Woese: Life could have started “millions of times”

In Ron Kotulak’s article below, he interviews Carl Woese about the latter’s skepticism concerning the monophyly of life on Earth. “Woese next went after a big stumbling block in classical evolution,” writes Kotulak. “Darwin’s doctrine postulated that all living things eventually could be traced back to a single founding cell.” Woese says No — life could have started “millions of times,” and no single cell was ancestral to all organisms on Earth.

THE COSMIC CONVERSATION
How can lifeless particles evolve into living things? They basically
talk themselves into it, a group of scientists say.

By Ronald Kotulak
Chicago Tribune

Published January 8, 2006
This story contains corrected material, published Jan. 13, 2006.
Additional material published Jan. 10, 2006:

CORRECTIONS AND CLARIFICATIONS

A quotation in a Chicago Tribune Magazine story Sunday about
communication among particles at the atomic and molecular levels
was mistakenly attributed to Cornell University physicist Paul
Ginsparg. In fact the quoted material was part of a question
posed by reporter Ronald Kotulak during a lengthy e-mail
exchange with Ginsparg, whose views differed.

THE ONLY REALLY BAD ARGUMENT University of Chicago
physics professor Henry Frisch can remember his parents having
was purely academic. The question: If a lightning bolt struck a
primitive soup of basic chemical building blocks enough times,
is there a chance it could eventually make a baby?

Frisch’s father, an MIT physicist immersed in the knowledge that
inanimate atoms combine to make living things said the probability
was vanishingly small, but it was not zero. Given enough chances,
such an event could conceivably arrange all the necessary atoms
in the right order to produce an infant.

His mother, a Harvard biologist steeped in the choreography of
living cells, said that was utter nonsense. Life evolved slowly from
the very simplest forms to more complex ones. There isn’t an
extremely small chance that lightning striking a concoction of
chemicals, even an infinite number of times, could produce a baby.
There was no chance.

“They were sailing along and they ran onto a rock that they couldn’t
deal with,” Frisch said.

Although Frisch didn’t take either parent’s side, he now finds himself
drawn into an offshoot of the lightning-bolt question: How could
something as complex as intelligence and consciousness evolve
from the inorganic, elementary particles of the early universe?
And is intelligence limited to humans and some animals, or do plants
and even inanimate objects possess it?

The scientists raising these questions are part of a fascinating new
field called emergent properties, which someday may reveal how
complexity in nature ultimately crosses a threshold to produce
intelligence and self-awareness.

Their research goes to the heart of a pivotal question in evolution,
one that has become a hot-button political issue: Why is it that things
that are very large and very complicated, and have many, many
pieces to them, have structure and order?

For advocates of “intelligent design,” life seems too complex to
have just happened. Some supernatural force had to guide it.

But to emergent-properties scientists, it is clear that all things
from the very beginning-atoms, molecules and so on, up to living
organisms-do their own “thinking” without any outside help. They
communicate, process information and form new unions, acquiring
capacities that are unpredictable and greater than the sum of
their parts.

Evolution, rather than being driven by competition among individual
organisms, is propelled forward into more complicated organisms
by symbiosis and cooperation among cells. Carbon atoms, for
example, can be thought of as “talking” to each other, exchanging
information on how to hold hands to create a diamond crystal.

It’s a concept that’s shattering a long-standing assumption-that the
behavior of atoms and of all life forms, except for human, is basically
preprogrammed, preordained and reflexive.

“All of life displays emergent properties,” says Utah State University
plant biologist Keith Mott. “Even a lot of things that are not life
display emergent properties. It means that when you get a bunch of
things together they do something that’s completely different from
what you would expect from all of the individual components.”

As information is concentrated, it has the capacity to move around,
be shared or seemingly amplify itself by providing a model for
less-organized neighboring systems, explains Cornell University
physicist Paul Ginsparg. “Once atoms form we can see how they
communicate to form molecules and eventually how genes communicate
to orchestrate life processes. It seems to me that information
processing is possibly the thread that ties together complexity
and the richness of the universe.”

The concepts that underlie the field of emergent properties are rooted
in the explosive development of the early universe. The Big Bang,
researchers agree, left behind oceans of elementary particles with
both positive and negative electrical charges. The oppositely charged
particles attracted each other, forming hydrogen, the simplest atom.

Gravity drew the hydrogen atoms into denser and denser clumps
until the pressure was sufficient to begin crushing them together,
forming helium and releasing enough energy to ignite the fusion
furnace that becomes a star. This process continued as new stars
aged, creating heavier elements as smaller atoms were fused
together to form bigger ones. Finally, when the stars reached the
end of their lives and exploded, they blasted into space both the
light and heavy elements, seeding the universe with the building
blocks of life.

These particles interact, pushing and pulling each other, constantly
throwing bits of information back and forth-their way of “talking.”
Electrons whiz around protons and the atoms they form are forever
chatting with nearby atoms, joining into molecules, whose chemical
reactions created the precursors of bacteria, plants and other
organisms.

Finding out how all that happens, how life emerges from the
interplay of inanimate matter, is the goal of a new $5 million grant
from the National Science Foundation. Its ambitious aim is to
duplicate the steps by which electrons, protons and all the other
atoms and molecules form sets of chemical reactions that set the
stage for life itself.

Among those whose work is funded by the grant are three University
of Illinois scientists: physicist Nigel Goldenfeld, who studies
snowflake formation in his pursuit of biological complexity;
microbiologist Carl Woese, who has unveiled new phases of
evolution; and chemist Zaida Luthey-Schulten, an expert in
determining the molecular pathways needed for early metabolic
activity.

They are, essentially, trying to create life in a test tube.

“All of these particles are inanimate,” says Goldenfeld of the
early universe, “but their dynamics are such that they form
self-reproducing chemical reactions that feed on each other
and the environment. There’s a gradual buildup of complexity
as one stage creates elements that are then used to form the
next stage.

“Although people have understood that process in a general way,
we’re trying to understand it in a very specific way.”

For Woese, the opportunity to try his hand at creating life is a
dream come true. A deep thinker who likes to cut through
science’s Gordian knots, he bears the academic scars from
repeatedly upsetting biology’s apple cart, and in the process
bringing evolution into sharper focus.

In 1977, his brilliant analysis of the genetic composition of cells
revealed a third form of life, after bacteria and plants and animals:
the archea. They joined bacteria, whose genes are free floating in
cells, and plants and animals, whose genes are packaged in a nucleus.
Archea’s genes are arranged in a way that lies somewhere between
the system used by bacteria and animals.

Classical biologists were miffed at Woese’s third life form, believing,
as did Darwin, that the “tree of life” had only two main branches.
Archea, they insisted, are not a separate branch but members of the
bacteria family. How could an unknown upstart whose background was
biophysics overturn a tenet of biology that had stood for nearly
150 years? One Nobel Laureate warned a colleague of Woese’s to
stop working with him if he wanted to salvage his own career.

As technology improved and it became easier to trace the evolutionary
history of life in genes, Woese’s finding was finally accepted a decade
later, and his three-branch tree of life is standard in biology texts.

Woese next went after a big stumbling block in classical evolution.
Darwin’s doctrine postulated that all living things eventually could be
traced back to a single founding cell. But the odds against that
happening are astronomically large. It would require all the building
blocks of life to come together in one place at the same time to form
the first founding parent.

Instead, Woese announced in 2002 that life did not start just once,
as had long been taught, but possibly millions of times. It was relatively
simple for raw chemicals, he said, to do what they do best-communicate
and form bonds-and build the first primitive genes. These early organisms
readily swapped genes among themselves, evolving more efficient survival
skills in the exchange. Most of the early life forms consolidated or died
off as three strains became dominant, he said, founding the three
domains of life.

This time, recognition of his work was swift. In 2003 the Royal Swedish
Academy of Sciences embraced the “Woesian revolution” by awarding
him the $500,000 Crafoord Prize, which is given for scientific research
not covered by the Nobel Prize.

His elevated stature hasn’t changed Woese’s work habits. He still sits
in an old swivel chair, puts his feet up on a cluttered desk and with a
computer keyboard on his lap lets his mind travel back in time more
than 3.5 billion years to try to envision how life on Earth first started.

The microbial world, he believes, holds the key to the genetic history
of human evolution.

Biologists have long thought that the life of a cell depends on a
two-step process: a source of energy and the molecules that take
that energy and use it to perform their life-giving functions. But Woese
thinks there is a crucial third step-organization. Things have a preferred
way of getting together and that sets the course for evolution.

“Organization is not an arbitrary random ordering of things,” he says.
“Organization is something that evolves from within. It is the nature
of the universe to organize with the passage of time.”

And the laws of physics regulate that organization, he says. “Physics
has changed. Physics is now talking far more about organization
of our complex dynamic systems.”

Woese made a discovery years ago that is now recognized as the
possible missing link between physics and biology. He showed that
long before amino acids became the building blocks of proteins,
they had a special property, preferring either to associate with water
molecules or be repelled by them, kind of like the 0’s and 1’s of
computer code.

By communicating their preference, Woese and his colleagues believe,
amino acids may have set about organizing how nucleic acids, the
chemicals of genes, pair up with individual amino acids to knit them
together into proteins. This dependence between amino acids and
nucleic acids ultimately evolved into the universal genetic code of
all living things.

“Evolution is the fundamental base of biology,” he insists. “It’s not
that biology gives rise to just this incidental tinkering around called
evolution. It is that evolution gives rise to biology.”

Goldenfeld calls Woese’s insight the turning point on the road to life.
“This property that Carl measured is, in biology, like a relic of the Big
Bang. It seems to be something that relates to very early properties
of living matter, of the amino acids themselves before they became
deeply involved in the molecules of life.”

Evolution comes in two forms, Woese says. The first is the kind
that he and his colleagues talk about, the natural inclination of the
universe to organize into more complex structures, from atoms to
living organisms. If the universe started over again, according to this
line of thinking, it would have some interesting differences, but it
would still end up very similar to the one we have now, complete
with single-celled organisms, plants and animals.

THE SECOND IS the kind of evolution Darwin described from his
observations of the variations in species caused by environmental
pressures. So now we have Woesian evolution driven by the free
exchange of genes among the first primitive cells, followed by the
random mutation of genes that Darwinian evolution showed bestows
better survival skills on organisms.

Norman Pace, professor of molecular, cellular and developmental
biology at the University of Colorado, Boulder, says that the
condemnation that Woese’s ideas initially aroused evoked the
ostracism Copernicus faced when he challenged existing dogma
that the sun revolves around the Earth.

“It wasn’t patently obvious to people in Copernicus’ time that the
Earth traveled around the sun, and in Woese’s case they weren’t
prepared to think about the microbiological and deep evolutionary
stuff he came up with,” Pace says. “Woese has done more for
biology than anyone since Darwin. What Darwin provided was
mechanism, natural selection. What Woese gave us was evolution’s
map-here’s what happened.”

The U. of C.’s James Shapiro, a pioneer of emergent properties,
faced similar skepticism when he first published his insights about
cellular communication 17 years ago to an incredulous scientific
community. In studying the behavior of bacteria he found that, although
they consist of single cells, they do not behave like loners. They act
together, just like an animal or any other multicellular organism.

His colleagues found this hard to swallow. “It wasn’t well-received,”
he recalls. “I later learned that the people who study higher organisms
didn’t want bacteria to be able to do things higher organisms could do.”

But now it’s widely accepted that bacterial colonies of many parts can
act as whole organisms. How they communicate and cooperate in large
numbers has become the basis for studying how bacteria maintain the
Earth as a livable planet. Because they make up the vast majority of
living organisms, bacteria and archea drive biology’s energy cycle,
and they balance the atmosphere’s oxygen and carbon dioxide content,
among other things.

The communication among bacteria is similar to how our cells talk to
each other. Human cells chat on a much more sophisticated level,
doing such things as warding off cancer and repairing cellular damage.
The chatter begins at conception when a fertilized egg starts dividing
and daughter cells busily inform their neighbors whether they are headed
off to become a brain, liver or toenail, so that they all don’t try to do
the same thing.

“What’s going on in biology, and is really very major, is we’re
understanding how really spectacular cells are at figuring things
out, processing information, analyzing complicated situations and
making good decisions about them,” Shapiro says. “The research
agenda, at least for the beginning of the 21st Century, is focusing
on cells and organisms as very sophisticated and powerful
processors of information.”

Others have shown how various organisms have evolved different ways to
exchange this information. Ants, for example, communicate by chemical
“words” called pheromones, as Harvard’s E. O. Wilson discovered, leading
him to develop the scientific discipline called sociobiology.

“The interesting point to be made is that different organisms and different
cells use different modalities to communicate,” Wilson says. “Humans
are in a very small select group that use AV, audiovisual communication.
Ants belong to the vast majority of organisms that use chemical
pheromones, smells and tastes as their signal.”

Organisms evolve these signals when it becomes advantageous to form
groups that improve survival. “The group is better than the individual
organism in competition for food, space and breeding,” notes Wilson.

When Wilson expanded his theory to say that humans have social instincts
that have a genetic basis, an irate scientist dumped a pitcher of ice water
on his head at a meeting in 1978. The water-pourer objected on grounds
that the brain was a blank slate and that whatever people do is learned.
Since then science has come to terms with the joint roles that genes and
learning play in behavior.

A key issue raised by the study of emergent properties is the nature of
intelligence and consciousness, and whether bacteria or even diamonds
can be said to think. Some scientists say this kind of communication is,
indeed, a basic form of thinking. Others vehemently disagree. Intelligence,
defined as the capacity to acquire and apply knowledge, is something
only humans and maybe some animals possess, they argue.

“When two atoms start forming a crystal lattice, that is information
transfer,” says Hans Bohner, a University of Illinois professor of
plant biology. “Some people would say a crystal has some
intelligence, a salt crystal or a diamond, because the atoms are
organized in a certain way. But I do not call that intelligence. It is
intrinsic in the quality of the atoms.”

While many scientists may be hesitant to give a diamond the benefit
of thought, they are not so sure anymore about non-human organisms
such as plants.

Plants process information and act on it, so they have a form of
intelligence, says plant scientist Anthony Trewavas of the University
of Edinburgh, Scotland, who has spent 40 years studying plant
communication. They have self-recognition in the sense that they
know the difference between another plant’s roots and theirs.
And they move and change shape, ever so slowly, to optimize
exposure to the sun, water and nutrients.

“Part of the problem when I talk about plant intelligence is that people
say, ‘Oh, rubbish. They don’t have a brain.’ OK, they don’t have a
brain, but you don’t need a brain for intelligence,” he says. “What
you actually need is an operating network of cells. If that network
has a way of controlling the flow of information and manipulating
it, in other words problem-solving, it is therefore regarded as
intelligent.”

Plants, for instance, can predict future shade from neighboring plants
by sensing their infrared emissions, and undertaking maneuvers to move
out of the way or to change their leaf structure so as to optimize the
area for collecting sunlight.

Once considered fringe science, plant intelligence is being taken more
seriously. Last May, an international group of scientists met in Florence,
Italy, for the first Plant Neurobiology Meeting. A second one is scheduled
for next spring in China. Trewavas believes that brains evolved in animals,
and not plants, because of the predator-prey relationship in animals.

Plants have no need for quick mobility because they depend on the sun, soil
and water for sustenance. But the first predatory organisms had to get smart
to capture prey, and the prey needed to get smarter to escape. This resulted
in a race to develop specialized cells to process information rapidly.

“You get this positive feedback system in which as predators become faster,
prey has to become faster or it doesn’t survive,” Trewavas says. “You evolve
even more nervous tissue to do it so you get up to organisms that now move
extremely fast, at the speed we are familiar with . . . Eventually the
brains continued to evolve until you end up with this complex structure with
large numbers of emergent properties coming out that you cannot predict
from the behavior of a few simple neurons-consciousness, for example,
speech and things like that.”

Giulio Tononi, a neuroscientist at the University of Wisconsin, says
consciousness may, in fact, result when lots of information is shared at
once. At the age of 16 in Italy, he decided that understanding consciousness
was the greatest puzzle in science and he wanted to solve it. Now he
believes the key may be understanding why consciousness fades when
we fall asleep.

Consciousness, his theory holds, emerges when a system integrates
information, such as when the different parts of the brain talk to each
other. As sleep sets in, those parts stop talking among themselves,
thereby dissolving the state of consciousness that emerged from that
communication network.

Scientists used to think that consciousness vanishes during non-dreaming
sleep because the brain rests and stops working. Researchers showed that
was wrong when they discovered that during slumber the brain is still
electrically and chemically as active as during wakefulness.

Consciousness fades away not because the brain takes a nap, Tononi
speculated, but because its different parts stop communicating. To
test his prediction, he and his colleagues performed an ingenious
experiment: When they electrically stimulated an area of the awake
brain, that part quickly sent out conference calls to many other
parts. But in the sleeping, non-dreaming brain, stimulation produced
no conference calls. The area of the brain that was dialed up by the
small jolt of electricity sat on the message.

“It fit exactly the key prediction of the information-integration theory,”
Tononi says. “The effect was very clear-cut.”

Even though self-awareness, or consciousness, is the least understood
property of matter, humans prize it for giving us the ability to quickly
adapt to changing situations and thus a tremendous evolutionary
advantage.

But all life forms solve problems, and Tononi says we may be
small-minded in asserting that other organisms, or for that matter
inanimate things, do not experience a degree of consciousness.

“If you say that consciousness is a system’s ability to integrate
information, then anything that’s made up of interacting parts will
have a little amount of consciousness,” he says. “Does a crystal
have consciousness? At one level I have to say yes, but
at another level I’d say it is so low that it’s basically nothing.
Animals will have it for sure, apes, monkeys, cats and dogs.”

Even single-cell organisms might be said to have consciousness. The
bacterium E coli, for example, can tell when its DNA has been
damaged and turns on repair systems. It holds up cell division until
all the DNA is mended so that daughter cells will be healthy. It can
then “sense” when the repair is complete.

“Do you call that self-awareness? I don’t know,” Shapiro ponders.
“You can get into a long debate about that. But until we understand
emergent properties like that more thoroughly than we do, it’s difficult
for us to deal with some of these large philosophical issues.

“There’s a lot of surprises coming up in biology and it’s precisely this
focus on information processing that is going to bring those
surprises to us.”