Friday, 29 May 2009


I think I might have been sent line drawings of my project after my next one...
Good draft. Stable as heck. Roomier than what I'm building (which is more like a glove). Wonder what its displacement is?
I should probably finish the stator that I started, first, I guess.

Genetic Bottlenecks

I'm not mucking with wolf systematics this week, not even a peek, as I'm focusing on another data set. I pushed out a manuscript to its completed first draft, and I'm starting to work on a second manuscript that unexpectedly grew out of the first. Re-reading one of my lab's papers turned out to be a good idea, as it's refreshed my thinking on Bottlenecks. And Bottlenecks are exactly what I want to discuss. .
No, Dave, not that kind of bottleneck

A bottleneck is when a population goes through an event that greatly reduces its size. I typically think of a bottleneck as being reduced to 10% of the pre-bottleneck population or less, but there's no hard, fast rules on what constitutes a bottleneck. Bottlenecks can occur from a variety of factors, but most frequently it's climate change that forces animals through them. Often, we find bottlenecks in species that were forced into refuges where they can survive, like Tahrs into the high mountains in a warm period, or Dall Sheep into foothills during glacial periods. Because the amount of space in the refugium (that's the fancy pants term for `refuge`) is limiting, the population is greatly reduced.

It's worth saying that these bottlenecks through refugia (pl. of refugium... I hate biologist-speak) are really important, evolutionarily. Because competition for resources is so high, animals tend to be come very well adapted to what they do. Anyone who doesn't doesn't leave behind as many kids, and are quickly outbred by their more successful cousins. But if bottlenecks are too tight, they can leave a species floundering on the shoals, because they've lost too much of their diversity, and too much of their capacity to adapt.

Here's a hand drawn figure!
This is what happens normally through time. The squiggly lines represent lineages, and the width of the tube represents the total population number. Since we frequently trace these with mtDNA (see my glossary to the right!), it represents the unbroken chain of female descendants. If you go back to your mother's great grandmother's grandmother, perhaps her sister had some children, but those children didn't have any children. Those would be a terminated lineage, represented by the little spurs that go out, but don't make it to the end of the tube. They stop early.

That's normal `lineage sorting,` as we call it. It doesn't require someone to have no children. It could be no female children, or no male children, or it could be that they didn't pass on the trait we're following. In a easy, simple example, if a tall female has children with a short male, but doesn't give any of the genes that made her tall to her children, they'll all be short. The lineage of descendants with the `tall` gene is broken, at that point. In our example, we start with three lineages, two of which are represented at the end. But each of the two lineages that made it has branched out, forming new spikes that persist. Some of them will go away, some of them will make up the successful families of tomorrow.

Here's what it looks like in a bottleneck
You can see that a lot of the lineages went away through the bottleneck. Only 1 of the 3 founding lines made it to the end. Compare this to the normal situation, where many more lineages persist. Because of the fewer surviving lineages, less diversity is passed on to the offspring, and the population at modern day is more alike itself (more monotypic) than those who didn't go through the bottle neck. By measuring the variability, we can look back and see which groups went through bottlenecks, and which didn't.

Warning: Dumb joke coming up.
So when I say I'm dating a bottleneck, it doesn't mean I'm going to a bar.

Some species that have gone through bottlenecks include Moose, Cheetahs, Galapagos Finches, some populations of Koalas, Northern Elephant Seals, and humans. At some point, the ancestral human population was reduced to around 15,000 people (possibly due to a volcano, I read?) which is part of why almost every human is closer related to every other human on earth than two random mallards, or caribou would be.

Thursday, 28 May 2009

Grey, Grey, Stay a day...

Some people are bemoaning the grey and rain, but I'm preversely pleased it's dampened up a bit. For one, it'll help with the fires. For another, 30C is just too hot for us in the interior! Okay, so it's too hot for me... It looks like it'll all clear up on Sunday, which I hope is enough for them to get a handle on the McGrath Fire.

Sadly, the rain has meant I can't apply a 3rd coat of varnish to the boat. That might seem an excessive amount of marine varnish, but for plywood, it's really a minimum. I'm looking at 3 coats of varnish, and one coat of over-sealant for the whole boat. Next one, I think I might go with bentwood to avoid plywood. Plywood is convenient for shaping, and doesn't need steamed to shape, but if there's a weak point in all of this, it's got to be the plywood crosspars. If I did bentwood cedar, then I wouldn't really need to do more than a single rubdown with linseed oil. And even that might be over-kill.

I've got the amiq coming to me in the mail, plus some some sealant. I won't get to sew it on until after I get all the chines lashed in good, which will come after I've got all the wood sealed. Ended up costing me quite a bit, but less than if I got it from Fairbanks.

Off to the east...

Who says I just do American politics? The Govern General, the Queen's representation in Canada, took part in a seal butchering in Nunavut. People are all atwitter over this, because catching seals is controversial in Canada (moreso than in the US).

I'm pretty glad she did. Ooops. Was that too moralistic?

Wednesday, 27 May 2009


We were doing whatnow?

According to the newspaper, the hiring freeze is going to be lifted June 1st.
Speaking only for myself, I completely forgot the state had a hiring freeze. I simply didn't notice. Funny thing, since I saw positions being posted and heard of people starting new jobs over at ADF&G.

It was a very serious freeze. Oh, yes.

Tuesday, 26 May 2009

Cauga una?

Here's lastweek's:
Of which I'm sad to report the one on the left is Brown Bear (Ursus arctos) and the one on the left that's been peroxide washed is Black Bear (Ursus americanus). The yugcetun for bear is pretty complex. It's one of those things that depends who you're talking to. Like `Cougar,` `Puma,` and `Mountain Lion.` Black bear tends to be tan'gerliq. Brownbear doesn't tend to be anything. Carayak, sometimes. But for other people, that's a ghost. Or something else.

You all were on the right track with the more disk like face, but really, the thing that gives it away is the slope of the muzzle. Brownbear pitches forward more near the brows, and blackbear is more smooth, gradual angle. Here, you can see it better with a picture. A brownbear:
Look where the pen tip touches.

On to new stuff! I like the way these guys (and it is a male!) look. I have a still frame, and a crummy video.
That's a picture from this weekend, to give you an idea of the plumage. Obviously, Alaska. Interior Alaska at that.
The bird won't show up for a few seconds, so be patient. My digital camera isn't a very good video camera recorder.

Who is this handsome beast?

The boat

Well, I promised photos once I could get a few without identifying stuff in there - a moot exercise, since all you have to do is drive around looking for the law with the boat in the lawn. But no point making it easier than it should be, eh?

My boat's really come together, with a mixture of muscle power, skill, and luck. I couldn't be more pleased with how well it's gone. Here's my kayak:
Now that I have the pai attached, I really don't have much wood working left to do. I started adding sealant, after these pictures. The Cedar doesn't really need it, but the marine plywood does.

What do you all suggest for names? `Qayaqa,` while accurate, lacks... something.

Monday, 25 May 2009

Dog breeds as species?

You all having a good Memorial Day? I am, thus far! I love rolling out of bed nice and late. It's a rare luxury!
Here's a little reading to go with your hot-dog eating! A person writing at Scientific America proposes we call dog breeds separate species. It's slightly tongue in cheek, but nut of the story is still there. And thanks to my previous post, you all can probably figure out why even though it's meant to be a joke, it's still kinda wrong. : )

Or! Don't! Go outside! Hassle some ducks! Have a hotdog! Or a moose-dog! I've got a friend who makes sheep-sausages that are second to none... mmm. Sheep dogs. ;)

Beer Notes from this weekend

If I haven't posted a beer review for some time, it's because I've been sober for about two months now. I decided it was appropriate to ease back into things, and after a few warm-up beers (on other days!) I've decided to tackle something new. Here's the review

Vuuve by Brouwerij De Regenboog

The bottle is minimalist. A brown 33cl container with a rose red label held on with what appears to be tape. Definitely not the work of a large manufacturer. The bottle is capped, not corked, and opens with a light spray. You're hit immediately with a floral bouquet of esters, even before you pour. Honey, coriander, and light citrus zest permeate the air. The beer pours easily, but is heavily carbonated. My first pour left more head than beer. I gently added more, allowing me to reveal the hazy amber colour against a backlight. The taste is sharp, both from citrus and carbonation, and leaves a crisp feeling on the roof of your mouth. At 5% ABV, there are no heavy overtones of ethanol. But the finish is dry, leaving your mouth like cotton. It's a very forceful witbier, and if there were a lineup, it would stand out like a Hockey Player surrounded by Cubscouts. It's vaguely sour, but not in a way you can put your finger on; it's not at all bitter. Unfortunately, it's yet another uni-dimentional citrus beer. Disappointing, given it's wonderful odour. 3.6 of 5. A solid B.

Friday, 22 May 2009

Presidential decisions

As soon as I can, I want to share pictures of the boat with you. I've been working on it without stopping for as long as I've been awake and not at work. In fact, yesterday, I ran out of parts I need (1/4th inch hardwood dowel rod) early, so I stopped early for the day (before 9pm being early). I wasn't sure what I was going to do with all this free time!

Does anyone else find Palin's claim that Obama is closing a car dealership in Alaska... kind of strange? I don't know much about the specifics of the situation, but she makes it sound like he woke up one morning and said "Morning hon. Kids off to school? I was thinking about closing a Soldotna auto dealership." I some how doubt this was the case. I'd think it'd have more to do with, you know, the fact that Chevrolet is blowing up like a poorly ventilated meth lab. Something that's been going on for quite some time, now.

Sometimes, I swear. Her being nominated for VP seriously effected her in the head.

Edit: Now with a link to a relevent story!

Thursday, 21 May 2009

Taxinomic Un-sure-ed-ness

I'm starting to look into the systematics of wolves, in preparation for a potential project. Systematics is the study of naming things as species, subspecies, genera, families, and so on. It's all the Latin you see thrown around after common names. The rules are arcane, complex, and written by rich dead guys from Europe who didn't know that biologists would be doing what we're doing with it today. People have tried to redesign the rules from time to time, but it rarely is met with success.

You think it'd be easy to say what a species is. After all, we're always talking about this species, or that species - it's the most fundamental unit of population biology. Superficially, it's easy to point to brown bears and Pintail Ducks and say "Oh, yes, different Species for sure!" But when you get to coyotes and wolves, how about then? Wolves and dogs? The rules start getting very fuzzy.

The dirty secret of biology is we're not sure how to define a species. There are as many as 22 different ways to define species, with little agreement between them. Some heathens, like myself, are beginning to doubt that species actually exist as "a discrete biological entity." I envision sliding scales of similarity where populations are free to become less similar through isolation, or more similar through interbreeding. I imagine a few numbers that describe, say, `bear-ish-ness,` where Brown Bears, Black Bears and Polar Bears all have different values. The idea of a monotypic species is beginning to become very suspicious to me.

So if there's so much uncertainty, fuzziness and doubt around what is and isn't a species, imagine how much there is around the idea of a subspecies. Depending on who you talk to, there's between one and sixteen subspecies of brown bear in Alaska. The truth probably lies closer to the smaller value.

This unclaritude is reflected in wolf systematics. According to once source, there were 5 recognized subspecies and two species of wolf in North America. According to another, there was twenty four subspecies and two species. That's a heck of a lot of space between the two. While I write this, there's probably someone out there conspiring to name yet another subspecies, ranging the estimate up towards 25 or more in North America. I don't envy the sucker who has to wrap their head around all this.

Oh, that sucker's me, isn't it?

I present C. Lupus Zoalis
Common Name: The Zoo Wolf.
Type Specimen: Anchorage Zoo

Wednesday, 20 May 2009


Bear Ranching

This is one of the things that are so stupid, I didn't believe the story was true until I got verification.

A man has been feeding bears for 20 years, to train them to... I don't know. Frankly, it doesn't matter. He could be training them to belch oh-come-all-ye-faithful for all I care. This is... words fail me. It's stupid. It's amazingly stupid. This is fantastically and confoundingly ill-advised, moronic, hairbrained, misguided, and plain old WACKO.

The stupid is so flaming hot. It burns us.
In case I'm not clear, don't feed the $#**##$#@ing bears!

Of course, the ADN brings out the best commenters by a long stretch. Take this gem:
graves wrote on 05/19/2009 11:59:29 AM:
Typical Fish and Game. Gotta be the boss, can't let it be.
Ah, yes. Damn those ADF&G people for enforcing the law! Damn them to heck! Next, well be angry when troopers start responding to robberies. They're not the ones getting robbed, so they should just let it be.
LonePony wrote on 05/19/2009 12:02:56 PM:
The thing that bothers me about this is that the State promotes hunters, sitting in a tree, luring bears in with stale doughnuts. That's just fine but they want to prosecute this guy. Both are habituating bears to human food.
There's a huge difference between feeding bears and bear baiting. Bear baiting can't be people's homes. This guy had neighbours. Bear baiting is done for short periods per year. This was a 20 year, year round activity. Bear Baiting involves... you know, shooting the bear. feeding bears involves not shooting bears, but allowing them to wander wherever they will, looking for more human handouts. Bear Baiting allows us to control predator numbers in sensitive areas where human game harvest is a big concern (esp. predator pits). Feeding bears... well. It just contributes to the problem.
kodiaks wrote on 05/19/2009 02:12:42 PM:
Habitat back? No just let them have waht they have now. Is it always humans first? Our we not the stwards of the earth or does that go to the way side when it is our own self interests
Call me crazy. But... what the heck is even remotely natural about feeding bears thousands of pounds of dogfood?! This guy isn't letting nature be, he's decided to subvert it for his own human pleasures!
akgem wrote on 05/19/2009 03:16:26 PM: say people should not domesticate wild animals? How many dogs or cats do you have? Friends or family members have? Do you turly think that dogs and cats have always been domestic? Where do you think they originally came from? What would they world be if we did not have our furry family members? Dog, cat, skink, raccoon, ferret, mouse, cow, pig, horse, bear, tiger, whatever! Any decent human can tame an animal. It is the bad owners who have pets that you should worry about. the 'cool' people who intentionally make a 'pit' or 'rottie' mean thinking it makes them cool. It is not just about the animal, but the people also. Treadwell was a moron who 'assumed' he was accepted to tresspass in the bears area. Vandergaw accepted the bears into his, and the bears accepted him, and his area. My point...thank god people have domesticated wild animals...I love my pets. It is people to worry about..not animals.
Did this person just compare bears to their pet dog? Seriously? Dog, which are the product of far over 10,000 years of domestication, and still occasionally mauls people? And this guy has been `domesticating ` them for less than 0.1% of that time... so they're just as safe?
Siegfried and Roy had the same thing, and even had the advantage of people who knew jack$*#! about tigers, and a tiger still attacked Roy.
Yes, tigers and bears, exactly like normal household pets.

My lord! How do people this dim survive? There is no justice in the world.

Tuesday, 19 May 2009

Caugak ukuk?

For those of you who forgot what we had up for naming, here's the picture again!This is on a lake near my home, and it contains the following!
x2 Bonaparte's Gull (Larus philadelphia). Naruraq (maybe?).
x2 Lesser Yellowlegs (Tringa flavipes) I don't know this one.
x1 Mallard (Anas latyrhynchos), or Curcurpak.

I like ducks much more than I like other birds. Sometimes, you see rpak on the end of animal names, which means big. So does vak, so Qimulvak would be a big dog, and tuntuvak is a big caribou (better known as a moose!). So a mallard is a big curcuq? There's no such word. Or, not anymore. :)

This if I were to just ask, it would be too easy. These are bears. One is a blackbear, and one is a brown bear.

But which is which? :)

Monday, 18 May 2009

Construction and Cat Fights.

As a vaguely nautical sort of update, my boat is coming along nicely. The family has been privy to photos my boat, but until it is a bit further along, and I can take it away from my home, I won't be sharing it at blogspot. I know my anonymity is razor thin, but there's no point blowing what little I have. Sorry, folks! I can add that saws work great on humans and wood, a fact that I'm slowly shaking off. Just because they're slower than powertools doesn't mean hand-tools can't inflict some ouch!

I'm not the only one in summer construction mode. Apparently they're getting ready to re-pave Chena Hot Springs road. They claim it'll only take 3 months, which is an optomistic lie. It'll probably take closer to 5+ months. Oh well, so long as they do it before the aurora is out, and it's cold again. I don't much care if tourists have to deal with ugly road equipment on their way to go soak in a tub... :}

In sanctomonious idiot related news, PETA is out targeting medical students again. This time, they're going after emergency technicians who are trained in intubation on anestized cats. I completely agree. When we have medical personel intubading people, I want them to have never done it on a living thing before. It's the `toss them into the river and watch them sink or swim` school of education taken to medicine.

I have one stipulation, though. Under this training system, no new medical technicians are allowed to intubate me until they've learnt by trial and error on a few PETA members, first.

Friday, 15 May 2009

I'm a bad person

I'm about to make a joke in exceptionally bad taste. People like me need punched in the face.
But I have proof Fairbanks doesn't have a drinking problem, despite what all those fussy outsiders say.
Headline: Intoxicated Fairbanks mom puts 7-year-old behind wheel of the car
See? She got a designated driver!

Yeah, I'm going straight to heck.

The Amazing Randi

I've always been fond of James Randi.

How many people can introduce themselves with `The amazing` as their title? The Amazing James Randi is a magician who shows how people could fake supernatural powers with slight of hand or gimmicks. In this way, he's like Hudini, who after he lost a loved one, was so infuriated by people offering to talk to the spirits of the dead (for a small money, of course) that he went on a crusade to expose their tricks to the public. James Randi is also a very funny guy.

There's a story in the Guardian about his Million Dollar Challenge. That's where if you can show that you have supernatural powers under scientific, observed conditions, you get a million dollars. It started back in the 60s, and all that money is still sitting around. And it's not because people don't try to win it...

I wish I had some of his funniest videos to share, but the best of them were taken down off YouTube. Sad.

Thursday, 14 May 2009

Outbreeding Depression in Arabian Oryx

As a reminder, if you need any definitions for terms, check out the link to my glossary in the righthand bar!

I've previously mentioned Outbreeding Depression, and given you a bit of a mechanism for it, in a previous post. However, outside the ibex example, there's not many good illustrations of the power of outbreeding depression in animals. Most of the good examples exist in plants, which are considerably easier to study.

I'd like to discuss one of the other examples of outbreeding depression, which was stumbled upon when conservation managers tried to save the Arabian Oryx. The advent of repeating rifles, motorized transport, and access lead quite a few Arabian rural users to dramatically over-harvest the Arabian Oryx, in addition to several species of Gazelle, Ibex, and the Arabian Tahr. All of these species were rendered endangered, and the Oryx was made completely extinct in the wild. Phoenix Zoo in Arizona instituted rescue breeding of Arabian Oryx to great success, and reintroductions began in 1980s. This is where the study of Marshall and Spalton (2000) really kicks in.

There's invariably some level of juvenile mortality, especially in that are reintroduced to the wild, and as part of on-going research to fine tune the reintroduction of the Oryx, they collected tissue and horn material post-mortum; additionally, they collected blood from live animals whenever possible. They went through and extracted DNA from the materials, and genotyped them at 6 microsatellite loci. Remember that microsatellites are meaningless repeat units in DNA that drift in frequency `randomly.`

Marshall and Spalton computed a few correlates of inbreeding and outbreeding - Heterozygosity (which I've previously defined/explained) and d^2, which is a measure of outbreeding, and it's the difference in size of alleles within an animal (measured in repeat units), squared. So if one animal has a 200 long allele at a loci that can grow or shrink by 2 units at a time, and a second allele that is 204, it is 204-200=4/2 and then 2^2=4. Sorry about the math! They also looked at protein content, and a few other factors

I'll spare you the statistical model they applied to see the effect that inbreeding and outbreeding had on mortality, but they found that analysed alone, neither seemed to be a major factor. That is to say, they couldn't detect it. In a low sample of 57, this isn't terribly surprising. But when they considered both together, they found both were significant factors.

Wait, how can you be both inbred and outbred? Well, to answer that, we need to go back to the re-introductions. The Oryx reintroduced into the Oman refuge, you see that they came from very different populations, and 5 of them. The unrelated populations can lead to intragenomic issues, when one part of their DNA is telling them to do one thing, and another part of their DNA is telling them to do another - they're not co-adapted. Alternatively, they could have traits from animals that might be really good in Saudi Arabia, but are terrible for Oman.

To add inbreeding on top of that, all you need to do is take these already out-bred individuals and have them mate with close relatives. Broken bits of DNA will accumulate as they always do, while they continue to have problems with the rest of their working DNA complement.

There's a few lessons we can learn from the Arabian Oryx, relating to over-harvest, land management, and so forth. Those are probably the issues that are going to doom the Arabian Oryx (if they're ignored), but let's just ignore them for the moment and focus on conservation implications. First, we need to take greater care to maintain better lines of animals. This is difficult, as we simultaniously seek to keep fairly diverse, non-inbred animals. Finally, Introductions need to be large enough that inbreeding is statistically unlikely.

(Photo credit: Wikipedia)
Cite: Marshal T.C. & Spalton J.A. 2000. Simultaneous inbreeding and outbreeding depression in reintroduced Arabian oryx. Animal conservation, 3, 241-248

Wednesday, 13 May 2009


Picture taken through my Snowmachine Goggles.

Administrivia and a quick personal note

Just a quick heads-up on Administrivia. I fixed commenting on the preceding post. I've no clue why Blogger suddenly turned comments off. Thanks to GPC for pointing it out!

Well, students are gone, grades were due yesterday, and most of my lab members are off in Anchoragua for an All Hands meeting from a funding agency. That means it's fairly quiet up here, and I've got a few moments of spare time to worth with again. Since I apparently haven't mentioned it before, I'm working on building a boat. I won't use here as a build-log, but I'll throw up pictures when I'm done. It's skin-on-frame, and I'll probably use PVC (or something similar) as its amiq.

Tuesday, 12 May 2009

Caugat agkut?

Hey! A couple of you got it spot on this week! No, it's not a Gerbil, it's an Ord's Kangaroo Rat (Dipodomys ordii)! No yuk name, obviously. These little folk are highly adapted to being desert critters (something I'm not!) and badland specialists, and aren't found north of Calgary, AB.

They're normally nocternal, and we'd catch them at night, and when we'd do trap checks in the morning, we'd weigh them, and then put them someplace cool until we could release them. We wanted to catch other small mammals, like Pocket Mice and Wood Rats. Here's a little guy who hid in my shadow, because he didn't like the sun.

Kangaroo Rats are so neat to watch run. Sadly, I don't have any good video, and YouTube doesn't have anything useful either. When they get up to speed, they can jump about a meter-per-stride.

Yakuleget! I know I'm a mammal guy, but here are some birds. All of them swimming or wading around in the small lake I have by my home. These are last year's birds. There's three species in here. Can you name them all? The picture is small and fuzzy, but I took it from ~400 yards.

Monday, 11 May 2009

Star Trek!

I'm not much of a Trek-nerd, though I did watch episodes with the family once upon a life - my Father, among all his faults, is a sometimes geek - so I didn't have anything invested in the new Star Trek film. On Friday, as a reward to myself for getting a huge amount done at work, I bought some tickets to one of our two local theatres. Yeah, that's right. Fairbanks has two! How do you like that, Bethel?!

Okay, one of them is actually a bar that they sometimes show old movies in. And it's in Ester.

So, I watched the Trek movie, and I have to say, I liked it. It's not very... cerebral, I guess, is the word I'm looking for. It doesn't call for much deep thought. There's no monologue on the human condition, and the techno-babble is kept to a minimum. But it was a fun little movie, and if you get access to a theatre in the next few weeks-months, it's worth the ticket.

I like how they made everything so shiney. It was very Flash-Gordan.

Picture credit: Paramount Pictures.

Sudden moose

As I sit here writing this, it's 10:10p on Sunday. Just a few minutes ago, I was typing away some stuff, watching a bit of TV, when I glanced over and noticed there was a moose about 4 feet from my head. It was on the other side of the window, but still, it was a bit of a shock to see this in your face:
Right now, I have a perfect lung shot. It's a cow, too. I do love cow. Young one, to boot. Alas, poaching is bad, so I'll just look and covet. You know, in another life, it would have been a crime not to catch it.

What is it the French say? C'est la vie.

Friday, 8 May 2009

Magic Trucks!

To the editor:

I have come to the conclusion, after long thoughtful hours, that I own a magic truck. Now, many people would believe that it is just an ordinary pick-up truck, but not me. It is magic. It must be magic!

I glanced at the news, while wondering what to have for lunch (I think I'll have Raviolis, instead of the cheddar and bacon stew), and I was intreagued by the magic truck. I want a magic truck! What's it do?

Of course, I intend to clean the bed out at least once every three months whether it needs it or not. But I have a magic truck. The truck bed cleans itself automatically. I think the magic comes into play when I drive to North Pole on the Richardson. When I arrive, the truck bed is clean as a whistle. I love my truck.

I wonder if it works along Farmer's Loop... :)

Now that we've had breakup... greenup!

It's green up! I hope you haven't blinked, or else you'll miss it. Green up `offically` started on Tuesday, when the first aspen leaves started to slowly push their way out. They're still tiny, though. Maybe because this year I'm counting the number of days it takes for them to leaf out, but it feels greenup is taking longer...

Thursday, 7 May 2009

Contrasting North America and European moose harvest

The radio is saying that the ice jam in Eagle is moving again, and the water level's going down. I'd provide a link, but it was on the radio, so I guess my link is "Http:// listen to your radio .radio," or some something.

Sweden, Norway and Finland (Fennoscandia) are at roughly the same latitude that Alaska, The Yukon, and the North-Worst Territories are - perhaps a trivial bit more southerly - but even a fleeting glance will reveal that the area is fairly different from North American areas of the same latitude. There's considerably more broad leaf plants, there are quite a few pines (I'm not sure, but I think there are no pine species in AK), and the average temperature is quite a bit warmer. I'm no climatologist, but I've been told it's because of a warm ocean current that pushes up into that area, moderating the effect of the arctic. I could be mistaken, though.

From the perspective of game, there is a huge difference. A good estimate is that in the whole state of AK, about 10,000 moose are harvested in a given year. I forget if this estimate considers unreported harvest... but yeah, it's pretty okay. Maybe high. (EDIT TO ADD: About 8,000, including unreported harvest). In just Sweden and Norway, they harvested 116,000 in 2007. There are a number of user groups in the state (and out of state) that'd like to see our harvest numbers approach theirs.

Scott Brainerd, now at ADF&G, but a guy we stole from Norway (sorry Norway!), had been talking to us about how this just doesn't seem likely. First, you have the productivity issue (the milder seasons, more plant growth, and favourable soil) which leads to a big difference in biomass between similar North American regions and Fennoscandian regions. Biomass is literally just that - the mass (weight) of biological stuff.

Second, Scandinavia has some very intensive forestry practices, which involve quite a bit of timber harvest. While timberharvest isn't great for many species, it tends to be very good for moose in a short period, as it creates a bloom of new second growth. This might not be sustainable in Scandinavia, and I've heard a few people mention that the good times won't always roll - that they're headed for a crash. Alaska doesn't have that sort of timber available to harvest in moose-relevent areas.

Third, access in that whole region is phenomenal. There is few areas in Norway or Sweden that you can't reach quickly through road and off-road vehicle access. They have about a 700 year head start on building roads. You can see a clip of the end effect in that picture to the right. I don't think there's any place where you can go 30km straight line and not intersect a road of some sort.

Predators are all but expatriated. Wolves were quite actively hunted (over-exploited in most areas) until 1976, when hunting and trapping was restricted. Wolf numbers remain very low, as do brown bears. As I mentioned before, Arctic Fox are also in a bad situation.

Finally, hunting itself is very different in Fennoscandian, compared to Alaska. This is far too big of a topic to go into with any coverage here, but in a nutshell, animals are owned by landowners, not the state, hunting is typically done in territories and by teams, as opposed to family units in an ad-hoc manner, and moose meat is commercially viable, whereas sale is restricted in Alaska, Yukon, etc.

Scott said the question shouldn't be `can we do it?`, but instead `would we even want to?` The factors that make the difference in moose numbers are fairly serious, and while we could make a best effort at copying the Fennoscandian model, the end effect looks mildly unpleasant for the United States and Canada.

Wednesday, 6 May 2009

Random thoughts

Can we make the Ducks-Wings series best of 15? Not because I want to give my boys in red and white more chance to win, but because there have been some great games. It's been genuinely enjoyable to watch.

Also, here's a poorly worded caption:
Bristol Palin on NBC's "Today Show" this morning with father Todd Palin and infant Tripp.
Uuuuuh. Ahem. Yeah. So!

So I'm drinking tea, and organizing my thoughts for the day. It's not been a great day, so far - I lost 3 hours of work this morning, when all the data I entered went ka-blammo before I even went into the office. I'm hoping things turn around before Avise swings by. Dr. Avise pretty much invented most of the scientific tools we use in my field, so I'm fairly humbled to have him visiting my few square metres of earth. And while I organize my notes, it occurs to me that people outside science don't really understand the importance of a lot of what we do.

No, I don't mean the math, and beaker, and measuring part of what we do. I think that's fairly understanble. But the social side - the meetings, seminars, symposia, poster sessions, and conferences... I'm not sure there's anything quite like it outside Science and Engineering. To someone else, it might look like I'm spending time getting ready to waste an hour with a big-wig, but to us, this is an important part of what we do. Ideas get exchanged, and you get feedback on where you're going. To scientists, ideas are king. Any idiot can count moose, but it takes ideas to turn that number into something useful, and productive.

And this is about where it dawned on me that I've got two feet in about three different cultures, here. The research world has its on social norms, its own language (That even scientists in other countries use), its own importent events... all it needs is its own foods, really.

Food for thought.


Tuesday, 5 May 2009

Cauga una?

First, some unintentional humour - Someone wrote, about the Eagle flooding, that we won't have a fiasco like Louisiana, because our state isn't crazy.

What planet do they live on? :)

Here's the answer to last week's critters! Arctic Ground Squirrel (Spermophilus parryii), or Cikiq in yup'ik, and apparently Siksrik in Inupiaq.

I know in written yup'ik (which is a whole different beast) there's a bunch of squiggles and archy things that you can't type (Like an arch that goes over ugasek or taugam), but inupiaq there's a lot more of those marks. I wonder how they manage typing it? It probably isn't a big issue - like yugcetun, the writing system is pretty new, and many speakers are probably illiterate in it.

Anyhow, here's cikiq again!
I love them. I wish Fairbanks had them. Brian Barns, at IAB (my department) has a colony of them for research, but that's not the same.

Here's a tricky one!
It's an animal I like a lot. It's definitely not found in Alaska - This one was caught in the badlands of Utah, but you could find it's brothers anywhere from Mexico to southern Washington, as well as parts of Alberta and Sasquatch-wan. They can grow fairly large (for a rodent) but are light - 60ish grams, or .1 lbs. The green marker on it's tail is our addition - it's so we know we've trapped it already, if we re-trap it.
Do you know what these little long-tailed beasts are?

Monday, 4 May 2009

Volcanos and MHC

The volcano is getting restless. Quick, someone sacrifice a goat. I hear Mike Kelly's not busy anymore...

With the Swine Flu getting quite a bit of attention these days, I figure I could make a topical post by reaching back into my work experience and making a post about immunogenetics. Swine Flu is both important and overblown by the media; a very bright epidemiologist from Ames Iowa can explain two reasons why it's concerning far better than I could.

An important thing in fighting off diseased cells in your body is recognizing that they're infected. When a Virus infects one of your body's cells (or any cells), it injects its DNA (or RNA, a close chemical cousin of DNA) into the cell, and tricks the cell into using that genetic material. That DNA or RNA makes the cell produce new virus parts, which self-assemble (Easier than the Ikea crap) and sometimes hang around until the cell explodes, releasing all the new viruses. It's actually kinda smart.

If you're reading this, and you have a spine (Sorry, shellfish readers), you have tools to fight off viruses. This comes in the form of what is called the Major Histocompatibility Complex, or MHC. It was discovered in the early 1900s, when surgeons of the day had a problem. Sometimes, tissue grafts, especially skin grafts, would take just fine. Other times, it would be violently and horribly rejected, sometimes killing the person in the process. In the 1930s, a Scientist named Gorer discovered that he could isolate 4 blood antigens that would strongly influence whether the tissue was rejected or not.

The antigens were MHC. So is MHC just there to make doctor's lives difficult? Obviously not, because I said it has something to do with fighting off viruses earlier! MHC is a critical part of the antigen recognition process. What happens is that as viruses replicate, they produce protein. Some of that protein is degraded by what we call Proteinases - protein-chopper-uppers. Also, protein naturally degrades on its own, over time. This produces lots of little fragments of protein floating around inside your cells, and outside your cells.

MHC's job is deceptively simple. It grabs these little chunks of protein floating around, and puts it out on the surface of the cell. This allows T-Cells, an important component of your active imune system, to go through and see if they recognize the MHC+Protein fragment combination. If they recognize it, then it's foreign, and it triggers an immune response, ultimately killing off the cell. Crazy, huh? You can see it in the second figure of this post: the peptide is the green bit.

The whole process is made tricky because of a few reasons. First, your MHC only has two `docking points` that it can grab these little floating protein chunks And these docking points can only grab specific forms of protein parts. Without getting into too much chemical detail, different parts of protein have different building material. Using a building analogy, if a stretch of protein is made out of wood, your MHC might be able to recognize it, but if it's made out of cinder blocks, it can't grab on to it.

Second, you only have two docks for each MHC type. Luckily, you have one MHC type for stuff inside your cells, and one for stuff outside, but that's still only 4 docks. And there's no guarantees that you'll get different sorts from your parents. If you get an identical sort from your mother and your father, then you're limited in what your MHC can detect.

Third, it's important to know that viruses are wiley beasts, and they mutate like crazy. If they have a mutation in a part of the peptide fragment responsible for being scooped up by the MHC - using my building analogy again, if they mutate from wood to brick in part of the docking segment - then that fragment can't be picked up by whatever MHC receptor that was recognizing it, anymore. All the new T-Cells that were made to recognize the fragment+dock combination are now kinda useless, and the virus has some breathing room until a new fragment is found, shown to a T-Cell, and more of those sorts of cells are made.

Finally, the last tricky bit is the T-Cell recognition itself. I said that it'll recognize foreign stuff... but how's the T-Cell know that it's foreign? When T-Cells are maturing, they go through a little squishy bit of organ called the thymus. The thymus isn't a very impressive organ. It's incredibly easy to miss that it exists at all, in a lot of critters. I don't think there's a yup'ik word for Thymus - I'll have to ask, but I don't know any. It's that small and unremarkable. Except while in the thymus, T-Cells get schooled. The thymus presents pretty much everything there is to express in the body, and the T-Cells either recognize stuff, or they don't. Those that recognize the stuff in the thymus are destroyed, leaving only T-Cells that can detect non-self-stuff. The process is called thymic education.

And you thought our school testing was high stakes!

There's literally reams more I could write about MHC. It's important for a billion and a half things, some of which have nothing in the least to do with disease. And you can imagine why a wildlife biologist might be interested in genes that help critters fight off diseases! I've got no doubt that I'll return to MHC in the near future.

The first figure is an excerpt of a figure graciously provided to me by WK Potts. The second figure comes from the URL cited at the bottom of the picture, but comes via WK Potts again.

Friday, 1 May 2009

Very important work

Sometimes, I get very important emails from colleagues. Material that simply cannot wait to be communicated in person. Things of the upmost importance that must be opened immediately. Emails that contain this:
Censored by yours truly.
I'm glad I got this very important communication.

PETA actually gets one right!

AN ANIMAL rights organisation has asked the Oxford English Dictionary to change its definition of the word ‘fisherman’.
Normally, that gets a Yawn. PETA does more moronic stunts all the time. Kentucky Derby's coming up - how much you want to bet at some point someone will have horse blood thrown at them? No doubt they'll compare someone to Nazis. One of their cretins will light some cars on fire, and maybe rough up a few stable hands before the race. The usual. But then I saw their definitions:

Peta offered the following revised definitions of the word: l A person ignorant of, oblivious to or indifferent to the fact that he or she is inflicting pain by catching, suffocating, stabbing and gutting fish; someone who is hooked on cruelty.

Yawn. Not even creative.

l A person who “relaxes” by impaling water-dwelling animals; often a person too out of shape to participate in a real sport.

Ever see PETA people up close? They tend to be really frail. Need to eat some fat and protein! Anyhow, yawn again.

l A man looking for an excuse to wear thigh-high waders.

Oooooooh. I actually like that one. 's true. I tend to wear chest waders, myself, but it's easy enough - just say `any excuse to wear waders.` My one complaint is that it leaves women out of fishing. I think they thought that'd be more insulting that it actually is... : )

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