Monday, May 24, 2010

OF MICROORGANISMS AND MAN

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More than 150 years ago, Darwin proposed the theory of universal common ancestry (UCA), linking all forms of life by a shared genetic heritage from single-celled microorganisms to humans. Until now, the theory that makes ladybugs, oak trees, champagne yeast and humans distant relatives has remained beyond the scope of a formal test. This week, a Brandeis biochemist reports in Nature the results of the first large scale, quantitative test of the famous theory that underpins modern evolutionary biology.

The results of the study confirm that Darwin had it right all along. In his 1859 book, On the Origin of Species, the British naturalist proposed that, "all the organic beings which have ever lived on this earth have descended from some one primordial form." Over the last century and a half, qualitative evidence for this theory has steadily grown, in the numerous, surprising transitional forms found in the fossil record, for example, and in the identification of sweeping fundamental biological similarities at the molecular level.

Still, rumblings among some evolutionary biologists have recently emerged questioning whether the evolutionary relationships among living organisms are best described by a single "family tree" or rather by multiple, interconnected trees—a "web of life." Recent molecular evidence indicates that primordial life may have undergone rampant horizontal gene transfer, which occurs frequently today when single-celled organisms swap genes using mechanisms other than usual organismal reproduction. In that case, some scientists argue, early evolutionary relationships were web-like, making it possible that life sprang up independently from many ancestors.

According to biochemist Douglas Theobald, it doesn't really matter. "Let's say life originated independently multiple times, which UCA allows is possible," said Theobald. "If so, the theory holds that a bottleneck occurred in evolution, with descendants of only one of the independent origins surviving until the present. Alternatively, separate populations could have merged, by exchanging enough genes over time to become a single species that eventually was ancestral to us all. Either way, all of life would still be genetically related."

Harnessing powerful computational tools and applying Bayesian statistics, Theobald found that the evidence overwhelmingly supports UCA, regardless of horizontal gene transfer or multiple origins of life. Theobald said UCA is millions of times more probable than any theory of multiple independent ancestries.

"There have been major advances in biology over the last decade, with our ability to test Darwin's theory in a way never before possible," said Theobald. "The number of genetic sequences of individual organisms doubles every three years, and our computational power is much stronger now than it was even a few years ago."

While other scientists have previously examined common ancestry more narrowly, for example, among only vertebrates, Theobald is the first to formally test Darwin's theory across all three domains of life. The three domains include diverse life forms such as the Eukarya (organisms, including humans, yeast, and plants, whose cells have a DNA-containing nucleus) as well as Bacteria and Archaea (two distinct groups of unicellular microorganisms whose DNA floats around in the cell instead of in a nucleus).

Theobald studied a set of 23 universally conserved, essential proteins found in all known organisms. He chose to study four representative organisms from each of the three domains of life. For example, he researched the genetic links found among these proteins in archaeal microorganisms that produce marsh gas and methane in cows and the human gut; in fruit flies, humans, round worms, and baker's yeast; and in bacteria like E. coli and the pathogen that causes tuberculosis.

Theobald's study rests on several simple assumptions about how the diversity of modern proteins arose. First, he assumed that genetic copies of a protein can be multiplied during reproduction, such as when one parent gives a copy of one of their genes to several of their children. Second, he assumed that a process of replication and mutation over the eons may modify these proteins from their ancestral versions. These two factors, then, should have created the differences in the modern versions of these proteins we see throughout life today. Lastly, he assumed that genetic changes in one species don't affect mutations in another species—for example, genetic mutations in kangaroos don't affect those in humans.

What Theobald did not assume, however, was how far back these processes go in linking organisms genealogically. It is clear, say, that these processes are able to link the shared proteins found in all humans to each other genetically. But do the processes in these assumptions link humans to other animals? Do these processes link animals to other eukaryotes? Do these processes link eukaryotes to the other domains of life, bacteria and archaea? The answer to each of these questions turns out to be a resounding yes.

Just what did this universal common ancestor look like and where did it live? Theobald's study doesn't answer this question. Nevertheless, he speculated, "to us, it would most likely look like some sort of froth, perhaps living at the edge of the ocean, or deep in the ocean on a geothermal vent. At the molecular level, I'm sure it would have looked as complex and beautiful as modern life."

(Photo: Brandeis University)

Brandeis University

A WOMAN'S TOUCH: PHYSICAL CONTACT INCREASES FINANCIAL RISK TAKING

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A woman's touch is all it takes for people to throw caution to the wind. That's the conclusion of a new study published online in Psychological Science, a journal of the Association for Psychological Science. If a female experimenter patted a participant on the back, they'd risk more money than if she just talked to them, or if a man did the patting. The researchers think this comes from the way that mothers use touch to make their babies feel secure.

When we are infants, we receive a lot of touch from our mothers. This creates a sense of attachment, which makes a baby feel secure. This helps the youngster's sense of adventure; they're more willing to take the risks that come with exploring unfamiliar contexts and strange situations. Jonathan Levav of Columbia University and Jennifer J. Argo of the University of Alberta wanted to know what happens when those babies grow up: Does physical contact also affect how willing adults are to take risks?

Participants were tested to see if they would take risks, such as investing money or taking a gamble. When they started the experiment, they were greeted in different ways: by a female or male experimenter and with a light, comforting touch on the shoulder, a handshake, or no physical contact at all. At the end of the experiment, they also filled out surveys that assessed how secure they felt. The researchers found that participants who were touched felt more secure and took bigger risks than those who weren't – but only if they were touched by a woman. The effect was stronger for a touch on the back than for a handshake, but went away entirely for participants who were touched by a man.

The results suggest that a woman's touch works the same on adults as it does on infants: making them feel more secure and more willing to take risks.

Association for Psychological Science

SPACE TECHNOLOGY REVOLUTIONIZES ARCHAEOLOGY, UNDERSTANDING OF MAYA

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A flyover of Belize's thick jungles has revolutionized archaeology worldwide and vividly illustrated the complex urban centers developed by one of the most-studied ancient civilizations -- the Maya.

University of Central Florida researchers led a NASA-funded research project in April 2009 that collected the equivalent of 25 years worth of data in four days.

Aboard a Cessna 337, LiDAR (Light Detection and Ranging) equipment bounced laser beams to sensors on the ground, penetrating the thick tree canopy and producing images of the ancient settlement and environmental modifications made by the inhabitants of the Maya city of Caracol within 200 square kilometers (77 square miles).

UCF anthropology professors Arlen and Diane Chase have directed archaeological excavations at Caracol for more than 25 years. The hard work of machete-wielding research scientists and students has resulted in the mapping of some 23 square kilometers (9 square miles) of ancient settlement.

The NASA technology aboard the Cessna saw beyond the rainforest and detected thousands of new structures, 11 new causeways, tens of thousands of agricultural terraces and many hidden caves – results beyond anyone's imagination. The data also confirm the size of the city (spread over 177 square kilometers or 68 square miles) and corroborate the Chases' previous estimates for the size of the population (at least 115,000 people in A.D. 650).

Until now, Maya archeologists have been limited in exploring large sites and understanding the full nature of ancient Maya landscape modifications because most of those features are hidden within heavily forested and hilly terrain and are difficult to record. LiDAR effectively removes these obstacles.

"It's very exciting," said Arlen Chase. "The images not only reveal topography and built features, but also demonstrate the integration of residential groups, monumental architecture, roadways and agricultural terraces, vividly illustrating a complete communication, transportation and subsistence system."

UCF Biology Professor John Weishampel designed the unique LiDAR approach. He has been using lasers to study forests and other vegetation for years, but this was the first time this specific technology fully recorded an archeological ruin under a tropical rainforest.

"Further applications of airborne LiDAR undoubtedly will vastly improve our understanding of ancient Maya settlement patterns and landscape use, as well as effectively render obsolete traditional methods of surveying," Chase said.

The images taken at the end of the dry season in Belize last April took about 24 hours of flight time to capture and then three weeks to analyze by remote sensing experts from the University of Florida. Now Caracol's entire landscape can be viewed in 3-D, and that already offers new clues that promise to expand current understanding of how the Maya were able to build such a huge empire and what may have caused its destruction.

"The ancient Maya designed and maintained sustainable cities long before 'building green' became a modern term," said Diane Chase, who has worked as co-director of the Caracol Archaeological Project beside her husband for the past 25 years. Her conclusion is based on the extensive agricultural terracing LiDAR revealed.

In addition to the UCF researchers, partners include Jason Drake with the U.S. Forest Service in Tallahassee and an adjunct professor at UCF; Ramesh Shrestha, K. Slatton and William Carter of the National Center for Airborne Laser Mapping; and Jaime Awe, director of the Institute of Archaeology in Belize.

Much more powerful information is anticipated from the data collected. UCF's Weishampel said rainforests play an important role in understanding and managing global warming today. The team's results also give him a snapshot of forest vegetation in that part of the world and how it was influenced by land-use practices 1,000 years ago. This may help scientists understand past human-environment interactions and changes that should be made today.

(Photo: Caracol Archaeological Project)

University of Central Florida

UNIVERSITY OF FLORIDA SCIENTISTS DISCOVER MEGALODON SHARK NURSERY

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University of Florida researchers have discovered a 10-million-year-old Neotropical nursery area for the extinct megalodon shark in Panama, providing fossil evidence the fish used these areas to protect their young for millions of years.

Appearing in the journal PLoS ONE, the article is the first thorough study of megalodon juveniles and gives scientists a better picture of shark behavior.

“The study provides evidence of megalodon behavior in the fossil record,” said lead author Catalina Pimiento, who just completed a master’s degree in zoology from UF and worked in the Florida Museum of Natural History’s vertebrate paleontology division. “Behavior doesn’t fossilize, but we were able to interpret ancient protection strategies used by extinct sharks based on the fossil record.”

Previously suggested fossil shark paleo-nursery areas, the Paleocene Williamsburg Formation and late Oligocene Chandler Bridge Formation of South Carolina, were based only on the anecdotal presence of juvenile teeth accompanied by marine mammals.

“Neither of the collections from previously suggested nursery grounds has been as rigorously analyzed as the specimens in this study, which better supports the presence of this paleo-nursery area,” Pimiento said.

In the current study, funded by the National Science Foundation, researchers collected 400 fossil shark teeth between 2007 and 2009 from the shallow marine Gatun Formation, which connected the Pacific Ocean and the Caribbean Sea during the late Miocene Epoch in Panama. Most of the 28 Carcharocles megalodon specimens were surprisingly small, Pimiento said, and analysis determined the size did not relate to tooth position in the jaw or the size of the species during the late Miocene.

“Our study suggests the specimens represent mostly juveniles with lengths between 2 and 10.5 meters,” Pimiento said.

Michael Gottfried, associate professor and curator of vertebrate paleontology at Michigan State University Museum, helped review the PLoS ONE article. His method of determining the skeletal anatomy of megalodon sharks based on comparisons with the great white shark was used in this study. Though Gottfried said he did not completely agree with all of the study’s conclusions, he believes the findings are interesting.

“Shark nursery areas are very poorly known, both for living and fossil species,” Gottfried said. “If the teeth from Panama described by Catalina and her collaborators do indeed come from a nursery area for the giant megalodon shark, they have the potential to provide a lot of interesting information on the paleobiology of this enormous, but still very enigmatic, fossil species.”

Nursery areas for sharks have ample food resources and serve as protection for juveniles and neonates from predators. Some scientists argue megalodon did not need nursery areas to protect their young because it was the largest shark that ever lived. But researchers discovered teeth in the study area from juvenile megalodon sharks as small as 2 meters long. Other studies also have confirmed present-day large sharks such as the tiger shark, great hammerhead and the white shark use nursery areas.

Other studies have shown white sharks, which belong to the same order as megalodon, seasonally return to the eastern Pacific and other coastal “hot spots” for feeding, foraging and mating. UF researchers considered the hypothesis that megalodon sharks used the grounds for feeding and reproduction rather than as a protective nursery area, but rejected the possibility based on the high number of juveniles, presence of neonates, shallow depth of the area and the scarcity of large mammals.

“This study of the megalodon teeth from Panama and its paleobiologic implications demonstrates the potential information that other fossil shark faunas can give us, including survival strategies, feeding habits and life histories,” said Dana Ehret, second author and vertebrate paleontology graduate student at the Florida Museum.

Other authors are Bruce MacFadden, Florida Museum of Natural History vertebrate paleontology curator, and Gordon Hubbell of Jaws International.

Most of the teeth collected are located in the Florida Museum of Natural History, which also houses the Florida Program for Shark Research and the International Shark Attack File.

(Photo: Jeff Gage/Florida Museum of Natural History)

University of Florida

THE JOKE IS ON US: A NEW INTERPRETATION OF BARED TEETH IN ARCHAEOLOGICAL ARTIFACTS

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Bared teeth are a prominent and eye-catching feature on many historical and archaeological artifacts, and are commonly interpreted as representing death, aggression and the shamanic trance. But a study in the forthcoming issue of Current Anthropology argues that the bared-teeth motif often expresses something a bit less sinister: the smile.

Alice V. M. Samson, Faculty of Archaeology at Leiden University, the Netherlands, and Bridget M. Waller, Department of Psychology, University of Portsmouth, examined the bared-teeth motif (BTM) of the Taíno, who lived in the Greater Antilles (the Caribbean) from AD 1000 to the early decades of European contact (1492-1550). Here the BTM was used on bodily adornments and items associated with healing and shamanic practices, usually as part of decorations depicting human and animal faces.

Interpretations of the BTM by early European observers reflect a western religious and cultural worldview rather than an understanding of indigenous practices. Some of these interpretations stem from eyewitness accounts of the first European observers, who feared the indigenous people and their idols. They described the BTM as "diabolical and associated with ferocity or aggression or the expression of malevolent deities who need to be appeased." These interpretations have never been challenged and as a consequence, the bared-teeth motif has mostly been interpreted negatively.

However, Samson and Waller argue that the negative interpretation misses the mark. "Exposed and clenched teeth are not common features of the universal facial expression of anger, which is instead characterized by widened eyes, tensed lower eyelids, and lowered, furrowed brows," they write. "Studies of facial expression in human and non-human primates have shown that the bared-teeth expression is used in social contexts as an unambiguous signal of non-aggression, affiliation and benign intent."

The Greater Antilles were home to several different societies. Samson and Waller believe that pendants and other adornments that carried the BTM "acted as a sort of Taíno social grammar, allowing the indigenous peoples of the islands to engage with each other and facilitating interactions while retaining their differences."

University of Chicago

NEW PLASTIC-LIKE MATERIALS MAY SAY 'SHHHH' TO HUSH DISEASE-CAUSING MICROBES

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Scientists are reporting success in a first attempt to silence the biochemical conversations that disease-causing bacteria use to marshal their forces and cause infections. In a study in ACS' monthly journal, Biomacromolecules, they describe use of specially designed plastic-like materials to soak up the substances that bacteria produce and pass to one another as messages.

Elena Piletska and colleagues point out that more and more disease-causing bacteria are developing resistance to the effects of antibiotics. The problem has sparked a global scientific quest for new antibiotics, and totally new approaches for dealing with bacteria that have caused millions of deaths throughout human history. One increasingly promising approach, they explain, blocks the chemical signals bacteria use to launch infection, a signaling process called "quorum sensing."

The scientists designed special plastics, similar to those dentists use to repair damaged teeth, to capture signaling molecules in laboratory experiments and thwart microbes' attempts to start an infection. The plastics also reduced the ability of the bacteria to form biofilms. Bacteria form these slimy layers inside medical tubing, water supply pipes, and other surfaces and use them as a refuge to grow and multiply.

(Photo: iStock)

American Chemical Society

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