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April 2009 Archives

ImmuneEssayIntro With swine flu circulating the globe, it’s appropriate that May’s Origins essay is “On the Origin of the Immune System.” Immunology is the study of how we and other animals defend ourselves against pathogenic microorganisms—bacteria, viruses, and parasites, for example—and this battle goes back to the beginning of evolution. The first multicellular creatures must have had to learn how to be nice to their own cells yet attack any invading cell trying to exploit their resources. Indeed, when biologists look at sponges and other “simple” creatures at the base of the evolutionary tree, they see many of the same microbial defenses that we and other complex animals use, which suggests that at least some form of immunity arose very quickly in the evolution of animals. But those ancient defenses only constitute what scientists call the innate immune response, an all-out molecular and cellular assault on infected tissue. Most vertebrates have a second level of defense, the adaptive immune response, that targets, and remembers, specific microbes. It’s this adaptive immune response, dependent on white blood cells called B and T cells, that physicians elicit when they vaccinate a person against a virus, for example. In a scientific detective story that has played out over the past few decades, researchers have shown how this adaptive immune response arose after innate immunity, and they have teased out the details of the fortuitous event, a random DNA insertion in an opportune spot, that was the key to its birth. The research on this “big bang of immunology” even played a key role in a 2005 trial pitting scientists and educators against those doubting evolution and seeking to diminish its teaching in school systems in the United States.

—John Travis

Illustration: Katharine Sutliff/Science

Students of human evolution are forever on the prowl for signs of positive selection in our genome. The detection of changes in the sequences of particular genes from one population to the next can signal an adaptive value for those genes and thus indicate how humans are evolving through time. Until recently, researchers have been quite limited in their searches, restricted to looking at particular genes. But with advances in genomics and in particular, the mapping of variation in the genome across populations, they have been able to look more broadly for chromosomal regions that change more quickly than others, and from there home in on genes under recent evolutionary pressure. In its issue celebrating Darwin’s anniversary, Genome Research explores human population genomics and other evolutionary aspects of genomics.

In particular, Jonathan Pritchard and Joseph Pickrell of the University of Chicago in Illinois and their colleagues have done the most extensive survey yet of the almost two dozen broad scans for positive selection done to date. In their report, they describe their examination of genetic variation in 53 populations and their discovery of new genes under positive selection, including ones involved in brain, heart, and breast development.

Other reports (freely available as abstracts) detected fine genetic substructure in United Kingdom populations as well as among castes in India, Malaysia, and Eastern Europe.

The journal’s special issue also covers rapidly evolving gene families and the role of alternative splicing in the evolution of plants, with one open-access paper on the evolution of the chimp and human transcriptome.

—Elizabeth Pennisi

darwinart2.jpgWASHINGTON, D.C.—Here, in the Rotunda Gallery of the National Academy of Sciences, an early 20th century bust of Charles Darwin offers a stoic gaze to visitors. But just beyond lies a much less traditional take on the famed naturalist, a new work in which the pages of his On the Origin of Species essentially serve as a canvas for artists.

The unusual concept was developed by Tim Rollins and his collaborators, "learning disabled" students of the South Bronx who call themselves K.O.S. (Kids of Survival). Since the 1980s, Rollins has engaged his students’ minds, and hands, encouraging them to draw or paint pictures in books of classic literature that the students were reading. Several of the students who started with Rollins in the beginning of K.O.S, when they were 11 to 13 years old, are still taking part in the program today as adults.

In 2007, Rollins and the K.O.S. were approached by J. D. Talasek, the director of cultural

Courtesy NASprograms at the National Academy of Sciences, to create a piece based on Darwin's seminal work. "We've been trying to tackle Darwin for years and years," says Rollins, but "[Talasek] really put a fire under us."

The group, which consists primarily of eight artists ranging from ages 16 to 37, plus Rollins, 53, pulled together any information they could find on Darwin. "It was a big scavenger hunt in terms of information," Rollins says. They read through On the Origin of Species, pondered the "poetic passages," watched documentaries on Darwin, gathered magazine articles, and researched existing art that was inspired by the text. "Painting on Darwin is like painting on the Bible; … it's a pretty daunting task," says Rollins.

The group decided early on that they did not want a traditional image of Darwin and evolution; they wanted something intuitive, not literal. "We wanted to see what evolution looked like,” says Rollins. Visually capturing evolution proved a real “struggle,” the artist says. The group abandoned two concepts, before pursuing the one that went on display at the National Academy of Sciences on 2 February 2009.

Their "eureka moment," Rollins says, was inspired by the original “Tree of Life” that Darwin sketched on a notebook page, and the statement that accompanies the image: "I think." They scanned Darwin’s rough diagram and decided to extend and expand it over the canvas—to "replicate the process of natural selection, the randomness, the excitement of life," Rollins says.

The final work includes pages from On the Origins of Species plastered on a large canvas.

Courtesy NAS

Darwin’s words, faintly visible beneath a thin veneer of white matte acrylic, are covered by a branching network of black ink made from beetle shells and carbon. A key decision, Rollins says, was to have the origin of this network remain hidden, with just a line to it extending off canvas, from above. This tries to capture the "amazing mystery of creation," according to Rollins.

The artist notes that people viewing the work often don’t see the connection of the branching pattern to Darwin, with some asking 'Where's the fish, the birds, the finches?' But Rollins says he and the K.O.S. wanted to capture Darwin's "intense free inquiry … the love of questioning where things come from, where things are, and where they are going." "I definitely think that you feel that flow in the painting," he says.

Rollins hopes to see the exhibit, which is on permanent loan to the National Academy of Sciences, in other venues. He and his fellow artists also plan to produce variations on their original concept, creating a series. But for now, The Origin of Species (after Darwin) runs through 15 June 2009 in the National Academy of Sciences' Rotunda Gallery.

—Jackie Grom

popcornSome 300,000 species strong, flowering plants dominate terrestrial landscapes, prompting awe and wonder dating from the days of Charles Darwin about how this group arose. (See this month's Origins essay.) And although the blossoms themselves contributed much to the success of angiosperms—attracting and making efficient use of insects and other pollinators—they are not the only feature that gave angiosperms a leg up on earlier seed plants. The way angiosperms provide nutrients for their seeds represents an underappreciated, cost-saving innovation that arguably made human civilization possible. It’s called the endosperm, and it's what pops in popcorn (left) and forms the bulk of what's in flour, rice, oats, and other grains, providing humans with two out of every three calories worldwide. “You take endosperm off the table, and you have fern fiddleheads and not much more [to eat],” says William "Ned" Friedman, a botanist at the University of Colorado, Boulder. “Even a grain-fed cow is really processed endosperm.”

Endosperm is the nutrient-filled tissue that sustains the growth of the embryo within a seed, sometimes early in development and sometimes later, once the seed has germinated. It arises through an innovation called “double fertilization.”  Each pollen grain produces two sperm, one of which fertilizes the “egg” and one of which merges with a so-called central cell that’s colocated with the “egg” in the female embryo sac. That latter fertilization sets off the growth and development of endosperm, which becomes packed with starches, proteins, lipids, or oil, depending on the species. Endosperm can be solid, as in wheat, or liquid, as in coconut milk. This double fertilization ensures that the embryo will have the sustenance it needs to complete its development.

embryoPines, firs, ginkgoes, and other gymnosperms also have nutritive tissue, but their tissue is prepared well in advance, laid down as the egg is maturing and well before fertilization. “It’s a slow process,” says Friedman, and should subsequent fertilization fail, this effort goes to waste. By jump-starting embryo and endosperm development simultaneously, angiosperms save time and cut down on wasted effort. “My sense is this [change] opened up all kinds of opportunities,” he adds. For example, now life cycles could be completed in a season, making possible annuals and other rapidly reproducing plants. But how did this just-in-time provisioning evolve?

Photo Credits:  William "Ned" Friedman.

...Stony Brook, NY; Stony Brook University: The Stony Brook Human Evolution Symposium, Hobbits in the Haystack: Homo floresiensis and Human Evolution: (L-R) Mark Moore (University of New England, Australia), Mike Morwood (University of Wollongong, Australia), Susan Larson (Stony Brook University), William Jungers (Stony Brook University), and Thomas Sutikna (National Research and Development Centre for Archaeology, Indonesia). Long Island, that is, where researchers studying the puzzling little people of the Indonesian island of Flores gathered for a public symposium at Stony Brook University on 21 April. The biggest news was archaeologist Mark Moore's detailed report on the stone tools throughout the Liang Bua, the cave where hobbit bones were found. See ScienceNOW and this Friday's Science for more on Moore’s surprising conclusion: that the modern humans who arrived 11,000 years ago at the cave made tools in the same way as hobbits, who lived there from 95,000 years ago to perhaps 17,000 years ago. Moore, of the University of New England in Armidale, Australia, even suggested the possibility of contact between the species, with Homo sapiens learning from hobbits. His work is also in press at the Journal of Human Evolution. (Pictured above, from left: Mark Moore, Mike Morwood, Susan Larson, William Jungers, and Thomas Sutikna with a cast of the hobbit and a modern human skull and limb bones for comparison.)

The meeting was a rare chance for U.S. researchers to hear from the team that discovered the hobbits, which they officially call H. floresiensis. Lead excavator Thomas Sutikna of the National Research and Development Centre for Archaeology in Jakarta and Mike Morwood, now of the University of Wollongong in Australia, flew across the globe for the meeting, which gathered only those researchers who already accept H. floresiensis as a new species. The lingering skeptics, who think the fossilized bones represent a diseased modern human, were not invited to give talks. (In 2007, a meeting in Indonesia chiefly featured critics.)

The public talks at the Long Island meeting reprised some previously published information. For example, researchers detailed features of the shoulder, wrist, and brain, suggesting that the 17,000-year-old hobbit skeleton resembled much older African hominids rather than a diseased modern human.

But bits of important news emerged: Hand specialist Matthew Tocheri of the Smithsonian Institution in Washington, D.C., reported that last summer he went through hundreds of bags of bone fragments recovered from Liang Bua, including those from a layer that has already yielded a second hobbit jawbone, known as specimen LB6. Tocheri was seeking one of the four fingernail-sized bones of the wrist, and he got lucky: He found one, called the capitate, presumably from LB6. The bone has the same peculiar and primitive configuration seen in the capitate of the main skeleton, suggesting that at least two individuals from Liang Bua have this oddly shaped wrist bone. Two individuals with such a primitive trait makes the disease argument less likely, Tocheri said.

A couple of relatively neutral observers praised the detailed skeletal analyses presented at the meeting but retained skepticism on some points. Archaeologist Paul Mellars of the University of Cambridge in the United Kingdom, who is at Stony Brook for the semester, said he started the day thinking there had been a bit too much fuss about the little people but was impressed by the data by the day's end—although he remains skeptical that humans learned from hobbits. Meanwhile, famed fossil hunter Richard Leakey, chair of the Turkana Basin Institute at Stony Brook, which hosted the conference, described himself as originally "needing a nudge" to be convinced that the hobbit was a new species. One of the few present with an African perspective, he remained quite doubtful about some presenters' ideas that H. floresiensis represents an extremely early migration out of Africa but said he was impressed by several talks and satisfied that the skeleton was not diseased.

Also at the meeting, researchers unveiled a model of the hobbit skeleton, made by materials scientists at Stony Brook who transformed CT scans of the original fossils into three-dimensional casts. The new model will be given to the Indonesian National Research and Development Centre for Archaeology for display, according to symposium organizer William Jungers of Stony Brook.

And finally, Sutikna and Morwood reported that they are still looking for more bones: This summer, they will excavate again at Liang Bua and also plan digs at other sites on Flores. 

—Elizabeth Culotta


Credit: Mark A. Klingler

Make sure to check out our latest ScienceNOW on the discovery of Puijila darwini, reported today in Nature. Puijila fills a fossil gap in the evolution of seals, sea lions, walruses, and other pinnipeds, by being the first of its kind to be found with legs and webbed feet in place of flippers. The fossil provides a glimpse of a terrestrial animal making the transition to an ocean-going creature.

Puijila dwelled in a freshwater habitat, suggesting an intermediate freshwater phase in pinniped evolution. The researchers chose the species name to pay tribute to Charles Darwin, who predicted a transitional land to sea creature with just that type of an intermediate stage in his seminal work On the Origin of Species: "A strictly terrestrial animal, by occasionally hunting for food in shallow water, then in streams or lakes, might have at last be converted into an animal so thoroughly aquatic as to brave the open ocean." Puijila means "young sea mammal" in Inuktitut, a native language of the Inuit people inhabiting the territory in which the fossil was found.

—Jackie Grom

Image Credit: Mark A. Klingler

Tetrahedraletes medinensis(3)No bigger than specks of dust, cryptospores are one of our largest windows into the deep history of plants. These ancient spores and pollen show up in the fossil record between 465 million and 407 million years ago, a key moment for Earth’s greenery. During the first half of that period, the nonvascular land plants—mosses, liverworts, and hornworts—held sway, dominating the landscape for 30 million years. But eventually, vascular plants—ferns and seed-bearing plants—evolved and gradually took over. By examining the shapes and structures of cryptospores collected during oil explorations, paleobotanists have been trying to pin down this transition. New finds now push back the date when vascular plants appeared by almost 30 million years, to about 450 million years ago, Philippe Steemans of the University of Li├Ęge, Belgium, and colleagues report in the 17 April issue of Science.

Cryptospores differ from modern spores and pollen in that they come in clumps of two or four, having failed to separate as modern pollen does into individual cells. Thus these dyads and tetrads (above; scale is 10 micrometers) are diagnostic for ancestral land plants. Spores that have disassociated from these clumps represent more modern plants, and folds and bumps on spore surfaces distinguish species and thus are indicative of diversity.

Since 1990, Steemans and Charles Wellman of the University of Sheffield in the United Kingdom have been retrieving fossils from boreholes dug for oil exploration in Saudi Arabia. They dissolve the rock in different solvents to remove carbonate and silicate materials and examine the remaining organic material under light and scanning electroambitisporites avitus(2)n microscopes. They typically find marine fossils, which help them determine the age of the rock, as well as spores and pollen.

In the most recent samples, the cryptospores at first seemed quite ordinary. But when they looked closely, Steemans and Wellman found single spores—called  trilete spores (left; scale is 10 micrometers)—dispersed among the dyads and tetrads. “Our first reaction was to think that the samples had been contaminated by younger material,” Steemans recalls. But an independent analysis in a second laboratory turned up the same ancient trilete spores.

“These generally don’t appear until much later,” about 436 million years ago, says Wellman. Thus these newly described, 450-million-year-old cryptospores “probably represent the origin of vascular plants.”

—Elizabeth Pennisi

Photo Credit: P. Steemans

As I pointed out in my essay on the origin of flowering plants, a key breakthrough came in the late 1990s when molecular studies showed water lilies and the New Caledonia plant Amborella to be toward the bottom of the angiosperm tree. With these basal lineages in place, botanists could begin to tease out the more primitive angiosperm traits. More recently, another plant, this one masquerading as a monocot, a major group of flowering plants that includes grasses, orchids, and palms, has been reassigned to the primitive part of the tree, near the water lilies. Found in Australia and New Zealand, with one species in India, these tiny plants, which make up the Hydatellaceae family, like to be submerged, sometimes more than a meter deep, sending up flower stems 1 to 3.5 centimeters high with flowers 1 or 2 millimeters in size. From afar, they can look like a lawn of underwater moss.

stevenson_trithuria_submersa_02Though very odd in appearance and lifestyle, the Hydatellaceae had seemed to fit best with grasses: Both have reduced flowers, for example, and their seeds seemed similar in having what looks like one seedling leaf and not two as in the majority of angiosperms. At least one gene study has placed one of this group, Trithuria submersa (left), squarely among the grasses—although later this turned out to be a contaminant sequence.

Fascinated by this oddball, Sean Graham of the University of British Columbia Botanical Garden and his colleagues did a more thorough gene analysis. They isolated chloroplast genes from Trithuria and compared them to the same genes in a variety of other species. To their surprise, Trithuria proved to be quite a distant relative to grasses. Instead, this plant branched off the angiosperm family tree at about the same place as water lilies. This arrangement held fast even after Graham and his colleagues analyzed the data several different ways. Analyzing sequences from a nuclear gene and chloroplast genes from another Hydatellaceae, Hydatella inconspicua, supported this new classification as well, which they reported on in 2007.

From this new perspective, botanists have begun to realize that Hydatella and Trithuria really do fit nicely down at the base of the angiosperm tree, not high up among the later-evolving monocots. Their seeds have a cap called an operculum just like water lilies. Their embryo sacs, specialized sexual tissue of seeds, have fewer cells compared to those of more later-evolving species. And their carpels, protective sheaths surrounding the seeds, start out as cup-shaped, with margins that do not completely fuse as in carpels of most other plants. These traits in Hydatella “fit with an emerging picture in which the earliest angiosperms likely had many of these features,” says Graham. It also raises the question about whether the first flowering plants were aquatic, but many botanists don't think that was the case.

Now firmly ensconced among the water lilies, the Hydatellaceae are attracting quite a bit of interest. “We are trying to develop Hydatellaceae as a model organism for early-divergent angiosperms and are successfully growing and flowering it at Kew, though so far we have not managed to set seed,” says Paula Rudall, a botanist at the Royal Botanic Gardens, Kew. Her team has even isolated many of its genes.

Rudall, Dimitry Sokoloff of Moscow State University in Russia, and their colleagues have been going over these species micrometer by micrometer as well as second by second, probing both the structure and the development for clues about the most ancient angiosperms. The Trithuria flower seems to be inside-out, with stamens at the center instead of rimming centrally located carpels, they reported earlier this year, illustrating their paper with stunning pictures of the flower’s development.

Graham is refining the relationships among these and other basal angiosperms. Others, including his student Will Iles, are taking a close look at the species within this group. Already, these botanists have concluded that there’s just one genus, not two as had been thought, and at least 12 species, not 10. "We found that previously, males and females of the same species (some species are sexually dimorphic) had been included in different genera,” notes Rudall.

Graham hopes that one day botanical gardens will exhibit Hydatellaceae. “It’s not going to be a spectacular [display],” he admits, but for the study of angiosperm evolution, these plants’ contribution could be enormous.

—Elizabeth Pennisi

Credit: Dennis Wm. Stevenson, New York Botanical Garden

Tracing the origin of flowering plants has long been a challenge for evolutionary researchers, as discussed in this month's Origins essay. Paleobotanist David Dilcher thinks part of the reason is that researchers in his field misidentified fossil plants as members of modern groups. Back in 1979, he and a colleague reanalyzed fossil leaves collected from 45-million-year-old clay pits in Tennessee. Careful cleaning revealed previously unnoticed stipules, small outgrowths from the base of the leaves, calling into question the fossils’ supposed identity as modern corkwood. A close examination of the venation pattern and the cuticle of the leaves convinced Dilcher that these leaves were an extinct group belonging to the coffee family. Dilcher, now at the Florida Museum of Natural History in Gainesville, talks about the impact of this and subsequent work by others on understanding flowering plants.

Often the phrase “the origin of the flowering plants is an abominable mystery” can be read in popular and scientific literature. This phrase is credited to Darwin and comes from a letter that Darwin wrote to J. D. Hooker on 22 July 1879 (Darwin, 1905). It represents Darwin’s frustration with the paleobotanical record of his time. The literature available to Darwin in the 1870s shows that when flowering plants are first found in the fossil record, they are nearly all given names of extant genera. At the time of Darwin, there was no evolution that could be demonstrated from the fossil record of flowering plants. This record was based almost entirely upon impressions and compressions of fossil leaves, and paleobotanists of the 19th and first half of the 20th centuries looked for “matches” or similar leaf types with the leaves of living flowering plant genera. This ”leaf matching” can be done if one does not look closely at detailed characters of fossil and living leaves. When characters such as fine venation, epidermal cell patterns, trichome types, and stomatal complexes are examined carefully (Dilcher, 1974), a different view of early flowering plants emerges.

Such was the case for Paleorubiaceophyllum eocenicum (far left), which was once classified as Leitneria floridana (near left) but which really represents an extinct group of plants.

Darwin’s “abominable mystery of the origin of the angiosperms” can be understood when careful observations of characters are made. With the study of detailed leaf venation and leaf epidermal cell characters, it is clear that many of the earliest flowering plants represent extinct species, extinct genera, extinct families, and perhaps even extinct orders (Dilcher 1974, 2000). This paradigm change has caused a revolution in the study of fossil flowering plants which only in the past 40 years has begun to present a realistic record of extinct flowering plants.

It seems to be human nature that when a fossil leaf is found, the first question asked is what is its living counterpart. When fossil leaves are examined only as hand specimens, using gross form, it is easy to find leaves of trees living today that “match” the fossils. The success of early paleobotanists depended upon making such matches. It has taken a philosophical shift in angiosperm paleobotany in order for researchers today to strive to understand relationships between fossil and living plants, based upon detailed characters, rather than feeling the need to find a living genus to which they can name a fossil. Using character analyses, we now have an emerging new fossil record of flowering plants with many extinct taxa that would have delighted Darwin. This new record is one he could have understood because it demonstrates the evolution of flowering plants, a major group of organisms on Earth. We do not yet know all the details, but there is no longer any “abominable mystery” to the origin of flowering plants.

—David Dilcher

Darwin, F. (Ed.). More letters of Charles Darwin. Vol. 2. (Murray, London, 1905).

Dilcher, D. Approaches to the identification of Angiosperm leaf remains. The Botanical Review, 40:1, 1 (1974).

Dilcher, D.  "Toward a new synthesis: Major evolutionary trends in the Angiosperm fossil record. pages." Variation and Evolution in Plants and Microorganisms: toward a new synthesis 50 years after Stebbins. F. J. Ayala, W. M. Fitch, and M. T. Clegg, Eds. (National Academy Press, Washington, D.C., 2000), pp 255-270.

Credits: Paleorubiaceophyllum eocenicum: H. Wang and D. L. Dilcher; Leitneria floridana: J. S. Peterson, USDA NRCS NPDC. Missouri Botanical Garden.


Last week, I had a rare opportunity to exchange ideas about the origins of art and symbolism with scientists, students, and the general public in India. After reading my 6 February essay, the president of the Indian Academy of Sciences, Dorairajan Balasubramanian of the L. V. Prasad Eye Institute in Hyderabad, invited me on a lecture tour as part of the academy’s 75th anniversary. For a busy 8 days, I gave lectures and met informally with small groups of students in both the “hard” sciences and the humanities at Jawaharlal Nehru University in New Delhi, the Centre for Cell and Molecular Biology in Hyderabad, and the Indian Institute of Technology Madras in Chennai (the city formerly known as Madras), among other places.

My talk, which I called “What Made Humans Modern?” after the title of an earlier story I had written for Science, focused on how archaeologists and anthropologists have tried to trace the origins of art and symbolism by using proxy indicators of the cognitive mechanisms involved, such as the ritual use of ochre and sophisticated toolmaking. I also described possible Darwinian explanations for the evolution of advanced cognition in modern humans.

I was very impressed with how serious and engaged my listeners were. One question that came up after nearly every lecture was why our species became so far advanced cognitively over all other animals. In response, I suggested (rightly or wrongly) that the human line, which split from the chimp line around 5 million to 7 million years ago, might have had a “lucky break” when it went bipedal while other animals did not, as that evolutionary development later allowed brain expansion and other adaptations such as greater flexibility of the hands.

Some audience members were skeptical that symbolic behavior, especially language, was unique to modern humans, citing the dances of honey bees, bird songs, and dolphin sounds, among other indications of sophisticated animal behavior. I suggested that although we should not minimize the talents of other animals, most of their impressive abilities are nevertheless stereotypical and instinctive. They bear little resemblance to the kind of nearly endless innovation and nuanced expression represented by human language, art, and music. (See my article about the apparent “gap” between animal and human cognition.)

But as I fielded such questions, and in the talk itself, I was careful to present the various scientific viewpoints about these often controversial questions and avoid coming down hard in favor of any particular conclusion. My audiences seemed particularly responsive to that more journalistic approach, which allowed them to make up their own minds about the mysteries of human origins.

—Michael Balter

Photo Credit: Vivek Handa