H00102--00A, Front mat Genesis

by Charles Baum

  goo that oozed out of our gold capsules held self-organizing molecules.

  That might be worth investigating, because we had started with a core

  metabolic molecule. It would be newsworthy if there were a facile path

  from primitive metabolism to membranes.

  On hearing my story, Dave immediately invited me to his specially

  equipped lab at UC Santa Cruz (where he had moved in 1994) to try

  the experiment. The following winter, I prepared some new pyruvate-

  plus-water capsules and subjected each of them to two hours at 2,000

  atmospheres and 250°C. I brought them, unopened, to the beautiful

  Santa Cruz campus.

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  GENESIS

  In spite of his insanely busy schedule as faculty member in two

  departments, supervisor of two laboratories, and mentor to several

  graduate students and postdocs, Dave was a gracious and attentive

  host. He welcomed me to his biochemistry lab and we set to work

  immediately.

  Once I had opened the capsules (which responded with the now

  familiar bang! and intense oily foaming), he led me step-by-step

  through the chloroform extraction, concentration, and preparation of

  a 10 × 10-inch glass plate for chromatography. I had pored over his

  1989 paper several times, so it was a delight to duplicate that work with

  my own samples under his supervision.

  Within a couple of hours, I had decorated a glass plate with a small

  yellow-brown dot of unknown chloroform-soluble compounds. We

  gently lowered the plate into a deep glass tank into which I had poured

  a half-inch layer of pungent ether. (The strong smell triggered a brief,

  vivid flashback to an early childhood moment—a menacing masked

  anesthesiologist bending over me, smothering my face prior to a ton-

  sillectomy. I had to shake away the disturbing image.) As with Deamer’s

  earlier work, the solvent pulled the glass plate’s single yellow-brown

  spot into a long streak. Then we rotated the plate and the chloroform

  smeared the streak into what we hoped would be a distinctive pattern

  of organic compounds.

  I felt more than a little tingle of anticipation as the lights went out

  and the UV fluorescent lamp flicked on. The results were gorgeous! A

  brilliant yellow, blue, and purple pattern appeared, blazing across the

  plate in a diffuse 7-inch-long arc of color. We were delighted to see

  several distinctly fluorescing areas, strikingly similar in detail to the

  Murchison sample [Plate 6]. Noting the correspondence, Dave sug-

  gested that we first concentrate on a blue fluorescing area most closely

  matching the position of his original “spot 1.”

  Again, we followed the 1988 procedures: Carefully mark the glass

  plate, scrape off the white powder from the area of interest, wash that

  powder with chloroform to redissolve the fluorescing molecules,

  and dry the extract (by this time the lab area smelled strongly of the

  chloroform–ether mix). Then the big test. Would my concentrated

  extract perform the self-organization trick?

  The test was quick and easy. We applied a bit of the extract to a

  droplet of water on a glass slide and watched in the microscope, which

  used a UV light to highlight fluorescent molecules. Sure enough, tiny

  ISOLATION

  151

  green fluorescing spheres appeared, like a fantastic display of Christ-

  mas lights. [Plate 7] Beautiful, but were they vesicles that trapped the

  surrounding liquid, or simply solid spheres? That was key to deter-

  mine if we had really made cell-like bilayer membranes.

  Deamer’s technique was to repeat the microscope observations,

  but this time starting with a strongly fluorescing red dye in the water.

  For a second time he applied a bit of the extract to the water and, once

  again, green fluorescing spheres formed. If we had made hollow

  vesicles, then they would capture the distinctive red dye. To find out,

  Dave carefully flushed the slide with new, nonfluorescing water. Lo and

  behold, the centers of the tiny green vesicles glowed red. We knew we

  had made bilayer membranes from nothing more than pyruvate and

  water.

  We celebrated that night with a bottle of Napa Valley cabernet and

  talk of next steps and publications. We both knew that the pyruvate

  results were at best a footnote to the Murchison and NASA Ames dis-

  coveries, but the experiments seemed to underscore the inevitable

  emergence of self-organizing molecular systems along the path to life.

  To be sure, many problems remain to be solved. Recent work by

  Deamer’s group suggests that lipid self-organization may be sharply

  limited by the presence of dissolved calcium and magnesium, seawater

  ingredients that would have been present in significant concentrations

  in Earth’s early ocean. Perhaps life can begin only in fresh water, or

  maybe some as yet unidentified varieties of lipid molecules were in-

  volved. And, as many biologists have been quick to point out, the

  vesicles produced in Deamer’s work are a far cry from actual cell mem-

  branes, which feature a mind-boggling array of protein receptors that

  regulate the flow of molecules and chemical energy into and out of the

  cell.

  These details will occupy researchers for decades to come, but the

  emergence of cell-like vesicles from simple molecules is now one of the

  best-understood features of life’s origin.

  AEROSOL LIFE

  New ideas about the emergence of self-organized molecular systems

  keep origin-of-life workers on their toes. An especially intriguing re-

  cent proposal comes from Oxford chemist Christopher Dobson and

  his collaborators at the National Oceanic and Atmospheric Adminis-

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  GENESIS

  tration (NOAA) in Boulder, Colorado. In 2000, they published a specu-

  lative yet persuasive hypothesis on lipid self-organization in the Pro-

  ceedings of the National Academy of Sciences. Elaborating on earlier

  unpublished work by the geophysicist Louis Lerman at Stanford,

  Dobson’s group focused on the possible roles of atmospheric aerosols

  in prebiotic synthesis and molecular organization.

  Many organic molecules—especially lipid molecules like the ones

  Deamer isolated from the Murchison meteorite—could have accumu-

  lated at the ocean’s surface like an oil slick. As wind kicked up white-

  caps and waves crashed onto the earliest shores, a continuous fine mist

  of aerosol particles—tiny droplets, some smaller than a thousandth of

  an inch across—would have sprayed into the atmosphere from the oily

  surface. Each water droplet would have contained a significant con-

  centration of organic molecules that almost immediately would have

  formed a membranous shell around the wet interior. The largest of

  these droplets would have fallen quickly back into the foam, but smaller

  aerosol particles are quite robust and could have remained suspended

  in the atmosphere for months or even years, riding wind currents like

  microscopic gliders high into the stratosphere.

  Dobson and colleagues speculate that lipids in each aerosol par-

  ticle formed a spherical, si
ngle-layer structure with the hydrophobic

  ends facing the atmospheric exterior and the hydrophilic ends facing

  the aqueous interior. Many of these aerosol particles would have incor-

  porated reactive, water-soluble organic molecules, which might have

  undergone further chemical reactions in sunlight. Each particle would

  have had weeks or months to experience such energetic transforma-

  tions; each would have been, in effect, a tiny chemical experiment.

  For hundreds of millions of years, aerosol particles in numbers

  beyond imagining drifted into the skies. Upon their return to the ocean,

  each hydrophobic aerosol particle would have been spontaneously

  coated by more lipid molecules at the ocean’s surface to form a bilayer

  structure—the emergence of the familiar membrane structure of cel-

  lular life. In the words of Dobson, “Organic aerosols offer more than

  freedom from the tyranny of the tidal pool or Darwin’s ‘warm little

  pond’; they offer a possible mechanism for the precursory production

  and the subsequent evolution of populations of cells.”

  In either scenario, whether in the form of wind-blown aerosols or

  water-bound vesicles, lipid self-organization seems to have been an es-

  sential step in isolating the insides from the outsides of cell-like struc-

  ISOLATION

  153

  A

  B

  C

  D

  According to the theory of Christopher Dobson and colleagues, the surface of the

  ancient ocean was coated with amphiphilic molecules. The action of ancient waves

  and winds would have formed aerosol particles surrounded by lipid molecules (A).

  These particles might have remained in Earth’s atmosphere for months (B), but

  would eventually return to the ocean (C), and form cell-like bilayer structures (D) (after Dobson et al., 2000).

  tures. But a membrane, by itself, is not life. Other essential

  biomolecules, including proteins, carbohydrates, and nucleic acids, had

  to be assembled from the soup. The trouble is that the building blocks

  of these macromolecules—amino acids, sugars, bases—are all water

  soluble. By themselves, they can’t self-assemble in water.

  What to do? Call in the rocks.

  12

  Minerals to the Rescue

  But I happen to know exactly how life arose; it’s brand-new

  news, at least to the average layman like yourself. Clay. Clay is

  the answer. Crystal formation in fine clays provided the

  template, the scaffolding, for the organic compounds and the

  primitive forms of life. All life did, you see, was take over the

  phenotype that crystalline clays had evolved on their own.

  John Updike, Roger’s Version, 1986

  The first living entity emerged from interactions of air, water, and

  rock—the same raw materials that sustain life today. Of these three

  chemical ingredients, rocks—and the minerals of which they are

  made—have generally received little more than a footnote in theories

  of life’s emergence. The atmosphere and oceans have long enjoyed the

  starring roles in origin scenarios, while rocks and minerals sneak in

  and out as bit players—or simply as props—and then only when all

  other chemical tricks fail.

  Some recent and fascinating experiments promise to change that

  misperception. Origin-of-life researchers have begun to realize that

  minerals must have played a sequence of crucial roles, beginning with

  the synthesis of biomolecules and during their subsequent assembly

  into growing and evolving structures.

  The Miller–Urey chemical process works by ionizing gas mol-

  ecules—blasting them with lightning or ultraviolet radiation and

  thereby stripping off electrons, so that small groups of atoms readily

  recombine into larger organic molecules. Interesting molecules inevi-

  tably emerge, but those energetic processes effectively prevent the for-

  mation of essential macromolecular structures, including the polymers

  and membranes required by all known life-forms. The Miller–Urey

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  156

  GENESIS

  scenario can’t have been the entire story. That’s why many researchers,

  especially those trained in geology, turn to rocks and minerals.

  MINERALS AS PROTECTION

  Rocky outcrops and overhangs—especially in tidal zones, where sea-

  water evaporates and thus concentrates organic molecules—might

  have promoted macromolecular formation. Imagine a shaded cove

  where increasingly concentrated mixtures of organic molecules accu-

  mulated and reacted, protected by a rocky ledge from the Sun’s harm-

  ful radiation. Rocks might have served as Earth’s earliest sunblock.

  They may well have provided protection at a smaller scale as well. Many

  volcanic rocks of the early Earth were laced with countless air pockets

  left by expanding volcanic gases. Evaporating seawater might have de-

  posited a rich mix of organic molecules in such tiny hollows, each like

  a small test tube where further reactions could proceed.

  Mineralogist Joseph V. Smith, professor emeritus at the University

  of Chicago, envisions even smaller protected environments. He cites

  electron microscopy studies of weathered mineral surfaces, which of-

  ten display myriad microscopic cracks and pores. Feldspar, the com-

  monest of all rock-forming minerals, sometimes features millions of

  tiny weathered pockets, each the approximate size and shape of living

  cells, each providing a place for molecules to congregate, each pore and

  crack a separate experiment in molecular self-organization. [Plate 7]

  POLYMERIZATION ON THE ROCKS

  The production of macromolecules requires two concerted steps: The

  correct molecules must first be concentrated and then organized into

  the desired structure. In the case of lipid membranes, these two tasks

  occur virtually simultaneously and spontaneously; lipids in water sepa-

  rate and self-organize into a bilayer. But other key biological macro-

  molecules, including proteins and carbohydrates, form from

  water-soluble units—amino acids and sugars. Consequently, they tend

  to break down, not form, in water.

  One promising way to assemble such molecules from a dilute so-

  lution is to concentrate them on a surface. For decades, the prevailing

  paradigm has been that the molecules of life assembled at or near the

  ocean–atmosphere interface. The surface of a calm tidal pool, or per-

  MINERALS TO THE RESCUE

  157

  haps a primitive slick of water-insoluble molecules might have done

  the job. But then, as noted, these environments are open to lightning

  storms and ultraviolet radiation.

  Origin scientists with a penchant for geology have long recognized

  that rocks might provide attractive alternative surfaces for concentra-

  tion and assembly—a kind of scaffolding for the assembly of protolife.

  More than a half-century ago, the British biophysicist John Desmond

  Bernal advocated the special role of clays, which are ubiquitous miner-

  als with regularly layered atomic structures.

  Clays come in a wide range of compositional and structural vari-

  ants, but
all of them feature layers of strongly bonded silicon and alu-

  minum atoms. The proclivity of clays to exhibit a surface electrostatic

  charge enhances their ability to adsorb organic molecules—a kind of

  molecular-scale static cling. What’s more, clays tend to occur as excep-

  tionally fine-grained flat particles. Consequently, a palm-sized pile of

  ordinary clay can boast a reactive surface area greater than 1,000 square

  feet.

  Subsequent experiments have supported Bernal’s speculations. In

  a 1978 study, Israeli biochemist Noam Lahav and colleagues discov-

  ered that amino acids concentrate and polymerize on clays to form

  small, protein-like molecules. Such reactions occur when a solution

  containing amino acids evaporates in the presence of clays—a situa-

  tion not unlike the evaporation that dries up a shallow pond or tidal

  pool. Of special note is the fact that this process relies on cycles of

  heating and evaporation—and cycles, recall, are one of the key factors

  in the emergence of complexity. Patterns of daily and seasonal changes

  doubtless fostered the emergence of new molecular structures.

  More recently, research by NASA-sponsored teams in California

  and New York has demonstrated that a variety of layered minerals can

  adsorb and assemble a variety of other organic molecules. In a tour de

  force series of experiments during the past two decades, chemist James

  Ferris and colleagues at Rensselaer Polytechnic Institute induced clays

  to act as scaffolds in the formation of RNA, the polymer that carries

  the genetic message enabling protein synthesis.

  Ferris relied on the simplest of procedures. First, he prepared a

  solution of “activated” RNA nucleotides, each consisting of a ribose

  sugar bonded to a phosphate and a base, plus a reactive molecule called

  imidazole that promotes, or “activates,” bonding between nucleotides.

  Such a solution can sit on the lab bench for weeks with little change.

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  GENESIS

  But sprinkle in a bit of a suitable clay mineral and the RNA pieces start

  to link up. In a matter of hours, lengths of 10 nucleotides form. By the

  end of 2-week experiments, the RPI team produced RNA strands of

  more than 50 nucleotides. The fine-grained clay particles had induced

  polymerization by a process not yet fully understood.

  Buoyed by the Ferris team’s success, other origin-of-life research-