Scientists finish a 53-year-old classic experiment on the origins of life

By Ed Yong | March 21, 2011 3:00 pm

In 1958, a young scientist called Stanley Miller electrified a mixture of simple gases, designed to mimic
the atmosphere of our primordial lifeless planet. It was a sequel to one of the most evocative experiments
in history, one that Miller himself had carried five years earlier. But for some reason, he never finished his
follow-up. He dutifully collected his samples and stored them in vials but, whether for ill health or
dissatisfaction, he never analysed them.

The vials languished in obscurity, sitting unopened in a cardboard box in Millers office. But possessed by
the meticulousness of a scientist, he never threw them away. In 1999, the vials changed owners. Miller
had suffered a stroke and bequeathed his old equipment, archives and notebooks to Jeffrey Bada, one of
his former students. Bada only twigged to the historical treasures that he had inherited in 2007. Inside,
were all these tiny glass vials carefully labeled, with page numbers referring Stanleys laboratory notes. I
was dumbstruck. We were looking at history, he said in a New York Times interview.

By then, Miller was completely incapacitated. He died of heart failure shortly after, but his legacy
continues. Badas own student Eric Parker has finally analysed Millers samples using modern technology
and published the results, completing an experiment that began 53 years earlier.

Miller conducted his original 1953 experiment as a graduate student, working with his mentor Harold
Urey. It was one of the first to tackle the seemingly insurmountable question of how life began. In their
laboratory, the pair tried to recreate the conditions on early lifeless Earth, with an atmosphere full of
simple gases and laced with lightning storms. They filled a flask with water, methane, ammonia and
hydrogen and sent sparks of electricity through them.

The result, both literally and figuratively, was lightning in a bottle. When Miller looked at the samples
from the flask, he found five different amino acids the building blocks of proteins and essential
components of life.

The relevance of these results to the origins of life is debatable, but theres no denying their influence.
They kicked off an entire field of research, graced the cover of Time magazine and made a celebrity of
Miller. Nick Lane beautifully describes the reaction to the experiment in his book, Life Ascending:
Miller electrified a simple mixture of gases, and the basic building blocks of life all congealed out of the
mix. It was as if they were waiting to be bidden into existence. Suddenly the origin of life looked easy.

Over the next decade, Miller repeated his original experiment with several twists. He injected hot steam
into the electrified chamber to simulate an erupting volcano, another mainstay of our primordial planet.
The samples from this experiment were among the unexamined vials that Bada inherited. In 2008, Badas
student Adam Johnson showed that the vials contained a wider range of amino acids than Miller had
originally reported in 1953.

Miller also tweaked the gases in his electrified flasks. He tried the experiment again with two newcomers
hydrogen sulphide and carbon dioxide joining ammonia and methane. It would be all too easy to
repeat the same experiment now. But Parker and Bada wanted to look at the original samples that Miller
had himself collected, if only for their considerable historical interest.

Using modern techniques, around a billion times more sensitive than those Miller would have used,
Parker identified 23 different amino acids in the vials, far more than the five that Miller had originally
described. Seven of these contained sulphur, which is either a first for science or old news, depending on
how you look at it. Other scientists have since produced sulphurous amino acids in similar experiments,
including Carl Sagan. But unbeknownst to all of them, Miller had beaten them to it by several years. He
had even scooped himself it took him till 1972 to publish results where he produced sulphur amino
acids!

The amino acids in Millers vials all come in an equal mix of two forms, each the mirror image of the
other. You only see that in laboratory reactions in nature, amino acids come almost entirely in one
version. As such, Parker, like Miller before him, was sure that the amino acids hadnt come from a
contaminating source, like a stray bacterium that had crept into the vials.
Imagine then, a young and violent planet, wracked with exploding volcanoes, noxious gases and lightning
strikes. These ingredients combined to brew a primordial soup, fashioning the precursors of life in
pools of water. On top of that, meteorites raining down from space could have added to the accumulating
molecules. After all, Parker found that the amino acid cocktail in Millers samples is very similar to that
found on the Murchison meteorite, which landed in Australia in 1969.

These are powerful images, so why arent people more excited? Echoing many sources I spoke to, Jim
Kasting, who studies the evolution of Earths atmosphere, said, I am underwhelmed by it. The main
problem with the study is that Miller was probably wrong about the conditions on early Earth.

By analysing ancient rocks, scientists have since found that Earth was never particularly teeming in
hydrogen-rich gases like methane, hydrogen sulphide or hydrogen itself. If you repeat Millers
experiment with a more realistic mixture heavy in carbon dioxide and nitrogen, with just trace amounts
of other gases youd have a hard time finding amino acids in the resulting brew.

Parker accepts the problem, but he suggests that a few specific places on the planet may have had the
right conditions. Exploding volcanoes, for example, throw up masses of sulphurous compounds, as well
as methane and ammonia. These gases, belched forth into lightning storms, could have produced amino
acids that rained out and gathered in tidal pools. But Kasting still isnt convinced. Even then the reduced
gases would not be as concentrated as they are in this experiment.

Even if our young planet had the right conditions to produce amino acids, thats a less impressive feat
than it appeared in the 1950s. Amino acids are old hat and are a million miles from life, says Nick
Lane. Indeed, as Millers experiments showed, its not difficult to create amino acids. The far bigger
challenge is to create nucleic acids the building blocks of molecules like RNA and DNA. The origin of
life lies in the origin of these replicators, molecules that can make copies of themselves. Lane says,
Even if you can make amino acids (and nucleic acids) under soup conditions, it has little if any bearing
on the origin of life.

The problem is that replicators dont spontaneously emerge from a mixture of their building blocks, just
as you wouldnt hope to build a car by throwing some parts into a swimming pool. Nucleic acids are
innately shy. They need to be strong-armed into forming more complex molecules, and its unlikely that
the odd bolt of lightning would have been enough. The molecules must have been concentrated in the
same place, with a constant supply of energy and catalysts to speed things up. Without that lot, life will
never get started, and a soup cant provide much if any of that, says Lane.

Deep-sea vents are a better location for the origins of life. Deep under the oceans surface, these rocky
chimneys spew out superheated water and hydrogen-rich gases. Their rocky structures contain a labyrinth
of small compartments that could have concentrated lifes building blocks into dense crowds, and
minerals that would have catalysed their get-togethers. Far away from visions of languid soups, these
churning environments are the current best guess for the site of lifes hatchery.

So Millers iconic experiment, and its now-completed follow-ups, probably wont lay out the first steps of
life. As Adam Rutherford, who is writing a book on the origin of life, says, Its really a historical piece,
like finding that Darwin had described a Velociraptor in one of his notebooks.

If anything, the analysis of Millers vials is a testament to the value of meticulous scientific work. Here
was a man who prepared his samples so cleanly, who recorded his notes so thoroughly, and who stored
everything so carefully, that his contemporaries could pick up where he left off five decades later.

Reference: Parker, Cleaves, Dworkin, Glavin, Callahan, Aubrey, Lazcano & Bada. 2011. Primordial
synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. PNAS
http://dx.doi.org/10.1073/pnas.1019191108

Photos by Carlos Gutierrez and Marco Fulle

A possible icy start for life
By Ed Yong | September 21, 2010 11:00 am

The origin of life is surely one of the most important questions in biology. How did inanimate molecules
give rise to the endless forms most beautiful that we see today, and where did this event happen? Some
of the most popular theories suggest that life began in a hellish setting, in rocky undersea vents that churn
out superheated water from deep within the earth. But a new paper suggests an alternative backdrop, and
one that seems like the polar opposite (pun intended) of the hot vents ice.

Like the vents, frozen fields of ice seem like counter-intuitive locations for the origin of life theyre
hardly a hospitable environment today. But according to James Attwater form the University of
Cambridge, ice has the right properties to fuel the rise of replicator molecules, which can make copies
of themselves, change and evolve.

When thinking about such replicators, DNA the molecule that is virtually synonymous with life
springs readily to mind. But a world of independent DNA strands makes no sense, because this famous
molecules accomplishes very little on its own. DNA needs special proteins in order to copy itself but it, in
turn, provides the blueprints for making proteins. So neither DNA nor proteins should be able to evolve
without the other.

The chicken-and-egg problem seems inescapably vexing, but it fades into irrelevance when you consider
a related molecule called RNA. Today, RNA messages are transcribed from information coded within
DNA and then translated into proteins. But RNA is much more than some unglamorous go-between; in
fact, it probably deserves to take centre-stage.

Since the 1980s, it has become abundantly clear that RNA is more than capable of performing the roles of
both of its partners. Like DNA, it stores information in the form of four letters (nucleotides) arranged in
specific sequences. But unlike the famous double helix of its relative, RNA is typically found as a single
spiral, which can fold into complex shapes. Many of these can speed up chemical reactions in the same
way that proteins do. RNA molecules that do this are called ribozymes, and they can even speed up the
production of RNA itself.

So RNA can store information, speed up chemical reactions, and make copies of itself without any
outside help. It evolves too stick it in a test tube with the right raw materials and a source of energy and
it eventually gets better and better at copying itself. This ability was first demonstrated in 1972 by Sol
Spiegelman and the brutally efficient RNA strand that resulted was melodramatically known as
Spiegelmans monster.

In RNA, we have a plausible candidate for the original replicating molecule, from which all life is
derived. This concept was deftly summarized by Nobel laureate Walter Gilbert when he coined the term
RNA world. Its a wonderfully evocative phrase that brings to mind a planet of evolving RNA
molecules that predated the later DNA revolution.

But RNAs unique physical properties arent enough. The molecule is also very fragile and it would
rapidly degrade under all but the gentlest environmental conditions. It also needs to be concentrated in
some way. A molecule that makes copies of itself needs to be kept in the same place as its constituent
chemicals; if the parts are allowed to disperse, the whole will never come together. So RNA may have the
right qualities, but it needs a stable and confined space to make the RNA world a reality. Attwater thinks
that ice provides just such a space.

At first glance, this seems like a bizarre idea. For a start, cold temperatures can slow many chemical
reactions to a crawl. Proteins that piece together RNA molecules stop working when theyre frozen. But
remember, RNA in the form of ribozymes can speed up its own creation without any proteins. And
Attwater found that one such ribozyme called R18 is still active at subzero temperatures. In fact, ice
actually stabilised the ribozyme, preventing it from breaking down. On ice, the ribozyme was slower than
at room temperature but it also carried on working for longer. As a result, it was actually more productive,
creating longer lengths of RNA with no less accuracy.
Thats one problem down, but theres also the fact that ice is solid. You might think that this would
prevent molecules from meeting each other with ease, but ice isnt completely solid. At a microscopic
level, weaving their way between the crystals, theres a complicated network of channels and spaces that
havent frozen completely.

The water in these spaces is salty; as the surrounding molecules froze, any dissolved impurities were
pushed away and became concentrated in the remaining liquid. Attwater found that this process boosts the
concentration of ions, nucleotides and other chemicals in the liquid compartments by over 200 times. That
accelerates the work of the ribozymes, and more than compensates for the slowing effects of the cold.

The liquid compartments provide everything that a RNA molecule needs to reproduce effectively. In these
closed quarters, chemical reactions arent dependent on the vagaries of open space. Concentrated
molecules have a high probability of bumping into one another and are slow to diffuse away.

Of course, this scenario only has a chance of being true if there was a lot of ice on primordial Earth.
Attwater pictures frozen lakes and ponds but a decade ago, that would have sounded far-fetched.
Scientists commonly assumed that, during our planets youth, temperatures on both land and ocean were
scorchingly hot. But over the last decade, various studies have suggested that this early climate include
more temperate conditions, which allows for the possibility of ice.

This isnt to say that life began in ice. Attwater has simply demonstrated that ice provides the right
conditions for a cold RNA world to take off. For now, theres little evidence that it did so; we simply
know that it might have.

There are other places that can provide similar conditions, including the undersea vents that I mentioned
at the start of this piece. They too can concentrate molecules within rocky cells, and their high
temperatures are a boon to many chemical reactions. Phil Holliger, who led Attwaters study, points out
that vents have high temperatures and high levels of heavy metals, both of which accelerate the
breakdown of RNA. Its hard to imagine them as the places where RNA-based life could have arisen or
thrived, he says.

But the vent idea has the backing of decades of research. Bill Martin from the University of Duesseldorf
certainly thinks that they are the more likely alternative. Of Attwaters work on ice, he says, Interesting
experiments, I suppose, but holes in ice had as much to do with the origin of life as the electric toaster.

Ultimately, as I wrote last week in a post about the origin of complex cells, it is predictable that these
questions should generate debate. As Holliger concedes, The actual events of the origin of life are
unknown and probably unknowable. What can be tested is the plausibility and consistency of theories.

Reference: Nature Communications http://dx.doi.org/10.1038/ncomms1076

Tree or ring: the origin of complex cells
By Ed Yong | September 13, 2010 3:16 pm

The natural world is full of great partnerships. Bacteria give animals the guts to digest all manner of
otherwise inedible foods. Algae allow corals to harness the power of the sun and construct mighty reefs.
Ants cooperate to become mighty superorganisms. But the greatest partnership of all is far more ancient.
Its so old that we can only infer that it took place by looking for signals of history, embedded into the
genomes of modern species. The details of how and when it happened are still the source of fierce debate
but this was undoubtedly the most important merger in the history of life on Earth: a partnership between
two simple cells that would underlie the rise of every living animal, plant, fungus and alga.

All complex life belongs to a single group called the eukaryotes, whose members, from humans to
amoebas, share a common ancestry. Their cells are distinguished by having several internal
compartments, including the nucleus, which shelters their precious DNA, and the mitochondria, which
provide them with power.

This internal organisation sets the eukaryotes apart from the two other domains of life: the prolific
bacteria; and the archaea, masters of extreme environments. These two groups are very different in their
biochemistry but they are look superficially similar. Both are comprised of solitary cells that lack
mitochondria or any other internal compartments; their DNA is unfettered by a nucleus. A chasm of
organisation separates these simple cells from the complex eukaryotes, and the crossing of this chasm,
several billion years ago, is one of the most important events in the planets history.

An event so deep in time was always going to be difficult to piece together. Those ancestral cells are
hardly going to leave fossils behind, but there are clues to their ancient prehistory in the genomes of
living species. Some genes are so important that theyre shared between all living things neither
bacterium nor human could do without them. These core genes have diverged over the course of
evolution, but theyre similar enough to reflect a shared history. By comparing them across modern
species, biologists can look at which are more closely related than others.

In the 1970s, the great biologist Carl Woese used one such gene to construct a grand tree of life, where
eukaryotes and archaea are sister lineages, both descended from bacterial ancestors (left image above).
This is the traditional view of the origin of eukaryotes, but it was based on just one gene. As others were
analysed, a more confusing picture emerged. While many eukaryotic genes are indeed closely related to
those of archaea, as predicted by Woeses tree, others have more similar counterparts in bacteria.

These two classes also tend to have different roles. The archaea-like genes tend to be informational
genes, which are involved in DNA: decoding it, using it to produce proteins, and making new copies of it.
The bacteria-like genes tend to be operational theyre involved in dogsbody jobs like making amino
acids, fat molecules and so on.

Now, in a new study, James Cotton and James McInerney have found that the archaea-like genes also
seem to be more important than the bacteria-like ones, even though theyre less common. The duo looked
at every one of the 6,700 gene in the bakers yeast Saccharomyces cerevisiae. They found that around
2,000 are most closely related to bacterial genes and just 500 or so are most closely related to archaeal
ones.
But not all genes are equal. Some are so indispensible that if they dont work, the yeast dies. And these
vital genes are more than twice as likely to have archaeal counterparts as bacterial ones. There are other
indicators of importance: the archaea-like genes are also about twice as active as the bacteria-like ones;
theyre more likely to interact with other genes; and theyre present in fewer copies. So in the yeast
genome, the archaea-like genes are a small group but an elite one.

Cotton and McInerney think that their results support a model for the origin of eukaryotes thats very
different to Woeses tree. In this scenario the so-called ring of life eukaryotes arose from a fusion of
the other two domains of life. In a fateful encounter, an archaeon swallowed a bacterium, setting up an
alliance that would allow both of them to escape the restraints of their simple structures.

The bacterium was eventually domesticated, becoming the mitochondria of today. It transferred many of
its genes into the host genome, producing the chimeric mash-up of archaeal and bacterial DNA that we
see in modern eukaryotes. Meanwhile, it retained some of its own genes and indeed, mitochondria still
have a small genome of their own.

Cotton and McInerneys results certainly fit with this idea. The genes of the archaeal host have been
interacting with each other for longer, well before any bacterial genes were added into the mix. Once that
happened, some archaeal genes were displaced, but the essential few remained inviolate. Even after some
2 billion years of evolution, theyre still doing the same fundamental job. The bacterial additions had to
be integrated around this core network. This explains why the archaea-like genes of yeast have a central
importance out of all proportion to their small number.

That is not to say that the addition of the bacterium wasnt a pivotal event. Nick Lane has written about
this subject extensively in his beautiful book, Life Ascending, and cautions against over-interpreting the
new study. The impression might be created that the host cell was somehow in charge all along and the
mitochondria had a relatively minor, certainly less important, involvement in the evolution of the
eukaryotic cell, he says. That would be totally wrong.

The host cell was utterly transformed by the mitochondria, he says. The fact that a few archaeal genes
seem to be more important than bacterial genes should not distract from the fact that the eukaryotic cell is
not an archaeon. It has transformed utterly and has thousands of new genes (even in yeast), none of which
would have been possible without the mitochondria.

Bill Martin, who also supports the ring of life model, thinks that its important that bacteria have made a
greater quantitative contribution to yeast (and eukaryote) genomes than archaea. To him, this runs
counter to the classical tree of life model, where archaea are the sisters to eukaryotes. It can only be
explained by a symbiotic origin of eukaryotes, where archaea and bacteria both contributed to the
origin of these complex cells.

Tom Cavalier-Smith, who still champions the tree of life model, sees things differently. To him, the
archaea-like genes of yeast were simply those present in the last common ancestor of eukaryotes and
archaea; they reflect the fact that the two groups are sisters. According to this view, the first eukaryotes
had already evolved many of their complex features before they swallowed the bacterium that would
eventually become mitochondria. The bacteria-like genes in yeast and other modern eukaryotes either
come from these domesticated bacteria, or theyre slow-changing remnants of extremely ancient bacterial
ancestors.

Cavalier-Smith also says that the new study doesnt account for the fact that genes evolve at very different
rates. Some of the most important genes that shaped the evolution of the early eukaryotes have changed
so much that they cant be ascribed to either archaea or bacteria. Those genes tell an important story, but
theyre largely ignored by Cotton and McInerney.

And if theres one thing that everyone agrees on, its that yeast genes are only part of the picture. For a
start, yeast can survive without mitochondria. In eukaryotes that cant, such as animals, Lane thinks that
knocking out the bacterial genes would be far more costly. Martin agrees he thinks that the
importance of the archaeal hand-me-downs might vary from one species to another. Time and more
analyses will tell, he says.

This is not a debate thats going to be settled any time soon. Indeed, Woese emailed me simply to say that
he didnt want to get involved. Perhaps this is inevitable. The origin of eukaryotes whether through the
branching of a tree or the fusion of a ring was a critical event that took place billions of years ago. Its
singular importance makes it both endlessly fascinating and perhaps endlessly difficult to resolve.
Reference: PNAS http://dx.doi.org/10.1073/pnas.1000265107