Episode Transcript
[00:00:04] Speaker A: ID the Future, a podcast about evolution and intelligent design.
Welcome to ID the Future. I'm your host, Eric Anderson, and I'm excited to have Dr. Brian Miller back on the show with us today. Welcome, Brian.
[00:00:19] Speaker B: Thank you. It's a pleasure to be here.
[00:00:21] Speaker A: So, Brian, tell me what you're working on these days before we dive into our topic. Exciting things going on. I know you guys have the Science and Faith conference coming up pretty soon, right?
[00:00:30] Speaker B: Yeah. There's going to be some really nice talks about things like wonders of the animal kingdom. So that's going to be really enjoyable. People like Daniel Reeves will be there, Emily Reeves, we've got a person who's an extra in Earthworm. So I think it's going to be particularly exciting for people to bring their, like, their children too, because they'll really see the awe and wonder of creation. And I will not be there that year, but this year. But I'll definitely be at other events this year.
[00:00:55] Speaker A: Yeah, yeah, we've got. I know you guys have a lot of stuff coming up. We've got cells coming up later this year and of course, the summer seminars and lots of things going on that'll keep you busy. I know you have your fingers in a lot of things.
[00:01:06] Speaker B: Yes. And definitely I'm really excited about the projects. I'm working with you and others in the our engineering group on about just sort of the application of engineering principles of biology. And I think this year we're going to see some really significant breakthroughs. So listeners can just stay tuned.
[00:01:21] Speaker A: Excellent, Excellent. Good stuff. Well, I do want to talk about one of our favorite topics today. I know it's a favorite of yours as well as mine, and that's Origin of Life.
So let's start this way. If you kind of back up a little bit, Brian, kind of, you know, to Steve Meyer, some of his work, maybe we could talk about him first and then Jim Tour and then some of your own research. Just kind of give us a summary, if you will, of some of the challenges and some of the issues that have been raised.
[00:01:46] Speaker B: Yeah, certainly. So Stephen Meyer obviously wrote the book Signature in the Cell, and that dovetailed with earlier books such as the Mystery of Life's Origin. And what Stephen Meyer did was it was really related to his PhD thesis as he was making the case that you can come up with a robust scientific argument for there being design in biology. And part of the way that argument works is you show that a system could not realistically occur through chance or natural processes. And you can also show that in some way, it's specified, it's special, it points to purpose. And in his arguments, he made both of those cases. So he talked about how everything we know about chemistry and physics, all the origin of life research, suggests that chemicals will not naturally move towards the state of life. In fact, quite the opposite. What he also showed, though, is that even beyond the challenges of chemistry and physics, the problem is what's central to life is information.
So what happens, and you've talked about this, and many of us have talked about this, but what he articulated so clearly in his book was that if you want to do something in a cell, the cell has to have enzymes. It has to have these molecular machines to make things happen. And those machines themselves are composed of things like amino acids. So you have this chain of amino acids, much like letters in a sentence. In the same way you've got 26 letters in English Alphabet, you've got 20amino acids, or occasionally an extra one or two. What happens is you have to have the right order, the information in the same way you have the information in a sentence for the sequence of amino acids to fold into the right structure to do something useful. So Stephen Meyer made the case that information is absolutely essential to life. So those are two arguments that he's made very effectively.
[00:03:34] Speaker A: Right, good, good. And then if we jump to Jim Tour and some of the stuff that he's been doing, particularly over the last couple years, I would say, how does that dovetail?
[00:03:43] Speaker B: Well, what happens is, while Meyer was creating, was presenting these very general arguments and using some specific examples, James Tour went very, very, very deep in the chemistry. So what James Tour was showing is that it's exceptionally difficult, even in an advanced laboratory setting, to create complex molecules. And as our listeners have heard many times before, James Tour creates these really amazing molecular machines that can cure cancer potentially in the future and things like that. Yeah, well, he has to use incredibly complex protocols to create his machines, but the machines in life are far more complicated than what he creates. So what he argued is that if you look at what chemistry naturally does, either today or on the early Earth, you're never going to expect natural processes to produce something like RNA or proteins. And what he. He went into great detail of of those challenges. But what he also did was he showed that the origin of life research that claims to solve the problem of life's origin, or at least parts of the problem, the only way they make progress is by using exceptionally complicated chemical procedures, where there's constant intervention, where they change conditions, where they add molecules to assist in the process. And he said, look, this has no relevance to what would have happened on the early earth. So those are the sorts of arguments he's made.
[00:05:02] Speaker A: Right. And if you're using these complex protocols, you know, just to give an example, or, you know, I'm just sort of pulling it out of the, out of the air here, but you have to have a particular ph, or you have to have a particular temperature, you have to mix a certain chemical a particular amount of time and leave it, and then purify it and do another step. This all requires information. Right. So it's that information aspect again that is being highlighted in all of the effort that the researchers are doing to move this set of reactions in the right direction.
[00:05:34] Speaker B: Yeah, that's an exceptionally insightful point that you just made. And it's something also that Stephen Meyer addressed in his book, his writings, his essays, is that what these origin of life researchers are actually doing is they're showing the absolute necessity of information to move molecules towards life. So in the same way an enzyme has these very specific ordering of amino acids, these scientific protocols have these very specific conditions, steps, interventions that serve the same function as these enzymes. So what happens is Stephen Meyer talks about how information constrains possibilities. It ensures only a certain set of desired outcomes take place. And the same way the enzymes constrain what happens in a cell, the researchers use information to force the chemical processes that produce what they want.
[00:06:27] Speaker A: Right, right. Well said. I like that. And, and I guess it sort of highlights something. I think Jim Tours said this, but I'll state it this way.
You know, he says that molecules left to their own devices have, have no interest in moving toward life and, and no tendency to do so. Frankly. Left to their own devices, they're pretty helpless.
[00:06:49] Speaker B: Yeah, in fact, it's really interesting. One of my favorite papers is by Stephen Benner, who is a really one of the world most respected origin of life researchers. He's operating from the assumption that life must have happened through a natural process. But in his paper, Paradoxes of the Origin of Life, he states explicitly that everything we know about chemistry, everything we know about physics, processes like thermodynamics, and even all the research we've seen reinforces the idea that molecules do not move towards life, but they move away from life. That what all this research does, if it's at all realistic, is it creates complex mixtures that referred to often as tars or asphalts. So I was shocked at the honesty of the article. Of course, at the end of the article, he says but we should still have hope. We should just sort of assume it happened naturally. And maybe our assumptions are wrong or something along those lines. But. Yeah, so James Tour actually was very generous to the field compared to other people within the field, Right?
[00:07:49] Speaker A: Well, yeah. In fact, one of my criticisms of Jim Tour is that he's been too soft.
[00:07:54] Speaker B: Yeah, yeah.
[00:07:55] Speaker A: Which is kind of funny if you've heard him, because he's very passionate about.
[00:07:59] Speaker B: Oh, yes, yes.
[00:07:59] Speaker A: He's talking about there. But that's great. Yeah. And. And you know, what's. What's Benner's approach here? Is he hoping for some new physics, as some people have claimed, or is he just.
[00:08:08] Speaker B: Well, this is what's so fascinating, and this will get into future podcasts. I won't spoil it for our listeners, but what Stephen Benner does is the whole point of this paper was to describe the problems. So he really offered no solutions. He says these are the problems, and he gave five very, very serious problems. In fact, he articulated the problems as well as anyone I've ever seen. It was really a beautiful article, and I'm sure he's really happy how much I quote it and give him honor for what he did.
But what he does, and this is what everyone does, actually, practically, is they appeal to natural selection, or what would people just say? Selection as the means by which nature overcomes these challenges.
[00:08:51] Speaker A: Oh, boy.
[00:08:52] Speaker B: Okay. It's really fascinating because people don't even always mention something replicating, like there's nothing reproducing, but they still just invoke the word selection to state that nature knows to select the right thing to move towards life. That's usually how they respond to it. And I see, Steve, Stephen Benner's had papers that have made those sorts of claims.
[00:09:11] Speaker A: Right. Well, okay, we're throwing back 100 years, then to the early, early days of prebiotic selection, then. Okay. Yeah. And the other approach I've heard a lot of people argue for, I think what's her name, Sarah Walker, and some others have argued that we need to have new physics, new understanding. I know you have a degree in physics from Duke, a PhD in physics, so maybe we could have you back sometime to pursue that point. But let's set that aside for another time. I did want to say, I know you wrote up an article recently for Evolution News about a paper, and you had mentioned something about circular reasoning. I don't want you to get in the details yet because we'll dive into it in a minute, but maybe just highlight real quickly what you meant by circular Reasoning and then we'll dive into the paper.
[00:09:57] Speaker B: Yes, this is really, I think, a very important observation about this research that people don't talk about enough. But whether you're talking about origin of life or the origin of complex animals in the Cambrian explosion, what happens is a biologist rarely have, or chemists rarely have details. They really have a specific set of steps to explain how this happened. What they'll do is they'll look at something that exists today. For instance, what some researchers do is they'll look at various proteins that exist today and then they'll envision what did the ancestor protein look like? They just assumed they all came from an ancestor. They'll then envision what the ancestor looks like. They'll then look at the difference between the ancestor and the modern protein. They'll then sort of break up the differences into a series of steps and then they'll somehow order the steps.
[00:10:50] Speaker A: Right.
[00:10:50] Speaker B: And they'll say, just because then they'll say these steps occurred to turn this ancestor into the modern version.
[00:10:56] Speaker A: Right.
[00:10:57] Speaker B: But they rarely give serious thought about the details of the steps. They just assume the steps happened. But when you actually look at the steps, often they face very clear, insurmountable hurdles.
[00:11:09] Speaker A: Yeah.
[00:11:09] Speaker B: Or at least what would seem insurmountable hurdles. So it's all based on circular reasoning. They assume it evolved from an undirected process. And it's that assumption that drives those stories.
[00:11:19] Speaker A: Right, right, right. And then, and then the press release can come out and say, we've got new insights into the evolution of X or Y. Yeah, it's kind of an interesting approach. So we've got this new paper that came out just recently, December 2024. It's kind of a mouthful. It of amino acid recruitment into the genetic code resolved by last universal common ancestors protein domains. This is by seven researchers. I think five of them were from the University of Arizona, one from Germany and one from Australia. So there's some international collaboration, particularly on the computational side. Tell us a little bit about this paper. What are they looking at?
[00:11:55] Speaker B: Well, one of the big challenges with explaining how life formed is explain the genetic code. Because what you have in life is you have all these essential proteins in cells, but proteins don't reproduce themselves like a single protein won't copy itself. So you have to have a very complex process to manufacture them. And what happens is inside of DNA, or if you're in, let's say an RNA world hypothesis, in these RNA chains, you have the sequence of amino acids in proteins encoded into either RNA or DNA through the codons. So just as a reminder to listeners who might be new to this podcast, every amino acid in a protein corresponds to what's called a codon, which is a set of three nucleotides, and there's four nucleotides, Z, A, C, T and G. And what happens is multiple codons could correspond to a single amino acid. You have this encoded information in DNA or rna. And what happens, you've got to get the information from the, the, the, the nucleotides into the amino acid sequence. And that's no easy task. So that requires very complex molecular machines. You've got to, if in the case of DNA, you have to break the DNA in two, you've got to somehow, what's called, transcribe the information from the DNA onto what's called messenger rna. And then you've got to have this very complex machine that does the conversion. It's called the ribosome. So what happens is this ribosome gets fed into this molecular machine and then the three nucleotides in a codon is converted to an amino acid. Incredibly complicated. And then you've got these special proteins which will link the right, what's called a TRNA to the right amino acid. I won't go into all the details, but the point is.
[00:13:40] Speaker A: Now you're getting into the details here.
[00:13:41] Speaker B: Yeah. The point being that this is a really complicated process. So the question becomes, how do you explain this? And they really have no serious explanations. So what they do is they simply say, well, we'll look at the amino acids and we'll sort of assume that the early code must have been simpler. So modern proteins primarily use 20amino acids. So the early code probably used some smaller number, maybe roughly half, around 10. And then what they do is they figure out, or they try to guess which extra amino acids were added to the code later, which amino acids were added to proteins later. And that's how it works. So previous research, what they've done is they looked at things like which amino acids could easily form in an ancient earth environment, like the Miller Urey experiment. What did the Miller Urey experiment produce in non trace quantities? Right. And they might look at which amino acids are most complex, and if it's simpler, that's easier to form. And they might look at which are stable. So which amino acids would break apart quickly in the ocean or in a lake or someplace. And then they say, well, let's look at cells. And you look at the metabolic pathways and you think, well, if a cell starts with this amino acid and then turns it into some more complex amino acid. The simpler amino acid probably happened first. That's how it works.
[00:14:58] Speaker A: Right, okay, so. So let me. Let me restate that piece because you said a lot there. So on this particular approach that's been taken, which it sounds like has been the primary. Well, let's back up even further. The reason why we want to try to explain some kind of a simpler approach is because it's assumed and recognized by everybody that the current system couldn't have arisen by. On its own. Okay.
[00:15:17] Speaker B: Yeah.
[00:15:18] Speaker A: So then we back up and say, well, it must have been simpler. It must have arisen from some more primitive ancestor. And so we're going to figure out what that was. And what you're saying, Brian, is that the prior approaches, primarily to date, have focused on the types of conditions that might have existed on the early Earth, what kind of prebiotic conditions existed. Therefore, we're going to start with those amino acids, whereas the new paper is doing something different. What are they looking at?
[00:15:43] Speaker B: Yeah, this is a very different approach. What they're doing is they're looking at modern proteins. They look at proteins in a lot of different organisms throughout the kingdom of life. And then what they do is they compare sequences and they try to reconstruct, based on looking at proteins that are in organisms closer to each other and further apart from each other. And through very complex processes, they try to reconstruct what they believe were the proteins in what's called the last universal common ancestor of life. In other words, all life today is believed to have evolved from something, and that something is called luca, or the last universal common ancestor. So they try to figure out what were the sequences of amino acids in those proteins. And then they use very complicated techniques to say, well, what might have been the sequences of proteins even earlier. And what they assume is that if the earliest proteins didn't have some amino acids, but they had a lot of others, and the ones that they had a lot of are probably the ones that were in the code first.
And then what happens if you see other amino acids added as you go from these ancient organisms to more recent reconstructions and so forth, that's kind of the way they reconstruct the order in which these amino acids were added to the genetic code. That's the approach.
[00:16:57] Speaker A: Okay. And the term that's used in the field is recruitment of amino acids into the genetic code. This is sort of a funny term. It's like. It's like the code is out there recruiting new participants to come participate. It should say accidental, but any rate, that's the term that they're talking about is the order of recruitment. So that's part of the title, the order of the amino acid recruitment. Now we know what they're talking about. We start with a certain number of amino acids, and then over time, additional amino acids get added to the code until we end up with our, you know, roughly 20 that we have today. Right?
[00:17:30] Speaker B: Yeah, exactly.
[00:17:31] Speaker A: Okay. And so what they found was. What did they find through their statistical research? And is theirs primarily statistical statistical research or are they doing lab research here?
[00:17:41] Speaker B: No, they're not doing really lab research themselves. It's much more statistical.
[00:17:44] Speaker A: Okay.
[00:17:44] Speaker B: What they found is that there was a lot of similarities from what they expected or what they found with previous attempts to, To. To reconstruct this order of incorporation recruitment. They said the simplest amino acids were the ones that were in the earliest code. That's. That's pretty standard. But then what they did is they sort of said other amino acids may have been in a different order from what people believed before.
[00:18:08] Speaker A: Right.
[00:18:09] Speaker B: So that's really the only difference is that the specific ordering in which they were incorporated is different than the ordering that was. That was suspected before. Partly like the amino acids with sulfur, they thought may have been a bit earlier. The ones with rings may have been earlier. That's. That's some of them they thought might have been later. That's really the only difference.
[00:18:26] Speaker A: Right. Okay. So the metal binding I think they mentioned in the sulfur containing amino acids they felt should have been earlier in time than maybe some other prior researchers had.
[00:18:35] Speaker B: Yeah, exactly. That was. That's the basic difference in conclusions.
[00:18:38] Speaker A: Yeah. Okay. And so how many amino acids do they think life started with or LUCA had, or how. Which approach did they take there?
[00:18:47] Speaker B: Right. And they were mainly focusing on sort of the later ordering. But the general sense is that there was probably nine or 10amino acids that were the original amino acids in the earliest genetic code. And I can't recall exactly what they said were the very, very earliest. That wasn't their focus. But generally the Census is about 10 or so that were the earliest.
[00:19:08] Speaker A: Are there organisms today that use only 9 or 10amino acids? Is that.
[00:19:14] Speaker B: I haven't specifically researched that. But what you generally find today is that organisms today generally will have a large number percentage of the amino acids today are used in their various proteins. Some use all 20, some may not use all 20. But there's a, there's gonna be a, a wide variety of the amino acids used today, which would be more than what they would've expected from the early Earth. But I can't remember the exact details of what that looks like today. That's part of the research we'll do later.
[00:19:41] Speaker A: Yeah, yeah. All right. Yeah, that'd be interesting to know if there's any living organism that can get away with just nine or ten amino acids.
[00:19:48] Speaker B: Yeah, I don't think they have much like that. They haven't had much success unless it's a super simple thing like sticking to something.
[00:19:54] Speaker A: Well, okay, but that's not a living organism. Yeah, yeah. Okay. All right. Okay. So they've decided that there's. Based on their statistical research there, they're proposing a slightly different ordering of the amino acids being recruited, we'll use that term, into the genetic code over time.
And what's your thinking here in terms of.
Is the statistics. Fine. Is the approach that they took to this Fine. Where does it kind of go off the rails if it does, in your opinion?
[00:20:24] Speaker B: Right. And again, this is really just. It's kind of just circular reasoning. Like if you take some set of. I mean, and I love the titles, like the title's like. I mean, the title is basically like, we've solved this. This shows this. It's a very, you know, it's been resolved. It says, yeah, yeah, I mean that's, that's quite a statement. And I guess that's what's helpful to get papers published. But the reality is it's all circular reasoning. They just reconstructed from the sequences today with some proteins, and then they saw that certain amino acids were, were less common. And they just said, well, that probably suggests this is when they're recruited. But, but there's a huge problem with this, is that they're not exactly examining some of the essential proteins in life, like something like a topoisomerase, which tell us about topoisomerase. Topoisomerase is a remarkable enzyme. In fact, there's a video online with, there's Discovery YouTube channel that shows this. This enzyme, what topobisomerase is necessary for is untangling knots in DNA. And it's really remarkable that people like Francis Crick recognized really early that this thing would be necessary even before it was discovered. But what happens with DNA is you've got two separate strands, they have to be opened up and that allows for the information to be accessed. But when you open up these strands, it. The DNA starts to twist. Like for those of us that remember telephone cords back in the day or something like that, they would twist in this very inconvenient pattern. So what happens is as that twisting or super supercoiling takes place, you can no longer open the DNA to gain the information.
So you have to have, in a DNA translation system, you've got to have a, a machine, a molecular machine that will essentially snip the DNA into passed part of it through the broken piece and then reassemble the DNA. It's called topoisomerase. It's, it's incredibly sophisticated.
[00:22:21] Speaker A: So that video is great. I would certainly encourage everybody to check that out. Our colleague Joe deweese has done a lot of work on topoisomerase. But that's, you know, it's an interesting. Let me pause here for a second, Brian, because this is an interesting situation where one solution to an engineering problem creates another. So if you're trying to untwist DNA, you need DNA helicase. Right. Which is running along unzipping the DNA.
[00:22:44] Speaker B: Yeah. To unzip it.
[00:22:45] Speaker A: And then because of that, you end up with supercoiling in the DNA which can also prevent, do two things, I guess, prevent it from being accessed and also potentially break, cause breakages within the DNA strand. And so now you need another system which is called topoisomerase, to come along and resolve the supercoiling.
So, yeah, it's sort of this cascade of engineering problems as you start to go down the track of figuring out how you're going to actually translate this and build these amino acids that we've been talking about. Okay, so that's all. All right. So sorry to, sorry to sidetrack you there, but, but you were mentioning topoisomerase and other machines that are required to do this translation and transcription and translation process.
[00:23:27] Speaker B: Yeah. And then another machine is like what's called the polymerase. And what that'll do is that will go along your, you have different types. One will, let's say with, with DNA, will copy one strand of DNA. So that's in cell division. Before a cell can break into two cells and divide, you have to copy the DNA. And you need a very complicated machine that does that. And then of course, if you want to make proteins, you've got to have, you have to have a polymerase set will take your DNA and turn it into MRNA or into sort of the message protein that goes to your ribosome. And again, these particular machines have to have the amino acids that are some of the most complicated.
So in other words, before you can evolve the genetic code, before you can change genetic code, before you can even have a genetic code, you've got to have complex machines which require the amino acids that are believed to have occurred long after the code was in existence.
This is the problem.
[00:24:26] Speaker A: Yeah. And are you seeing people address that or they're just kind of leaving that for future, you know, we'll deal with that problem later.
[00:24:33] Speaker B: Well, there's people that acknowledge that this is a challenge.
They say, yeah, this is an unresolved problem. But usually it's an unresolved problem. What they'll say is, well, yeah, today maybe topoisomerase and polymerase, they require these very advanced amino acids. But maybe back in the day when you have your original genetic code, maybe the topoisomerase, like protein didn't have the more complicated amino acids. That's sort of the logic. But there's an enormous.
[00:25:04] Speaker A: What's that must be a simpler way that it was done in the past. Right, exactly.
[00:25:08] Speaker B: And that's again circular reasoning. The problem is, from a purely engineering perspective, to do what you need to do with these machines, to actually identify the amino, the nucleotides, to break DNA, to do a lot of these various tasks, even to have the structural stability, you absolutely must have more complicated amino acids. A simple amino acid simply can't do what you need to do. And this is the huge problem.
[00:25:33] Speaker A: Okay, so let me see if I can restate the circular reasoning piece here then. So if you take an engineering approach and you look at this system and you say what is required to do these various functions, you end up somewhere similar to what we have today, what we see in living organisms. You know, the simplest living organism, if you want to even use that term, you know, let's say a single celled organism. You need something along those lines. Okay, but here's where the circular reasoning comes into place, because we start with the recognition that I think everybody has that, well, it couldn't have started this complex because that doesn't work for evolutionary theory. So it must have started more simply.
And therefore we're just going to assume that there were these hypothetical, I could say made up, but I know you're a nice guy, Brian, so we'll just say hypothetical organism, hypothetical genetic code, hypothetical copying process, hypothetical replication process must have existed because that's what our theory says. And so therefore we're going to then use those assumptions to try to then flesh out the theory. But we're falling back on the circularity because we've assumed the very thing that is in question here.
[00:26:49] Speaker B: Yeah, and they assume that the simpler thing, however they imagine it could have, through natural processes, turned into more complicated thing.
[00:26:56] Speaker A: That too. Yeah.
[00:26:57] Speaker B: So that's one of the. How the circular reason. Oh, and this is my favorite part. Then they'll say, because we quote, unquote, know that this simple thing turned into a complicated thing. We know that natural processes have the ability to make complicated things, which is.
[00:27:11] Speaker A: The question on the table in the first place.
[00:27:13] Speaker B: Exactly.
[00:27:14] Speaker A: Right, yeah, yeah. Okay, good, good. All right, so let's, let's move on from that because there is a circular aspect of life that is really important to understand. I'm not talking about circular reasoning here, but what we might call causal circularity. What do we mean by that and how is that different?
[00:27:31] Speaker B: And this is, this is a concept that, that a biologist, Ann Gager, who's a colleague of ours, really highlighted as she was doing her research and writing. And it's an idea that, that actually goes earlier. Like you, you can go to much earlier papers and they use that language, causal circularity. But the basic idea is that you want to produce like a cell wants to produce something important like an enzyme.
The problem is the system needed to produce that important thing requires that important thing to already exist.
[00:28:02] Speaker A: Yep.
[00:28:03] Speaker B: So one of the examples that Engager talked about is that if you want to create ATP, you've got to have all these various enzymes. But the problem is the process to produce ATP requires ATP to drive the process.
[00:28:15] Speaker A: Yep, yep.
[00:28:16] Speaker B: And there's countless, countless examples of that. But that's sort of the idea of causal circularity.
[00:28:20] Speaker A: Well, and you gave us an example a minute ago, right, when you talked about the various machines required to open up DNA, to transcribe it, to translate it, which in turn required that transcription, translation process to build those machines in the first place. So that's another example, right?
[00:28:38] Speaker B: Oh, absolutely. And it gets so much worse because even if you look at one step in this translation process, you have to have an enzyme to do like one step. We talked about the topoisomerase. Well, these, these enzymes have the amino acids that are not supposed to be there yet. They're supposed to be something that appears much, much later. And what happens is the complex metabolic pathways to produce these enzymes require those. I'm sorry, the complex metabolic pathways require these machines, these enzymes, but those enzymes again, have to have the very proteins that the enzymes are creating or the amino acids that the enzymes are creating. Yeah, Something like tyrosine, which is this complex amino acid. And there's a complex metabolic pathway to produce this amino acid, but that amino acid is essential in the enzymes that produce it. So again, it's this causal circularity challenge. And again, people Assume that maybe these enzymes worked with simpler amino acids in the past. But the problem is there are certain activities that only the complex amino acids can perform.
You simply can't take the amino acids that are believed to be on the first genetic code and use them to do a whole lot. That's very interesting.
[00:29:58] Speaker A: Okay, so we've got causal circularity at this, at the very biochemical stage where various things are being built like ATP or whether where amino acids are being produced. But what I'm hearing you say is that there's also in a sense, kind of a historical aspect to this as it relates to the theory, because we need all of these things to do what would have been required to have this earlier organism that could then evolve into the later organism in the first place.
[00:30:26] Speaker B: Yeah, because the problem is you simply cannot have the simpler genetic code that they think existed because you've got to have a genetic code that has, that's coded for the amino acids that can produce the essential enzymes to translate the genetic code to go from nucleotides to protein space. So the genetic code depends on the genetic code always having these very complex amino acids incorporated into them.
[00:30:53] Speaker A: Right. And we should point out this is the kind of thing that designers are able to handle on a regular basis, these kinds of causal circular chains, but doesn't work in an unguided, undirected process. So.
Yep, good, good. So are you seeing other researchers, Brian, who are recognizing this? Or is everybody just sort of saying, well, you know, it had to work, so therefore we're going to make up a story about what must have been, even though it doesn't make sense either from an engineering or biochemical standpoint.
[00:31:23] Speaker B: What do you usually see? And this is, I've, you know, I have a PhD in physics, so I understand how the academy works. Often you get focused on some very simple question, like you'll have a researcher saying, what is the exact process of, let's say, topoisomerase mending DNA? What is going on there? Very often people lose the forest for the trees. They don't take a step back and think, what is the big picture here? What story is taking place and how should we think about it? And there are some people that write about this problem. In fact, I was just reading this article written in 2012, it's autopiosis 40 years later, the review and the reformulation that actually does talk about specifically causal circularity. Okay, so there are people that have recognized this. Even Polani is a mathematician, I believe Steve Meyer quotes from that recognizes decades ago, but it really is these big thinkers, these people that have the ability to take a step back and examine the problem. But most people think, oh, that's interesting, and they go back to their work with their particular chemical reaction. That's the challenge we're facing.
[00:32:27] Speaker A: Right, Right. Okay. All right. Well, what's the big takeaway from all of this in terms of those of us who are interested in origin of life and research in the field generally?
[00:32:37] Speaker B: Well, there's two major takeaways. The first takeaway is when you hear a headline, how we've solved this, or we've corrected this mistake, whatever. Recognize what's happening is you're not seeing researchers who are doing very detailed experiments to show that these things could have come about in a natural way. That's not what's happening. What they're typically doing is circular reasoning. They look at what's here today, they imagine what was in the past, they assume the past became the present, and then they say, that's the evidence for the power of nature to make these transformations. So be wary of circular reasoning and identify it. And two, recognize that this problem of causal circularity is central to the genetic code. It's central to producing things like complex amino acids, and it's central to life in general. So, again, this is just an example that highlights this problem of causal circularity, which is a form of irreducible complexity, which, again, points to the fact that you need information from the beginning. You have to have a mind that plans everything in advance and puts it together in the right way so it functions the way it needs to function. Those are the takeaways.
[00:33:44] Speaker A: Right? Well said. Well said. Yeah. And this. This question about the circular reasoning. You know, I was just thinking about another field where this is absolutely rampant, and that's in comparative genomics.
You know, huge numbers of those papers fall prey to that circular reasoning in that. In that regard. But, yeah, it's. It's definitely a big takeaway. All right, so we want to watch out for circular reasoning. We want to watch for causal circularity. And I like your point at the end there, Brian, that this is really a hallmark of design. This is something that we see in design. This is something a designer has the capability to do.
In fact, every time you build something, every time you design a new machine or your iPhone or a TV or whatever, you're going through this process of identifying the various things and how you're going to solve them at once in order to get this to work. And things are going to interact together. They're going to be playing off of each other. And that's how you get a system that can actually function in the real world, not by adding, you know, accidental molecules bumping into each other over time.
[00:34:51] Speaker B: Very well said.
[00:34:52] Speaker A: All right, anything else you want to flag for us today, Brian? Or if not, we'll look forward to having you back to talk a little more maybe about the physics side of things.
[00:35:01] Speaker B: That would be great. And just as sort of, we could say it's almost like a post movie trailer, like an Avenger movie. What will be fun to talk about in the future is the actual design logic, the engineering where you really see evidence of a top down design, where a mind planned the highest top level of the design hierarchy in advance and ensured everything fits together perfectly with everything else. So that's something that'll be for a future episode.
[00:35:25] Speaker A: Excellent, Excellent. That'll be great to have you back to talk about that. Well, thank you so much for being with us, Brian. For ID the Future, I'm Eric Anderson. For anybody who's interested in Origin of Life, please check us out again at ID the Future or at our YouTube channel, Discovery Science. Until next time, have a good day.
Visit us@idthefuture.com and intelligentdesign.org this program is copyright Discovery Institute and recorded by its center for Science and Culture.
