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We desperately need a bioGNU.

Something like iGEM might be what you're looking for. IANAL, but I think you can still use CRISPR/Cas9 for non-commercial purposes (I think the patent system allows for this?). There are also other CRISPR/Cas systems that rely on other version of Cas, and those may not be patented. They're less well-characterized, but they do exist.

I suggest diving into the synthetic biology movement. Take a look at the BioBricks Foundation. Search the Registry of Standard Biological Parts. Maybe there is something missing that you might contribute. Join iGEM, the International Genetically Engineered Machine competition. It is a worldwide synthetic biology competition aimed mostly at undergraduate university and high school students. Some people there are doing amazing eco-friendly projects. And don't be scared by the recent anti-science hysteria. Genetic engineering in general and synthetic biology in particular is not as hard as people tend to think. It doesn't even has to be too serious. For example, in 2006 the MIT team engineered E. coli to produce a wintergreen scent during exponential phase and a banana scent during stationary phase, known as the "banana-fart" bacteria. Some kids are engineering just amazing DNA to produce bacteria that help to digest pollution, or converts sunlight into energy that is easy to use. There is a lot to be done in synthetic biology and both BioBricks and iGEM are directed towards young people who want to experiment and collaborate, without the need to synthesise everything from scratch. You don't need sunlight to do that and you don't need expensive equipment any more. These days people are sending DNA by email and change it like it was just a computer program - which it is in a sense, but it is software that builds hardware. This is truly amazing stuff and I believe this the future of fixing our planet. We have to help mother nature. And this is the most optimal way to do it - from the ground up. iGEM and BioBricks is a great way for young students to dive into it.

Yes, it's more impressive than an "OR" gate (which could simply be two different mechanisms that trigger the same effect), but the word Logic circuit just doesn't do it for me.

You really want to impress me, show me an "XOR" - either of two indications, but not both.

http://2008.igem.org/Team:Davidson-Missouri_Western/DNA_Encoded_XOR_Gates

Looks like these undergrads still have some bugs to work out, but in principle such a thing should be eminently possible given that most genes already have tons of positive and negative regulators that can be easily co-opted and transplanted. The trick is making a robust system with enough dynamic range that you can easily read the output, but with enough finesse that it can dampen the noise as well as mother nature does it.

That's a proposal that I just made here. No self-destruct system was included in the engineered T cells mentioned in the paper. However, it's not an uncommon concept in synthetic biology, and has been included in (for example) numerous iGEM projects. It is a fairly easy pathway to construct and implement.

The minimal mammalian self-destruct mechanism probably consists of a single gene that gets turned on in the presence of a foreign steroid hormone not normally present in the body, but doesn't cause an immune response. Steroid hormones are convenient in that they can pass through cellular membranes without transport, and can directly effect the activation of genes designed to respond to them (although another gene might be required to create an appropriate DNA-binding cofactor; I don't remember my endocrine lectures that well.) This single gene can then direct the cell to produce a protein, such as the peptide described in this paper, which causes T cells to perform self-lysis (to kill themselves, typically for the good of the body.) However, more blunt instruments can be used; directing a cell to very aggressively use up all of its metabolic energy producing something useless is a common mistake often made by inexperienced genetic engineers, and usually causes the cell to die due to resource exhaustion. Thus, adding this foreign hormone would trigger self-destruction of the engineered T cells.

There are other methods, too; one could, for example, make the engineered T cells look like invaders (by introducing an adapter protein that fuses with the original receptor and turns it into a foreign epitope.) The body would then eliminate these T cells just as they originally eliminated the cancerous B cells. This has the advantage of being applicable to the original test patient (since it doesn't require genetic engineering), but requires a lot of tricky pharmaceutical engineering to prevent the adapter drug from getting destroyed before it's bound.

Actually, it's a little trickier than that. Worms have to be microinjected. But that hasn't stopped people from trying to make worm engineering widely accessible. This is the seminal work on the topic, I believe.

Yeah, it's not like the biologists working on this would have thought of that themselves, oh wait...

Outside of this article, there's no indication that these E. coli actually exist. Check the U Tokyo iGem page: http://2010.igem.org/Team:UT-Tokyo/Sudoku_construct

I guess it's difficult since their page keeps talking about 'our E. coli', but we also never see any results from 'their E. coli'. I think they're more hypothetical at this point.

They have an interesting model and system, but nothing on their actual E. coli or their results. Everything is idealized and simulated. I think there must have just been some kind of miscommunication. If they had actually created bacteria that solved sudoku, they would have done better in the contest.

Try this URL instead.

There are three principal parts to the filler produced by these bacteria. First, the bacterium naturally produces calcium carbonate as a byproduct of breaking down urea as a nitrogen source; this activity has been greatly increased in the engineered bacterium. The second part is a "glue" made from levan, a polysaccharide that the bacterium is able to produce from sucrose; this activity is also natural, but highly upregulated in the engineered bacterium. The final part is the bacterial cells themselves; the cells are made long and threadlike by expressing a protein that halts cell division, and these filamentous cells act as reinforcing fibers. In practical usage, a solution of nutrients (including sucrose in particular) would need to be sprayed along with the bacterial spores in order for them to display this concrete-filling activity. This information comes from here.

Also, the concrete repair activity is produced by upregulation of genes natural to Bacillus subtilis, not by anything transgenic. The upregulation of these genes presents an energy cost to the engineered bacterium while providing no benefit- if these bacteria mutate, it is more likely to be towards the wild phenotype. In addition, the team responsible has added a kill switch which tells the bacteria to commit suicide if sucrose is not present.

Also, the concrete repair activity is produced by upregulation of genes natural to Bacillus subtilis, not by anything transgenic. The upregulation of these genes presents an energy cost to the engineered bacterium while providing no benefit- if these bacteria mutate, it is more likely to be towards the wild phenotype. In addition, the team responsible has added a kill switch which tells the bacteria to commit suicide if sucrose is not present.

This engineered bacterium system was entered into the International Genetically Engineered Machine competition, so there's a lot more information about this project at the team's project page. In particular, there's a more thorough description of the kill switch the team engineered to prevent the spread of this bacterium beyond the target environment, the underlying mechanism being that sucrose must be available in the environment to prevent the bacterium from producing a toxin which kills itself.

This engineered bacterium system was entered into the International Genetically Engineered Machine competition, so there's a lot more information about this project at the team's project page. In particular, there's a more thorough description of the kill switch the team engineered to prevent the spread of this bacterium beyond the target environment, the underlying mechanism being that sucrose must be available in the environment to prevent the bacterium from producing a toxin which kills itself.

This engineered bacterium system was entered into the International Genetically Engineered Machine competition, so there's a lot more information about this project at the team's project page. In particular, there's a more thorough description of the kill switch the team engineered to prevent the spread of this bacterium beyond the target environment, the underlying mechanism being that sucrose must be available in the environment to prevent the bacterium from producing a toxin which kills itself.

International Genetically Engineered Machines competition Look forward to some very affordable kits to be introduced this year.

Turns out a lot of the coolest results in synthetic biology have been produced by teams of college students for less than $1500. See the iGEM competition http://2010.igem.org/ (and follow links to older competitions), order some biobricks from New England Biolabs http://www.neb.com/nebecomm/products/productE0546.asp , and check out the tutorials at http://syntheticbiology.org/ It's all open source, too. The price of DNA sequencing and DNA synthesis are both dropping exponentially. It's a lot like the Homebrew Computer Club times in molecular biology right now...

It looks like the University of Edinburgh entered this project in the International Genetically Engineered Machine competition, so they have a project page with a lot of information. From what I gather, it would appear that the system is based on a system of enzymes that break down soil nitrites which have been linked to Green Fluorescent Protein. Nitrites are a natural byproduct of the breakdown of nitro-based explosives like TNT and PETN. Of course, soil nitrites from non-leaking landmine sources, like chemical fertilizers would also trigger fluorescence, so the team engineered a non-natural gene promoter protein. The genes to produce the fluorescent complex only get transcribed and translated into protein if the promoter is active. The activator for that promoter is a molecule of TNT, so the bacteria will only glow if TNT is present.

I'd also encourage people to take a look at the other iGEM projects. Lots of interesting reading.

It looks like the University of Edinburgh entered this project in the International Genetically Engineered Machine competition, so they have a project page with a lot of information. From what I gather, it would appear that the system is based on a system of enzymes that break down soil nitrites which have been linked to Green Fluorescent Protein. Nitrites are a natural byproduct of the breakdown of nitro-based explosives like TNT and PETN. Of course, soil nitrites from non-leaking landmine sources, like chemical fertilizers would also trigger fluorescence, so the team engineered a non-natural gene promoter protein. The genes to produce the fluorescent complex only get transcribed and translated into protein if the promoter is active. The activator for that promoter is a molecule of TNT, so the bacteria will only glow if TNT is present.

I'd also encourage people to take a look at the other iGEM projects. Lots of interesting reading.

http://2008.igem.org/Team:University_of_Alberta This project was about creating a synthetic organism that would be able to detect and destroy this stuff

(AC, so I'm not as much a karma whore)

http://diybio.org/ - open source hardware, biology, XMLizing lab protocols, the goods.
http://openwetware.org/
http://biopunk.org/
http://syntheticbiology.org/
http://partsregistry.org/
http://igem.org/ (international genetically engineered machines competition)
http://ponoko.com/
http://shapeways.com/
http://thingiverse.com/
http://instructables.com/
lifeboat foundation (AKA "fearmongers click here")

cat * > /dev/trend-spotting-machine

Not now per se.. but give it 5 years. Around then there will be enough biobricks to make this more like programming than electronics. I also expect that, by then, you'll be able to do your design work entirely in silico, and send the compiled DNA sequences (at most a few plasmids) off to a lab to be synthesized, implanted into a specified bacterium, cloned, mailed to you - and for a cost that is affordable to hackers. Note that this is almost already here. Mr Gene will send you whatever DNA sequence you want for pretty cheap prices ($0.49/bp) but that needs to go down a whole lot more and they need to send the entire organism, not just the DNA they extract for you. Most their current customers don't want the whole organism, so they don't currently offer it, but I expect that could change as easily as getting the necessary paperwork done.

What kind of stuff can you make? Depends how creative you are. This year's iGEM Jamboree produced some amazing stuff.. and most every one of these projects had to make a new biobrick.. and that's the time consuming part, and cuts into the limited amount of time they had to get their entry in. If you're doing this in 5 years time it'll be hard to come up with a new biobrick that does something that hasn't been done. Instead, people will be working on reusable systems of biobricks.

This will all explode faster than computing technology ever did, because we're talking about machines that can manipulate the physical world here. If there's a single industry, 10 years from now, that doesn't include some kind of engineered biology then it'll be for a very good reason.. hopefully not legislative :)