Saturday, December 13, 2008

The Miller-Urey Experiment

The Origin of Life

Though Darwin’s theory of evolution applies to the diversification of biological life, not the origin of biological life, scientists have nonetheless attempted to find a naturalistic explanation of life’s origin through recourse to Darwinian type events. Competition between the first self-replicating molecules is thought to have led to increasingly efficient and complicated bio-molecules until the first primitive cell emerged. The question then is: where did these first self-replicated molecules come from? Every living thing known to science utilizes the same set of bio-molecules to reproduce: DNA, RNA, and proteins. These are enormously complicated molecules that, respectively, contain genetic information, the ability to translate and transport genetic information, and the ability to construct molecular machines (including other proteins) based on that information. Without all three components in place and functioning, there is no self-replication. The difficult task facing origin of life scientists is to discover which bio-molecule came first, and how, and then to show how the other bio-molecules developed to form the first reproducing organism.

Darwin himself thought that life may have arisen from a “warm little pond,” and in the early 20th century the scientists J.B.S. Haldane and A.I. Oparin independently speculated that a pre-biotic organic soup must have arisen early in the Earth’s history. Haldane and Oparin postulated a reducing atmosphere for the early Earth, an atmosphere containing abundant hydrogen, methane, ammonia, and water vapor. It was a logical assumption, as hydrogen is the most abundant element in the universe, and methane and ammonia are both hydrogen containing compounds. In this environment organic molecules were thought to naturally accumulate into the organic soup, and eventually, into life itself.

Miller’s Experiment

In 1953 a graduate student name Stanley Miller decided to test what may be called the “Oparin-Haldane Hypothesis.” Working under his advisor, Harold Urey, Miller created an experimental set-up to explore whether synthesis of organic molecules was possible in the hypothetical atmosphere of the early Earth.

Miller’s device (see Figure 1) contained three main compartments filled with water, methane, ammonia, and hydrogen. The water was boiled and electrical charges were sent through the vapors, which then passed into the next compartment and cooled and condensed. He ran the device for a week and then analyzed the resulting compounds. Miller discovered that among the compounds were some amino acids, the building blocks of proteins. This result sent a ripple through the scientific community. Miller had uncovered experimental evidence demonstrating the first steps of how life could have arisen purely through natural means. The experiment has become a staple in science textbooks, often accompanied by words like "the Miller-Urey experiment has shown that biological molecules can accumulate through natural means, and events like these led to the formation of life on Earth.1" But just how significant were Miller’s results?

Figure 1

First, it had been known for a century that organic compounds could be synthesized from inorganic ones, so the fact that organic materials can result from reactions with non-biological materials had already been discovered (Schopf 2002).

Second, it turns out that Miller’s experiment has several problems. One major problem with the Miller experiment is the assumption of a reducing atmosphere. Electrical sparks in an oxidizing atmosphere (like our current atmosphere) do not lead to any organic compounds. As mentioned above, the atmosphere was originally thought to be reducing (composed of hydrogen, methane, and ammonia) because of the abundance of hydrogen in the universe. The problem is that hydrogen is too light for earth's gravity to hold it, and it escapes out of our atmosphere (Brinkman 1969)(Catling et al. 2001). Geochemists and atmospheric scientists currently believe the Earth’s original atmosphere was neutral, not reducing (Miyakawa et al. 2002)(Shapiro 1986)(Schopf 2002)(Stanley 1999). The atmosphere came from the interior of the earth through volcanic outgassing. Small amounts of oxygen also had to be present due to photodissociation2, though the exact levels at which oxygen was present remain unclear (Brinkman 1969)(Stanley 1999). What is clear is that oxygen is present as far back as the rock record goes (Rosing and Frei 2003). In any case, it is now recognized that the early atmosphere was neutral and consisted of nitrogen, carbon dioxide, and water vapor with trace amounts of hydrogen, oxygen, and other gases (Schopf 2002)(Shapiro 1986)3.

In addition to hydrogen not being present except in trace amounts, the existence of methane and ammonia on the early Earth are also problematic. Since there was little oxygen on the early Earth, there was no ozone (O3) layer to absorb ultra-violet light. In addition, the younger sun would have produced ultra-violet light levels 30 times stronger than current levels (Schopf 2002)4. Methane and ammonia are both rapidly decomposed by UV rays and plausible suppliers of large amounts of these gases on the early earth do not exist. Neither could have been present on the early earth except in trace amounts (Schopf 2002)(Shapiro 1986). So, hydrogen, methane, and ammonia could at best be trace gases in the early atmosphere, but Miller's experiment postulated an atmosphere containing only them and water vapor. Clearly this is a fundamental flaw. Neutral atmospheres when sparked create only the simplest biological molecules, and this only with considerable hydrogen sources (Schopf 2002.) Since there are no plausible significant hydrogen sources for the early Earth's atmosphere, Miller’s experiment is something of a non-starter. However, there are other problems still.

Though it may seem trivial, the spark itself in Miller’s experiment is problematic, as there is no natural counterpart to the type of spark Miller used. He actually has tried simulating a lightning-type spark and, in his own words "very few organic compounds were produced and this discharge was not investigated further” (Shapiro 1986).

Miller's apparatus also contained a crucial piece: a trap which separated some of the resulting compounds, saving them from further exposure to energy. In nature, there is no such convenient trap, and the same energy that caused any molecules to bond would just as quickly (and in fact more commonly) break down those molecules. Energy is far more likely to break things down than to build them up. Effectively harnessing energy requires delicate, complicated, specific processes carried out by appropriate molecules. These processes do not occur in organic soup, and the soup would have moved toward equilibrium (the breakdown of all biological molecules is energetically favored in water) (Shapiro 1986)(Schopf 2002).
Interestingly, the specific arrangement of the device itself is in part responsible for the result of biological molecules. Miller had previously done the same experiment, with the same chemicals and spark, but with the pieces of the apparatus in a different arrangement and no biological molecules formed. The design of the apparatus favored the production of certain types of organic molecules, but in nature the process would not be so ordered (Shapiro 1986).

Ignoring all these problems, let us consider Miller's results anyway. The majority (85%) of the result can be referred to as tar, or organic goo, bearing no relevance to biological life (Shapiro 1986)(Schopf 2002). Of the approximately 50 major small organic compounds relevant to life, two were produced in Miller's experiments in a meaningful amount. These were the two simplest amino acids, glycine and alanine. There are twenty amino acids relevant to life, and though six were produced in Miller's experiment, only the aforementioned two were present in more than a miniscule amount. In addition, around half of the already small amounts of amino acids that were present are irrelevant to life due to the chirality problem (Shapiro 1986)(Schopf 2002). The chirality problem is that amino acids come in two forms, mirror images of the other. Only one type (the left-handed ones) are relevant to biology, and amino acids which spontaneously form will end being about half one type and half the other.

Miller’s results consisted of small amounts of a few of the molecules needed for life.5 The majority of a simple organism like a bacterium is composed of proteins (microscopic molecular machines), nucleic acids (DNA and RNA), polysaccharides (sugars), and lipids (fatty membranes). "None have been detected, in any amount, in a Miller-Urey experiment" (Shapiro 1986).


In short, even if the Miller experiment had turned out to simulate realistic conditions on the early Earth, its results are truly a most insignificant step toward figuring out how life arose. It is clear that the significance of this experiment has been grossly exaggerated. Miller himself has said as much. The severe problems with the experiment have led to interest in a variety of other ideas to explain the origin of life, including hydrothermal vents, meteorite seeding, and even panspermia (the idea that extraterrestrials planted the first life forms here).
So then, students should be taught that the Miller experiment is what it appears to be: a historically important but outdated and flawed experiment.

A further note: even if Miller’s experiment had generated every last biological molecule known to man, present in exactly the right proportions, we still would not have solved the origin of life. One could have all the right pieces together, in any conditions, and still “life” would not emerge. Scientists are unable to re-create any kind of cell even with all the right materials and controlled conditions. How then did it happen by accident on the early Earth?

1. Some modern textbooks do acknowledge the deficiencies in Miller’s experiments, but the Miller experiment remains an icon of pre-biotic evolution.
2. Photodissociation is the breakdown of H2O into hydrogen and oxygen by sunlight.
3. Scientists estimate that oxygen levels just 1% of current levels would prevent organic molecules from forming at all on the early earth.
4. The strong UV rays would have also instantly destroyed any biological molecules that had formed.
5. Subsequent Miller-type experiments have resulted in the production of almost all of the 20 amino acids found in proteins. While interesting, see the rest of this essay.

Works Cited

Brinkman, R.T., 1969, The photodissociation of water vapor, evolution of oxygen and escape of hydrogen in the earth’s atmosphere. PhD. Diss., California Institute of Technology,

Catling et al., 2001, Biogenic Methane, Hydrogen Escape, and the Irreversible Oxidation of the Early Earth. Science, 839-843

Miyakawa et al. 2002. Prebiotic synthesis from CO atmospheres: implications for the origin of life. PNAS, 14628-14631

Rosing, M.T. and Frei, R., 2003. U-rich Archaean sea-floor sediments from Greenland – indications of > 3700 Ma oxygenic photosynthesis. Earth and Planetary Science Letters, 237-244.

Schopf, W., ed. 2002. Life’s Origin: the beginnings of biological evolution, California, UCAL Press

Shapiro, R. 1986. Origins: a skeptic’s guide to the creation of life on earth, New York, Simon & Schuster Inc.

Stanley, S. 1999. Earth System History, New York, W.H. Freedman and Company

Friday, December 12, 2008

My Job

I am a manager, administrator, secretary, and accountant.

I am an evaluator, psychologist, counselor, and diplomat.

I am a scholar, scientist, historian, and student.

I am a teacher, and I don't get paid enough for this job.

Thursday, December 4, 2008

The Omnivore's Dilemma

I'm almost through the audiobook version of The Omnivore's Dilemma, and it's one of the most interesting books I've read in a while. If you eat food (and I'm pretty sure you do) you must read this book.