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Sunday, February 12, 2012
Here’s my weekly evolution column, which appears Monday Feb 13 in the Philadelphia Inquirer:
On Star Trek, the aliens often look so human that crew members fall in love with them. But in real life, scientists in the field known as astrobiology can’t be sure alien life would even be carbon-based like us, or use DNA to carry a genetic code.
Some insight now is coming from earthly labs, where scientists are building alternative kinds of genetic codes, and showing how they can evolve.
Whether life could be built with an alien biochemistry was among the more interesting questions that came up during a public event with famed biologist Richard Dawkins and physicist Lawrence Krauss, author of the book The Physics of Star Trek.
Dawkins saw the question as a biological equivalent of one posed by Einstein: Did God have any choice in making the universe? Not that Einstein believed in a biblical God, as the famously atheistic Dawkins was quick to point out.
Dawkins noted that most of the species that ever existed are now extinct. The way carbon-based life works on Earth is downright wasteful, he said. “Any decent engineer would have sent it back to the shop.”
The event, which drew more than 3,000 people, was held at Arizona State University in Tempe. Dawkins didn’t lecture but instead took part in an onstage discussion with Krauss, who runs a multidisciplinary program there on the origins of humanity, life, and the cosmos.
Krauss — while not going so far as to say alien chicks would be hot — did say the laws of physics and chemistry might favor carbon-based life resembling ours.
Dawkins said he was inclined to think life could exist in more diverse forms, as long as it included some kind of code-carrying system equivalent to DNA, copying itself with high fidelity. Such genetic material is critical for Darwinian evolution, which, to Dawkins and many others, is the defining characteristic of life.
Perhaps it wasn’t a complete coincidence that at the same university, biochemist John Chaput was creating an alternative version of DNA, called TNA, and had last month published the first evidence that the stuff can undergo Darwinian evolution.
Chaput, who works at ASU’s Biodesign Institute, said Dawkins is correct to emphasize the need for genetic material — something that can carry a code. All known life does this with DNA and RNA.
NASA has taken a great interest in such possible alternative code-carriers. In late 2010 the space agency claimed that scientists had forced bacteria to substitute arsenic for phosphorus in its DNA. Despite the fanfare, the team never presented adequate evidence that alternative life really existed, said chemist Steve Benner of the Florida-based Foundation for Applied Molecular Evolution.
And when biochemist Rosemary Redfield of the University of British Columbia tried to replicate this, she discovered that the bacteria failed to grow when fed arsenic and no phosphorus.
Benner said the original arsenic life paper admitted to a small amount of phosphorus contamination. From the start, he said, he thought the contamination was fooling the team into thinking the organism was using arsenic the way we use phosphorus.
Benner said this new TNA work is just as exciting and relevant to astrobiology as the arsenic bacteria would have been if it had been proved.
This alternative genetic material is like RNA in that it’s single-stranded and it carries a chemical code with four different units. But the backbone that holds it together has a different structure, incorporating a sugar called threose where RNA has a sugar called ribose.
Threose is found in meteorites, said Chaput, suggesting it can form spontaneously in the absence of life. It’s also simpler than RNA, making it a reasonable candidate for a precursor to our current genetic material.
The existence of a precursor fits with the widely held view that life didn’t start out as complex as even the simplest microbes today. Instead, the simplest known living things evolved from yet simpler life that no longer exists.
Chaput showed that, like RNA, TNA can undergo Darwinian evolution. In theory, then, life elsewhere could use TNA as its genetic code, and if early life on Earth used it, TNA-based life could evolve into DNA-based life.
To demonstrate TNA evolution, he used selection to prompt the molecules to do a fairly simple task — to stick to a specific protein. This is what so-called receptors do in our bodies. He continued to select those TNA molecules that best stuck to the protein until he had a decent receptor.
TNA evolution worked the same way as in DNA, with accidental mutations leading to variation, and natural selection amplifying those variants that are best at surviving and reproducing themselves. He published the results last month in the journal Nature Chemistry.
That suggests the possibility of TNA-based life elsewhere, said Benner. It’s also possible, he said, that arsenic-using DNA would be stable, say, under the frigid conditions of Saturn’s moon Titan.
So now we have TNA as well as PNA, GNA, FNA and code-carrying molecules that use six or 12 characters rather than the usual four. With these increasing possibilities known, Benner sides more closely with Dawkins on the question of life forms with alternative chemistries.
Our life is not the best of all possible forms, Benner said, but a product of chance, our biochemistry hinging on which molecules happened to bump into each other. God did have alternatives, in other words, but perhaps no power to choose which one would evolve to create works like Star Trek.
Contact staff writer Faye Flam at 215-854-4977, firstname.lastname@example.org, on her blog at www.philly.com/evolution, or @fayeflam on Twitter.
While nature has used nanotechnology for millennia in the form of DNA, a team of scientists have created GNA as a less expensive and more durable replacement. Until a better replacement comes along, GNA is looking to be the building block for future nanotechnology.
Imagine any piece of technology in science fiction you have ever read or watched on film, and then realize that, barring self-destruction, it is only a matter of time before those capabilities become reality. If you have doubts, just taking a look around at what has already become commonplace over the last century or so that was once considered impossible.
Unfortunately, a lot of those people who dreamt of the possibilities in the past have not lived to see the reality. Therein lies what is a major part of the problem, our own mortality.
While a few may want death to come unexpectedly and without warning at any time in their lives, or trust in their own deity of choice, perhaps helping ourselves to not only extend life, but make death an option, would be preferable to inevitability.
Realizing that any problem today, including death, could be solved through nanotechnology, one would think it would be the utmost priority. Unfortunately, some Luddite type thinking, fear mongering, ignorance, and religious absolutism have delayed or even stopped technological progress in some areas of the globe.
Fortunately, this is not the case with the United States and other developed countries, at least when it comes to nanotechnology or technology on the scale of a billionth of a meter. At the atomic and molecular scale, however, many difficulties occur.
While Deoxyribose Nucleic Acid (DNA), or Nature’s nanotechnology, has proven to be useful for evolution over millennia, adapting it for use in recently developed nanotechnology has proven difficult, time-consuming, and expensive.
Helping to solve this problem is John Chaput and his research team at the Biodesign Institute of Arizona State University, who have now created a more flexible alternative: Glycerol Nucleic Acid (GNA). The advantages include faster mirror image replication, less expense, greater connectivity, and a higher heat tolerance. While still fairly new, the Journal of the American Chemical Society claims the team has been the first to make self-assembled nanostructures with GNA.
With these and many other tools currently available and on the horizon, the only problems left in the future seem to be those we create. Perhaps with enough foresight and responsibility, we will succeed in becoming more than human.
Chemical cousin of DNA new nanotechnology building block
April 28, 2008
In the rapid and fast-growing world of nanotechnology, researchers are continually on the lookout for new building blocks to push innovation and discovery to scales much smaller than the tiniest speck of dust.
In the Biodesign Institute at Arizona State University, researchers are using DNA to make intricate nano-sized objects. Working at this scale holds great potential for advancing medical and electronic applications. DNA, often thought of as the molecule of life, is an ideal building block for nanotechnology because they self-assemble, snapping together into shapes based on natural chemical rules of attraction. This is a major advantage for Biodesign researchers like Hao Yan, who rely on the unique chemical and physical properties of DNA to make their complex nanostructures.
Biodesign Institute scientist John Chaput and his research team have made the first self-assembled nanostructures composed entirely of glycerol nucleic acid — a synthetic analog of DNA. The nanostructures contain additional properties not found in natural DNA, including the ability to form mirror image structures. The ability to make mirror image structures opens up new possibilities for nanotechnology.
While scientists are fully exploring the promise of DNA nanotechnology, Biodesign Institute colleague John Chaput is working to give researchers brand new materials to aid their designs. In an article recently published in the Journal of the American Chemical Society, Chaput and his research team have made the first self-assembled nanostructures composed entirely of glycerol nucleic acid (GNA)—a synthetic analog of DNA.
“Everyone in DNA nanotechnology is essentially limited by what they can buy off the shelf,” said Chaput, who is also an ASU assistant professor in the Department of Chemistry and Biochemistry. “We wanted to build synthetic molecules that assembled like DNA, but had additional properties not found in natural DNA.”
The DNA helix is made up of just three simple parts: a sugar and a phosphate molecule that form the backbone of the DNA ladder, and one of four nitrogenous bases that make up the rungs. The nitrogenous base pairing rules in the DNA chemical alphabet fold DNA into a variety of useful shapes for nanotechnology, given that A can only form a zipper-like chemical bond with T and G only pair with C.
In the case of GNA, the sugar is the only difference with DNA. The five carbon sugar commonly found in DNA, called deoxyribose, is substituted by glycerol, which contains just three carbon atoms.
Chaput has had a long-standing interest in tinkering with chemical building blocks used to make molecules like proteins and nucleic acids that do not exist in nature. When it came time to synthesize the first self-assembled GNA nanostructures, Chaput had to go back to basics. “The idea behind the research was to start with a simple DNA nanostructure that we could just mimic.”
The first self-assembled DNA nanostructure was made by Ned Seeman’s lab at Columbia University in 1998, the very same laboratory where ASU professor Hao Yan received his Ph.D. Chaput’s team, which includes graduate students Richard Zhang and Elizabeth McCullum were not only able to duplicate these structures, but, unique to GNA, found they could make mirror image nanostructures.
The only chemical difference between DNA and a synthetic cousin, GNA, is in the sugar molecule. GNA uses a three carbon sugar called glycerol rather than the five carbon deoxyribose used in DNA. The sugar provides the chemical backbone for nucleic acid polymers, anchoring a phosphate molecule and nitrogenous base (B).
In nature, many molecules important to life like DNA and proteins have evolved to exist only as right-handed. The GNA structures, unlike DNA, turned out to be ‘enantiomeric’ molecules, which in chemical terms means both left and right-handed.
“Making GNA is not tricky, it’s just three steps, and with three carbon atoms, only one stereo center,” said Chaput. “It allows us to make these right and left-handed biomolecules. People have actually made left-handed DNA, but it is a synthetic nightmare. To use it for DNA nanotechnology could never work. It’s too high of a cost to make, so one could never get enough material.”
The ability to make mirror image structures opens up new possibilities for making nanostructures. The research team also found a number of physical and chemical properties that were unique to GNA, including having a higher tolerance to heat than DNA nanostructures. Now, with a new material in hand, which Chaput dubs ‘unnatural nucleic acid nanostructures,’ the group hopes to explore the limits on the topology and types of structure they can make.
“We think we can take this as a basic building block and begin to build more elaborate structures in 2-D and see them in atomic force microscopy images,” said Chaput. “I think it will be interesting to see where it will all go. Researchers come up with all of these clever designs now.”
To read the online publication, go to:
Hawaii-Tribune Herald, Sunday, July 1, 2012
Onishi, Ikeda come under fire
Ethics complaint filed against councilmen for low attendance
By TOM CALLIS Tribune-Herald staff writer
Hawaii County Council members Dennis Onishi and Donald Ikeda are both facing an ethics complaint targeting their attendance records.
Terri Napeahi, vice president of the Pele Defense Fund, filed the complaint with the county Board of Ethics Committee on June 14.
Napeahi cites the absence of the Hilo council members during recent testimony regarding geothermal power and their attendance rate during votes.
According to figures provided by Chairman Dominic Yagong’s office, the two council members have the worst records when it comes to casting their votes on the ninemember council.
Onishi has missed 30 percent of the 1,557 votes taken in committee and council meetings between Dec. 6, 2010, and April 18, 2012, and Ikeda has missed 23 percent of the votes during that time period.
Percentage of missed votes for the other council members are: Vice Chairman Angel Pilago, 15 percent; J Yoshimoto and Pete Hoffman, 12 percent; Fred Blas, 7 percent; Brittany Smart and Yagong, 3 percent; Brenda Ford, 1 percent.
The Pele Defense Fund had requested the same figures from Yagong’s office.
Yagong said he provided them with the information, rather than sending the request through the County Clerk’s Office, because his office already had compiled the data in response to an earlier records request.
“When they asked me for that, I said we had the information available and we provided that to them,” Yagong said.
A check of the figures by the Tribune-Herald found that Yagong’s office counted some excused absences as votes, but no other discrepancies between their vote tallies and county records was seen. Ikeda and Onishi both said Thursday they were unaware of the complaint.
The council members in separate interviews defended their voting records and said they don’t think they are neglecting their offices.
Onishi attributed recent absences to marathon public testimony sessions that have pushed meetings into the evening hours.
“I know in the past couple council meetings … testimony has been for eight hours,” he said.
“The council meeting started after that. I know I had prior commitments in the evening part and later part in the afternoon.”
Onishi said those commitments included “other meetings in the community.” He said he couldn’t elaborate because he didn’t have his calendar on hand.
While Onishi has missed 471 out of 1,557 votes during that time period, the records show he has only missed three council or committee meetings.
Asked why he makes some votes during a meeting but misses others, he repeated that he has other commitments that sometimes conflict with the meeting.
“At this time I don’t have my calendar in front of me,” he said when asked to elaborate. “I can’t tell you for sure.”
Ikeda has missed 365 votes during that time period, but he said in an interview that he doubts he missed that many.
“I think I have a high percentage of votes,” he said. Ikdea said he couldn’t estimate how many votes he has made or missed.
In regards to the ones he has missed, Ikeda said he gets called out of meetings sometimes to speak to constituents. “I go out and listen to them and as soon as I get done there I come back in,” he said.
Ikeda, who is running for state Senate, said he didn’t have another reason for missing votes. He said he tries not to schedule other commitments during council meetings. Ikeda has missed nine committee or council meetings during that time period. The council holds two council and two committee meetings each month unless a special meeting is called.
All nine council members are voting members of the committees.
Onishi and Ikeda acknowledged that they haven’t sat through all of the public testimony at recent meetings, but said they choose instead to listen to it in their council offices while they catch up on their council work.
“We have video screens,” Onishi said. “I’m listening to the testimony at my office on the computer.”
Napeahi said she thinks it’s important for the council members to be present during testimony so that residents know they are listening.
“They are there to serve the public,” she said.
“They were elected as public officials to listen to the concerns of our people, and they are not engaging with us as we’re giving passionate testimony.”
Ford, who has an almost flawless attendance record, said she sees it as essential for council members to sit through all votes and testimony.
“I think it’s my obligation … to be there as much as possible,” she said.
Ford said she also ensures that her schedule is clear for all council meetings.
“If serving your constituents is your priority, then you will make those meetings your priority,” she said.
Ikeda and Onishi have both voted against several of the recent geothermal bills, supported by the PDF.
Palikapu Dedman, PDF president, denied that the complaint is politically motivated; he said it’s about ensuring that testifiers are heard by all council members.
“We take off work,” Dedman said, “and we only talk to a few people.”
Napeahi said the ethics board will address the complaint during a preliminary hearing July 11.
Renee Schoen, county deputy corporation counsel, said the board decides during those hearings whether to proceed with the complaint further or drop it.
A violation of county ethics rules can be punished by up to $1,000 for each offense. Yagong said there is no attendance requirement for council members, leaving little likelihood that penalties would be issued.
He said he couldn’t comment on whether he thinks the complaint is valid but added that he values attendance at the meetings.
“Do I believe people should listen to those who take the time to come to the council … Do I think that’s important? Absolutely,” he said.
“I think they deserve an audience of the council. That’s who they came to see.”
Email Tom Callis at email@example.com.