Al Stahler: Life-or-death chemistry |

Al Stahler: Life-or-death chemistry

Al Stahler

Fire can be dangerous — especially in a hospital room, with a patient breathing oxygen.

Normal air is mostly nitrogen, just one-fifth oxygen. With so much nitrogen in the air, we’re lucky fire can even burn at all. (As I describe fire, please forgive me for describing atoms as “happy.” Atoms are not alive, but they do seem to have “wants” and “desires.”)

Fire: Atoms of oxygen, at over 1,000 mph, slam into atoms of carbon and hydrogen, jettisoned from the burning fuel.

Atoms of oxygen “want”, very much, to bond to atoms of carbon and hydrogen. When they bond … when they glue together … they are so “happy”, they release energy: heat and light. Fire.

Again, air is mostly nitrogen — atoms of nitrogen, packed, two atoms at a time, into molecules. The two nitrogen atoms in each molecule are glued so tight, even the fire cannot loose them from one another. Nitrogen does not burn.

Not only does nitrogen not burn … it gets in the way of atoms that do. More often than not, an oxygen atom, on-course to hit a carbon or hydrogen atom, slams into a nitrogen molecule instead. Nothing happens. The few times oxygen atoms hit carbons or hydrogens give us a fire that burns slowly.

Slow-burning fire is manageable, so it’s good that nitrogen does not react. But that reluctance of nitrogen to interact with other atoms is a problem, when it comes to keeping ourselves alive. (By “ourselves,” I include all life on Earth).

All life needs nitrogen atoms, as building blocks when we make protein, DNA, many other parts of our bodies.

No animal, no plant, no fungus has ever evolved an enzyme — a machine — powerful enough to separate the two nitrogen atoms in a nitrogen molecule.

Bacteria to the rescue. Only certain bacteria can pull apart the atoms in a nitrogen molecule, then attach those nitrogens to other atoms, putting nitrogen into a form they (bacteria) and we (fungi, plants, animals) can use to keep ourselves alive.

Pulling one nitrogen atom off another takes a lot of energy.

Deep within the muck on the edge of a lake live microbes that don’t use oxygen to get energy from food. Billions of years ago, there was no oxygen at all in the air, and all life lived by such anaerobic metabolism. (Truth be told, we oxygen-breathers still do — when we exercise so hard that we run out of oxygen, and fall back on fermentation (producing, in our muscles, lactic acid — the acid of yogurt — which “burns”).

But anaerobic metabolism is very inefficient. We aerobes — we oxygen-breathers — get more than 10 times as much energy out of every bite of food as the anaerobes.

Pulling apart nitrogen molecules takes lots of energy, and oxygen-breathing aerobic metabolism is great for producing that energy. But the enzymes that pull apart nitrogen molecules are super-high energy machines. Allowing such high-energy machines to come into contact with oxygen would be like lighting a match in a hospital room.

Solutions and evolutions

What to do?

The Scotch broom is blooming. The flowers are pretty … but the plant is a pest. Scotch broom overgrows native plants, kills them, and ruins the lives of the critters that depend on native plants.

And then, come fire season, Scotch broom really “likes” to burn.

The annual Scotch Broom Challenge would normally have work parties out right now, removing the pest … but, of course, something came up ….

What a good chance for all of us to move our bodies! It’s not hard — I’ve got excellent results, simply cutting the broom, with clippers, just above ground. A few plants might grow back next year, but nothing like what got cut.

This is also a chance to see a major factor that makes Scotch broom such a successful competitor in our thin foothill soil. Find a plant growing in moist soil, where it’s easy to pull. Pull the plant up gently, roots and all. Notice, on the roots, tiny nodules, a sixteenth, maybe an eighth of an inch across. Notice that some of those nodules are pink.

Pink for the same reason our blood is red. Host plant and bacteria, living in the nodules, together produce hemoglobin — the molecule that hauls oxygen through our bodies. With hemoglobin, the bacteria in the nodules bring oxygen to their energy-producing metabolic “furnaces” … and to keep oxygen away from the high-energy enzyme machinery pulling nitrogen molecules apart.

Another biochemical story:

Life on Earth is close to 4 billion years old … but, for its first 3 billion years, nothing alive had more than one cell … there were no animals.

When the first animals evolved, something under a billion years ago, they were soft, squishy things – they were defenseless. Fortunately, nothing around could eat them – teeth and jaws and claws had yet to evolve.

Eventually — inevitably — meat-eaters evolved, and thus began an arms race: Weapons for hunting vs. weapons for defense. One such defensive weapon was the shell, inside of which a critter could hide its soft, tasty body.

Shells remain a good strategy for defense. But building a shell can be a challenge.

Most of the sea shells we find at the beach are made of calcium carbonate — the stuff of marble, limestone, the chalk kids use to draw on the sidewalk. To assemble such a shell, a critter glues a charged-up atom of calcium (the same atom we put into our bones) to a small clump of atoms called carbonate. The problem arises if either charged-up calcium atoms or carbonate clumps are scarce. Lacking either puts the brakes on building a shell.

I’m sure I’m not the only one who has been frustrated by a product that comes in a package that cannot be opened. It’s tempting to take the thing and trash it … or grab a hammer and smash it. Either way, it’s a total loss.

The clump of atoms that make up carbonate are in constant interplay with the atoms in the water around. Under ideal conditions, the carbonate clumps are free and ready to join up with calciums. But — when large amounts of carbon dioxide dissolve in the water — the carbonate clump gets tied-up — packaged — with other atoms, making it unavailable for shell-building.

Adding insult to injury, mixing carbon dioxide with water creates carbonic acid … the acid that gives a tart tang to soda and beer … and that tends to dissolve sea shells.

The ocean will never become truly acidic … but measurements and calculations show dissolved CO2 causing it to drift in a more-acid direction … making it harder for clams and oysters, corals and — most critically — the base of the oceanic food chain — single-cell plankton — making it harder for all of them to build shells.

Al Stahler enjoys sharing science and nature with friends and neighbors on KVMR-FM, and can be reached at

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