Saved by The MetaGenomics of Dirt

Below are some annotated bits from an article in Wired that describe the early successes in the battle to find weapons against the increasingly numerous and increasingly virulent microbes that are resistant to all known antibiotics.

We worry about the Russians or the Chinese or the North Koreans or Dr Strangeloves in power around the world, when all along, if the human population suffers the Malthusian reduction many fear, it will most likely come from invaders far too small to see.

HOW DIRT COULD SAVE HUMANITY FROM AN INFECTIOUS APOCALYPSE

The culprit, pan-resistant Klebsiella pneumoniae, is not the only superbug overpowering humanity’s defenses; it is part of a family known as carbapenem-resistant Enterobacteriaceae. The carpabenems are drugs of last resort, and the CDC considers organisms that evade these antibiotics to be nightmare bacteria.

So it’s difficult to envision a future that resembles the pre-antibiotic past—an era of untreatable staph, strep, tuberculosis, leprosy, pneumonia, cholera, diphtheria, scarlet and puerperal fevers, dysentery, typhoid, meningitis, gas gangrene, and gonorrhea.

But that’s the future we are headed for.

This is not the coming plague. It’s already upon us, and it spells the end of medicine as we know it.

That’s why Brady and others turned to metagenomics—the study of all the genetic information extracted from a given environment.

Brady came to realize that he did not need to trek to some pristine or remote ecosystem to explore the world’s biodiversity. The requisite material for building new drugs could be found much closer to home.

The more we use antibiotics, the less effective they become; the more selective pressures we apply, the more likely resistant strains will emerge.

Think about this the next time you stand quietly in the park or in the forest or meadow near your house. Reach down and gather a teaspoon full of everyday soil in your palm, and realize there are likely to be some 3000 different microbes nestled in the hollow of your hand.

Here is enough genetic information to solve many of humanity’s problems–if only we ask the right questions. And move with sufficient speed to do the work in advance of the inevitable and urgent need.

Snows of Narnia

If every snowflake is different, then every snowfall must be too.

This one was unique. It was the last snow to fall before my personal odometer turns to a new zero.

And so I am trying to pay attention to the details. And the details of this snow were worth attending.

I confess I used PixelBender oil paint filter to attenuate the branching snow shapes just a little; it impressed me as a scene out of a fairy tale–maybe Chronicles of Narnia, and so I rendered the image to bring that out a bit. [click to enlarge image ]

SomeWhere

From Bethlehem Church Road, Floyd County Virginia. Click image to enlarge.

And SomeWhen.

Finding the pot of gold means a bit of good luck. And keeping your eyes open. And having a camera in your pocket 24/7. And stopping in the rain to step out of your car in the middle of a county road to save the moment.

I once reflected on the place of photographs in my life:

“Film became a way to preserve present moments in a clear resin of recall. Every photograph set a benchmark in time, held a unique instant in the emulsion of memory, captured in perfect synchrony that vertical line of precise moment that intersects the coordinates of particular place.”

It may be maudlin and saccharine, but Kodak moments anchor us in person, place, space and time. And I am thankful to have had more than my share of them.

And a bit more of the reflection on time (from What We Hold in Our Hands):

“No two photographic markers were the same, and there was no going back. With my lens, I fished from the moving stream of time as days flowed through the faces I knew, past the places I loved, leaving the lived, the known moments bobbing on its glassy surfaceÑdeeper down, farther back, receding Doppler-like across a realm that I could photograph, could know just once, just now.

I have spent decades more behind the camera, no longer wishing I were older, happy for the past, but savoring photographic instants in the present when one face or one flower, one sunset, yet another family pet or one more grandchild’s candle-covered birthday cake fills the viewfinder and moves on downstream.”

 

A Season To Be Mired in Quicksand

To everything there is a season, we are told:

A time for effective and meaningful engagement in  a full life; and a time to be mired up to your acetabulum in an unending, onerous, complex, emotionally draining and impossible slog through quicksand.

There is a time for effortless, natural progression from passion to passion; and a time for soul-sucking, bizarre and out of control obligation to duty.

I, as you might have guessed, I find myself in the second of these seasonal possibilities.

Way busy; stressed; uncertain; sad; exhausted; and not all that agreeable to be around.

So when the going gets tough, the tough (or even wimps like me) get doodling.

Yep, I have recently spent a bit of our children’s inheritance and purchased an iPad Pro with Apple Pencil. And when I should be creating agendas, sending out Doodle polls, writing complex position statements toward conflict resolution or otherwise moving forward toward one mission statement or another, I pull out the pad and pen and do the visual version of nothing at all.

A better person would feel regret and shame at such a retreat from responsibility. Me, I lean into purposelessness–with some flare and success, I add in all modesty.

So fire me.

 

Gandy, Going, Gone

Gandy is gone as of an hour ago, after seven years and four months. That’s a lot of dog years, and they were good ones. She had an enchanted life on Goose Creek after being a rescue puppy that could have ended up anywhere, and in not such expansive wilderness with two creeks! Think trailer park tied to a tree.

Three days ago she was chasing squirrels on the ridge. Then she went into a rapid decline, and was having difficulty standing, breathing, moving. The end was near. We found a vet from FloydCo who makes house calls. She came right away. Gandy did not suffer.

She is buried out the kitchen window where we could never get a pear tree to grow. And that was one of the most difficult things we have done together in 47 years of marriage—in sickness and in health. We never buried a dog together before.

It will take some while before we stop expecting her to greet us in the morning and run ahead of us on the pasture loop. I just glanced up to see a copper colored flash go past the window and thought “there she is” but it was one of the red chickens.

It is a good exercise just now to think of our friends and family and those that knew us, and knew us with Gandy, through all the ups and downs; through the Feather years. Feather left the story a year ago January 23rd and Gandy never stopped missing her, I feel sure. Maybe there are dogs in heaven after all.

We never had a smarter companion, or more faithful or more helpful–bringing in wood, doing anything in the truck, she was involved in all family activities. And so her absence, all the more the loss.

And life goes on.

There are a lot of reasons why Gandy should be our LAST dog. But the “heart has reasons that reason does not know” Pascal said. And I expect he is on to something.

Plate is Full, Blog is Empty

Earth in Ice: Image from Goose Creek January 2008

I made the mistake a few weeks back of saying I hoped to be doubling down on efforts to apply the brake to the creening path of humanity towards the brink–as if one person can make a difference; and yet…

One person can be a bystander or can give aid at the scene of a horrific accident.

Where we are as a species today is a horrific consequence of ignorance early on, followed by full intention in the past decades–since the Great Accelleration of 1950–to push the pedal to the medal, calamitous consequences (for all but the present stockholders and CEOs) be damned.

And so since I made that declaration here (I am too lazy to make a link) I have had new obligations and opportunities to man the oars and paddle against the currents.

I am now serving on the Volunteer Core Group for the nomination then election of Anthony Flaccavento to Congress from the 9th district of Virginia; and have a multitude of new hats to wear with SustainFloyd, perhaps more about that at some point.

Also i have elaborated on the Personal Climate Pledge project of SustainFloyd and that essay will be up on Fragments in excerpt tomorrow, with a link to the full piece at medium.com

So I intend–because it is something I want to attempt to do for the first time in years–to post to the blog every day this week. The posts will come mostly from material already generated elsewhere (like the two Forestry-related presentations for the Living in Our Forests series at the Floyd library, yesterday and on January 11th.

Also now will be planning for an hour-long presentation (vs the 20 minute versions at the library) for an organization in Roanoke probably in July.

Idle hands…not so much. But I like it that way–up to a point that might have been passed a couple of weeks ago. Balance. Serenity Now! World peace!

The High Places Made Low

Talus field along Nameless Creek–moss and fern-covered boulders tumbled down from Nameless Mountain –a high place that was gone long before there could be human views from the top.

One of the places I stand and ponder in our daily silvan peregrinations is up back, beyond the last extent of floodplain of which our five-acre pastureland is the remainder. Beyond that point, the path skirts high above the rock shelves and tumbling waters of Nameless Creek.

What now stands as the high country above us rises at least 150 feet above the creek, and so steep we have never been to it. This is all that remains of Nameless Mountain, as I think of it. It calved all these boulders that hikers dread to pass over and call scree, and which geologists refer to as talus slopes. Erosion, gravity and time lay green and jumbled, in place now for a thousand human generations.

Nameless Mountain–a crest pushed up during the Ancient and Early Blue Ridge mountain-building epoch or orogeny–would have been as high as today’s Himalayas or Rockies. Coming to full acceptance of this truth (remember truth? It was popular once) is easy to achieve after much practice, standing quietly above the creek and below the wasted remnant of mountain crest.

We are surrounded by traces of time to which our now-ness  makes us blind. Unfortunately, we have also become blind to time to come, and do little or less to make ready for the gravity of those challenges. They are as real as the mountain that once rose above Goose Creek and Floyd County and dominated what we think of as Southwest Virginia.

This is the place we call the Valley of the Bones. Our dogs often find remnants of mammals who have sought out the dark spaces under boulders to die.

Here is how one writer describes talus:

The very random placement of fallen boulders, slabs of rock and massive pieces of stone creates an abundance of small caverns, nooks, cubbies, and grottos connected by a labyrinth of narrow passageways, chimneys and tunnels. In shady places, such as in ravines, on north-facing slopes, and along the edges of streams and rivers, a carpet of moss frequently covers the surface of these piles of rock. In heavily forested settings, a layer of organic debris may develop in cracks and crevices that promotes the growth of some species of ferns, herbaceous plants and small shrubs.