[Hplusroadmap] Fwd: Stuart Kauffman: Rethink Evolution, Self-Organization Is Real

[Bryan Bishop]

---------- Forwarded message ----------
From: Tony Smith <ts at meme.com.au>
Date: Mon, May 5, 2008 at 5:57 PM
Subject: Re: FYI
To: Bryan Bishop <kanzure at gmail.com>




On 06/05/2008, at 1:31 AM, Bryan Bishop wrote:
On Mon, May 5, 2008 at 6:55 AM, Tony Smith <ts at meme.com.au> wrote:
http://www.scoop.co.nz/stories/HL0805/S00052.htm

Google tells me that it's a new Kauffman book, but the page doesn't
load for me, and it's not on the Internet Archive.


S Kauffman: Rethink Evo, Self-Organization Is Real
Monday, 5 May 2008, 1:21 pm
Column: Suzan Mazur

Stuart Kauffman: Rethink Evolution, Self-Organization Is Real

By Suzan Mazur


Stuart Kauffman in Santa Fe

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
2x2x2 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. . .

*************

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 at aol.com







Tony Smith

Complex Systems Researcher

Meme Media

Melbourne, Australia


http://www.meme.com.au/