Perceiving Wholes

Science is Not a Game

2011-10-28T23:31:00.000-07:00

Janet Stemwedel at Doing Good Science has been blogging about Marcus Ross, the young earth creationist who earned a mainstream Ph.D. in paleontology. She's trying to pin down exactly what scientists and science-minded people think is wrong with what he did. Where exactly is that gut feeling of something not being quite right coming from?

One of the possibilities she examines is that, "It’s wrong for Ross to maintain his young earth creationist beliefs after the thorough exposure to scientific theories, evidence, and methodology that he received in his graduate training in geosciences". Here, however, she says that young earth creationism is a religious belief, not a scientific one, and scientists typically have all kinds of non-scientific beliefs. This seems like a weak argument to me, as Ross' particular religious beliefs directly contradict scientific ones. This isn't a case of a scientist simply not applying their training to certain belief; it's a case of irreconcilable conflict.

Still, I think that the problem here goes deeper than that. I would argue that when Marcus Ross was doing his dissertation research, he was not doing science, despite using completely standard methods. Ross is not a scientist. He only plays one on TV.

I make this claim because I think that science is defined by its goals, not its methods. The goal of basic research is to improve your understanding of the Universe and share this understanding with others. Janet Stemwedel has referred to the "inferential machinery" of science several times in her blog series, but this machinery (to the extent that a general scientific method even exists) is only a tool. We do experiments, make observations and carry out statistical analyses because doing so is a fairly reliable method of learning about the natural world. If carrying out Ouija board seances while standing on your head was a better way of learning about the world, graduate students would have to master inverted Ouija board use.

This is how we can distinguish Ross from real scientists. His belief in young earth creationism was fixed, so he can't be said to have believed the conclusions in his dissertation. Therefore, Ross' understanding of the world was not and could not have been improved by his work. His research was only a pantomime of science -- maybe a good pantomime, but a pantomime nonetheless.

An Ethical Ad Blocker?

2011-10-24T20:49:00.000-07:00

I just read George Monbiot's new essay about advertising and it got me thinking about how we might reduce ad exposure on the web. Like many people, I sometimes use an ad blocker. However, because I'm aware that the free content and services I depend on are paid for by advertising, I generally only use the blocker for sites with really annoying ads. Still, it would be better for the environment if we weren't exposed to so many messages telling us to buy stuff.

I propose that somebody develop a subscription-based ad blocker that would automatically make micropayments to the sites you visit. Content providers would register and the ad blocker plug-in would keep track of where you go on the web. (Ideally, for privacy reasons, this data would only be stored on your computer.) For practical reasons, you would probably pay a fixed amount of money each month. At the end of the month, the money would be divided among content providers according to how much you used them. If you disabled the blocker on certain sites, they wouldn't get any money.

So, what do people think? Is this workable? How would you modify the idea?

On Not Being a Fish

2011-10-01T13:49:00.000-07:00

There's a quote that's been making the rounds on the internet and elsewhere. Attributed to Albert Einstein, it says, “Everybody is a genius. But if you judge a fish by its ability to climb a tree, it will live its whole life believing that it is stupid.” (I very much doubt Einstein actually said this, as I've never been able to find a source for it. If you know where this quote comes from, please tell me in the comments.)

I have very mixed feelings about the "everybody's different" meme in education. On one hand, it's (trivially) true -- everybody IS different. On the other hand, I think it causes people to internalize their limitations as part of their identity. "Oh, I'm just not good at art/math/writing/music." Worse, it can cause teachers to give up on certain students.

I've been on the receiving end of this. In seventh grade, I started algebra and went from getting A's in math to getting C's. After a while, I concluded -- with ample support from people around me -- that I simply wasn't a "math person". This lasted until my fourth year of college when, for some reason, I decided to take a mathematical ecology class. To make a long story short, I bombed the midterm and was going to drop the course. When I went to see the professor and started talking about dropping, he just said, "Don't do that. That would be a mistake". He then sat down with me and we spent half an hour going over what I had gotten right on the test and what he thought that meant about my thinking. Result: I got help from a friend who was excelling in the course, earned a B+, and then went back and relearned the algebra and calculus I hadn't mastered earlier. In grad school, I successfully took several undergrad math classes and a large part of my research is now theoretical. So much for being a fish!

The fundamental flaw in the "fish trying to climb a tree" metaphor is the hidden assumption that people have fixed abilities and talents. But this is just wrong. My favorite example of the flexibility of our abilities is John Mighton, who was interested in both math and creative writing as a child, but was discouraged from pursuing them by some low grades and the belief that he would have to have been born a prodigy to do well in either field. Eventually, though, he became an award-winning playwright by deliberate practice, following the example of Sylvia Plath. While trying to make ends meet in theater, he started tutoring kids. His first student was a teenager who had been told by his teacher that he was too dumb to do well in math. (We'll return to him later.)

Mighton ended up creating a program called JUMP Math that allows kids who were far working below grade level to catch up and excel. Even more remarkably, when used as a full-class program, JUMP both increases achievement and drastically shrinks the gap between "stronger" and "weaker" students. It does this by combining careful step-by-step instruction with a strong emphasis on developing self-confidence.

Confidence in one's ability to learn is absolutely critical to learning. My grandfather, a retired engineer who was appalled at my calculus grades, once offered to pay for a tutor for me -- and I declined because I didn't think it would do any good. When a student doesn't believe their work will pay off, doing the minimum amount of work necessary to get by isn't laziness but a perfectly rational strategy. Why waste your time? Conversely, experiments have found that kids who are taught that intelligence can be developed with practice do better in school.

The bottom line: Most of us have the ability to excel in many fields and they can inform each other. While letting kids have time to explore their interests is certainly valuable, we should err on the side of educational breadth. So let's work to find worldchanging ways of teaching that work for everyone!

Oh, and about John Mighton? He ended up going back to school and earning a Ph.D. in mathematics. So did his first student.

What Am I Not Talking About?

2007-12-12T13:00:00.000-08:00

Ahhh, finals. The urge to waste valuable study time on random websites is almost irresistible... so I'm not resisting it. Instead, I give you a list of mondegreens from England Dan and John Ford Coley's song "I'd Really Love to See You Tonight".

Original lyrics:
I'm not talkin' 'bout movin' in
and I don't want to change your life.

Misheard as:
I'm not talkin' 'bout:

forgivin'
the linen / the linens / my linens (How romantic!)
aluminum (chemical element #1)
a live in
bulimia
Lavinia
Malydian (huh?)
Bolivia
committing (At least that makes some kind of sense)
millennia / millennium /millenniums
museum
religion
the limit
'ma lady' (Is that medieval or ghetto?)
John Lennon
Meridian
molybdenum (chemical element #2)
Mullet Inn (Come for the haircuts, stay for the fish?)
a wedding / no wedding
believin'
iridium (chemical element #3. We're into some really obscure ones now!)
my Lydia
my layin' ya (A little too bold for the mood of this song, wouldn't you say?)
my winnings
my livin' / the livin'
the women / my women (Again, not really a soft sell, is it?)
relating
relentin'
that idiot (The speaker or somebody else?)
that idiom
the lily liver (That doesn't even scan!)
the weather (Yes, Virginia, we can get more prosaic than "the linen".)
Aborigine
blamin'
oblivion
bellinin (Try googling it.)
merlinin (Is that a little Merlin?)
mood rhythm
the Lady in Green (Continuing the "mythology of the British Isles" theme.)
the Leonids
the lenient
the weekend
more than friends (Sensible but doesn't scan.)
no Indian (Next line: "And I don't want to join your tribe". Really!)
Marillion
but booty is
relivin'
melanin (More science!)
the lady

Wally Schirra: 1923 - 2007

2007-05-03T19:41:00.000-07:00

Wally Schirra died today.
I'm playing "Fire in the Sky" and "Hope Eyrie" in his honor.

Silly Article About Mushroom Foraging

2007-03-26T20:09:00.000-07:00

A promising-looking article about mushroom hunters in northern California focuses mostly on the "dark side" of the activity -- fines and possible poisonings. While these, particularly the latter, are real threats, people go overboard over them. One spectacularly silly quote, from the director of the Sacramento division of the California poison control system: "If you're going to eat mushrooms, buy them from the store." (Such a kicker sentiment!) Um, how about, "Don't eat anything you haven't positively identified and have an experienced forager accompany you if you're a beginner".

Another paragraph in the article is flat-out dangerous. "Serious hunters eat only what they can identify. Keller said once he learned to identify the distinctive color and sheen of death caps, he noticed them everywhere."

First, it's not just "serious hunters" who eat only the mushrooms they can identify, it's anyone who would rather not be poisoned. Many poisonings occur among immigrants who eat mushrooms that look like edible species from the old country. If you eat wild mushrooms, identify them. To species. And save a sample in case you do get sick.

The second sentence of the above pernicious paragraph is almost as bad as the first. The death caps are members of the genus Amanita and are actually quite easy to identify. In addition to having a fairly distinctive shape and a white spore print, Amanitas have a volva (an underground cup surrounding the stem) and, very often, scales on the cap and a ring around the stem. Maybe some species do have a distinctive sheen, but I wouldn't rely on that for ID.

If you're interested in getting out into the field to study (and eat!) mushrooms, check out the North American Mycological Association.

This Made My Evening

2007-02-24T19:40:00.000-08:00

Human solidarity and the power of international connections, both at their best.

LA Koreans Angry at Anti-Jewish Cartoon - Forbes.com: "Korean-American community leaders said they plan to launch a protest against the publisher of a popular South Korean comic book that contains anti-Semitic images."...
Yohngsohk Choe, co-chairman of the Korean American Patriotic Action Movement in the USA, said, "I don't have words to describe the outrage I feel."
The group met Friday with Rabbi Abraham Cooper, associate dean of the Simon Wiesenthal Center, a Jewish advocacy group. Cooper said he would travel to Seoul on March 15 to raise concerns about the book.

Oekologie Carnival

2007-02-15T20:35:00.000-08:00

Hello and welcome to the (slightly delayed) February 15, 2007 edition of oekologie, the carnival of ecology and environmental science. Let's start off by clarifying what ecology actually is. Jeremy Bruno of The Voltage Gate starts off a series of basic ecological concepts by asking "What Is Ecology? ". My favorite definition is one of the oldest -- the study of how organisms interact with each other and with their environment. It is distinct from environmental science, which focuses on humans and, as Jeremy makes clear, it is a very broad field of study.

From here, let's move to posts on the science of ecology. James Millington at Direction not Destination presents a description of Characterizing wildfire regimes in the United States. Johan A. Stenberg of Insect-Plant Ecology presents a post on the open journal PLoS one and a call for less explanatory factors in experimental ecology. If you read ecology papers, you'll probably get behind that second one!

Yours truly has a post on feedbacks between climate and volcanic activity. You might say this is more Earth science than ecology, but I think anything on global self-regulation is ecologically relevant.

Greg Laden presents two evolutionary biology posts, The Evolution of Human Diet and Models of Sexual Selection. I learned quite a bit from these.

Finally, Marcia Bonta presents Grasslands of Central Pennsylvania. This excellent description of Pennsylvania grasslands and the forces that maintain them leads to our next subject area, natural history.

We start off with two posts from GrrlScientist at Living the Scientific Life. Gyroscopes Tell Moths How to Fly Straight explains, well, how gyroscopes at the base of moth antennae tell them how to fly straight and C'mon Baby, Light my Fire gives us a fascinating look at courtship among fluorescent spiders. Did you know fluorescent spiders existed? Cool! Reigh Belisama at Save The Ribble! has a nice post about a riverside nature walk, Locals Enjoy The Ribble's Winter Wildlife. Finally, Dave at Via Negativa gives us two posts, Bluestem and Forester-think: a brief primer. Both are thought provoking discussions on the relationships between humans and nature, which segues nicely to our third subject area, the environment.

Here, we start off with the ever-controversial subject of exotic species. Mike Bergin at 10,000 Birds, presents What is Wild?, which distinguishes between individual "fugitives" and established populations. On the other hand, Nuthatch at bootstrap analysis gives us shooting mute swans versus mute swans shooting blanks. What has more ethical standing, individuals or ecosystems?

Let's continue the water theme for a while. Don Bosch, The Evangelical Ecologist, presents The Desert Blooms, a piece about the recovery of marshes in Iraq and the establishment of Iraq's Ministry of Environment. Garry Peterson at Resilience Science discusses the role of an obscure fish in coral reef recovery from an algal-dominated state in Hidden Ecological Functions and Ecological Hysteresis. Jennifer Pinkley at The Infinite Sphere gives us Karst geology and water pollution and Sewage treatment plant on karst floodplain??? .

What can we do to protect the environment? Wenchypoo at Wisdom From Wenchypoo's Mental Wastebasket presents an appropriately contrarian post titled Green is Making Me See Red. Meanwhile, Vihar Sheth at green | rising discusses the environmental benefits of vegetarianism in You Are What You Eat.

On the political level, Justin Lowery at blog4brains.com presents America: Pro-Immigration? Then Pro-Oil Dependence!. Vihar Sheth at green | rising presents Wasted Gas, on the use of landfill methane. John Feeney at Growth is Madness! points out that the problem isn't population or consumption, it's both, in An unholy matrimony. And Marcelino Fuentes at Biopolitical brings up the issue of scientific uncertainty at Crichton, Laurance, Lomborg, and their agendas .

We finish up on a light note. Avant News presents Ostrich Charged With Multiple Ostricides posted at Avant News, saying,

That concludes this edition. Submit your blog article to the next edition of oekologie using our carnival submission form. Past posts and future hosts can be found on our blog carnival index page.

Climate Affects Volcanoes, Volcanoes Affect Climate...

2007-01-02T09:37:00.000-08:00

We know that volcanic eruptions can change the climate. The ash they throw up into the atmosphere blocks sunlight, cooling Earth. (The 1815 eruption of Mount Tambora in Indonesia caused the "Year Without a Summer" in Europe and North America -- and led to the writing of Frankenstein.) But can climate affect volcanic activity? Several discoveries reported in 2006 say yes.

The first discovery concerns isostatic rebound after glaciation. The rock continents are made of is less dense than the molten rock of the mantle, so continents float on the mantle like a rubber duck floats in your bathtub. Push down on the rubber duckie, or put an ice sheet on top of the continent, and they sink a little bit. When the ice sheet melts, the continent slowly rebounds to its former height. Patrick Wu of the University of Calgary have found links between isostatic rebound and seismic activity. Wu's research indicates that melting ice makes earthquakes, and maybe even volcanic eruptions, more likely as the crust rises to its new equilibrium height.

The work of Allen Glazner, of the University of North Carolina, is even more dramatic, finding a possible link between the dry climate of interglacial periods and supervolcanoes. Essentially, rainfall and groundwater can cool a volcano's magma chamber, making it less likely to build up the amounts of magma needed for a supereruption.

Let's look at this a bit more closely. Interglacial periods are warm and dry, which, according to this new work, makes volcano eruptions more likely. Volcanoes produce both suspended particles, which cool the Earth, and carbon dioxide, which warms it. Depending on which effect is more important in the long run, we may have a climate-stabilizing or destabilizing feedback loop. Either way, the connections are intricate and interesting. I look forward to learning more about this topic.

The Real Reason for "Happy Holidays"

2006-12-25T16:49:00.000-08:00

Thank you, Bill O'Reilly. For the last two years, the normally pleasant holiday season has been polluted by heated arguments over a purported "War on Christmas". The allegation, for those of you living under rocks, is that political correctness is forcing Christmas out of the public sphere and "Merry Christmas" is being replaced by the generic "Happy Holidays".

Never mind that New Year comes just a week after Christmas and "Happy Holidays" can easily be understood to mean "Merry Christmas and Happy New Year". Christians who see themselves as victims of the "Happy Holidays" phenomenon insist that its purpose is to avoid offending folks who don't celebrate Christmas by avoiding explicit mention of it.

But is that really what's going on? I grew up in a secular Jewish family and was never offended by people wishing me a merry Christmas. Geoffrey Pullum of Language Log points out that neither are most people who don't observe the holiday. But there is more to saying "Happy Holidays" than just avoiding reference to a particular one.

Think back to the brouhaha over the removal of Christmas trees from Seattle-Tacoma Airport. (BTW, folks, a Christmas tree is not a Christian symbol. It's an adopted pagan custom, like Easter eggs.) That unfortunate decision was triggered by an Orthodox Jewish rabbi's request that the airport display a menorah along with its Christmas trees. The rabbi never asked for the removal of the trees. He simply wanted another holiday included.

The key word here is "included". Yes, very few non-Christians will be offended at hearing, "Merry Christmas" or seeing a Christmas tree. But it is nice to hear a greeting that you can interpret as including your holiday, whether that's Christmas, Hanukkah, Diwali or Eid al-Adha. In the same vein, I have no objection to public holiday displays, as long as they include symbols of many of the religions practiced in a community and secular holidays like New Year and Winter Solstice.

With this shift in viewpoint, I hope we can call a truce in the Christmas Wars. Now, can someone please explain "Season's Greetings" to me?

Tribute to Carl Sagan

2006-12-20T12:52:00.000-08:00

Today is the ten-year anniversary of Carl Sagan's death and he is being memorialized in the blogosphere. Here is my own little contribution:

Sometime in the eleventh grade, I was browsing the shelves of my local public library and came upon a copy of Pale Blue Dot. That was not my first encounter with Carl Sagan's work -- I had read The Dragons of Eden a couple of years earlier -- but it was the one that took. I read Pale Blue Dot, renewed it and reread it. Reaching the renewal limit, I brought the book back -- and checked it out again on my very next library trip. (Of course, I was reading Sagan's other books at the same time.) I eventually bought a softcover copy of Pale Blue Dot, wore it out in a couple of years and finally invested in a hardcover edition.

What about that book captured my attention so durably? It wasn't just the fascinating descriptions of the Solar System or the luminous visions of future space exploration. What touched me the most was Sagan's sense of the unity of humankind. We occupied a tiny mote of dust in a vast Cosmos, and the way we treated each other had to reflect that. Against the backdrop of space, all the subgroups of Homo sapiens are essentially one. Sagan wrote:

Look again at that dot. That's here. That's home. That's us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. The aggregate of our joy and suffering, thousands of confident religions, ideologies, and economic doctrines, every hunter and forager, every hero and coward, every creator and destroyer of civilization, every king and peasant, every young couple in love, every mother and father, hopeful child, 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 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 this pixel on the scarcely distinguishable inhabitants of some other corner, 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.

If you have a high-bandwidth connection, please watch the YouTube video below. Quite honestly, it gave me goosebumps.

Imagining the Future We Want

2006-12-06T18:01:00.000-08:00

Chris Clarke of Creek Running North asked readers to describe what the world would look like "if our side won". We're not talking about getting out of Iraq or implementing Kyoto but about having a vision. What kind of world do we really want to live in?

Several years ago, I ran a few Future History Project workshops in which participants imagined the world they wanted to exist in a hundred years and then outlined its history. The article below describes one such experience. (WFA is the World Federalist Association, which has since transmogrified itself into the much less visionary Citizens for Global Solutions.)

Conversations for a Century
by Jane Shevtsov

What happens when we set aside the problems of the present and give ourselves permission to dream?

  "It is now the year 2102. What are your favorite things about the world right now?" I ask this question at the beginning of the Future History Project workshop Tad Daley and I are conducting at WFA's October 2002 assembly in Denver. The thirty or forty people attending spend the next five minutes writing about a time when the troubled years of the early 21st century are safely in the history books.
  Why are we indulging in these flights of fancy when there are so many pressing issues right here and now? When the president seems hell-bent on bombing an already suffering nation, when the global climate is changing unpredictably and the rate of extinction is higher than at any point in the past 65 million years, when tens of thousands of children die every day from fully preventable causes, what is the use of speculation about a better world a century hence?
  The very existence of these problems makes it important to dream of a world without them. Once we envision a world in which problems like these do not exist, we can see why they do not exist. And the Future History Project goes more deeply into this than most other visioning processes because Future History participants develop the history of that happy world of 2102. They draw a road map from here to utopia.

  Such grandiose plans can be difficult to get into. So right after brainstorming, I ask participants a simple question. I ask them what their community is like.
  My co-facilitator corrects me immediately. What do I mean by community?
  It is a good question, since even now, virtual communities are important and growing exponentially. So I define community as both physical neighborhood and any virtual communities to which you belong.
  After a few questions, the discussion takes on a life of its own. Occasionally Tad and I remind people of the ground rules -- if it's desirable and doesn't break the laws of physics, then it's possible; no miracles or aliens, "now" is 2102 -- but mostly we're just along for the ride, keeping order and taking notes but letting ideas flow.
  People speak of social contracts and sustainable architecture, of food and livelihood. This being WFA, government, particularly global government, gets much attention. (At a Future History Project, sometimes a person who has no idea world federalists even exist will be the first to bring up global government.) We discuss schools, families and values -- especially values. People seem eager to discuss a shift to more inclusive, communitarian values.

  After about 45 minutes, we shift gears. It is time for the hard part -- inventing the history of 2102. A timeline hangs on the wall and we try to fill it in, going backwards from 2102 to 2002. As co-facilitator, I try to get people to think in terms of logical steps -- A had to happen before B could occur -- but mostly people just want to fill in that blank sheet.
  And fill it in they do. We go to Mars in 2012. In 2032, a reformed UN General Assembly becomes a world government. By 2042, everyone uses renewable energy. And so on.

  It's over too soon. Ten minutes of written and shared reflection and we go our separate ways. But people leave inspired. Utopia is not impossible -- it's just very, very improbable. And the improbable happens.

The Creek is Running Again!

2006-10-24T16:38:00.000-07:00

Creek Running North is back up after dealing with anonymous threats. What does the writer's dog have to say about it?

"When I brush Chris’ cactus plants
I sometimes wince or cry aloud,
But for an online thug? Fat chance.
My leg is lifted, and bow-wowed."

Threats Against a Blogger

2006-10-23T20:12:00.000-07:00

Creek Running North, to which I have linked several times, is down. Its owner, Chris Clarke, who is an environmentalist and progressive activist, has had his dog threatened. From prior experience, Chris does not expect the police will be of any help. In a comment on Pharyngula (you'll have to scroll down), he writes:

"My blog is one of the least important things I do. Becky and Zeke are up top, and quite honestly Zeke's impending demise makes him edge Becky out, as he's edged me out in Becky's priorities. In descending order after that: a few good friends, my longer-term writing projects, political activism, my day job, hiking, my blog. I appreciate the fact that my blog has fans. But really now. My effective speech takes place at my day job and doing politics. I am not one of those people who has confused writing a blog post with political activism."

About the only thing I disagree with in that is the last sentence. If you have an audience, blogging can indeed be political activism. Although it probably won't influence decision-makers directly, it may well help awaken your fellow citizens. Chris' blogging has done this to me more than once.

This whole situation has made me think about threats to bloggers, particularly in repressive societies. The Committee to Protect Bloggers has shut down, although the people behind it are doing related work. The Electronic Frontier Foundation has some information on bloggers' rights, but it appears to be mostly written for US readers and toward avoiding civil lawsuits and other relatively mild consequences. Is there anything else out there, in the US or elsewhere?

Good luck, Chris, and I hope the creek starts running again soon.

Rediscovering a Favorite Song

2006-10-22T13:13:00.000-07:00

I have a confession to make: I don't like Charlotte's Web. At least, I didn't care for it in the third grade, when my class read it. (I disliked all fantasy and fairy tales at the time.) However, seeing the movie was completely different and one song from the film has stayed with me to this day. And a couple of days ago, I finally got around to looking it up.

The song is called "How Very Special are We" and is a gentle, poetic lyric about the seasons and the cycle of life. There doesn't seem to be a formal site of Charlotte's Web soundtrack lyrics, but a user going by TherealRNO has posted the words to "How Very Special are We" in an Amazon.com review. There's also a short clip of the song at reelclassics.com.

Here are the words:

How very special are we
For just a moment to be
Part of life's eternal rhyme
How very special are we
To have on our family tree
Mother Earth and Father Time

The summer larks return to sing
Oh, what a gift they give
The autumn days grow short and cold
Oh, what a joy to live

He turns the seasons around and so she changes her gown
But they always look in their prime
They go on dancing their dance of ever-lasting romance
Mother Earth and Father Time

How very special are we
For just a moment to be
Part of life's eternal rhyme
How very special are we
To have on our family tree
Mother Earth and Father Time...

The autumn days grow short and cold
It's Christmastime again
The snows of winter slowly melt
The days grow long
And then

He turns the seasons around and so she changes her gown
Mother Earth and Father Time
How very special are we
For just a moment to be
Part of life's eternal rhyme

Friday Random Ten

2006-10-13T10:30:00.000-07:00

Emerald Rose, "Penny in the Well". A warm song about searching for fulfillment.
Tim McGraw, "Tiny Dancer". I like this version of the song.
Alabama, "Fiddle in the Band". Can you listen to this and not tap your toes?
John Denver, "Islands"
Jackson Browne, "Running on Empty". A very LA song about growing up.
Bruce Cockburn, "All the Diamonds in the World". Gentle and lyrical.
Vladimir Vysotsky, "Vyet Eto Nashi Gory (These are Our Mountains)". Russian song that tells of a WWII battle in which Soviet alpine fighters faced German soldiers they themselves had trained. Has anybody tried to translate Vysotsky into English?
John Denver, "Rhymes and Reasons". The first John Denver song I ever heard and still one of my favorites. Hopeful and comforting.
Trisha Yearwood, "Real Live Woman". An honest, solid song that matches Yearwood's style perfectly.
The Highwaymen, "Against the Wind". Good song, but I like Bob Seger's version better.

Now I'm off to the Smokies!

What Does It Feel Like to be On Top of a Nuclear Test?

2006-10-10T19:56:00.000-07:00

Since North Korea claimed to have tested a nuclear weapon on Monday, geologists and policy wonks have been wondering why the tremor the detonation caused was so small. Was the bomb small, not very good, or fake -- simply a pile of regular explosives? While the authorities study and debate, I am struck by the surrealness of the situation. Human beings have weapons that imitate tectonic plate movements!

I grew up in southern California and have been through several earthquakes, including the magnitude 6.6 Northridge Earthquake in 1994. When I read about the North Korean nuclear-seismological debate, I wondered what it would feel like to be on top of an underground nuclear test.

To find out, I combined a Wikipedia chart of the Richter scale magnitudes of various earthquakes and explosions with a chart giving rough conversions between earthquake magnitudes on the Richter scale and their felt intensities on the Modified Mercali Scale. Here is the result.

Event	Richter magnitude	TNT Equivalent	Intensity
WWII conventional bombs	1.5	178 kg (392 lb)	Detected only by seismographs
late WWII conventional bombs	2.0	1 metric ton	Detected only by seismographs
WWII blockbuster bomb	2.5	5.6 metric tons	Detected only by seismographs
Small atomic bomb	4.0	1 kiloton	Resembling vibrations caused by heavy traffic.
Nagasaki atomic bomb	5.0	32 kiloton	Sleepers awakened and bells ring.
Little Skull Mtn, NV Quake, 1992	5.5	178 kilotons	Trees sway, some damage from overturning and falling objects.
Double Spring Flat, NV Quake, 1994	6.0	1 megaton	General alarm, cracking of walls.
Northridge quake, 1994	6.5	5.6 megatons	Chimneys fall and there is some damage to buildings.
Tsar Bomba, largest thermonuclear weapon ever tested	~7.0	50 megatons	Ground badly cracked and many buildings are destroyed. There are some landslides.
Landers, CA Quake, 1992	7.5	178 megatons	Ground badly cracked and many buildings are destroyed. There are some landslides.

Friday Random Ten

2006-10-06T18:57:00.000-07:00

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

2006-10-03T21:03:00.000-07:00

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

2006-10-01T07:59:00.000-07:00

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?

2006-09-29T18:51:00.000-07:00

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

2006-09-29T18:09:00.000-07:00

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?

2006-09-27T21:22:00.000-07:00

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

2006-09-26T20:11:00.000-07:00

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

2006-09-25T18:39:00.000-07:00

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

2006-09-25T18:33:00.000-07:00

A lizard and a dolphin.

WorldChanging On E. coli Spinach

2006-09-23T09:14:00.000-07:00

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

2006-09-22T17:28:00.000-07:00

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?

2006-09-21T19:54:00.000-07:00

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

2006-09-20T20:39:00.000-07:00

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

2006-09-17T19:26:00.000-07:00

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

2006-08-04T20:39:00.000-07:00

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

2006-08-03T23:23:00.000-07:00

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

2006-08-02T19:54:00.000-07:00

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

2006-08-02T12:23:00.000-07:00

Check out the new Tangled Bank at Science and Reason.

A Blogger After My Own Heart!

2006-08-01T00:31:00.000-07:00

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!

2006-07-31T23:28:00.000-07:00

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

The Parasite Web

2006-07-31T13:01:00.000-07:00

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?

2006-07-31T12:55:00.000-07:00

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!

2006-07-30T23:13:00.000-07:00

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

2006-07-29T14:57:00.000-07:00

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...

2006-07-29T14:45:00.000-07:00

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

2006-07-28T23:15:00.000-07:00

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

2006-07-26T11:31:00.000-07:00

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

2006-07-25T00:18:00.000-07:00

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

2006-07-23T23:07:00.000-07:00

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.

Farting Alien Cows?

2006-07-21T13:28:00.000-07:00

Steinn Sigurðsson at Dynamics of Cats has a great post with a title I couldn't possibly hope to top: "What if Cows Don't Fart in Space?". It's all about finding planets with life by examining their atmospheres. The problem is picking appropriate biomarkers.

We currently are limited to remote sensing, which pretty much boils down to optical and near-IR spectroscopy, so we're looking at upper atmosphere molecules.

Well, first thing to look for are atmospheres out of chemical equilibrium; but that in itself is not sufficient as a biosignature, since there is significant flow of free energy from the star, and photolytic chemistry can produce chemical disequilibrium, including molecular oxygen.

But how far out of chemical equilibrium could you get without life? It doesn't seem to happen too much in our solar system. Not only, as Lovelock pointed out, does life have to use its environment to obtain resources and dump wastes, living things tremendously increase the surface area available for various interesting reactions. Maybe each planet should be compared to others in the same solar system.

Sigurðsson continues:

Now, 'we' think we understand photolytic gas chemistry, and bottom line is that if you see oxygen (or ozone proxy) AND methane, in the presence of water (and we expect some carbon dioxide as well), then we have carbon based photosynthetic life... or some funky chemistry we didn't predict.

BUT, for a large fraction of the Earth's history, there was no significant photosynthesis, and life utilized anaerobic metabolism, but it was still life.

So, what is that signature: we're talking methanogens, free-hydrogen metabolising critters, others living on sulphur compounds or metal ions. We don't even know what the Earth's atmosphere was like at different stages in the archaean, much less what the range of possible atmospheres was which was consistent with pre-aerobic life.

OK, so that should be corrected to read, "for a large fraction of the Earth's history, there was quite a bit of photosynthesis and it was even oxygenic, but the oxygen was getting mopped up by iron until the iron ran out". Still, it's a valid point and a fascinating question. What set of characteristics would allow us to distinguish a planet with life from one without it?

Friday Random 10

2006-07-21T11:07:00.000-07:00

Dar Williams, "If I Wrote You"
Jackson Browne, "Lives in the Balance". Written in the 80s but oh, so timely. "I want to know who the men in the shadows are. I want to hear somebody asking them why they can be counted on to tell us who our enemies are, but they're never the ones to fight or to die."
Leslie Fish, "Grandma Went Out With a Bang". I know this one's come up before. One of the funniest songs ever written!
Animaniacs, "Noel". Animaniacs take on the Christmas song. It's July? Oh well.
Kathy Mar, "Daughters and Sons". Struggling for progress takes generations.
Jackson Browne, "Rock Me on the Water". Getting through times of change.
Karen Linsley, "The Challenge". A tribute to the astronauts killed in the Challenger explosion.
Gaia Consort, "Every Sacred Thing". We live in a sanitized society.
John Denver, "What One Man Can Do". Written in honor of Bucky Fuller.
Animaniacs, "The Presidents". Yes, I like Animaniacs songs.

Time Won't Drive Us Down to Dust Again

2006-07-20T23:28:00.000-07:00

Today is the 37th anniversary of the Apollo 11 moon landing. Please listen to Leslie Fish's song, "Hope Eyrie". (The title is a bit of a pun -- "eyrie" means "eagle nest".) The lyrics are below:

Worlds grow old and suns grow cold
And death we never can doubt.
Time's cold wind, wailing down the past,
Reminds us that all flesh is grass
And history's lamps blow out.

CHORUS:

   But the Eagle has landed; tell your children when.
   Time won't drive us down to dust again.

Cycles turn while the far stars burn,
And people and planets age.
Life's crown passes to younger lands,
Time brushes dust of hope from his hands
And turns another page.

CHORUS

But we who feel the weight of the wheel
When winter falls over our world
Can hope for tomorrow and raise our eyes
To a silver moon in the open skies
and a single flag unfurled.

CHORUS

We know well what Life can tell:
If you would not perish, then grow.
And today our fragile flesh and steel
Have laid their hands on a vaster wheel
With all of the stars to know

CHORUS  That the...

From all who tried out of history's tide,
Salute for the team that won.
And the old Earth smiles at her children's reach,
The wave that carried us up the beach
To reach for the shining sun.

CHORUS  For the...

When Statistical Mistakes Don't Matter

2006-07-19T23:47:00.000-07:00

The famous "hockey stick" reconstruction of Northern Hemisphere temperatures over the last 600 years has recently come under fire because of an error in using a statistical technique called principal components analysis. RealClimate points out that this really doesn't matter. At a Congressional hearing on the subject, "no-one (with sole and impressive exception of Hans von Storch during the Q&A) went on to mention what the effect of the PC centering changes would have had on the final reconstruction - that is, after all the N. American PCs had been put in with the other data and used to make the hemispheric mean temperature estimate. Beacuse, let's face it, it was the final reconstruction that got everyone's attention. Von Storch got it absolutely right - it would make no practical difference at all."

Tangled Bank #58

2006-07-19T14:21:00.000-07:00

The new Tangled Bank is up at Salto sobrius. Check it out! I particularly like Daniel Collins' short but sweet post about erosion, carnivores and Aldo Leopold. Also, I want to welcome everybody visiting Perceiving Wholes for the first time. Please leave a comment and tell me what you think!

Causes, Effects and Networks in the Genome

2006-07-17T12:34:00.000-07:00

Carl Zimmer at the Loom has a great piece on
gene expression networks in E. coli. It turns out that a particular pattern of connections, called a feed-forward loop, is common in the E. coli genome. Since feed-forward loops act as noise filters, the scientists who originally found them in bacterial genes thought they evolved for that reason. That, however, may not be the case:

"A few days ago Dutch scientists launched another attack on the feed-forward loop, called simply 'Feed Forward Loop Circuits as a Side Effect of Genome Evolution'....

The Dutch scientists wondered whether an abundance of feed-forward loops could emerge spontaneously, even if natural selection was not favoring them... They built a network of genes, each of which had sites at which proteins could bind to them and cause them to be expressed. They then allowed the network to evolve according to rules based on what scientists know about how actual genes evolve. The genes could lose their binding sites or they could acquire an extra copy of a binding site. The entire genome could be accidentally duplicated. Genes sometimes disappeared, and sometimes proteins that switched on one gene began to switch on another.

Initially the model produced a random network, which came as no surprise... But over time, something odd occurred. Some genes began to get more and more connected to other genes. And after about 100 generations, a large number of feed-forward loops appeared in the network, in what the scientists liken to an avalanche... The scientists did not have to build in any advantage to feed-forward loops that could make them the object of natural selection. They emerged spontaneously from mutating networks. 'Selection on individual circuits,' the scientists conclude, 'is not needed to explain their abundance.'"

What interests me is not so much the origin of the feed-forward loops as their function. Even if the loops originated as byproducts of other evolutionary processes, are they useful to the organism that has them? Do they still work as noise filters?

These kinds of functional questions are important in the study of food webs, which almost certainly don't evolve by natural selection but do link the species in an ecosystem to each other. How does network structure affect ecosystem dynamics?

On World Government and Being an Oddball

2006-07-16T19:44:00.000-07:00

"Hope and hardship and a worthy task
That's all I offer and it's all I ask"
--Echo's Children, "The High Frontier"

Yesterday, I came to the annual meeting of the Southern California chapter of Citizens for Global Solutions, which went rather better than I expected. CGS is a descendant of the World Federalist Association, which itself used to be known as the United World Federalists. During the movement's 1940s heyday, it counted Albert Einstein and E.B. White as supporters; Isaac Asimov was a world federalist until the end of his life.

Today, global government is not a mainstream issue. The overwhelming majority of people are neither for it nor against it -- they've simply never seriously thought about it. The basic idea is simple. World federalists believe we need a system of democratic global governance on top of (not instead of) national governments. Such a system would provide enforceable legal mechanisms for resolving conflicts, protecting human rights and safeguarding the environment. Present-day countries would be in a position similar to that of US states or Swiss cantons.

The idea may be simple but its consequences would be profound. The two that resonate most deeply with me are abolishing war and allowing freedom of movement. When speaking on the subject, my good friend Tad Daley likes to say, "It is within the power of the human imagination to envision abolishing war itself". Why not? When formerly independent, sovereign entities unite politically, armed forces beyond police become unnecessary. Their borders no longer need to be defended and people are free to come and go. It is from this freedom that World Beyond Borders, the global government website I co-founded with Eli Williamson-Jones, takes its name.

Although technology is bringing the world closer together, global government is a long way off -- a couple of decades at best, centuries at worst. Much of the work to be done is simply raising awareness -- trying to get the idea of global government into the public eye. The rest consists of changing international institutions such as the UN and working toward the basic levels of democracy and economic development that will allow a stable world democracy to exist.

Working on such a generational project is not for everyone. It takes courage, imagination and the ability to stand alone. I am reminded of physicist Charles Sheffield's words about space exploration:

"If you want to be on the leading edge of anything, you have by definition to be a couple of standard deviations away from most people. That makes you an odd-ball. The trick is to learn to accept it, then to like it -- and keep on making lots of noise for what you believe in."

Majoring in Organic Farming?

2006-07-16T00:00:00.000-07:00

How does WorldChanging find this cool stuff? Today, they let us know that Washington State University is now offering a major in organic farming!

Virology with Attitude!

2006-07-14T12:31:00.000-07:00

I've done some work modeling HIV infection, so I really enjoyed the rebuttals to HIV deniers on Moment of Science.

Mushroom Photos

2006-07-14T12:22:00.000-07:00

Via Negativa has posted some truly artistic photographs of mushrooms. Check them out!

Friday Random 10

2006-07-14T10:47:00.000-07:00

Jackson Browne, "These Days". A simple, sad song. "Don't confront me with my failures -- I had not forgotten them."
Bruce Cockburn, "The Coldest Night of the Year"
Lonestar, "Mr. Mom". The trials and tribulations of a guy staying home with the kids.
Johnny Cash, "Jackson". A sassy duet with June Carter Cash.
John Denver, "The Flower that Shattered the Stone". Expresses a gentle sense of wonder.
Jackson Browne, "Lawyers in Love" A song about yuppies? Very '80s!
Gaia Consort, "Cry Freedom". One of their best. "Do you trust a creed that claims to set you free by spending half a lifetime begging on your knees?"
Trisha Yearwood, "X's and O's".
Alabama, "Dancin', Shaggin' on the Boulevard". Sweet beat!
Jackson Browne, "The Naked Ride Home"

The Jellyfish Takeover

2006-07-13T21:56:00.000-07:00

Off the southwestern coast of Africa, a current flowing from the east hits land and forms an upwelling that brings cold, nutrient-rich water to the surface. These nutrients, promote plankton growth and the plankton, in turn, supports a productive fishery. Or, at least, it used to.

In the 1980s, the Namibian sardine and anchovy fisheries collapsed from overfishing. With fish populations down, jellyfish thrived. Freed from predators and competitors, they took over the place to the point where a recent study estimated that the Namibian continental shelf supported 3.6 million tons of fish -- and 12.2 million tons of jellyfish!

The authors of the study credit the jellyfish population explosion to the removal of competitors, but I think predators may be playing a role. In their trawls, 99% of jellyfish (by weight) were one species, Aequorea forskalea. To me, this hints at the removal of a predator, since classic field experiments have found that predators help maintain biodiversity by keep superior competitors from getting too common. I do not know of evidence for a similar effect with competitors.

The difficulty with this idea is that not much eats adult jellyfish. I certainly don't think sardines or anchovies do. But what if these fish helped support a jelly predator? (Sea turtles?) Alternatively, it's possible that zooplankton-eating fish, which include the aforementioned sardines, consume jellyfish larvae, keeping populations under control.

To be fair, the authors' hypothesis is not impossible. If one or more kinds of fish competed mainly with A. forskalea rather than other jellies, then removing that competitor would have the observed effect. Alternatively, it could be that A. forskalea was just as dominant before overfishing began, although it would mean the other jellyfish species were extremely rare. Further investigation of this question could yield scientifically interesting results.

Jelly populations are rising from the Bering Sea to the Gulf of Mexico to the Black Sea. The causes appear different in each place (although overfishing may have played a role in the Black Sea), but it looks like jellyfish have what it takes to take advantage of disturbed ecosystems. Somewhat worryingly, it looks like they may delay the recovery of fish stocks by consuming eggs and fry. While it doesn't look like much can be done with existing jellyfish blooms, preventing overfishing and bioinvasions should be priorities for keeping the gelatinous predators under control.

Paradoxical Screenshot

2006-07-11T21:23:00.000-07:00

Seen while submitting a paper to the Journal of AIDS:
'

What's the proper response here? How about, "The following comment is not a comment"?

Real Headline!

2006-07-09T18:29:00.000-07:00

Isn't it nice when businesspeople know biology?
Rare flower found on site is a plant, says developer

Friday (OK, early Saturday) Random Ten

2006-07-08T00:22:00.000-07:00

Collin Raye, "A Bible and a Bus Ticket Home"
Tim McGraw, "Drugs or Jesus". A weird, emotional song. Tim McGraw sings it like it's just a religious song... but it compares Christians to drug addicts! I'm honestly surprised it got much play on mainstream country radio.
John Voorhees, "A Sad Man". Spare melody, poetic lyrics. Good stuff.
Collin Raye, "One Desire"
Jo Dee Messina, "You're Not In Kansas Anymore". As an Angeleno, I really like this one.
Leslie Fish, "Grandma Went Out with a Bang". Grandma the radical and her plutonium-powered pacemaker...
Rainbow Warriors, "Rainbow Warriors". Based on a Hopi prophecy, although I don't know how authentic it is. A bit preachy but otherwise good.
Dar Williams, "When I was a Boy". How do we get stuck in narrow gender roles?
the Wilkinsons, "26 Cents". Rather similar to today's first song.
Paul Metsa, "Jack Ruby". A biographical story song.

Blog Carnival Update!

2006-07-05T19:41:00.000-07:00

Perceiving Wholes is being featured on two blog carnivals! The Tangled Bank links to "Nature Green in Leaf and Shoot" and Carnival of the Liberals has "Left, Right and What?". I want to welcome my new readers and encourage the rest of you to check out these excellent compilations.

A Thought for the Fourth

2006-07-04T12:54:00.000-07:00

We hold these truths to be self-evident,
  that all men are created equal,
  that they are endowed by their Creator
    with certain unalienable Rights,
  that among these are Life,
    Liberty
    and the pursuit of Happiness,

--That
to secure these rights,
  Governments are instituted among Men,
    deriving their just powers from the consent of the governed

What if we applied this to the world?

EarthBall Ironies

2006-07-03T23:17:00.000-07:00

"At a few hundred kilometers altitude, the Earth fills half your sky, and the band of blue that stretches from Mindanao to Bombay, which your eye encompasses in a single glance, can break your heart with its beauty. Home you think. Home. This is my world. This is where I come from. Everyone I know, everyone I ever heard of, grew up down there, under that relentless and exquisite blue." --Carl Sagan, Contact

I've long been fascinated by world maps and photographs of Earth from space -- and taking a geography class that put them in historical perspective didn't help the situation. So, when I saw the EarthBall, it was a must-buy.

An EarthBall is an inflatable photographic globe. The image on the ball is a composite of satellite photographs, since you cannot take a picture of the whole planet at once. This means there was never a moment when the clouds, oceans and continents looked precisely the way they do on my globe. Yet this depiction of Earth is much closer to reality than a conventional globe would be. There's a nice paradox here. In order to approach the truth, you have to lie.

Exact photographic veracity aside, the EarthBall is lovely. Subtle shades of brown, green and blue convey the rich diversity of environments on Earth. (Look at the African rift lakes in the photo.) Cloud patterns suggest air circulation. Although the cities on my EarthBall don't glow in the dark the way they're supposed to, you can still see clusters of human settlements. All in all, it's a wonderful globe.

The EarthBall comes with an edicational handbook that combines information, games and quotes, mostly from astronauts. My favorite part is the list of tips on caring for the globe:

The EarthBall does not like extremes in temperature. A hot stove or very, very cold weather can be harmful. For optimum operating temperature try to maintain an average distance of 92 million miles to the sun.
Toxic chemicals can also damage your EarthBall and pollute valuable groundwater supplies, lakes, streams, and oceans. Avoid exposure to these. An abundance of fresh, clean water is very beneficial.
Excess radiation is extremely hazardous. Do not expose your EarthBall to unnecessary nuclear warfare or nuclear power plant accidents.
Too much ultraviolet radiation can also be harmful. Avoid excessive sunlight and ozone depleting substances.

There's just one problem that I must discuss. Opening the package the EarthBall came in released a very strong chemical smell that clung to the ball for several days. I don't know what it is, but anything that smells that irritating can't be good for you. Worse, according to the packaging, the EarthBall is made of vinyl and while that word can refer to several types of plastic, it most commonly means PVC.

PVC is an environmental bad actor. Like almost all plastics, it's made out of fossil fuels. It is hard to recycle, releases poisons when burned and usually contains toxic additives. Worst of all, its manufacture and incineration produce extremely toxic chemicals known as dioxins. Dioxins disrupt hormones in the body and have been linked to cancers, reproductive problems and immune system dysfunction in humans and wild animals.

Ironically, dioxin is a truly global pollutant. Being stable and fat-soluble, dioxin that gets into the environment travels through food chains and ends up in top carnivores, particularly in the Arctic. Inuit people who eat fish and marine mammals are exposed to especially high dioxin concentrations.

I've come full circle in this post. Images of global interconnectedness are powerful and necessary, but we must act on the reality of that interconnectedness. (Here, that might mean using a more benign plastic or natural rubber.) I will continue to enjoy and learn from my EarthBall -- and hope that in the future, its message might change its medium.

Left, Right and What?

2006-07-01T00:36:00.000-07:00

I just finished watching the 20/20 special on political polarization in the US and feel rather conflicted about it. On one hand, I understand the need for people with different political views to be able to talk to one another. On the other hand, this "meta" position isn't enough. I have strongly held political views myself, and most of them are quite liberal. I really think that we as a society would be better off with, for example, more social freedoms and a more equal distribution of wealth. People with views opposite mine are, for the most part, just as sincere. So where do we go from here?

The first thing that comes to mind is the inadequacy of the "left-right" political spectrum. The folks at the Political Compass have designed a two-dimensional system that rates a person as being more authoritarian or libertarian on separate social and economic scales. (I might add a "parochial-cosmopolitan" axis.) Science fiction writer and physicist David Brin has some great stuff on his blog about alternative models of politics and lots of provocative ideas about what modern societies need to prosper.

Unfortunately, the American political system enshrines the left-right dichotomy in its two major parties. The Democrats and Republicans present us with packages of issues that may be completely unrelated (what does gay marriage have to do with the war in Iraq?), but most of us feel we have to choose one or the other. In Europe and much of the rest of the democratized world, citizens have more choices in selecting a party that truly represents their views, but Americans appear to be stuck with two. I remember doing a short presentation on the Green Party in my high school government class. Greens are fairly left-wing on most issues, but my teacher pointed out that two of the party's Ten Key Values, decentralization and personal responsibility, are traditionally associated with conservatives, at least in the US. The Green Party is not centrist but it does take on elements of several philosophies.

While there are several reforms I could recommend, especially instant runoff voting (you rank several candidates in order of desirability) and the prevention of gerrymandering, I don't think it's enough in the long run. If voters are getting more polarized, why are there so few supporters of creative, potentially radical ideas in Congress? Why do so few Democrats campaign for universal health care or the Department of Peace? I don't know, but merely responding to the issues of the day is not going to get us through this century. This is where sites like WorldChanging.com come in.

WorldChanging is a repository of ideas, inventions, tools and projects for a better world. Reading it, you become excited about Brazil and India. You learn about green buildings, serious games and dialogue. WorldChanging's strength and weakness is that it's non-political, but there are websites with a similar spirit that include politics. Check out the Radical Middle and the Global Ideas Bank -- and start working for something new. In the end, we won't meet in the middle, but we may reach higher ground together.

Friday Random 10

2006-06-30T09:46:00.000-07:00

Sorry for not posting much this week. I've been crazy busy but hope to make up for it next week and possibly this weekend. There's good stuff in the pipeline!

And now, without further ado, the random ten:

Echo's Children, "How Far Back Does Music Go?". A neat a capella song from an unfortunately disbanded duo.
John Denver, "Rhymes and Reasons". One of my all-time favorites.
Alan Jackson, "Midnight in Montgomery". Talk about atmosphere!
ARKA, "Tear Down the Walls". A Chilean rock group sings about "tearing down the walls" that divide us. Bury your chains! (In English.)
Bruce Cockburn, "When the Sun Falls"
Vince Gill, "Worlds Apart". Sweet, sad and wise.
Larry Warner, "The Archivist". A filk song of a wasted life.
Kathy Mar, "The Word of God". Evolution vs. creationism. "Humans wrote the Bible; God wrote the rocks!"
Animaniacs, "Several Drops of Water". Remember Animaniacs? A cartoon take on the water cycle.
Collin Raye, "Sweet Miss Behavin'". Fun!

Stars to Brains

2006-06-27T23:41:00.000-07:00

Just a quickie tonight. There's a post on illuminating science about a "Stars to Brains" conference held in honor of physicist Paul Davies. If you have a moment, check it out.

Brilliant, Just Brilliant!

2006-06-26T23:24:00.000-07:00

A poem about spam!

"In my in-box, every morning,
Greetings from a slew of spammers,
Each, to fool the filters, using
In the header and the body,
Random lines from 'Hiawatha'"...

Zooming in on Salmon

2006-06-25T20:35:00.000-07:00

There's a cool post on WorldChanging about salmon restoration in the Pacific Northwest. From a global perspective, salmon are just a pixel. But look closer:

Zoom in once, and you learn that the forests ringing the north Pacific glean nitrogen from marine sources — ocean-borne nutrients that the salmon brought upstream in their bodies, and then left behind when they died. Their lives nurture 137 species of wild animals, plus a 138th that scientists habitually overlook: Homo sapiens.

Look closer at the health of the salmon populations, and you can see how a host of human impacts, from hydro dams to ill-conceived hatcheries, from irrigation projects to poor stream crossings, have conspired to reduce their populations. Keep zooming in, to the solutions that people are beginning to try, and it comes down to something as prosaic as installing a better culvert or replacing flood irrigation with sprinklers.

Friday Random 10

2006-06-23T17:58:00.000-07:00

Stephen Longfellow Fiske, "Eagle Fly"
Johnny Cash, "Guess Things Happen That Way"
Dar Williams, "Bought and Sold". Takes on Wal-Mart and weapons manufacturers in the same song.
Collin Raye, "I Know That's Right". If this song doesn't make you feel good, nothing short of drugs will!
Mariah Carey, "Hero"
Julia Ecklar, "Ladyhawke!". Ever heard of filk? Nice example -- a fantasy song.
Leslie Fish, "Sequoia sempervirens". Yes, it's a song about a tree and yes, I'm enough of a nerd to properly format the Latin name.
Julia Ecklar, "Survivor's Song". The thoughts of a nuclear war survivor. Powerful!
John Lennon, "Imagine". A perfect contrast with the previous song.
Gaia Consort, "Evolve" (live version). I blogged about this one. You can hear it here.

The Beauty of Evolution

2006-06-22T20:20:00.000-07:00

There's a lovely post on Pharyngula about the evolutionary connection between fish gills and our thyroid glands. Fish use their gills not just for gas exchange but also to control the concentration of salts in their bodies. So what does a fish do when it finds itself on land and needs to regulate calcium in its blood? Read the post to find out!

Nature Green in Leaf and Shoot

2006-06-21T23:36:00.000-07:00

Debates about the nature of ecological communities have shaped many aspects of the science. Ecologists of the late 19th and early 20th centuries generally saw communities as highly interdependent systems or even superorganisms whose composition was shaped by biotic interactions and coevolution. The contrary view, that the physical environment in a location pretty much controlled what plants lived there, gained ascendency later. This idea, modified to included the effects of chance and some competition, is still dominant today. However, mutualism is finally beginning to get some recognition as an important factor determining community composition. (The word "mutualism" refers to an interaction between two species that benefits both of them -- what laypeople typically think of as "symbiosis".) The debate is not merely academic. It has real consequences for conservation and restoration of damaged ecosystems.

The May 2006 issue of Frontiers in Ecology and the Environment contains a review paper by Francisco M. Padilla and Francisco I. Pugnaire about the use of nurse plants in ecological restoration. This approach involves planting the plants you want next to larger plants already growing in the area. (Yes, I get paid for each use of the word "plant".) The nurse plants may shield the target species from harsh weather, bring up water and nutrients, protect against grazers and attract pollinators. However, this approach doesn't always work. Environment matters, as does the identity of the nurse and target plants.

Nurse plants are most helpful in harsh environments like chapparral and alpine tundra. In easier conditions, competition between the two plants trumps any beneficial effects. For the same reason, nurse plants are more useful in dry years than wet years. This counterintuitive effect may occur because the deep roots of the nurse plant bring up water and the shade it casts helps the establishing seedling conserve water.

The species of the nurse and target plants also makes a difference. Plants that release growth inhibitors into the soil don't make good nurse plants. (Duh.) Late successional species benefit more from having nurse plants than early successional ones. And, although the authors don't discuss this, I'd bet pairing close relatives will increase competition and reduce beneficial effects.

The importance of this synthesis goes beyond practical restoration work to providing key insights for community ecology. If nurse plants matter in restoration succession, they probably also make a difference in natural succession. Since these interactions show at least some species specificity, we can draw a similar conclusion about species interactions in succession and ecosystem development. Finally, both biotic interactions and physical conditions make a difference; indeed, physical conditions can determine the nature of the interaction between nurse and target plants. The same effect can be expected in the wild.

No Cats were Harmed in the Making of This Website...

2006-06-21T23:09:00.000-07:00

But you should check it out anyway! I refer to Cat Flinging: An Illustrated History of Catflinging in Europe and North America, the first scholarly work on this much under-appreciated sport. An excerpt:

The cat is much like the bagpipe in that there are few people who are entirely indifferent toward either. (The similarity does not end there, however, a fact that will be documented hereinafter.) For the sake of illustration, let us assume it possible to create a list objects in the environment ordered according to their ability to engender collective indifference in the human observer. At the top of our indifference index one would probably find such things as tofu and Ed Sullivan, objects with the capacity to engender violent indifference. The cat and the bagpipe, however, would have their place at the bottom, somewhere in the vicinity of Monte Python and chewing tobacco. It is perhaps largely the cat's low indifference index that best explains the controversy surrounding the art of cat flinging.

What Kind of Whole is North Korea?

2006-06-20T21:55:00.000-07:00

According to this, North Korea might be among the few states -- perhaps the only one -- that might be said to form a real whole. Seems fragile.

Wife Swap Leads the Way

2006-06-19T23:35:00.000-07:00

One of my guilty pleasures is watching the ABC reality show Wife Swap with my mom. For those who don't know how Wife Swap works, the show has the wives in two families change places for two weeks. For the first week, each woman lives by her new family's rules; at the beginning of the second week, she gets to make some changes. Usually, both families come away having learned something, or at least give the impression of having done so.

The episode I saw today, which originally aired on November 28, 2005, featured two families, the Stonerocks and the Finleys. Both families learn to pay more attention to their childrens' needs, but the key theme in the episode is religion. The Finleys are hard-core atheists, while Jeff Stonerock preaches in what looks like a pretty fundamentalist church. Kelly Stonerock takes over Reggie Finley's Infidel Guy radio show while Amber Finley hires a secular tutor for the homeschooled Stonerock kids. Predictably, fur flies.

For me, the key moment came when Amber discussed discrimination against atheists with Jeff, explaining that she rarely goes out because of it. That topic NEVER comes up on TV. Later, when the families meet, they again discussed prejudice against atheists/agnostics/Brights and the religious Stonerocks sympathized, telling the Finleys, "We are on your side". The show's finale? Jeff Stonerock preaches a sermon at his church, saying that atheists are worthwhile individuals and God loves them and Christians equally. Amen to that! :-)

Seriously, I hope today's show starts to open a discussion of the civil rights of secular individuals. Religion is here to stay, and so is doubt. With tolerance, reason and separation of church and state, we can get along while disagreeing and build a better society for everyone.

Networks in Epidemics and Ecology

2006-06-19T12:35:00.000-07:00

Tara Smith at Aetiology has a neat post about networks, particularly in disease transmission. Studying networks allows you to see and analyze how entities, like people in a society or species in an ecosystem, interact. Sometimes, you discover neat and useful patterns. For example, many infectious diseases, including HIV in America, are primarily spread by hyper-connected individuals. Other times, a person does more than their share of disease transmission by simply shedding more of the infectious agent than other people. SARS is an example of this.

To me, the coolest application of network science is to ecological networks such as food webs. Neo Martinez, Jennifer Dunne and their colleagues at PEaCE Lab have done some fascinating work on food web structure. One of their basic results shows that you can create realistic food webs using very simple rules -- animals have a certain size and eat things that are a given fraction of that size. Their simulations also show that the ability of a food web to withstand species extinctions depends on how richly interconnected the species are.

A different approach to the study of ecological networks is that practiced by Bernie Patten and the Systems and Engineering Ecology group at the University of Georgia. Their work looks less at network structure than at dynamics and general principles. I'll be joining this group in mid-August, so expect more on ecological networks starting then.

Displaying the Flag

2006-06-15T23:24:00.000-07:00

Rigor Vitae explains why it won't be displaying an American flag any time soon. I wish I'd said it that clearly!

Nationalistic chest-thumping is one thing if you're Lithuanian or Gambian, but when you're a member of the most privileged and powerful group on Earth, it's more than a little unseemly. I would no sooner don a t-shirt that read “Proud to be an American” than I would one that proclaimed “Proud to be a White Man.”

I'd say there should be limits even if you are Lithuanian or Gambian. Some very bloody conficts have resulted from nationalism in small countries -- look at the Balkans.

Science, Poetry and the Sun

2006-06-15T22:35:00.000-07:00

BLDGBLOG reviews The Music of the Spheres, an out-of-print book about astronomy. Some of the quotes are pure poetry. Enjoy!

"As the sun unceasingly explodes in arching structures of storm and prominence, 'glowing veils of gaseous calcium' escape. In others words, the same mineral responsible for animal bones bursts outward from the sun in astrophysical shells that 'look like gnarled trees with blazing rain pouring downward from their branches in beautiful magnetic curves that have been clocked at speeds up to 400 miles a second.'
"

Tracking the Nitrogen Cascade

2006-06-13T22:48:00.000-07:00

This isn't quite pure ecology (we'll get there, I promise), but I thought I'd post it today.

Global warming is in the news. Small increases in the amount of carbon dioxide in the atmosphere are changing Earth’s climate, with unpredictable results. By now, almost everybody has heard of this human impact on the carbon cycle. Yet impacts to the nitrogen cycle are even more dramatic. We have doubled the amount of biologically available nitrogen annually cycling through the environment, with complex and sometimes subtle consequences.

It has been said that the first law of human ecology is, “we can never do merely one thing”. This is the major challenge in thinking and writing about impacts to the nitrogen cycle. Effects form a complex cascade that has to be considered as a whole. In addition, there may be effects we are not even aware of yet.

Consider a molecule of nitrogen, N₂. The two atoms making it up are held together by a strong and stable triple bond, making the nitrogen inaccessible to the vast majority of living things. Yet this element is the fourth most common one in living things, necessary to make the amino acids that make the proteins that make most structures inside you, your goldfish and the fly on the wall.

The reason all three of you are alive is that a few kinds of bacteria called nitrogen fixers have mastered the trick of fixing inert atmospheric nitrogen, turning it into forms they and everyone else in the biosphere can use. Nitrogen fixers live both in the ocean and on land. They commonly associate with certain plants, forming root nodules on clover, beans, acacia trees and other members of the legume family. Using special enzymes to speed up a process that would otherwise be unbelievably slow, they combine it with oxygen or hydrogen to form nitrate or ammonia. These compounds find their way into plants and from plants go to animals, fungi and bacteria.

Eventually, they reach the denitrifiers. These bacteria live in oxygen-poor waters and sediments, where they use dissolved nitrate ions to extract energy from food. They give off nitrogen gas as a waste product, lowering the amount of biologically available nitrogen in the biosphere.

Following this cycle one nitrogen atom at a time, we may travel from the nitrogen-fixing nodules on an alder’s roots to a moose, a wolf, and denitrification by bacteria in a marsh. Another journey might take us from a pea plant to a human, bacteria in a sewage treatment plant, algae, an insect larva, more bacteria and, as always, eventual denitrification. Until less than a century ago, this would have summed up the basics of the nitrogen cycle.

At that time, farmers, who often need extra nitrogen for their crops, applied animal or human manure to their fields or planted nitrogen-fixing crops. People also got some nitrogen, for both industry and agriculture, from Chilean deposits of guano (aka bird poop). At the turn of the 20th century, Chile led the world in commercial nitrogen production. This, of course, gave Chile – and whoever could control access to Chile – much political and economic power.

Nitrogen compounds are used not only for agriculture but also to make explosives and gunpowder. So when German chemist Fritz Haber discovered how to make ammonia from nitrogen in the air, he made possible both modern agriculture and modern warfare. Working with engineer Carl Bosch, Haber developed mass production of ammonia. Without the Haber-Bosch process, Germany would have run out of food and munitions by 1916, with who knows what consequences for the modern world.

Even more important, though, is the Haber-Bosch process’s impact on our food supply. It has been estimated that 40% of the people alive today owe their lives to artificial fertilizer. Humans are now responsible for more nitrogen fixation than all natural processes combined. The environmental consequences have been correspondingly enormous.

Let us now take a step back from nitrogen and think about how elements move through the biosphere. All living things take in some substances and excrete others. From these small flows, cycles emerge. For an example, think about food. Eat a slice of bread and as your body combines it with oxygen to release energy, you exhale CO₂. A wheat plant can take that CO₂ and use it, with water and sunlight, to make seeds that then become flour for your bread. The wheat also releases oxygen that you inhale and then release as water and CO₂.

Scale up these processes over a large area or even the whole Earth. You will now see biogeochemical cycles in which water, air, life and even the slow movements of geology transport the chemicals of life throughout the world. Without knowing all the details of every process involved, we can get an idea of how much of what substance flows from where to where each year. How much carbon from the soil to the atmosphere? How much phosphorus from land to ocean? How much nitrogen from the atmosphere to nitrogen-fixing bacteria?

Globally, these numbers remain roughly constant year to year, at least on time scales meaningful to us. But the amount of biologically available nitrogen cycling through Earth’s systems has doubled in about a hundred years. Think of putting twice as much electricity as usual through the wiring in your house. You don’t know what will be damaged by the power surge, but you know something will.

What if we could follow a single nitrogen atom fixed in the Haber-Bosch process? Part of a nitrate ion in a bag of fertilizer, it is bought by a corn farmer in Iowa and applied to his field. An atom of nitrogen stands only a 14% chance of becoming part of a corn plant and helping feed someone.

Our atom is not among the 14%. Instead, it sinks into the groundwater, where it has plenty of company. A well supplies water to the farmhouse, but its water now contains high levels of nitrates. If the farmer’s baby drank this water, bacteria in her stomach would convert the nitrates to nitrites, which can bind to hemoglobin and cause a potentially serious condition called methemoglobinemia or blue baby syndrome. Luckily, the community knows about the threat and residents give infants bottled water.

Some water from the well goes on the family’s vegetable garden and our atom comes along for the ride. The garden receives its own fertilizer, much of which gets washed into a pond after a summer rain. Algal growth goes haywire from this bounty. In a process called eutrophication, the algae grow, die and decay, robbing the water of oxygen and killing fish.

A heavier rain comes and the farm pond overflows. The nitrate ion with our atom of nitrogen flows from stream to stream, eventually reaching the Mississippi River. Here, more and more nitrogen is added as you go downstream. Wetlands along the river’s edge that could absorb some of this excess were destroyed long ago. Eventually, the water with its load of fertilizer reaches the Gulf of Mexico.

Here, eutrophication takes place on a huge scale, creating a dead zone thousands of square miles in area. Fish and other marine organisms die or are driven out, with devastating impacts on both biological and, potentially, human communities. While fishermen have, so far, largely managed to work around the dead zone, in the end, people cannot fish where there are no fish! In some places, however, the problem is even worse because algae there produce toxins that accumulate in shellfish and can sicken or kill people who eat the shellfish.

Finally, the nitrate ion is denitrified and becomes a nitrogen atom that spends several years floating around in the atmosphere as part of a nonreactive N₂ molecule. Eventually, though, it reaches Beijing and gets sucked into a businessman’s car engine, where high temperatures combine it with oxygen to form a gas called nitric oxide, NO. Even more NO forms from the nitrogen present in gasoline, as does nitrous oxide, NO₂. If nitrous oxide reaches the upper atmosphere, it contributes to ozone depletion and acts as a greenhouse gas 200 times more potent than CO₂.

NO comes out through the car’s exhaust pipe and becomes part of the city’s infamous smog. It also contributes to the formation of ground-level ozone, a respiratory irritant. Sitting in traffic, the businessman coughs.

A little later, wind blows the NO a few miles out of the city, when rain begins to fall. The molecules containing our atom and a few million of his closest pals dissolve in rainwater and change into nitric acid. When this acid rain falls on the ground, it injures plants. When lakes become acidic, fish and amphibians die.

The root of a plant absorbs our nitrogen atom. This is another, more subtle, effect of nitrogen deposition. In many ecosystems, nitrogen abundance limits plant growth. Plants must compete for this critical nutrient and the competition helps maintain diversity. When more nitrogen is added, it becomes easier for a few species to take over. If that happens, the ecosystem can become less able to resist shocks like droughts.

What can we do to get the nitrogen cascade described earlier under control? There are three major types of strategies: reducing the amount of biologically available nitrogen we create, keeping it where we want it and increasing denitrification.

Reducing fossil fuel use is an important component of the first strategy. In addition, technologies that greatly reduce nitrogen oxide emissions are available right now. Their universal use would make human contribution to the atmospheric concentration of these chemicals quite minor. Preventing emissions is generally better (and, in the long run, cheaper) than cleaning them up at the end of a pipe.

Keeping nitrogen where we want it means working with farmers to reduce fertilizer use and improve its efficiency. Farmers certainly don’t benefit from wasting money on fertilizers that aren’t even taken up by plants! However, they sometimes use more than the recommended amount as a sort of gamble. Most years, water availability limits how much benefit a fertilized crop can derive from nitrogen. Some years, however, are wetter than usual and the crop could grow more with extra nitrogen. Farmers don’t want to miss out on that kind of chance, so they apply more fertilizer than recommended by the USDA.

One proposed solution is a kind of insurance policy. Under a program providing such insurance, farmers would apply the USDA recommended amount of fertilizer to most of their land but fertilize some small patches as much as they want. If there was a substantial difference in yields, the insurance company would compensate the farmer. This is being tried on a small scale in the US.

Improving the efficiency of irrigation can help prevent fertilizer runoff. So can more ambitious plans, such as a switch to year-round cropping to keep soil nutrients in place. Individuals can reduce or eliminate fertilizer use on their own lawns and gardens.

The final strategy, encouraging denitrification, typically boils down to encouraging wetlands. Protection of existing wetlands is important, as is restoration, particularly along streams and rivers. Constructing wetlands on farmland is another promising approach because it puts denitrification close to the nitrogen runoff source.

The nitrogen cascade is a beautifully complex problem that makes global warming seem straightforward. Solving it requires us to think on multiple scales and in terms of whole systems. In the end, we can’t double the amount of an important nutrient flowing through the biosphere each year without expecting consequences.

Sources

Carlisle, Elizabeth. 2000. “The Gulf of Mexico Dead Zone and Red Tides”.

Charles, Dan. 2002. “The Tragedy of Fritz Haber”.

Fields, Scott. 2004. “Global Nitrogen: Cycling Out of Control”. Environmental Health Perspectives 112(10). (Slightly technical, but excellent.)

Fisher, David E. and Marshall Jon Fisher. 2001. “The Nitrogen Bomb”. Discover. 22(4)

Galloway, James N., et al. 2003. “The Nitrogen Cascade”. BioScience. 53:341-356. (Comprehensive but technical.)

Pafko, Wayne. "Nitrogen: Food or Flames". "The History of Chemical Engineering".

Raloff, Janet. 2004. “Dead Waters”. Science News. 165:360

Raloff, Janet. 2004. “Limiting Dead Zones”. Science News. 165:378. (This two-part series on dead zones is aimed at interested non-scientists.)

Science Museum of Minnesota. “The Gulf of Mexico Dead Zone”. (Mostly for kids, but works for anyone.)

Vitousek, Peter M., et al. 1997. “Human Alteration of the Global Nitrogen Cycle: Causes and Consequences”. Issues in Ecology 1. (Excellent introduction. Somewhat technical, but aimed at general public.)

My Dream House

2006-06-12T21:16:00.000-07:00

Worldchanging and Inhabitat have posts about using trees to grow the walls of a house. The technique, called pleaching, bends and weaves the trees together into a structure, which can even provide fruit for its inhabitants. The walls are then covered with cob (a mixture of mud and straw) for insulation and waterproofing. You end up with a genuine treehouse. Talk about fun!

I wonder whether these kinds of houses could prove beneficial in the developing world.

Good Advice from Robert Muller

2006-06-12T18:51:00.000-07:00

Robert Muller has what I think would be a truly worldchanging idea if implemented:

No student should be allowed to study economics before having studied ecology or he should study the two disciplines together.

Expect some ecology here tomorrow.

On Being an Imperfect Girl

2006-06-12T12:56:00.000-07:00

Tara Smith at Aetiology comments on over-achieving girls in high school and college. You've seen the type -- the straight-A student who plays tennis, competes in Academic Decathlon, is a student body officer (if not president) and somehow squeezes in volunteer work. I know her but I wasn't her.

In high school, I quickly discovered that cerebral palsy would prevent me from taking the same number of honors and AP classes that my friends were -- I simply couldn't do things fast enough. So I decided to just focus on what interested me. I took a mixture of classes, from AP to regular. I joined the debate team in eleventh grade and was in the ecology club as long as it existed, but mostly I did my own thing. I gardened. I organized an online volunteer pledge drive among fellow Collin Raye fans. I became known as the school's environmental activist. And I got into every college I applied to.

UCLA was more of the same. I was elected co-vice president of the Astrobiology Society but quit CALPIRG after finding no room for creativity. I devoted a lot of time to working for global government and volunteering on Dennis Kucinich's presidential campaign. I took lots of classes outside my major, completed several truly independent research projects, created my own positions at two out of three summer internships and co-founded the UCLA Math and Biology Society. Basically, I kept busy but blazed my own trail.

Result? Despite a less-than-stellar GPA, I got into the Ecology Ph.D. program at the University of Georgia -- my top choice -- and was awarded a very nice fellowship.

Tara Smith writes:

I worry a lot about my daughter... She's already very independent and wants to be the best at whatever she does. I want her to be competitive and to succeed, but I want her to define for herself what 'success' means. I don't want her to be obsessed with perfection and to be overly critical of herself. I don't want her to put what others think of her above what she thinks of herself. I want her to have a realistic view of life and a good work ethic, and not to expect things to be handed to her on a platter. I want her to be able to see the light at the end of the tunnel, even when things are difficult and stressful. I want her to have some kind of balance between work and play, even if she chooses a challenging career path. In short, I still want her to have it all--but I want to help her keep her perspective and not fall into the 'imbalanced, anxiety-ridden, perfect girl' stereotype 'crumbling under the weight of their own expectations' that Martin describes.

My advice to Tara? Encourage your daughter to choose activities that are either fun, helpful to others, or learning experiences. (Hint: student government is often none of the above.) Teach her to compete with herself more than with others and let her know it's okay not to be perfect. Most importantly, help her find her passions. It's all right to be consumed by your work if you are doing what you love.

Irresponsible Perfectionism

2006-06-11T14:37:00.000-07:00

Several green blogs, including bootstrap analysis, are complaining about Wal-Mart's decision to sell organic food at prices no more than 10% higher than regular. Echoing many enviros, bootstrap analysis writes:

"More organic foods are being shipped from far-flung places; they may be organic, but the environmental costs of the amount of fossil fuel needed to ship them is just as bad if not worse than those of conventionally-grown foods purchased locally."

True, in the short run, buying local is easier on the environment than consuming food that has travelled thousands of miles, even if it is organic. And, yes, supporting small, local farmers is a good thing, both socially and environmentally. The problem is that a farmer doesn't need to do anything to be local. An organic farmer, on the other hand, needs to change deeply entrenched practices. Organic certification takes several years. Farmers who make these changes deserve our support.

On a related note, raising demand for organic food encourages farmers, most of whom are local to somebody, to go organic. Selling organic food, which does cost more to produce, only to local consumers may not be enough to support a farm. Increasing local demand would be ideal, but shipping produce to more distant locations is frequently necessary. As increased demand causes the number of organic farms to rise, buying locally grown organic food will be easier and the need to support far-away farmers transitioning to low-input agriculture will decrease.

Author Michael Pollan, in commenting on Wal-Mart's decision, asserts that, "To index the price of organic to the price of conventional is to give up, right from the start, on the idea...that food should be priced not high or low but responsibly." But what does it mean for food to be responsibly priced? Surely, part of "responsible pricing" is affordability. Already, poor people in America are at a much greater risk for obesity than the rich or middle-class. Why? Because calorie-dense foods are cheap and fruits and vegetables are not. Raising food, particularly produce, prices will increase the health gap between rich and poor. (In the long run, such things as urban agriculture and living wage legislation can help address this problem.)

No, selling organic food at Wal-Mart prices isn't a perfect or complete solution to the problems of our food system. But at this stage, to demand perfection would be irresponsible.

Relaunching "Perceiving Wholes"

2006-06-11T14:02:00.000-07:00

I have posted nothing on this blog since January. However, I hope to restart regular posting now. There's so much good stuff to write about!

Strogatz's "Dangerous Idea" and the Nature of Insight

2006-01-05T00:04:00.000-08:00

Disclaimer: My background is in biology and I have no right to comment on mathematics. That said, I will proceed to do so.

Edge.org has once again asked over a hundred prominent scientists and other thinkers a provocative question. This year, the question was, "What is your dangerous idea?".

Steven Strogatz's answer is particularly intriguing. Strogatz, of network and complex systems fame, comments on the use of computers in mathematical proofs, writing "we're able to figure out what's true or false, we're less and less able to understand why". Somehow, to him this means that "insight is becoming impossible". He concludes,

When the End of Insight comes, the nature of explanation in science will change forever. We'll be stuck in an age of authoritarianism, except it'll no longer be coming from politics or religious dogma, but from science itself.

But what is insight and do computers threaten it? Mathematical facts -- theorems -- automatically come with explanations -- proofs. In other sciences, however, facts and the theories that explain them are distinct. Rocks fall. The Galapagos Islands have 14 slightly different finch species. I submit that insight is what it takes to go from these sundry observations to the theories of evolution and gravity.

The first step in science is making observations. Mathematicians have not traditionally been able to do this, at least not as an initial step. Now they can, and the nature of the discipline may approach that of the other sciences. Facts may get ahead of structures of thought and require ex post facto explanations. Is this really a tragedy?

There is one more response to Strogatz' worries. Computers, for all their power, do what they are programmed to do. No computer can test a conjecture that did not originate in a human brain or answer a question that a human did not ask. Surely there's room enough for insight in questioning and conjecturing.

How Much of an Explosion was the Cambian Explosion?

2005-12-31T12:26:00.000-08:00

A very cool new post on Pharyngula examines new research attempting to work out the phylogeny of animal phyla. As a bonus, there's an important place for fungi in this work -- always a good thing. More on the fungi below.

The researchers compared the sequences of 50 genes in 9 phyla to try to create a family tree. (I am under the impression that this is way more genes than are normally used for systematics. Is this correct?) Some of the branch points could be resolved fine, but it was not possible to distinguish branching times for others. Various modifications, detailed in the Pharyngula post, didn't help. The conclusion? The Cambrian explosion 543 million years ago was quite rapid, so branching times are too close together to be sorted out by the methods used.

As one of their tests of this idea, the investigators tried the same techniques on fungal phylogeny, since fungal evolution appears to lack anything like the Cambrian explosion. Walla! The methods worked just fine, producing a clean and reasonable family tree. This research agrees with the fossil record, suggesting that the Cambrian explosion was a real event.

Now, anyone who can refer to events that took tens of millions of years as an "explosion" is either a geologist or an evolutionary biologist. The term is confusing to laypeople and plays into the hands of creationists. "Rapid adaptive radiation" is too technical, plus the word "radiation" doesn't help. My poetic side wants to borrow Brian Swimme's renaming of the Big Bang and call the event the "animal flaring forth", but that suffers from the same problems as "explosion". How about "animal branching out"?

Guardian Unlimited | Special reports | US boy's answer to a school essay on Iraq: take a trip to Baghdad

2005-12-31T11:31:00.000-08:00

Guardian Unlimited | Special reports | US boy's answer to a school essay on Iraq: take a trip to Baghdad

Farris Hassan is one of the coolest people I have heard of in a long time. In an earlier age, he may have run off to be a sailor or have become an explorer. Yes, going to Baghdad is a dangerous thing to do. Precisely for this reason, it takes savvy and daring.

In this safety-obsessed society, we need kids like Hassan. I wish him well.

Evolve -- A Song That Gets It Right

2005-11-13T13:36:00.000-08:00

A group in the Pacific Northwest, Gaia Consort, performs music that might be described as secular pagan folk rock. One of their songs, "Evolve" has got to be the coolest thing I've heard in a long time.

Life teaches life teaches life teaches life
One thing: evolve

Not only does this make me think of Chris Adami's work on increasing information content in evolution (although Adami, at least in what I've read of him, doesn't specifically address co-evolution), it really appeals to the ecology buff in me. Living things adapt to one another, whether in arms races or mutually beneficial relationships. "Life teaches life" is a beautiful way of saying this.

There's a full-length live version of the song on the Gaia Consort homepage (scroll down). I might use it for a celebration of the origin of life.

Hello World!

2005-11-08T00:35:00.000-08:00

OK, so I really ought to be studying for a physicochemical biology midterm. Instead, I'm creating a blog. I've thought about starting one for a while, so you'd think it could wait -- but have this weird habit of doing things precisely when I don't have time to do them.

I am a student, an ecology geek and interested in life, the Universe and everything. (Really -- I'm a member of UCLA's Astrobiology Society.) The idea is to search for patterns and try to put things together. Expect posts on ecology, space, world citizenship, big history, bizarre connections, speculations and a fair amount of miscellany.