domingo, 21 de octubre de 2012

"The Mars' Strain" --Searching for Martian DNA


MIT's Technology Review reports that two renowned entrepreneurs say they want to put a DNA sequencing machine on the surface of Mars in an effort to prove the existence of extraterrestrial life. In a first-ever search for for the first extraterrestrial genome, Human genome-pioneer J. Craig Venter and Jonathan Rothberg, founder of Ion Torrent, a DNA sequencing company have announced seperately that they are developing machines capable of sequencing and beaming backDNA data from Mars.

“There will be DNA life forms there,” Venter predicted Tuesday in New York, where he was speaking at the Wired Health Conference. Venter said researchers working with him have already begun tests at a Mars-like test site in the Mojave Desert.
Their goal, Technology Review reports, is to demonstrate a machine capable of autonomously isolating microbes from soil, sequencing their DNA, and then transmitting the information to a remote computer. 
"This will work only if the DNA on Mars is exactly the same in its fundamental structure as on Earth," says Steven Benner, president of the Foundation for Applied Molecular Evolution in Gainesville, Florida told Technology Review. "It is very unlikely that Terran DNA is the only structure able to support Darwinian evolution."
Christopher Carr of MIT's Department of Earth, Atmospheric and Planetary Sciences, wants to see if Earth and Mars have exchanged life at some point in ancient history, which is why his research team at MIT is building the DNA-detecting machine for possible use on a future Mars rover.
If we can find DNA on Mars would mean the red planet held life and that finding DNA on Mars could mean that life on Mars spawned life on Earth via a Mars-to-Earth rock shuttle.  Earth's stronger gravity and thick atmosphere make it more likely that DNA based life might have a higher probablity of having a Mars-based origin.

"It's an interesting thing to try," said Steven Squyres, a Cornell University planetary scientist and lead scientist for NASA's Mars Exploration Rover Project. 

Seth Shostak, lead astronomer at the SETI Institute, which looks for evidence of extraterrestrial life, thinks it's too soon to narrow the search down to DNA. "I admire their audacity, but it's a very restrictive set of assumptions" that completely overlooks the possibility that life arose independently on Mars, he said. 

Norman Pace, a microbial ecologist from the University of Colorado at Boulder, also supports a broad approach. "We haven't even found organic material on Mars," he pointed out. And Tori Hoehler, an exobiology research scientist at NASA's Ames Research Center, believes in an even wider search. He thinks the expeditions should first determine whether Mars was ever habitable, and then look for organic molecules. If they find organics, he said, only then should they check for DNA. 

While Carr acknowledges the value of the broader studies Pace and Hoehler advocate, he still sees a potential benefit in getting more specific. "We can't really envision what a second genesis would look like, but we can envision what something that's related to us would look like," he said. "We should do the most straightforward thing first."

A little-known fact is that each year Earth is hit by by half a dozen or so one-pound or larger rocks that were blasted off the surface of Mars by large impacts and found their way into Earth-crossing orbits. A little-known fact is that nearly 10% of all rocks blasted off into space from the Red Planet end up crashing into Earth.

This natural "interplanetary transportation system" begs a fascinating question: If primitive and nearly indestructible micro-organisms exist on a given planet, must they by definition as a natural act of nature, travel to their immediate solar-system neighbors?

Recent research on lunar rocks discovered in Antarctica has shown that rocks greater than 10 kilograms in mass could be ejected from terrestrial planets -these are rocks capable of carrying living microbes- and survive the searing violence of the launch.

Over the history of the Earth, billions of football-sized rocks have landed on its surface, some only slightly heated by the launch, reaching Earth in a matter of a few months.

A study by a team of scientists at Oregon State University of a meteorite that originated from Mars revealed a series of microscopic tunnels that are similar in size, shape and distribution to tracks left on Earth rocks by feeding bacteria. Although the researchers were unable to extract DNA from the Martian rocks, the finding nonetheless adds intrigue to the search for life beyond Earth.

Martin Fisk, a professor of marine geology in the College of Oceanic and Atmospheric Sciences at Oregon State University and lead author of the study, said the discovery of the tiny burrows do not confirm that there is life on Mars, nor does the lack of DNA from the meteorite discount the possibility.

"Virtually all of the tunnel marks on Earth rocks that we have examined were the result of bacterial invasion," Fisk said. "In every instance, we've been able to extract DNA from these Earth rocks, but we have not yet been able to do that with the Martian samples.

"There are two possible explanations," he added. "One is that there is an abiotic way to create those tunnels in rock on Earth, and we just haven't found it yet. The second possibility is that the tunnels on Martian rocks are indeed biological in nature, but the conditions are such on that the DNA was not preserved."

More than 30 meteorites that originated on Mars have been identified. These rocks from have a unique chemical signature based on the gases trapped within. The noble gas trapped in glass in the meteorites serve as a "fingerprint" that matches the composition of the Maritian atmosphere measured by the Viking Mission  spacecraft that landed on in 1976. These rocks were "blasted off" the planet when was struck by asteroids or comets and eventually these Martian meteoritescrossed Earth's orbit and plummeted to the ground.

One of these is Nakhla, which landed in Egypt in 1911, and provided the source material for Fisk's study. Scientists have dated the igneous rock fragment from Nakhla – which weighs about 20 pounds – at 1.3 billion years in age. They believe that the rock was exposed to water about 600 million years ago, based on the age of clay found inside the rocks.

"It is commonly believed that water is a necessary ingredient for life," Fisk said, "so if bacteria laid down the tunnels in the rock when the rock was wet, they may have died 600 million years ago. That may explain why we can't find DNA – it is an organic compound that can break down."

Fisk and his colleagues have spent more than 15 years studying microbes that can break down igneous rock and live in the obsidian-like volcanic glass. They first identified the bacteria through their signature tunnels then were able to extract DNA from the rock samples – which have been found in such diverse environments on Earth as below the ocean floor, in deserts and on dry mountaintops. They even found bacteria 4,000 feet below the surface in Hawaii that they reached by drilling through solid rock.

In all of these Earth rock samples that contain tunnels, the biological activity began at a fracture in the rock or the edge of a mineral where the water was present. Igneous rocks are initially sterile because they erupt at temperatures exceeding 1,000 degrees C. – and life cannot establish itself until the rocks cool. Bacteria may be introduced into the rock via dust or water, Fisk pointed out.

"Several types of bacteria are capable of using the chemical energy of rocks as a food source," he said. "One group of bacteria in particular is capable of getting all of its energy from chemicals alone, and one of the elements they use is iron – which typically comprises 5 to 10 percent of volcanic rock."

Another group of OSU researchers, led by microbiologist Stephen Giovannoni, has collected rocks from the deep ocean and begun developing cultures to see if they can replicate the rock-eating bacteria. Similar environments usually produce similar strains of bacteria, Fisk said, with variable factors including temperature, pH levels, salt levels, and the presence of oxygen.

The igneous rocks from are similar to many of those found on Earth, and virtually identical to those found in a handful of environments, including a volcanic field found in Canada.

One question the OSU researchers hope to answer is whether the bacteria begin devouring the rock as soon as they are introduced. Such a discovery would help them estimate when water – and possibly life – may have been introduced on Mars.

"There seems to be little doubt that spores of microbes could survive the thousands of years a typical 'journey' by a rock from Mars to Earth would take," says Shostak. 

But that doesn't mean NASA will decide to put Carr's instrument on the next rover. It's a typical debate in space exploration, said Hoehler: given limited time, money and weight, what are the most important instruments to send? 

Before NASA has to decide, however, Carr's team must finish building the instrument. It will need to be tiny, durable and reliable. They'll need to consider how the equipment will be affected by conditions on Mars and how to distinguish between the DNA of Martian microbes and Earthly contaminants.

Compelling new data that chemical and fossil evidence of ancient microbial life on Mars was carried to Earth in a Martian meteorite is being elevated to a higher plane by the same NASA team which made the initial discovery in 1984 in Victoria Land, in the Eastern region of Antarctica, at the end of the Transantarctic Mountains range, where numerous meteorites have been discovered.
The new data are providing a powerful new case for the Allen Hills Meteorite to have carried strong evidence of Martian life to Earth -- evidence that is increasingly standing up to scrutiny as new analytical tools are used to examine the specimen. It is about 4.5 billion years old and is thought to have been blasted off of Mars by a meteor impact about 16 million years ago.
A possible microfossil, found in a sample of the meteorite, measures less than 1/100th the width of a human hair. This microfossil has caused much debate about whether or not it is evidence for past life on Mars.The latest findings are the product of new research using more advanced High Resolution Electron Microscopy than was in existence when the initial findings were made and announced by NASA and the White House in 1996. Those laboratory sensors were focused directly on carbonate discs and associated tiny magnetite crystals present inside the meteorite Allen Hills ALH 84001.

Now, 16 years after the Martian meteorite life story emerged, the science team finally feels vindicated. Their data shows the meteorite is no smoking gun but is full of evidence that supports the existence of life on the surface of Mars, or in subsurface water pools, early in the planet's history.

The distinct environments of the two planets at present might not allow an organism adapted to one planet to grow on the other. But meteoritic exchange in the solar system was 100 to 1000x more intense during the heavy bombardment stage 4 billion years ago. There are signs of numerous fluid flows a possible ancient ocean, and sedimentary formations that suggest a warmer and wetter Mars 3 to 4 billion years ago, an environment more similar to Archean Earth.
Thus at the time of maximal meteoritic exchange 3.5-4 billion years ago,  microbial life on Earth may have already possessed a shared core of 500 genes, including the 16S ribosomal RNA gene. The last common ancestor with life on Mars may have also shared this core of genes. Thus at the point of high meteoritic exchange, there may have been microbial life on Earth detectable by 16S  gene PCR  and an environment on Mars more similar to Earth than today.
The environments on Mars and Earth have diverged:  the appearance of oxygen on the Earth 2 billion years ago led to decreased UV radiation, while Mars lost its atmosphere as its magnetic field decayed causing an increase in UV flux, cooling of the surface, and loss of surface water. Current life on Mars would need to survive temperatures and pressures below the triple point of water, high UV flux and the oxidizing surface chemistry induced by UV radiation. 
While there is no doubt that Mars is currently an extreme environment, given the adaptability of microbial life on Earth, it is not unreasonable to propose that Martian microbes could have adapted to the gradual decline in water, temperature, and UV protection over the past few billion years. And just as the adapted and diverged microbes on Earth still bear the signature of their common ancestry in their 16S ribosomal RNA genes, the Martian biota may also bear this signature.
Until recently, NASA's strategies for detecting life on other planets have sought to avoid the assumption it would share any particular features with life on Earth. The most general strategies — seeking polymers, structures of biogenic origin, or chemical or isotopic signatures of enzymatic processes — look for features that all life is expected to exhibit. But strategies in the search for extraerrestrial life are not particularly sensitive, and more importantly, there are abiological routes to these life signatures. But if life on Earth is actually related to life on other planets, we can use a far more powerful and information-rich technique developed to detect the most extreme forms of life on Earth.

With funding from NASA, Ruvkun is working on a sensor designed to test the soil of for DNA -the first part of a project he has dubbed the "Search for Extraterrestrial Genomes," which will be a part of a lander mission during the decade. If the device finds any, it could then analyze the genetic code to see if the "Martians" microbes are related to us.

A SETG prototype will have its first field test this year with funding from NASA's Astrobiology Science and Technology Instrument Development program using powerful methods to detect life by the DNA polymerase chain reaction (PCR) are now in standard use. The PCR detector for on site analysis on other planets, most immediately, Mars, is so sensitive it should allow the detection very low levels of microbial life on Mars,  and will determine its phylogenetic position by analysis of the DNA sequence of the detected genes.   

Ruvkun points out that the project represents a stark break from the current operative philosophy of life detection: avoiding an Earth-centric view of what life might look like, which tainted earlier efforts.

Instead, inspired by evidence that microbes can shuttle between planets on meteors, Ruvkun argues it is most likely that any life on would be related to life on Earth and have somewhat similar DNA. We already have evidence that some biologically important molecules, such as the ingredients for amino acids, are delivered by comets. 

Ruvkun and his collaborators have looked for a stretch of DNA that would likely be conserved in both Martians and Earthlings. They believe this common thread should be in the 16S ribosomal RNA gene, which is vital to the protein-making process in cells. This gene has regions of its sequence that have barely changed over billions of years of evolution. Short segments in the 16S ribosomal RNA sequence are exactly identical in more than 100,000 species that have so far had their ribosome genes analyzed.

The proposed strategy is for the SETG instrument to receive a Martian sample and add small extracts from the 16S ribosomal RNA gene as "primers" for DNA replication. If the sample contains DNA and if some part of that DNA's genetic code matches the primer's, then a suite of chemical reactions will produce a million or so copies of the sample's DNA.

The amplified DNA can be detected with special markers and part of its code can be sequenced in order to identify what sort of life-form is the owner of this DNA. If the sample were contaminated by Earthling DNA, then the SETG researchers should be able to recognize signatures in the sequenced code that will pinpoint whether the contamination comes from a human or a bacteria or something else familiar to us. However, if nothing on Earth matches the observed sequence, Ruvkun and his colleagues will claim to have found our Martian relatives.

Ruvkun's team has constructed  a prototype of their DNA analyzer and are currently calibrating it. The team will travel to Argentina's Copahue Volcano, which is considered to be one of the most Mars-like environments on Earth. There, they will test whether the prototype can sequence the DNA of some of the hearty microbes that live in the acidic runoff from the volcano.

The project's prospects depend on a fascinating backstory: about 3.5  billion years ago the planets experienced a period of intense bombardment. Meteors came crashing down to the surface, ejecting more rocks into space, some of which came crashing down onto other planets. Life on Earth appeared very quickly after the bombardment -- to quickly, not to have been seeded, Ruvkun believes, by microbe-bearing meteors.

Martian rocks have been found on earth, and an analysis revealed that its core never experienced superheating as it fell to earth, showing that meteors could be viable shuttles for microbial life.

Extremeophile research has shown that there are microbes that have adapted to almost unbelievably extreme environments -- they are the ultimate adventurers. These organisms thrive where other microbes don’t dare venture: boiling water holes, freezing lakes, and toxic waste dumps. Researchers have sequenced the genomes of two extremophiles that live at the bottom of Ace Lake in Antarctica, where there is no oxygen and the average temperature is a brutal 33 degrees below Fahrenheit.

Image credit: NASA

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