Tuesday, 29 December 2009

Huzzahs are in order

What could drag me back from vacation to blog about something? Two words: Jurassic Park.

Technically, it's Holocene Park. Here's the meat and potatoes of the story, as the cool kids say: Researchers have successfully cloned an extinct subspecies of Ibex, where they had tissue preserved from the last surviving individuals. The Daily Telegraph has the story. This is a long sought holy-grail of conservation Genetics - to revive extinct species means that the end is no longer the end. Right now, when we lose biodiversity, it's 100% gone forever; impossible to recreate. But if whole-organismal cloning can be used to recreate extinct species, then then suddenly it opens the prospects that maybe we could get a second chance at a few species.

Especially the big, fuzzy lovable ones. You know, like Pandas.

Of course, whole organismal cloning is very crude currently, and the technique... well... it has issues. Our success rate with it is still very low. I can't help but wonder if our lack of success in cloning has to do less with DNA damage, and more to do with inappropriate epigenetic enviroment. How I hate that word, epigenetic. It basically means `Anything inherited, but not from the DNA, and we're not sure where.` Or maybe it's my cynicism showing through.

Still, our first subspecies cloned. To quote a TV show, Huzzahs are in order. I hope we do better, and we can make this work. Of course, the underlying causes of the species' extinction must be addressed, otherwise we'll just bring them back to die off all over again. But with some species, who knows? Maybe we stand a chance.

Tuesday, 22 December 2009

Mox Jousting

I know I'm on vacation, but here's a video I made before the public tours at Lars. :)

Thursday, 17 December 2009

Doing it wrong

Here's a sign that you might be doing it wrong:
Wanted: PR firm to fight species listings

The Alaska Legislature is paying for a conference and public relations campaign to persuade Congress to limit the Endangered Species Act.
The argument goes "Polar Bears cost us money as an endangered species. So, we should have them unlisted as endangered species." If you can't spot the numerous non-sequitors in there, give it another read.  Since apparently it needs said, Polar Bears are very probably endangered by habitat loss.

I'm disappointed by this - it's nothing more than politicization of Science - but I'm not surprised by it. There's a phrase we hear often that goes "We need more science." That means, "We need more people who agree with us." It's one of the things you realize early on in the critter management field. If you're unscrupulous, it also means you found a willing payer to revisit some topic.

Wednesday, 16 December 2009

Ahhh, winter break.

It's that time of year in the University, when the campus is a ghost town. Things are quiet, as students work on their finals, professors work on hiding from students, and Graduate Students try to slip out the back for a long vacation. You can hear a pin drop in the hall. Many of us choose to work at home if we can - I did yesterday, where I paradoxically got heaps more done than I ever do at work. There's no end of parking, which pleases me greatly, since I hate parking in Sri-flipping-Lanka.

As a side note, worrying about Parking is such a strange luxury. Just a hair over 100 years ago, some of my ancestors were worrying about starvation. Now, in 2009, I worry about having to walk 10 more minutes for parking.

This is one of the few times that a Academic job really shines. When people realize that working 50+ hour weeks for the previous 51 weeks has entitled them to slack off just a little bit. The rest of the year it seems like the onslaught is never ending: an endless parade of students, meetings, deadlines, expected overtime, proposals... It's almost bizarre, when you think about it, how much time goes to these alien tasks.

Some of us will take work home with us over the next week or so - I'm trying to limit myself to a book, "Genetics and the Extinction of Species." It seems potentially interesting, and I've been meaning to read it for a while. Maybe I'll blog it, if I'm feeling ambitious.

Pictures


Tuesday, 15 December 2009

Yellowstone Cauldera Bigger than previously thought

And they laugh at us for living in a place where -20°C weather is toasty warm. At least we're not living on top of a giant, 250 mile deep bomb.

Well, except those of us in the Aleutians. 

For those of you who didn't know, Yellowstone sits on top of a massive Caldera that's still active, geologically. It last erupted a few hundred thousand years ago, when it sent a few hundred square miles of material into the air, raining it down as far as the other side of the world. It's a big-un', as the cool kids say. Whether it goes soon (In the next 100,000 years)  or not depends on whether now having the Rocky Mountains on top of it is enough to bottle it in, but when it goes it'll take out a chunk of Idaho, Utah, and Montana with it.

If Utah, Idaho and Montana still exist, when it explodes. 

Monday, 14 December 2009

Breath Deep!

This is very cool: SEM microscope Pictures of Spider Lungs. Makes me wish I had an SEM lying around. ;)
Spiders don't have tidal lungs as you or I have, but instead folded structures called book lungs. They're so-called because they're folded in like ridges, hanging down like pages from a book. The folds are highly vascularized, and take up oxygen directly into the blood through a passive process. They're quite remarkable, and something that makes Spiders and Scorpions quite amazing!

Rejected hypothesis

This is the way science works. You make a hypothesis, you form a prediction, you test the prediction, and then evaluate your hypothesis.

We are forced to reject the hypothesis of massive rural influx into urban areas as the data does not support it. I, myself, was wrong. This graph pretty much says it all:

More at the ADN, where the story is from.

Not only do we need to revise our hypothesis, but it appears the data supports an nearly opposite mechanism! a) Students come from primarily urban areas and b) Among rural areas, those worse off economically appear to export less students! Speculating, this may be because households worse off economically cannot afford to move their households. Or, they tend to value living in situations like their current situation more than the additional leap in economic opportunity.

No one else would put it in economics speak like that, so here's an example: C lives in Alakanuk. With commercial fishing having crashed in the area (and subsistence having been slashed), C decides to move his family. C compares other places - Bethel, Dillingham, Anchorage, Nunapitchuk, Kwigillingok etc - for characteristics including 1) economic oppertunity, 2) current relations 3) similarity to C's preferred ideal of a village/city/whatever. Among those options, he makes a decision where more than immediate economic oppertunity factors in. ("Anchorage has more jobs, but I've got family in Dillingham, and he can get me work on a boat"). 

You'd test this by finding out who moved, who moved where, and whether presence of relatives or some other similarity factors influence movements more than chance. Sounds like a project for some young aspiring masters student out there. ;)

Saturday, 12 December 2009

It sounds barbaric when you put it like that...

From an issue of "The Citizen" from 1910
There were forty-seven homicides in Louisville during the year just closed, and not a single hanging. Life in the Falls City is much cheaper than property.
Also, elsewhere, there's a mention of Taft's visit to the Canal. I wonder what we think is important, that 100 years from now will be laughable. I wonder what we do now that will seem totally inhumane 100 years from now. The idea of chasing down a person and stringing them up is, I think most of feel, repellent. Contrary to the course of justice.

Friday, 11 December 2009

Phew! And, was Alaska Worth it to the States?

I've finished my week long sprint to the finish line, yesterday, and I was so burnt out I loitered around drinking Moose Drool and doodling while watching TV for the rest of the day. A friend of mine told me I look like hell, which means I probably look positively monstrous to the public at large (since my friend is not exactly the `most polished` of people...). Still, it's done, which means I can go back to normal life for a week, before the holidays strike. :)

Enough about me! Was Alaska worth it? To the states, that is. Arctic Economics makes a great point:
An annual gross state product of over $40 billion is not the appropriate benefit measure.  That's gross, not net.  Moreover, $40 billion - or whatever the right benefit figure is - would have been heavily discounted in 1867.  Still more - Alaska costs a lot to maintain; the $7.2 million was a start; we had to defend it from the Japanese, rebuild it after the 1964 earthquake, and pay the heavy costs of governing in this large, remote, and often hostile environment.
Instead, they argue, you need to look at the differences between the outcomes if the US had bought Alaska (what we have today) and what would happen if it hadn't. It's hard to quantify things such as the benefit of having a military base near the far east (apparently it's at least worth Eielson Airforce Base's operational budget), but Dave Barker at the University of Iowa takes a crack at it.

Of course, the more ego-centric question is "Is Alaska better off having been bought by the US?" That's harder to quantify. If we were to assume Alaska would be bought by England (and ended up part of Canada), politically it would depend on whether Alaska ended up acquiring provincial status. Given the comparably large population of AK, I think it might have (~600k is larger than the population of Newfoundland and Labrador) - it's my gut feeling that Candian Provinces enjoy slightly greater autonomy than American States.  Definitely the Alaska would have better representation - Somewhat better than 3% representation, compared to our <<2% representation currently. While whether Eskimo have done better living under US law than their counterparts living under Canadian law is highly debatable (there's a Ph.D. dissertation for Rural Development somewhere in that topic!), the fact that NWT spun off Nunavut as a separate territory and Quebec is granting areal autonomy to Nunavik definitely speaks somewhat better of modern outcomes.

It would be very interesting to quantify each outcome, but it appears at least politically, Alaska drew the short straw!
I don't have an appropriate picture to go with this post, so here is a random fox:

Monday, 7 December 2009

We're number 1!

We're number one!

... in food stamp usage.

The Wade Hampton Census area, generally called the lower Yukon River region, is tied for the nation's highest rates of food stamp use, a state official said.
"It's 49 percent of all people," said Craig Kahklen, senior research analyst at the Division of Public Assistance.
A county in Kentucky and South Dakota share that rate, he said.
"It's a dubious honor," he said.
The region had one of the nation's lowest per capita income rates during the 2000 U.S. Census, so it stands to reason that food stamp use would be high there, he said.
Food stamp use grew rapidly across the state last year, mostly in urban areas, Kahklen said.
I'd thought it'd be higher, honestly.

Other news, aside from my normal Wed post (which I've already picked out), I'm laying low until Friday. I need to buckle down and work on prepping for Thursday. And I anticipate being too bleery on Thursday to make a serious attempt at a blog post.

Friday, 4 December 2009

The Parnell plan for reducing Domestic violence contrasted

When Governors announce that they'll reduce Domestic violence, rape, incest, or anything of that sort, it feels a bit like when teachers from the states come here and announce that they'll solve all our problems - you know they mean well, but they don't have a clue what they're doing. Parnell, bless him, says he'll be the man to reduce domestic violence rates.
  • They plan to aggressively pursue stiff sentencing for offenders.
  • The sex offender list will become unavoidable through plea bargains.
  • New sexual assault and domestic violence investagors will be added to the roll.
  • Increased funding to shelters.
  • An expansion to the VPSO project.
I'm afraid the end result will not be a reduction in the real rate, but that the real rate will remain unchanged, and we'll see an increase in the observed rate thanks to the increase in enforcement. Domestic violence is not a pre-meditated thing. It's typically a crime of passion, where deterrence just doesn't work. In fact, there's been a study on just this subject, where Sherman et al 1991 found, "Contrary to deterrence theories, arrest had no overall crime reduction effect in either the official or victim interview measures of repeat domestic violence." In fact, there's a chapter in a book, titled, "Does Arrest Deter Domestic Violence." The answer seems to be 'no.'

Even more problematic, it appears not only arrest appear to be ineffectual, but it may actually increase domestic violence in the long run as those penalized through stiff sentences increase the rate of battery. This may be due to the increased disruption in the batterers' leading to a poor economic situation, and this hypothesis would be supported by the fact that increased arrest increases the rate of domestic violence and sexual assault among the unemployed. It seems that the situation is positively hopeless!

The current situation is clearly not tenable, so what would a better plan be? The bush suffers differentially from domestic violence, with some areas it being positively epidemic. There are a few strong links to domestic violence that we could address, possibly with greater success. Most studies have focused on male to female violence, so please keep that in mind.

  • Female highest level of education is negatively associated.
  • Having multiple partners is positively associated.
  • Conflict over his drinking is positively associated.
  • Greater income inequality between partners is positively associated.
  • Other conflict in their lives was positively associated.
  • General increasing income equality was negatively associated.
  • Family income is negatively associated.
  • Living with more extended family members is positively associated.

I've only listed the things we societally could address. For example, the older you are, the less likely domestic violence is, but we can't go out and age people. In the light of this information, it should seem highly unsurprising that many bush communities have high rates of violence, because they are on the increased risk end of many of these factors. My arm-chair quarterback suggestions for reducing the rate of domestic violence in Alaska would be:
  • Invest very heavily in rural economic development.
  • Continue to invest in domestic violence shelters.
  • Increase the availability and desirability of bush student scholarships.
  • Increase the amount of available affordable, energy efficient housing in the bush.
In my last point, energy efficiency is important, because households (in my purely observational opinion) tend to consolidate over the inability to keep two houses running at once. Typically over heat. As a side note, I went to AZ once, and a lot of the old BIA houses are the exact same ones they use on the Navajo reservation. And they wonder why they leak heat!

The problem with the TwoYaks proposal is it'd be slow. It would take a long time to see the fruits we've planted, but I don't know of any method to give the state an immediate short-term drop in domestic violence. There just doesn't seem to be a quick and easy fix. But the TwoYaks proposal has the advantage of being based on sound science and observation, and also effecting other things we find societally undesirable too. For example, poor opportunities for employment is associated with high levels of murder and alcoholism, two things we also don't like.

Sadly, I'm not Governor, so I just make them start. That means it's time to hit the pen and paper, and write some letters to my congress critters.

Thursday, 3 December 2009

Check for flying pigs!


This is the corner of my desk. Notice anything? My coffee pot is clean. That's right. Hell froze over, and I finally scrubbed 6(±1?) years of grime off the pot. This photo is to prove to the world (and the relevant family) that I can, in fact, clean the coffee pot.

I just choose not to. Now the coffee tastes weird! :p

Climate Gate matters, but not really.

A few years back, a group of Scientists called `bullshit` on a Korean scientist who had claimed to human embryos to make batches of embryonic stem cells from nine patients. Far from data manipulation, the data of Hwang Woo-Suk was outright invented, and was as grounded in reality as hairymen and UFOs.

(Un)interestingly, no one used the scandal to doubt that scientists were doing this cloning business at all. It wasn't an opportunity for the public to go `Right, now that we've disproven stemcells, we can go back to treating humours like people should.` People rightly realized that there's more than one horse in town. Science is done by networks of people, and rarely does science rest or fall on one person working alone.

This is Tyler Cowen's point in an incredibly eloquently written post on the so-called "Climate Gate" scandal:
I am by no means an expert in climate science but I will explain in more detail why I would stress different issues.  (Please do set me straight where I am wrong.)  I see science, including climate science, as very much a decentralized process, based on the collective efforts of thousands of researchers.  The evidence for our current understanding of climate change also comes from a wide variety of disciplines, including chemistry, meteorology, oceanography, geography, tree ring studies, ice sheet studies, and a good body of theory, which has held up well.  These results all point in broadly similar directions.  Call me naive but, with apologies to Robert Sugden, I don't think many scientific results depend on what comes out of East Anglia, even if you include its emailing affiliates from Penn State and the like.  Even very, very simple climate models generate many of the basic results.
He forgot growing times, distribution of species in terms of biological evidence. Otherwise, spot on. I'd encourage you to read the rest.

And that's leaving aside whether there was foul play with the East Anglian data - far from some random emails, the papers from their group will be dissected and either stand on their own in the face of independent verification, or be redacted.

It's worth noting that redaction is Scientist-death. And rarely do dead scientists get the opportunity to shamble around as a zombie. Science is self correcting, and carries a wooden stake.

Tuesday, 1 December 2009

2nd Grade Math.







Find your nearest 2nd grader and show them this. Maybe they can tell Fox News what they did wrong when making a piechart. :p

Priming the Pump


You've probably seen it a million times in the newspapers. "Alcohol was not a factor." It seems innocuous enough, but it's actually journalistically unethical. The biggest objection to the phrase comes when you apply it to something else, such as `Teenaged Drivers were not a factor in the accident.` There might be good reason to suspect Teen drivers were involved in an accident, since they're more prone to crashing their truck. However, because they're not relevant, it's not mentioned. In fact, there's a great deal of non-relevant things that are not mentioned.

But far from wasting page space, these kinds of phrases when given by authority figures (such as a newspaper, or a police agency) actually have the opposite effect. It's called `priming,` and Obama has a lot of problems with it. The meat of the issue is when an authority figure discusses something, even to say it's not associated, it almost instantly becomes associated. Because of how the Human Brain works, when you hear Obama say "There are no death Panels," people are more likely to think Death Panels exist. The more time an authority figure spends dispelling a rumour, the more authority that rumour takes. It seems backwards, but the human brain often is.

So, when people talk about accidents and say `Alcohol was not involved,` readers are more likely to take away the message that alcohol was involved. Or, at least, they're primed to consider that as a possibility, if they weren't before.  The News Miner is terrible about this, when they say that drugs were found at the scene of some crime, but drugs were not a factor in the crime. Instantly, people begin to assume it is a drug related crime, when in reality it's a totally false association. My favourite example of this is  when someone pointed  out that both Hitler and Stalin had moustaches, so history books should mention that mass-murder is not moustache related.

And the worst bit is, Journalists aren't ignorant of this. If the journalist went to that fancy pants college place, they almost invariably have learnt that a) this stuff happens and b) doing this is unethical. Sadly, many reporters and editors don't seem to be able to remember their actual training. Now, I'm probably never going to the battle on accident reports, when when people detail crime victims, and say they were in possession of, say, an once of marijuana in a totally drug-unrelated crime, that really cheeses me off.

Alcohol was not a factor in this post.