Secret Codes in Bacteria

Neat:

Researchers have invented a new form of secret messaging using bacteria that make glowing proteins only under certain conditions. In addition to being useful to spies, the new technique could also allow companies to encode secret identifiers into crops, seeds, or other living commodities.

[...]

The new scheme replaces the fuse with seven colonies of Escherichia coli bacteria, each given a gene for a different fluorescent protein. When, and only when, these genes are turned on do the bacteria make these proteins and light up. The colors, including yellow, green, and red, vary based on which gene is expressed. All are clearly visibly different to the naked eye. With their colorful bacterial colonies in hand, the researchers then created a code using pairs of different colored bacteria. Having seven colors gave them 49 combinations, which they used to encode the 26 different letters and 23 alphanumeric symbols such as "@" and "$." They wrote a message by simply blotting pairs of colored bacteria in rows. To "print" the message, the researchers transferred the bacteria onto a plate containing agar, a bacterial growth medium, into which they pressed a sheet of nitrocellulose "paper" that immobilizes the bacteria.

At this point, the bacteria on the nitrocellulose paper remain invisible. But the message receiver can turn on the key genes and make the colors light up by pressing the nitrocellulose paper into an agar plate containing a chemical trigger that activates expression of the fluorescent proteins. (The proteins chosen to light up are ones the bacteria don't normally use, so unless the researchers activate them, they stay quiescent.) As long as the receiver knows which colors correspond to which characters, the message is revealed. But Walt and his colleagues added one more safeguard as well. Into some bacteria they inserted genes for resistance to particular antibiotics; the idea is that only the antibiotic-resistant bacteria are carrying the real message. If the message fell into the wrong hands, the receiver would see a mix of colors once the genes were activated and be unable to read it. But if the decoder added the right antibiotic, nonresistant bacteria and their colors die away, and the message becomes clear. The first example, reported in today's issue of the Proceedings of the National Academy of Sciences reads "this is a bioencoded message from the walt lab @ tufts university 2010."

Posted on October 27, 2011 at 12:01 PM • 28 Comments

Comments

RandyOctober 27, 2011 12:45 PM

This is a good idea...until...WE ALL DIE from all the antibiotic-resistant bacteria.

Randy -- broughttoyoubythelawofunintendedconsequences

Fred POctober 27, 2011 12:49 PM

My immediate thought is that an attacker could:

1) Activate the genes on all the bacteria
2) Take a picture
3) Culture the bacteria, being careful to keep the different types and their origins separate.
4) Then either kill and sequence the bacteria (to find the antibiotic resistant strains), or use small samples to test antibiotics until you find the correct one.

So to me, it sounds mostly like obfuscation of a message and making it more expensive to crack.

edOctober 27, 2011 1:01 PM

I don't see it being useful to spies. Once the chemical trigger is known, then anyone can read the messages. And you need the chemical to read any messages, so if a spy is carrying the chemical, then it can be captured. It seems unlikely that the spy-handlers could quickly switch triggers (it's coded in the bacterial genes, no?), or develop new bacterial strains to respond to new chemical triggers. Messages in color-coded glowing bacteria is a nice movie-plot element, though. And remember, kids, you don't have to color within the lines.

vwmOctober 27, 2011 1:07 PM

I understand the cloak and dagger application (plus having antibiotic-resistance ready for a plot twist towards a disaster or horror movie).

But how do you use that stuff as a commodity identifier? When applying the bacteria on anything else but the immobilising nitrocellulose, wont they start growing into a colourful alphabet soup soon?

Furthermore they will mix with the identifier of the last commodity carried in the same container. Which is fine, as long as you don't get a key collision. That is re-use the same resistance. Which might happen soon, as you'll need to throw in some resistances for the decoy-bacteria in each batch as well.

Laurent GauthierOctober 27, 2011 1:07 PM

I actually remember watching on Youtube a symposium on bio-security where they were talking among other things about encoding codes in DNA to enable identification of synthetic DNA. I will try to dig a reference.

vwmOctober 27, 2011 1:20 PM

@ed: I guess the trigger is part of the protocol (some kind of salt at its best) and is assumed to be generally known.

The secret key is resistance to particular antibiotics. Given enough antibiotics and resistances, you can even implement asynchronous encryption (If you capture a spy, the antibiotics he uses to read do not tell you what kind of resistance he uses to write).

Of course, wasting antibiotics and resistances on communication might not be the best idea.

XOctober 27, 2011 1:21 PM

You know, as soon as this is used commercially, we're going to start seeing youtube videos showing how if you mix item X with 409 cleaner (or some other common household chemical), it glows...

I do wonder what happens when someone using that antibacterial-alcohol grabs the bacteria end of the stick... Or how resistant they are to UV (aka sunlight).

Petréa MitchellOctober 27, 2011 1:34 PM

Given the problems with antibiotic resistance, maybe it would be better to design some invented vulnerability into the non-coding bacteria. Then you aren't running the risk of spreading resistance to useful drugs, and the range of substances you can use as the key is much broader.

Jordan BrownOctober 27, 2011 1:34 PM

It's interesting, but it seems more like invisible ink than like a code. (Yes, there's a cypher in how you encode letters into colors, but you could use that same cypher with crayons.)

Clive RobinsonOctober 27, 2011 1:53 PM

The idea of a "DNA Switch" is not new and is offten seen in nature in plants of the potato/tabacco species as well as several others.

In the case of a potato, it is quite safe to eat provided it has not been exposed to light for a sufficient time to cause the trigger.

When a potato has been triggered it starts to turn green and as a side effect also produces a toxin which can quite easily kill people.

When I was young my parents where quite aware of this and taught me to discard green potatoes and also make sure I fully dug out any eyes that had sprouted.

Oddly this knowledge does not appear to have been passed on through the TV Dinner generation.

But it has made it into a fairly recent Spy Thriller for children as one of the books in the Alex Rider series, which my son quite enjoys.

MarioOctober 27, 2011 2:38 PM

This reminds me of speculation concerning extra-terrestrials trying to communicate with us. Some people think that if aliens arrived on this planet, ages ago, that they would have encoded a message in the DNA of the creatures on this planet -- a message that would be found when intelligent and sufficiently advanced life evolved.

dilbertOctober 27, 2011 3:24 PM

@Mario,

Actually this was done millions of years ago... a secret group of scientists have already decoded the message. It said "So long and thanks for all the fish"

Clive RobinsonOctober 27, 2011 3:49 PM

@ Mario,

"Some people think that if aliens arrived on this planet ages ago, that they would have encoded a message in the DNA of the creatures on this planet"

Hmm there is also a number of respected scientists who believe that life on this planet might have started with alien DNA ariving on comets/meteors and other bits of space bourn debris.

However as has been observed from examining space debris. from around earth, most of it is contaminated by a very fine layer of human biological waste.

Thus one or two people have speculated if life on this planet is actually the outgrowth of alien sewage...

Of one thing we do appear reasonably certain all life on this planet derived from a sludge of Blue-Green algae, which lets face it does look like the contents of your average cess pit...

Which when you think about it kind of alters your outlook on life ;-)

vexorianOctober 27, 2011 8:05 PM

the new technique could also allow companies to encode secret identifiers into crops, seeds, or other living commodities.
What could possibly go wrong?

Clive RobinsonOctober 27, 2011 9:29 PM

@ vexorian,

"What could possibly go wrong?"

You forgot the obligatory sarcasm quotes ;-)

But you do raise a valid point in that we realy don't know enough to say what is and is not safe when it comes to splicing bits of DNA from one organism to another.

Lets be honest man has been practicing Genetic Modification for several thousand years, by selective cross breeding. In most cases its goal has been to improve foods in one way or another.

The earliest was selective cross breeding of grasses to produce cereal crops such as wheat.

Now as some know something between 1.5 and 2% of the population of the Western world are sufficiently allergic to wheat that it can kill them if they ingest it for a period of time. However in many cases they can still tolerate other older less cross bred cereal crops. However this is only part of the problem quite a few foods that are a result of genetic modification by cross breeding are linked to other allergies and syndromes (IBS being just one catchall).

In short even where the genetic modification has been by semi-natural methods, the result has been to cause the immune response in a significant percentage of the population to be activated to a level where it can cause significant harm or death.

And in some cases (such as causing cancer) it can take far longer than the testing time required by the likes of the FDA for problems to show up (which is one reason why drugs get withdrawn). It has been shown with some GM crops that they can cross breed with existing crops and therefore the GM part can escape. We also see cases of viral disease jump for reasons we don't yet sufficiently understand from one species to another such as swine and avian flu.

I guess if you want to "play at being God" then you should be mindful of areas "where Angels fear to tread"...

AntibioticsOctober 28, 2011 3:07 AM

@Randy This is a good idea...until...WE ALL DIE from all the antibiotic-resistant bacteria.

Yeah, and the invasion has begun already:

The bacteria methicillin-resistant Staphylococcus aureus, or MRSA may be found on the skin and in the noses of nearly 30
percent of the population without causing harm. Experts believe it
survives on surfaces in 2 percent to 3 percent of homes, cars and
public places.

http://well.blogs.nytimes.com/2007/10/23/...

@Fred P So to me, it sounds mostly like obfuscation

Yeah, and about obfuscation in bacteries, prior art that is far better: http://www.schneier.com/blog/archives/2011/01/...

This post http://www.schneier.com/blog/archives/2011/10/... shows a decoding methods which only needs antibiotics. But what about juste encrypting the message before laying the bacteries on the paper, instead of spreading antibiotic-resistant bacteries as dangerously as GMO seed industry does ?

Toby SpeightOctober 28, 2011 3:47 AM

I don't think it's likely that anyone will seriously use this for hidden communication (in my lifetime, anyway). But I fully expect to see it used for that another purpose - identification. Imagine you're a researcher, and want to know if your modified organisms out-compete the natural ones in a particular environment, for example (and if so, then which of the many modifications you made were most effective).

The key quote for me is "the new technique could also allow companies to encode secret identifiers into crops, seeds, or other living commodities". GM crop manufacturers want tight control over the farmers who grow their crops, and often disallow the use of seed from the grown crop. This kind of watermarking would enable them to identify a crop sample as being derived from their product, and perhaps even which customer, allowing them to enforce their license terms.

Whether you think that's a good thing or not is entirely up to you.

SteveOctober 28, 2011 9:33 AM

I'd be much more impressed if they could encode into the genetic material of an ossifrage. (Particularly one that was, say, squeamish?)

elkhornNovember 1, 2011 9:01 PM

This is one of those things that falls into the category of "Just because we can do it doesn't mean that we should do it".

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