Sunday, July 16, 2017

Could DNA Evolve?

I recently posted about the nature of DNA,1 how it is found in every living thing on Earth, and how every living thing—no matter how far back you go—uses the same DNA-RNA-protein coding system. It’s not just similar in every microbe, plant, and animal. It’s the same system, down to the smallest details of chemistry, arrangement, and function.

To me, this is like discovering that every car on the road has the same motive power: a four-stroke, four-cylinder, inline, fuel-injected, internal-combustion engine, all with the same valve timing and compression ratio, and all burning the same grade of gasoline. With a little imagination, you might be able to conceive of an internal-combustion engine that burned kerosene or diesel fuel. You could invent a block with two, six, eight, or ten cylinders. You could design in your head a configuration with the cylinders arranged in either flat opposed pairs or a V shape. With more imagination, you could imagine the power cycle simplified to two strokes, so that exhaust and intake occurred on the same stroke, and every combustion stroke was followed by a compression stroke. You could think of ways to introduce the fuel into the cylinder other than by injecting it with a nozzle—say, by spritzing it into the air flow through the throttle body and call it “carburation.” You could even think of external combustion processes, like a steam engine. Or engines that had no cylinders and pistons at all, like a turbine.

All of these variations are possible to think about. But in the world I’m describing, they don’t exist. Every car on the road is a fuel-injected inline four. More than that, every pickup truck, semitrailer tractor, farm tractor, and motorcycle has this type of engine. So, too, does every weed whacker, lawn mower, water pump, and air compressor. Also every airplane, helicopter, and railroad locomotive. If it moves in this world, it is powered by an inline four-cylinder engine of the same exact specifications. Some engines would have larger or smaller cylinder volumes than others, but all have the same arrangement, operating principle, and fuel needs.

After thinking about this for a bit more, you might reach one of two conclusions. The first is that the fuel-injected inline four is just so perfect an engine that the designers, manufacturers, and users of cars, trucks, airplanes, and farm equipment simply had no reason to try anything different. The second thought is that maybe the engine wasn’t invented around here but brought into this world in its fully developed state from someplace else.

This is where I end up thinking about DNA. Either the DNA-RNA-protein coding system was just so robust and efficient that it outperformed and overcame all other possible chemical coding systems during Earth’s earliest history—so early that no trace of these competing systems remains on the planet. Not as some feeble microbe hiding in a deep cave somewhere. Not as a tiny mite making an inconspicuous living on DNA’s droppings in the sandy desert soil or the ooze at the bottom of the deep ocean. Either that, or coding system for all the planet’s known life forms went through its development and evolutionary stages somewhere else in the universe and blew into Earth’s early atmosphere as a microbial spore, or arrived as skin cells shed inside a visiting astronaut’s lost glove, or was seeded here with a package launched by galactic gardeners from another star system.2

The obvious answer—once you accept either premise, ultimate efficiency or astronaut’s gift—is that the DNA system itself simply can’t evolve. Once the fragile molecular chain floating in the salt brine of a tide pool stops trying to arrange itself and starts calling for the protein and lipid sequences to build a membrane around the first single-celled, prokaryotic organism, the system is locked in place. That first cell, whether it leaned toward the plant-way or the animal-way, used the DNA coding system to build its internal organelles and external membrane, to regulate its operations by a cascade of enzymes, to feed itself through the breakdown of carbon compounds and the buildup of the energy molecule adenosine triphosphate (ATP) inside its mitochondria, and to conduct all the other processes to which the cell had become accustomed. Once the living organism was dependent on using this coding system to process the amino acids it needed to build proteins, and then to build those same proteins over and over again as the cell grew and expanded, its fate was sealed.

The DNA code—its sequence of its base pairs—might be changed, or mutated, either by chemical challenges or by radiation effects from the external environment. Change the letters of the code, and it will—sometimes, but not always, depending on the letter’s position in the three-base codon—call for a different amino acid and so create a different protein. The new protein might be slightly different in structure and function from what the code called for before, or it might be very different. That is how evolution works: accidents to the DNA sequence create changes in proteins that either hurt the cell inheriting the new code, or that have no present effect but allow this cell to prosper amongst its sisters when the environment changes—as the environment continually does—or, occasionally, that improve the cell’s functioning right away in the present environment.

The code itself is resilient, because many of the sixty-four possible combinations of four bases in a three-base reading frame call for the same amino acid, and the third base in the codon can usually be changed without effect—which is why it’s called the “wobble.” But also, most proteins are big enough and complex enough—with enough amino acids chained together—that changing out one or two amino acids in their makeup has little effect on structure or function. And then, most protein changes are not either beneficial or lethal to the organism right away, but instead they hang around and make themselves felt when the environment changes and then they either benefit or kill off one set of genetic inheritances over a competing sister line with a different inheritance.

The whole system is slippery and wobbly in its effects, in the exact sequence of DNA and RNA bases, the choices among amino acids, and the production of proteins. But this is like saying that a flatbed printing press can produce many different documents, based on how the lines of monotype letters are arranged in its iron frame. To create all those different documents, however, the press always uses a predetermined alphabet of type blocks, sets them up in the same framework, inks them the same way every time, lays the paper on them in the same place, and applies the same amount of pressure with the platen. The coding changes all over the place, but the coding system remains the same.

If the DNA-RNA-protein system could evolve and change, that would create chaos within the cell—wouldn’t it? If a new fifth purine or pyrimidine base were added to the existing four, it would scramble the DNA sequence. First, because it would have no complementary base to pair with, as A always pairs with T, and C pairs with G. A fifth base—say, the purine xanthine (X)—would just sit there filling a hole, like the empty socket in a jaw that’s missing a tooth. Having nothing to pair with, the new base would scramble the code, much as the upper tooth over an empty socket has no way to provide bite pressure. Second, if somehow two bases could be added and paired up at the same time—matching that X with, say, the pyrimidine orotic acid (O)—their popping up together in the sequence would still scramble the code. Even if the new bases could be recognized and transcribed into messenger RNA, the existing ribosome in the cell body would have no way to translate either of them into one of the possible amino-acid choices for the next position in the developing protein strand. And if somehow the new X and O bases were added to the existing code and intended to call for some new amino acid—beyond the twenty that now make up all microbial, animal, plant, and human proteins—that would simply create another toothless gap, because the cell’s internal processes are not yet geared to manufacture, collect, or supply this new amino acid in any quantity.

And all this is just to consider the evolution of the DNA-RNA-protein system inside a single prokaryotic cell. Such cells reproduce by continually growing all their contents and expanding to the point of rupture, at which time they replicate their DNA strands, divide and haul off the resulting new chromosomes to opposite ends of the cell body, pinch off the cell membrane in the middle, split into two new cells, and trot on. If the existing parent cell had somehow survived the chaos of introducing at least two new bases, transcribing them successfully into messenger RNA, happening to have the right kinds of new amino acids on hand, and then using the new protein in a constructive manner … then no problem. The two daughter cells produced by the split would inherit this newly evolved DNA-RNA-protein coding system and continue to function with it.

But in the eukaryotic domain, whose cells contain their DNA in a separate nucleus, most reproduction is by sexual joining.3 Two organisms come together, usually by one contributing an egg and the other fertilizing it with sperm, in order to create a new and unique individual. That individual differs genetically from either parent, and so sexual reproduction increases the amount of genetic variation—and thus the possibility for new combinations of mutations, more changes, more adaptations—in the species. But sexual reproduction puts a powerful limit on the evolution of the DNA coding system. An individual who might somehow evolve in his or her germline a new set of X-O base pairs, a new corresponding messenger RNA sequence, a modified ribosome to translate the new code, and a new and unusual set of amino acids to be used by it … would then be a genetic freak. To reproduce and pass all this newness along to the next generation, she or he would have to meet up with a breeding partner who had similar equipment. Chromosomes in sexually reproducing species come in pairs, one from the mother aligning with one from the father. Unless the individual with the newly evolved DNA could meet someone with the same evolved system, the breeding line would die out. The evolved system would disappear in the first, nonexistent generation.

Or would it? If the evolved DNA was in a male, it would probably disappear, because the sperm provides nothing but raw coding to the next generation. But if the altered individual was female, and her egg contained the mechanisms for the novel transcription and translation—appropriate RNA, ribosome, and amino-acid processes—then the offspring might survive. It would make the usual proteins from the traditional DNA chromosome pairs supplied by both the mother and the father, and it would make new proteins with the X-O-contaminated chromosomes and adapted cellular machinery supplied by the mother. Over time, and with enough generations—probably passing down the female side at first, like the mitochondria in the mother’s egg, because of all that cellular machinery—the new DNA system might spread through the population of both females and males. In fact, it probably would spread if it conferred advantages of more flexibility, more adaptability, more robustness. Eventually, certain species that had an improved six-base DNA, perhaps in a larger, four-base reading frame, and calling on more than twenty amino acids to create novel proteins, would appear in generations that could be traced back to the evolutionary split. Eventually, the older style of DNA with just four bases in a three-base reading frame might disappear in all the different animals or plants that evolved from that revolutionary ancestor. As a result, we might see two separate populations differing in their fundamental DNA system.

Such a systemic evolution would not be easy. It might first appear as a byproduct: one gene on a fragmentary chromosome, off to one side in the cell body or in the nucleus, making its own special proteins, and not interfering with the regular business of the cell. It would have its own RNA. And the ribosome out in the cell body, being a highly adaptable structure, might quickly evolve to make use of these new messenger RNAs with their strange coding. The new system might start out sex-linked to the female line, as certain genes are now linked to the male line’s Y chromosome. If a six-base DNA—or any other systemic variant—had any greater adaptive power or offered more evolutionary advantage to a cell line, it might certainly develop out of the existing four-base system. And some of its daughter cells might not be so chaotically disrupted that the old system would out-compete them in every environment. A hybridized cell, using both DNA systems at first, but perhaps eventually singling up on the newer model, could survive somewhere, in some environment, someplace on Earth.

With a little imagination, it could happen. But it didn’t. We live in a world without two-stroke engines, without two- or six- or eight-cylinder engines, and with no trace of a steam engine or a carburetor in our developmental history. Everywhere we look it’s just fuel-injected, four-cylinder, inline engines and always has been. And I still wonder why.

1. See The God Molecule from May 28, 2017.

2. The third alternative is that the DNA-RNA-protein coding system was thought up and then cooked up by a genius god with a PhD in molecular biology. But as soon as you start allowing for the supernatural, then all sorts of “just-so” stories become possible and the whole world is simply a giant miracle.

3. Once you get beyond the single-celled eukaryote variants such as the algae, yeasts, and protozoa.

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