Monday, February 28, 2011

Happy Birthday, Kenneth Koch

So, yesterday (February 27) would have been Kenneth Koch's 81st birthday, had he not passed away in 2002. He is among the poets that I find I can always go back to when I grow tired of poetry. He is associated with the "New York School" of the 50s and 60s, which included Frank O'Hara, John Ashberry, and James Schuyler. He is reasonably well known, although not super famous, in part, I think, because he sort of falls in the gap between the two main categories that define contemporary American poetry.

For simplicity, we could call these two categories "high art" and "popular," although I am sure that more accurate and more descriptive terms exist. On the one hand, much contemporary poetry seems to be written primarily for consumption by other poets. It grapples with language and imagery in a way that is often self-consciously designed to challenge the reader. Typically, unless you read a lot of poetry, this work tends not to be a lot of fun, and it can be hard to distinguish between good and bad versions of it.

On the other hand, we have poetry that is self-consciously aimed at a popular audience, maybe people who haven't read a poem since high school. This work tends to be playful with language, reveling in rhyming or puns, and is accessible on a first read (Maya Angelou or Billy Collins would be examples). These poets tend not to be valued highly by academics and poets (typically the same people), in part because these poems tend to give you everything they have on that first reading, yielding little additional satisfaction on rereading.

Koch's poetry is part of a movement that was deliberately reacting against the dense, highly referential poetry of, say, Eliot, and trying to recapture the playfulness of language. In this sense, he is a progenitor of the contemporary popular strain of American poetry. On the other hand, he was often motivated by very artsy, high-culture things, like abstract expressionist painting (which was still high art in the 1950s) and music.

To my mind, this position, straddling popular and high art, is an admirable place to aim for. The ideal poem would be one that welcomes the reader with something that is broadly accessible, whether sound or humor or imagery. At the same time, there should be layers that nag at the reader, encouraging them to return to the poem, and giving them a glimpse of something new on each read.

What I love most about Koch, however, is his emotional stance. Probably ninety percent of the poetry in the world is either about poetry, or about being sad or mistreated. At least half of it is about being a sad or mistreated poet. Throughout his career, Koch kept returning to the project of writing poems about happiness. This is a dangerous thing to do, because you set the bar higher for yourself when you write about being happy. You especially open yourself up to being criticized for sentimentality when you dare to write about simple, universal sources of happiness, like having your wife sit on your lap. But again and again, in my opinion, at least, he set himself a high happy-poem bar and then cleared it.

In honor of Koch's birthday, and the example he set both for how to live a happy life and how to write poetry about it, I wanted to share this poem of mine from Transistor Rodeo. It is a pseudo-sestina prompted by a passage in Koch's poem "Days and Nights." The sestina form consists of six six-line stanzas that use the same six end words. The end words occur in a prescribed order in each stanza. The poem ends with a three-line stanza that also contains these six words. In this pseudo-sestina, I have followed the canonical pattern in terms of the order in which the six words are used, but have used a different transformation rule on each word to introduce variation each time it comes up. Only the word "dream" is repeated in the standard way.


Kenneth Koch's Unfinished Sestina

            William Carlos Williams I wrote
            As the end word of a sestina.  And grass
            Sleepy, hog snout, breath, and dream.
            I never finished it.
                                    – Days and Nights

After the prom William Carlos Williams
and I lay out in the grass
behind the stadium, drunk and sleepy,
bare-naked and laughing about the hog snout
in the punch bowl, catching our breath,
and curling up to dream

a dream
worthy of Samuel Taylor Coleridge
(who was also not wearing pants
at the time).  The opium
and strapless dresses, god knows,
had finally transformed at least one grumpy

teen into a free-spirit, happy
enough to dream
deep, diving hundreds of fathoms
through unconscious visions, past Edgar Allen Poe
and even past Jung.  It was there, at the hub of my mind, that I saw her, the heroine
of the story.  My jaw went slack,

my knees and arms buckled and fell limp.
Bashful
as a schoolboy, I offered her a Coke
(now this part of the dream
I was familiar with, although she had always previously been Mean Joe Green).
Before this point I would have said she was out of my league,

but our union
was written in the stars that night!  She opened the gate
and I drove the flock in, like a pastoral Henry Wadsworth Longfellow.
Pretty soon I was twitching like a sneezy
old man in a pepper factory dream-
ing of dander.  But then, just as she and I were approaching the cornice of ecstasy,

I was awakened to a ring of narcotics
officers saying if we were cooperative
no one would get hurt.  But my dream
was already destroyed.  I walked through the doors
of the police station humiliated, feeling dopey,
not sure I would ever see Elizabeth Barrett Browning

again.  In the cell I told William Carlos Williams, "Doc, we gotta dream
us up a plan to bust out of this joint before her husband catches up with her.
I love her madly, and you know he's dangerous when he's jealous."


Sunday, February 27, 2011

Genomic Imprinting VI: Hemimethylation

So, last time, we discussed the fact that the expression differences associated with genomic imprinting rely on the existence of epigenetic differences, such as DNA methylation. We also mentioned that those differences are established separately in the male and female germ lines. That is, one methylation pattern is established in the female germ line during oogenesis (egg formation), while a different pattern is established in the male germ line during spermatogenesis (sperm formation).

It is straightforward to understand how such differences could be established, since oogenesis and spermatogenesis occur in physically distinct locations, where different patterns of gene expression can produce the epigenetic differences. But, after fertilization, these parent-of-origin-specific epigenetic marks are maintained across many rounds of cell division. So, a cell in, say, your liver, will exhibit different epigenetic states on maternally and paternally alleles, despite the fact that they have occupied the same cellular environment throughout development.
Alleles at an imprinted locus maintain substantial epigenetic differences, despite occupying the same environment across many cell divisions.
The allele-specific maintenance of the methylation state depends on the fact that methylation occurs at "palindromic" sequences. When we're talking about language, a palindrome is a word or phrase that contains the same sequence of letters when read forwards or backwards, like "a man, a plan, a canal, Panama," or "eat tea." In genetics, a palindrome is where the nucleotide sequence on one strand of the DNA is the same as the sequence on the complementary strand (which is read in the opposite direction).
The palindrome we will be concerned with here is a really short one: CpG (where the "p" indicates the phosphate linker between the cytosine (C) and guanine (G) nucelotides).  CpG is a palindrome because C pairs with G (and G pairs with C), so that the complementary DNA strand has a CpG at the same site. Methylation occurs on the cytosines, so that if we have two alleles with different methylation states at a CpG site, they will look like this:
Here we have a schematic representation of two alleles with palindromic CpG sites that differ in their epigenetic state. In the top figure, the cytosines on both strands of the double-stranded DNA are methylated. In the bottom figure, both cytosines are unmodified.
So, how is this methylation difference maintained when the cell undergoes DNA replication and mitosis? The key lies in the fact that DNA replication is semi-conservative. That is, in order to make a copy of a double-stranded piece of DNA, what you do is pull the two strands apart and synthesize a new strand complementary to each of them.
When Watson and Crick published their paper on the structure of the DNA double helix, they noted that this structure suggested a mechanism by which the specific DNA sequence could be replicated. Crick later went on to establish a reputation for himself as a neuroscientist. Watson went on to establish a reputation for for himself as an asshole.
The newly-synthesized strands will contain normal, unmethylated cytosine, whether or not the template strand was methylated.  So, starting from unmethylated DNA, each daughter cell inherits an unmethylated copy of the allele. But, if we start from methylated DNA, each daughter cell inherits hemimethylated DNA, where one strand of the DNA double helix has a methylated cytosine, but the cytosine on the complementary strand is unmethylated.

There an enzyme, Dnmt1, that specifically targets the unmethylated cytosine at a hemimethylated CpG and methylates it. So, after the action of this enzyme, the methylated state has been restored in each of the daughter cells. The combination of the hemimethylase (or maintenance methyltransferase) activity of Dnmt1 and the semiconservative replication of DNA set up a system in which the epigenetic state of an allele can be set once, and it will be propagated across multiple cell divisions.
DNA replication of a fully methylated CpG site results in two hemimethylated copies. The hemimethylase Dnmt1 then restores these hemimethylated sites to their fully methylated form.
In the next installment, we'll talk about another epigenetic mechanism, histone modification, and the possibility of an analogous propagation mechanism for propagating those epigenetic marks.

Yoder, J., Soman, N., Verdine, G., & Bestor, T. (1997). DNA (cytosine-5)-methyltransferases in mouse cells and tissues. Studies with a mechanism-based probe. Journal of Molecular Biology, 270 (3), 385-395 DOI: 10.1006/jmbi.1997.1125

Tuesday, February 22, 2011

Tomorrow, Utah – The Day After Tomorrow, well, also Utah

So, tomorrow I am headed to Salt Lake City for a poetry reading. I'll be reading from my book, Transistor Rodeo, as well as some newer poems, primarily from a series called Thus in the Limit, which tackles the topic of immigration. If you're in the Salt Lake area please come by!

The reading will be on Thursday (Feb 24) at 7 pm. The location is: Finch Lane Gallery/Art Barn, 1340 East 100 South, SLC, UT. There will also be a "noontime conversation" at the same location on Friday at – let me check – noon. Both events are free and open to the public.

I'll be reading with Ander Monson, who has published books of poetry and essays, which are worth reading, and I am certain will be worth hearing as well. I'm not sure how to describe Ander's work, so I'll describe him instead.

When you first see his name, you're like "Ander Monson! That's awesome. It's just like 'Another Monsoon.'"

Then, you meet him, and you're like "He so totally should have been named 'Another Monsoon.'"

Then, you find out that his twitter is @angermonsoon, and you're like "Anger Monsoon!  What did I tell you? See, it's perfect!  What!  No, why, what did you think I said? No, 'Anger Monsoon' is so much better than 'Another Monsoon.' Why would I say 'Another Monsoon'? That's just dumb."

Also, he is a connoisseur of beer, which already makes him one of America's Heroes, but more importantly, he recognizes that many microbrews lazily try to make their beer fancy by just adding more hops, which is sort of like trying to make your poetry better by just making it less comprehensible.

Anyway, his writing is sort of like the kind of thing that that guy would write. Come to the reading, and you'll see what I mean.

Monday, February 21, 2011

Self-Doubting Monkeys

So, this is motivated by reports about a session at the 2011 AAAS meeting titled Thinking About Thinking. The BBC coverage includes a video.


URL for sharing: http://www.darwineatscake.com/?id=7
URL for hotlinking or embedding: http://www.darwineatscake.com/img/comic/7.jpg

Come see more at Darwin Eats Cake.

Sunday, February 20, 2011

Eight

So,

URL for sharing: http://www.darwineatscake.com/?id=6
URL for hotlinking or embedding: http://www.darwineatscake.com/img/comic/6.jpg

More geek humor available at Darwin Eats Cake.

Saturday, February 19, 2011

Jeopardy

So,

URL for embedding: http://www.darwineatscake.com/img/comic/5.jpg

Unfortunately, this keeps getting that Weird Al song, "I Lost on Jeopardy" stuck in my head.

Come get stuff stuck in your head at Darwin Eats Cake.

Tuesday, February 15, 2011

Snowflakes

So,

URL for embedding: http://www.darwineatscake.com/img/comic/4.jpg

For sketches of the 80 different snowflake types, see the referenced paper, which presents them taxonomically, or check out the key figures here and here.

For more Darwin Eats Cake, go here.

Magono, C., & Lee, C. W. (1966). Meteorological Classification of Natural Snow Crystals Journal of the Faculty of Science, Hokkaido University, Japan, Ser. VII, 2 (4), 321-335

Monday, February 14, 2011

Dunning-Kruger Effect

So,

URL for embedding: http://www.darwineatscake.com/img/comic/3.jpg

More comics at darwineatscake.com.

Kruger, J., & Dunning, D. (1999). Unskilled and unaware of it: How difficulties in recognizing one's own incompetence lead to inflated self-assessments. Journal of Personality and Social Psychology, 77 (6), 1121-1134 DOI: 10.1037/0022-3514.77.6.1121

Grass und Gaga - Im Ei

So, here's something you probably already know, but wish you didn't. Lady Gaga showed up at the Grammy Awards last night in an outfit that, in evolutionary terms, represents a sort of neoteny relative to the meat dress she was sporting at the MTV Video Music Awards. Here she is arriving. She's the one you can't see, because she is inside the egg.

Lady Gaga is carried inside an egg by four of her muscular servants, who are so poorly paid that two of them can not even afford shirts. Later, the slave-mistress would mount the egg and let out guttural screams until the singer emerged, soaked in amniotic fluid. At least, I am assuming that is what happened. Image via CBS News.
But really, I just wanted to use this as an excuse to share a poem that I love. It is by G√ľnter Grass, and is probably a reasonable approximation of what Lady Gaga was muttering to herself in a Gollum-like rasp while contemplating which of her servants she would consume first. The difference is that she would no doubt be muttering in the original German, whereas I am presenting you with an English translation, taken here from the 1977 bilingual edition of In the Egg and Other Poems. The English translation of this poem was done by Michael Hamburger.

Enjoy!

In The Egg

We live in the egg.
We have covered the inside wall
of the shell with dirty drawings
and the Christian names of our enemies.
We are being hatched.

Whoever is hatching us
is hatching our pencils as well.
Set free from the egg one day
at once we shall make an image
of whoever is hatching us.

We assume that we're being hatched.
We imagine some good-natured fowl
and write school essays
about the colour and breed
of the hen that is hatching us.

When shall we break the shell?
Our prophets inside the egg
for a middling salary argue
about the period of incubation.
They posit a day called X.

Out of boredom and genuine need
we have invented incubators.
We are much concerned with our offspring inside the egg.
We should be glad to recommend our patent
to her who looks after us.

But we have a roof over our heads.
Senile chicks,
polyglot embryos
chatter all day
and even discuss their dreams.

And what if we're not being hatched?
If this shell will never break?
If our horizon is only that
of our scribbles, and always will be?
We hope that we're being hatched.

Even if we only talk of hatching
there remains the fear that someone
outside our shell will feel hungry
and crack us into the frying pan with a pinch of salt.
What shall we do then, my brethren inside the egg?

Sunday, February 13, 2011

Proximate vs. Ultimate Causes

So, here's another one. For a more viewable version, go here.

URL for embedding: http://www.darwineatscake.com/img/comic/2.jpg

Saturday, February 12, 2011

Guillaume the Adaptationist Goat

So, here is the premiere of Darwin Eats Cake:



URL for embedding: http://www.darwineatscake.com/img/comic/1.jpg

For the latest, go to the website.

Thursday, February 10, 2011

Dissent among Philippine separatist MILFs

So, here is a story that proves the old adage that everything is funny in translation.

Apparently, the government of the Philippines has entered into talks with the Moro Islamic Liberation Front, which has been fighting to establish an independent Islamic state for nearly thirty years, since it split from the less-insurgency-minded Moro National Liberation Front. But now, some of the more militant MILFs are splitting from that group.

It's the same moral that we've seen in every other installment of the Real Housewives franchise: some MILFs don't even want to get along.

Tuesday, February 8, 2011

Reflected Glory: Agha Shahid Ali

So, I'm a few days late with this post, as I had intended for it to coincide with Agha Shahid Ali's birthday, but there you have it. Had he not passed away in 2001, he would have turned 61 on February 4.

Although I never had the opportunity to meet him, I feel personally indebted to him, and sad that I did not know him. My poetry book was published last year after it won the 2009 Agha Shahid Ali Poetry Prize. Since then, I have had a number of conversations with people who did know him, and they invariably go on and on about what a fantastic human being he was. And it's not at all in the way that people tend to speak well of the dead. In every one of these conversations, people speak in an almost trance-like state. Their voices and eyes soften, as if his immense kindness were channeled through them.

He was born and raised in Kashmir, attended the Universities of Kashmir and Delhi, and then came to the United States, where he earned a PhD from Penn State and an MFA from the University of Arizona. He taught at creative writing programs across the country, leaving behind a trail of devoted students and colleagues.

He wrote several books of poetry, but is perhaps best known for his championing of the ghazal, an ancient Arabic poetic form that dates back to like the 6th century. It long ago spread across southern Asia, and has become a common form in Persian and Urdu poetry. He translated a collection of ghazals by Faiz Ahmed Faiz into English, and his best-known work is probably his posthumously published collection Call Me Ishmael Tonight: A Book of Ghazals.

The ghazal form consists of a series of couplets, where the second line of each couplet ends with a sort of extended rhyme. What I mean by that is that there are one or a few words at the end of the line that are repeated exactly in each couplet, preceded by a conventional rhyme. It also conventionally contains the poet's name in the last couplet. Agha Shahid Ali's most famous ghazal is the title(ish) poem "Tonight" from his posthumous collection. You can find it easily on the internet, and you should.

Here is his poem "Land," where you can see the ghazal form as well as the soul of the man who was so well loved.

Land

     For Christopher Merrill

Swear by the olive in the God-kissed land –
There is no sugar in the promised land.

Why must the bars turn neon now when, Love,
I'm already drunk in your capitalist land?

If home is found on both sides of the globe,
home is of course here – and always a missed land.

Clearly, these men were here only to destroy,
a mosque now the dust of a prejudiced land.

Will the Doomsayers die, bitten with envy,
when springtime returns to our dismissed land?

The prisons fill with the cries of children.
Then how do you subsist, how do you persist, Land?

"Is my love nothing for I've borne no children?"
I'm with you, Sappho, in that anarchist land.

A hurricane is born when the wings flutter ...
Where will the butterfly, on by wrist, land?

You made me wait for one who wasn't even there
though summer had finished in that tourist land.

Do the blind hold temples close to their eyes
when we steal their gods for our atheist land?

Abandoned bride, Night throws down her jewels
so Rome – on our descent – is an amethyst land.

At the moment the heart turns terrorist,
are Shahid's arms broken, O Promised Land?

Monday, February 7, 2011

Well Thank God for THAT: 24 The Fragrance

So, remember how just the other day you were saying that you wished you could smell like a blend of gunpowder, blood, and moral relativism? Well, you're in luck! Park Fragrance has introduced a new fragrance just for you: 24.

If you're a big fan of torture porn, you've probably seen the TV show 24. For the rest of you, it's the one where Kiefer Sutherland assembles an action-packed argument justifying the abandonment of all principles when dealing with one's enemies.

24™ toilet water.  Not just for waterboarding!

There are two "24" eaux de toilette: Classic and Gold. Classic has a "blend of bergamot, lemon, mandarin, and orange." It is "masculine and self assured," just like you were that time you were working over Earl Grey with a pair of pliers in a citrus grove. It is "quickly [sic] underpinned by a spicy oriental core." Just like a North Korean nuclear facility!

Gold is for both men and women and "opens with emotions of vibrancy created by notes of jasmine, sandalwood, amber, and vanilla." Gold is "precious and captivating," recapitulating the show's characters and most overused plot device, respectively.

Sunday, February 6, 2011

Evolution Made Us All

So, it's Sunday morning here in the States. If you're reading this now, it means you're skipping church, which means you might also enjoy this awesome video by Ben Hillman. I came across it via Boing Boing.

Evolution Made Us All from Ben Hillman on Vimeo.

Reflected Glory: Picture Songs

So, we all know that you, Cathy, and Garfield all Hate Mondays. But that's probably just because you haven't been watching Nice Peter's Picture Songs. They're songs. That he writes about pictures. Every monday. I honestly don't know how he does this every week, especially since he appears to do other things. Here is last week's:



And links to some previous editions:

Old, Shiny, Awesome

Really Really Bad Day

Nom Nom Nom Nom, Babies!

Enjoy!

Saturday, February 5, 2011

Egypt Week - Resources

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.

Egypt Week – Oxytocin and Ethnocentrism

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

Wednesday, February 2, 2011

Egypt Week – Genetic Conflict and Social Dominance

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 – Pro-Mubarak Thugs Damage National Treasure

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.