Episode 103: Neo-Darwinism vs Post-Darwinism

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Transcript

[00:00:01]  Blue: Hello out there. 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 master’s 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]  Red: Welcome to The Theory of Anything Podcast. Hey, Peter. Hello, Bruce. How are you today? Good. 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 when I actually ended up putting it together, it 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. Oh, here it is. 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 Dennis 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 on line yet. So, there’s some definite similarities between Michael Levin’s work and particularly Ray and Dennis Noble, but Dennis 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 Dennis 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, 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.

[00:03:41]  Red: And, you know, like Third Way is very controversial, and in fact, we are going to talk about that probably not in this episode so much, but in the next episode where I’m going to talk about criticisms.

[00:03:50]  Blue: I’ve heard it called post -Darwinism too, so it’s kind of… Post -Darwinism, interesting.

[00:03:56]  Red: This is

[00:03:56]  Blue: neo -Darwinism versus post -Darwinism. It could be a good title here.

[00:04:00]  Red: So, I jokingly call it neo -neo -Darwinism. Okay. Which I think is a better term for it.

[00:04:06]  Blue: Or a return to Lamarckism. Oh, I hate that.

[00:04:10]  Red: Oh, my gosh.

[00:04:12]  Blue: Can I just interject one thing? This is going to be a podcast where I am listening more than speaking for sure. 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 Dennis 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. By the way,

[00:04:57]  Red: remember that you just said that. Neo -Darwinism, the gene -centered view of evolution. I want to call it right now that Peter said that. But anyhow, continue.

[00:05:04]  Blue: Okay, fair enough. But even Dawkins seemed quite open to some of Dennis Noble’s arguments. He didn’t seem like he thought it was preposterous or anything. It was actually a very good debate. If there’s anyone who’s listening to this, that things were crazy, they should check out that debate and see how open Dawkins was to these arguments.

[00:05:29]  Red: So it’s interesting that debate is probably what catapulted Dennis Noble in particular into the public eye and kind of got some of his ideas and theories. And I’ve seen numerous magazines have… Evolution is purposeful and it’s freaking scientists out, right? Which is probably just very typical clickbait, totally untrue headlines from journalism, right? But it’s always based on Dennis Noble’s work. So I wanted to actually cover this. Here’s the thing, though. I’m actually not a huge fan of Dennis Noble. I shouldn’t say that in a super negative way. Of course, I think he’s great. But I’ve tried to read some of his books and honestly, I think they’re a little crappy, right? And I’ll talk more about my criticisms of Dennis 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? Like all… Is the name of the paper? Excellent, excellent paper and I highly recommend that paper. But like when I try 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, you know, Ray and Dennis Noble and then James Shapiro. And I got… 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?

[00:07:14]  Red: Shapiro is giving away what the point of the book is in the name of the title right there. And I started reading his book and it really kind of impressed me, right? Like with Dennis’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 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, a view from the 21st century, fortified. And that’s the one I actually have. 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 layman. 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. Okay. So, and that’s the stuff meant for layman, right? So I wanted to, like, I suspect most people who read his blog posts, even when intended for layman, 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.

[00:08:51]  Red: 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 Dennis Noble. And I honestly find the criticisms to be rather devastating. So I don’t want to make it sound like I’m necessarily in favor of Shapiro’s theories. You 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 tried to understand them with a critical eye, right? We’re just interested in trying to understand the various points of view. I do, we’ll 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? Like that may be one of the least important statements I could have possibly made, right? Like every theory is going to need revisions, right?

[00:10:00]  Blue: Yeah.

[00:10:02]  Red: But 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 it’s somebody trying to take seriously that there’s some sort of problem that needs to be resolved.

[00:10:40]  Blue: 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?

[00:10:49]  Red: 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. We just know it. Like there should be no doubt about that, okay? And I know most people just don’t think that way. 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 firsthand 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?

[00:12:17]  Red: 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? 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 just dislike about creationism. Now Shapiro agrees with me. 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]  Blue: 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 kind of like leads to people thinking that evolution has just figured out. We know how it

[00:14:03]  Red: works.

[00:14:04]  Blue: The reality is there are mysteries at every step of this process. Really intriguing mysteries. Yes.

[00:14:12]  Red: 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 paparian epistemological approach to dealing with them. Which I think is very much different than how it’s actually been handled. I think we have touched on that a little bit. Even just little things like how did life even get started? That’s such an obvious problem with evolution that it has no good answer today. Vague theories on the table, some interesting though, but vague ideas of how to answer that question. Go talk to evolutions about that and you can’t even get them to admit it’s a problem. Lee Cronin talks about how he’s… 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. 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. This is not a creationist we’re talking about, right? And they’ll say, oh no, that’s a solved problem. And he’ll go, no it’s not. In his interviews, he talks about the funny conversations he’s had with scientists on this.

[00:15:57]  Red: 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? Because there’s a blindness to them. 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 proselyter for his undoubting and absolutist version of atheism confirms this conclusion. This is from page 17. By the way, if that quote rankles you wrong, it should have. And I’m going to explain why I actually rankles me wrong too, but let’s continue. I’m intentionally picking some of the more, you know, rankling quotes that he makes. One of the creationist’s main tools is the argument that evolutionists are simply militant atheists in drag who care more about dishing 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. That was from page 18. Now, I have a sincere question here. Is Shapiro being unfair to Dawkins?

[00:17:44]  Blue: Yeah,

[00:17:44]  Red: he is. 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. However, here’s the problem. Dawkins really does come across bad to me in general as a religious person, right? 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 get solved problems. 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. And I think Shapiro at least vibe wise has got Dawkins correct.

[00:18:47]  Blue: To be fair, Dawkins is a complicated character, I think. He is. I mean I’ve seen him lecture live and where he just 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 you know 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. There is, I think.

[00:19:22]  Red: When he’s talking religion, it’s like he’s a different person. Yeah. And I agree, Dawkins is one of the great scientists of our times. I love his book, The Selfish Gene, right? 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. Okay. And so I can at least vibe wise kind of agree with what Shapiro’s saying. However, keep in mind those quotes are Shapiro’s viewpoint not mine. Okay. But I’d be lying if I did admit that I at least do overall agree with the vibes of what he’s saying here. Okay. So I like Shapiro’s approach because he’s one of the rare examples about 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. Okay. 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 -weir, 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. He’s talking about evolutionists there.

[00:21:16]  Red: 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. They’ll often say, well, who knows? Maybe it’s aliens, right? 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 layman. 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. Hancock on YouTube. And apparently, we’re also going to talk about Jerry Tone. But do yourself a favor and don’t listen to that yet. First wait for me to give you Shapiro’s view.

[00:23:04]  Red: 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. And that’s what we’re interested in. What do they agree on? 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 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 that 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. It really just is. 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. And because of that, this is going to be yet another epic three -hour three -of -anything podcast. And that’s okay. And this just isn’t for everybody. This is easier than reading the book.

[00:25:05]  Red: And I’m going to, 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. 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. Okay. 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. Okay. 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 that that even is what neo -darwinian evolution means. But that is certainly what 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.

[00:26:48]  Blue: 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]  Red: Yes.

[00:27:00]  Blue: That is absolutely

[00:27:01]  Red: the selfish gene viewpoint that is expressed by Dawkins. Yes. And most people would see that as equivalent to neo -darwinian evolution. Okay. So if somebody says neo -darwinian evolution there’s a very good chance it’s not a 100 % chance but it’s a very good chance they mean that view. So 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. In

[00:28:46]  Red: fact I even remember the little movie my teacher played in high school biology which I’m pretty sure was done by Disney that 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 all that in the animation that I saw that was in my classroom. Yeah I remember that too. I got to go back and watch that. Yes. So 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 by like Ernest Mayer 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.

[00:30:25]  Red: 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 America article on this subject titled cataclysmic evolution the distinguished 20th century evolutionist G. Ledyard -Stevens explained how flour wheat evolved suddenly by hybridization that’s from page 6 also so how does this even work if DNA is supposed to be hard to vary whenever we so 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

[00:32:36]  Red: 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 all within a single generation and again I want to ask how does that even work given that if you were taking 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 genes 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 school room 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 teach me wrong in school about evolution like I seriously doubt that that is happening at this moment hybridization is it’s a well -known exception to gradualism but it’s well known right like everybody knows biologists know hybridization play 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 up front having said that at least as a non biologist though though classically educated which means that I had college level courses in biology okay

[00:34:31]  Red: 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 science sciences 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

[00:35:07]  Red: 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 started 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 there’s 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? 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

[00:36:41]  Red: it so happens that there is a different species of finches that they don’t interbreed with by definition species don’t interbreed that’s what species means and it’s always a little fuzzy what counts as a species because interbreeding happens more than we usually admit okay so they start to die off that other species starts to die off as well so we have an island something has gone wrong with the environment 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 they 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 functional functionalities capable of generating organisms with complex novel phenotypes this process occurs prominently following interspecies hybridization itself a response to reduction of population reduced population size and can be followed in real time and biological systems as diverse as Galapagos finches and cancer progression discussed later in a future section this is from page XXI

[00:38:10]  Red: of his book 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 inches the weaker members of this new species die off of course the remaining ones are better suited for 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 neodarwinian evolution at all is it I mean everything you just described 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 neodarwinian 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 okay but do they 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

[00:39:44]  Red: very much a form of natural selection or neodarwinian evolution so arguably not really at odds with neodarwinian 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 you know people in college like me right um so let’s continue to maybe dig into some of Shapiro’s maybe deeper examples here so Shapiro to get to a slightly more controversial example since hybridization is very much uncontroversial right so Shapiro’s key slightly more controversial counter example to the standard neodarwinian evolution is the super bug again Shapiro seems to really be attacking gradualism rather than truly attacking neodarwinian evolution and he seems to almost treat those two as if they’re one and the same okay 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 how do they become pathogens we currently know a great deal about the genetic basis of these critically important bacterial properties we also know how resistance resistance and virulence 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 scarer quotes consists of more than experimentally confirming hypothetical predictions by the way as Deutschians we should have loved that last quote right because it’s not about prediction so basic neo -Darwinian version of the theory

[00:41:50]  Red: 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 enzyme 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 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 okay and it requires several different generations so he talks about conformation in the lab 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 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 -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

[00:43:51]  Red: there were probably there were problems both with the science and the new public health policy based on it the surgeon general mis underestimated 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 flagellum okay which I raised we raised earlier 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 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

[00:45:05]  Red: 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 school room 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 flagellum okay 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 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 an 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 okay 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 microorganisms 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

[00:47:25]  Red: he just used a term natural genetic engineering which is a term that he himself created or NGE for short so let’s do a quick aside on that 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 this theory is in no way supernaturalistic but 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 I can’t pronounce that term Akai have probably 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 it’s not knowledge contained in DNA

[00:49:01]  Red: 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 sorts of learning algorithms 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 often of different species or even different kingdoms

[00:50:01]  Red: also on page 24 multiple genomically encoded functions can be acquired at once in a single DNA transfer event in other words evolutionary change can be sudden and does not have to proceed one trait or once 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 not neo -Darwinian evolution the bacteria gain this ability via natural selection presumably and it would come as no shock to any biologists that some organisms such as bacteria utilize or at least no shock today back maybe it was

[00:51:12]  Red: 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 it is 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 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 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 so let’s keep digging all right 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 let’s 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 this is a quote at graduate student at Cambridge University in the UK I characterized a series of spontaneous mutations affecting I can’t pronounce the term but E.

[00:52:49]  Red: 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 molecular geneticists in the mid 1960s they were neither they were neither nucleotide changes substituting one base 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 more over 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 this is by the way from page xvii he was initially expecting E. coli to mutate according to the gradualist account of neodarwinism that most of us know about and instead these 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 it was causing a certain gene that was unchanged to create a different phenome characteristic okay so the need for some sort of explanation of non vertical transfer DNA seems apparent so page 26 working under minimalist conduct conditions he demonstrated that sexual recombination of E.

[00:55:00]  Red: coli required an infectious factor that he called f for fertility bill demonstrates as 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 this so they say it 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 are plasmids autonomous replicating elements in question so for example from wikipedia a plasmid is a small extra chromosomal 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 wrinkle duetions in particular wrong and I’m not going to be waiting 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 so from page xvii these homogeneous 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’s a very real possibility that the plants themselves or herbivorous insects fungi, bacteria or viruses that prey on them may spread the

[00:57:09]  Red: bioengineered DNA encoding resistance to others less desirable species

[00:57:16]  Red: before reading Shapiro 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 out -compete the regular plants which have much more variety of DNA 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 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 feel new ecological niches one case involves acquiring anti -fungal defense proteins from a beetle whose dead body serves as the food for the fungi that feed the nematode 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

[00:59:56]  Red: 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 trance trance spoonson TN7 TN7 has two specialized proteins to target its trance transposition the TNSD protein directs TN7 to insert into a special I can’t pronounce it sight in the chromosomes of many bacterial species where it does not disrupt any host functions and so causes no effects so notice that in this example here this is an actual studying experiment where it 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 so that’s kind of I didn’t know that was possible 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 transplant 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 bacteria therefore the bacteria can gain resistances faster than they can replicate

[01:02:05]  Red: again I didn’t know this was possible this really doesn’t match my understanding of traditional neodarwinism 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 so 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 hot spots 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 that’s from page 48 now

[01:03:16]  Red: famously Barbara McClintock Nobel prize winner by the way discovered in May’s 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 ninth chromosome as the May’s 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 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 May’s 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 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 be

[01:05:20]  Red: that would cause a mutation or some sort of problem for the cells but what it actually did in the May’s was it would take the chromosomes and it would fuse them back together again okay 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 homostatic 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 and scare quotes or put another way the genome contains sensory and react mechanisms and is controlled by learning algorithms that’s me saying that

[01:07:02]  Red: conventional wisdom this is from page 8 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 cells 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 they are part of the elaborate set of biochemical functions essential for making changes to DNA sequence which do not happen without these functions page 29 unlike the gene 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 I would never have guessed that as the author notes and continue to quote Shapiro here mobile genetic 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 X Xaptation so they could actually take the genes and target locations where they will confer advantageous regulatory functions that’s called Xaptation our data reveal over 280,000 mobile element Xaptations 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

[01:09:22]  Red: Euthyrian radiation we can trace greater than 19 percent to mobile element Xaptations I mean that’s huge right like again from page 9 by the way totally outside of what I had been taught in school okay 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 embedded in the genome resemble genetic engineering more than a mutational random walk that’s from page 9 also okay 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 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 primitive animals and there’s maybe an open question of does this scale to higher organisms okay and in many ways that is the question that we need to be asking

[01:11:07]  Red: 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 rewrite 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 and even we’ve talked about the immune system I’m going to use that as an example 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 and I don’t mean that in a pejorative sense 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 okay so okay so now talking about self -monitoring

[01:13:06]  Red: page 76 he says complex cells with a nucleus so that would be your cariotes 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 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 of mutation as 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

[01:14:24]  Red: the process cares more about certain this makes sense 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 because of this certain areas can mutate faster than others now this isn’t too surprising 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 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 junk DNA is supposed to mutate faster because it doesn’t actually code for proteins but the cells decide how much mutation takes place and they actually decide that certain areas are more important that does extra error correction on those 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 symbiogenesis so perhaps the most important evolutionary step of all took place this is Shapiro from page 6 took place at least 1 billion years ago when two or more cells fused to produce the first

[01:16:12]  Red: eukaryote cell having a defined nucleus a 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 are known as symbiogenesis long championed as an evolutionary force by the recently deceased biologist Lynn Margules so he goes on to say

[01:16:46]  Red: 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 that’s one major reason why the conventional theory is an inadequate explanation of evolution that’s from page 42 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 it’s a tough book so that’s why I put off doing a podcast on it 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 Deutsche 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 and 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

[01:18:45]  Red: and two animals got fused together became a single new organism that replicated in one generation and you started having nucleated cells cells with nuclei and that that was the necessary jumped universality that allowed every single higher organism to come into existence okay 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 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 okay 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

[01:20:19]  Red: 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 I thought that was hilarious 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 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 that was from page 74

[01:22:20]  Red: another interesting thing that he brings up is this concept of modularity so coding 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 okay I need to explain that that when they made changes they would maintain their functions okay even when they were combined in new ways 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

[01:24:26]  Red: did 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 would be rapid ways of copying and modifying the DNA encoding the network components on a whole sale basis although such processes were ruled out a priority by the founders of conventional evolutionary theory they were 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 this is from page 64 now

[01:25:35]  Red: 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 um it creates knowledge in the genes in fact right but doesn’t do it via the sex cells so it doesn’t become part of the germline passed down generations and I use that as a way of showing that the two sources hypothesis David Deutch’s two sources hypothesis is actually incorrect um obviously having talked with many crit rats about this they typically just redefine um knowledge to not include what the immune system actually creates these recipes for antibodies so I suggested well can we at least call them simul knowledge can we call them something that’s like a simulacrum of knowledge and I got a very negative reaction of crit rats even for that they didn’t even want to talk about it they want to even think about 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 it’s happening with you and me today 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 Deutch’s theories on knowledge and why I think the two sources hypothesis really should function as a a poor version of the open problem of open -endedness I think it’s something to it but it’s not what David Deutch thinks it is

[01:27:14]  Red: um 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 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 he doesn’t mean across generations here he means the organism itself evolves they change to adapt to new circumstances 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 but that is correct right that the immune system basically does many evolution of like the cells inside the body trying to find the right recipe to fight the antibody okay 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

[01:29:06]  Red: invaders immune system cells have to produce antibody molecules that combine 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 couldn’t splice DNA but diversity is strictly limited to a specific part of the antibody molecules and again we covered this in a past episode that is exactly how it works it knows to hyper mutate 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 hyper mutation 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 higher animals and then he’s saying look even in the higher animals

[01:31:13]  Red: if you’re looking at body cells non -sex cells soma cells it’s not true there either the body knows how to do hyper mutation 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 instead what we want is we want the genes to have a learning algorithm that can hyper mutate 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 hyper mutation evolution and targeted evolution to try to discover a hyper 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 right so 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 so he then goes on to say the burden of explaining what other cells lack that lymph lymphocytic cell 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

[01:33:11]  Blue: now

[01:33:13]  Red: despite all this evidence let’s put the evidence in scare quotes here Shapiro really seems to have no clear cut testable theory here and I think this is where I am going to take issue with what he’s saying 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 ok so here’s a quote from him natural genetic engineering is not an explanatory principle in this it differs from 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 experiment 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 paparian 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

[01:35:11]  Red: 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 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]  Blue: Bruce this is extremely interesting there’s a lot of details I’m still absorbing what you’re saying this is probably one of our headier more dense episodes I do have one kind of big picture question on this that might be too far out even for us that we can cut if it doesn’t go anywhere but thinking about like does this have implications for you know I’m thinking as you know I’ve read books I think in the last year by Paul Davies Thomas Nagel Phillip 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 so

[01:37:53]  Red: I don’t think anywhere I’ve seen Shapiro try to advocate for a Phillip 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]  Blue: Sure 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 probably don’t want to go there but you know I don’t have that I don’t have skin in the game there It has some definite tie -ins to that viewpoint let me see if I can explain why so

[01:38:28]  Red: we will have to cover the work of Michael how do we pronounce his last name Michael Levin

[01:38:34]  Blue: Levin?

[01:38:36]  Red: in a separate podcast it won’t even be the next podcast maybe I’ll touch upon it in the next podcast 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 Dennis Noble is wrong about evolution by Zach B. Hancock it’s on YouTube go watch it before the next episode where I’m going to go through it

[01:39:01]  Blue: particularly

[01:39:02]  Red: now that I biased you by giving you Shapiro’s viewpoint first I think it’s really helpful to have Shapiro’s viewpoint first it was certainly helpful to me and he has like I said it’s a fairly devastating critique and he kind of defends that no Neo Darwinian evolution is not not wrong and you can easily find criticisms of Dennis Noble Ray Noble, James Shapiro out on the internet, out on YouTube go try to look up Michael Levin you know is wrong you won’t find a thing believe me I’ve tried right 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 that’s not what Levin is doing Levin is 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 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

[01:40:45]  Red: Michael Levin he actually does an interview of Dennis Noble and talks very positively about it right in his different things 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 like it’s like you just don’t do it it’s just not worth the effort this guy’s got way too much evidence okay but he also doesn’t ever put things in kind of the silly ways that Dennis Noble does he never claims Lamarckism is back which by the way just isn’t true like it’s if you define Lamarckism vaguely enough yeah maybe 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 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 pan -psychist or something but in probably better in Deutsche in 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

[01:42:34]  Red: now does this mean we need a new theory of evolution it’s a difficult question to even ask 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

[01:43:37]  Red: so when Dennis Noble says neo Darwinian evolution is wrong I think what we’re going to find when we go through the next up with the 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 get that was that we tweak our existing theories to be correct and we air correct them and from that standpoint I’ve got a problem with Dennis Noble saying neo Darwinian evolution is wrong because it gets it elites 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 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 what I call it neo neo Darwinian evolution but it’s not so different like it down plays 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 that it’s not even that the gene centric views entirely wrong they’re clearly

[01:44:52]  Red: 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’s 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 now what is that new theory that’s emerging I don’t think we have it yet 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 it shouldn’t be so controversial it bothers me that it is particularly in the Deutsche community that because the two sources hypothesis they are so insistent that there is only two sources of knowledge genes and memes and they are missing the plethora the overwhelming number of knowledge creating

[01:46:12]  Red: 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 you know it’s an like we know this, cells are little animals that 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 and 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 and then they’ll try to replicate on their own that’s called cancer, right 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 know 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 you know 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 and it’s a fuzzy boundary it’s not that there is no boundary clearly there are differences between them right and that’s why we have both 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 so and again I don’t think anyone’s challenging any of this like Levin

[01:48:41]  Red: 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 and that’s clearly not what we mean and the word cognition maybe it would be best if we reserved 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 read 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 your 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 it’s all the way down you can start thinking about it being on a spectrum of intelligence

[01:50:13]  Red: and eventually you do get to a rock that has no intelligence so it’s not like he’s being a panpsychist but that we should expect that life came from something in physics that had some level of intelligence you know very very very small level and that that was what life got built out of it wasn’t just chance 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 wrongly maybe I haven’t read Philip’s book yet I’ll read that and then we’ll talk about that I’ve read Bobby Azarian’s book and I think Azarian’s 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 and that’s okay right like Bobby Azarian’s kind of advocating for a sort of cosmic religion that will combine traditional religious ideas into a scientific realm that’s kind of what Deutsch is doing he wouldn’t call it that but it’s not that different right I

[01:52:02]  Red: 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

[01:52:16]  Blue: compared to Goff and Azarian just to put that out there 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]  Red: alright sounds good

[01:52:40]  Blue: okay thank you Bruce

[01:52:43]  Red: bye bye

[01:52:51]  Blue: 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 B Nielsen 01 also please consider joining the Facebook group the mini worlds of David Deutsch where Bruce and I first started connecting thank you

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