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Scientists develop synthetic genome

Hydrogen

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A very interesting topic and worth the read. The legal and ethical issues are to be the type that will enrage and terrify a considerable segment of the population (particularly the patenting issues).
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Scientists develop synthetic genome

CAROLYN ABRAHAM
Globe and Mail Update
January 24, 2008 at 6:04 PM EST

If you thought that designing life was the sole domain of nature or a divine power – think again.

A team of U.S. scientists is reporting that it has constructed the genome of a living organism for the first time. Assembling bits of lab-made DNA, researchers at the J. Craig Venter Institute in Maryland say they have built the genetic structure of a bacterium from scratch in the lab.

The feat marks an historic, and controversial, milestone in the fledgling field known as synthetic biology. It uses chunks of synthetic DNA like Lego blocks, with an aim to creating life forms that can be genetically programmed to perform useful tasks.

Its proponents envision making micro-organisms that gobble up pollution, produce hard-to-make drugs, pump out clean energy, or, at the whimsical end, flowers designed to bloom on your birthday.

The field has raised profound ethical questions about human control of creation and its potential to produce new weapons of bio-terror. But the Venter project is also drawing criticisms of a different kind.

Bio-ethicists, and some scientists, allege the researchers have applied for such broad patents on their human-made genome that, if granted, they might give the group a monopoly on the making of all synthetic life forms – which some believe will fuel the next industrial revolution.

Until now, researchers had not crossed the technical barriers of putting together the whole DNA sequence of a single living organism, or even stretches of genetic code nearly 20 times smaller. But in a paper published online by the journal Science yesterday, the Venter group says it has done exactly that with Mycoplasma genitalium, a bacterium common to the human reproductive tract.

“It's the largest molecule made by humans… we don't know if there is an upper limit now,†said co-author J. Craig Venter, the upstart U.S. biologist and businessman who heads the not-for-profit institute. “The broader implications of this work have not been missed by us – we could enter into a new design phase of biology.â€

The lab-made genome has not so far resulted in a living microbe that functions or replicates. But Dr. Venter said it is just a matter of time before they figure out how “to boot it up†by inserting the synthetic DNA into the shell of another bacterium. (The team showed last year that transplanting the genome of one bacterium inside the casing of another could bring it to life.)

“It is not just a slam dunk or we would be announcing it today,†Dr. Venter acknowledged. “There's multiple steps we have to overcome … but we are confident that they can be overcome. I will be equally surprised and disappointed if we can't do it in 2008.â€

Dr. Venter, who also launched a company in 2005 called Synthetic Genomics, has received a multimillion-dollar grant from the U.S. Department of Energy to find a clean energy source, possibly from microbes. But he said the current version of the M. genitalium genome will not be the template for that project.

With advances in computer technology, making bits of DNA from scratch has become relatively easy and cheap in recent years. Even amateurs can type up genetic code with keystrokes, e-mail it to a commercial lab that spits it out as chemical dots on a glass sheet, synthesizes it, tucks it into a bacteria for transport and returns a live version to the customer.

In the wake of the Venter group announcement, the ETC Group, a Canadian-based bioethics watchdog, dubbed the lab-made genome “Synthia†and distributed a statement calling the work “unacceptable.â€

“While synthetic biology is speeding ahead in the lab and in the marketplace … there has been no meaningful or inclusive discussion on how to govern synthetic biology in a safe and just way,†said group member Jim Thomas. “In the absence of democratic oversight, profiteering industrialists are tinkering with the building blocks of life for their own private gain.â€

Dr. Venter, who mapped a private version of the human genome in 2000 and last fall became the first person to have his DNA fully sequenced, is no stranger to controversy and flatly rejected the accusation that social debate has been skimpy.

Before his group published the assembly of a viral genome in 2003, Dr. Venter said there were extensive discussions and reviews with bio-ethicists, the National Academy of Sciences and “every branch of the (U.S.) government.†Given fears that the work could be misused to build novel pathogens, Dr. Venter said the government thought about blocking its publication, but ultimately decided to move the research forward and keep the technology in the public domain.

Different groups, and corporations, have used synthetic biology to construct new genes that do not exist in nature. But the longer the stretch of genetic code researchers try to assemble, the more brittle DNA becomes.

The Venter group, which began its work in 1995, opted to assemble a small bug, initially to build the leanest genome possible and determine which genes are essential for life. M. genitalium contains just one circular-shaped chromosome, 517 genes and some 583,000 nucleotides, the chemical units that make up DNA. The largest lab-made DNA previous to this was about 32,000 nucleotides long.

During a news conference yesterday, the researchers, led by Nobel Laureate Hamilton Smith, described the assembly as though it were a laborious jigsaw puzzle that “started with four bottles.†Those bottles refer to the four nucleotide chemicals contained in DNA – adenine, cytosine, guanine and thymine, usually represented by the letters A,C,G and T.

The genome – the natural version of which the group had already sequenced – was then divided into 101 pieces, Dr. Smith said. Those pieces were then synthesized at three different commercial labs before the group figured out a multi-step process for putting them all together. Dr. Venter noted that having commercial labs synthesize the pieces cost less than a dollar for each base pair of nucleotides.

Robert Holt, a scientist at the Genome Science Centre of the BC Cancer Agency, and a former collaborator with the Venter group, called the report “an important technical accomplishment†because the size of the DNA molecule constructed dwarfs previous efforts.

“While they haven't yet shown that their synthetic Mycoplasma genome is functional … it is now feasible to activate a genome by inserting it into an existing cell of the same or closely related organism.â€

Ensuring the synthetic genome does not essentially reject its host shell is among the hurdles researchers have described.

Stephen Davies, an assistant professor of biomaterials and biomedical engineering at the University of Toronto, said the work could well be a template for others.

“It's not rocket science that they have done. Rather their achievement is to be the first to build something this large. This was done through a judicious selection of methods to address the barriers they encountered along the way,†said Prof. Davies, who works in the synthetic biology field.

“Their work clearly demonstrates a way to make whole genomes with good yields … it would make sense for others to follow this process…â€

But the ETC Group has likened the Venter group's patent applications to “a bid for extreme monopoly†that could stymie the field.

Prof. Davies said the controversy stems in part from the fact that pioneers of synthetic biology, particularly at the Massachusetts Institute of Technology, have pushed the new science as an “open-source†technology, with genetic code freely available online. But, he added, it is essentially an engineering field, where patenting is commonplace.

It could be, said Prof. Davies, that the methods of making synthetic organisms should not be patented, only their commercial applications.

Dr. Venter dismissed the allegation of a monopoly grab yesterday, arguing that protecting intellectual property is the norm and lifeblood of most other industries. He said his group would be willing to license its technologies and that there could be other methods to do the work.
 

afransen

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I'm sure the mainstream media will have a hard time moving past the 'playing God' debate.
 

Prometheus The Supremo

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i read about this yesterday. amazing! imagine creating a bacteria that eats (whatever) and craps out hydrogen? (not the UT member hydrogen but the fuel)
all of a sudden, hydrogen would become economically viable to produce and we can start moving toward hydrogen cars, etc. imagine being able to program the bacteria to die of after a period of time and to have gene that will only allow a certain amount of generations to be spawned so as to keep it in check. imagine creating a virus that eats HIV, cancerous tissue, other viruses, etc!


of course the technology can be used for evil but this is why we have to develop it first. if a dangerous country develops a virus that can turn our brains to liquid shit, if we are experienced in creating life, we can create a virus that will eat their virus.

i think the greatest issue would be keeping evolution in check. hopefully they can create a gene that says if "mutation takes place = self destruct".


p.s, does this technically make craig venter god? i know the church is going to be against this, but why? how much more pro-life can you get? :p
 

Mongo

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I'm sure the mainstream media will have a hard time moving past the 'playing God' debate.

If people start using that argument, then it should be pointed out that we have been 'playing God' for thousands of years. Almost every variety of domestic animal on Earth is the result of thousands of generations of selective breeding, and bears very little resemblance to their wild ancestors (i.e. basset hounds and wolves). The same is true (perhaps even more so) with domesticated plants -- for example, modern maize (corn) looks nothing like its ancestor, teosinte.

It is true that this technology opens the door to potential danger. I dread the day when small terrorist groups, or wealthy but deranged individuals, will be able to create 'designer plagues'. But if the research is suppressed here, it will only be done in places beyond our control. Out best chance to survive in my opinion is to push ahead with all necessary research, and hope that when the engineered plagues are released (which I am sure WILL happen at some point) the ability exists to contain and eliminate them as they happen.

I expect that in a few decades, we will see something like the current internet malware environment, with new bugs being released all the time, but an artificial 'immune system' looking for new bugs and counteracting them when found.

Bill
 

Hydrogen

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i read about this yesterday. amazing! imagine creating a bacteria that eats (whatever) and craps out hydrogen? (not the UT member hydrogen but the fuel)

:D


What is also interesting is how this branch of biology now appears as a branch if information processing. I find this blending of metaphors fascinating. Much more so than the "playing god" thing that will inevitable pop up.
 

Prometheus The Supremo

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:D


What is also interesting is how this branch of biology now appears as a branch if information processing. I find this blending of metaphors fascinating. Much more so than the "playing god" thing that will inevitable pop up.

a human is nothing more than +/- 6GB of data. LOL! remember that scene in casino where they put that guys head in a vice? were they trying to winzip him?
 

Prometheus The Supremo

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Maybe, but I think the result was some considerable data corruption.

maybe they should have used winrar instead?


p.s, future sex ed.....

the man inserts his floppy into the females slot. he then proceeds to transfer data at a upload rate of 370mb a second. there is considerable packet loss but a few bytes find their way in the form of 1sperm.exe. the woman then knows if the transfer is complete and some data has been written to her disk by TCP/IP'ing onto a device. if it turns blue that means the upload was successful. 9 months later a human is downloaded from uterus. of course, if you want to prevent a download, use copy protection or pull out the floppy before the data transfer starts. don't forget to scan for malware before linking up for data transfer.

:confused:
 

Hydrogen

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the man inserts his floppy into the females slot. he then proceeds to transfer data...

It'll be wireless, broadband, open source...

Let your imagination run wild. ;)
 

Prometheus The Supremo

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adma

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p.s, future sex ed.....

the man inserts his floppy into the females slot. he then proceeds to transfer data at a upload rate of 370mb a second. there is considerable packet loss but a few bytes find their way in the form of 1sperm.exe. the woman then knows if the transfer is complete and some data has been written to her disk by TCP/IP'ing onto a device. if it turns blue that means the upload was successful. 9 months later a human is downloaded from uterus. of course, if you want to prevent a download, use copy protection or pull out the floppy before the data transfer starts. don't forget to scan for malware before linking up for data transfer.

:confused:

And it used to be as simple as this...
 

AlvinofDiaspar

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prometheus:

the man inserts his floppy into the females slot. he then proceeds to transfer data at a upload rate of 370mb a second. there is considerable packet loss but a few bytes find their way in the form of 1sperm.exe. the woman then knows if the transfer is complete and some data has been written to her disk by TCP/IP'ing onto a device. if it turns blue that means the upload was successful. 9 months later a human is downloaded from uterus. of course, if you want to prevent a download, use copy protection or pull out the floppy before the data transfer starts. don't forget to scan for malware before linking up for data transfer.

That's nothing new. Let me quote from Greg Egan's Diaspora, p. 205:

They made love with their almost-traditional bodies - and brains; Paolo was amused to the point of distraction when his limbic system went into overdrive, but he remembered enough from the last occasion to bury his self-consciousness and surrender to the strange hijacker. It wasn't like making love in any civilized fashion - the rate of information exchange between them was minuscule, for a start - but it had the raw, insistent quality of most ancestral pleasure.

Context: Sex between two software-based post-humans, running as simulations of humans in amphibian form.

re: Human being = 6 GB

The size of the genome, yes - but the mechanisms that utilizes, expresses and ultimately got changed by the genome is certainly much bigger than 6GB. Likely in the Exabyte range or more.

re: Venter

As groundbreaking as it maybe, it's still pretty tame - the fundamental system (Genome, protein transcription, etc) are still fundamentally natural in origin. To really push the envelope, one would have to develop alternate biochemical and cellular processes - e.g. DNA with non-ATGC bases, artificial biochemical and biomechanical pathways, etc...that to me would be truly "artificial". What they are doing right now is merely the beginning.

re: Playing God

Like it or not, the Pandora's box is now open - that, along with whole hosts of other exotic technologies (e.g. quantum computation, nanotechology, etc.) will likely change human society fundamentally. While the technology itself is not bad per se, I think we should tread carefully - I am not convinced we (human civilization) are collectively wise enough to wield the powers we are about to receive. Either way, these are interesting times we're living in.

AoD
 

Prometheus The Supremo

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LOL!





re: Human being = 6 GB

The size of the genome, yes - but the mechanisms that utilizes, expresses and ultimately got changed by the genome is certainly much bigger than 6GB. Likely in the Exabyte range or more.

i don't understand. do you mean a living human? the total?

exabyte! is that a million terabytes?



re: Playing God

Like it or not, the Pandora's box is now open - that, along with whole hosts of other exotic technologies (e.g. quantum computation, nanotechology, etc.) will likely change human society fundamentally. While the technology itself is not bad per se, I think we should tread carefully - I am not convinced we (human civilization) are collectively wise enough to wield the powers we are about to receive. Either way, these are interesting times we're living in.


09_frozen.jpg


"Moon Pie.... What a time to be alive!"
 

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