05.05.08
S. Kauffman: New book, Reinventing the sacred
Stuart Kauffman: Rethink Evolution, Self-Organization Is Real
Column: Suzan Mazur
In his new book, Reinventing the Sacred, legendary complexity pioneer Stuart Kauffman continues to challenge the view of most biologists that natural selection is the only source of order. However, Kauffman is more charitable than hundreds of other evolutionary scientists (non-Creationists) who contend that natural selection is politics, not science, and that we are in a quagmire because of staggering commercial investment in a Darwinian industry built on an inadequate theory.
True to his research roots in self-organization, Kauffman says life is not based on the replication of DNA and RNA. He also questions whether biology can be reduced to physics, writing that lovers walking along the Seine are not just particles in motion.
He thinks the biosphere constructs itself using sunlight and free energy and that the universe is “ceaselessly creative.” And because the future is not really predictable, Kauffman (writing from the Canadian Rockies) recommends we all calm down, remix science with the ancient Greek model of “the good life, well lived,” and treat ALL in our global culture as sacred.
Stuart Kauffman draws on 40 years of work for the book, from his investigation of snowflakes to “coherence-decoherence” of the conscious mind.
Kauffman tackles evolution of the economy as well. Yes, it’s ceaselessly creative.
He comes clean in a chapter called “Broken Bones” revealing he has advised the US Joint Chiefs of Staff on asymmetric warfare and terrorism (Kauffman’s been a consultant to Los Alamos too). He notes that “all sought to prevent war,” but that “history shows us that war is often excused by a trumped-up atrocity or threatened atrocity.”
I telephoned Stuart Kauffman because I wanted to discuss self-organization, an area he trailblazed in the 1960s at New Mexico’s Santa Fe Institute.
Kauffman began his career as a medical doctor, has been honored as a MacArthur Fellow, a Marshall Scholar and awarded the Gold Medal of the Academia Lincea Rome. He is a founder of the University of Calgary’s Biocomplexity and Informatics Institute and is currently an adjunct professor in the university’s philosophy department.
His three previous books are: The Origins of Order, At Home in the Universe: The Search for the Laws of Self-Organization and Complexity, and Investigations.
Stuart Kauffman spoke passionately about self-organization for much of the 45 minutes of our pre-scheduled talk, taking me on a shamanic flight through his rugged landscapes theory and to the edge of chaos throughout the universe. Then after several pleas (they grew loud) from his handler that my allotted time was up — the vision ended — and Kauffman agreed to move on to his next appointment.
Excerpts from our interview follow.
Suzan Mazur: You were one of the pioneers of self-organization. I’ve looked at your new book, Reinventing the Sacred. You’re thinking in a much bigger way.
Stuart Kauffman: It has to do with getting older. You don’t write a book called Reinventing the Sacred when you’re 30. . . .
Suzan Mazur: Are there alternatives to natural selection?
Stuart Kauffman: I think self-organization is part of an alternative to natural selection. .
Let me try to frame it for you. In fact, it’s a huge debate. The truth is that we don’t know how to think about it.
Suzan Mazur: You said in your forward to Investigations: “Self organization mingles with natural selection in barely understood ways to yield the magnificence of our teeming biosphere. We must, therefore, expand evolutionary theory.”
Stuart Kauffman: I’m still there. . . . Investigations is the weirdest book I’ve ever written and it is the prelude to Reinventing the Sacred. I’ve gone through a trajectory in my life. I started with pure self-organization and I originally thought 40 years ago – let’s see how far we can get without any selection at all. . . . Just think about a snowflake.
Suzan Mazur: You’ve said: “The snowflake’s delicate six-fold symmetry tells us that order can arise without the benefit of natural selection.” So it can arise without natural selection, but it’s not living.
Stuart Kauffman: But it’s not living. Right. There are all sorts of signatures of self-organization. I’ll give you one that very few would doubt I don’t spend time talking about it in any of my books. But here it is.
If you take lipids like cholesterol and you put them in water, they fall into a structure – a liposome, which is called a bilipid membrane, that forms a hollow vesicle. . . . Now if you look at the structure of this bilipid membrane, it’s virtually identical to the bilipid membrane in your cells. So this is a self-organized property of lipids . .
That’s physics and chemistry. . . . And evolution has made use of it to make lipid membranes that balance cells. So that’s a snowflake. It’s hard to look at that and doubt it. Nothing mysterious or mystical. . . .
Suzan Mazur: No genes in the mix.
Stuart Kauffman: Genes by themselves are utterly dead. They’re just DNA molecules. It takes a whole cell in the case of a fertilized egg to grow into an adult. So there’s a lot of physics and chemistry. . . .
And somehow the right answer is that this is a whole integrated system in which matter, energy, information, whatever that means – it turns out to be a very slippery concept – and the control of process is all organized in some way.
The philosopher Immanuel Kant talked about this – the self-propagating organization of process. . . .
Suzan Mazur: You say in Reinventing the Sacred: “I have always believed that the basis of life is deeper and that it rests on catalysis. The speeding up of chemical reactions by enzymes.”
Stuart Kauffman: And then I have a chapter called “The Cycle of Work”.
Suzan Mazur: You say: “My second intuition is that it’s based on some form of collective autocatalysis.”
Stuart Kauffman: Right. So remember that Charles Darwin starts with life. He doesn’t get you to life. . . .
Suzan Mazur: Are you saying form came first and genes later?
Stuart Kauffman: You mean in the origin of life.
Suzan Mazur: Yes.
Stuart Kauffman: I’ll tell you what I think. Current cells use DNA, RNA and proteins. It’s really unlikely that the earliest life on Earth used anything as complicated as contemporary DNA, RNA and protein, because the machinery by which our DNA gets translated into proteins is incredibly complicated and it includes the fact that the genes code for that protein that carries out the translation for those proteins. They’re called amino acid synthesizers. So life couldn’t have started out that complex.
Assuming life started on Earth – it had to start somehow else and evolve into current life. People are working on the origin of life, including me, including my idea on collective autocatalysis. It is a debate about self-organization. But it’s before there is life.
There’s a guy named Reza Ghadiri. And Reza has made a collectively autocatalytic system of proteins where protein 1 catalyzes the formation of protein 2 out of protein 2 parts and protein 2 catalyses the formation of protein 1 out of protein 1 parts.
There’s no molecule in Ghadiri’s system. This system catalyzes its own formation. The set as a whole is collectively autocatalytic. It achieves catalytic closure. That’s a done deal experimentally. Molecular application’s in the bag. Ghadiri at Scripps Research Institute has done it.
Now before he did that he also made a protein that catalyzed its own formation. So that’s both logically possible and that’s in the bag experimentally too.
Next thing to tell you is that a cell really is a collectively autocatalytic whole. There is no molecule in the cell that catalyzes its own formation. The cell as a whole builds itself. . . .
Suzan Mazur: Originally genes were or were not part of the story?
Stuart Kauffman: Nobody knows.
Suzan Mazur: Your sense is that it was more of a mechanical and chemical process first.
Stuart Kauffman: My sense is that it was a catalytic process. Collectively autocatalytic. I have a whole theory about it – chapter 5 in the new book. But that’s just a theory.
What Reza’s done is fact. Whether the theory turns out to be correct, we don’t know. It’s a beautiful theory.
Suzan Mazur: But in the beginning when you had this simple cell there were no genes.
Stuart Kauffman: It depends what you mean by genes. If you mean by a gene a sequence of nucleotides that codes for a protein, I think it’s extremely unlikely that at the start of life — if life started on Earth or wherever it started — that you started with genes that coded for proteins. That’s just utterly remote.
But it may have been that the earliest catalysts were polynucleotides rather than proteins or something else. In that sense of gene – yes. But they wouldn’t have coded for proteins. It’s just remote.
So what we’re talking about is how do you get life in the first place?
Suzan Mazur: Where do the work cycles fit in?
Stuart Kauffman: Think about choo-choo trains. A train uses heat. It turns it into mechanical work train pistons. That’s a work cycle. It uses the transfer of heat from a hot to a cold place. And it manages to get the pistons to go around.
It’s been around since 1830. A guy named Sadi Carnot worked out the principles of a thermodynamic work cycle.
I think that an essential part of life is that it does work cycles. It’s not enough that life is markedly reproducing. . . Every free living cell, in fact, all the cells in your body do work cycles – chemical work cycles and mechano-chemical work cycles. And that’s missing from what most people think about life. . . Buried in this are the roles of self-organization and natural selection.
Selection couldn’t have played a role before there were organisms. You couldn’t have had natural selection because there were no organisms. It’s a different debate whether some other form of selection for chemical stability might have played a role.
There are some physicists who are asking questions like: Is natural selection an expression of some more general process? Like entropy production. And it’s all up in the air. But at least people are thinking about it. Meanwhile, we’ve got self-organization.
Suzan Mazur: Are evolution and development the same thing?
Stuart Kauffman: Sure.
Suzan Mazur: You mention Nobel laureate Murray Gell-Mann in your book. I know you were colleagues at the Santa Fe Institute. Do you think similarly about self-organization?
Stuart Kauffman: Probably not. . . . Murray is a profound reductionist. He’s been a major voice in the Santa Fe Institute and is a superb scientist. I’m not a reductionist. Reductionism meaning everything is due to the physical laws down there.
What’s happening is that the physics community is dividing now. . . .
But let me tell you where I started 40 years ago. And where it is now. I literally started on this when I was 24 and I’m 68. . . That was about 1964.
You know that cells get to be different from one another – cell differentiation. You make liver cells and kidney cells and spleen cells. And the question at the time was: So how do cells get to be different?
We thought – different cells get different genes from the fertilized egg. That turned out to be false. Just wrong. All the cells in your body have the same genes.
Suzan Mazur: Right.
Stuart Kauffman: Now it’s essential to know that different cells in your body make different proteins. Red blood cells make hemoglobin. That’s because different genes are active. Where active means making more protein.
Two guys who got the Nobel prize for this, Francois Jacob and Jacques Monod, in 1961 showed in bacteria that genes could turn one another on and off. This is absolutely essential now. One gene can make a protein that binds to a little DNA region near another gene and turn the other gene on or turn it off.
Suzan Mazur: Right.
Stuart Kauffman: So there’s a sense — leaving out the rest of the physics and chemistry of the cell, which we cannot do, but just for the moment — then you could imagine genes turning one another on and off.
Jacob and Minod published a document in which they said imagine you’ve got two genes.
You and I are the two genes. And we’re both spontaneously active, if nothing happens to us. But Stu makes the Stu protein which goes over and binds next to the Suzan gene and shuts Suzan off. And vice versa. Suzan makes a protein that shuts Stu off.
So it’s a tiny circuit, a genetic circuit. You can think of it like an electrical circuit. Then that circuit – and I think you can see this immediately – has two alternative steady states. Suzan on. Stu off. And Stu on. Suzan off. Can you see it?
Suzan Mazur: I think so.
Stuart Kauffman: So what they said was – look the same genome is giving rise to two patterns of gene activity. Suzan on. Stu off. And the other way around.
Suzan Mazur: Right.
Stuart Kauffman: This could be what controls cell differentiation. And they revolutionized the whole field of developmental biology with that paper.
I came along about a year later. And what I said was – we used to think 100,000 genes. We now know it’s about 25,000 or 30,000 genes. And I thought, well, there’s some sort of regulatory circuitry among these 25,000 or 30,000 genes. And there is. Forty-four years later we know something about it.
Imagine you’ve got 30,000 genes and somehow they’re turning one another on and off in some complicated way. Okay. What I did — this is Stu’s early foray into self-organization. . .
Suzan Mazur: So how many of the 25,000 or 30,000 are doing the turning on and off?
Stuart Kauffman: Nobody knew 40 years ago. . . Here’s what we know now. In the human, there are approximately 2,000 genes that seem to play the role of turning one another on and off and the rest of the genes on and off. . . . They’re called transcription factors. And they’re also regulating the other genes.
Hemoglobin is probably not regulating anything. It’s regulated, but not regulating.
Suzan Mazur: Right.
Stuart Kauffman: So here’s what I did. This is an essential core of current biology.
Suzan Mazur: The endogenous variables. . . .
Stuart Kauffman: Right. You also have all the proteins. . . . Let’s suppose that there are 25,000 genes. And 2,000 of them are playing the role of regulating one another and regulating the other 22,500. Just imagine that genes can only be on or off. That’s false. That’s an idealization. Then how many possible patterns of gene activity are there?
Well there’s 25,000 genes. So each could be on or off. So there’s 2×2x2 25,000 times. Well that’s 2 to the 25,000th. Right?
Suzan Mazur: Right.
Stuart Kauffman: Which is something like 10 to the 7,000th. Okay? There’s only 10 to the 80th particles in the whole universe. Are you stunned?
Suzan Mazur: It’s getting pretty staggering . . .
Stuart Kauffman: So, 25,000 is plenty if you start thinking about all the possible combinations of their activities. It’s super- hyper-astronomical.
Suzan Mazur: Right.
Stuart Kauffman: The next idea you need is somehow this network among the genes is controlling their activities. We don’t know what this network is. My colleagues and I have just published a paper in which we think we maybe know. We have the first sketch of what this regulatory network looks like. . . .
Anyway here’s what I did when I was young. I asked the following radical question. . . I said does this regulatory network have to be really really special and tuned by natural selection to give rise to normal development? Or could it be spontaneously self-organized so that there’s a huge set of possible networks and they’re sort of all good enough? In other words, is it a spontaneous self-organized property of complex networks that they just do the right thing? . . .
So I was saying ignore selection. Let’s just ask whether or not there’s a self-organized property and complex network of genes.
And what I showed in my mid 20s – I was 27 when I published it for the first time – was that my intuition was right. There really are. And so I modeled genes like they were lightbulbs, which they’re not. And I made random lightbulb networks.
They’re called Boolean networks because of a guy named George Bool. We now know a vast amount about the behavior of really complicated Boolean networks. Even random Boolean networks. So I’m just going to tell you a couple of things.
Suzan Mazur: Okay.
Stuart Kauffman: You know how I had you and me turning one another on and off and we had two steady states.
Suzan Mazur: Yes.
Stuart Kauffman: So the fancy word for those two steady states is attractor. That’s the mathematical word. And you can think of it like a mountain region with a bunch of lakes in it. And each lake is like an attractor. And you know how streams flow into a lake. So in the space of all the possible pattern of gene activity, most of them constitute streams that flow into the attractor lakes. So the hypothesis I’ve had for 45 years, partially taken from Jacob and Monod, is that cell types – livers, kidneys, etc. – are these attractors.
Suzan Mazur: I see.
Stuart Kauffman: So one lake is a liver. Another lake is a kidney. Another lake is. . . You with me?
Suzan Mazur: Yes.
Stuart Kauffman: So we’ve got evidence that that hypothesis is true. Cell types look like they’re attractors. Now, if that’s true, cells getting to be different from one another happens in basically one of two ways.
You hop out of one lake into a mountain pass and flow down a creek into another lake. And then there’s a fancier way in which you wiggle the mountains and change where the lakes are. That’s called a bifurcation.
So this is sort of the two ways that it can happen. And we’ve got evidence for both. So we’re beginning to understand that the cell and the organism is a very complicated set of processes activating and inhibiting one another. It’s really much broader than genes.
Suzan Mazur: And form arises?
Stuart Kauffman: To say we know nothing about how form arises is wrong. There’s been 70 years of superb developmental biology. . . .
Suzan Mazur: Can you, for instance, do plastic surgery embryonically where the correction will take – say to an arm? . . .
Stuart Kauffman: You mean could you conceivably take a thalidomide baby and do surgery and make it grow a normal arm?
Suzan Mazur: Yes.
Stuart Kauffman: Conceivably.
Suzan Mazur: You can?
Stuart Kauffman: No. Nobody’s ever done it. But it doesn’t seem impossible. And this has to do with what I’m working on right now. A lot of people are working on controlling and steering cell fates. That’s exactly what I’m doing right now. I’m trying to get cancer cells to differentiate into normal cells. I’m trying to get a new way to treat cancer. . . .
But to get back to self-organization, I showed two main things. Years ago I showed lakes of the kind you would need to explain cell types as lakes as attractors. And we know that cell types are actually attractors. It’s early evidence. I think that it’s very likely that it’s true. . . .
Now I’m going to tell you something that’s just stunning. All of this work that has been done on random Boolean knots — it turns out that they can behave in three broad ways: ordered, chaotic, and there’s a phase transition between the ordered regime and the chaotic regime where cells are poised at the “edge of chaos.”
That’s a phrase we came up with at Santa Fe Institute. A whole bunch of us – Chris Langdon, Norman Packard and I are the three main people who focused on all of this.
I have ever since 1987 believed that cells are poised on the edge of chaos. You’ll find it in my first two books.
The easiest book of mine to read, by the way, is my second book: At Home in the Universe, which a lot of people have read. Al Gore read it. I wrote it with Gore in mind. . . .
So there’s this poised edge of chaos state between order and chaos. Here’s what we’re beginning to know now, 20 years later. There’s evidence that cells are at the edge of chaos. The mathematical term is critical. Ordered, chaotic and critical. Edge of chaos will do.
So two main papers have been published. One came out just a couple of weeks ago and I’m one of the authors on it . . It is the first direct evidence that maybe cells are at the edge of chaos. There’s really dramatic evidence. It’s gorgeous. But it’s only one example.
Suzan Mazur: Can we draw conclusions?
Stuart Kauffman: No. But could you say – neat, let’s explore it further? Yes.
Suzan Mazur: If it’s right?
Stuart Kauffman: I suspect, I hypothesize that we may have found something general about life anywhere in the universe. That cells or whatever the analog of cells are anywhere are going to have to be at the edge of chaos because they could do all sorts of neat things.
They can coordinate the most complicated behavior. They can propagate information most efficiently. There are all sorts of neat reasons why it’s incredibly advantageous to be at the edge of chaos.
Notice that I just used the word advantageous. Now you start hearing natural selection creep in. So it turns out that to be at the edge of chaos, networks have to be pretty special. They can’t just be any old network. They have to be tuned to be at the edge of chaos.
And what could possibly be do that tuning? Well, natural selection, because it’s highly advantageous. So here is a marriage of self-organization and selection. Both are necessary.
In other words, the self-organization part is that large classes of networks have a property that they’re either ordered, chaotic or edge of chaos – critical. . . . So self-organization affords the capacity to be critical and then selection gets it and maintains it. And maybe it’s so general that it’s a law for any biosphere.
Suzan Mazur: So natural selection exists throughout the universe?
Stuart Kauffman: Well, yes, wherever there’s life. But notice that there’s self-organization too. . .
There are people who are spouting off as if we know the answer. We don’t know the answer.
Suzan Mazur: So you’re saying we should enjoy life.
Stuart Kauffman: Well, we should enjoy life. But we have to rethink evolutionary theory. It’s not just natural selection. Self-organization is real. . .
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Suzan Mazur says her interest in evolution began with a Cessna single engine flight into Olduvai Gorge, across a closed Kenyan-Tanzanian border, to interview the late paleoanthropologist Mary Leakey. Their meeting followed discovery of the 3.5 million year old hominid footprints by Leakey and her team at Laetoli http://en.wikipedia.org/wiki/Laetoli. Mazur says Leakey was the only reason the Tanzanian authorities agreed to give landing clearance. Her reports have since appeared in the Financial Times, The Economist, Forbes, Newsday, Philadelphia Inquirer, Archaeology, Connoisseur, Omni and others, as well as on PBS, CBC and MBC. She has been a guest on McLaughlin, Charlie Rose and various Fox Television News programs. Email: sznmzr@aol.com