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August 2003

Microbe From Depths Takes Life To Hottest Known Limit
Posted: Friday, August 15, 2003
Source: National Science Foundation

[B]Researchers Find Iron-reducing Archaeon 'Strain 121' Respires To Greatness[/B]

ARLINGTON, Va. -- It may be small, its habitat harsh, but a newly discovered single-celled microbe leads the hottest existence known to science. Its discoverers have preliminarily named the roughly micron-wide speck "Strain 121" for the top temperature at which it survives: 121 degrees Celsius, or about 250 degrees Fahrenheit.

Announcing Strain 121's record-breaking ability to take the heat in the August 15 issue of the journal Science, researchers Derek Lovley and Kazem Kashefi write, "The upper temperature limit for life is a key parameter for delimiting when and where life might have evolved on a hot, early Earth; the depth to which life exists in the Earth's subsurface; and the potential for life in hot, extraterrestrial environments."

Previously, the upper known temperature limit for life had been 113 C (235 F), a record held by another hyperthermophilic--or extreme-heat-liking--microbe called Pyrolobus fumarii.

The work by Lovley and Kashefi, researchers at the University of Massachusetts, Amherst, was supported by the National Science Foundation's Life in Extreme Environments program. Their NSF project may also yield clues to the formation of important ore deposits, the remediation of toxic contaminants, and more efficient recovery from petroleum reserves.

On a standard stovetop, water boils at 100 C, or 212 degrees F. Strain 121, however, comes from water at the ocean bottom, from a surreal deep-sea realm of hydrothermal vents. Heated to extremes by the earth's magma, water there spouts forth through leaks in the ocean floor. The pressure of the immense depths prevents such hot water from turning to steam--even as it sometimes emerges at temperatures near 400 C (750 F).

The sample cultured by Lovley and Kashefi was collected about 200 miles offshore from Puget Sound and nearly a mile and a half deep in the Pacific Ocean by a University of Washington team led by biological oceanographer John Baross.

Baross's crew, also supported by NSF, used a remotely operated submarine to retrieve it from the Pacific Ocean's Juan de Fuca Ridge, a lightless seascape where vents called "black smokers" rise up like three- and four-story chimneys and continuously spew a blackening brew laced with iron and sulfur compounds.

While suffocating, crushing, scalding, toxic and downright abysmal by most living standards, the arrangement is not so bad for Strain 121 and its ilk. They are archaea, single-celled microbes similar to, but not quite, bacteria. They often live amid extreme heat, cold, pressure, salinity, alkalinity, and/or acidity.

Archaea literally means "ancient," and Lovley and other biologists tend to call them "deep branchers" because these microbes were among the first branches on the "tree of life."

According to Lovley, Strain 121--it will be given a species name after his lab finalizes the microbe's description--uses iron the way aerobic animals use oxygen.

"It's a novel form of respiration," Lovley says, explaining how Strain 121 uses iron to accept electrons. (Many archaea also use sulfur). As oxygen does in humans, the iron allows the microbe to burn its food for energy. Chemically, the respiration process reduces ferric iron to ferrous iron and forms the mineral magnetite.

The presence of vast deposits of magnetite deep in the ocean, its presence as a respiratory byproduct of some archaea, and the abundance of iron on Earth before life began all led Lovley and Kashefi to write that "electron transport to ferrous iron may have been the first form of microbial respiration as life evolved on a hot, early Earth."

The researchers tested the process with Strain 121 cultures kept at 100 C in oxygen-free test tubes.

"It really isn't technically difficult. You just need some ovens to get it hot enough--and remember not to pick it up with your bare hands," Lovley says, speaking from experience.

They discovered that Strain 121 grew at temperatures from 85-121 C (185-250 F). (Meanwhile, Pyrolobus fumarii, the former top-temperature record-holder, wilted. After an hour at 121 C, only 1 percent of its cells were intact and none appeared viable).

"Growth at 121 C is remarkable," report Lovley and Kashefi, "because sterilization at 121 C, typically in pressurized autoclaves to maintain water in a liquid state, is a standard procedure, shown to kill all previously described microorganisms and heat-resistant spores."

Not only did Strain 121 survive such autoclaving, its population doubled in 24 hours at such heat and pressure. While they could not detect growth at higher temperatures, the researchers found that cultures that spent two hours at 130 C (266 F) still grew when transferred to a fresh medium at 103 C (217 F), with each new single-celled member appearing like a tiny tennis ball filled with cytoplasm and covered with about a dozen whip-like flagella.

The original news release can be found here
 

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Cross-species Mating Lead To Rapid Change
Posted: Friday, August 8, 2003
Source: Indiana University

Cross-species Mating May Be Evolutionarily Important And Lead To Rapid Change, Say Indiana University Researchers

BLOOMINGTON, Ind. -- Like the snap of a clothespin, the sudden mixing of closely related species may occasionally provide the energy to impel rapid evolutionary change, according to a new report by researchers from Indiana University Bloomington and three other institutions. Their paper will be made available online by Science magazine's "Science Express" service on Thursday (August 7) at 2 p.m. EDT.

A study of sunflower species that began 15 years ago shows that the sudden mixing and matching of different species' genes can create genetic super-combinations that are considerably more advantageous to the survival and reproduction of their owners than the gene combinations their parents possess.

"This is the clearest evidence to date that hybridization can be evolutionarily important," said IUB biologist Loren Rieseberg, who led the research. "What's more, we were able to demonstrate a possible mechanism for rapid evolutionary change by replicating the births of three unusual and ecologically divergent species within an extremely short period of time -- just a few generations."

The finding comes a month after IUB biologist Jeffrey Palmer and colleagues suggested in a letter to Nature that genetic exchange between completely unrelated species has occurred more often than experts previously thought.

There are many modern examples of hybridization in nature, some forced, some natural. Mules are bred by humans from horses and donkeys, are completely sterile, and represent an evolutionary dead-end. But there are other species-crossings that do just fine, such as offspring of the notoriously promiscuous oak tree species, which hybridize so often species-namers commonly joke about not being able to keep up.

Still, cross-species matings usually result in sickness or sterility, if the offspring get that far -- many naturally abort. Hybrid offspring that are fertile but sick or weak will not be able to compete with the purer offspring of either parent in passing on their genes to future generations. As a result, many evolutionary biologists have thought hybridization to be evolutionarily unimportant.

But Rieseberg's new report suggests that even weak, hybrid offspring can acquire new, strong combinations of genes from their parents. As long as those offspring are just virile enough to transmit their useful genes to their own offspring, those genes may fight their way into populations of either or both parent species and become evolutionarily important. Hybridization has been used to great effect in the creation of successful crops and animal breeds, but many evolutionary biologists have resisted accepting hybridization's importance in a world before the appearance of modern humans.

"We're all aware hybridization and intensive cross-breeding has produced better corn and better cows," Rieseberg said. "Yet there's been resistance in the evolutionary biology community to the notion that evolution might sometimes be facilitated by hybridization."

Rieseberg and his team compared the physical, physiological and genetic traits of several sunflower species. Two of the species, Helianthus annuus and H. petiolaris, are considered "parental," or more ancient. Another three species the scientists studied, H. anomalus, H. deserticola and H. paradoxus, are believed to have evolved somewhat recently, as hybrids of the two parental sunflower species, between 60,000 and 200,000 years ago. The three hybrid species are remarkable in being adapted to very extreme habitats: sand dunes, dry desert floor and salt marshes, respectively. The researchers also created their own hybrids of H. annuus and H. petiolaris.

The researchers found that their synthetic hybrids quickly acquired the traits necessary to colonize the extreme habitats of their naturally evolved hybrid counterparts, suggesting that potentially useful traits can be created quickly. Rieseberg and his team also found that the traits were largely the same as those produced by natural selection during the evolution of the natural hybrid species. Through cross-breeding, the researchers were able to simulate the birth of three new species and the large and dramatic evolutionary changes that accompanied their origins.

"It's often very easy to explain small differences we see within a species, but harder to account for larger differences between species that require changes in multiple traits or genes," Rieseberg said. "We have provided an explanation for how some of these more difficult changes might happen. Dramatic evolutionary changes are most likely to occur when parental species are very different from each other, creating a much broader array of gene and trait combinations."


Researchers at La Laboratoire de Biologie Moleculaire et Phytochimie (Villeurbanne, France), the University of Georgia and Kent State University also contributed to the report. It was funded by grants from the National Institutes of Health and the National Science Foundation.

The original news release can be found here.
 

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When did we start talking?
Posted: Thursday, August 7, 2003
http://www.guardian.co.uk/

We began talking as early as 2.5m years ago, writes Stephen Oppenheimer. Is that what drove the growth of our brains?

When did we start talking to each other and how long did it take us to become so good at it? In the absence of palaeo-cassette recorders or a time machine the problem might seem insoluble, but analysis of recent evidence suggests we may have started talking as early as 2.5m years ago.

There is a polar divide on the issues of dating and linking thought, language and material culture. One view of language development, held by linguists such as Noam Chomsky and anthropologists such as Richard Klein, is that language, specifically the spoken word, appeared suddenly among modern humans between 35,000 and 50,000 years ago and that the ability to speak words and use syntax was recently genetically hard-wired into our brains in a kind of language organ.

This view of language is associated with the old idea that logical thought is dependent on words, a concept originating with Plato and much in vogue in the 19th century: animals do not speak because they do not think. The advances in communication and abstract thought demonstrated by chimps and bonobos such as the famous Kanzi put this theory in doubt.

The notion of a great leap forward in the quality of human thinking is further reflected in a common interpretation of the flowering of Upper Palaeolithic art in Europe. European cave paintings in Lascaux and Chauvet in France and carved figurines that have been dated to over 30,000 years ago are seen, according to this perspective, as the first stirrings of symbolic and abstract thought and also of language.

The problem with using art as prehistoric evidence for the first human that could speak is that, quite apart from its validity, the further back one looks the more chance the evidence for art itself would have perished.

An alternative to the Chomskian theory, is that language developed as a series of inventions. This was first suggested by the 18th-century philosopher Etienne Bonnot de Condillac. He argued that spoken language had developed out of gesture language (langage d'action) and that both were inventions arising initially from the simple association between action and object. The Condillac view, with some development, can be traced to the present day with the recent work of New Zealand psychologist Michael Corballis and others. The theory sees gesture language as arising originally among apes as sounds accompanying gestures, with these sounds gradually becoming coded into "words" as the new skill drove its own evolution. Subsequently, coded words developed into deliberate, complex communication. Evolutionary pressures promoted the development of an anatomy geared to speech - the larynx, vocal muscles and a specific part of the brain immediately next to that responsible for gestures.

This view, that spoken language was ultimately a cultural invention like tool-making, which then drove the biological evolution of the brain and vocal apparatus, seems obvious when you think of the development of different languages.

The unique features of a language such as French clearly do not result from any biological aspect of being French but are the cultural possessions of the French-speaking community. Each language evolves from one generation to the next, constantly adapting itself to cope with the learning biases of each new set of young, immature minds.

Several skull and spinal modifications relating to speech production (arched base of skull and enlargement of the channel for nerves to the tongue in early human fossils, a lopsided brain and changes in relative proportions of the brain) have all been used to shift speech way back to early humans 2.5m years ago or even earlier.

Anthropologists and fossil experts who accept that speech started early, still tend to think of language evolution as a gradual 2m year process with our own modern human species (Homo sapiens) way out at the top and our older human ancestors cast as mumbling, hooting parodies of ourselves. A major reason for this is the perception that brain growth among humans was gradual over the same 2.5m year period. Several recent changes in the fossil evidence bring this into doubt.

The first of these is a redating of soil layers from the famous Olduvai Gorge in east Africa where many key fossil remains have been found. A number of big-brained human species appear to be much older than previously thought, with several specimens dating over a million years old. When brain sizes for all available skulls are plotted against time, using the revised dates, the result is startling: the bulk of increase in brain size was over by around 1.2m years ago with some African human species having brain volumes easily within the modern human range by that time. Those in our own African ancestry stopped growing their brains perhaps 200,000 years ago and even started shrinking them over the past 150,000 years - the period of our own species' time on Earth.

So we have the paradox that over the period when our brain was growing most rapidly, our material cultural development, as measured by stone tools, advanced only marginally; then, over a million years later, when the culture of anatomically modern humans finally started to accelerate, artistically and technologically, our brains were actually getting smaller.

The additional piece of evidence that makes this paradox all the more significant is that brain size did not just leap between human species in a direct line of ascent towards ourselves. Over the period from 2.5 to 1.5m years ago, it turns out brains were growing more rapidly than at any time since, within all the different human species and also in Paranthropus species. The logical conclusion is that there must have been a unique new behaviour driving brain growth, shared between all species of humans and Paranthropus, with its origin, presumably, in their immediate shared walking ape ancestor.

So, what was driving rapid brain growth right at the beginning 2.5m years ago? The answer may have been staring us in the face. Namely, that not only were early humans and Paranthropus communicating but their ancestor, a walking ape, had started the trend in this very useful skill. Around 2.5m years ago the weather took a decided turn for the worse, becoming more variable and colder and dryer. The search for food became more taxing, and there would have been a real need to communicate more effectively and cope with the worsening environment in a cooperative way.

Speech, a complex system of oral communication, is the only inherited primate skill that would self-evidently benefit from a larger computer than that of a chimp. The near maximum in brain size achieved by 1.2m years ago indicates that those early ancestors could already have been talking perfectly well. It was all over bar the shouting. Our new Rolls Royce brain, developed to manipulate and organise complex symbolic aspects of speech internally, could now be turned to a variety of other tasks.

So what happened in the million gap years after that? Why did we take so long to get to the moon? Cultural evolution aided by communication and teaching is a cumulative interactive process. If each new generation invented just one new skill or idea and passed it on with the rest to their children and cousins, you could predict exactly the same curve of cultural advance as we see from the archaeological and historical record - first very slow, then faster and faster.

Reproduced from:
http://www.guardian.co.uk/life/lastword/story/0,13228,1013222,00.html


Out of Eden: the Peopling of the World by Stephen Oppenheimer
Out of Eden: the Peopling of the World
by Stephen Oppenheimer
 

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Early Hominids May Have Behaved More 'Human'
Posted: Thursday, August 7, 2003
Source: Ohio State University

Early Hominids May Have Behaved More 'Human' Than We Had Thought

COLUMBUS, Ohio Our earliest ancestors probably behaved in a much more "human" way than most scientists have previously thought, according to a recent study that looked at early hominid fossils from Ethiopia.

Previously skeptical, an Ohio State University anthropologist now supports the idea that the minimal size differences between male and female pre-hominids suggest that they lived in a more cooperative and less competitive society.

The evidence centers on the extent of sexual dimorphism differences in size based on sex -- that existed among these early primates and what it suggests about the social structure of these creatures.

In a paper published in the August 5 issue of the Proceedings of the National Academy of Sciences, researchers at Kent State University reported that remains of both male and female specimens of Australopithecus afarensis showed fewer differences based on size than most paleontologists had earlier expected.

After comparing these bones with the near-complete skeletons of the fossil "Lucy," the researchers argue that the social structure of our earliest ancestors compared more to that of modern humans and chimpanzees than it does to gorillas and orangutans, as had previously been thought.

Gorillas, orangutans and baboons are known to have social structures built around fierce competition among males. Chimps and humans however, while still competitive, are more cooperative, giving them a greater degree of "humanness."

In a commentary in the journal, Clark Spencer Larsen, distinguished professor and chair of anthropology at Ohio State, argued that the Kent State study was the best to date at linking sexual dimorphism in early hominids to their probable social structure.

"These researchers have been able to show convincingly that, from the fossil remains, there was very little sexual dimorphism in these early hominids," Larsen said. "From that, I think we can extrapolate some behaviors specifically that males were cooperating more than they were competing among themselves a distinctly 'human' behavior."

Larsen believes that this male cooperation is the product of evolutionary change. "The success of this cooperation proved valuable to these early ancestors and has become a trait among humans," he said.

Paleontologists knew that there were minimal size differences between males and females since Homo sapiens evolved but the fossil record is so sparse, they were unsure of whether pre-Homo species showed more of less sexual dimorphism. Modern humans show no more than 15 percent size difference on average, Larsen said.

This new study, however, took advantage of a novel fossil find at Site 333 in the Afar Triangle of Ethiopia where remains of 13 individuals were discovered in 1975. Scientists believe that they all died at the same time, giving a possible "snapshot" view of how they lived.

Using the "Lucy" skeleton from a nearby site as a template, the Kent State researchers were able to use femur "head" size as a key to extrapolate the size of the individuals from Site 333.

"Only in the last few years have we realized that an individual's femur head size is a good proxy for its body weight," Larsen said.

The comparison showed that the sex-based size differences among the fossils at Site 333 were no greater than those for modern humans, suggesting that the same kind of modern social structure with cooperating males also occurred in the days of Australopithecus afarensis.

"I think what we are seeing here are the very first glimpses of 'humanness' in these early hominids dating back 3 million to 4 million years," he said.

The original news release can be found here.
 

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Cellular Reaction Processes From Ancient Life
Posted: Tuesday, August 5, 2003
Source: Virginia Tech

Discoveries Made About Cellular Reaction Processes From Ancient Life

Blacksburg, Va. (Aug. 4, 2003) -- How did life begin? What chemical combination launched the first organism with self-contained metabolism? And then what happened? Researchers in Robert H. White's group at Virginia Tech are tracing the family tree of life on earth by tracing the biochemical mechanisms within the cell -- specifically those that are used in the formation of peptide bonds. The building blocks of enzymatic and functional structures in living organisms are proteins created by linking amino acids into peptides (sub units of proteins). The mechanisms for creating peptides in proteins and some coenzymes are the clues that White and colleagues are following. "Enzymes that mechanistically do the same thing are included into a family, and we believe that there is an ancestral enzyme for this family," says David Graham, who was an NSF postdoctoral fellow in microbial biology at Virginia Tech.

In their attempt to reconstruct biochemical history, White's group has discovered two enzymes in Methanococcus jannaschii that may predate the cell's use of ribosome to build proteins. Their research will be reported in the Proceedings of the National Academy of Science (PNAS) by Hong Li, a post doc at Virginia Tech; Huimin Xu, a Virginia Tech technician, Graham, now at the University of Texas at Austin, and White, professor of biochemistry. The article (#3391), "Glutathione synthetase homologs encode a-L-glutamate ligases for methanogenic coenzyme F420 and tetrahydrosarcinapterin biosyntheses," will be published in the PNAS online Early Edition during the week of Monday, Aug. 4 Friday, Aug. 8, 2003.

"We found two enzymes, MptN and CofF, which are descendants of the ATP-grasp superfamily," says White.

The ATP superfamily is a group of enzymes that use ATP -- the nucleotide energy source for the cell. "ATP-grasp" refers to a shared nucleotide-binding method. Every self-sustaining, living organism has ATP superfamily enzymes. "We are interested in determining the functions of genes and how coenzymes are made," says Graham.

The two newly discovered genes share a common ancestor with the ribosomal protein S6:glutamate ligase and a putative a-aminoadipate ligase, defining the first group of ATP-grasp enzymes with a shared amino acid substrate specificity.

"Most people learn in high school biology about ribosomes' role in making protein, but there is a whole other world without ribosomes - interesting predecessors to how peptides were formed before ribosomes," says Graham.

White's group studies archaea, one of the earliest forms of life -- from when the earth was hot and soupy. Archaea are now found in such places as ocean vents and camel guts. "We are looking at present metabolism to extrapolate to ancient life," says White.

"MptN and CofF both produce alpha glutamate bonds (the same as in proteins), so we infer that an ancestor protein was also making alpha glutamate bonds," says Graham. "The mechanism is the same, but the substrate that the glutamate is attaching to is really different."

The compounds range from a protein to a small molecule, says White.

"We have defined a family that shares the same ability to add alpha glutamate," says Graham. "But we don't know why, yet."

Li also discovered another enzyme, CofE, which may predate ribosome. It makes gamma-linked glutamate bonds. Her article, "CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii" is forthcoming in the journal Biochemistry.

"Our initial interest in how F420 is made led to discovery of one new enzyme in sarcinpterin and two enzymes in F420 that are mechanistically related. They all have glutamate in their chemical structure and share a common reaction method for adding this amino acid," says White. "This work has shown how changes in members of a superfamily of enzymes can lead to a wider diversity in their function - in this case the biosynthesis of coenzymes."

After millions of years, the genealogy of life is more like a spider web, White says. "You never know where you will end up, which makes it exciting. We are working on one spoke of the spider web and want to go back to the center.

"In the meantime, we have expanded our knowledge of gene function, which is a central goal of our work."

The reviewers of the PNAS article commented that the research increased the understanding of the ATP superfamily and appreciated the elucidation of the relationships between two members in terms of coenzyme biosynthesis.

Li received her Ph.D. in biochemistry from Virginia Tech in May 2002 and plans to continue her research.


This story has been adapted from a news release issued by Virginia Tech.
 

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