Friday, July 21, 2006

Farting Alien Cows?

Steinn SigurĂ°sson 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.

SigurĂ°sson 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

  • 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.

Thursday, July 20, 2006

Time Won't Drive Us Down to Dust Again

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.


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.


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.


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...

Wednesday, July 19, 2006

When Statistical Mistakes Don't Matter

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

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!

Monday, July 17, 2006

Causes, Effects and Networks in the Genome

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?

Sunday, July 16, 2006

On World Government and Being an Oddball

"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?

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