Environmental News From China

I was unable to access this blog last week while I was in Changchun—sorry!

But I’m back in Singapore now, so here’s some news, mostly from the 2 August 2011 edition of China Daily, the government’s official English newspaper. As you’ll see, they’re pretty concerned about environmental problems. But to balance the picture, here’s a picture from Changbai Mountain, illustrating the awesome beauty of the parts of China that remain wild:

The Chinese have fallen in love with cars. Though less than 6% of Chinese own cars so far, that’s already 75 million cars, a market exceeded only by the US.

The price of real estate in China is shooting up—but as car ownership soars, you’ll have to pay a lot more if you want to buy a parking lot for your apartment. The old apartments don’t have them. In Beijing the average price of a parking lot is 140,000 yuan, which is about $22,000. In Shanghai it’s 150,000 yuan. But in fancy neighborhoods the price can be much higher: for example, up to 800,000 yuan in Beijing!

For comparison, the average salary in Beijing was 36,000 yuan in 2007—and the median is probably much lower, since there are lots of poor people and just a few rich ones. On top of that, I bet this figure doesn’t include the many undocumented people who have come from the countryside to work in Beijing. The big cities in China are much richer than the rest of the country: the average salary throughout the country was 11,000 yuan, and the average rural wage was just 3,600 yuan. This disparity is causing young people to flood into the cities, leaving behind villages mostly full of old folks.

Thanks to intensive use of coal, increasing car ownership and often-ignored regulations, air quality is bad in most Chinese cities. In Changchun, a typical summer day resembles the very worst days in Los Angeles, where the air is yellowish-grey except for a small blue region directly overhead.

In a campaign to improve the air quality in Beijing, drivers are getting subsidized to turn in cars made in 1995 or earlier. As usual, it’s the old clunkers that stink the worst: 27% of the cars in Beijing are over 8 years old, but they make 60% of the air pollution. The government is hoping to eliminate 400,000 old cars and cut the emission of nitrogen oxide by more than 10,000 tonnes per year by 2015.

But this policy is also supposed to stoke the market for new automobiles. That’s a bit strange, since Beijing is a huge city with massive traffic jams—some say the worst in the world! As a result, the government has taken strong steps to limit car sales in Beijing.

In Beijing, if you want to buy a car, you have to enter a lottery to get a license plate! Car sales have been capped at 240,000 this year, and for the first lottery people’s chances of winning were just one in ten:

• Louisa Lim, License plate lottery meant to curb Beijing traffic, Morning Edition, 26 January 2011.

Why is the government trying to stoke new car sales in Beijing while simultaneously trying to limit them? Maybe it’s just a rhetorical move to placate the car dealers, who hate the lottery system. Or maybe it’s because the government makes money from selling cars: it’s a state-controlled industry.

On another front, since July there has been a drought in the provinces of Gansu, Guizhou and Hunan, the Inner Mongolia autonomous region, and the Ningxia Hui autonomous region, which is home to many non-Han ethnic groups including the Hui. It’s caused water shortages for 4.3 million people. In some villages all the crops have died. Drought relief agencies are sending out more water pumps and delivering drinking water.

In Gansu province, at least, the current drought is part of a bigger desertification process.

Once they grew rice in Gansu, but then they moved to wheat:

• Tu Xin-Yi, Drought in Gansu, Tzu Chi, 5 January 2011.

China is among the nations that are experiencing severe desertification. One of the hardest hit areas is Gansu Province, deep in the nation’s heartland. The province, which includes parts of the Gobi, Badain Jaran, and Tengger Deserts, is suffering moisture drawdown year after year. As water goes up into the air, so does irrigation and agriculture. People can hardly make a living from the arid land.

But the land was once quite rich and hospitable to agriculture, a far cry from what greets the eye today. Ruoli, in central Gansu, epitomizes the big dry-up. The area used to be verdant farmland where, with abundant rainfall, all kinds of plants grew lush and dense; but now the land is dry and yields next to nothing. All this dramatic change has come about in just 50 years—lightning-fast, a mere blink of an eye in geological terms.

Rapid desertification is forcing many parties, including the government, to take action. Some residents have moved away to seek better livelihoods elsewhere, and the government offers incentives for people to relocate to the lowlands Tzu Chi built a new village to accommodate some of these migrants.

Tzu Chi is a Buddhist organization with a strong interest in climate change. The dramatic change they speak of seems to be part of a longer-term drying trend in this region. Here is one of a series of watchtowers near Dunhuang, once a thriving city at the eastern end of the Silk Road. I don’t think this area was such a desert back then:

Meanwhile, down in southern China, the Guanxi Zhuang autonomous region is seeing its worst electricity shortage in the last 2 decades, with 30% of the demand for electric power unmet, and rolling blackouts. They blame the situation on a shortage of coal and the fact that the local river isn’t deep enough to provide hydropower.

On the bright side, China is investing a lot in wind power. Their response to the financial crisis of of 2009 included $220 billion investment in renewable energy. Baoding province is now one of the world’s centers for producing wind turbines, and by 2020 China plans to have 100 gigawatts of peak wind power online.

That’s pretty good! Remember our discussion of Pacala and Socolow’s stabilization wedges? The world needs to reduce carbon emissions by roughly 10 gigatonnes per year by about 2050 to stay out of trouble. Pacala and Socolow call each 1-gigatonne slice of this carbon pie a ‘wedge’. We could reduce carbon emissions by one ‘wedge’ by switching 700 gigawatts of coal power to 2000 gigawatts of peak wind power. Why 700 of coal for 2000 of wind? Because unfortunately most of the time wind power doesn’t work at peak efficiency!

So, the Chinese plan to do 1/20 of a wedge of wind power by 2020. Multiply that effort by a factor of 200 worldwide by 2050, and we’ll be in okay shape. That’s quite a challenge! Of course we won’t do it all with wind.

And while the US and Europe are worried about excessive government and private debt, China is struggling to figure out how to manage its vast savings. China has a $3.2 trillion foreign reserve, which is 30% of the world’s total. The fraction invested in the US dollars has dropped from 71% in 1999 to 61% in 2010, but that’s still a lot of money, so any talk of the US defaulting, or a drop in the dollar, makes the Chinese government very nervous. This article goes into a bit more detail:

• Zhang Monan, Dollar depreciation dilemma, China Daily, 2 August 2011.

In a move to keep the value of their foreign reserves and improve their ratio of return, an increasing number of countries have set up sovereign wealth funds in recent years, especially since the onset of the global financial crisis. So far, nearly 30 countries or regions have established sovereign wealth funds and the total assets at their disposal amounted to $3.98 trillion in early 2011.

Compared to its mammoth official foreign reserve, China has made much slower progress than many countries in the expansion of its sovereign wealth funds, especially in its stock investments. Currently, China has only three main sovereign wealth funds: One with assets of $347.1 billion is managed by the Hong Kong-based SAFE Investment Co Ltd; the second, with assets of $288.8 billion, is managed by the China Investment Corporation, a wholly State-owned enterprise engaging in foreign assets investment; the third fund of $146.5 billion is managed by the National Social Security Fund.

From the perspective of its investment structure, China’s sovereign wealth funds have long attached excessive importance to mobility and security. For example, the China Investment Corporation has invested 87.4 percent of its funds in cash assets and only 3.2 percent in stocks, in sharp contrast to the global average of 45 percent in stock investments.

What’s interesting to me is that on the one hand we have these big problems, like global warming, and on the other hand these people with tons of money struggling to find good ways to invest it. Is there a way to make each of these problems the solution to the other?

Azimuth News (Part 1)

Here’s some good news about Azimuth:

1. George Musser, a science writer who is an editor for Scientific American, is coming to the Centre for Quantum Technologies here in Singapore from 10 October to 17 December 2011. I found this out in a Google Plus conversation when I happened to mention I was in Singapore. He will be visiting to write a book on “nonlocality and emergent spacetime”. But when I said I’m also interested in climate change, he suggested that we write a couple of joint blog posts on that! This is great news. He has written about “detection and attribution” questions.

2. I am hiring Brendan Fong as an intern during September 2011. He has just graduated from the mathematics department at Australian National University and is starting a masters in mathematics and the foundations of computer science at Oxford in October 2011. He has written a thesis on algebraic geometry, but now he’s working on image analysis for plant growth modelling, with Jinhai Cai of the Phenomics and Bioinformatics Research Centre at the University of South Australia. He wants to help with the ‘network theory’ program we’ve been discussing here

3. On Google Plus, Cameron Smith has expressed interest in writing an article for the Azimuth Blog. He has done work on synthetic biology, but now he’s interested in gene regulatory networks and multi-level selection theory in evolutionary biology. Best of all, he’s interested in applying elegant math, like category theory, to these topics! So, I’m hoping he’ll explain some of his thoughts here, and we can discuss them, and ideally push them forwards a step or two.

As you’ll note, two of these three items are directly due to Google Plus. (The third is due to this blog, which Brendan has been reading.) So, Google Plus may be a useful way of making connections and accelerating the growth of the Azimuth Project!

Meanwhile, over on the Azimuth Forum, we’ve been having an interesting discussion of Milankovitch cycles, enlivened by the new presence of Marcel Bökstedt, an algebraic topologist who has gotten interested in climate science. A lot of what we’re discussing will eventually find its way into This Week’s Finds, so I mention it only in case you want to peek into the kitchen and see what’s cooking!

On another note, Lisa and I are going to China tomorrow. First to Beijing, where I’ll give a talk on Energy, The Environment and what Mathematicians Can Do at Capital Normal University, and she’ll try to buy a guqin:

That’s not Lisa, but you get the idea: a guqin, also simply known as a qin is a zither-like instrument. The prefix gu- means ‘old’, and this instrument is mentioned in Chinese writings dating back almost 3,000 years.

Then, on Tuesday, we’ll take a train up to Changchun, which is about 500 kilometers west of Vladivostok:

There will be a mathematics workshop at Jilin University up there, and I’ll give a series of lectures on how the octonions let us construct category-theoretic structures good for doing superstring theory.

But before the workshop, there will be an excursion to Changbai Mountain from August 3rd to 6th. This is part of a mountain range near the border with North Korea:

or, on a warmer day:

Changbai Mountain is actually a volcano, and the lake occupies a caldera formed by an explosive eruption that occurred around 969 AD. Debris from this eruption has been found as far as the island of Hokkaidō in Japan. In 2011, experts in North and South Korea met to discuss the chances of a significant eruption in the near future.

So, if it blows up while I’m in Changchun: goodbye, it was nice knowing all of you!

Otherwise, I’ll be back on August 12th.

Azimuth on Google Plus (Part 1)

Google Plus is here… and it’s pretty cool.

If you’re on Google Plus, and you want to get Azimuth-related news items, please let me know, either here or there. I’ll add you to my Azimuth circle.

Or even better, tell me how to broadcast items on Google Plus so that 1) everyone can see them, but 2) only people who want Azimuth stuff needs to see them. I can send stuff to “Public”, but so far I’ve been using that for fun stuff I think everyone would enjoy. Maybe future improvements to Google Plus will help me solve my dilemma.

Here’s a sample of Azimuth items on Google Plus. But note: these look a lot nicer on Google Plus.

• Solar panels could reduce heat reaching the rooftop by as much as 38%. So, while making electricity you also spend less energy cooling your building in the summer. Not so nice in the winter, maybe.

• Japan has been paying the dues for other countries in the International Whaling Commission — and then these countries vote against banning whaling. Japanese academic Atsushi Ishii said that this form of vote-buying was “very likely,” but added “I would not call it corruption.” Yeah, right. But the good news: now things may change a bit, since the International Whaling Commission has decided to ban this practice!

• A plastic bottle filled with water refracts sunlight and acts like a 55-watt bulb — during the day, if you have a hole in your roof. For many that would be a good thing.

• Congress may finally kill a $6 billion annual subsidy for turning corn into ethanol. This would be a good thing in many ways. Even some bioethanol producers say they don’t need this subsidy anymore. After all, there are laws requiring the use of ethanol in fuels, and as oil prices continue to rise, ethanol is becoming competitive.

• Koch Industries Inc. and Exxon Mobil helped write legislation that’s been introduced in Montana, New Mexico, New Hampshire, Oregon, Washington and other states in the USA. It includes these words: “a tremendous amount of economic growth would be sacrificed for a reduction in carbon emissions that would have no appreciable impact on global concentrations of carbon dioxide.” They did this through an organization called the American Legislative Exchange Council (ALEC).

• See all the things that are wrong with scientific publishing today. On Google Plus we’ve been discussing ways to solve these problems.

• Paleoecologist Micha Ruhl of Utrecht University has a new paper on the Permian-Triassic extinction. It argues that a fairly small release in CO₂ from volcanoes was enough to make the sea floor release methane and cause the world’s worst mass extinction event. How much is “fairly small”, I wonder?

• There’s a new Canadian study on “astroturfing”. Students who viewed a fake “grassroots” website with arguments against the existence of manmade global warming not only became less certain about the cause of global warming; they also believed that the issue was less important than before! Worst, the responses of participants who had viewed sites “Funded by Exxon-Mobil” weren’t different than those who had viewed sites funded by the “Conservation Heritage Fund,” by “donations by people like you,” or sites that didn’t list the source of funding at all.

And just for fun, especially for those of you suffering from the US heat wave… here’s what happens when you throw boiling water into the air at -35 °C:

But why isn’t she wearing a hat?

This Week’s Finds (Week 317)

Anyone seriously interested in global warming needs to learn about the ‘ice ages’, or more technically ‘glacial periods’. After all, these are some of the most prominent natural variations in the Earth’s temperature. And they’re rather mysterious. They could be caused by changes in the Earth’s orbit called Milankovich cycles… but the evidence is not completely compelling. I want to talk about that.

But to understand ice ages, the first thing we need to know is that the Earth hasn’t always had them! The Earth’s climate has been cooling and becoming more erratic for the last 35 million years, with full-blown glacial periods kicking in only about 1.8 million years ago.

So, this week let’s start with a little tour of the Earth’s climate history. Somewhat arbitrarily, let’s begin with the extinction of the dinosaurs about 65 million years ago. Here’s a graph of what the temperature has been doing since then:

Of course you should have lots of questions about how this graph was made, and how well we really know these ancient temperatures! But for now I’m just giving a quick overview—click on the graphs for more. In future weeks I should delve into more technical details.

The Paleocene Epoch, 65 – 55 million years ago

The Paleocene began with a bang, as an asteroid 10 kilometers across hit the Gulf of Mexico in an explosion two million times larger than the biggest nuclear weapon ever detonated. A megatsunami thousands of meters high ripped across the Atlantic, and molten quartz hurled high into the atmosphere ignited wildfires over the whole planet. A day to remember, for sure.

The Earth looked like this back then:

The Paleocene started out hot: the ocean was 10° to 15° Celsius warmer than today. Then it got even hotter! Besides a gradual temperature rise, at the very end of this epoch there was a drastic incident called the Paleocene-Eocene Thermal Maximum— that’s the spike labelled "PETM". Ocean surface temperatures worldwide shot up by 5-8°C for a few thousand years—but in the Arctic, it heated up even more, to a balmy 23°C. This caused a severe dieoff of little ocean critters called foraminifera, and a drastic change of the dominant mammal species. What caused it? That’s a good question, but right now I’m just giving you a quick tour.

The Eocene Epoch, 55 – 34 million years ago

During the Eocene, temperatures continued to rise until the so-called ‘Eocene Optimum’, about halfway through. Even at the start, the continents were close to where they are now—but the average annual temperature in arctic Canada and Siberia was a balmy 18 °C. The dominant plants up there were palm trees and cycads. Fossil monitor lizards (sort of like alligators) dating back to this era have been found in Svalbard, an island north of Greenland that’s now covered with ice all year. Antarctica was home to cool temperate forests, including beech trees and ferns. In particular, our Earth had no permanent polar ice caps!

Life back then was very different. The biggest member of the order Carnivora, which now includes dogs, cats, bears, and the like, was merely the size of a housecat. The largest predatory mammals were of another, now extinct order: the creodonts, like this one drawn by Dmitry Bogdanov:

But the biggest predator of all was not a mammal: it was
Diatryma, the 8-foot tall "terror bird", with a fearsome beak!

But it’s not as huge as it looks here, because horses were only half a meter high back then!

For more on this strange world and its end as the Earth cooled, see:

• Donald R. Prothero, The Eocene-Oligocene Transition: Paradise Lost, Critical Moments in Paleobiology and Earth History Series, Columbia University Press, New York, 1994.

The Oligocene Epoch, 34 – 24 million years ago

As the Eocene drew to a close, temperatures began to drop. And at the start of the Oligocene, they plummeted! Glaciers started forming in Antarctica. The growth of ice sheets led to a dropping of the sea level. Tropical jungles gave ground to cooler woodlands.

What caused this? That’s another good question. Some seek the answer in plate tectonics. The Oligocene is when India collided with Asia, throwing up the Himalayas and the vast Tibetan plateau. Some argue this led to a significant change in global weather patterns. But this is also the time when Australia and South America finally separated from Antarctica. Some argue that the formation of an ocean completely surrounding Antarctica led to the cooling weather patterns. After all, that lets cold water go round and round Antarctica without ever being driven up towards the equator.

The Miocene Epoch, 24 – 5.3 million years ago

Near the end of the Oligocene temperatures shot up again and the Antarctic thawed. Then it cooled, then it warmed again… but by the middle of the Miocene, temperatures began to drop more seriously, and glaciers again formed on the Antarctic. It’s been frozen ever since. Why all these temperature fluctuations? That’s another good question.

The Miocene is when grasslands first became common. It’s sort of amazing that something we take so much for granted—grass—can be so new! But grasslands, as opposed to thicker forests and jungles, are characteristic of cooler climates. And as Nigel Calder has suggested, grasslands were crucial to the development of humans! Early hominids lived on the border between forests and grasslands. That has a lot to do with why we stand on our hind legs and have hands rather than paws. Much later, the agricultural revolution relied heavily on grasses like wheat, rice, corn, sorghum, rye, and millet. As we ate more of these plants, we drastically transformed them by breeding, and removed forests to grow more grasses. In return, the grasses drastically transformed us: the ability to stockpile surplus grains ended our hunter-gatherer lifestyle and gave rise to cities, kingdoms, and slave labor.

So, you could say we coevolved with grasses!

Indeed, the sequence of developments leading to humans came shortly after the rise of grasslands. Apes split off from monkeys 21 million years ago, in the Miocene. The genus Homo split off from other apes like gorillas and chimpanzees 5 million years ago, near the beginning of the Pliocene. The fully bipedal Homo erectus dates back to 1.9 million years ago, near the end of the Pliocene. But we’re getting ahead of ourselves…

The Pliocene Epoch, 5.3 – 1.8 million years ago

Starting around the Pliocene, the Earth’s temperature has been getting every more jittery as it cools. Something is making the temperature unstable! And these fluctuations are not just getting more severe—they’re also lasting longer.

These temperature fluctuations are far from being neatly periodic, despite the optimistic labels on the above graph saying “41 kiloyear cycle” and “100 kiloyear cycle”. And beware: the data in the above graph was manipulated so it would synchronize with the Milankovitch cycles! Is that really justified? Do these cycles really cause the changes in the Earth’s climate? More good questions.

Here’s a graph that shows more clearly the noisy nature of the Earth’s climate in the last 7 million years:

You can tell this graph was made by a real paleontologist, because they like to put the present on the left instead of on the right.

And maybe you’re getting curious about this “δ¹⁸O benthic carbonate” business? Well, we can’t directly measure the temperatures long ago by sticking a thermometer into an ancient rock! We need to use ‘climate proxies’: things we can measure now, that we believe are correlated to features of the climate long ago. δ¹⁸O is the change in the amount of oxygen-18 (a less common, heavier isotope of oxygen) in carbonate deposits dug up from ancient ocean sediments. These deposits were made by foraminifera and other tiny ocean critters. The amount of oxygen-18 in these deposits is used as temperature proxy: the more of it there is, the colder we think it was. Why? That’s another good question.

The Pleistocene Epoch, 1.8 – .01 million years ago

By the beginning of the Pleistocene, the Earth’s jerky temperature variations became full-fledged ‘glacial cycles’. In the last million years there have been about ten glacial cycles, though it’s hard to count them in any precise way—it’s like counting mountains in a mountain range:

Now the present is on the right again—but just to keep you on your toes, here up means cold, or at least more oxygen-18. I copied this graph from:

• Barry Saltzman, Dynamical Paleoclimatology: Generalized
Theory of Global Climate Change, Academic Press, New York,
2002, fig. 1-4.

We can get some more detail on the last four glacial periods from the change in the amount of deuterium in Vostok and EPICA ice core samples, and also changes in the amount of oxygen-18 in foraminifera (that’s the graph labelled ‘Ice Volume’):

As you can see here, the third-to-last glacial ended about 380,000 years ago. In the warm period that followed, the first signs of Homo neanderthalensis appear about 350,000 years ago, and the first Homo sapiens about 250,000 years ago.

Then, 200,000 years ago, came the second-to-last glacial period: the Wolstonian. This lasted until about 130,000 years ago. Then came a warm period called the Eemian, which lasted until about 110,000 years ago. During the Eemian, Neanderthalers hunted rhinos in Switzerland! It was a bit warmer then that it is now, and sea levels may have been about 4-6 meters higher—worth thinking about, if you’re interested in the effects of global warming.

The last glacial period started around 110,000 years ago. This is called the Winsconsinan or Würm period, depending on location… but let’s just call it the last glacial period.

A lot happened during the last glacial period. Homo sapiens reached the Middle East 100,000 years ago, and arrived in central Asia 50 thousand years ago. The Neanderthalers died out in Asia around that time. They died out in Europe 35 thousand years ago, about when Homo sapiens got there. Anyone notice a pattern?

The oldest cave paintings are 32 thousand years old, and the oldest known calendars and flutes also date back to about this time. It’s striking how many radical innovations go back to about this time.

The glaciers reached their maximum extent around 26 to 18 thousand years ago. There were ice sheets down to the Great Lakes in America, and covering the British Isles, Scandinavia, and northern Germany. Much of Europe was tundra. And so much water was locked up in ice that the sea level was 120 meters lower than it is today!

Then things started to warm up. About 18 thousand years ago, Homo sapiens arrived in America. In Eurasia, people started cultivating plants and herding of animals around this time.

There was, however, a shocking setback 12,700 years ago: the Younger Dryas episode, a cold period lasting about 1,300 years. We talked about this in “week304”, so I won’t go into it again here.

The Younger Dryas ended about 11,500 years ago. The last glacial period, and with it the Pleistocene, officially ended 10,000 years ago. Or more precisely: 10,000 BP. Whenever I’ve been saying ‘years ago’, I really mean ‘Before Present’, where the ‘present’, you’ll be amused to learn, is officially set in 1950. Of course the precise definition of ‘the present’ doesn’t matter much for very ancient events, but it would be annoying if a thousand years from now we had to revise all the textbooks to say the Pleistocene ended 11,000 years ago. It’ll still be 10,000 BP.

(But if 1950 was the present, now it’s the future! This could explain why such weird science-fiction-type stuff is happening.)

The Holocene Epoch, .01 – 0 million years ago

As far as geology goes, the Holocene is a rather silly epoch, not like the rest. It’s just a name for the time since the last ice age ended. In the long run it’ll probably be called the Early Anthropocene, since it marks the start of truly massive impacts of Homo sapiens on the biosphere. We may have started killing off species in the late Pleistocene, but now we’re killing more—and changing the climate, perhaps even postponing the next glacial period.

Here’s what the temperature has been doing since 12000 BC:

Finally, here’s a closeup of a tiny sliver of time: the last 2000 years:

In both these graphs, different colored lines correspond to different studies; click for details. The biggish error bars give people lots to argue about, as you may have noticed. But right now I’m more interested in the big picture, and questions like these:

• Why was it so hot in the early Eocene?

• Why has it generally been cooling down ever since the Eocene?

• Why have temperature fluctuations been growing since the Miocene?

• What causes the glacial cycles?

For More

Next time we’ll get into a bit more detail. For now, here are some fun easy things to read.

This is a very enjoyable overview of climate change during the Holocene, and its effect on human civilization:

• Brian Fagan, The Long Summer, Basic Books, New York, 2005. Summary available at Azimuth Library.

These dig a bit further back:

• Chris Turney, Ice, Mud and Blood: Lessons from Climates Past, Macmillan, New York, 2008.

• Steven Mithen, After the Ice: A Global Human History 20,000-5000 BC, Harvard University Press, Cambridge, 2005.

I couldn’t stomach the style of the second one: it’s written as a narrative, with a character named Lubbock travelling through time. But a lot of people like it, and they say it’s well-researched.

For a history of how people discovered and learned about ice ages, try:

• Doug Macdougall, Frozen Earth: The Once and Future Story of Ice Ages, University of California Press, Berkeley, 2004.

For something a bit more technical, but still introductory, try:

• Richard W. Battarbee and Heather A. Binney, Natural Climate Variability and Global Warming: a Holocene Perspective, Wiley-Blackwell, Chichester, 2008.

To learn how this graph was made:

and read a good overview of the Earth’s climate throughout the Cenozoic, read this:

• James Zachos, Mark Pagani, Lisa Sloan, Ellen Thomas and Katharina Billups, Trends, rhythms, and aberrations in global climate 65 Ma to present, Science 292 (27 April 2001), 686-693.

I got the beautiful maps illustrating continental drift from here:

• Christopher R. Scotes, Paleomap Project.

and I urge you to check out this website for a nice visual tour of the Earth’s history.

Finally, I thank Frederik de Roo and Nathan Urban for suggesting improvements to this issue. You can see what they said on the Azimuth Forum. If you join the forum, you too can help write This Week’s Finds! I could really use help from earth scientists, biologists, paleontologists and folks like that: I’m okay at math and physics, but I’m trying to broaden the scope now.

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We are at the very beginning of time for the human race. It is not unreasonable that we grapple with problems. But there are tens of thousands of years in the future. Our responsibility is to do what we can, learn what we can, improve the solutions, and pass them on. – Richard Feynman

This Week’s Finds (Week 316)

Here on this This Week’s Finds I’ve been talking about the future and what it might hold. But any vision of the future that ignores biotechnology is radically incomplete. Just look at this week’s news! They’ve ‘hacked the genome’:

• Ed Yong, Hacking the genome with a MAGE and a CAGE, Discover, 14 July 2011.

Or maybe they’ve ‘hijacked the genetic code’:

• Nicholas Wade, Genetic code of E. coli is hijacked by biologists, New York Times, 14 July 2011.

What exactly have they done? These articles explain it quite well… but it’s so cool I can’t resist talking about it.

Basically, some scientists from Harvard and MIT have figured out how to go through the whole genome of a bacterium and change every occurrence of one codon to some other codon. It’s a bit like the ‘global search and replace’ feature of a word processor. You know: that trick where you can take a document and replace one word with another every place it appears.

To understand this better, it helps to know a tiny bit about the genetic code. You may know this stuff, but let’s quickly review.

DNA is a double-stranded helix bridged by pairs of bases, which come in 4 kinds:

• adenine (A)
• thymine (T)
• cytosine (C)
• guanine (G)

Because of how they’re shaped, A can only connect to T:

while C can only connect to G:

So, all the information in the DNA is contained in the list of bases down either side of the helix. You can think of it as a long string of ‘letters’, like this:

ATCATTCAGCTTATGC…

This long string consists of many sections, which are the instructions to make different proteins. In the first step of the protein manufacture process, a section of this string copied to a molecule called ‘messenger RNA’. In this stage, the T gets copied to uracil, or U. The other three base pairs stay the same.

Here’s some messenger RNA:

You’ll note that the bases come in groups of three. Each group is called a ‘codon’, because it serves as the code for a specific amino acid. A protein is built as a string of amino acids, which then curls up into a complicated shape.

Here’s how the genetic code works:

The three-letter names like Phe and Leu are abbreviations for amino acids: phenylalanine, leucine and so on.

While there are 4³ = 64 codons, they code for only 20 amino acids. So, typically more than one codon codes for the same amino acid. If you look at the chart, you’ll see one exception is methionine, which is encoded only by AUG. AUG is also the ‘start codon’, which tells the cell where a protein starts. So, methionine shows up at the start of every protein, at least at first. It’s usually removed later in the protein manufacture process.

There are also three ‘stop codons’, which mark the end of a protein. They have cute names:

• amber: UAG
• ochre: UAA
• opal: UGA

UAG was named after Harris Bernstein, whose last name means ‘amber’ in German. The other two names were just a way of continuing the joke.

And now we’re ready to understand how a team of scientists led by Farren J. Isaacs and George M. Church are ‘hacking the genome’. They’re going through the DNA of the common E. coli bacterium and replacing every instance of amber with opal!

This is a lot more work than the word processor analogy suggests. They need to break the DNA into lots of fragments, change amber to opal in these fragments, and put them back together again. Read Ed Young’s article for more.

So, they’re not actually done yet.

But when they’re done, they’ll have an E. coli bacterium with no amber codons, just opal. But it’ll act just the same as ever, since amber and opal are both stop codons.

That’s a lot of work for no visible effect. What’s the point?

The point is that they’ll have freed up the codon amber for other purposes! This will let them do various further tricks.

First, with some work, they could make amber code for a new, unnatural amino acid that’s not one of the usual 20. This sounds like a lot of work, since it requires tinkering with the cell’s mechanisms for translating codons into amino acids: specifically, its set of transfer RNA and synthetase molecules. But this has already been done! Back in 1990, Jennifer Normanly found a viable mutant strain of E. coli that ‘reads through’ the amber codon, not stopping the protein there as it should. People have taken advantage of this to create E. coli where amber codes for a new amino acid:

• Nina Mejlhede, Peter E. Nielsen, and Michael Ibba, Adding new meanings to the genetic code, Nature Biotechnology 19 (2001), 532-533.

But I guess getting an E. coli that’s completely free of amber codons would let us put amber codons only where we want them, getting better control of the situation.

Second, tweaking the genetic code this way could yield a strain of E. coli that’s unable to ‘breed’ with the normal kind. This could increase the safety of genetic engineering. Of course bacteria are asexual, so they don’t precisely ‘breed’. But they do something similar: they exchange genes with each other! Three of the most popular ways are:

• conjugation: two bacteria come into contact and pass DNA from one to the other.

• tranformation: a bacterium produces a loop of DNA called a plasmid, which floats around and then enters another bacterium.

• transduction: a virus carries DNA from one bacterium to another.

Thanks to these tricks, drug resistance and other traits can hop from one species of bug to another. So, for the sake of safe experiments, it would be nice to have a strain of bacteria whose genetic code was so different from others that it couldn’t share DNA.

And third, a bacterium with a modified genetic code could be resistant to viruses! I hadn’t known it, but the biotech firm Genzyme was shut down for three months and lost millions of dollars when its bacteria were hit by a virus.

This third application reminds me of a really spooky story by Greg Egan, called “The Moat”. In it, a detective discovers evidence that some people have managed to alter their genetic code. The big worry is that they could then set loose a virus that would kill everyone in the world except them.

That’s a scary idea, and one that just became a bit more practical… though so far only for E. coli, not H. sapiens.

So, I’ve got some questions for the biologists out there.

A virus that attacks bacteria is called a bacteriophage—or affectionately, a ‘phage’. Here’s a picture of one:

Isn’t it cute?

Whoops—that wasn’t one of the questions. Here are my questions for biologists:

• To what extent are E. coli populations kept under control by phages, or perhaps somehow by other viruses?

• If we released a strain of virus-resistant E. coli into the wild, could it take over, thanks to this advantage?

• What could the effects be? For example, if the E. coli in my gut became virus-resistant, would their populations grow enough to make me notice?

and more generally:

• What are some of the coolest possible applications of this new MAGE/CAGE technology?

Also, on a more technical note:

• What did people actually do with that strain of E. coli that ‘reads through’ amber?

• How could such a strain be viable, anyway? Does it mostly avoid using the amber codon, or does it somehow survive having a lot of big proteins where a normal E. coli would have smaller ones?

Finally, I can’t resist mentioning something amazing I just read. I said that our body uses 20 amino acids, and that ‘opal’ serves a stop codon. But neither of these are the whole truth! Sometimes opal codes for a 21st amino acid, called selenocysteine. And this one is different from the rest. Most amino acids contain carbon, hydrogen, oxygen and nitrogen, and cysteine contains sulfur, but selenocysteine contains… you guessed it… selenium!

Selenium is right below sulfur on the periodic table, so it’s sort of similar. If you eat too much selenium, your breath starts smelling like garlic and your hair falls out. Horses have died from the stuff. But it’s also an essential trace element: you have about 15 milligrams in your body. We use it in various proteins, which are called… you guessed it… selenoproteins!

So, a few more questions:

• Do humans use selenoproteins containing selenocysteine?

• How does our body tell when opal is getting used to code for selenocysteine, and when it’s getting used as a stop codon?

• Are there any cool theories about how life evolved to use selenium, and how the opal codon got hijacked for this secondary purpose?

Finally, here’s the new paper that all the fuss is about. It’s not free, but you can read the abstract for free:

• Farren J. Isaacs, Peter A. Carr, Harris H. Wang, Marc J. Lajoie, Bram Sterling, Laurens Kraal, Andrew C. Tolonen, Tara A. Gianoulis, Daniel B. Goodman, Nikos B. Reppas, Christopher J. Emig, Duhee Bang, Samuel J. Hwang, Michael C. Jewett, Joseph M. Jacobson, and George M. Church, Precise manipulation of chromosomes in vivo enables genome-wide codon replacement, Science 333 (15 July 2011), 348-353.

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Pessimists should be reminded that part of their pessimism is an inability to imagine the creative ideas of the future – Brian Eno

Rationality in Humans and Monkeys

Cosma Shalizi wrote a great review of this book:

• David Easley and Jon Kleinberg, Networks, Crowds and Markets: Reasoning about a Highly Connected World, Cambridge University Press, Cambridge, 2010.

Apparently this is one of the first systematic textbooks on network science, which Shalizi defines as:

the study of networks of semiautonomous but interdependent units and of the way those networks shape both the behavior of individuals and the large-scale patterns that emerge from small-scale interactions.

This is not quite the same as what I’ve been calling network theory, but I’d like to see how they fit together.

Shalizi’s review includes a great putdown, not of the book’s authors, but of the limitations of a certain concept of ‘rationality’ that’s widely used in economics:

What game theorists somewhat disturbingly call rationality is assumed throughout—in other words, game players are assumed to be hedonistic yet infinitely calculating sociopaths endowed with supernatural computing abilities.

Clearly we have to go beyond these simplifying assumptions. There’s a lot of work being done on this. One important approach is to go out and see what people actually do in various situations. And another is to compare it to what monkeys will do in the same situations!

Monkey money

Here’s a video by Laurie Santos, who has done just that:

First she taught capuchin monkeys how to use money. Then, she discovered that they make the same mistakes with money that people do!

For example, they make different decisions in what mathematically might seem like the same situation, depending on how it’s framed.

Suppose I give you $1000, and then ask which game would you rather play:

1) a game where I give you either $1000 more or nothing more, with equal odds.

2) a game where I always give you $500 more.

Most people prefer game 2), even though the average, or expected amount of money collected is the same in both games. We say such people are risk averse. Someone who loves to gamble might prefer game 1).

Like people, most capuchin monkeys chose game 2), although Santos used grapes rather than money in this particular experiment.

So, like people, it seems monkeys are risk averse. This is not a ‘mistake’: there are good reasons to be risk averse.

On other hand, suppose I give you $2000 — twice as much as before! Feel all those crisp bills… think about all the good stuff you can buy. Now, which game would you rather play:

1′) a game where I either take away $1000 or nothing, with equal odds.

2′) a game where I always take away $500.

Most people prefer game 1′). The strange thing is that mathematically, the overall situation is isomorphic to the previous one. It’s just been framed in a different way. The first situation seems to be about ‘maximizing gains’. The second seems to be about ‘minimizing losses’. In the second situation, people are more likely to accept risk, in the hopes that with some chance they won’t lose anything. This is called loss aversion.

Monkeys, too, prefer game 1′).

This suggests that loss aversion is at least 35 million years old. It’s survived a long process of evolution! To me that suggests that while ‘irrational’, it’s probably a useful heuristic in most situations that commonly arise in primate societies.

Laurie Santos has a slightly different take on it. She says:

It was Camus who once said that man is the only species who refused to be what he really is. But the irony is that it might only be by recognizing our limitations that we can really actually overcome them.

Does economics elude mathematical reasoning?

For yet another approach the enormous project of reconciling economics to the reality of human behavior, see:

• Yanis Varoufakis, Foundations of Economics: A beginner’s companion, Routledge, London, 1998.

• Yanis Varoufakis, Joseph Halevi and Nicholas J. Theocarakis, Modern Political Economics: Making Sense of the Post-2008 World, Routledge, London, 2011.

For the introduction of the first book go here. The second is described on the Routledge website:

The book is divided into two parts. The first part delves into every major economic theory, from Aristotle to the present, with a determination to discover clues of what went wrong in 2008. The main finding is that all economic theory is inherently flawed. Any system of ideas whose purpose is to describe capitalism in mathematical or engineering terms leads to inevitable logical inconsistency; an inherent error that stands between us and a decent grasp of capitalist reality. The only scientific truth about capitalism is its radical indeterminacy, a condition which makes it impossible to use science’s tools (e.g. calculus and statistics) to second-guess it. The second part casts an attentive eye on the post-war era; on the breeding ground of the Crash of 2008. It distinguishes between two major post-war phases: The Global Plan (1947-1971) and the Global Minotaur (1971-2008).

The emphasis is mine here, not because I’m sure it’s true, but because of how important it could be. It seems quite plausible to me. People seem able to squirm out of any mathematical framework we set up to describe them, short of the laws of physics. Still, I’d like to see the book’s argument. If there’s a ‘logical inconsistency’ in something, I want to actually see it.

You can get a bit more feeling for the second book in a blog post by Varoufakis. Among other things, he makes a point reminiscent of one that Phil Henshaw has repeatedly hammered home here:

Imagine a theorist that tries to explain complex evolving ecosystems by means of engineering models. What would result but incongruity and a mindset bent on misunderstanding the essence of the explanandum; a flight from that which craves explanation?

(By the way: I thank Mike Stay and Miguel Carrión-Álvarez for pointing out some items that appear in this blog entry. They did this on Google Plus. More on that later, maybe.)

Heat Wave in the USA

It’s hot in the United States! This picture from the NOAA Environmental Visualization Laboratory shows the temperature at 5 pm Eastern Time on the 12th of July:

Half the population is suffering under ‘heat advisories’. These kick in when the heat index—a measure of perceived temperature that takes humidity into account—surpasses 105°F (about 40 °C), or when the nighttime low exceeds 80°F (about 27 °C) for two consecutive nights.

Here’s what the Capital Weather Gang has to say:

East of the continental divide, it’s difficult to escape today’s searing heat. NOAA reported that as of 1 p.m., heat advisories or excessive heat warnings affected 150 million Americans in 23 states. Washington, D.C. had been under a heat advisory earlier today, but it was canceled when it became clear temperatures would fall just below advisory criteria.

Almost all of the south central and southeast states have seen heat indices exceed 105 degrees Tuesday afternoon. Some sample readings at 3 p.m.: Little Rock 109, St. Louis 109, Raleigh 105, Memphis 111, Charleston 108.

In recent days, the searing heat has set scores of new record high temperatures across the eastern two thirds of the country. Yesterday alone, 41 record highs were set including Ft. Smith, Ar. (107), Indianapolis, In. (96), Louisville, Ky. (97), Watertown, Ny. (90), Altoona, Pa. (94), and Charleston, WV (95).

Record high minimum temperatures have been more even pervasive, offering little nighttime relief from the oppressive afternoon heat. On Monday, 132 record high lows were set.

In Louisville, Kentucky this morning, the low dropped to a mere 84 degrees. Meteorologist Eric Fisher at The Weather Channel tweeted: “That. Is. Filthy. Heat Index was still above 100 at 5am.”

Some of the most remarkable heat occurred on in central Plains on July 9 and 10. Oklahoma City reached 110 degrees on the 9th, tying its all-time high for the month. Wichita, Kansas rose to 111 degrees on the 10th, its hottest temperature in 30 years. See CapitalClimate for more on the records which extended into Arkansas and Missouri.

In both Oklahoma City (13 days) and Dallas (10 days), the mercury has reached 100 or better for at least ten straight days. Hot weather is predicted to persist there through the weekend, at least.

Across the country during the month of July, record highs have outnumbered record lows 349 to 68 (or more than 5:1).

Could any of this be related to, umm, global warming? Joe Romm has a blistering critique of the American media’s failure to mention this possibility:

• Joe Romm, After Story on Monster Heat Wave, NBC Asks “What Explains This?” The Answer: “We’re Stuck in a Summer Pattern”!, Climate Progress, 13 July 2011.

Inference is a tricky business. It’s easy to spot patterns where they don’t exist, especially when the patterns are as subtle as an increase in extreme weather events, also known as ‘global weirding’. If there’s a flood, or a drought, we can easily explain it this way. The human mind, after all, is programmed to seek out patterns: we can see faces in clouds.

But it’s also easy to fail to recognize patterns where they do exist—especially when acknowledging them would require difficult changes in behavior. “Am I an alcoholic? No, I just got really drunk last night… and, okay, the night before…”

Earlier this spring, Bill McKibben had a sarcastic editorial about this:

• Bill McKibben, A link between climate change and Joplin tornadoes? Never!, Washington Post, 24 May 2011.

It starts:

Caution: It is vitally important not to make connections. When you see pictures of rubble like this week’s shots from Joplin, Mo., you should not wonder: Is this somehow related to the tornado outbreak three weeks ago in Tuscaloosa, Ala., or the enormous outbreak a couple of weeks before that (which, together, comprised the most active April for tornadoes in U.S. history). No, that doesn’t mean a thing.

It is far better to think of these as isolated, unpredictable, discrete events. It is not advisable to try to connect them in your mind with, say, the fires burning across Texas — fires that have burned more of America at this point this year than any wildfires have in previous years. Texas, and adjoining parts of Oklahoma and New Mexico, are drier than they’ve ever been — the drought is worse than that of the Dust Bowl. But do not wonder if they’re somehow connected.

If you did wonder, you see, you would also have to wonder about whether this year’s record snowfalls and rainfalls across the Midwest — resulting in record flooding along the Mississippi — could somehow be related. And then you might find your thoughts wandering to, oh, global warming, and to the fact that climatologists have been predicting for years that as we flood the atmosphere with carbon we will also start both drying and flooding the planet, since warm air holds more water vapor than cold air.

It’s far smarter to repeat to yourself the comforting mantra that no single weather event can ever be directly tied to climate change. There have been tornadoes before, and floods — that’s the important thing. Just be careful to make sure you don’t let yourself wonder why all these record-breaking events are happening in such proximity — that is, why there have been unprecedented megafloods in Australia, New Zealand and Pakistan in the past year. Why it’s just now that the Arctic has melted for the first time in thousands of years. No, better to focus on the immediate casualties, watch the videotape from the store cameras as the shelves are blown over. Look at the news anchorman standing in his waders in the rising river as the water approaches his chest.

Luckily, scientists are busy at work on these questions. For example, these papers on floods came out in February:

• Pardeep Pall, Tolu Aina, Dáithí Stone, Peter Stott, Toru Nozawa, Arno Hilberts, Dag Lohmann, and Myles Allen, Anthropogenic greenhouse gas contribution to flood risk in England and Wales in autumn 2000, Nature 470 (17 February 2011), 382–385. Supplementary information available for free online.

• Seung-Ki Min, Xuebin Zhang, Francis W. Zwiers and Gabriele C. Hegerl, Human contribution to more-intense precipitation extremes, Nature 470 (17 February 2011), 378-381.

I believe that someday we will understand whether and how extreme weather events are linked to global warming—if not individually, at least statistically. Whether we’ll understand it soon enough for it to make much difference—I’m less sure about that.

Luckily, I’m back in Singapore now, so I don’t personally have to worry about the heat wave in the USA. No heat advisory here! The weather is quite normal, with the heat index a nice cool 100 °F (or 38 °C).