Contingent History

I think the importance of “path dependence” is highly overlooked in science. Anytime someone invokes an equation that is based on equilibrium or steady-states (which is often), they are implicitly saying that we can ignore all of the system’s past history. We just wait until everything settles down at some fixed state, which we can determine more easily based on balancing some first derivatives. However, many real situations have multiple equilibria, and the final state of the system depends very strongly on previous trajectory. A recent paper in Nature provides a clear example regarding antibiotic resistance in which bacteria colonies that are exposed to an drug gradually are much more likely to survive than if the drug is introduced suddenly. The explanation is that the trait of resistance at high concentrations of the antibiotic may require multiple mutations, but having exactly single mutation is NOT adaptive at either zero or high concentrations. [Since mutations that confer resistance are costly, they provide negative fitness if no antibiotic is around. And if a lot of antibiotic is around, having just one mutation usually isn’t enough] As a result, bacterial with just one mutation will only be selected for at intermediate concentrations. But, of course, you have to have one before you can have two. A simplified chart with the arrows pointing to states with higher fitness would be:


Low Concentration: Zero Mutations <— One Mutation <—- Two Mutations
Medium Concentration: Zero Mutations —> One Mutation <—- Two Mutations
High Concentration: Zero Mutations —> One Mutation —-> Two Mutations

So there is a “barrier” to having a single mutation that can only be overcome if the system spends time at intermediate concentrations. [There is a strong analogy here with the free energy landscape vs reaction coordinate in chemistry] This allows for the first, “potentiating mutation,” which will be essential when the antibiotic is increased to the high concentration. Since evolution cannot “look ahead,” it can only select for mutations that provide fitness in the current landscape. This is what prevents the first mutation from occurring before the antibiotic is applied (unless we want to include the possibility of random “genetic drift,” but this is would be much less frequent). The bottom line is that our common practice of putting antibiotics into everything – like soap and cleaning sprays – is worse than we thought, since it creates the prefect environment to “train” bacteria to become resistant. Also, this shows why the schedule of administering antibiotic pills is so important. If the concentration in the body is too low for a long time, if can also lead to the evolution of resistant populations.

The current experiment made use of the ability to freeze generations of bacteria for later DNA sequencing so that the complete evolutionary history could be traced. The researchers also used genetic engineering to create bacteria with specific combinations of mutations so that the relative fitness could be quantified.

In the Ancestor’s Tale, Richard Dawkins raises the possibility of using the traits (and DNA) of living species to learn about the past environments its ancestors lived in, since some to the adaptations will still be reflected in the progeny.


Our power grid is complicated enough to count as a complex system, in which changes in any one part can have unexpected effects on other parts. For example, the great northeast blackout of 2003 was caused by a small error that cascaded , causing failures in larger and larger swaths to the system. Thus, a power-line contacting a tree near Cleveland led to the lights going out in New York City. To prevent serious damage, automatic shutoffs are usually installed. However, while this prevents the need for expensive repairs, it also greatly increases the chances that a cascade will start in the first place. This is likely the causal factor in the famous Super Bowl blackout of 2013. The setting for a relay was set too low, so it “…activated the switch gear, which is designed to cut some power to isolate any problem and prevent system damage and a larger outage.” Therefore, learning about complexity theory, especially as it applies to power systems, is very important.

Bell Labs

I just finished reading The Idea Factory by Jon Gertner, a loving, mostly oral history of Bell Laboratories. Not only is the list of innovations (as complied by the Wikipedia page) including the transistor, the laser, the charge-coupled device (CCD), information theory, the UNIX operating system to come out of Bell Labs amazing,but it is important to remember that this was a part of a private corporation. Back when AT&T was a government regulated monopoly, the labs could rely on an uninterrupted flow of funding for applied and basic research. While modern tech companies are loathe to spend money on open-ended research that may or may not provide tangible profits decades hence, Bell Labs was charged with finding the technology that would support the national phone system as it rapidly expanded to provide “universal connectivity” for all citizens. It may not be an exaggeration to say that Bell Labs invented the information age, since it is hard to imagine the internet enjoying the widespread appeal that it has without the bandwidth and computing power made possible by transistors and fiber optics connections. Yet, Bell Labs was also sowing the seeds of its own demise.


Zombie Game Theory

I just watched the movie Warm Bodies, which is not so much a Zombie movie as a Romantic Comedy rehash of Romeo and Juliet in which half of the eponymous couple is of the undead persuasion. Which is probably why I enjoyed it so much (my second favorite: Shaun of the Dead). In any case, I think that the fact that the genre has enjoyed a great resurgence (AMC’s Walking Dead, the forthcoming World War Z) is a good oppertunity to talk about the game theory of zombies.

There is something very primal about the survival instinct aroused by the threat of a mindless horde of humanoids motivated only by a desire to kill you and take your most precious resource. The fact that these foes feel no compassion and cannot be bargained with, appeased, or deterred by show of force is almost written into the definition. In this case, there is no alternative than to fight or seek refuge. The compassion “switch” in our brain gets turned off, and we are prepared to kill in self-defense without hesitation. The fact that these beings resemble (or recently were) humans equipped with compassion or remorse is of no consequence, we are told to regard zombies as killing “machines” that will not stop for anything. This is an almost explicit version of tit-for-tat reasoning, in which thou shall not show compassion to those who cannot reciprocate is the only directive.

As Max Brooks, the author of the World War Z novels said:

The lack of rational thought has always scared me when it came to zombies, the idea that there is no middle ground, no room for negotiation. That has always terrified me. Of course that applies to terrorists, but it can also apply to a hurricane, or flu pandemic, or the potential earthquake that I grew up with living in L.A. Any kind of mindless extremism scares me…

Now we are entering the realm of game theory, as formulated by evolutionary psychology. It is adaptive to cooperate (and generally not harm) your friends, with whom you cooperate. However, should your friend have the misfortune of becoming a zombie, it is greatly maladaptive (to you) to show mercy. For your own survival, you must go into an antagonist mindset towards your (erstwhile) friend. This is the same antagonism you would generally feel towards strangers who encroached on your territory and are much more likely to kill you than come bearing goods with an opportunity to trade for mutual benefit. What is interesting is that this attitude can switch, at least towards the strangers, if they prove to be capable of cooperation after all. Then you might even learn to change your worldview to accommodate their change in status from mortal enemies to co-parties. In a world of shifting alliances, this must occur often, but importantly, never if the person is physically unable to show empathy, or at the very least, some enlightened self interest. Here mindless, as in “mindless zombie,” means an inability to have either.

But what if it is not apparent which classification to put a person into? Zombies resemble humans, after all. The movie Blade Runner confronted this issue head on. There is an inherent unease about not knowing if someone is a human capable of empathy, or a replicant, who is not. It is very wrong to murder fellow humans. It is obligatory to kill replicants. Making enemies into “other than human” is a very important goal of propaganda. This is also why zombies are “the dead,” since it is hard to achieve a greater state of “otherness” than entering the “other world.” Warm Bodies takes up this theme as well, but in a more Montague and Capulet sort of way.

There is, amazingly, an inverse of zombification. And that is love. As Steven Pinker points out, when searching for a mate, you would ideally want to find someone who won’t ditch you the moment it is to his/her advantage. He compares it to the signing of a long-term lease – you only want to commit if you can rely on something more than the rational choices of your potential mate, which could be swayed by other options, should they become available.

That is why many (all?) love songs proclaim the singer to be in the thrall of love and cannot escape, even if he (usually it is a he proclaiming his undying love) wanted to. Love is not just the ability to show compassion, it is inability to do otherwise.  If you think that “lover” is the additive inverse of “zombie,” Warm Bodies makes a lot more sense.

PS. Zombies are real. Some parasites affect the behavior of their hosts in ways that are very beneficial to the parasite (and detrimental to the host). Such as:

…the virus is harmful only to caterpillars of insect species, like gypsy moths. When a caterpillar bites a baculovirus-laden leaf, the parasite invades its cells and begins to replicate, sending the command “climb high.” The hosts end up high in trees, which has earned this infection the name treetop disease. The bodies of the caterpillars then dissolve, releasing a rain of viruses on unsuspecting hosts below.

Probably the most well-known example, are the zombie rats infected with Toxoplasma gondii, a protozoa that has part of its life-cycle in rats, and part in cats. The parasite, while in a rat, makes its host less afraid of cats, increases the probability that the protozoa will make it to its next phase.