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January 2009 Archives

January 28, 2009

Visualizing Life's Origins

Janet Iwasa creates the pictures worth 1000 words. After earning a Ph.D. in cell biology, she decided to pursue a career in science animation and landed what she called a "dream" postdoctoral position with Jack Szostak, an origin-of-life researcher at Harvard University. Her job was to show what the earliest life looked like. Her work is showcased in the Boston Museum of Science, in the 2008 International Science & Engineering Visualization Challenge, and in Science's first monthly "Origins" essay, "On the Origin of Life on Earth." She is now a lecturer in molecular visualization at Harvard Medical School. Here's her story in her own words.

What did Earth's earliest forms of life look like? This was one of the central questions that I faced as I started a postdoc in Jack Szostak's lab at Massachusetts General Hospital in the fall of 2006. My postdoc was a very unconventional one--through NSF's Discovery Corps, and I was being funded to carry out a 2-year project to work with the Szostak lab and Boston's Museum of Science to launch a multimedia exhibit on the chemical origins of life. Not only was I jumping into a scientific field that felt far removed from my former area of expertise, but the numerous molecular animations I proposed to create for the project would require mastery of 3D animation techniques that I had only just begun learning. It was my dream postdoc, one that I hoped would launch my career in scientific visualization, and I couldn't wait to get started.


bookcover.jpgLove him or hate him, British artist Damien Hirst is at least always provocative. He continues that tradition with the ghoulish cover for Penguin Books' 150th anniversary edition of On the Origin of Species. In a Guardian blog post today (which includes a larger version of the cover titled "Human skull in space"), Hirst calls it an honor to do the cover and notes enjoying the "contentious aspects" of the book when he read it many years ago. The artist offers this description of his work:

The painting sits firmly in the tradition of "still life" and is made up of objects I've come to imbue with my own meanings, some of them Darwinian in origin, and that I guess are seen in other areas of my work. The painting has an X-ray-like quality to it, as if it is revealing something about the structure of the objects painted. I suppose the work, in a modest way, acknowledges Darwin's analytical mind and his courage to believe in those ideas that questioned the very fabric of existence and belief in his time.

—John Travis 

Stephen J. O'Brien is chief of the Laboratory of Genomic Diversity at the National Cancer Institute in Frederick, Maryland. He spoke last week at the U.S. National Academy of Sciences Sackler colloquium on evolution, Two Centuries of Darwin, and came away with these thoughts.

There are few science paradigms that survive and continue their influence for very long—most disappear within a decade. So it was a remarkable gathering at the Beckman Center of the National Academies of Science and Engineering in Irvine, California (hosted by John C. Avise and Francisco J. Ayala), where a group of eclectic evolution experts—biologists, philosophers, thinkers, historians, and empiricists—met to reflect upon 150 years of influence exerted by On the Origin of Species and the 200th birthday of its author, Charles Darwin. In 17 brilliant and colorful lectures, we heard updates, details, and advancements centered on nature’s examples of natural selection and two carryover concepts that intrigued Mr. Darwin: artificial and sexual selection. The historians and philosophers revealed timeless insights into the prescience of Darwin's logic and dismissed as rubbish conspiracy theories that imply he purloined ideas from Alfred Russel Wallace. Francisco Ayala marveled at Darwin's propensity to erect hypotheses over any biological observation and then to begin the scientific process of falsification (or validation) a century before granting bodies began to instruct us to follow this format in our research proposals. Elliott Sober reminded us that adaptive characters offer evidence of their cause, natural selection, while nonadaptive or even maladaptive characters are better for imputing common ancestry. Adaptation happens frequently, leading to parallel, independent origins of flight and of aquatic and terrestrial locomotion, but neutral traits form the currency for modern coalescent and phylogenetic reconstructions. Darwin’s rough sketch of a bifurcating tree of life connecting related species was shown often to remind us that temporal transition of species is a continuous branching process that continues today.

With but 17 talks, the speakers’ examples proved but a snippet of the possible richness of study and empiricism that the Origin has since spawned; indeed, a score of Darwin's birthday celebration symposia scheduled this year across the globe testify not only to the expansiveness of evolutionary theory and practice to all corners of biology but also to its critical role as a bedrock in modern biology, from medicine to agriculture to natural history and ecology. Rich, natural illustrations of sexual selection in beetles and small terrestrial, aquatic, and marine critters affirmed the notion that there are countless discoverable strategies for how to proliferate and survive in our world. Darwin perceived artificial selection of domesticated animals and plants by human agency as providing a cogent natural laboratory example of how selection can change things. And change things it did: When Neolithic farmers in the Near East set up the first villages and communities, domestic species were chosen and selected almost simultaneously. Some believe this event changed the world enormously, providing a ready food supply, clothing, servile labor, sport, transport, and even home companions. Charles Darwin saw domestication as a validation of the force of natural selection, while others see it as the lever by which civilization overtook the globe in so short an interval.

Pause to consider the influence of evolutionary theory and practice, the Darwinian Revolution, as Michel Ruse termed it, made us remember how much it really changed science. Darwin’s genius was not only deductive and empirical; he was also a master communicator, the Abraham Lincoln of his day. His ideas were understood clearly and embraced widely despite the cacophony of theist protestations. His image appears on the 20-pound English note; his legacy is celebrated in a three-story marble mural of his notebook in Beijing; and academic departments of evolutionary theory and practice flourish in the world’s universities to inform us of the intricacies of the process in the era of DNA sequencing and genomics. I wish I could have known Mr. Darwin, but instead, perhaps I should simply try to attend all the celebrations of his theory and influence now, so many years since his birth.

—Stephen J. O'Brien

originavisepix

Credit: Jesse Willis, NAS

One of the first of many scheduled events to commemorate the bicentennial of Charles Darwin's birth and the sesquicentennial of Darwin's On the Origin of Species took place in Irvine, California, this past weekend. Sponsored by the Sackler program of the U.S. National Academy of Sciences and hosted by John C. Avise (left) and Francisco J. Ayala as part III in their annual In the Light of Evolution (ILE) colloquia, the event (entitled Two Centuries of Darwin) included 17 keynote talks divided into four half-day sessions. Three of these sessions dealt with modern scientific evidence on the three forms of selection that Darwin illuminated during his career: natural selection (e.g., in The Origin, 1859), artificial selection (in The Variation of Animals and Plants Under Domestication, 1868), and sexual selection (in The Descent of Man, and Selection in Relation to Sex, 1871). In the fourth session plus an evening plenary, five prominent historians and philosophers of science evaluated the Darwinian legacy. A few of the many highlights from this eclectic set of lectures follow.

Regarding natural selection, Scott Hodges and Dolph Schluter reviewed evidence from plants and animals, respectively, on how selective pressures can promote prezygotic reproductive isolation in "ecological speciation" events that differ quite fundamentally from more traditional staid speciation scenarios in which postzygotic barriers accumulate gradually in allopatry. As phrased by Schluter, such findings demonstrate that "species really do originate by means of natural selection." Another theme to emerge from this session was the incredible complexity of biological evolution under selection. Sara Via showed how the sexual genome is a heterogeneous mosaic of selected and neutral DNA sequences with distinctive evolutionary dynamics during speciation and varied porosities at the species boundary. Julius Lukes documented cascades of convergent evolution at the molecular level in protists, as well as the accumulation of bizarre genomic features, all of which seem indicative of natural evolutionary processes and contradictory to any notions of sentient design in the remarkable genomes of these single-celled organisms.

Regarding artificial selection, Ed Buckler and Steve O'Brien addressed molecular transformations during the human-mediated evolution of domesticated plants (notably maize) and animals (cats). Fred Allendorf showed how hunting and trophy fishing by humans can generate "unnatural selection" (disfavoring the biggest or best) that differs diametrically from the artificial selection regimes (typically favoring the biggest or best) in traditional crop science or animal husbandry. Frances Arnold discussed a novel form of artificial selection in the modern era. Under "directed protein evolution," geneticists synthesize and mutagenize alternative forms of specific proteins (such as cytochrome P450s) and then subject them to repeated rounds of artificial selection for particular biochemical functions. A common result is the rapid emergence, in test tubes, of novel molecules (not known in nature) with a wealth of potential applications in fields such as medicine and pharmacology.

Regarding sexual selection, Adam Jones and Stephen Shuster reviewed and contrasted modern thought about mate choice and mating systems with the sentiments that Darwin had expressed in the Victorian era. Patty Gowaty presented a new model on how time constraints on individuals in various ecological and life-history settings might translate into the mating decisions that underlie sexual selection. And William Eberhard reviewed modern evidence on an important aspect of sexual selection—postcopulatory phenomena, including sperm competition and cryptic female choice—that Darwin had overlooked entirely.

Daniel Dennett, Francisco Ayala, Michel Ruse, Elliott Sober, and Robert Richards each addressed the broader Darwinian legacy, 150 years later, from various historical and philosophical vantages. Perhaps the most controversial suggestion came from Richards, who used selected quotations from Darwin's writings to suggest that Darwin retained for many years a more goal-directed or teleological view on evolution than has commonly been assumed.

In his concluding comments, John Avise reminded the audience that the intent of the colloquium had been not to idolize Darwin (idolatry, or appeal to authority, has no valid place in science), but rather to celebrate Darwin's pioneering role in launching a revolutionary discipline that continues to grow in its vibrancy and relevance to all of the biological sciences. Proceedings of the ILE III colloquium will be published later this year as a special edited issue of PNAS and as a book from the National Academies Press.

—John C. Avise and Francisco J. Ayala

University of California, Irvine, January 2009

darwintree90.jpgThe University of Cambridge rang in its 800th anniversary with church bells and a light show on Saturday the 17th. The light show, created by projection artist Ross Ashton, included specially commissioned illustrations of Cambridge alumni Charles Darwin and Isaac Newton by Roald Dahl's illustrator, Quentin Blake. Above, a graying Darwin ponders the tree of life, whose branches recapitulate the origins of the species. Other images evoked the scientific, musical, and debaucherous achievements of 800 years of Cambridge students and alumni. 

—Lucas Laursen (additional pictures after the break)

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January 19, 2009

An Origin-al: Stanley Miller

Miller1999.jpgIn On the Origin of Life on Earth, the first of our monthly Origins essays, Carl Zimmer briefly notes Stanley Miller's "iconic" 1953 spark-discharge experiment indicating that amino acids could be created in what was then thought to have been the gases in our planet's early atmosphere. Indeed, countless researchers credit Miller for fathering the modern experimental study of life's origins. And Carl Sagan, who as an undergraduate student attended the Chicago lecture where Miller first presented his work, once noted that "the Miller-Urey experiment is now recognized as the single most significant step in convincing many scientists that life is likely to be abundant in the cosmos."

It's not surprising then that the International Society for the Study of the Origins of Life, whose meeting Miller regularly attended till his death in 2007, in 2003 established a Web site honoring the 50th anniversary of this pivotal experiment. It includes an interview with the man himself, reflections on his career by current origin-of-life researchers Jeffrey Bada, Miller's second graduate student, and Antonio Lazcano, and photographs and videos of the celebrated experiment. (Science published its own anniversary tribute by Bada and Lazcano, and the pair wrote more extended reflections on Miller after his death.)

Bada and Lazcano provide this account of the 1953 lecture by Miller:

After the lecture [the audience] sat in silence, unable to find any flaws in what Stanley had done. At one point, someone - according to Arnold, Enrico Fermi - politely asked if it was known whether this kind of process could have actually taken place on the primitive Earth. Harold Urey, Stanley's research advisor, immediately replied, saying 'If God did not do it this way, then he missed a good bet'. The seminar ended amid the laughter and, as the attendees filed out, some congratulated Stanley on his results.

At the risk of self-promotion, Science played a role in the experiment's claim to fame—and in perpetuating its legacy. The journal published the original paper by Miller and Urey. More recently, Bada rediscovered some of Miller's vials from the original spark-discharge work and conducted an analysis that Science published. (Here's our ScienceNOW story on that modern work and a podcast with Bada about the fascinating backstory that led to it.) Miller's 1953 classic continues to spark our thoughts.

—John Travis

January 15, 2009

Sizing Genomes

Irene Chen is a Bauer research fellow at Harvard interested in the origins of life and in particular, in the emergence of complexity. In this entry, she explores why there are limits to the size of a genome, using an example from real life to get across the point that the longer the genome, the harder it is to pass information faithfully from one generation to the next:

telephone game image Have you ever played the game Telephone? In this game, several people sit in a circle, and the first person whispers an arbitrary message to his or her neighbor, as quietly as possible. The message is passed by successive whispers around the circle, and the last person attempts to repeat the message out loud. Typically, the message has become completely garbled by the time it reaches the last player. Why is this? The problem (or the game) is that whispering is a rather inaccurate mode of information transfer, so mistakes accumulate around the circle until the message is lost. In fact, errors can plague transfer of information in any form, including biological genomes.

The information for making a living organism is encoded in the genome as a series of chemical letters (adenine, guanine, cytosine, and thymine). Longer genomes have the potential to encode more information and thus more complex organisms. In 1971, Nobel laureate Manfred Eigen realized that the probability of making a mistake limits the length of the genome. If errors are relatively rare, most daughter genomes are faithful copies of the original. However, if errors are too common, daughter genomes usually contain mistakes, and their daughters would contain even more mistakes, and so on. In that case, the information of the genome would degrade over time.

Eigen proved that the maximum length of the genome is inversely proportional to the rate of mistakes per letter, simply because longer genomes contain more opportunities to make mistakes (Eigen, M., Naturwissenschaften 58, 465). If the genome is longer than this critical threshold, then an "error catastrophe" ensues: Error-ridden replication essentially randomizes the genome after several generations. This principle also suggests that mechanisms to reduce mistakes can set the stage for the evolution of more complex organisms. Indeed, modern organisms generally have multiple proofreading mechanisms, such that mistakes are usually very rare. (Some viruses, like HIV, are notable exceptions and appear to exist near the edge of the error catastrophe.)

Although the concept of the error threshold was originally developed to understand the limits of biological information, we can see surprising illustrations of this idea in everyday life. Take a look at the name of this lake in central Massachusetts:

sign with lake name

Photo: Irene Chen

According to locals, it means "You fish on your side, I fish on my side, and nobody fishes in the middle" (see the Wikipedia article for more information). Now, check out this sign from the Massachusetts Turnpike Authority:

road sign

Photo: Bree Bailey

Looks the same, right? But look again:

lake name spelled out

sign spelling mistakes noted

There are two errors in this sign! Notice that the short, four-letter word "Lake" was copied correctly, but that the long, 45-letter word "Chargoggagoggmanchauggagoggchaubunagungamaugg" was copied with two errors, for an error rate of approximately 4%. If the MTA were to use its sign as a template for more signs, you can imagine how the information in the lake name would quickly disappear. Fortunately for humans, whose genome is more than 3 billion letters long, our DNA replication is substantially more accurate!

—Irene Chen

January 14, 2009

Good News for Lost Tiger

Don't call it a comeback, but the regal Caspian tiger--thought to have gone extinct nearly 40 years ago--lives on in a closely related subspecies, a new genetic analysis reveals. Conservationists say they can use these relatives to help reestablish the Caspian tiger in Central Asia, parts of which are no longer inhabited by people and have plenty of suitable prey. In ScienceNOW, read about the DNA studies that demonstrate the close affinity between this extinct subspecies and the Siberian, or Amur, tiger and that reveal how tigers spread from China to Central Asia. The scientific report was published today in PLoS ONE.

Origin_of_Species_title_page3.jpgAll the Darwin celebrations this year will certainly make some of us reread On the Origin of Species and others pick it up for the first time. One of the latter is John Whitfield, who trained as an evolutionary biologist before turning to science writing. (He's written several stories for Science including one on cheating ants and another on the junk-food hypothesis as an explanation for why certain marine predators are struggling--subscription to Science required for access.)

On a new blog, Whitfield ruefully admits he's never read Darwin's celebrated manuscript. He vows to read almost a chapter a day, informing readers of his thoughts along the way and discussing the issues with those who comment.

Will I be thrilled? Horrified? Sceptical? Baffled? Bored? Let's use part of our brains to try and ignore all that we now know about Darwin's biography and legacy, pretend that this is our first encounter with his theory, and that evolution must stand or fall on the quality of the science and writing in the Origin

Whitfield plans to finish reading the book by 12 February, Darwin's birthday.

—JohnTravis

January 9, 2009

RNA Begets RNA

As Science's essay on the origin of life on Earth points out, many researchers think RNA was central to early life. But one challenge has been to show that RNA could make copies of itself without help from another biological molecule--DNA or proteins, for example--and that it could do this for long enough to allow evolution to gain a foothold. "That's no small feat," says molecular biologist Joan Steitz of Yale University. Yet molecular biologist Gerald Joyce of the Scripps Research Institute in San Diego, California, reports success this week in Science Express.

rna-rna-th.gif

Credit: Gerald Joyce, Scripps Institute

Piece by piece. Researchers designed two RNA strands (blue and red) that could replicate indefinitely and evolve, showing how life could have arisen from these simple molecules.

When RNA replicates itself, it tends to make perfectly complementary copies that stick together like the jaws of a zipper. Once an RNA molecule has found its complementary match, it tends not to split off and make more copies. Joyce says his goal was to create an RNA molecule that was just unstable enough to keep replicating.

For almost a decade, his team played with different combinations of the four RNA nucleotides--A, U, G, C--to create an RNA that would replicate indefinitely. Nothing kept dividing. But finally, Joyce's team hit on the idea of creating an RNA molecule that would replicate by copying and assembling whole chunks of molecule at a time rather than working letter by letter. They engineered two such RNA molecules, called E and E-prime, and dropped them into a solution with four strands of nucleotides, precursors that might have been available on the young Earth. Within an hour, the number of RNAs had doubled, and the molecules kept replicating until all the other nucleotides in the solution had been used up, the researchers report. The replicated RNAs aren't perfect copies, and Joyce's team has shown that some of these mutants can outcompete their parent RNAs, becoming more populous over time. Despite being simple--the RNAs are just 70 nucleotides long--they demonstrate primitive evolution, Joyce points out.

Although the work almost certainly doesn't reflect what happened at the start of life, it models how self-replication and mutation might have arisen--a significant accomplishment, says Andy Ellington, a molecular biologist at the University of Texas, Austin.

—Rachel Zelkowitz

Rachel Zelkowitz is a science writer in Washington, D.C.