All posts by jonfwilkins

Behavior, culture

Naming Advice for New Parents

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So, you’re having a baby. There’s one rule, really. Are you listening?

Don’t give your kid the middle name “Lee.”

Here’s the latest “*Lee*” in the news, Ricky Lee Kalichun:

from the Evansville Courier & Press, via Geekologie

Broke into ex-roommate’s apartment. To get back his video games. With a sword.

He was wearing a camouflage jacket, and camouflaged his face as well, with a marker. Maybe he was hoping to be mistaken for one of Jesse James’s girlfriends.

Now, I’m glad that your Grampa Lee was a World War II hero and all, but, really, just – just don’t.

culture, Hemiscience, Sports

Can you spell scrappy without crappy?

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So, I’m among those who believe that a baseball player only gets a reputation for being “scrappy” if they are not very good. You only get called scrappy if you scramble around and smother a ground ball that a fielder with better range would have gotten to easily. (I’m looking at you, David Eckstein.)

I decided to address this question by collecting some data that really has nothing to do with the original question. Using a method similar to that used by the Negative Log Google Naked Ratiometer, I looked at each position to see how often the position was referred to as “scrappy” and how often it was referred to as “crappy.”

For example, the Log Scrappiness for second basemen is calculated by taking the logarithm (base 10) of the number of google hits for “scrappy second baseman” divided by the number of hits for just “second baseman.” Similarly for Log Crappiness. Positions are more often referred to as “crappy” if they are higher on the graph. They are more often “scrappy” if they are further to the right.

If we look at the infielders and outfielders separately, the positions fall close to two straight lines with similar slopes.[1] Within each group, the relative scrappinesses are more or less what you might expect. The interesting thing is that each group has an inverse relationship between scrappiness and crappiness.[2] The scrappier a position is, the less crappy it is.

The solid diagonal line is the iso-(s)crapocline, or the line indicating equal scrappiness and crappiness. First basemen (1B), left fielders (LF), and right fielders (RF) are crappier than they are scrappy. Third basemen (3B), shortstops (SS), second basemen (2B), and center fielders (CF) are more scrappy than crappy.

Pitchers and catchers were left off, since there is too much cross talk on Google with non-baseball uses.

But, let’s get back to the original question: “Can you spell scrappy without crappy?” One answer is, “Yes, if you spell it in Albanian.” Via Google Translate: you can definitely spell i copëzuar without i mutit.

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[1] You may have noticed that these straight lines represent power laws. If I were a physicist, I would say something about universality classes, and publish this blog post in Physical Review E.[3]

[2] This seems to violate the assertion I made at the beginning of the entry, but the right way to do address that question would actually be to look at how often “scrappy” is used to describe individual players, and then to compare this to an objective measure of crappiness, based on player statistics.

[3] Oh, SNAP!

Politics, religion, science

Venn-Diagram Guide to 2012 Predictions

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So, a lot of people have been making predictions recently about how the world is going to end, or when the rapture is going to start, or what will be the new vampire.  It all just gets so gosh-darned confusing!

Never fear! I have produced this handy-dandy Venn diagram that graphically tells you what things could, conceivably happen in 2012, and which of those things actually will happen:

You’re welcome!

biology, evolution, genomic imprinting, primers, science

Genomic Imprinting IV: Escalation Between Loci

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So, in the previous installment, we introduced the “Loudest Voice Prevails” principle, which describes the evolutionarily stable pattern of gene expression at an imprinted locus where there is an intragenomic conflict over the total level of gene expression. Basically, the allele that favors lower expression becomes transcriptionally silenced. Expression from the other allele (the “louder” voice) evolves to the level that maximizes its inclusive fitness. In this sense, the active allele at an imprinted locus “wins.”

But what is going to happen if we have a pair of imprinted genes that exert opposite effects on the phenotype? If we have a paternally expressed growth enhancer, it will evolve to bring the growth phenotype up to the paternal optimum. If we have a maternally expressed growth suppressor, it will evolve to bring the growth phenotype down to the maternal optimum. But what if we have both?

Well, intuitively, if there is conflict between maternally and paternally derived genes over the optimal growth phenotype, then the phenotype can’t simultaneously satisfy the paternal and maternal optima. One or the other (or both) of these genes will always be under selection to increase its gene expression level (or, equivalently, the activity or longevity of the gene product, etc.). Thus, these two opposing genes will become involved in a kind of arms race.

In the simplest possible model that we can write down, this arms race goes on indefinitely, with natural selection driving each of the genes towards infinite expression. Clearly, in a real biological situation, this will not be the case, and something will step in to bring this escalation to a halt. The questions then become: What stops the escalation? And, what does the system look like at its new, escalated, evolutionarily stable state?

To think about this, let’s return to our analogy from last time, where Pat and Chris are sharing an office, but disagree about what temperature the office should be kept at. Recall that genes are totally passive aggressive, so Pat and Chris don’t compromise or communicate. They just use the tools at their disposal to move the office closer to their preferred temperature. Pat wants the office at 71 degrees. Chris wants it at 70.

We saw that if Pat and Chris both have space heaters, eventually Chris’s space heater is off, while Pat’s holds the temperature at 71. On the other hand, if they both have air conditioners, Pat will turn his/her A/C off, and Chris will get to have the room at 70.

If each of them has a space heater and an air conditioner, we have an arms race on our hands. Whenever the temperature is below 71, Pat will turn up the space heater. Whenever it is above 70, Chris will turn up the air conditioner. In passive-aggressive-allele fashion, this will go back and forth until the space heater and air conditioner are both blasting away. In the absence of any constraints or side effects, it will go on until both are blasting away infinitely.

There are several ways that the escalation could stop, however, each of which has a biological analog.

     (1) Mechanical limitation. There will be some limit beyond which gene expression / activity can not increase. Once one of the genes reaches its limit, the other will win. Like if Pat’s Tufnel-brand space heater goes to eleven, Pat wins. Of course, this will depend on the mechanisms through which the two genes exert their influence. For instance, if Chris’s air conditioner is actually a combination air conditioner / food processor / exfoliator, Chris might have to turn it way way up to get the air conditioning equivalent of a little bit of space heating. Similarly, a gene product might perform multiple tasks, and this pleiotropy could limit its competitive ability in the arms race.

     (2) Production costs. One difference between the single-locus solution and the two-locus solution is the level of energy consumption. If Chris’s space heater is off, Pat’s holds the temperature at 71. If Chris’s air conditioner is maxed out at ten, Pat’s space heater (which goes to eleven, remember) holds the temperature at 71. The difference is that the second solution comes with a huge-ass electricity bill. Can this sort of cost actually halt the escalation? Maybe. This requires either that there are diminishing returns to increased escalation, or that there are accelerating costs to production (like utility rates where your thousandth kilowatt-hour costs more than your first one).

     (3) Intervention. In a real office, we might expect that the manager would come in and yell at Pat and Chris, telling them to turn down their space heater and air conditioner. Maybe the manage would mandate an office temperature of 70.5 degrees. Does this ever happen with genes? Could a consortium of unimprinted genes step in and stop the escalation? There is no evidence to my knowledge of such things happening in the context of genomic imprinting, but this type of intervention is thought to be responsible for meiotic sex-chromosome inactivation, where the autosomes all gang up and put the sex chromosomes in a headlock in order to prevent meiotic drive.

     (4) Side effects. What if turning up Pat’s space heater also makes the music louder in the office? What if Chris’s air conditioner draws so much power that it causes occasional brown-outs? This is the other way in which the escalation between imprinted genes might be self limiting. If we consider a monolithic “growth phenotype” in isolation, then each allele has a simple, monolithic optimum. But genes are seldom like that. A paternally expressed allele may benefit from increased expression due to the effect of that increased expression on growth. But what if that increased expression has other consequences, as well? Maybe those other effects are detrimental to the allele’s inclusive fitness. If those deleterious side effects outweigh the growth-related benefits, then natural selection will not drive further escalation.

In future installments, we’ll look at some specific examples of escalating genes. But first, we’ll step back and look at some of the other features and consequences of imprinted genes.

Kondoh, M., & Higashi, M. (2000). Reproductive Isolation Mechanism Resulting from Resolution of Intragenomic Conflict The American Naturalist, 156 (5), 511-518 DOI: 10.1086/303409

Wilkins, J., & Haig, D. (2001). Genomic imprinting of two antagonistic loci Proceedings of the Royal Society B: Biological Sciences, 268 (1479), 1861-1867 DOI: 10.1098/rspb.2001.1651

Books, Remarkable

Yes, I married up

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So, for those of you who know us personally, this will not come as a surprise, because you already know that my wife is a hundred times smarter and more talented than I am. But here’s the new news. She has just sold her book manuscript, Remarkable, to Dutton publishing as part of a two-book deal. Other authors in their list includes authors ranging from Ken Follett and Eckhart Tolle to John Hodgman and Jenny McCarthy. Their backlist includes, among other classics, the Winnie-the-Pooh books.

Remarkable is a middle-grade reader, which, as I understand it, is the age group just below young adult. I think that this is approximately the same group as the Harry Potter and Percy Jackson books. Or, if you’re actually familiar with the genre, the Mysterious Benedict Society books.

I don’t want to give anything away, other than to say that it is the BEST FREAKING BOOK YOU WILL EVER READ IN YOUR LIFE, EVER.  The target age group is, technically, 9-12, so buy it for your kids. But, like all the best children’s literature, it has layers of nuance in its themes and characters that will engage adult readers.

Obviously, I’m not an unbiased reviewer here, but this book moved to tears and to laugh out loud – sometimes at the same time – and even after reading multiple previous drafts.

For those in the population genetics community, you can look forward to a cameo appearance by John Novembre.

The editor is hoping to include the book in Dutton’s Spring 2012 catalog. When more information becomes available, I’ll pass it along.

If you’re connected to her on Facebook or Twitter, say hi and congratulations, because she’ll no doubt be too modest to adequately blow her own horn (yet another way in which she is a hundred times better than I am). Or, stop by her sadly neglected blog and say hi in the comments.

From me, congratulations Lizzie K. Foley!! You deserve everything good that is coming to you. And congratulations to her agent, Faye Bender, and her brand-new editor, Nancy Conescu!

culture, media, poetry, science, Well Thank God for THAT

Well Thank God for THAT: Mr. Peabody and Sherman headed to the big screen

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So, what do you do with the two guys who wrote the screenplay for Yogi Bear, which was filmed in approximately three too many dimensions and made as much money as sense? Well, if you’re Dreamworks, you pay them to make another fifty-year-old cartoon into a movie. Or rather, a cartoon that was part of another cartoon. And then you cast Robert Downey Jr. as a dog. Presumably because his complete lack of talent complements the complete lack of creativity at the studio.

Following similar logic, I assume that the soundtrack will be composed by feeding beans to a room full of monkeys.

The movie will be based on Peabody’s Improbable History, which was a regular feature on The Rocky and Bullwinkle Show. In it, Mr. Peabody, a bespectacled dog-genius, and his sidekick, Sherman, a bespectacled boy-not-genius, use the WABAC machine to travel back in time and visit famous historical events.

The historical events in question unfold in humorous ways.

To be fair, this was the second best segment on the show, after Bullwinkle reading poetry. But still, why would Dreamworks do this? With real money that could have been better spent feeding the poor, or, if we’re honest, teaching the poor Esperanto?

Here’s the good news. Director Rob Minkoff says,

Mr. Peabody is this genetic anomaly. He does have brothers and sisters, all of them non-speaking, no[n] super-smart dogs. He’s an outcast, but has overcome it by being so great at so many things.

So yay, genetics, presumably in the form of a mutation at FOXP2, or that X-Men locus. And overcoming the adversity of being a genius – through the “being so great at so many things.”

The other good news? At the time of this writing, at least, Ed isn’t in it.

biology, Books, culture, Reflected Glory

Reflected Glory: Axe Cop

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So, you may be familiar with the opening of Nietzsche’s Also sprach Zarathustra, where he describes the three metamorphoses: spirit becomes camel, camel becomes lion (and slays dragon), and lion becomes child. I think that Nietzsche’s metaphor works really nicely in a lot of circumstances. I most strongly associate it with biology graduate training, but I think that similar reasoning probably applies in a lot of other fields.

In the early stages of education, through high school and college, and into the beginning of graduate school, the student is like the camel, who has to develop a strong back by learning to carry all of the received knowledge. Then, starting typically in grad school, you learn that all of the things that are in the textbooks you’ve been using are not strictly true. This is like the transformation into the lion, who has to slay the dragon covered with scales, where each scale has golden letters that read “Thou Shalt!” It is only after passing through these two stages that the third transformation occurs (maybe while you’re a postdoc?), where the lion becomes the child. The child is innocence and creativity, and it is this child who advances knowledge by possessing skills and knowledge, but no longer being beholden to them.

Now, one of the problems with the system is that not everyone makes it all the way through the transformations. Many scientists never fully shed the camel phase. They are quite skilled at the type of incremental research that NIH and NSF love to fund, and are often successful, but are excessively (IMHO) tied to the dogma and assumptions that define their discipline.

Other people get stuck in the lion phase. These are the compulsive paradigm shifters. They are Don Quixotes who spend their lives slaying imaginary windmill-dragons. In evolutionary biology this is the phenomenon responsible for the perennial “Darwin was WRONG!!” headlines.

That last step is really the hardest one. It requires us to recapture the innocence and creativity of childhood, but to wield it tempered with skill and knowledge. Unfortunately, the implementation of most science education is such that the camel and lion stages are coupled with a soul-crushing strangulation of the childlike curiosity that we are all born with.

So, what does this all have to do with Axe Cop? Axe Cop is a web comic (and now a book) written by a pair of brothers, Ethan and Malachai Nicolle. The twist? Ethan is 29 years old, and Malachai is 5. Ethan has clearly absorbed the illustrating and storytelling skills of the comic-book camel, and has slain the comic-book dragon. The comic itself is just bursting with a child-like creativity that is easy to recognize but difficult to produce. How do they do it? I suspect that Ethan was able to retain and/or recapture his creativity and innocence better than most, but the biggest thing is probably the co-authorship with Malachai, who has not yet entered the camel phase.

There is undoubtedly a lesson here about how to do great science, although I can’t quite figure out the mechanics. One possibility is this.

So, in the spirit of understanding Nietzsche, and biology graduate school, and education reform, and dragons, and ninjas, unicorns, avocados, vampires, dinosaurs, and robots, go read Axe Cop.

Also, it’s AWESOME!

culture, religion

I can haz rapshur? Bible pwns doomsday n00bz

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So, wickd preechr sez teh rapshur cumn dis May. Him sez did da calclashunz. An go on teh muzik box an sez evrywun gotta lisn 2 him kthx. But dat crazy cuz jesus sez in teh matthew book chaptr 24 dats liez:

36 “but bout dat dai or hour no wan knows, not even teh angels in heaven, nor teh son, [e] but only teh fathr.37 as it wuz in da dais ov noah, so it will be at teh comin ov teh son ov man.38 4 in da dais before teh flood, peeps wuz eatin an drinkin, marryin an givin in marriage, up 2 teh dai noah enterd teh ark;39 an they knew nothin bout wut wud happen til teh flood came an took them all away. Dat iz how it will be at teh comin ov teh son ov man.40 2 doodz will be in da field; wan will be taken an teh othr left.41 2 women will be grindin wif hand mill; wan will be taken an teh othr left.42 “therefore keep watch, cuz u do not knoe on wut dai ur lord will come.43 but understand dis: if teh ownr ov teh houz had known at wut tiem ov nite teh thief wuz comin, he wud has kept watch an wud not has let his houz be brokd into.44 so u also must be ready, cuz teh son ov man will come at an hour when u do not expect him.

Wen Ceiling Cat cummin, dis preechr no can haz cheezburger kthxbai.

biology, evolution, genomic imprinting, journal club, primers, science

Genomic Imprinting III: The Loudest Voice Prevails

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So, it’s been a while since the last installment of the Primers on Imprinting feature, but they should be posted with greater regularity in the upcoming weeks. This time we’re going to introduce something that we will see again in future installments: small differences in selection lead to large differences in behavior.

Last time, we introduced the most widely discussed and most successful explanation of the evolutionary origins of genomic imprinting, the “kinship” or “conflict” theory. According to this theory, imprinted gene expression is a consequence of the fact that natural selection acts differently on alleles depending on their parent of origin. There are several ways to think about the origin of this differential selection, but we talked about it in terms of the framework that I find most intuitive: inclusive fitness.

As we also noted last time, even in the cases where the asymmetry in selection on maternally and paternally derived alleles is sufficiently large to drive the evolution of imprinted gene expression, the actual magnitude of this asymmetry is actually incredibly small. Why? Well, even for a allele with large effects on the survival and reproduction of related individuals, the dominant factor in the inclusive fitness of that allele is still going to be the survival and reproduction of the individual organism carrying that allele around.

But, the standard pattern observed with imprinted genes is that the allele-specific expression is all or nothing. For example, an allele might be expressed when it is inherited from a male, but completely silent when inherited from a female. So this small difference in the optimal expression levels of the maternally and paternally derived alleles leads to – in a way – the largest possible difference in the realized expression levels of the two alleles.

I like to think of this in terms of an analogy. Imagine that Pat and Chris share an office, and that they have a slight disagreement over the temperature they want the office at. Say Pat wants the office to be at 71 degrees (Fahrenheit), while Chris wants it to be 70. Each of them has control over a small space heater, and this is the only mechanism that they have for manipulating the temperature. [1]

What’s going to happen? Let’s say the temperature is 70 degrees. Pat will turn up his/her space heater until the temperature reaches 71. In response, Chris will turn his/her space heater down until the temperature comes down to 70. They will go back and forth like this until, eventually, Chris’s space heater is completely turned off. Pat will then turn his/her space heater up to get the room to 71. Then we’re done. Chris is unhappy about the temperature of the room, but no longer has any ability to make it any cooler.

Two things about this outcome. First, a small disagreement over the ideal temperature has led to a large divergence in the strategies: Chris’s space heater is all the way off, while Pat’s is on and doing all the work. Notice that the outcome would be exactly the same, in principle, if Chris’s ideal temperature were 70.9 degrees, or even 70.999 degrees. [2]

Second, Pat wins. This is a consequence of the fact that we are talking about space heaters, and that Pat prefers the higher temperature. If, instead of space heaters, Pat and Chris each had control of an air conditioner, Chris would be the winner. At equilibrium, Pat’s air conditioner would be all the way off, and the room would be at 70 degrees.

This is also the way it works with alleles at an imprinted locus. Let’s consider the case of a gene where increased expression results in increased prenatal growth. The inclusive fitness argument says that the optimal amount of this growth factor is higher for an allele when it is paternally inherited than when it is maternally inherited. Say this patrilineal optimum is 105 units, while the maternal optimum is 95 units.

If the gene is not imprinted we might expect it to produce about 100 units, with each allele producing 50. However, once the evolutionary dynamics of imprinting take over, the pattern of expression will evolve to one where alleles are transcriptionally silent when maternally inherited, but where a paternally expressed allele is making 105 units.

For a growth-suppressing gene, where increased expression actually reduces prenatal growth, we expect the opposite pattern, where alleles are silenced when paternally inherited, but are expressed when maternally inherited. This set of predictions – that imprinted growth enhancers will be paternally expressed, and imprinted growth suppressors will be maternally expressed – matches the empirically observed pattern by and large, although there are a few counterexamples that are not fully understood at the moment.

This pattern of allele silencing has been dubbed the “loudest voice prevails” principle. The phenotype evolves to the optimum of the allele favoring higher expression. Now, you can argue that this is the sort of thing that does not really need its own name. Fair enough. It’s really just saying that the evolutionarily stable state of the system is an edge solution. But, “loudest voice prevails” is sort of catchy, and has the advantage of reminding us which allele is expressed at equilibrium.

The Haig 1996 citation is the paper that introduces the phrase. The other three citations are papers published around the same time that use different mathematical frameworks to address the evolution of gene expression at an imprinted locus. Generically speaking, the answer is the one described here, although the Spencer, Feldman, and Clark paper identifies certain regimes in parameter space where apparently different results can be obtained. In a future post, we will delve into the differences in the assumptions and conclusions of different modeling frameworks as they have been applied to imprinting.

Now, what if you consider more than one imprinted gene? What if Pat and Chris each have a space heater and an air conditioner? We’ll talk about that next time.

Haig, D. (1996). Placental hormones, genomic imprinting, and maternal-fetal communication Journal of Evolutionary Biology, 9 (3), 357-380 DOI: 10.1046/j.1420-9101.1996.9030357.x

Mochizuki A, Takeda Y, & Iwasa Y (1996). The evolution of genomic imprinting. Genetics, 144 (3), 1283-95 PMID: 8913768

Haig, D. (1997). Parental antagonism, relatedness asymmetries, and genomic imprinting Proceedings of the Royal Society B: Biological Sciences, 264 (1388), 1657-1662 DOI: 10.1098/rspb.1997.0230

Spencer HG, Feldman MW, & Clark AG (1998). Genetic conflicts, multiple paternity and the evolution of genomic imprinting. Genetics, 148 (2), 893-904 PMID: 9504935

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[1] Of course, in the real-life situation, we might assume that Pat and Chris would discuss the situation and come to some sort of agreement. This is a key difference between people interacting in strategic situations and genes evolving under natural selection. Alleles at a locus are like people sharing an office, where both of them are incredibly passive aggressive. If it helps, imagine that Pat and Chris won’t talk to each other.

[2] In practice, of course, there is going to be some minimum level of disagreement required in order to trigger this passive-aggressive escalation. In this analogy, the minimum level will be set by a combination of things such as the sensitivity of Pat and Chris to small changes in temperature, the precision with which the space heaters control the temperature of the room, and the extent to which they care about each other’s comfort. Similar reasoning holds in the case of genes, and we will address this in a future installment of the series, where we ask why there are any genes that are not imprinted.

Hemiscience, science

Google Violates Benford’s Law, Arrest Warrant Issued

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So, Google has already had it’s Twitter account subpoenaed, and can look forward to months of molestation enhanced screening at the airport, all thanks to its brazen violation of Benford’s Law.

What is this Benford’s Law thing?

It is a statement that if you look at lists of numbers in empirical data, the first non-zero digit is distributed in a very specific way. At least for certain kinds of data. Specifically, if the logarithms of the numbers you are looking at are uniformly distributed, then the first digits of those numbers will be Benfordly distributed.

Here’s what the relative probabilities of different first digits look like:

Here’s a graphic that shows the frequencies of different letters and numbers in Google searches. The numbers are way down at the bottom.

Image via Gizmodo

The thing that you’ll notice about this is that 6 is by far the most common digit (and that J/j is sad). Here’s a plot of these relative frequencies on the same scale as the Benford’s Law plot above.

Roughly speaking, this plot has the same shape as the one above, except for the fact that it includes 0, and that 6 is crazy. But, look at where the 0 value is: pretty much even with where you might expect the 6 to be. What happens if we assume that this was actually a transcription error that happened somewhere along the way? If we switch the 6 and 0 values, and then look at the relative probabilities of all of the non-zero digits, we get this:

The dark blue dots are the Benford’s Law points that we showed before. The reddish squares are the new empirical distribution.

Now that we’ve switched the 6 and the 0, we get something that looks to me like a mixture of the Benford’s Law distribution and a uniform distribution. But remember, Benford’s Law applies to first digits. This is data from all google searches. So, that’s going to be a mixture of first digits and non-first digits.

If we assume that 35% of the non-zero digits in searches are first digits, and that the other 65% are uniformly distributed between 1 and 9, we can back out the relative frequencies of the digits specifically in the first digit context.

The blue circles are the Benford’s Law expectations, and the red squares are the inferred empirical distribution of first digits. The choice of 35% was established through manual trial and error, and the fit was done by visual inspection. So, you know, don’t go and make any medical decisions based on this.

This is actually a reasonably good fit for this sort of thing, and constitutes fairly compelling evidence in support of the “sumbudy dun messed up” theory to my mind. Either that, or you have to invoke roughly 6 billion instances of people googling ‘666’.

Frank Benford (1938). The law of anomalous numbers Proceedings of the American Philosophical Society, 78 (4), 551-572