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.

A New Pest. And an Old One

Spotted Lantern Fly now in Virginia.

“A potentially very serious pest of grapes, peaches, hops, and a variety of other crops, the spotted lanternfly (SLF), Lycorma delicatula, was detected in Frederick County, Virginia, on Jan. 10, 2018.”

It’s host plant for hatching its eggs and hosting its young: Ailanthus–Tree of Heaven. A match made in, well…

In Pennsylvania…

“The red and black spotted lanternflies are native to China and feed on sap, essentially sucking plants dry. They go after grapes, but researchers have seen them invading apple trees as well. In December, Pennsylvania state officials quarantined Christmas tree growers in 13 counties to prevent the insect eggs from traveling to other states.”

We are likely to hear more–a lot more–about insect issues as winters get milder and natural cycles become disrupted by unpredictable patterns of temperature and rainfall: climate chaos.

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.

On Not Killing Our Environmental Puppies

Yesterday, your neighbor’s yellow lab gave birth to a litter of puppies.

Today, the owner has made up his mind to do one of the following: to turn them outdoors to fend for themselves in the heat and take their chances with the traffic; to poison them outright; or to simply ignore their whining there in the next room until they die from starvation.

The dogs are his. They live, however briefly or unwell, on his private property. But if we heard about irresponsible treatment of creatures in this way, we’d think it fitting that the local sheriff visit your neighbor to explain to him the consequences of reprehensible treatment to animals. Animal cruelty is a behavior universally abhorred — against certain cherished and cuddly animals, at least.

And yet some very vocal people of our times are convinced that a godless, liberal, socialist one-world-government conspiracy is ramming down our throats the notion that other animals than pets have “rights” that limit how they ought to be treated.

Read More at medium.com…

Mountain Lake(less)

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Mountain Lake (on Salt Pond Mountain) in Giles County, Virginia, was familiar territory once upon a time. I took five-week-long studies at the UVa Biological Station there in the summers of 1977 and 1978.

I have been back a few times since, doing author tables maybe twice. The last time I was there, I think there was still a lake. Last week’s visit was sad: there is now no lake at all.

Memories abolished by cataclysm, “progress” or decay are bitter sweet.

I remember diving off the large boulder nearest to what used to be the center of the lake. This part of the lake was called the Garden of the Gods. The water was unbelievably cold–even in July.

This, by the way, is (or was) one of only TWO naturally occurring lakes in the Commonwealth of Virginia. The other is Lake Drummond, in Dismal Swamp. At least that is what I have stated as being accurate and think it to be true (vs alternative) fact.

A trail follows the perimeter of the lake. I’ve walked it many times, finding amazing bird life, which, like human visitors, came for the water.

If you know of the Lodge (off image far right) it might be because it was the site of filming for some of Dirty Dancing.

I’ve told the geological story of the lake before, I know, but I can’t locate it just now. You can read some of the history of the lake and the lodge here.

 

 

The Fading Faint Colors of Fall

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It has not been a spectacular year for fall colors in our part of the Southern Appalachians.

The prolonged late-summer drought seems likely to have contributed to the subdued palette, but the alchemy of autumn is a many-splendored mystery with regard to the exact combination of temperature and moisture and sun and wind and plant attitude.

So we did not expect and did not see spectacular maples, hickories or beech on the parkway in our short walk a few days back. But there is color in places not seen from a tourist’s vehicle. You can find it if you look for it. Even the understory B-string of fall has something to show in its way out.

Here, the summer greens of cinnamon ferns fade to reveal the other-than-chlorophyll pigments that contribute to the work of photosynthesis. And another year concludes–at least above ground–until the days lengthen again in another six long-night short-day months.

When The Bottom Falls Out of the Food Web

Single blister beetle hanging out, ready to make whoopie.

Most people might think it’s a good thing–that there are demonstrably and significantly fewer insects than there were three decades ago.

But consider that these morels are critical links between the primary producers (grasses and other greenery that turns sun into food) and the chain of upper-tier eaters that depend on insect biomass to keep their own bodies warm and populations from crashing.

Scientists have long suspected that insects are in dramatic decline, but new evidence confirms this.

Research at more than 60 protected areas in Germany suggests flying insects have declined by more than 75% over almost 30 years.
And the causes are unknown.

“This confirms what everybody’s been having as a gut feeling – the windscreen phenomenon where you squash fewer bugs as the decades go by,” said Caspar Hallmann of Radboud University in The Netherlands.

“This is the first study that looked into the total biomass of flying insects and it confirms our worries.”

I always monitor the goldenrod of September as a kind of biological clock telling me where we are on the celestial rotatation towards autumn. In particular, there is a tan blister beetle that uses this plant as a “hooking up” spot, to meet, greet, eat and procreate.

There are usually numerous pairs on every plant around the edge of the garden. This year, there were four pairs–total. I could go on with similar stories about other insects gone missing.

Turns out our canary in the cage might be an insect after all.