All right. One more lecture. All right. So today we're going to be talking about amino acid metabolism. And if I could have your attention, I know it is so painful to be in here. It's so nice outside. So, but it isn't that painful. We're learning about amino acids. Okay. So today we're going to learn about amino acid metabolism. And so today's lecture is a bit painful because when you think about it, there's really 20 metabolic pathways for degradation and 20 anabolic pathways for building amino acid. So if we were actually to cover every pathway, I mean, we could spread this out over four or five lectures. So instead of covering hundreds of new enzymes and all these new pathways, we're going to sort of dip in a little bit to just a subset of the pathways, some of the easier pathways. And so if you want to have a comprehensive understanding, that would not be a requirement for an examination, but a lot of, even the textbook doesn't have all the pathways. Many of the steps are described as something magic happens here, and then something comes out of that. Okay. So we're going to start with catabolism. And then we're going to move to anabolism. We're going to look at both. We're going to sort of have a clinical slant today where we're going to be looking at a variety of metabolic diseases that come up with defects in amino acid catabolism. But then at the end of the lecture, we're going to be looking more holistically, you know, so where, how do we get some of the feedstocks of amino acids, these ammonia? Where does ammonia come from when all, there's all this nitrogen gas in the air? So we're going to be taking an ecological slant at the end of the lecture. Okay. So let's start with catabolism. So it's a two step process that is pretty separable. So first you remove the amino group, and that reaction forms alpha keto functionality on the, the amino acid without the amino group. And then we're going to process those two parts separately. The ammonia produced from the removal of this, that amino group is going to be ultimately processed, either recycled to be available for synthesis of new amino acids, or if we're burning amino acids, if you're eating tons and tons of, like an Atkins diet, you're eating tons of protein, well, you're going to have to get rid of some of those amino groups. And that comes out of a urea cycle. And the urea cycle is intertwined with the citric acid cycle by this so-called shunt. But then we have the carbon skeleton. And literally what we can do with that is just burn it for fuel. So we can feed it into a variety of pathways, either a Krebs cycle, or we can transfer some remnants of those carbon skeletons to other tissues from the liver. So liver is where the urea cycle is occurring. And we can, you know, transfer it as a ketone body and regenerate the acetyl-CoA, and then burn it that in the Krebs cycle. But ultimately, the idea here is burning fats, so fully oxidizing the carbon atoms in those, or burning amino acids, so fully oxidizing the carbon atoms in the amino acid to CO2 ultimately. Okay, so that's an overview of where we're going today. So let's look at the first part, this, the manipulation of the amino group. So there's lots of different sources for amino acids. So if you have, you know, a diet that is high in protein, well, you're going to have a lot of amino acids coming in. But also there's a certain amount of turnover. So you have cellular proteins that are degraded to amino acids, and those need to be processed. And there's different ways, but the thing of it is that the liver is the critical organ. So obviously you're going to have amino acid metabolism all over, but you need to transport those amino groups from whatever tissue they're produced in to the liver. And so there's two different molecules that are used to transport the amino groups to the liver. And so we have ingested protein or liver cellular protein gives you amino acids, and those amino groups are transaminated onto alpha ketoglutarate to make glutamate. Okay, and producing the alpha keto acid corresponding to the amino acid. So if you look at this, you see this is oxidized, right, and this is reduced. So this is not a redox process. It occurs very close to equilibrium. There's no ATP hydrolysis. One molecule is oxidized, the other molecule is reduced. So we're transferring electrons between the molecule by transporting this ammonia group and having the end product of these reactions be a keto group. Okay, and so alanine can come in here and from muscle predominantly, and that can be processed to pyruvate, right? So if you look at this, this is the alpha keto skeleton of a deaminated alanine, or you can have glutamine, right? And so you can shed this amido nitrogen and the amide functionality of this amino acid. You can give that up to make glutamate, and then glutamate can be deaminated to make ammonia. But what are we going to do with ammonia? So ammonia is toxic. We need some way to encapsulate the reactivity in the chemical properties. This is a very alkaline substance, right? So if you have a high level of ammonia, your pH is going to be really high. So you need to do something with that to safely remove it from the organism. So let's look at this transamination. So this is not a net redox process, but the molecules are changing oxidation states. So you have alpha-ketoglutarate, receives an amino group, right? So this is reduced, and then this carbon is oxidized, and so you're transferring from each of the 20 possible amino acids, the amino group, onto a glutamate molecule. So glutamate forms the pool of amino groups, the storage pool for amino groups in the cell. And so each of these amino transferases is able to remove the amino group, forming the alpha-keto form of that amino acid, and place that amino group on alpha-ketoglutarate to make glutamate. Okay, so there's no net gain. We're transferring amino groups. We're changing oxidation states, but there's no net change of amino groups or oxidation states. Okay, so this is a transamination. There's cofactor. So it's sort of a new type of chemistry. We need a cofactor for transamination reactions, and it's this periodoxal phosphate cofactor. So this cofactor is originally stored on the enzyme by forming this imine, or shift base, with a lysine. So the epsilon amino group of a lysine forms a shift base with this cofactor. But that's not a form of this cofactor that's going to be reacting with our amino acid. We have to remove this periodoxal group from the lysine, and then it can react and form a shift base with our amino acid. And so there's an aldehyde form of this, and then when it removes the amino group, ultimately you form periodoxamine phosphate. So you have the amino group that's been removed from whatever we're transferring amino group from, and put on the cofactor. And so I've added a slide at this point that describes the mechanism of this reaction. The whole strategy here is to avoid the formation of unfavorable carbanion. So instead of forming a carbanion, so if we just had a base pull off a proton, well you would get a carbanion. But instead we have this, you can see how this is highly conjugated, right? And so first we form a shift base between our periodoxal group and our amino acid. And then when we remove this proton, we can just rearrange the electrons, and so that there ends up being a double bond here. And then we can add a proton there and then get to this form of the shift base. So now instead of having a shift base here, you have it with your amino acid. So you've changed the orientation. You're about to release this amino group. And then you just reverse this, such that out the other end when you add water is the alpha keto acid. And our amino group is now placed on the cofactor. And we can do a similar reaction where we take an alpha keto acid and then place this amino group in lieu of that alpha keto acid. So we're transferring an amino group from one molecule to another. Does that make sense? It's a little crazy. Just hit a little mechanism today. Okay, so what we need to do is transport amino acids that come from proteins from all the tissues in your body to your liver. And the way this is done is you can imagine, well, glutamate is not a very good transport molecule. It's highly charged. Getting that across membranes is going to be difficult. So if we could first convert that into a less charged molecule, that would help us in our transport. So in the tissues, you have glutamate can be activated by forming a phospho-n hydride bond. And of course this could be hydrolyzed. That would release some energy. Or it's a great leaving group. So ammonia can react with this to make glutamine. That glutamine is less charged. It's great for transport of an ammonia. So we're taking ammonia from the tissue. Taking ammonia from the tissue. And then you see how we're releasing it in the liver. So the glutamine goes into the liver where we can hydrolyze off that ammonia. And then that ammonia can be processed in a type of tissue that has the enzymatic machinery to deal with the ammonia. And so this is just a simple transport. But in muscle, there's other ways, the other carriers for ammonia that we could use. So muscles have a high glycolytic rate. So there's a large amount of pyruvate in muscles. And so pyruvate is an alpha-keto acid. So it has alpha-keto group, carboxylate, and a methyl group. And so we can transfer from glutamate our storage form of ammonia. We can transfer that amino group to pyruvate to make alanine. So alanine, so pyruvate is the corresponding alpha-keto acid for alanine. Alanine is then less charged than pyruvate. Or it's about the same charge. When you think about it, pyruvate, but alanine is what's transported. Because alanine is wither ion. So alanine is transported anyway. Alanine is transported. It's received in the liver where the reverse reaction can occur. We can transfer those amino groups back to our storage molecule, glutamate, and we can convert an alpha-ketoglutarate to pyruvate. So transfer that, or we convert the alanine to pyruvate, alpha-ketoglutarate to glutamate. So the net effect is to take ammonia from the muscle and move it into the liver. These are hanging out of the liver, but it's actually occurring within the liver. So now we have glutamate. That's storing our ammonia. But to make urea, we have to release some of that ammonia back into solution so it can be fed into the urea cycle. And so glutamate, you can react or convert glutamate to the alpha-keto acid with release of ammonia. So this is changing the oxidation state here because here, this is reduced, this is oxidized. And so we're transferring those electrons from glutamate to NADP to form the alpha-ketoglutarate. So now we have ammonia in solution. That's good because we need that to process it as waste. So here's the overall picture. We came in either with alanine or glutamine.  So now we need to process those ammonia molecules. Currently we're in the liver. The urea cycle occurs in two organelles, in the liver and in the cytosol. But we're starting in the liver with the, or in the, I'm sorry, we're in the mitochondria and then with the ammonia. And that urea cycle occurs in the mitochondria and the cytosol. I'll get it eventually. And so there's different ways we can deal with this ammonia. If you're a fish, you can just release the ammonia into solution because you have all this water and as soon as you release the ammonia into solution, it's massively diluted. So we don't have to worry about the alkalinity of that molecule. If you're a vertebrate for us, we make molecules of urea. But urea is a denaturant. So if you had a really high concentration of urea, that would be bad. You would start to denature your proteins. So when we make urea, we put that in lots of water. We dilute it out so that it's less denaturing. But you know, that wastes water. You have to use a lot of water in order to dilute urea. And so the other option for birds is to make a molecule that looks a little similar to urea. It's uric acid. You can see, well, here's a urea. Here's a urea. And so this molecule is released as a slurry. Anybody that has received a gift from a bird has known about the slurry of uric acid. And that's just, it's doing the same thing we do but with less water. So it's a little more goopy. Okay. So let's look at us. You know, we're sort of focused here on vertebrates. And so we have, first, we need to begin to build our urea molecule. So we have ammonia, right? And so this ammonia is, or needs to be added to a carbon atom. Basically we need to have two ammonia and a carbon atom, right? That's the structure of urea. So let's start with bicarbonate. There's lots of bicarbonate in the cell. And the bicarbonate can be activated, right? And so this involves one high energy, phospho and hydride bond being broken. We've now activated the bicarbonate so that it can react with directly with ammonia. And so that synthesizes carbamate with release of inorganic phosphate. And you could see, man, we're so close. And you might think, well, you know, why not just do that again on the other side? Well, energetically, that's not very favorable. And we need a very complicated pathway. And all we're going to end up doing is just adding another amino group on the other side of this molecule. But first, we're going to activate, right? So this is our second high energy, phospho and hydride bond broken, transferring phosphate from ATP to make this carbamoyl phosphate. And this reaction is catalyzed by carbamoyl phosphate synthetase, right? So in your original slides it said synthase, but this involves ATP. So we call those synthetases. That was a mistake. This occurs, as I've already mentioned, in the mitochondrial matrix. And so now we have carbamoyl phosphate. Our goal is to synthesize urea. How are we going to do this? So this is, I think, the last cycle in the whole semester. And that must make you very sad. But it's a pretty cool cycle. So here you have carbamoyl phosphate coming in, right? And so what we want to do is condense carbamoyl phosphate with ornithine. Now, ornithine is an amino acid. It's not one of the 20 naturally occurring amino acids in proteins, but you know, it has amino group. It sort of looks almost a little bit like, it's almost lysine, right? It's just a little bit shorter. And so ornithine, wherever that comes from, is combined with carbamoyl phosphate to make citrulline. Do you see how we've removed the phosphate? And we sort of color coded these atoms. You can see it sitting on the end of this amino group of ornithine to make citrulline. Now we're going to activate citrulline, right? And so we're going to make a new AMP-alated version right here, okay? And then we're going to condense that citrulline with aspartic acid to make arginosuccinate. And so you would say, well, where is this aspartic acid just came out of nowhere? This seems like, you know, it would be a bad thing to do. If you keep doing this cycle, every time you do this cycle, you'd be using aspartic acid. We need aspartic acid to make proteins. So we'll have to deal with that at some point. So here we have aspartic acid combining with citrulline to make this arginosuccinate. And if you can see here, if we were to break this bond, that would release fumarate, and say fumarate, I remember that from the TCA cycle. So that can feed into the TCA cycle, and it can make arginine. And then you have this guanidinium group in arginine, which can be cleaved to regenerate our ornithine and release our urea molecule. So all we've done, you know, in the big picture is taking that carbonyl phosphate and put an amino group there. And we've done it in sort of a roundabout way. But there's some problems here. This is not really a cycle. It's going to, if we just keep doing this, the amount of aspartate in the cell is going to go down, and the amount of fumarate in the cell is going to go up. So we need a way to interconvert fumarate to aspartate. Obviously, that way these two can feed into each other. And the way this is done is by this so-called shunt. So fumarate in the cytosol, remember we moved into the cytosol for part of the urea cycle, especially when we generated fumarate. Fumarate can be converted to malate, and either fumarate or malate can be transported back into the mitochondria, where it can be converted to acetylacetate. So we have this malate dehydrogenase. And that's sort of cool, because up to this point, we've spent some energy doing this cycle to make the carbonyl phosphate. It took some energy, and actually I should point out here, here we cleaved ATP to AMP. So we've used a total of four phospho- and hydride bonds to make this urea molecule. But in this shunt, when we're reconverting malate back to aspartate, we're generating NADH, one molecule, and that's equivalent of 2.5 ATPs. So this net process has only taken 1.5 ATPs. And the good thing is we've reconverted the output of the urea cycle into the input of the urea cycle. Fumarate has been converted back to aspartate. Aspartate has been exported out and is now ready for another revolution. So this is, again, a carbon-neutral pathway. The input is ultimately the ammonia stored on glutamate, our storage form of ammonia, is transferred to aspartate transfers that ammonia ultimately onto the urea molecule. Do you see how that works? So think about urea. So the carbonyl group came from bicarbonate. One of the amino groups came from ammonia, and the other one came from glutamate. Do you see how that comes together? And so we've accomplished our goal. We have a safe way to deal with excess amounts of ammonia. We can just take the urea, dilute it up, and release it. So that's the urea cycle. Any questions on that? Yes. Yeah, so what is the pathways that make uric acid? You might guess. Well, I don't know offhand, but I would guess maybe urea, maybe at some point there would be some urea that's combined together. But I don't know the biochemical pathways that make uric acid. Maybe the BIRD researchers, if there are any, can tell us. And you don't know, have to know either. We're studying humans right now. Okay, so we have acetyl-CoA. It can be combined with glutamate to make a regulatory molecule. Remember that fructose 2,6-bisphosphate? It's not really a metabolite. It's sort of a signaling molecule. We have a similar form of regulation on the carbonyl-phosphate synthetase, right? And so this signaling molecule in acetyl-glutamate is an allosteric activator of the carbonyl-phosphate synthetase. And this sort of makes sense, right? So if we have a large amount of ammonia, we're going to have a large pool of glutamate because that's where we're storing the ammonia. Arginine also is involved in the urea cycle, but it also contains lots of nitrogens, right? So in some sense, that's also a sensor for the amount of ammonia in the cell. And so if we're building up the amount of ammonia in the cell, we need to start to deal with that issue by activating the enzyme that feeds into the urea cycle. And so this is how this process is regulated. So overall, we've cleaved four phosphonohydride bonds, so we've used three ATPs to make two ADPs and one AMP. That's four ATP equivalents, and we fed in aspartate, and we got out a fumarate, right? And then, but we can convert mallet and oxidize mallet and reduce NAD to NADH. And so that gives us back 2.5. Remember, if we did from the oxidative phosphorylation lecture, it was about 2.5 ATPs. So the net cost to this cycle is less than it would be if we didn't have this cool way to shunt the fumarate back into aspartic acid. And so the cell is being resourceful here. All right, so we've only dealt with half of the problem. We've looked at really a lot of the fine details there. Now we're going to come out a little bit and look at some of the ways in which these alpha keto acids that are remaining, these carbon skeletons, are metabolized. But ultimately, what we want to do is use amino acids as fuel. So we're going to feed them in to the Krebs cycle or feed them into a formation of ketone bodies, which then can be transported to another tissue and then be fed into the Krebs cycle in that other tissue because they come out as acetyl-CoA. So these different pathways, different amino acids give rise because they have different structures, give rise to different entry points into the pathway. And they can be called glucogenic or ketogenic. So glucogenic means that once you feed directly into Krebs cycle, you can take oxaloacetate and push that off to make some glucose and gluconeogenesis. So that's why we call it glucogenic. Ketogenic, well, we cannot use those to make glucose because there are these two carbon units here, right? And so there's no way to do that. But you can see that some of these amino acids show up in bulk. So as we're disassembling these carbon skeletons, oftentimes we can take one product when we maybe break an intermediate form of the amino acid into two pieces. We can take one of those pieces, feed it into ketone body formation. In the other piece, we feed in directly to the Krebs cycle. So let's look at some of these reactions. These are the cofactors that are involved. You've already seen pyridoxyl phosphate. Biotin, you've seen. Remember, carboxylation reactions. THF is new. And so this is important in one carbon transfers. You can transfer between molecules, either a single carbon or a single carbon that's in various oxidation sites, either being alcohol or an aldehyde. We'll see that in a moment. Atomet is only used for transfer of methyl groups between different molecules in THP, which we won't talk that much about today. It's very similar in structure to THF, but it's more involved in oxidation reduction reactions and enzymes. So there's a whole host of different cofactors in general that are used in the catabolism of those carbon skeletons of amino acids. So by the time we've seen it, like 15 zillion times, carbon dioxide binds, gets transported to the second active site where it is combined with another molecule to increase the number of carbons in that molecule by one. And so those are important. Atomet's new to us, so Atomet, so we have a methionine molecule attached to adenosine.  So here you have S plus. And so what we can do with this is we can transfer that methyl group to this some other substrate molecule that we need to increase by one methyl group generating this acidinosil homocysteine. And so there's a way that we're hitching a ride on this cofactor making this Atomet and then depositing that methyl group on some other molecule. So here's THF. So you have three parts. You have glutamate attached to amino-benzoate. But then the business end of this cofactor is this six-methyl-terrin, methyl-terrin, methyl-terrin, I think the P is silent. And so this cofactor, this part of the cofactor has these two nitrogens. And these two nitrogens can be involved in making new bonds to carbon atoms. And so this cofactor is only involved with transferring single carbon atoms between molecules, either as the fully reduced form or in these different oxidation states. And so if we bind with the two nitrogens, we get the equivalent of CH2OH. And if we make this bond, we get an aldehyde equivalent. So we can transfer those between substrates. Okay, so we have some cofactors. Let's do some catabolism. So we have a variety of amino acids that can be converted to pyruvate. And so we're just going to start scanning through some of these. Some of these are really easy. Yes, hi. Two slides ago. Right. So here, you can't really see. Is that an aldehyde? No, it looks like something. When it is released, it becomes an aldehyde. Or when this carbon here is released, it becomes an alcohol. So for example, serine. That last methyl group on serine is by taking this CH2OH equivalent off of here and putting it onto glycine. I think it's a glycine. We'll see in a moment. Yeah, it's a glycine. So that's the delivery form and the receiving form of carbon atoms for that cofactor. So we have three anine. And you'll see many of these pathways. You might guess, well, there's probably 20 different pathways, and they're all completely independent. But that wouldn't make much sense. We want to minimize the number of enzymes that we're using in these pathways. So in many steps along the way, we'll pass it to another, to another, to another until you get to something you can burn in a Krebs cycle, ultimately, or form a ketone body. And so here you have, for example, three anine. We can disassemble a three anine, right? And so first we're oxidizing this carbon to a carbonyl. We can now disassemble this to make an acetyl-CoA and a glycine molecule. So here's our glycine, and here's our acetyl-CoA. And so when we make glycine, we can take two glycine molecules. One of the glycine molecules, we can pick off that alpha carbon in an oxidation state of CH2OH and put it on THF. The other thing is we can react a second glycine molecule with that, you know, methyl from the methyl with the hydroxyl on it from the THF to make serine. So we've converted three anine to glycine to serine. But we need to feed into some pathway that generates energy here. And see, also, here's a similar set of reactions. Is this slide? I think eventually we deal with the serine later. So tryptophan, you can disassemble this aromatic ring. We're not going to look at that. It's really complicated. But you can sort of see that, oh, okay. That has this alanine equivalent in it. So you can break this bond, deal with this part of the tryptophan separately, and then you have alanine. Alanine can be converted directly to pyruvate. Do you see that? So the transamination, remember, transamination with that periodoxyl phosphate produces an alpha-keto acid. So you have alanine, and you've removed the amino group and put a keto group. That's a direct reaction. Serine, you can dehydrate to form pyruvate. And cysteine can be converted into pyruvate as well. In a lot of these, we've color-colored the atoms to get a sense, not for every single step what's going on, but generally what parts of the molecule end up in which of our metabolites. And so let's look at some aromatic amino acids. So a lot of metabolic diseases occur with the processing of aromatic amino acids. So if you're interested in medicine, pay attention here. So we have phenylalanine. And you can think, well, phenylalanine is very similar in structure to tyrosine. So it would be a simple matter to add that parahydroxyl group to phenylalanine to make tyrosine. So that's catalyzed by an enzyme. If that enzyme has a defect, if it's not functional, then we're going to begin to build up a phenylalanine. And the best we can really do with that is do an amino transferase reaction to make a keto group. But so if you have a deficiency in that enzyme, you're going to build up early metabolites of phenylalanine. You're not going to really have a way to deal with those carbon skeletons. And that build-up causes the disease, causes the mental retardation in PKU. And each of these steps, you can see there's all these different steps. And at every step, there's a deficiency in an enzyme. You're not going to be able to fully metabolize that amino acid. So something unnatural is going to build up. So you have various tyrosinemias. So tyrosine, you can look at the way that we're disassembling the aromatic ring. You say, well, that's pretty hard to do to bust open an aromatic ring. That's a pretty stable structure. And so what we're doing is activating it to this form here, where we have these two hydroxyl groups. And in the next step, we pry the ring apart. And that requires some energy. So we have an oxygen molecule involved there. And now we have a linear form of the molecule, where these carbons that are highlighted here end up over here. And then through a few more steps, we can get to fumarate, which feeds directly into the TCA cycle, or acetoacetyl-CoA, which can be used to make ketone bodies. So this is ketogenic and glucogenic. Okay? So branch chain amino acids. I know it's sort of tedious. There's a lot of amino acids. We're not going to look at them all. We're looking at quite a few of them. So here's a branch chain amino acid. These things, first, you have the amino transferase. You see a common theme. In general, you deal with the amino group right away, and then you disassemble the carbon skeleton. So we transfer the amino group away, onto our storage molecule. And now we have the alpha-keto acids. But conveniently for all these amino acids, we have the alpha-keto acids, but you have this carboxylate. And so we can decarboxylate these molecules and add a CoA functionality. And so this is a dehydrogenase enzyme. So right, we're oxidizing this molecule. So we have an aldehyde equivalent that's oxidized to a carboxylic acid equivalent. This is the exact same enzyme that we saw with pyruvate dehydrogenase, right, when we converted pyruvate to S-til-CoA. The exact same set of cofactors are involved with that. And so then we have this CoA metabolite, which can be converted into a variety of in-products that can be used to make energy. Either ketone bodies are fed directly into the citric acid cycle, these two. Okay, and so here we have another disease. So if you have a deficiency in this enzyme, you begin to build up, especially this isoleucine metabolite, which is converted into this structure, which smells like maple syrup, right? And so the reason that people have a deficiency in this disease, they have this peculiar aroma.  And that's because they have this sotolone hanging out in their bodies, because their bodies cannot feed these carbon skeletons into energy-generating pathways. This is an aromatic volatile compound. Maple syrup, urine disease. Back in the old days, they used to taste and smell, just so you know. Luckily, doctors don't have to do that anymore. Okay, we can take asparagene or aspartate and move it into oxaloacetate. And so asparagene, you can say, oh, okay, yeah, I can just hydrolyze off that amido group to make the carboxylic acid. So we're at aspartate, and then the aspartate, we can deaminate here to make the alpha-keto acid. And as it turns out, because of the original structure of this molecule, we do these two simple steps, and we're already at oxaloacetate. We can feed that right into Krebs cycle. So that one's pretty easy straightforward. So what we're doing here is we're just feeding all these molecules. We're first dealing with the amino group that gets eventually put on urea, and the carbon skeletons are degraded so that they can feed into Krebs cycle, either in the liver tissue or being transferred as ketone bodies to other tissues where they feed into Krebs cycle. Okay, any questions so far on catabolism of amino acids? There's a lot of stuff I know. Painful. Okay, we're going to start building up again. So let's look at the biosynthetic pathways. And so ammonia is incorporated through glutamate and glutamate. So obviously we're making amino acids. So we're going to assemble the alpha-keto-carbon skeleton separately, and then we're going to add the amino group. And the amino group is being transferred from glutamate or glutamine. And so glutamate can be interconverted into glutamine. And so first you activate the carboxylic acid with the synthetase that uses ATP hydrolysis. And then you have this gamma-glutamyl phosphate, which can be used to react directly with an ammonia molecule to make glutamine. Okay, so both glutamate and glutamine are important in adding nitrogen atoms to amino acid structures. Okay? And so this is an amidation step here. Okay? Does that make sense? All right, and so this is an early step or an important step in the pathway, so it's heavily regulated. And you might think about it, well, this is a little bit dicey. We have 20 amino acids. And proteins sort of need, you know, all of those amino acids to make proteins. And so we need some way to have the regulation in these pathways since and correct for precisely the right amount of each amino acid. But here we have sort of a set of feedback inhibitions. So glutamine can be fed into incorporating nitrogen in things like AMP, CTP, tryptophan, histidine. So those are feeding back. But you might say, okay, well, red acts its digital, right? It feeds back. And if any one of those molecules is there, it cuts it off. But that wouldn't be good because there's other molecules that we need to make. And so this is a rheostat. Each of these inhibitors, allosteric inhibitors, is just slowing down the rate just a little bit. And so the combination, so if you begin to have all of these present, then the rate of this greatly diminishes. But with just one present, one of these products present, it just goes down a little bit. Okay, and so there's a variety of feedback inhibitors and you can see, ah, carbonyl phosphate. Why would the cell want to regulate this thing by carbonyl phosphate? Anybody have an idea, Trink? Where did we see that bad boy? You remember? It was way back 10 minutes ago. Yes. Yeah, right. So that was a catabolic pathway. And so why my carbonyl phosphate turned off this pathway? Yes. Say again? I'm sorry. Exactly. So this is a form of reciprocal regulate. Remember, I bring this up again and again. You don't want to necessarily just be, you know, building up, breaking down, building up, breaking down. And so by having carbonyl phosphate regulate the formation of the thing that's going to be adding amino groups to amino acids. Well, that's helpful, right? Because then you won't be doing both at the same time. So there's all kinds of levels of activation. But wait, it gets better. This is a rheostat with each of these inhibitors turning up the rheostat, but you can adjust the global sensitivity of this rheostat, making the inhibitors more efficacious by another mechanism. So you have the adenylation of the glutamine synthetase. So you're adding an adenyl group to a tyrosine. That turns up the sensitivity of this allosteric regulation of this enzyme. So it becomes more sensitive to inhibitors. So in the presence of some of those inhibitors, we just saw if the enzyme is adenylated, then that's going to make it more, it's going to be more inhibited. So it's going to be decreased. But this enzyme is also activated or inhibited by a urodylation. So the urodylation of the adenylyl transferase turns off the adenylyl transferase. And this urodyl transferase is itself allosterically regulated. So we've sort of bumped, this is a cascade of inactivations, but the starting point is here, at this urodyl transferase. And so this is turned on by alpha-ketoglutarate and ATP. These are indicators of energy. There's lots of energy present. We have ATP, we have alpha-ketoglutarate, or it's inactivated by glutamine, right? Or inorganic phosphate, being a marker for low amount of energy in the cell. And so this enzyme is going to be more active when it's time to do an anabolic process, when there's high ATP or high alpha-ketoglutarate. And it's going to be less active with glutamine or inorganic phosphate. So there's layers of regulation giving us amplification of the regulatory pathways. But that is not the only form of regulation of synthesis of amino acids. That's a bulk regulation, right? We need something to uniquely regulate the formation of each amino acid, and we'll see how that's done in a moment. So now we have synthesized a glutamine, and we need some way to transfer that to a substrate. And this is catalyzed by glutamine ametotransferases. So we're transferring the ametonitrogen, not the amenonitrogen, by first releasing it from the glutamine, making a covalent bond to the enzyme. This ammonia then moves through a channel to a second active site, where it then reacts with some kind of activated molecule. And then we release the glutamate. So we loaded the ammonia on to glutamine, and then it's used to be transferred to some other molecule and regenerating the glutamate. So these are in the general class of enzymes. They allow us to utilize that glutamine that we've synthesized. So here's all the amino acids. We're going to go into even less detail on how we make each of these amino acids. Each of the amino acids are built from different building blocks. Alpha-ketoglutarate, for example, is used to make this group of amino acids. Three-phosphoglycerate is from what pathway? Glycolysis, yeah. So we're using bulk TCA intermediates and glycolytic intermediates. TCA, right? This is sort of both, because it feeds between the two pathways. PEP or erythros, you might say, or ribose 5-phosphate. Where do we see that bad boy? So remember the pentose phosphate pathway, that evil pathway. One of the evil outcomes of that pathway is to make histidine amino acids with the ribose 5-phosphate. Okay, so let's put this together. Let's look at the big picture. So you have both glycolytic intermediates and Krebs cycle intermediates feeding into the synthesis of these molecules. We know, well, so they sort of all attach, and glycolysis is attached to pentose phosphate, right? So we can make ribose phosphate, 5-phosphate and histidine. 3-phosphoglycerate can be used in this way, PEP and pyruvate. So there's all of these different ways to make molecules. You shouldn't be ultra concerned with memorizing which comes with which.  So pyruvate, we can also use Krebs cycle intermediates, pyruvate, oxaloacetate, and alpha-ketoglutarate to make a variety of amino acids. So this is the, you know, from 10,000-foot view of how we make amino acids. So we'll look at a few of these. So here's alpha-ketoglutarate. The same strategy is used as before. We overlap the pathways for efficiency, right? And so we, from glutamate, we can make glutamine, proline, and arginine. Okay, so we have overlap pathways, but we're not going to look at the individual reactions for that one, but we are going to look at this one because it's pretty straightforward. Phosphoglycerate is first converted to serine. That serine can then be converted to glycine or cysteine. And so here's three-phosphoglycerate. You might think about it. It's like, wow, we're pretty close. If we just turn this into an alpha-ketoacid, then we can transaminate that thing and make something very close to a serine. So first, we oxidize the hydroxyl group to a carbonyl. That's an alpha-ketoacid. So we can use an amino-transferase enzyme to transfer an amino group from glutamate to this three-phosphohydroxypyruvate to make our three-phosphoglycerate. And so then we just need a phosphatase.  So this is pretty straightforward. You can see that these are, let's see, here you have three carbons. Here you have three carbons. You just had to rearrange stuff a little bit. The three-phosphoglycerate. Serine, okay. That can feed into other molecules. So we can take the serine and we can use the phosphatase to make a serine. And then we've already seen sort of a similar reaction here, but we can take the serine and use our THF cofactor to make glycine. So we can take that CH2OH group and stick it on the THF cofactor, or at glycine, okay? All right. The cysteine gets a little bit more complicated. So it turns out the cysteine is sort of conditionally essential. So methionine is essential amino acid, but methionine is used to make cysteine. So we make cysteine technically, but we make it out of an essential amino acid. And so you have homocysteine, right? And so homocysteine can be condensed with serine. And look at this thing. We're making a new bond where we can have, we bring a sulfur in between these two metabolites, and then we have options. We can break on either side, right? So we come together like this and then we cleave over here. So we're taking that sulfur off the homocysteine and sticking it on a, to make a cysteine molecule. And we've just bound the two together and then cleave the other bond releasing cysteine. So that was pretty straightforward. But where did the homocysteine come from? Well, that came from methionine. So here's homocysteine. Methionine can be reacted to make our SAM, this prosthetic group. And so we can take the AMP, and the AMP is reacted with methionine, releasing pyrophosphate, which pushes the reaction forward. But that gives us this acidinacyl methionine, where we have this positively charged sulfur atom in our methyl group. We can then use that to transfer the methyl group to something else. And then all we have to do is release this adenosine group to make homocysteine. So this is basically homocysteine. Cysteine just has one methylene group, remember, not two. And so we can make that just by releasing the adenosine group. So this methionine is essential. We can't make it. And it's used to make the non-essential cysteine. So cysteine is sort of conditionally essential. Do you essentially get it? All right. That wasn't very good. I try. Okay. So oxaloacetate. Now we're getting very distanced. There's a lot of pathways underneath here. Oxaloacetate can be used to make aspartate, which then is fed into a synthesis of these four amino acids. Pyruvate can be used to make these amino acids. In general, the pathways that synthesize these amino acids require ATP, NADPH, and transamination reactions to put the amino group on. Many of them involve carbon group transfers on our carbon group transfer molecule. All right. This one is pretty straightforward. OAA to aspartic acid, because that's the alfaketo acid of aspartic acid. Yes. So aspartate. Say again. So aspartate. Yeah. There's options. You can... Right. Undoubtedly, there's a fine set of allosteric regulations. There's separate enzymes that lead to different fates for the aspartate molecule. Right? And so you can regulate each of those enzymes so that you get the right amount of each of these amino acids. And also you're able to do the urea... Urea cycle is aspartate neutral. Because remember, aspartate is always regenerated from fumarate. So in some sense, you could sort of ignore that. It's not depleting aspartate. It's just cycling aspartate to fumarate, back to aspartate to fumarate, because of the shunting reaction. So... But if we want to make molecules, we have to take aspartate molecules out and then make these other amino acids. I guess... Yeah. Makes sense. Okay. So in pyruvate, remember, that's the alfaketo acid of alanine. So you have carboxylate, carbonyl, methyl group, and pyruvate. And we just transaminate to make alanine, which just has a methyl group side chain. Okay. Pretty straightforward. We can stitch together these molecules to make the beginning molecules using the synthesis of aromatic amino acids. This is an important precursor in the synthesis of aromatic amino acids. Phenylalanine and tryptophan are essential. So the pathways that stitch these molecules together are found in plant cells. And so the plant cells make those amino acids, and then animals eat them up. Okay. Histidine is crazy. So you have this ribose 5-phosphate, right? One, two, three, four, five carbons. That ribose 5-phosphate gets in, ends up in the histamine molecule, all spread out. So you break that ring open and you lay it out like this, and then you attach some other groups to it. We're not going to talk about, you know, exactly how that's done, but it involves PRPP, which is not only important in the synthesis of histidine. It's also used in the synthesis of nucleotides. And so that's an important precursor. And yeah, so this pentose phosphate intermediate are in the product of pentose phosphate pathway. It can be used to make histidine. Okay. So general can sort of see how they're stitched together. All right. So here's a summary of everything from 10,000 feet. We have each of these amino acids is synthesized from different precursors, and some of the synthetic pathways are overlapping. So now we need to deal with this issue that we left unresolved, the regulation of this pathway. So we need just the right amount of each of the 20 amino acids. If we regulate upstream, way upstream, that's not going to give us the fine-tuning we need for regulating the exact amount of each of the amino acids. So we need to think about how this comes together. So there's all these different pathways that feed into amino acid synthesis, but many of them share common precursors and have overlapping pathways. So we need to deal with this problem. And the way that we deal with this is isoenzymes. And so here, for example, we have a stacked pathway. Aspartate leads to the synthesis of lysine, lead synthesis of methionine, and then isoleucine. So if we just turned off this enzyme here, we would turn off the synthesis of all of these amino acids. We need a way of dialing down the enzymes, not a digital switch, an analog switch. So by having different forms of the enzymes that are each subjectable to different allosteric regulation, we can dial things down, but not completely off. For example, you have these feedback regulators from threonine. So if those are inhibited, we still have some flux through this pathway in here to make our isoleucine, because we always need to, in the last step, convert threonine to isoleucine. So for lysine, that feedback's here, but some of those substrates can get through, get past that regulation by using the different forms of the enzyme. We have this fine tuning of all these different, very similar protein sequences that are catalyzing the same reaction, allowing us to get exactly the amount of flux through each part of the overlapping segments of the pathway. So does that make sense? Okay. That is the 10,000-foot view of amino acid synthesis with a little bit of details here and there. But now you think about amino acids. Where did the amino group come from? We don't have the capability to make ammonia. So there's lots of nitrogen. It's like 80% nitrogen or so in the air, into gas. So if you would just let things go to their thermodynamic endpoint, you would end up with just oxidized form of nitrogen. So ammonia is the most reduced form of nitrogen. So we need some way to synthesize ammonia. So there's this nitrogen cycle that goes through each of the oxidation, possible oxidation states of nitrogen. So there's a set of bacteria. Remember, fish are releasing ammonia directly. And then there's a set of bacteria that can oxidize that. So they literally are burning ammonia. Oxidation reactions are highly exergonic. So these organisms derive synthesis of ATP from burning ammonia to nitrate or nitrite to nitrate. But then there's other bacteria that do the opposite reaction. And so they take a fully oxidized molecule and convert it into a more reduced form of the molecule. Why would they do that? Let me give you a hint. These are necessarily anaerobic bacteria that do this. So what do we do? So we're aerobic organisms, right? What do we do with the oxygen? Why do we need oxygen? We're bringing all the pathways together. Exactly. So if you're an anaerobic bacteria, you don't have anything to pass your electrons to. You don't have the oxygen to pass your electrons through. But you could just pass it to some other oxidized molecule. So this is how you deposit those electrons that have come through the same similar electron transport chains. And then you just, in the last step, instead of depositing the electrons on oxygen, you deposit them on nitrate to make nitrogen gas. And so we have all this nitrogen gas around. But then there's this other conversion. Conversion of nitrogen gas to ammonia. In other words, fertilizer synthesis. And so this reaction, you might think, well, surely exergonic, right? Is it? Would you guess that the reduction here is exergonic? Okay. Well, this is, let's see, the full oxidation. That's this part here. And so that's exergonic. The other way, could that be exergonic? This nitrogen fixing? It is. And that's very surprising. Nitrogen gas converted to ammonia releases 33 kilojoules per mole. So that's an easy reaction, right? Well, there's this little problem. That bond is about a thousand kilojoules per mole in strength. The bond between those two nitrogen atoms. It is exergonic. At equilibrium, there would be 100,000-fold excess of ammonia compared to nitrogen gas. But there's this little problem in between. A thousand kilojoules per mole is necessary to crack those two nitrogen atoms apart. So although it's exergonic, delta G double dagger is huge. It's a thousand kilojoules per mole. There's a huge activation barrier to this reaction. So it's thermodynamically very favorable, but kinetically impossible. Do you see that? So you can read it, too. So you might think, well, you can do this chemically. You can take your nitrogen and a billion people on Earth are dependent on this reaction. If this reaction didn't occur, billions of people would die. This is how we make fertilizers. We take nitrogen and we put tremendous amount of energy into that molecule. We would bake it at 400 degrees and put it under hundreds of pounds of pressure because we're trying to pry those two nitrogen atoms apart. That's a tremendous amount of energy that's necessary chemically to transform nitrogen gas to ammonia. But if we want to do this with enzymes, these enzymes have been evolved such that they can do this reaction at atmospheric pressure at room temperature. So you think about it. It's what an amazing enzyme. You take something that requires tremendous amounts of energy and you are able to do it under standard conditions. So this occurs in these denitrogenase enzymes and there's a little electron transport going on here. So here's a complex between the two enzymes that are involved in this reaction. So you have the dinitrogenase reductase, which is transferring electrons here to our dinitrogenase in the center, I believe. So here's our dinitrogenase in the center. And inside of the dinitrogenase are all these very ornate and elaborate metal clusters. Remember that? Remember that oxygen-evolving complex that we saw before? These are batteries. See the batteries? They're right here. And we're taking these electrons and charging the batteries one electron at a time, transferring from some original source down into this reductase. The reductase transfers electrons one at a time. It begins to charge up the batteries in these metal centers to the point where we've invested a tremendous amount of energy in here and in one step it takes into and makes ammonia. We don't want to get stuck somewhere in between for the same reason that we talked about with the oxygen-evolving complex. We don't want any free radicals going on. Okay, so let's look at each of these steps. The dinitrogenase reductase is a, literally, it's just a one-electron carrier. So it accepts an electron from ferrodoxin. Where did we see ferrodoxin before? There's a lot of questions today. Zorro. Yep, yep, photosystem one. Very good. And what was it used to do there in photosystem one, that ferrodoxin? NADP, oxido, reductase enzyme. It's making NADPH molecules, transferring electrons to the NADPH synthesizing enzyme. But here we can also use those electrons on ferrodoxin to transfer them to the dinitrogenase enzyme by first transferring them to the reductase. So the ferrodoxin binds to the dinitrogenase reductase, transfers one electron at a time. This reductase then cleaves two ATP molecules, which allows to jam those electrons into the dinitrogenase and also give some energy into the dinitrogenase. So for every electron we jam into the dinitrogenase, we cleave two ATP molecules. So what do we have here? We have a six electron transformation of our N2 to make NH3. So now those electrons are received on the dinitrogenase one at a time and stored in these elaborate metal clusters. So there's a molybdenum metal ion here, and that's also involved in holding this thing together. So we charge it up. We put a tremendous amount of energy, hundreds and hundreds of kilojoules promote energy into this dinitrogenase. So then when it binds nitrogen in one bolt, it transfers those electrons to its final product. And so here we derive those electrons from metabolism so we take pyruvate dehydrogenase, for example. We can make some NADH, which then eventually you can transfer those electrons onto ferrodoxin one at a time to make the reduced form. Transfer from one electron at a time from ferrodoxin to the dinitrogenase reductase, which when ATP is hydrolyzed, it allows you to transfer electrons from this enzyme to this enzyme, the dinitrogenase. So you have this conformational change of the dinitrogenase reductase, which is catalyzed by ATP hydrolysis. And that allows you to have enough energy to insert these electrons where they need to go in the dinitrogenase when they're transferred. And you say, well, wait a minute. The reaction we're doing here involves six electrons. But because of the mechanism of this enzyme, we're not only reducing nitrogen to ammonia, we're also reducing protons to hydrogen gas. That's a necessary part. So actually it takes eight electrons in this process. So, and that means 16 ATP molecules needed to be used up to make this NH4, this ammonia molecule. So that's a tremendous amount of energy. Any questions so far? Any of that stuff? All right. That's a tough one, huh? Hey, test, test, test. Okay, turn off the clicker. Turn off the clicker. Turn off the clicker. So why was I chuckling? And people were struggling up here, you know? So one of the answers was reductive deamination. Why is that wrong? Yes, it's going the other way. And what is NADP, a cofactor? Yes. She's sure. Okay, so the correct answer was D. D, good for you.


Welcome to the 34th episode of Patterson in Pursuit. This is a very special episode because I'm coming to you from Auckland, New Zealand, and I'm very happy to announce that my first book on philosophy is finally complete and you can now pick up a copy. It's called Square One, The Foundations of Knowledge, and as I've said before, it's literally the most important thing that I've ever written. You can pick up a copy of Square One on Amazon. There's a paperback version and a Kindle version, and in the next couple of months there's also going to be an audiobook edition. Or another way you can get a copy is by becoming a patron on Patreon.com slash Steve Patterson, where if you sign up to be a contributor to the show, then you immediately get a copy of What's the Big Deal About Bitcoin, which is my previous book, and Square One, The Foundations of Knowledge, the book that I just released. You get a free copy immediately. And so I want to talk to you today about Square One, why I consider this book to be so important and why I chose to write this one first of the several philosophy books that I have planned. But before I do, I want to give a massive shout out to all of the supporters that have been following my work and supporting me on Patreon for the last year or so. Without you guys, I would not have a career in the world of ideas outside of academia. Every support is making it possible for work like this to be produced, and it's about to be ramped up majorly in the future. Now that the book is done, I'm super excited to go back to writing frequent articles from my website.  The book was awesome, and I'm so, so dang proud of it, but it's been kind of a bottleneck for some of the other work I wanted to accomplish because I wanted to make sure that this one was done perfectly. And right now there are more than 50 patrons on Patreon.com who are contributing. Every time I post a new episode or a new article or a new video, and I want to give you my heartfelt thanks for demonstrating your support for valuing the mission of creating a rational worldview, it's very exciting and encouraging and humbling for me. And I think this community of rationalist renegades is going to be really growing significantly in the coming year. I've got big ambitions for 2017, and I want to start by telling you guys about Square One. Why you guys, who have demonstrated that you are interested in a new, clear-headed approach to thinking about big ideas, why you can get excited about what's in Square One. You can tell your friends about what's in the book, because I think you'll find the ideas force people who have not heard them, maybe life changing, and the way that it's written is immensely approachable. I explicitly tried to make it as non-academic as possible. There's almost no jargon in the book because there doesn't need to be. One of my suspicions is that the reason that academics write so poorly is because they actually aren't clear thinkers. If you can be a very clear thinker, you should be able to be a very clear writer. All right, so let's dive into the book. A great summary of why I wrote the book and what the general purpose of it is is on the back cover. It says, truth is discoverable. It's not popular to say. It's not popular to think, but you can be certain of it. Ultimately, if you had to sum up my whole project as a philosopher and the purpose of the book, it is to say that right now we live in a culture which denies the existence of truth. They think it's naive to say there's such a thing as objective truth, much less to say that the mind can grasp some parts of what objective truth is. Well, that is my position and I'm not just gently claiming that that is true. I'm saying you can actually have certain knowledge, knowledge that is objectively true that cannot be false. It may not be a great list of knowledge that is objective certain truths, but we can still have an underlying foundation of certain knowledge. Now, this in context of modern philosophy is heresy and it's naive, right? To address topics like, is there objective truth? Is not really a topic that's written a whole lot about in philosophy. Yeah, some people write about it, but it's not a central issue. In my mind, there is no more central issue. We shouldn't be talking about anything else really until we resolve whether or not it's the case that objective truth exists and whether or not it's discoverable. There is no such thing as any kind of objective truth and why are we talking about anything? Why are we trying to sort through and discover things? If all there is is opinion, then when we're doing philosophy, we're essentially just sharing one another's opinion and I'm not a big fan of that. There are some popular philosophers out there who think that the role of philosophy is akin to poetry because there's no such thing as objective truth. So we're essentially just assembling words together that sound nice and make us feel nice and represents some kind of artistic perspective on the world. I completely disagree with this and that is one of the reasons I wrote this book. It's called the foundations of knowledge because I'm not just claiming this is arbitrary truth that we can know. I'm claiming that underpinning all knowledge, 100% of knowledge, is the same foundational truth. That truth I've talked a little bit about on the show, it's logic. It is logical necessity, which I'll talk a little bit more later in this episode. So the book starts with a couple of analogies to try to help people understand the connections that we have in our worldview. I say that ideas are not held in isolation from one another. Our worldviews are like trees. Each part is connected to another part. When you look at a tree, you have the leaves of the tree that are connected to little branches. The branches are connected to bigger branches which are connected to the trunk. The trunk grows out of its roots. All of these things are connected together. And I claim worldviews work the same way. Conclusions you can think of like leaves. They're connected to premises, which are the branches. Premises are connected to deeper premises. All of those deeper premises ultimately grow out of foundations. And the foundations is what this book is about. I want to examine, first of all, is it the case that there are foundations? And second of all, if there are foundations, what are they? And my discovery is the foundations of everybody's worldview. Without exception, share the same core presuppositions. The exact same truths are the foundation of my worldview as they are somebody else's worldview in Africa that I've never met. So the first chapter is really trying to get people to realize that they have a worldview and they shouldn't just view things in isolation. Our ideas grow out of one another. And the more foundational the idea, the more base level the idea, the closer to the roots, the more important, because the more ideas follow from those base level ideas. So, for example, if you have a flawed theory of physics, if you think that the earth is flat or you think that the earth is in the center of the solar system, a great number of ideas you hold will be incorrect, versus if you think that the surface temperature of the sun is a little bit hotter or colder than it actually is, well, there's not that many ideas that have to be revised if you get that particular belief wrong. So the deeper we go into our worldviews, the more foundationally critically important those ideas become. And if you get the foundations wrong, these ultimate inescapable foundations, these logical foundations, if you get those wrong, your entire worldview is essentially based on sand. So the next part of the book is trying to frame some of the most popular objections to the idea that there is foundational knowledge. And I categorized two types of ideas. I call them the arguments from impossibility and the arguments from implausibility. So the implausible arguments say that maybe it's the case there is objective truth and foundational knowledge, but even if there is, it's totally implausible to think that humans could ever access it, were too limited and finite creatures to think that we could ever know such a thing as objective truth. The arguments from impossibility say that it's not even true in principle that there are such things as objective truths, or some of them argue that there are actual logical contradictions in the world, which means that we can't actually be certain about anything. So I give brief summaries of these positions in anticipation of refuting them, which I do in chapters 3 and 4. Now, if you are already a philosopher, and for whatever reason you don't want to read, you know, 25 introductory pages, and you want to jump straight into the higher level important philosophic ideas of square one than starting chapters 3 and 4. That's really the whole meat of the book. And it's an idea that I've spoken a bit about on the pie-cast, but I'll give you a taste of these ideas. What I consider to be the foundations of knowledge can be discovered through a process of internal doubt, introspection, and skepticism. So there's all kinds of ideas that we hold about the world that might be wrong, right? Whether or not a physical world exists, maybe everything is illusory and we're just brains in a vat and we're hallucinating everything and maybe it's the case I'm not even a human, maybe I'm a Martian that's dreaming and there's all kinds of possible ways that my ideas might be wrong. Are there any ideas then that can withstand radical skepticism, doubt, and scrutiny? And I say, yes, in fact there are. So I'll give you a simple example. There are no square circles. Since you guys have been listening to the show, you know, I actually talked about this particular idea with the professor at Columbia and he was saying, well, maybe there are square circles. So this is an important idea and what I'm claiming to be certain knowledge is still doubted by some people. Nevertheless, when you unpack the meaning of the terms square and circle, you discover a certain truth. There cannot be any square circles or spherical cubes, given what we mean by the terms. You cannot have things which have mutually exclusive properties. Another simple example of a certain truth be something like this. All of the students in class with blonde hair are students. This is another certain truth. Now, some people might disagree. They might try to have some weird circumstance. Well, if somebody we think is a student isn't actually a student. They come up with all kind of silly objections, but if you unpack the meaning of your words, you will discover that indeed, if it's the case that somebody is a student in class with blonde hair, then it is the case that they are a student. That is a necessary truth. Okay, so then we have to go one step farther. We have to ask, why is it the case that all the students with blonde hair are students? Why is it that there are no square circles? Why is it that there are no married bachelors? The answer is logic. Logic is the reason that there are no square circles. Logic is the reason that 2 plus 2 equals 4. It's the reason that all the students in class with blonde hair are students. Logic is necessary. When you understand necessariness, what is meant by the term necessary, you discover logic and it is extraordinarily powerful. Logic is the reason that contradictions are false. If somebody contradicts themselves, that means what they're claiming is necessarily false. And logic points to the foundation of knowledge, what I call square one. You simply have to ask, why is logic necessary? Could there be any exceptions to the laws of logic? My answer is this, the laws of logic are necessary and inescapable, universal, because logic and existence are inseparable. Logic and existence are inseparable. That is the foundation for knowledge. What I mean is this, that for anything that exists in any circumstance whatsoever, it's a physical thing, mental thing, conscious thing, some kind of existent that we can't even comprehend, for any existent thing, it is the case that it exists the way that it exists and it does not exist the way that it does not exist. So in other words, anywhere that you have existence, you must have logic. You have the law of identity, which is A is A, a thing is exactly what it is and it is not the case that things are not the way they are not. This is true for everything. So this means when we're talking about the world that literally doesn't matter what we're talking about, we can know that any existent thing whatsoever must play by the laws of logic. So if that is true, which I make the case for in obviously more detail, that is true, that implies that any contradiction is necessarily false. Reality cannot be contradictory, that doesn't make sense and I give explanations for why that's the case. There are no true mystical paradoxes in the world where something is and it isn't and we just have to throw our minds away and say, well, this is something we can never comprehend. This is the reason why when talking with some Christian evangelicals about the Trinity, they say things like, well, maybe it's a logical contradiction, but God is bigger than logic, God supersedes logic, God is transcendent. And my position is, if it's the case that your conception of God contains a logical contradiction, it is necessarily true that your conception of God is false or that God does not and cannot exist because there cannot be logical contradictions. It is not the case that God created the laws of logic, I'm certain of it. And if you don't believe me, that's fine, but pick up a copy and see why I say that's the case. Because if it's true that God exists, then it is true that God exists and it is not true that God does not exist. Or God also plays by the laws of logic, to the extent that he exists. The only thing to which logic does not apply is nothing, as I've spoken about on this show before. And because nothing isn't something that exists, logic applies to everything. Now this, friends, is why I wrote this book first. In my own pursuit of truth for the last, I don't know, 10, 15 years, whatever, I have been seeing whether or not there's any kind of objective truth out there. I've been interested in these topics. I discovered this several years ago and my life changed. I realized this is it. This is actually certain truth. You can build an entire world view based on the fact that logic and existence are inseparable, based off of logic and logical consistency. So this is my mission. I want to build an entire world view based on the truths that you will find in square one the foundations of knowledge. There's no faith involved. There's no trust involved. Don't take my word for anything. I am completely convinced that in chapters three and four of this book, as I explain, when you, in your mind, you conceive of things the way that I conceive of them, you understand the meaning of my words, you will agree with me that there is certain truth. Even if it's limited in scope, we can only say things like, you know, things are the way that they are, which doesn't tell you a whole lot about the world. But it tells you a limited amount of things that you can be certain of. And one of the nice things about working outside of academia is I don't have to be quiet and have this fake humility about it. I'd be like, oh, well, I'm just adding to the conversation and maybe my ideas are wrong and I don't know. I'm just commenting on somebody else's ideas that they wrote about 3,000 years ago. No, that's, I don't have to say any of that, right? I can say very honestly, I sincerely believe that if you read this book with an open mind, don't take one thing that I say based on the fact that I said it, scrutinize, be skeptical about every single thing. The purpose of the book, the methodology of the book is skepticism and doubt first. So that obviously applies to me, the author. But try to understand what I have tried to clearly communicate about the necessity of logic, and I am all but convinced that you will agree. So it is square one. It is the foundation I say for everybody's worldview. It's certainly the foundation for mine, and I'm trying to build off of it. So the next book that I'm going to be writing is on metaphysics. And I've got books planned on politics and economics and language and mathematics. And eventually I'm going to write a book on ethics, all of which are going to draw from the ideas of square one. If the ideas in this book are wrong, then you can unsubscribe from the podcast. You can ignore anything that I say, because everything I'm going to say is going to contain a fundamental catastrophic flaw in it explicitly. And I'm the first to admit it, right? If it's the case that there is some true logical contradiction out there, then nobody should take anything that I say seriously, not even myself. So after I lay out the case that logic and existence are inseparable, therefore is an explanation of kind of where we can go from there. So it's an explanation of conceptual reasoning, of a little bit of the relationship between our minds and the world, how we can build theories, some of the problems with rationalism, some of the problems with empiricism. And I make the case that there is an objective hierarchy of knowledge, that if it's the case we value understanding truth about the world, then it must be the case that philosophy is more fundamental and more important than art history, right? Philosophy affects virtually every single idea you have in your worldview. Art history affects very few, so we have to acknowledge there is indeed a hierarchy.  Well, no, the reason I got involved in philosophy is because I recognize philosophy is categorically more important than political theory and economics, which is how I got into philosophy in the first place. And this is true regardless of the field of study. As you get more fundamental in whatever you're studying, you will eventually discover philosophy, the primacy of philosophy. So I also lay out in chapter 4 a bit of methodology, a bit of technique for building a rational worldview. And then the last chapter is devoted to responses to objections. So I have the first thing I talk about is the Liar's Paradox, which is the most popular objection to this idea that there is certain knowledge, that logic is inescapable. People say, oh, this sentence is false, as they try to make a true contradiction out of that. And I give a fairly thorough refutation of the idea that that somehow is a logical paradox. It certainly isn't. It's entirely resolvable, as are all other paradoxes. And I give several more examples. So I talk about the bittersweet paradox, the logic of nothing, this idea of vagueness. It's a similar idea to what I was talking with Dr. Giazzo at Harvard about this idea of universal flux, that everything is constantly moving and there's kind of an infinite regress all the way down to nothing. And so therefore, no thing really exists per se. I address all that in chapter 5. And then I address a popular objection, at least in coming from the 20th century, that, oh, all these ideas are mere tautologies. You can't actually prove anything just by saying A is A. That's a tautology, which means it's devoid of content. This is certainly mistaken, and I address it in some detail in chapter 5. Though I'm sure I'll have more to say on my next book about the philosophy of mind. This is not a one-off book. This is the first step in creating an entire world view. And it is written in a style that is meant to be read. I'm not trying to impress anybody. I'm trying to communicate ideas as clearly as I can. So as somebody who's just obsessively interested in the world of ideas, I think there's nothing more important than the world of ideas and the truth that we discover, you can see why I say, and this is the most important thing I've written. And of all the books I intend to write, I'm going to continue coming back to this one and look if you find anything that I say interesting or plausible or worth investigating, read this book. It's a little bit more than 100 pages and anybody from the philosopher who's been studying philosophy for 40 years to the complete novice is going to be able to get something out of it. And I also know based on some of the emails that you guys sent me that I'm not isolated in seeing that we live in a culture of what I call irrationalism, that denies everything I've just said. Truth is indiscoverable or non-existent and it's just a complete waste of time and everything is gray and fuzzy. It's all around us. That is the dominant cultural philosophy is something like an epistemological nihilism and a relativism. And it's frustrating as heck because a lot of these people don't mind if they end up contradicting themselves. I know you guys can sympathize with that and this book you can also hand to those relativists and nihilists and say, look, just read this one and if you disagree with the ideas in this book, tell me where and then talk about it. My claim I make very explicitly in the book is if you can't agree on the laws of logic, the law of identity and non-contradiction, then you cannot make meaningful progress in any kind of intellectual discourse. You must presuppose the laws of logic in order to make sense. I think, I'm not sure, but I think this will get through to a lot of people who are stuck in kind of an intellectual cloud where they are convinced that truth is indiscoverable. I think this book might reach them, at least that's my goal. So if I've piqued your curiosity and you think this is a worthwhile goal, a worthwhile purpose for a book, then pick up a copy. You can get it on Amazon, you can get a paperback version, you can get the Kindle version, there will be an upcoming audiobook version which will be me narrating the book. You can become a patron, patreon.com, where you can immediately get a PDF version and quite frankly, if for some reason committing a dollar a month or the $9.99 on Amazon, if that's too much and you're somebody that can't afford it, I understand, been there, done that. I don't want these ideas to be restricted from anybody, so find a pirated copy. I'm sure online, if you Google around, you'll be able to find a pirated version. It's much more important that if somebody is interested in these ideas, that they have access to them and can have a clear voice to say that truth exists, then it is, I get a couple of dollars of royalty or a supporter. So one way or another, pick up a copy of the book. Thanks so much for listening and I'll talk to you guys next week.


Everybody forced here on Origins release day. We got 22 23 origins hobbies six box half case number one picker team style AJ with the magic Eric Y Mavericks Frank C Clippers How he with the Knicks sons hung see bulls Jeanette has the Sixers Jeffery Rockets Jesse Nets Jin Tian with the Wizards Jose Hawks Justin Cavs Kenneth T Wolves Raptors Kim with the heat Lersack Spurs Lee Juan warriors Long J Hornets Luke M Pelicans Marvin N Nuggets Miguel with the Lakers Muhammad has the Thunder Paul Oh Bucks Robert R Grizzlies Robert P Blazers Sean M. King Steve R. Pistons Tim V jazz and US has the pagers. Good luck everybody. Let's see what we got here Let's see what are those SSPs Tiger Kyle wants to see one of the dawns as well. All right two autos or mem so two hits per box Also, what one insert I think is what it was Yeah, two hits two parallels one insert. So, let's see. Oh, that's pretty cool roots are great And it's sixers dual here dwelling be James Harden the 75 Like glossy they're not like a matte finish like glossy. Oh That's different nice insert for the Sixers Those guys are good at basketball Yeah, they're all glossy.  This one's a parallel. I think Is that Katie look different than the other two? It does. Well, he's a red It's a that's a guy KD was a red. So like a Ace parallel. All right first hit goes to the Raptors rookie Jersey auto Christian Coloco Colocamo Go Christian Coloco first hit of the day and second one is an Isaiah Mobley two rookie Jersey autos in the first box Cavaliers Isaiah Mobley Mobley fam Mobley fam out here Second break is sold out everybody Second break is sold out Third one has five to go teams on sale Nets Nick's Wizards Nugget Sixers five to go There we go box to Again, these are half cases So if you have like one and two would be the same case three and four would be the same case So if you do buy a team with like seven and eight or nine and ten That would be a full case. There's a dawn of Jake Laravia for the Grizzlies Cal's favorite. No friggin Murray there's a Patrick Baldwin, Jr. He was red Mike Conley For Utah and an orange rookie AJ Griffin hawk 67 to 75 and glossy finish on Oregon I'm about it doesn't really change the product a whole lot, but I'm about it. You know thunder Jalen Williams, rookie Jersey Hit for the Thundernail Jumbo rookie Jersey Big balancer join the Niners. Why would they have why would the Niners have done and a David Roddy rookie Jersey auto for the Grizzlies Why the Niners would would do that David Roddy Grizzlies rookie Jersey auto Yeah, I would gather's that but Their backup backup also good back up to the backup to the backup got hurt as well though So they have signed him like their mid-mid game. All right, let's see an on-card this box here See an on card. I think we do have an on-card. Yeah, that's a lot thinner That originals tie-tie Washington Rockets Originals insert tie-tie Washington, Jr. Rockets There's another Keegan Murray rookie for the Kings Johnny Davis rookie for the Wizards red RJ Barrett and Blue rookie Benedict Matherin Pacers 97 a 99 We go eggs Benedict Matherin Cumberbatch as you're gonna hear a lot tonight. I'm sure was Sam Good stuff there. We got a Damian Lillard Jersey car for the Blazers 18 out of 35. That's game worn The vets should all be game worn in this Blazers Dame Jersey And our first on-card Rookie auto goes to the Warriors Patrick Baldwin, Jr. If only our economy, David Yeah, or or or a Nick Bosa Or a Simeon rice We go Trying to think of one for Kyle there. Do you want cards? Is that what is that what I'm seeing? Team origins Jalen Green Rockets Caprice aviak Caprice av as well I'll allow I'll allow it crispy John Morant Anna LeBron James Red Cole Anthony magic with a green to 49 Tyler hero heat The greens my favorite parallel so far 28 to 49 Nuggets rookie on card auto Christian Brown Thunder rookie auto Usman dang both on card two on cards in the box. That's what we like to see in origins Go thunder. There you go. Nuggets All right, still at five to go on number three nine on number four Good to see spots coming in. Thanks again, everybody Let's get these filled up. We also got McDonald's all American chrome later on Nine boxes left in that case. You do get a random box. So two autos plus parallels every card in the box is going to ship to you Hang on Originals Johnny Davis wizards box with a LeBron James Oh, it's a variation. That's what it is. LeBron James variation. Is that the with hair without hair variation? Is that Cut cut Kyle off guard. Uh, red rookie Usman's. Yeah, you're the thunder Uh-oh bronze can come after me now and blue Donovan Mitchell number to 99 for the calves The on cards are not glossy. They're like regular origins I don't think it would I like it. It would work on it Nice Donovan Mitchell calves could parallel there first year jake larivia rookie patch to 35 for the grizzlies Go grizzlies. What do we have? Elevation rookie auto 86 of 99 magic palo ben caro Magic with a monster AJ Elevation signatures palo ben caro. That is a pretty neat design Yep to 99 that's going into a mad congrats magic On card palo it's our uh That's our let's say it's like he's like a god around around these parts the elevation looks cool. I like that a lot Is that new to this year? That's gotta be new Because usually the only on cards were the like just the regular autos Team origins John Morant grizzlies I'm about that. I'm all in on that hallow burden devin booker Red levine for chicago with an orange to 75 mark williams rookie for the hornets He's been quietly really good mark williams former uh Just he's just a carolina guy through and through I guess Dude Peyton watson on the rookie jersey one of the nuggets to 49 What's up, AJ? Congrats, dude, and a max christie rookie on card auto for the lakers Lakers thanks for joining everybody. Let's do a really quick recap I'm not sure if we're going to be a recap every single one of these because they're just Pretty quick but Do our best recap them all All right, relics of Peyton watson jake laravia Damian lillard Jalen williams autos of christian brown again. These will be the on cards Usman yang mostly what you're looking for in this product is on cards uh patrick balvin jr Jersey autos of david roddy Isiah mobley christian colloco another on card of christie and then the elevation rookie auto palo ben carter 99 Congrats magic on to number two. Thanks everybody