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Elizabeth Pennisi: 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

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.

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 Liège, 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.

 http://plants.usda.gov/java/profile?symbol=LEFL&photoID=lefl_004_ahp.jpg

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.

balter

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

April 10, 2009

Darwin's Lost Egg

Darwin Egg2

The University of Cambridge’s zoology museum has come across a long-forgotten egg that Charles Darwin collected during his famous voyage on the Beagle. The 4.7-centimeter-long egg (left), from a partridge-like bird, is cracked: “The great man put it into too small a box, and hence its unhappy state,” according to records found with it.

“It’s the only egg that we know for sure was collected by Darwin,” even though he collected eggs and nests from at least 16 types of birds on his travels, says museum Director Michael Akam.

A museum volunteer rediscovered the egg while cataloging the museum’s egg collection, which has lain uninventoried for a century. It was in a collection belonging to Alfred Newton, a zoologist and friend of Darwin’s, who noted in his journal: “One egg, received through [Darwin's son] Frank Darwin, having been sent to me by his father who said he got it at Maldonado [now in Uruguay] and that it belonged to the Common Tinamou [now the spotted nothura, Nothura maculosasa] of those parts.”

“This is an extremely interesting and significant ornithological find,” says Douglas Russell, bird curator at the Natural History Museum in London. It should encourage other researchers "looking for famous missing specimens."

—Claire Thomas

Photo Credit: University Museum of Zoology Cambridge

Although angiosperms outnumber other land plants nine to one, there’s still a vast “green” world beyond those blossoming trees, herbs, shrubs, and grasses. Indeed, land plants are but a twig on the tree of green eukaryotic life (below), one that extends from a major branch called the streptophytes.

archibaldfig_x480

The other branch, Chlorophyta, includes many of the green algae. Sprouting off toward the bottom of the chlorophyte branch are tiny organisms called Micromonas, thought to most closely represent this tree’s earliest ancestor. Two of their genomes are newly described in today's issue of Science.

No bigger than a bacterium, these minuscule marine eukaryotes have surprisingly sophisticated genomes, says Alexandra Worden, a marine microbial ecologist at the Monterey Bay Aquarium Research Institute in Moss Landing, California. Her team has deciphered the genomes of two strains of Micromonas (lower left), which proved different enough to qualify as independent species. She chose these organisms because they thrive from the tropics to the poles and likely play an important role in the ocean’s food chain and carbon cycle. They are so small that they are hard to characterize and understand without the genes in hand, and she’s very eager to learn how they will respond to a changing environment and how they fit into the marine food chain. (See video.)

Overall, the Micromonas genome is about 21 million bases long, with 10,000 genes, 2000 more than its much more streamlined relative, Ostreococcus, which has already been sequenced, twice. About 20% of the genes found in Micromonas but not in Ostreococcus are genes generally thought to have evolved only in land plants, not earlier, her team reports. For example, the team finds that Micromonas has a gene called YABBY, which is missing from other green algae and even moss, and is thought to be related to the development of leafy plants. Given that leaves don’t exist in these algae, she thinks YABBY must have played another role early in green eukaryotic evolution.

One challenge is that many genes unique to Micromonas “are genes we don’t know the function of,” she points out. “That’s disappointing. If we can figure out their functions, that’s really going to give us new insights into what these organisms have to deal with [in their environments] that we are not thinking about.”

—Elizabeth Pennisi

Diagram: Adapted by P. Huey/Science

Image: A. Z. Worden, T. Deerinck, M. Terada, J. Obiyashi, and M. Ellisman (MBARI and NCMIR).

Chancellor's House double burial After weeks of protest from anthropologists, University of California, San Diego (UCSD), officials have withdrawn their request to the federal government to rebury the skeletal remains (left) of Paleoindians unearthed near the chancellor’s home in La Jolla. The rare, 10,000-year-old bones were found in 1976. Anthropologists and the university’s own scientific working group wanted to keep the remains for further scientific study, but a local American Indian group wanted them reburied. The withdrawal comes not necessarily because of the researchers’ protests but mainly because Kumeyaay nation leaders object to the wording of the UCSD request to the federal Native American Graves Protection and Repatriation Act (NAGPRA).

In an official statement, university officials said that they withdrew the request late last week “upon learning that the Kumeyaay Cultural Repatriation Committee (KCRC) does not support the university’s request submitted to the Review Committee" of NAGPRA, according to Jeff Gattas, senior director of university communications and public affairs.

In a statement issued Monday, the Kumeyaay committee members wrote that they opposed the UCSD request because UCSD Vice Chancellor for Resource Management and Planning Gary Matthews filed a request with NAGPRA to repatriate the remains as “culturally unidentifiable.” Even though the Kumeyaay leaders want the remains—and filed a request for them in 2006—they firmly believe that the remains are indeed culturally affiliated with the Kumeyaay and Dugueno people and that the wording of the request should reflect that. The Kumeyaay committee wrote that they have provided “a mountain of evidence from linguistic, anthropological, archaeological and historical scholars to support their claim that these individuals were indeed culturally affiliated with today’s Kumeyaay/Dugueno people,” according to the statement. “This process sets a dangerous precedent for future claims, both from KCRC and other tribes whose ancestors may be in the possession of the UC.”

But the UCSD scientific advisory group that reviewed the claims (and a separate systemwide UC research committee) drew a different conclusion. It found that the remains of the three individuals have no cultural or biological affinity with the Kumeyaay or any living Americans Indians, according to UCSD anthropologist Margaret Schoeninger, who is co-director of the UCSD working group that reviewed the request. It also found that the Kumeyaay language moved into the region 2000 years ago and that they traditionally cremated their dead rather than burying them. Moreover, preliminary DNA evidence shows no connection between Kumeyaay and known older American Indian groups. Indeed, in a talk Saturday at the annual meeting of the American Association of Physical Anthropologists in Chicago, Schoeninger reported that her lab’s analysis of stable isotopes from samples of the skeletons indicated that they ate a diet of marine mammals and offshore fish—a coastal adaptation that contrasts with the desert origins of the Kumeyaay (see Origins, 3 April). Anthropologists who study the bones and DNA of Paleoindians also agree that the remains are probably too old to have any affiliation, cultural or otherwise, with tribes living in southern California today. And, at such an early age, they are important for scientific analysis, particularly because new methods are being developed to extract and study ancient DNA, and to analyze the diet and lifestyles of ancient people.

To acknowledge that the remains are too ancient to be affiliated with living people, however, might weaken the Kemeyaay’s strongest argument to claim ancient remains in this and other cases before the NAGPRA review committee, which meets next in May in Seattle, Oregon. Kumeyaay spokesperson Steve Banegas says, “We cannot rest until the remains of our ancestors are cared for properly and interred as they should be.” But by quibbling over the wording of UCSD’s request, the Kumeyaay put UC officials in a no-win situation where they were opposed by anthropologists, on the one hand, and the Kemeyaay, on the other hand. The Kumeyaay committee members may have just lost their best ally in their process to get these bones for reburial.

—Ann Gibbons

Photo credit: Jan Austin, Santa Monica Community College

April 6, 2009

Evolution Rocks

What happens when you mix rock music with evolution?

You get Darwin Rocks!, a team of eager ecologists who have made a music video and a computer game to get people interested in Charles Darwin’s seminal theory. The scientists, from the University of Tübingen in Germany, have put together a music clip called “Struggle for Love” featuring a rock soundtrack designed to grab the attention of 15- to 25-year-olds. “We were aiming for a simple message,” says team leader Nico Michiels. “Most people misunderstand what evolution is all about: In the end all that counts is reproduction.”

The video opens with a Darwin look-alike scientist staring intently into a petri dish. The dish contains a strange sci-fi world where the “survival of the fittest” is battled out by microscopic people on a tiny soccer pitch. Several generations later, it’s not the team with the strongest and most ambitious players that wins but the team with the most players—that is, the one that reproduces most. “That’s why the song is written around love and reproduction, instead of focusing on strength,” says Michiels. “Also, we used [sports] to attract the attention of people who would never normally look at a clip like this.”

The video was made in collaboration with students from music schools in Heidelberg and Mannheim and a film school in Munich and thus received a lot of input from the age group it is targeting, says Michiels.

The team also designed a computer game based on the idea that it’s not just animals and plants that evolve—so can music. The game starts with a "musical primordial soup" where the user selects tunes he or she likes from a list. Based on that subset, the program creates "offspring" tunes, which the user also rates. This process of listening and rating hones the evolution of the music. “The user is basically the selective environment. They stand for natural selection,” explains Michiels.

Michiels says the music video and game are nonprovocative ways of demonstrating evolution: “I’d rather generate curiosity about evolution instead of being critical about other people’s beliefs,” he says. “If you provoke moderately religious people, you might lose them. But if we just talk about evolution, you might just win them.”

The video and game were made after the team won a German “creativity contest,” in which evolutionary scientists had to come up with innovative ways of presenting Darwin’s theory. Both Michiels's team and the contest were funded by the Volkswagen Foundation.

—Claire Thomas