Well Thank God for THAT: Thunderwear

March 14, 2011 jonfwilkins 1 Comment

So, this comes to us from the file of things you didn’t even know you needed: Thunderwear! What is Thunderwear, you ask? Obviously, it is underwear with a built-in holster for your gun. Well, I guess technically it is a holster that you wear under your pants, but over your underwear. But, that assumes that you actually own and wear underwear, and I don’t like to make assumptions about my readers. You know what happens when you assume!

On the Thunderwear website, the filename for this photo is actually “happy.jpg.” Insert “is that a ___ in your pocket . . .” joke here.

Anyway, I wanted to draw attention to this product, because most of this blog’s readers are probably academics, and the current wave of gun-lobby insanity is for states to allow concealed weapons to be carried at universities. Or, more specifically, to require universities to allow concealed weapons on campus. I believe that Utah has already passed such a law, and legislation has been proposed in a number of other states, including Texas and Arizona. So, next time a student comes in to argue about their grade on a test, you’ll be ready.

Pretty cool, but I’m going to wait for the one that I can customize with the name of my sorority across the backside.

The site also provides testimonials. Here, by far, is the best one:

“I have been wearing it tonight with the P230 and it works fine. Tried it out at dinnertime in jeans & a t -shirt, neither wife nor kids were the wiser. thanks.” A.P Los Angeles CA.

No, indeed, they were not.

Books, Remarkable

My wife is still much too good for me, and now has a website to prove it

March 13, 2011 jonfwilkins Leave a comment

So, a couple of months ago, I posted an announcement that my wife had gotten a two-book deal for her middle-grade book Remarkable. If you want to experience my going on and on about the book, I’ll just refer you back to that post. For the just-the-facts version: her agent is Faye Bender, her editor is Nancy Conescu, and the book should be coming out in 2012 under Penguin’s Dial Books imprint.

Anyway, the point of this post is to let you know about her new author website, which you can find at http://www.lizziekfoley.com. You’ll find pictures and factoids and a lot of little things that will give you a sense of the book.

Who is this parrot? Is it going to eat this Basset Hound’s nose? Go to http://www.lizziekfoley.com to find out!

So, go check it out. Then come back here and read some more blog posts. You will come away with a good sense of how lucky I got when she married me.

biology, evolution, evolutionary psychology, homosexuality, science, sex

Re: Homophobia and Evolutionary Psychology

March 12, 2011 jonfwilkins 4 Comments

So, a couple of days ago, Jesse Bering published an interesting post on his Scientific American blog, where he attempts to revive interest in a research topic that was hotly debated in the mid 1990s, but has since fallen dormant. He describes a debate between two evolutionary psychologists – Gordon Gallup and John Archer – over the evolutionary origins of negative attitudes towards homosexuality.

Bering does an excellent job describing the debate, so I will just provide the briefest synopsis here. Gallup argues that, all else being equal, natural selection would favor negative attitudes towards homosexuality. The argument is basically that people who encourage heterosexual behavior in their children will have more grandchildren. The counter-argument championed by Archer is basically, no, it’s all cultural: homosexuals are identified as “other” and are demonized in the media.

Silly girl is so unfamiliar with cultural norms, she does not even recognize that she should be vilifying anyone who looks different from her.

Bering’s stated purpose is to stir up some debate, and hopefully to prompt some new research. He takes the position – the correct one in my view – that we should not refrain from asking such questions out of fears driven by political correctness. However, the thing that caught my attention, and prompted my to write my own response, was his opening paragraph:

Consider this a warning: the theory I’m about to describe is likely to boil untold liters of blood and prompt mountains of angry fists to clench in revolt. It’s the best—the kindest—of you out there likely to get the most upset, too. I’d like to think of myself as being in that category, at least, and these are the types of visceral, illogical reactions I admittedly experienced in my initial reading of this theory. But that’s just the non-scientist in me flaring up, which, on occasion, it embarrassingly does. Otherwise, I must say upfront, the theory makes a considerable deal of sense to me.

This, in a sense, encapsulates exactly what is wrong with so much evolutionary psychology. I don’t mean that as a criticism of Bering, who writes conscientiously and consistently well about a host of tricky topics. In fact, what I am doing here is a bit unfair to him, but I want to make a lot of hay out of that last statement: “the theory makes a considerable deal of sense to me.”

Back in the late 1970s, evolutionary biology was rent by a conflict over sociobiology. The debate was perhaps at its hottest and most divisive at Harvard, where the author of the book Sociobiology, E. O. Wilson, and two of its strongest critics, Richard Lewontin and Stephen Jay Gould, were all on the faculty. The debate focused particularly on the use of adaptationist reasoning to describe the origins of human behaviors, but it had methodological implications that reverberated throughout evolutionary biology.

Like sociobiology before it, evolutionary psychology has been accused of using the veneer of objective science to promote a socially conservative agenda, reinforcing social norms. Image via imageshack.

I won’t go more into the history here, but if you’re interested in a highly entertaining historical account, which delves particularly into many of the biggest personalities involved, I highly recommend this article, published originally in the sadly now defunct Lingua Franca.

As with many such schisms, the field eventually healed, primarily through retirement and replacement. Nowadays, most practicing evolutionary biologists take a more synthetic view, one that integrates the ambitions of the sociobiology program with the demands of a more rigorous scientific foundation demanded by the critics.

Basically, the lessons of the whole sociobiology episode boil down to this: plausibility is NOT scientific proof.

In fact, it is trivially easy to come up with a plausible-sounding evolutionary argument to describe the origin of almost any trait. More importantly, it is often just as easy to come up with an equally plausible-sounding argument to describe the origin of a hypothetical scenario involving the exact opposite trait.

If you have students, you can try this little experiment, which provides a nice learning exercise for the students as well:

Divide your class into two groups. Give one group a card that describes a pattern of behavior of the form: “In species X, the females do Y, and the males do Z.” Tell them that their job is to work together to come up with an evolutionary argument for why the females do Y and the males do Z. A group of a few modestly engaged undergraduates will have little trouble constructing such an argument. The argument will likely seem plausible on its face, and the students will probably emerge from the exercise convinced of its correctness.

Give the other group the same exercise, but with the modification that their card says that the females do Z and the males do Y. You will likely find that this group also has little trouble coming up with a plausible explanation, and that they will also be convinced of its correctness. For extra fun (for you, anyway), have the two groups come back together to debate the evolutionary question, but don’t tell them at first that they were given opposite patterns to explain.

If you can create a set of journals in which you can publish evolutionary claims with no requirement that any of those claims be scientifically tested, eventually, you can generate a whole parallel literature that is self-citing, a group of researchers that are self-refereeing, and review panels that are self-funding. Congratulations! You’ve just invented an academic perpetual motion machine!

The problem with much of the early work in sociobiology was that it was based on assertions of plausible-sounding mechanisms, where not enough thought was put into consideration of alternative scenarios. One of the dangers is that the plausible-sounding mechanisms that most readily come to mind are often those that resonate with the cultural norms in which we are all immersed. This is part of the reason why molecular evolution has focused so much over the past few decades on statistical tests to look for evidence of natural selection.

While most evolutionary biologists have taken on board the cautionary tales that emerged from the sociobiology debate, most evolutionary psychologists are not evolutionary biologists. When evolutionary psychology started to become a field in the early 1990s, it basically recapitulated many of the errors of early sociobiology. It deflected criticism by claiming that politically correct academics didn’t want them to ask these questions, painting itself as a field of martyrs who were bravely trying to do science, when the actual criticism was that the science was bad.

Evolutionary biology is one of those areas, like linguistics or sociology or film, where many people have some basic understanding or exposure, and so they tend to assume that they have an expertise on the topic, and that there is nothing more to understand beyond what they know.

Evolutionary psychology is to evolutionary biology as physics is to everything.

I would not want to criticize Gallup’s methods, nor his results, insomuch as they relate to psychology. However, the leap to the evolutionary argument is complete nonsense. That is not to say that he is not right. He might be. It simply means that the studies that are the focus of the debate do not contain the information required to construct and test an evolutionary argument as a scientific question.

Gallup’s premise is that an impulse to discourage homosexuality in one’s children would be evolutionarily favored. Fine. The argument is supported by surveys about parents’ levels of discomfort with homosexuality in different scenarios, specifically that they are less comfortable having their children exposed to homosexuality at age 8 than at age 21, and that they are more comfortable with a homosexual brain surgeon than with a homosexual pediatrician. Again, Bering does a nice job of describing the studies and the arguments against them, and I won’t reproduce those here.

I will just note (as Bering does) that this interpretation hinges on the assumption that exposure to homosexuals at an early age increases the likelihood of growing up to be homosexual. Gallup has some evidence to suggest that this might be the case, although we could easily put forward, for example, the “exotic becomes erotic” theory, which might be interpreted as suggesting that early exposure to homosexuality would decrease the erotic appeal of homosexuality in later life.

Basically, the structure of Gallup’s argument is that his studies show that A * B > 0. He wants to conclude that A > 0. Therefore, he asserts that B is probably greater than zero.

The problem is that the claim that A > 0 sounds plausible. Having straight kids gives you more grandkids. Makes sense, right? Therefore, we don’t demand a real test to figure out what B is.

Let me throw out a few alternative evolutionary stories:

1) Parents should want their own children to be straight, but they should support a culture that is broadly supportive of homosexuality, thereby reducing the number of children that other people’s children have. That would reduce the competition faced by their own grandchildren, giving them more great-grandchildren.

2) Parents should favor sex-specific homosexuality in the general culture, facultatively based on the sex ratio among their own children. Parents with lots of sons should favor male homosexuality in the broader community, but should disfavor female homosexuality, in order to maximize the number of mates available to each of their sons.

3) Parents should favor having their older children be homosexual during the early part of their lives, so that they stick around and help to raise the younger children, but once the younger children are old enough to fend for themselves, they should want all of their children to be straight.

Do any or all of these sound plausible to you? Maybe they do, or maybe they don’t. However, my point is that it does not matter. Whether some or all or none of these sound plausible to us depends a lot on the cultural milieu we inhabit, and almost nothing to do with the actual evolutionary origins of human sexual orientation.

It would be straightforward to construct mathematical models to support any of these verbal arguments. The key to turning this into science is to construct those models and see what other implications they have, and to look for evidence that supports or contradicts those other implications. The key is to measure what B is. The key is to uncover the genetic and neural mechanisms that underlie sexual orientation, and to subject those mechanisms to a rigorous statistical and molecular analysis. The key is to consider as broad a set of hypotheses as possible, and to be creative in identifying tests and observations capable of differentiating among those hypotheses.

I’m with Jesse Bering in hoping that there will be more research on this topic in the future. But I would add the caveat that if the research is done by psychologists in isolation, it will ultimately go nowhere, even if they are evolutionary psychologists. What is needed is a broad, transdisciplinary collaboration involving psychologists, for certain, but also evolutionary biologists, neuroscientists, anthropologists, sociologists, and who knows what else.

Gallup GG Jr, & Suarez SD (1983). Homosexuality as a by-product of selection for optimal heterosexual strategies. Perspectives in biology and medicine, 26 (2), 315-22 PMID: 6844119

biology, Books, evolution, Genetical Book Review, genetics, science

The Genetical Book Review: White Cat

March 1, 2011 jonfwilkins 1 Comment

So, welcome back to the Genetical Book Review, where we use concepts from evolutionary biology and genetics to talk about novels. In this installment, we are going to talk about White Cat, written by Holly Black. This is the first book in the Curse Workers fantasy series, the second book of which is set to be published in April. Holly Black may be familiar to some readers as one of the authors of The Spiderwick Chronicles.

White Cat is, broadly speaking, the same flavor of book as the Spiderwick series. The story has a contemporary setting, but in an alternate history in which a subset of people, known as “curse workers” or just “workers,” possess special abilities. The book’s protagonist, Cassel, comes from a worker family, but has no special abilities himself. One of his brothers is a “luck worker,” who is able to give people good (or bad) luck, while his other brother is a “body worker,” meaning that he is able to hurt people. His mother is an “emotion worker” who is able to manipulate people by, for example, convincing them that they are in love with a particular person. His grandfather is a “death worker,” who is able to kill people with his touch.

In fact, all workers’ skills require that the worker touch their target. Thus, in this alternate history, everyone wears gloves, and approaching someone with bare hands represents a potential act of aggression. In this world, curse workers are subject to “blowback,” which results from a sort of conservation law. For instance, whenever Cassel’s grandfather uses his ability to kill someone, a part of his body dies, such that when we first meet him, his fingers are blackened stumps, the consequence of a lifetime of death work.

Artist imitates art. Holly Black dons eponymous gloves in an effort not to accidentally curse herself when she touches her face. Image from the Holly Black website.

In this alternate history, curse work has been outlawed, so that curse workers live somewhat in the shadows and are employed by organized crime families. Much of the book’s social commentary focuses on issues that arise from this situation. There are discussions that parallel arguments about prohibition and drug legalization. There is a political movement to require people with abilities to register with the authorities. These subjects are handled largely in subtext, providing a layer to the book that will be interesting to adult readers.

I won’t go on further here about the premise or plot, as describing more would risk revealing some of the book’s twists. In terms of summary judgment, let me just recommend the book. It is fast moving and well written, and easily the sort of book you might find yourself finishing in a single sitting. It has some dark elements that might make it inappropriate for younger independent readers, so I would not necessarily buy it for your grade-school son or daughter. On the end of the spectrum, if you are an adult who enjoys this genre of young-adult fiction (e.g., if you like the Bartimaeus trilogy by Jonathan Stroud), I suspect you’ll have a great time reading this book, which is aimed at an older age bracket than Spiderwick.

What we will focus on here is the nature of the genetic variation that underlies the ability to perform curse work. The ability clearly has a genetic basis and seems to run strongly in families. There is also an explicit discussion of the fact that there is a high frequency of workers in Australia, due to a high frequency of the trait in the founding population.

The premise of a magical ability with a genetic basis underlies many fantasy franchises, including Harry Potter, X-Men, and television’s Heroes. In each case, there is some variation in the extent of the ability among those who have it, but there is fundamentally a binary distinction between those with abilities and those without them.

The clean, binary division between wizards and muggles means that no matter how enthusiastically you grip that broom between your legs, you’re never actually going to fly. Image of the fourth annual Quidditch World Cup. A real thing that real people do. For real.

Franchises differ in how they conceive of the structure of variation among those with abilities. In Heroes and X-Men, for instance, each mutant has unique abilities. (Or, to the extent that two mutants share abilities, it is generally looked upon as a lack of creativity or lack of attention to detail on the part of the writers.) By contrast, in Harry Potter, witches and wizards have, by and large, the same set of abilities. They differ in the degree of proficiency they display in different skills, but the variation seems to be fairly continuous.

We could say the franchises differ in the extent to which the mutant phenotype is canalized. In contemporary usage, the term canalization is used to refer to mechanisms that buffer the phenotype against genetic and/or environmental variation. It is an inherently relative term, in that it makes no sense to talk in isolation about a trait being canalized or not. However, it is sometimes possible to compare the extent to which a trait is canalized in two systems. For example, if the pattern of wing veins in one species of fly is invariant in response to changes in the temperature at which the flies are raised, while the pattern in a second species changes with temperature, we could say that the patterning was more canalized (with respect to temperature) in the first species than the second. The term comes from a metaphor in which different genetic variants or environmental influences get channeled into a “canal” representing normal development.

The canalization concept is usually used in the context of stabilization of the wild-type, but we can just as easily talk about canalization of a mutant phenotype. In Heroes and X-Men, it seems that the mutant phenotype is almost completely uncanalized. These franchises employ the “Anna Karenina Principle.” To quote the most over-quoted Tolstoy passage ever, “Happy families are all alike; every unhappy family is unhappy in its own way.” Despite the fact that a specific mutation is responsible for the superpowers in Heroes and X-Men, some interaction involving the mutation (presumably with other loci in the genome) results in a wildly different phenotype in each individual.

Whenever scientists want to say that something breaks in all sorts of different ways, while at the same time establishing their credentials as cultured intellectuals, they cite the “Anna Karenina Principle,” referencing a book that they know to be important, even if they have not actually read it themselves. This mapping of a diverse array of scientific observations onto a single reference represents a kind of literary canalization.

In the Harry Potter books, the genetic basis for wizardry is less clearly articulated, but the trait appears to be more canalized than the analogous traits in Heroes and X-Men. If there were less variation in the abilities of different witches and wizards in different areas of magic, we would say that the trait was even more highly canalized.

While canalization is often currently thought of as a buffering mechanism that applies to the entire phenotype, when the idea was first introduced by C. H. Waddington, he was also interested in the idea of cell-type differentiation. He introduced the concept of the “epigenotype” to refer to distinct sets of traits that could develop from the same underlying genotype. The cells in your brain and the cells in your liver have the same set of genetic material, but the morphology and behavior of the cells is wildly different. Thus, in this original concept of canalization involved the notion of multiple, distinct canals, each of which uses some sort of buffering to produce a stereotyped outcome.

Waddington represented development as a ball following one of a set of distinct, stereotyped pathways, like the character arcs on “reality” television.

The curse-worker phenotype in White Cat is like this notion of canalization. There are a handful of very distinct types of curse work that seem to occur in fairly well defined relative frequencies. Based on Cassel’s family, the capacity to do curse work seems to be strongly genetic, but the type of curse work one is able to do may be largely stochastic. It is sort of like Plinko: the genetic mutation hurls you onto the board of being a worker, but then random processes determine which curse-work canal you wind up following.

A Plinko contestant drops a hockey-puck type thing onto a board with a bunch of pegs on it to determine which kind of curse work he will spend his life doing. Genetics works exactly like this.

There is another form of canalization that we can see in the world of White Cat, a sort of historical canalization. Like many books in this genre, White Cat takes place in a world much like our own, but with a couple of key changes. Part of the appeal of many science fiction and fantasy books of this sort is seeing how the author takes a couple of key changes and imagines how history might play out differently. What if the Roman Empire had never fallen? What if Germany had won World War II? What if Martin Sheen had only had one son? And so forth.

The characters in White Cat occupy a world that is as precisely like our own as it can be and still support the premise of the story. The forces of history are so highly canalized that you can rewind the tape hundreds of years and give a small fraction of people magical powers, and you still wind up with Facebook. Tolstoy would be proud.

WADDINGTON, C. (1942). Canalization of Development and the Inheritance of Acquired Characters Nature, 150 (3811), 563-565 DOI: 10.1038/150563a0

Update: I had originally described the book as having been written by Michael Frost and Holly Black, which is what it says on the Kindle version, where I read it. Upon further investigation, it seems that Michael Frost is responsible for the cover art, but not the writing in the book. Everywhere else, Holly Black is the only listed author, so I have corrected my review accordingly. It strikes me as odd that the only place where he would be listed as a co-author is on the Kindle, where there is no cover art, but there you have it.

Buy it now!!

What’s that? You say you want to buy this book? And you want to support Lost in Transcription at the same time? Well, for you, sir and/or madam, I present these links.

Buy White Cat now through:

Books, poetry

Happy Birthday, Kenneth Koch

February 28, 2011 jonfwilkins 3 Comments

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.”

biology, evolution, genomic imprinting, primers, science

Genomic Imprinting VI: Hemimethylation

February 27, 2011 jonfwilkins Leave a comment

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

Books, poetry

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

February 23, 2011 jonfwilkins Leave a comment

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.

Darwin Eats Cake