SIO458: How Eye Color Reveals the Complexity of Genetics

Transcript

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

0:00:12 Thomas: Hello and welcome to Serious Inquiries Only. This is episode 458 and I'm excited to bring you two parts. Now, this is everyone's favorite dinosaur ologist. No, dinosaur constructor. Of genetic dinosaurs. Eric Jaffe. One thing Eric was really keen on explaining to us all, a subject he was really excited about, about teaching is us about CRISPR, but in a more detailed way than perhaps might've been in the kind of the popular coverage. That's hard to do in a podcast. First he wantedto lay a little foundation here by talking about genetics, talking and some other stuff. So this first part is how we get our eye color. And how eye color can teach us about a lot of other things in genetics. And I know, what the hell's going on with all that, I guess. But along the way, there's some really interesting stuff. He talks about why there really are no binaries in genetics, and it's very silly to call sex, for example, a binary in genetics there's, just so much more complicated. Like if I were to summarize the kind of the tension that I think this helps explain, it's like, OK, on one hand, as a layperson, I know there's the genetic code. I know we cracked that human genome sometime in like, I don't know, what was it, 2000s, early 2000s or something.

0:01:32 Thomas: And that would seem to a lay person like, oh, OK. So we should have the answer to like, you know, everything like we should just know how everything works. In the human body, where everything comes from. You know, like you would think that's it. Like we should have everything. But obviously that's not true. And obviously, even with a technology like CRISPR, which we'll get to in part two, still really complicated. It's still incredibly hard to figure out what exactly is happening. And so this episode really helps illustrate why, like, why is it so much more complex than just like, oh, Gattaca, you like we got those letters, G -A -T -C, and then if you know the right code of them, then you can just do anything. There's so much more going on. And this episode really helps elucidate that. It is absolutely a tricky topic, especially for me. It's not one of my strong suits. It may take careful listening, but one thing's for sure, we have an enthusiastic teacher in Dr. Eric Jaffe, and I really think that's a lot of the battle. If you've got someone who's enthusiastic and wants to teach you something, I think that goes a long way. So without further ado, we'll take our normal ad break that you can avoid at patreon.com/seriouspod, and then we'll get going. And I'm once again, joined by Dr. Eric Chaffee. What are we going to build today? How are you doing?

0:02:48 Eric: I'm doing great. And today we're going to build an eye very quickly, and then we're going to peel back the layers.

0:02:54 Thomas: Do we have to build onions first, though, then? Are we also building onions?

0:02:58 Eric: Luckily, the divergence between onions and people happened far enough away that we're not going to do too much onion genetics.

0:03:02 Thomas: Phew.

0:03:03 Eric: Plant genetics actually gets really weird. They have way too many chromosomes a lot of times. Be no, no DNA discussion in this episode.

0:03:06 Thomas: Sound Oh, thank God. So, yeah. Love that building a dinosaur episode. Still think about that from time to time. And now I'm wondering, you hinted that there's some stuff to perhaps clean up or add to that.

0:03:21 Eric: As a teacher, I always like to do something called spiraling. And when you spiral, you add new topics, but then you kind of layer in the stuff we've already talked about. This is both from kind of discussions with you and some of my friends and family that listened to the podcast. There was a lot of confusion around the question of like, how do these changes in genetics actually drive changes in that perspective bird slash dinosaur. I thought today would be a good topic would be like, how do genes actually make us who we are? What do genes do that make us the things that we use to survive? And how does changing genes then change the person itself?

0:03:54 Thomas: I want to note, you and I have a different idea of what spiraling is, but that's okay. I like your version. It's probably better.

0:03:59 Eric: There's another spiraling that I'm trying not to do after the recent Supreme Court rulings and debates, and that is we're going to try healthier spiraling.

0:04:06 Thomas: So you are familiar with my kind of spiral. I got you. Okay.

0:04:09 Eric: I think we've all been in it. I want to kind of go back to, again, my high school biology roots, and we're gonna talk about something very biologically simple, eye color. And we're gonna go from there, and we're gonna peel back how we get our colored eyes, and then what are the different ways that complexity and regulation gets layered into a fairly simple logic. To get started on that project, we are first going to have to talk about — now, biology isn't a religion, but there is a central dogma in biology, a kind of organizing thing that makes genetics make sense. And it's called the central dogma because by and large, it holds for every cell that is going to do biology. It is how genes work and it's what makes us who we are.

0:04:46 Thomas: Are there any cells that go into accounting or anything or?

0:04:49 Eric: There are cells that don't hold to this dogma super well. And there are also viruses that really don't hold to this dogma well. So AIDS is a great example of a virus that just kind of rebels against the central dogma. In general, the central dogma is this. You start with your DNA, which is one form of genetic information. DNA gets what we call transcribed into RNA. You can think of RNA as like the temporary cousin of DNA. And we'll talk about what those differences are as we go through this topic of the eye. Once you get the RNA, that's what gives you the instructions you need to make the protein of the day that's actually going to do the thing. I think in the last episode, we likened it to a restaurant, right? Where the DNA is the menu. It's permanent, it's unchanging, and it's always there as like the background of what makes the restaurant the restaurant. RNA is like the ticket that a waiter writes, right. It is going to change based on customer preferences, the time of the season, the time of day even, right? Busyness of the crowd, customer modifications. Then the food is the protein. In biology, in general, proteins are what actually does things. They're the real workhorses of the cell. We have four major biomolecules. Sugars, carbohydrates, are mainly important for two things. They help provide some structure. They also give us our daily energy, right. You've heard of sugar rush, that's because we're converting those bonds, tons of carbon and oxygen into energy in the form of this molecule called ATP. The other major biomolecule that we're not going to talk about today is lipids. Lipids are these kind of fat molecules that form our cell membranes. They can be used to send messages between cells, but they don't really do the heavy duty lifting that our DNA and our proteins do for biology. Those are the two major molecules that we are going to focus on, our nucleic acids and our protein.

0:06:26 Thomas: So RNA is like the RAM kind of.

0:06:29 Eric: RNA way I like to think about it is it's like the, it's the RAM. It's the temporary processing power of the computer. Yes.

0:06:34 Thomas: Okay. Temporary. Yeah. Gotcha.

0:06:35 Eric: It changes based on usage. It changes based upon a host of other factors. It's also really fun because DNA is always known for that nice, perfect double helix, right? It's got two strands and it forms that nice winding helix. And that's important for its stability and its its ability to resist change, right? It is largely going to stay the same across your cell replications, across your cell divisions, across differentiation. It's everything else that changes, right. RNA, because it needs to change so dynamically, doesn't have that second strand. And that's going to play a huge role as we start sketching this process out. The way I always think about RNA, it's like, have you ever had headphone cords back before AirPods were universal that like, always get twisted and tangled in your pockets, they always get caught on

0:06:43 Thomas: It's It's known for it. Interesting. They still do. I still have those.

0:07:17 Eric: Yeah, RNA, unlike DNA, is single-stranded. Its base pairs are free to make base pair bonds the same way our DNA does, you know, like C bonds with G in our DNA. C bonds with G in RNA, too. But because it's single-stranded, it doesn't have an opposite partner to kind of nicely line up with and form that crisp helix. It's constantly making these hairpin turns, these sharp right angles, these bundles of messes as these base pairs are transiently temporarily bonding with each other and then losing those associations.

0:07:46 Eric: So RNA is much more dynamic in both structure and function than DNA. And that's going to play a huge role in the story we're about to tell. Let's frame that story. I mentioned that we're going to build an eye, right? I really mean is we're gonna talk about the genes that give us our eye color. In general, right, we have three major colors of eyes that we know of. We have our brown eyes, our green eyes, and our blue eyes. And then within that, there's a huge gradient in between, right? Let's talk about how we get our blue eyes, green eyes and brown eyes. The way you get color in your eyes is from a pigment protein. So again, proteins are the workhorses of the cell. Your genes have one protein that it produces that's called melanin. It is the same pigment that gives us our skin color. It also gives you your eye color. I know what you're thinking. Don't we have blue skin then, right? Why don't we have green skin? The reason is, is the same reason why you can have blue water, green water, and brown water, you go to one of those really pristine, um, beaches in the Bahamas, that water is like crystal clear blue or teal, right, and that's because there's very little stuff in there. Like the way our sky is blue, the way light diffracts in our atmosphere just scatters it in such a way that it appears blue to us. If you start putting in little bits of sediment, little pieces of dirt, animals, that water quickly becomes less blue and more of that green color, right? Then when you get a mudslide and there's just tons of mud and sediment, that's when you got that brown water. It's the same with our eyes. When you have a lot of that protein being produced, that melanin, you get brown eyes. You get an intermediate amount of that protein being produced. You get green eyes. When you have none of that protein being produced you get blue eyes. That's why green eyes are often considered that incomplete dominance. You have brown allele, right, one that's producing the pigment. You have a blue allele, one that — or blue version of the gene — one that doesn't produce the pigment, and if you have two of those, right, one blue one brown, you're not getting quite as much as if you have two brown eye genes, so you're not going to get brown eyes, but you don't have zero protein at all. So you're not getting blue eyes. And that's why you end up with green eyes.

0:07:46 Thomas: Interesting, Hmm. Hmm. That is interesting. So I have to imagine this about — in our evolution — at a certain point in time, right? Cause I, I imagine like apes, unless they, I know there's like albinism probably or or whatever, but I mean, their eyes are all brown, right? Or was there a point when this came about? And if, if so, was it an accident or was it something that was like, Ooh, this is a cool by-product that's now sexually selected or what?

0:10:00 Eric: I love the way you phrase that, because the answer is always both, right. Things in genetics are always accidents at first. Then it's whether they have selective pressure that they either get more prevalent or less prevalent. Right?

0:10:11 Thomas: I think I used the wrong term. Cause I actually meant like, I know there's — to be different between like, Oh, this is adaptive versus, Oh this is like a by-product of something else. Like it may still be being selected, but like indirectly, or maybe something that comes along with something else that's useful. Right. So, like, I was just wondering if it's that kind of thing, oh, like, our skin adapted to be a certain way. And along with that comes an eye adaptation that isn't really the key thing there. I was wondering the difference between those two things.

0:10:36 Eric: So you're thinking of something like sickle cell anemia, where the reason why sickle cell anemia is so prevalent in African-American populations is because they come from regions of sub-Saharan Africa where malaria is super present. If you have both copies of this mutated gene that alters the way your blood cells work, you have sickle cell anemia, which is deeply harmful. So you would think that that wouldn't be selected for, right? If you're a heterozygote, if you have one copy that functions normally, and one copy that has that sickle-cell allele trait, you actually have protection from malaria.

0:11:05 Eric: So the heterozygote protects it from selective pressures against the more harmful version of the homozygous. That's actually a very good point that you're making, that there are often complicating factors for these selective pressures. In this case, actually, blue eyes is actually a weird thing. You're absolutely right that the standard is brown eyes. What's interesting, when you look at the mutations that cause blue eyes, they're very narrow. There's only a select few and they're not very diverse, which suggests that this is one of those things that was kind of one of those random things that happen in a population. Because there wasn't any selective pressure to select against it, it just happened to keep existing at that low level of quantity because it's not the standard. You're only going to be able to get it if you have a non-functional copy of the gene. It does seem that pretty much all blue eyes come from a like select few mutational events a hundred thousand years ago. That's actually a very good point. But there is another point that we should be picking up on here. We don't have only three colors, right? Clearly there is a lot more going on than just if you have a copy that works, you have brown eyes. If you have copy that doesn't work, you have blue eyes. And if you have one copy that worked, you green eyes,

0:12:04 Eric: Right.

0:12:04 Thomas: I, I I was assuming it was just like different gradients or something.

0:12:07 Eric: And we'll get into why those gradients exist, because to me, that's what makes biology, biology. But I did want to also mention, this is why blue eyes is the recessive trait, as right, long as you have one copy of that functional gene, you're going to make the protein that prevents from becoming blue because you need that complete lack of pigment in order to get those blue eyes. That's why blue eyes is the recessive trait, because if one of your parents gives you a functional gene then by definition you're not going to be able to have blue eyes. So as we mentioned, we have those three cases, but we've got to start building in complexity, and the real reason is that I think we think of most mutations that interrupt proteins, right, it just renders them non-functional, that's not really how it works, and the reason why that is is because of that central dogma of biology. So let's take the absolute easy case with blue eyes, right. I have a mutation in my gene that is going to cause me to have blue eyes. I now try to produce that melanin protein, but it doesn't work, it's not functional, or it gets degraded immediately, right? Now I don't have that protein in my eyes. That's going to change the way that light scatters. That's going to give me that blue-eyed appearance. If I have one copy, I'm going to have — because I have two chromosomes, right, I'm gonna have one copy of the gene that's functional and produces some amount of that protein. Then my other copy is going to be useless. So I don't have as much as if both of those genes were working at full speed, right. As we mentioned, there's also hazel eyes, there is dark brown, light brown, amber eyes, light blue, blue-green, right? So how do we get that range from a simple process? The first step is, while we think of eye color as being controlled by one gene, right, you produce that pigment or not, that's not really true, because nothing in biology can really exist independently, right, you still need genes that can deposit that pigment in the correct location, make sure that that pigment stays stably expressed, right. Make sure that no other proteins are messing around and trying to interfere with that pigment. There's roughly about 16 genes actually that control our eye color. And there might even be more that we haven't yet elucidated. Just always keep in mind that when we teach things in like model systems, like eye color, we're giving that simplified version, but there's a lot of complexity underneath the hood. The other real reason is we think of mutations as like an on or off switch, right? You get the X gene as an X -Men, you then have the powers. Whereas as

0:14:11 Eric: If you don't get it, you don't. That's not really how genetics works. Genetics works more on efficiency. So going back to that RAM, right? If you have a computer working at 70% capacity, you can still play your video game, but you might get a frustrating amount of lag, right. Then eventually, you'll drop to a point where that efficiency is so low that it's not even worth playing the game anymore. But there's plenty of stages in between where you're willing to put up with that two to three seconds of lag and you go, okay, this isn't optimal, right? It's still able to be used. There's food that you can cook that's way too salty, but you're like, it's still edible. And then all of a sudden you get that salt bomb. I once in college baked cookies with salt and that was inedible. There were times where I've just used too much butter and those weren't ideal, but those goopy messes were still edible, right. It's much like our genetics. Let's think about why that happens. We have our gene, right, this gene is going to produce melanin. I think we briefly touched on this in the last episode, but there's two major parts of the gene. There's the regulatory region, and then there's the region that actually produces the protein, You right? Can think of this as like the package is what needs to be delivered in order to, you its thing, right. I need a birthday cake, I need it delivered at my house, Otherwise, I'm not celebrating a birthday. But before that birthday cake is at my my house, I have to put in an order to the bakery. I have to tell them what time I need to pick it up. I need to, you know, the correct location of that bakery and then bring it back to the correct location in my house. All of that is the regulatory sequences of our DNA. It's the packing slip for the package in our UPS package, right? Mutations can happen either in that protein region or in that packing slip. Let's first start with the protein one, because I think that's a simpler one to unpack — the pun. You have a mutation in this gene that produces melanin, right? Some of the time, you will get a gene that renders that protein completely non-functional, right, in the genetic code, because this is probably obvious, but your DNA is kept in a long string of base pairs, right? Genes are kept one after the other in that long string of A, C, G, T, A, C, G, T, those letters, right? But

0:14:43 Thomas: Interesting long are we talking but

0:16:00 Eric: There are thousands of genes and millions to billions of bases in the human body.

0:16:04 Thomas: Like if you stretched one out, like whoa, no

0:16:07 Eric: Yeah. If you stretched out all of the DNA in your body, like base pair after base pair.

0:16:10 Thomas: I I guess I mean like so isn't it I I this is so hard to keep in mind because it's crazy but it doesn't every cell basically have your entire genetic whatever so it can't be like, like infinitely big, but like, so every — so how, how much is, how does it hold all that? How much is that?

0:16:28 Eric: We're going to talk about some of the ways it holds all of it. But if you were to take all the DNA and unwind it — so the way it stores it is by coiling it over and over again. Think of that as like when you have rubber bands and they start like twisting in on themselves, and they get more and more compact as they get twistier and twistier.

0:16:42 Eric: DNA does that same thing. It's called supercoiling. But if you were to uncoil all of your DNA in your body, it would stretch to the moon and back, I think it was hundreds to thousands of times. We have an unimaginable amount of DNA in our body. As we mentioned, not every piece of DNA in every cell at every time is going to be used, right? So what we're going to talk about now is how does that eye cell know to produce this gene? And once it's producing that gene, what does that mean? And how does that actually translate? And that'll be a pun for later. How does that translate to the traits that we know and love? We start with the gene. We have our melanin gene. It's got a series of bases, right? It might be like ACG, CGT, TCA. Note that I'm reading these in sequences of three base pairs at a time, right. DNA is organized in series of triplets that we call codons. The reason they're called codons is because they're what codes the protein. So the first step of our central dogma of biology is we need to transcribe, make a copy of our DNA, that permanent form, into that temporary form of RNA that's going to be used in the day-to-day of the cell. What happens is a protein comes down called RNA polymerase. RNA polymerase recognizes and binds the DNA. Then it's going to take RNA bases. After it unwinds that double strand, it's gonna start base pairing the same way when we replicate our DNA, right? If it sees an A on the DNA strand that it's reading, it's gonna place a U there. If it sees a C, it's gonna place a G,

0:18:01 Thomas: What

0:18:01 Eric: U for uracil. So RNA uses one base differently than DNA. While DNA has a T as the fourth letter, RNA uses a U.

0:18:09 Thomas: The hell?

0:18:09 Eric: That's probably an accident of evolution.

0:18:11 Thomas: That's so interesting.

0:18:12 Eric: Or Actually, now that I think about it, it might be the way that thiamine is structured and its ability to store.

0:18:17 Thomas: It's like a different file system. We got Mac and PC going on.

0:18:21 Eric: Exactly. It's very similar to... If you've ever signed those things on the carbon copy sheets where some of the letters come out a little janky on the second page, a little like that, where as you're making this copy of the DNA for the temporary form, you're using the template of the DNA to elongate your RNA strand. And eventually you have a fully produced transcript. Something we should mention is how does the RNA know when to stop? How does the RNA polymerase know when to stop producing, right?

0:18:46 Thomas: I don'T KNOW HOW I KNEW WHEN TO START, WHERE TO GO, WHAT DAY IT IS. I DON'T KNOW how it knows anything to be honest uh

0:18:51 Eric: I did skip the start, didn't I? Remember when we did how to build a dinosaur, we talked about how transcription factors, right, bind DNA and direct the cell to produce certain genes and certain proteins. That's the first step in our journey. A transcription factor, another protein itself, is going to bind and recognize certain sequences of DNA, right? That's based entirely on the shape and structure of the protein and what amino acids that protein is comprised of. So amino acids are the building block for proteins in the same way that the individual letters and base pairs are the building blocks of DNA. Each of those three base pairs that I said are the codons will code for one amino acid,

0:19:27 Thomas: Say so I'm Not sure how what level I need to understand this but

0:19:30 Eric: Yeah, it will be more clear once we get into the process of transcription and translation. A transcription factor will come and based on its own sequence of amino acids, it will recognize certain pieces of the DNA. Right. That's basically like the horn blowing in the Lord of the Rings where it's — it's sending up signal flares. It's recruiting all of what we call the transcription machinery to come to this site on the DNA strand. It's saying we need to produce this RNA transcript so we can make the protein, come on over RNA polymerase. And it brings RNA polymerase to that exact part of the gene that it needs to produce the protein. Make sense so far?

0:20:02 Eric: So then RNA polymerase is going to, and I'm using air quotes here, it's going to read the DNA, right? It's going to unwind that DNA so that it only takes one strand at a time. It's going to give the opposite letter that it pairs to and build an RNA strand that we call complementary to the original strand. Again, if it reads a DNA strand as like ATTT, it will put one as UAAA, right? It is doing the reverse base of its base pair. And that builds a single-stranded piece of RNA that now has the code that you need to turn into the protein. We are still in the nucleus here. And the way you know that is because we're dealing with DNA, right. All of the things that the proteins need to do are going to be in the cytoplasm. We are going to have to, over this process, go from that nucleus where the DNA is to the cytoplasm where all this stuff is happening, right? Eventually, you need to leave Washington, D.C. and actually go to the place where your infrastructure program is taking place.

0:20:51 Thomas: Are we in the — like, uh, whatever, whatever development stage, or does this matter — is this every

0:20:55 Eric: This is every cell, every cell every time you produce a protein.

0:20:58 Thomas: Time you produce a protein. How often am I producing proteins? All the time? And

0:21:02 Eric: It would depend on the gene. But in general, yes, you are always producing proteins unless you are dead.

0:21:07 Thomas: What am I doing with these proteins? So

0:21:08 Eric: You're using them to do various functions. So let's say I need to... It's

0:21:11 Thomas: I wasn't sure when you talk about eye color, I wasn't sure if we were talking about like, well, this develops in the fetus or whatever, when — some early stage — but you're talking about all the time.

0:21:18 Eric: Both, Both. Yes. Because proteins, right, just like every other biological thing, has a shelf life. Eventually they degrade. Eventually they turned over.

0:21:23 Thomas: Is Is that why old people tend to have like lighter, lighter eyes, or is that unrelated? Related, yeah, yeah.

0:21:32 Eric: I guess it is somewhat related in that as you accrue either scarring and DNA damage, it will affect the rates of replenishment and it will affect the way those proteins get replenished. But I didn't specifically look that up and I don't want to.

0:21:44 Thomas: I feel like they do. I could be entirely making that up, but I'm pretty sure they do, I don't know. At least people who had non -brown eyes. I'm actually not sure about brown eyes, but

0:21:51 Eric: The general principle is the same. As your DNA gets, you up up a couple of changes here and there over life as you doing this process and altering your environment slightly, you get less and less efficient at the protein build and turnover over time. And that's part of the aging process. But let's get back to the main point. So we have a transcription factor that bound the DNA. And it's saying we need more of this brown pigment, this melanin in this eye. Let's produce a transcript that produces the RNA that tells our body we need to make more, right? The RNA polymerase then binds the DNA right at the site of that melanin gene. And it starts just making a copy of that RNA transcript. It's going to do base pairs, and it's going to give a transcript that's hundreds to thousands of base pairs long, right, and tons of base pairs. As I mentioned, there's multiple parts of the gene, right. There's the packing slip, and there's the actual thing that gets produced, right? We only need the part that's going to turn into the protein once we're doing this process called translation. What needs to happen is that RNA gets processed in the nucleus in a process that we call splicing. Splicing is the first step where you can — or the second step besides the transcription factors — where you can add an extraordinary amount of regulation. The reason why is because, while I've originally told you that each gene produces one protein, once again, a kind of oversimplified version of the story. In reality, each RNA transcript can be changed, rearranged, and cut in different ways that you end up with different versions of that transcript that will produce different versions of similar proteins. So maybe you want one protein that has a huge, like, part of the protein that can work as a molecular scissor. You're going to process that RNA transcript one way, then if you need a version of that protein that doesn't have that molecular scissor, you want to get rid of that piece of the RNA.

0:23:28 Thomas: Molecular scissor. You can't just introduce things like this and move on, but

0:23:30 Eric: A A molecular scissor would be something that like cuts DNA. That's what we'll get into when we talk about CRISPR, because CRISPR is really a case of molecular scissors gone crazy.

0:23:38 Thomas: Am I making molecular scissors? Oh, wow, they're natural.

0:23:40 Eric: Yes, molecular scissors are what we call our nucleases. They help kind of cleave DNA, cut it up. You also have of things like proteases, which get rid of different protein groups, right? You're constantly changing, modulating, and cutting your proteins the same way you would in like a do -it -yourself version of building your house, right. Body is constantly a DIY house builder for your body. It is constantly making these adjustments and changes and modifications, using things like scissors and glues and transferases, all of the things that you would expect it in like building and construction. The main point is, right, already we have this way to produce many different types of protein from just one RNA transcript. Again, we are only interested in melanin, right? We're going to chop out what we call introns, pieces of the RNA that we are not using in producing this protein. Then we're gonna take that RNA, now that we have kind of made it the one that we want, we've sanded the edges, we have drawn our blueprints. We have kind of cut it down to the thing that we need, right? Now we send it away from the nucleus. I want to put a pin in one thing. People were freaking out about the mRNA vaccines and COVID and how it would alter our DNA. Notice as this RNA is being turned into protein, what is it doing with regards to the nucleus? It's leaving, right. It's leaving — the RNA in those vaccines isn't going to enter the nucleus, they cannot alter your DNA. And that was pure fearmongering.

0:24:56 Thomas: Interesting.

0:24:56 Eric: But our RNA has now left the nucleus. It is in the cytoplasm. We have made a copy of our DNA in a temporary form. We call that process transcription because you're still sticking with nucleic acids, went from deoxyribonucleic acid, DNA, to ribonucleic acid, RNA. The language is still the same. You're using those base pairs and letters. You are just making a thin copy. And that's why it's called transcription.

0:25:18 Eric: Transcription. You're transcribing what the DNA does into a copy you can use. A protein isn't built on nucleic acids. It's built on amino acids. And that's a slightly different language. Now we have to take our transcript, our RNA, and we need to translate it into the protein. It does that using what we call the genetic code. Now, we're finally going to learn why the letters we have matter. Let's say I have an ATG as my first three letters. As a hint, every gene starts with that ATG. It is what we call the start codon.

0:25:48 Thomas: Oh, interesting.

0:25:49 Eric: Those three letters will always recruit what's called — so let me back up a second. We have our RNA, right? And it needs to be translated. There's a machine that we use in our cell to translate RNA into protein in that cytoplasm called a ribosome. A ribosome is a mix of RNA and proteins that basically works like a conveyor belt for the RNA. It will read through the RNA letters and it will start grabbing amino acids and kind of like forcing them together like Lincoln Logs into the protein that it's going to be. Let me try and do one helpful image for you. Have you ever tried to put like a thread through the eye of a needle?

0:26:22 Eric: That's what you're doing with the RNA transcript to the ribosome. Or you're like feeding in something through like a paper reader, right? Like one of those scanner things. And you have to constantly feed the tickets into the arcade game that gives you a prize as it's counting, right. You have to feed it through that slot. It's going to register each one as it comes in and make some informational assessment. It's going to do the same thing in the cytoplasm with our RNA and ribosome. We have those first three letters, ATG. It gets fed into that hole in the ribosome. The ribosome reads those letters. And just remember when I say read, we're talking biochemical stuff, biophysics,

0:26:22 Thomas: Sure Yeah,

0:26:53 Eric: Right? Not actual reading and scanning. It reads those three letters. Then just like with DNA, it's going to take another molecule that has the opposite base pairs to that molecule. It's going to take a molecule that has the letters — if we have ATG, it's gonna have TAC attached to the other molecule, right? The way the A binds with the T, T binds with A, and the C binds with G. Makes sense? It's, again, all about that base pairing, right, there's right, there's not a choice in the matter. It's only going to recruit the tRNA has this right base pairs that's complementary to those first three letters of the RNA. It's going to bring in that first amino acid. Then just like a ticket reader, it's gonna shove and continue to thread that needle, right? it'S going to push in the next three letters. And let's say those next three letters are CTG. I want to note, I don't have the genetic code in front of me. I'm just using random amino acids here.

0:27:20 Thomas: What you did there you don't have the genetic code we all have a different one, or do we have like the same first several?

0:27:46 Eric: CTG, what? No, No, we all have. So this is actually one of the best proofs of evolution is the fact that every single organism on Earth uses the exact same genetic code. The reason why is because the amino acid at the top of the molecule that is recognized — right, the mRNA is the transcript, what we call the tRNA is what brings the amino acid to the messenger RNA to build the protein. Again, the tRNA is using those three base pairs that it recognizes on the mRNA and base pairs. So, right, if I have ATG in the mRNA, the tRNA is going to have TAC, right. There is no reason why the particular amino acid in this tRNA happens to be the same one across all other species, because the site of the amino acid and the site of the base pair recognition are not all that related to each other. The only reason they're the same across every species on Earth is because we all got the same genetic code from the same common ancestor.

0:28:38 Eric: But if you really want to disprove evolution by common descent, show me someone that uses a different genetic code and I will concede that they likely had a different common ancestor,

0:28:47 Thomas: Well, you know, they just say God probably made that common ancestor, so it doesn't really — but I guess it doesn'T just prove evolution though because evolution yeah it's like yeah

0:28:52 Eric: But right, it supports evolution by common descent. It doesn't necessarily disprove creationism, is I think the way you want to put it. But either way, we have those three letters, right? And it just brought over methionine because Because it had the only, that tRNA that has methionine has the three letters that recognizes and is base pair complementary to the three -letters in that mRNA transcript. You continue to thread that needle through the ribosome, right? That mRNA transcript through theribosome. So after those first three letters, you then feed in the next three letters. And once again, a tRNA with the correct complementary base pairs, so let's say I have CTG this time. The tRNA with the base pairs GAC, right, which are the base pair for CTG, are then going to bind by the laws of physics, right? That CTG is going to have a different amino acid that's associated with it. We have 20 different amino acids, 20 amino acids can combine over the course of hundreds to thousands of chains of those amino acids into the dizzying array of proteins that have so many different functions because each amino acid has three parts of it that are exactly the same. And then one part called the R group that gives it its functional properties, right? Like, let's say I need to be one of those molecular scissors and I need do a lot of cutting of things, right. Acid -based reactions are a great way to have that cleaving, that scissoring in molecules. So that protein will probably have a collection of either acidic or basic amino acids right at the part where it's doing its scissoring. That's the sequence determining the function of the protein. And it's because each time you get those three base pairs, a different amino acid with a different property is being recruited to build that chain of protein. Okay, let me try to zoom out then. We've got our mRNA transcript, your mRNA transcript, that thing that will become the protein, is organized in groups of three base pairs. Three base pairs tells you I need a different amino acid. Amino acids will then stack together to build your proteins. Just like if I'm using different ingredients to build my cake, that will give it different flavors. If I use different amino acids to build my protein, that's going to give it a different function. So what mutations do is they change those three letter sequences, right?

0:30:55 Thomas: All right.

0:30:56 Eric: Then you start getting different amino acids. As you start getting different amino acids, the function of that protein is going to change. The reason why eye color forms a gradient is because most of the changes that you make to proteins are less at the grand scale of this protein either fully works or it doesn't work, but it's more like, oh, well, one amino acid changed. That amino acid, it matters, but it's not the off-on switch of this entire protein. So maybe this protein functions slightly differently, but it's largely doing the same thing. That is, as an aside, why you can use mouse genes in human cells and human genes in mouse cells, right? Because as long as it's largely functional, it will do most of its job, but that's what gives you the variation — the little bits that are different, but not necessarily like we're going to completely submarine this protein's ability to function. Every three base pairs in your DNA, you have a chance to introduce a change that will change that amino acid and change the structure or function of your protein. Does that make a little more sense? So once you have those amino acids built, right, you have this long string of amino acids. Those are then, based on those laws of physics, going to fold in a three-dimensional way to build that protein that's actually going to do the thing. Now you have things that can actually function in the cell, right? I'm producing pigment, that's going to start to bend light. That's going to give us our eye color. But if I have a mutation in one of those codons, and now the part that's bending light is slightly different, that's going to bend the light slightly differently now, right? Maybe instead of dark brown, you're going to get a lighter brown because the way the light is scattering in that protein is no longer exactly the same. But there's still a protein there that's scattering light. That's what most mutations are. They're not big, they're not dramatic, they're not what we call knockouts that remove the function of the protein. But they're things that alter the shape and structure of the protein ever so slightly that changes the way it works in the cell, which then changes the way that you look at a higher level because your cells are what make you who you are. Let's talk about some of the different types of mutations. The simplest mutation we have is what we call a substitution mutation. These are often not very harmful, right? The reason is because you're only changing one amino acid at a time. When you get a substitution mutation, maybe instead of a glycine amino acid, you're going to add a leucine amino acid instead. Most of the time, those changes are perfectly tolerated by the protein. We call these missense or silent mutations, but they might or might not have functional effects. You're changing the sequence and you're challenging the structure of the protein, right? There's something we didn't bring up quite yet. We have 20 amino acids. We have four bases that are organized in groups of three, right? If you take four to the third, you end up with 64 different combinations. We have 64 different combinations of codons, but only 20 different amino acids. That means that there's redundancy in there. And so you can get mutations in your DNA. And this is part of why it's less of a miracle than you would think that every human is born, because there is some elasticity. You can tolerate some mutations that won't actually affect your genes at all

0:33:43 Eric: Because they're silent. If both CTG and ATG code for the same amino acid, it doesn't matter if that C turns into an A or that A turns into a C because that codon is going to be exactly the same. So you're going to get the same amino acids. You change one of those nucleic acids such that you're getting a different amino acid now, Now, that's when you don't get a silent mutation, you get those missense mutations. And those missense mutations are like our sickle cell anemia that can have pretty drastic effects on the protein function, Sickle cell is a one base pair change that changes the structure of that hemoglobin protein and then alters the function of those red blood cells.

0:33:52 Thomas: Interesting. Think what's interesting to think about. So, yeah, it makes sense that there would have to be some redundancy, you some air protection. Otherwise, one just little thing and we're just like, ah, can't exist. Exist but what's interesting to me and not the topic probably of the show is like what forces would determine how much redundancy there's got to be some return and kind of return on investment there to that's almost like a meta evolutionary question you know it's

0:34:40 Eric: Actually is, and because I don't want to get even more in the weeds, we're not going to talk about like codon optimization and the way that like you have different codons that will affect the way RNA polymerase can flow through and read the RNA or the way the ribosome can scan and read the RNA. That will change your rates of transcription and translation, which can alter your protein in transcript levels in subtle ways. So that's another of those layers of complexity in addition to the transcription factors, in addition to the splicing. That redundancy actually does work as regulation. Now we have our protein produced with those sequences of amino acids. We folded them, and we have them ready to go and be functional, right? Haven't actually brought the pigment to the right part of the eye yet, though, right? It's got to be processed in the center called the Golgi complex, that's the warehouse distribution center of the cell. It's taking all these newly formed proteins, it's reading the packing slips in those regulatory sequences, it're reading the what we call post -translational modifications, and it's going, okay, based on these things, you are now going to this part of the cells, and you are going to be there for this long. That's what really is happening in that central dogma. The simple step is we go from DNA, we make a copy of it in RNA, those RNAs are then spliced and refit together to form that mature mRNA transcript. Transcript gets read by the ribosome in groups of three at a time. And every three base pairs, you add an amino acid, which then folds into the proteins that we know and love. That is genetics at its most simple. And it's why brown eyes have that pigment, blue eyes don't. The blue eyes, a mutation happens where that protein no longer gets made, and so it's not going to produce that pigment. Now, the reason why one simple mutation can cause a protein to not be made is because of a much more complicated mutation than a simple substitution, right? Just talked about if you switch an A for a C, that can have an effect on the protein, but it could also be silent, right. Much more troubling mutations are what we call frameshift mutations. About it this way. Way. Read our RNA in groups of three, right? If I have a sentence with a bunch of three letter words, right, the cat ate the rat, is perfectly intelligible, Let's right. Substitute the E in the for an A. How does

0:36:43 Eric: That sentence read to you?

0:36:42 Thomas: Still gonna figure it out yeah but But then guessing if it offsets it all by one or something, is that what this frame shift is?

0:36:48 Eric: Exactly.

0:36:48 Thomas: Like, yeah, clumps

0:36:49 Eric: The frame shift is when you have an insertion or a deletion.

0:36:52 Thomas: Differently. Yeah.

0:36:53 Eric: Becomes completely unintelligible, right? Then you might have the, yeah, you know, like you end up with nonsense words. And

0:37:01 Thomas: Hmm. It like so if the E is missing, it's going to take the C and put it there. Right. And so is that why? OK, so it'd be like click at in like pretty quickly. It's becoming unreadable.

0:37:12 Eric: Because now all of the groups of three after that insertion or that deletion are no longer with their original groups of 3.

0:37:18 Thomas: So the whole friggin thing is out of order.

0:37:20 Eric: Exactly. That's the real problem with frameshift and that's why a lot of our really harmful mutations are a lot of those frameshifting mutations because they're really disrupting not not just one amino acid, but all of them. And it gets even worse. A lot of times what happens in those frame shift mutations is the ribosome eventually has to know when to stop producing this translated protein, It right? Needs to know When to stop reading the RNA. We need a codon just like we had that same three base pairs at the start of every protein, that's our start codon, you need to code on that to stop codon. Right?

0:37:49 Thomas: Yeah.

0:37:50 Eric: If you get a frame shift, where you're not supposed to have the sequences of three letters, the way they're organized, the odds of you getting a stop codon where you shouldn't have a stop codon go up a lot more because because normally a tight regulation of where stop codons are because that's under high evolutionary pressure because if you don't produce the protein not going to work but if you have this frame shift and now all of a sudden there's a stop codon in the middle of that protein if you only have half the protein it's just not going to do its thing and your cells recognize that so it's actually going to clear that protein away for what we call nonsense mediated decay, it's the quality assurance of the cell going, this is not right, we need to just get rid of this protein.

0:38:24 Thomas: This is so much like computing. Like know, you got like file headers.

0:38:27 Eric: Really is very similar logic.

0:38:28 Thomas: It's just, it's amazing how similar it is.

0:38:31 Eric: Just remember that all of this is constrained by laws of physics, right?

0:38:34 Thomas: It's all the right?

0:38:35 Eric: Base pairs of that tRNA can only bond with the base pairs of that mRNA that are complementary, right. ATG can't bind GGG. It's just not going to work.

0:38:45 Thomas: So is computing. It is obviously the laws of physics. When I you get right down to it, the ones and zeros can only interact in a way. The charges and the not charges can only interact through certain gates by the the laws of physics. It's amazing how similar it is, even though it is of course also vastly different, but a like lot of these principles, it's

0:39:02 Eric: Why I don't think biological computing is like that science fiction a concept, right, it really does seem like you should with with complete knowledge of biology, or at least near complete knowledge of biology be able to build really complicated and high -powered biological machines.

0:39:16 Thomas: You would think.

0:39:16 Eric: But as we've kind of been discussing in this podcast, unpeeling all of that complexity and fully understanding it is the rub, right? We haven't even talked about things like, now you've made that protein. Just as we talked about earlier, that protein has a set life, right, eventually it's going to be cleared for decay so that new proteins can replace it, or it's no longer necessary. So these other proteins called ubiquitin kind of attach onto it like globs and then tell the cells this protein is ready for destruction. It's basically like earmarking it for obsolescence.

0:39:43 Thomas: Wow. Absolute.

0:39:45 Eric: RNA, and again, I want to remind everyone about the fears that were being parroted by very prominent biologists and doctors about this vaccine. For the mRNA vaccine, right, also has a shelf life, especially because unlike DNA, it's really not stable. It's going to eventually degrade itself or be broken down by those molecular scissors. So again, those vaccines are not staying in your body for more than about 48 hours. That's because RNA by its very nature has to be temporary. You're stuck with the same problem of DNA where you have all the information, but you can't use it dynamically. So you need these systems to dynamically both create and then clear all of this RNA protein. Protein. Then we have other layers of regulation, right? You can have a gene that's what we call epistatic to eye color. And by that, I mean, the protein is what gives you your color. Another protein has to physically bring that pigment to the right place, right? So if you have a mutation in the protein, not in the pigment, but in the thing that develops and deposits the pigment. Then you're still going to have effectively a mutation in your eye color, right? Even though your pigment's being properly produced, it's not being properly cargoed and escorted to the correct place. So epistatic mutations are when you have mutations that are either upstream or downstream. And by that, I mean, they're either responsible for producing or responsible for kind of affecting the original gene you're interested in. That interaction being disrupted has now made that gene either less or non -functional. So just to recap, we have this very simple workflow of DNA to RNA to protein. Along the way, because that DNA gets transcribed into RNA that gets spliced and chopped up in many different ways, that one gene can produce many different types of transcripts, right? So that's one layer of regulation. Then when it gets escorted to the nucleus and it gets taken by the ribosomes, we have different ribosome with different levels of efficiency. We have different ribosoms in different locations that recognize different transcripts. Be another layer of regulation that you have, which ribosom is the one that's translating our RNA, right? You have that next layer of organization of, okay, well, we've made the protein with the correct sequences, is, but have we folded it correctly? Have we built it up properly? Just like if you have a mutation in the gene that can deposit the pigment, you Have a mutation, what we call chaperone proteins that help fold proteins, you can also get a protein that's no longer functioning properly. We have that next layer of regulation where we have our tRNAs, right? Things that recognize we have redundancy in our t RNAs that help determine whether our codons are optimal or or not? And then finally, we have, is it going to the right place? Is it being cleared or stabilized on what timeframe? In all of these ways, you can choose what protein is being produced, slight slight modifications to the protein, slight changes to when and where it's being produced, and slight changes To how long and how effective it is. And all of those things take that simple gene to RNA to protein, and makes it the huge gradients that we see in everyday life. And And that's why I really want to caution anyone that thinks that biology deals with binaries in anything, you

0:42:37 Eric: Are thinking about biology wrong. It is always going to turn into gradients because of these layers of interacting complexities and genes that are constantly regulating each other, right?

0:42:46 Thomas: I imagine there's going to be some stuff that comes down to binaries, right? Or really think not at all?

0:42:52 Eric: Depends what you mean by that, right? Because you could say that sex is a binary until you realize, well, we have different levels of sexual development, right.

0:42:58 Thomas: I don't mean that. I mean like certain genetic stuff. I I mean, I, there's gotta be certain things where it's like, you're missing this or not, or, you that generic thing with cilantro, where - if

0:43:08 Eric: You're talking about the PCC gene where you can taste bitter on the paper or not, depending on that one gene mutation that it's so that itself is binary, but well, yes, exactly. Right. Maybe you taste bitter, but how bitter is it going to be is going to depend on other things like the strength of your receptors, how tightly that interfaces with your brain to register that your emotional regulation and dealing with the bitterness, right? Of these things are going to build complexity complexity into that taste of bitter.

0:43:13 Thomas: You say so, something like that. Yeah, thought that was pretty binary, but maybe it's not. Oh, oh, oh - to get - okay. OK, so like the trait is binary, but the way to get there maybe isn't or something.

0:43:42 Eric: Whether

0:43:28 Thomas: Mm hmm. Interesting. Well, I was just I message taken, but I was actually just talking about binaries in terms of the the mechanisms of biology is all I'm sure there's got to be examples of like, oh, you're missing this thing. That's yes or no. You don't have it.

0:43:47 Eric: But almost always gets subsumed by the complexities of the system. You're right that in very reduced cases, you were going to have those binaries. But then they become part of this multifactorial polygenic and dynamic systems that then alter the effects of that binary and modulate it.

0:43:57 Thomas: Interesting. Mm hmm, mm hmm. Interesting. Sure. Sure.

0:44:09 Eric: So that's really, and what I I want to drive in. There's two other things I want to put a pin in for when we talk about CRISPR. RNA can also regulate itself in a dynamic way. Because I mentioned that RNA is single -stranded and DNA is double -straded, right? Way you typically get double -standed RNA in your body is by viruses that have double -standing. So double - stranded RNA a lot of times is like a recognition that something is wrong and is often targeted for degradation. And so your body has these things that they produce called micro RNAs and silencing RNAs. What they are is just like the tRNA, they're complementary transcripts to the RNA, if the RNA that you produce has like a 20 base pair sequence of all A's, it's going to produce a micro RNA that's a 20 based pair sequenceof all T's. It's going to bind to that RNA and make it double stranded. Now that's telling your body we want to get rid of these RNAs, so one of the ways your body can splice when it's making those RNA transcripts is instead of producing a protein and an mRNA transcript, it can produce either those microRNAs that regulate the other transcripts and target them for degradation, or even produce what we call long non -coding RNAs, which basically interact with proteins and DNA and RNA and chromosomes based on their sequence and kind of work as like decoys and modulators, right? You want to block the binding or the process of something starting, stick a long non -coding RNA in the active side of the protein that you're relying on, and it's going to remain inactive until that long non coding RNA removes itself from the active part of that protein. And now that protein is free to do its thing. RNA is really the thing that like gives us our levels of regulation in dynamic space and time. DNA gets all the like headlines, but I actually think RNA is the much more interesting molecule when talking genetics.

0:45:52 Thomas: DNA gets all the attention. RNA is the like sibling that, does actually like a lot of really important work, but just hasn't made it big.

0:45:58 Eric: Exactly. DNA is like the older child. And then RNA would be like the middle child with protein being like the younger golden child that gets all the credit. And RNA is like that workhorse in the middle, like actually making things happen behind the scenes. Just really want to stress that because of those layers of complexity, every gene coding for one protein is a simplification because you're going to be able to make those RNAs in different ways. And then the other thing I want to stress is that most mutations are not the dramatic mutations that we think about. Those subtle ones, changing an amino acid here or there that changes that efficiency slightly, changes the localization or timing of a gene ever so slightly. And that's how you get those minute variations in a population while everyone is still able to be born.

0:46:40 Thomas: Yeah. So interesting. Because you got to figure, I mean, I think you said early on, yes, obviously this is all a miracle in a sense, and it really is. But also there has to be that redundancy for this to work as a high percentage as it does. You know, it's really to think about both how precise this is, but also, I means, obviously there's room for error in a lot of this.

0:46:59 Eric: Mention also, there's also redundancy in the genes themselves, right? Remember how we talked about the knife and the fork and how the fork gets created after you have two knives? But in a pinch, you can still use that proto fork knife, right, to cut the meat before it turns fully into a fork. So let's say I have three family members of a certain protein, gene I studied in graduate school is grainy head like three. On that naming, it probably wouldn't shock you to learn that there was also a grainy head like one and a grainy head like two. A big problem that I was encountering was grainy head like to and grainy had like three were expressed at the same place in time in the embryos I was studying. And so when I'd remove grainy, had like, three, it was hard to know exactly what grainy. Had like three was doing because grainy Had like two could come in and say, well, grainy Head like three really dropped the ball here. I probably need to get back to my old role of doing this or that. Even within or genes, even between individual genes, we have that layer of redundancy and complexity that can slightly alter traits and introduce that gradient that we talk about in biology.

0:48:01 Thomas: Interesting. Okay. Well, Well, this was fascinating, and I think we're setting a bit of a teaser here for another part on CRISPR, right?

0:48:07 Eric: CRISPR is where it will really all come together, and it is both fascinating and a little terrifying.

0:48:13 Thomas: Yeah. Can't wait to listen to that. We've laid a foundation that I hope we followed. I don't know. But always fascinating. Can't Wait to Build Our Eye, possibly. Or did we do that? Built the eye color.

0:48:22 Eric: Built the pigment of our

0:48:23 Thomas: Yeah, that's the pigment of a big difference.

0:48:23 Eric: Eye. So if you really want to build the eye, remember how we talked about those morphogens like Sonic Hedgehog and Wnt?

0:48:29 Thomas: Yeah, we got to get back into the sonic universe.

0:48:31 Eric: Let's, let's actually, now we actually have the picture of how those genes work. So I have Wnt signaling, right? Wnt will bind a cell receptor on the outside of my cell. It will start what we call a cascade where it's going to be like those signal flares in like medieval armies, right, it is going from like one receptor to the next until it it eventually degrades a protein. Protein that it degrades frees up another protein to enter the nucleus. Because before that protein was like holding on to what we call beta -catenin and telling you, you can't go into the nucleus, you are going away. Once Wnt binds that receptor and that signal starts to propagate in the cell, all of a sudden beta -catinin now goes into the nucleus. And what's in the nucleus?

0:49:09 Thomas: Treasure chest.

0:49:09 Eric: DNA, right? Our DNA. So that DNA DNA with beta -catenin is then going to recruit one of those transcription factors. Going to bind the DNA for the genes that are under control of that particular transcription factor, which is recognizing certain sequences of DNA. Then those mRNA are going to be produced. Those mRNA manuscripts are produced, they get translated by the ribosome. And then you have what you call the Wnt signaling program being expressed in that cell. Because Wnt bound that one receptor, it recruited a series of transcription factors that made certain mRNA transcripts be produced. Get translated into the proteins. Those proteins do functions. And that's how you build your different cells using selective parts of the genome.

0:49:48 Thomas: Right. Right. Well, more on that and more on CRISPR in next part. But I want to thank you, Dr. Eric Traffey, so much for coming on again. It's always fascinating.

0:49:56 Eric: Course, anytime. When we talked about transcription factors in the last episode?

0:50:15 Thomas: Is now define the last episode I'm not entirely sure how everything will have come out I'm

0:50:19 Eric: The day the dinosaurs died. How there were these things that directed the cell, what program to turn on, what genes to produce.

0:50:25 Thomas: Sorry we did the day the dinosaurs died I just blew my mind I was like jesus I know my mind's a little

0:50:27 Eric: That, sorry, let's back up five minutes. Yeah. Yeah, sorry. When we did how to build a dinosaur, we

0:50:33 Thomas: Yeah yeah if