Earth’s chemical energy powered early life through ‘the most revolutionary idea in biology since Darwin’

For 80 years it has been accepted that early life began in a ‘primordial soup’ of organic molecules before evolving out of the oceans millions of years later. Today the ’soup’ theory has been over turned in a pioneering paper in BioEssays which claims it was the Earth’s chemical energy, from hydrothermal vents on the ocean floor, which kick-started early life.

“Textbooks have it that life arose from organic soup and that the first cells grew by fermenting these organics to generate energy in the form of ATP. We provide a new perspective on why that old and familiar view won’t work at all,” said team leader Dr Nick lane from University College London. “We present the alternative that life arose from gases (H2, CO2, N2, and H2S) and that the energy for first life came from harnessing geochemical gradients created by mother Earth at a special kind of deep-sea hydrothermal vent – one that is riddled with tiny interconnected compartments or pores.”

The soup theory was proposed in 1929 when J.B.S Haldane published his influential essay on the origin of life in which he argued that UV radiation provided the energy to convert methane, ammonia and water into the first organic compounds in the oceans of the early earth. However critics of the soup theory point out that there is no sustained driving force to make anything react; and without an energy source, life as we know it can’t exist.

“Despite bioenergetic and thermodynamic failings the 80-year-old concept of primordial soup remains central to mainstream thinking on the origin of life,” said senior author, William Martin, an evolutionary biologist from the Insitute of Botany III in Düsseldorf. “But soup has no capacity for producing the energy vital for life.”

In rejecting the soup theory the team turned to the Earth’s chemistry to identify the energy source which could power the first primitive predecessors of living organisms: geochemical gradients across a honeycomb of microscopic natural caverns at hydrothermal vents. These catalytic cells generated lipids, proteins and nucleotides giving rise to the first true cells.

The team focused on ideas pioneered by geochemist Michael J. Russell, on alkaline deep sea vents, which produce chemical gradients very similar to those used by almost all living organisms today - a gradient of protons over a membrane. Early organisms likely exploited these gradients through a process called chemiosmosis, in which the proton gradient is used to drive synthesis of the universal energy currency, ATP, or simpler equivalents. Later on cells evolved to generate their own proton gradient by way of electron transfer from a donor to an acceptor. The team argue that the first donor was hydrogen and the first acceptor was CO2.

“Modern living cells have inherited the same size of proton gradient, and, crucially, the same orientation – positive outside and negative inside – as the inorganic vesicles from which they arose” said co-author John Allen, a biochemist at Queen Mary, University of London.

“Thermodynamic constraints mean that chemiosmosis is strictly necessary for carbon and energy metabolism in all organisms that grow from simple chemical ingredients [autotrophy] today, and presumably the first free-living cells,” said Lane. “Here we consider how the earliest cells might have harnessed a geochemically created force and then learned to make their own.”

This was a vital transition, as chemiosmosis is the only mechanism by which organisms could escape from the vents. “The reason that all organisms are chemiosmotic today is simply that they inherited it from the very time and place that the first cells evolved – and they could not have evolved without it,” said Martin.

“Far from being too complex to have powered early life, it is nearly impossible to see how life could have begun without chemiosmosis”, concluded Lane. “It is time to cast off the shackles of fermentation in some primordial soup as ‘life without oxygen’ – an idea that dates back to a time before anybody in biology had any understanding of how ATP is made.”

February 2, 2010.
GAINESVILLE, Fla. — A 60-million-year-old relative of crocodiles described this week by University of Florida researchers in the Journal of Vertebrate Paleontology was likely a food source for Titanoboa, the largest snake the world has ever known.

Above: GAINESVILLE, Fla. — On Feb. 1, 2010, Alex Hastings, a graduate student at UF’s Florida Museum of Natural History, measures a jaw fragment from an ancient relative of crocodiles that lived 60 million years ago. The fossil came from the same site in Colombia as fossils of Titanoboa, indicating the crocodyliform was a likely food source for the giant snake. Photos by: Jeff Gage/University of Florida.

Working with scientists from the Smithsonian Tropical Research Institute in Panama, paleontologists from the Florida Museum of Natural History on the UF campus found fossils of the new species of ancient crocodile in the Cerrejon Formation in northern Colombia. The site, one of the world’s largest open-pit coal mines, also yielded skeletons of the giant, boa constrictor-like Titanoboa, which measured up to 45 feet long. The study is the first report of a fossil crocodyliform from the same site.

“We’re starting to flesh out the fauna that we have from there,” said lead author Alex Hastings, a graduate student at the Florida Museum and UF’s department of geological sciences.

Specimens used in the study show the new species, named Cerrejonisuchus improcerus, grew only 6 to 7 feet long, making it easy prey for Titanoboa. Its scientific name means small crocodile from Cerrejon.

The findings follow another study by researchers at UF and the Smithsonian providing the first reliable evidence of what Neotropical rainforests looked like 60 million years ago.

While Cerrejonisuchus is not directly related to modern crocodiles, it played an important role in the early evolution of South American rainforest ecosystems, said Jonathan Bloch, a Florida Museum vertebrate paleontologist and associate curator.

“Clearly this new fossil would have been part of the food-chain, both as predator and prey,” said Bloch, who co-led the fossil-hunting expeditions to Cerrejon with Smithsonian paleobotanist Carlos Jaramillo. “Giant snakes today are known to eat crocodylians, and it is not much of a reach to say Cerrejonisuchus would have been a frequent meal for Titanoboa. Fossils of the two are often found side-by-side.”

The concept of ancient crocodyliforms as snake food has its parallel in the modern world, as anacondas have been documented consuming caimans in the Amazon. Given the ancient reptile’s size, it would have been no competition for Titanoboa, Hastings said.

Cerrejonisuchus improcerus is the smallest member of Dyrosauridae, a family of now-extinct crocodyliforms. Dyrosaurids typically grew to about 18 feet and had long tweezer-like snouts for eating fish. By contrast, the Cerrejon species had a much shorter snout, indicating a more generalized diet that likely included frogs, lizards, small snakes and possibly mammals.

“It seems that Cerrejonisuchus managed to tap into a feeding resource that wasn’t useful to other larger crocodyliforms,” Hastings said.

The study reveals an unexpected level of diversity among dyrosaurids, said Christopher A. Brochu, a paleontologist and associate professor in geosciences at the University of Iowa.

“This diversity is more evolutionarily complex than expected,” said Brochu, who was not involved in the study. “A limited number of snout shapes evolved repeatedly in many groups of crocodyliforms, and it appears that the same is true for dyrosaurids. Certain head shapes arose in different dyrosaurid lineages independently.”

Dyrosaurids split from the branch that eventually produced the modern families of alligators and crocodiles more than 100 million years ago. They survived the major extinction event that killed the dinosaurs but eventually went extinct about 45 million years ago. Most dyrosaurids have been found in Africa, but they occur throughout the world. Prior to this finding, only one other dyrosaurid skull from South America had been described.

Scientists previously believed dyrosaurids diversified in the Paleogene, the period of time following the mass extinction of dinosaurs, but this study reinforces the view that much of their diversity was in place before the mass extinction event, Brochu said. Somehow dyrosaurids survived the mass extinction intact while other marine reptile groups, such as mosasaurs and plesiosaurs, died out completely.

The crocodyliform’s diminutive size came as a surprise, Hastings said, especially considering the giant reptiles that lived during the Late Cretaceous. The fossil record also points to the possibility of other types of ancient crocodyliforms inhabiting the same ecosystem. “In a lot of these tropical, diverse ecosystems in which crocodyliforms can thrive, you often see multiple snout types,” he said. “They tend to start speciating into different groups.”

Feb. 1, 2010
Speed is not a word typically associated with trees; they can take centuries to grow. However, a new study to be published the week of Feb. 1 in the Proceedings of the National Academy of Sciences has found evidence that forests in the Eastern United States are growing faster than they have in the past 225 years. The study offers a rare look at how an ecosystem is responding to climate change.

For more than 20 years forest ecologist Geoffrey Parker has tracked the growth of 55 stands of mixed hardwood forest plots in Maryland. The plots range in size, and some are as large as 2 acres. Parker’s research is based at the Smithsonian Environmental Research Center, 26 miles east of the nation’s capital.

Parker’s tree censuses have revealed that the forest is packing on weight at a much faster rate than expected. He and Smithsonian Tropical Research Institute postdoctoral fellow Sean McMahon discovered that, on average, the forest is growing an additional 2 tons per acre annually. That is the equivalent of a tree with a diameter of 2 feet sprouting up over a year.

Forests and their soils store the majority of the Earth’s terrestrial carbon stock. Small changes in their growth rate can have significant ramifications in weather patterns, nutrient cycles, climate change and biodiversity. Exactly how these systems will be affected remains to be studied.

Parker and McMahon’s paper focuses on the drivers of the accelerated tree growth. The chief culprit appears to be climate change, more specifically, the rising levels of atmospheric CO2, higher temperatures and longer growing seasons.

Assessing how a forest is changing is no easy task. Forest ecologists know that the trees they study will most likely outlive them. One way they compensate for this is by creating a “chronosequence”—a series of forests plots of the same type that are at different developmental stages. At SERC, Parker meticulously tracks the growth of trees in stands that range from 5 to 225 years old. This allowed Parker and McMahon to verify that there was accelerated growth in forest stands young and old. More than 90% of the stands grew two to four times faster than predicted from the baseline chronosequence.

By grouping the forest stands by age, McMahon and Parker were also able to determine that the faster growth is a recent phenomenon. If the forest stands had been growing this quickly their entire lives, they would be much larger than they are.

Parker estimates that among himself, his colleague Dawn Miller and a cadre of citizen scientists, they have taken a quarter of a million measurements over the years. Parker began his tree census work Sept. 8, 1987—his first day on the job. He measures all trees that are 2 centimeters or more in diameter. He also identifies the species, marks the tree’s coordinates and notes if it is dead or alive.

By knowing the species and diameter, McMahon is able to calculate the biomass of a tree. He specializes in the data-analysis side of forest ecology. “Walking in the woods helps, but so does looking at the numbers,” said McMahon. He analyzed Parker’s tree censuses but was hungry for more data.

It was not enough to document the faster growth rate; Parker and McMahon wanted to know why it might be happening. “We made a list of reasons these forests could be growing faster and then ruled half of them out,” said Parker. The ones that remained included increased temperature, a longer growing season and increased levels of atmospheric CO2.

During the past 22 years CO2 levels at SERC have risen 12%, the mean temperature has increased by nearly three-tenths of a degree and the growing season has lengthened by 7.8 days. The trees now have more CO2 and an extra week to put on weight. Parker and McMahon suggest that a combination of these three factors has caused the forest’s accelerated biomass gain.

Ecosystem responses are one of the major uncertainties in predicting the effects of climate change. Parker thinks there is every reason to believe his study sites are representative of the Eastern deciduous forest, the regional ecosystem that surrounds many of the population centers on the East Coast. He and McMahon hope other forest ecologists will examine data from their own tree censuses to help determine how widespread the phenomenon is.

 Domestic dogs have followed their own evolutionary path, twisting Darwin’s directive ‘survival of the fittest’ to their own needs – and have proved him right in the process, according to a new study by biologists Chris Klingenberg, of The University of Manchester and Abby Drake, of the College of the Holy Cross in the US.

Huxley, a basset/lab mix. ©JCM Natural History Photography.

The study, published in The American Naturalist  (20 January 2010), compared the skull shapes of domestic dogs with those of different species across the order Carnivora, to which dogs belong along with cats, bears, weasels, civets and even seals and walruses.

It found that the skull shapes of domestic dogs varied as much as those of the whole order. It also showed that the extremes of diversity were farther apart in domestic dogs than in the rest of the order. This means, for instance, that a Collie has a skull shape that is more different from that of a Pekingese than the skull shape of the cat is from that of a walrus.

Above, the diversity of dog skulls suggests rapid evolution. Photo credit: Abbey Drake.

Dr Drake explains: “We usually think of evolution as a slow and gradual process, but the incredible amount of diversity in domestic dogs has originated through selective breeding in just the last few hundred years, and particularly after the modern purebred dog breeds were established in the last 150 years.”

By contrast, the order Carnivora dates back at least 60 million years. The massive diversity in the shapes of the dogs’ skulls emphatically proves that selection has a powerful role to play in evolution and the level of diversity that separates species and even families can be generated within a single species, in this case in dogs.

Much of the diversity of domestic dog skulls is outside the range of variation in the Carnivora, and thus represents skull shapes that are entirely novel.

Dr Klingenberg adds: “Domestic dogs are boldly going where no self respecting carnivore ever has gone before.

“Domestic dogs don’t live in the wild so they don’t have to run after things and kill them – their food comes out of a tin and the toughest thing they’ll ever have to chew is their owner’s slippers. So they can get away with a lot of variation that would affect functions such as breathing and chewing and would therefore lead to their extinction.

“Natural selection has been relaxed and replaced with artificial selection for various shapes that breeders favour.”

Domestic dogs are a model species for studying longer term natural selection. Darwin studied them, as well as pigeons and other domesticated species.

Drake and Klingenberg compared the amazing amount of diversity in dogs to the entire order Carnivora. They measured the positions of 50 recognizable points on the skulls of dogs and their ‘cousins’ from the rest of the order Carnivora, and analyzed shape variation with newly developed methods.

The team divided the dog breeds into categories according to function, such as hunting, herding, guarding and companion dogs. They found the companion (or pet) dogs were more variable than all the other categories put together.

According to Drake, “Dogs are bred for their looks not for doing a job so there is more scope for outlandish variations, which are then able to survive and reproduce.”

Dr Klingenberg concludes: “I think this example of head shape is characteristic of many others and is showing it so clearly, showing what happens when you consistently and over time apply selection.

“This study illustrates the power of Darwinian selection with so much variation produced in such a short period of time. The evidence is very strong.”

Drake, A. G. and C. P. Klingberg. 2010. Large-scale Diversification of Skull Shape in Domestic Dogs: Disparity and Modularity. The American Naturalist, March

The photo above is not a prehistoric creature, it is a tentacled snake. Tentacled snakes belong to the family Homalopsidae, a small, old lineage of semi-aquatic and aquatic snakes found in southern Asia and Australia. The swamps of Vietnam, Cambodia and Thailand support a diverse aquatic fauna, including the unique tentacled snake, Erpeton tentaculatum. Erpeton is the most distinctive of snakes. It has a pair of scale covered tentacles extending from its snout, the scales on its body are heavily keeled, and in the wild the snake’s body is covered with protists to aid in concealing it. Kenneth Catania of Vanderbuilt University, Duncan Leitch and Danielle Gauthie have worked out the function of the tentacles on the tentacled snake. Previous authors have hypothesized that they served as camouflage to break up the out line of the head, while others proposed a sensory function. Catania and colleagues found tiny nerve branches on the middle surface of the tentacles.They found the tentacles to be very sensitive using von Frey hairs they gently deflect the tentacles and then measured the tentacle’s responses in the trigeminal ganglion. The snake responded to even the tiniest displacement produced by the finest hair. Catania and colleagues also mapped the tentacle’s inputs to the snake’s optic tectum (the region of the brain that receives sensory inputs and then coordinates behavioral responses). The region of the optic tectum that received signals from the tentacles was close to regions that responded strongly to visual inputs, suggesting vision and the mechanical information from the tentacles was  highly integrated. The team fooled the snake into hunting by sight alone and found they would strike at the video image of a cartoon fish and found the to be surprisingly accurate. Erpeton has exceptionally large eyes for a homalopsid snake.

Full Citation: Catania, K. C., Leitch, D. B. and Gauthier, D. (2010). Function of the appendages in tentacled snakes (Erpeton tentaculatus). Journal of Experimental Biology 213, 359-367.

Scientists have long puzzled over how iguanas, a group of lizards mostly found in the Americas, came to inhabit the isolated Pacific islands of Fiji and Tonga. For years, the leading explanation has been that progenitors of the island species must have rafted there, riding across the Pacific on a mat of vegetation or floating debris. But new research in the January issue of The American Naturalist suggests a more grounded explanation.

Fiji Banded Iguana  (Brachylophus fasciatus). Wikimedia Commons.

Using the latest genetic, geological and fossil data, biologists Brice Noonan of the University of Mississippi and Jack Sites of Brigham Young University have found that iguanas may have simply walked to Fiji and Tonga when the islands were still a part of an ancient southern supercontinent.

The two islands, located about 2000 miles east of Australia, are home to several iguana species, and their presence there is “one of the most perplexing scenarios in island biogeography,” Noonan says. The other islands in the region, and closest continental landmass, Australia, have no iguanid species at all. In fact the closest iguanids are found about 5,000 miles away in the Americas. So how did these species get to these remote islands?

Some scientists have hypothesized that they must have rafted there—a journey of around 5,000 miles from South America to the islands. There is some precedent for rafting iguanas. There are documented cases of iguanas reaching remote Caribbean islands and the Galapagos Islands on floating logs. But crossing the Pacific is another matter entirely. Noonan and Sites estimate the trip would take six months or more—a long time for an iguana to survive on a log or vegetation mat.

So Noonan and Sites tested the possibility that iguanas simply walked to the islands millions of years ago, before the islands broke off from Gondwana—the ancient supercontinent made up of present-day Africa, Australia, Antarctica and parts of Asia. If that’s the case, the island species would need to be old—very old. Using “molecular clock” analysis of living iguana DNA, Noonan and Sites found that, sure enough, the island lineages have been around for more than 60 million years—easily old enough to have been in the area when the islands were still connected via land bridges to Asia or Australia.

Fossil evidence backs the finding. Fossils uncovered in Mongolia suggest that iguanid ancestors did once live in Asia. Though there’s currently no fossil evidence of iguanas in Australia, that doesn’t necessarily mean they were never there. “[T]he fossil record of this continent is surprisingly poor and cannot be taken as evidence of true absence,” the authors write.

So if the iguanas simply migrated to Fiji and Tonga from Asia or possibly Australia, why are they not also found on the rest of the Pacific islands? Noonan and Sites say fossil evidence suggests that iguana species did once inhabit other islands, but went extinct right around the time humans colonized those island. That’s an indication that iguanas were on the menu for the early islanders. But Fiji and Tonga have a much shorter history of human presence, which may have helped the iguanas living there to escape extinction.

The molecular clock analysis combined with the fossil evidence suggests a “connection via drifting Australasian continental fragments that may have introduced [iguanas] to Fiji and Tonga,” Noonan says. “The ‘raft’ they used may have been the land.”

The researchers say that their study can’t completely rule out the rafting hypothesis, but it does make the land bridge scenario “far more plausible than previously thought.”

Full Citation: Brice P. Noonan and Jack W. Sites Jr., “Tracing the Origins of Iguanid Lizards and Boine Snakes of the Pacific.” The American Naturalist 175:1 (January 2010).

 Jan. 14, 2010 - University of Utah scientists discovered that air flows in one direction as it loops through the lungs of alligators, just as it does in birds. The study suggests this breathing method may have helped the dinosaurs’ ancestors dominate Earth after the planet’s worst mass extinction 251 million years ago.

Before and until about 20 million years after the extinction - called “the Great Dying” or the Permian-Triassic extinction - mammal-like reptiles known as synapsids were the largest land animals on Earth.

The extinction killed 70 percent of land life and 96 percent of sea life. As the planet recovered during the next 20 million years, archosaurs (Greek for “ruling lizards”) became Earth’s dominant land animals. They evolved into two major branches on the tree of life: crocodilians, or ancestors of crocodiles and alligators, and a branch that produced flying pterosaurs, dinosaurs and eventually birds, which technically are archosaurs.

Above: Computerized tomographic (CT) X-ray images of side and top views of a 24-pound American alligator, with 3-D renderings of the bones and of airways or bronchi within the lungs. The windpipe and first-tier of bronchi are not shown. A University of Utah study found that air flows in one direction through a gator’s lungs. It flows from the first-tier bronchi through second-tier bronchi (blue), then through tube-like third-tier parabronchi (not shown) and then back through other second-tier bronchi (forest green). Photo Credit: C.G. Farmer and Kent Sanders.

By demonstrating one-way or “unidirectional” airflow within the lungs of alligators, the new study - published in the Friday, Jan. 15 issue of the journal Science - means that such a breathing pattern likely evolved before 246 million years ago, when crocodilians split from the branch of the archosaur family tree that led to pterosaurs, dinosaurs and birds.

That, in turn, means one-way airflow evolved in archosaurs earlier than once thought, and may explain why those animals came to dominance in the Early Triassic Period, after the extinction and when the recovering ecosystem was warm and dry, with oxygen levels perhaps as low as 12 percent of the air compared with 21 percent today.

“The real importance of this air-flow discovery in gators is it may explain the turnover in fauna between the Permian and the Triassic, with the synapsids losing their dominance and being supplanted by these archosaurs,” says C.G. Farmer, the study’s principal author and an assistant professor of biology at the University of Utah. “That’s the major reason this is important scientifically.”

Even with much less oxygen in the atmosphere, “many archosaurs, such as pterosaurs, apparently were capable of sustaining vigorous exercise,” she adds. “Lung design may have played a key role in this capacity because the lung is the first step in the cascade of oxygen from the atmosphere to the animal’s tissues, where it is used to burn fuel for energy.”

Farmer emphasized the discovery does not explain why dinosaurs, which first arose roughly 230 million years ago, eventually outcompeted other archosaurs.

Farmer conducted the study - funded by the National Science Foundation - with Kent Sanders, an associate professor of radiology at the University of Utah School of Medicine. They performed CT scans of a 4-foot-long, 24-pound alligator.

The synapsids - which technically include modern mammals - occupied ecological niches for large animals before the Permian-Triassic extinction.

“Some got up to be bear-sized,” says Farmer. Some were meat-eaters, others ate plants. They were four-footed and had features suggesting they were endurance runners. Their limbs were directly under their body instead of sprawling outward like a lizard’s legs. There is evidence they cared for their young.

The cause of the mass extinction 251 million years ago is unknown; theories include massive volcanism, an asteroid hitting Earth and upwelling of methane gas that had been frozen in seafloor ice.

“A few of the synapsids survived the mass extinction to re-establish their dominance in the early Triassic, and the lineage eventually gave rise to mammals in the Late Triassic,” says Farmer. “However, the recovery of life in the aftermath of the extinction involved a gradual turnover of the dominant terrestrial vertebrate lineage, with the archosaurs supplanting the synapsids by the Late Triassic.”

From then until the dinosaurs died out 65 million years ago, any land animal longer than about 3 feet was an archosaur, says Farmer, while mammal-like synapsid survivors “were teeny little things hiding in cracks. It was not until the die-off of the large dinosaurs 65 million years ago that mammals made a comeback and started occupying body sizes larger than an opossum.”

No one knows much about the archosaur that was the common ancestor of crocodilians and of pterosaurs, dinosaurs and birds, Farmer says.

It probably was “a small, relatively agile, insect-eating animal,” Farmer says. Illustrations of early archosaurs look like large lizards.

“Our data provide evidence that unidirectional flow [of air in the lungs] predates the origin of pterosaurs, dinosaurs and birds, and evolved in the common ancestor of the crocodilian and bird [and pterosaur and dinosaur] lineages,” Farmer says.

In the lungs of humans and other mammals, airflow is like the tides. When we inhale, the air moves through numerous tiers of progressively smaller, branching airways, or bronchi, until dead-ending in the smallest chambers, cul-de-sacs named alveoli, where oxygen enters the blood and carbon dioxide moves from the blood into the lungs.

It long has been known that airflow in birds is unidirectional, and some scientists suggest it also was that way in dinosaurs.

In modern birds, the lungs’ gas exchange units are not alveoli, but tubes known as “parabronchi,” through which air flows in one direction before exiting the lung. Farmer says this lung design helps birds fly at altitudes that would “render mammals comatose.”

Some researchers have argued that unidirectional airflow evolved after crocodilians split from the archosaur family tree, arising among pterosaurs and theropod dinosaurs, the primarily meat-eating group that included Tyrannosaurus rex. Others have argued it arose only among coelurosaurs, a group of dinosaurs that also includes T. rex and feathered dinosaurs.

Unidirectional air flow in birds long has been attributed to air sacs in the lungs. But Farmer disagrees, since gators don’t have air sacs, and says it’s due to aerodynamic “valves” within the lungs. She believes air sacs help birds redistribute weight to control their pitch and roll during flight. Farmer says many scientists simply assume air sacs are needed for unidirectional airflow, and have pooh-poohed assertions to the contrary.

“They cannot argue with this data,” she says. “I have three lines of evidence. If they don’t believe it, they need to get an alligator and make their own measurements.”

Farmer did three experiments to demonstrate one-way airflow in alligators’ lungs:

* She performed surgery on six anesthetized alligators and inserted flow meters called thermistors into the lungs to measure airflow speed and direction.

* Farmer pumped air in and out of lungs removed from four dead alligators sent to her by a wildlife refuge in Louisiana. The flow was monitored, showing the air kept going the same direction to loop through various tiers of bronchi and back to the trachea.

* Using lungs from another dead gator, she pushed and pulled water with tiny fluorescent beads through the lungs, making movies showing the unidirectional flow.

Farmer says the fact gator lungs still had unidirectional flow after being removed shows unidirectional airflow is caused by aerodynamic valves within the lungs, and not by some other factor, like air sacs or the liver, which acts like a piston to aid breathing.

How does air loop through an alligator’s multichambered lungs?

Inhaled air enters the trachea, or windpipe, and then flows into two primary bronchi, or airways. Each of those primary bronchi enters a lung.

From those primary airways, the bronchi then branch into a second tier of narrower airways. Inflowing air jets past or bypasses the first branch in each lung because the branch makes a hairpin turn away from the direction of airflow, creating an aerodynamic valve. Instead, the air flows into other second-tier bronchi and then into numerous, tiny, third-tier airways named parabronchi, where oxygen enters the blood and carbon dioxide leaves it.

The air, still moving in one direction, then flows from the parabronchi into the bypassed second-tier bronchi and back to the first-tier bronchi, completing a one-way loop through the lungs before being exhaled through the windpipe.

CAMBRIDGE, Mass. (January 13, 2010) – Contrary to a widely held scientific theory that the mammalian Y chromosome is slowly decaying or stagnating, new evidence suggests that in fact the Y is actually evolving quite rapidly through continuous, wholesale renovation.

Above: A human x and y chromosome from a male karyotype. Photo credit: National Human Genome Research Institute (NHGRI)

By conducting the first comprehensive interspecies comparison of Y chromosomes, Whitehead Institute researchers have found considerable differences in the genetic sequences of the human and chimpanzee Ys—an indication that these chromosomes have evolved more quickly than the rest of their respective genomes over the 6 million years since they emerged from a common ancestor. The findings are published online this week in the journal Nature.

“The region of the Y that is evolving the fastest is the part that plays a role in sperm production,” say Jennifer Hughes, first author on the Nature paper and a postdoctoral researcher in Whitehead Institute Director David Page’s lab. “The rest of the Y is evolving more like the rest of the genome, only a little bit faster.”
The chimp Y chromosome is only the second Y chromosome to be comprehensively sequenced. The original chimp genome sequencing completed in 2005 largely excluded the Y chromosome because its hundreds of repetitive sections typically confound standard sequencing techniques. Working closely with the Genome Center at Washington University, the Page lab managed to painstakingly sequence the chimp Y chromosome, allowing for comparison with the human Y, which the Page lab and the Genome Center at Washington University had sequenced successfully back in 2003.

The results overturned the expectation that the chimp and human Y chromosomes would be highly similar.  Instead, they differ remarkably in their structure and gene content. The chimp Y, for example, has lost one third to one half of the human Y chromosome genes–a significant change in a relatively short period of time. Page points out that this is not all about gene decay or loss. He likens the Y chromosome changes to a home undergoing continual renovation.

“People are living in the house, but there’s always some room that’s being demolished and reconstructed,” says Page, who is also a Howard Hughes Medical Institute investigator. “And this is not the norm for the genome as a whole.”

Wes Warren, Assistant Director of the Washington University Genome Center, agrees. “This work clearly shows that the Y is pretty ingenious at using different tools than the rest of the genome to maintain diversity of genes,” he says.  “These findings demonstrate that our knowledge of the Y chromosome is still advancing.”

Hughes and Page theorize that the divergent evolution of the chimp and human Y chromosomes may be due to several factors, including traits specific to Y chromosomes and differences in mating behaviors.

Because multiple male chimpanzees may mate with a single female in rapid succession, the males’ sperm wind up in heated reproductive competition. If a given male produces more sperm, that male would theoretically be more likely to impregnate the female, thereby passing on his superior sperm production genes, some of which may be residing on the Y chromosome, to the next generation.

Because selective pressure to pass on advantageous sperm production genes is so high, those genes may also drag along detrimental genetic traits to the next generation. Such transmission is allowed to occur because, unlike other chromosomes, the Y has no partner with which to swap genes during cell division. Swapping genes between chromosomal partners can eventually associate positive gene versions with each other and eliminate detrimental gene versions. Without this ability, the Y chromosome is treated by evolution as one large entity. Either the entire chromosome is advantageous, or it is not.

In chimps, this potent combination of intense selective pressure on sperm production genes and the inability to swap genes may have fueled the Y chromosome’s rapid evolution. Disadvantages from a less-than-ideal gene version or even the deletion of a section of the chromosome may have been outweighed by the advantage of improved sperm production, resulting in a Y chromosome with far fewer genes than its human counterpart.

To determine whether this rapid rate of evolution affects Y chromosomes beyond those of chimps and humans, the Page lab and the Washington University Genome Center are now sequencing and examining the Y chromosomes of several other mammals.

This research was funded by the National Institutes of Health (NIH) and the Howard Hughes Medical Institute (HHMI).

Full Citation: Hughes, J. et al. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content” Nature, online January 13, 2010.

JUPITER, FL – Scientists from The Scripps Research Institute have determined for the first time that prions, bits of infectious protein devoid of DNA or RNA that can cause fatal neurodegenerative disease, are capable of Darwinian evolution.

The study from Scripps Florida in Jupiter shows that prions can develop large numbers of mutations at the protein level and, through natural selection, these mutations can eventually bring about such evolutionary adaptations as drug resistance, a phenomenon previously known to occur only in bacteria and viruses. These breakthrough findings also suggest that the normal prion protein – which occurs naturally in human cells – may prove to be a more effective therapeutic target than its abnormal toxic relation.

The study was published in the December 31, 2009 issue of the journal Science Express, an advance, online edition of the prestigious journal Science.

“On the face of it, you have exactly the same process of mutation and adaptive change in prions as you see in viruses,” said Charles Weissmann, M.D., Ph.D., the head of Scripps Florida’s Department of Infectology, who led the study. “This means that this pattern of Darwinian evolution appears to be universally active. In viruses, mutation is linked to changes in nucleic acid sequence that leads to resistance. Now, this adaptability has moved one level down – to prions and protein folding – and it’s clear that you do not need nucleic acid for the process of evolution.”

Infectious prions (short for proteinaceous infectious particles) are associated with some 20 different diseases in humans and animals, including mad cow disease and a rare human form, Creutzfeldt-Jakob disease. All these diseases are untreatable and eventually fatal. Prions, which are composed solely of protein, are classified by distinct strains, originally characterized by their incubation time and the disease they cause. Prions have the ability to reproduce, despite the fact that they contain no nucleic acid genome.

Mammalian cells normally produce cellular prion protein or PrPC. During infection, abnormal or misfolded protein – known as PrPSc – converts the normal host prion protein into its toxic form by changing its conformation or shape. The end-stage consists of large assemblies (polymers) of these misfolded proteins, which cause massive tissue and cell damage.

“It was generally thought that once cellular prion protein was converted into the abnormal form, there was no further change,” Weissmann said. “But there have been hints that something was happening. When you transmit prions from sheep to mice, they become more virulent over time. Now we know that the abnormal prions replicate, and create variants, perhaps at a low level initially. But once they are transferred to a new host, natural selection will eventually choose the more virulent and aggressive variants.”

In the first part of the study, Weissmann and his colleagues transferred prion populations from infected brain cells to culture cells. When transplanted, cell-adapted prions developed and out-competed their brain-adapted counterparts, confirming prions’ ability to adapt to new surroundings, a hallmark of Darwinian evolution. When returned to brain, brain-adapted prions again took over the population.

To confirm the findings and to explore the issue of evolution of drug resistance, Weissmann and his colleagues used the drug swainsonine or swa, which is found in plants and fungi, and has been shown to inhibit certain prion strains. In cultures where the drug was present, the team found that a drug-resistant sub-strain of prion evolved to become predominant. When the drug was withdrawn, the sub-strain that was susceptible to swainsonine again grew to become the major component of the population.

Weissmann notes that the findings have implications for the development of therapeutic targets for prion disease. Instead of developing drugs to target abnormal proteins, it could be more efficient to try to limit the supply of normally produced prions – in essence, reducing the amount of fuel being fed into the fire. Weissmann and his colleagues have shown some 15 years ago that genetically engineered mice devoid of the normal prion protein develop and function quite normally (and are resistant to prion disease!).

“It will likely be very difficult to inhibit the production of a specific natural protein pharmacologically,” Weissmann said, “You may end up interfering with some other critical physiological process, but nonetheless, finding a way to inhibit the production of normal prion protein is a project currently being pursued in collaboration with Scripps Florida Professor Corinne Lasmezas in our department.”

Another implication of the findings, according to the study, is that drug-resistant variants either exist in the prion population at a low level prior to exposure or are generated during exposure to the drug. Indeed, the researchers found some prions secreted by infected cells were resistant to the drug before exposure, but only at levels less than one percent.

The scientists show that prion variants constantly arise in a particular population. These variants, or “mutants”, are believed to differ in the way the prion protein is folded. As a consequence, prion populations are, in fact, comprised of multiple sub-strains.

This, Weissmann noted, is reminiscent of something he helped define some 30 years ago – the evolutionary concept of quasi-species. The idea was first conceived by Manfred Eigen, a German biophysicist who won the Nobel Prize in Chemistry in 1967. Basically stated, a quasi-species is a complex, self-perpetuating population of diverse and related entities that act as a whole. It was Weissmann, however, who provided the first confirmation of the theory through the study of a particular bacteriophage – a virus that infects bacteria – while he was director of the Institut für Molekularbiologie in Zürich, Switzerland.

“The proof of the quasi-species concept is a discovery we made over 30 years ago,” he said. “We found that an RNA virus population, which was thought to have only one sequence, was constantly creating mutations and eliminating the unfavorable ones. In these quasi-populations, much like we have now found in prions, you begin with a single particle, but it becomes very heterogeneous as it grows into a larger population.”

There are some unknown dynamics at work in the prion population that leads to this increased heterogeneity, Weissmann added, that still need to be explored.

“It’s amusing that something we did 30 years has come back to us,” he said. “But we know that mutation and natural selection occur in living organisms and now we know that they also occur in a non-living organism. I suppose anything that can’t do that wouldn’t stand much of a chance of survival.”

LAWRENCE — A group of University of Kansas researchers working with Chinese colleagues have discovered a venomous, birdlike raptor that thrived some 128 million years ago in China. This is the first report of venom in the lineage that leads to modern birds.

Above: Top reconstruction from Robert DePalma/KU. Bottom photo: Sinornithosaurus teeth contain long, grooves to carry venom molecules to prey. It lived in prehistoric forests of northeastern China that were filled with a diverse assemblage of animals including other primitive birds and dinosaurs. Photo Credit: David A. Burnham.

“This thing is a venomous bird for all intents and purposes,” said Larry Martin, KU professor and curator of vertebrate paleontology at the Natural History Museum and Biodiversity Institute. “It was a real shock to us and we made a special trip to China to work on this.”

The KU-China team’s findings will be published in the early edition of the Proceedings of the National Academy of Science this week.

“We think it’s going to make a big splash,” said Martin.

The article’s authors are Enpu Gong, geology department at Northeastern University in Shenyang, China, and researchers Martin, David Burnham and Amanda Falk at the KU Natural History Museum and Biodiversity Institute.

The dromaeosaur or raptor, Sinornithosaurus (Chinese-bird-lizard), is a close relative to Velociraptor. It lived in prehistoric forests of northeastern China that were filled with a diverse assemblage of animals including other primitive birds and dinosaurs.

“This is an animal about the size of a turkey,” said Martin. “It’s a specialized predator of small dinosaurs and birds. It was almost certainly feathered. It’s a very close relative of the four-winged glider called Microraptor.”

The venom most likely sent the victim into rapid shock, shrinking the odds of retaliation, escape or piracy from other predators while the raptor manipulated its prey.

“You wouldn’t have seen it coming,” said Burnham. “It would have swooped down behind you from a low-hanging tree branch and attacked from the back. It wanted to get its jaws around you. Once the teeth were embedded in your skin the venom could seep into the wound. The prey would rapidly go into shock, but it would still be living, and it might have seen itself being slowly devoured by this raptor.”

The genus had special depressions on the side of its face thought by the investigators to have housed a venom gland, connected by a long lateral depression above the tooth row that delivered venom to a series of long, grooved teeth on the upper jaw. This arrangement is similar to the venom-delivery system in modern rear-fanged snakes and lizards. The researchers believe it to be specialized for predation on birds.

“When we were looking at Sinornithosaurus, we realized that its teeth were unusual, and then we began to look at the whole structure of the teeth and jaw, and at that point, we realized it was similar to modern-day snakes,” Martin said.

Sinornithosaurus is represented by at least two species. These specimens have features consistent with a primitive venom-delivery system. The KU-China research team said it was a low-pressure system similar to the modern Beaded lizard, Heloderma, however the prehistoric Sinornithosaurus had longer teeth to break through layers of feathers on its bird victims.

The discovery of features thought to be associated with a venom-delivery system in Sinornithosaurus stemmed from a study of the anatomy and ecology of Microraptor by the joint Chinese-KU team. They now are seeking to discover if Microraptor may have possessed a similar poison-delivery system.