Carbon and nitrogen stable isotopes in fast food

There’s something intrinsically hilarious about a stable isotope geochemistry paper that begins:

By purchasing and eating 1 serving of the substrates of this study (i.e., 1 hamburger, 1 chicken sandwich, and 1 small order of fries), the consumer has gained 50% of that day’s recommended calories, 80% of carbohydrates, 75% of protein (90% if the consumer is a woman), and the full day’s limit of dietary fat at a cost of $3.

and includes the sentence:

Fastfood was purchased from America’s top 3 chains: McDonald’s, Burger King, and Wendy’s; each rest aurant was sampled at 3 locations within 6 major U.S. cities: Los Angeles, San Francisco, Denver, Detroit, Boston, and Baltimore [supporting information (SI) Table S1]. At each location, 9 items were purchased: 3 hamburgers, 3 chicken sandwiches, and 3 orders of fries.

Nonetheless, the point the paper makes — that corn permeates the American diet through a multitude of intermediaries — is quite serious.  Simon Donner has more.

Nature endorses…

In what I believe is a first, Nature (the scientific journal, not the universe) has issued a presidential endorsement, for Barack Obama.

There is no open-and-shut case for preferring one man or the other on the basis of their views on these matters. This is as it should be: for science to be a narrow sectional interest bundled up in a single party would be a terrible thing. Both sides recognize science’s inspirational value and ability to help achieve national and global goals. That is common ground to be prized, and a scientific journal’s discussion of these matters might be expected to stop right there.

But science is bound by, and committed to, a set of normative values — values that have application to political questions. Placing a disinterested view of the world as it is ahead of our views of how it should be; recognizing that ideas should be tested in as systematic a way as possible; appreciating that there are experts whose views and criticisms need to be taken seriously: these are all attributes of good science that can be usefully applied when making decisions about the world of which science is but a part. Writ larger, the core values of science are those of open debate within a free society that have come down to us from the Enlightenment in many forms, not the least of which is the constitution of the United States…

The Oval Office is not a debating chamber, nor is it a faculty club. As anyone in academia will know, a thoughtful and professorial air is not in itself a recommendation for executive power. But a commitment to seeking good advice and taking seriously the findings of disinterested enquiry seems an attractive attribute for a chief executive. It certainly matters more than any specific pledge to fund some particular agency or initiative at a certain level — pledges of a sort now largely rendered moot by the unpredictable flux of the economy.

This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama.

The Anti-Science Party

John McCain is against Adler Planetarium.

Sarah Palin is against research in fruit flies, one of the most basic model organisms in animal genetic research.

If the worst examples of earmarks the GOP ticket can come up with are a token amount of support for a major institution promoting science education and fundamental biological research, they’re really hard up.

GPlates on the Mac

This post will probably be of interest to very few people, but it should go somewhere, so it’s here. GPlates is a promising new program for managing four-dimensional geological GIS-type data. Right now, it mostly handles reconstructing plate positions based on data in text files, though it also has some simple features for digitizing new data. It also doesn’t compile on the Mac as the code is shipped, but it can with a few slight changes.

Freezing Science

According to Science, Ike Brannon, a senior policy advisor to the McCain campaign, indicated that science funding would be frozen at FY 2009 levels in the first budget proposed by a McCain administration:

Next year’s federal budget may not contain a penny more for research and education if Republican Senator John McCain (AZ) is elected U.S. president and has his way with Congress. An aide to the McCain campaign delivered that sober fiscal message today to science lobbyists, who pressed him unsuccessfully for leeway in the candidate’s promise to curb federal spending by imposing a 1-year freeze on domestic discretionary spending.

Such a freeze would translate into many hundreds of fewer grants funded by NSF, as well as a couple hundred fewer graduate research fellowships. Leaving science out to dry: that’s putting country first.

The Musical Stylings of Richard Alley

These speak for themselves, I think. (More here.)

What I Learned from the Microbial Ecologists

I’m not a microbial ecologist, though I’ve studied the field a bit. I was invited to speak at the International Symposium on Microbial Ecology in the climate change session, to talk about my work on the Paleocene/Eocene Thermal Maximum and what magnetofossils indicate about changing microbial ecology during that ancient global warming event.

The big new breakthrough since I last took a microbial ecology class four years ago seems to be a technique known as “tag  sequencing”, in which researchers target short, highly variable sub-sequences of small sub unit RNA. Rather than sequencing the whole SSU RNA (the gene sequencing traditionally used for identifying organisms), which is typically a couple thousand base pairs long, they focus on regions of a hundred base pairs or so that are subject to relatively rapid evolutionary change. The shorter sequence length allows sequences from many more organisms to be sampled, which means that environmental studies capture a more accurate profile of all the microbes in a community.

In a session on the human microbiome, Rob Knight presented a comparison of tag sequencing analyses from a variety of environments. It turns out that the first order division in microbial community composition is between freshwater and saltwater environments. Invertebrate gut microbiota resembles those of the environment they live in; vertebrate gut microbiota resemble neither freshwater or saltwater environments. Among the vertebrate gut microbiota, the second order division of diversity is based upon diet: carnivores, omnivores, hind-gut herbivores, and fore-gut herbivores all fall into different classes. Humans have fairly typical omnivore gut microbiota.

But… that’s the higher order pattern of diversity. When looked at in detail, there’s quite a bit of variability in microbes between different individuals. They are very few specific taxa that are common to all human gut microbiota, and it’s similar for the rest of the human microbiome. Fun fact: on average, less than 20% of the taxa present in the skin microbiome of your right hand are present in the skin microbiome of your left hand.

On another topic, a number of people talked about the interaction between methane oxidation and nitrogen cycling in soil. Apparently, fertilizing soil with ammonium causes some bacteria to shift from oxidizing methane to oxidizing ammonium, thereby increasing the flux of methane into the atmosphere. Nobody presented estimates as to how significant this effect is globally, but it’s something worth thinking about.

Something else I learned: the word “Eocene” in a title apparently frightens audiences away. It shouldn’t be this way. The Eocene needs to become as much a popular concept as the Jurassic, and a representing of the sort of world that can develop under global warming. Eocene Park, anybody?

Cairns

Needless to say, the Arctic Bay, Nunavut, Canada to Cairns, Queensland, Australia itinerary is one of the least travelled in the world. Nonetheless, ten days after I was sleeping on the floor of the Arctic Bay gym, waiting for our plane’s engine to be repaired, I was on the other side of the planet in Cairns, waiting for the 12th International Symposium on Microbial Ecology to begin.

Cairns in the major city in Far North Queensland. Once primarily a port town, the city of 120,000 is now primarily a jumping off point for tourists visiting the tropical rainforest and the reef. Aside from its proximity to these exciting places, it is notable primarily for its high food prices. (Not unlike Princeton in those two respects, actually.) My colleagues and I found a few restaurants that were at least worth the price. In the unlikely event you’re looking for restaurants in Cairns, I recommend the Indian places (especially Marinades), the Lily Pad (a California-cuisine type place), and the Balinese restaurant Bayleaf.

The most exciting place in Cairns, in my experience, was the area in the north of the city containing the Centennial Lakes, the Botanical Garden, and (especially) Mt. Whitfield Conservation Park. The last has about seven kilometers of sometimes rough hiking trail through rainforest — particularly nice because organized tours of the Daintree rainforest seem not to leave much time for walking. Watch out for the cockatoos in the park, though — one irritable flock started ripping branches off a tree to throw down upon me and my friends. Signs around the park warn you about the cassowaries — flightless birds that grow up to two meters in height — but they don’t warn you about that.

I went on two reefs tours and a Daintree tour while I was in Cairns. Two of the three tours — to the Daintree and the Low Isles — began by driving about an hour north to Port Douglas, which suggest to me that Port Douglas is probably a better base for visitors than Cairns. Both my reef tours — to the Low Isles and to the Frankland Islands — were enjoyable. The Low Isles are a coral cay, built upon reef that accreted above sea level. There’s a beautiful diversity of soft corals visible in the reef there. Apparently, there were more hard corals there eighty years ago, but — perhaps due to increased sediment input associated with sugar cane farming on land — the soft ones are thriving now.

In contrast to the Low Isles, the Frankland Islands are built upon continental basement. Here, I discovered to my surprise that quite a few species of corals can survive above low tide line. During low tide here, it’s possible to walk among corals and giant clams — pretty cool, and more conducive to good photos than snorkling.

My Daintree trip was nice as well, but a bit disappointing by comparison. I could have done with less driving around and more hiking in one place. But the low-lying Daintree is a different flavor of rainforest than the hilly conservation park in Cairns, and that difference was good to see. Plus, the crocodiles were kind of cool.

My one other touristy activity while in Cairns was the conference party at Rainforestation in Kurunda, one of a number of animal parks in the region. While it’s not the same as seeing them in the wild, it was a good opportunity to see the local animal life — koala, roos, wallabees, wombats, and crocs. Those koalas are pretty darn cute.

Three Earth Stories from West Greenland

To a geologist’s eye, West Greenland has three overarching stories to tell, set at times that span from the earliest days of the Earth to the present. One story is told by the deformed, metamorphosed basement rocks, three billion and more years old, that underlie not just West Greenland but most of the eastern Canadian Arctic. Another is told by far younger sedimentary and volcanic rocks, dating to the Cretaceous and Paleocene epochs. The third is told in the present tense: the story of retreating glaciers and melting ice.

The oldest story is also the most pervasive. Metamorphic rocks dating back three billion years, to the Archean eon, greeted us when we stepped off the plane in Iqaluit, Nunavut, and followed us along almost all the Greenland coast. Most of what we saw was orthogneiss, the metamorphic product of ancient granites, a sign that something resembling plate tectonics was alive and well in the middle of the Archean. If we had turned south rather than north at Sisimiut, we would have travelled even farther back in time, to the 3.8 billion-year-old metamorphosed volcanic and sedimentary rocks of Isua, some of the oldest in the world. These rocks, formed initially not within the Earth but at the bottom of the ocean, convey hints of Earth’s earliest biosphere. These rocks include schists rich in organic matter that may have been produced by ancient photosynthetic microbes, as well as banded iron formations — perhaps a hint that these microbes were making a living by oxidizing iron dissolved in the water column.

Disko Island and the Nuussuaq peninsula tell a different story. The far younger, nearly flat-bedded rocks there date back to between 60 and 80 million years ago, the Cretaceous and Paleocene eras. These rocks filled a basin called the Nuussuaq basin. While deposition began in the middle Cretaceous, most of the rocks are basalts that erupted between 61 and 59 million years ago. These basalts are associated with the beginning of the rifting of Baffin Island from Greenland and the opening of Baffin Bay.

The final story is still ongoing: the story readily visible at Ilulissat of the fast retreat of Jakobshavn Isbrae. Though the town of Ilulissat, where we visited, is now about 80 km from the glacial front, the calving of icebergs of the glacier is obvious as you approach the town from Disko Bay. When you look go on a short hike and look just out of town, into the great fjord carved by the glacier, you can see a long line of icebergs that have broken off the glacial front, and are now on their way to sea.

The People of Nunavut and Greenland

My trip in the Arctic began in Iqaluit, a town of about six thousand people in the southeast corner of Baffin Island and the capital of the Canadian territory of Nunavut. Nunavut, which has a total population of about thirty thousand, became a territory of Canada nine years ago, in April 1999; previously, it had been part of the Northwest Territories. Sovereignty has, I gather, been a boon for the town, bringing money and people from the south. Our tour guide in town, Claude, was one of these migrants; he was an artisan from the Maritimes who had moved north to teach craftsmanship and expand the range of materials he was working with. He had taught all over the territory and employed materials that included such exotics as polar bear teeth and whale baleen — both available to the Inuit, who are allowed to hunt bears and whales under a quota system.

Life in the North is pricy. Housing is scarce and expensive. Nineteen percent of Nunavut residents live in rooms with more than one person, four times the rate for the rest of Canada. Heating prices are high — unsurprising, given the average December low temperature of -26 C. Claude estimated that he spent about $100 a month on utilities, not including his $1000 a month gas bill. The buildings in Iqaluit, as elsewhere in the Arctic, are generally built on stilts so as to avoid melting the underlying permafrost. A few are built upon cement blocks, but these blocks then need to be refrigerated so that their temperatures never rise above the melting point of ice, a rather expensive proposition. The new, glass-rich Legislative Assembly building, one of the centerpieces of Iqaluit is, like most of the house, elevated.

Add to the cost of heating the cost of transporation. Food and other consumer products in Nunavut must be shipped from the south in a process that accentuates the high cost of oil. In the Northern grocery store in Arctic Bay, at the northwestern tip of Baffin Island, my father spent several minutes staring and trying to convince himself that a 64 oz bottle of cranberry juice really did cost $30. (They go for about $6 in the continental US). Non-perishable and nutritious perishable foods can be shipped at deep discounts through Canada Post’s Food Mail program, but the jug of cranberry juice clearly was not. The same grocery store also had rotting bananas for sale the first time we took a look inside. (It was a Sunday morning; by early afternoon, that had been replaced by green bananas.)

Southerners who come north to Nunavut are sometimes given a stipend to cover the high cost of living. The Inuit residents supplement by hunting a wide range of local animals, from Arctic hares and foxes to polar bears and whales. (A press release from the government posted in the Arctic Bay Northern protested the U.S. decision to list polar bears as a threatened species.)

Because of the governmental presence, Iqaluit is one of the best-off communities in Nunavut. Arctic Bay, where we ended the trip, presented a rather more grim view of the territory. In this town of seven hundred, many people live in houses with boarded-up windows. Orphaned kids roam the streets. I don’t know where they go in the wintertime, but in the 24-hour daylight of summer they seemed to be up all night, even at two in the morning. The two nicest buildings in town are the Northern store and the government health clinic. Alcoholism is rampant; the tour guide our expedition leader had hired to show us around town Sunday morning forfeited the money she would have earned for guiding one hundred people because she was home with a hangover. The steep skree slopes on the hillsides, with inclines approaching sixty degrees, are marked where thrill-seeking kids have tried to ride their skidoos up them. Late on Sunday morning, three girls were racing around town on a skidoo. At one point, we saw the skidoo overturn; fortunately, nobody was hurt, but they easily could have been.

The three towns we visited in West Greenland — Sisimiut (pop. 6200) and Ilulissat (pop. 4500) especially, and to some extent also Uummannaq (pop. 1500) — were by comparison better off than anywhere in Nunavut — perhaps related to the fact that Greenland has been a self-governing territory for twenty years longer than Nunavut has existed. Unlike Iqualuit or Arctic Bay, Sisimiut and Ilulissat have deep-water ports; our ship, the Akademik Ioffe, docked and took on supplies at Sisimiut. Almost all roads in these towns were paved; those with Blackberries reported receiving data as well as voice signals. (Iqaluit had a CDMA cell phone signal, which provided voice service to those with Verizon phones.) The buildings, like those of Scandinavian towns, are brightly colored, which is probably better for the mental health of the inhibatants than the drab colors of Iqaluit. (Arctic Bay was also drab, but the buildings of that town have rather more severe problems than their choice of paint.)

Ilulissat sits near the mouth of the fjord carved by Jakobshavn Isbrae, the fast-retreating glacier that drains about 6% of the Greenland Ice Sheet, produces abundant icebergs, and whose front has retreated rapidly over the last 160 years — clocked at about 6 kilometers per year from 1992 to 1997, and accelerating to about 12 kilometers per year by 2003. In 2004, the region, under the name of Ilulissat Icefjord, was named a World Heritage Site. According to a figure in the recently-renovated Ilulissat museum, tourism to the region has increased rapidly since the declaration, a fact most likely reflected not only by the renovation of the museum, but also by the active road crews we encountered.

In short, West Greenland, with nearly three decades of self-government and a boom of tourist interest driven by climate change, appears to be prospering. (Mineral resources made accessible by the melting glaciers may also contribute to the economic boom in the future.) Nunavut, less than a decade old, still seems to be finding its way.