Friday Random Ten

• Jackson Browne, "Doctor My Eyes". "Doctor, my eyes cannot see the sky. Is this the price for having learned how not to cry?" A classic.
• Aladdin soundtrack, "A Whole New World". We learned to sing and sign this one in fifth grade!
• Peter, Paul and Mary, "Oh, Rock My Soul"
• Kathy Mar, "Child's Song". A melancholy song about leaving home.
• John Lennon, "Imagine". Music just doesn't get much better than this. Certainly a song we need to hear.
• Jackson Browne, "For a Dancer". "Keep a fire for the human race."
• Gaia Consort, "Falling". Walking is falling and catching yourself.
• Johnny Cash, "The One on the Left is on the Right". No, it's not about Congress, but it is a very funny song about a folk group torn apart by political differences.
• Kathy Mar, "Flowering Green". Talk about getting what you deserve!
• Wishing Chair, "Three Doors". A song about Ellis Island.

Home and the Big Here

If you've been reading this blog for any length of time, you know that I'm a fan of WorldChanging, and a couple of weeks ago, they posted an essay that I've been meaning to comment on. The question raised in the essay is, "Where is home?".

"Home is a fiercely individual concept: it's hard to articulate all the elements that make a 'home'; our location, and notion, of home may change over time; we may not be able to live at home for various reasons; and how we are comfortable with our environment and the people around us are all, I think, wrapped up in this notion of 'home.'"

I lived in Los Angeles for 16 years but don't think it was ever home to me. Some parts of it felt comfortable and I developed emotional attachments to my high school and the LA Eco-Village, but the city itself was simply there. Furthermore, I did not particularly like the there. When I think of good things about LA, I think of people, not places.

Where is home, then? For most of my life, I've had a deep emotional connection to temperate deciduous forests. I don't know what it is about the forest landscape that makes me feel peaceful and comfortable, but it's powerful. Two years ago, I got to spend a summer at Cranberry Lake Biological Station in the Adirondacks and upon arrival, I immediately felt it to be home. It was there that I hit upon the phrase, "Home is where what is inside you matches what is outside you".

What about now? I'm living in Athens, GA, which has the forests I so love, although many areas are still dominated by pine. There are many things -- and people -- I like here, but the city does have problems. (The public transportation system sucks!) Will Athens become home? I don't know yet.

In connection with this, I will start doing Kevin Kelly's "Big Here" quiz, which provides a structure for exploring the place where you live. Stay tuned for question 1!

Fungal Blogging

The new Festival of the Trees is up and seems to have an unusual number of fungal posts. There's a post about a huge artist's conk (Ganoderma applanatum) and one with pictures of several fungi, most likely wood-rotters, growing on trees. But the close-up mushroom photos on Riverside Rambles take the cake!

Is There Really a Connection between E. coli and Farming Methods?

Last Saturday, I linked to a WorldChanging post that said that E. coli O157 is linked to factory farming because it prefers to grow in grain-fed cows. I have just become aware that Tara Smith at Aetiology has written on this topic and the issue is not really clear-cut. There may indeed be a connection between grain-feeding and pathogenic E. coli, but the evidence is hardly unequivocal. Tara mentions a study that found

that when a long-term diet of hay was fed (greater than a month), the cattle still shed O157 (Appl Environ Microbiol. 2005 71:7974-9.) Another one found diet had no effect on O157 (J Anim Sci. 2006 84:2523-32). If anything's clear, it's that the link between diet and shedding of O157 *isn't* clear, despite what Plank claims.

Of course, knowing where our food comes from is important for many reasons and some links between factory farming and disease, like the evolution of antibiotic-resistance bacteria, are widely accepted. However, it is important that we base our decisions on the best science available and learn to tolerate some uncertainty.

Friday Random Ten

An unusual amount of very good stuff came up today. I guess it's my lucky music day!

• Bruce Cockburn, "All the Diamonds in the World". Cockburn's usual lyrical imagery, spirituality and perfect guitar. Good stuff!
• Kathy Mar, "Flowering Green". A fairy tale for the modern world.
• Kathy Mar, "Everybody's Moon". Thoughful but light folky song.
• Jackson Browne, "For Everyman". Life will be good for all of us or none of us.
• Echo's Children, "O, Sumer!". An allegory describing the sacking of ancient Sumer.
• Jackson Browne, "Tender is the Night". Searching for that right person.
• Julia Ecklar, "Burnish Me Bright". The story of a mute child who learns to communicate through mime.
• Gaia Consort, "Moon in Your Teeth". Spare and mystical.
• Collin Raye, "It Could Be That Easy"
• Peter, Paul and Mary, "The Times They are a' Changin'". Wrong generation? Maybe not...

What Does It Mean to Respect Nature?

I've never watched Steve Irwin, but I'm a member of the ECOLOG mailing list and lately my inbox has been filling up with ecologists' commentary on his approach to education and entertainment. Commenters seem to fall into two categories: those who admired Irwin and those who thought he wasn't serious enough, that his wildlife-based entertainment had little value.

I can't comment on Irwin specifically, but two assumptions came up often enough in the writings of the second group that I feel they must be discussed. The first is that respecting nature means taking a hands-off approach as much as possible. The second is that scientific research is intrinisically more valuable than, say, entertainment.

The title of the Charles Jonkel article linked to above, "Save a Grizzly, Visit a Library", exemplifies the first assumption. To a certain extent, I share it. Humans certainly are capable of harming nature and animals while enjoying them. But must I be a pair of eyes on a stick? While some of Steve Irwin's actions may certainly have been questionable, is there anything seriously wrong with my herpetology professor's lizard-catching or my munching on various woodland edibles? Promoters of the "hands-off" attitude often decry the fact that many modern kids learn more about nature from TV and computers than first-hand experience, but isn't this perfectly consistent with the "do not disturb" ethic? Under what circumstances may we participate in nature, and doesn't even posing the question separate us from the rest of the natural world?

Several list members have commented that handling, marking and sometimes even killing wild animals is justified only if it is for scientific purposes. Entertainment, even if educational, just isn't good enough. This claim is frequently followed by the assertion that the use of wild animals in research is acceptable because it helps with conservation or management. However, most zoological research has essentially nothing to do with conservation or management! While I agree that animal welfare is extremely important, I would argue that mist-netting 100 birds to band them is more problematic than capturing one or two such birds to show off on television. Furthermore, many (if not most) biologists chose their careers because they love nature and the outdoors. Biologists generally enjoy their work and this enjoyment is the primary motivation for the work. However, it is hard to argue that the satisfaction of a scientist's curiousity is inherently more worthwhile than the satisfaction of another person's desire for entertainment.

When animals are used in either science or entertainment, the animal's well-being must be paramount. Beyond that, it is hard to criticize Steve Irwin.

Kudzu, Hurricanes and Soybean Rust

I may be a fungus freak, but learning life cycles is, well, a necessary evil. Rusts, plant pathogens with up to five types of spores, are a particular pain. So today's lecture on rusts in my mycology class was a bit less than exciting -- that is, until we got to soybean rust. The organism is not particularly fascinating, but the story of how it got to the United States is worth telling.

Like soybeans, soybean rust is native to East Asia. As soybean cultivation spread worldwide, so did the rust. In the 1950s and 1960s, it spread through South Asia and Australia. In 1994, it reached Hawaii, but the continental US was protected by long distances and careful inspection of imported plants.

The beginning of the end of this isolation came in 1997, when a cyclone carried the fungus from India to central Africa. In a few years, it reached both South Africa and the Atlantic coast. Then, transported by either wind or airplanes, the rust showed up in Paraguay in 2002. From Paraguay, the fungus' highly mobile spores dispersed to Venezuela and Brazil. After that, it was only a matter of time before soybean rust showed up in the continental US.

It didn't take long. In September 2004, Hurricane Ivan blew spores from South America to the American South, introducing the rust to Louisiana, Mississippi, Georgia and Florida. Farmers are now trying to control the pathogen, which attacks a wide range of legumes. So far, damage has not been serious.

So what's up with kudzu? It turns out that this vine, a Japanese import ubiquitous in the South, is one of the hosts of soybean rust. This means it can become a reservoir for the disease -- unfortunately, without sustaining much damage itself. You gotta love ecology!

Cool Space Blogging

Have you heard of Anousheh Ansari? She's a space tourist, the fourth one in history and the first woman, and she has a blog that gets updated several times a day. (She can't blog live because of Internet connection outages during orbit; instead, she sends down emails that her friends post on the web.)

Only the very wealthy can afford space travel right now, but what will happen in 15 or 20 years? Will the merely well-off be able to go up? Will there be private space stations catering to the ultimate in tourism? And what would happen if many people experienced a view of Earth from space? That could be one of the drivers of Homo sapiens' maturation.

On a related note, Thomas P.M. Barnett notes a New York Times article about Mike Griffin, the director of NASA, visiting China. I hope we do start to cooperate in space.

Two Tales of Missing Tails

A lizard and a dolphin.

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!