Synthetic Genome Drives Bacterial Cell 174
Dr. Eggman writes "Physorg.com brings us news of a synthetic genome, produced by the J. Craig Venter Institute, being used in an existing bacterial cell for the first time. Using a combination of biological hosts, the technique produces short strings of DNA by machine which are then inserted into yeast to be stitched together via DNA-repair enzymes. The medium sequences are passed into E. coli and back into yeast. After three rounds, a genome of three million base pairs was produced." (More below.)
"Specifically, the genome of M. mycoides was synthesized from scratch. This synthetic genome was then inserted into the cells of a bacteria known as Mycoplasm capricolum. The result is a cell, driven by a synthetic genome, producing not the proteins of Mycoplasm capricolum, but of M. mycoides. The institute has far-reaching plans for its synthetic life program, including designing algae that can capture carbon dioxide, make new hydrocarbons for refineries, make new chemicals or food ingredients, and speed up vaccine production."
The BBC has coverage of the hybrid cell as well.
Take that, IDers! (Score:3, Insightful)
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Re:Take that, IDers! (Score:5, Insightful)
Not that I disagree with your sentiments when it comes to ID proponents (they're morons) but I don't think this really counts as "making life." Not yet, anyway. It's a step in that direction, though.
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Yeah, but it's hard to argue that it will never happen now.
Agreed.
Now, whether that's a good thing or not is somewhat debatable. I can come up with arguments on both sides of that one.
Re:Take that, IDers! (Score:5, Interesting)
Re:Take that, IDers! (Score:4, Insightful)
The grandparent post was modded as flamebait, but the religious flame war is in real life. From the parent's article:
However, with this step forward comes a new set of ethical considerations, say experts. “We need to be critically aware of the profound implications of creating synthetic life,” said Karl Giberson, director of the Forum on Faith and Science at Gordon College in Wenham. “I don’t think this is something to be scared of. I don’t think Mother Nature is being violated in some egregious way. But this is an area of science with important ethical considerations, and religious sensibilities and higher priorities need to be on the table, under discussion.”
It's a pretty moderate response, but even so, it conflates ethics and religion, implying that the ethical decisions should be based on theology. The grandparent is right - this is going to be a culture war thing.
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I don't think you're an artist, a writer, or a programmer. If you are, you need to turn around an look at yourself.
This is a first step into the grey area. Creation isn't an area of sharp divisions. Almost everything worthwhile is based on extensive predecessors. This is taking one kind of cell, and converting it into another (closely related) kind. This *IS* creation. It's not creating all that much, but it's creating a new species. (Whatever that means at the level of yeasts.) The new species has
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It would prove that it doesn't require a divinity to create life. That doesn't demolish the stated premise of ID but it is a blow to the implied premise of ID, namely "We all know that it was Yahweh but came up with this as a roundabout way of not actually saying it."
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Yeah, they left out the word supernatural before creator.
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I'd say it may well be creating life. It's not exactly designing life (and not exactly NOT designing life either...).
Consider:
1) The cell they injected the new DNA into had the old DNA removed first - hence it has dead.
2) The new DNA started out as chemicals in a bottle - certainly dead too.
3) The new DNA put into the cell "rebooted" / reanimated it so that it started dividing again. Certainly back alive now!
This experiment may not LOOK that impressive, but consider that the exact same technique can be used
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Except of course they blindly programmed. They copied the DNA, no more no less. All that they did was prove that a DNA photocopy machine can work. Yup, we knew that years ago. We could make DNA years ag
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I'm not surprised by it either, but it's :
1) A necessary step on one path to creating more interesting types of designer life (from oil producing microbes all the way up to whatever your imagination can conjure up - chickens turned back into dinosaurs, etc)
2) Certainly significant to those who do think that life is something magical and not merely a systems property.
Incidently, what Craig Venter is really working is a minimal organism whose DNA started out as that of some simple bacteria (from a venereal di
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I agree that it is unsurprising in that it has long been obvious that we could and eventually would be able to create synthetic life passing any arbitrary bar anyone wanted to set on defining "creating synthetic life". Or at least, it has long been obvious to anyone familiar with science and who is not blinded by some ideology that life involves some magik essence beyond the reach of science.
This story is both a trivial step and enormous progress. It reminds me of Neil Armstrong's "One small step for a man,
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What would count as creating life?
How much does one need to synthesize?
How much needs to be totally original?
You can get to the point where I would think that even if we can do it, we shouldn't. Because it would be impossible to predict with surety how dangerous it would be.
(OTOH, if you're really a young Earth creationist... Sorry. I can't believe that. You can write a coherent paragraph.
But postulating that you were, would anything count as creating life where the atoms weren't synthetic as well as th
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I came up with the "Cosmic Garbageman" theory of the creation of life on Earth when I was in high school ... but I never believed it seriously.
Still, here it goes:
There's this alien spaceship passing by, and they think that Sol III would be a good place to hold a picnic, so they do. And they're careless about how they dispose of their garbage.
Not exactly "Intelligent Design", but definitely not "life evolved naturally in the seas of earth" either.
There are lots of reasonable possibilities. There aren't ma
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And science is only ever an approximation to the truth, it doesn't try to be anything else (though people try to make it more than it is).
The only people who try to make science into more than it is are religious people. Scientists are keenly aware of the approximations in their search for truth.
BTW, how nice of your God to keep moving the goal posts. It used to be: you can't create life out of dirt. Now you have to create dirt, too? And I presume that the goal posts will keep moving until they arrive at "Use your own space/time continuum."
Where's my nobel? (Score:3, Insightful)
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Waits for... (Score:5, Interesting)
... the first fully patented life forms. I'm really curious how that would work.... let's say an egg gets a fully artificial set of chromosomes that include patented genes for fixing Thyroid diseases, preventing breast cancer, and purple hair with green skin. Let's also say that that egg develops into a regular person. Is that person property? What happens if they have kids? Do they need to pay royalties?
I can't wait for this stuff, because it will allow for some truly awesome fixes to truly terrible diseases. But I'm also pretty sure that this will result in legal messes of epic proportions. Monsanto will be a side show compared to that.
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legal messes of epic proportions
Only in America.
Though it will spawn the new industry of genetic engineering tourism.
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legal messes of epic proportions
Only in America.
Though it will spawn the new industry of genetic engineering tourism.
Yeah, only in America because other countries don't do stupid shit with their legal system [slashdot.org].
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Re:Waits for... (Score:4, Insightful)
It can be done, and that means it will be done. The first applications will be medical; synthetic gene therapy could offer cures for many diseases we currently have no way to treat, and only "it's bad 'cause it's got DNA in it!!!" Luddites will object. Yes, there will be harmful side effects, including death, but people with terminal cancer, or parents of children with terrible birth defects, will be willing to take the risk. Once the therapeutic principles are established, we'll inevitably see more frivolous applications. And at that point, whether or not it's "welcomed by society" will be irrelevant -- as long as there are people with the money to pay for it, someone will do it.
That being said, we're a long way from that point. There's a hell of a lot of difference between building a bacterial genome and modifying a human one at will.
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I'm kinda surprised that our special forces don't have cyber eyes with natural night-vision and HUDs yet. Of course, super-soldiers take time to grow.
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"Is that person property? What happens if they have kids? Do they need to pay royalties?"
This is just silly. "Parents" will probably pay through the nose, but not the person or his kids.
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[citation needed]
In the only cases I'm aware of, the defendant claimed their crops were pollinated from the wind, etc. But at trial it was revealed the defendant had bags of the plaintiff's seed.
(insert Bevis-and-Butthead style joke here)
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In which world? In the world where the laws about humans and plants are generally the same?
How do you imagine this argument in court?
"Your honor, the corn plant seeds are subject to this regulation, babies are nothing more than human seeds, so they should be subject to it to".
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Is that person property? What happens if they have kids? Do they need to pay royalties?
if we take a look at the universal declaration of human rights I think it's clear that no special rules need to be made to protect the interests on individuals according to the kind of birth or technique involved in their conception. Taking the example of clones, after they're born it really is not possible to say that they are different from anyone else and therefore should have special status. right?
Article 6 Everyone has the right to recognition everywhere as a person before the law.
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purple hair with green skin
You really shouldn't say things like that on Slashdot.
Now a whole bunch of slashdotters are going to have to go wash off their sticky keyboards.
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Awesome & aweinspiring (Score:2)
Pandora's box has been opened. I'm excited to see what pours out over the next decades. We all know we need radical new technology to fix the energy crisis and reduce climate gas emissions. Hopefully, we can engineer more efficient organisms, providing clean(er) energy and food for the world's ever-growing population.
Re:Awesome & aweinspiring (Score:5, Insightful)
Pandora's box has been opened. I'm excited to see what pours out over the next decades.
Uh, I think you need to read up on your Greek mythology a bit more. Opening Pandora's Box [wikipedia.org] was not such a good thing.
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Re:Awesome & aweinspiring (Score:4, Insightful)
Or maybe he was being so subtly ironic that I missed the point entirely.
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I enjoy being ambiguous. It makes people think harder.
Yeah, but thinking hard makes my head hurt, so stop it!
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Let's see, we create a problem with misguided policies and practices. Now we fix said problem with a new, complex technology. What could possibly go wrong?
This planet will become a barren desert and mankind will vanish. Rightfully so.
Did the institute "make" it and is this "life"? (Score:5, Insightful)
I guess we should wait until the actual Science article comes out, but it looks like they basically synthesized an entire bacterial genome, as opposed to the normal way of having a bacteria copy it's own genome with it's own enzymes, and then they put it into a different bacterial strain.
Is that "making" a cell artificially? They didn't make most of the bacterial cell themselves, the bacteria did that. They didn't design the genome from scratch, they just copied an existing one that nature made and modified it a bit. I'm not sure that constitutes actually making a cell artificially. If you buy a mac at a store, print out the ones and zeros to make windows vista, manually retype them, make a boot disk, and install that on the mac and it worked, that would be an impressive feat, sure, but did you "make a completely new computer?" (Best comparison I could come up with, sorry about that in advance). I don't think this can be considered making life yet.
Second, is this "life?" Life seems to be impossible to define, but it's pretty certain that "genome was stitched together in a lab and inserted into a dummy cell" is unique to this thing, nothing else we'd call life has that feature. Does that disqualify it as life and make it something else?
To their credit, Venter doesn't seem to be claiming they made new life, but they are aiming for that eventually, and I'm curious as to what slashdot thinks about when we can actually say we've created artificial life.
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To their credit, Venter doesn't seem to be claiming they made new life, but they are aiming for that eventually, and I'm curious as to what slashdot thinks about when we can actually say we've created artificial life.
I'd say it's life once the constructed bacteria show that they're able to reproduce, and keep doing so for a number of generations (which can take place pretty quickly for bacteria.) Until then it's an interesting piece of machinery.
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That would be a good readout that it is functional, and undoubtedly they did that already. Working with a single bacterium is I guess possible, but pretty much everyone just works with whole colonies.
They wouldn't have had much to screen from to see if they got the genome in had they not gotten a colony rather than a single cell.
Anyway, the reason "reproducing" isn't a good standard for defining life is there are many live things, such as mules, which aren't capable of reproducing, and some non-living thin
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Re:Did the institute "make" it and is this "life"? (Score:4, Interesting)
"The new bacteria replicated over a billion times, producing copies that contained and were controlled by the constructed, synthetic DNA." - http://news.bbc.co.uk/1/hi/science_and_environment/10132762.stm [bbc.co.uk]
Yes, it really is life.
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"The new bacteria replicated over a billion times, producing copies that contained and were controlled by the constructed, synthetic DNA." - http://news.bbc.co.uk/1/hi/science_and_environment/10132762.stm [bbc.co.uk]
Yes, it really is life.
Or we Pluto it :)
Re:Did the institute "make" it and is this "life"? (Score:4, Insightful)
As an aside, I really was conflicted whether to state my opinion here or mod you up to increase the chances of getting more opinions. Ultimately, I decided yours is strong enough to stand on its own. Good luck in getting to 5!
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Is it life? Yes. It's true that life is somewhat difficult to define, but bacteria lies well within any definition I've heard.
Did they make it? Well, that's a bit more complex.
Bacteria is basically a self-replicating machine that has software to encode it's own building instructions. Its software gets replaced, so it won't any more build copies of itself, but rather a different machine. That new machine is also a self-replicating machine, just a different one (down to protein level). Now both machines build
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but it looks like they basically synthesized an entire bacterial genome
They didn't really synthesize the DNA; they just cut'n'pasted a bunch of existing DNA and inserted it into a new cell. This is like grafting 100 trees together and calling the conglomeration a synthetic tree.
What is the function of the E. coli? (Score:3, Informative)
Because current machines can only assemble relatively short strings of DNA letters at a time, the researchers inserted the shorter sequences into yeast, whose DNA-repair enzymes linked the strings together. They then transferred the medium-sized strings into E. coli and back into yeast. After three rounds of assembly, the researchers had produced a genome over a million base pairs long.
I read this as:
Sequencer-> Yeast -> E. coli -> Yeast -> Repeat
Short segments-> Merged segment -> ? -> ??? -> Full M. mycoides Genome
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They always include E. Coli. Shit happens, you know.
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1. The JCVI team designed specific cassettes of DNA that were 1,080 base pairs long with overlaps of 80 base pairs (bp) at their ends to aid in building the longer stretches of DNA. These were made according to JCVI’s specifications by the DNA synthesis company, Blue Heron Biotechnology.
2. Then the team employed a three stage process using yeast to build the genome using 1,078 cassettes that are 1,080 bp in length. The first stage involves taking 10 cassettes of DNA at a time to build 10,000 bp long segments. In the second stage, these 10,000 bp segments are taken 10 at a time to produce eleven 100,000 bp long segments. Finally, all 11 segments are assembled into a complete synthetic genome as an extra chromosome in a
yeast cell, by using yeast genetic systems. 3. The complete synthetic M. mycoides genome is then released from the yeast cell and transplanted into M. capricolum recipient cells that have had the gene for a restriction enzyme removed. Following incubation, viable M. mycoides cells are produced in which the only DNA present is the synthetic genome. These cells are controlled only by that synthetic genome.
Which then makes sense of the chart which states the sequence as:
1. Oligonucleotide Synthesizer
2. Yeast
3. ?
4. Extract Complete Genome from Yeast
1. Oligonucleotides in 1,080 bp cassettes (1,078)
(Assemble109X)
2. 10,080 bp assemblies (109)
(Assemble 11X)
3. 100,000 bp assemblies (11)
(Assemble 1X)
4. 1,077,947 bp
So I guess the ?? in step 3 is the E. coli, which assembles the 10,000bp segments into 100,000 bp segments, which are finally stitched together back i
That's new? (Score:3, Insightful)
The natural algae already do this. Even more, they produce oxygen at the same time!
Ugh (Score:3, Interesting)
Asimov will be pleased (Score:2)
This will really help when we finally get around to terraforming the galaxy. Instead of sending off a huge Noah's Ark to each one, we'll just ship whatever raw materials can't be found on the new planet and build the lifeforms onsite.
Re:What... (Score:4, Insightful)
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This sounds exactly like Jurassic Park, except replace Dinosaurs with Yeast and Frogs with E. Coli.
Need I explain what happens next?
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Oh wait, that's already been invented [wikipedia.org].
You forgot the quote (Score:2)
God destroys dinosaurs.
God creates man.
Man destroys God.
Man creates dinosaurs...
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Women inherit the earth.
What happens next is (Score:4, Funny)
Uruk-hai
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Humans create microbial park which goes horribly wrong, causing untold havoc as artificial E. Coli stalks innocent humans in the jungles of Mexico causing uncontrollable diarrhea.
No, wait...
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This sounds exactly like Jurassic Park, except replace Dinosaurs with Yeast and Frogs with E. Coli.
Need I explain what happens next?
Newman steals the bacteria (WHICH IS NOT E.COLI FYI!!!) and then a velociraptor eats Samuel L Jackson?
Re:What... (Score:4, Insightful)
FTFA
Perhaps there is a difference between random changes directed solely to furthering of DNA propagation ...
and the short term goals of greedy men?
whatcouldpossiblygowrong?
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whatcouldpossiblygowrong?
People use to say the same thing about computers... and still do about robots. The question a rational person asks is "what is the risk vs possible return."
Re:What... (Score:4, Insightful)
That's what you meant by risk vs. return right?
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The question a rational person asks is "what is the risk vs possible return."
The typical American asks "What is the possible return" and ignores the risk in pursuit of personal gain.
Re:What... (Score:4, Insightful)
Oh come on, the likely hood of an oil spill in the gulf is 1/10,000. Do we really want to block drilling based on the 1/10,000 chance of a 200 million barrel leak that could kill all life in the gulf and do substantial damage to most of the eastern seaboard and destroy the fishing industry in four states and potentially do a lot of damage to the atlantic ocean and carribean as well? Be reasonable.
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Choose your rate.
Let's say 1/10,000 per year per rig.
Let's say 1/10,000 per year per thousand rigs.
Does it really make a difference?
For low frequency events, we underweight the potential damage.
The gulf should be fine by 2045. Life recovers pretty fast. All they have to do is stop fishing for 20-30 years and the gulf would be teaming with life.
Re:What... (Score:4, Insightful)
The typical American asks "What is the possible return" and ignores the risk in pursuit of personal gain.
Given the amount of Luddism that is invariably displayed with respect to genetic engineering, I'd say that in this particular case the reverse is true. There's a level of ignorance driven fear on this topic that I haven't seen since the days when a lot of people genuinely believed that computers were malevolent "thinking machines" that would try to take the world away from their human creators.
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the days when a lot of people genuinely believed that computers were malevolent "thinking machines" that would try to take the world away from their human creators.
Interesting, your post does not have an origin IP address.
It appears to come..... {DUM dum dum!} from the network itself.
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We wish the programmer of the Therac-25 HAD asked himself whatcouldpossiblygowrong.
At the same time, just like with computers, there are many potential benefits to be had. Perhaps more than computers. Of course, computers aren't free to roam the earth, multiply, and then colonize our bodies, so we need to make really sure the right questions are asked.
This particular research was reasonably well thought out and probably couldn't produce anything viable that can't be produced through random mutation anyway.
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I don't think a kill switch is the right answer, I'm more in favor of creating a dependence. Design the things to require an amino acid not to be found in the wild, and don't design any of them to make it. I believe that there are only around 20 amino acids that exist in the natural world, but it would be easy enough to synthesize an additional one through normal chemical processes. (Use one of the 20 as a starter, and add a new side chain, e.g. Possibly one incorporating iron or cobalt. Things that a
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Computers and robots can't reproduce without our help. The same criticism (whatcouldpossiblygowrong) would hold when they can.
Re:What... (Score:5, Interesting)
The genome was produced by machine (from a digital copy of a sequenced genome). Presumably, if somebody wrote a brand new genome, it could be inserted into a living organism by the same procedure.
I guess we can now start finding out which genes are really necessary for an organism to function...
(I am not a biologist.)
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Not a troll. "What could possibly go wrong" is a common meme used here at Slashdot for any sort of experiment with even the slightest possibility of catastrophic, world ending consequences. We've all seen the movies where the genetically engineered thingy eats everyone, so it's funny, not a troll. It does not generally indicate that the writer even believes something will go wrong.
Now, that being said, selective breeding is not the same thing as genetic engineering. Not that I really think this sort of work
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How is this different: let me count the ways (Score:3, Insightful)
It's different for a a lot of reasons. I'll just focus on three. The bio-weapon fear: the viruses and bacteria that we harbor have co-evolved with us. Viruses and bacteria shape evolution in a myriad of subtle ways but one way to look at even the most pathogenic forms is that their habitat is you and me. So despite the suffering inflicted by TB, Ebola, HIV etc. fundamentally it is not in the best interest of the microbe to cause the extinction of its habitat -- although it probably happens. The bio-weapon
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If you go to Indiana you don't see the Monsanto soybeans growing wild in a ditch.
That's because Monsanto seeds are sterile. You can't simply buy once and plant some of the seeds from that crop, you have to buy from Monsanto each year. Seriously, this is basic bio-tech information from the 90's.
Completely false. (Score:3, Informative)
This article [monsanto.com] on monsanto.com makes it very plain:
"Monsanto has never developed or commercialized a sterile seed product. Sharing many of the concerns of small landholder farmers, Monsanto made a commitment in 1999 not to commercialize sterile seed technology in food crops. We stand firmly by this commitment. We have no plans or research that would violate this commitment in any way."
In spite of this reassurance, one can't rule out the possibility that Monsanto will decide later that it's in their own best
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Here's [freezerbox.com] the best article I could find on the topic. You have to get all the way to the bottom before hearing how Monsanto backed off due to political pressure.
Of course, the wiki page [wikipedia.org] also spells it out. And apparently some [mit.edu] people [healthy-ea...litics.com] simply get it wrong.
I believe that th
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Not true. Turns out nobody would buy the "sterile" seeds when they were introduced by another firm.
Who would have thought that farmers know more about farming than geeks in their parent's basements?
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However now it is possible to accelerate this "artificial sex" to rates that far exceed the norm. Plant-Animal hybrids here we come -- and let's use our imagination. Plant a seed, up grows the plant, a flower fruits, a butterfly emerges which lays -- seeds. Pretty kewl huh.
Pfffft!
Plant a seed and out pops a horny green babe with three tits.
Just let her lie in the sun all day, water her twice a week, and as you said "it is possible to accelerate this 'artificial sex' to rates that far exceed the norm".
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1. It would be directed, allowing it to create things that evolution just wouldn't.
2. Nature doesn't have a great track record itself so adding yet more adds more risk. I'm sure all the life that did exist before cyanobacteria evolved and killed everything else buy spewing out toxic oxygen would have prefered a bit less unsupervised genetic twidling...
But don't get me wrong, I think this is great stuff and we should keep on doing it.
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So there are two completely separate issues to be addresses here. In this specific case if you read the article, these scientists went to extraordinary lengths to ensure that their work wouldn't lead to potential negative impact. Bioethicists were involved from the get go, and that is distinctly different than the unsupervised genetic twiddling that happens naturally.
As for genetic experimentation as a whole, there are things happening in labs that are seriously more dangerous to humanity and life as we kno
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Unsupervised? Anything genetically defective didn't really reach the next generation.
Re:What... (Score:5, Interesting)
But the funny part is that Monsanto would welcome any sort of biological catastrophe, as they're the only ones that would be capable of fighting it. Kind of like how my paranoid father thinks the majority of viruses are produced by Norton and McCafee on the side just to stir up business, Monsanto could produce a better fungus to drive up business.
Evil, malicious, and a wonton disregard for human suffering, but massively profitable.
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.... could possibly go wrong?
You should write for Hollywood.
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Holy crap? Hulu? I thought it was only available on laser disc? I have a set of laser disc rips from a hell of a long time ago, but the audio was screwed up in half the episodes.
It was my favorite cartoon when I was young. It was pretty edgy back then, the only cartoon that even attempted to deal with things like death and emotion.
Re:Linux (Score:5, Funny)
Sony says no Linux on the Cell.