Episode 103: Neo-Darwinism vs Post-Darwinism

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Unofficial, reviewed transcript. It may still contain mistakes; check the podcast when wording matters.

Speakers are labeled by first name where identified. Unidentified-speaker labels may refer to different people. Bracketed question marks indicate uncertain wording.

Transcript

[00:00:01]  Unidentified speaker: Hello out there.

[00:00:03]  Peter: This week on the Theory of Anything podcast, we discuss neo-Darwinism versus post-Darwinism. Neo-Darwinism, meaning a gene-centric view of evolution, which is also called the great synthesis since it unifies natural selection with genetics, paleontology, and perhaps even human psychology. Post-Darwinism is the view that emphasizes factors outside random mutation, like epigenetics or the assertion that organisms and cells can alter their own genome in a beneficial way. Here, Bruce specifically concentrates on the work of biologist James Shapiro's critical look at Richard Dawkins' neo-Darwinism. Does it really, truly make sense to see our cells, bodies, and minds as tools governed by our masters' DNA? Does post-Darwinism, also called third-way evolution, offer a meaningful alternative to both neo-Darwinism and intelligent design? Does this way of looking at biology say something about the very nature of reality, maybe even the laws of physics? I admit, I'm barely holding on to what Bruce is saying at times, but I find this to be a super interesting topic with all kinds of implications, and I hope someone out there does too.

[00:01:40]  Bruce: Welcome to The Theory of Anything Podcast. Hey, Peter.

[00:01:43]  Peter: Hello, Bruce.

[00:01:44]  Unidentified speaker: How are you today?

[00:01:45]  Unidentified speaker: Good.

[00:01:46]  Bruce: I'm excited for today's episode, but also nervous about it. I have wanted to do this topic for forever, and Peter will testify that I kept putting this one off because it was so hard to put together, and what I actually ended up putting together kind of sucks, but it's just a tough topic to try to cover. So if you were to go back in time, there was an episode that we did. Let me see if I can actually find it. Way in our early days.

[00:02:17]  Unidentified speaker: Ah, here it is.

[00:02:18]  Bruce: It's episode 21, Evolution Outside the Genome. I saw a video by Michael Levin, so we decided to do an episode about his stuff, and while I was doing that, I came across a paper by Ray and Denis Noble, although embarrassingly, I think I called him Denise Noble, because his name is spelled weird, and I didn't know how to, I hadn't met him, you know, like, online yet.

[00:02:45]  Unidentified speaker: Yeah.

[00:02:46]  Bruce: So there's some definite similarities between Michael Levin's work, and particularly Ray and Denis Noble, but Denis in particular seems to be the face of this group. And so it makes sense that I pulled those two together and covered them together. But Denis Noble is kind of the leader of something called The Third Way. There's like a website out there where they talk about a third way approach to evolution. So the idea, I think, is supposed to be there's the traditional Neo-Darwinian evolution, that there's like intelligent design, and then there's like this third way, which isn't supernaturalistic like intelligent design, but that it admits that there's purposefulness to evolution. And you know, I like third way is very controversial.

[00:03:43]  Unidentified speaker: And in fact, we are going to talk about that.

[00:03:45]  Bruce: Probably not in this episode so much, but in the next episode where I'm going to talk about criticisms.

[00:03:50]  Unidentified speaker: I've heard it called post-Darwinism too.

[00:03:54]  Unidentified speaker: So it's kind of-

[00:03:54]  Unidentified speaker: Post-Darwinism, interesting.

[00:03:55]  Peter: This is neo-Darwinism versus post-Darwinism, could be a good title here.

[00:04:00]  Bruce: So I jokingly call it neo-neo-Darwinism.

[00:04:02]  Unidentified speaker: Okay.

[00:04:04]  Unidentified speaker: Which I think is a better term for it.

[00:04:05]  Peter: Or a return to Lamarckism.

[00:04:09]  Unidentified speaker: I hate that.

[00:04:10]  Unidentified speaker: Oh my God.

[00:04:11]  Peter: Well, no, let me just, can I just interject one thing? This is going to be a podcast where I am listening, more than speaking for sure. I don't, I'm not sophisticated in this argument in the slightest. However, I did, the one thing that really sticks with me, that I've checked out, is that debate between Dawkins and Denis Noble. There's a really good debate on YouTube, where they were obviously, I mean, they obviously have a lot of respect for one another. I think that they even have had worked together or done research together or something. And I mean, Dawkins, obviously the founder of neo-Darwinism, a gene-centered view of evolution.

[00:04:55]  Bruce: By the way, remember that you just said that. Neo-Darwinism, the gene-centered view of evolution. I want to call out right now that Peter said that, but anyhow, continue.

[00:05:04]  Unidentified speaker: Okay, fair enough.

[00:05:05]  Peter: But even Dawkins seemed quite open to some of Denis Noble's arguments. He didn't seem like he thought it was preposterous or anything.

[00:05:16]  Unidentified speaker: It was actually very good debate.

[00:05:17]  Peter: If there's anyone who's listening to this, that thinks we're crazy, they should check out that debate and see how open Dawkins was to these arguments.

[00:05:28]  Bruce: So it's interesting that debate is probably what catapulted Denis Noble in particular into the public eye and got some of his ideas and theories. I've seen numerous magazines have, evolution is purposeful and it's freaking scientists out, which is probably just very typical click bait, totally untrue headlines from journalism. But it's always based on Denis Noble's work.

[00:06:02]  Unidentified speaker: So I wanted to actually cover this.

[00:06:03]  Unidentified speaker: Here's the thing though.

[00:06:05]  Bruce: I'm actually not a huge fan of Denis Noble.

[00:06:07]  Unidentified speaker: I shouldn't say that in a super negative way.

[00:06:09]  Unidentified speaker: Of course, I think he's great.

[00:06:11]  Bruce: But I've tried to read some of his books. Honestly, I think they're a little crappy. I'll talk more about my criticisms of Denis Noble's books. I love that one paper that we covered in episode 21, which is like, is the blind watchmaker blind or is she one-eyed or something like that?

[00:06:31]  Unidentified speaker: Is the name of the paper.

[00:06:32]  Bruce: Excellent, excellent paper and I highly recommend that paper. But when I tried to read some of his books, I don't really particularly enjoy them and they seem very strange to me, and I don't feel like I'm getting to the point of what he's getting at. So I came across the fact that on the Third Way website, there's this guy named James Shapiro, who's kind of the less well-known of the three members, Ray and Denis Noble and then James Shapiro. And he has a book about his views on evolution, which is called Evolution, A View from the 21st Century, Why Evolution Works As Well As It Does. And so that title right there says it all, right? Shapiro is giving away what the point of the book is, you know, in the name of the title right there. And I started reading his book and it really kind of impressed me, right? [Unlike?] with Denis's book, where I feel like it's just a bunch of metaphors and I can't make sense of what he's saying. James Shapiro gets right into the weeds with exactly what he's talking about in terms of actual biological experiments, right? And why he thinks they're significant. And I think that's part of what I find so intimidating by it, is that I'm like, this book is this giant book, it's huge, and I've only read the first section. So the first, so the original book was like, is the middle of the book, like there's a first version of the book, then there's one that's called Evolution of a View from the 21st Century, Fortified. Okay, and that's the one I actually have.

[00:08:04]  Bruce: The original book is the middle of the book, and then he has a bunch of blog posts at the beginning of the book, meant for laymen, and then he has a bunch of papers, white papers meant for people who are serious scientists at the end of the book. I only made it through the blog posts, and they kicked my tail.

[00:08:23]  Unidentified speaker: Okay.

[00:08:25]  Bruce: So, and that's the stuff meant for laymen, right? So, I wanted to, like, I suspect most people who read his blog posts, even when intended for laymen, are really going to struggle with what he's trying to say. And I feel like I can add some value here by trying to yank together what it is he's trying to say, and why he thinks it's significant, okay? So, he, let me say this, that I do think he's saying something that is of some significance, but I'm also going to, in the next episode, cover criticisms of him and Denis Noble. And I honestly find the criticisms to be, to be rather devastating. So, I don't want to make it sound like I'm necessarily in favor of Shapiro's theories, I have to see me as someone who's just interested in exploring ideas as best I can. I use my critical rationalism to try to understand these ideas, and I try to understand them with a critical eye, right? We're just interested in trying to understand the various points of view. I will say this much. I think that the idea that we need revisions to neo-Darwinism is absolutely true. So I guess I at least agree with them that much. But then again, wasn't that just a given? That may be one of the least important statements I could have possibly made, right? Every theory is going to need revisions, right?

[00:10:00]  Unidentified speaker: Yeah.

[00:10:00]  Bruce: So I, but we've, on this show, we've kind of talked specifically about the problem of open-endedness in particular, but various problems with Darwinism in its current form, neo-Darwinism in its current form. And like we know there's something just not right about it and that we don't really understand it and that really there's stuff just missing from it. And so that's why I think I'm attracted to the work of someone like James Shapiro. Maybe his approach is going to turn out to be total garbage, right? But at least that somebody trying to take seriously that there's some sort of problem that needs to be resolved.

[00:10:40]  Peter: And just to clarify that, are you saying there's a problem because of this thing, this property of natural selection, that it's open-ended?

[00:10:48]  Bruce: That we don't understand what that even means, right? Like, if we really understood biological evolution, we would know how to program open-endedness, and we can't, right? So we know that there's something giant missing from our theory.

[00:11:05]  Unidentified speaker: We just know it.

[00:11:05]  Bruce: Like, there should be no doubt about that, okay?

[00:11:08]  Unidentified speaker: And I know most people just don't think that way.

[00:11:10]  Bruce: Most people, when I bring up this idea that there's something missing in evolution, it's like, no, as a creationist turned evolutionist, I got to encounter that first-hand in a way that your average evolutionist would never get to encounter it, right? So I have an awareness of this fact that there's a very deep denial. Now, there's various scientists out there. Lee Cronin, who is somewhere between complete genius and bat crazy, is someone else who's pointed out that we've got giant things missing in evolution, and his assembly theory is an attempt to try to address some of those problems. And I'm excited about assembly theory for much the same reason. I mean, anytime I see somebody who actually tries to address that there's something wrong, something missing from evolutionary theory, it catches my interest and I want to look into it, and then I want to see if there's anything to it or if they're just kind of really on the wrong path, right? Which, you know, it wouldn't be too surprising if they really are just on the wrong path, okay? So, let me just say, Shapiro quotes somebody from his blog early on in the book about how he lives in a state that passed laws to, quote, teach the controversy in regards to controversial sciences, quote, which is rather obviously a way to get special creation and flood geology and other such hypotheses of no relevant intellectual value into the classroom, from page 17 of his book. Shapiro asks, what is the best way to deal with such intrusions into science education?

[00:12:47]  Bruce: The conventional approach has been to circle the wagons around the mid-19th and mid-20th century ideas, Darwinism and neo-Darwinism, page 17. So now at this point, if you're a regular listener, you know why I already am interested in what this guy has to say. I'm a former creationist turned hardcore Darwinian evolutionist, and I think most of the evolutionists I've talked to about Darwinian evolution back when I was a creationist had pretty awful arguments. That smacked of the same sort of vague manning that I grew to dislike about creationism.

[00:13:19]  Unidentified speaker: Now, Shapiro agrees with me.

[00:13:21]  Bruce: He says on page 17, this approach has not been successful. So in past podcasts, I've claimed that evolutionists will use fairly bad arguments when engaging creationists, and will ignore or downplay what are really actually pretty obviously very real problems with the existing theory of Darwinian evolution.

[00:13:38]  Peter: I think that's a very intriguing point that you've really convinced me on, is that this whole debate between evolutionists and creationists or intelligent design people, it almost leads to people thinking that evolution is just figured out.

[00:14:02]  Unidentified speaker: We know how it works.

[00:14:03]  Unidentified speaker: That's right.

[00:14:04]  Peter: The reality is there are mysteries at every step of this process, really intriguing mysteries.

[00:14:10]  Unidentified speaker: Yes.

[00:14:11]  Bruce: By the way, when we're eventually done with this, won't be in this episode, ask me for my opinion on how to handle the controversies between intelligent designers versus evolutionists. Because I actually have my own approach of what I think is the scientifically correct way to handle them, the correct Popperian epistemological approach to dealing with them. So which I think is very much different than how it's actually been handled.

[00:14:39]  Unidentified speaker: I think we have touched on that a little bit.

[00:14:40]  Unidentified speaker: We have, yeah.

[00:14:41]  Unidentified speaker: Yeah.

[00:14:42]  Unidentified speaker: Okay.

[00:14:44]  Bruce: So even just little things like how did life even get started? Like, that's such an obvious problem with evolution, okay, that has no good answer today. Vague theories on the table. Some interesting though, right? But vague ideas of how to answer that question. Go talk to evolutionists about that. And you can't even get them to admit it's a problem, right? Like, Lee Cronin talks about how he's... So Lee Cronin obviously is advancing his theory, assembly theory, which is an attempt to explain evolution in a far more general way that includes non-biological sources of evolution, okay? So that is one of his attempts to make a small step towards trying to explain how life got started in the first place. It doesn't really answer that question yet, but it creates a broader view of evolution that creates a way in which we might have a way forward on that question. And when he brings it up to scientists, they shut him down. Like, this is not a creationist we're talking about, right? And they'll say, oh no, that's a solved problem.

[00:15:48]  Unidentified speaker: And he'll go, no, it's not.

[00:15:50]  Bruce: You know, in his interviews, he talks about the funny conversations he's had with scientists on this, okay? So in many ways, the fact that there's such a drive to claim there are no problems is keeping us from addressing the problems that exist, right?

[00:16:05]  Unidentified speaker: Because there's a blindness to them.

[00:16:07]  Bruce: So Shapiro continues, 30 years ago, I was at a conference in Cambridge, England, to celebrate the centennial of Darwin's death. There, Richard Dawkins began his lecture by saying, I will not only explain that Dawkins had the right answer, but I will show that he had the only possible right answer. Hearing this and knowing that the alternative explanations invariably arise in science—that alternative explanations inevitably arise in science— I said to myself that the creationists have a point. They are dealing with a form of religious belief on the evolution side. Dawkins' transformation into an aggressive proselytor for his undoubting and absolutist version of atheism confirms this conclusion.

[00:16:49]  Unidentified speaker: This is from page 17.

[00:16:51]  Bruce: By the way, if that quote rankles you wrong, it should have. And I'm going to explain why it actually rankles me wrong too.

[00:16:58]  Unidentified speaker: But let's continue.

[00:16:59]  Bruce: I'm intentionally picking some of the more wrinkling quotes that he makes. One of the creationists' main tools is the argument that evolutionists are simply militant atheists in drag who care more about dissing religion than about understanding evolution. Dawkins' ill-considered crusade just bolsters their position. Rather than accept that evolution science is always a tentative work in progress, conventional evolutionists make absolutist statements like, all the facts are on my side, making obviously inflated and unrealistic assertions is hardly likely to convince anyone who has serious questions.

[00:17:36]  Unidentified speaker: That was from page 18.

[00:17:38]  Unidentified speaker: Now, I have a sincere question here.

[00:17:40]  Bruce: Is Shapiro being unfair to Dawkins?

[00:17:44]  Unidentified speaker: Yeah, he is.

[00:17:45]  Bruce: Okay, like he's portraying, I mean, what Dawkins actually said there, at least the part he quotes from Dawkins, is it seems to me that he's kind of taking him out of context.

[00:17:56]  Unidentified speaker: Okay.

[00:17:57]  Unidentified speaker: However, here's the problem.

[00:17:59]  Bruce: Dawkins really does come across bad to me in general.

[00:18:03]  Unidentified speaker: As a religious person, right?

[00:18:05]  Bruce: The way Dawkins talks, the way he handles things, he does not come across to me as at all sincerely trying to have a dialogue or trying to solve problems. Let me just to compare him with one of the other militant atheists, Sam Harris. Sam Harris comes totally differently across to me as a religious person. Okay, so I can understand not maybe so much from this particular quote, which I think Shapiro is kind of taking out of context, but in general, I think Dawkins is not a good example of how to engage religious people on the question of creationism versus evolution. I think Shapiro, at least vibe wise, has got Dawkins correct.

[00:18:47]  Peter: To be fair, Dawkins is a complicated character, I think.

[00:18:51]  Unidentified speaker: He is.

[00:18:51]  Peter: I've seen him lecture live and where he comes across as a very humble and cool guy, and he's talking about, I remember so clearly him talking about memes, and it was just like aha moment after aha moment, and I think probably what you're talking about is more his literal debates with creationists and things. There's kind of like almost like a different persona that comes out.

[00:19:20]  Unidentified speaker: There is.

[00:19:21]  Unidentified speaker: I think.

[00:19:21]  Bruce: When he's talking religion, it's like he's a different person.

[00:19:25]  Unidentified speaker: Yeah.

[00:19:27]  Bruce: I agree, Dawkins is one of the great scientists of our times.

[00:19:29]  Unidentified speaker: I love his book, The Selfish Gene, right?

[00:19:32]  Bruce: So I'm not knocking his work, but I do think that he does come across very dogmatic to me when he's trying to engage the question of evolution versus say intelligent design.

[00:19:44]  Unidentified speaker: Okay.

[00:19:46]  Bruce: So I can at least vibe wise kind of agree with what Shapiro is saying. However, keep in mind, those quotes are Shapiro's viewpoint, not mine, okay? But I'd be lying if I [did/didn't] admit that I at least do overall agree with the vibes of what he's saying here.

[00:20:03]  Unidentified speaker: Okay.

[00:20:04]  Bruce: So I like Shapiro's approach because he's one of the rare examples of an evolutionist who is really trying to solve what seems to me like some very specific problems with evolution. And he's not that interested in winning an argument.

[00:20:17]  Unidentified speaker: Okay.

[00:20:20]  Bruce: So he's perfectly willing to engage something like Intelligent Design directly if they raise a fair problem. So, quote, the Intelligent Design ID advocates point to the bacterial flagellum as an example of an irreducibly complex structure that could not have evolved by Darwinian evolutionary processes. So Shapiro's opponents have characterized him as a crypto-intelligent designer. And it doesn't help that Shapiro has identified himself as a third-wayer, which is a term for a path somewhere between Intelligent Design and traditional neo-Darwinian evolution. But reading Shapiro directly, he is exactly as critical of Intelligent Design as I would want him to be. So, for example, here's a quote from page 23. They need to address how such intricate and clearly related biological inventions have come to be diversified for so many different uses.

[00:21:14]  Unidentified speaker: He's talking about evolutionists there.

[00:21:16]  Bruce: Then he says, certainly the ID argument is greatly undermined if it has to invoke supernatural intervention for the origin of each modified adaptive structure. Okay, so right there, you basically can see he's not on the Intelligent Designer's side, right? He's against how they will invoke supernatural interventions for things, effectively supernatural.

[00:21:39]  Unidentified speaker: They'll often say, well, who knows?

[00:21:40]  Unidentified speaker: Maybe it's aliens, right?

[00:21:41]  Bruce: So they're not necessarily talking about God. But I can appreciate that Shapiro is also critical of the near religious fervor evolutionists tend to fall into. So also from page 23, at the same time, it is fair to recognize that the evolutionary science community is also challenged to come up with detailed explanations for the origins and diversification of a basic complex functional design of, for example, the bacterial flagellum. This is what Shapiro sets out to do. Among other problems, he wishes to address problems like this by amending existing neo-Darwinian evolution to explain how it's possible for something like the bacterial flagellum to evolve in the first place. So in this episode, I'm going to go over several examples of his non-standard evolution that he talks about in his book, and I'm only covering the blog post section which was meant for laymen. So my goal is to bias you as much as possible towards this theory. Then in the next episode, I'm going to cover a devastating critique of third-way views, including Shapiro's, by Zach B.

[00:22:52]  Unidentified speaker: Hancock on YouTube.

[00:22:53]  Bruce: And apparently, we're also going to talk about Jerry Coyne. But do yourself a favor and don't listen to that yet. First, wait for me to give you Shapiro's view, okay? I sincerely think that if you're familiar with the specific example Shapiro gives, it doesn't make the critique less devastating, but it does allow you to counter-read Hancock more easily, such that it's easier to pick out what he agrees with Shapiro and the third way on.

[00:23:22]  Unidentified speaker: And that's what we're interested in.

[00:23:24]  Unidentified speaker: What do they agree on?

[00:23:26]  Unidentified speaker: Okay?

[00:23:27]  Bruce: This will be more obvious if you listen to Shapiro's view first before you see the critique. Now, let me say that I probably could have made this episode, you know, 45 minutes, and I probably could have summarized Shapiro's views. And I thought about doing that a whole bunch of times. And I realized at some point, so let's call this Bruce's rule of summarization, which would be the summary of an idea doesn't resemble the idea that much. And when you're really trying to understand a point of view, it's the details that matter. I mean, it really just is, right? Like if all you get to hear is the summary of the view, it's just so easy to dismiss the view. Because of that, I am going to go into an enormous amount of detail quoting Shapiro from the book, and I'm going to attempt to pull a lot of his examples together and have some commentary on my part to try to link them together. But I'm going to mostly read what he's saying in detail, because I really feel like if you're going to assess the viewpoint, you must be familiar with the experiments and the details of the experiments that have affected his view. Because of that, this is going to be yet another epic three-hour Theory of Anything podcast, and that's okay. This just isn't for everybody, right? This is easier than reading the book, and I think I've got some value add here. But ultimately, if you really want to understand this, it's really important that you do allow yourself to be impacted by the details.

[00:25:16]  Bruce: And so because of that, and because I feel so strongly about that, we are going to do an epic long episode where I'm going to read a lot from the book.

[00:25:23]  Unidentified speaker: Okay.

[00:25:24]  Bruce: So what sort of issue does Shapiro have with neo-Darwinism slash modern synthesis? By the way, for what I can tell, Shapiro uses those two terms interchangeably. And one of the things we're going to talk about in the next episode from Hancock is whether those are actually the same thing or not.

[00:25:41]  Unidentified speaker: Okay.

[00:25:42]  Bruce: So I think the right starting point for the discussion is probably the least controversial example that he uses, which is hybridization. So recall that under traditional neo-Darwinian evolution, all the knowledge of a phenotype is contained solely within the genes. Now I say traditional neo-Darwinian evolution, but one of the things we're going to discuss in the critique from Hancock is whether that even is what neo-Darwinian evolution means. But that is certainly what I thought it meant, and it's what, according to what Peter just said a second ago, is what Peter thought it meant, okay? And I think what you're going to find is that most people do understand neo-Darwinian evolution from a Dawkins-like, gene-centric viewpoint, okay? So under that viewpoint, the phenotype is contained solely within the genes, in the DNA, and that can only be interacted on via organisms mutating one base pair at a time, and then surviving and replicating their genes, or not doing so.

[00:26:47]  Peter: So to explain it to someone like me, the genes are essentially, or our bodies are essentially like slaves to our genes wanting to replicate themselves.

[00:26:59]  Unidentified speaker: Yes.

[00:27:00]  Bruce: That is absolutely the selfish gene viewpoint that is expressed by Dawkins.

[00:27:04]  Unidentified speaker: Yes.

[00:27:05]  Bruce: Most people would see that as equivalent to Neo-Darwinian evolution. If somebody says Neo-Darwinian evolution, there's a very good chance, it's not 100 percent chance, but it's a very good chance they mean that view. Shapiro points out that the schoolroom version of Neo-Darwinian evolution concentrates on clean examples of members of the same species mating together. This way of looking at evolution lacks some important explanatory power, and it's too slow to explain real biological evolution. Now, what do I mean by lacks explanatory power? So it's well-known, and even critic Zach Hancock, who we're going to cover in the next episode, agrees with this, that natural variance across the species tends to even out over time. So, for example, if you get one extra large member of the species, it will still have to mate with normal members of the species. Their offspring will be a mix. Those in turn must mate with other members of the species. The effect eventually becomes diluted. According to Zach Hancock, who we're going to cover in the next episode, Darwin was so worried about this problem ruining his theory, that Darwin made up a theory that there must be some other means of variance, of inheritance, stored in the bloodstream, and that somehow this got around the problem. Now today, we'd say that we've ruled out this possibility, and instead, we now know there is a constant unintentional variance due to, say, cosmic rays causing mutations in the DNA. This account of biological evolution is certainly how I was taught it in school.

[00:28:46]  Bruce: In fact, I even remember the little movie my teacher played in high school biology, which I'm pretty sure was done by Disney, because Disney did stuff like that back then. They would hire Disney to put these together, that showed the little cosmic ray hitting the nucleotide, and it changing color to show that it was mutated. I can recall that in the animation that I saw.

[00:29:08]  Unidentified speaker: That was—

[00:29:08]  Unidentified speaker: Yeah, I remember that too.

[00:29:09]  Unidentified speaker: I got to go back and watch that.

[00:29:11]  Unidentified speaker: Yes.

[00:29:13]  Bruce: This account of biological evolution, where single mutations via something like cosmic rays, is the key source of variation, is known as gradualism. But Shapiro points out that this gradualist account of things is very slow, a very slow process, and that in real life, hybridization injects massive change into DNA all at once. This is what I mean by the traditional account is too slow. So, quoting Shapiro now, page 17, while neo-Darwinian theories focus on the bourgeoisie model of mating, wherein well-defined population boundaries are articulated by major figures like Ernst Mayr, the evidence increasingly tells that evolutionary novelty comes from the more adventurous and improper bohemian matings that are excluded in many conventional accounts. Shapiro points out that we can detect this in the actual DNA via genomic studies. From page 6, there has always been controversy about whether random variation and natural selection for improved fitness can truly explain biological evolution over time. Today, we can apply genomic sequence data to test Darwin's theory. It answers clearly about gradualism. Many genome changes at key stages of evolution have been neither small nor gradual. For example, plant breeders are familiar with rapid speciation. When we wish to create new plant species artificially, we do not use gradual natural selection. We generate hybrids by mating the different species. In a fine 1951 Scientific American article on this subject, titled Cataclysmic Evolution, the distinguished 20th century evolutionist G.

[00:31:06]  Bruce: Ledyard Stebbins explained how [flowerweed?] evolved suddenly by hybridization.

[00:31:12]  Unidentified speaker: That's from page 6 also.

[00:31:14]  Bruce: So how does this even work if DNA is supposed to be hard to vary? From page 17, whenever we find there was high inherited variability in a particular population, examination of the DNA indicates that it arose from introgression from a different species. So consider how hybridization gets around gradualism. From page 6, he says, hybridization frequently leads to a process of whole genome doubling. Doubling the genome takes one generation and potentially affects all hereditary traits. Note that the production of new species with novel characters by hybridization occurs too rapidly for regular natural selection to act creatively. So hybridization represents a single generation big bang change to a species, often creating a whole new species in a single generation. So from page 17, he says, the grants also describing the formation of what would be classed as a new finch species resulted from the full hybridization of two distinct species. So this probably is the easiest example of Shapiro's point. I'm going to give you a bunch of much more difficult examples to follow. You were likely, like me, taught gradualism in school, as if that was the account of how evolution works. But gradualism, while true in many cases, is not the only way life evolves. Hybridization is a much quicker way to inject variation into a population, and even change the chromosome count.

[00:32:55]  Unidentified speaker: All within a single generation.

[00:32:57]  Bruce: And again, I want to ask, how does that even work, given that if you were to take the stance that the gene-centric view, that the genes are a specific program or recipe for building a specific phenotype, that's hard to vary, then doubling the gene should just make a mess. It shouldn't lead to a whole new species in a single generation, right? So hopefully, Shapiro and I have you convinced of this now that at a minimum, the schoolroom version of evolution is wanting. However, I have to ask the following question. Is it really all that radical a change in view? It's not like biologists around the world are at this point listening to my podcast, because of course, famous biologists listen to my podcast. And all of them just went, oh my gosh, are you kidding me? I never knew about hybridization. How dare they teach me wrong in school about evolution? I seriously doubt that that is happening at this moment. Hybridization, it's a well-known exception to gradualism. But it's well-known, right? Everybody knows, biologists know, hybridization plays some sort of role in how evolution works. And school does normally concentrate on simplified versions of science, rather than giving all the messy truth upfront. Having said that, at least as a non-biologist, though classically educated, which means that I had college-level courses in biology, okay, because in classically educated people, they're trying to give you a little bit of everything, right? At a college level, they're trying to introduce you to all the different sciences.

[00:34:39]  Bruce: And it never occurred to me prior to reading Shapiro that hybridization, which I was well aware of and knew existed, that it was an important counter-example to the gradualism taught in school. I had never made the connection prior to reading Shapiro. So reading Shapiro caused two pieces of knowledge that I already had to snap into place for me. I could see that he was right, that if you want to understand why evolution happens, happens to be so effective compared to our feeble attempts to model it via genetic programming or genetic algorithms, that only model gradualism, that things like hybridization need to be modeled better. Okay, now I've been very interested in this. Like I started studying AGI and I bought the famous books on genetic programming and genetic algorithms, trying to understand how you might go about creating an AGI and what we currently knew on the subject. And they are absolutely modeling gradualism and it has never occurred to them to try to model hybridization. And it's not even clear how you would, okay? And that's, again, if you don't know how to program it, you don't really understand it, okay? So this is the sign that something more is going on here. So hybridization is nothing like the schoolroom version of evolution that we've all been taught. It's a giant bang that happens all at once in response to stress, that is a reduced population, that suddenly causes the species to hyper mutate for reasons entirely unrelated to cosmic rays and mutations, okay? So how might we understand its relationship to biological evolution better?

[00:36:22]  Bruce: Shapiro suggests we look at it as a baked-in response to stress on an organism or to a species. Say there is some sort of stressor in a population of, say, finches. Finches is the example that we've been kind of using. Suddenly, they start to die off because of a change in the environment. It so happens that there is a different species of finches that they don't interbreed with.

[00:36:45]  Unidentified speaker: By definition, species don't interbreed.

[00:36:47]  Unidentified speaker: That's what species means.

[00:36:48]  Bruce: And it's always a little fuzzy what counts as a species because interbreeding happens more than we usually admit.

[00:36:55]  Unidentified speaker: Okay.

[00:36:56]  Unidentified speaker: So they start to die off.

[00:36:58]  Bruce: That other species starts to die off as well.

[00:37:00]  Unidentified speaker: So we have an island.

[00:37:01]  Unidentified speaker: Something has gone wrong with the environment.

[00:37:03]  Bruce: You've got two species of finches that don't interbreed and both start to die off. Because of this reduction to both populations, these two species of finches suddenly start to interbreed because there just aren't enough of their own species around to breed with and to hope to pass on their genes. So it's kind of a Hail Mary that they're taking, right? They go ahead and start to interbreed even though they don't normally do that. Now, as Shapiro puts this, quote, how do organisms determine when genome innovation for a new adaptions becomes necessary? A growing body of research links stress conditions to the activation of genome restructuring functionalities capable of generating organisms with complex novel phenotypes. This process occurs prominently following interspecies hybridization, itself a response to reduction of reduced population size, and can be followed in real time in biological systems as diverse as Galapagos-Finches and cancer progression discussed later in a future section.

[00:38:08]  Unidentified speaker: This is from page XXI of his book.

[00:38:12]  Bruce: The animal is merely struggling to find a mate and make do with what's available. But from an evolutionary account of things, this is identical to saying that the species, when under stress, makes decisions that force rapid genomic change that create sudden large variations in the population. In this case, breeding a whole new species of Finches. The weaker members of this new species die off, of course. The remaining ones are better suited to the environment than either of the two previous species. This is such a stupidly obvious example that it is embarrassing to me that I had never thought of it this way prior to reading Shapiro. But you might object here, but wait, this isn't really at odds with Neo-Darwinian evolution at all, is it? I mean, everything I just described still boils down to a kind of variation, though in this case very fast variation, and natural selection. So isn't it still Neo-Darwinian evolution? All throughout this book, Shapiro makes questionable claims like this, quote, conventional evolution theoreticians completely exclude any connection of the genome change to lifetime experiences as a first principle of their theory.

[00:39:30]  Unidentified speaker: Okay, but do they?

[00:39:31]  Bruce: I mean, is it really true that evolutionary theoreticians exclude hybridization? So we might argue that hybridization is still, at the very end of the day, a part, very much a form of natural selection or Neo-Darwinian evolution. So arguably not really at odds with Neo-Darwinian evolution or modern synthesis per se, but merely at odds with a certain way of teaching those, the way we teach it to, at least at a minimum, classically trained people in college like me. So let's continue to maybe dig into some of Shapiro's deeper examples here. So Shapiro, to get to a slightly more controversial example, since hybridization is very much uncontroversial, so Shapiro's key, slightly more controversial counter-example to the standard Neo-Darwinian evolution is the super bug. Again, Shapiro seems to really be attacking gradualism rather than truly attacking Neo-Darwinian evolution, and he seems to almost treat those two as if they're one and the same.

[00:40:40]  Unidentified speaker: Okay.

[00:40:41]  Bruce: But in this case, he's now going to go over the standard story of vertical transfer of genes from generation to generation, which he argues is too slow and too rigid to ever explain the bacterial flagellum, better known as the whiptail. So, quoting Shapiro here, how do bacteria acquire antibiotic resistance?

[00:41:03]  Unidentified speaker: How do they become pathogens?

[00:41:05]  Bruce: We currently know a great deal about the genetic basis of these critically important bacterial properties. We also know how resistance and virulence are acquired and spread to new species. The story of how we came to this knowledge is a fascinating and instructive chapter in the history of science. It illuminates the insight that scientific fact, he puts that in scare quotes, consists of more than experimentally confirming hypothetical predictions. By the way, as Deutschians, we should have loved that last quote, right?

[00:41:41]  Unidentified speaker: Because it's not about prediction.

[00:41:44]  Bruce: So basic neo-Darwinian version of the theory, this is quoting from page 21 again, in the early days of molecular biology, bacterial geneticists applied conventional evolutionary concepts from the pre-DNA period to explain the evolution of antibiotic resistance. The theory was that mutations could alter the structure of cell components and either block entry of the drugs into the bacteria or prevent their action on cellular targets, such as the enzymes essential to cell wall synthesis. Even if the initial mutation did not confer a high degree of resistance, accumulation of several sequential changes would result in resistance to the antibiotic levels used in clinical medicine. In plain English, what he's saying is the conventional account of how this should work, they're trying to look at how to—they're trying to use the general theory of mutation, and that the mutations have a slow accumulation of resistance, and that it would therefore take a certain amount of time for the bacteria to become resistant to the antibiotics. It requires several different generations.

[00:43:06]  Unidentified speaker: He talks about confirmation in the lab.

[00:43:08]  Bruce: He says, indeed, a wide variety of laboratory experiments confirmed this theory, and bacterial geneticists isolated the predicted mutant strains. In virtually all cases, the resistant mutants grew less well than the parental sensitive bacteria, leading to the comforting conclusion that resistant bacteria would not significantly accumulate in nature. So now here's what's interesting from that. He says, this is quoting him from page 21 and 22, The degree of confidence was so great that the US. Surgeon General in 1967 declared that the war against infectious disease has been won. There were probably problems both with the science and the new public health policy based on it. The Surgeon General misunderstood the bacteria, which followed their own evolutionary rules, and did not listen to what the scientists said they should do, although experimentally confirmed in the laboratory the mutation theory of antibiotic resistance failed to account for most cases in the real world. Resistance continued to spread amongst bacteria isolated in clinics around the globe. Also from page 22, even more ominously, different strains of pathogenic bacteria increasingly displayed resistance to more than one antibiotic at a time. Now we're starting to see the connection with the question of bacteria flagella, okay, which we raised earlier.

[00:44:37]  Bruce: Just as it seems impossible under neo-Darwinian evolution, or at least what we're currently calling that, for a bacterial flagellum to form because it requires coordinated changes to several survival and, um, to—coordinated changes to create survival and reproduction value, it seems like bacteria should not be able to display resistance to more than one antibiotic at a time. Doesn't resistance to antibiotic happen not in response to antibodies, but due to a change or a mutation in one of the genes? Would it even make sense for two random mutations to two different antibodies to just happen to form at the same time? So here we have bacteria violating our understanding, or at least the schoolroom understanding of neo-Darwinian evolution, or so Shapiro is arguing, unless we want to explain it as wild coincidence. Note how this is quite similar to the intelligent design challenge to biological evolution using the bacterial flagella.

[00:45:44]  Unidentified speaker: Okay.

[00:45:45]  Bruce: Shapiro proposes a solution out of the literature, so not necessarily controversial. So page 22, research pioneered in Japan found that multiple antibiotic resistances could be transferred simultaneously from one bacterial species to another. The DNA agents responsible for this transfer are circular molecules that are called multi-drug resistance plasmids, plasmids is the word here, which can move from one cell to another. Multiple antibiotic resistance clearly represented genome change and evolution of a type unimagined in the pre-DNA period. DNA molecules could be transferred horizontally between unrelated cells, rather than inherited from ancestral cells. The plasmids would move the DNA between bacteria rather than being inheritance. Moreover, horizontally transferred DNA could carry complex sets of genetic information encoding multiple distinct biochemical activities. Evolutionary leaps involving several characteristics at once could occur through horizontal DNA transfer from page 22. Continuing from there, over time, it became increasingly clear that bacteria and other micro-organisms engage in a great deal of horizontal DNA swapping. In addition, these small cells have an ample toolbox of natural genetic engineering mechanisms to incorporate and rearrange this horizontally acquired DNA. So he just used a term natural genetic engineering, which is a term that he himself created or NGE for short.

[00:47:31]  Unidentified speaker: So let's do a quick aside on that.

[00:47:33]  Bruce: Shapiro's key contribution here is the concept of natural genetic engineering. It is the idea that evolution has given the organism cells the ability to change its DNA, making DNA read-write instead of just read, to accomplish certain kinds of goals, such as developing antibiotic resistance at a much faster rate than theory says should be possible. I would note that this theory is in no way supernaturalistic, so it wouldn't be helpful to believers in intelligent design. Bear in mind that CRISPR, which famously is today used for genetic engineering by humans, is a natural process taken from bacteria. From page XXV, from his book, Bacteria and Acha-

[00:48:18]  Unidentified speaker: I can't pronounce that term.

[00:48:19]  Unidentified speaker: Acha-

[00:48:22]  Bruce: [Archaea?] have possibly been using this now famous CRISPR to defend themselves longer than nucleated eukaryote cells have existed on earth. Eukaryote cells are cells that have a nucleus. This is actually not that different from the idea that animals can create knowledge in the lifetime of the organism via learning algorithms. So now even Deutsch, when we looked at this, was forced to admit that animals have memes, which is a kind of knowledge that is not found in the genes, though he argued it was non-explanatory. But it's also not knowledge contained in DNA. What we are saying here is that the [phenome?] or body of the animal contains learning algorithms that perform [many evolutionary survival of the fittest?] within the lifetime of the animal at the level of DNA. This may at first sound sort of controversial, but we've previously discussed an entirely non-controversial version of it, the immune system, which I'm going to cover a little later in this podcast. The work of Michael Levin has shown that the body cells have a far more of these learning algorithms than we thought. See episode 21, Evolution Outside the Genome, or discussion on that. So, from page 24, living cells are not solely dependent upon vertical inheritance for acquiring DNA encoding new traits. They can definitely acquire DNA by horizontal transfer from other cells, be often of different species or even different kingdoms. Also on page 24, multiple genomically encoded functions can be acquired at once in a single DNA transfer event.

[00:50:08]  Bruce: In other words, evolutionary change can be sudden and does not have to precede one trait or one small change at a time. This second is Shapiro's proposed response to the bacterial flagellum problem. Now, while this example is not as mainstream as hybridization, I doubt there is yet much here that would be considered controversial. Shapiro gives plenty of evidence that superbugs don't follow standard evolutionary theory that assumes gradualism and shows how that led to bad predictions among scientists at the time. Bacteria, the true inventors of CRISPR, are well known to have advanced abilities to do natural genetic engineering. And I think someone might easily argue here, but how is this not neo-Darwinian evolution? The bacteria gained this ability via natural selection, presumably. And it would come as no shock to any biologist that some organisms, such as bacteria, utilize, at least no shock today, maybe it was a shock back in the 60s, utilize horizontal instead of vertical transfer of genes. So does this example really count as a counter example of neo-Darwinian evolution either? Even though it is clearly now a very non-standard, less well-known example of evolution that is nothing like gradualism, and it's even sexier now because it seems to require a bit of intelligence, in that the bacteria seem to be able to coordinate necessary changes due to their DNA-based learning algorithms. Again, I'm personally struck with how none of my classical training in biology prepared me for any of this, and when I read this, this was all a shock to me.

[00:51:55]  Bruce: I suspect many of you, if you're layman or even scientists outside the field, will find this example a bit shocking too. But I agree that this could certainly still fit into a neo-Darwinian framework if we stretch a bit.

[00:52:09]  Unidentified speaker: So let's keep digging, all right?

[00:52:11]  Bruce: So let's dig a bit deeper into Shapiro's concept of natural genetic engineering. So Zach Hancock, who we're going to cover in the next podcast, in his critique is going to argue that calling it natural genetic engineering is misleading because it's pretty poor at engineering much. But before we dig into that in the next episode, let's go over Shapiro's examples of natural genetic engineering in detail. Now, as a graduate student at Cambridge, this is a quote, a graduate student at Cambridge University in the UK, I characterized a series of spontaneous mutations affecting I can't pronounce the term, but E coli bacterial sugar metabolism. Spontaneous means that no chemical or radiation treatments were used to induce the mutations. As I study these mutations, they did not follow the rules established by molecular geneticists in the mid-1960s. They were neither nucleotide changes, substituting one base pairing specificity for another, nor the recently discovered frameshift mutations, which either deleted or inserted one or two nucleotides of the DNA coding strands. Moreover, these mutations had extremely strong effects on the expression of nearby unmutated coding sequences. Eventually, I hypothesized correctly as it turns out that these mutations resulted from the insertion of extra DNA into the target sequence on the bacterial chromosome. In other words, my E coli bacteria were telling me that they could modify their genes in totally unexpected ways. So, in plain English, what he's talking about is his own research.

[00:53:56]  Unidentified speaker: This is, by the way, from Page XVII.

[00:54:00]  Bruce: He was initially expecting E coli to mutate according to the gradualist account of neo-Darwinism that most of us know about. And instead, they were mutating in these unexpected, sudden ways. And they were, not only were they just inserting DNA into sequences where they wanted it, and self-modifying their own DNA, but when they would do this, it would change how the DNA next to it that was unchanged, how it changed the phenome, right? So it was causing a certain gene that was unchanged to create a different phenome.

[00:54:46]  Unidentified speaker: Characteristic.

[00:54:47]  Unidentified speaker: Okay.

[00:54:48]  Bruce: So the need for some sort of explanation of non-vertical transfer DNA seems apparent. So page 26, working under minimalist conditions, he demonstrated that sexual recombination of E coli required an infectious factor that he called F for fertility. Bill demonstrated, since he's quoting somebody else's research, demonstrated that F was independent of the E coli chromosome by studying the kinetic of this spread in a bacterial population. He found that F could replicate and spread through the population far faster than the 30-minute division time of the bacteria. So let me say that again. He could replicate, they could replicate and spread; the DNA could replicate and spread through the population faster than the 30-minute division time of the bacteria. This kind of autonomously replicating element came to be called a plasmid, page 26. So to be clear, this specific example does not seem to be in question. [No/Nor?] are plasmids' autonomous replicating elements in question. So for example, from Wikipedia, a plasmid is a small extra chromosomal DNA molecule within a cell that is physically separated from the chromosomal DNA and can replicate independently. Shapiro gives one of the more clear-cut example explanations on why some are worried about GMOs to try to explain this. I know this is one that may rankle Deutschians in particular wrong, and I'm not going to be wading into the controversy at all, but I thought that it was a very good example of the type of evolutionary processes that a strict reading of neo-Darwinian evolution as taught in school can't explain well.

[00:56:36]  Bruce: So, from page XVII, These homogenous bioengineered genetically modified organisms, GMO crops, crowd out natural varieties without consideration for the many advantages of biological diversity. Every time a GMO is planted widely across the planet, there is a very real possibility that the plants themselves, or herbivorous insects, fungi, bacteria, or viruses that prey on them may spread the bioengineered DNA encoding resistance to others, less desirable species. Before reading Shapiro, I admit I had no idea whatsoever that DNA could just horizontally transfer between species of plants due to bacteria, insects, or fungi. It never occurred to me that insects might spread the DNA of plants across species via hybridization. So, to be clear here, what he's saying is the reason why people are worried about genetically modified plants is because they outcompete the regular plants, which have much more variety of DNA.

[00:57:53]  Unidentified speaker: Okay.

[00:57:54]  Bruce: So if you put these plants down and you start to grow them, I would have thought using my classically trained biology and evolutionary theory that there's no danger, that you've got a field, you put these genetically modified organisms out there, you grow them, they have certain advantages, and that there would be no impact on any other species, right? Because you're not actually mating them with any other species. So I would not have understood why there was a concern here. What he's saying is that the very fact that you put them down into a field, immediately you have to worry about their DNA, their genetically modified DNA getting transferred to all other species, even entirely different species of plants via insects or bacteria or fungi, okay, via horizontal transfer of DNA. Now you stop and you think about that for a second. I had no idea that was even possible, right? I mean, like, I kind of had a vague idea that you could have some hybridization, that, you know, but this idea that you would have to worry about the DNA just escaping into the wild and getting into other plants and therefore making these other plants less resilient never would have occurred to me, okay? So maybe that's true for plants, but what about animals? Okay, so page 44, he says, nematode genomes reveal further horizontal transfer events that help them fill new ecological niches. One case involves acquiring antifungal defense proteins from a beetle, whose dead body serves as the food for the fungi that feed the nematode.

[00:59:41]  Bruce: What has become clear from these plant parasitic nematode examples, is that horizontal DNA transfer occurs into the animal germline and plays a key role in adaptive evolution. This example I'm about to read is really hard to read, and I don't know that it makes a lot of sense, but bear with me. One fascinating case of highly biased integration is the bacterial transposon TN7. TN7 has two specialized proteins to target its transposition. The TNSD protein directs TN7 to insert into a special, I can't pronounce it, site in the chromosomes of many bacterial species where it does not disrupt any host functions and so causes no effects. Notice that in this example here, this is an actual study and experiment where it can actually take DNA and it knows where to insert it into the bacterial species, such that it does not disrupt any host functions.

[01:00:52]  Unidentified speaker: I didn't know that was possible.

[01:00:53]  Bruce: That was beyond my understanding of neo-Darwinian evolution. Another more interesting protein, TNSE, directs TN7 to insert into replicating DNA molecules. The reason this is important is that transmissible plasmids replicate their DNA as they transfer from one cell to another. The TNSE, targeting to [transmit?] plasmids in transit to new cells, thus enhances the spread of TN7 and the resistance it carries to many different kinds of bacteria. So the bacteria actually gain resistance by doing a targeting modification to a plasmid, which then replicates itself, and then that DNA gets inserted into the bacteria, which then picks up the resistance. So the resistance can transfer amongst the population of bacteria much faster than their 30-minute replication cycle, because it simply has to transfer it to the plasmids, which then transfer it to the entire population of the bacteria. Therefore, the bacteria can gain resistances faster than they can replicate.

[01:02:04]  Unidentified speaker: Okay.

[01:02:05]  Bruce: Again, I didn't know this was possible, right? This really doesn't match my understanding of traditional neo-Darwinism. He then goes on in page 52 and 53 to explain how to detect this via experiment, but I'm not going to cover that part. Now, here's bigger examples, because we're still talking about nematodes, which are little tiny animals, very primitive. We've recently learned that mouse cells exert control over recombinatorial hotspots in meiosis. They produce a blocking protein that binds to cleavage sites that coincide with highly evolved combinations of expression signals in the DNA. This inhibition protects those adaptive combinations from disruption by recombinatorial exchanges. As we often find in cell biology, one specificity leads to another. So biochemical processes are tightly controlled against bad outcomes. As DNA sequencing reveals, genomes are full of repeated segments of many different locations. Our own genome contains over 40% of their DNA as dispersed repeats.

[01:03:11]  Unidentified speaker: That's from page 48.

[01:03:15]  Bruce: Now, famously, Barbara McClintock, Nobel Prize winner, by the way, discovered in maize corn, Indian corn, that its genes could jump around the chromosome. So from Wikipedia, in 1944 to 1945, McClintock planted corn kernels that were self-pollinated. These kernels came from a long line of plants that had been self-pollinated, causing broken arms on the end of their 9th chromosome. As the maize plants began to grow, McClintock noted unusual color patterns on the leaves. For example, one leaf had two albino patches of almost identical size, located side by side with the leaf. When comparing the chromosomes of the current generation of plants with the parent generation, she found certain parts of the chromosomes had switched positions. This refuted a popular genetic theory of the time, that genes were fixed in their position on the chromosome. McClintock found that genes could not only move, but could also be turned on and off due to certain environmental conditions or during different stages of cell development. So here are several quotes now from Shapiro about McClintock's work. Using experimentally generated breaks, McClintock demonstrated conclusively that maize cells can detect, juxtapose, and fuse broken chromosome ends. McClintock realized that the X-rays broke chromosomes whenever they happened to strike. Breakages alone, however, was insufficient to generate a mutant chromosome. The cell's ability to repair the damage by fusing broken ends was essential. In other words, X-ray mutagenesis provoked cell action.

[01:05:05]  Bruce: This was not simply a passive consequence of physical damage induced by radiation. To put this into plain English, the old theory was that if you used X-rays and you broke a chromosome, that that would cause a mutation or some sort of problem for the cells. But what it actually did in the maize was it would take the chromosomes and it would fuse them back together again.

[01:05:34]  Unidentified speaker: Okay.

[01:05:34]  Bruce: This realization had profound implications, as McClintock wrote in her Nobel lecture. The conclusion seems inescapable, that cells are able to sense the presence in their nuclei of ruptured ends of the chromosomes and then to activate a mechanism that will bring together and then unite these ends one with another. The ability of a cell to sense these broken ends, to direct them towards each other, and then to unite them so that the union of the two DNA strands is correctly oriented is a particularly revealing example of the sensitivity of cells to all that is going on within them. Broken chromosome repair was thus an example of action by what McClintock came to call smart cells. McClintock said, There must be enormous homeostatic adjustments required of cells. The sensing devices and the signals that initiate these adjustments are beyond our present ability to fathom. A goal for the future would be to determine the extent of knowledge the cell has of itself and how it utilizes this knowledge in a thoughtful manner when challenged, thoughtful in scare quotes. Or, put another way, the genome contains [sensory and react?] mechanisms and is controlled by learning algorithms.

[01:06:59]  Unidentified speaker: That's me saying that.

[01:07:02]  Unidentified speaker: Conventional wisdom, this is from page eight,

[01:07:04]  Bruce: Conventional wisdom has it that genetic changes underlying evolution are random accidents, each having a small chance of making incremental improvements in fitness. Now that we have almost 60 years of DNA-based molecular genetics and genome sequencing behind us, a different picture has emerged. Molecular science reveals built-in cell systems for restructuring genomes in times of stress and challenge. The mobile genetic element, first discovered by Barbara McClintock, have proved to be everywhere. Sometimes these are also called transposable elements, TEs. They are part of the elaborate set of biochemical functions essential for making changes to DNA sequence, which do not happen without these functions.

[01:07:53]  Unidentified speaker: Page 29.

[01:07:54]  Bruce: Unlike the genes hypothesized by pre-DNA genetic theory, transposable elements do not occupy a permanent location on particular chromosomes. They can be distributed throughout the genome. In fact, dispersed mobile genetic elements account for between 40 and 65 percent of our own DNA.

[01:08:15]  Unidentified speaker: I would never have guessed that.

[01:08:18]  Bruce: As the author notes, and continue to quote Shapiro here, mobile elements provide an elegant mechanism for distributing a common sequence across the genome, which can then be retained in locations where it confers advantageous regulatory functions to the host, a process termed exaptation. They could actually take the genes and target locations where they will confer advantageous regulatory functions.

[01:08:54]  Unidentified speaker: That's called exaptation.

[01:08:57]  Bruce: Our data reveal over 280,000 mobile element exaptations, common to mammalian genomes, covering approximately 7 megabase pairs of the 1.1 million constrained elements that arose during the 90 million years between the divergence from marsupials and the eutherian radiation. We can trace greater than 19% to mobile element exaptations.

[01:09:29]  Unidentified speaker: I mean, that's huge, right?

[01:09:30]  Bruce: Like, again, this is from page 9, by the way, totally outside of what I had been taught in school.

[01:09:37]  Unidentified speaker: Okay?

[01:09:38]  Bruce: In other words, new DNA signals in the genome do not need to evolve independently by random mutation at each site, where they play an important role. Different DNA signals can be distributed to many sites by the biochemical systems that mobilize defined segments of DNA, mobile genetic elements, to new locations. In this way, evolution of the DNA signals imbedded in the genome resembles genetic engineering more than a mutational random walk.

[01:10:08]  Unidentified speaker: That's from page 9 also.

[01:10:10]  Unidentified speaker: Okay.

[01:10:12]  Bruce: I think that's all pretty impressive. But maybe this is true for bacteria, but is it true for higher organisms? All the examples we used here were bacteria. So, that is an open question, okay? And I think that this is, and I'll come, I'll circle back to this near the end of this particular podcast, but kind of keep it in your mind right now, that while I'm giving you some fairly impressive examples from Shapiro, they're usually from plants or from bacteria, and or we did have some with like nematodes, very, very primitive animals. And there's maybe an open question of, does this scale to higher organisms?

[01:11:01]  Unidentified speaker: Okay.

[01:11:02]  Bruce: And in many ways, that is the question that we need to be asking. So now another interesting quote, and I kind of already hinted at this, but I thought this was a really interesting quote that people should know about. So from page XXII, organisms actively restructure their genome in the course of evolution, using a set of biochemical and cellular natural genetic engineering tools to rewrite their DNA. This means in informatic terms that the genome is rewrite data storage system, not a read-only memory system that changes only by copying errors. Genome change is not a blind process, but involves sensing and control circuits that both activate natural genetic engineering functions in response to ecological distress and bias the nature of the modifications that result. The time has come to view read-write genome evolution from an informatic smart system perspective rather than from the more conventional and atomistic view as a collection of independently and randomly evolving gene units. Now, this is something you might hear and it's true, right? Genes are a read-write system, at least for some of these lower organisms that we've talked about.

[01:12:20]  Unidentified speaker: And even we've talked about the immune system.

[01:12:23]  Unidentified speaker: I'm going to use that as an example.

[01:12:25]  Bruce: Even for higher organisms, the immune system, genes are a read-write system, right? Where we have this gene-centric view of the genes are the center of the universe, a very reductionistic view.

[01:12:39]  Unidentified speaker: And I don't mean that in a pejorative sense.

[01:12:41]  Bruce: Where we're looking things from the genes, from the point of view of the DNA, the genes in the DNA. Once you understand that genes, that DNA is in fact a read-write system, it does seem a little weird that we look at it from such a gene-centric view.

[01:13:01]  Bruce: Okay, so now, talking about self-monitoring. Page 76, he says, Complex cells with a nucleus, so that would be eukaryotes, display a tightly controlled multi-stage cell division cycle. Each stage involves intricate processes such as cell growth, DNA replication, and accurate transmission of genome copies to their daughter cells. Elaborate biochemical reactions regulate passage from one stage to the next. On top of the stage-to-stage control circuitry, a self-monitoring system makes sure everything comes out right. If the different biochemical and biomechanical processes fall out of sync, or if there is either a mistake or damage, sensory molecules detect the problem. They activate a checkpoint to hold up the entire cycle until everything has been set right, by renewed progress. Set right for renewed progress. So in other words, mutation is at least partially non-random, because cells put more effort into making sure some areas copy without a mutation. So we often think a mutation is just a random process. There's these passive genes that exist in DNA, and a cosmic ray comes along and hits one and it changes it. That just isn't how this works.

[01:14:25]  Bruce: The process cares more about certain areas.

[01:14:27]  Unidentified speaker: This makes sense.

[01:14:29]  Bruce: Certain areas would be more essential for life than others. So it allows certain areas to mutate faster than others due to this basically error-checking mechanism that exists within the cells when it's trying to do a copy.

[01:14:42]  Unidentified speaker: Okay.

[01:14:42]  Bruce: Because of this, certain areas can mutate faster than others.

[01:14:47]  Unidentified speaker: Now, this isn't too surprising.

[01:14:49]  Bruce: It's surprising the way I'm putting it. But like this idea of junk DNA, by the way, Shapiro claims there isn't such a thing as junk DNA. I'm not going to cover that, but that is one of his claims and I find that maybe one of the more questionable claims.

[01:15:02]  Unidentified speaker: Junk DNA is supposed to mutate faster because it doesn't actually code for proteins.

[01:15:06]  Unidentified speaker: But the cells decide how much mutation takes place.

[01:15:12]  Bruce: And they actually decide that certain areas are more important and it does extra error correction on those. Okay, meaning that the mutation is partially non-random. So from page 77, the network is capable of responding to completely unpredictable events such as external damage or experimental interventions. It displays reliability and enviable in any complex human manufacturing process. So let's move on to... This is actually an uncontroversial example because I've read something about it. But it was actually a little bit of a shock to me when I first heard about it. So symbiogenesis. So perhaps the most important evolutionary step of all took place. This is Shapiro from page 6. Took place at least one billion years ago when two or more cells fused to produce the first eukaryote cell having a defined nucleus. So eukaryote cell is a cell with a nucleus and a prokaryote is one that doesn't have a nucleus. This nucleated cell was apparently the progenitor of all higher forms of life, including plants and animals. Such cell mergers are known as symbiogenesis, long championed as an evolutionary force by the recently deceased biologist Lynn Margulis. So he goes on to say, symbiogenetic events included the origin of the eukaryotic cell. This major step enabled all the following evolutionary leaps up to multicellular organisms, including us. Let me repeat that last point for emphasis. The formation of the eukaryotic cell, setting the stage for all subsequent eukaryotic evolution, did not happen by gradual change and natural selection.

[01:17:11]  Bruce: That's one major reason why the conventional theory is an inadequate explanation of evolution.

[01:17:17]  Unidentified speaker: That's from page 42.

[01:17:19]  Bruce: Now, maybe this sounds controversial, right? Like that seems like a really, really big claim. And if it were true, then certainly it is a gigantic counter example to how we would normally think of Darwinian evolution and the way it's taught in schools today. But this is really an uncontroversial claim that he's making. So if you're interested in this, just what a huge step in evolution eukaryotic cells were, see Nick Lane's book, The Vital Question. Excellent book, by the way, where he tries to figure out how eukaryotic cells came to be. I can confirm that, and we'll probably do a podcast on just his book.

[01:17:59]  Unidentified speaker: It's a tough book, so that's why I put off doing a podcast on it.

[01:18:02]  Bruce: I can confirm that Lane concurs with Shapiro, that it was the evolution of eukaryotic cells that allowed the necessary jump to universality, to use the Deutschian term, that allowed all higher life forms to evolve, and that that jump to universality, according to Lane, did not happen via gradualism, and it happened once, or at least one that we know of. What he claims happened is two kinds of cells got fused together, just as Shapiro just said in my quotes I just gave, into a single new kind of organism. And it happened all within one generation. That is to say, we had no nuclei in cells, and two animals got fused together and became a single new organism that replicated in one generation. And you started having nucleated cells, cells with nuclei. And that was the necessary jump to universality that allowed every single higher organism to come into existence.

[01:19:08]  Unidentified speaker: Okay.

[01:19:10]  Bruce: This really is a strong counter example to the traditional view of Darwinism that we've been taught in school. And it's a completely uncontroversial example. So as Shapiro puts this on page seven, it's remarkable that even though processes like hybridization and symbiogenesis have been well known for decades, many neo-Darwinists firmly insist on gradualism in evolutionary change.

[01:19:39]  Bruce: So all of this comes down to kind of where we started this episode. This idea of the gene-centric view. So this is really what Shapiro is attacking.

[01:19:51]  Unidentified speaker: Okay.

[01:19:53]  Bruce: Here's a quote from page XXIII. A major shortcoming of the modern synthesis is that it was based on a gene-centric view, which assumed that the genome is basically a collection of genes that are both the protein coding units of heredity and the major sites of heritable variation. This view failed to take the evolutionary importance of chromosome structure into account. It also blinded evolutionary biologists to the importance of McClintock's mid-20th century discovery of mobile controlling elements. The idea of genetic transposition and control of gene expression by these non-coding mobile elements were heretical notions that did not fit within the narrow confines of the modern synthesis concept of genome function and variation. Barbara McClintock told me how angry looks from her colleagues greeted her after the first presentation on controlling elements at a Cold Spring Harbor Symposium in the 1950s.

[01:20:55]  Unidentified speaker: I thought that was hilarious.

[01:20:56]  Bruce: Keep in mind that Barbara McClintock did go on to win a Nobel Prize, but it wasn't for this, and she was still considered an outsider and kind of a bit of a heretic, despite that fact. So I think a lot of her work is kind of proven out over the years, but there was definitely a bad reaction to these discoveries because it went against existing. It was perceived at the time as going against existing theory. The basic idea, this is from page 74, is that molecular genetics has made it impossible to provide a consistent or even useful definition of the term gene. In March 2009, I attended a workshop at the Santa Fe Institute titled Complexity of the Gene Concept. Although we had a lot of smart people around the table, we failed as a group to agree on a clear meaning for the term gene. The modern concept of the genome has no basic unit. It has literally become systems all the way down. There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other quote DNA elements that participate in the multiple functions involved in genome expression, replication, transmission, repair, and evolution.

[01:22:17]  Unidentified speaker: That was from page 74.

[01:22:19]  Bruce: Another interesting thing that he brings up is this concept of modularity. So quoting him again from page 40 and 41, the fact that single amino acid changes could not easily account for many aspects of protein evolution was generally ignored. For example, how proteins change their size, formed completely novel structures, or combined the capacities to bind multiple different molecules, was difficult to account for on the basis of successive single amino acid substitutions. These difficulties were even used by intelligent design advocates to argue that proteins could not evolve by natural means. By laboratory genetic engineering, it was possible to add domains together in new combinations. The results show that the domains retained their functions when combined in new ways.

[01:23:11]  Unidentified speaker: Okay, I need to explain that.

[01:23:14]  Bruce: That when they made changes, they would maintain their functions.

[01:23:19]  Unidentified speaker: Okay, even when they were combined in new ways.

[01:23:22]  Bruce: Thus, they were truly independent modules capable of rearrangement, or they were modular. From the point of view of genetic novelty, the ability to combine different pre-existing functional modules in new ways is far more efficient than taking a slow random walk through protein sequence space, one amino acid at a time, as per the dominant theory. Domain combinations arise in a single cell generation. So, the process is far more rapid than accumulating single amino acid changes. Since the modules each have functionality, it is likely that new combinations will maintain some functionality as well, whereas many amino acid changes will either make no difference because they maintain their functionality even when a change happens, or prove detrimental. In addition, there are some functional protein structures that cannot be reached from other structures by changing individual amino acids, and yet are reached. How do genome-encoding complex networks evolve to provide novel functions in any reasonable period of time? According to the conventional view of evolution, a random succession of independent, localized, slight changes, each providing its own selective advantage. The evolutionary process appears hopelessly slow and subject to taking too many steps backwards before it takes one forward. The ideal solution would be rapid ways of copying and modifying the DNA, encoding the network components on a wholesale basis.

[01:25:00]  Bruce: Although such processes were ruled out a priori by the founders of conventional evolutionary theory, they were just what molecular biologists studying DNA change in genome sequences have discovered. Duplication and natural genetic engineering processes for amplifying and distributing DNA encoding network components throughout the genome. In other words, natural genetic engineering is a way to build molecular circuits Lego-like, thus rapidly.

[01:25:30]  Unidentified speaker: This is from page 64.

[01:25:33]  Bruce: Now, we've covered in the past the immune system. And I used that as an example of a process that creates knowledge, but isn't part of... It creates knowledge in the genes, in fact, right? But doesn't do it via the sex cells.

[01:25:54]  Unidentified speaker: So it doesn't become part of the germline passed down generations.

[01:25:58]  Bruce: And I used that as a way of showing that the two sources hypothesis, David Deutsch's two sources hypothesis, is actually incorrect. Obviously, having talked with many crit rats about this, they typically just redefine knowledge to not include what the immune system actually creates, these recipes for antibodies. So I suggested, well, can we at least call them simulknowledge? Can we call them something that's like, you know, a simulacrum of knowledge? And I got a very negative reaction of crit rats even for that.

[01:26:31]  Unidentified speaker: They didn't even want to talk about it.

[01:26:32]  Unidentified speaker: They didn't want to even think about it.

[01:26:33]  Bruce: They just said, oh, it's so boring and uninteresting, I'm just not even willing to talk about it. But the immune system is this really interesting example of everything we've been talking about up to this point, and yet it's happening with higher organisms, okay?

[01:26:46]  Unidentified speaker: It's happening with you and me today.

[01:26:48]  Bruce: And in fact, we could not survive without it, okay? Now, I've given the examples of this in past episodes, including episode 21 and also where we talked about David Deutsch's theories on knowledge and why I think the two sources hypothesis really should function as a poor version of the problem of open-endedness. I think it's something to it, but it's not what David Deutsch thinks it is. So here are some quotes from page 56 to 57 about the immune system. And you can kind of see how he's pulling it all together here. Your life depends on purposeful, targeted changes to cellular DNA. Although conventional thinking says directed DNA changes are impossible, the truth is, is that you could not survive without them. Your immune system needs to engineer certain DNA sequences in just the right way to function properly. Your immune system has to anticipate and inactivate unknown invaders. Living organisms deal with unpredictable events by evolving.

[01:27:54]  Unidentified speaker: He doesn't mean across generations here.

[01:27:56]  Bruce: He means the organism itself evolves.

[01:27:59]  Unidentified speaker: They change to adapt to new circumstances.

[01:28:02]  Bruce: Variation comes from their capacity for self-modification. Cells have many molecular mechanisms that read, write and reorganize the information in their genome. The DNA molecules used for data storage. The adaptive immune system executes basic evolutionary principles in real time. Now, we covered this in a past episode in detail, but we're going to cover it again from Shapiro's viewpoint.

[01:28:30]  Unidentified speaker: But that is correct, right?

[01:28:31]  Bruce: The immune system basically does mini evolution of the cells inside the body, trying to find the right recipe to fight the antibody. And then it allows the ones that are successful to replicate and proliferate, and the ones that are unsuccessful die off. So it's just basically survival of the fittest, but it's not at the organism level. It's at the level of the cells, okay? So again, the adaptive immune system executes basic evolutionary principles in real time. It has to recognize and combat unknown and utterly unpredictable invaders. Immune system cells have to produce antibody molecules that can bind to any possible molecular structure. How do cells with finite DNA and finite coding capacity produce a virtually infinite variety of antibodies? The answer is that certain immune cells, B cells, become a rapid evolutionary factories. Immune cells achieve both diversity and regularity in antibody structures. They accomplish this by a targeted yet flexible process of natural genetic engineering. They cut and splice DNA, but diversity is strictly limited to a specific part of the antibody molecules.

[01:29:49]  Unidentified speaker: And again, we covered this in a past episode.

[01:29:51]  Bruce: That is exactly how it works. It knows to hypermutate the genome, but only parts of the genome, so that it's the parts that will try to search for the correct antibody recipe. Three remarkable things about somatic hypermutation, somatic means non-sex cells, are explicitly excluded from the prevailing philosophy of genetic change. First, they are adaptive and purposeful genome changes. Second, they are functionally targeted. Third, [partially involves targeting?] involves intercellular signals that depend on how other cells in the immune system perceive a particular infection. If immune cells do all the above, is there any scientific reason we should assume that other cells cannot do the same? So, let me see if I can explain the argument here, okay? So, he's trying to show that evolution does not take place using the standard story of gradual evolution through mutation to genes, and is not even gene-centric if you're looking at bacteria, if you're looking at plants, okay? That the story only seems to apply, if at all, to higher animals. And then he's saying, look, even in the higher animals, if you're looking at body cells, non-sex cells, soma cells, it's not true there either. The body knows how to do hypermutation and to do evolution, because it wouldn't make sense to try to store only antibodies that were known in the past in the genes.

[01:31:34]  Bruce: Instead, what we want is we want the genes to have a learning algorithm, that can hypermutate its own genes until it finds in real-time the necessary antibody to defeat this bacteria, so that you can overcome the sickness and you don't die with every new novel bacteria that you encounter. You could not survive if your body didn't know how to do hypermutation, evolution and targeted evolution to try to discover a hypermutation, a mutation that is specifically meant to deal with a problem that you have right now, the fact that you have COVID or something like that. He's saying, look, we know it's not controversial that soma cells can do this. Why are we assuming that sex cells can't do it, and that there isn't something like this that is affecting overall evolution? He then goes on to say, The burden of explaining what other cells lack, [that lymphocytic cell process/processes?] lies with those who wish to adopt the position that the immune response is unique and does not reflect a more general capacity to target genome change. Evolution has obviously refined antibody producing cells for their immune system functions. But do immune cells have unique capabilities for natural genetic engineering, that it's missing in other cells? If the answer is no, as I believe, then we need to incorporate adaptive genome restructuring into our most fundamental thinking about biology. Now, despite all this evidence, let's put the evidence in scare quotes here, Shapiro really seems to have no clear-cut testable theory here.

[01:33:23]  Bruce: And I think this is where I am going to take issue with what he's saying. Okay, it's more a matter of saying, well, DNA can actively perform natural genetic engineering. So maybe this can explain some of the anomalies that are currently understood as problems for neo-Darwinianism. And I was happy to see that James Shapiro outright admits that this is the case.

[01:33:48]  Unidentified speaker: Okay, so here's a quote from him.

[01:33:50]  Bruce: Natural genetic engineering is not an explanatory principle. In this, it differs from the use many evolutionary biologists have made of the descriptive phrase natural selection to cover gaps in their account of adaptive novelties. Natural genetic engineering is only a set of well-documented DNA change operators. While natural genetic engineering can help in understanding the molecular details of rapid and widespread genome change, it does not tell us what makes genomic novelties turn out to be useful. How NGE leads to major new innovations of adaptive use remains a central problem in evolution science. To address this problem experimentally or testably, we need to do more ambitious laboratory evolution research looking for complex coordinated changes in the genome. Or to put this in slightly less positive terms, this is an early conjecture, not a Popperian-style falsifiable theory. Shapiro is basically saying there are these strange aspects of evolution that we never talk about that much that don't fit the traditional account. I think maybe if we go explore them, we're going to find answers to big unanswered questions. But from a critical rational standpoint, until he proposes a specific testable theory, this is just a wild conjecture and that's all it really is. It can never attain a best theory status without also being falsifiable. And this is where I'm going to actually leave off for this episode.

[01:35:29]  Bruce: I've given you several, I think, really interesting examples of how biology does not follow the rules of what I thought Neo-Darwinian evolution was and doesn't seem to care about the gene-centric view that typically gets taught in schools. On the other hand, I think Shapiro is making it sound like, he admits that it's not a true testable theory yet, but he makes it sound like we know more than we do. There's more like a set of problems here and a set of interesting ideas that maybe could be formed into a theory in the future. But this really strikes me more as hope of a future theory than a true theory as of yet.

[01:36:19]  Peter: Bruce, this is extremely interesting. There's a lot of details I'm still absorbing on what you're saying. This is probably one of our headier, more dense episodes. I do have one big picture question on this that might be too far out even for us, or that we can cut if it doesn't go anywhere. But thinking about, does this have implications for, I'm thinking, as you know, I've read books, I think, in the last year by Paul Davies, Thomas Nagel, Philip Goff, Bobby Azarian, that seem to be making the case that there is something inherent in this laws of physics that's almost like a creative force that tends towards novelty, I guess, that meaning is something that isn't just arbitrarily created by humans, but that has, you know, there's something in the nature of reality that trends toward meaning or life or something. Does this theory of Shapiro's play into this idea? Or is it completely separate?

[01:37:52]  Bruce: So I don't think anywhere I've seen Shapiro try to advocate for a Philip Goff type or Bobby Azarian type, inherent meaning. I think he's more interested in trying to solve evolutionary problems that he feels are getting ignored.

[01:38:09]  Unidentified speaker: Sure.

[01:38:10]  Peter: I think some of these scientists, if they go off on this weird stuff, it kind of like discredits their ideas a little bit. Some people say they probably don't want to go there, but I don't have skin in the game there.

[01:38:21]  Bruce: It has some definite tie-ins to that viewpoint. Let me see if I can explain why.

[01:38:26]  Unidentified speaker: Okay.

[01:38:27]  Bruce: So we will have to cover the work of Michael, how do we pronounce his last name, Michael Levin?

[01:38:34]  Unidentified speaker: Levin.

[01:38:35]  Unidentified speaker: In a separate podcast.

[01:38:36]  Unidentified speaker: It won't even be the next podcast.

[01:38:38]  Unidentified speaker: Maybe I'll touch upon it in the next podcast.

[01:38:40]  Bruce: He's got so many interesting ideas. He's not considered a third wayer like Shapiro. And if you go out and you check, you know, like the episode, homework for next episode, we're going to talk about Denis Noble is Wrong About Evolution by Zach B.

[01:38:57]  Unidentified speaker: Hancock.

[01:38:57]  Unidentified speaker: It's on YouTube.

[01:38:58]  Bruce: Go watch it before the next episode where I'm going to go through it. Now, particularly now that I biased you by giving you Shapiro's viewpoint first.

[01:39:06]  Unidentified speaker: Okay.

[01:39:07]  Bruce: I think it's really helpful to have Shapiro's viewpoint first.

[01:39:10]  Unidentified speaker: It was certainly helpful to me.

[01:39:12]  Unidentified speaker: Okay.

[01:39:13]  Bruce: And he has, like I said, it's a fairly devastating critique, okay? And he kind of defends that, no, neo-Darwinian evolution is not wrong. And you can easily find criticisms of Denis Noble, Ray Noble, James Shapiro, out on the internet, out on YouTube. Go try to look up Michael Levin, you know, is wrong.

[01:39:38]  Unidentified speaker: You won't find a thing.

[01:39:39]  Unidentified speaker: And believe me, I've tried, right?

[01:39:42]  Bruce: And I kind of get the feeling, part of the reason why is because he's really, when it gets right down to it, Shapiro and Noble and these others, they're trying to pull together research done by others and trying to say, wake up, you're missing something.

[01:40:00]  Unidentified speaker: That's not what Levin is doing.

[01:40:02]  Bruce: Levin is doing, coming up with interesting theories and then creating the necessary empirical evidence for them. And the evidence is overwhelmingly impressive, right? Like where he actually has the little Xenobots that he's created out of a cell that can survive and replicate on their own. And he's got like the planarian worms where he splits their heads, it tells it to grow two heads. And then the genes haven't changed, but then when they replicate, they keep two heads because the information for two heads isn't contained within the genes. It's actually contained within the soma cells. And like he's come up with these things that are exactly the same. Like this is why there's, it's the third wayers, like Michael Levin, he actually does an interview of Denis Noble and talks very positively about it, right?

[01:40:51]  Unidentified speaker: In his different things.

[01:40:53]  Bruce: But you would think that he would get attacked along with the other third wayers, but he doesn't. And I honestly feel like he's trying to pick a fight with Superman, right?

[01:41:02]  Unidentified speaker: Like it's like, you just don't do it.

[01:41:04]  Unidentified speaker: It's just not worth the effort.

[01:41:06]  Bruce: This guy's got way too much evidence.

[01:41:08]  Unidentified speaker: Okay.

[01:41:09]  Bruce: But he also doesn't ever put things in kind of the silly ways that Denis Noble does. He never claims Lamarckism is back, right? And which, by the way, just isn't true. Like if you define Lamarckism vaguely enough, yeah, maybe, right? But like Lamarckism is just not back. And it doesn't therefore rile up his peers to try to go attack him. Instead, he comes up with, basically, Michael Levin's main thing is, is that it's agency all the way down. Not to the level of physics necessarily, but into a realm that we would consider non-living. And so when you decide you're going to look at cells as agents that are cognitive and that they have their own will, we're not talking about like consciousness here, okay? He's not like a panpsychist or something. But probably better in Deutschian terms to say that they are learning algorithms that create knowledge, right? Something very much at odds with the two sources hypothesis, okay? And when you decide to look at cells in that way, you decide to look at what's inside the cells in that way, and you continue to look at it in that way, it turns out it leads to really direct research programs that have empirical evidence, because that is the way life actually works. Now, does this mean we need a new theory of evolution?

[01:42:39]  Unidentified speaker: It's a difficult question to even ask.

[01:42:41]  Bruce: That's why I jokingly call it Neo-Neo-Darwinian evolution. You can, the cutoff between an old theory and the advent of a new theory is usually not clear cut. Like, we tend to think of, I've used this as an example in past podcasts, we tend to think of general relativity as this paradigm shift away from Newtonian physics, and that it broke off Newtonian physics, showed it was wrong, and it replaced it. But one could argue, rightly, I think, that general relativity is really just Neo-Newtonianism, because they're so similar in so many ways. And whether you consider a theory, a new theory that refutes the old one, or a tweak on the old one, is often an aesthetic choice. And it's based on a whole bunch of different things that maybe aren't that important. So when Denis Noble says Neo-Darwinian evolution is wrong, I think what we're going to find when we go through the next episode with Zach Hancock, is that it sort of depends on what you mean by Neo-Darwinian evolution. And that it sort of doesn't matter if it's right or wrong. What matters is that we tweak our existing theories to be correct, and we error correct them. And from that standpoint, I've got a problem with Denis Noble saying Neo-Darwinian evolution is wrong, because it gets, it alights people, right? Like it just brings them up for a fight. And, you know, I kind of do it jokingly, and then it brings people up for a fight, even when I'm doing it jokingly. And then I'll say, no, no, I mean, it's like Neo-Neo-Darwinian evolution. Like it's clearly not totally at odds with the original theory.

[01:44:21]  Bruce: And, in fact, you can fit it into the original theory, but you have to adapt the theory to what we now know. And I think it's a big enough jump, what Michael Levin is finding, that to me, it's like a new theory. That's why I call it Neo-Neo-Darwinian evolution. But it's not so different. Like it downplays the gene-centric view, and that's one of the things that we're going to talk about in the next episode as well. And says, it's not even that the gene-centric view is entirely wrong. Clearly, reductionism has been very successful, right? Where we try to look at things, not in terms of emergent explanations, but in terms of reductionist explanations. It's been so overwhelmingly successful in physics. It's been so overwhelmingly successful in biology. It wasn't a blind wrong path, right? Like it's looking at things from the point of view of the gene was a super useful way of looking at biology, but it's not the only way to look at biology. And if you insist, it's the only way of looking at biology, you are blinding yourself to other processes that exist, that are emergent, that need to be a part of the explanation.

[01:45:27]  Unidentified speaker: Okay.

[01:45:28]  Bruce: Now, what is that new theory that's emerging?

[01:45:32]  Unidentified speaker: I don't think we have it yet.

[01:45:33]  Bruce: I think that it is going to turn out to be that Levin is basically correct, that cells have sources of knowledge that are outside the genes, that there is a... You know, this shouldn't be so controversial. It bothers me that it is, particularly in the Deutschian community, that because the two sources hypothesis, they're so insistent that there's only two sources of knowledge, genes and memes, and they're missing the plethora, the overwhelming number of knowledge-creating learning algorithms that exist all throughout nature. And that simply, you would never have the gene-centric view if you hadn't had all these supporting systems that are error-correcting mechanisms, that are agentic, right? That exist in nature and are part of how everything works. And we are going to have to do a restructure of the way we look at evolution, to take this agentic nature, agentic meaning that, like a cell is its own individual cognitive agent.

[01:46:42]  Unidentified speaker: You know, it's like we know this.

[01:46:44]  Unidentified speaker: Cells are little animals.

[01:46:45]  Bruce: They used to be eukaryotes that existed on their own, and they've gained the ability to exist in a giant collective. And that collective is us, right? And it has its own identity as an animal on its own. It doesn't mean the cells aren't still animals. And they'll even try to break themselves off and go back to being an individual animal and not being part of the collective.

[01:47:09]  Unidentified speaker: And then they'll try to replicate on their own.

[01:47:11]  Unidentified speaker: That's called cancer, right?

[01:47:13]  Bruce: Like, that's what it is, and it kills the organism. And Levin, and this is something we'll cover in a future podcast, he's actually figured out in animals, not in humans, how to tell the cancer cell, no, you're part of the collective. And it goes back to being a non-cancer cell. And he does it by communicating to it through bioelectricity. And what he's basically found is that the cells communicate with each other using the exact same means of bioelectricity as is used by the nervous system. So the whole body is a giant brain. And the nervous system is just a specialized case of it that was needed for certain types of animals for a much faster response times. But all the different things that we think of as being unique to brains and nervous systems, the communication across neurons, things like that, they exist amongst regular cells too. And there's no actual cut between regular cells and neurons and having a nervous system.

[01:48:17]  Unidentified speaker: And it's a fuzzy boundary.

[01:48:18]  Unidentified speaker: It's not that there is no boundary.

[01:48:20]  Unidentified speaker: Clearly, there are differences between them, right?

[01:48:22]  Unidentified speaker: And that's why we have both.

[01:48:23]  Bruce: But a lot of the processes that exist in that we thought were unique to brains and nervous systems, they exist amongst just regular cells. And therefore exist in animals that don't have nervous systems. And again, I don't think anyone is challenging any of this. Like Levin, because he puts it not as a giant challenge to existing theories, he's managed to create excitement around this other way of looking at biology in terms of agents, and that the cells have their own agency. He uses the term cognition, which Hancock is going to take really strong exception to, and for good reason, by the way. It possibly makes you think wrongly that cells can think and they have their own little lives where they're wanting to watch television at night and they're like humans, right?

[01:49:14]  Unidentified speaker: And that's clearly not what we mean.

[01:49:16]  Bruce: And the word cognition, maybe it would be best if we reserve the word cognition. But the reason why Levin uses that term is because it allowed him to think, well, what if these did have their own cognition, which really just means learning algorithms. It doesn't mean they're conscious in any way. And by thinking of it in that way, it led to ideas and it led to a research program, which in turn was testable and which he then tested and corroborated it. And therefore, he's going to stick with that term because it was the term that allowed him to not be blind to what was going on. And in many ways, this is just the way this works, right? So how does this get back to the original question? What Levin is really getting at is this idea that it's not just cells that have agency and cognition, it's the parts within the cells.

[01:50:07]  Unidentified speaker: It's all the way down.

[01:50:08]  Bruce: You can start thinking about it being on a spectrum of intelligence. And eventually, you do get to a rock that has no intelligence, right?

[01:50:16]  Unidentified speaker: So it's not like he's being a panpsychist.

[01:50:19]  Bruce: But that we should expect that life came from something in physics that had some level of intelligence, you know, very, very, very, very small level, and that that was what life got built out of.

[01:50:32]  Unidentified speaker: It wasn't just chance, right?

[01:50:34]  Bruce: It was that certain physical processes could be thought of as a kind of cognition, and that this idea of cognition, used in this more general way, so we're not talking about consciousness, that it exists all the way through life, all the way to the bottom, and then must exist outside the bubble of what we currently considered alive. And that once we can see that, and once we understand that, that will explain how life actually got started, and it will solve the mystery of how life got started. And it will turn out to be that evolution works in some really unique ways with these processes. And yes, it's not hard to see that this is exactly what Bobby Azarian and Philip Goff are getting excited about, right?

[01:51:19]  Unidentified speaker: Like wrongly, maybe.

[01:51:21]  Unidentified speaker: Like I haven't read Philip's book yet.

[01:51:23]  Bruce: You told me to read it, and I'll read that, and then we'll talk about that. I've read Bobby Azarian's book. And I think Azarian's kind of right to get excited about a lot of these things, but I don't think he fully knows what he's talking about either. And he's maybe getting prematurely excited about a lot of things.

[01:51:42]  Unidentified speaker: And that's OK, right?

[01:51:43]  Bruce: Like Bobby Azarian's kind of advocating for a sort of cosmic religion that will combine traditional religious ideas into a scientific realm.

[01:51:56]  Unidentified speaker: That's kind of what Deutsch is doing.

[01:51:57]  Unidentified speaker: He wouldn't call it that.

[01:51:59]  Unidentified speaker: But it's not that different, right?

[01:52:01]  Peter: Yeah, I think Philip Goff might be too. In terms of the other, the four thinkers that I named before, I think that Paul Davies and Thomas Nagel might be making the more sober minded arguments compared to Goff and Azarian.

[01:52:18]  Unidentified speaker: Just to put that out there.

[01:52:21]  Peter: Well, Bruce, I don't care what anyone else says about you. I think you're an interesting and compelling and unique thinker. And I enjoy listening to you. And I will look forward to next week.

[01:52:38]  Unidentified speaker: All right.

[01:52:39]  Unidentified speaker: Sounds good.

[01:52:40]  Unidentified speaker: Okay.

[01:52:41]  Peter: Thank you, Bruce.

[01:52:44]  Unidentified speaker: Bye-bye.

[01:52:51]  Unidentified speaker: Hello again.

[01:52:53]  Peter: If you've made it this far, please consider giving us a nice rating on whatever platform you use, or even making a financial contribution through the link provided in the show notes. As you probably know, we are a podcast loosely tied together by the Popper Deutsch Theory of Knowledge. We believe David Deutsch's Four Strands tie everything together. So we discuss science, knowledge, computation, politics, art, and especially the search for artificial general intelligence. Also, please consider connecting with Bruce on X at BNielsen01. Also, please consider joining the Facebook group, The Many Worlds of David Deutsch, where Bruce and I first started connecting.

[01:53:36]  Unidentified speaker: Thank you.