Wing-bat envy

Here in Alaska, we only get senate candidates who 

• go on unemployment, and then argue unemployment should get removed, 
• lie about why they won't release their records, 
• fail to pay their taxes, 
• apply for low-income resident hunting licenses that they aren't qualified for, 
• want to abolish the federal minimum wage,
• apply for medicare money, which they're vehemently against,
• accept farm subsidies which they're vehemently against,
• and who think that the 17th amendment was just a crummy idea because really, what to voters know anyhow?

Well, that and Lisa Murkowski, who should really have her name legally changed to something like "Lisa Smith" for her write in campaign, if she wants any chance in heck. But let's be honest, how boring is that? There's no style. It's just boring old rank-hypocrisy from a self-important group of blowhards who lust after power like I lust after a big bowl of ice cream. There's nothing new or exciting there. We have Palin going around talking about Death Panels, and other forms of verbal diarrhoea, but she's pretty much gone national now. She's the 'States' problem now (sorry guys). Oh, and I've heard rumours we got some other guy running, too.

But Delaware? They have candidates who say that although they dabbled in witch-craft once upon a time, that honestly, they've stopped being a witch. She also denies evolution, and has a strange obsession with... well... topics that are really none of her business. And honestly, that makes our craziest candidates look sane and well adjusted. I guess when people say we should go back to the root of what makes this country great, they mean going back to the 1600s:

Can we agree F-st has run its course?

Other scientists out there! Hi. Can we agree that Fst, as wonderful as it's been, has run its course? It was a good idea - a great first crack at population genetics. When Wright came up with it, it was a wonderful idea. And for some applications - those where heterozygosity is generally low (I'm looking at you allozymes) - it works quite nicely. But once you're outside the Hs of .4 to .6, your Fst value starts becoming highly constrained. Fst = (Ht - Hs)/Ht. If Hs is large, it doesn't matter how much skewed your heterozygostity partitioning is, Fst will be small. There may be a way around this in Jost's D. I'm not a math biologist, so I'm not qualified to review his equations. But Fst is deader than a door nail. It's been a good run

Not convinced? Fair enough. Consider this figure from Gerlach et al 2010.

Why should diversity have any effect on population sub-structure? This makes no sense. Imagine two herds of caribou, one in Alaska, and the other in Quebec. All the herds between them are wiped out by Caribou flu (and you thought pig flu was bad!), so there's no gene flow. They both diversify, generating new genotypes - Alaska generates Alleles A, B, [...] L, M. Quebec generates alleles N, O, L [...] Y, Z. Both populations lose their ancestral form. All alleles are represented at equal frequencies. Neither population has a single allele in common. Divergence is total. And Fst is only 0.04* for this population pair. Fst will only get lower as you add more unique alleles to each population. This is absurd. Adding alleles does nothing to alter the fact that there is no gene flow from Quebec to Alaska in my example.

Jost's D would calculate differentiation as 1.0, which I think is a more accurate reflection of the fact that they have no diversity in common. But, IANAMB**.

Two reasons I bring this up. First, because I'm reading Gerlach et al 2010, which took the approach of using a variety of datasets to show that Fst*** does not reflect true levels of differentiation. It's a heap of data that show that when corrected, Jost's D neatly tracks true population divergence while Fst... well, it's flogging a dead horse at this point. The second reason will become clear in a moment.

I propose the following. You're allowed to use Fst in your publications for one more year. But at the end of 2011, that's it. Either move to other metrics, or take up under-water basket weaving. I've got two manuscripts I've got in prep. that I really hate having to report both Fst and Jost's D within. And in my case, Fst is awful because my species have high heterozygosity all around. I'm to be told that subspecies on different continents have an Fst of ≥0.05. If I were to take the most simpleminded, naïve interpretation of this, I would be to believe that I have around 4 migrants successfully swimming the arctic ocean to Eurasia each generation.

How about not?

*If I got my exact math wrong, you have permission to beat me with a stick. My point stands, though.**I am not a math biologist, so I'm not sure if Jost D's derivation is completely correct.
***Technically Gst, but Fst and Gst are used interchangeably, so 'nuff said.

GERLACH, G., JUETERBOCK, A., KRAEMER, P., DEPPERMANN, J., & HARMAND, P. (2010). Calculations of population differentiation based on GST and D: forget GST but not all of statistics! Molecular Ecology, 19 (18), 3845-3852 DOI: 10.1111/j.1365-294X.2010.04784.x

Good oppertunity for the sciency people!

I'm on a few professional mailing lists, which are good for various questions, finding out about conferences, new journals, and so forth. One of which is Evol-Dir, one of the oldest biology mailing lists on the internet. This morning, I got a very interesting announcement from Evol-Dir. While I can't take advantage of it myself, perhaps someone of you can. The prize is a free trip to North Carolina! In the middle of Jan, a trip to the tropics-that-are-the-states would be niiiiice. I'll reproduce the email here:

Win a travel award for best evolution-themed blog
Application deadline: December 1, 2010

Are you a blogger who is interested in evolution? The National
Evolutionary Synthesis Center is offering two travel awards to attend
ScienceOnline2011, a science communication conference to be held January
13-15, 2011, in North Carolina¢s Research Triangle Park.

The awards offer the opportunity to travel to North Carolina to meet with
several hundred researchers, writers, editors and educators to explore how
online tools are changing the way science is done and communicated to the
public. Each winner will receive $750 to cover travel and lodging expenses
to attend the conference. For more information about ScienceOnline2011,
visit http://scienceonline2011.com/.

To apply for an award, writers should submit a blog post that highlights
current or emerging evolutionary research. In order to be valid, posts
must deal with research appearing in the peer-reviewed literature within
the last five years.  Posts should be 500-1000 words, and should mention
the NESCent contest. Two recipients will be chosen by a panel of judges
from both NESCent and the science blogging community.  Please send your
name, contact information, the title and date of your blog post, and a
URL to travel.award@nescent.org.

Winners will be notified by December 15th, 2010.

For the results of last year's contest, visit http://bit.ly/a5wtbt

For more information contact Craig McClain at cmcclain@nescent.org,
or Robin Smith at rsmith@nescent.org.

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Coming to theatres soon

I just read that there's serious talk about there being a Myst movie. For those of you who haven't wasted as much time on computers as me, Myst is a puzzle solving game where you wander around an island pulling levers, getting inside a tree, and trying to unsink a ship. It's actually far less boring than you think, and is a great, non-violent puzzely game for getting the kids to think. But it's the absolutely worst material to make into a movie.

What's next? "Tetris 2: Revenge of the Z Shaped Block." Of course, everyone will agree that Tetris 2 was no where as good as Tetris 1: Crazy Blocks Falling From the Sky.

Don't worry people! I've got a biology post ruminating in my brain. I just need to plot it out on paper.

New Toys

Yeah, I know I've been hiding for a bit. Hopefully my situation will change soon, but until then, here's something neat I saw in the Tundra Drums: Someone modified a Polaris 6 wheeler to act as a mini-ambulance. I'm surprised no one thought of the idea sooner - now that I see it, it's pretty obvious. The problem is that ambulances can't really work in most villages because of poor roads, or often no roads at all. How do you get a seriously unwell person to the clinic?
Previously, you'd stick someone in the back of a gator or argo, or in the seat of a bigger ATV. If you can run a truck, maybe that might help out, but that's hit and miss. But this, converting a 6 wheeler into an ambulance? It might have some problems in snow, but this is pretty brilliant.

Okay, speaking of ambulances, I can't help but think of a mildly NSFW monologue by Tim Minchin on the subject of ambulances, taking a cab in London, and lipsycing.

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Little Bobby Tables strikes again And Intertidal Neatness

For you code geeks out there, this is too funny to pass up. Amid all the stupid that happened in the Swedish Elections viz. nazis (sorry Sweden. :( ), some more anarchical voters subbmited votes for... well, they did a write in vote for an SQL injection attack. :P They were counting on people compiling their vote and entering it as written, so when the vote 'software' hit it, it would think it was a code and treat it as such. Sweden clearly has an educational system that works. ;)

For you non-code geeks, here's some intertidal neatness. :)

More Economics of Drugs (It's the incentives, stupid)

I've been reading a lot about the economics of drugs lately (again, I don't touch the stuff myself, but this stuff is fascinating!), and it was very interesting to see a blog post by Marginal Revolutions, a wonderful economics blog, discuss the groups most actively lobbying against the legalization of marijuana. Before you click, care to guess?

...

It's the Police and beer distributors. At first you might think there's a crime watch aspect from the police - good health and safety and all that. Instead, the cause turns out to be far more banal:

[...] Police forces are entitled to keep property seized as part of drug raids and the revenue stream that comes from waging the drug war has become a significant source of support for local law enforcement. Federal and state funding of the drug war is also a significant supplement to local forces' budgets.

Legalization means a cut in budget, and less material seized. Any economist would say that life is all about incentives, and in this case all the incentives are for police to oppose legalization. They must have done some form of calculus to find that the amount of money garnered for police budgets through taxation would be less than the amount they achieve from property seized. This is presumably because they would have to share tax revenue with other departments. This raises the question of whether incentives could be reworked to favour police departments (And that, of course, raises the issue of should incentives be re-worked at all, which is an entirely different question).

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Croudsourcing consumer expenses.

Very particular consumer expenses. Since I'm apparently in a controversial mood today, there's a neat link I found called priceofweed.com. You can probably guess what it's about. While I don't do them, I find drug economics very interesting. The products are illegal, expensive, and in some cases dangerous to acquire, and yet according to the Author of Freakanomics, crack dealing has much the same business organization as McDonalds.

Anyhow, back to weed pricing: you can't trust police estimates of drug worth, since they have a vested interest in exaggerating the prices both to dissuade use and to make them look like they've accomplished something. When you spent several hundred thousand dollars, you need to justify it by saying you stopped some equal or greater amount of illegal activity, and the greater the estimate of the activity stopped, the more cost effective you can claim to be. "You should fund me, because for every one dollar, we can stop six thousand dollars of drugs." It gets so absurd that on the TV, I once heard police claim they had interdicted something along the lines of 1% of the US's GDP in drugs. 100 Billion dollars worth of drugs is... well... in 2008, it would have been the equivalent of trying to smuggle in the net worth of IBM. I imagined somewhere, an economist saw that on TV and promptly choked in his own spittal over the absurdity of the claim.

What happens when someone performs an act that's entirely legal in a majority of countries including the one they're in, causing no material harm to any person, through making an artistic political statement?

They have to change their identity and hide from death. That's exactly what happened to Molly Norris, of Draw Mohammed Day. Now, I won't pretend like the situation is not a bit more complex than a cut and dry instance of freedom of speech trumping all, but dangit it shouldn't be. Even granting that it is an "insult" just for a moment, well adjusted human beings should not react to insults with murder. This whole thing is like Salman Rushdie all over again.

He's not anti-science. He's just anti-science.

Here's a gambit you might recognize:

"Just because you are anti-evolution doesn’t mean you are anti-science," [John May] said. "I deeply respect science [...]"

It's a similar gambit to the "I have tons of black friends" gambit, or sentences that go "I'm not a homophobe, but I'm about to say they sleep with Satan himself." Sure he deeply respects science... as long as you're not talking about palaeontology, biology, zoology, phylogeography, or any of the other fields that don't make a lick of sense without invoking evolution. Normally, it's easy enough to ignore a crank, or point out he is a crank - and John May is a crank - but the problem comes from the fact that he has backing from Ireland's science minister.

Well, there's a rub.

Mister Lenihan backed out after it came out that John May ran some torrid magazine at some point. To be honest, I have less problems with that than he was backing this vacuous crap to begin with. After all, politicians are always in some sex-scandal or another. But a Science Minister who endorses creationism is a bit like a pacifist general, or a minister for finance who never really could do the sums, and thinks poplar leaves are accepted as a form of currency. It's a sign you might have problems.

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*Tap Tap* Is this thing on?

Hello!

You might have noticed I've been absent for a little bit again. I was out in the field again, wrapping up the season with some various and sundry work. I've run into a tiny snag in my personal life, and although I'll try to have some posts out, it'll definitely be fewer and longer between posts until everything is peachy again.

In the interim, here's a moose staring at you.

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