Decoding the secret DNA code in Venter's synthetic bacterium

Craig Venter recently created a synthetic bacterium with a secret message encoded in the DNA. This is described in more detail at singularityhub. (My article will make much more sense if you read the singularityhub article.)

I tried unsuccessfully to decode the secret message yesterday. I realized the problem was that I was thinking like a computer scientist, not a biologist. Once I started thinking like a biologist, the solution was obvious.

I won't spoil your fun by giving away the full answer (at least for now), but I'll mention a few things. [Update: I've written up the details here.] There are four watermarks. The first contains HTML. (That's right! They put actual HTML - complete with DOCTYPE - into the DNA of a living creature. That's just crazy!)
The HTML in the genome
I sent email to the link, and they told me I was the 31st person to break the code. I guess I'll need to be faster next time.

The second, third, and fourth watermarks each contain co-authors and an interesting scientific quote. The first watermark also contains the full character set in order, to help verify the decoding, although I was unable to decode a few of the special characters because they only appear once.

I found the following quotes (which match the quotes given by JCVI and in the singularityhub article):
Note that the quotes are one per watermark, not all in the fourth watermark as the singularityhub article claims.

If you want to try decoding the code, the DNA of the watermarks is at Science Magazine. The complete genome is a NCBI, in case you want it.

My loyal readers will be disappointed that I didn't use the Arc language to decode this, unlike my previous cryptanalysis and genome adventures. I started out with Arc, but my existing Arc cryptanalysis tools didn't do the job. I switched to Python since I'm faster in Python and I wanted to do some heavy-duty graphical analysis.

I tried a bunch of things that didn't work for analysis. I tried autocorrelation to try to determine the length of each code element, but didn't get much of a signal. I tried looking for common substrings between the watermarks both visually and symbolically, and I found some substantial strings that appeared multiple times, but that didn't really help. I discovered that the sequence "CGAT" never appears in the watermarks, but that was entirely useless. I tried applying the standard genetic code (mapping DNA triples to amino acids), since apparently Craig Venter used that in the past, but didn't come up with anything. I tried to make various estimates of how many bits of data were in the watermarks and how many bits of data would be required using various encodings. I briefly considered the possibility that the DNA encoded vectors that would draw out the answers (I think a Pickover book suggested analyzing DNA in this way), or that the DNA drew out text as a raster, but decided the bit density would be too low and didn't actually try this.

Then I asked myself: "How would I, myself, encode text in DNA?" I figured Unicode would be overkill, so probably it would be best to use either ASCII or a 6-bit encoding (maybe base-64). Then each pair of bits could be encoded with one of C, G, A, and T. Based on the singularityhub article I assumed the word "TRIUMPH" appeared, so I took "riumph" (to avoid possible capitalization issues with the first letter), encoded it as 6-bits or 8-bits, with any possible starting value for 'a', and the 24 possibilities for mapping C/G/A/T to 2-bits, and then tried big-endian and little-endian, to yield 15360 possible DNA encodings for the word. I was certain that one of them would have to appear. However, a brute force search found that none of them were in the DNA. At that point, I started trying even more implausible encodings, with no success, and started to worry that maybe the data was zipped first, which would would make decoding almost impossible. I started to think about variable-length encodings (such as Huffman encodings), and then gave up for the night. I was wondering if it would be worth a blog post on things that don't work for decrypting the code or if I should quit in silence.

In the middle of the night it occurred to me that the designers of the code were biologists, so I should think like a biologist not a computer scientist to figure out the code. With this perspective, it was obvious how to extend the genetic code to handle a larger character set. The problem was there were 64! possibilities. Or maybe 64^26 or 26 choose 64 or something like that; the exact number doesn't matter, but it's way too many to brute force like I did earlier. However, based on the quotes in the singularityhub article, I assumed that the substring " OUT O" appeared in the string, made a regular expression, and boom, it actually matched the watermark, confirming my theory. Then it was a quick matter of extending the technique to decode the full watermarks. As far as I can tell, the encoding used was arbitrary, and does not have any fundamental meaning. As I mentioned earlier, I'm leaving out the details for now, since I don't want to ruin anyone else's fun in decoding the message.

In conclusion, decoding the secret message was a fun challenge.

Your relationship: mathematically doomed or not?

I came across an interesting paper that uses a mathematical model of relationships to show that relationships are likely to fall apart unless you put more energy into them than you'd expect. To prove this, the paper, A Mathematical Model of Sentimental Dynamics Accounting for Marital Dissolution by José-Manuel Rey, uses optimal control theory to find the amount of effort to put into a relationship to maximize lifetime happiness. Unfortunately, due to a mathematical error, the most interesting conclusions of the paper are faulty. (Yes, this is wildly off topic for my blog.)

To briefly summarize the paper, it considers the feeling level of the relationship to be a function of time: x(t). The success of the relationship depends on the effort you put into the relationship, which is also a function of time: c(t). In the absence of effort, the feelings in the relationship will decay, but effort will boost the relationship. This is described with the catchphrase "The second thermodynamic law for sentimental interaction", which claims relationships deteriorate unless energy is added.

Next, your overall happiness (i.e. utility) is based on two more functions. The first function U(x) indicates how much happiness you get out of the relationship. The better the relationship, the happier you are, but to a limit. The second function D(c) indicates how much it bothers you to work hard on the relationship. All else being equal, you want to put some amount of effort c* into the relationship. Putting more effort than that into the relationship drains you, and putting a lot more effort drains you a lot more.

To summarize the model so far, you need to put effort into the relationship or it will deteriorate. If you put more effort into the relationship, you'll be happier because the relationship is better, but unhappier because you're working so hard, so there's a tradeoff.

The heavy-duty mathematics comes into play now. You sum up your happiness over your entire life to obtain a single well-being number W. (A discount rate is used so what happens in the short term affects W more than what happens many years in the future.) Your total happiness is given by this equation:
Equation W
Your goal is to figure out how much effort to put into the relationship at every point in the future, to obtain the biggest value of W. (I.e. determine the function c(t).) By using optimal control theory, the "best" effort function will be a solution to the paper's Equation 2:
Equation 2
From this, you can compute how much effort to put into the relationship at every point in the future, and what the final destiny of the relationship will be. The paper determines that there is an optimal equilibrium point E for the relationship, and you should adjust the effort you put into the relationship in order to reach this point.

However the paper has one major flaw at this point. It assumes that all trajectories satisfy Equation 2, not just the optimal one. (As the paper puts it, "The stable manifold is the only curve supporting trajectories leading to equilibrium.") From this, the paper reaches the erroneous conclusion that relationship dynamics are unstable, so a small perturbation will send the relationship spiraling off in another direction. In fact, a small perturbation will cause a small change in the relationship. The paper's second erroneous conclusion is that "effort inattentions" (small decreases in the effort put into the relationship) will cause the relationship to diverge down to zero and relationship breakup. In fact, the paper's model predicts that small decreases in the effort will cause small decreases in the relationship.

To make this clearer, I have annotated Figure 3 from the paper. My annotations are the "yellow notes":
Annotated Figure 3
The trajectories that the model obtains according to Equation 2 are mostly nonsensical, and exclude sensible trajectories, as I will explain.

Black line A' shows what happens if you start off putting "too much" effort into the relationship. You end up putting more and more effort into the relationship (upper-right), which will yield worse and worse well-being (W), turning the relationship into an obsession. Obviously this is neither sensible or optimal.

The model claims that Black line A'' is explains relationship breakups, where the relationship effort drops to 0, followed by the collapse of the relationship below xmin. Again, this is a nonsensical result obtained by using Equation 2 where it does not apply. According to the model, effort c* is the easiest level of relationship effort to provide. Thus, a trajectory that drops below c* is mathematically forced to worsen well-being function W, and doesn't make sense according to the model of the paper.

The paper poses the "failure paradox", that relationships often fail even though people don't expect them to. This is explained as a consequence of "effort inattention", which drops your relationship from a good (equilibrium) trajectory to a deteriorating trajectory such as A''. I show above (in orange) two alternate trajectories that recover the relationship, rather than causing breakup. The horizontal orange line assumes that after some decline, you keep the relationship effort fixed, causing the relationship to reach the stable orange dot above Wu. The diagonal orange line shows that even if your relationship is on a downwards trajectory, you can reverse this by increasing the effort and reach the "best" point E. Note that both of these trajectories satisfy the basic model of the paper, and the trajectories achieve much higher wellbeing than trajectory A''. This proves that A'' is not an optimal trajectory. (I believe the optimal trajectory would actually be to jump back up to the yellow-green line as soon as possible and proceed to E.)

Another erroneous conclusion of the paper is that E is the unique equilibrium point and is an unstable equilibrium. In fact, any point along the upwards dotted diagonal line is a stable equilibrium point. Along this line, the effort c is the exact amount to preserve the relationship feeling level x at its current value. Any perturbation in the relationship feeling x will be exponentially damped out according to Equation 1. In other words, if the feeling level in the relationship gets shifted for some reason (and the effort is unchanged), it will move back to its original path. Alternatively, if the effort level changes by a small amount, it will cause a correspondingly small (but permanent) shift in the relationship feeling, moving along the diagonal line. The relationship will not suddenly shift to line A' or A'' and go crazy.

To summarize, the paper makes the faulty assumption that all relationship trajectories (and not just the optimal one) will follow Equation 2. As a result, the paper yields nonsensical conclusions: relationships can surge up to infinity (line A') or down to 0 (line A''). The paper also reaches the mistaken conclusions that relationships have a single equilibrium point, this equilibrium point is unstable, and temporary inattention can cause relationships to break up. These conclusions are all erroneous. According to the paper's model followed correctly, relationships are stable to a rather boring degree.

Overall, I found the mathematics much more convincing in Gottman's The Mathematics of Marriage: Dynamic Nonlinear Models which applies catastrophe theory (the hot math trend of the 70s) to marriage. To vastly oversimplify, once your relationship is in an unhappy state, it takes a great deal of effort to flip it back to a happy state. This is pretty much the exact opposite of the linear model that Rey uses.

Disclaimer: My original posting was rather hand-waving; I've significantly edited this article to fill in some of the mathematical details.

Credits: I came across this article via Andrew Sullivan. ("Hat tip" is just too precious a term for me to use.)