Tuesday, 26 October 2010

Picturesque Copper River

Here's a picture of the copper river outside of chitna, when I went down there this year supposedly to fish. I never really did get a chance, since the water level was all wrong, and I had to go home soon after. But Chitna is a great place. The Chitnites are easy to get along with, there's a great little bar in 'town' (Uncle Tom's), and when things aren't so crowded, its easy to get to talking to people from all over the state. Soon after I took this, I was passed by a guy on a bike who was out sheep hunting south of there, and we got to talking about his trip - he also was unsuccessful in getting any meat that day. For all you transplants to AK, as soon as you're legal, you should go give dipnetting at Chitna a try. It's an experience and a half for most people, and even I find it a whole lot of fun.

I heard it called "Subsistence for College Students" once, and I had to laugh because that isn't so far from the truth!

Monday, 25 October 2010

Yugcetun demonstratives

A friend of mine went to Montana for graduate studies in linguistics - she's studying to be a speech pathologist - and was apparently in a conversation with someone down there about Yup'ik. She'd told him that Yup'ik has an incredibly elaborate set of demonstratives (ways of saying "This" or "That"), and when she told him that there were 30+ demonstratives, he refused to believe her. :p

But it's true! There are over 30 demonstratives in Yup'ik, not counting all the positional words. Why so many? Well, I got told this explanation about how the tundra is confusing to navigate on, and so the system gets elaborated to work out where things are. I'm not sure if I believe that - I think it's more likely that it's complicated because it's complicated. English has a very complicated and irregular system of plurals, like Goose-Geese, Cow-Cattle, Moose-Moose, Dog-Dogs, and so on. Over time, we lose a lot of the complication in English (the irregular forms are purged), and the same is true with Yup'ik - people use a smaller selection of demonstratives than before. But no one would argue that in English's primordial environment, people had to be very good at quantifying animals. It's just a silly argument.

In grammar person talk, Yugcetun demonstratives can be either 'extended,' 'restricted,' or 'obscured'. That is, they can refer to something at one spot, not moving (restricted), something spread out or moving (extended) or something we can only infer is there (obscured). For example, we have man'a, which is by me (the speaker) in the spread out sort of way. Or unegna, which would translate so elegantly as "that downriver one that is spread out." Pamna would be "that one upslope that you can't see." The translations don't really roll off the tongue in English!

In a simple sentence, I could say "Kan'a Angsaq cukaituq." Which would be "That boat (down below) is slow." With nouns you use them pretty normally, except the plurals get funny. If I wanted to say boats, I'd say Kankut angsat cukaitut... so instead of just changing the ending like most words (Kavirliq->kavirlit) you have to strip it down, add on a -ku- and then you get to end it. Adverbs are even more different.

I've wondered if inupiaq has a similar system of demonstratives, or if it's different. The languages borrow a lot of vocab from each-other, but I'm told the grammar of inupiaq is different in ways. If someone knows, I'd be very curious to hear.

Here's a really cool shirt my friend made for yup'ik demonstratives. He gave me one, and I've worn it around town! :)

Friday, 22 October 2010

Using Physics to save a life

There's this wonderful story making the rounds about how an engineer in Washington used a basic knowledge of physics to save the life of an elderly driver passed out behind the wheel. You can read all about it at the Seattle Times. Mr. Innes saw the driver of a truck was passed out and heading for a busy intersection, but the vehicle was still going. So he took his van, got ahead of the truck and matched the speed. Then, decelerating, he let the truck rear-end him, and then used that contact to slow down the truck. The trick here is that while both vehicles were travelling fast, they were both travelling in the same direction, so at the time of the crash, the difference in speed was only a few miles per hour. This resulted in a much less dramatic crash, after which he could slow presumably by breaking thus avoiding a crash with a larger difference in speed (like 80+ mph).

In a bizarre show of humanity, Mr. Innes was told that he wouldn't have to cover damages for the collision. The Insurance Company promises not to act humanely twice.

Thursday, 21 October 2010

Egg eating Snakes

While I'm 'nomming' my lunch (As the cool kids say), I was reading about this interesting group of critters. See, I learnt a rule in college that says you should never eat anything bigger than your head. Clearly, these egg eating snakes have never heard of this rule.

You can read more about them over at Jerry Coyne's blog, WEIT. While mammals have a reasonably diverse group of modes of feeding, I can't think of anything as outlandish as this in the species I study. No one who owns a dog will be impressed by how fast a wolf can eat, and moose and caribou have comparatively boring feeding ecology. It's days like this I'm envious of other scientists for working on really crazy weird critters. :P

Tuesday, 19 October 2010

Does your doctor have a conflict of interest?

This morning, I was listening to KUAC when I heard a story about Doctors who had been disciplined in the past, but were now receiving money from pharmaceutical companies. You can read the original ProPublica story here. I think most people are vaguely familiar with this happening - or at least I hope most people are - but along with that story came a wonderful utility to find out if your doctor had reported income from the drug companies. Immediately, I checked for a doctor that had behaved very strange and found that their strange behaviour was all their own (or is hiding their pharmaceutical income). But perhaps you'd like to check your own too; I've gone ahead and linked the entry on Alaskan doctors here.

I should hasten to add that I'm not against pharmaceutical companies per se, as I'm a huge fan of new and modern drugs. I'll take a refined and purified analgesic over some willow bark and mashed up porcupine quills any day of the week (or at least those days where I need an analgesic). I am slightly leery of their marketing arms though, which can get up to some... morally dubious things. What really surprises me is that the amount that Doctors have received is so small; 257 million since 2009 seems like chump change. We're talking about 7 massive companies what have far more than that to throw around...

Monday, 18 October 2010

Beer Notes from Sunday

Jubelale by Deschutes, Oregon.

The bottle is a typical 12 oz Deschutes bottle, with a purple label that informs me that Jubelale is a "festive winter ale," and little else. There's a best by date stamped by the UPC, but no indication when it was bottled. You can smell the hops before you've even poured; the beer is a dark oak colour, just edging on transparent, with little evident carbonation. The head is down to a thin ring in short order.

The aroma is dominated by hops, with just the faintest hint of caramelized sugar. The flavour is more balanced, with the smoky coffee flavour that Deschutes does so well blended with hops and something malty. The beer finishes dry, with just a slight bitter aftertaste. It seems to improve as it warms, the flavours becoming more distinct. Not terribly drinkable for for my money, though - just a touch too dry. 3.7 out of 5. B.

Tuesday, 12 October 2010

Was hiring Mike Modano a good call?

About 70 days ago, the big question for the Detroit Red Wings was whether or not Mike Modano would sign on with the team for a year contract. Modano is an amazing player, and one of the all-time goal leaders. He is also a local boy, having been raised in Michigan. But Modano is also old for an athlete, having turned 40 in June. And his season average goals has been on the decline for some time. So when Modano agreed to sign a contract about 67 days ago, the question quickly became "is this a good idea?"

The idea is that Babcock will use Modano as a centre on the third line, with Jiri Hudler and Dan Cleary. Nominally, this is to provide third-line depth that most people don't have, but that's not the real reason he's there. The real reason is so that Datsyuk, Zetterberg and to a lesser extent Holmstrom can be put on the same line. It's all about getting the Eurotwins back together and hoping Zetterberg's Swedish Magic™ will come out in his pairing with Datsyuk.

By the way: Thank god for Sweden. :) And anyone else notice how few Russians there are on the team right now? Bizarre.

But. This is all predicated on the idea that Modano will keep the third line strong enough to shuffle things around. And while Modano has had a nice first few games, I'm going to point out the obvious - He's old. Even in a club like the Red Wings, which has been at times jokingly called the senior centre on ice. He doesn't have many years of good hockey left in him, if he has any at all. Yes, his first shot in his first game was a goal. But long-term, will he have the staying power? In the regular season they can just idle him down for a game or two, but in the playoffs, what then?  There's no nap time in the play offs, when Modano will be expected to consistently bring his A-Game. So while the experts are saying good things about Modano and the Red Wings, I remain cautiously optimistic at best. I'm often wrong, and I look forward to being wrong about this too.

If life was like a political debate...

I can't resist sharing this comic from the always funny, though sometimes NSFW, Saturday Morning Breakfast Cereal.

Monday, 11 October 2010

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:

Friday, 8 October 2010

Can we agree F-st has run its course?

ResearchBlogging.orgOther 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, na├»ve 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

Wednesday, 6 October 2010

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.


Monday, 4 October 2010

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.

Friday, 1 October 2010

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.