Etech Session Liveblogging: Real Hackers Program DNA (Ginkgo Bioworks)

GB is “Making the process of engineering biology easier.”

ben-plasmid.jpgSynth bio is the idea that biology is a technology to engineer novel systems- say drugs, biofuels, other sexy sexy projects.

This is to be a flavor of what engineering biology is all about.

We will be installing a program into E coli to make it turn red, glow in the dark, or smell like bananas… We get to pick!

The DNA is stapled to the pages that describe them in the notebook.
quinn-plasmid.jpg
Some of the tools of synth bio: biobricks, interchangeable components that can be strung together into programs. The parts registry lets you snap programs together.

iGem participants get a kit in the mail and pick out parts and mix and match them into new programs they want- much like the one we’re holding. The Scottish team made and E coli that turned red in response to arsenic contamination.

Standardized interchangeable components are limited, but let a lot more people get involved and democratizes access to the tools. This is still biology- it can seem kind of scary- do you trust your neighbor to engineer biology?

Question from the audience: how do you prevent the terrorists from building smallpox?
Answer: You can’t perfectly. “How do you prevent a car bomb from blowing up outside?” You don’t, but you can limit it, and create a community that self polices.

Question from the audience: What about release? Would the arsenic detector be scattered on the ground?
Answer: We don’t understand how manufactured organisms will interact with the environment. We work with safe organisms, and we don’t release our stuff. These E coli are pretty innocuous, so we’re going to wash our hands before lunch.

It’s pretty unlikely that anyone is going to make anything in a lab that’s dangerous right now, but we should think about that.

It’s a bit legally gray, the guidelines everyone follows are only required for people receiving NIH funding, and there’s some places with local laws (like Cambridge) … There’s no clear answer.

We’re punching out our DNA and dropping it in cells. (Ben has returned our vial, #19 and #10 to ice, while the receptive cells take up our dna)

We’re installing on a plasmid. “You’re literally just mixing the plasmid DNA with the cells.” These cells are competent, which means they can take up DNA easily. We cool the DNA, then do a heat shot- then shock it in a 42 degree water bath for 30 seconds, time it, put it back on ice for two minutes. We’re disrupting the membrane of the cells and letting them recover. Then we’re adding media, food for the cells. Then we’re incubating them with our bodies. I’m going to keep mine in my armpit, I think.

Can’t mix the three bit of dna, because they’re the same plasmid – they are ampecillin resistance plasmid, so there’s a space collision, things aren’t likely to play well together.

DIYbio.org is a good place to learn about good lab practices.

I am now heading to lunch, incubating a tube of e coli in each armpit. (Will update with pictures after lunch)

Update: I’ve now transferred my E. coli to a petri dish and a vial, freeing my arms.ecoli.jpg

…and no, I was in a hurry, and I didn’t wash my hands before lunch. Phear my bad lab skillz. (& Know your organisms.)

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  • http://basiscraft.com Thomas Lord

    One time I was with a very young guy (barely adolescent) who had just then gotten his very first C compiler. He was experienced playing with his DOS-based PC but this was a first way to get into programming of the sort his older brother did.

    He was walked through the mechanics of writing “hello world” and getting it to compile and running it. It’s an important first lesson to make sure you know how to run the compiler and run the resulting program.

    Quiz time: “Ok, make it say something else other than hello world.” Just to make sure he’s got the basics down (and thus can be left to learn on his own).

    Clever lad: he fires up a binary file editor, opens hello.exe, looks around for the string “hello world” and changes it.

    We don’t currently have the skill to program organisms and, in fact, it isn’t clear we much ever will. What we’re doing is binary patching and just as that kid could create unintended consequences (e.g., by making the new string too long) same here. And just as that kid didn’t have even the beginning of a framework of understanding to grok the nature of such possible consequences – same thing in synthbio.

    It’s nice that the notes from the talk mention the concept that we don’t know how these organisms interact with the larger biosphere when released. That’s refreshingly honest.

    It’s disappointing that people are still claiming the particular organisms they make are “safe” (they are of unknown safety). It’s a flat out lie to claim they aren’t released into the wild given the very weak protections against such afforded by popular protocols.

    I am now heading to lunch, incubating a tube of e coli in each armpit. (Will update with pictures after lunch)

    Shame on you.

    -t

  • http://basiscraft.com Thomas Lord

    Phear my bad lab skillz. (& Know your organisms.)

    May I instead fear them? Do we need the hipster spin of sarcasm? Really? This is your argument? Authority and style? And how am I supposed to know that which you do not. Ms. Curie, what’s that you’re carrying in your pocket?

    -t

  • Martin Haeberli

    Thomas,

    While I fear “gray goo” (nanotech) or over-optimistic biologists as much as the next person, I also know key members of Drew Endy’s extended team pretty well, and have known them for a long time, and trust them, to a degree, to be “very very careful”.

    Quinn, thanks for liveblogging this – sorry I missed it.

    Best,

    Martin

  • http://basiscraft.com Thomas Lord

    Martin,

    An interesting thing about e. coli is that after we are born but shortly thereafter we tend to acquire from the environment certain strains that will be dominant there, as part of our gut bacteria. Later in life, these strains that come dominate early tend to exclude most replacements. Sometimes a medication or other experience will flush our long-term colonies and then there’s actually a period there where part of recovery means growing new ones.

    First thing to note here is that Ms. Norton is a bit cavelier towrds any parents of infants (or infants present) as she goes to get lunch.

    Now, the synthbio folks will point out that (a) e. coli is fairly wimpy, comparatively speaking, and (b) the particular strains into which they playfully inject plasmids are purposely selected so as to be especially wimpy compared to even e. coli in general – in fact, each is selected for its extreme vulnerability to one or more very banal and already widely used anti-biotics. A drop of bleach? A drop of amoxicillin? Heck, just slapping some on your hand? The parent strains of what they create are (in theory) very banal. Not quite “you can put them in your tea” (not recommended) but actually pretty close.

    And they’ll be quick to tell you that the plasmids they inject don’t change that and, stochastically, that’s an empirically solid result with lots and lots of verification. [Disclaimer: I don’t know if amoxicilin is literally correct an an example of an applicable antibiotic – maybe that isn’t one of the one’s commonly used or not – but the idea is clear and correct.]

    They’ll also, if you tour their labs and inquire about their practices, make it clear that their controls are extremely weak. They don’t spend much effort double checking that the strains they are working with are the one’s they are labled as. They don’t do much of any checking at all to see whether or not any of this is actually surviving the protocol and thriving in the sewage system – they don’t check. They argue it must be so as they flush stuff down the ordinary drain but they don’t check.

    They don’t badge and test people entering and leaving containment areas. They don’t much vet for admission to these areas. Ordinary medical X-Ray machines in veterinary clinics are handled with far greater care than these guys handle their creations. No kidding.

    The Endy-related society will also be quick to say – at least if you ask them or keep pressing the point in harsh blog comments – that they don’t actually understand how these organisms will do once released in the wild or how they evolve. Not even close.

    So now, put two and two together. We have obvious threats like the vector to an infants gut colonies. We have negative knowledge about the severity of those threats but reason to be highly suspicious. And we have protocols not only in place but BEING PIMPED AND ADVERTISED BY THESE PEOPLE that pretty much guarantee release into the wild.

    These people use the rhetoric of engineering but I do not think that word means what they think it means, as the saying goes. They are not engineers nor are they on a path to becoming engineers.

    That society, for all of its rhetorical sophistication, is a bunch of monkeys who found a resonant part of the biosphere to start banging on ’cause when they do it sparks of pretty things. And there’s a boatload of folks in the VC-related society egging them on.

    These are dangerous bozos.

    There, I said it.

    There quite analogous to “quant” professionals in finance, if you look at it right — resonance as excuse for unwise pounding, potentially leading to a system that shakes itself into collapse. Only with the Synthbio-crowd, the collapse we’re talking about is, indeed, our species and its biosphere.

    -t

  • http://biblek12.org Kirk W. Fraser

    E.coli and E.bola are different by two characters. I’ve had a denial of service attack and more by a hacker so I know they are evil little dudes. Even Ray Kurzweil failed to respond to a question on how he was going to keep the singularity (AI cloud) safe for humans.

    The only place to look for future hope is the Bible. It says world without end. So dispite all the plagues of nature and those mankind brings on itself (like trying to nuke Apophis) some people will survive. Things will be better for the Rev. 12:5 manchild than the 12:6 left behind. Join me at http://biblek12.org

  • http://88proof.com/synthetic_biology/blog JonathanCline

    You said “heat shot”… I think you mean, “heat shock”.

    To the previous commenter who said, “The Endy-related society will also be quick to say – at least if you ask them or keep pressing the point in harsh blog comments – that they don’t actually understand how these organisms will do once released in the wild or how they evolve. Not even close” :

    The answer is that the organisms most likely die if ever they had to compete in the wild — survival amongst competitors is how common organisms are already evolved, and right now by changing things it makes the GMO significantly weaker. Though this does not 100% rule out something else being possible and I am also very interested in the safety aspect.

  • http://www.techiestuff.org TechieStuff

    Are those viruses that you are handling? Daang….