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.

Tomorrow,
I'll be at the table
When company comes.
Nobody'll dare
Say to me,
"Eat in the kitchen,"
Then.

Besides,
They'll see how beautiful I am
And be ashamed--

I, too, am America.

Peace be upon you.

Egypt Week – Corruption and Cooperation

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]

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[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.

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.