UCLA Genomicist James Lake Offers a New View on Evolution

James Lake has spent the past several years searching for insights into evolution by studying the genomes of single-celled organisms that lack a nucleus, like bacteria—prokaryotes—and organisms with a cellular nucleus, like plants, animals and fungi—eukaryotes. The research, conducted with his UCLA colleague Maria Rivera, has led to a startling conclusion: Where scholars had long thought that evolution resembles a tree, with life growing upward and branching out into new and more complex species, he found that it is also like a ring, with new species evolving from the transfer of genetic material between unrelated organisms.

"We wanted to title our research report 'One Ring to Rule Them All,'" Lake said in a presentation at AAAS, "but reviewers quickly threw that idea out."

The research seems esoteric, but it has dramatic implications for evolutionary science. And it is highly relevant for religious interpretations of the world and the origin of life.

"The realization that gene swapping, or horizontal gene transfer as it is called, is a common phenomenon has thrown the field into a tizzy," according to a story in the 16 July 2004 edition of the journal Science. "Borrowed genes can spread antibiotic resistance from one pathogen to another or help an organism survive new or stressful conditions. And it happens often enough to alter the dynamics of microbial communities and even affect the course of evolution."

Lake is an evolutionary genomicist and a professor in the department of molecular, cell and developmental biology at the University of California, Los Angeles. He detailed his findings in a 5 November lecture in Washington, D.C., sponsored by AAAS's Dialogue on Science, Ethics and Religion.

His analyses of four complete genomes showed that both prokaryotes and eukaryotes contain two classes of genes: informational and operational. The informational genes are involved in replication, transcription, translation and related processes. These genes are difficult to transfer, and their evolutionary lineage diverges resembling a tree-like pattern. Operational genes are primarily involved in essential functions, such as metabolic cycles, and are much easier to transfer. These genes transfer from organism to organism in a much more dynamic, horizontal manner.

We ordinarily think of gene transfer occurring between generations—from parents to offspring. But, it has become clear that genetic material, DNA, is released by organisms into the environment, where it picked up by other organisms not related by reproduction.

This horizontal gene transfer is genetic cooperation, and can be likened to the Internet. "Before the days of the Internet, we might take several years to write a program," said Lake. "Now we can usually find what we need on the Internet, and it saves us a lot of time." Similarly, he went on to say, "if a bacterium is missing a gene that it needs to survive, it'll go searching for what it needs, sometimes getting it, sometimes getting a virus."

This genetic cooperation that has led to the high amount of diversity in prokaryotes because it has made possible a greater degree of genetic exchange than is possible through reproductive processes. Bacteria that do not share genes, that attempt to isolate themselves from horizontal gene transfer, do not thrive as well. The diversity in eukaryotes is not as deep. The discovery of the vast amount of horizontal gene transfer at the bacterial level enriches contemporary evolutionary theory that descends from Darwin's original insights.

In addition, horizontal gene transfer provides a possible new understanding of the formation of eukaryotes from prokaryotes. Lake and his colleagues at UCLA's Molecular Biology Institute[link: http://www.mbi.ucla.edu/] have found evidence from gene analysis that supports a model of eukaryote formation through the fusion of two disparate prokaryotes. Such a model is consistent with other fusion theories in evolution, such as the evolution of mitochondria and other organelles.

The interconnectedness of life in evolutionary terms is often described in relation to common ancestors, But horizontal gene transfer allows different organisms to be related in another way, by sharing genes through horizontal transfer. Having genetically diverse organisms in an environment, where they are able to draw on that diversity in the face of environmental pressures, increase the viability of the population.

"Life is interrelated," said Lake. "Every change we make affects the environment. Diversity is necessary to maintain a robust population."

Antje Jackelén, director of the Zygon Center for Religion and Science at the Lutheran School of Theology in Chicago, discussed the implications of models of evolutionary cooperation instead of competition. She noted that "concepts used in science often have an ideological component," and advocated care in how these terms are discussed.

"To use the word 'cooperation' with eukaryotes anthropomorphizes them," Jackelén said. But she also observed that in the larger society common language "has to be used to explain scientific concepts. One can't just use equations and fully understand. Ordinary language is important."

The impact on contemporary discussions of science and religion may also be that once-simple arguments are now more complicated. Reflecting on the contrast between bacteria that isolate themselves to their evolutionary disadvantage and those that engage actively in horizontal gene transfer and so are able to draw on a richer reservoir of genetic material, she suggested an analogy in the arena of religious thought.

"Neatly separated and closed systems are less likely to be true," or viable, and she cautioned against a theological paradigm in which "disorder," like the freewheeling messiness of horizontal gene transfer, "is ignored, explained away, or worse, written off as sin." Being able to draw on theological resources beyond the historically linear tradition is likely to result in a more robust theological position.

Instead, said Jackelén, as in the case of informational and operational genes, "we must find a way to accept the dual experience of stability and change."

— Kelly Gayden

16 November 2004