Thursday, July 28, 2011

Chicken and Egg

The toughest problem in evolution has always been origins. Once scientists figured out the way the skills of life were partitioned among DNA, RNA and proteins, the question became how the whole complex system could have originated. Bacterium, yeast, tree, worm, dinosaur and human looked pretty different until we started figuring out how they all worked, but once we had they all started looking pretty similar. Inside each is (almost) the very same system of DNA genes, RNA helpers and proteins, doing the same things to keep us all alive. This fact is stupendously obvious signal of the common origin of all life, but it’s a lot more silent on the question of what those origins were.

We have a pretty clear if imperfect picture of how tree and dinosaur evolved out of bacteria, but we have many fewer clues as to how the first bacteria evolved out of non-living chemicals. The real problem is that neither contemporary life nor the fossil record has preserved anything much in the way of intermediate types.

Proteins are the great general purpose contractors of life. Living systems rely heavily on them for construction, and they are both the builders and much of the building materials. They are girders, scaffolds, and master chemists regulating each other. One thing they don’t seem to be able to do is store plans for building themselves or each other. The plan storing has been outsourced to DNA, and DNA does a very good job. It has hardly any other. But DNA unaided can’t transform its stored plans into proteins, nor can DNA and protein alone together do that job. For that you need RNA. One form of RNA (mRNA) temporarily stores working copies or construction plans for genes, and two other, with some help from proteins, do the actual work of protein manufacture.

It’s an intricate and highly interdependent system. Each part is highly complex and deeply dependent on the others, so how could the whole intricate apparatus have come into being? How could intermediate steps have sustained themselves long enough to evolve? This is the great puzzle of origins.

Nobody knows the answer, but a promising clue was found half a century ago, and clever scientists have been putting the resulting idea to the test. The clue was that RNA was capable of doing the crucial functions of both the other key ingredients of life. Like DNA, is has the capability to store information, and like proteins it can catalyze chemical reactions. It’s not as good at either of those things as DNA and protein, but in a pre DNA world, we can imagine a self-sufficient RNA world.

There is a critical step without which nothing can work. You need a chemical that can catalyze its own formation – the simplest kind of reproduction we can imagine.

Such a chemical solves the old chicken versus egg problem (which came first?) by being both chicken and egg. It seems that researchers in artificial life have solved that problem – they have created RNA molecules which, given appropriate nutrients, can reproduce themselves. Not only that, they can evolve in a test tube.

Dennis Overbye, writing in the New York Times, has some of the interesting details and some hints of where this could go next.

Four years ago Dr. Joyce and a graduate student, Tracey A. Lincoln, now a researcher at the University of Massachusetts Medical School, evolved a molecule in a test tube that could replicate and evolve all by itself, swapping little jerry-built genes in a test tube forever, as long as it was supplied with the right carefully engineered ingredients.

An article in the Joyce Laboratory newsletter called it “The Immortal Molecule.” Dr. Joyce’s molecule is a form of RNA, or ribonucleic acid, which plays Robin to DNA’s Batman in Life As We Do Know It, assembling proteins in accordance with the blueprint encoded in DNA. Neither RNA nor DNA is alive by itself, any more than any other chemical, like bleach, or a protein. But in Dr. Joyce’s test tube, his specially engineered RNA molecule comes close, copying itself over and over, and evolving.

But, Dr. Joyce says, “We really would hope for more from our molecules than just replicating.”

Reproduction is the job of any life, he explained, but Earthly organisms have evolved a spectacular set of tricks to improve the odds of success — everything from peacock feathers to whale songs. Dr. Joyce’s molecules have not yet surprised him by striking out on their own to invent the molecular equivalent of writing a hit pop song.

It is only a matter of time, he said, before they do.
“Our job is to give them the running room to do that,” Dr. Joyce said.

It’s much easier how to imagine how one molecule with autocatalytic capabilities could have arisen by spontaneous and accidental processes than to imagine how three intricately interconnected such systems could have.

We are still well short of a detailed theory of the origin of life, but now we have a promising candidate.