This year science has made important progress on one of the truly big questions in biology: The origin of life.
There are three general theories about the origin of life:
1. Special creation. Some scientists believe life was placed on earth by a supernatural or divine power.
2. Extraterrestrial origin. Others believe that life was carried to earth from a planet of some other star.
3. Spontaneous origin. Most scientists accept — tentatively — the theory that life arose spontaneously here on earth from inanimate matter, as associations of molecules became more and more complex.
Only the third of these theories is subject to test, and for many years scientists have been trying to do just that. The logical way to test the spontaneous origin theory is to repeat the process. In 1953 Stanley Miller and Harold Urey assembled in a glass flask an atmosphere similar to what the early earth’s atmosphere is thought to have been like. It was a smelly sort of atmosphere, composed of hydrogen-rich molecules like hydrogen sulfide [SH2] (“rotten eggs”), methane [CH3] (“swamp gas”), and ammonia [NH4] (“smelling salts”).
Bombarding the mixture with lightening in the form of sparks, Miller and Urey found that within a week 15% of the carbon originally present as methane gas had been converted into other carbon compounds, including amino acids (the building blocks of proteins) and nucleotides (the building blocks of nucleic acids like DNA and RNA). They concluded that the basic building blocks used in the construction of living organisms could indeed have arisen spontaneously.
The next step predicted by the spontaneous origin theory has not been so easy to test — that these building blocks spontaneously linked together to form the large molecules of which cells are made. Somehow, the individual amino acids produced in the Miller-Urey experiment must have linked together in chains to form proteins, like pearls coming together to form a necklace.
This linking-together presents what at first seems an insurmountable problem: theory tells us that it is chemically impossible for amino acids to aggregate spontaneously in water. Without going into the chemistry, the basic problem is that water will tend to push the chemical reaction backwards, towards breaking up proteins rather than forming them.
One way out of this quandary is to imagine that life first arose away from water, say within a clay or mineral. While a little zany, this idea has attracted serious consideration, at least to some degree because it is hard to think of other water-free alternatives.
Another way out of the quandary is to step back and look at the problem from a different perspective. There is lots of water in each cell of your body, and yet proteins get
assembled in your cells with no difficulty. Water presents no problem there, because in cells the process of protein assembly does not actually occur out in the water. Instead, it is carried out within great contraptions called ribosomes, and there is no water inside a ribosome.
Ribosomes are very complex cellular machines. Each ribosome is made of over 50 different proteins, as well as three chains of RNA composed of some 3000 nucleotides (RNA is a nucleic acid similar to DNA but single-stranded). It has been traditionally assumed that the proteins act as enzymes to catalyze the amino acid assembly process, with RNA adding the information saying which amino acid goes where.
But if proteins in ribosomes catalyze the linking together of amino acids to form proteins, then where did the ribosome proteins come from?
This year we learned the answer to that chicken-or-egg question, and a surprising answer it turned out to be. Over the last 12 months, several research groups have used powerful X-ray diffraction to determine the complete detailed structure of a ribosome at atomic resolution.
The researchers found that the many proteins of a ribosome are scattered over its surface like decorations on a Christmas tree. The role of these proteins seems to be to stabilize the many bends and twists of the RNA chains, the proteins acting like spot-welds between the RNA strands they touch. Importantly, there are no proteins on the inside of the ribosome where the chemistry of protein synthesis takes place — just twists of RNA. Thus it is the ribosome’s RNA, not its protein, that catalyzes the joining together of amino acids! Science, the most widely-read scientific journal in the United States, chose this discovery as the second-most-important scientific discovery of 2000 (runner-up to completion of the human genome project).
This discovery that protein synthesis is RNA-catalyzed dissolves the quandary of spontaneous assembly. RNA nucleotides are produced in Miller-Urey experiments and can spontaneously link together to form chains. RNA chains can act as enzymes to catalyze the linking together of amino acids to form proteins. There is a great deal we don’t know, but the theory of spontaneous origin seems to have passed another hurdle.
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