My horse in the race finishes.

FAIRBANKS — Newton Marshall belied his humble Jamaican upbringing by dreaming big. On Thursday morning, he finished the Yukon Quest in lucky 13th place.

Woo! I'm glad he finished. I thought he would, but I'm still glad! I am, however, surprised he placed as high as he did! Not top 10, but definitely not bad for a guy who had never seen snow a few years ago!

Flaming Wombats

Sage advice to Dave from the Onion:

Australian wild fires spur large increase in flaming animal attacks It's the onion radio, news this is Doyle Redland reporting. Wildfires in the Australian outback have reportedly doubled the number of attacks on humans by kangaroos, snakes, and wombats currently engulfed in flames. Zoologist doctor Janet Nordean says that even creatures long believed harmless to man can be a major concern went on fire.

"Now even the gentle Wallaby can be quite deadly."

Nordean added that upon encountering a flaming animal in the bush people should not repeat not douse it with gasoline as one would with an ordinary, household pet.

Can you sex goats?

ADF&G has a great quiz, testing your ability to tell male mountain goats from female mountain goats. I'm no goat/sheep hunter myself, so I did miserably. How well did you?

Here's a question I have: How often do mountain goats fall to their death? I'm very curious to know. Think about it: there's no reason that mountain goats are immune to stepping on loose rock near big drops. It's not as if they can fly if they misstep. Or, rather, they would fly, but they would have an uncontrolled landing. And if monkeys fall from trees, why not goats slip from rocks?

I'm very curious.

Jindal vs. The Volcano

Bobby Jindal delivered the Republican response, and staying true to the current fad in the party, decided to pick out several minute spending items that total a fraction of a fraction of a percent, and single them out to damn the whole thing (ignoring the larger question of whether Gov't. spending can actually stimulate the economy, which is frankly a more interesting issue). So he decided to criticise a few things that weren't actually in the bill at all, and one thing...

I stood agast - well, not stood. I was busy driving when I heard that. But I drove agast. Turns out people from states with volcanos? They think he made a pretty big ass of himself. Like Washington, and Alaska. I can't find the Hawaii story I saw yesterday, but you can imagine that comment wasn't especially popular there, either. One person went as far to sarcastically ask,

Volcano Monitoring? Is that sort of like Huricane Forecasting? Who gets Huricanes, anyhow?

which got a smile out of me. Scientific America has a story about what Volcano Monitoring is all about, and while it's on par for an average Sci-Am story (which is to say, it could use some work), it's got the basics.

Apparently, his collegues are derriding the response in general as especially awful. Except Rush Limbaugh, but he'd defend a lump of frozen dog crap if it called itself a Republican. What's it take to go from `rising star of the party` to `yet another Lousiana political hack?` Apparently, it takes Little Bobby Volcano.

Meant to repost this earlier. From the village telegraph:

Federal Subsistence Board bans lead shot for hunting wildlife in Unit 18

2-19-09

The Federal Subsistence Board has approved a special action to prohibit the possession or use of shot shells containing size “T” lead shot or smaller for the taking of wildlife in Unit 18 in Western Alaska.
The use of lead shot for waterfowl hunting has been banned since 1991, due to the high mortality of waterfowl related to ingestion of lead shot. However, it was not banned for the harvest of other wildlife under Federal subsistence regulations. Officials with the Yukon Delta National Wildlife Refuge believe this ban would benefit waterfowl by helping to decrease the amount of lead shot in the environment.
Two species of eider that inhabit Unit 18, the spectacled eider and the Steller’s eider, are listed as threatened under the Endangered Species Act. Concerns over the effects of lead shot on these species resulted in this action. For additional information contact Chuck Ardizzone at (907) 786-3871.

I understand the rational behind this, but I don't think its an especially good call. A more gradual shift to a total ban would be better, so it gives people a chance to use up their lead shot as they transition to steel shot. If this is a major issue at all - I'm a bit unsure how they they estimate the amount of lead shot used in larger game to be anything but negligible. Most folks use centrefire rifles for large game, and furbearers etc. tend to get .22.

Pictures

Yukon Quest Rules

There's news that Hugh Neff, second place in the Yukon Quest, has been penalized for two hours. Here's the story in the Daily News Miner, but the long and short of it is that he mushed on the road for a number of miles, thus cheating. I agree, mushing on the road is kinda skeezy. He deserves punished. However, the reason why surprised me.

Neff violated the trail procedure rule that states: “All teams must follow the trail as marked or as instructed by the race marshal.”

Well. That seems dumb. Isn't this supposed to be a race of skill, talent, and physical prowess? If people think they can shave time off by going and bushwacking, more power to them. So long as they make it to the checkpoints, and they don't use roads, that's all that should matter. But saying `there's one way between these two points` is silly.

In fact, call me old fashioned, but I wouldn't mind seeing the trail go away. I've got no illusions this'll happen, but in the dim and distant yesteryear, the mushers had to make their own way along. Hard? Sure. But the 'Quest bills itself as the toughest race on earth.

Desk!

There's an internet meme going around where you take a picture of your desk and post it (where your desk is supposed to be a reflection of yourself, I suppose). Since I'm in the office mostly today, here's mine:
In that vein, I have no clue what my desk says about me - other than I have a landslide of papers, and I need food to work. I took the picture at a jaunty angle, so you can see my half a billion maps and references I have taped to my wall. I've got the 1:250 layout for the state, habitat type for the state, GMUs for the state, caribou herds for the state, a map of prince of wales island's middle, caribou around the whole arctic, a diagram of the mitochodria's DNA, a calendear, no fewer than three phylogenies (Caprinae, Cervidae, and cervids with dates), four stickie notes with indeciperable reminders exhorting me to do things a year ago, a list of phone numbers, and a sheet reminding me what my own address is.

I suppose all those maps and so forth means I have a hard time remembering where things are. :p

Population and diversity.

A little while ago, I left you all with this graph, and I asked which had more diversity, and why.
The answer is `Caribou,` because for each loci, there's a wider range of possible values (or `alleles` as we call them in the biz). While diversity in µsats (these chunks of DNA) doesn't translate 1:1 into total diversity, they're often a good proxy for them. Take Muskox, for example: They're monomorphic (meaning they have no diversity) at many regions of neutral diversity. Additionally, they're monomorphic at regions that are important to the function of the animal - such as MHC, which is important for disease resistence in us critters with backbones.

Part of the reason why Caribou have so much more diversity than Moose is probably due to the sheer number of critters - there's so many more Caribou than there are reindeer. Why, taken together, The Western Arctic Herd and the Mulchatna Herd of caribou outnumber the humans in the state of Alaska! That's not a trivial number of animals, and that's before you add in other major herds. Moose, to contrast, probably number between 60 and 80,000 animals in the state, depending on who's doing the counting. They exist at a pretty low density overall.

Why does population matter? Well, there's two reasons why. And I'll use two anologies.
First, imagine you have ten marbels, each a different colour. You have them all on the ground, when you drop a hammer and smash one accidentally. One of your colours is now no longer represented in your pool of marbels. But if you have 100 marbels, with 10 of each colour, and you drop your hammer, you could smash many more marbels before you lose any colours. The same is true with animal diversity - the more animals you have, the less likely you are to accidentally kill off all the animals with one sort of `allele.`

Second, imagine you're running a poor-man's xerox place. Instead of machines, you've hired a bunch of teenagers to copy things by hand. Teenagers are flakey, and make mistakes while copying pages. Right now, you're xeroxing stuff for the national archives, so all their mistakes will be preserved as they're made. If 1 in 10 teens makes a mistake, then on average, your shop of 10 teens will make one mistake each job. But if you're running a larger shop of 100 smelly, moody teenagers a) you're to be pittied and b) you'll, on average, make 10 mistakes per job.
The same is true with animals. When DNA is replicated so it can be passed on to baby animals, we invariably make mistakes in copying it. Some of it is bad, most of it doesn't matter, and a little fraction of the mistakes are good - this leads to some of the variation we see in nature. Each human, for example, carry around about 400 new `copy mistakes` that most other humans don't have. The more animals you have, the more new forms of `alleles` will be formed through copy mistakes.

Things I did not want to see.

Over the last two hours, I've been watching the alaska 511 page for the interior. Everything started out yellow (which is good, for this time of year), and slowly, one by one, the roads have been turning red. Now 12 mile and Eagle Summit are effectively closed (if not outright) and Ptarmigan Pass (where I need/want to get over) is impassible for the time. And not even just `conditions are bad` impassible, but `it's going to take us a bit to clear` impassible.

So I guess I'm in Fairbanks for the foreseeable future.

Sunrise from a week or so ago.

Pictures

Spare a thought...

Spare a thought for this poor dog.He's forced to live his life near/at the Turtle Club, eating leftover prime rib every single night. The thing was so well fed he had problems walking more than a few feet. I went to the Turtle Club for a friend's birthday, and the qimulvak was visibly confused when we didn't feed him any of our leftovers.

I bet he's only 4. :)

A hot cup of... what?

What's the non-alcoholic drink of choice in AK? In the bush, and lots of the road system, it's not coffee like most people would guess. It's tea. Tea is popular in ways most people outside wouldn't guess. The big one is lipton, but people love Hidden Stash too. People buy lipton by the bulk, and go through it as quickly. Part of it is, in a lot of places if you show up to someone's house, you'll get offered tea (and frequently food, but this is a post about tea). 9 times out of 10. I promise you, if you show up at my house, I'll offer you tea. It's just sort of what people do. Now, I have coffee too. In fact, Kuuvviarsugtua. Taugam, instead I'm having tea because I didn't think through breakfast. The hidden stash orange one.


Somehow, in my upbringing, I got it in my head that you shouldn't accept what people offer you, because it's inconveniencing them, or being a burden. But the saying is out here, if someone offers you food, you make room in your stomach - it's rude to refuse. It makes it awkward for me, because to be polite, I have to act in a way I think is rude.

I blame my parents, society, and TV. Oh, and the devil's music.

AWT looks for Supercub.

Hard to believe I missed this:

Feb. 9, 2009
PR# 09-017

AWT Asks Public’s Help in Locating Aircraft

(ANCHORAGE, Alaska) - Alaska Wildlife Troopers are investigating an illegal big game guiding operation that involved the use of a super cub N191AK. Alaska Wildlife Troopers currently have a seizure warrant for this airplane. Information leading to the seizure of this aircraft may result in a cash reward. Please contact Wildlife Safeguard at 1-800-478-3377 if you have information about this plane.

Word on the grape vine (which I've verified by looking up the tail number) is the guy who owns the plane is the same guy who has been arrested for baiting wolves with poisoned moose before. And breaking dozens of non-trivial laws as a Guide (like landing and shooting; letting clients ditch moose because `it wasn't big enough`). This guy is a grade-a scum dog. You see this plane, call it in.

Yukon Quest Rookie

With the home town hero, Lance Mackey, not racing in the Yukon Quest, who are we supposed to root for?
I'm going to root for this guy here.

Gatt said Wednesday that he met Melville at a dinner with Quest officials in Whitehorse, where the businessman invited him to visit Jamaica. Gatt accepted, and once there, “Danny came up with the idea it would be possible to run the Yukon Quest with a Jamaican musher. He needed to find somebody that knew how to do it so he approached me,” Gatt said.

Marshall, 25, is proving to be a quick learner. He placed seventh and won the sportsmanship award at the 2008 Percy DeWolfe Memorial Race. This season, Marshall was 21st among 47 starters at the Sheep Mountain 150 and 13th in an extreme Copper Basin 300 that featured frigid cold, a stretch of open water and sugar-snow conditions. Like any rookie, he’s had accidents but nothing catastrophic.

I love rooting for people with class, like Mackey, or the Wings, and I like people who are good at what they do. But I want this guy to place because it's just such a great story.
Go Marshall!

Advanced Robotic Limbs

This is pretty cool. The story on the page is pretty fluffy, but the video off to the right is very neat indeed. In it, amputees use an advanced limb to do all sorts of things that require fine motor control, including picking up a cracker, tearing open a packet of sugar, and what appears to be setting a tissue box on end. The engineering challenge is pretty substantial.

Very, very cool!

Photo Credit: DEKA Research and Development, and The Rehabilitation Institute of Chicago

Happy Darwin Day!

Born this day in 1809, today would be the 200th birthday of Charles Darwin, were he still alive today. Among other things, Charles Darwin almost single handedly unified the subject of biology. It's hard to overstate the effect the man has had on science; science that now touches most facets of our lives in the `developed` world.

A number of organizations are holding Darwin Day calibrations, and you can go to the Darwin Day homepage to find one near you! Sadly, there is none near Fairbanks (or at least none registered). I'm undaunted, though: After work, I'll have a beer to toast the man. Could you spare a moment for one of the most influential minds of the last 1,000 years?

Pictures

AntiTerrorist Strikeforce=Mall Cops

Anti-terrorist force. On Segways. They'll incapacitate the enemy with laughing.
The world's a very silly place.

PETA opposes both bacon and doctors.

Ah, PETA. Where would we be without you.
According to the Daily Minor News, the latest thing making them angry is that Army doctors are getting training on live animals, as opposed to half-assing it by playing `Operation` followed by watching a few episodes of House, M.D. They call it `using sophisticated simulators.` I agree. I think doctors should only learn on simplified, non-realistic proxies for living biology. The less life like, the better, so that way when complications arise in real humans, they have no clue what to do. That might sound like a bad thing, but remember that doctors are arrogant bastards, and they need put in their place!

Here's my own suggestion: To simulate battlefield medicine, done under stress, they should play Operation as a drinking game. Each time they buzz, they have to take a shot. Let's see them remove the funny bone after a few shots of tequila!

You know, your priorities are totally screwed up when you look at an organization who's job is to kill people and decide that the most inhumane part about them is that they train to save lives on animals.

Dick and Jane does Alaska Politics

Cabin Dweller has a very funny post that will explain current Alaskan politics for the uninitiated.
Check it out! Though, I don't think it'll work as well for the post-Dick and Jane generation. :)

Careless Language

That's James Randi, a funny man, and one of the few people I'd listen to with the title `The Amazing` before their name. I kinda like his comments about how `natural` is flung around with reckless abandon. All natural this, and natural herbal that, it's enough for someone to gouge their ears. Totally independently of Mr. Randi, I have about the same sarcastic response to the suggestion that natural is a priori better: Methylmercury, cyanide, and botulism are all natural, but you'd do well to steer clear of all of them.

Unless someone wants to suggest that manufactured cyanide would be worse for you than the sort that some plants produce.

Organic is another poorly conceived term. I understand it's supposed to be a stand in for a suite of farming characteristics, but frankly, Organic was the wrong label to put to this suite. When I first started hearing about organic this, that and the other, I wanted to know what an inorganic banana looked like. Did organic potatoes have extra carbon? Are non-organic carrots made in a plastic injection mould?

The term organic implies that there's something unilaterally, fundamentally wrong or unnatural with non-organic foods, which is a sweeping generalization that I'd take issue with. Plying on the whole `natural=good` misconstrusion, it suggests that their goods are all around better, healthier, more sustainable. This is also not true. Yet based solely on the label, and the mistique about it, a growing number of people assume just that. Including, I'll add, quite a number of educated people who should really know better.

Gene Diversity

Diversity is how many different forms of a region of DNA exist within a group of critters. By way of example, in my building there's genes for red hair, black hair, blond hair, and brown hair. So for that region of DNA, there's quite a bit of diversity. But inside this room, there's only the genes for a one hair colour. Much less diversity. In some fish, you have life history strategies: some have genes for becoming huge, mature adults, while others have genes for spawning young. If all the members of a species who would spawn young die out before breeding, then there's less diversity - now there's only genes for becoming big mature adults left.

One way we test for diversity is to look at neutral areas of DNA - these are areas that don't do anything. Much of it is just repetitious garbage, copy errors, and viruses that snuck in and went dormant. Most of your DNA, as far as we can tell, is non-functional. Some of it is very patently useless.

Because it doesn't do anything, neutral areas of DNA (loci) are free to do pretty much whatever they want through mutation, and they're passed on in the population. We can look at this as a proxy for total diversity*, which is harder to look at.

So, I want to show you two groups of loci, one of the loci in Caribou, and one in Moose. The length of the bars shows how widely the locus of DNA can vary.The colours mean something, but nothing important for here. Which species more diverse? Why do you think that species is more diverse?*Kinda sorta. Lots of boring caveats go here.

Wild and crazy.

This weekend has been one of the more physical, most mentally demanding, and just plain bizarre times to date. I drove absurd distances, shovelled enough snow to build a cabin sized hill, ended up broke down outside of Minto, got `bumped` off the road by a semi trailer on the Dalton, had to pull people out of the ditch (had to be pulled out myself), chased moose through deep snow, got made fun of by moose (don't ask, but they were clearly mocking me), and got racially profiled (Or so I was told).

I reek of gasoline.
I ended up talking to a random person in the butt middle of nowhere about why Eugenics doesn't work, and why NCBL is a joke on America.
I was told to get bent in new and exciting ways.
I unwillingly played chicken with a grader/plough.
I wrote a post being vague about what a crazy weekened I've had in bloody clothes.

I really, really, really need a weekend to recover from this weekend.

Inversion Layers

As I've eluded to, I've spent some time in Utah (aka, the firey furnace) doing various Utah things. Any strangeness on my part is because I had my (very few) brain cells roasted alive in the sweltering heat. Never seen Railroad tracks go wavy gravy like Dave-y. I digress.
Utah is fantastically gorgeous, but it's got its problems. Let me tell you, the local beer selection in Salt Lake City (SLC) is awful. Oh, and for much of the winter, the air is neigh unbreathable. They get inversion layers too. Actually, they get worse inversion layers, in depth, duration, and pollution trapped in it. Everyone knows about Mexico City's bad air, but fewer people know that in an SLC inversion, the air can get much, much worse than Mexico City.

There's a very lovely post from a physicist at the U (what they called University of Utah, since `U of U` sounds dumb) about the role physics and geography play in making and keeping inversion layers. Something Fairbanks and SLC have in common!

Seal Control

This doesn't explain why there was less support for predator control than expected in areas currently asking for predator control, but the mistranslation sure is good for a laugh. :)

Sadly, 90% of the comments to the stories are from racist assholes:

Assimilation should be encouraged. The government does people a disservice when it enables their failed cultures to hang on a little longer.

The other 10% consists of people saying `holy hell, you're racist assholes.`

Outbreeding Depression is just plain depressing.

Opposite of Hybrid Vigour (sometimes), when you have two individuals of different populations, subspecies, breeds or species mate, Outbreeding Depression might occur. Unlike Hybrid Vigour, there's much less to explain here, but unlike it, Outbreeding Depression is less common in nature.

As generations of animals roll on, and nature does it's thing with picking the winners to have more babies than the losers (or even the slightly less winners), animals start to become very good at what they do, and often very adapted to where they do it. Their DNA has been winnowed down to genes that make them outstanding whatevers1. Arabian Gazelles are great at being arabian gazelles, and Turkish Gazelles are fantastic at being gazelles in Turkey. But what makes a good Caribou over here in North America doesn't make a good wild-reindeer over in Eurasia...

Take this case from Templeton (1986):

"...when the Tatra Mountain ibex (Capra ibex ibex) in Czechoslovakia became extinct through overhunting, ibex were successfully transplanted from nearby Austria (Greig 1979). However, some years later, bezoars (C. i. aegagrus) from Turkey and the Nubian ibex (C. i. nubuana) from Sinai were added to the Tatra herd. The resulting fertile hybrids rutted in early fall instead of the Winter (as the native ibex did), and the kids of the hybrids were born in February - the coldest month of the year. As a consequence, the entire population went extinct (Greig 1979)."

There's a number of species we're worried about outbreeding depression. Scottish Wildcats interbred with domestic felines, heavily burdening its genes with domestic copies. The same is true for Sand Cat in Saudi Arabia, and the Ethopian Wolf. Closer to home, there's evidence that domestic reindeer from our reindeer herding past (and lesser reindeer herding present) have introgressed into caribou herds - that is, left reindeer genes where they ought not be. No one's sure how extensive it is, and what, if any, consequences it has for North American caribou.

1 Though sometimes, natural selection traps them in a nasty situation (such as the Irish Elk, whose antlers were simply too big).

Greig, J.C. 1979. Principles of genetic conservation in relation to wildlife management in southern Africa. S. African Journal of Wildlife 9:57-78.
Templeton, A.R. 1986. Coadaptation and outbreeding depression. 105-116 in M.E. Soulé (ed.) Conservation Biology: The Science of Scarcity and Diversity. Sinauer Assoc., Sunderland, MA.

Pictures

Writing Hell

If it seems like I've been slacking off on the blog, it's true. I've been stuck in writing hell for the last week or so - so much so that I decided tomorrow I'm going to do menial lab chores to take a break. To give you an idea what excitement I've been enduring, here's a sample paragraph:

Using Fstat 2.9.3.2 (Goudet 2001), we characterized the variability within each locus by the number of alleles (A), the observed heterozygosity (Ho) and the expected heterozygosity (He). Additionally, we utilized Fstat to calculate FIS for each population, and overall f and θ following Weir & Cockerham (1984), and relatedness following Queller & Goodnight (1989). Fstat was also used to test for linkage disequilibrium, Beonferroin correcting for multiple comparisons (Rice 1989).

I dunno if that's English. Until yesterday, I was writing an in-house technical note that went like this -

We subsequently attempted extraction using a Qiagen® QIAmp DNA Mircro Kit (Valencia, CA). Contrary to our previous methods, which utilized a Guanidinium Thiocyanate (GuSCN) digestion, and a caustic digestion respectively, the Qiagen® QIAmp DNA Mircro Kit (Micro Kit) utilizes a GuSCN digestion in concert with Proteinase K and Dithiothreitol (DTT) digestion (QIAamp® DNA Micro Handbook, August 2003). We suspect that this allows the liberation of DNA product from protein, while causing minimal incidental damage to the DNA.

Just reading it makes my brain bleed. And this stuff follows me home at night.
Wildlife Biology - it's all glamorous and stuff.

A quickie from work - someone forwarded me this, from Penny Arcade, a foulmouth, Avant-garde comic about computer games -

You may not be aware that both Fisher Price and Nintendo are colluding with Muslim terrorists to ensnare the young, which might make it difficult to understand today's comic. You may not think that unintelligible samples or scarves are an effective weapon for global jihad, but that just means you're a part of the problem, Mohammed.

This reminds me of the uproar when a bunch of Muslims accused Nike of having something that looked like `Allah` on the bottom of one type of shoes. People can recognize stupidity when its some other bunch in another country. It's trickier seeing the stupid around ourselves.

Two hypotheses

First hypothesis - there is some evil terrorist or Muslim evangelist targeting little girls through patterns in baby babble, because we all know young girls love to repeat baby babble to themselves. There is a conspiracy by Nintendo to cover up this ebil do-er's doings. This one, brave woman is standing up to the system. Standing up to The Man.

Second hypothesis - Pareidolia strikes again. Both the doll and the computer game bought stock sound tapes from the same company - you notice this all the time, when you start to listen for it in movies (there seems to be only a few different variants of `shell casings bouncing` recorded). The woman is an overprotective wackaloon.

Occam's razor says we should go with the hypothesis that makes the least undemonstrated assumptions. One hypothesis is full of unfounded assumptions. The other full of stuff we see everywhere else. I'll let you pick which is which.