Wednesday, October 29, 2008
Jonathan Coulton
Just a quick note to plug a musician and his website (which includes a fan blog). I've followed Jonathan Coulton's alt-geek-folk-rock music ever since he brought down the house at a National Association of Science Writers do in Baltimore. Hard to describe his stuff, but if you can picture an unlikely but surprisingly apt blend of Fountains of Wayne and Tom Lehrer you won't be far off. Check it out.
Monday, October 27, 2008
Where I Get Off
There are two kinds of professional writer.
The first is the staff writer: the schlub who, day after day, hammers out copy — which may range in quality from routine boilerplate to high art, depending on the taste and needs of the employer — for a regular paycheck. Some of these folks work for publications like newspapers and magazines; but the great majority are “work for hire” employees in some sort of public relations or internal communications shop — they sell their copyright to their employer, who therefore owns everything they write.
The National Writer’s Union considers work for hire to be inherently exploitive; they may be right, but it’s also the only reason why many of us can make a living at writing. Certainly, staff writers’ employment can be precarious, because writers tend to be regarded as a luxury at many companies, and an early item to go when there are cutbacks.
The patron saint of staff writers, therefore, is Scheherazade.
The second kind of pro writer constitutes the glory corps of writing — the freelancers, people who live from project to project and contract to contract. The stars of the writing world number among them; but so do some very under-paid, hard working folks who, because they freelance, live from hand to mouth. So, also, are many people who write the occasional piece, do it well enough to get paid (often very well), but for lack of time, inclination, ambition, or sometimes just luck can’t make a go at it full-time.
The deal with freelancers is that, myths of “choose your own hours” aside, they actually tend to have less free time than staffers. Every full-time freelancer I’ve ever known worked at least as many hours as staff people, because freelancers have to spend so much (unpaid!) time marketing their writing rather than writing.
The patron saint of freelancer writers, therefore, is Thoreau’s basket maker — the fellow who, unclear on the supply/demand thing, made baskets and was puzzled why nobody would buy them as a matter of course.
That may sound stark: Certainly, the literary life has offered me a lot of joy over the years. Eighteen years after they ceremonially ripped the stripes off my lab coat and sent me out into the cold, cruel world of the professional writer, I’m still — so far — making a living at it, so I have far less cause to complain than many.
But I confess: I’m sick of being Scheherazade, and I’m sick of wanting to make baskets nobody (or no publications) seem to want. To pay the bills, I plan to keep the day job; to make some extra money, and to keep myself a bit sharper as a wordsmith, I hope to continue writing paid freelance pieces. But I wanted a space for myself — a space where I could write what interested me, not what I thought I could sell (or had the time to market, anyway).
Maybe it will be a space for things that interest you, too. I hope so; but in all honesty what I’m really doing is nurturing my inner basket maker. We’ll see whether he has enough to offer to warrant a readership. Hell, a writer who can’t take risks isn’t much of a writer.
So what will you be reading here? Well, checking out my bio, you’ll see that I have a peripatetic, typically University of Chicago background. So I plan to have a somewhat peripatetic site. Most of what you’ll see will probably reflect my ongoing fascination, as a former biochemist and current volunteer search-and-rescue dog handler and professional science writer, with the sense of smell (hence the blog’s title). SAR subjects may often come up, in that context or alone; so may navel-gazing pieces on writing like this one (though I promise to try to minimize these, as they get old). I write science fiction as well, so SF topics may also appear.
And like any bloggist, I reserve the right to mouth off on current political (and other) issues about which I’m not well enough educated to illuminate.
Ya fires up yer browser, ya takes yer chances. Reading, like writing, poses its risks.
The first is the staff writer: the schlub who, day after day, hammers out copy — which may range in quality from routine boilerplate to high art, depending on the taste and needs of the employer — for a regular paycheck. Some of these folks work for publications like newspapers and magazines; but the great majority are “work for hire” employees in some sort of public relations or internal communications shop — they sell their copyright to their employer, who therefore owns everything they write.
The National Writer’s Union considers work for hire to be inherently exploitive; they may be right, but it’s also the only reason why many of us can make a living at writing. Certainly, staff writers’ employment can be precarious, because writers tend to be regarded as a luxury at many companies, and an early item to go when there are cutbacks.
The patron saint of staff writers, therefore, is Scheherazade.
The second kind of pro writer constitutes the glory corps of writing — the freelancers, people who live from project to project and contract to contract. The stars of the writing world number among them; but so do some very under-paid, hard working folks who, because they freelance, live from hand to mouth. So, also, are many people who write the occasional piece, do it well enough to get paid (often very well), but for lack of time, inclination, ambition, or sometimes just luck can’t make a go at it full-time.
The deal with freelancers is that, myths of “choose your own hours” aside, they actually tend to have less free time than staffers. Every full-time freelancer I’ve ever known worked at least as many hours as staff people, because freelancers have to spend so much (unpaid!) time marketing their writing rather than writing.
The patron saint of freelancer writers, therefore, is Thoreau’s basket maker — the fellow who, unclear on the supply/demand thing, made baskets and was puzzled why nobody would buy them as a matter of course.
That may sound stark: Certainly, the literary life has offered me a lot of joy over the years. Eighteen years after they ceremonially ripped the stripes off my lab coat and sent me out into the cold, cruel world of the professional writer, I’m still — so far — making a living at it, so I have far less cause to complain than many.
But I confess: I’m sick of being Scheherazade, and I’m sick of wanting to make baskets nobody (or no publications) seem to want. To pay the bills, I plan to keep the day job; to make some extra money, and to keep myself a bit sharper as a wordsmith, I hope to continue writing paid freelance pieces. But I wanted a space for myself — a space where I could write what interested me, not what I thought I could sell (or had the time to market, anyway).
Maybe it will be a space for things that interest you, too. I hope so; but in all honesty what I’m really doing is nurturing my inner basket maker. We’ll see whether he has enough to offer to warrant a readership. Hell, a writer who can’t take risks isn’t much of a writer.
So what will you be reading here? Well, checking out my bio, you’ll see that I have a peripatetic, typically University of Chicago background. So I plan to have a somewhat peripatetic site. Most of what you’ll see will probably reflect my ongoing fascination, as a former biochemist and current volunteer search-and-rescue dog handler and professional science writer, with the sense of smell (hence the blog’s title). SAR subjects may often come up, in that context or alone; so may navel-gazing pieces on writing like this one (though I promise to try to minimize these, as they get old). I write science fiction as well, so SF topics may also appear.
And like any bloggist, I reserve the right to mouth off on current political (and other) issues about which I’m not well enough educated to illuminate.
Ya fires up yer browser, ya takes yer chances. Reading, like writing, poses its risks.
Sunday, October 26, 2008
Broken Bottle Fight
Ya gotta love a broken bottle fight.
OK, that’s pure hype: I’ve heard no rumors of olfaction researchers actually resorting to smashing Pellegrino bottles and offering to rearrange each other’s faces at any recent symposia. But since Buck and Axel issued the first major installment in their Nobel-winning research on how the nose detects smells in 1991, two schools of thought in the science of smell have shared a major bone of contention.
Namely, is bigger necessarily better?
Here’s the rub: In 1991 Buck & Axel discovered a huge family of genes that encode the olfactory receptor proteins: A family of sensor molecules that sit on the outside of olfactory neurons in the main olfactory epithelium, deep in the nose, and detect the small molecules that constitute smells.
The OR family was one of those rare discoveries that suggest compelling answers to important questions. The sheer quantity of genes for the olfactory receptors, and the subsequently discovered fact that each olfactory neuron appears to express only one type of receptor, suggested how we detect so many complex smells: Olfactory neurons specialize in the specific odor-carrying molecules they respond to by virtue of carrying specialized detectors. Each receptor type matches a specific odorant — or, more likely, a small family of similar odorants [1]. The odorant fits the receptor much as a key fits into a car’s ignition; the receptor fires up its nerve cell, which in turn reports that odorant’s presence via an electrical jolt to the brain’s olfactory bulb.
The idea had legs for two reasons: First, in this model the receptors would act a lot like other receptor proteins and enzymes previously described in detail, and that’s always a reassuring sign you’re not going off the deep end. Second, it offered one explanation for why we use dogs to search for lost people: They can smell more things than we can.
Humans have about 900 olfactory receptor genes; dogs, around 1,200; and mice, 1,500. Now, by biological standards those numbers aren’t terribly different; it really gets interesting when we account for pseudogenes — genes that have a mistake in them that makes them non-functional. In humans, at least a whopping 63 percent of the receptor genes are such molecular dead weight — and so the actual numbers of working receptor types for each species are 350 for humans and roughly 1,000 apiece for dogs and mice.
Aha, a lot of us thought: That’s why they smell better than we do (after a fashion). They’ve got more receptors, ergo they’re detecting smells we can’t even imagine.
That’s when people started busting fizzy-water bottles against lecterns. For scientists love nothing more than to shoot down a simple idea for being too simple: People make careers from demolishing comfortable assumptions.
And some data seemed to do exactly that. Humans had far fewer total types of receptor; but if you looked at a more detailed structural level, much of the mouse "superiority" began to seem redundant. The mouse genes comprise 228 families of similar receptors, and it turned out that humans have a comparable number of gene families — we just have many more "only children" within each family. What this might mean is that mice carry around a bunch of receptors that detect pretty much the same stuff, and therefore, humans’ smaller repertoire of receptors can cover the same ground.
Enter Anna Lesniak and colleagues at the Polish Academy of Sciences: In the Sept./Oct. 2008 issue of the Journal of Heredity, they present a study of a group of 35 detector dogs from different scent specialties (human identification, explosives detection, drug detection, and tumor detection), that may rescue the more-is-better hypothesis after all.
The group tested these dogs for polymorphism — genetic diversity — in five randomly selected olfactory receptor genes. They asked: If a dog inherits two different versions of a receptor gene from its parents, does it carry out a scent-based task better than a dog who inherits the same version from each parent?
The situation turned out a bit differently for each of the five genes: For three of them, the version didn’t matter to the dog’s ability to carry out the scent task. But for the other two, an interesting, if not yet conclusive, pattern emerged [2].
* Dogs with two versions of one of these genes tended to be among the best performers for a scent task based on their specialty.
* The gene seemed to have a "better" version and a "worse" version: With two copies of the former, the dog tended to rank on average among the best performers; two copies of the latter put him among the slackers.
* It’s not clear whether having two versions is actually better than one: It may be simply that the existence of two versions gives you a better chance of having the good one.
* With the other gene, a similar pattern emerged, but only in the explosives dogs — lineup-identification dogs, tumor detectors, and drug dogs showed no difference.
* Taking the above together with the three genes that showed no difference, in no case were the dogs with two versions doing worse: They were either better off or indistinguishable.
So here’s the simple, if tentative, explanation: More receptors — even more versions of roughly the same receptor — give you a better chance of having a more-sensitive version that puts you ahead of the game in scenting ability. So the "redundant" receptors in the mouse and dog genomes may not be so redundant after all. (And yet another nail goes into the coffin of the quaint 19th-century notion that inbreeding produces superior working dogs, but that’s another issue.)
There are always provisos:
* The researchers aren’t completely satisfied with their scenting-ability tests, and they’ve got a point. The specialty based performance test hinges on the dog/handler relationship, and so doesn’t completely isolate pure scenting ability — though creating a more abstract, if lab-friendly, test might miss some important nuances in how the scent task unfolds.
* Worse, a second test, based on the dog’s ability to find treats, showed no effect for any of the genes, and its results didn’t correlate all that well with the specialty-specific tests. I think they might have gotten themselves into trouble here by using a poorly thought-out test, but they did use it, and its lack of a result is awkward.
* All the negative results could devolve from the simple expedient that, in the case of the negatives, those particular tasks simply don’t require those receptors. But we can’t rule out that the few positives were a fluke.
* For our larger, "is more better" question, we have to keep in mind there’s an apples-to-oranges going on here: We were talking about having more receptor types within each family of genes, while this experiment actually suggests what happens when you have more diversity within one type. My bet is that won’t make a difference to the validity of the argument, but it’s a possibility.
The good news is that Lesniak and her crew are well aware that their result is preliminary, and are planning to sharpen up their methods in future reports. So stay tuned.
But I wouldn’t blame conference organizers if they went for the plastic Pellegrino bottles, at least for now ...
[1] The number that people have thrown around is about 10 odorants per receptor, for a total of about 10,000 odorants. The only problem is that it doesn’t seem to come from any published scientific findings (even though the Nobel press release cited it). But here’s a wild one that suggests the whole issue is moot (or at least a vast oversimplification): In a 1993 theoretical biophysics paper that I only just found out about, Doron Lancet and posse calculated — calculated, mind you — that the olfactory system needs 300 to 1,000 receptors with the average sensitivity of the olfactory receptors to recognize, well, everything.
[2] For the wonks, they carried out their analysis with an ANOVA and subsequent Tukey testing, so they’ve presumably ruled out false discovery.
OK, that’s pure hype: I’ve heard no rumors of olfaction researchers actually resorting to smashing Pellegrino bottles and offering to rearrange each other’s faces at any recent symposia. But since Buck and Axel issued the first major installment in their Nobel-winning research on how the nose detects smells in 1991, two schools of thought in the science of smell have shared a major bone of contention.
Namely, is bigger necessarily better?
Here’s the rub: In 1991 Buck & Axel discovered a huge family of genes that encode the olfactory receptor proteins: A family of sensor molecules that sit on the outside of olfactory neurons in the main olfactory epithelium, deep in the nose, and detect the small molecules that constitute smells.
The OR family was one of those rare discoveries that suggest compelling answers to important questions. The sheer quantity of genes for the olfactory receptors, and the subsequently discovered fact that each olfactory neuron appears to express only one type of receptor, suggested how we detect so many complex smells: Olfactory neurons specialize in the specific odor-carrying molecules they respond to by virtue of carrying specialized detectors. Each receptor type matches a specific odorant — or, more likely, a small family of similar odorants [1]. The odorant fits the receptor much as a key fits into a car’s ignition; the receptor fires up its nerve cell, which in turn reports that odorant’s presence via an electrical jolt to the brain’s olfactory bulb.
The idea had legs for two reasons: First, in this model the receptors would act a lot like other receptor proteins and enzymes previously described in detail, and that’s always a reassuring sign you’re not going off the deep end. Second, it offered one explanation for why we use dogs to search for lost people: They can smell more things than we can.
Humans have about 900 olfactory receptor genes; dogs, around 1,200; and mice, 1,500. Now, by biological standards those numbers aren’t terribly different; it really gets interesting when we account for pseudogenes — genes that have a mistake in them that makes them non-functional. In humans, at least a whopping 63 percent of the receptor genes are such molecular dead weight — and so the actual numbers of working receptor types for each species are 350 for humans and roughly 1,000 apiece for dogs and mice.
Aha, a lot of us thought: That’s why they smell better than we do (after a fashion). They’ve got more receptors, ergo they’re detecting smells we can’t even imagine.
That’s when people started busting fizzy-water bottles against lecterns. For scientists love nothing more than to shoot down a simple idea for being too simple: People make careers from demolishing comfortable assumptions.
And some data seemed to do exactly that. Humans had far fewer total types of receptor; but if you looked at a more detailed structural level, much of the mouse "superiority" began to seem redundant. The mouse genes comprise 228 families of similar receptors, and it turned out that humans have a comparable number of gene families — we just have many more "only children" within each family. What this might mean is that mice carry around a bunch of receptors that detect pretty much the same stuff, and therefore, humans’ smaller repertoire of receptors can cover the same ground.
Enter Anna Lesniak and colleagues at the Polish Academy of Sciences: In the Sept./Oct. 2008 issue of the Journal of Heredity, they present a study of a group of 35 detector dogs from different scent specialties (human identification, explosives detection, drug detection, and tumor detection), that may rescue the more-is-better hypothesis after all.
The group tested these dogs for polymorphism — genetic diversity — in five randomly selected olfactory receptor genes. They asked: If a dog inherits two different versions of a receptor gene from its parents, does it carry out a scent-based task better than a dog who inherits the same version from each parent?
The situation turned out a bit differently for each of the five genes: For three of them, the version didn’t matter to the dog’s ability to carry out the scent task. But for the other two, an interesting, if not yet conclusive, pattern emerged [2].
* Dogs with two versions of one of these genes tended to be among the best performers for a scent task based on their specialty.
* The gene seemed to have a "better" version and a "worse" version: With two copies of the former, the dog tended to rank on average among the best performers; two copies of the latter put him among the slackers.
* It’s not clear whether having two versions is actually better than one: It may be simply that the existence of two versions gives you a better chance of having the good one.
* With the other gene, a similar pattern emerged, but only in the explosives dogs — lineup-identification dogs, tumor detectors, and drug dogs showed no difference.
* Taking the above together with the three genes that showed no difference, in no case were the dogs with two versions doing worse: They were either better off or indistinguishable.
So here’s the simple, if tentative, explanation: More receptors — even more versions of roughly the same receptor — give you a better chance of having a more-sensitive version that puts you ahead of the game in scenting ability. So the "redundant" receptors in the mouse and dog genomes may not be so redundant after all. (And yet another nail goes into the coffin of the quaint 19th-century notion that inbreeding produces superior working dogs, but that’s another issue.)
There are always provisos:
* The researchers aren’t completely satisfied with their scenting-ability tests, and they’ve got a point. The specialty based performance test hinges on the dog/handler relationship, and so doesn’t completely isolate pure scenting ability — though creating a more abstract, if lab-friendly, test might miss some important nuances in how the scent task unfolds.
* Worse, a second test, based on the dog’s ability to find treats, showed no effect for any of the genes, and its results didn’t correlate all that well with the specialty-specific tests. I think they might have gotten themselves into trouble here by using a poorly thought-out test, but they did use it, and its lack of a result is awkward.
* All the negative results could devolve from the simple expedient that, in the case of the negatives, those particular tasks simply don’t require those receptors. But we can’t rule out that the few positives were a fluke.
* For our larger, "is more better" question, we have to keep in mind there’s an apples-to-oranges going on here: We were talking about having more receptor types within each family of genes, while this experiment actually suggests what happens when you have more diversity within one type. My bet is that won’t make a difference to the validity of the argument, but it’s a possibility.
The good news is that Lesniak and her crew are well aware that their result is preliminary, and are planning to sharpen up their methods in future reports. So stay tuned.
But I wouldn’t blame conference organizers if they went for the plastic Pellegrino bottles, at least for now ...
[1] The number that people have thrown around is about 10 odorants per receptor, for a total of about 10,000 odorants. The only problem is that it doesn’t seem to come from any published scientific findings (even though the Nobel press release cited it). But here’s a wild one that suggests the whole issue is moot (or at least a vast oversimplification): In a 1993 theoretical biophysics paper that I only just found out about, Doron Lancet and posse calculated — calculated, mind you — that the olfactory system needs 300 to 1,000 receptors with the average sensitivity of the olfactory receptors to recognize, well, everything.
[2] For the wonks, they carried out their analysis with an ANOVA and subsequent Tukey testing, so they’ve presumably ruled out false discovery.
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