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Elizabeth Pennisi: February 2009 Archives

Nescent Darwin Meeting Image A chilling tale of science, romance, politics, and death in the Soviet Union set the stage for the National Evolutionary Synthesis Center’s (NESCent's) third annual Darwin Day Symposium, held on 21 February at the Sigma Xi Center in Durham, North Carolina. The birthday boy himself was rarely mentioned; rather, the event emphasized modern applied evolution. Theodosius Dobzhansky famously wrote in 1973, "Nothing in biology makes sense except in light of evolution." But, as speaker Fred Gould pointed out, evolution has become far more than a way to make sense of things. “Today, your quality of life depends on application of a rigorous understanding of evolution,” he argued. And thus began a series of talks that addressed evolutionary approaches to practical challenges in agriculture, disease, and conservation.

But first, Gould provided the opening historical overview—a convoluted story centered on Soviet geneticist Nikolai Vavilov (1887-1943) and his nemesis, state-supported pseudoscientist Trofim Lysenko (1898-1976). Vavilov is best known for his studies of global crop evolution and diversity, as well as his efforts to breed better cereal crops based on Mendelian genetics. Lysenko, on the other hand, is remembered as a proponent of crackpot notions about the inheritance of acquired traits. Despite his more valid scientific approach, Vavilov fell out of favor with socialist leaders and died of starvation in prison, after criticizing Lysenko’s unfounded claims. Gould’s account (like this recent article in The New York Times) was a clear reminder that the practice of science has been, and still is, shaped by its political and ideological milieu.

“You trashed our heroes,” lamented one audience member after hearing how the evolutionary giants Ronald Fisher, Francis Galton, and J.B.S. Haldane supported eugenics or Lysenkoism. But Gould and the other speakers were ready to add their own stories of how politics and ideology affect the way they fund or present their work. Gould, for instance, believes that genetically engineered insects can be used to manage medically and economically important insect pests. But he worries that this approach will meet with resistance because of current attitudes toward genetically modified crops and the big businesses that market them.

Barbara Schaal encountered a different kind of roadblock in her work on the evolutionary genetics of cassava. Although it is a dietary staple in much of the developing world, cassava lacks many important nutrients. Millions would benefit from an improved cassava—but because it is not a cash crop and is not grown in the United States, Schaal found it difficult to fund her initial research. Eventually, her team produced molecular phylogenies of cassava and its wild relatives to pinpoint the crop’s likely origin in the Brazilian Amazon. There, they discovered that villagers were growing varieties with vitamins, pigments, and sugars unknown in the common domestic cassava. Some of those varieties are now involved in a project, funded by the Gates Foundation, to produce a nutritionally complete cassava for widespread cultivation.

Daniel Faith came all the way from Sydney, Australia, to discuss how evolutionary biology can help prioritize conservation areas. His research is part of a growing body of work that highlights the importance of plant phylogenetic diversity, rather than total species diversity, in preserving the characteristics of an ecosystem. Regions with the greatest phylogenetic diversity include more distantly related species and represent evolutionary history more completely—even if they include fewer total species. Faith argues that phylogenetic diversity should, therefore, inform conservation decisions, but he also talked about the challenge of communicating and applying the results without embracing a “naïve efficiency” that sanctions extinction as long as phylogenetic diversity is preserved.

Katia Koelle left the macroscopic world of plants and entered the invisible realm of viruses. She described how an improved understanding of rapid viral evolution can inform efforts in disease control. And in an excursion from the applied theme of the day, Steven Benner talked about how he and his colleagues use evolutionary trees to infer the sequences of ancestral proteins. By recreating those ancestral proteins and studying their function, Benner tries to make evolutionary “just so” stories more concrete.

Although free and open to the public, the symposium drew a largely academic crowd of biology students, faculty members, and postdocs. About 80 people sacrificed at least part of a sunny Saturday to sit in a dim auditorium and take in the talks.

NESCent plans to post video of the symposium online—watch the symposium site for updates.

—Elsa Youngsteadt

February 20, 2009

Deconstructing the Ribosome

Our lives depend on a microscopic tangle of molecules called the ribosome. The job of the ribosome is to use the sequence of DNA in a gene to build a corresponding protein. Other enzymes first build a single-stranded copy of the gene from RNA, and then a ribosome grabs onto the RNA and "reads" it, using the information to decide which building block to grab next in order to build a protein. (Here's a video of the process.)

The ribosome has two parts that come together around the RNA like a pair of jaws, and each one is a fiendish nest of complexity. Each of the jaws, known as subunits, is a mix of protein and RNA. This animation, created by David S. Goodsell, shows the structure of the large subunit in bacteria. It contains two RNA molecules in it, a big one here colored orange, and a small one colored yellow. The proteins wrapped around them are in blue. The big RNA molecule alone is a marvelous migraine of complexity. It measures 2900 nucleotides long, and it twists and folds in on itself again and again to form the supreme Gordian knot.

All living things make ribosomes and use them for the same essential purpose. It is a sign of our common heritage with baobabs and starfish, with plague and mold. But the fact that the ribosome is everywhere makes its evolution difficult to study. There is no partial ribosome in nature to offer clues to how it emerged. But in this article in the 19 February issue of Nature, Konstantin Bokov and Sergey Steinberg, two biochemists from the University of Montreal, offer some new hope: It's possible that the evolution of the ribosome is recorded in its very own tangles.

Bokov and Steinberg show that the ribosome is like an onion, with outer layers that can be peeled away from inner ones. The proteins of the ribosome help keep it stable, but they themselves do not actually weld together new proteins. That's the work of the ribosomal RNA. As I wrote in my January Origins essay, many researchers now argue that DNA and proteins were not the first biological molecules to emerge; before they existed, life was based on RNA alone. The origin of the ribosome, Bokov and Steinberg argue, is really the origin of the ribosomal RNA.

Ribosomal RNA is made up of dozens of loops, and loops upon loops, all folded in on each other. But Bokov and Steinberg point out that they have an onionlike order of their own. They inspected all the loops, looking for ones that could be removed without altering the rest of the RNA molecule. They found 19 of these expendable loops. Next, they looked at the loops that had kept those 19 loops stable but which could be eliminated without affecting the rest of the RNA. They found 11 such loops. Below these two layers, Bokov and Steinberg found yet another layer of loops, and another, and another, until they had reduced the ribosomal RNA to a tiny fragment, a core on which all the rest depended.

Bokov and Steinberg propose that the seeming complexity of the ribosome is something of a mirage. Its evolution was actually pretty simple. It evolved from a tiny piece of RNA, perhaps only 110 nucleotides long. At first, this molecule didn't build proteins; it may have carried out some kind of reaction on other RNA molecules in RNA-based cells. Then mutations accidentally duplicated the fragment, building new units that could fold back on the older units. This protoribosome may have been able to add random building blocks together. New layers of loops evolved, making the ribosome more precise, able to build specific proteins when it read specific pieces of RNA. Newer loops made the ribosome even more stable and thus able to crank out proteins even faster. The last major step in the evolution of the ribosome was the addition of its proteins.

The most practical way to test Bokov and Steinberg's hypothesis will be to build the intermediate ribosomes and see if they work as predicted. But perhaps we should not give up on nature just yet. As I have reported, RNA-based life could conceivably still be hiding in refuges somewhere here on Earth, eking out an existence with ribosomes that are a little less hideous than our own.

Carl Zimmer

February 17, 2009

Findings From the AAAS Meeting

Don't miss the chance to check on what happened at the annual meeting of AAAS this past weekend at Findings. In just a few busy days, researchers squeezed in discussions on everything from the evolution of kissing to the genetics of dog shape. There were talks on Neandertals and hobbits, even a science dance contest. Also, hear about the origins of emotions or the origins of the human diet in podcasts.

In a letter to the governor of Louisiana, the Society for Integrative and Comparative Biology announced it would not hold its 2011 annual meeting in New Orleans because of the state's antievolution policies. For more on the issue, check out The Chronicle of Higher Education story.

—Elizabeth Pennisi

February 6, 2009

Extraterrestrial Evolution

Science writer and author of Microcosm: E. coli and the New Science of Life Carl Zimmer wrote the "On the Origin of Life on Earth"  last month. Today he discusses evolution on other worlds.

Imagine you spent your whole life on a tiny island, with only some tortoises and snails to give you a clue to what life was like. You'd be forgiven for failing to imagine a Venus flytrap or an armadillo. Evolutionary biologists are in much the same bind. They are, for the time being, stuck on a planetary island, only able to study life on Earth. While life on Earth takes many forms, every living thing is nevertheless a variation on the common theme of DNA, RNA, and protein. What kind of life, if any—exists on other planetary islands we don't know?

If we do discover life someday on another planet, evolutionary biology would leap to a new level. Biologists would be able to compare how evolution played out on two separate planets. If life began independently on another world and ended up a lot like life on Earth, that might mean that evolution must follow certain rules no matter where on the universe it plays out. Or perhaps evolution has the potential to be a lot weirder than we know, because we're stuck here on our little island of life. The closest place where it makes sense to look for life is Mars. Its surface may have been warm and wet in the past, and puffs of methane discovered in recent years just might be a sign that microbes are still thriving deep under the surface. The best way to see if that's the case is to drill into the Martian soil and find them.

But Chris McKay of NASA warns in this week's Science that in our search for a second biosphere, we may contaminate it with our own. As McKay points out, space scientists were already concerned about contaminating other planets in the 1960s. NASA completely sterilized the Viking Probe that landed on Mars in 1976, but the results of that mission suggested that the Red Planet was so harsh that no life could survive and so fewer protections were necessary. The Mars rovers that we've all watched wandering across the Martian landscape probably brought hundreds of thousands of bacteria with them.

Yet, over the years, scientists have grown more concerned again. The surface of Mars is clearly an awful place for even the hardiest microbe. But if we start drilling down into the ground, we might well be injecting microbes from Earth down into a Martian ecosystem. We unfortunately know all too well what happens when we accidentally introduce species to new places. At worst, the new species becomes invasive and drives native animals and plants extinct. At best, native ecosytems are dramatically altered. Do we have an ethical obligation to protect what McKay called "indigenous biospheres"?

Later this year, a meeting will be held to consider just this question. We do need to take responsibility for our actions, but we also should not forget another lesson of evolution here on Earth: Invasive species don't always need people to deliver them to a new home. Darwin himself first recognized that seeds and eggs can been carried to distant islands on the feet of birds. In space, meteorites may act as interplanetary birds, bringing microbes from Earth to Mars—or perhaps the other way as well. Even if we take every possible precaution, the life we find on Mars may turn out to be invasive after all. It just invaded Mars a billion years ago.

Carl Zimmer

Arizona State University joins in the global celebration of Darwin‘s 200th birthday, and commemorates the 150th anniversary of the publication of On the Origin of Species, with Darwinfest—a celebration of how the expression of radical thinking and scientific and technological enterprise can and has changed the world.

Why does Darwin matter? Arizona State University takes that question to students and the public in Arizona 4 to 13 February with core events that capture how Darwin’s bold thinking has evolved into new understanding about some of the most fundamental questions about humanity and the human spirit, including our origins and life beyond Planet Earth.

See the full calendar of events and information for details.

Events include:

· Origins Symposium (3-6 April)

· The Darwin Distinguished Lecture Series (through November 2009)

· The Future of Evolution Lecture Series (4-25 February)

· Looking for Life: Adventures and Misadventures in Species Exploration (11 February)

· Darwin Days (4-13 February) with a Tea Party and Darwin Look-alike Contest


Margaret Coulombe

Coordinator, ASU Darwinfest.


Arizona State University, Tempe

February 4, 2009

Animal Life's Spongy Origins

Researchers analyzing the chemistry of ancient sedimentary rock in southern Arabia have answered a question that has plagued scientists for more than a century and a half: whether animals appeared on Earth slowly and sporadically or suddenly and spectacularly. A story today on ScienceNOW discusses the rise of Demospongiae, a class that includes modern-day sponges, some 635 million years ago, more than 100 million years before the Cambrian explosion of oxygen-breathing animals. The rocks were chock-full of a protein made only by these sponges.

—Elizabeth Pennisi

The idea that life arose from RNA got a boost 8 January when researchers reported the creation of RNA molecules that could replicate themselves indefinitely. But the debate over life's beginnings continues. Geochemist George Cody of the Carnegie Institution for Science in Washington, D.C., spoke to Science about a competing view of how life got started called "metabolism first."

In brief, what does the "metabolism first" (MF) argument say?

GC: It's basically that the first living organisms, being autocatalytic, could make entire biochemical assemblages based on carbon dioxide, ammonia, etc. The MF idea is that first you have these chemosynthetic systems, then downstream you have these information-based macromolecules [RNA and DNA], and then, genomic emergence. ...

The problem with the RNA-first world is that whereas RNA chemistry is elegant and functional and now developing critical qualities of self-replication, these experiments are done under very carefully controlled conditions. ... I don't think anyone in the RNA world would propose doing these experiments in seawater.

So what's the evidence for the MF idea?

GC: In the so-called MF camp, one seeks to demonstrate that the natural environment is capable of synthesizing molecular intermediates that lie along the chemical reaction pathways [that break down chemicals and nutrients and produce energy] and that these are superficially similar to extant metabolic pathways.

Basically, you're looking at two different ways of making amino acids. The “RNA firsts” say you have to have purines [nucleotides used in building RNA and DNA] and rely on hydrogen cyanide [HCN] chemistry to make amino acids, and metabolists say you can use reductive animation [a type of redox reaction]. In the lab, we can make amino acids either way; ... for example, we can use transitional metal sulfides to make pyruvate.

When will we know who is right?

GC: The question is what kind of chemistry can you do under the actual geochemistry [conditions on early Earth].

I don't think there's going to be an experiment that resolves things satisfactorily. With continued experimentation at the level of what [Scripps’s Gerald] Joyce did on these systems, things will pile on, and slowly the fog will clear. The veils of time are actually being pulled backward, and we're starting to learn more about the early Earth than we ever dreamed we could have.

The best evidence [for the MF idea] would be to discover that the natural world only has one way of synthesizing [life’s] molecular precursors and that [this] one way looks identical to the real-life system. Then extant metabolism is a primordial pathway, directly connected to the chemistry of the planet.

And if not?

GC: If we find out that the early atmosphere is more like Stanley Miller's idea, with an excess of HCN, then the RNA-first explanation might be more satisfying. We're just not there yet.

—Rachel Zelkowitz