Egypt Week – Resources

February 5, 2011 jonfwilkins Leave a comment

So, this brings us to the end of the Egypt Week posts here at Lost in Transcription. Of course, the protests are still going on in Egypt and elsewhere. Here in Santa Fe, New Mexico, I just drove by a rally down by the State Capitol Building in support of the Egyptian protesters. And, as many people have been pointing out recently, if the protests succeed in removing Mubarak (and it is seeming more likely that they will), this is just the beginning of a very messy process that will likely continue for some time.

At this point, Lost in Transcription is going to be returning to its regularly scheduled mix of science, literature, and snarky pop-culture commentary. But that does indicate any lessening of the desire to support the protests or goodwill towards them. For any readers interested, I have tried to compile a short list of resources for keeping up with what is going on in Egypt.

Al Jazeera in English – for current information about events on the ground

Asmaa Mahfouz’s vlog – which helped to trigger the protests

Virtual March – Facebook online “event” to show solidarity with the protesters

Wikio Egypt – aggregated recent blog entries on Egypt

The New Republic – overview of the major players in the current crisis

If there is a site that you have found to be particularly helpful in understanding the current situation in Egypt, please post it in the comments. Or, if you know of things that can be done to more actively support the protesters, please include information on that in the comments as well.

Peace be upon you.

Behavior, biology, Egypt Week, science

Egypt Week – Oxytocin and Ethnocentrism

February 5, 2011 jonfwilkins Leave a comment

So, as we approach the end of Egypt Week, we are going to talk about recent paper in PNAS. The researchers examined the effects of oxytocin on the extent to which people exhibit in-group favoritism. They use ethnic markers to indicate in-group versus out-group membership. In this study, which was performed in the Netherlands, the in-group was Dutch and out-groups were German or Arab.

Here’s the bottom line: subjects who were given oxytocin were more likely to favor in-group members relative to placebo-treated subjects. There was also a hint that oxytocin enhanced negative attitudes towards out-group members, but this second effect was quite weak.

Oxytocin causes people to exhibit greater affection and favoritism towards people with whom they share identifying characteristics.

They examined the effects in the context of three different types of experiment. The first was a set of Implicit Association Tests, which asks subjects to identify in-group members by pressing one key and out-group members by pressing a different key. At the same time, individuals use the same two keys to categorize positive and negative words. The test measures how quickly people are able to perform the task when the positive words and in-group members use the same key, and compares this to their performance when positive words use the same key as out-group members.

People are deemed to exhibit in-group bias if they perform the categorization task more quickly when the “in-group key” is the same as the “positive words key” relative to when positive words use the same key as out-group members. The average extra time it takes in the slower arrangement is a quantitative measure of the degree of in-group bias. It was this measure that was enhanced by treatment with oxytocin.

If you’re interested in this sort of test, researchers at Harvard have an online setup, where you can test your own implicit biases about race, sexuality, and other things, and you can see how you compare to the distribution of other people who have taken the test. Check it out here.

The second test looked at “infrahumanization.” It measured how likely subjects were to associate someone with emotions that are commonly perceived to be “uniquely human,” here embarrassment, contempt, humiliation, admiration, hope, and surprise. (This is not a claim that these emotions are actually limited to humans, just that they are often perceived to be so.) Again, people are more likely to associate these with people of their own ethnicity, and treatment with oxytocin appears to enhance this bias.

The third test was a moral dilemma task of the sort that I have described previously. Subjects had to decide whether to take an action that would kill one person in order to save a group of other people. The ethnicity of the one person whom the subject would have to sacrifice was signaled through middle names that were stereotypically Dutch (e.g. Dirk), German (e.g. Helmut), or Arab (e.g. Ahmed). In this test, treatment with oxytocin made the Dutch subjects less likely to sacrifice someone with a Dutch name, but did not affect their willingness to sacrifice Germans or Arabs.

In a March 2010 Playboy interview, “musician” John Mayer bemoaned the fact that he has “a Benetton heart and a fuckin’ David Duke cock.” This may be a consequence of a currently undescribed genetic disorder that produces a highly non-uniform distribution of oxytocin in the body. If true, this disorder will someday be known as “John Mayer Syndrome.” Alternatively, it is possible that he is just a douche. Image via Jezebel.

A lot of studies have investigated the effects of oxytocin on behavior, and it is has previously been shown to enhance trust, cooperativeness, empathy, and prosociality. The authors of this paper interpret their results as saying that oxytocin should not be viewed as a general-purpose feel-good chemical that makes everyone all happy and want to share things. Rather, they argue that these effects may be limited to those with whom the individual shared a common identity. In more complex social settings, they suggest, the in-group bias that is enhanced by oxytocin can lead to actions that are perceived as unfair by out-group members, and can actually enhance between-group conflicts.

Peace be upon you.

De Dreu CK, Greer LL, Van Kleef GA, Shalvi S, & Handgraaf MJ (2011). Oxytocin promotes human ethnocentrism. Proceedings of the National Academy of Sciences of the United States of America, 108 (4), 1262-6 PMID: 21220339

Behavior, biology, Egypt Week, evolution, genetics, genomic imprinting, journal club, science

Egypt Week – Genetic Conflict and Social Dominance

February 3, 2011 jonfwilkins Leave a comment

So, our next scientific Egypt Week post concerns a paper just published in last week’s issue of Nature, where the authors describe novel behavioral effects of the imprinted gene Grb10 in the mouse.

If you’re not familiar, genomic imprinting is the phenomenon where the expression pattern of a gene depends on its parental origin. So, most of your genes come in two copies, one of which came from your mom, and one of which came from your dad. For most genes, the function of the allele, or gene copy, depends just on its DNA sequence. But something like 1% of our genes are imprinted, meaning that they retain a chemical memory of which parent they came from, so that the two gene copies will function differently, even if the DNA sequences are identical.

The most widely accepted theory for the evolutionary origin of gene expression suggests that it is the result of an intragenomic conflict between maternally and paternally inherited gene copies. That is, from a gene’s-eye point of view, natural selection acts differently on maternally and paternally derived alleles.

Many imprinted genes in mammals have growth effects in early development, and these most of these effects are well described by models where selection favors more growth (and a greater demand on maternal resources) when alleles are paternally derived, and less growth (preserving more maternal resources for the mother’s other offspring) when maternally derived.

There is also evidence for large-scale imprinted gene expression in the brain, and evidence that these imprinted genes may have substantial effects on cognition and behavior. We are still at the early stages of describing these effects, and at even earlier stages of understanding the relevant evolutionary pressures.

Elsewhere on this blog, I have begun writing a series of primers on genomic imprinting, links to which can be found here, if you are interested in more background.

Today’s paper describes the effects of the two parental knockouts of the Grb10 gene. Grb10 is a particularly interesting imprinted gene, because it is maternally expressed in many peripheral tissues, but paternally expressed in the central nervous system. So, when you knock out the maternally inherited copy, you get a complete loss of function in the periphery, but don’t impact Grb10 expression in the brain. Conversely, when you knock out the paternally inherited copy, you lose gene function in the brain, but leave expression in the periphery unaffected.

The phenotype of the maternal knockout is more or less what is expected in terms of growth effects, and is consistent with previous studies of this gene. Theory predicts that if a growth-related imprinted gene is maternally expressed, it likely functions as a suppressor of growth. When the maternal copy of Grb10 was knocked out, the result was overgrowth, due to the loss of this growth-suppressing function.

The knockout of the paternally inherited results in a behavioral phenotype associated with increased social dominance, as indicated by two specific behaviors. The first dominance behavior was observed in a “tube test.” In this test, two mice who don’t know each other are forced to encounter each other in a tube. In this setting, the knockout mice are less likely to back down than the wild-type (normal) mice are.

The second observation was an increase in allogrooming and barbering. Let’s pause for a moment to talk about what that means. Allogrooming is where one individual grooms another individual (in contrast to autogrooming, where you groom yourself). Barbering is where the grooming gets out of hand, and the groomee gets big bald (and sometimes bruised and bloody) patches.

Now, intuitively, you might assume that grooming behavior is submissive, like the handmaid combing out the princess’s hair. In mice, at least, it’s not like that. If you have a pet mouse, and it is grooming you, it is actually being dominant. It’s more like when you sit your little sister down in a chair and put makeup on her – the goal is NOT to make her look good. And, if you are feeling really mean, you give her a haircut, too.

The researchers argue that the behavioral effect is specific to social dominance, as tests designed to look at anxiety, locomotion (moving), olfaction (smelling), and aggression all found no differences between these knockouts and wild-type (normal) mice.

A conflict-based interpretation of these behavioral results would suggest that, for some reason, maternally inherited genes place a greater premium on establishing social dominance than do paternally inherited genes. (In the nervous system, the gene is paternally expressed, and knocking it out increased dominance behaviors. This implies that the gene normally acts to limit dominance behaviors.)

A bemedallioned Hosni Mubarak helps to illustrate the intragenomic conflict over social dominance behaviors. Natural selection favors alleles that enhance socially dominant behaviors when they are maternally derived, but limit socially dominant behaviors when paternally derived. The study was performed in mice, and it is important to note that the patterns of imprinted gene expression can vary among species, so we can not extrapolate from these results to the influence of Grb10 on human cognition and behavior. However, mice and rats are closely related, so we are probably safe extrapolating to Mubarak.

The next question is why would alleles favor more socially dominant behaviors when maternally derived? Fundamentally, at this point we have no idea. This is where the modeling has to come in. In this type of situation it is always possible to come up with a host of possible explanations, all of which sound plausible, and all of which would predict that a paternally expressed gene would limit dominance. The key thing is to model each of those explanations formally, so that we know what key ecological and demographic factors underlie the explanation. Then, we find other species where those factors differ, and examine the imprinting status and phenotypic effect of Grb10 in those species.

For the less politically oriented, the intragenomic conflict over social dominance is like this. Nadya “Octomom” Suleman is like your maternally inherited genome, while the guy with the moustache and the milk bottle is like your paternally inherited genome. Image from the Daily Mail.

Peace be upon you.

Garfield AS, Cowley M, Smith FM, Moorwood K, Stewart-Cox JE, Gilroy K, Baker S, Xia J, Dalley JW, Hurst LD, Wilkinson LS, Isles AR, & Ward A (2011). Distinct physiological and behavioural functions for parental alleles of imprinted Grb10. Nature, 469 (7331), 534-8 PMID: 21270893 [1]

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[1] Disclosure: I didn’t really intend for Egypt Week to devolve into blog-posts-about-papers-by-collaborators-of-mine week, but there you have it. I have an ongoing collaboration with Anthony Isles, and know some of the other authors.

Egypt Week, media

Egypt Week – Pro-Mubarak Thugs Damage National Treasure

February 2, 2011 jonfwilkins Leave a comment

So, there have been some reports this week of looters damaging some of Egypt’s national treasures, including the decapitation of two mummies (although we should probably not discount the Highlander scenario there). There have also been reports of civilians organizing to protect treasures from looters. Most disturbingly (but, sadly, most plausibly, in my view), there have been reports that much of the looting was actually by Mubarak’s security forces, in an effort to cast the protesters as an unruly mob, thereby justifying a violent crackdown.

So, are Mubarak’s thugs deliberately destroying Egypt’s national treasures? We don’t know right now, and we may never know for sure. What we do know is that they have deliberately damaged one of America’s national treasures, blue-eyed, silver-maned Anderson Cooper.

Somewhere in America, Kathy Griffin is weeping.

Peace be upon you.

Books, Egypt Week, poetry, race

Egypt Week – I, Too, Sing Egypt

January 31, 2011 jonfwilkins Leave a comment

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.

biology, cooperation, Egypt Week, evolution, journal club, science

Egypt Week – Corruption and Cooperation

January 31, 2011 jonfwilkins Leave a comment

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.

biology, cooperation, Egypt Week, evolution, journal club, science

Egypt Week – Spiteful versus Altruistic Punishment

January 30, 2011 jonfwilkins Leave a comment

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]

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[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.

biology, Egypt Week, evolution, science

Egypt Week – Solidarity

January 29, 2011 jonfwilkins Leave a comment

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.

Behavior, biology, culture, journal club, math, science, scientific misconduct

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

January 28, 2011 jonfwilkins Leave a comment

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

biology, evolution, genomic imprinting, primers, science

Genomic Imprinting V: DNA methylation and gene silencing

January 27, 2011 jonfwilkins 1 Comment

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

Science, Poetry, and Current Events, where "Current" and "Events" are Broadly Construed