by Charles Baum
Those similarities provide a clear focus for experimental studies of
emergent biochemistry.
The greatest challenge in understanding life’s emergence lies in find-
ing mechanisms by which just the right combination of smaller mol-
ecules was selected, concentrated, and organized into the larger
macromolecular structures like RNA and in self-replicating cycles of
molecules like the citric acid cycle. But regardless of how much or-
ganic stuff was made, the primordial ocean—with an estimated vol-
ume greater than 320 cubic miles—formed a hopelessly dilute soup in
which it would have been all but impossible for the right combination
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GENESIS
of molecules to bump into one another and make anything useful in
the chemical path to life. Complex emergent systems require a mini-
mum concentration of interacting agents. Many scientists have there-
fore settled on an obvious solution: Focus on surfaces, where
molecules tend to concentrate.
Interesting chemistry takes place on surfaces where two different
materials meet and molecules often congregate. The surface of the
ocean, where air meets water, is one such promising place. Perhaps a
primordial “oil slick” concentrated organic molecules. Evaporating
tidal pools, where rock and water meet and cycles of evaporation con-
centrate stranded chemicals, represent another appealing location for
origin-of-life chemistry. Deep within the crust and in hydrothermal
volcanic zones, mineral surfaces may have played a similar role, select-
ing, concentrating, and organizing molecules on their periodic, crys-
talline surfaces. Whatever the mise-en-scène, a surface seems a logical
site for life’s origin.
But just suppose a collection of organic molecules could organize
themselves in such a way that they provided their own surface? Now
that would be a trick worth learning!
11
Isolation
The self-assembly process seems to defy our intuitive expecta-
tion from the laws of physics that everything on average
becomes more disordered.
David Deamer, 2003
Water provides the universal medium for life. All known cells are
mostly water on the inside, and most are surrounded by water
on the outside. That aquatic lifestyle poses a problem, however, be-
cause water is one of the best solvents. You don’t want your body’s cells
to dissolve every time you take a bath. Life had to develop an insoluble
protective membrane, but what chemical to use?
Lipid molecules, which feature hydrocarbon chains (a row of car-
bon atoms surrounded by hydrogen atoms), provide the perfect an-
swer to the problem. Lipids, including various fats, oils, and waxes, are
characterized by their insolubility in water—oil and water don’t mix.
The special phospholipid molecules that form most modern cell mem-
branes are no exception. Each of these molecules is shaped something
like a tiny bobby pin, with two long hydrocarbon chains of atoms at-
tached to a rounded end. The two exposed hydrocarbon chains are
hydrophobic (“water hating”), so most of the elongated molecule is
water-repellent. By contrast, the rounded end incorporates a phosphate
group (phosphorus and oxygen atoms); that hydrophilic (“water lov-
ing”) end attracts water. Such molecules, with both hydrophobic and
hydrophilic regions, are called amphiphiles.
SELF-ORGANIZATION
When placed in water, amphiphilic lipids deal with their love-hate re-
lationship in a remarkable way. All natural systems tend to rearrange
143
144
GENESIS
themselves to reduce their total energy content: A tightly stretched elas-
tic band snaps, a precariously perched boulder tumbles to the valley
below, a firecracker explodes. By the same token, a solution of lipid
molecules searches for a state of lower energy in which only the hydro-
philic phosphate ends contact water. In the early 1960s, Alec Bangham,
a biophysicist from Cambridge, England, discovered that lipids that
were extracted from egg yolk and immersed in water spontaneously
organized themselves into tiny spheres—structures now known as
vesicles.
The energy-reducing strategy employed by the molecules that
form cell membranes is nothing short of magical. Millions of indi-
vidual amphiphilic molecules quickly clump together, forming a
smooth, flexible double layer of lipids—a lipid bilayer. The resilient
lipid bilayer provides a simple and elegant solution to the
phospholipid’s ambivalence toward water. All of the hydrophobic
chains of atoms point toward the middle of the structure, well away
from water, while the hydrophilic phosphate ends all wound up on the
outside of the cell facing the wet environment or on the inside facing
the water-based contents of the cell. This arrangement accomplishes
the vital functions of holding the cell together while separating its in-
side from the outside.
Life has perfected this task of separating the inside from the out-
side, but could such an emergent, self-organizing process have arisen
naturally in the lifeless prebiotic soup? The answer, once again, is to be
found in the laboratory. Some amazing experiments have been per-
formed by the Swiss biochemist Pier Luigi Luisi, who has spent de-
cades studying lipid self-organization.
Not only can Luisi and co-workers form vesicles with ease, but
they also demonstrate that these structures can grow, gradually incor-
porating new lipid molecules from solution. They’ve also shown that
vesicles are autocatalytic—that is, they can act as templates that trigger
the formation of more vesicles. And, under the proper circumstances,
vesicles can even divide—a kind of self-replication.
These intriguing emergent behaviors have led Luisi to propose the
“Lipid World” scenario for life’s origin. In this conceptually simple
model, prebiotic lipids formed abundantly on Earth and in space. Once
in solution, these lipids self-organized into cell-like vesicles that cap-
tured a primitive genetic molecule, some early, simpler version of DNA
or RNA. Now the Swiss team has set its sights on incorporating self-
ISOLATION
145
B
C
A
Cell membranes are formed from amphiphiles, which are elongated molecules that
have both water-attracting and water-repellent ends (A). When placed in water, these molecules self-organize into a bilayer (B), which can form a spherical vesicle (C).
replicating pieces of RNA into self-replicating vesicles, perhaps even to
make the first synthetic life-form. It hasn’t happened yet, but the
chemical pieces are close to falling into place.
MEMBRANES FROM SPACE
In the relatively brief history of origins research, a mere handful of
experiments may be counted as classics. Louis Pasteur’s refutation of
146
GENESIS
spontaneous generation and Stanley Miller’s electric-spark synthesis
experiments have achieved that status, as
has the novel vacuum-cham-
ber research of Lou Allamandola and his colleagues at NASA Ames.
Their results changed the way we think about life’s origins. The same
high regard is accorded David Deamer’s remarkable discoveries of lipid
self-organization in spaceborne molecules.
For almost three decades, Dave Deamer has been a popular profes-
sor of biochemistry in the University of California system. Lean, bright-
eyed, with a neat graying beard and dark-rimmed glasses, he delivers
lectures in a gentle and reassuring voice, like a scientific Mister Rogers.
Listening to his low-key delivery, you might not guess that he is one of
the world’s most respected experts on the origin of life. [Plate 6]
Deamer caught the origins bug in 1975, when he took a sabbatical
from the Davis campus of the University of California and went to
study lipids with Alec Bangham at Cambridge. Their work revealed
that the size and resilience of vesicles depends on the size and shape of
the dissolved lipid molecules. In the course of these investigations, they
realized that vesicles might have provided the first sheltering environ-
ment for life. If lipids existed in the early oceans, then prebiotic vesicles
may have been abundant.
Deamer returned to Davis and continued this line of research,
which led to his most famous experiment. That work, completed in
1988, focused on carbon-based molecules extracted from the
Murchison meteorite. Ever since it landed in the Melbourne cow field
in 1969, origins scientists all around the world had been bargaining
and pleading for a piece of the prize. Deamer’s precious 90-gram
Murchison fragment, about the size of a walnut, arrived from the Field
Museum in Chicago. Dave and his collaborator, chemist Richard
Pashley of the Australian National University, went straight to work.
Their focus was the lipids, essential biomolecules but ones that did not
seem to be produced in sufficient abundance by Miller’s spark process.
Perhaps, they thought, carbonaceous chondrites provided those neces-
sary raw materials for life’s membranes.
Deamer and Pashley ran their sample through a series of chemical
steps to break apart the dense black meteoric mass into chemically
distinct fractions—steps that in some ways mimicked millennia of
chemical weathering processes on the primitive Earth. Whatever mol-
ecules they found were thus likely to have occurred on the prebiotic
Earth, as well. First they pulverized a portion of the meteorite into fine
ISOLATION
147
black powder. Their straightforward procedure involved grinding the
rock while it was submerged in a liquid mixture of water, alcohol, and
chloroform. These solvents don’t affect the crystalline minerals that
form the bulk of the Murchison, but they do dissolve different suites of
interesting organic molecules. After several minutes of grinding,
Deamer and Pashley poured their fine-grained slurry into a test tube,
placed it into a centrifuge, and let it spin.
In the centrifuge, the pulverized meteorite solution rapidly sepa-
rated into three fractions. A small pile of dense mineral fragments
settled to the bottom of the tube, to be set aside just in case more
studies were required. On top was a layer of water–alcohol solution,
which dissolved and concentrated amino acids, sugars, and a variety
of other water-soluble organic species. This fraction, too, was set aside.
In the middle was a layer of chloroform, an effective solvent for any
lipids the meteorite might hold. They found that the chloroform frac-
tion had extracted more than a tenth of a percent of the meteorite
fragment’s mass—a surprisingly high concentration of tantalizing or-
ganic species.
Further separation was performed using chromatography. Follow-
ing much the same protocols as Stanley Miller had employed decades
earlier to separate his amino acids, Deamer and Pashley evaporated a
portion of their chloroform sample to reveal a yellowish-brown con-
centrated solution. They placed a drop of this concentrate on the cor-
ner of a 4 × 4-inch glass plate that had been coated with a soft, porous
white powder (an effective replacement for the older-style chromatog-
raphy paper). They used ether, a colorless strong-smelling solvent, for
the first chromatographic stage, stretching the dried dot into a streak.
Then they rotated the plate 90 degrees and used chloroform to spread
the streak into a distinctive two-dimensional array of compounds.
Viewed in daylight, the dried glass plate was unimpressive, with
only the original brownish spot and a few faint yellowish areas nearby.
But Deamer knew that many otherwise invisible compounds fluoresce
brightly under “black light.” When he darkened the room and shone
an ultraviolet lamp on the plate, he was delighted to see a rich display
of colors sweeping across it in a broad arc.
Deamer and Pashley identified a half-dozen distinct fluorescent
regions, each with a different, as yet unknown suite of ancient cosmic
organic molecules. They meticulously outlined each area by scratching
the soft, powdery white surface; then they scraped off and collected
148
GENESIS
powder from each of those areas into test tubes. A quick wash in chlo-
roform was all that it took to recover the precious suites of Murchison
molecules.
Keen with anticipation, the chemists placed the chemical fractions
one-by-one into water and watched to see if anything interesting hap-
pened. They began with “spot 1,” with molecules that had concentrated
in an elongated area close to the original drop on the chromatography
plate. Deamer and Pashley watched transfixed as the invisible mol-
ecules, once dispersed throughout the meteorite, spontaneously ar-
ranged themselves into tiny spheres no more than a hundredth of an
inch across—about the size of many modern microbes. What’s more,
they found, these weren’t just little drops of oil or fat floating in water.
These structures had an inside and an outside. The molecules had or-
ganized themselves into bilayers, just like a cell membrane—an elegant
example of emergence.
It was a breakthrough moment for origin researchers. Deamer and
Pashley had shown that ancient lipid molecules, synthesized at some
distant place in space and delivered intact to Earth, form tiny enclosed
structures that are in many ways like the membranes encasing living
cells. One of life’s most basic requirements—the isolation of inside
from outside—suddenly seemed to have been hard-wired into the fab-
ric of the universe.
SELF-ORGANIZATION, REPRISE
Dave Deamer’s Murchison experiments were conceptually simple and
beautifully executed. So when new lipid-rich samples came along, he
repeated the process.
Lou Allamandola and his NASA Ames team realized that their
growing inventory of organic molecules, synthesized under simulated
deep-space conditions of ultracold vacuum with ultraviolet radiation,
contained a significant
fraction of yellowish oily stuff just as the
Murchison meteorite did. In particular, when they irradiated an ice
made principally of water and alcohol with a bit of ammonia and car-
bon monoxide thrown in, they produced an intriguing residue of fluo-
rescent material. Much of that material was known to be the familiar
multiringed hydrocarbons known as PAHs, but other molecules ap-
peared to have an amphiphilic character. Naturally, they turned to Dave
Deamer to check it out.
ISOLATION
149
Samples in hand, it took Deamer less than a day to confirm what
the Ames researchers had hoped. Once the correct fraction of fluores-
cent molecules was concentrated, stunning vesicles appeared sponta-
neously in water. The press trumpeted the result, and a colorful
photograph of the delicate tiny spheres graced the front page of the
Washington Post above the headline “IN SPACE; CLUES TO THE
SEEDS OF LIFE.” The implications were profound: Even before the
formation of planets and moons, in the tenuous vacuum of frigid
space, the raw materials for life abound, ready to organize spontane-
ously into cell-like structures.
PYRUVATE REDUX
I got the chance to work with Dave Deamer following a conversation at
one of NASA’s first astrobiology meetings, in April 2000. Dave had been
asked to present a keynote lecture on self-organization to the audience
of geologists, chemists, biologists, and astronomers, not to mention a
smattering of philosophers and ethicists.
Some scientific lecturers try to snow their audiences. Deamer is
different; he meets the audience more than halfway, with comfortable
metaphors, familiar examples, and elegant demonstrations. At this lec-
ture, he held up two large beakers, both with colorless solutions. When
mixed, the resulting liquid immediately became cloudy white; we were
looking at the spontaneous self-organization of lipids, he explained.
At Carnegie, my group’s 1996 pyruvate work had been sitting on
hold for years. We knew we’d made a lot of interesting organic mol-
ecules by heating and squeezing pyruvate, but other than the fact that
the reactions occurred rapidly under hydrothermal conditions, the rel-
evance to life’s origin wasn’t clear. Perhaps, we thought, the yellow, oily