YouSaid · the spoken record

Betül Kaçar

lines on the record: 191
first: 2022-12-29
most recent: 2022-12-29
sittings or episodes: 1
sources: podcast

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“If you just do genetic codon charts, we can pull that up. Yeah, it's a very standard table. So I can explain why this is so amazing. So you're looking at, like, this is life's alphabet, right? And so I also want to make a very quick link now to your first question, the tree of life. When we try to understand ancient languages or the cultures or the cultures that use these extinct languages, we start with the modern languages, right? So we look at Indo-European languages and try to understand certain words and make trees to understand this is what Slavic word is for snow, something like snig. Now we jump.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Yeah, because the informatic capacity is made possible together with other components. And not only that, but also the product yields a function, no, in this case, enzyme or protein, right? So that's really amazing to me.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Yeah, we don't have a good reason But because roughly 20 out of 60 states are used, you're using one third of your possible states in your information system. So this may seem like a waste, but informatically it's important because it is abundant and it is redundant, right? So this called degeneracy, you see this implemented by this translation missionary inside the cell. It means we can make errors, right? You can make errors. But the message will still get through. You can speak missing some letters to the information can miss some parts, but the message will still get through. So that's two-thirds of the not-use states gives you that robustness and resilience within the system.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Don't know, so we would be fooling ourselves if we said we know exactly how many amino acids existed early on. But there's no reason to think that it wasn't the same.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Is only one code that says start. There's only one. And then there's two, if not three, that says stop. So that's what you work with, but you can have 64 possible states, but life only uses 20 amino acids. So we used life uses 64 possible states minus four of the start and stops to code for 20 amino acids in different combinations. That is really amazing if you think about it, there are 500 different phenomenino acids life can choose, right? Narrowed it down to training. We don't know why. A lot of people think about this genetic code is quite fascinating I mean, it didn't do it for 4 billion years. I don't know. We may wait for another 4 billion years.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Yes, and chemistry can happen even if you strip some of the parts out. You can get very minimal level of information processing that does not look anything like the translation that cells relies on, but chemists showed from linear, you can generate information that arrives to a processing center in the form of a linear polymer. informatic part of this system that I think sets the part from computation and from metabolism comes in if you think about the information itself right so we have four nucleotide letters that compose DNA and they are processed in the translation in triplets so you have in triplet codon fragments so you have four times So you have 64 possible states that can be encoded by four letters in three positions.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Because it's far more than chemistry. You need biology, obviously. You need biochemistry. You need to think as, I think, network systems folk. You need to think about computation. You need to think about information. And that is not happening yet, except we are trying to bring this perspective. But the more you understand how information systems work, you cannot, once you see it, you cannot unsee it. It's one of those things.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“I love that you said jazz, it's definitely true, it's a party, and it's like everybody's invited, and they need to offerate together, right? And what's really cool about it, I think, there are many things that are very interesting about this thing, but if you take, if you remove it from the cell and put it in a cell for environment, it works just fine, right? So you can get cell-free translation systems, put this translation in a test tube and it is doing its thing. It doesn't need the rest of the cell to translate information. Of course, you need to feed the information, at least so far, but because we are far from evolving a translation, maybe not so far, evolving a translation in the lab or a machinery that can process information as it generates it. We have not done that yet.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“I cannot separate the two. I think what makes this machinery fascinating is that those five components that I listed are they coexist. So for instance, Talking about the chemistry part, we know a certain rate constant, all these proteins that operate in this machinery needs to harbor in order to get the mechanism going. If you are bringing the information to the translation machinery and you are the initiator of this computation system, you need to have You can only afford a certain range of mistakes. If you're too fast, then the next message cannot be delivered fast. If you're too slow, you may stall the process. So there is definitely a chemistry constant going on within the machinery. Again, it's not perfect, far from it, but they all have their own margin of error that they can tolerate versus they cannot otherwise call.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Where the biology comes in. But in terms of chemistry, you absolutely cannot have a translation machinery without chemistry. As I said, there are four main steps. These are the core steps that are conserved in all translation missionary. And I should say all life has this machine, right? Every cell, everything. Yes.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“You cannot have life without chemistry. You cannot have any cellular process without chemistry. What makes life interesting is that even if the chemistry is imperfect, even if there are accidents along the way, if something binds to another chemical in a way it shouldn't, there is resilience within the system that it can maybe not necessarily repair itself, but it moves on however imperfect mistakes can be handled.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Well, chemically, I think that's it. You have enzymes, you have proteins, enzymes are doing their thing. They know how to chew energy using ATP or GTP. They know what to do in their own way. They do their enzymatic thing. So it's not just the ribosome that is at the heart of the transition, but there are a lot of different proteins. You're looking about a hundred different components that compose this machinery.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Just make sure that you have good chemist friends if you're interested in Origin of Life. That's 100% requirement. It should be mandatory.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“I'm not sure if that's what they call it, but that's how I think of it because it is all combined in a test tube, and you know the outcome, and it's very mathematical once you know the right environment and the right chemistry that needs to get into this container or this part, you know what the outcome is. There's no luck there anymore. It's a pretty rigid established input output system and it's all chemistry”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Yeah, so, well, we can start with the more, I guess, the ones that are more established, which is the chemical aspect of the translation machinery. The specific compounds make up the assembly of RNA. Chemists showed this in many different ways. We can rip apart the entire machinery. We know that the core of it, there's an RNA That operates not only as an information system itself or information itself, but also as an enzyme. And origin of life chemists make these molecules easily now. We know we can manipulate RNA. We can make even the single-pot chemistries. We can create compounds.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Exactly. And the computers don't have, don't link information to function, right? They are not tightly coupled nowhere close to what translation Or the way translation does it. So that's the number one, I think, difference between the two. And yes, it's informatic. And we can discuss this further too.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Yeah, and it tracks this information, so it is almost a mini computer device inside ourselves. And that's the oldest computational device of life. It's likely the key operation system that had to evolve for life to emerge”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“I would divide it into actually even four more additional steps or disciplines than what would it take to study it by the way you described it. It's a chemical system. It's the compounds that make it up are chemicals. It's physical. It tracks the energy to make its job, to do its job. It's informatic. What is processed are the bits. It's computational. The discrete states that the system is placed when the information is being processed that's itself is computational and it's biological. There's variability and inheritance that come from imperfect replication even and imperfect computation.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Converts a linear sequence of mRNA into a folded later folded protein. That's when that's the core processing center for information for life. It has multiple steps, it initiates, it elongates, it terminates, and it recycles. discrete bits of information itself is like a chemical decoding device and that is incredibly unique for translation that I don't think you will find anywhere else in the cell that does this”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“So I will start with one of the most fascinating machineries that we target, which is the translation machinery. It is a very unique subsystem of cellular life in comparison to, I would say, metabolism. And we used to, you know, when we are thinking about cellular life, we think of cell as the basic unit. building block. But from a key perspective, that's not the case. That one may argue that everything that happens inside the cell serves the translation and the translation machinery. There is a nice paper that called this, that entire cell is hopelessly addicted to this main informatic. Computing, biological, chemical system that is operating at the heart of the cell.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“So, some biological engineers E. coli to fix nitrogen, I believe, not us. We use the nitrogen fixing bug and engineer it with the nitrogen fixing metabolism that we resurrected using our computational and phylogenetic tools.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Absolutely. We tried to replicate in the most simplest way what nature has come up with. We do this by taking nitrogen using a lot of pressure and then generating ammonia. Life does this in a more sophisticated way, relying on one single enzyme called nitrogenase. It's the nitrogen that is used together with eight electron donor and ATP together with a lot of hydrogen. Life pushes this metabolism down to create fixed nitrogen. It's quite remarkable.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Is the schnapps, right? Carbon, hydrogen, oxygen, nitrogen, sulfur. So there are five elements that life relies on. We don't quite know whether that's the only out of many options that life necessarily needs to operate on, but that's just how it happened on our own planet. And there are many abiotic ways to fix nitrogen, like lightning, right? Lightning can accumulate ammonia. Humans found a way about 100 years ago, I think around World War I, the Haber Bosch process that we can abiotically convert nitrogen into ammonia. Actually, 50% of the nitrogen in our bodies comes from the human conversion of nitrogen to ammonia. It's the fertilizer that we... Use urea comes from that process. It's now our food. So we helped, we found a way to fix our own nitrogen for ourselves.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“I cannot think of it, no, it's essential to life, as we know. You and I are having this conversation because life found a way to fix nitrogen”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“So far we know there's only one nitrogen fixation pathway as opposed to say carbon you can find up to seven or eight different carbon based microbes invented to fix carbon. That's not the case for nitrogen. It's a singularity across geologic time. We think it evolved around 2.7 maybe roughly three probably less than three billion years ago and that's the only way that nature invented to fix the nitrogen in the atmosphere for the subsequent use.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Well, it's actually a very important element. It's one of the most abundant elements on our planet that is used by biology. It's in ATP, it's in chlorophyll, that relies on nitrogen. So it's a very important enzyme for a lot of cell functions.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“So nitrogen is a triple bond gas that's pretty abundant in the atmosphere. But nitrogen itself cannot be directly utilized by cells given it is triple bond. It needs to be converted to ammonia that is then used for the downstream cellular functions.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“We inject pretty much all the bacteria that we work with, with foreign DNA. We also work with diazotrophs. These are azotobacteria. They're one of the prime nitrogen fixers, nitrogen-fixing bacteria.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Established sort of a pet lab pet that we use it a lot for cloning and for understanding basic functions of the cell, given that it's really well studied.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“We study a variety of different bacteria depending on the questions that we ask. We engineer bacteria. So ideally, we want to work with bacteria that we can engineer. Seldom we developed the tools to engineer them. And it depends on the question that we are interested in. If we are interested in connecting the biology and geology to understand the early life and fundamental innovations across billions of years, there are really good candidates like Cyanobacteria. So we use cyanobacteria very frequently in the lab. We can engineer its genome. We can perturb its function by poking its own DNA with the foreign DNA that we engineer in the lab. We work with E. coli. It's the most simple in terms of model systems, organism that one can study.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Well, they'd get themselves invited in a way. So, we and they're definitely older and definitely very sophisticated, very resilient than anything else as someone working as a bacteriologist. I feel like I need to. Defend them in this case because they don't get much shout out. Maybe you think about life”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Bacteria. We should be very grateful to bacteria. First of all, they are our great, great ancestors. I like this quote by Douglas Adams. Humans don't like their ancestors. They rarely invite them over for dinner. But bacteria is in your dinner. Bacteria is in your gut. Bacteria is helping you.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Even further. And I like that you said fog. It is pretty foggy. And it gets foggier and fogier. The more further you try to see into the past. Biology is, you basically study the survivors, broadly speaking. And you're trying to put together their history based on whatever you can recover today. What makes biology fascinating also erased its own history in a way, right? So you work with this four billion year product that's genome, that's the DNA. It's great. It's a very dynamic, ever-evolving chemical thing. And so you will get some information, but you're not going to get much unless you know where to look because it is responding to the environment.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“that enabled you and I to have this conversation. We have very little understanding of the biological innovations that took place in the past of this planet. We work with a very limited set of, I don't want to even say data because they are fossil records. So let's say imprints. Either that comes from the ROC and the ROC record itself. Or what I just described, these trees that we create and whatever we can infer about the past. So we have two distinct ways that comes from geology and biology. And they each have their limitations.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“So, I will tell you the more interesting things for us. One is the origin of life or what happened right following the emergence of life. How did the first cells look like? And then pretty much anything that we think shaped the environment and was shaped by the environment in a way that impacted the entire planet.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Fun stuff is what people think is boring, I think. The face that two different times in the geologic history. One is the first life, past origin of life, how the first life looked like. And the second is why do we think that over certain periods of geologic time, no significant innovation happened to the degree of leaving no record behind?”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Yeah, sold dinosaurs or all these mammals, at least for us is. Exciting thing already happened by the time we hit to the larger organisms or to eukaryotes.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“We approached it in every way we can. So it's the gene could be protein, the product of the gene, or species, or could be even groups of species. It totally depends on what you want to do with your tree. If you want to understand certain past events, whether an organism exchanged a certain DNA with another one along the course of evolution, you can be able to tree accordingly. If you rather use the tree to reconstruct or resurrect ancient DNA, which is what we do, then in our case, for instance, we do both gene, protein, and species because we want to compare the tree. We create using these different information.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Exactly. So the tree itself, by just taking a few steps back and looking at the entire tree itself, can give you an idea about the connectedness, the relatedness of the organisms or whatever. Again, you use to create your tree. There are different ways. But in this case, I'm imagining entire diversity of life today is sitting on the tips of the branches of this tree. look at biologists look at the tree itself we like to think of it as the topology of the tree to understand when certain organisms or their ancestry may have merged over time depending on the tools you use you might use this tree to then reconstruct the ancestors as well”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Starts from the branches. It starts from the tip of the branch, actually. And then depending on what you collected to build the tree. So depending on the branches, depending on what's on the tip of the branch, and I will explain what I mean, the root will be determined by what is really sitting on the tip of the branch of the tree.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source
“Think phytogenetic trees could be one of the most romantic and beautiful notions that can come out of biology. It shows us a way to depict the connectedness of life and all living beings with one another. Itself is an ever evolving notion. Biologists like visualizations, they like this graphics, this diagrams and tree of life is one of them.”
2022-12-29 · Lex Fridman Podcast · #350 – Betül Kaçar: Origin of Life, Ancient DNA, Panspermia, and Aliens · IDENTIFIED FROM THE TRANSCRIPT · source