All posts by jonfwilkins

biology, evolution, genomic imprinting, primers, science

Genomic Imprinting I

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So, one of the things that I study is genomic imprinting. What is that, exactly?

Even if you’re not a biologist, you are probably familiar with the fact that, for most of your genes, we carry two different copies, or alleles. You get one of those alleles from your mom, and one from your dad. Those two alleles could be the same (have identical DNA sequences) or different (usually only at a small number of positions within DNA sequence). If they are different, then the consequences of those alleles on your traits, like how tall you are or what color your eyes are, are determined by the dominance relationship between those two alleles. For example, the main allele responsible for red hair (at the MC1R locus) is recessive in relationship to alleles for brown or black hair. So, if you have only one copy of the red-hair allele, you will probably have dark hair. Importantly, in terms of what follows, it does not depend whether the recessive red-hair allele you have came from your mother or father.

If you are a biologist, you already knew all of that, but you may or may not be familiar with imprinted genes. About one percent (or possibly more) of our genes are imprinted. For these genes, it does matter which allele came from your mother and which one came from your father. That’s because imprinted genes retain a chemical memory of which parent they came from, and function differently depending on their parental origin. More specifically, at an imprinted locus, alleles are subjected to epigenetic modifications in the germ lines (ovaries or testes). These epigenetic modifications can be chemical modifications applied directly to the DNA itself, or modifications to proteins that are closely associated with the DNA. These modifications alter how the allele functions, without modifying the DNA sequence itself. The key thing is that, for imprinted genes, the epigenetic modifications that are established in the male germ line are different from those established in the female germ line. So the allele that came from your father will function differently from the allele that came from your mother, even if the DNA sequences are identical.

In the simplest cases, one of the two alleles is inactivated, or turned off. The effect of that gene on a given trait, then, depends only on the active allele. To return to the red-hair example, imagine that the MC1R locus was imprinted (which it is not, as far as we know), and that only the paternally inherited copy was expressed. Now, if you had one copy of the red-hair allele, and one of the more common dark hair allele, you would not necessarily have dark hair. Your hair would be dark if your red-hair allele came from your mom, but if it came from your dad, your hair would be red.

Of course, as with all things in biology, once you start looking at the details, everything becomes a lot messier and more confusing. But, that is the basic gist.

Genomic imprinting was one of the biggest surprises to come out of molecular biology in the past few decades. Both the origins of imprinting of particular genes, and the effect of imprinting on the evolution of those genes, are interesting questions that we will return to in future posts. At some point along the way, we will get deeper into those messy and confusing details.

culture, linguistics

Humanity as an emergent property: of douches and douchbags

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So, why is it an insult to call someone a douchebag?

The “douche” part is easy. Anything associated with the crotchal region, however tangentially, eventually makes its way into the lexicon as an insult. These terms are insults because they carry a connotation of being “dirty,” physically and/or morally. However, I think that most people would agree that calling someone a douchebag is a step up in the degree of insult, and that is what is curious. If we naively try to interpret its meaning based on what a douchebag actually is, it should be, if anything, a milder insult, if not a complement, as it is an implement with the specific function of remedying the very dirtiness that is the basis of any crotch-related insult.
Obviously, that is not the right way to parse “douchebag.” When we call someone a douchebag, we are really calling them a douche + bag. It works through analogy to the other “-bag” insults, like dirtbag or scumbag. Suffixes like “-bag,” “-sack,” and “-bucket” function as as intensifiers, or perhaps insultifiers. They can be productively added to just about anything, and it sounds more insulting. “Jerkbag” sounds worse than “jerk.” In many contexts (e.g., volleyball), calling someone a “wall” might be a complement. Calling someone a “wallsack” would be mostly confusing, but could probably safely be interpreted as an insult.
I think that these modifiers implicitly deny the emergent humanity of the insultee, by reducing them to no more than the sum of their constituent parts. Stick with me here. The fact is, the very thing that makes us human — or alive for that matter — is not the components that make us up, but rather the complex relationships among those components. To quote Patty Loveless, “Break us down / to our elements, / and you might think He failed. / We’re not copper for / one penny or / even iron for one nail.” [1] The critical attribute of a bag or a sack is that its contents are disordered, and that complex functional or structural relationships among those contents are unlikely to exist. If someone calls you a douchebag, they are both calling you a douche and implying that your value is not greater than the sum of your parts.
What I like is that the productive family of suffixes “-bag,” “-sack,” etc. implies a sophisticated, if unconscious, understanding that the essence of our humanity is a classic emergent property, not derivable from a simple summation of our human components. For those of you who aspire to greater explicitness when insulting people (I know you’re out there), let me suggest the following variant next time you are thinking of calling someone a scumbucket: “high-entropy scum.”
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[1] This is not technically true anymore, since the introduction of copper-plated zinc pennies in 1982. According to Wikipedia, penny weighs about 2.5 grams, and is now about 2.5% copper, which means that it takes about 62 mg of copper to make a penny. According to the Copper Development Association, the human body contains perhaps 100-200 mg of copper, depending on the size of the particular human body in question. So, we are, in fact, copper for one penny, but most of us are not copper for four pennies. In Patty’s defense, the song was released in 1994, and, given that coins can commonly last for 25 years or more, the majority of the pennies in circulation at the time may well have been of the pre-1982 variety, containing 15 to 20 people worth of copper.
About this blog

Pilot

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So, here’s what I’ve noticed about the web. There are not enough blogs! I aim to remedy that by creating this one. (Pregnant pause) Alright, NOW there are enough blogs. Whew.

Like you, I am a number of things, but the two that are relevant here are: evolutionary biologist and poet. This will be a place for discussion of various topics in evolutionary biology (and science more generally), poetry (and language more generally), and the places where these things intersect.
Some of the topics will be discussions of individual poems or books, or recent scientific publications. Some will be more meta-discussions of nebulous topics like, “What constitutes poetry?” or “What is the relationship between the societal roles played by science and poetry?” Some will be shameless promotions of my own work and ideas in these areas. And, undoubtedly, some will be unprincipled rantings about unrelated topics, such as politics or reality television.
Hopefully, some coherence will emerge, or, if not, perhaps a pleasing decoherence.
Welcome!