Breaking down biology

Thermodynamics started out as steam punk physics, but now explains, well, everything.

There is a non-trivial element of faith the the Second Law of Thermodynamics, one we dance around when we toss the idea of the Big Bang around in science class. Every time there's an energy exchange in a closed system there's less useful energy available to do work--and that's the natural world in a nutshell.

Everything eventually falls apart, drifts to a state of uselessness.

From The Onion,

If students spent any time delving into the implications of that, they'd go from the nutshell to the nuthouse. Instead we toss serious equations at them, with serious sounding names for all the serious parts, and we got them playing in abstract la-la land, which is a fine place to be in you've studied physics for years, but a psyche-killer for the neophytes.

How did the energy get packed into a point billions of years ago? We have a don't ask, don't tell policy.  That kids blithely except the concept of the universe contracted to a point just assures me no one's really paying attention.

My goal this year? Get them paying attention.


So here's my question for the more experienced out there. Would it be crazy to design the biology course around the Second Law of Thermodynamics, starting out each class every day with a brief discussion of how energy transformations guide everything in biology?

Evolution is the Big Daddy of Biology--should I spend as much time on Grandpa Entropy?

I'm not going to lie to you--first time I saw this photo I thought it was a real protest. Things have gotten that crazy.

Photo lifted from The Onion--where else?

On nothing in particular

Students seem amazed that the idea of "0" as a number is a relatively new concept, but students also see "0" as a numeral, as solid and inevitable as a "3" or a "7"--as most of us do. How could zero be invisible to the Greeks? (It wasn't, of course...but we only think so because we misunderstand our own concept of "0".)

XKCD rules!

That's not how we use it, though, at least not most of the time in the simple measurements or arithmetic we use in class. Zero serves mostly as a placeholder.

Take the number "306"--the "0" means there are no chunks of tens beyond those already captured by the three hundreds signified by the "3". We have 6 units, true, not quite enough to form a chunk of ten, so we need a way to show this: 3_6.

This is glaringly obvious to many of us who grew up without electronic calculators. The calculator we occasionally used in elementary school was the abacus, which requires grasping the concept of placeholders in order to manipulate the beads, and the slide rule, which requires the use of mental placeholders to make any sense at all.

If you do not grasp the very real difference between zero and the other nine digits, subtle problems arise, which become not so subtle when playing with significant figures ("sig figs"), those numerals that carry any real meaning when we apply math to the natural world.

We too often teach sig figs as a set of rules, which make little sense if the student has a poor grasp of zero, which many--through no fault of their own--do. The rules seem arbitrary and arcane, when, in fact, they define the limits of numerical reality when we measure the natural world.

"Numerical reality" comes off a bit too abstract. I should rephrase this: significant figures define the limits of observable mathematical relationships found in the natural world. The relationships are real, inasfar as they can be measured by independent observers. In class, however, sig figs become an exercise in futility for many.

I think it gets down to the zero. Electronic calculators add a level of abstraction to numeracy, leading to the ridiculous assertion science teachers hear at least once a week: "But my calculator says..."

And indeed, the calculator says exactly what it's supposed to say, when its operators plug in numbers without any feeling for what they represent.

And how could they? The Greeks had the concept without the symbol. We, alas, now have the symbol without the concept.

Yes, I know, the Mayans and Indians and Phoenicians and on and on and on had it down pat.
Thank Fibonacci for getting it to the western folk.

XKCD comic used wtihin his guidelines--very broad ones at that. Thanks! 

And yes, the sig fig rules are a tad arbitrary--range of error makes more sense.

Bats!

Last night was Perseids night--we had our lawn chairs out, the full moon's light blocked by the garage at our backs. The mosquitoes, our state bird, were scarce enough that we had not slathered on whatever state-of-the-art organic compounds we use to ward off 6-legged critters these days.

Joe Westerberg, Joshua Tree National Park, California, Aug. 11, 2007

We saw a bat, a welcome sight. Then two. Now a third.

We held still, lying on our chairs, watching the bats chase bugs and each other, a spectacular aerial show against the deep gray-violet of the late dusk sky. And we realized that, really, the mosquitoes were remarkably scant.

A bat swooped up from the ground by our feet, no doubt, munching away. We watched the acrobats flip from their invisible trapezes a few more moments, then one swooped inches from our heads.

Now we know that bats tangling in your hair is an old wives' tale, but the few mosquitoes buzzing about our heads was tempting enough to the bats to show off their aerial skill a tad too close, and as much as we appreciated their predation, we scurried back inside.

Though we missed the main event, the Perseids changed our world in subtle ways:

• We spent the whole afternoon outside, as well as a good chunk of dusk. The dust of Perseid micro-meteorites fell on our hair. (Heck, you can catch micro-meteorites at home--really!)

• A few of my red blood cells gulped by a mosquito (or two) ended up in the belly of a bat, now broken down into tiny pieces. Some of it will become part of that bat, some released as carbon dioxide in the bat's breath, possibly captured by the Brussels sprouts nearby, which I will eat after November's first frost.

Communion.

The meteor photo was taken by Joe Westerberg, lifted from Spaceweather.com, used with permission.

August light

The tomatoes came from a farm within a stone's throw, the eggplant from our front yard. Our neighbor two homes down gave us the flounder he caught within a couple of miles of here. The basil got plucked from the backyard patch. The peach melomel came from local honey and peaches brewed under our roof a year ago, with help from a local vintner when I ran out of yeast nutrient. I biked over to the Cape May Winery, and he shared what he had.

This is how humans made it before the industrial age, when we depended on this year's sun, this year's crops, and this year's kindness.

Leslie's secret to her cooking in August--keep out of the way of the ingredients.

***

The sun went as far north as it's going to go, and is now sliding back, picking up momentum day by day. The bees know this, more frantic now as they store their honey. The plants know this, shedding captured calories into the fruit we call vegetables.

Food is good, food is abundant in these parts. We eat, and we put some by.

We'll freeze tomatoes and basil and beans. We'll ferment peaches and blueberries and honey. We'll collect seeds and store them in brown paper bags, in the pantry closet, until the creaking light of February prompts us to start sowing again.

***

By February, I will be diving into ribonucleic acids and adenosine triphosphates with kids who will be diving into McDonald's as we defrost last summer's pesto. McDonald's is cheap, and McDonald's is, to many, tasty.

A year ago I grew a batch of basil in class, eventually making a batch of pesto. I offered to share it, but my students were shocked I'd eat something we grew in class.

We are so disconnected from our earthy roots that even food has become abstract.

Biology, or any science for that matter, is not abstract. Oh, the models can get a bit wacky, and just about all of them are wrong here or there, but none of them come from thin air. Our hypotheses are human inventions, true, but our conclusions are not--our ideas are weathered by the natural world, by reality, by an uncertain sense of truth.

We eat, we breathe, we shit, we pee--pretty much all animals do. You can get through formal education all the way to a PhD and not have even a vague notion of how life works, how matter is transformed, and energy caught.

August is the month of accounting--the solar feast wanes, do we have enough to survive the winter? For most living things on this part of the world, the answer comes in a slow unraveling, as mitochondria are no longer fed pyruvate, as another life ends beneath the snow, silently, held in ice until the feast resumes in March.

And what do we offer the nascent adult? A diet of DNA, ATP, and ribosomes, a subcellular abstraction that answers nothing that matters to a child just starting to shave.

I hope to fix that....

And while we're at it, food is not energy.

P.S.: Perseids tonight!

Fracking logic

According to the New York State Department of Environmental Conservation, fracturing fluids typically contain about 90 percent water, about 9 percent propping agents like silica sand and less than 0.5 percent chemicals.

International Business Times, August 11 2011

*thunk*

When experts spew out statements like this, hiding absolute numbers behind safe-sounding percentages, when they deliberately obfuscate the word "chemicals" to make a political point, and when "journalists" cannot be bothered to research what the "less than 0.5 percent chemicals" contains, my heart trembles for any hope of an enlightened citizenry.

But all that sounds like fearful piffling on my part, and even responding to it makes me sound like a liberal loser wonky type.

Heck, air is mostly nitrogen, with a small chunk of oxygen tossed in. I wonder if the committee that spewed this nonsense would mind sitting in a room with only 0.5% carbon monoxide during one of its meetings.

No, that was not a threat. Allowing fracking near someone's water supply, however, is a threat.
We're letting them frack with our water--what would Thomas Jefferson do?

Cartoon lifted without permission from here.

Grain moon

The Grain moon of summer moves perceptibly
Through the white birch we did not plant
But showed up as a sapling when our child still suckled
And now drapes over the pond that a young one
Dug when she needed to dig.
Daphnia dance in the shadows of the birch
As unexpected, as unplanned
As every birth of every human
That mouthed the word mama.


We know how it ends, as does
The birch, as does the mosquito
Who drills into my skin to
Provide, blood drier than nectar
(which she prefers), but she does what she must,
As we all do, all beings, all all.


The little boy slaps at her, laughing
Because he got her, amused
By the splash of ruby now on his arm,
“I got one! I got one!”
And the white birch kneels over the pond,
As it does, as it does,
As the moon slides through its branches.

The full moon is approaching. I was reading Seamus Heaney as I saw it peek over the book in the steel gray of dusk.

Nothingness is a huge part of everything

I ramble on a lot. I edit a lot, too, hard as that might be to believe, tossing out about 7 or 8 words for every one that I leave. Yes, I know, anything less than a 10:1 scrub ratio marks me as an amateur too in love with his darlings....

Mary Ann Reilly and I have never met, though we have collaborated on a project I tossed at our state  Ed Commissioner Christopher Cerf--ain't the internet grand? She's building a high school, one I'd like to be part of, but enough of the full disclosure nonsense.

I wrote this: "The atoms taught in elementary school  do not exist. If a nucleus is the size of a dime, the electrons would fling as far as half a football field, and even that's just an average. What's in-between? Nothing. Nothingness is a huge part of everything."

She wrote that: "Nothingness is a huge part of everything and there is never the accounting for nothingness in the slick state and now national standards. They are overfilled with their own self importance."

The national standards are like our universe 14.6 billion years ago--no space, no wiggle room, no humanity.

Life found in the spaces, in the niches, in the shadows of the corners works the same way as the stuff that spews forth in the elevated air of Mount Hubris. And matters just as much.

Thank you, Mary Ann, for helping me see this.

Mary Ann Reilly is an artist who is fascinated by edges, by borderlands.

The photo is by her, used without permission.