On the Human Condition
Volume XXVIII Number 2
Photo © Tyagan Miller
Daphnia pulex, the water flea
Photo by P.D.N. Herbert, University of Guelph
Evolution By Chance
By the close of 2005, scientists had sequenced the full set of genetic information--or genomes--of more than 300 organisms, from bacteria to human beings. We know now that relatively large organisms, like humans, have enormous, messy genomes. The genomes of tiny organisms, like bacteria, are compact and neat.
Common sense might dictate that our human genome needs to be more complex simply because we are large organisms. But it turns out that much of the additional material in our genome serves no clear purpose. It's just clutter. So why is it there?
Distinguished Professor and evolutionary biologist Michael Lynch came to Indiana University Bloomington in 2001 to answer that question. In doing so, he has provided new insight into how evolution works.
Lynch studies two of the broadest and most divergent categories of life on earth. First are the prokaryotes, a wildly diverse group of tiny organisms united only by their lack of a nucleus, a compartment that in other types of organisms houses genetic material. All the bacteria on Earth are prokaryotes, as are a peculiar group of organisms known collectively as Archaea, which live in places including geysers, sewage, and the guts of termites.
At the other end of the spectrum are eukaryotes, a division including every organism that has a nucleus. We are eukaryotes. So are plants, insects, and the parasites that cause malaria, amebic dysentery, and giardiasis.
Part of what makes our human genome so much more complicated than that of bacteria is the structure of our genes. Composed of the genetic material DNA, genes can be thought of as "words" made up of the letters A, T, C, and G, which are DNA's chemical alphabet.
A bacterium's genes consist of unbroken strings of these letters. All the genes in a bacterium's genome are laid out end to end. When one gene sequence ends, another begins. There's so little wasted space that the endpoints of some genes even overlap the beginnings of others, Lynch says.
Compared to the bacterial genome, ours is a neat freak's worst nightmare. Our genes are broken up by stretches of DNA thousands of letters long that serve no apparent purpose. Many thousands or even millions of letters separate one gene in the genome from the next. Reading our genome is akin to reading a book in which each word is broken up with extra letters, and individual words are separated by pages and pages of gobbledygook.
In 2003, Lynch proposed a groundbreaking hypothesis to explain this disparity in genetic organization. Ancient populations of eukaryotes were far smaller than those of prokaryotes, he says. And according to the laws of population genetics, natural selection--the phenomenon that culls less-than-stellar variation from populations--simply isn't as effective in smaller populations.
In Lynch's scenario, random mutations that arose by chance, such as the inclusion of extra DNA in a gene, slipped past natural selection, building up in populations over the billions of years that eukaryotes have evolved. The buildup of mutations in small populations--a phenomenon known as "drift"--can outpace natural selection, leading some characteristics to become established in populations even if they don't make evolutionary sense. It all boils down to a game of numbers: the smaller the number of individuals in a species, the greater the role chance plays in the evolution of its genome.
Lynch's approach turns some of the conventional thinking about the genome on its head. "I argue that a lot of the complexity you see in genomes can't be explained by natural selection. It's the ineffectiveness of natural selection that leads to what we see," he says.
His idea hasn't gone unnoticed in the scientific community, says Eugene Koonin, a senior investigator with the National Center for Biotechnology Information in Bethesda, Maryland. "Mike's theory is the baseline from which everyone will start to explain how the evolution of complex genomes took place," he says. "It gives us for the first time the simplest explanation for how high levels of complexity could have evolved in the absence of natural selection."
Nor has his research been ignored by the intelligent design (ID) community. "I push this idea of what we call non-Darwinian processes--drift and mutation," says Lynch. "But people in the ID community always take it out of context. They hear 'non-Darwinian,' and they read that as non-evolution, because they equate evolution with natural selection. So they love to quote me."
It's a subtle but significant point. Natural selection, sometimes called "Darwinian selection," is only one of several mechanisms by which evolution proceeds. Even Charles Darwin himself argued that natural selection was not the only agent of evolution. Lynch agrees, emphasizing the role of chance events in genome evolution.
An Evolving View of Evolution
As it turns out, Lynch's approach to explaining genome complexity might be just what evolution needs to withstand criticisms leveled by the ID community. The popular misconception about evolution is that it proceeds entirely by natural selection and that it always benefits species, Lynch explains. The problem with this understanding is that it makes evolution via natural selection sound to some like evolution with a purpose. "Explaining everything in the natural world with natural selection is not that different from intelligent design," he says. "An intelligent design person just says well, here's something complex, let's just invoke an intelligent designer. If you're willing to invoke natural selection to explain everything, that's not science. It doesn't explain anything to simply say, 'natural selection did it.' Mutations don't arise de novo [anew] at the whim of natural selection."
Numerous random changes accumulate in the genome. Some of those changes work, but most don't. What we see in organisms today isn't necessarily the most ideally adapted form, but instead what's simply good enough. Indeed, many experts in evolution share this view, but it's a view that has not made it into the popular understanding.
For proof that evolution doesn't always produce the most ideally or intelligently designed organism, we need look no further than our own DNA. "You can really think of the human genome as the epitome of an unintelligent design," Lynch says. "It's the biggest mess of a genome." If anything, maybe our genomes could learn a lesson or two in organization from the tidy bacteria.
For additional proof, Lynch points to the mathematical underpinning of evolution.
"There's a rigorous theoretical framework behind evolution, and we know it works. It's a quantitative framework. Evolution is not a soft science," he says.
Evolution works at the level of the population, which means the mathematical laws of population genetics explain how evolution behaves. Unfortunately, Lynch says, many students today don't learn this mathematical framework. This leaves them ill equipped to make valid arguments about evolution based in the laws of inheritance, mutation, and drift, he says. "You need population genetics to tell you where reality is," Lynch says.
He believes much of the public misconception surrounding evolution stems from a disconnect between how evolution actually works and how it is taught to students and represented in much of the popular press. "Many spokespersons for evolution don't have a thorough understanding of evolution," he says. "I think they're doing somewhat of a disservice to our field by focusing just on Darwinian processes, which allows IDers to push them into a corner."
"It's partly our fault," he says of his larger community of evolutionary biologists. "If you're a physicist, you don't want to spend your career convincing flat-earthers that the earth is round," he quips. "I don't want to spend all my time defending and explaining evolution."
To mend the disconnect, he suggests that he and his colleagues start teaching evolution differently in high school and college classrooms. "Some of evolutionary theory is grounded in basic algebra, which would provide a lot of good exercises for basic biology students."
The Accidental Biologist
For someone who's made so many significant contributions to his field, Lynch attributes much of his success to serendipity. He grew up fascinated by the natural world, but as the first in his family to attend college, he says he didn't recognize the range of possibilities in studying biology. "I thought since I enjoyed biology I should become a doctor," he says. He began applying to medical schools his junior year. At the same time, he started working with an ecologist at his college, and by the time his medical school acceptance letters arrived, Lynch had changed his mind about his future. He applied to several graduate schools and headed off to the University of Minnesota, where he performed some of the first studies to manipulate predator and prey communities in freshwater lakes and ponds. Those studies helped form the foundation for countless future studies of community ecology.
One of the organisms Lynch studied early in his career is a tiny crustacean--a relative of crabs, shrimp, and lobsters--called Daphnia. His career drifted away from Daphnia as he moved into population genetics and evolution. Today, though, Lynch has come full circle as one of the principal investigators of the just-launched Daphnia Genomics Consortium, an international collaboration housed at IU's Center for Genomics and Bioinformatics and supported by the National Science Foundation.
Lynch and his colleagues recently completed a sequence of the Daphnia genome--the first crustacean to have its genome sequenced. They plan to use it as a model organism in the emerging field of ecological genomics, or the study of genes in their natural environments. Daphnia have been the subject of ecological studies in their natural environments for more than 100 years, making it "a great new model organism," Lynch says. "We don't know anything about the natural ecology of the standard model organisms in biology such as the worm or the fruit fly." By pairing genetics with ecological studies, Lynch and his colleagues aim to better understand what it takes, at the genetic level, to survive in a given environment.
Daphnia also happens to be one of the primary animals the U. S. Environmental Protection Agency uses to set regulatory limits for pollution levels, Lynch says. Toxicity tests, however, tell researchers only the lethal dosage of a compound without providing any information about how a toxin kills. "In these tests, you put the organism in some effluent, and see how long it takes for it to die. But you never know why--you just know there's something bad in there," he says.
With the Daphnia genome in hand, he and his colleagues will now be able to show, for the first time, which genes are affected by environmental toxins. "Now we'll be able to put Daphnia in some environment and know the expression of every gene in its genome. Presumably, this will help unravel what's going on with any number of environmental toxins," he says.
Early in his career, Lynch says, there was no good way to combine his ecological and genetic approaches to studying Daphnia. Now, he says, "we finally have a way to do that, and a critical mass of colleagues interested in pursuing such studies, especially in the IU Center for Genomics and Bioinformatics. It's been really interesting to finally get to IU where we have the whole genome, the genetic map, the whole works."
Evolution operates in the context of the environment, Lynch says--a dictum that applies equally to genomes and scientific careers.
Jennifer Cutraro is a freelance science writer in Boston, Mass.