Saturday, May 22, 2010
Sunday, January 27, 2008
Team claims synthetic life feat (July 2007)
Chris Street comments are in bright green;
highlights in yellow blockquotes.
| By Neil Bowdler BBC science reporter |
Scientists in the US say they have taken a major step towards producing life from scratch in the laboratory. 
Dr Craig Venter says in the journal Science that his team successfully transplanted an entire genome from one bacterium cell to another.
He says he hopes eventually to use the technique to create designer microbes, which could produce artificial fuel or help clean up toxic waste.
Dr Venter was a pioneer in mapping the human genome.
Organic tools
The ultimate plan is to stitch together artificial chromosomes, proteins and other building blocks with the aim of jumpstarting their designer microbe to life. But Dr Venter concedes that this may be a long way away, but he says he has taken an important key step towards that goal.
His team, essentially, snatched the body of another life-form and invaded it with a new genetic code.
This, he says, will be a key tool in testing the artificial chromosomes - or DNA bundles - he plans to make.
"What's in this paper is the result of taking a native chromosome from one species," Dr Venter explained.
"That chromosome was transplanted, inserted through the cell walls, the cell membrane of a second species and, after several days of growth and cell division, the original chromosome in the cell disappears and we have cells containing only the transplanted chromosome."
Different views
But there are those who are worried about what Dr Venter is doing.
Some fear the technology could be used to create biological weapons or simply that something unforeseen may emerge from the laboratory.
Others are concerned that his institute's efforts to patent research could restrict scientific advances elsewhere.
But Dr Venter says he is doing nothing that other institutes do not already do.
"Over the last several years we have had to develop novel techniques and approaches that have not existed before because this field has not existed before," he said.
"The Venter Institute and the Synthetic Genomics Company are doing what most major institutions do - that is we file patents on these unique techniques."
Creating life in the laboratory
Chris Street comments are in bright green;
highlights in yellow blockquotes.
| By Rebecca Morelle Science reporter, BBC News |
The race to create life version 2.0 is under way.
And rumours abound that closest to the finish line in constructing a lifeform in the laboratory is US genome-entrepreneur Craig Venter's research team.
The J Craig Venter Institute scientists are aiming to craft a "minimal genome"- the smallest group of genes an organism needs to survive and function - and insert it into an empty cell.
This stripped-down genome has been established with the help of a simple bacterium, Mycoplasma genitalium, by knocking out its genes, one by one, until only the genetic material vital for survival was found.
The plan is to re-synthesise these DNA sequences from simple chemicals, stitch them together and create an artificial organism. Some believe the team may be on the cusp of doing just that. 
Dr Venter's work on synthetic life is described by some as "top-down", meaning that he is taking an existing organism and changing it to create something new.
Drew Endy from the Massachusetts Institute of Technology, US, says:
"Venter is not creating life from scratch.
"He is constructing a genome, which is more or less a slightly modified copy of an existing genome, then putting it back into an existing cell."
Dr Endy, who is working on standard building blocks, called BioBrick parts, which can be assembled to build larger biological systems, says he sees Dr Venter's work as a "genome construction project", albeit "an incredibly significant" one.
But building life from scratch, from the "bottom-up", is a challenge that some synthetic biologists have decided to take on. 
If you can build the biological parts, they argue, then creating something that meets the criteria for life - has a metabolism, replicates and evolves - is surely the next step.
Cell 'blueprint'
Anthony Forster from Vanderbilt University Medical Center, Tennessee, US, says: "There has been a fair amount of talk about how you might synthesise self replication and life in a test tube, but nobody really had a detailed plan for it."
Dr Forster, along with George Church from Harvard Medical School, US, has created a "blueprint" for a synthetic cell, defining the 151 genes that they believe are needed to create life. 
We have abandoned so much of what traditional biology is doing, many biologists view us as heretics 
The team is now in the process of using the blueprint to begin to piece together its prototype cell.
But what are the reasons for creating synthetic life?
Dr Venter hopes to modify genes in his new organism so that it can mop up greenhouse gases. Other tasks such organisms might be able to do include cleaning up oil spills or producing plastics.
Giovanni Murtas, from the Enrico Fermi Centre, University of Rome Three, Italy, plans to build a new lifeform to look at the more fundamental question of the origins of life.
"We are creating these semi-synthetic minimal cells that recall the early living cells," he says. 
So far, his team has successfully built a cell system that can synthesise proteins, which is important for demonstrating that a basic metabolism can be created. Replication is the next step, he explains.
"If you want to understand more about how life was set up, then you want to recreate the principal steps for life; and you can obviously learn something new about life from using this approach," Dr Murtas tells BBC News.
Ron Weiss from Princeton University, US, who is focussing on programming biological organisms, believes the technology could also have biomedical applications.
"One thing people are trying to do is to use cells as factories to make drugs or fabricate structures," he says.
New take on life
The top-down and bottom-up teams have something in common: they are mimicking what nature does already. Some scientists, though, have gone back to the drawing broad in their quest to produce synthetic life.
Steen Rasmussen from Los Alamos National Laboratory, US, is one of them.
"We are the radical kids on the block. We have abandoned so much of what traditional biology is doing. Many biologists view us as heretics," he says. The biggest challenge is not necessarily creating life, but knowing that you have created life
Rather than turning to biological cell design as his starting point, Dr Rasmussen is looking to see if there might be simpler structures that he can use as the basis of his synthetic organism.
He is creating a cell in which the essential parts, such as genes and metabolic chemicals, are stuck to the surface of it rather than held inside like a traditional cell.
He says: "This means you can exchange resources and waste directly with the environment and that simplifies things enormously."
Synthetic biologists think that although life created by a top-down approach may be imminent, synthetic life built from the bottom up is a few more years away - at least five to 10. 
However, George Attard from Southampton University, UK, adds a word or two of caution.
"The biggest challenge is not necessarily creating life, but knowing that you have created life - doing the experiment that unambiguously tells you that you've got it," he says.
"That's because you are going to be looking at a 'soup' that contains several hundred, possibly several thousand, chemical species. How on Earth can you tell that what you have isn't just a chemical waste bottle but something that is exhibiting the signs of life?"
Synthetic life 'advance' reported
Chris Street comments are in bright green;
highlights in yellow blockquotes.
| By Helen Briggs Science reporter, BBC News |
An important step has been taken in the quest to create a synthetic lifeform. 
A US team reports in Science magazine how it built the entire DNA code of a common bacterium in the laboratory using blocks of genetic material.
The group hopes eventually to use engineered genomes to make organisms that can produce clean fuels and take carbon dioxide out of the atmosphere.
Publication of the research gives others the chance to scrutinise it. Some have ethical concerns.
It sets the stage for what we hope is going to be a new approach to engineering organisms 
These critics have been calling for several years now for a debate on the risks of creating "artificial life" in a test tube.
But Dr Hamilton Smith, who was part of the Science study, said the team regarded its lab-made genome - a laboratory copy of the DNA used by the bacterium Mycoplasma genitalium - as a step towards synthetic, rather than artificial, life.
He told BBC News: "We like to distinguish synthetic life from artificial life.
"With synthetic life, we're re-designing the cell chromosomes; we're not creating a whole new artificial life system."
Gene cassettes
The team of 17 scientists constructed the bacterial genome by chemically synthesising small blocks of DNA.
These were grown up in a bacterium, and knitted together into bigger pieces, so-called "cassettes" of genes.
The researchers ended up with several large chunks of DNA that were joined to make the circular genome of a synthetic version of Mycoplasma genitalium.
They have named it Mycoplasma JCVI-1.0, after their research centre, the J Craig Venter Institute in Rockville, MD, US.
Dr Craig Venter, who was involved in the race to decode the human genome, believes tailor-made micro-organisms can become efficient producers of non-polluting fuels such as hydrogen. Other synthetic bacteria could be made to take up greenhouse gases, he believes.
"It sets the stage for what we hope is going to be a new approach to engineering organisms," said co-researcher Dr Smith.
Operating systems
To achieve this goal, the researchers must overcome a crucial, and tricky, obstacle.
They must transplant the synthetic genome into another cell so that it can use the existing machinery to "boot up" and start growing and reproducing.
| STEPS TO SYNTHETIC LIFE 2002: synthetic virus created - a lab version of polio 2007: a genome from one cell is placed in another 2008: publication of synthetic genome study |
"We're simply re-writing the operating software for cells - we're not designing a genome from the bottom up - you can't drop a genome into a test tube and expect it to come to life," he added.
This is the stage which raises the most concern among critics, and where a new lifeform could be said to be truly created. How precisely will it behave? What will its impact be on other organisms and the environment? Some say it is a step too far, but others argue that the new field of synthetic biology is an important science.
Even bigger
The UK's Royal Society is seeking views from the public on the issue.
Adviser on synthetic biology, Dr Jason Chin, said the increasing ability to design and construct DNA sequences would, in principle, allow the construction of organisms for particular purposes, such as biofuels production.
He added: "Understanding how you construct organisms artificially is an important first step. But scientists still need to understand what effect altering the DNA sequence of an organism - such as bacteria - will have upon their behaviour."
Dr Drew Endy of the Department of Biological Engineering at Massachusetts Institute of Technology, US, said that re-constructing a natural bacterial genome from scratch was a great technical feat.
He said genomes 10 times larger than Mycoplasma JCVI-1.0 had already been assembled from existing DNA fragments by a Japanese group.
Dr Endy added: "Given the work already done in Japan, building genomes almost 10 million base-pairs long - I would be surprised if by 2012 it were not technically possible to routinely design and construct the genomes of any bacteria or single celled eukaryote, which also means that it will be possible to construct some mammalian chromosomes."
Dr Simon Woods, a bio-ethicist at the Policy, Ethics and Life Sciences Research Centre at the University of Newcastle, UK, said scientists were acting in a regulatory vacuum.
"On the one hand it's an amazing piece of science but the real concern is that it's another example of science delving into matters that have potentially dangerous consequences," he said.
"It's not necessarily going to stay in the hands of well-intentioned scientists."
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CREATING A SYNTHETIC GENOME
In 2007, scientists put genome from one organism into cell of another, taking over cell's machinery.
Bacterial synthetic genome was built up chemically by sewing together short DNA segments.
Synthetic genome to be put (1) into cell, reproduce and (2) create plants for biofuels and petrochemical substitutes.
Thursday, October 25, 2007
Synthetic life 'no terror threat'
Scientist Craig Venter on his latest project
| By Cristina Jimenez Science reporter |
Synthetic biology can help in the fight against emerging infections, rather than aid the design of bioweapons, controversial scientist Craig Venter has told reporters.
The US scientist, who led the private sector race to map the human genome, used a briefing in central London to allay fears that his work may fall into the wrong hands.
Critics of Dr Venter's research, which aims to design the world's first synthetic life, have expressed concern.
They say that artificial microbes may have dangerous consequences, such as either escaping into the environment or being used to manufacture bioweapons.
"If Venter succeeds in creating a working bacteria then he also lifts the lid on creating bacterial bioweapons, such as anthrax, in the near future," said Jim Thomas of the ETC Group, a Canadian campaign group that has concerns over the development of genetic technology.
When there is a big shift of knowledge, we go through a cycle of fear, in which people are afraid of the unknown
"An equally real concern in the longer term is bio-error, the synthetic creation of organisms that escape out of our control," he added.
Dr Venter insisted that such worries about synthetic organisms were unfounded.
He maintained that antibiotic-resistant infections, such as MRSA, were much more of a threat.
According to the maverick scientist, synthetic biology could provide the most effective way of stopping infections in developing countries, such as malaria, and emerging drug-resistant superbugs.
"In the US, MRSA kills more people than Aids,"
he said.
Campaigners say that there are currently no international laws or oversight mechanisms to assess the safety of synthetic organisms.
They suggest that an international process is needed to put in place controls before anything is commercialised.
Dr Venter defended himself against any claims that he was exploiting the human genome for financial gain.
"If you look at the record, my institution has no human gene patents, yet my biggest critics do," he said. "The Human Gene Project has human gene patents."
In an effort to explain why his work had attracted so much critical attention, he pointed out that a similar controversy occurred at the beginning of the molecular biology era.
He said: "When there is a big shift of knowledge, we go through a cycle of fear, in which people are afraid of the unknown."