live, is how best to elucidate microbial function?that is, how they malee their liv- ing. No one technique is yet sufficiently well developed to do this; however, func- tional gene microarray systems, which look for expression of genes coding for enzymes involved in specific functions, are currently under development (13). An associated challenge is to determine the role of community microbial activity in shaping geochemical consequences. Geochemical interest in microbial activity is often restricted to a single metabolic function with a relevant geochemical con- sequence, such as metal sequestration (5, 7). However, the microbe responsible for that geochemical impact likely exists with- in a microbial community or consortium (12). The by-products from one organism's metabolic pathway are the nutrients of the next strain. Both the series of metabolic re- actants and products associated with a mi- crobial community, and the reaction ener- getics involved, are therefore likely to dif- fer from one location to the next. Thus, even though commonality of metabolic pathways ensures widespread occurrence of certain microbially driven geochemical processes in different envi- ronments, variability in microbial consor- tia and microgeochemical conditions will selectively refine that geochemical impact. In doing so, they may create community- specific microbial fingerprints on geo- chemical processes. Microbial growth and activity can only proceed through inputs of energy, and are thus constrained geochemically to reac- tions that are thermodynamically feasible. High-resolution analytical tools for geo- chemistry and culture-independent molec- ular microbial techniques have yielded ex- citing insights. Today, microbial activity is viewed to play an important?and quantifi- able?role in aqueous geochemistry. New molecular techniques for evaluating micro- bial functional activity will provide key in- formation on how microbes engineer geo- chemical processes, and how they, in turn, are constrained by the geochemical world in which they find themselves. Systematic examinations of the links between genome and geochemistry will ex- plore gene expression (that is, function) and determine reaction kinetics of micro- bial communities growing under differing geochemical and physical conditions (14). Such studies will provide microbial finger- prints for important geochemical processes under microbial control. Moreover, such PERSPECTIVES studies should help to quantify the micro- bial influence on important aqueous geo- chemical processes, determine the linked controls for these key processes, and show how feedback between microbial ecology and geochemical conditions influences the geochemical outcomes. References 1. K. Takai, T. Komatsu, F. Inagaki, K. Horikoshi, Appl. Environ. Microbiol. 67, 3618 (2001). 2. P. L. Bond, S. P. Smriga, J. F. Banfield, Appl. Environ. Microbiol 66, 3842 (2000). 3. F. H. Chapelle et ai, Nature 415, 312 (2002). 4. Aqueous Microbial Ceochemistry in Extreme and Contaminated Environments, Fall AGU Meeting, San Francisco, CA, 6 to 10 December 2002. See www.agu.org/meetings/fm02/program.shtml. 5. G. Morin et ai. Fall AGU Meeting, San Francisco, CA, 6 to 10 December 2002, abstract B22E-05. 6. C. M. Hansel etal.. Fall AGU Meeting, San Francisco, CA, 6 to 10 December 2002, abstract B22E-10. 7. E. A. Haack, L. A. Warren, Fall AGU Meeting, San Francisco, CA, 6 to 10 December 2002, abstract B22E-06. 8. P.A. O'Day, Rev Ceophys. 37, 249 (1999). 9. N. R. Pace, Science 276, 734 (1997). 10. B. J. Finlay, Science 296,1061 (2002). 11. K. H. Nealson, D. A. Stahl, in Ceomicrobiology: Interactions Between Microbes and Minerals, J. F. Banfield, K. H. Nealson, Eds. (Mineralogical Society of America, Washington, DC, 1997), vol. 35, pp. 5-34. 12. D. K. Newman, J. F. Banfield, Science 296, 1071 (2002). 13. A. S. Beliaeveta/.,/Bacter/o/. 184,4612 (2002). 14. A.-L. Reysenbach, E. Shock, Science 296,1077 (2002). 15. K. J. Edwards, P. L. Bond, T. M. Gihring, J. F. Banfield, Science 2S7, 1796 (2000). ARCHAEOLOGY Invisible Clues to New World Plant Domestication Vaughn M.Bryant Decades ago, excavations in the Tehuacan Valley of Mexico (1) con- vinced many archaeologists that they now had physical proof of how, when, and where plants Enhanced online at were first domesti- www.sciencemag.org/cgl/ cated m the New content/full/299/5609/1029 World. The proof came in the form of preserved seeds and fruits, maize kernels and cobs, fibers, and the rinds of cultigens found in cave soils and in preserved human ^ feces originally dated as early as 7500 to o 9000 years old. Little did these archaeolo- 0 gists realize that the puzzle of New World 1 plant domestication was far from solved. 0 Decades later, they would learn that the 1 most critical clues come not from the large Q and visual remains of plants, but from tiny The author is in the Center for Ecological Arch- aeology, Department of Anthropology, Texas A&M University, College Station, TX 77843, USA. E-mail: vbryant@neo.tamu.edu microscopic particles that most archaeolo- gists unknowingly discarded. Fortunately, a few researchers (2, 3) were not convinced by the traditional sto- ry of New World cultigen origins. Piperno and a few others devoted more than three decades to searching the archaeological soils of Central and South America for microscopic phytoliths (plant crystals), tiny starch grains from domesticated plants, and fossil pollen (see the figure). As noted by Piperno and Stothert on page 1054 of this issue (4) and by Piperno and Pearsall in a recent book (5), these microscopic traces of plants reli- ably record the earliest use of domesti- cated plants. Early speculation about the origins of New World plant domestication focused on the upland regions of Mexico and South America. These regions were fa- vored because they were easy to reach, of- ten contained caves or rock shelters filled with preserved plant remains, and had yielded previous successes that ensured Archaeology under the microscope. (A) Radiocarbon-dated 10,000-year-old phytollth (diameter 100 |xm) of domesticated Cuc?rbita, collected from soil at the Vegas Site 80 In Ecuador. (B) Reserve starch grains from the root of a modern manioc plant. (C) Maize pollen grain (diameter 75 |j.m) from cultural levels of the Kob Site, Belize, radiocarbon dated to -5000 years ago. www.sclencemag.org SCIENCE VOL 299 14 FEBRUARY 2003 1029 PERSPECTIVES continued funding. Few archaeologists were willing to search for the origin of plant cultigens in lowland and jungle re- gions, where seeds, wood, rinds, and cobs did not preserve well. Many also won- dered how tropical lowlands could have supported foragers making the switch to early sedentary farming. And most be- lieved incorrectly that all lowland and jungle soils were infertile, similar to ones known from the non-flood plain regions of the Amazon. But Piperno and a few others remained convinced that the long search for cultigen origins had focused on the wrong areas and the wrong kind of clues. It is true that, except for charcoal, the visual evidence of plant remains quickly disappears in most tropical soils. But some clues remain, if you know where to look. By the early 1990s, Piperno (2, 6) had shown that plant phytoliths were plen- tiful in the lowland soils of many regions of Central and South America. She noted that the size and shape of phytoliths were often unique to a family, genus, or species of plant (see panel A of the figure). Piperno and Pearsall then led the way in developing phytolith keys to a wide vari- ety of New World cultigens and tropical plants (5). Armed with this knowledge, scientists began to search for microscopic clues in the soils of early, well-dated ar- chaeological sites throughout Central and South America. New studies based on phytolith data (3, 6) soon began to contradict the long-held theory that plant domestication began in upland regions, where many envisioned cave-living foragers switching to raising cultigens (1). Archaeologists challenging the new discoveries pointed to potential er- rors in dating, saying that the phytolith ev- idence could not possibly be as old as the dates indicated. To quell the critics, phy- tolith researchers developed new ways of dating tiny bits of carbon trapped inside phytoliths as they were formed. The new techniques, which use acceler- ator mass spectrometry (AMS) dating, re- quire the careful collection and separation of many phytoliths (4). Precise phytolith identification is also critical. Piperno and Stothert (4) collected and measured phy- toliths from more than 150 mature fruits from wild and domesticated species of Cuc?rbita (squash and gourds) grown in 100 different locations. The phytoliths from domestic species were substantially larger than those from wild species. The authors then used phytolith size to confirm that domesticated Cuc?rbita were grown and used during the early Holocene in coastal Ecuador, between 9000 and 10,000 years ago. Piperno (7) has also been at the fore- front of searching for archaeological evi- dence of cultigen starch grains. In tropical regions of Central and South America, root crops?including yams, sweet potatoes, and manioc?are the mainstay of many in- digenous cultures. These high-calorie tuber crops grow well in the wet soils and areas created by recently cleared tropical forests. But it has been difficult to prove when and where these plants were first domesti- cated. Tuber-producing crops do not car- bonize well; ?irthermore, most produce small amounts of pollen and do not pro- duce diagnostic phytoliths. However, they do produce copious numbers of water- insoluble granules called "reserve starch grains" (panel B), which preserve well on the surfaces of food preparation imple- ments and in many types of tropical soils. Starch grains from tuber cultigens have re- cently been identified on early Holocene grinding stones used in Colombia and cen- tral Panama {8). In 1957, the British pollen analyst Dimbleby (9) stated that soils with a pH above 6 are virtually useless for fossil pollen studies. Because the pH values of almost all tropical soils exceed 6, pollen analysts have for decades rarely searched the tropical soils of Central or South America. I was one of those pollen ana- lysts who spent more than 30 years work- ing at sites in Mexico and South America. I never found well-preserved pollen in any of those sites. IMMUNOLOGY To the astonishment of many, Jones and colleagues recently recovered pollen from key archaeological sites in Central America (70). His pollen data confirm the use of early cultigens, including maize and man- ioc, from the San Andres site in the Mexican tropical lowlands near La Venta, Tabasco. Radiocarbon dating shows that the archaeological deposits containing cultigen pollen are 5800 to 6200 years old. Perhaps DNA studies of soils in archae- ological sites may soon replace our current techniques. Until then, our best New World records for cultigen origins are coming from the invisible clues: phytoliths, starch grains, and fossil pollen. References 1. R. S. MacNeish, in The Prehistory of the Tehuacan Valley: Environment and Subsistence, D. S. Byers, Ed. {Univ. of Texas Press, Austin, TX, 1967), vol. 1, pp. 290-309. 2. D. R. Piperno, Phytolith Analysis: An Archaeological and Geological Perspective (Academic Press, San Diego, CA, 1988). 3. D. 1^. Pearsall, in Current Research in Phytolith Analysis: Applications in Archaeology and Paleoecology, D. M. Pearsall, D. R. Piperno, Eds. {University Museum of Archaeology and Anthropology, Philadelphia, 1993), pp. 109-122. 4. D. R. Piperno, K. E. Stothert, Science 299, 1054 {2003). 5. D. R. Piperno, D. M. Pearsall, The Origins of Agriculture in the Lov/landNeotropics (Academic Press, San Diego, CA, 1998). 6. D. R. Piperno,/ WorldPrehist. 5, 155 {1991). 7. I. Hoist,/ Archaeol. Sei. 25, 765 {1998). 8. A. J. Ranere, P. Hansell, Phytolitharien 13, 1 {2001). 9. C.W. Dimbleby New P/iyto/. 56, 12 {1957). 10. K. O. Pope etal.. Science 292, 1370 {2001). Regulating the Regulators Fiona Powrie and Kevin J. Maloy Recently, there has been an explosion of interest among immunologists in a subset of T lymphocytes that pre- vent harmful immune pathology. These regulatory T cells (TR), most of which ex- press the activation marker CD25, consti- tute a small number (5 to 10%) of the to- tal population of CD4^ T lymphocytes present in healthy individuals. CD4^ TR cells prevent a number of immune-medi- ated diseases, including autoimmune dis- orders, transplant rejection, and inflam- matory bowel disease (1). Recent studies including two papers in this issue, by Hori et al. (2) on page 1057 and Pasare and Medzhitov (3) on page 1033, are begin- The authors are at the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. E-mail: fiona.powrie@path. ox.ac.uk ning to elucidate TR cell biology in more detail, particularly aspects of their differ- entiation and functional capabilities. These studies emphasize that TR lympho- cytes do not act in isolation, but are them- selves influenced by cells of the innate immune system. An equilibrium is there- by established that allows effective re- sponses against dangerous microbes while minimizing immune pathology. The identification of transcription fac- tors that direct the differentiation of na?ve CD4^ T cells into functionally distinct T helper 1 (THI) and TH2 cells has trans- formed our understanding of the molecu- lar basis of CD4^ effector T cell responses (4). The study by Hori et al. (2) identifies the forkhead/winged helix transcription factor Foxp3 as a master regulator that promotes TR cell differentiation. These in- vestigators noted that both humans and 1030 14 FEBRUARY 2003 VOL 299 SCIENCE www.sciencemag.org