Slashdot Mirror
Synthetic Genome Drives Bacterial Cell
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.
.... could possibly go wrong?
I don't know how many times I've heard the young earth creationists and intelligent designers say that since man can't make life, life must be special. Dear FSM, I wish I could send this article to all those IDiots on all the message boards to which I've posted over the years.
Tic-Tac-Toe, Global Thermonuclear War, and relationships all have the same winning move.
sudo dd if=genome.helix of=/dev/nucleus0
... 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.
Those who can, do. Those who can't, sue.
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.
Stop the brainwash
Sony says no Linux on the Cell.
No sig? Sigh...
Sorry, it's Windows only. They were required to place a limiter on it, so it wouldn't stay alive forever, and Windows just seemed a natural fit.
Who would win this election: Andrew Weiner vs Andrew Weiner's weiner.
God creates dinosaurs.
God destroys dinosaurs.
God creates man.
Man destroys God.
Man creates dinosaurs...
Computer Science is Applied Philosophy
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.
Uruk-hai
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 fear is that pathogens can now be created whose long term interest is not in the "cruel but fair" hands of Darwinian Evolution but in the possibly malevolent (or hopefully beneficent) hands of a bona-fide "CREATOR/DESTROYER". Let's hope Venter is nice. The second: the lateral gene transfer mechanism has been shown to play a role on evolution. 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. Three: Genetic twiddling -- there are some parts of the cell that evolution just doesn't take a chance in messing around with. It is now possible to mess around.
My two cents: weeds win...the reason algae for fuel doesn't work is weeds. If you go to Indiana you don't see the Monsanto soybeans growing wild in a ditch. And there are no wild packs of Shih Tzus. I'm not sharpening the pitchfork yet.
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
The natural algae already do this. Even more, they produce oxygen at the same time!
The Tao of math: The numbers you can count are not the real numbers.
Well, that specific requirement can be met with other operating systems. For example, I don't think the Nexus series (and I don't mean the Google Phone) will run under Windows.
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 many that it's reasonable to assign a high probability. One that *WOULD* qualify as "intelligent design" and has a reasonable possibility is directed panspermia:
Long ago and far away an intelligent life form desired to spread it's descendents throughout the galaxy, but they couldn't figure out an FTL drive. So the whipped up a mix of primitive life forms that would have at least one survive in a mix of environments, wrapped them in a bunch of preservative capsules (designed to protect the contents from cosmic rays, etc., and to give the mass driver something to hold onto, and shot them out at every reasonable target they could find. LOTS of them.
OK. That's "Intelligent Design". I can't prove it was wrong. It actually seems to have a reasonable probability. We might have come from something like that. But do note that that's intelligent design of life, not of humans. I can't think of anything plausible that yields "intelligent design of humans" except the "The Universe is a Simulation" hypotheses. (No way to disprove that one, or estimate it's probability, either. Some variants say "Historical Simulation", others say "Video Game". They're all unfalsifiable.)
I think we've pushed this "anyone can grow up to be president" thing too far.
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."
Those who can, do. Those who can't, sue.
It'd never work. A bacteria has enough redundancy so that DNA polymerase's error rate usually won't cause any issues. Linux is built with the assumption that data replication is flawless. Therefore, the two differ dramatically in regulatory strategies.
(Even though you jest, there is some debate as to whether DNA and its enzymes are Turning-complete or not. Obviously, at one extreme, a human can function as a Turing machine, but at the other, DNA & protein synthesis don't quite work that way.)
I love the complete bullshit rhetoric that is in use here. This is about as "synthetic" as a plagiarized paper is original. Hacking up a bunch of real genomes is easypeasy compared to actually making life from scratch. The way this was done you dont even have to know the rules, you just put it all together and hope it works.
Life can never be "synthetic." Life is a process, and maybe we will one day be able to stick some genetic code into a cell composed of protiens and lipids and carbohydrates that were all synthesized in a lab, but until then we will always have to steal and cheat our way by taking what evolution has given us.
This article 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 interest to market a sterile seed technology.
Monsanto has persecuted many farmers for allegedly saving the seeds of their GM plants (corn, soybeans, and cotton) for planting. See http://www.monsanto.com/seedpatentprotection/monsantos_position.asp for one of the several Monsanto resources that discusses this practice. There's very little a farmer can do to protect his business when Monsanto makes such an accusation. The legal battles can last years, and are devastating.
I am not learning to program in DNA. That's like the assembly language of the molecular biology world. Could someone come up with a nice ruby module so I can just mixin the traits I want?
I'm trying to teach myself to set people on fire with my mind... Is it hot in here?
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.
... in Belgium: a completely artificial country was synthesized by joining the Southern Netherlands and a Northern piece of what was once France.
A latin world and a germanic world joined without LHC.
Only kept together by utter latin arrogance: " La Belgique sera latine où elle ne sera pas." (dixit Cardinal Mercier).
So, an intelligent designer has created life. No surprises here then.
No left turn unstoned.
Genetic design != patching up a genome using DNA fragments of known function. It is not possible at this time to design a gene that can perform a given biological function. So basically, what they have done is, they have engineered a 3 Mbp plasmid using genes that exist in nature. That in itself is an accomplisment but I would not call the result a "synthetic genome". The concept of genome implies a consistent and complete biological function set and that, nobody has managed to "synthesize" yet.
The word `God` has limited connotations in English. If it just means creator then the creator is god to this form of life.
If alien life plants us a long time ago then would that alien life be god?
What if that alien life views not only out reality but knows much more than we do, such as operating through other dimensions... and the only way to communicate this at the time was through genetic knowledge of a creator and the concept of `god` that the meaning of which has changed over time.
If that is so, then does the relationship between the bacteria and the scientist mirror religious legend? (allowing for variation in the passed down knowledge by averaging what all the religions say).
Remember, most disagreements are misunderstandings on what a word means. God means different things to different people.
Every time we witness disagreement, examine the meaning of the words involved and develop agreement on what the words mean.
A blog I run for the wealth
Students of genetics know that organisms with short life spans and simpler structures evolve much quicker that complex organisms.
A while back I had an idea to modify saccharomyces cerevisiae to include code for generating ligninase, xylanase, and cellulase. This would allow me to brew alcohol from wood etc. Presently the enzymes are harvested from aspergillus niger. Production and recovery are expensive.
So in comes a brewing bacteria that can "liquify wood." Wait. What if this bacteria were released into the environment in an uncontrolled fasion? What if it mutates? Wouldn't the result be catastrophic?
/\/\icro/\/\uncher