Molecular Evolution: Investigating the Genetic Books of Life Reveals New Details of 'Descent with Modification' and the Forces Driving It

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Charles Darwin didn't know about genes and DNA. In fact, hardly anyone noticed when Gregor Mendel, a monk whose pea experiments eventually led to modern genetics, published his findings in an obscure journal a few years after Darwin's On the Origin of Species appeared in 1859. It would take nearly a century more before James Watson and Francis Crick deciphered the structure of DNA, the molecule that contains the manual for building an organism. Yet Darwin was still able to describe a mechanism--natural selection--for how evolution shapes life on Earth. That's like describing how a car works without knowing about the existence of internal combustion engines.

While Darwin achieved his insights without molecular help, biologists today are intimately familiar with the molecules responsible for the diverse array of organisms that populate the planet. The study of genes has revealed evolution as essentially a high-stakes poker game in which organisms draw randomly from a deck of genetic choices. At stake is the chance to pass along genes to the next generation. Sometimes the hand is good enough to get ahead, but some hands are losers, perhaps to the extent of extinction. By studying the winners, scientists are learning how the forces of evolution work on DNA, the biochemical repository of an organism's entire natural history. DNA records the mutations that helped some animals to survive ice ages while others perished, the nips and tucks that make animals more attractive to mates, the big leaps that allowed plants to become domestic crops--they're all there, written out in a simple alphabet of four letters.

Each organism's book of life is contained in its genome, and scientists have been hard at work creating a library of species's books. Comparing the genomes of different creatures will help researchers learn the history of how life on Earth has evolved.

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But many questions remain. Scientists still don't know how cells first formed, including how former bacteria came to live inside cells as mitochondria or chloroplasts. Another mystery is how the complex structure of genes in eukaryotes--organisms in which the genetic material is encased in a nucleus--evolved. One of the biggest issues is whether life on Earth was destined to evolve the way it has.

Limits on evolution Play a poker game, rewind it to the beginning, start again and see what happens. Would the game play out the same every time? Stephen Jay Gould, the late paleontologist, didn't think so. If you restart the game, the shuffled cards will turn up a little different each time, and the exact order in which the cards are drawn can have profound consequences for the outcome. Replaying the "tape of life" from some point in the past would produce very different life-forms than the ones we have today, Gould thought.

Other scientists disagree. Organisms are dealt a finite number of genes and so must choose from a limited menu of evolutionary options, narrowing the directions the organisms can go in a particular environment. "The evolutionary routes are many, but the destinations are limited," says paleontologist Simon Conway Morris of the University of Cambridge in England. As a result, organisms often end up independently developing the same sorts of structures to solve a particular problem. Although the details of how eyes work vary between species, for example, the basic structures are similar.

While it's impossible to turn back time (no matter how easy Superman makes it look) and replay all of evolution again, scientists have devised other ways to investigate the issue.

Richard Lenski, an evolutionary biologist at Michigan State University in East Lansing, is among the scientists hitting the rewind button on evolution. Meter-high letters taped to the windows of his lab spell out the lab's motto: EVOLVE. In the center of the "O," the face of Charles Darwin peers out toward the football stadium. …