Latest on Evolution

Collection of some interesting developments from around famous laboratories of the world

How did life on Earth originate?
Did life arrive from space? Rather than developing here, could the first life forms have been catapulted to Earth on a chunk of rock from outer space? Investigations show that microbes are capable of surviving just such a journey. At the mention of life forms from other planets, images of green Martians, ET-like creatures or Klingons immediately spring to mind, largely influenced by the film industry. They travel through space in UFOs in order to conquer the Earth. Something similar may well have happened a long time ago: The ‘UFOs’ could have been lumps of rock that broke off from a planet when it was hit by a meteorite, and their ‘crews’ could have been microbes. This is the assumption on which the panspermia hypothesis is based. However, assuming that there are microbes on other planets, Mars for example, would they be able to withstand the pressure that arises when a meteorite crashes into their planet and catapults their rocky UFO into space – a pressure that is 400,000 times higher than that of the Earth’s atmosphere?

Researchers at the Fraunhofer Institute for High-Speed Dynamics, Ernst-Mach-Institut, EMI have systematically investigated this question for the first time: “We simulate the shock wave that occurs when a meteorite crashes into Mars,” says Dr. Ulrich Hornemann, who is in charge of the experiments at the EMI. “To do that, we detonate an explosive cylinder that accelerates a metal plate. This metal plate then hits a steel canister containing two thin stone plates between which there is a thin layer of microbes.” When the metal plate crashes into the container, a shock wave is generated that passes through the stone plates and the layer of microbes. The astonishing thing is that even at 400,000 times atmospheric pressure, one ten thousandth of the microbes survive the impact of the metal plate; the main reason for this

being that the inhospitably high pressure only lasts for a fraction of a second just like the impact of a meteorite. Because the rocks that are broken off by meteorites usually have small cracks and crevices in them, the experts have also investigated the feasibility of porous rocks as ‘UFOs’. The result: Microorganisms can also survive here. And the small fissures are also advantageous to the tiny organisms in other ways, providing them with protection on their journey through space against UV radiation, solar wind and the icy cold and thus increasing their chances of survival, as the EMI’s project partners at the German Aerospace Center (DLR) found out. “It is therefore possible,” says Hornemann, “that life on Earth came here from other planets.”

When fish first started biting
Before fish began to invade land, about 365 million years ago, they had some big problems to solve. They needed to come up with new ways to move, breathe, and eat. Take the latter, for example. Fish usually pucker up and suck prey into their mouths. But air is 900 times less dense than water, so land-livers must bite into their food to get a meal. Researchers at Harvard University have just completed a study that gives a clear picture of how that change was made. “Aquatic creatures developed the tools they needed to feed on land before they completely left water,” notes Molly Markey, a lecturer on earth and planetary sciences. “Our research suggests that these first tetrapods, four-footed animals, bit on prey in shallow water or on land. Although they may have occasionally captured a meal by suction.” To become biters, the invaders had to change their teeth and skulls, and learn to walk. Along with Charles Marshall, a professor of biology and of geology at Harvard’s Museum of Comparative Zoology, Markey compared the boney remains of a 365million-year-old fish named Eusthenopteron, two ancient tetrapods called Acanthostega and Phonerpeton, and a modern fish. The salamanderlike Acanthostega spent much of its life in the water, Phonerpeton lived on land. Both Acanthostega and Eusthenopteron possessed lungs and gills, so they could breathe air or water, like today’s lungfishes. All three ancients boasted pointed teeth, indicating that they were meat-eating predators. Studies done by Jenny Clark at Cambridge University in England show that Acanthostega had short legs that stuck out to its sides, ending in what look like webbed toes. Such limbs would not be very supportive, so it’s likely that the old tetrapod slithered or scooted, rather than walked, when it ventured on land. Slithering and chewing One big question is why Acanthrostega and its relatives left their aquatic domain in the first place. Were they trying to get away from bigger predators, or were they looking for new prey to feed on? “It’s likely that both reasons are true,” Markey says. Markey and Marshall compared models of the ancient tetrapods and Eusthenopteron, the fish that stayed at home. They published their findings in the April 16 online edition of the Proceedings of the National Academy of Sciences.

The comparison found that the key to evolving from sucking to biting lay in the tops of the animals’ skulls. These boney skull roofs, rather than being solid, were made up of lots of different pieces. Markey compares them to pieces of a jigsaw puzzle. “Imagine that skull bones are puzzle pieces,” she explains. “Places where they touch each other are known as sutures, and the bones can move around them a bit. The sutures get wider or narrower depending on motions such as chewing.” By analyzing sutures in the skulls of the ancient tetrapods and fish, then comparing them with those in a living fish, the researchers could determine how the skull roof deformed under the compression and tension of eating. Such analyses led to the conclusion that Eusthenopteron was a sucker and the awkward-moving Acanthostega was a biter — perhaps the first one in the animal kingdom. Think of that next time you suck in strands of spaghetti or chew on a piece of chicken.

Ancient T. rex and Mastodon Protein Fragments Discovered, Sequenced
Scientists have confirmed the existence of protein in soft tissue recovered from the fossil bones of a 68 million-year-old Tyrannosaurus rex (T. rex) and a half-million-year-old mastodon. Their results may change the way people think about fossil preservation and present a new method for studying diseases in which identification of proteins is important, such as cancer.

When an animal dies, protein immediately begins to degrade and, in the case of fossils, is slowly replaced by mineral. This substitution process was thought to be complete by 1 million years. Researchers at North Carolina State University (NCSU) and Harvard Medical School now know otherwise. The researchers’ findings appear as companion papers in this week’s issue of the journal Science. “Not only was protein detectably present in these fossils, the preserved material was in good enough condition that it could be identified,” said Paul Filmer, program director in the National Science Foundation (NSF) Division of Earth Sciences, which funded the research. “We now know much more about what conditions proteins can survive in. It turns out that some proteins can survive for very long time periods, far longer than anyone predicted.” Mary Schweitzer of NCSU and the North Carolina Museum of Natural Sciences discovered soft tissue in the leg bone of a T. rex and other fossils recovered from the Hell Creek sediment formation in Montana. After her chemical and molecular analyses of the tissue indicated that original protein fragments might be preserved, she turned to colleagues John Asara and Lewis Cantley of Harvard Medical School, to see if they could confirm her suspicions by finding the amino acid used to make collagen, a fibrous protein found in bone.

Bone is a composite material, consisting of both protein and mineral. In modern bones, when minerals are removed, a collagen matrix–fibrous, resilient material that gives the bones structure and flexibility–is left behind. When Schweitzer demineralized the T. rex bone, she was surprised to find such a matrix, because current theories of fossilization held that no original organic material could survive that long. “This information will help us learn more about evolutionary relationships, about how preservation happens, and about how molecules degrade over time, which could have important applications in medicine,” Schweitzer said. To see if the material had characteristics indicating the presence of collagen, which is plentiful, durable and has been recovered from other fossil materials, the scientists examined the resulting soft tissue with electron microscopy and atomic force microscopy. They then tested it against various antibodies that are known to react with collagen. Identifying collagen would indicate that it is original to T. rex–that the tissue contains remnants of the molecules produced by the dinosaur. “This is the breakthrough that says it’s possible to get sequences beyond 1 million years,” said Cantley. “At 68 million years, it’s still possible.” Asara and Cantley successfully sequenced portions of the dinosaur and mastodon proteins, identifying the amino acids and confirming that the material was collagen. When they compared the collagen sequences to a database that contains existing sequences from modern species, they found that the T. rex sequence had similarities to those of chickens, and that the mastodon was more closely related to mammals, including the African elephant. The protein fragments in the T. rex fossil appear to most closely match amino acid sequences found in collagen of present-day chickens, lending support to the idea that birds and dinosaurs are evolutionarily related. “Most people believe that birds evolved from dinosaurs, but that’s based on the ‘architecture’ of the bones,” Asara said. “This finding allows us the ability to say that they really are related because their sequences are related.” “Scientists had long assumed that the material in fossil bones would not be preserved after millions of years of burial,” said Enriqueta Barrera, program director in NSF’s Division of Earth Sciences. “This discovery has implications for the study of similarly well-preserved fossil material.” The research was also funded by grants from the David and Lucille Packard Foundation, the Paul F. Glenn Foundation and Beth Israel Deaconess Medical Center.

Paleontologists Discover New Mammal from Mesozoic Era
An international team of American and Chinese paleontologists has discovered a new species of mammal that lived 125 million years ago during the Mesozoic Era, in what is now the Hebei Province in China. The new mammal, documented in the March 15 issue of the journal Nature, provides first-hand evidence of early evolution of the mammalian middle ear–one of the most important features for all modern mammals. The discovery was funded by the National Science Foundation (NSF).

“This early mammalian ear from China is a rosetta-stone type of discovery which reinforces the idea that development of complex body parts can be explained by evolution, using exquisitely preserved fossils,” said H. Richard Lane, program director in NSF’s Division of Earth Sciences, which cofunded the discovery with NSF’s Division of Environmental Biology and its Assembling the Tree of Life (AToL) program. Named Yanoconodon allini after the Yan Mountains in Hebei, the fossil was unearthed in the fossil-rich beds of the Yixian Formation and is the first Mesozoic mammal recovered from Hebei. The fossil site is about 300 kilometers outside of Beijing. The researchers discovered that the skull of Yanoconodon revealed a middle ear structure that is an intermediate step between those of modern mammals and those of near relatives of mammals, also known as mammaliaforms. “This new fossil offers a rare insight in the evolutionary origin of the mammalian ear structure,” said Zhe-Xi Luo, a paleontologist at the Carnegie Museum of Natural History (CMNH) in Pittsburgh, Pa. “Evolution of the ear is important for understanding the origins of key mammalian adaptations.”

Mammals have highly sensitive hearing, far better than the hearing capacity of all other vertebrates, scientists have found. Consequently, paleontologists and evolutionary biologists have been searching for more than a century for clues to the evolutionary origins of mammal ear structure. Mammalian hearing adaptation is made possible by a sophisticated middle ear of three tiny bones, known as the hammer (malleus), the anvil (incus) and the stirrup (stapes), plus a bony ring for the eardrum (tympanic membrane). The mammal middle ear bones evolved from the bones of the jaw hinge in their reptilian relatives. However, paleontologists long have attempted to understand the evolutionary pathway via which these precursor jaw bones became separated from the jaw and moved into the middle ear of modern mammals. “Now we have a definitive piece of evidence, in a beautifully preserved fossil split on two rock slabs,” said Luo. “Yanoconodon clearly shows an intermediate condition in the evolutionary process of how modern mammals acquired their middle ear structure.” Yanoconodon is about 5 inches (or 15 cm) long and estimated to weigh about 30 grams. Its teeth are notable for the three cusps in a straight line on molars (thus known as a triconodont) for feeding on insects and worms. It has a long body, short and sprawling limbs and claws that were ideal for either digging or living on the ground. In addition to its unique ear structure, Yanoconodon also has a surprisingly high number of 26 thoracic (”chest”) and lumbar (”waist”) vertebrae, unlike most living and extinct terrestrial mammals that commonly have 19 or 20 thoracic and lumbar vertebrae. The extra vertebrae give Yanoconodon a more elongated body form, in contrast to its relatively shorter and very primitive limb and foot structures. The new mammal also has lumbar ribs, a rare feature among modern mammals. “The discoveries of exquisitely preserved Mesozoic mammals from China have built the evidence such that biologists and paleontologists are able to make sense of how developmental mechanisms have impacted the morphological evolution of the earliest mammals,” said Luo. The article is authored by Luo and his collaborators, Peiji Chen and Gang Li of Nanjing Institute of Geology and Palaeontology, China, and graduate student Meng Chen of Nanjing University. The researchers also received support from the National Natural Science Foundation (China), Ministry of Science and Technology (China), and National Geographic Society.

Human Ancestors had Short Legs for Combat, not Just Climbing
Ape-like human ancestors known as australopiths maintained short legs for 2 million years because a squat physique and stance helped the males fight over access to females, a University of Utah study concludes. “The old argument was that they retained short legs to help them climb trees that still were an important part of their habitat,” says David Carrier, a professor of biology. “My argument is that they retained short legs because short legs helped them fight.”

The study analyzed leg lengths and indicators of aggression in nine primate species, including human aborigines. It is in the March issue of the journal Evolution. Creatures in the genus Australopithecus – immediate predecessors of the human genus Homo – had heights of about 3 feet 9 inches for females and 4 feet 6 inches for males. They lived from 4 million to 2 million years ago. “For that entire period, they had relatively short legs – longer than chimps’ legs but shorter than the legs of humans that came later,” Carrier says. “So the question is, why did australopiths retain short legs for 2 million years? Among experts on primates, the climbing hypothesis is the explanation. Mechanically, it makes sense. If you are walking on a branch high above the ground, stability is important because if you fall and you’re big, you are going to die. Short legs would lower your center of mass and make you more stable.” Yet Carrier says his research suggests short legs helped australopiths fight because “with short legs, your center of mass is closer to the ground. It’s going to make you more stable so that you can’t be knocked off your feet as easily. And with short legs, you have greater leverage as you grapple with your opponent.”

While Carrier says his aggression hypothesis does not rule out the possibility that short legs aided climbing, but “evidence is poor because the apes that have the shortest legs for their body size spend the least time in trees – male gorillas and orangutans.” He also notes that short legs must have made it harder for australopiths “to bridge gaps between possible sites of support when climbing and traveling through the canopy.” Nevertheless, he writes, “The two hypotheses for the evolution of relatively short legs in larger primates, specialization for climbing and specialization for aggression, are not mutually exclusive. Indeed, selection for climbing performance may result in the evolution of a body configuration that improves fighting performance and vice versa.” Great Apes’ Short Legs Provide Evidence for Australopith Aggression All modern great apes – humans, chimps, orangutans, gorillas and bonobos – engage in at least some aggression as males compete for females, Carrier says. Carrier set out to find how aggression related to leg length. He compared Australian aborigines with eight primate species: gorillas, chimpanzees, bonobos, orangutans, black gibbons, siamang gibbons, olive baboons and dwarf guenon monkeys. Carrier used data on aborigines because they are a relatively natural population. For the aborigines and each primate species, Carrier used the scientific literature to obtain typical hindlimb lengths and data on two physical features that previously have been shown to correlate with male-male competition and aggressiveness in primates:

The weight difference between males and females in a species. Earlier studies found males fight more in species with larger male-female body size ratios. The male-female difference in the length of canine teeth, which are next to the incisors and are used for biting during fights.

Carrier used male-female body size ratios and canine tooth size ratios as numerical indicators for aggressiveness because field studies of primates have used varying criteria to rate aggression. He says it would be like having a different set of judges for each competitor in subjective Olympic events like diving or ice dancing. The study found that hindlimb length correlated inversely with both indicators of aggressiveness: Primate species with greater male-female differences in body weight and length of the canine teeth had shorter legs, and thus display more male-male combat. There was no correlation between arm length and the indicators of aggression. Carrier says arms are used for fighting, but “for other things as well: climbing, handling food, grooming. Thus, arm length is not related to aggression in any simple way.” Verifying the Findings

Carrier conducted various statistical analyses to verify his findings. First, he corrected for each species’ limb lengths relative to their body size. Primates with larger body sizes tend to have shorter legs, humans excepted. Without taking that into account, the correlation between body size and aggression indicators might be false. Another analysis corrected for the fact different primate species are related. For example, if three closely related species all have short legs, it might be due to the relationship – an ancestor with short legs – and not aggression. Even with the corrections, short legs still correlated significantly with the two indicators of aggressiveness. The study also found that females in each primate species except humans have relatively longer legs than males. “If it is mainly the males that need to be adapted for fighting, then you’d expect them to have shorter legs for their body size,” Carrier says. He notes there are exceptions to that rule. Bonobos have shorter legs than chimps, yet they are less aggressive. Carrier says the correlation between short legs and aggression may be imperfect because legs are used for many other purposes than fighting. Humans “are a special case” and are not less aggressive because they have longer legs, Carrier says. There is a physical tradeoff between aggression and economical walking and running. Short, squat australopiths were strong and able to stand their ground when shoved, but their short legs made them ill-suited for distance running. Slender, longlegged humans excel at running. Yet, they also excel at fighting. In a 2004 study, Carrier made a case that australopiths evolved into lithe, long-legged early humans only when they learned to make weapons and fight with them. Now he argues that even though australopiths walked upright on the ground, the reason they retained short legs for 2 million years was not so much that they spent time in trees, but “the same thing that selected for short legs in the other great apes: male-male aggression and competition over access to reproductively active females.” In other words, shorter legs increased the odds of victory when males fought over access to females – access that meant passing their genetic traits to offspring. Yet, “we don’t really know how aggressive australopiths were,” Carrier says. “If they were more aggressive than modern humans, they were exceptionally nasty animals.” Why Should We Care that Australopiths Were Short and Nasty? “Given the aggressive behavior of modern humans and apes, we should not be surprised to find fossil evidence of aggressive behavior in the ancestors of modern humans,” Carrier says. “This is important because we have a real problem with violence in modern society. Part of the problem is that we don’t recognize we are relatively violent animals.

Many people argue we are not violent. But we are violent. If we want to prevent future violence we have to understand why we are violent.” “To some extent, our evolutionary past may help us to understand the circumstances in which humans behave violently,” he adds. “There are a number of independent lines of evidence suggesting that much of human violence is related to male-male competition, and this study is consistent with that.” Nevertheless, male-male competition doesn’t fully explain human violence, Carrier says, noting other factors such as hunting, competing with other species, defending territory and other resources, and feeding and protecting offspring.

Research shows how animals adapt their behavior to the environment
Male Anole lizards signal ownership of their territory by sitting up on a tree trunk, bobbing their heads up and down and extending a colorful throat pouch. They can spot a rival lizard up to 25 meters away, says National Science Foundation (NSF)-funded biologist Terry Ord of the University of California at Davis. Ord and colleagues published their results this week in the journal Proceedings of the Royal Society B. The lizards’ signals need to be strong enough for a rival to see, but not vivid enough to interest predators. Their forest homes, however, can be “visually noisy” environments, with branches and leaves waving in the breeze. “They have to have a strategy to get their message across,” Ord says. “We all know that people speak more loudly in a noisy party,” says John Byers, program director in NSF’s division of organismal systems. “These researchers have shown that lizards can do the same. We are only beginning to understand how perfectly adapted the behavior of animals can be.” Ord videotaped two species of Anole lizards, Anolis cristatellus and Anolis gundlachi, in the Caribbean National Forest of Puerto Rico.He found that the more “noise” in the background, the faster and more exaggerated the movements of the lizards. Anole lizards are interesting to evolutionary biologists because different species are found on different islands throughout the Caribbean. The lizards are not closely related — they are separated by 30 million years of evolution — but they live in similar environments with the same obstacles to communication. Co-authors of the paper are Richard Peters, Australian National University, Canberra, and Barbara Clucas of the University of California at Davis. The work was also supported by grants from the National Geographic Society and the Australian Research Council.

New dating evidence of skull suggests that modern humans originated in sub-Saharan Africa
Oxford researchers have used new dating techniques on a human skull to help find out where our most recent common ancestor came from. The skull, which was discovered more than 50 years ago near the town of Hofmeyr in the Eastern Cape Province of South Africa, is thought to be 36,000 years old, according to the study published in the Science journal. The finding by researchers from Oxford University in collaboration with Stony Brook University, New York, supports a growing body of genetic evidence, which suggests that modern humans originated in sub-Saharan Africa and migrated about this time to colonise the Old World. The international team of scientists relied on a new application of dating methods developed by Dr Richard Bailey and his colleagues from the School of Geography and the Environment, the Research Laboratory for Archaeology and the Department of Earth Science at Oxford University. Traditional radiocarbon dating of the Hofmeyr skull was not possible because so much carbon had been leached from the bone while it lay buried in sediment. Instead, the researchers measured the amount of radiation that had been absorbed by sand grains that filled the inside of the skull’s braincase. Measurements of radioactive isotopes in the sediment, combined with a sophisticated radiation transport model using data from a CT scan of the skull, allowed them to calculate the yearly rate at which radiation had been delivered to the sand grains. From this, the researchers were able to determine that the Hofmeyr skull had been buried for 36,000 years. Dr Richard Bailey, from Oxford’s School of Geography and the Environment, said: ‘Grains of sand have the ability to record the amount of radiation they have absorbed. It is this remarkable property of crystals that makes this kind of dating possible. ‘ Many problems we face in understanding the evolution of humans and the evolution of the wider natural environment can be expressed in terms of hypotheses related to the timing of key events. This is why the range of dating techniques available to us is so important in so many areas of science.’ This discovery is key to knowing more about a critical period in human evolutionary history, given the lack of human fossils in sub-Saharan Africa between 70,000 and 15,000 years ago. During the middle of this period, sophisticated stone and bone tools and artwork first appeared in sub-Saharan Africa, and anatomically modern people are

seen for the first time in Europe and western Asia in what archaeologists refer to as the ‘Upper Paleolithic’ period. Research conducted in the Max Planck Institute in Leipzig, Germany, established similarities between the Hofmeyr skull and contemporaneous Upper Paleolithic skulls from Europe. These findings, combined with the new dating evidence, provides strong support for the genetics-based ‘Out of Africa’ theory, which predicts that modern humans inhabiting western Asia in the ‘Upper Paleolithic’ period should also be found in subSaharan Africa around 36,000 years ago. The skull from South Africa provides the first fossil evidence in support of this prediction. Lead author, Professor Frederick Grine of the Departments of Anthropology and Anatomical Sciences at Stony Brook University in New York, said: ‘The Hofmeyr skull gives us insights into the morphology of such a sub-Saharan Africa, which means the most recent common ancestor of all of us – wherever we come from.’

How did our Ancestors’ Minds really work?
How did our evolutionary ancestors make sense of their world? What strategies did they use, for example, to find food? Fossils do not preserve thoughts, so we have so far been unable to glean any insights into the cognitive structure of our ancestors. However, researchers at the Max Planck Institute for Psycholinguistics and their colleagues at the Max Planck Institute for Evolutionary Anthropology were able to find answers to these questions using an alternative research method: comparative psychological research. In this way, they discovered that some of the strategies shaped by evolution are evidently masked very early on by the cognitive development process unique to humans. Being able to remember and relocate particular places where there is food is an asset to any species. There are two basic strategies for remembering the location of something: either remembering the features of the item (it was a tree, a stone, etc.), or knowing the spatial placement (left, right, middle, etc.). All animal species tested so far - from goldfish, pigeons and rats though to humans - seem to employ both strategies. However, if the type of recall task is designed so that the two strategies are in opposition, then some species (e.g. fish, rats and dogs) have a preference for locational strategies, while others (e.g. toads, chickens and children) favor those which use distinctive features. Until now, no studies had systematically investigated these preferences along the phylogenetic tree. Recently, however, Daniel Haun and his colleagues have carried out the first research of its kind into the cognitive preferences of a whole biological family, the hominids. They compared the five species of great apes - orangutans, gorillas, bonobos, chimpanzees and humans - to establish which cognitive strategies they prefer in order to uncover hidden characteristics. The researchers worked on the assumption that if all five species share particular preferences, these are very probably a part of the evolutionary legacy of our most recent common ancestors, who died out some 15 million years ago. At the Wolfgang Koehler Primate Research Center at the Leipzig Zoo, the researchers hid coveted items using two different strategies (see the above picture): In the place condition, the item remained in the same place it was hidden in previously, but under a different object (e.g. a stone); in the feature condition the object remained the same, but the place changed. It was established that all four great ape species and one-year-old

children actually use the location as a way of finding something hidden, even if it is hidden under a completely different object. This outcome suggests that this preference has been part of our cognitive structure for 15 million years. The researchers then investigated three-year-old children and discovered a difference: Unlike younger children, they considered the object under which the item was hidden to be the most reliable indication of its whereabouts, even if the location had changed completely. The scientists have sufficient evidence to conclude that 1-year-old children and great apes do not lack the capability to develop a feature-based strategy, but simply prefer to use a place-based strategy. Evidently, humans reassess these preferences as their cognitive development continues. “The unique human cognitive development seems to mask some of our evolved strategies even before we reach the age of three,” says Daniel Haun. “In future experiments, we therefore want to find out which areas of cognitive development in humans, for example language acquisition, are responsible for this restructuring of cognitive preferences.” The new methodical approach and the results it yields pave the way for the systematic study of the cognitive structures of our evolutionary ancestors and thus ultimately to an improved understanding of the origins of human thinking.

Life finds a way in unlikely circumstances
Australian and US scientists have discovered a new group of organisms living in the pH equivalent of battery acid at a Californian mine. University of Queensland scientist Rick Webb was working with scientists from the University of California when they uncovered the extraordinary life forms in acid mine drainage at the Richmond Mine on Iron Mountain in California.

He said the existence of these organisms was nothing short of remarkable considering the harsh environment they were found in. “The samples for our project were collected from acid mine drainage which is at a pH of about 0.5 to 1,” he said. “This is the equivalent of battery acid…so the fact that these organisms are living in this extreme environment is no mean feat in itself.” Even more astounding is the minute size of the organisms. “When observed with the electron microscope it became apparent to us that they are small - smaller than other organisms in the mine, and they appear to be similar in size to viruses,” he said. “In fact they are so tiny that they are smaller than the minimum size expected on the basis of theoretical considerations for free-living cells.” Had it not been for the use of a new method of studying the entire genomic information of the samples, this new group of organisms would have gone undiscovered. Rick Webb and his colleagues did not isolate the microbes in the laboratory or use polymerase chain reaction (PCR), the methods typically employed to identify new microbes in the environment. “Instead, we found them by directly isolating genomic DNA from the mine and sequencing the genomes of the organisms present,” he said. “We have called these new organisms ARMAN - Archaeal Richmond Mine Acidophilic Nanoorganisms.”

Rick Webb, who was called into the project on the back of his expertise in the field of electron microscopy, said the discovery could open the possibilities for discovering new groups of organisms in different environments around the world. “One of the important things about this study is that it illustrates that direct genomic sequencing of the environment is beginning to reveal entirely new groups of life overlooked using common methods,” he said. In this case, the research could also have significant environmental implications, helping scientists to develop their understanding of the forces involved in acid mine drainage. “Here, we discovered new groups of microorganisms, present everywhere we look in the mine, which significantly increases our understanding of life associated with this worldwide environmental problem known as acid mine drainage.” The Iron Mountain site, which was mined for iron, silver, gold, copper, zinc and pyrite until it was closed in 1963, is well known for its problem with acid mine drainage. “Historic mining activity has fractured the mountain, exposing its minerals to surface water, rain and oxygen. “When pyrite is exposed to moisture and oxygen, sulfuric acid runs through the mountain and leaches out copper, cadmium, zinc and other heavy metals. “These heavy metals, along with the acid run-off, drain into the local water system and eventually into the Sacramento River, causing a serious environmental problem.” The research was part of a project to identify bacteria living within the acid mine drainage, [that are] involved in the reaction that releases heavy metals from the pyrite deposits. Rick Webb said further study would be required for scientists to get a firm grip on the existence of the newly discovered organisms. “We will need to isolate these ARMAN cells and grow them in the laboratory to be certain they are viable,” he said. The research will be published in the December 22, 2006 edition of the prestigious international journal SCIENCE.

UCLA Geneticists Aim to Unravel Where Chimp and Human Brains Diverge
Six million years ago, chimpanzees and humans diverged from a common ancestor and evolved into unique species. Now UCLA scientists have identified a new way to pinpoint the genes that separate us from our closest living relative and make us uniquely human. The Proceedings of the National Academy of Sciences reports the study in its Nov. 13 online edition. “We share more than 95 percent of our genetic blueprint with chimps,” explained Dr. Daniel Geschwind, principal investigator and Gordon and Virginia MacDonald Distinguished Professor of Human Genetics at the David Geffen School of Medicine. “What sets us apart from chimps are our brains: homo sapiens means ‘the knowing man.’” During evolution, changes in some genes altered how the human brain functions, he noted. “Our research has identified an entirely new way to identify those genes in the small portion of our DNA that differs from the chimpanzee’s,” Geschwind said.

By evaluating the correlated activity of thousands of genes, the UCLA team identified not just individual genes, but entire networks of interconnected genes whose expression patterns within the brains of humans varied from those in the chimpanzee. Gene expression is the process by which a gene’s DNA sequence is converted into cellular proteins. “Genes don’t operate in isolation — each functions within a system of related genes,” said first author Michael Oldham, UCLA genetics researcher. “If we examined each gene individually, it would be similar to reading every fifth word in a paragraph — you don’t get to see how each word relates to the other. So instead we used a systems biology approach to study each gene within its context.” The scientists identified networks of genes that correspond to specific brain regions. When they compared these networks between humans and chimps, they found that the gene networks differed the most widely in the cerebral cortex — the brain’s most highly evolved region, which is three times larger in humans than chimps. Secondly, the researchers discovered that many of the genes that play a central role in cerebral cortex networks in humans — but not in the chimpanzee — also show significant changes at the DNA level.

“When we see alterations in a gene network that correspond to functional changes in the genome, it implies that these differences are very meaningful,” said Oldham. “This finding supports the theory that variations in the DNA sequence contributed to human evolution.” Relying on a new analytical approach developed by corresponding author Steve Horvath, UCLA associate professor of human genetics and biostatistics, the UCLA team used data from DNA microarrays — vast collections of tiny DNA spots — to map the activity of virtually every gene in the genome simultaneously. By comparing gene activity in different areas of the brain, the team identified gene networks that correlated to specific brain regions. Then they compared the strength of these correlations between humans and chimps. Many of the human-specific gene networks identified by the scientists related to learning, brain cell activity and energy metabolism. “If you view the brain as the body’s engine, our findings suggest that the human brain is like a 12-cylinder engine, while the chimp brain is more like a 6-cylinder,” explained Geschwind. “It’s possible that our genes adapted to allow our brains to increase in size, operate at different speeds, metabolize energy faster and enhance connections between brain cells across different brain regions.” Future UCLA studies will focus on linking the expression of evolutionary genes to specific regions of the brain, such as those that regulate language, speech and other uniquely human abilities.

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