Showing posts with label DNA. Show all posts
Showing posts with label DNA. Show all posts
Thursday, September 20, 2012
Neanderthal nookie notion nixed
Will Parker
14 August 2012
http://www.scienceagogo.com/news/20120713195113data_trunc_sys.shtml
Hybridization, the idea that modern humans and Neanderthals once interbred is probably wrong, say researchers at the University of Cambridge who suggest that a common ancestry better explains the DNA we share with Neanderthals. The new work, that details an alternative explanation for the 1-4 percent shared Eurasian and Neanderthal DNA, appears in the journal PNAS.
Central to the new research is the fact that Africans have almost none of the Neanderthal genome. In previous studies this was explained by suggesting hybridization occurred after modern humans exited Africa and later bred with the Neanderthals who already inhabited Europe.
Study leader, Dr Andrea Manica, explained that Neanderthals and modern humans likely once shared a common ancestor who spanned Africa and Europe about half a million years ago. "Just as there are very different populations across Europe today, populations of that common ancestor would not have been completely mixed across continents, but rather closer populations would have been more genetically similar to each other than populations further apart," she said.
Then, about 300-350,000 years ago, the European range and the African range became separated. The European range evolved into Neanderthal, the African range eventually turned into modern humans. However, explains Manica, because the populations within each continent were not freely mixing, the DNA of the modern human population in Africa that were ancestrally closer to Europe would have retained more of the ancestral DNA (specifically, genetic variants) that is also shared with Neanderthals.
Exploring this idea, Manica's team created a model to determine whether the differences in genetic similarities with Neanderthal among modern human populations, which had been attributed to hybridization, could be down to the proximity of modern humans in northern Africa (who would have later gone on to populate Europe) to Neanderthals.
By examining the different genetic makeup among modern human populations, the scientists' model was able to infer how much genetic similarity there would have been between distinct populations within a continent. The researchers then simulated a large number of populations representing Africa and Eurasia over the last half a million years, and estimated how much similarity would be expected between a random Neanderthal individual and modern humans in Africa and Eurasia.
Manica concluded that when modern humans expanded out of Africa 60-70,000 years ago, they would have brought out that additional genetic similarity with them, making Europeans and Asians more similar to Neanderthals than Africans are on average - undermining the theory that hybridization, and not common ancestry, explained these differences.
"Based on common ancestry and geographic differences among populations within each continent, we would predict out of Africa populations to be more similar to Neanderthals than their African counterparts - exactly the patterns that were observed when the Neanderthal genome was sequenced; but this pattern was attributed to hybridization. Our work shows clearly that the patterns currently seen in the Neanderthal genome are not exceptional, and are in line with our expectations of what we would see without hybridization. Hopefully, everyone will become more cautious before invoking hybridization, and start taking into account that ancient populations differed from each other probably as much as modern populations do," she noted.
Wednesday, February 2, 2011
Beam My DNA Up, Scotty
A Nobel prizewinner is reporting that DNA can be generated from its teleported "quantum imprint"
A STORM of scepticism has greeted experimental results emerging from the lab of a Nobel laureate which, if confirmed, would shake the foundations of several fields of science. "If the results are correct," says theoretical chemist Jeff Reimers of the University of Sydney, Australia, "these would be the most significant experiments performed in the past 90 years, demanding re-evaluation of the whole conceptual framework of modern chemistry."
Luc Montagnier, who shared the Nobel prize for medicine in 2008 for his part in establishing that HIV causes AIDS, says he has evidence that DNA can send spooky electromagnetic imprints of itself into distant cells and fluids. If that wasn't heretical enough, he also suggests that enzymes can mistake the ghostly imprints for real DNA, and faithfully copy them to produce the real thing. In effect this would amount to a kind of quantum teleportation of the DNA.
Many researchers contacted for comment by New Scientist reacted with disbelief. Gary Schuster, who studies DNA conductance effects at Georgia Institute of Technology in Atlanta, compared it to "pathological science". Jacqueline Barton, who does similar work at the California Institute of Technology in Pasadena, was equally sceptical. "There aren't a lot of data given, and I don't buy the explanation," she says. One blogger has suggested Montagnier should be awarded an IgNobel prize.
Yet the results can't be dismissed out of hand. "The experimental methods used appear comprehensive," says Reimers. So what have Montagnier and his team actually found?
To read the entire article:
Scorn over claim of teleported DNA
12 January 2011 by Andy Coghlan
Magazine issue 2795.
http://www.newscientist.com/article/mg20927952.900-scorn-over-claim-of-teleported-dna.html
A STORM of scepticism has greeted experimental results emerging from the lab of a Nobel laureate which, if confirmed, would shake the foundations of several fields of science. "If the results are correct," says theoretical chemist Jeff Reimers of the University of Sydney, Australia, "these would be the most significant experiments performed in the past 90 years, demanding re-evaluation of the whole conceptual framework of modern chemistry."
Luc Montagnier, who shared the Nobel prize for medicine in 2008 for his part in establishing that HIV causes AIDS, says he has evidence that DNA can send spooky electromagnetic imprints of itself into distant cells and fluids. If that wasn't heretical enough, he also suggests that enzymes can mistake the ghostly imprints for real DNA, and faithfully copy them to produce the real thing. In effect this would amount to a kind of quantum teleportation of the DNA.
Many researchers contacted for comment by New Scientist reacted with disbelief. Gary Schuster, who studies DNA conductance effects at Georgia Institute of Technology in Atlanta, compared it to "pathological science". Jacqueline Barton, who does similar work at the California Institute of Technology in Pasadena, was equally sceptical. "There aren't a lot of data given, and I don't buy the explanation," she says. One blogger has suggested Montagnier should be awarded an IgNobel prize.
Yet the results can't be dismissed out of hand. "The experimental methods used appear comprehensive," says Reimers. So what have Montagnier and his team actually found?
To read the entire article:
Scorn over claim of teleported DNA
12 January 2011 by Andy Coghlan
Magazine issue 2795.
http://www.newscientist.com/article/mg20927952.900-scorn-over-claim-of-teleported-dna.html
Sunday, July 25, 2010
Rats fed junk food pass down cancer risk through multiple generations
http://www.naturalnews.com/029198_cancer_epigenetics.html
Rats fed junk food pass down cancer risk through multiple generations of offspring
Wednesday, July 14, 2010
Ethan A. Huff, staff writer
(NaturalNews) A recent study out of Georgetown University Medical Center has concluded that what you eat can affect your children's and grandchildren's health, even if they eat healthy themselves. Sonia de Assis and her colleagues observed that rats fed fatty, unhealthy food pass on an increased cancer risk to their children and grandchildren.
The study, which was presented at the American Association for Cancer Research in Washington, D.C., illustrates that a fatty diet can actually contribute to "epigenetic" DNA modifications, which are inherited changes in DNA patterns. Essentially, one's offspring can inherit DNA changes caused by their parents' unhealthy diets and other environmental factors.
The findings also seem to explain why diseases like breast cancer are more likely to manifest in certain family lines and not in others. If epigenetic DNA changes are altering genes like BRCA1 and BRCA2, then this would explain why some people are more prone than others to develop certain degenerative diseases.
"We think that there may be other means of transmission that are not genetic that can account for breast cancer," explained de Assis in response to the study's findings.
And Assis' perspective is warranted based on her findings.
According to Breastcancer.org, only about 20-30 percent of women diagnosed with breast cancer have any family history of breast cancer. This means that the other 70-80 percent must be developing it for reasons other than simply genetics.
If a person's parents or grandparents ate a diet rich in processed, chemical-laden foods throughout their lives, then the DNA changes that likely occurred in their bodies may be passed down to their children. Even if they themselves didn't develop cancer, the children will be more likely to develop it, based on the findings of the study.
And if the children also eat junk food diets that lack proper nutrients, antioxidants, vitamins and other necessary life components, then their children will be even more prone than they were to develop degenerative diseases like cancer.
But your personal diet and lifestyle choices are still the primary deciding factors for whether or not you develop a degenerative disease. Even if your parents and grandparents ate unhealthy diets all their lives does not mean that you have to get sick. Eating a strong, healthy diet and regularly exercising will do wonders for your health.
Rats fed junk food pass down cancer risk through multiple generations of offspring
Wednesday, July 14, 2010
Ethan A. Huff, staff writer
(NaturalNews) A recent study out of Georgetown University Medical Center has concluded that what you eat can affect your children's and grandchildren's health, even if they eat healthy themselves. Sonia de Assis and her colleagues observed that rats fed fatty, unhealthy food pass on an increased cancer risk to their children and grandchildren.
The study, which was presented at the American Association for Cancer Research in Washington, D.C., illustrates that a fatty diet can actually contribute to "epigenetic" DNA modifications, which are inherited changes in DNA patterns. Essentially, one's offspring can inherit DNA changes caused by their parents' unhealthy diets and other environmental factors.
The findings also seem to explain why diseases like breast cancer are more likely to manifest in certain family lines and not in others. If epigenetic DNA changes are altering genes like BRCA1 and BRCA2, then this would explain why some people are more prone than others to develop certain degenerative diseases.
"We think that there may be other means of transmission that are not genetic that can account for breast cancer," explained de Assis in response to the study's findings.
And Assis' perspective is warranted based on her findings.
According to Breastcancer.org, only about 20-30 percent of women diagnosed with breast cancer have any family history of breast cancer. This means that the other 70-80 percent must be developing it for reasons other than simply genetics.
If a person's parents or grandparents ate a diet rich in processed, chemical-laden foods throughout their lives, then the DNA changes that likely occurred in their bodies may be passed down to their children. Even if they themselves didn't develop cancer, the children will be more likely to develop it, based on the findings of the study.
And if the children also eat junk food diets that lack proper nutrients, antioxidants, vitamins and other necessary life components, then their children will be even more prone than they were to develop degenerative diseases like cancer.
But your personal diet and lifestyle choices are still the primary deciding factors for whether or not you develop a degenerative disease. Even if your parents and grandparents ate unhealthy diets all their lives does not mean that you have to get sick. Eating a strong, healthy diet and regularly exercising will do wonders for your health.
Friday, August 28, 2009
Artificial life is only months away
http://www.timesonline.co.uk/tol/news/uk/science/article6804599.ece
From The Times
August 21, 2009
Artificial life is only months away, says biologist Craig Venter
Mark Henderson, Science Editor
Artificial life will be created within four months, a controversial scientist has predicted. Craig Venter, who led a private project to sequence the human genome, told The Times that his team had cleared a critical hurdle to creating man-made organisms in a laboratory.
“Assuming we don’t make any errors, I think it should work and we should have the first synthetic species by the end of the year,” he said.
Dr Venter, who has been chasing his goal for a decade, is already working on projects to use synthetic biology to create bacteria that transform coal into cleaner natural gas, and algae that soak up carbon dioxide and turn it into hydrocarbon fuels. Other potential applications include new ways of manufacturing medicines and vaccines.
Dr Venter’s prediction came after scientists at his J. Craig Venter Institute, in Rockville, Maryland, announced that they had developed a new method of transplanting DNA into bacteria, promising to solve a problem that has held up the artificial life project for two years.
The team took the first step in 2007 by implanting the genome of a bacterium, Mycoplasma mycoides, into cells belonging to a close relative, Mycoplasma capricolum. This transformed the host bacteria into Mycoplasma mycoides.
Last January the team built a bacterium’s entire genetic code from scratch. The next step was to transfer this synthetic genome into a host cell, using the 2007 transplant technique, to “reboot” it with genetic instructions written by humans. This has failed so far because the synthetic genome will not work when it is transplanted into host cells.
The new research, published in Science, has identified the probable reason for this failure and developed a new approach that should address it.
Natural bacterial genomes, such as the one that was successfully transplanted, are chemically modified by a process called methylation. When they are inserted into other cells this process appears to protect them against chemicals called restriction enzymes, which defend against viruses.
The synthetic genome, however, is not methylated, as it has to be grown in yeast, which does not provide the necessary chemical modifications, thus leaving it open to attack by the restriction enzymes.
In the new study, the Venter team grew the natural M. mycoides genome in yeast, under similar conditions to the synthetic genome, so that it had no methylation. These genomes failed to take when they were transplanted into host cells.
The team then remethylated the M. mycoides genome in the laboratory before placing it into the host cell. This time the transplants worked and the cells were rebooted as M. mycoides.
The success suggests that methylating the synthetic genome before transfer should allow it to take over host cells and reboot them with its DNA. Experiments in this have now begun.
Methylation should protect the synthetic genome against the host cells’ defences, much as drugs that suppress the immune system protect transplanted organs against rejection.
Hamilton Smith, a Nobel laureate who is another leader of the research, said: “I believe this work has important implications in better understanding the fundamentals of biology to enable the final stages of our work in creating and booting up a synthetic genome. This is possibly one of the most important new findings in the field of synthetic genomics.”
Dr Venter said the research was particularly important because it opened the door to altering algae and bacteria to perform useful functions.
“This could be one of the most powerful tools in biology,” he said.
From The Times
August 21, 2009
Artificial life is only months away, says biologist Craig Venter
Mark Henderson, Science Editor
Artificial life will be created within four months, a controversial scientist has predicted. Craig Venter, who led a private project to sequence the human genome, told The Times that his team had cleared a critical hurdle to creating man-made organisms in a laboratory.
“Assuming we don’t make any errors, I think it should work and we should have the first synthetic species by the end of the year,” he said.
Dr Venter, who has been chasing his goal for a decade, is already working on projects to use synthetic biology to create bacteria that transform coal into cleaner natural gas, and algae that soak up carbon dioxide and turn it into hydrocarbon fuels. Other potential applications include new ways of manufacturing medicines and vaccines.
Dr Venter’s prediction came after scientists at his J. Craig Venter Institute, in Rockville, Maryland, announced that they had developed a new method of transplanting DNA into bacteria, promising to solve a problem that has held up the artificial life project for two years.
The team took the first step in 2007 by implanting the genome of a bacterium, Mycoplasma mycoides, into cells belonging to a close relative, Mycoplasma capricolum. This transformed the host bacteria into Mycoplasma mycoides.
Last January the team built a bacterium’s entire genetic code from scratch. The next step was to transfer this synthetic genome into a host cell, using the 2007 transplant technique, to “reboot” it with genetic instructions written by humans. This has failed so far because the synthetic genome will not work when it is transplanted into host cells.
The new research, published in Science, has identified the probable reason for this failure and developed a new approach that should address it.
Natural bacterial genomes, such as the one that was successfully transplanted, are chemically modified by a process called methylation. When they are inserted into other cells this process appears to protect them against chemicals called restriction enzymes, which defend against viruses.
The synthetic genome, however, is not methylated, as it has to be grown in yeast, which does not provide the necessary chemical modifications, thus leaving it open to attack by the restriction enzymes.
In the new study, the Venter team grew the natural M. mycoides genome in yeast, under similar conditions to the synthetic genome, so that it had no methylation. These genomes failed to take when they were transplanted into host cells.
The team then remethylated the M. mycoides genome in the laboratory before placing it into the host cell. This time the transplants worked and the cells were rebooted as M. mycoides.
The success suggests that methylating the synthetic genome before transfer should allow it to take over host cells and reboot them with its DNA. Experiments in this have now begun.
Methylation should protect the synthetic genome against the host cells’ defences, much as drugs that suppress the immune system protect transplanted organs against rejection.
Hamilton Smith, a Nobel laureate who is another leader of the research, said: “I believe this work has important implications in better understanding the fundamentals of biology to enable the final stages of our work in creating and booting up a synthetic genome. This is possibly one of the most important new findings in the field of synthetic genomics.”
Dr Venter said the research was particularly important because it opened the door to altering algae and bacteria to perform useful functions.
“This could be one of the most powerful tools in biology,” he said.
Tuesday, August 18, 2009
A Human Genome in Record Time
http://blogs.sciencemag.org/scienceinsider/2009/08/a-human-genome.html
August 10, 2009
A Human Genome in Record Time
A new type of technology has sequenced a human genome in a month and for less than $50,000 worth of reagents, according to a report today in Nature Biotechnology. But this step toward fast, cheap genomes doesn't spell the end for large sequencing centers.
Human genomes produced to date have all required many instruments running in parallel and have cost up to $500,000 per genome, says Stephen Quake, a biophysicist at Stanford University in Palo Alto, California, and founder of Helicos Biosciences of Cambridge, Massachusetts. The HeliScope Single Molecule Sequencer is the first commercial single-molecule sequencing instrument, so called because it does not require the production of millions of copies of the target DNA for the analysis. Instead, DNA is cut into small pieces and mounted at very high densities in a flow cell, where a very sensitive camera monitors the step by step addition of bases for each sequencing reaction.
In the new paper, Quake and colleagues report how the machine generated enough data to cover the 3-billion base human genome 28 times over. That sequence data consisted of short stretches of sequences 24 to 70 bases long, which were compared with the reference human genome sequence in public databases to piece together Quake’s own genome.
The demonstration brings “plug and play” sequencing one step closer to reality, wherein individual labs will be able to do what today is accomplished primarily in large sequencing centers. “This is the main coming out party for the Helicos machine,” says Jeffery Schloss of the National Human Genome Research Institute in Bethesda, Maryland.
However, the machines cost $1 million. That’s several times the price of other sequencing machines, notes Schloss. While such machines hint at a future where individual labs sequence large genomes, Schloss emphasizes that large centers will continue to play a role in improving technologies and their uses and developing analytical tools for genome projects.
— Elizabeth Pennisi
August 10, 2009
A Human Genome in Record Time
A new type of technology has sequenced a human genome in a month and for less than $50,000 worth of reagents, according to a report today in Nature Biotechnology. But this step toward fast, cheap genomes doesn't spell the end for large sequencing centers.
Human genomes produced to date have all required many instruments running in parallel and have cost up to $500,000 per genome, says Stephen Quake, a biophysicist at Stanford University in Palo Alto, California, and founder of Helicos Biosciences of Cambridge, Massachusetts. The HeliScope Single Molecule Sequencer is the first commercial single-molecule sequencing instrument, so called because it does not require the production of millions of copies of the target DNA for the analysis. Instead, DNA is cut into small pieces and mounted at very high densities in a flow cell, where a very sensitive camera monitors the step by step addition of bases for each sequencing reaction.
In the new paper, Quake and colleagues report how the machine generated enough data to cover the 3-billion base human genome 28 times over. That sequence data consisted of short stretches of sequences 24 to 70 bases long, which were compared with the reference human genome sequence in public databases to piece together Quake’s own genome.
The demonstration brings “plug and play” sequencing one step closer to reality, wherein individual labs will be able to do what today is accomplished primarily in large sequencing centers. “This is the main coming out party for the Helicos machine,” says Jeffery Schloss of the National Human Genome Research Institute in Bethesda, Maryland.
However, the machines cost $1 million. That’s several times the price of other sequencing machines, notes Schloss. While such machines hint at a future where individual labs sequence large genomes, Schloss emphasizes that large centers will continue to play a role in improving technologies and their uses and developing analytical tools for genome projects.
— Elizabeth Pennisi
Friday, February 20, 2009
Scientists unravel Neanderthal genome
http://www.guardian.co.uk/science/2009/feb/12/neaderthal-genomeScientists unravel Neanderthal genome
Extraordinary feat will shed light on what it means to be human
Ian Sample, Chicago
Thursday 12 February 2009
Scientists have unravelled the genetic make-up of the Neanderthal, the long-faced, barrel-chested relative of modern humans.
Anthropologists analysed more than a billion fragments of ancient DNA plucked from three Croatian fossils to reconstruct a first draft of the Neanderthal genome.
The extraordinary feat gives scientists an unprecedented opportunity to clarify the evolutionary relationship between humans and Neanderthals that may ultimately shed light on the great mystery of how we became the most formidable species on the planet.
Neanderthals were the closest relatives of modern living humans. They lived in Europe and Asia until they became extinct around 30,000 years ago. The reason they died out is not clear, but likely factors are dramatic swings in the climate that affected the availability of food, and competition with early humans.
By comparing the genomes of modern humans with Neanderthals and chimps, scientists hope to unravel the genetic differences that define what it is to be human.
The Neanderthal genome was built up from strands of DNA, most of which came from a 38,000-year-old fossilised leg bone unearthed in a cave in Vindija, Croatia. Other material came from older remains dating back 70,000 years. Together, the fragments make up more than 60% of the Neanderthal genome.
Svante Pääbo, who led the project at the Max Planck Institute for Evolutionary Biology in Leipzig, Germany, said the team would spend the rest of the year analysing the DNA. They will focus on genes linked to modern human evolution, such as FOXP2, which is involved in speech and language.
The draft genome was announced at the American Association for the Advancement of Science meeting in Chicago.
Two years ago, the same group used the ancient DNA to pinpoint the moment, about 500,000 years ago, when modern humans split from Neanderthals.
The analysis should clear up once and for all the ongoing debate as to whether Neanderthals and modern humans continued to mate with each other after separating along the path of evolution.
Remains of Neanderthals dating back to 400,000 years ago suggest they were proficient at crafting basic tools and weapons and buried their dead. The last Neanderthals died out shortly after Homo sapiens migrated to Europe and settled.
Neanderthals were stocky and well-adapted to a cold climate, with brains that were on average larger than those of modern humans. Some fossil evidence suggests they were occasionally cannibalistic, though they more commonly hunted large animals including horses and mammoths.
Thursday, December 20, 2007
Synthetic DNA on the Brink of New Life Forms
http://www.washingtonpost.com/wp-dyn/content/article/2007/12/16/AR2007121601900.html
Synthetic DNA on the Brink of Yielding New Life Forms
By Rick Weiss
Washington Post Staff Writer
Monday, December 17, 2007; A01
It has been 50 years since scientists first created DNA in a test tube, stitching ordinary chemical ingredients together to make life's most extraordinary molecule. Until recently, however, even the most sophisticated laboratories could make only small snippets of DNA -- an extra gene or two to be inserted into corn plants, for example, to help the plants ward off insects or tolerate drought.
Now researchers are poised to cross a dramatic barrier: the creation of life forms driven by completely artificial DNA.
Scientists in Maryland have already built the world's first entirely handcrafted chromosome -- a large looping strand of DNA made from scratch in a laboratory, containing all the instructions a microbe needs to live and reproduce.
In the coming year, they hope to atransplant it into a cell, where it is expected to "boot itself up," like software downloaded from the Internet, and cajole the waiting cell to do its bidding. And while the first synthetic chromosome is a plagiarized version of a natural one, others that code for life forms that have never existed before are already under construction.
The cobbling together of life from synthetic DNA, scientists and philosophers agree, will be a watershed event, blurring the line between biological and artificial -- and forcing a rethinking of what it means for a thing to be alive.
"This raises a range of big questions about what nature is and what it could be," said Paul Rabinow, an anthropologist at the University of California at Berkeley who studies science's effects on society. "Evolutionary processes are no longer seen as sacred or inviolable. People in labs are figuring them out so they can improve upon them for different purposes."
That unprecedented degree of control over creation raises more than philosophical questions, however. What kinds of organisms will scientists, terrorists and other creative individuals make? How will these self-replicating entities be contained? And who might end up owning the patent rights to the basic tools for synthesizing life?
Some experts are worried that a few maverick companies are already gaining monopoly control over the core "operating system" for artificial life and are poised to become the Microsofts of synthetic biology. That could stifle competition, they say, and place enormous power in a few people's hands.
"We're heading into an era where people will be writing DNA programs like the early days of computer programming, but who will own these programs?" asked Drew Endy, a scientist at the Massachusetts Institute of Technology.
At the core of synthetic biology's new ascendance are high-speed DNA synthesizers that can produce very long strands of genetic material from basic chemical building blocks: sugars, nitrogen-based compounds and phosphates.
Today a scientist can write a long genetic program on a computer just as a maestro might compose a musical score, then use a synthesizer to convert that digital code into actual DNA. Experiments with "natural" DNA indicate that when a faux chromosome gets plopped into a cell, it will be able to direct the destruction of the cell's old DNA and become its new "brain" -- telling the cell to start making a valuable chemical, for example, or a medicine or a toxin, or a bio-based gasoline substitute.
Unlike conventional biotechnology, in which scientists induce modest genetic changes in cells to make them serve industrial purposes, synthetic biology involves the large-scale rewriting of genetic codes to create metabolic machines with singular purposes.
"I see a cell as a chassis and power supply for the artificial systems we are putting together," said Tom Knight of MIT, who likes to compare the state of cell biology today to that of mechanical engineering in 1864. That is when the United States began to adopt standardized thread sizes for nuts and bolts, an advance that allowed the construction of complex devices from simple, interchangeable parts.
If biology is to morph into an engineering discipline, it is going to need similarly standardized parts, Knight said. So he and colleagues have started a collection of hundreds of interchangeable genetic components they call BioBricks, which students and others are already popping into cells like Lego pieces.
So far, synthetic biology is still semi-synthetic, involving single-cell organisms such as bacteria and yeast that have a blend of natural and synthetic DNA. The cells can reproduce, a defining trait of life. But in many cases that urge has been genetically suppressed, along with other "distracting" biological functions, to maximize productivity.
"Most cells go about life like we do, with the intention to make more of themselves after eating," said John Pierce, a vice president at DuPont in Wilmington, Del., a leader in the field. "But what we want them to do is make stuff we want."
J. Craig Venter, chief executive of Synthetic Genomics in Rockville, knows what he wants his cells to make: ethanol, hydrogen and other exotic fuels for vehicles, to fill a market that has been estimated to be worth $1 trillion.
In a big step toward that goal, Venter has now built the first fully artificial chromosome, a strand of DNA many times longer than anything made by others and laden with all the genetic components a microbe needs to get by.
Details of the process are under wraps until the work is published, probably early next year. But Venter has already shown that he can insert a "natural" chromosome into a cell and bring it to life. If a synthetic chromosome works the same way, as expected, the first living cells with fully artificial genomes could be growing in dishes by the end of 2008.
The plan is to mass-produce a plain genetic platform able to direct the basic functions of life, then attach custom-designed DNA modules that can compel cells to make synthetic fuels or other products.
It will be a challenge to cultivate fuel-spewing microbes, Venter acknowledged. Among other problems, he said, is that unless the fuel is constantly removed, "the bugs will basically pickle themselves."
But the hurdles are not insurmountable. LS9 Inc., a company in San Carlos, Calif., is already using E. coli bacteria that have been reprogrammed with synthetic DNA to produce a fuel alternative from a diet of corn syrup and sugar cane. So efficient are the bugs' synthetic metabolisms that LS9 predicts it will be able to sell the fuel for just $1.25 a gallon.
At a DuPont plant in Tennessee, other semi-synthetic bacteria are living on cornstarch and making the chemical 1,3 propanediol, or PDO. Millions of pounds of the stuff are being spun and woven into high-tech fabrics (DuPont's chief executive wears a pinstripe suit made of it), putting the bug-begotten chemical on track to become the first $1 billion biotech product that is not a pharmaceutical.
Engineers at DuPont studied blueprints of E. coli's metabolism and used synthetic DNA to help the bacteria make PDO far more efficiently than could have been done with ordinary genetic engineering.
"If you want to sell it at a dollar a gallon . . . you need every bit of efficiency you can muster," said DuPont's Pierce. "So we're running these bugs to their limits."
Yet another application is in medicine, where synthetic DNA is allowing bacteria and yeast to produce the malaria drug artemisinin far more efficiently than it is made in plants, its natural source.
Bugs such as these will seem quaint, scientists say, once fully synthetic organisms are brought on line to work 24/7 on a range of tasks, from industrial production to chemical cleanups. But the prospect of a flourishing synbio economy has many wondering who will own the valuable rights to that life.
In the past year, the U.S. Patent and Trademark Office has been flooded with aggressive synthetic-biology claims. Some of Venter's applications, in particular, "are breathtaking in their scope," said Knight. And with Venter's company openly hoping to develop "an operating system for biologically-based software," some fear it is seeking synthetic hegemony.
"We've asked our patent lawyers to be reasonable and not to be overreaching," Venter said. But competitors such as DuPont, he said, "have just blanketed the field with patent applications."
Safety concerns also loom large. Already a few scientists have made viruses from scratch. The pending ability to make bacteria -- which, unlike viruses, can live and reproduce in the environment outside of a living body -- raises new concerns about contamination, contagion and the potential for mischief.
"Ultimately synthetic biology means cheaper and widely accessible tools to build bioweapons, virulent pathogens and artificial organisms that could pose grave threats to people and the planet," concluded a recent report by the Ottawa-based ETC Group, one of dozens of advocacy groups that want a ban on releasing synthetic organisms pending wider societal debate and regulation.
"The danger is not just bio-terror but bio-error," the report says.
Many scientists say the threat has been overblown. Venter notes that his synthetic genomes are spiked with special genes that make the microbes dependent on a rare nutrient not available in nature. And Pierce, of DuPont, says the company's bugs are too spoiled to survive outdoors.
"They are designed to grow in a cosseted environment with very high food levels," Pierce said. "You throw this guy out on the ground, he just can't compete. He's toast."
"We've heard that before," said Jim Thomas, ETC Group's program manager, noting that genes engineered into crops have often found their way into other plants despite assurances to the contrary. "The fact is, you can build viruses, and soon bacteria, from downloaded instructions on the Internet," Thomas said. "Where's the governance and oversight?"
In fact, government controls on trade in dangerous microbes do not apply to the bits of DNA that can be used to create them. And while some industry groups have talked about policing the field themselves, the technology is quickly becoming so simple, experts say, that it will not be long before "bio hackers" working in garages will be downloading genetic programs and making them into novel life forms.
"The cat is out of the bag," said Jay Keasling, chief of synthetic biology at the University of California at Berkeley.
Andrew Light, an environmental ethicist at the University of Washington in Seattle, said synthetic biology poses a conundrum because of its double-edged ability to both wreak biological havoc and perhaps wean civilization from dirty 20th-century technologies and petroleum-based fuels.
"For the environmental community, I think this is going to be a really hard choice," Light said.
Depending on how people adjust to the idea of man-made life -- and on how useful the first products prove to be -- the field could go either way, Light said.
"It could be that synthetic biology is going to be like cellphones: so overwhelming and ubiquitous that no one notices it anymore. Or it could be like abortion -- the kind of deep disagreement that will not go away."
The question, if the abortion model holds, is which side of the synthetic biology debate will get to call itself "pro-life."
Synthetic DNA on the Brink of Yielding New Life Forms
By Rick Weiss
Washington Post Staff Writer
Monday, December 17, 2007; A01
It has been 50 years since scientists first created DNA in a test tube, stitching ordinary chemical ingredients together to make life's most extraordinary molecule. Until recently, however, even the most sophisticated laboratories could make only small snippets of DNA -- an extra gene or two to be inserted into corn plants, for example, to help the plants ward off insects or tolerate drought.
Now researchers are poised to cross a dramatic barrier: the creation of life forms driven by completely artificial DNA.
Scientists in Maryland have already built the world's first entirely handcrafted chromosome -- a large looping strand of DNA made from scratch in a laboratory, containing all the instructions a microbe needs to live and reproduce.
In the coming year, they hope to atransplant it into a cell, where it is expected to "boot itself up," like software downloaded from the Internet, and cajole the waiting cell to do its bidding. And while the first synthetic chromosome is a plagiarized version of a natural one, others that code for life forms that have never existed before are already under construction.
The cobbling together of life from synthetic DNA, scientists and philosophers agree, will be a watershed event, blurring the line between biological and artificial -- and forcing a rethinking of what it means for a thing to be alive.
"This raises a range of big questions about what nature is and what it could be," said Paul Rabinow, an anthropologist at the University of California at Berkeley who studies science's effects on society. "Evolutionary processes are no longer seen as sacred or inviolable. People in labs are figuring them out so they can improve upon them for different purposes."
That unprecedented degree of control over creation raises more than philosophical questions, however. What kinds of organisms will scientists, terrorists and other creative individuals make? How will these self-replicating entities be contained? And who might end up owning the patent rights to the basic tools for synthesizing life?
Some experts are worried that a few maverick companies are already gaining monopoly control over the core "operating system" for artificial life and are poised to become the Microsofts of synthetic biology. That could stifle competition, they say, and place enormous power in a few people's hands.
"We're heading into an era where people will be writing DNA programs like the early days of computer programming, but who will own these programs?" asked Drew Endy, a scientist at the Massachusetts Institute of Technology.
At the core of synthetic biology's new ascendance are high-speed DNA synthesizers that can produce very long strands of genetic material from basic chemical building blocks: sugars, nitrogen-based compounds and phosphates.
Today a scientist can write a long genetic program on a computer just as a maestro might compose a musical score, then use a synthesizer to convert that digital code into actual DNA. Experiments with "natural" DNA indicate that when a faux chromosome gets plopped into a cell, it will be able to direct the destruction of the cell's old DNA and become its new "brain" -- telling the cell to start making a valuable chemical, for example, or a medicine or a toxin, or a bio-based gasoline substitute.
Unlike conventional biotechnology, in which scientists induce modest genetic changes in cells to make them serve industrial purposes, synthetic biology involves the large-scale rewriting of genetic codes to create metabolic machines with singular purposes.
"I see a cell as a chassis and power supply for the artificial systems we are putting together," said Tom Knight of MIT, who likes to compare the state of cell biology today to that of mechanical engineering in 1864. That is when the United States began to adopt standardized thread sizes for nuts and bolts, an advance that allowed the construction of complex devices from simple, interchangeable parts.
If biology is to morph into an engineering discipline, it is going to need similarly standardized parts, Knight said. So he and colleagues have started a collection of hundreds of interchangeable genetic components they call BioBricks, which students and others are already popping into cells like Lego pieces.
So far, synthetic biology is still semi-synthetic, involving single-cell organisms such as bacteria and yeast that have a blend of natural and synthetic DNA. The cells can reproduce, a defining trait of life. But in many cases that urge has been genetically suppressed, along with other "distracting" biological functions, to maximize productivity.
"Most cells go about life like we do, with the intention to make more of themselves after eating," said John Pierce, a vice president at DuPont in Wilmington, Del., a leader in the field. "But what we want them to do is make stuff we want."
J. Craig Venter, chief executive of Synthetic Genomics in Rockville, knows what he wants his cells to make: ethanol, hydrogen and other exotic fuels for vehicles, to fill a market that has been estimated to be worth $1 trillion.
In a big step toward that goal, Venter has now built the first fully artificial chromosome, a strand of DNA many times longer than anything made by others and laden with all the genetic components a microbe needs to get by.
Details of the process are under wraps until the work is published, probably early next year. But Venter has already shown that he can insert a "natural" chromosome into a cell and bring it to life. If a synthetic chromosome works the same way, as expected, the first living cells with fully artificial genomes could be growing in dishes by the end of 2008.
The plan is to mass-produce a plain genetic platform able to direct the basic functions of life, then attach custom-designed DNA modules that can compel cells to make synthetic fuels or other products.
It will be a challenge to cultivate fuel-spewing microbes, Venter acknowledged. Among other problems, he said, is that unless the fuel is constantly removed, "the bugs will basically pickle themselves."
But the hurdles are not insurmountable. LS9 Inc., a company in San Carlos, Calif., is already using E. coli bacteria that have been reprogrammed with synthetic DNA to produce a fuel alternative from a diet of corn syrup and sugar cane. So efficient are the bugs' synthetic metabolisms that LS9 predicts it will be able to sell the fuel for just $1.25 a gallon.
At a DuPont plant in Tennessee, other semi-synthetic bacteria are living on cornstarch and making the chemical 1,3 propanediol, or PDO. Millions of pounds of the stuff are being spun and woven into high-tech fabrics (DuPont's chief executive wears a pinstripe suit made of it), putting the bug-begotten chemical on track to become the first $1 billion biotech product that is not a pharmaceutical.
Engineers at DuPont studied blueprints of E. coli's metabolism and used synthetic DNA to help the bacteria make PDO far more efficiently than could have been done with ordinary genetic engineering.
"If you want to sell it at a dollar a gallon . . . you need every bit of efficiency you can muster," said DuPont's Pierce. "So we're running these bugs to their limits."
Yet another application is in medicine, where synthetic DNA is allowing bacteria and yeast to produce the malaria drug artemisinin far more efficiently than it is made in plants, its natural source.
Bugs such as these will seem quaint, scientists say, once fully synthetic organisms are brought on line to work 24/7 on a range of tasks, from industrial production to chemical cleanups. But the prospect of a flourishing synbio economy has many wondering who will own the valuable rights to that life.
In the past year, the U.S. Patent and Trademark Office has been flooded with aggressive synthetic-biology claims. Some of Venter's applications, in particular, "are breathtaking in their scope," said Knight. And with Venter's company openly hoping to develop "an operating system for biologically-based software," some fear it is seeking synthetic hegemony.
"We've asked our patent lawyers to be reasonable and not to be overreaching," Venter said. But competitors such as DuPont, he said, "have just blanketed the field with patent applications."
Safety concerns also loom large. Already a few scientists have made viruses from scratch. The pending ability to make bacteria -- which, unlike viruses, can live and reproduce in the environment outside of a living body -- raises new concerns about contamination, contagion and the potential for mischief.
"Ultimately synthetic biology means cheaper and widely accessible tools to build bioweapons, virulent pathogens and artificial organisms that could pose grave threats to people and the planet," concluded a recent report by the Ottawa-based ETC Group, one of dozens of advocacy groups that want a ban on releasing synthetic organisms pending wider societal debate and regulation.
"The danger is not just bio-terror but bio-error," the report says.
Many scientists say the threat has been overblown. Venter notes that his synthetic genomes are spiked with special genes that make the microbes dependent on a rare nutrient not available in nature. And Pierce, of DuPont, says the company's bugs are too spoiled to survive outdoors.
"They are designed to grow in a cosseted environment with very high food levels," Pierce said. "You throw this guy out on the ground, he just can't compete. He's toast."
"We've heard that before," said Jim Thomas, ETC Group's program manager, noting that genes engineered into crops have often found their way into other plants despite assurances to the contrary. "The fact is, you can build viruses, and soon bacteria, from downloaded instructions on the Internet," Thomas said. "Where's the governance and oversight?"
In fact, government controls on trade in dangerous microbes do not apply to the bits of DNA that can be used to create them. And while some industry groups have talked about policing the field themselves, the technology is quickly becoming so simple, experts say, that it will not be long before "bio hackers" working in garages will be downloading genetic programs and making them into novel life forms.
"The cat is out of the bag," said Jay Keasling, chief of synthetic biology at the University of California at Berkeley.
Andrew Light, an environmental ethicist at the University of Washington in Seattle, said synthetic biology poses a conundrum because of its double-edged ability to both wreak biological havoc and perhaps wean civilization from dirty 20th-century technologies and petroleum-based fuels.
"For the environmental community, I think this is going to be a really hard choice," Light said.
Depending on how people adjust to the idea of man-made life -- and on how useful the first products prove to be -- the field could go either way, Light said.
"It could be that synthetic biology is going to be like cellphones: so overwhelming and ubiquitous that no one notices it anymore. Or it could be like abortion -- the kind of deep disagreement that will not go away."
The question, if the abortion model holds, is which side of the synthetic biology debate will get to call itself "pro-life."
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