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Post Info TOPIC: Ancient life


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Tree of Life

In 1870 the German scientist Ernst Haeckel mapped the evolutionary relationships of plants and animals in the first 'tree of life'. Since then scientists have continuously redrawn and expanded the tree adding microorganisms and using modern molecular data, yet, many parts of the tree have remained unclear. Now a group at the European Molecular Biology Laboratory (EMBL) in Heidelberg has developed a computational method that resolves many of the open questions and produced what is likely the most accurate tree ever. The study, which appears in the current issue of the journal Science, gives some intriguing insights into the origins of bacteria and the last common universal ancestor of all life on earth today.

"DNA sequences of complete genomes provide us with a direct record of evolution. For a long time the overwhelming amount of data (the human genome alone contains enough information to fill 200 telephone books) has made it very difficult to pinpoint the information needed for a high-resolution map of evolution. But our study shows how this challenge can be tackled by combining different computational methods in an automated process"- Peer Bork, Associate Coordinator for Structural and Computational Biology at EMBL, whose group carried out the project.

Bork's lab specialises in the computational analysis of genomes, and recently they applied this expertise to the tree of life. Since all organisms descend from the same ancestor, they share some common genes. Francesca Ciccarelli and Tobias Doerks of Bork's group managed to identify 31 genes with clear relatives in 191 organisms, ranging from bacteria to humans, to reconstruct their relationships.

"Even using such genes, you might get the wrong answer. Organisms inherit most genes from their parents, but over the course of evolution, a few have been obtained when organisms swapped genes with their neighbours in a process called horizontal gene transfer (HGT). Obviously, the latter class of genes does not tell you anything about your ancestors. The trick was to identify and exclude them from the analysis." - Francesca Ciccarelli

"This procedure drastically reduced the 'noise' in the data, making it possible to identify as yet unknown details of early evolution. For example, we now know that the first bacterium was probably a type called gram-positive and likely lived at high temperatures -- suggesting that all life arose in hot environments." - Tobias Doerks

The improved tree has also shed light on other research carried out by the group. Bork and colleagues are participating in projects that collect genetic material of unknown species en masse from environments such as farm soil and ocean floor.

"With the new high-resolution tree in hand, it is now possible to classify genetic material from this unexplored microbial world and further our understanding of life on the planet."




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When the space shuttle Columbia broke apart during re-entry February 1, 2003, more than 80 on-board science experiments were lost in the fiery descent.

Texas State University-San Marcos biologist Robert McLean, however, has salvaged some unexpected science from the wreckage. A strain of slow-growing bacteria survived the crash, a discovery which may have significant implications for the concept of panspermia. The findings will be published in the May 2006 issue of Icarus, the international journal of solar system studies.

Panspermia is the idea that life--hitchhiking on rocks ejected from meteorite impacts on one world--could travel through space and seed other worlds with life under favourable conditions. Because the conditions under which panspermia could function are so harsh, however, there's been little direct testing of the hypothesis.

"That might have been in the back of my mind when we recovered our payload. My first thinking when we found our payload was, 'Let's look for survivors.'" - Robert McLean.

McLean, along with a team of Texas State researchers, had placed an experiment package aboard the Columbia to investigate the interactions of three different bacterial species in microgravity. When the shuttle broke up over Texas, they assumed the experiment lost--until it turned up, relatively intact, in the parking lot of a Nacogdoches convenience store.
And he found survivors - a bacterium called Microbispora.
Ironically, Microbispora wasn't one of the three species McLean expected to find. The slow-growing organism is normally found in the soil, and McLean determined that it had contaminated the experiment prior to launch. With the Icarus publication, McLean anticipates request for samples of this rugged strain to come in from researchers around the world.

"This organism appears to have survived an atmospheric passage, with the heat and the force of impact. That's only about a fifth of the speed that something on a real meteorite would have to survive, but it is at least five or six times faster than what's been tested before. This is important for panspermia, because if something survives space travel, it eventually has to get down to the Earth and survive passage through the atmosphere and impact. This doesn't prove anything - it just contributes evidence to the plausibility of panspermia. Realistically, that's all it can do. Out of respect for the seven people who gave their lives for this research, I feel it's very important these results don't get lost"- Robert McLean.




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RE: Ancient life

On Tuesday an international two-day meeting at the Royal Society, the UK's academy of science, in London, will explore the latest thinking on the origin of life on Earth.

"It is about 140 years since Charles Darwin suggested that life may have begun in a 'warm little pond'. We are now testing Darwin's idea, but in 'hot little puddles' associated with the volcanic regions of Kamchatka and Mount Lassen. The results are surprising and in some ways disappointing. It seems that hot acidic waters containing clay do not provide the right conditions for chemicals to assemble themselves into 'pioneer organisms.
The reason this is significant is that it has been proposed that clay promotes interesting chemical reactions relating to the origin of life. However, in our experiments, the organic compounds became so strongly held to the clay particles that they could not undergo any further chemical reactions
" - David Deamer, emeritus professor of chemistry at the University of California at Santa Cruz.

Experiments carried out in volcanic pools suggest they do not provide the right conditions to spawn life. Life is unlikely to have emerged from volcanic springs or hydrothermal vents.
Amino acids and DNA, the "building blocks" for life, and phosphate, another essential ingredient, cling to the surfaces of clay particles in the volcanic pools.

"Understanding how life emerged on Earth within 1,000 million years of its formation is both a fascinating scientific problem and an essential step in predicting the presence of life elsewhere in the Universe. One possibility is that life really did begin in a 'warm little pond', but not in hot volcanic springs or marine hydrothermal vents" - Professor Ian Smith, from the University of Cambridge.

Professor Deamers research, which is not yet published, will help to narrow down the theories about how life on Earth emerged.



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Clay made animal life possible on Earth, a University of California Riverside-led study finds. A sudden increase in oxygen in the Earth’s recent geological history, widely considered necessary for the expansion of animal life, occurred just as the rate of clay formation on the Earth’s surface also increased, the researchers report.

"Our study shows for the first time that the initial soils covering the terrestrial surface of Earth increased the production of clay minerals and provided the critical geochemical processes necessary to oxygenate the atmosphere and support multicellular animal life" - Martin Kennedy, associate professor of sedimentary geology and geochemistry at UCR, who led the study.

Study results appear in the Feb. 2 issue of Science Express, which provides electronic publication of selected Science papers in advance of print.
Analysing old sedimentary rocks, the researchers found evidence of an increase in clay mineral deposition in the oceans during a 200 million year period that fell between 1.1 to 0.54 billion years ago – a stretch of time known as the late Precambrian when oxygen suddenly increased in the Earth’s atmosphere. The increases in clay formation and oxygen shortly preceded – in geological time – the first animal fossils about 600 million years ago.

"This study shows how we can use principles developed from the study of modern environments to understand the very complex origin of life on our planet – studying a time in history that has left us only a scanty record of its conditions" - Lawrence M. Mayer, professor of oceanography at the University of Maine and a co-author of the Science paper.

Clay minerals form in soils through biological interactions with weathering rocks and are then eroded and flushed to the sea, where they are deposited as mud. Because clay minerals are chemically reactive, they attract and absorb organic matter in ocean water, and physically shelter and preserve it.
The UCR-led study emphasises the possibility that colonisation of the land surface by a primitive terrestrial ecosystem (possibly involving fungi) accelerated clay formation, as happens in modern soils. Upon being washed down to the sea, the clay minerals were responsible for preserving more organic matter in marine sediments than had been the case in the absence of clays. Organic matter preservation results in an equal portion of oxygen released to the atmosphere through the chemical reaction of photosynthesis. Thus an increase in the burial of organic carbon made it possible for more oxygen to escape into the atmosphere, the researchers posit.

"One of the things we least understand is why animals evolved so late in Earth history. Why did animals wait until the eleventh hour, whereas evidence for more primitive life dates back to billions of years? One of the best bets to explain the difference is an increase in oxygen concentration in the atmosphere, which is necessary for animal life and was likely too low through most of Earth’s history" - Martin Kennedy.

To establish a change in clay abundance during the late Precambrian, the researchers studied thick sections of ancient sedimentary rocks in Australia, China and Scandinavia, representing a history of hundreds of millions of years, to identify when clay minerals increased in the sediment from almost nothing to modern depositional levels.

"We predicted we would only find a significant percentage of clay minerals in sediments toward the end of the Precambrian, when complex life arose, while earlier sediments would have less clay content. This test is easier than it sounds. Because clay minerals make up the bulk of sediment deposited today, we are saying that it should be largely absent in ancient rocks. And this is just what one finds" - Martin Kennedy.

The study attracted the attention of the National Aeronautics and Space Administration during the proposal stage, and the agency helped fund the research.

NASA is interested in what conditions to look for on other planets that might lead to the arrival of life. What are the processes? Using earth as our most detailed study site, what are the necessary steps a planet needs to go through to enable complex animal life to arise? If oxygen is the metabolic pathway, then we need to know what conditions have to allow for that to happen. The geologic record provides us with a record of these steps that occurred on Earth”- Martin Kennedy.

UCR’s Mary Droser and David Mrofka; and David Pevear collaborated on the study, which was supported also by the National Science Foundation.




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Ancient DNA

Scientists at the Weizmann Institute of Science recently discovered a new source of well-preserved ancient DNA in fossil bones. Their findings were published in the Proceedings of the National Academy of Sciences (PNAS).

Fossil DNA is a potential source of information on the evolution, population dynamics, migrations, diets and diseases of animals and humans. But if it is not well preserved or becomes contaminated by modern DNA, the results are uninterpretable.

The scientists, Prof. Steve Weiner and Michal Salamon of the Institute's Structural Biology Department, working in collaboration with Profs. Baruch Arensburg, Tel Aviv University, and Noreen Tuross, Harvard University, may have found a way to overcome these problems.
It was in 1986 that Weiner first reported the existence of crystal clusters in fresh bones. Even when these bones are ground up and treated with sodium hypochlorite – a substance that removes all traces of organic matter – the clusters of crystals remain intact and the organic material embedded in them is unaffected. Now, almost 20 years later, Weiner and Salamon have returned to these findings, reasoning that fossil bones might possess such crystal structures containing preserved ancient DNA.

After treating two modern and six fossil animal bones with the sodium hypo-chlorite, they found that DNA could be extracted from most of these crystal aggregates that is better preserved and contains longer fragments than DNA from untreated ground bone. The technique for reading the DNA worked better, as well, and the use of sodium hypochlorite reduces the possibility of modern contamination.

The crystal aggregates act as a "privileged niche in fossil bone," protecting the DNA from hostile environments and leaving it relatively undamaged over time. The team's findings suggest that the DNA in these aggregates should be preferred, whenever possible, over DNA from untreated bone.

This method holds much promise for the future analysis of ancient DNA in bones in yielding more reliable and authentic results than has previously been possible, and may help in unearthing the mysteries of our ancestral past.




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Black Smokers

Arizona State University geochemist Dr Lynda Williams and her colleagues have discovered that certain clay minerals at the bottom of the ocean may have acted as incubators for the first organic molecules on Earth.
Primordial clay "wombs" that lie scattered around ocean floors played a crucial role in fostering early life on Earth. The clay structures were found in deep waters, in and around ocean floor volcanic vents called black smokers, so named because they churn out hot black particles from the Earth's crust.

By providing a haven for molecules brought up from the Earth's interior, the wombs protected them from the harsh environment until they formed the most basic building blocks of life. Black smokers form along the edges of mid-ocean ridges. The rich variety of chemicals they emit supports a unique ecosystem including bizarre bacteria and unique species of worms. Scientists believe that these hot, sulphur-rich waters may have been ideal for life to evolve.
Until now researchers have been puzzled as to how molecules such as methanol could have survived the 300 to 400 C temperatures in volcanic vents, but the researchers found that lumps of clay that build up on the inside walls of the vents could have captured, then protected, key molecules for around six months. The clay deposits eventually break away and spill out onto the ocean floor, where they break open, releasing the molecules into cool surrounding waters.

One of four pinnacles that form the summit of the 200-foot tall carbonate chimney called Poseidon in the Lost City hydrothermal field. The white chimney in the foreground is actively venting 55°C fluids. As the chimneys age they turn grey to brown in colour, such as the one shown towards the back. Image courtesy of University of Washington.

"When I first heard that, I thought, 'that's strange, Methanol is supposed to break down at those temperatures. I asked myself, 'what can protect it?' The answer is common clay minerals" - Dr Lynda Williams.

Dr Williams's group recreated the high temperature and pressure environment of a black smoker in the laboratory to examine whether organic molecules, the building blocks of life, could grow on various types of clay surface.

"We simulated the reactants that we know can exist in black smoker environments, to see what organic compounds would form in nature" - Dr Lynda Williams.

Six weeks into the experiment they discovered that one type of clay mineral, known as smectite, helped organic molecules to survive.
Smectite owes its protective properties to the layers of silicate it is formed from, allowing it to expand easily and let water, ions and molecules to flow inside.

"It is a bit like a peanut butter and jelly sandwich. The bread slices are the silicate layers, the sticky peanut butter represents the ions that are attracted to the bread and the jelly is like the organic compounds" - Dr Lynda Williams.

The rich chemical soup that rises through black smoker chimneys has all the right ingredients to form simple organic compounds, such as methanol. Dr Williams and her colleagues believe that clay stuck to the vent walls eventually gets pushed out of the chimney by flowing water, carrying the molecules inside to a safer place.

"If the organic compounds are released into cooler ocean water, which it is less acidic, some molecules might survive" - Dr Lynda Williams.

Similar womb-like structures may also exist on other planets, suggesting that the first step towards starting life may is not confined to Earth.

"This research tells us that as long as there is water and the right chemical ingredients, common clay minerals can help produce the ingredients for biomolecules (chemical components used by living organisms)" - Dr Lynda Williams.

The Mid-Atlantic Ridge hosts numerous hydrothermal fields (coloured dots). Lost City is currently the only known hydrothermal field composed solely of carbonate chimneys.
Logatchev, Rainbow and Saldahna are underlain by variable mixtures of deeper crustal rocks (gabbros and peridotite) and both Logatchev, Rainbow host high-temperature black smokers. The other fields are also sites of black smokers, but are hosted on volcanic rocks.
The Lost City Hydrothermal Field, lies about 762metres below the surface of the Atlantic Ocean.

Not everyone is convinced that Dr Williams's work, "Organic Molecules Formed in a Primordial Womb,"which appears in the November issue of Geology, explains how life on Earth got started. Mike Russell from the Centre for Life Detection at the California Institute of Technology, thinks life is more likely to have originated in a less extreme environment, such as the cooler hydrothermal springs, known as Lost City, discovered five years ago on the floor of the Atlantic Ocean. These warm springs also have all the necessary ingredients for the formation of organic carbon, but are only slightly hotter than human body temperature, so primordial wombs would not be needed to foster new life.

Additional experiments are planned to find out what chemical conditions would be required to form the building blocks of life.

"We have only started investigating the influence of clays on the origin of life" - Dr Lynda Williams

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RE: Amino Chirality

Recent laboratory simulations show that space radiation preferentially destroys specific forms of amino acids.
The research suggests that the molecular building blocks that form the "left-handed" proteins used by life on Earth took shape in space, bolstering the case that they could have seeded life on other planets.
Amino acids can exist as mirror-image right- and left-handed forms. But all the naturally occurring proteins in organisms on Earth use the left-handed forms - a puzzle dubbed the "chirality problem".

"A key question is when this chirality came into play" - Uwe Meierhenrich, a chemist at the University of Nice-Sophia Antipolis in France.

One theory is that proteins made of both types of amino acids existed on the early Earth but "somehow only the proteins of left-handed amino acids survived".
It was thought that minerals, such as quartz could have acted as a template for early life; for example planets such as Mercury has an over-abundance of left-handed quartz.

"We say the molecular building blocks of life were already created in interstellar conditions" - Uwe Meierhenrich.

The researchers think that "handed" space radiation destroyed more right-handed amino acids on the icy dust from which the solar system formed. This dust, along with the comets it condensed into, then crashed into Earth and other planets, providing them with an overabundance of left-handed amino acids that went on to form proteins.

The naturally occurring UV radiation is called circularly polarised light because its electric field travels through space like a turning screw, and comes in right- and left-handed forms, and preferentially produce, in the case of our solar system, left-handed varieties in interstellar space.
The radiation is thought to be produced when dust grains become aligned in the presence of magnetic fields threading through regions of space much larger than our solar system. Circularly polarised light is estimated to make up as much as 17% of the radiation at any given point in space.

In 2000, an experiment showed that when circularly polarised ultraviolet light of a particular handedness was shone on an equal mix of right- and left-handed amino acids, it produced an excess of 2.5% by preferentially disintegrating one type.
But that experiment was done using amino acids in a liquid solution, which behave differently than those in the solid conditions of icy dust in space.
To avoid absorption by water molecules, it was also necessary to use light at a wavelength of 210 nanometres – significantly longer than the peak of 120 nm radiation actually measured in space.

Now, Meierhenrich's team has performed a similar experiment. The group shone circularly polarised light at a wavelength of 180 nm on a solid film of both right- and left-handed forms of the amino acid leucine. It found that left-handed light produced an excess of 2.6% left-handed amino acids.

"Going towards greater realism by exploring another wavelength of light and solid samples is definitely a good thing and a logical step forward" - Max Bernstein, chemist at NASA's Ames Research Centre in California, US, who is not part of the team.

He says the research adds to previous measurements of an excess of left-handed amino acids in two meteorites. If the bias exists in these meteorites, "then the same bias should exist at least across our solar system".


But other solar systems may harbour right-handed amino acids if they are subjected to the other type of circularly polarised light.

"The chiral amino acids might have been delivered to other planets, to other solar systems. The probability that life arose somewhere else is increased with this experimental result" - Uwe Meierhenrich.

Meierhenrich will continue to reduce the wavelength of the experimental radiation by using a synchrotron facility, due to begin operating in 2006. But the real test of his theory may come in 2014, when the European Space Agency's Rosetta spacecraft lands a probe on Comet 67P/Churyumov-Gerasimenko.
He designed an instrument for the lander that will measure the handedness of any amino acids it finds.
The robotic lander Philae (RoLand) will detach from the orbiter of the ROSETTA spacecraft and set down on the surface of the comet in order to separate and identify cometary organic compounds. Chiral organics will be separated into their enantiomers by application of 3 capillary columns coated with different kinds of stationary phases.

"If we identify left-handed amino acids on the cometary surface, this would underline the hypothesis that the building blocks of proteins were created in interstellar space and were delivered via comets or micrometeorites to early Earth" - Uwe Meierhenrich.

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RE: ICE life

Did life begin in ice?

New findings are backing up a theory that life originated in ice.
If it’s true, it could boost the chances that life might turn up in places considerably colder than our planet.
Ice might have been an ideal environment for the first self-replicating molecules, some researchers argue.

The theory departs from mainstream thinking on the origins of life, which usually assumes a warm, or hot, and wet environment was necessary.

"Conditions associated with freezing, rather than ‘warm and wet’ conditions, could have been of key importance" for the chemical reactions that led to life, wrote four researchers in the July 21 advance online issue of the Journal of Molecular Evolution, a research publication.

The scientists, including Laura F. Landweber of Princeton University in Princeton, N.J., argue that ice might have been a favourable environment to generate the first self-replicating molecules, a precondition for life.

These molecules would be of a type called ribonucleic acids, or RNA - a chemical cousin of DNA, which makes up genes.

Many researchers believe the first self-replicating molecule was RNA, not DNA. This is because RNA can do various things in addition to carrying genetic information, which is all that DNA basically does.

Some of RNA’s activities seem to be similar to what would be required for self-replication, something that DNA can`t do, strictly speaking. DNA needs the help of other molecules to copy itself. Also, RNA still exists in living cells, where it has various functions—some so basic to life that many scientists think RNA must have been there from the beginning.

The theory that RNA started it all, a 20-year-old proposal called the "RNA world hypothesis," holds that RNA was not only the first self-replicating molecule, but also that it initially carried out most of life’s functions, such as metabolism and cell formation.

Most biologists consider the RNA world hypothesis at least plausible, but it has some problems. It’s not easy to explain how the first self-replicating RNA molecules might have arisen.

RNA molecules tend to fall apart under warm conditions outside of cells. This would prevent the build-up of the rather long, complex RNA molecules that would probably be needed to conduct life processes, according to Landweber and her colleagues.

Various conditions can prevent RNA molecules` breakdown, the researchers argue. These include various types of water solutions, and freezing. But freezing may have been the one that most likely occurred on the early Earth, they argued.

Freezing usually slows down chemical reactions, which is why cold places are generally considered hostile to life. But freezing actually speeds up some of RNA’s key activities, Landweber and colleagues argue.

This is because ice contains hard, tiny compartments that hold the molecules in one place, where they can react together. Some of these reactions result in the creation of bigger RNA molecules.

In liquid water, by contrast, the molecules don`t come close enough together often enough to react as much. Thus they tend to fall apart faster than they can react to create bigger products.

In essence, the small compartments in ice play the role that cells today play in bringing the molecules together to react, Landweber and her colleagues argue. Dehydrated substances - a sort of primordial sludge, for instance - could also have provided a function similar to ice, they added, but ice works better.

Landweber’s group conducted an experiment to test the theory. Led by Alexander Vlassov of SomaGenics, a Santa Cruz, California - based biotechnology company, the researchers broke to pieces some RNA molecules found in normal cells. This process yielded more, smaller, RNA molecules.

By doing this, the researchers produced RNA molecules of sizes that biologists think might have been available on early Earth. They then experimented to find out what sort of capabilities these smaller RNAs had.

Reporting their results in the May 25, 2004 issue of the journal Nucleic Acids Research, the researchers noted that the broken-up RNAs still could carry out some of the same functions as normal RNAs, but only in ice or sometimes other extreme conditions, such as dehydration.

These activities included grabbing other pieces of RNA and attaching them together, an activity called `ligation` that is similar to self-replication.

To fully self-replicate, a molecule must attach other molecules together in such a way as to match the sequence of chemical pieces that characterize the first molecule. This process is called "template-directed" ligation.

But the ligation alone—even without the self-replication—can build up ever larger and more complex RNA molecules, which according to the RNA world hypothesis could eventually develop self-replicating abilities.

The theory that an icy environment might have helped jump-start life isn’t new. Researchers proposed in 1994, for example, that repeated cycles of freezing and thawing could help accelerate some of the chemical reactions necessary for life.

Such a scenario might have existed on early Earth, where according to some researchers, repeated meteor and comet impacts might have periodically melted an otherwise icy environment.

However, Landweber and her team seem to be the first to have provided an account of how the "RNA world" might have fit into this scenario, according to Leslie Orgel, an origins-of-life researcher at the Salk Institute for Biological Studies in San Diego, California.

The work "has important implications," said Jeffrey L. Bada, director of the NASA Specialized Centre in Research and Training in Exobiology in La Jolla, California, one of the original proponents of the freeze-thaw cycle theory.

Although Landweber and her colleagues also wrote that freeze-thaw cycles are helpful for the processes they describe, such cycles aren`’t strictly necessary in their proposal.

Moreover, they wrote in their Journal of Molecular Evolution paper, "It is worth noting that Jupiter’s moon Europa and even Mars are also thought to contain large amounts of liquid water and ice now or at some time in the past."

The possibility of RNA activities in ice, they added, "lends some credibility to claims that the rather extreme environments of these extraterrestrial locations could have provided suitable conditions for the emergence of life."

However, as Sergei Kazakov of Somagenics noted in an email, the origin of life and the RNA world aren’t necessarily the same thing.

"The RNA world as complex self-replicating molecular society could appear at multiple places in Universe, but not necessarily result in the appearance of life as we know it," he explained. This transition may actually be rare, he added.

"I also think that Earth is a possible but not necessarily the best place where the RNA world could start. Rather, I would bet on Europa or a giant comet," he continued. If the transition to life as we know it did occur, he added, "it could spread across many planets through cross-contamination" carried by comets or meteorites.




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RE: Ancient life

A number of hypotheses have been used to explain how free oxygen first accumulated in Earth's atmosphere some 2.4 billion years ago, but a full understanding has proven elusive.
Now a new model created by Mark Claire, a University of Washington doctoral student in astronomy and astrobiology, offers plausible scenarios for how oxygen came to dominate the atmosphere, and why it took at least 300 million years after bacterial photosynthesis started producing oxygen in large quantities.

The big reason for the long delay was that processes such as volcanic gas production acted as sinks to consume free oxygen before it reached levels high enough to take over the atmosphere.
Free oxygen would combine with gases in a volcanic plume to form new compounds, and that process proved to be a significant oxygen sink.
Another sink was iron delivered to the Earth's outer crust by bombardment from space. Free oxygen was consumed as it oxidized, or rusted, the metal.
Just by changing the model to reflect different iron content in the outer crust makes a huge difference in when the model shows free oxygen filling the atmosphere. Increasing the actual iron content fivefold would have delayed oxygenation by more than 1 billion years, while cutting iron to one-fifth the actual level would have allowed oxygenation to happen more than 1 billion years earlier.

"We were fairly surprised that we could push the transition a billion years in either direction, because those levels of iron in the outer crust are certainly plausible given the chaotic nature of how Earth formed" - Mark Claire.

Claire and colleagues David Catling, a UW affiliate professor in atmospheric sciences, and Kevin Zahnle of the National Aeronautics and Space Administration's Ames Research Centre in California will discuss their model on August 9th in Calgary, Alberta, during the Geological Society of America's Earth System Processes 2 meeting.

Earth's oxygen supply originated with cyanobacteria, tiny water-dwelling organisms that survive by photosynthesis. In that process, the bacteria convert carbon dioxide and water into organic carbon and free oxygen.
But, in the early Earth, free oxygen would quickly combine with an abundant element, hydrogen or carbon for instance, to form other compounds, and so free oxygen did not build up in the atmosphere very readily. Methane, a combination of carbon and hydrogen, became a dominant atmospheric gas.
With a sun much fainter and cooler than today, methane build-up warmed the planet to the point that life could survive. But methane was so abundant that it filled the upper reaches of the atmosphere, where such compounds are very rare today. There, ultraviolet exposure caused the methane to decompose and its freed hydrogen escaped into space.
The loss of hydrogen atoms to space allowed increasingly greater amounts of free oxygen to oxidize the crust. Over time, that slowly diminished the amount of hydrogen released from the crust by the combination of pressure and temperature that formed the rocks in the crust.

"About 2.4 billion years ago, the long-term geologic sources of oxygen outweighed the sinks in a somewhat permanent fashion. Escaping to space is the only permanent escape that we envision for the hydrogen, and that drove the planet to a higher oxygen level" - Mark Claire.

The model developed by Claire, Catling and Zahnle indicates that as hydrogen atoms stripped from methane escaped into space, greenhouse conditions caused by the methane blanket quickly collapsed. Earth's average temperature likely cooled by about 30 degrees Celsius, or 54 degrees Fahrenheit, and oxygen was able to dominate the atmosphere because there was no longer an overabundance of hydrogen to consume the oxygen.

The work is funded by NASA's Astrobiology Institute and the National Science Foundation's Integrative Graduate Education and Research Traineeship program, both of which foster research to understand life in the universe by examining the limits of life on Earth.

"There is interest in this work not just to know how an oxygen atmosphere came about on Earth but to look for oxygen signatures for other Earth-like planets" - Mark Claire.




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Scientists crack 40-year-old DNA puzzle and point to ‘hot soup’ at the origin of life

A new theory that explains why the language of our genes is more complex than it needs to be also suggests that the primordial soup where life began on earth was hot and not cold, as many scientists believe.

In a paper published in the Journal of Molecular Evolution this week, researchers from the University of Bath describe a new theory which they believe could solve a puzzle that has baffled scientists since they first deciphered the language of DNA almost 40 years ago.
In 1968, Marshall Nirenberg, Har Gobind Khorana and Robert Holley received a Nobel Prize for working out how proteins are produced from the genetic code. They discovered that three letter ‘words’ - known as codons - are read from the DNA code and then translated into one of 20 amino acids. These amino acids are then strung together in the order dictated by the DNA code and folded into complex shapes to form a specific protein.
As the DNA ‘alphabet’ contains four letters - called bases - there are as many as 64 three-letter words available in the DNA dictionary. This is because it is mathematically possible to produce 64 three-letter words from any combination of four letters.
But why there should be 64 words in the DNA dictionary which translate into just 20 amino acids, and why a process that is more complex than it needs to be should have evolved in the first place, has puzzled scientists for the last 40 years.
Dozens of scientists have suggested theories to solve the puzzle, but these have been quickly discounted or failed to explain some of the other quirks in protein synthesis.

"Why there are so many more codons than amino acids has puzzled scientists ever since it was discovered how the genetic code works. It meant the genetic code did not have the mathematical brilliance you would expect from something so fundamental to life on earth" - Dr Jean van den Elsen from the Department of Biology and Biochemistry.

One of quirks of the genetic code is that there are groups of codons which all translate to the same amino acid. For example, the amino acid leucine can be translated from six different codons whilst some amino acids, which have equally important functions and are translated in the same amount, have just one.
The new theory builds on an original idea suggested by Francis Crick - one of the discoverers of the structure of DNA - that the three-letter code evolved from a simpler two-letter code, although Crick thought the difference in number was simply an accident `frozen in time`.

The University of Bath researchers suggest that the primordial ‘doublet’ code was read in threes - but with only either the first two ‘prefix’ or last two ‘suffix’ pairs of bases being actively read.
By combining arrangements of these doublet codes together, the scientists can replicate the table of amino acids - explaining why some amino acids can be translated from groups of 2, 4 or 6 codons. They can also show how the groups of water loving (hydrophilic) and water-hating (hydrophobic) amino acids emerge naturally in the table, evolving from overlapping ‘prefix’ and ‘suffix’ codons.

"When you evolve our theory for a doublet system into a triplet system, you get an exact match up with the number and range of amino acids we see today. This simple theory explains many unresolved features of the current genetic code. No one has ever been able to do this before, so we are very excited" - Dr van den Elsen, who has worked with Dr Stefan Babgy and Huan-Lin Wu on the theory.

The theory also explains how the structure of the genetic code maximises error tolerance. For instance, ‘slippage’ in the translation process tends to produce another amino acid with the same characteristics, and explains why the DNA code is so good at maintaining its integrity.

"This is important because these kinds of mistakes can be fatal for an organism. None of the older theories can explain how this error tolerant structure might have arisen" - Dr van den Elsen.

The new theory also highlights two amino acids that can be excluded from the doublet system and are likely to be relatively recent ‘acquisitions’ by the genetic code. As these amino acids - glutamine and asparagine - are unable to hold their shape in high temperatures, this suggests that heat prevented them from being acquired by the code at some point in the past.
One possible reason for this is that the Last Universal Common Ancestor (LUCA), which evolved into all life on earth, lived in a hot sulphurous pool or thermal vent. As it moved into cooler conditions, it was able to take up these two additional amino acids and evolve into more complex organisms. This provides further evidence for the debate on whether life emerged from a hot or cold primordial soup.

"There are still relics of a very old simple code hidden away in our DNA and in the structures of our cells" - Dr van den Elsen, who points to several aminoacyl-tRNA synthetases - molecules involved in protein synthesis - which only look at pairs of bases in triplet codons, as well as other physical evidence in support of the theory.

"As the code evolved it has been possible for it to adapt and take on new amino acids. Whether we could eventually reach a full complement of 64 amino acids I don’t know, a compromise between amino acid vocabulary and its error minimising efficiency may have fixed the genetic code in its current format."


-- Edited by Blobrana at 02:27, 2005-08-09

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