All posts by jonfwilkins

Comedienne skewers false prophets

So, gifted comedienne Cindy Jacobs has set the cyberverse aflame with her dead-on satirical portrayal of a manipulative, dishonest, bigoted snake-oil salesman. You may already have seen her outstanding video, which has been circulating the past few days. In it she spins a yarn about how the recent large-scale die-off of fish and birds in Arkansas are the result of the repeal of Don’t Ask, Don’t Tell.

For those of you who are not familiar with this particular brand of irony, let me break it down for you. You see, it paints this completely ridiculous picture of God as a homophobe with tendency to lash out, where he takes out his anger about homosexuals serving openly in the U. S. Miliatry on a bunch of defenseless animals. I actually worry a bit that she may have gone too far, and that this disrepectful portrayal may be viewed as blasphemous by some.

And she nails the pseudo-logic that these false prophets use. It’s like something straight out of a Tina Fey skit. Here’s a snippet:

. . . the blackbirds fell to the ground in Beebe, Arkansas. Well the Governor of Arkansas’ name is Beebe. And also, there was something put out of Arkansas called “Don’t Ask, Don’t Tell,” by a former Governor this was proposed – Bill Clinton.

Great stuff! And there’s more. Like she’s got a whole thing on how California will be destroyed by earthquakes if Prop 8 is repealed.

Back before the 2010 midterms, she had a skit about how if Latinos would support candidates who opposed gay marriage and abortion, God would reward them with comprehensive immigration reform. More Bible humor! See, it’s just like the Book of Job. Elect right-wing candidates, and you get immigration “reform,” like in Arizona.

Even her website is hilarious. She starts off with an oxymoronic description of herself as a “respected prophet.” She then goes on to . . .

Wait . . . what now?

She’s not being ironic?

Nevermind.

Reflected Glory: Vi Hart

So, here is the debut of yet another new feature: Reflected Glory. This series will contain my callous and cynical attempts to convince you that this blog is really interesting and valuable because it is interested in and values interesting and valuable things.

To launch this feature, we have the math, music, and awesomeness blog of Vi Hart. You can get instructions on how to slice apples into Platonic Solids. You can listen to original stories set to original music. And you can watch the Doodling in Math Class video series, which covers things like how to draw an infinite line of camels such that they reach exactly to the edge of the page.

If you’re a math geek, this is probably already bookmarked on your browser. If you’re not, don’t let that stop you from checking it out. The site is not about math in the sense of memorization, abstract notation, and jargon. It is about the beauty of patterns and music and fun. You’ll want to spend plenty of time exploring.

The downside is that you will feel totally inadequate after seeing what this talented artist, composer, musician, mathematician, and expositor can do.

The Genetical Book Review: Middlesex

So, welcome to the first installment of Lost in Transcription’s newest feature: The Genetical Book Review. For the maiden voyage, we’ll cover the 2002, Pulitzer-prize-winning Middlesex by Jeffrey Eugenides.

You’re surprised? Because you assume that an eight-year-old Pulitzer winner must already have been reviewed?

Fair enough. But, here’s the gimmick: we’ll use the genetics angle to talk about some things that have not already been covered extensively elsewhere.

First, though, the precis and value judgement. If you’ve not read the book, or read about it, it follows three generations of the Greek-American Stephanides family, who traipse through a slice of historical events in Smyrna and Detroit over the course of nearly a century. It’s sort of a Forrest Gump for the NPR set. Cal Stephanides and his relatives witness genocide at the hands of the Turks, emigrate to America, build cars for Henry Ford, and run booze during prohibition. They are present for the founding of the Nation of Islam and the 1967 Detroit race riots. They flee to the suburbs and watch Watergate unfold on the television.

As in Forrest Gump, some of the historical context feels a bit like pandering, an attempt to draw the reader in through nostalgia. On the other hand, many of the events are local enough to be only passingly familiar to most readers, so there’s learning to be had. More importantly, those events are always portrayed through the lens of how they shaped the trajectories of the characters in the book. And, they are charmingly and engagingly written, with a varied style that is pleasurable to read.

Basically, if your book group has not already read this book, and you’re sick of plodding stories about alcoholic mothers and victims of sexual abuse, but want something with some literary gravitas (so that you don’t lose social status by suggesting it to your book-group frenemies), this is the book for you!

There you have it. Hit the jump for the role of genetics in the book.

The book is written in a memoir style, told by Cal, who periodically takes on the persona of a chromosome being passed down, or an egg sitting in an ovary as s/he relates the events from previous generations. I say “s/he” because – and I’m not giving anything away here – the key twist to the coming-of-age story is that Cal is intersex, having ambiguous genitals as a result of a recessive, genetic 5-alpha-reductase deficiency.  For reasons reaching back to Smyrna, Cal’s condition is not identified at birth, and our protagonist is raised as a female, Calliope. It is not until puberty hits that Calliope discovers her condition and transforms into her male alter ego, Cal.

The 5-alpha-reductase gene encodes an enzyme that converts testosterone into dihydrotestosterone (DHT). In early development, testosterone is responsible for certain internal male reproductive structures, such as the vas deferens, while DHT is responsible for the external genitalia. Upon the onset of puberty, testosterone drives the male increase in muscle mass and deepening of voice, while DHT is responsible for the growth of facial hair. One of the reasons for the female-to-male switch that happens at puberty is that there are actually two different 5-alpha reductases. The type 2 enzyme is the one that is primarily responsible for DHT production, particularly in early development, and it is this enzyme that Cal lacks. The other one, the type 1 enzyme, is substantially upregulated at puberty, which results in an uptick in DHT production.

So, there are two things that combine at puberty to drive the sudden appearance of male characteristics: (1) Testosterone and DHT start sharing the load for creating external male-typical characteristics, and (2) a second pathway appears for the generation of DHT.

I have to say, as I have read about this disorder, I have been impressed with the depth of understanding that Eugenides seems to have brought to the novel.

[As a side note, this disorder was first identified in the remote village of Salinas in the Dominican Republic, where it occurred in about 2% of live births. Locally, these individuals are known as “guevedoces.” Whenever I have seen reference to the guevedoces, it is followed by the phrase “literally ‘penis at twelve.'” Actually, it turns out that ‘gueve’ is derived from ‘huevos,’ which is slang for ‘balls.’ Thus, a better translation might be “balls at twelve.” Although, if you’re going to precede your translation with “literally,” you would need to acknowledge that this slang for ‘balls’ is literally the word for ‘eggs.’ Of course, referring to the appearance of male sexual characteristics at the onset of puberty as “eggs at twelve” is just weird and confusing, because it sounds like something you would order at Denny’s, and because it is sort of the exact opposite of what is going on.]

Incest is one of the recurring themes in the book, which traces the paths through which Cal came to inherit two defective copies of the 5-alpha-reductase gene. This particular disorder is straight-up recessive, so if you have one functional copy of the gene, you develop normally.

Cal’s grandparents on his/her father’s side are brother and sister. They hailed from the same tiny village outside of Smyrna, were orphaned, and fell in love. Their immigration to America permitted them the opportunity to fabricate a non-consanguinous past. The interesting thing is that the inbreeding involving Cal’s grandparents bears absolutely no responsibility for Cal’s condition. Their son, Milt is unaffected, which means that he inherited one defective gene copy from one of his parents. It doesn’t actually matter whether the other parent carried a copy or not.
More specifically, what is required for the story is that Milt be a carrier, but not express the condition. If one of his parents is a carrier, the probability that he is a non-expressing carrier is 1/2. If both of his parents are carriers, the probability that he is a non-expressing carrier is 1/2. It will not have escaped your attention that 1/2 = 1/2.

There is a second case of inbreeding, however, that does contribute to Cal’s condition. Milt and his wife, Tessie, are second cousins, and each of them is heterozygous for the deficiency. Now, statistically speaking, the fact that Milt and Tessie are second cousins barely counts as incest. For a rare disorder such as 5-alpha-reductase deficiency, the elevation in risk due to a second-cousin marriage is small. How small? Let’s see.

Assume that the frequency of the defective version of the gene is q = 0.001, or one in a thousand. This is in the ballpark of what we might expect for a recessive mutation maintained at mutation-selection balance. The probability that an outbred individual inherits two defective copies is approximately q2, or one in a million. What if the mother and father are related? If their degree of relatedness is r, then the probability that their child will inherit two copies is:

         p = q (r/2q (1 – r/2))

What is this r thing? Well, if they are brother and sister, r = 1/2, so the probability p would be about 0.00025. For first cousins, r = 1/8, and p = 0.0000634. For second cousins, r = 1/32, and p = 0.0000166.

That is, for second cousins, the probability goes from one in a million to about one in 60,000. Basically, you will have a bigger impact by taking prenatal vitamins.

Diane Paul and Hamish Spencer published an interesting piece a couple of years ago about the history of the stigmatization of first-cousin marriage, particularly in the United States. They make a number of interesting points, and I recommend the article, which can be found here. It is short, fascinating, open access, and requires no background in genetics to follow.

One of the points they make is that there is pretty much no way to interpret a ban on first-cousin marriage as anything other than eugenics. And yet, somehow, this prohibition has managed to escape that label. Another of their points is that the genetic risks associated with first-cousin marriage are actually small compared with a lot of behaviors that are completely acceptable in our society, such as women having children over the age of 40, or the use of in vitro fertilization techniques. (That second one was not mentioned by them, but it’s true.) So, there is some inconsistency there, which they trace to nineteenth century misconceptions about heredity and prejudice against immigrants and the rural poor.

But, back to the book.

To recap, in terms of causal things leading to Cal’s genetic composition, the fact that his/her parents are second cousins matters. The fact that the grandparents are brother and sister does not. Why, then, does the story, much of which is driving towards Cal’s conception, spend so much more attention on the (genetically) irrelevant grandparental love story?

Obviously, I can’t speak to the author’s intention, but to me, having two separate incidents provides a nice, clean separation between the psychological and genetic consequences of incest. Cal’s grandmother is wracked with guilt about her transgression, and this guilt drives the story in several places. In fact, one of the motifs in the book is that action (or, often, lack of action) is often motivated by superstitious beliefs. –– Sorry about the vagueness here. I’m in spoiler-avoidance mode. –– Hypothetically speaking, let’s say one of the characters is eating toast, and then that character’s mother falls down and breaks her hip. The character would blame him/herself for eating toast and refuse to eat toast again for a long time. You get the idea.

Anyway, my point is that by having two separate incests, we are able to distinguish more clearly between the genetic consequences of consanguinity from the EWWWW consequences of knocking boots with your sister.

Paul, D., & Spencer, H. (2008). “It’s Ok, We’re Not Cousins by Blood”: The Cousin Marriage Controversy in Historical Perspective PLoS Biology, 6 (12) DOI: 10.1371/journal.pbio.0060320

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 Middlesex now through:

Amazon

Barnes and Nobleicon

indiebound

Alibrisicon

Well Thank God for THAT: Novelization of Gulliver’s Travels

So, this week at Lost in Transcription we’ll be rolling out a few new features. The first of these is Well Thank God for THAT, which will cover some of those “current” “events.”

If you haven’t been to your local bookstore recently, you may have missed the fact that Simon Spotlight has published a novelization of Gulliver’s Travels. Now a generation will not be deprived of this Jack Black classic during a power outage that is long enough for their laptops to run out of juice, but not so long that their kindles run out of juice.

If you’ve never read it, Gulliver’s Travels offers an almost swiftian satire of human nature. It focuses particularly on two of our most enduring foibles: (1) being fat, and (2) saying “awesome” a lot.

Introducing the Negative Log Google Naked Ratiometer

So, one of the interesting things about having a website is that you can track the keywords that people Google that lead them to you. I get a lot of hits from people searching on “Jon Wilkins naked.” It turns out that’s not as exciting as it sounds. One of the other Jons Wilkins is one of the cofounders of the marketing firm Naked Communications. So, I assume that some fraction of those people were actually looking for him.

It got me interested, though, in the relative web presences of “Jon Wilkins” and “Jon Wilkins naked,” and, by extension, in the relative naked and non-naked web presences of people in general. I’m going to call this the Negative Log Google Naked Ratio (NLGNR): the ratio of the number of hits when you Google “[Person’s Name] naked” to the number of hits when you just Google “[Person’s Name]” in log base 10. Negative.

Here’s an example. When I searched for “Kanye West” today, Google found approximately 38,600,000 hits. I then searched for “Kanye West naked” and got approximately 428,000 hits. The ratio of these two is about 0.011088, and the logarithm base 10 of that is about –1.95.

So, Kanye West’s NLGNR is 1.95.

If your NLGNR is 1, that means that 10% of all of the hits for your name actually come from pages where your name is followed by the word “naked.” If your NLGNR is 2, it is one in a hundred pages. NLGNR of 3 means one in a thousand, and so on.

Just like in golf, low scores are better, assuming that your goal is to have your internet presence primarily associated with nakedness.

I did this for 93 people, and I have to tell you the internet is a weird place. Before presenting the whole chart, here are some of the highlights.

Top among the people I surveyed was Mia Hamm, whose NLGNR is an impressive 0.83. That means nearly 15% of the sites containing the phrase “Mia Hamm” contain the phrase “Mia Hamm naked.” Weird? No. That actually seems low to me.

Mia’s equally dreamy husband, Nomar Garciaparra, came in 64th, at 4.52.

Number two on the list, just behind Mia Hamm? Rosalind Franklin, who edges out Charlie Sheen. Umm.

Where is Jon Wilkins in all this? My NLGNR is 2.32, just behind Angelina Jolie, Lindsay Lohan and Britney Spears, and just ahead of Kathy Griffin, LeBron James and Queen Elizabeth.

Other weird stretches: just behind Kanye West come, in order, Anderson Cooper, Marie Curie, Ron Jeremy, Kim Kardashian, and Bill Nye.

Yes, Bill Nye the Science Guy has almost as high a ratio of naked to non-naked web hits as porn icon Ron Jeremy. And, yes, both of them have lower ratios than Marie Curie.

Betty White beats out Saddam Hussein and David Beckham.

Barney Frank beats out Ke$ha.

Glenn Beck beats out Maya Angelou, but just barely.

Most of the poets appear way down at the bottom of the chart, which makes you wonder, what’s the point of being a poet at all.

Evolutionary biologists did even worse, with many having absolutely no naked internet presence.

A bunch of people actually returned zero naked hits, giving them infinity for their NLGNR. Most impressive among these was “Ted Williams,” whose nearly 46 million hits cover both the Red Sox legend and the golden-voiced, formerly homeless internet sensation. Others, from most non-naked hits to least, include: Jerry Coyne, James Watson, Francis Crick, HRP-4c, J. B. S. Haldane, Stephen Jay Gould, Louis Macneice, E. O. Wilson. John Ashbery, Doris Kearns Goodwin, Jorie Graham, Ronald Fisher, Sewall Wright, and Richard Lewontin.

I’m afraid I could not bring myself to do the analysis for Justin Bieber.

The 78 finite NLGNR scores at time of publication

Find any other interesting NLGNR scores? Add them in the comments.

Reading the Constitution: Democrats Lose Again

So, today was the big day when the U. S. Constitution was read into the congressional record. This was preceded by a discussion of which parts, exactly, would be read. It was agreed that they would not read those sections of the Constitution that had been made irrelevant by amendments. That means, for instance, that they did not have to read all of the stuff about slaves.

And so, the Democrats lose again.

Why? Because the game being played here by the Republicans is part of the new Constitution-as-sacred-text push that is being fueled by the tea partiers. The founding fathers (sorry, I mean Founding Fathers) are being cast as infallible geniuses who set down immutably true principles of governance. Then, they can oppose any policy or piece of legislation on the moral principle that it is not what the Founding Fathers would have wanted.

The problem with reading the abridged Constitution is that it takes something that is a living, evolving entity and casts it as fixed. If the congress had read out all of the parts about slaves being three fifths of a person, and then read out the amendments abolishing slavery, the effect would have been the opposite. They would have emphasized that the Constitution as a document was not infallible. It would have emphasized the notion of the Constitution as a process.

The founding fathers were clever. They got a lot of things right. They also recognized that they were not going to get everything right, and that times and values would change.

I wish that they had read the entire Constitution into the congressional record. I am moved not by an America in which the government is something that we revere, but by an America in which the government is something that we do.

Spokeo: Protection Racket, or just Doucheracket?

So, I’m reading teh Boing Boing the other day, and they have this article about Spokeo, which I assume is having a burst of coverage right now because its founder, Harrison Tang, was just elected Grand Sucktard of Douchebekistan.

This is a “service” where you can type in your name (or presumably the name of someone you want to rob, terrorize, and/or murder), and it will show you a satellite image of their house, along with a bunch of personal information about things like number of children and estimated wealth.

Just how much of a wankwad is this Tang dude? As Boing Boing point out, “Tellingly, Mr. Tang opted out of his own site over privacy concerns.”

A full set of instructions on how to opt yourself out can be found here. I clicked on the privacy button, and was greeted by the statement that “Spokeo cares about data privacy.” You can then have yourself removed from Spokeo’s public searches (although presumably not from their database) “for free.”

BUT, they are quick to point out, YOUR PRIVACY IS STILL AT RISK!!1!11! Your information will still be available through other sites, and you will have to contact them “one-by one . . . to protect your online identity.”

Fortunately, the heroes at Spokeo have “partnered with” the company “Reputation Defender,” which will protect your online identity for a modest fee. What I’m wondering is, what’s the deal with that? Is that Spokeo’s actual business model? How is this any different from having the guy who threatens your family “partner with” Vito Corleone?

I’m not breaking any news here. I just wanted to post something because I thought that the protection-racket aspect of this whole thing did not receive enough emphasis in the article by Boing Boing’s Xeni. Not a complaint, as that article had a somewhat broader point, and is a great read for anyone interested in online privacy issues.

Also, I had about a million HILARIOUS ways to misspell “Harrison Tang”, but then decided to spare you.

The Cost of Christmas

So, if you haven’t already, you’ll probably soon receive the credit card bill with all of your Christmas purchases on it. Was it worth it? Well, was it, punk?

If you’re like most people, some of your presents were probably intended to impress someone. The question is, what’s the best kind of present for that? Should I give the girl from math class diamond earrings, or new batteries for her calculator? Should I give my boss a mug, or a gift certificate to Glamour Shots?

Fortunately, Science!™ has the answer. Today’s journal club entry concerns a model of gift-giving that considers three different types of gift that differ in their cost to the giver and their value to the recipient. “Cheap” gifts are, well, cheap. “Valuable” gifts are expensive to give, and have value to the recipient. The interesting category is the third one, the “extravagant” gifts, which are expensive to give, but have little inherent value to the recipient.

The specific context is gift-giving and mating. The model is of a sequential game with three or four stages. First, the male offers a gift to the female. Second, the female either accepts or rejects the gift. Third, she chooses whether or not to mate with the male. Then, in one version of the game, the male decides whether or not to stick around and contribute to the care of the offspring.

This $305 luxury frisbee is an example of an extravagant gift.

The conclusion of the paper is that there are many combinations of parameter values that will lead to males giving extravagant gifts. There are two critical features of the model that seem to be necessary in order to get this result.

First, there is uncertainty. The female has a guess about the quality of the male (or, equivalently, in the version of the model with paternal care, the probability that he will stick around after mating). By accepting the gift, she gains additional information about his quality or intentions. Similarly, the male is uncertain about the quality and intentions of the female – whether it is worth it for him to stick around after mating, and whether or not she is a gold-digger, who will just take his gift and skip town with his cousin.

[Editorial note: the term “gold-digger” is from the paper. Those of you who know me know me know that I would never have gone with such a politically incorrect term. I would have used “■■■■■■■■■■”.]

[[Meta-editorial note: parts of the previous editorial note have been redacted.]]

The other key feature is that there must be some cost to the female in accepting the gift.

Now, there are lots of parameters in a model like this, and several equilibrium solutions are possible. The interesting one is the one where males give cheap gifts to unattractive females (females whom they judge, with some uncertainty, to be of low quality), and give extravagant gifts to attractive females.

The key to getting the interesting equilibrium is that the ability or willingness to provide and extravagant gift has to correlate with the male’s quality or intentions. For example, a male can’t afford to spend two-months salary on a diamond ring every time he wants to have a one-night stand. Therefore, an extravagant engagement ring becomes a reliable indicator of his intentions. Ideally, the gift has to have no inherent value to the female, for example, if it were impossible to sell the engagement ring for cash money. Recall also that it has to cost her something to accept the gift. Then, taking the gift constitutes a commitment on her part as well. Otherwise, she benefits most from accepting the gift and walking away.

In the salacious application-to-human-mating case, this cost to the female is easiest to envision as a reputation cost (e.g., the risk of being labeled as a ■■■■■■■■■■). In certain species, where females mate with multiple males, store the sperm, and then use it selectively, there may be direct opportunity costs that do not require catty moralizing.

Just one last point.

The paper starts with, “Gift-giving is a feature of human courtship”. The authors cite Geoffrey Miller’s 2000 book, The Mating Mind. If the paper were being written today, I assume they would have cited more recent work by Hefner and Harris.

Sozou, P., & Seymour, R. (2005). Costly but worthless gifts facilitate courtship Proceedings of the Royal Society B: Biological Sciences, 272 (1575), 1877-1884 DOI: 10.1098/rspb.2005.3152

2010: The Year in Jon Wilkins

So, here’s what I got up to last year, presented for your viewing pleasure in three word clouds.

This blog launched on July 29, and talked about the following topics:

My poetry book, Transistor Rodeo, which was published this year, contains the following words, in marginally less random order:

And finally, here are the papers that I published this year. Note the prominence of “et” and “al,” which really tells you all you need to know about science:

Thanks, Wordle!

Top 10 ABBA songs

So, the year is almost over, which means it’s all top-ten lists all the time. Lost in Transcription is no different. Do we really need a top-ten ABBA song list, you ask? I mean, aren’t they dead – and Swedish?

Do we need an electric spin-the-bottle game? A motorized ice-cream cone? A combination fork and pizza cutter?

Yes, yes, and yes.

Let’s get started.

10. Lovers (Live a Little Longer)
     The premise in this one is that a woman reads in the paper about a scientific study finding that romance increases lifespan. The science writing apparently moves her to burst into song. The high point is the sassy emphasis on she, indicating that the lead scientist on the study was a womyn.

9. Hey, Hey Helen
     Half feminist anthem, half catty anti-feminist anthem. She’s a single mother, making it on her own, but her children are becoming irrevocably twisted by the absence of a male role model, and will probably wind up being serial killers. Was it worth it? Well, was it?

8. Love Isn’t Easy (But it Sure is Hard Enough)
     Um, what?

7. Kisses of Fire
     Kisses of fire, burnin’ burnin’
     I’m at the point of no returnin’

6. When I Kissed the Teacher
     Companion song to Don’t Stand So Close to Me by the Police. That teacher is SO fired!

5. Bang-a-Boomerang
    Bang a boom a boomerang 
    Dum de dum dum de dum de dum dum
    Bang a boom a boomerang
    Love is a tune you hum de hum hum

4. King Kong Song
     A song about a guy writing a song about watching a King Kong movie. It’s just like Inception. My mind is, like, totally blown.

3. I Do, I Do, I Do, I Do, I Do
     Awesome in part because this is actually the title, with five “I”s, five “Do”s and four commas, and in part because this was the song that my wife and I went back down the aisle to at our wedding.

2. So Long
     In which the narrator repeatedly asserts that she is NOT a prostitute.

1. Waterloo
     Extended “love is war: metaphor. You see, she is defeated utterly and completely by his romantic advances, just like Napoleon was defeated utterly and completely at Waterloo. Then, just like Napoleon, she contracts syphilis and dies alone on an island in the middle of the ocean.

Where are Chiquitita and Dancing Queen, you ask? Yeah, well, where are your mom and the – um – guy – um – who’s not your dad?