Prolonged Climatic Stress Main Reason for Mass Extinction 65 Million Years Ago, Paleontologist Says

ScienceDaily (Mar. 27, 2010) — Long-term climate fluctuations were probably the main reason for the extinction of the dinosaurs and other creatures 65 million years ago. This conclusion was reached by PD Dr. Michael Prauss, paleontologist at Freie Universitaet Berlin, based on his latest research results.

According to new research from a German paleontologist, long-term climate fluctuations -- not a giant meteorite impact -- were likely the main reason for the extinction of the dinosaurs and other creatures 65 million years ago. (Credit: iStockphoto/Adrian Chesterman)

Prauss thus challenges the almost 30-year-old theory that a meteorite impact at the Mexican Yucatan peninsula was the single cause for one of the five largest mass extinctions in Earth history, which has most recently been reiterated in a publication in the journal Science. According to Prauss, the impact was only one in a chain of catastrophic events that caused substantial environmental perturbations, probably largely controlled by the intermittent activity of the Deccan volcanism near the then-Indian continent, that continued over several million years and peaked at the Cretaceous-Paleogen boundary.

"The resulting chronic stress, to which of course the meteorite impact was a contributing factor, is likely to have been fundamental to the crisis in the biosphere and finally the mass extinction," says Michael Prauss. In a research project funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) and in collaboration with Prof. Dr. Gerta Keller, paleontologist at Princeton University, U.S.A., Prauss analyzed several drill cores and rock sections covering the extended Cretaceous-Paleogene boundary interval at Brazos River, Texas, USA. The investigated region is located about 1000 km northwest of the Chicxulub impact crater and is well known among geologic scientists for its exceptionally complete preservation of Upper Cretaceous sediments.

Based on an analysis of the appearance and distribution of organic-walled microfossils such as Algal cysts, pollen, and spores of terrestrial plants, Prauss shows that significant and persistent variations in the ecosystem of the Upper Cretaceous started long before the meteorite impact. Among others, these are reflected by fluctuations in sea-level and marine algae productivity.

Prauss also considers it highly problematic to equate the meteorite impact with the position of the Cretaceous-Paleogene boundary: "The actual impact took place well before the geochemically and micropaleontologically defined Cretaceous Paleogene boundary." He supports his assertion with the position of the so-called fern spike, an episodic, significant increase in the proportion of fern spores caused by the pioneering phase of ferns in repopulating landscapes of destroyed ecosystems. In all sections of the investigated area the fern spike occurs well before important stratigraphic evidence for the Paleogene.

The new results contradict a publication by Schulte et al. (2010) in the March 5 issue of Science. Schulte et al. summarize the Cretaceous-Paleogene issue only to arrive at the 30-year-old theory of the impact as the sole cause of mass extinction. The occurrence of substantial fluctuations within the ecosystem of the Upper Cretaceous before the impact is disputed and the impact event is equated in time with the biostratigraphic Cretaceous-Paleogene boundary. "In the light of the new data, both of these points have to be refuted," says Prauss.

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How Did Flowering Plants Evolve to Dominate Earth?

ScienceDaily (Dec. 1, 2009) — To Charles Darwin it was an 'abominable mystery' and it is a question which has continued to vex evolutionists to this day: when did flowering plants evolve and how did they come to dominate plant life on earth? A new study in Ecology Letters reveals the evolutionary trigger which led to early flowering plants gaining a major competitive advantage over rival species, leading to their subsequent boom and abundance
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Colorful tulips and other spring flowers in the Keukenhof Gardens, the Netherlands. How did flowering plants come to dominate plant life on earth? (Credit: iStockphoto/Monika Lewandowska)

The study, by Dr Tim Brodribb and Dr Taylor Field of the University of Tasmania and University of Tennessee, used plant physiology to reveal how flowering plants, including crops, were able to dominate land by evolving more efficient hydraulics, or 'leaf plumbing', to increase rates of photosynthesis.

"Flowering plants are the most abundant and ecologically successful group of plants on earth," said Brodribb. "One reason for this dominance is the relatively high photosynthetic capacity of their leaves, but when and how this increased photosynthetic capacity evolved has been a mystery."

Using measurements of leaf vein density and a linked hydraulic-photosynthesis model, Brodribb and Field reconstructed the evolution of leaf hydraulic capacity in seed plants. Their results revealed that an evolutionary transformation in the plumbing of angiosperm leaves pushed photosynthetic capacity to new heights.

The reason for the success of this evolutionary step is that under relatively low atmospheric C0₂ conditions, like those existing at present, water transport efficiency and photosynthetic performance are tightly linked. Therefore adaptations that increase water transport will enhance maximum photosynthesis, exerting substantial evolutionary leverage over competing species.

The evolution of dense leaf venation in flowering plants, around 140-100 million years ago, was an event with profound significance for the continued evolution of flowering plants. This step provided a 'cretaceous productivity stimulus package' which reverberated across the biosphere and led to these plants playing the fundamental role in the biological and atmospheric functions of the earth.

"Without this hydraulic system we predict leaf photosynthesis would be two-fold lower then present," concludes Brodribb. "So it is significant to note that without this evolutionary step land plants would not have the physical capacity to drive the high productivity that underpins modern terrestrial biology and human civilisation."

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Plodding Amoeba Flips Into Free-Swimming Flagellate: Naegleria Genome Sheds Light on Transition from Prokaryotes to Eukaryotes

ScienceDaily (Mar. 5, 2010) — In the long evolutionary road from bacteria to humans, a major milestone occurred some 1.5 billion years ago when microbes started building closets for all their stuff, storing DNA inside a nucleus, for example, or cramming all the energy machinery inside mitochondria.

Top: N. gruberi flagellate-stage (microtubules are highlighted in green, basal bodies in red, and DNA is stained blue). Bottom: N. gruberi, amoeba-stage. (Credit: Photos by Lillian Fritz-Laylin, UC Berkeley)

Scientists have now sequenced the genome of a weird, single-celled organism called Naegleria gruberi that is telling biologists about that transition from prokaryotes, which function just fine with all their proteins floating around in a soup, to eukaryotes, which neatly compartmentalize those proteins?

The sequence, produced by the Department of Energy Joint Genome Institute (JGI), and an analysis by scientists from the University of California, Berkeley, Lancaster University in the United Kingdom and institutions elsewhere in the United States and the U.K. are published in the March 5 issue of the journal Cell.

"In a sense, analyzing the Naegleria genome shows us what it would be like to be on this planet more than a billion years ago, and what kind of organisms were around then and what they might have looked like," said Simon E. Prochnik, a JGI and UC Berkeley bioinformaticist and coauthor of the Cell paper.

Naegleria is a common soil amoeba -- the sequenced organism was isolated from the mud in a grove of eucalyptus trees on the UC Berkeley campus -- that, under stress, quickly grows two flagella, like sperm tails, that it uses to swim around. It has a third identity, a hard cyst, that can persist in the soil until conditions become damp and warm enough for it to turn into an amoeba.

"This one-celled organism hunts and eats bacteria as an amoeba, swims around looking for a better environment as a flagellate, and then hunkers down and waits for good times as a cyst," Prochnik said. "It is a very rare process to go from amoeba to flagellate like this."

Not surprisingly, the organism is packed with genes that help support these three personalities, he said. He and his colleagues report that this amoeboflagellate contains 15,727 genes coding for proteins, while humans have 23,000 protein-coding genes.

"Naegleria has a lot of genes because it has a complicated lifestyle; most single-celled organisms -- in particular, parasites -- have a simpler lifestyle, and therefore have fewer genes," Prochnik said. "These single-celled organisms are highly versatile, containing all the genetic information necessary to survive in a wide range of environments and under a wide range of stresses."

The researchers compared the Naegleria genome to the genomes of 16 other eukaryotes, ranging from humans and fungi to green plants and other unicellular eukaryotes, shedding light on the set of perhaps 4,000 genes that may have been part of the first, most primitive eukaryotes, according to UC Berkeley graduate student Lillian Fritz-Laylin, first author of the paper. The number of genes surprised the researchers, because previous genome comparisons that included parasites came up with a much lower number. That may be because parasites live off their host and have been able to shed many genes that are critical for a free-living organism, they said.

"Now that our analysis focuses on data from free-living organisms, including Naegleria, that haven't lost all these genes and functions, we can make a broader comparison, and we find a lot more proteins were probably present in the eukaryotic ancestor than we previously thought," Fritz-Laylin said.

"This is the first genome comparison that includes not only Naegleria, but representatives of all six sequenced groups of eukaryotes," Prochnik said. Naegleria is part of a diverse group that includes a cousin, Naegleria fowleri, that can fatally infect swimmers. The other eurkaryotic groups are animals and fungi; plants and green algae; chromalveolata, which include diatoms, red tide and malaria; amoebozoa, which include various single-celled amoebae; and the diverse group that includes parasites like giardia.

Among other things, Naegleria's genes shed light on how cells move, how they signal one another and how they metabolize nutrients.

As an amoeba, Naegleria pushes out little feet, called pseudopods, that propel it in its hunt for food. Yet, once the food disappears, the amoeba creates flagella from scratch and uses them to swim about in search of new hunting grounds.

What is interesting, Fritz-Laylin said, is that pseudopods and flagella use different proteins for movement. Amoebae make use of actin, which provides the internal scaffolding for the cell and for the pseudopods that help amoebae explore their environment. Flagella, on the other hand, are made mostly of the protein tubulin. Because Naegleria has both types of movement, the organism can help scientists understand the origins of these parallel systems during the evolution of eukaryotes.

Scientists can starve populations of Naegleria in its amoeba form and have seen it switch quickly and simultaneously to its flagellar form. This suggests that the switch from an actin-based system to a microtubule-based system of movement is very highly regulated and synchronized across a population.

"The sequence helped us identify the genes associated with each type of motility," she said. "Although this has been done for flagellar motility, it had not been done for amoeboid motility."

The genome also reveals versatility in how Naegleria produces energy. The organism can use oxygen to burn nutrients -- glucose, amino acids or fatty acids -- for energy or, in the absence of oxygen, utilize other nutrients and possibly produce hydrogen as a byproduct.

Like the recently sequenced, free-living alga Chlamydomonas, Naegleria likely uses its metabolic flexibility to survive the intermittent hypoxia common to muddy environments, the researchers concluded. Prochnik suggests that Naegleria could help biologists understand hydrogen production that, in other organisms, might be used to produce energy.

Fritz-Laylin noted that, while the genome will be a boon to the small number of biologists who study the organism, it also will help in understanding the evolution of more complicated organisms.

"By comparing diverse organisms like Naegleria from all over the family tree of eukaryotes we can begin to understand where we come from," she said.

Other co-authors of the paper are Michael L. Ginger of the School of Health and Medicine at Lancaster University; Meredith L. Carpenter, Alex Paredez, W. Zacheus Cande and Daniel S. Rokhsar of UC Berkeley; Rochak Neupane of UC Berkeley's Center for Integrative Genomics; Alan Kuo, Jarrod Chapman, Shengqiang Shu, Asaf Salamov, Erika Lindquist, Hank Tu, Harris Shapiro, Susan Lucas and Igor V. Grigoriev of JGI; Joel B. Dacks of the University of Alberta Edmonton in Alberta, Canada; Jonathan Pham, Michael Cipriano and Scott C. Dawson of UC Davis; Joel Mancuso of Gatan Inc. in Pleasanton, Calif.; Mark C. Field of the University of Cambridge, U.K.; and Chandler Fulton of Brandeis University in Waltham, Mass.

Rokhsar is the program head for computational genomics at JGI and a professor of molecular and cell biology and of physics at UC Berkeley.

Funding for the project came primarily from the Department of Energy.

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Unselfish Molecules May Have Helped Give Birth to the Genetic Material of Life

ScienceDaily (Mar. 8, 2010) — One of the biggest questions facing scientists today is how life began. How did non-living molecules come together in that primordial ooze to form the polymers of life? Scientists at the Georgia Institute of Technology have discovered that small molecules could have acted as "molecular midwives" in helping the building blocks of life's genetic material form long chains and may have assisted in selecting the base pairs of the DNA double helix.New research suggests that small molecules could have acted as "molecular midwives" in helping the building blocks of life's genetic material form long chains and may have assisted in selecting the base pairs of the DNA double helix. (Credit: iStockphoto)

The research appears in the online early edition of the Proceedings of the National Academy of Sciences beginning March 8, 2010.

"Our hypothesis is that before there were protein enzymes to make DNA and RNA, there were small molecules present on the pre-biotic Earth that helped make these polymers by promoting molecular self-assembly," said Nicholas V. Hud, professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology. "We've found that the molecule ethidium can assist short oligonucleotides in forming long polymers and can also select the structure of the base pairs that hold together two strands of DNA."

One of the biggest problems in getting a polymer to form is that, as it grows, its two ends often react with each other instead of forming longer chains. The problem is known as strand cyclization, but Hud and his team discovered that using a molecule that binds between neighboring base pairs of DNA, known as an intercalator, can bring short pieces of DNA and RNA together in a manner that helps them create much longer molecules.

"If you have the intercalator present, you can get polymers. With no intercalator, it doesn't work, it's that simple," said Hud.

Hud and his team also tested how much influence a midwife molecule might have had on creating DNA's Watson-Crick base pairs (A pairs with T, and G pairs with C). They found that the midwife used could determine the base pairing structure of the polymers that formed. Ethidium was most helpful for forming polymers with Watson-Crick base pairs. Another molecule that they call aza3 made polymers in which each A base is paired with another A.

"In our experiment, we found that the midwife molecules present had a direct effect on the kind of base pairs that formed. We're not saying that ethidium was the original midwife, but we've shown that the principle of a small molecule working as a midwife is sound. In our lab, we're now searching for the identity of a molecule that could have helped make the first genetic polymers, a sort of 'unselfish' molecule that was not part of the first genetic polymers, but was critical to their formation," said Hud.

The work was supported by the National Aeronautics and Space Administration and the National Science Foundation.

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Why birds are NOT descended from dinosaurs

By Daily Mail Reporter
Last updated at 12:02 PM on 10th June 2009

Birds did not descend from dinosaurs, scientists claim after studying how our feathered friends move and breathe.

It has been known for decades that the femur, or thigh bone in birds is largely fixed making birds 'knee runners.'

But researchers from Oregon State University found the bone also stops their lung collapsing, allowing the breathing capacity for flight.

The thigh bone stops a bird's lungs from collapsing, allowing them the breathing capacity to fly unlike dinosaurs like sauropods

Every other animal that has walked on land, including humans, elephants, lizards and theropod dinosaurs - a family that includes the T Rex, had a moveable thigh bone.

The find may force paleontologists to reconsider their long-held belief that modern birds are direct descendants of ancient, meat-eating dinosaurs.

'It's amazing we didn't understand a basic aspect of bird biology,' said US researcher Professor John Ruben.

'A velociraptor did not just spout feathers at some point and fly off into the sunset.

Running and walking is generated mostly at knee and ankle joints in birds

'Birds probably evolved on a parallel path alongside dinosaurs, starting that process before most dinosaur species even existed.'

Characteristics such as feathers, wings and a bird's unique way of moving therefore developed separately.

Dinosaurs and birds both thrived in the Cretaceous period between 145 and 65 million years ago.

The Archaeopteryx, long considered the oldest bird, lived 150million years ago, while dinosaurs emerged earlier around 200million years ago.

However, Professor Ruben said he didn't discount birds and dinosaurs sharing an ancient ancestor such as the small, reptilian 'thecodonts' that roamed Earth 250million years ago.

'It just seems pretty clear now that birds were evolving all along on their own and did not descend directly from the theropod dinosaurs,' he concluded.

There study has been published in The Journal of Morphology.

Read more: http://www.dailymail.co.uk/sciencetech/article-1192019/Why-birds-NOT-descended-dinosaurs.html#ixzz0hnJtScr9

Bird-from-Dinosaur Theory of Evolution Challenged: Was It the Other Way Around?

ScienceDaily (Feb. 10, 2010) — A new study just published in the Proceedings of the National Academy of Sciences provides yet more evidence that birds did not descend from ground-dwelling theropod dinosaurs, experts say, and continues to challenge decades of accepted theories about the evolution of flight.

An image drawn in 1915 by naturalist William Beebe suggests a hypothetical view of what early birds may have looked like, gliding down from trees - and it bears a striking similarity to a fossil discovered in 2003 that is raising new doubts about whether birds descended from ground-dwelling theropod dinosaurs.

A new analysis was done of an unusual fossil specimen discovered in 2003 called "microraptor," in which three-dimensional models were used to study its possible flight potential, and it concluded this small, feathered species must have been a "glider" that came down from trees. The research is well done and consistent with a string of studies in recent years that pose increasing challenge to the birds-from-dinosaurs theory, said John Ruben, a professor of zoology at Oregon State University who authored a commentary in PNAS on the new research.

The weight of the evidence is now suggesting that not only did birds not descend from dinosaurs, Ruben said, but that some species now believed to be dinosaurs may have descended from birds.

"We're finally breaking out of the conventional wisdom of the last 20 years, which insisted that birds evolved from dinosaurs and that the debate is all over and done with," Ruben said. "This issue isn't resolved at all. There are just too many inconsistencies with the idea that birds had dinosaur ancestors, and this newest study adds to that."

Almost 20 years of research at OSU on the morphology of birds and dinosaurs, along with other studies and the newest PNAS research, Ruben said, are actually much more consistent with a different premise -- that birds may have had an ancient common ancestor with dinosaurs, but they evolved separately on their own path, and after millions of years of separate evolution birds also gave rise to the raptors. Small animals such as velociraptor that have generally been thought to be dinosaurs are more likely flightless birds, he said.

"Raptors look quite a bit like dinosaurs but they have much more in common with birds than they do with other theropod dinosaurs such as Tyrannosaurus," Ruben said. "We think the evidence is finally showing that these animals which are usually considered dinosaurs were actually descended from birds, not the other way around."

Another study last year from Florida State University raised similar doubts, Ruben said.

In the newest PNAS study, scientists examined a remarkable fossil specimen that had feathers on all four limbs, somewhat resembling a bi-plane. Glide tests based on its structure concluded it would not have been practical for it to have flown from the ground up, but it could have glided from the trees down, somewhat like a modern-day flying squirrel. Many researchers have long believed that gliders such as this were the ancestors of modern birds.

"This model was not consistent with successful flight from the ground up, and that makes it pretty difficult to make a case for a ground-dwelling theropod dinosaur to have developed wings and flown away," Ruben said. "On the other hand, it would have been quite possible for birds to have evolved and then, at some point, have various species lose their flight capabilities and become ground-dwelling, flightless animals -- the raptors. This may be hugely upsetting to a lot of people, but it makes perfect sense."

In their own research, including one study just last year in the Journal of Morphology, OSU scientists found that the position of the thigh bone and muscles in birds is critical to their ability to have adequate lung capacity for sustained long-distance flight, a fundamental aspect of bird biology. Theropod dinosaurs did not share this feature. Other morphological features have also been identified that are inconsistent with a bird-from-dinosaur theory. And perhaps most significant, birds were already found in the fossil record before the elaboration of the dinosaurs they supposedly descended from. That would be consistent with raptors descending from birds, Ruben said, but not the reverse.

OSU research on avian biology and physiology has been raising questions on this issue since the 1990s, often in isolation. More scientists and other studies are now challenging the same premise, Ruben said. The old theories were popular, had public appeal and "many people saw what they wanted to see" instead of carefully interpreting the data, he said.

"Pesky new fossils...sharply at odds with conventional wisdom never seem to cease popping up," Ruben wrote in his PNAS commentary. "Given the vagaries of the fossil record, current notions of near resolution of many of the most basic questions about long-extinct forms should probably be regarded with caution."

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Did Bacteria Develop Into More Complex Cells Much Earlier in Evolution Than Thought?

ScienceDaily (Feb. 8, 2010) — Monash University biochemists have found a critical piece in the evolutionary puzzle that explains how life on Earth evolved millions of centuries ago.

The team, from the School of Biomedical Sciences, has described the process by which bacteria developed into more complex cells and found this crucial step happened much earlier in the evolutionary timeline than previously thought.

Team leader and ARC Federation Fellow Trevor Lithgow said the research explained how mitochondria -- the power house of human and other cells, which provide complex eukaryotic cells with energy and ability to produce, divide and move -- were thought to have evolved about 2000 million years ago from primitive bacteria.

"We have now come to understand the processes that drove cell evolution. For some time now the crux of this problem has been to understand how eukaryotes first came to be. The critical step was to transform small bacteria, passengers that rode within the earliest ancestors of these cells, into mitochondria, thereby beginning the evolution of more complex life-forms," Professor Lithgow said.

The team found that the cellular machinery needed to create mitochondria was constructed from parts pre-existing in the bacterium. These parts did other jobs for the bacterium, and were cobbled together by evolution to do something new and more exciting.

"Our research has crystallised with work from other researchers around the world to show how this transformation happened very early on -- that the eukaryotes were spawned by integrating the bacterium as a part of themselves. This process jump-started the evolution of complex life much more rapidly than was previously thought."

The research consisted of two components, the first used computers to read, compare and understand DNA sequences. From this, experiments were designed to do actual laboratory testing using a bacterium that is the closest living relative to the original ancestor of the mitochondria.

The research was published in the journal Science.

Professor Lithgow said the latest findings were only made possible due to a gradual gathering of evidence within the scientific community and recent developments in genome sequencing. "We can now "read" with great care and insight genome sequences -- the complete DNA sequence of any organism. From these sequences we find tell-tale clues to the past. Our findings are relevant to all species, including the evolution of humans," Professor Lithgow said.

"It continues to amaze that this theory, proposed in the century before the advent of molecular investigations, is so accurate on a molecular scale. This improved understanding is directly relevant to the big picture timeline for the evolution of life."

Professor Lithgow said the findings will be regarded by some scientists as controversial as many have long-held views on the process of evolution as a tinkerer. "This will surprise and may even spark debate. However our research compliments the basic rules of life. Even at the molecular level, the rules of the game are the same. Evolution drives biology to more and more complex forms," Professor Lithgow said.

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