A fair amount of hysteria in this article, and even more in the forums. But it's not your guy's fault - society has a bad habit of...well, treating scientists like alchemists and wizards. We haven't really moved past the Dark and Middle Ages in that sense.
This is probably just spitting into a hurricane, but let's see how this goes...
"The Pentagon's mad superscience branch DARPA..."
Truism. Everything associated with the government is mad. But that's beside the point.
"Included in the Pentagon's budget for next year is a relatively piddling $6 million dedicated to a project called BioDesign, a relatively unassuming moniker for a project with the goal of eradicating
'the randomness of natural evolutionary advancement.'"
Here's an idea of the kind of thing on which we're (hopefully) on the cusp. Someone's suffering from sickle cell anemia because the protein is defective. This defect starts right at the level of a DNA sequence that isn't quite right. So what if we could introduce something into the cells to cut out that bad sequence of DNA and paste in a piece of DNA with the "proper" sequence near the cells with the defective sequence.
People are hoping that with <a href=http://en.wikipedia.org/wiki/Zinc_finger#Engineered_zinc_finger_arrays>zinc fingers, we may be able to do this sort of thing in the near future. And this is just on the speculative side; this isn't counting the thousands of experiments that are run every year in which we alter DNA sequences in various organisms to get the kinds of proteins we want. The majority of insulin production at present (I believe) is thanks to genetically modified bacteria that we've reprogrammed for that purpose. So if they're just sticking to modifying pre-existing genomes (which seems more reasonable than creating your own genome from scratch, with this kind of budget minus government inefficiency), then the principle of it is not so exotic.
"The final goal of the project is to create living, breathing organisms from scratch that have been genetically engineered to "produce the intended biological effect."
This is rather ambiguous. Create very simple organisms from "scratch" or heavily modify slightly more complicated ones? "Living breathing organisms", by the way, is quoted off the Wired article, not the Pentagon review. I wouldn't be surprised if there was some exaggeration here; there are quite a few interesting organisms that don't "breathe" in the normal sense, and would probably make more sensible targets.
On the other hand, it makes very little sense to be mucking around with human DNA. There are plenty of NIH grants trying to do similar things. So I'd put away the Captain America fantasies. ;-)
Said organisms will ideally have their cells bolstered with special molecules that prevent cell death, so that these artificial life forms can be "programmed to live indefinitely."
This makes me suspect that we're dealing with smaller, maybe unicellular organisms. Cell death is covered by a specific set of events with clearly defined checkpoints. In a unicellular context, it's a "simpler" matter of knocking out these events (although we probably haven't characterized all of them, and moreover, one thing usually affects another, so such specific knock-outs can be complicated).
In a multicellular context, however, this becomes very complicated. A big reason for controlled cell death in the human body is to keep cell counts balanced relative to each other. If this doesn't happen, we get...well, tumors, since cells are preprogrammed (for the most part) to divide at a certain rate. So in a multicellular organism, you would not only only have to stop cell death but also arrest further cell growth. That's...double the problems. And that $6 million could run out fairly quickly.
"But if that weren't enough, the organisms will also have genetic serial numbers so that they can be tracked - and as a very last resort in case it all goes out, these aberrations of nature will come equipped with self-destruct devices:"
Assuming a random distribution of DNA bases (which is an oversimplification, but bear with me), one would require only a 16 base pair sequence to be
reasonably sure that such a sequence will only occur once in the human genome. Probability hits pretty hard, so such a "genetic tag" would, in theory, be not so difficult.
As far as self-destruct goes, cell death is much easier to encode than cell life. I could think of all sorts of crazy things that could a cell to just quit. The interesting thing though, would be making the trigger specific to the organisms in question. Sulfuric acid kills, for instance, but it is a little non-specific. ;-)
"Naturally, despite DARPA tossing $20 million at a new synthetic biology program, there are some serious roadblocks in the organization's plan."
I can see you're excited, but $6 million versus $20 million is a big difference...
Ok, I'm just nitpicking.
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In sum, I don't really see a terrible lot here to be worried about, except that millions of dollars are being poured into this as opposed to helping NASA, oh I don't know, keep up manned space flights? There is one way I could see this being turned to something more nefarious than has been brought up here, but it's an application that has been looming over the world's heads for a while, and I don't feel like adding to the Luddite panic.
As far as the ways in which this is playing God (altering DNA, creating recombinant lifeforms), a lot of your taxpayer dollars are going towards laboratories that are already doing such things. So if you're having ethical conflicts now, I suggest you leave the first world countries.