Egypt Week – I, Too, Sing Egypt

So, this will be a non-science Egypt Week post. Opposition organizers in Egypt have called for a massive protest on Tuesday, anticipating that millions will march on Tahrir Square in the morning. Here is hoping that this leads to better things.

Below is the text of the Langston Hughes poem I, Too, Sing America. While it was obviously written in the context of racial dynamics and inequality in the United States, its sense of hope, defiance, and the inevitability of justice speaks for oppressed and dismissed people everywhere.

I, too, sing America.

I am the darker brother.
They send me to eat in the kitchen
When company comes,
But I laugh,
And eat well,
And grow strong.

I’ll be at the table
When company comes.
Nobody’ll dare
Say to me,
“Eat in the kitchen,”

They’ll see how beautiful I am
And be ashamed–

I, too, am America.

Peace be upon you.

Egypt Week – Corruption and Cooperation

This post was chosen as an Editor's Selection for So, our next Egypt Week feature is a theoretical paper on a topic closely related to the last post. Once again, we are interested in understanding the mechanisms that are responsible for encouraging or enforcing cooperation, thereby facilitating collective action. Last time, we talked about a paper that found that “altruistic” or “third-party” punishment is common in large-scale, complex societies, but is rare in small-scale societies, while “spiteful” punishment is universal.

Many empirical and theoretical studies of cooperation focus on punishment as a mechanism for enforcing societal norms. Basically, you set up a situation where the group benefits if people cooperate, but each individual benefits by not cooperating. If mechanisms exist to punish people for not cooperating, you get cooperation. Which is to say that the existence of punishment changes the individuals’ incentives. The benefits of not cooperating are outweighed by the cost of being punished. No big mystery there.

But what if punishment itself is costly? Punishment can stabilize cooperation, but what stabilizes punishment? Some models rely on an infinite succession of punishments, where people punish people who fail to punish people who fail to cooperate, and people punish people who fail to punish people who fail to punish people who fail to cooperate, and people punish … well, you get the idea.

Today’s paper asks if cooperation can be enforced by corrupt punishment. That is, while punishment is still treated as costly, punishers are not necessarily cooperators themselves, as is commonly assumed in models of this sort. Furthermore, the corrupt punishers (“policers”) suffer a lower cost when punished than do non-punishers (“civilians”).

A corrupt policer looks forward to a cushy retirement, thanks to his hypocritical enforcement of others’ cooperation. Little does he suspect how a new, young partner, who colors outside the lines, but has a heart of gold, will turn his whole life upside-down, with hilarious consequences.

The model shows that in the presence of a modest power imbalance, cooperating civilians and corrupt policers can coexist. That is, a moderate level of corruption is consistent with, and can even stabilize cooperation. However, when the power imbalance becomes large, corrupt policers overrun the population, the system breaks down, and cooperation is lost.

The first part of the result is nice because it provides a degree of robustness to the “cooperation through punishment” paradigm, as it does not require the punishers to be acting altruistically themselves.

The second part of the result is perhaps more directly relevant to Egypt Week. Societies can function in the presence of a degree of inequality, and they can tolerate a certain amount of hypocrisy from their leaders. But too much hypocrisy and inequality is inconsistent with the type of collective action that governments are meant to facilitate.

It is heartening to see that when a less corrupt alternative presents itself, people are still capable of collective action on a massive scale.

Peace be upon you.

Úbeda, F., & Duéñez-Guzmán, E. (2010). POWER AND CORRUPTION Evolution DOI: 10.1111/j.1558-5646.2010.01194.x [1] [2]


[1] This is an online, ahead-of-print publication, which is why there are no page numbers, but it should be findable through the DOI.

[2] Disclosure: The first author on this paper is a long-time friend and colleague, and we have worked together on issues of intragenomic conflict. Here is photographic evidence of our friendship, from when we were traveling around Lyon, France like Thelmo and Louis following the 2010 SMBE meeting:

On our way to the Palais de Justice, we accidentally activated our Wonder-Twin Powers. Francisco took the shape of an evolutionary biologist, and I took the form of a French trash can. Photo by Gleek.

Egypt Week – Spiteful versus Altruistic Punishment

So, welcome to the first Egypt Week edition of Lost in Transcription. We’re going to kick it off with an anthropology paper that uses a cross-cultural approach to study the origins of human punishment and cooperation.

If you’re not familiar with this vein of research, let me set the stage for you. The “problem” of cooperation when people talk about it in anthropology, biology, and economics is this. If you take a super naive view of natural selection, it would say that we should have evolved to ruthlessly pursue our own self interest. In particular, if we have an opportunity to cheat and get away with it, the logic of self interest suggests that we should. From this perspective, the whole idea of successfully engaging in collective action seems absurd.

Contrary to this naive expectation, we observe that people do forego opportunities to pursue their own narrow self interest, and the history of civilization is one of successful collective action on an enormous scale.

Of course, at some level, we know what the answer is.[1] Natural selection does not act only on the short-term self interest of the individual, but favors behaviors that enhance survival, reproduction, and the propagation of the genes carried by the individual. Those things are all affected by more that just who gets the biggest piece of the pie in a given interaction. Other factors that come in to play include selection on kin or social groups, the establishment and enforcement of social norms, and systems of reward, punishment, and reputation.

So, much of the work in this field focuses on trying to figure out which among these various effects has played the greatest role in the origin of the enormous capacity for cooperation that underlies all human societies.

This paper uses a standard set of experimental protocols, applied to twelve societies that differ enormously in size and complexity of social organization. The societies studied span the range from the Hadza, hunter-gatherers from Tanzania, to the people of Accra, the capital city of Ghana. Each experiment is a two-player or three-player game in which the players make decisions that determine how money is distributed. The goal here is to measure the degree of “altruism” in each society, the degree of “second-party” punishment (how willing are people to punish someone who is not generous to them), and the degree of “third-party” punishment (how willing are people to punish someone who is not generous to someone else).

The first experiment used was the Dictator Game (DG), in which the experimenter provides Player 1 with an allotment of money, and Player 1 determines how that money will be divided between themselves and Player 2. The game is played once, and is played anonymously, so there is nothing to stop Player 1 from offering nothing to Player 2. This experiment establishes a baseline level of cooperation or altruism, quantified by the average proportion of the money that Player 2 receives.

The second experiment is the Ultimatum Game (UG). This is like the Dictator Game, but Player 1 proposes a division of the allotment of money, and Player 2 can either accept or reject this proposal. If Player 2 rejects, both players walk away with nothing. This measures the willingness to punish ungenerous individuals who make low offers. Note that for any non-zero offer, Player 2 actually has to give up money in order to punish Player 1, making this a “spiteful” form of punishment.

The third experiment is the Dictator Game, but involves a third player, who receives an allotment of money from the experimenter. After Player 1 determines how the primary allotment will be divided between him/herself and Player 2, this third player has the option of paying back a portion of their allotment in order to have three times that amount taken away from Player 1. This again measures the willingness to punish an ungenerous offer, but this time the punishment is “altruistic” rather than “spiteful,” since the punisher was not actually the one who suffered the ungenerous offer.

A few general patterns emerged from this set of experiments.

(1) Small-scale societies were less generous (Player 1 made lower offers) across all three games compared with larger societies.

(2) Second-party punishment was observed at similar rates across all societies. Thus, in the small-scale societies, individuals “expect to get a fair share even when they do not want to give a fair share.”

(3) Third-party punishment was much more common in larger societies. And, in fact, in those larger societies, third-party, “altruistic” punishment occurred more often than “spiteful” second-party punishment.

Taken together, what these patterns support the idea that human cooperation may have emerged first in the context of spiteful punishment, rather than through altruistic or community-oriented enforcement of social norms. They suggest that third-party punishment arises only with the establishment of more complex societies. In particular, once a society exceeds a certain size, it becomes difficult to keep track of individual reputations. In such groups, collective-action problems require the existence of institutions that promote and reward third-party punishment.

Peace be upon you.

Marlowe, F., Berbesque, J., Barrett, C., Bolyanatz, A., Gurven, M., & Tracer, D. (2010). The ‘spiteful’ origins of human cooperation Proceedings of the Royal Society B: Biological Sciences DOI: 10.1098/rspb.2010.2342 [2]


[1] Editorial note: This is a version of the answer that comes up again and again in science. The world is a complicated place. We (scientists) come in and try to describe it using a really simple model. Then we feign surprise that the simple model does not adequately describe the behavior of the system that we are supposedly modeling. We declare that there is a paradox and build a field around resolving it. This is all fine, as it is just the way that science works, but it is worth remembering that many of the “problems” in science are really artifacts of simplistic models that have achieved an iconic status.

[2] Disclosure: Frank Marlowe, who is the first author on this paper, is a friend, and we have written a paper together on the genetic and ethnographic evidence regarding sex-biased migration in humans.

Egypt Week – Solidarity

So, unless you are in China, you are undoubtedly aware of the massive protests that have been going on in Egypt for the past few days. If you’re like me, you are filled with a mixture of hope and anxiety. I sincerely hope that the Egyptian people will be able to establish a new government that is actually responsive to their needs, and that it can be done with a minimum of bloodshed. But I also know that it is possible that this ends with a brutal crackdown and the Egyptian government resuming business as usual.

Also, if you’re like me, you feel a sense of solidarity with the protesters, but feel completely powerless to do or contribute anything. I am thousands of miles away, and do not have any inside information or clever insights on Egyptian politics and culture. I am a poet and a theoretical evolutionary biologist – two things that find little practical application even in the best of circumstances.

Still, I feel that I want to do something, so I will do what I know. I am going to dedicate this week’s blog entries to the protesters in Egypt and to people everywhere who long for more freedom and better government. Topic-wise, I will discuss a number of recent scientific papers from the evolutionary literature on cooperation, punishment, and corruption.

I have no illusion that this can have any impact on the course of events in Egypt, or on the protests in Jordan, Yemen, and elsewhere. I simply hope that I can contribute something to the knowledge that we are all in this together.

The desire for freedom and safety and a better life for ourselves and our children is not defined or limited by nationality or religion or race or language. As an American, I am fully aware that my government’s rhetoric about freedom and democracy is often at odds with its support of corrupt and anti-democratic regimes, including Mubarak’s. But a government is rarely the same thing as a people. All of the people I have spoken with, American and not, are hoping and praying that this will be a turning point in history, and that the people of Egypt (and Iran and Myanmar and Uganda and on and on) can move forward together into a better future.

Peace be upon you.

Mathematicians and Mongeese: Peeing to Defend Territory? or Mates?

So, you may have heard about Tihomir Petrov, the math professor at Cal State, Northridge who was arrested for urinating on his colleague’s office door. Campus security got video footage of Petrov in the act when they set up video cameras following the discovery of “puddles of what they thought was urine.”

You may be asking yourself, what the heck was this dude thinking? How should we interpret the behavior of this Homo mathematicus (not that there’s anything wrong with it) specimen?

What Professor Petrov was probably thinking.

Fortunately, once again, Science!™ has an answer for you. Urine is commonly used as a scent marker to deter competitors. But deter them from what? Traditionally, it has been assumed that scent marking is primarily used to defend territory against intruders, thereby safeguarding resources such as food and space. However, some recent studies have suggested that scent marking may be used to defend mates and mating opportunities. One of the difficulties in studying such a question, however, is that in many systems, competitors for territory and competitors for mates are the same individuals.

A recent study by a group of researchers in the UK, Uganda, and Switzerland have attempted to separate out these two forms of competition in a study of the wild banded mongoose. This species lives in large social groups that share a territory. Thus territorial competition occurs primarily between different social groups, whereas competition over mates occurs primarily within groups.

“Anal gland secretion (AGS) and urine samples were collected under anaesthesia during routine trapping events”  Image licensed under creative commons from Mike Rohde’s Flickr photostream.

The researchers found that the mongoose populations marked uniformly throughout their territory, and did not appear to increase the frequency of marking in those regions where two territories overlapped. This suggests that, in this species at least, defense of mates and mating opportunities represents a major contribution to scent-marking behavior, perhaps more so than territorial defense.

So, can we extrapolate from the behavior of the wild banded mongoose to the behavior of wild banded mathematician Tihomir Petrov? Of course we can! Should we extrapolate? Absolutely not! But, here at Lost in Transcription, we’re all about the possible, so here is the take-home message. Castle and Beckett should look beyond professional disputes between the two mathematicians. They need to be looking at the love-triangle angle (Love angle4?) for motive.

Alternate theory: As Northridge is, like, the pr0n capital of the country, Petrov might not have been the original urinator. When he saw that the cameras had been set up, he might have assumed that he had been cast in a movie, and that peeing on the floor was what was expected of him. Just sayin’.

Jordan, N., Mwanguhya, F., Kyabulima, S., Rüedi, P., & Cant, M. (2010). Scent marking within and between groups of wild banded mongooses Journal of Zoology, 280 (1), 72-83 DOI: 10.1111/j.1469-7998.2009.00646.x

Genomic Imprinting V: DNA methylation and gene silencing

So, we’ve already discussed the fact that genomic imprinting is mediated through epigenetic differences between the maternally and paternally inherited gene copies. That is, at an imprinted locus, the maternally inherited allele will have one pattern of epigenetic modifications, while the paternally inherited allele has a different pattern. These differences are first established in the male and female germ lines, when the alleles that will eventually become maternally and paternally derived are in physically different locations. It is not hard to imagine, then, how these differences could be established. One pattern of gene expression in spermatogenesis results in the paternal-specific epigenetic modifications. A different pattern of gene expression in oogenesis results in maternal-specific epigenetic modifications.

But what are these epigenetic modifications, and how do they change the expression pattern of the gene?

There are a number of modifications involved in imprinting, but for the moment, we’re going to focus specifically on the simplest and best-understood mechanism: DNA methylation.

The two horizontal lines in this picture represent the two copies of a gene.  The big, solid box is the part of the gene that actually codes for the protein. The open box is the promoter region, which is the part of the DNA sequence responsible for regulating expression of the gene. The lollipop things indicate DNA methylation on cytosine residues (the “C” of the A, C, G, T alphabet that makes up DNA).

In this simplest type of scenario, the DNA sequence in the promoter region binds to a variety of proteins that recruit the molecular machinery that will transcribe the gene, leading eventually to production of the corresponding protein. The addition of methyl groups to the DNA changes its binding properties, so that it no longer binds to this machinery, and that copy of the gene is not transcribed.

If you’re not a molecular biologist, you can think of it like this. The transcription machinery is a bit like a Xerox machine, and the gene is like the master copy of some document. The promoter region is like a lock that has to be unlocked before you can copy this particular document. There are a number of proteins called “transcription factors” that function like a key to this lock. These transcription factors fit nicely on the promoter region, unlocking the gene and resulting in the production of many copies of the gene product.

Adding methylation to the promoter region is a bit like squirting epoxy into the lock. The presence of the methyl groups actually changes the physical shape and chemical properties of the DNA. So, when you try to put the key in, it no longer fits right, and the gene can not be copied.

In the top part, we see the red transcription factor binding to the black promoter region, which will activate transcription from the gene. In the bottom part, methyl (CH3) groups have been chemically added to the promoter region, preventing binding, and thereby preventing transcription.

So, these relatively subtle chemical changes are able to completely alter the functional properties of the gene.

Next time, we’ll talk about how these methylation patterns are maintained through development, and how the two gene copies are able to maintain distinct epigenetic states across multiple rounds of cell division and DNA replication. Make sure to tune in, because it’s really slick!

The two references represent the first proposals that DNA methylation might be the thing that permits the stable transmission of patterns of gene expression across cell divisions.

Holliday, R., & Pugh, J. (1975). DNA modification mechanisms and gene activity during development Science, 187 (4173), 226-232 DOI: 10.1126/science.1111098

Riggs, A. (1975). X inactivation, differentiation, and DNA methylation Cytogenetic and Genome Research, 14 (1), 9-25 DOI: 10.1159/000130315

Naming Advice for New Parents

So, you’re having a baby. There’s one rule, really. Are you listening?

Don’t give your kid the middle name “Lee.”

Here’s the latest “*Lee*” in the news, Ricky Lee Kalichun:

from the Evansville Courier & Press, via Geekologie

Broke into ex-roommate’s apartment. To get back his video games. With a sword.

He was wearing a camouflage jacket, and camouflaged his face as well, with a marker. Maybe he was hoping to be mistaken for one of Jesse James’s girlfriends.

Now, I’m glad that your Grampa Lee was a World War II hero and all, but, really, just – just don’t.

Can you spell scrappy without crappy?

So, I’m among those who believe that a baseball player only gets a reputation for being “scrappy” if they are not very good. You only get called scrappy if you scramble around and smother a ground ball that a fielder with better range would have gotten to easily. (I’m looking at you, David Eckstein.)

I decided to address this question by collecting some data that really has nothing to do with the original question. Using a method similar to that used by the Negative Log Google Naked Ratiometer, I looked at each position to see how often the position was referred to as “scrappy” and how often it was referred to as “crappy.”

For example, the Log Scrappiness for second basemen is calculated by taking the logarithm (base 10) of the number of google hits for “scrappy second baseman” divided by the number of hits for just “second baseman.” Similarly for Log Crappiness. Positions are more often referred to as “crappy” if they are higher on the graph. They are more often “scrappy” if they are further to the right.

If we look at the infielders and outfielders separately, the positions fall close to two straight lines with similar slopes.[1] Within each group, the relative scrappinesses are more or less what you might expect. The interesting thing is that each group has an inverse relationship between scrappiness and crappiness.[2] The scrappier a position is, the less crappy it is.

The solid diagonal line is the iso-(s)crapocline, or the line indicating equal scrappiness and crappiness. First basemen (1B), left fielders (LF), and right fielders (RF) are crappier than they are scrappy. Third basemen (3B), shortstops (SS), second basemen (2B), and center fielders (CF) are more scrappy than crappy.

Pitchers and catchers were left off, since there is too much cross talk on Google with non-baseball uses.

But, let’s get back to the original question: “Can you spell scrappy without crappy?” One answer is, “Yes, if you spell it in Albanian.” Via Google Translate: you can definitely spell i copëzuar without i mutit.


[1] You may have noticed that these straight lines represent power laws. If I were a physicist, I would say something about universality classes, and publish this blog post in Physical Review E.[3]

[2] This seems to violate the assertion I made at the beginning of the entry, but the right way to do address that question would actually be to look at how often “scrappy” is used to describe individual players, and then to compare this to an objective measure of crappiness, based on player statistics.

[3] Oh, SNAP!

Venn-Diagram Guide to 2012 Predictions

So, a lot of people have been making predictions recently about how the world is going to end, or when the rapture is going to start, or what will be the new vampire.  It all just gets so gosh-darned confusing!

Never fear! I have produced this handy-dandy Venn diagram that graphically tells you what things could, conceivably happen in 2012, and which of those things actually will happen:

You’re welcome!

Genomic Imprinting IV: Escalation Between Loci

So, in the previous installment, we introduced the “Loudest Voice Prevails” principle, which describes the evolutionarily stable pattern of gene expression at an imprinted locus where there is an intragenomic conflict over the total level of gene expression. Basically, the allele that favors lower expression becomes transcriptionally silenced. Expression from the other allele (the “louder” voice) evolves to the level that maximizes its inclusive fitness. In this sense, the active allele at an imprinted locus “wins.”

But what is going to happen if we have a pair of imprinted genes that exert opposite effects on the phenotype? If we have a paternally expressed growth enhancer, it will evolve to bring the growth phenotype up to the paternal optimum. If we have a maternally expressed growth suppressor, it will evolve to bring the growth phenotype down to the maternal optimum. But what if we have both?

Well, intuitively, if there is conflict between maternally and paternally derived genes over the optimal growth phenotype, then the phenotype can’t simultaneously satisfy the paternal and maternal optima. One or the other (or both) of these genes will always be under selection to increase its gene expression level (or, equivalently, the activity or longevity of the gene product, etc.). Thus, these two opposing genes will become involved in a kind of arms race.

In the simplest possible model that we can write down, this arms race goes on indefinitely, with natural selection driving each of the genes towards infinite expression. Clearly, in a real biological situation, this will not be the case, and something will step in to bring this escalation to a halt. The questions then become: What stops the escalation? And, what does the system look like at its new, escalated, evolutionarily stable state?

To think about this, let’s return to our analogy from last time, where Pat and Chris are sharing an office, but disagree about what temperature the office should be kept at. Recall that genes are totally passive aggressive, so Pat and Chris don’t compromise or communicate. They just use the tools at their disposal to move the office closer to their preferred temperature. Pat wants the office at 71 degrees. Chris wants it at 70.

We saw that if Pat and Chris both have space heaters, eventually Chris’s space heater is off, while Pat’s holds the temperature at 71. On the other hand, if they both have air conditioners, Pat will turn his/her A/C off, and Chris will get to have the room at 70.

If each of them has a space heater and an air conditioner, we have an arms race on our hands. Whenever the temperature is below 71, Pat will turn up the space heater. Whenever it is above 70, Chris will turn up the air conditioner. In passive-aggressive-allele fashion, this will go back and forth until the space heater and air conditioner are both blasting away. In the absence of any constraints or side effects, it will go on until both are blasting away infinitely.

There are several ways that the escalation could stop, however, each of which has a biological analog.

     (1) Mechanical limitation. There will be some limit beyond which gene expression / activity can not increase. Once one of the genes reaches its limit, the other will win. Like if Pat’s Tufnel-brand space heater goes to eleven, Pat wins. Of course, this will depend on the mechanisms through which the two genes exert their influence. For instance, if Chris’s air conditioner is actually a combination air conditioner / food processor / exfoliator, Chris might have to turn it way way up to get the air conditioning equivalent of a little bit of space heating. Similarly, a gene product might perform multiple tasks, and this pleiotropy could limit its competitive ability in the arms race.

     (2) Production costs. One difference between the single-locus solution and the two-locus solution is the level of energy consumption. If Chris’s space heater is off, Pat’s holds the temperature at 71. If Chris’s air conditioner is maxed out at ten, Pat’s space heater (which goes to eleven, remember) holds the temperature at 71. The difference is that the second solution comes with a huge-ass electricity bill. Can this sort of cost actually halt the escalation? Maybe. This requires either that there are diminishing returns to increased escalation, or that there are accelerating costs to production (like utility rates where your thousandth kilowatt-hour costs more than your first one).

     (3) Intervention. In a real office, we might expect that the manager would come in and yell at Pat and Chris, telling them to turn down their space heater and air conditioner. Maybe the manage would mandate an office temperature of 70.5 degrees. Does this ever happen with genes? Could a consortium of unimprinted genes step in and stop the escalation? There is no evidence to my knowledge of such things happening in the context of genomic imprinting, but this type of intervention is thought to be responsible for meiotic sex-chromosome inactivation, where the autosomes all gang up and put the sex chromosomes in a headlock in order to prevent meiotic drive.

     (4) Side effects. What if turning up Pat’s space heater also makes the music louder in the office? What if Chris’s air conditioner draws so much power that it causes occasional brown-outs? This is the other way in which the escalation between imprinted genes might be self limiting. If we consider a monolithic “growth phenotype” in isolation, then each allele has a simple, monolithic optimum. But genes are seldom like that. A paternally expressed allele may benefit from increased expression due to the effect of that increased expression on growth. But what if that increased expression has other consequences, as well? Maybe those other effects are detrimental to the allele’s inclusive fitness. If those deleterious side effects outweigh the growth-related benefits, then natural selection will not drive further escalation.

In future installments, we’ll look at some specific examples of escalating genes. But first, we’ll step back and look at some of the other features and consequences of imprinted genes.

Kondoh, M., & Higashi, M. (2000). Reproductive Isolation Mechanism Resulting from Resolution of Intragenomic Conflict The American Naturalist, 156 (5), 511-518 DOI: 10.1086/303409

Wilkins, J., & Haig, D. (2001). Genomic imprinting of two antagonistic loci Proceedings of the Royal Society B: Biological Sciences, 268 (1479), 1861-1867 DOI: 10.1098/rspb.2001.1651