Lex Fridman PodcastLee Cronin: Controversial Nature Paper on Evolution of Life and Universe | Lex Fridman Podcast #404
EVERY SPOKEN WORD
150 min read · 30,137 words- 0:00 – 1:15
Introduction
- LCLee Cronin
... every star in the sky-
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
... probably has planets.
- LFLex Fridman
Yep.
- LCLee Cronin
And life is probably emerging on these planets. But I think the commentorial space associated with these planets is so different. Our causal cones are never gonna overlap, or not easily. And this is the thing that makes me sad about alien life, why- it's why we have to create alien life in the lab as quickly as possible, because I don't know if we are gonna be able to- be able to build, um, architectures that will intersect with alien intelligence and architectures.
- LFLex Fridman
In- in intersect, you- you don't mean in time or space?
- LCLee Cronin
Time and the ability to communicate.
- LFLex Fridman
So the ability to communicate.
- LCLee Cronin
Yeah. My biggest fear, in a way, is that life is everywhere, but we've become infinitely more lonely because of our scaffolding in that commentorial space.
- LFLex Fridman
The following is a conversation with Lee Cronin. His third time on this podcast. He is a chemist from University of Glasgow who is one of the most fascinating, brilliant, and fun to talk to scientists I've ever had the pleasure of getting to know. This is a Lex Fridman podcast. To support it, please check out our sponsors in the description. And now, dear friends, here's Lee Cronin.
- 1:15 – 21:45
Assembly theory paper
- LFLex Fridman
So your big assembly theory paper was published in Nature.
- LCLee Cronin
Yeah.
- LFLex Fridman
Congratulations.
- LCLee Cronin
Thanks. (laughs)
- LFLex Fridman
It created, uh, I think it's fair to say, a lot of controversy, but al- also a lot of interesting discussion. So maybe I can try to summarize assembly theory and you tell me if I'm wrong.
- LCLee Cronin
Go for it.
- LFLex Fridman
(laughs) So assembly theory says that if we look at any object in the universe, any object, that we can quantify how complex it is by trying to find the number of steps it took to create it, and also we can determine if it was built by a process akin to evolution by looking at how many copies of the object there are.
- LCLee Cronin
Yep. That's spot on. Yep.
- LFLex Fridman
Spot on?
- LCLee Cronin
Spot on.
- LFLex Fridman
I was not expecting that. Okay. So le- let- let's go through definitions.
- LCLee Cronin
(laughs)
- LFLex Fridman
So there's a central equation that I'd love to, uh, talk about, but definition wise, what is an object?
- LCLee Cronin
(laughs) Um, yeah. Uh, an object, so from- so if I'm gonna try to be as meticulous as possible, objects need to be finite, um, and they need to be decomposable into sub-units. All human made artifacts are objects. Um, is a planet an object? Probably yes in the- if you scale out. So an object is finite and countable and decomposable, um, I suppose mathematically. But, uh, yeah, I still- I still wake up some days and go- to- think to myself, "Wh- what- what is an object?" Because it's- it's- it's n- a non-trivial, um, question.
- LFLex Fridman
"Persists over time..." I'm quoting from the paper here. "An object is finite, is distinguishable."
- LCLee Cronin
Mm-hmm.
- LFLex Fridman
Sure, that's a weird adjective. Distinguishable. (laughs)
- LCLee Cronin
We've had so many people h- help- offering to rewrite the paper after it came out.
- LFLex Fridman
Yeah.
- LCLee Cronin
You wouldn't believe it. It's so funny. (laughs)
- LFLex Fridman
"Persists over time and is breakable such that the set of constraints to construct it from elementary building blocks is quantifiable. Such that the set of constraints to construct it from elementary building blocks is quantifiable."
- LCLee Cronin
The history is in the objects. It's kinda cool, right?
- LFLex Fridman
So, okay, so what defines the object is its history or memory.
- LCLee Cronin
Yeah.
- LFLex Fridman
Whichever is the sexier word.
- LCLee Cronin
I'm happy with both, depending on the day. (laughs)
- LFLex Fridman
Okay. So the set of steps it took to create the object, so there's a sense in which every object in the universe has a history.
- LCLee Cronin
Yep.
- LFLex Fridman
And that is part of the thing that is used to describe its complexity.
- LCLee Cronin
Yeah.
- 21:45 – 34:57
Assembly equation
- LFLex Fridman
before we get too far, let's talk about the assembly equation. (sighs) Okay. How should we do this? Uh, lemme just even read that part of the paper. "We define assembly as the total amount of selection necessary to produce an ensemble of observed objects, quantified using equation one." The equation basically has A on one side, which is the assembly of the ensemble.
- LCLee Cronin
Mm-hmm.
- LFLex Fridman
And then, a sum from one to N, where N is the total number of unique objects, and then there is a few variables in there that include the assembly index, the copy number, which we'll talk about. That's an interesting, I don't remember you talking about that. That's an interesting addition and I think a powerful one. Has to do with what? That you can create pretty complex objects randomly.
- LCLee Cronin
Mm-hmm.
- LFLex Fridman
And in order to know that they're not random, that there's a factory involved, you need to see a bunch of them.
- LCLee Cronin
Yep.
- LFLex Fridman
That's- that's the intuition there. It's an interesting intuition. And then, uh, some normalization. What else is it? And...
- LCLee Cronin
N minus one, just to make sure that more than one object, one object could be a one-off and random.
- LFLex Fridman
Yep.
- LCLee Cronin
And then you have more than one identical object, that's interesting.
- LFLex Fridman
When- when there's- when there's two of a thing.
- LCLee Cronin
Two of the thing...
- LFLex Fridman
That's interesting.
- LCLee Cronin
... is super important, especially if the ind- index, assembly index is high.
- LFLex Fridman
So, uh, we could say, several questions here. One, let's talk about selection.
- LCLee Cronin
Mm-hmm.
- LFLex Fridman
What is this term selection? What is this term evolution that we're referring to? Which- which aspect of Darwinian evolution are we referring to that's interesting here?
- LCLee Cronin
So, yeah, so (laughs) this is probably, what, you know, the paper, we should talk about the paper for a second. The paper did, what it did is it kind of annoyed, um, well it didn't annoy, I mean, it got attention. And obviously, angry people, the angry people were annoyed.
- LFLex Fridman
There's angry people in the world, that's good.
- LCLee Cronin
So what happened is the evolutionary biologists got angry. We were not expecting that, 'cause we thought evolutionary biologists would be cool. I knew that some, not many, computational complexity people will get angry 'cause I'd kinda been poking them, and maybe I deserved it. But I was trying to poke them in a productive way.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
And then, the physicists kinda got grumpy because the initial conditions tell everything. The prebiotic chemists got slightly grumpy because there's not enough chemistry in there. Then finally, when the creationists said it wasn't creationist enough, I was like...
- LFLex Fridman
Right.
- LCLee Cronin
"I've done my job."
- LFLex Fridman
The phys- well, you're saying the physics they say... Because you're basically saying that physics is not enough to tell the story of how biology emerges?
- LCLee Cronin
I think so. Classic phy-
- LFLex Fridman
And then they said, "A few physics is the beginning and the end of the story."
- LCLee Cronin
Yeah.
- LFLex Fridman
Okay.
- LCLee Cronin
So what happened is, the r- reason why people put the phone down on the call for the paper, if you're, if you're view- reading the paper like a phone call, they got to the abstract.
- 34:57 – 53:16
Discovering alien life
- LCLee Cronin
- LFLex Fridman
Okay. What- what about if- if I show up to your planet, we'll go to Mars or some other planet from a different solar system, and how do we use assembly index there to discover alien life?
- LCLee Cronin
Um, in, very simply actually. If we, let's say we'll go to Mars with a mass spectrometer with a sufficiently high resolution. So what you have to be able to do... So a good thing about mass spec, um, is that you can, um, select a molecule from the mass, and then if it's high enough resolution, you can be more and more sure that you're just seeing, um, identical copies. You can count them, and then you fragment them and you count the number of fragments and look at the molecular weight. And the higher the molecular weight, and the higher the number of fragments, the higher the assembly index. So if you go to Mars and you take a mass spec with a high enough resolution and you can find molecules... And I'll give- a- a gu- a guide on earth. If you could find molecules, say, greater than 350 molecular weight with more than 15 fragments, you have found artifacts that can only be produced, at least on earth, by life. Now you would say, "Oh, well, maybe the geological process," I would argue very vehemently that that is not the case, but we can say, look, if you don't like the cutoff on earth, go up higher, 30, 100.
- LFLex Fridman
(laughs)
- LCLee Cronin
Right? Because there's gonna be a point where you can find a molecule with so many different parts, the chances of you getting a molecule that has 100 different parts, um, and finding a million identical copies, you know, that's- that's just impossible, that could never happen in an infinite set of universes.
- LFLex Fridman
C- can you just linger on this copy number thing? A million different copies?What do you mean by copies, and why is the number of copies important?
- LCLee Cronin
Yeah. That- that was so interesting in that, um, I always understood the copy number is really important but I never explained it properly, (laughs) for ages. Um, and it be- I kept having this... It goes back to this, if I give you a, um, a- a- I don't know, a really complicated molecule, and I say "It's complicated," you could say, "Hey, that's really complicated." But is it just really random?
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
And so, so I realized that ultimate randomness and ultimate complexity are indistinguishable, until you can, um, you can see a structure in the randomness, so you can see copies.
- LFLex Fridman
So copies implies structure?
- LCLee Cronin
Yeah.
- LFLex Fridman
(inhales)
- LCLee Cronin
The factory.
- LFLex Fridman
I mean, there's a deep, profound thing in there 'cause like if you just have a random, random process, you're going to get a lot of complex, beautiful, sophisticated things.
- LCLee Cronin
Mm-hmm.
- LFLex Fridman
What makes them complex in the way we think life is complex or, um... Yeah. S- s- something like a, a factory that's operating under a selection processes, there should be copies. Is there, like, some looseness about copies? Like, what does it mean for two objects to be equal?
- LCLee Cronin
It- it's- it's all to do with the- the telescope or the microscope you're using. And so at the r- the maximum resolution... So in the nice thing about, the nice thing about chemists is they have this concept of the molecule, and they're all familiar with a molecule. And molecules, you can hold, uh, you know, in your hand, um, lots of them-
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
... identical copies. Uh, a molecule is actually a super important thing in chemistry to say, look, you can have a mole of a molecule, so an Avogadro's number of molecules, and they're identical. What does that mean? That means that their molecular composition, the bonding, and so on, the configuration is all... is- is indistinguishable. You can hold them together, you can overlay them. So the way I do it is if I say, "Here's a bag, um, of 10 identical molecules. Let's prove they're identical." You pick one out of the- the- out of the bag and you basically observe it using some technique, and then you put it- you take it away and then you put- take another one out. If you observe it using technique and you see no differences, they're identical. It's really interesting to get right because if you take, say, two molecules, molecules can be in different vibrational and rotational states, they're moving all the time. So with this respect, identical molecules have identical bonding.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
In this case, we don't even, uh, um, talk about chirality 'cause we don't have a chirality detector. So two ident- identical molecules in one conception assembly theory basically, um, considers both hands as being the same. Um, but of- but of course they're not, they're different. As soon as you have a chiral d- distinguisher detect- to detect the left and the right hand, they become different. And so it's to do with the detection system that you have and the resolution.
- LFLex Fridman
So I wonder if there's an art and science to the which detection system is used when you show up to a new planet.
- LCLee Cronin
Yeah, yeah, yeah.
- LFLex Fridman
So like you- you're talking about chemistry a lot today. We have kind of standardized detection systems, right? Of how to compare molecules. So when you start to talk about emojis, and language, and, uh, mathematical theorems, and, uh, I don't know, more sophisticated things at- at different scale, at a smaller scale than molecules, at a larger scale than molecules, uh, like what detection... Like if- if we look at the difference between you and me, Lex and Lee, are we the same? Are we different?
- LCLee Cronin
Sure. I mean, of course we're different close up. But if you zoom out a little bit-
- LFLex Fridman
Yeah.
- LCLee Cronin
... we'll morphologically look the same.
- LFLex Fridman
Yeah.
- LCLee Cronin
Not- not... Well, you know, height and characteristics, hair length, stuff like that.
- LFLex Fridman
Well- well also, like, the species and...
- 53:16 – 1:01:12
Evolution of life on Earth
- LCLee Cronin
because one of the things we've done, um, it's a secret but I can tell you (laughs) .
- LFLex Fridman
(laughs)
- LCLee Cronin
I think it's a- (laughs) .
- LFLex Fridman
Nobody's listening. (laughs)
- LCLee Cronin
Well, is that we've just mapped the tree of life using assembly theory.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
'Cause everyone said, "Oh, that, you can't do it from biology." And what we were able to do is, so you, I think there's three way- well, two ways of doing tree of life traphi- uh, um, well, three ways actually.
- LFLex Fridman
Yeah, what's the tree of life?
- LCLee Cronin
So the tree of life is basically, um, tracing back the history of life on Earth, all the different species going back what, who evolved from what, and it all goes all the way back to the first kind of life forms, and they branch off, and like you have plant kingdom, the animal kingdom, the fungi sys- uh, kingdom, you know, and different, and different branches all the way up. Um, and the way this was classically done, and I'm no evolutionary biologist, evolution biologists are very, uh, tell me every day-
- LFLex Fridman
(laughs)
- LCLee Cronin
... at least 10 times, um, uh, I wanna be one though. I kinda like biology, it's kinda cool, but-
- LFLex Fridman
Yeah, it's very cool.
- LCLee Cronin
Um, but basically-
- LFLex Fridman
Evolutionary.
- LCLee Cronin
... what, uh (laughs) , what Darwin and Mendeleev and all these people do is just they draw pictures, right? And they collect taxa. They just con- they were able to draw pictures and, and say, and say, "Oh, these look like common classes."
- LFLex Fridman
Yeah.
- LCLee Cronin
Then... (laughs)
- LFLex Fridman
They're artists, really. They're just, you know.
- LCLee Cronin
But they're, they're, but they're, they were able to find out a lot, right? In looking at vertebrates, invertebrates, Cambrian explosion, all this stuff. And then, um, then came the genomic revolution, and suddenly everyone used gene sequencing, and Craig Venter's a good example. I think he's gone around the world in his yacht just taking up samples, looking for new species, where he's just found new species of life just from sequencing. It's amazing.... so you have taxonomy, you have sequencing, and then you can also do a little bit of kind of molecular, um, uh, kind of archeology like, you know, measure the samples and- and kind of form some inference. What we did, um, is we were able to fingerprint... So we took a load of random samples from all of biology, and we used mass spectrometry. And what we did now is not just look for individual molecules, but we looked for coexisting molecules where they hadn't looked at their joint assembly space, and where we- we were able to cut them apart and re- and undergo recursion in the mass spec and infer some relationships, and we were able to recapitulate the tree of life using mass spectroscopy. No sequencing and no drawing.
- LFLex Fridman
All right. Can you, uh, try to say that again with a little more detail? So recreating, what does it take to recreate the tree of life? What does the reverse engineering process look like here?
- LCLee Cronin
So what you do is you take an unknown sample, you bung it into the mass spec, you get a... 'Cause this comes from what you're asking, like what do you see in E. coli.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
And so in E. coli, you don't just see, it's not a, it's not a, it's not the- the most sophisticated, um, cells on- on earth make the most sophisticated molecules. It is the coexistence of lots of complex molecules above a threshold.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
And so what we realized is you could fingerprint different life forms. So fungi make really complicated molecules. Why? 'Cause they can't move. They have to make everything on site.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
Um, whereas, you know, some animals are like lazy, they can just go eat the fungi-
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
... and they don't need to- to make very much. And I, um, and so what you do is you look at the... So you take, I don't know, the fingerprint, maybe the top number of high molecular weight molecules you find in the sample, you fragment them to get their assembly indices, and then what you can do is you can af- infer common origins of molecules. You can do a kind of molecular, um, um... When the reverse engineering of the assembly space, you can infer common roots and look at what's called the joint assembly space. Um, but what, let's translate that into the experiment. Take a sample, bung it in the mass spec, take the top, say, 10 molecules, fragment them, and then, and that gives you one fingerprint. Then you do it for another sample, you get another fingerprint. Now the question is, you say, "Hey, are these samples the same or different?" And that's what we've been able to do, and, um, by basically looking at the assembly spaces these molecules create. Without any knowledge of assembly theory, you are unable to do it. With a knowledge of assembly theory, you can cons- reconstruct the tree.
- LFLex Fridman
Uh, how does- how does knowing if they're the same or different give you the tree?
- 1:01:12 – 1:18:50
Response to criticism
- LFLex Fridman
- LCLee Cronin
Yeah. (laughs)
- LFLex Fridman
So, y- you've been saying a lot of chemistry examples for assembly theory. What if we zoom out and look at a bigger scale of an object?
- LCLee Cronin
Mm-hmm.
- LFLex Fridman
Ah, you know, like really complex objects, like humans. Or living organisms that are made up of, you know, millions or billions of other organisms. How- how do you try to apply assembly theory to that?
- LCLee Cronin
At the moment, um, we're- we're thi- we should be able to do this to morphology and cells, so we're looking at cell surfaces. And really, um, try and extend further. It's just that, you know, we worked so hard to get this paper out and people to start discussing the ideas, and I was, and I... (laughs) But- but it's kinda funny because I think the peb- the- the penny is falling on this. So, yeah, so, th-
- LFLex Fridman
What's that even... What- what- what's it mean for a penny to be fallen?
- LCLee Cronin
Well, I mean, you know, the- the- the penny's dropped, right? 'Cause a lot of people were like, "It's rubbish, it's rubbish. You've insulted me. It's wrong." And I'm- and I, you know, I mean, the paper got published on the 4th of October.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
It had 2.3 million engagements on Twitter.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
Right? And it's been downloaded over a t- few hundred thousand times. And someone actually said to me, wrote to me and said, "This is an example of really bad writing, and what not to do." And I was like, "If all of my papers got read this much," 'cause that's the objective, if I have a publishing a paper, I want people to read it, "I wanna write that badly again."
- LFLex Fridman
Yeah. I don't know what's the deep insight here about the negativity in the space. I think it's probably the immune system of the scientific community making sure that there's no bullshit that gets published. That's-
- LCLee Cronin
Uh...
- LFLex Fridman
And then it can overfire, it can do a lot of damage, it can shut down conversations in a way that's not productive.
- LCLee Cronin
We are gonna go back... I mean, I'll answer your question about the hierarchy and assembly, but let's go back to the reception. People saying the paper was badly written, I mean, of course we could improve it. We could always improve for clarity.
- LFLex Fridman
Let's go there before we go to the hierarchy.
- LCLee Cronin
Yeah.
- LFLex Fridman
Um, you know, it has been criticized quite a bit, the paper. Uh, what has been some criticism that you found most powerful? Like, that you can understand and... Can you explain it?
- LCLee Cronin
The... Yes. The most exciting criticism came from the evolutionary biologists telling me that they thought that- that, uh, it w- origin of life was a solved problem. And I was like, "Whoa, we're really onto something, because it's clearly not." And when you poke them on that, they just said, "No, you don't understand evolution." And I said, "No, no, I don't think you understand that evolution had to occur before biology, and we need... There's a gap."
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
That was really, for me, that misunderstanding, and that- that did cause an immune response, which was really interesting. Um, the second thing was the fact that physicists... Well, the physicists were actually really polite, right? Really nice about it. But they just said, "Heh, we're not really sure about the initial conditions thing, but this is a really big debate that we should certainly get into because, you know, the in- the- the- the emergence of life was not encoded in the initial conditions of the universe."
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
Um, and it can't, and I think assembly theory shows why it can't be. I'll say-
- LFLex Fridman
O- okay.
- LCLee Cronin
... I'll say that ag-
- LFLex Fridman
Sure. If you, if you could say that again.
- LCLee Cronin
I, the- the- the origin of the- the emergence of life was not and cannot, in principle, be encoded in the initial conditions of the universe.
- LFLex Fridman
Just to clarify what we mean by life is like, what, high assembly index objects?
- LCLee Cronin
Yeah. And this goes back to your favorite subject.
- 1:18:50 – 1:30:40
Kolmogorov complexity
- LCLee Cronin
- LFLex Fridman
Okay. Another piece of criticism, or by way of question is, how is assembly theory, or maybe assembly index different from Kolmogorov complexity? So for people who don't know Kolmogorov complexity of an object is the length of a shortest computer program that produces the object as output.
- LCLee Cronin
Yeah, I'm- I- I seem to- there seems to be a disconnect between the computational approach. So yeah, so Kolmogorov measure-... requires a Turing machine.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
Requires a computer, um, and that's one thing. And the other thing is, um, assembly theory is supposed to trace the process by which life evolution emerged, right? That's the main thing there. There are lots of other layers. So, so Kolmogorov complexity, you can, you can approximate Kolmogorov complexity, but it's not really telling you very much about the actual, um, it, it's really telling you about, like, your da- your dataset, compression of your dataset.
- LFLex Fridman
Sure.
- LCLee Cronin
And so, that doesn't really help you identify the, the turtle, in this case, is the computer.
- LFLex Fridman
Mm-hmm.
- LCLee Cronin
And so what assembly theory does is... I- I'm gonna say, (laughs) it's a trigger warning for anyone listening is, uh, uh, who loves complexity theory, I think that we're gonna show that AIT is a very important subset of assembly theory, because here's what happens. The, um, I think that it- assembly theory allows us to build, um, go, uh, understand when we're selections occurring, selection produces, um, factories and things, factories in the end produce computers, and you can go, then algorithmic information theory comes out of that. The frustration I've had with, with looking at life through this kind of information theory is it doesn't take into account causation. So the main difference between-
Episode duration: 3:19:21
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