are. Wherever the C remains, that's where the methyl groups are.

• 1:03:07Lester Nare?

  Right, and then now we know where the methylated cytosine is.

• 1:03:10Krishna Choudhary?

  Yeah, because any cytosine that survived had to have had a methyl group on it, right?

• 1:03:15Lester Nare?

  That makes sense. Okay. Now gives us a different map to analyze. That's not just in indistinguishable Cs, methylated versus non-methylated.

• 1:03:26Krishna Choudhary?

  Now, you can imagine treating a molecule like DNA with chemical is not a good idea. Okay, and of course not, because what ends up happening is something called catastrophic DNA degradation. Here's how sequencing works, okay? You've got a giant thing of DNA. When I treat it with detergent, it's gonna break up into short parts, okay? And I'm gonna get a bunch of different short parts. And now I have a combinatoric puzzle to stitch together all of these short parts into a big part, right?

• 1:03:55Lester Nare?

  Yes.

• 1:03:56Krishna Choudhary?

  The problem is, the short reads are about 150 base pairs long, max. It's not a lot, okay? Because a lot of times, nothing happens, okay? And so, if I've got repetitive sequences of DNA, I could just fool myself into thinking, oh, this is all part of the same sequence. Rather than this is the first repeat, this is the second repeat. It's kind of like, have you seen that like crazy puzzle of the Beetle White album? Right, where it's just, it's the Beatles White album, and it just says The Beatles with a white. And like, it's incredibly difficult because everything is white. So imagine here, like if I've got repeated sections of DNA, I don't know whether this thing came from this part, or this part, or this part, right?

• 1:04:35Lester Nare?

  Hundred percent, and some puzzle pieces go together when they're not supposed to be next to each other.

• 1:04:39Krishna Choudhary?

  Yeah, yeah, yeah, because, because just, you know.

• 1:04:42Lester Nare?

  Just kind of.

• 1:04:43Krishna Choudhary?

  Yeah, it's like, it's like this side of the puzzle piece goes together. But when you put it together with the rest, the other three parts don't make any sense. Yeah, like, it's a really incredibly hard puzzle, right? So that's one reason why you don't want that. The next is loss of allelic phasing, right? If I want to study non-Mendelian inheritance, what I'd really like to know is which parent the epigenetic mark came from. That's, that's why the maze thing was such a big deal, right? Because I could tell like what was happening.

• 1:05:08Lester Nare?

  Right.

• 1:05:08Krishna Choudhary?

  But in order to do that, what that requires is each of these short reads. To have a mutation from the parent, from one parent and not from the other, right? It's like, it's like, oh, this part is a T. I know that the mom had the T here and not the dad had a C here. So I know that this part comes from the mom. But if I have short enough reads that are 150, the probability of getting one of these single nucleotide permutations in my short read is very low.

• 1:05:35Lester Nare?

  Mm hmm.

• 1:05:36Krishna Choudhary?

  Right? Because the shorter the thing is, the probability of something going wrong is

• 1:05:40Lester Nare?

  Right.

• 1:05:40Krishna Choudhary?

  is not that high.

• 1:05:41Lester Nare?

  Right.

• 1:05:42Krishna Choudhary?

  So the methylation could be different between two identical, but I don't know which one came from the mom, which one came from the dad.

• 1:05:47Lester Nare?

  That's actually a really good point. And that's, that's fundamentally.

• 1:05:51Krishna Choudhary?

  Yeah. That fundamentally, the whole point of what you're trying to do.

• 1:05:53Lester Nare?

  Why I was trying to do is you need to be able to make that, that connection.

• 1:05:56Krishna Choudhary?

  Yeah, I, I'd like to know which paternal chromosome it came from, from the entire whole genome.

• 1:06:01Lester Nare?

  It's like you have two white puzzles. One is the Beatles' white album and one is whatever, the White Stripes' white album. And it's like the white.

• 1:06:08Krishna Choudhary?

  Yeah, and now you're taking the white piece from what?

• 1:06:09Lester Nare?

  Yeah, it's like they're all white.

• 1:06:11Krishna Choudhary?

  Yeah.

• 1:06:11Lester Nare?

  And but is this the white album? Like, and so now you're.

• 1:06:13Krishna Choudhary?

  That's exactly right. That's a, that's a good, good analogy. Exactly.

• 1:06:16Lester Nare?

  Okay, okay.

• 1:06:17Krishna Choudhary?

  So that's been the problem. I don't know how to do it.

• 1:06:19Lester Nare?

  Yeah.

• 1:06:19Krishna Choudhary?

  It's like, we've been relying on the sequencing technology that gives us the sequence of DNA, but it's not designed for methylation reads.

• 1:06:30Lester Nare?

  Right.

• 1:06:30Krishna Choudhary?

  Right?

• 1:06:30Lester Nare?

  Which, which is key for us to be able to identify, you know, where we're going to see these mutations that cause the dominant to get suppressed.

• 1:06:40Krishna Choudhary?

  Yeah, yeah. And all of this weird shenanigans.

• 1:06:42Lester Nare?

  All the weird stuff.

• 1:06:42Krishna Choudhary?

  All the weird stuff.

• 1:06:43Lester Nare?

  Kind of derives, at least in part, from, from this.

• 1:06:46Krishna Choudhary?

  From understanding where, which chromosome is the parent, right? Which chromatid came from which parent? Okay, so now we get to why it's happening now. The Oxford nanopore revolution. Okay? This is an insanely cool technology. Here's how it works. Okay? It's, it goes to biophysical detection. What you do. Is you take your native DNA strand and you pass it through a nanopore. It's a little hole in a membrane, kind of like ion channels, like the, the, the, the, there's a membrane that separates in and out. And then you've got a, you've got a little hole that's made out of protein that one strand of DNA goes through.

• 1:07:27Krishna Choudhary?

  There, there's a thing above it that unzips the DNA so that one strand goes this way, one strand goes through. Okay. And what you're going to do is measure the current across the membrane. Okay. The, the, the current that's going through from, from this side to this side. Now, AT, G and C are different molecules. They're, they have different sizes, they have different little residues, one, they have different shapes. And so every time the four goes through, there's going to be a tiny different current for each of the four.

• 1:08:04Krishna Choudhary?

  Isn't that sick?

• 1:08:05Lester Nare?

  I'm so, we're so smart, dude.

• 1:08:07Krishna Choudhary?

  Isn't that so sick?

• 1:08:09Lester Nare?

  That's very clever. The visual analogy I started thinking about is like if you unzip the zipper of your jacket. It's like the unzipping of the DNA. And each of these are then going into something that's going to read each segment of four, which is basically just going to have a different fingerprint.

• 1:08:21Krishna Choudhary?

  Exactly. Like imagine, imagine your zipper, let's go with that analogy. I like that. Imagine your zipper, but each of those tiny little zip thingies is a different, um, composition of plastic. Okay. And so when I go through this like little hole, it's going to sound different, right? The, the red plastic is going to sound different from the white plastic. And so if I've got a little sound recorder that just records the, the, the, the, the, the, the, right? I can, I can then have a computer program decode what type of plastic was the four zipper part. And that's what's happening here. And so on the right hand side, you see the current versus the time.

• 1:08:56Lester Nare?

  Yeah, yeah, yeah.

• 1:08:58Krishna Choudhary?

  Completely different signatures. And then you've got like, you know, it's probably not even machine learning. This is a very simple, like computational task to do.

• 1:09:06Lester Nare?

  This is really good.

• 1:09:07Krishna Choudhary?

  Okay. Now this was originally, um, this was originally invented for just genome sequencing because ATs, Gs and Cs, right? But now a C with a methyl group is gonna sound even more different.

• 1:09:20Lester Nare?

  Bingo.

• 1:09:21Krishna Choudhary?

  You see?

• 1:09:22Lester Nare?

  Bingo. Yeah.

• 1:09:22Krishna Choudhary?

  And so there's just gonna be a fifth signature that I have to look for.

• 1:09:27Lester Nare?

  Yep. That it makes, I mean, it makes total sense. It makes total sense.

• 1:09:31Krishna Choudhary?

  Why is this advantageous? One, you can do ultra-long reads. You're not treating the thing with detergent. Right? You just, you just, you just, you just stick this thing through and you can get hundreds of thousands of base pairs. We're going from 150 to now several orders of magnitude of like how long you can make the read, right? So it's like the, it's like, you know, when, when sometimes you, you like go to the Airbnb and like you open the puzzle box and half of it's done. You're like, Joe.

• 1:09:59Krishna Choudhary?

  Right? Cause then, cause then you can post on Instagram like two hours later. I did it.

• 1:10:05Lester Nare?

  That, that's, it's a really interesting note though, that through this biophysical detection method, which again was used for sequencing, the point is because we understood the methylation process in and of itself, you could then extrapolate that the C in this biophysical detection is going to just have again, that slightly different fingerprint. And that's all, that's, yeah, that's all you need to look for now. And again, just this narrow, now we can, and again, now being able to sequence longer.

• 1:10:35Krishna Choudhary?

  Yeah, it's huge.

• 1:10:36Lester Nare?

  Gets back to this chromatin.

• 1:10:38Krishna Choudhary?

  Yeah, because now you've got a longer sequence. There's in a hundred thousand base pairs, you're gonna be able to identify which one came from the mom and which one came from the dad.

• 1:10:46Lester Nare?

  Hundred percent.

• 1:10:47Krishna Choudhary?

  Wow. Isn't that sick?

• 1:10:49Lester Nare?

  And, and the thing is, this Oxford nanopore evolution was not necessarily for methylation.

• 1:10:54Krishna Choudhary?

  No, no.

• 1:10:55Lester Nare?

  Detection. It's just someone was like, wait a minute.

• 1:10:58Krishna Choudhary?

  Yeah, this is the, the physics works out here, right? It's called Oxford nanopore detection because it was a technology licensed by Oxford Nanopore Technologies of Oxford, UK. They licensed the patent, but the patent actually is a University of California patent. Okay, it was developed in UC Davis and UC Santa Cruz. The fundamental research comes from David Deemer, who he started in UC Davis and then Santa Cruz poached him. He's like, yeah, I'll go, I'll go live in Santa Cruz.

• 1:11:27Lester Nare?

  Santa Cruz is kinda nice.

• 1:11:28Krishna Choudhary?

  Yeah.

• 1:11:29Lester Nare?

  It's kinda nice.

• 1:11:30Krishna Choudhary?

  And I really do think that this is something that is Nobel Prize worthy. Because it is now the foremost way of not just doing methylation, but also just sequencing DNA, right?

• 1:11:40Lester Nare?

  In general.

• 1:11:41Krishna Choudhary?

  In general, like this is now, it's super fast because you go right, and then have a computer just read the whole thing. And these ultra-long reads are just good regardless.

• 1:11:52Lester Nare?

  Right.

• 1:11:52Krishna Choudhary?

  Right?

• 1:11:52Lester Nare?

  For any number of contexts, we have a specific focus for this episode, but the

• 1:11:57Krishna Choudhary?

  Yeah, the applications are endless. And Oxford Nanopore Technologies, they created something called a mini-on sequencing device. It's like a tabletop sequencing device. So you can just like have it, it's not like the giant machines that you used to be. It's just a tabletop, just stick your pipette in and then it'll just do the thingy.

• 1:12:14Lester Nare?

  Is it analogous maybe to the sort of the phase shift from vacuum tubes to like desktop personal computer or desktop to mobile in the

• 1:12:22Krishna Choudhary?

  Yeah, I would say like, yeah, desktop to like laptop.

• 1:12:26Lester Nare?

  Okay, desktop to laptop.

• 1:12:27Krishna Choudhary?

  You know what I mean? Because laptop, I can now like go anywhere.

• 1:12:29Lester Nare?

  I don't have to be plugged into a wall somewhere.

• 1:12:31Krishna Choudhary?

  Exactly, and things like that. And so I think it's a very big deal. And they actually took one to the International Space Station because they do like weird genetics experiments up there with like plants and like how they deal with microgravity.

• 1:12:43Lester Nare?

  Makes sense.

• 1:12:44Krishna Choudhary?

  Makes sense, right? Like, how does bacteria deal with microgravity? Because ultimately, if you want to extend life to several years in space, you need to understand how, like, does the genetics at the molecular biology level, do they care? Probably they shouldn't because the gravitational potential difference between like one end of the cell and the other shouldn't be that much. But you know, you never know with biology.

• 1:13:06Lester Nare?

  Right, right.

• 1:13:06Krishna Choudhary?

  You gotta, yeah.

• 1:13:07Lester Nare?

  Is the factory gonna shut down?

• 1:13:08Krishna Choudhary?

  Yeah, like just because I took out like a tiny bit of wind effectively, right? That's like going in one direction. So the ISS is using a mini ion sequencing device on it.

• 1:13:19Lester Nare?

  That's really cool.

• 1:13:20Krishna Choudhary?

  Yeah. So now finally, with this, we can get to the paper at hand. An hour in.

• 1:13:26Lester Nare?

  Yes.

• 1:13:26Krishna Choudhary?

  An hour into our episode, this is the paper that we were talking about. Okay, non Mendelian inheritance of DNA methylation patterns in mice. It was out in Nature Genetics. It was during my paternity break and I was like, oh, this is really cool.

• 1:13:38Lester Nare?

  But now I can read that title and understand why this is a big deal.

• 1:13:44Krishna Choudhary?

  That's right. You miss me?

• 1:13:45Lester Nare?

  Yeah, like this is, ladies and gentlemen, the greatest. This is why it's the greatest, but like, and it's, it's important because these words have meaning.

• 1:13:53Krishna Choudhary?

  Yeah.

• 1:13:53Lester Nare?

  A lot of times people see these titles and they're just like, ah, it's just big words. They don't mean anything. There's actually real, even in the short title.

• 1:13:59Krishna Choudhary?

  Even the short title, you get it, and it's in mice, not transgenic mice, not like special mice, just mice. Just plain old mice. That's why it's very important. He's doing it in mammals, right?

• 1:14:08Lester Nare?

  Because this is from the 2006 one, this is basically the next stage, the next development there.

• 1:14:13Krishna Choudhary?

  Yeah, the, um, one of the key authors, Andrew Feinberg, he's from Johns Hopkins, okay? He has a career in disease genetics and epigenomics. He's like one of the epigenomics guys at the conferences, right? Like that's like giving the presidential lecture or whatever. Um, and then David Threadgill at Texas A&M, he's been studying human-like complex genetics in mice. So they decided that they wanted to collaborate about 10 years ago, um, trying to study epigenomics in the mouse model. And they're trying to compare methylation patterns in response to diet in these inbred strains. And they realized that in order to do that, they, what they really want to observe is allele-specific epigenomics. Meaning this allele came from the mom, this allele came from the dad.

• 1:14:56Krishna Choudhary?

  How is the methylation changing? All of that kind of stuff.

• 1:14:59Lester Nare?

  Which this methodology we just talked about before is an enabling layer to that specific research question.

• 1:15:05Krishna Choudhary?

  Exactly, yeah. And so now we can, we can start doing that. The model that they chose was something called the collaborative cross model. This is key here because what this collaborative cross mouse model is, is it's derived from eight distinct founder strains. So the founder strains are kind of like your P generation in the Mendels, like the true breeding. But because now you're combining these eight different.

• 1:15:29Krishna Choudhary?

  Models, you get a lot of genetic diversity. And so it's much more closer, it's much closer to like, you know, normal organisms. But they're still lab in the sense that I still have very nice sequencing data about them. So I can still do very nice nitty gritty comparisons. Okay, so that's the strains they use. The specifically one, the strains that they use was the CC 019 and the CC 037. Those are the two specific like sort of F2 or in this case like FN generations, right? There's so many that you can make. And the experimental design is actually quite simple. It's kind of like Mendelian experiments. Okay, what you do is you take your, um, you're, you take your CC 019 and your CC 037.

• 1:16:14Krishna Choudhary?

  Those lines, very well established what the epigenetic markers are there and what the genetics are there. So even though they're not like true breeding in a sense, you have a good understanding of like what the genetics are. Now you cross them and then you cross those again, right? Just like in Mendel's experiments. But in this case, what we're looking at is the methylation pattern on the chromatin. Instead of the actual genetic sequence.

• 1:16:39Lester Nare?

  Yep.

• 1:16:39Krishna Choudhary?

  Okay, so the genetic sequences could be the same, but depending on whether this chromatin came from the mom, this one came from the dad, all of these things are now going to start changing. Okay?

• 1:16:49Lester Nare?

  Eric, this is very, and it, and it makes sense now why it would be changing. One, because we understand the sex chromosomes, so you get one from each. Two, because the methylation is going to change what proteins are actually produced or what's suppressed. And so now with all of that understanding and background and context, and the ability to actually detect and sequence the methylated C.

• 1:17:14Krishna Choudhary?

  Nice.

• 1:17:15Lester Nare?

  Like that, that is, they can now do real statistical analysis.

• 1:17:19Krishna Choudhary?

  Exactly.

• 1:17:19Lester Nare?

  That's meaningful in this, because they've done, they have the correct, they've done the mice work. They've done all the other background work. Anyway, so that I.

• 1:17:28Krishna Choudhary?

  It's very, very cool.

• 1:17:28Lester Nare?

  It's all kind of just.

• 1:17:29Krishna Choudhary?

  Yeah, and one final thing that I want to mention before we get into the results.

• 1:17:33Lester Nare?

  Yes.

• 1:17:33Krishna Choudhary?

  Is again about methods, because we do want to focus on methods in this. So we've got the. The you've got the model mouse models of CC 19 and CC 37. Now, when you sequence the offspring's DNA, right? Usually, when you want to put together, even when you've got these long reads, you've got to have a reference genome to put stuff together to. But we don't really have a reference genome for the offspring of these two lines, right? And it's not great to just use one or the other. Because you really you're gonna have to have like some middle ground. And so one thing that I do want to talk about is like in traditional bioinformatics pipelines, right? You've got these and I think photo 30 will show that in a traditional bioinformatics pipeline, right?

• 1:18:17Krishna Choudhary?

  You've got fragmented DNA, even if they're long. You sequence the DNA, then you get all these unaligned sequences. And then you try to align those sequences to a reference genome. Okay, and the reference genome is something that you get like if you've got a human genetics, right? You've got the human genome project and you align your own DNA to that. Because there's not going to be that many differences, right? But here, those tiny differences are going to matter in this study, right? And so what they did was they actually solved it by constructing a pseudo hybrid intermediate genome, which is, I think, very cool that they were careful enough, you know, to create this kind of custom software that constructs a synthetic reference genome for every single cross, right?

• 1:18:57Krishna Choudhary?

  And it includes all of the strain specific insertions of the parent genomes. But it's like unbiased analysis of what the what the kids are gonna be showing in terms of methylation.

• 1:19:11Lester Nare?

  And that this this is important because again, that reference genome is otherwise you're kind of you have no right. You have literally no reference.

• 1:19:17Krishna Choudhary?

  Yeah, exactly. And then it's impossible, but you can't use one or the other. You gotta use this like hybrid. And so they were careful enough to do that. I thought that was quite cool.

• 1:19:25Lester Nare?

  That's that's an important again, shows the they're really trying to do it in a robust.

• 1:19:31Krishna Choudhary?

  Yeah, very meticulously.

• 1:19:32Lester Nare?

  Fashion, especially also from a replication perspective.

• 1:19:35Krishna Choudhary?

  Exactly, yeah. So now we can finally get to the results figures, okay? So let's talk about the control, okay? So Mendelian baseline, 93% of the time, the epigenetics is doing what Mendel's laws say. Here's how we're going to read these figures, okay? All of the subsequent figures are going to be the same way. So the pink is coming from the mom, the green is coming from the dad. What we're looking at on the Y axis is the percent methylation, the amount of methylation, meaning how much of the Cs have a methyl attached to it, okay? Hundred percent would mean every single C has a methyl group attached, zero means none

• 1:20:18Krishna Choudhary?

  of the Cs have a methyl attached, right? And what we're looking at on the X axis is just along the DNA, okay? So along the DNA, you can see that there's a certain region where the mom has almost no methyl groups attached to the Cs and the dad has a bunch, okay? The solid green lines and the solid purple lines are the parent generation and then there's dotted green lines and dotted purple lines for the kids. The key thing to see here is that the dotted green is on top of the solid green and the dotted purple is on top of the solid purple, meaning the methyl pattern of the kids is

• 1:21:02Krishna Choudhary?

  the same as the moms or the dads. Nothing's changed.

• 1:21:05Lester Nare?

  Right.

• 1:21:05Krishna Choudhary?

  Like I got the chromatin, I got the methyl, nothing changed, nothing weird happened in between. So this is the Mendelian baseline.

• 1:21:12Lester Nare?

  Yes.

• 1:21:12Krishna Choudhary?

  Okay? And they actually use two different tissues from the liver and from the muscle to see how like if there's any organ dependent effects that are happening, right?

• 1:21:21Lester Nare?

  That's actually good.

• 1:21:22Krishna Choudhary?

  Yeah, yeah, so this is, this is, this is like normal, okay? This is something that we thought should happen every single time.

• 1:21:28Lester Nare?

  Yes.

• 1:21:30Krishna Choudhary?

  All right, now let's look at our first anomaly.

• 1:21:32Lester Nare?

  And because, and what we're saying is 93% of the time Mendelian genetics holds up.

• 1:21:37Krishna Choudhary?

  Yeah.

• 1:21:38Lester Nare?

  But there's the 7% outlier where it doesn't and that's what.

• 1:21:42Krishna Choudhary?

  And that's, that's, that's weird.

• 1:21:43Lester Nare?

  Yeah.

• 1:21:44Krishna Choudhary?

  And that's where the weirdness is, okay? Now let's look at non-dominant, transacting.

• 1:21:52Krishna Choudhary?

  Methylated, what is it? Something, QTLs, I forget what the full form is. But the ME is the methylated part.

• 1:21:59Lester Nare?

  Yeah, yeah, yeah.

• 1:21:59Krishna Choudhary?

  Okay. Here, what we're looking at is, let's look at the liver, which is the first figure. The first sort of middle figure, okay? At the top. Over there, what you're seeing is, the top line is the pink solid. The bottom line is the green solid. So that's the mom methylation and the dad methylation. You can see the mom has a lot of methylation in this region. The dad has almost no methylation in this region.

• 1:22:24Lester Nare?

  Which is an invert of what we just looked at.

• 1:22:25Krishna Choudhary?

  Right, yeah, yeah. But that's not what's important. Because this part of the gene might be different. What's important is, the dotted lines are all in the middle. They're not coinciding to one or the other. Meaning that the, I got the DNA from them, but then the methyl parts are half and half.

• 1:22:41Lester Nare?

  They're blended, the methylation is blended.

• 1:22:43Krishna Choudhary?

  That's non Mendelian. That's what we're looking at, okay? The offspring, some of the methylation is there, some of the methylation is not. Some of the, some of the female chromosome is getting more methylated. Or, sorry, no, some of the female chromosome is getting less methylated. And some of the male chromosome is getting more methylated.

• 1:23:02Lester Nare?

  Yeah, because, because based on where they are, they're in, they're in, again, the male is the one that almost has none. But the offspring are blended and so.

• 1:23:11Krishna Choudhary?

  And yeah, that's why the dotted lines are all in the middle.

• 1:23:13Lester Nare?

  In the middle. So you can see higher and the, higher and the opposite are, very interesting, okay?

• 1:23:17Krishna Choudhary?

  Okay.

• 1:23:18Lester Nare?

  Okay.

• 1:23:18Krishna Choudhary?

  Now let's go to the next one.

• 1:23:19Lester Nare?

  Yes.

• 1:23:20Krishna Choudhary?

  This one's weird. This is the CAPN11 gene. What we're looking at here is effectively paramutation.

• 1:23:29Lester Nare?

  Okay.

• 1:23:29Krishna Choudhary?

  Okay?

• 1:23:32Krishna Choudhary?

  So, in this one, in this particular region, the mom has, let's say, intermediate methylation, the solid pink line is like 50%. The dad is all the way down to like 10%. Okay, those are the solid green line that's way down there in that highlighted region. And the mom is down, there's a dip, but it's only 50%. The dotted pink line and the dotted green line are all on top of the green.

• 1:24:01Krishna Choudhary?

  None of the mom's effects of methylation have come through in the in the subsequent offspring. Okay, so that's that top part. Now let's look at the F2 generation. Okay, which is in the bottom.

• 1:24:11Lester Nare?

  Yes.

• 1:24:12Krishna Choudhary?

  Every single offspring has the methylation pattern of the dad. It's like the mom's methylate, like obviously the genes are there.

• 1:24:19Lester Nare?

  Right.

• 1:24:19Krishna Choudhary?

  But the mom's methylation pattern is completely gone. The mom's epigenetics have been completely silenced.

• 1:24:25Lester Nare?

  In both F1 and F2?

• 1:24:27Krishna Choudhary?

  Yes, and and and in F2 subsequently, yes.

• 1:24:30Lester Nare?

  Yeah.

• 1:24:30Krishna Choudhary?

  F2 is there to show that like whatever happened to F1, it didn't recover.

• 1:24:35Lester Nare?

  Right.

• 1:24:35Krishna Choudhary?

  Right, whatever happened in that first generation, the grandkids now just get no influence from the mom's epigenetics. All of the epigenetic influence is coming from the dad.

• 1:24:45Lester Nare?

  That's.

• 1:24:45Krishna Choudhary?

  In this particular allele.

• 1:24:46Lester Nare?

  Right, right, right, right.

• 1:24:47Krishna Choudhary?

  Right?

• 1:24:48Lester Nare?

  Right.

• 1:24:49Krishna Choudhary?

  This is very weird.

• 1:24:50Lester Nare?

  This is very weird. Because.

• 1:24:52Krishna Choudhary?

  This is something that we saw in the maze, right?

• 1:24:54Lester Nare?

  Right.

• 1:24:54Krishna Choudhary?

  Where it's like, it's like even when when I crossed the the purple with the green.

• 1:24:58Lester Nare?

  It was only green.

• 1:24:59Krishna Choudhary?

  Even the grandkids all were all green.

• 1:25:01Lester Nare?

  This was the suppression thing we talked about there.

• 1:25:03Krishna Choudhary?

  This is now the the the allele is completely suppressed.

• 1:25:07Lester Nare?

  And so we're now we're seeing this in animals as well. We'd seen it in the the maze before, but now we're seeing it in more complex.

• 1:25:13Krishna Choudhary?

  Yeah.

• 1:25:13Lester Nare?

  Biology, which is fascinating.

• 1:25:17Krishna Choudhary?

  Mm hmm. And there there's some very cool like consequences of this that we'll talk about at the very end, okay? Um, the last few figures that I want to talk about, um, this next one, figure number thirty four. This is, I think, figure six and seven. This shows um some emergent epigenetic patterns. Again, the main thing to see is that the dotted pink and green lines are different from the solid ones. The one on the left, figure six, that shows something very weird, which is that the offspring sometimes just have more methylation than either of the parents. So that I don't even know how that got there.

• 1:25:53Lester Nare?

  Right, right.

• 1:25:53Krishna Choudhary?

  And neither of your parents had it. It's not even a blend or one of the parent is dominant over the other.

• 1:25:58Lester Nare?

  Which would it make almost more sense?

• 1:25:59Krishna Choudhary?

  Yeah, yeah, this this was just like.

• 1:26:01Lester Nare?

  This doesn't.

• 1:26:02Krishna Choudhary?

  Yeah, that's why they're calling it emergent epigenetic. You know, it's just like, put it in that bin.

• 1:26:07Lester Nare?

  Yeah, well, we'll come back to that later.

• 1:26:08Krishna Choudhary?

  Yeah, yeah, yeah, it's like, it's like this happens, um, and we report it. So now you gotta say this. And then and then on the right hand side, we've got genomic imprinting. This is, um, again, this is similar to the mom and dad thing, but here, so in the in the mom and dad one, um, it didn't actually matter. Which chromosome, which, if the, if the allele came from the mom, or if the allele came from the dad? Because both sets of alleles, if they were from the mom or the dad, it was allele specific. Here, it's actually mom and dad specific. It's a process where certain genes are expressed in a parent of origin specific manner. In this case, the epigenetics is expressed in a parent of origin matter. Okay?

• 1:26:53Krishna Choudhary?

  So if the methylation is with the mom, only then is there going to be methylation in the kid. Okay? Doesn't matter what type of allele it is.

• 1:27:05Lester Nare?

  Which is actually an important distinction.

• 1:27:07Krishna Choudhary?

  Yeah. So it's a parent of origin.

• 1:27:12Lester Nare?

  So there can both be allele specific divergence in methylation in, you know, the FN generations.

• 1:27:21Lester Nare?

  And that can be true on top of the fact that there's this genomic imprint.

• 1:27:25Krishna Choudhary?

  Yeah, yeah.

• 1:27:26Lester Nare?

  Like, they're not necessarily independently true.

• 1:27:28Krishna Choudhary?

  Yeah. It's a, it's super, super, super complex.

• 1:27:33Lester Nare?

  Yeah, because the commona torx becomes...

• 1:27:35Krishna Choudhary?

  Right, the commona, yeah, exactly.

• 1:27:36Lester Nare?

  Becomes quite difficult.

• 1:27:38Krishna Choudhary?

  The last one I thought was actually really, really cool.

• 1:27:42Krishna Choudhary?

  I mean, I think, I think all of this stuff is really, really cool. But here, what we're seeing is a difference in one organ dependent methylation. So the same region in the liver versus the muscle. The muscle has about 80% methylation in both males and females. And in the liver, the males have 80% methylation, but the females have something like 50% methylation.

• 1:28:07Lester Nare?

  This is crazy.

• 1:28:08Krishna Choudhary?

  Highly significant difference.

• 1:28:10Lester Nare?

  This is crazy.

• 1:28:10Krishna Choudhary?

  Okay?

• 1:28:10Lester Nare?

  So you can also have divergence across organs and top of...

• 1:28:14Krishna Choudhary?

  And on top of sex. Now, why is this important? This was found, so it's hypermethylated in females, and then not that much in males, right? Why is this important? Well, it's found exclusively in the liver. What does the liver do? One of the big things that the liver does is...

• 1:28:31Krishna Choudhary?

  Dictate tissue specific, like it dictates hormonal environments. It dictates how drugs are detoxified. So this could be one of the main reasons why certain drugs work one way in one sex. And then not in another sex.

• 1:28:49Lester Nare?

  Yeah, yeah.

• 1:28:49Krishna Choudhary?

  Right? Because that's a known effect.

• 1:28:52Lester Nare?

  Right.

• 1:28:52Krishna Choudhary?

  That's kind of mysterious.

• 1:28:53Lester Nare?

  Right, right.

• 1:28:54Krishna Choudhary?

  This could be it. Like the epigenetics is different in the liver, but not in other, other places.

• 1:28:59Lester Nare?

  Really important potential insight among many in this is that there is this organ specific epigenetic difference in methylation in the liver, which would affect drug delivery.

• 1:29:16Krishna Choudhary?

  Yeah, a drug like efficacy.

• 1:29:18Lester Nare?

  Efficacy, yeah, right, right.

• 1:29:21Krishna Choudhary?

  Kind of crazy.

• 1:29:21Lester Nare?

  I, yeah, oh my, I'm thinking about so many things, but I, I want to be not, we, we will talk for the next three hours.

• 1:29:29Krishna Choudhary?

  Yeah, I mean, obviously this has very deep implications.

• 1:29:31Lester Nare?

  That's, that's right. That's the main headline.

• 1:29:33Krishna Choudhary?

  And what, what it's really saying is, look, future clinical genetics is now going to need to focus on genetics and epigenetic risk. Okay, if we want to start charting, you know, like how an individual's genome is going to affect their life and so on and so forth, right? There's also some very cool, just like fundamental science things that are happening here.

• 1:29:59Krishna Choudhary?

  That have to do with like, for example, evolution, right? The foundational science of evolution. There used to be this theory called the Waddington's theory of genetic assimilation. Basically, it's saying that environmentally induced traits can become hardcoded into the DNA, right? This is not very Darwinian. Darwinian is just natural, natural selection, survival of the fittest. It's like the offspring get a random assortment and then they live their lives and then if they survive, they procreate, right? What Waddington's theory is saying, it's, it's more Lamarckian in the sense that your life is going to dictate the genetic, your genetic makeup. Now, for a long time, this was discredited and for good reason, because genetics is

• 1:30:42Krishna Choudhary?

  like, as I said, the DNA part is like very hardcoded, right? But now there's a link between the software and perhaps the hardware.

• 1:30:50Lester Nare?

  Yeah.

• 1:30:51Krishna Choudhary?

  Because. Methylated cytosines, which are the Cs with the methyl groups, those are inherently chemically unstable. Okay, so what that means is they frequently mutate into thymine Ts. So if I have more methylation, I'm gonna have more mutations, and I'm gonna have more Ts where there should be Cs at three times a higher rate. So what's the conclusion? That means that if among the inherited epigenetic traits, right? If my life is changing the methylation pattern, that methylation pattern could change the hardware itself because of this 3X difference in mutation rate.

• 1:31:34Lester Nare?

  It's a recursive self-improvement or not.

• 1:31:38Krishna Choudhary?

  Or not improve, yeah, it could go either way.

• 1:31:40Lester Nare?

  It could go either way.

• 1:31:41Krishna Choudhary?

  Kind of crazy.

• 1:31:42Lester Nare?

  That's a really, you know, it's always been the conversation about nature versus nurture. It's more like nature and nurture. And it's, there's this combination between the two. And as this sort of continues to permeate as now posing some very difficult questions,

• 1:32:02Lester Nare?

  there is, and obviously the sort of epigenomics and epigenetics conceptually have now been around for some time. These are the kind of big results that I think put us into a new frame, you know, a new, what do they call it? The Overton window on this is moving a little bit to now really think about, okay, because I think your point is right. Over the course of your life, if your, your life itself is impacting the methylation on these cytosines that then become, go from C to T, and your offspring fundamentally get different genetics as a result of that, that's pretty meaningful.

• 1:32:45Krishna Choudhary?

  Yeah, yeah, that's, that's pretty huge, right? I mean, even, even in terms of disease risk.

• 1:32:52Lester Nare?

  Right.

• 1:32:52Krishna Choudhary?

  This is a big deal, right?

• 1:32:53Lester Nare?

  Right.

• 1:32:54Krishna Choudhary?

  Because you can explain now how a mutated allele could epigenetically silence a healthy allele.

• 1:33:01Lester Nare?

  Yeah.

• 1:33:02Krishna Choudhary?

  Right, so it's not just all about genetics. Even if you're a heterozygote and you've got the correct allele to like survive the disease, if you've got some shenanigans going on like this, and the healthy allele just doesn't even get expressed.

• 1:33:15Lester Nare?

  Yeah.

• 1:33:16Krishna Choudhary?

  You're biologically null for that gene, right?

• 1:33:20Lester Nare?

  This makes me think about things like

• 1:33:25Lester Nare?

  like anemia being more prominent in like Mediterranean or African populations.

• 1:33:32Krishna Choudhary?

  Yeah.

• 1:33:33Lester Nare?

  And it's like, is there?

• 1:33:35Krishna Choudhary?

  Well, that one, that one is actually a single nucleotide polymorphism. Yeah, that's actually, there's like a straight up hardwired genetic difference. That's not an epigenetic thing.

• 1:33:43Lester Nare?

  That's very.

• 1:33:44Krishna Choudhary?

  And that one's well documented because the, the, the mutation is, I believe, in the

• 1:33:49Lester Nare?

  That's great.

• 1:33:49Krishna Choudhary?

  In the Heme protein or something like that, that like affects the shape of red blood cells.

• 1:33:55Lester Nare?

  Yeah, where you cannot store the hemoglobin as well.

• 1:34:01Krishna Choudhary?

  Yeah.

• 1:34:01Lester Nare?

  Hemoglobin is.

• 1:34:02Krishna Choudhary?

  It's like, it's like in a weird shape.

• 1:34:04Lester Nare?

  Weird.

• 1:34:04Krishna Choudhary?

  Some of them are a weird shape, so then that makes the cell a weird shape. So, but there's so many other things, right? And this is like, there, there are traits, I forget which, but like, there's some traits where like the, there's like weak evidence that shows that the grandmother's exposure to stuff alters the disease risk of grandchildren. Okay, and maybe that's another episode that we could do. But like, this is, this is now getting to that question, right?

• 1:34:28Lester Nare?

  And we can now ask, we can actually probe at the, probe at it much more, in a much more robust fashion.

• 1:34:37Krishna Choudhary?

  Yeah.

• 1:34:38Lester Nare?

  Not just create a framework or have things that we can't quite then follow up with empirical data.

• 1:34:45Krishna Choudhary?

  Yeah, and I mean, the next step, the next clear step, and this is something that Feinberg and his colleagues are doing next, is to do this long read sequencing stuff.

• 1:34:52Lester Nare?

  Yeah.

• 1:34:53Krishna Choudhary?

  For humans.

• 1:34:53Lester Nare?

  Yeah.

• 1:34:54Krishna Choudhary?

  Right, and see permutation in humans.

• 1:34:56Lester Nare?

  Which makes total sense.

• 1:34:57Krishna Choudhary?

  So, because if it's like 7% in mice, it could even be higher in humans because humans are a relatively recent evolutionary organism, right? And our mutation rate is hella high, and that mutation rate. We've only, we're really talking at the hardware level. If the hardware level is already high, imagine what the mutation rate at the software level is. You know?

• 1:35:20Lester Nare?

  This is fascinating. A big, big return episode for our resident PhD, Krishna Choudhary. New rules for this idea of non-Mendelian inheritance of epigenetics. I mean, there's so much here that we, again, we can't cover everything in these pods. There's a lot of detail that we can't quite dive as much into. But hopefully, we gave a nice overview for folks who are interested in this conversation. And again, like I mentioned, there's so many, you know, social, cultural conversations around this idea of quote unquote generational trauma and its impacts on your, your actual

• 1:36:04Lester Nare?

  physical outcome. And we're starting to be able to actually poke at some of these areas in interesting ways. Do we want to leave? Because this is a long one. So if you've made it this far, congratulations. You are a lifelong learner like the rest of us. Do we want to have any questions for folks to leave in the comments for this episode?

• 1:36:24Krishna Choudhary?

  Oh, yeah. Well, I was gonna say, what we, what you guys should do is tell us what books to put on the, as you said, in the, the thing.

• 1:36:31Lester Nare?

  Yes.

• 1:36:32Krishna Choudhary?

  But if you made it this far, and do you have any advice for, for a new father?

• 1:36:40Lester Nare?

  That's a good one.

• 1:36:40Krishna Choudhary?

  Even if you're single and you don't have kids, just give me some like really terrible advice. I want to see like the, the worst advice you can think of.

• 1:36:50Lester Nare?

  My name is Lester Nare, joined as always by my co-host and our resident PhD. Welcome back to Zaddy Krishna Choudhary. It's great to have you back. This is always so, so fun.

• 1:37:03Krishna Choudhary?

  It's good to be back.

• 1:37:04Lester Nare?

  We got some fun ones coming up for you guys here in the next couple of weeks as we get back on our regular scheduling cycle. We appreciate you all for staying with us and we will see you all next week.