WorldChanging On E. coli Spinach

WorldChanging has a great piece called Spinach, Feedlots and Knowing the Backstory. Did you know that E. coli O157:H7, the dangerous strain that is now contaminating spinach, thrives primarily in the digestive tracts of grain-fed feedlot cows? Where does our food come from, anyway?

Friday Random Ten

• Animaniacs, "Parts of the Brain". Sung, of course, by the Brain.
• Linda Beck, "La Tierra Misma". A gentle song in English and Spanish.
• Bruce Cockburn, "My Beat". Impressionistic word painting of a city.
• Collin Raye, "Twenty Years and Change". Definitely the best thing Collin's written so far.
• Mindy McCready, "Guys Do It All the Time". Oh yeah!
• Collin Raye, "Sweet Miss Behavin'" Pun-filled dance tune.
• Peter, Paul and Mary, "500 Miles". I enjoy singing this one.
• Julia Ecklar, "Walkabout". Weird song of disillusionment.
• Jo Dee Messina, "Bye Bye". The boyfriend is history!
• Stephen Longfellow Fiske, "No Easy Answers". A song about homelessness; not Fiske's best.

Should HIV Testing be Routine?

Faced with a room full of premeds, my undergrad statistics professor enjoyed giving us problems like, "If one person in a thousand has a certain disease and the test for the disease gives a positive result X percent of the time if the person has the disease and Y percent of the time if they don't, how many false positives does it give if 100,000 people are tested?" For rare diseases, even very high test accuracy often resulted in more false positives than true ones.

Those old assignments came to mind when I read that the CDC is now recommending HIV testing for all adults and adolescents. This is supposed to reduce spread of the virus and ensure that those infected get anti-retroviral treatment before they actually get sick, but I was worried about false initial positives. Fortunately, the numbers are more favorable here than they were in Stats 13.

About 1% of the US population is estimated to have undiagnosed HIV infection. New rapid tests have a false positive rate of about 0.2% and a false negative rate of about 0.1%. So, screening 100,000 individuals would give 0.999*0.01*100,000=999 true positives and only 0.002*0.99*100,000=198 false positives, a pretty good ratio.

Conclusion? Although it makes sense to opt out of testing if you're sure you have no chance of having HIV, universal screening appears to be a good public health measure and I hope it's implemented quickly.

Nutrition, Solar Design and Buying Local

Now that organic is going mainstream, buying locally grown food has become the hot new trend among environmentally-oriented foodies. While I think the trend can go to entertaining but impractical lengths and some of the arguments in favor of locally grown food do not work, there's no doubt that buying local saves energy, since your veggies don't have to be trucked cross-country. And fresh food just plain tastes better.

There's just one small problem: winter. For those of us in temperate or northern climates, a local diet would be seriously vitamin-deficient -- not to mention boring -- for four to six months of the year. As a South Dakota resident colorfully put it:

If all I bought was local production in the wintertime, I wouldn't be buying anything but meat. I would have the same vitamin-deficient, fruit-deficient, vegetable-deficient diet that people had in the 1800s, when they lived on bread, beans, bacon, and potatoes for 6 months out of the year, and died in their 50s. A flu germ would kill me. If you want vitamin C, you're gonna have to import.

So, is there a way out of this dilemma? Yes, and its name is passive solar design. In one incarnation, described by Tom Philpott in Grist Magazine, this involves combining greenhouses built right into hills with using large barrels of water to store up heat. Another version, which even works in Maine, uses cold frames and varies crops with the seasons. Almost certainly, other possibilities exist that haven't been invented yet.

I do not think it is necessary or desirable to rely entirely on local produce, but it should certainly become more common than it is. (Why is Florida orange juice so common in California? What are California peaches doing here in Georgia?) The big lesson of passive solar design in agriculture is that we shouldn't automatically accept trade-offs between truly desirable things. Very often, we can have our fresh tomatoes and eat them, too.

I'm Back

It's good to be posting again! Past readers will notice the change in my profile -- I officially started graduate school a few weeks ago. Moving to Athens, getting set up and then obtaining my forgotten password from Blogger took far longer than I thought it would. Expect a new post sometime in the next few days. In the meantime, check out my fellow Athenian blogger Wayne at Niches.

Friday Random 10

I'm moving, so there won't be any new posts for at least a week and a half. In the meantime, enjoy my blogroll -- there's lots of good stuff there.

• Johnny Cash, "Orange Blossom Special"
• Jo Dee Messina, "That's the Way". Life isn't simple, but you've got to roll with the punches!
• Bruce Cockburn, "Arrows of Light"
• Peter, Paul and Mary, "Because All Men are Brothers". An anthem of solidarity.
• Gloria Gaynor, "I Will Survive". What is it with all the '70s stuff coming up today?
• Leslie Fish, "PGP". A total nerd song.
• Collin Raye, "I Can Still Feel You". I like the video for this one.
• John Denver, "Today". Lovely and gentle.
• Peter, Paul and Mary. "500 Miles". Slow and very singable.
• Tim McGraw, "Angry All the Time". Haunting.

Science, Wonder and Creativity

Today, Chaotic Utopia, Creek Running North and The Scientific Activist are all discussing various aspects of the connections between science, art, metaphor and poetry. I wish I had time to post something substantive on this, but I'll have to leave you with a poem and two quotes.

---

Molecule Moment
by Jane Shevtsov

Earth’s endless life-stuff cycles
-- Sun-energy flows --
make, as an eddy, me

I will someday be over
but flowing cycling
will go on
creating more uniquenesses

I eat, I drink, I breathe
and I excrete,
exhale
Life flows through me

i am a part of an immense intelligence
a Life spinning through space

My future, past, and present all connect
to all the Earth
to the whole Universe,
all of the knowledge of which
is required
to truly comprehend
the single cell
of an amoeba
living in my mouth

The Universe is glorious
and all of human artwork,
dancing,
singing,
celebration
is inadequate
to capture it.

I know my joy,
my thoughts,
my words.
The name does not matter
Only the acts.
I act
to celebrate,
invigorate,
and prolong Life

I'm a moment for all my molecules

---

""Spirit" comes from the Latin word "to breathe." What we breathe is air, which is certainly matter, however thin. Despite usage to the contrary, there is no necessary implication in the word "spiritual" that we are talking of anything other than matter (including the matter of which the brain is made), or anything outside the realm of science. On occasion, I will feel free to use the word. Science is not only compatible with spirituality; it is a profound source of spiritually. When we recognize our place in an immensity of light-years and in the passage of ages, when we grasp the intricacy, beauty, and subtlety of life, then that soaring feeling, that sense of elation and humility combined, is surely spiritual. So are our emotions in the presence of great art or music or literature, or of acts of exemplary selfless courage such as those of Mohandas Gandhi or Martin Luther King, Jr. The notion that science and spirituality are somehow mutually exclusive does a disservice to both."
--Carl Sagan, The Demon-Haunted World

---

"Poets say science takes away from the beauty of the stars -- mere gobs of gas atoms. Nothing is "mere." I too can see the stars on a desert night, and feel them. But do I see less or more? The vastness of the heavens stretches my imagination -- stuck on this carousel my little eye can catch one-million-year-old light. A vast pattern -- of which I am a part -- perhaps my stuff was belched from some forgotten star, as one is belching there. Or see them with the greater eye of Palomar, rushing all apart from some common starting point when they were perhaps all together. What is the pattern, or the meaning, or the *why?* It does not do harm to the mystery to know a little about it. For far more marvelous is the truth than any artists of the past imagined! Why do the poets of the present not speak of it? What men are poets who can speak of Jupiter if he were like a man, but if he is an immense spinning sphere of methane and ammonia must be silent?"
--Richard P. Feynman

Science as a Voice of Sanity

Science Magazine is one of the most reliably cosmopolitan publications coming out today. A couple of weeks ago, they printed a letter that seems especially poignant in light of the current madness in the Middle East. Its author responds to an article about collaboration between Israeli and Palestinian scientists. (Access most likely isn't free.) He writes:

In these days of debates on borders that impede the free movement of people--the U.S.-Mexican border, the European Union-African maritime borders, and the Israeli-Palestinian separation wall--Bohannon reminds us that science is an international activity that knows and should know no border.

Scientists understand the importance of the free flow of ideas, knowledge, and professionals. When scientific collaboration is seen as enemy collaborationism, science is losing against confrontational politics. While the battle against terrorism is of great importance, walls and barriers are against the essence of science.

While scientists are not immune to various chauvinisms, many have spoken out for larger loyalties. A couple of years ago, I studied cosmopolitan thought in Cold War America. One of my areas of focus was the attitudes of scientists, as expressed in the front matter of Science. Here are a few representative quotations.

"[S]cience is universal in that its truths are part of the universe accessible to all investigators; ... we gain as much by original discoveries made elsewhere as by those which we make." --Edward U. Condon, physicist, 1948

"We should deplore every display, whether by statesman or journalist, of dunghill courage that lessens the hope of mutual understanding, good-will, and ultimate collaboration among human beings." --Paul B. Sears, conservation scientist, 1958

"[I]nternational groups of scientists seem able to achieve cooperation of great importance when they are free of political entanglements and can act freely with the tropism toward cooperation which is traditional among scientists." --James R. Killian, Jr., former MIT president, 1961

"From a spaceship it is hard to see the logic of political boundaries. A new concept of sovereignty of nations might turn out to be the most important product of joint space stations." --Walter Orr Roberts, atmospheric scientist, 1970

Why is this view so widespread among scientists? Maybe because science studies an external world that exists independently of humans and their divisions. Maybe there is a trace in science of enlightenment universalist ideals. Maybe there are other reasons. Whatever the roots of the connection between science and world citizenship, I hope it leads to real change in the world.

Tangled Bank #59

Check out the new Tangled Bank at Science and Reason.

A Blogger After My Own Heart!

I've just discovered Science and sensibility and I like what I see there. Although the blogger, David Winter, is a biochemistry student, he writes about cool things like butterfly biogeography. (I can't remember the last time I saw biogeography in the science blogosphere!) And his front page has a post about fungi, including a very nice photo of Amanita muscaria, the fly agaric. Now, if he'd just do something on food webs...

Let's Go to the Circus!

Circus of the Spineless is up at Words & Pictures. Enjoy the show!

The Parasite Web

Food webs -- diagrams of who eats whom in an ecosystem -- are among the first aspects of ecology that most of us encounter in school. However, much is unknown about the rules governing the structure, formation and dynamics of these networks.

A large part of the reason is that reasonably complete food webs are extremely difficult to produce. A moderately large web can involve from tens to hundreds of species (even though many communities have far more) and it is necessary to trace feeding interactions for every single one of them. This can involve such pleasant tasks as examining the stomach contents of fish -- lots of fish. Tracking the feeding interactions of insects isn't easy either. And parasites, especially those that feed on other parasites? Forget about 'em!

That may not be a good idea, says a new study published in Proceedings of the National Academy of Sciences. (It is freely available here.) The authors took four published food webs that included parasites and examined the effects of removing them.

While much of the paper is devoted to methodological issues, the bottom line is that parasites are important. "Parasites dominated food web links; on average, a food web contained more parasite–host links than predator–prey links." Including parasites raised food web connectivity, which, computer models suggest, makes extinctions less likely to propagate.

The authors repeatedly return to the question of proper and improper methods of including parasites in food webs. However, I wonder whether they should be included at all. The problem is that many parasites have complex life cycles, requiring several hosts to mature and reproduce. In normal trophic interactions, having more than one food source makes an organism less vulnerable to extinction. But for a parasite, all links may be crucial. In other words, a predator-prey arrow doesn't have exactly the same meaning as a parasite-host arrow. To avoid confusion and develop robust theory, it may be best to distinguish between predator-prey and parasite-host interactions, at least where complex life cycles are involved.

---

References:

Dunne, Jennifer A., Richard J. Williams and Neo D. Martinez. (2002) Network structure and biodiversity loss in food webs: robustness increases with connectance. Ecology Letters 5:558-567

Lafferty, Kevin D. Andrew P. Dobson and Armand M. Kurls. (2006) Parasites dominate food web links. Proceedings of the National Academy of Sciences 103:11211-11216

Healthy Childhood, Healthy Elderhood?

From the Bizarre Connections department: FuturePundit and Aetiology discuss a New York Times article that shows evidence that reducing infectious disease in early childhood may reduce chronic disease in old age.

The biggest surprise emerging from the new studies is that many chronic ailments like heart disease, lung disease and arthritis are occurring an average of 10 to 25 years later than they used to. There is also less disability among older people today, according to a federal study that directly measures it. And that is not just because medical treatments like cataract surgery keep people functioning. Human bodies are simply not breaking down the way they did before.

Gorgeous!

There is a truly gorgeous piece of writing at Creek Running North you owe it to yourself to read.

The wind raked her hair — the color of the dried grasses atop the bluff. Eyes the shade of the horizon followed a line from my finger to the rock. Fifteen feet up, emerging, a nest of scallops five million years dead. The next storm will shatter them, an evanscence there with us and over far too soon.

Discovering Lady Beetles

Karmen at Chaotic Utopia has a post about discovering a lady beetle colony on a tree in her front yard. The initial encounter was less than promising.

"One of the reasons I chose my house was the giant maple tree by the front porch. The foliage provides shade and privacy in the summer and a terrific Halloween backdrop in the fall. So, a few weeks ago, when I noticed the tree was infested with something, I was a bit concerned. Ok, maybe that's putting it lightly. I threw science out the window and freaked out. 'The tree's covered with insects! It's gonna die! Ew!! Call somebody! Quick!'"

Eventually, she becomes a close observer of the colony, chronicling its development.

Mushroom Pictures And...

Via Negativa has posted some mushroom photographs and an atmospheric story that, to be honest, I don't quite get. Maybe I'll understand it in the evening, in a more relaxed mood. In any case, the pictures are worth checking out.

Friday Random 10

• Cheryl Cloud and Common Ground, "In a World Gone Mad". Incredibly appropriate today.
• Echo's Children, "Bold Adventurer". Fun twist at the end!
• Bruce Cockburn, "Pacing the Cage". Melancholy and thoughtful.
• Johnny Cash, "Get Rhythm". A nice change of pace after "Pacing the Cage".
• Animaniacs, "I'm Mad"
• Wishing Chair, "Keep Me Simple". A celebration of nature and simplicity.
• Lee Ann Womack, "Make Memories with Me"
• Collin Raye, "Twenty Years and Change". This song about maturation is one of Collin's best. I don't agree with everything it says, though. You don't have to lose your idealism!
• Jackson Browne, "Farther On". A meandering lyric.
• Gaia Consort, "Illumination"

Gore's Global Imagery

Yesterday, I finally got out to see An Inconvenient Truth. The film is well done, so if you haven't seen it, go! It's definitely worth eight bucks! (And if you're in LA, try seeing it at the Westwood Crest. It's a gorgeous, old-fashioned movie theater.)

I will not analyze the movie's science here -- RealClimate does an excellent job -- other than to say it's very largely correct but ebola and avian flu have nothing to do with global warming. What really got my attention was Gore's juxtaposition of local and global imagery, particularly how they complement each other.
The film starts at a river near the Gore family farm. A minute later, we see the most famous photographs of Earth from space -- Earthrise and the full-frame Apollo 17 shot known only as 22727.

The images continue. Before even really getting into global warming, Gore shows a film of Earth's rotation taken by the Galileo spacecraft and a composite cloudless photograph of Earth (somewhat similar to the one I blogged about here). While the composite is used many times later in the film, the animation and other photos seem to be shown mostly for their emotional effect.

And they certainly do have an effect. Even for somebody who has spent a lot of time examining these images and studying their cultural meanings, it is hard to look closely at Earthrise or 22727 without being moved. The emotion is a complex mix of esthetic appreciation, awe and humility at our place in the Cosmos. If this feeling isn't spiritual, I don't know what is.

At this point, the movie gets into the nitty-gritty of global climate change. Here, the only significant global images are maps, often superimposed on the composite image mentioned above. Instead, we see a lot of clips of particular places on Earth where global warming has been studied or is having an effect. The movie shows the disappearing glaciers of Kilimanjaro, a collapsed building on melting Siberian permafrost, drowning atolls in the South Pacific and New Orleans after Hurricane Katrina. There are also a few images of pollution sources, but Gore mostly presents this information in graphs.

Here, it makes sense to detour briefly into the relationship between the local and the global. The two perspectives are often presented as opposites, but this is a false dichotomy. "For this local scene to exist," writes geographer Denis Wood in Five Billion Years of Global Change, " the whole world had to be just so." Each place is an intersection of a myriad of global processes, from plate tectonics to the movements of plants and animals to cultural diffusion. Simultaneously, plate tectonics, biological range shifts and cultural diffusion result from local conditions in places all over the world. Everything happens somewhere, but global systems link localities. The local and the global co-create each other.

At the end of the film, Gore comes to another photograph of Earth, this one taken from beyond the orbit of the outermost planet. Usually referred to as the Pale Blue Dot image, this photograph shows Earth as a small dot, a mote of dust caught in a sunbeam. Carl Sagan, whose idea it was to take the picture, wrote eloquently about it in a book titled Pale Blue Dot. Unfortunately, Gore didn't quote him, so I will end by doing so.

That's here. That's home. That's us. On it, everyone you ever heard of, every human being who ever lived, lived out their lives. The aggregate of all our joys and sufferings, thousands of confident religions, ideologies and economic doctrines, every hunter and forager, every hero and coward, every creator and destroyer of civilizations, every king and peasant, every young couple in love, every hopeful child, every mother and father, every inventor and explorer, every teacher of morals, every corrupt politician, every superstar, every supreme leader, every saint and sinner in the history of our species, lived there on a mote of dust, suspended in a sunbeam.

The earth is a very small stage in a vast cosmic arena. Think of the rivers of blood spilled by all those generals and emperors so that in glory and in triumph they could become the momentary masters of a fraction of a dot. Think of the endless cruelties visited by the inhabitants of one corner of the dot on scarcely distinguishable inhabitants of some other corner of the dot. How frequent their misunderstandings, how eager they are to kill one another, how fervent their hatreds.

Our posturings, our imagined self-importance, the delusion that we have some privileged position in the universe, are challenged by this point of pale light. Our planet is a lonely speck in the great enveloping cosmic dark. In our obscurity -- in all this vastness -- there is no hint that help will come from elsewhere to save us from ourselves.

It's been said that astronomy is a humbling, and I might add, a character-building experience. To my mind, there is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly and compassionately with one another and to preserve and cherish that pale blue dot, the only home we've ever known.

To Understand and Protect Our Home Planet

WorldChanging reports that the phrase, "To understand and protect our home planet" has been deleted from NASA's mission statement.

NASA's mission statement used to be “To understand and protect our home planet; to explore the universe and search for life; to inspire the next generation of explorers ... as only NASA can.” Now, however, it's been changed:

In early February, the statement was quietly altered, with the phrase “to understand and protect our home planet” deleted. In this year’s budget and planning documents, the agency’s mission is “to pioneer the future in space exploration, scientific discovery and aeronautics research.” ...

Although this change is supposed to reflect a renewed focus on going to the moon and Mars, it is profoundly ironic in light of what astronauts have said about seeing Earth from space. Here are just a few samples:

"It isn't important in which sea or lake you observe a slick of pollution, or in the forests of which country a fire breaks out, or on which continent a hurricane arises. You are standing guard over the whole of our Earth." --Yuri Artyukhin

"As I looked down, I saw a large river meandering slowly along for miles, passing from one country to another without stopping. I also saw huge forests, extending along several borders. And I watched the extent of one ocean touch the shores of separate continents. Two words leaped to mind as I looked down on all this: commonality and interdependence. We are one world." --John-David Bartoe

"After an orange cloud -- formed as a result of a dust storm over the Sahara and caught up by air currents -- reached the Philippines and settled there with rain, I understood that we are all sailing in the same boat." --Vladimir Kovalyonok

I am a huge supporter of human space exploration, but I believe NASA's actions are short-sighted. Last year, they made deep cuts in the Life Sciences budget, including the development of bioregenerative life support systems that will almost certainly be necessary for long voyages. Now, the closely related Earth systems science is feeling the pinch. NASA's mission statement actually plays a role in the selection of research priorities. WorldChanging continues:

As we've said before, to truly know the Earth, we need to take to space. A whole array of useful information about our planet can only be learned by leaving it -- whether by launching satellites, sending unmanned probes to other planets, or even shooting ourselves into the depths of space. Space exploration is green, and, even more, the green benefits of space exploration may be the strongest argument for undertaking it.

They also suggest we spread the word about the mission statement change and put the deleted phrase on as many web pages as possible. I just did. Are you game?

Aspiring to be an Atypical Blogger

Freakonomics Blog points out that most blogs don't last. "The typical blogger, like most people who go on diets and budgets, quits after a few months, weeks, or in many cases, days." That's what happened to Perceiving Wholes the first time around, but its rebirth has been more lasting. Beginning to acquire an audience is a thrill. And there are so many neat things to write about that most people never see! I think I'll be here for a while yet.