March 21, 2011

Mostly just a bookmark

Found this article and really want to give it a more serious read so I am putting it here so that I remember. Have a look. See what you think.

A Romp Through Theories on Origins of Life --NY Times article

A Romp Into Theories of the Cradle of Life
Published: February 21, 2011

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TEMPE, Ariz. — We’re not in the Garden of Eden anymore.
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Elwood H. Smith

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Darwin speculated that life began in a warm pond on the primordial Earth. Lately other scientists have suggested that the magic joining of molecules that could go on replicating might have happened in an undersea hot spring, on another planet or inside an asteroid. Some astronomers wonder if it could be happening right now underneath the ice of Europa or in the methane seas of Titan.

Two dozen chemists, geologists, biologists, planetary scientists and physicists gathered here recently to ponder where and what Eden might have been. Over a long weekend they plastered the screen in their conference room with intricate chemical diagrams through which electrons bounced in a series of interactions like marbles rattling up and down and over bridges through one of those child’s toys, transferring energy, taking care of the business of nascent life. The names of elements and molecules tripped off chemists’ tongues as if they were the eccentric relatives who show up at Thanksgiving every year.

They charted the fall of meteorites and the rise of oxygen on the early Earth and evidence in old rocks that life was here as long as 3.5 billion years ago. The planet is only a billion years older, but estimates vary on when it became habitable.

In front of a 2,400-member audience one night they debated the definition of life — “anything highly statistically improbable, but in a particular direction,” in the words of Richard Dawkins, the evolutionary biologist at Oxford. Or, they wondered if it could be defined at all in the absence of a second example to the Earth’s biosphere — a web of interdependence all based on DNA.

Hence the quest for extraterrestrial examples is more than a sentimental use of NASA’s dollars. “Let’s go look for it,” said Chris McKay, a planetary scientist at NASA’s Ames Research Laboratory in Mountain View, Calif., who is involved with the Mars Science Laboratory, which will be launched in November.

The rapid appearance of complex life in some accounts — “like Athena springing from the head of Zeus,” in the words of Dr. McKay — has rekindled interest recently in a theory fancied by Francis Crick, one of the discoverers of the double helix, that life originated elsewhere and floated here through space. These days the favorite candidate for such an extraterrestrial cradle is Mars, which was once a water world. Perhaps, some think, its microbes hitched a ride to Earth on asteroids — unless, of course, the microbes went the other way and what’s to be found on Mars are the dead remains of long-lost cousins of Earth.

“We’ve crashed more space probes on Mars than anywhere else — it’s that interesting,” Dr. McKay said.

The conference was sponsored by the Origins Project at Arizona State University in an effort to get people together who don’t normally talk to each other, said Lawrence Krauss, a physicist who helped organize the meeting.

Talk is indeed hard across disciplines and geological ages. John Sutherland, a biochemist at Cambridge University in England, said geologists and astronomers were more interested in talking and speculating about the origin of life than chemists were, even though it is basically a problem of “nitty-gritty chemistry.”

The reason, he explained, is that “chemists know how hard it is.”

The modern version of the Garden of Eden goes by the name of RNA world, after the molecule ribonucleic acid, which plays Robin to DNA’s Batman today, but is now thought have preceded it on the biological scene. RNA is more versatile, being able not only to store information, like DNA, but also to use that information to catalyze reactions, a job now performed by proteins. That solved a sort of chicken-and-egg problem about which ability came first into the world. The answer is that RNA could be both.

“If you want to think of it that way, life is a very simple process,” said Sidney Altman, who shared a Nobel Prize in 1989 for showing that RNA had these dual abilities. “It uses energy, it sustains itself and it replicates.”

One lesson of the meeting was how finicky are the chemical reactions needed for carrying out these simple-sounding functions. “There might be a reason why amino acids and nucleotides are the way they are,” Dr. Krauss said.

What looks complicated to us might not look so complicated to a piece of a carbon molecule awaiting integration into life’s dance. “Complexity is in the eye of the beholder,” said Dr. Sutherland, who after 10 years of trying different recipes succeeded in synthesizing one of the four nucleotides that make up RNA in a jar in his lab.

With the right mixture and conditions, complicated-looking molecules can assemble themselves without help. “When everything is in the pot,” he said, “the chemistry to make RNA is easier.”

Dr. Sutherland’s results were hailed as a triumph for the RNA world idea, but there is much work to be done, said Steve Benner, who constructs artificial DNA at the Foundation for Applied Molecular Evolution, in Florida. Nobody knows whether Dr. Sutherland’s recipe would work on the early Earth, he said. Moreover, even if RNA did appear naturally, the odds that it would happen in the right sequence to drive Darwinian evolution seem small.
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“Other than that,” Dr. Benner said, “the RNA world is a great idea for origin of life.”

Some others, including astronomers and geologists, have another view of biological inevitability. Life is a natural consequence of geology, said Everett Shock, a geophysicist at Arizona State. “Most of what life is doing is using chemical energy,” Dr. Shock said, and that energy is available in places like undersea volcanic vents where life, he calculated, acts as a catalyst to dissipate heat from the Earth. In what he called “a sweet deal,” life releases energy rather than consuming it, making it easy from a thermodynamic standpoint.

“Biosynthesis is profitable — it has to be; they live there,” said Dr. Shock, referring to microbes in undersea vents.

Some scientists say we won’t really understand life until we can make it ourselves.

On the last day of the conference, J. Craig Venter, the genome decoding entrepreneur and president of the J. Craig Venter Institute, described his adventures trying to create an organism with a computer for a parent.

Using mail-order snippets of DNA, Dr. Venter and his colleagues stitched together the million-letter genetic code of a bacterium of a goat parasite last year and inserted it into another bacterium’s cell, where it took over, churning out blue-stained copies of itself. Dr. Venter advertised his genome as the wave of future migration to the stars. Send a kit of chemicals and a digitized genome across space.

“We’ll create panspermia if it didn’t already exist,” he said.

The new genome included what Dr. Venter called a watermark. Along with the names of the researchers were three quotations, from the author James Joyce; Robert Oppenheimer, who directed the building of the atomic bomb; and the Caltech physicist Richard Feynman: “What I cannot build, I do not understand.”

When the news came out, last year, Dr. Venter said, the James Joyce estate called up and threatened to sue, claiming that Joyce’s copyright had been violated. To date there has been no lawsuit.

Then Caltech called up and complained that Dr. Venter’s genome was misquoting Feynman. The institute sent a photograph of an old blackboard on which Feynman had written, “What I cannot create, I do not understand.”

And so his genome is now in the process of acquiring its first, non-Darwinian mutation.

Posted by michelle at 10:16 PM | Comments (0)

March 14, 2011

A thin line

The last viewing of Truth Project didn't go as well as the first few. Seems we have come to an impasse--to a place where we aren't arguing merits or facts but just relying on what we believe at a core level. There's no amount of debate that can change that. In either of our situations, from either of our perspectives, a change in belief system would require more than a set of proofs or persuasive reasoning. It would ultimately result in a complete paradigm shift. That point itself makes it much harder to foresee a change. When you then factor in traditions, cultures and heritage, it is never easy for someone to truly look inward and make such a significant change. This discussion is more of an exploration and an attempt to diversify the thought processes that have combined to mold the beliefs that we identify with currently. When you stop asking, when you stop learning, when you stop working on who you are and who you want to become, you just get tossed around by the currents and that is something that I don’t intend to do.
But now, watching is sometimes more upsetting than I thought it would be. I feel more defensive than I anticipated and more frustrated than I want to be. So we've come to an agreement that we'll watch only the ones that we think will lead to a good discussion and I will try very hard to not take notes so strenuously that I tear through the paper while it is going on.
I'm hoping we can still get through it.

Posted by michelle at 08:36 PM | Comments (0)