How screwed is the polar bear?

Even deniers like Akasofu wouldn't argue that the planet isn't warming. He just casts the blame elsewhwere, in a probably incorrect manner. It's the naïve who say that global warming is a hoax because "it snowed a lot last winter" (and so are those who believe in global warming because it's hot today, but for different reasons), that or the ideologues who view this through a partisan lens. Let there be no mistake, creatures like polar bears are adapted for conditions that won't occur again until the next ice age, and things are only going to change more as time goes on.

That's not to say we know everything about polar bears. The problems are not trivial - logistics are massive, the creatures elusive, and weather is ever your foe. It's difficult to get a reasonable trend on the species, in whole or in part, because counting is easier said than done. That's where morphemetrics supposedly can come in. The idea is that we can measure things, take masses, count the cubs, and figure out from there how well everyone is doing. In some respects, this has many advantages over census, where populations can be high, but unwell and ready for a massive decline.

And so, Dr. Rode, Dr. Amstrup and Dr. Regehr, all three Forest Service or USGS here in the state, have published a paper collating 28 years of morphometric data from polar bears in the southern Beaufort sea, which spans from midway between Point Hope and Wainwright, to somewhere just west of Nunavut's western most continental extreme. Thankfully, the spell out their study aims very nicely:

Specifically, we addressed the following four questions:
(1) Is reproductive output, quantified as litter mass, associated with maternal condition? If so, what measures of female stature/condition (condition indices, body mass, skull size) are most closely related to reproductive output?
(2) Did body mass, skull size, or condition relate to interannual variation in available ice habitat?
(3) Did body mass, skull size, or condition of polar bears exhibit a trend between 1982 and 2006?
(4) Did reproductive output (litter mass and cubs per-female) exhibit a trend between 1982 and 2006? Was it related to interannual variation in available ice habitat?

The study is deceptively simple in terms of field methods - they flew out in a helicopter oppertunistically tracking polar bears in May when polar bears are aggregated on the continental shelf, or in a few years in the Autumn when they're more on the shorefast ice or land. They would dart the bear, jab any cubs, and then take some basic measurements including skull width, body length, mass, they would age the bear (which can be done from the teeth), and quantify the cubs. In all, they captured between 5 and 152 bears a year

For the ice, things became more... mmm... abstract, we'll say. Instead of taking satellite measurements of ice, they use collar data to generate a resource selection function - which is to say, where the bears prefer to be. They called the top 20%, where 70% of the bears dwell, optimum habitat, or "Ice." From there, they dive into what I can only call model-mania, which is typical of a paper of this nature. They compete different models to see which are the best, and generate many tedious tables that all but the most interested individuals find themselves nodding off during. Don't get me wrong, the information of these models can be highly informative, as can their weights, but they're incredibly dry. I've sometimes caught individuals trying to use this fact to their advantage in sneaking through poor data and hoping people nod off after a hearty meal of model stew. I'll spare you the details of the growth curves, but suffice to say they broke the bears up into 2 age classes for each gender, and 1 for cubs which included all but bi-yearlings.

The answer to question (1) appears to be an unqualified yes, with high probability. Sow mass influences cub mass, and not inconsiderably. This is true of cubs of the year in both autumn and spring, and yearlings in just the autumn. This is unsurprising, but it's good to see that their variables are measuring what they think they're measuring, for purposes of our future analyses. The answer to (2) is also yes, but only for some age groups. Curiously, a trend over time is only evident if you look at age classes  (7-11yr olds), but there appears to be a simple explanation for this - lighter weight bears tend to die more. This leaves only the older bears, for whom there is no trend over time. They would be left at a reduced number, if this was the case. The best trends appear to come from skull width for females and "Ice", and Skull width and body length for both sexes early in life. This is curious, since neither variable acts fast. Bone is a slow growing (though dynamic) tissue, and you would expect it to react slowly to yearly variation of ice. This is to contrast with mass, which can change quite rapidly as conditions worsen. An explanation why it's a major factor for fast growing polar bears is that this is a key stage in their development, and environmental stress is getting 'recorded' in their body. An older bear just needs to pile on the pounds, and care for cubs, whereas a younger bear needs to do this as well as continue to grow larger and larger. As anyone who has been around teenagers know, this takes a lot of food.

Question (3) is a yes - there were trends over time in female skull width, body length, and some fewer variables in males. I'm less interested in this fact than I am in the trend in reproduction, where litter mass is trending down over time (while being positively associated with "Ice") at the same time that yearlings are trending down over time, with the same positive association with "Ice." This suggests there is a "Double Whammy" - not only are there fewer cubs, but lighter cubs. Recall that mass is good for survival, so these lighter cubs will be more likely to die earlier, and sire or whelp fewer cubs of their own. This is a real matter of concern, and should highlight how important it is to keep a close watch on the SB sea polar bears in the future.

They discuss the variance and trend in their "Ice" variable. As "Ice" doesn't truly measure ice, I'm hesitant to draw too much from this. What the graph I've put to the right really shows is that in some years, bears are more clustered than others, and over time the clustering is increasing. There are many  factors that could lead to this pattern, including decrease in true ice coverage, changing patterns of seal availability, and increased human related disturbance. The arctic is a changing place, and it is becoming a busy place, and I saw no attempts to disentangle their "Ice" from this. We don't actually know that true ice declines lead to any future trends we see in this paper, we only know that an increase in bear density (or a decrease in habitat selected) does. This is this paper's strongest weakness, and makes all further "Ice" models slightly weaker, in my mind.

Can be density increasing? If the population is declining, then a decrease in habitat selected could maintain the same density of bears. However, there is no statistically robust trend of bear population for the SB sea. The problem is that measurements in the 80s had a large deal of imprecision associated with them. I generally suspect bear census is declining, but as a properly skeptical scientist, I must point out this has not been well demonstrated. Discarding that hypothesis, density would increase, leading to many of the downstream
 findings that I've previously discussed. We know that density is bad for survival (males kill cubs), increases stress, and can decease resource availability to any given bear. Additionally, it can lead to an increased transmission of disease. The authors rightly discount selective hunting for large bears driving the trends (polar bears are shot opportunistically), and argue that contaminants are just as unlikely to be a source for a decline. But given the poor support for their "Ice' variable, we can equally argue that what we're seeing is density dependant effects from some other factor that might not stem from ice per-se. I am a fan of keeping my datasets simple. If I wish to measure ice's association with polar bears, I would prefer to measure the ice.

Rode KD, Amstrup SC, & Regehr EV (2010). Reduced body size and cub recruitment in polar bears associated with sea ice decline. Ecological applications : a publication of the Ecological Society of America, 20 (3), 768-82 PMID: 20437962

Carbon pawprints revisited.

Remember this qimulvak? He's been getting a ruff shake. People are barking up a storm about how he's a bad boy for having such a big carbon pawprint. The twitter version of the story is that medium sized dogs have bigger carbon emissions than a typical SUV. I linked an ABC version, but there are other agencies who reported on the story, too. I was somewhat sceptical when I read the story, but I figured most dogs up here are safe. Aside from the urbanites and their dogs, most dogs I know around here are heavily supplemented with fish and meat. Some eat nothing but locally harvested fish. The paw print on that is minuscule - just the oil burnt in getting out there to jig.

But most people I know bought into it without much critical review - even I gave some of the claims a pass, because they shook well with what I knew about the effects of agriculture on carbon emissions. Well, it turns out the numbers were much more worse-case than they probably realistically are. Clark Williams-Derry, a director for the Spotlight Institute, a pro-green environmental think-tank, spends some ink on explaining how the footprint of SUVs really is that bad, and how Landrovers are, in fact, worse than Rover.

Read the whole article. It's very well written, and entertaining (with even more dog puns than my post). But if you're too lazy, the big flaws are here:

• They underestimate how much driving people do.
• They underestimate how much oil is involved in car production and maintinance.
• They assume dogs get high quality meat and cereal, when dogs get trimmings meat in most dog chow. 

They also look top down, to show that practically, dogs have little impact on food from real buying habits.

So sleep easy, dog-outside-the-Turtle-Club. You're not worse than my truck.

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.

The future of Polar Bears is Styrofoam

There's a stock number of questions I get all the time. Usually the first question I get is something about whether I shoot wolves or not. But just as often, after a long discussion about predator control, I'll get asked about Polar Bears, and whether I support their listing.

My answer is, of course, that given my knowledge of Polar Bear biology (admittedly incomplete), it seems prudent to protect Polar Bears. People will then ask me if I support subsistence harvest for Polar Bears. Which, given my knowledge of Polar Bear ecology, I do. `Ah ha!` someone will cry. `You're biased to subsistence! You wouldn't let a bunch of white guys go out and shoot a Polar Bear, but you're happy to let natives do it even when you want to protect a species!`

This is when I get out the clue-by-four and begin beating them with it until they get a clue.

So how can a species need protection, but still be available to harvest? Well, unlike many things in biology, this is actually mostly straight forward.

Let's say you have a Polar Bear.

Yes, yes you are a Polar Bear. Incidentally, if you want my art skills using paint, check out this tutorial.

Okay, let's take that Polar Bear, and put it with all her buddies.

What a wacky bunch! They should have their own prime-time sitcom.

Now, in this system, we have something that is a limiting factor, and something that will become an increasingly large limiting factor - habitat. Particularly, ice habitat. We're going to have a lot less of it. Some Polar Bears are going to have it...

But what about those who won't? Or those who get sub-optimal habitat?

Well...

I joke. It's not curtains time for them, but those bears will be much worse off. The boars probably won't get to breed, and the sow will have very low cub survival, because the sows will be in poor condition. There may be some small contribution contribution to the next generation's numbers, but the contribution will be dominated by chance (stochasticity).

It's my contention, and the contention of US gov't., that harvesting a small number of Polar Bears is entirely acceptable (albeit unsustainable). If you shoot a Polar Bear, either a) it wasn't going to make a large contribution to the demographics (especially if male) or b) it frees up the limiting factor (habitat) for another animal who will now be able to make a larger contribution to the next generation. And if you keep your hunts low, the mortality will rarely make a blip on the population magnitude radar. The story is simplified slightly, yeah. And I glossed over a few things. But on the whole, it holds water.

"Wait! You said it was unsustainable. What's with that" Well, sure. Eventually, given the trends in habitat, there will be very little habitat left to Polar Bears. Short of building Styrofoam icebergs for them, there's nothing we can do about that. Thus, it's not a sustainable situation. However, it's got less to do with hunting pressure and more to do with people running coal fired power plants. Here's some cold hard facts to throw a damper on your day: There probably won't be many Polar Bears in the future, Yup'ik Language is dying, someone will have to take a cut in their lifestyle because every country can't all have it and Africans will eventually want to start eating food too, and eventually India will kick our ass economically. Oh, and there's no Santa.

So, that all said, the ban on importing Polar Bear rugs from hunts is pissing into an active volcano. Sure, it feels good, but it doesn't get anything done to Polar Bear conservation. Worse, it has the unintended consequences of cutting off the livelihood of people. And it will consume resources enforcing the ban which would be better spent doing conservation in other ways. Like, say, putting up a few few wind turbines. But if we were really serious about solving these problems, things would be different, wouldn't they?

Climate change skit

I found this little radio skit that almost perfectly represents the attitudes of many climate change denialists. You only need to go to the Daily News Miner's website to see this played out in text...

Climate Change and Rangifer

Here's a little something I wrote while sipping tea in my brother's home, obviously on vacation (that's why I had so many work related emails open! Because I was on vacation!). As you possibly remember, I have confidence in Global Warming as a actual phenomenon as it's born out by a variety of data sets. I can't comment on the mechanism, except to say I don't second guess nuclear physicists, so why should I treat climatologists any different.

That said, I was somewhat... appalled by the treatment of a finding I've known about for a while:

The scientists were shocked to discover that 34 of the herds were declining, while no data existed for 16 more. Only eight herds were increasing in number. Many herds had been declining for a decade or more.

"We were surprised at the ubiquity of the decline," says Vors.

Surprised? I'm not sure they should have been. The data's been around since 2004ish (more on that in a moment).

"When we delved into the status of European reindeer herds, we were surprised that so many were declining. We expected them to be in better shape than North America herds because reindeer, namely the semi-domestic herds, are closely managed by humans."

[...]

"If global climate change and industrial development continue at the current pace, caribou and reindeer populations will continue to decline in abundance," says Vors.

Oh dear. I suppose I should start with the initial statement. Reindeer herding on a whole is on the decline due to human factors. Namely, fewer people are doing it. In North America, little market exists for reindeer meat, and historical factors have sabotaged the development of herding as an industry. In Eurasia, the industry is on the wane for a variety of reasons.

As for the out-of-nowhere statement about Climate Change, I present this graph from Kofinas and Russel:
You can probably see the issue right from the get go.
I'll refrain from begrudging the point. After all, I haven't seen the paper yet (I am writing this while on vacation!), but it would take strong evidence to convince me that the competing hypotheses are incorrect.

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.

Global Warming: Don't care if you don't believe in it.

First things first: MERRY CHRISTMAS! And if you don't celebrate it, happy Thursday!
Second things first: What are you doing reading blogs today? :p

Okay. So, I think the evidence for Global Warming is pretty strong. I know just enough chemistry to be dangerous when I read over the papers on the subject, and enough about modelling to know that what climate modellers are doing is by and large legit. Partially, I trust the peer-review process, where scientists love to prove eachother wrong, and partially, I trust expertise - arguing about climatic science is like arguing about how things work inside a nuclear reactor, in that I'm ignoring the hell out of the person who isn't a nuclear chemist/physicist when they go on about the subject.

I don't need to place much faith in them, though, because there's many strong lines of biological evidence, not the least of which is the shifting of plant communities. And as Filmore's Bathtub - a blog from Utah - writes, even a lay person can see what's going on. This guy used to be a staffer for Sen. Hatch (R-UT), once upon a time, and is now an educator. He runs a neat blog, though one that's become increasingly left - it seems he's one of the many that the last 8 years of Bush have alienated from their party.

Here's the money shot:
Plants don't have a political agenda. They do, however, know when its getting warmer.