Grape Vine Red Blotch Associated Virus

Ebola is on our minds, but we easily forget that the biosphere is a churning cauldron of microbes whose tenure on the planet extends back several billion years. They live deep in the earth’s crust. They live in the mesosphere. They live in bedrock lakes beneath the ice in Antarctica. And that’s just where we’ve bothered to look. Any shovel full of dirt from your backyard would reveal creatures unknown to science if you had the patience to do a comprehensive survey.

Viruses and prions are scraps of nucleic acids that have found niches as wayfarers wandering through the genomes of more complex creatures. Most are submicroscopic and so poorly understood that you might well spend a good part of your life trying to catalogue these creatures in that same shovel full of dirt from your backyard.

We ignore them until they kick us in the butt.

When people began noticing red leaves on  grape vines that seemed to ripen slower late in the last decade  they tested for the leafroll virus that produces similar symptoms. Some actually had leafroll but others did not and further genetic investigation revealed a “new” circular, single stranded DNA virus distantly related to the Gemini viruses.


We tend to jump way too quickly from correlation to causation and many plants infected with the “new” virus are also infected with leafroll, but not all. Separate groups in several areas of the United States and Canada isolated the virus soon thereafter and gave it different names, but the consensus is that it is all the same virus and judging from its wide distribution it has probably been around for a long time, unnoticed.

Kind of like attention deficit disorder, completely undiagnosed when I was daydreaming through dull classes as a kid, but now the explanation for everything from laziness to psychopathic behavior.

But it is a serious problem if it is actually causing the reddening leaves slow ripening, which seems likely. One group has suggested the possibility that a fungus is associated with the disease and it seems very possible that a complicated set of interactions may affect the expression and virulence.

Underside redening veins

What seems to distinguish red blotch symptoms from Potassium and Phosphorus deficiencies, mite damage, and leafroll virus–all of which produce red leaves–is the reddening of the veins in the leaf. Sometimes this reddening of the veins is not apparent from the top and the leaf must be turned over like this one.

The biology of viruses and the knowledge of the sequencing techniques necessary to identify them is very difficult stuff that requires years of study to master, but the epidemiology of this disease–how it behaves and spreads in the vineyard–is virtually unknown. One can read the entire published knowledge base in an afternoon.

In cases like this, citizen scientists, those willing to carefully watch and learn, can be a valuable addition to the study of the disease.

We are accustomed to the leaves in our forests turning red in the harvest season and to the casual observer the sight of a red vineyard in the autumn can be a peaceful and beautiful spectacle. Grape vines should turn yellow, not red, and to those who work with the vines it is anything but a peaceful and beautiful spectacle. It means there is a lot of work to do because something is definitely wrong, and it may be a certain newly discovered circular virus with 3206 base pairs.


Posted in Biology, Microbial Dark Matter, Wine | Tagged , , | Leave a comment

Ecology Now!


This exhortation has a strange ring to it now, and it is likely that no one under the age of fifty ever heard it, but  the image above is a poster of an actual flag created by the activist organization Earth First that spun off from the Sierra Club in about 1970. It is interesting that they chose the flag as background because probably the prior change of this magnitude in the human world view was the nationalism that emerged in the 18th century.

Ecology Now! was the mantra of an ethic being born. Maybe it was the sheer size of the boomer generation. Maybe there were lots of reasons for generally bustin’ out new stuff back then, but the concept of studying biology in the form of unified systems was pretty new, and what we think of today as a university department and potential major was then a new holistic conception that the entire planet might be considered an organism.

Gaia, although not so named back then. Holism was being explored on many different levels. The social insects and their amazing command and control apparatus were likened to unified organisms.  There was a reaching out to study all human religions as if by understanding them all we could somehow define the whole of religion and the whole of life.


It is a beautiful ethic that has stood the test of time from when postage stamps were six cents. We must save our cities, soil, air and water, but to do so we must also save our fire.

Save our fire? We need to extend the concept of holism full circle to include ourselves. We humans are entirely natural. We did not create ourselves. We grew from the same soil, air, and water as all the organisms we share the planet with. We used fire to create cities. It is our nature, and the cities must be saved.

We have received a mysterious endowment of hydrocarbons, whether the more from decayed predecessors or bacterially modified mineral methane we can’t yet be sure. We can burn through this endowment like trust fund teenagers, scattering our packaging into continent sized plastic vortices in the oceans, or we can manage it to transition to a truly sustainable future. But burn it we will.

We don’t have a lot of room for error, but unfortunately the scientific community has made a very significant error and wasted enormous resources in its focus on Carbon dioxide as a serious risk to the planet. The combustion of hydrocarbons produces more water than Carbon dioxide and may well be that whatever slight warming we have caused is from adding the water to the air.

We simply can’t afford to vilify  gasses we exhale with every breath. We can never snuff the fire.

We need fire to scrub the truly dangerous combustion byproducts from our furnaces. We need fire to collect and recycle our packaging. We need fire to develop new technology and infrastructure, and we need a lot of fire to allow the developing world to build a decent standard of living.

So save our cities, save our soil, save our air, save our water, save our fire, and save our planet.

Ecology now!


Posted in Anthropology, Biology, Climate, Ecology, Ethics, History, Religion | Tagged , , , , | Leave a comment

The Pacific Triangle, The Pacific doughboy, and the wave

Folks just don’t seem to have their arms around the disarray in the earth sciences these days. Climate science and plate theory are going to have to be rebuilt from the ground up, or more appropriately from the core-mantle boundary.

Pacific Triangle, Doughboy. Wave

This rather ugly image shows the current position of the  Pacific Doughboy (LLSVP) in dark colored elevation contours above the core. This converted in an unsatisfying way from arcmap. The lighter colors are higher elevations and the highest points, some 2900 km above the core are supposed to be white but show only as unfilled contour line.

Of course, this doughboy should really be shown at its actual position far below, but it is impossible to turn off surface imagery in Google earth and all one would see is blue ocean.

The Pacific Triangle and the evolved seafloor isochrons that represent the wave or motion of the spreading ridge away from the triangle are shown in their Paleocene (60ma) position according to Christopher Scotese.

Google applied some emergent logic to decide which colors would express where, but all in all one can get some sense of the relationship of the forms. While it would have been fun to find the triangle at one of the peaks in the doughboy, the triangle seems to have moved modestly through time and we have no idea how the doughboys have behaved through time.

Austral view

Here is a more Austral view.

Our spreading ridges are clearly in motion. Our mantle is clearly stratified and not convecting in anywhere near the normal sense. We have two asymmetrical monstrous extrusions from the core (Doughboys). Something is supplying an enormous amount of energy to maintain mobile shallow pools of molten rock in both linear (ocean ridges) and point (hotspot) forms.

Oh well, venturing into the unknown is way more fun than reciting liturgy.

Posted in Geography, Geoid, Geology, Large Igneous Provinces, LLSVP, LLSVP's are Doughboys, Oceanography, Pacific Triangle, Paleogeography, Plate Tectonics, Seafloor Isochrons, Seismic Tomography | Tagged , | Leave a comment

Broke Down in Bishop

Kyle, my son in law, missed out on circumnavigating Mt. Whitney last October. Unsure if it would work out we latched onto the latest available permit for the North Fork of Lone Pine Creek last Christmas and listed our means of travel from the drop down list as “dogsled” and from another dropdown list asserted that we would be bring a goat. We left it to the powers that be to decide if the goat would be pulling the dogsled, but if you have ever been up the North Fork of Lone Pine Creek you would surely know that the goat would probably make it but the sled would have to be winched up and any dogs would be pretty iffy.

One can only wonder how many travelers in the Inyo wilderness actually bring dogsleds or goats so as to justify the dropdowns, but bureaucracy develops a logic of its own and it was our good fortune that when we went to collect our permit we found an official with a sense of humor.

But I get ahead of the story because driving through Yosemite on the way down we smelled some very bad smells from my old Honda hybrid and pulled into an overlook to find the belt to the air conditioner pump smoking and watch it snap before our eyes. The air conditioner was not a problem but we found as we proceeded that the very same belt drove the water pump and we began overheating as we climbed the hills.

We pulled in at this random icon promising a pay phone in the trees and discovered that we had lost all our pay phone skills and there was no cell reception whatsoever. We redeveloped a few rudimentary skills to the extent that we were able to get through to AAA who promised that although we had crossed the line into the province of Southern California a tow truck WOULD be coming.

The essence of wilderness is self sufficiency. After more than enough time for the tow to arrive and having further cajoled the pay phone into calling my daughter for connected outside help, we began to realize that we were in the wilderness and on our own. A little investigation revealed that although the belt drove the water pump, the radiator fan was electric and still functional. With a couple of brilliant suggestions from Kyle that we turn on the heater full blast and crack the hood, we basically drove air cooled Civic hybrid from Porcupine flat to Bishop, stopping to let that electric fan do its job when we began to overheat.

Bright and early the next morning as the service manager was putting his key in the door we delivered the wounded car to the Honda dealer, rented a replacement, and after what I believed was an understanding to “just fix it”, we were on our way to our meeting with the permit official with a sense of humor about dogsleds and goats.


The morning Iceberg Lake.


Kyle resting above Guitar Lake.

From the top of Mt. Whitney I called the dealer to find the progress and was informed my service manager was on vacation and the mechanic was awaiting my authorization to order the rather expensive air conditioning pump. He got it then and there and when I arrived the third of July I was informed that even if the parts arrived there would be no time before the holiday weekend to install them.

Rats! I kept the rental and drove back to Santa Rosa for the weekend, got up at 4AM the following Monday and arrived in Bishop to learn that in spite of our verification the prior week, the pump, but not the clutch, had arrived.

“Bloody cocksucking rats!”, in the words of a memorable aussie  mountaineer met during a storm many years ago in an alpine hut in British Columbia. He claimed to have harpooned several with his ice axe in a hut on Mt. Kenya

Fortunately I was prepared this time with the full regalia of modern connectivity and set to work with a laptop and mifi in a funky motel. As evening approached and the monsoon eased its grip on the mountains I headed up to Sierra View in the Inyo mountains.




The next morning I worked until check out time, dropped by the UC White Mountain field station at the end of Line Road to inquire after an old friend, Frank Powell, who had been director there for twenty years and got directions to Black Canyon.

Black Canyon must be an ancient fault as it cuts diagonally across the Inyos roughly parallel to the analogous Kern canyon in the Sierra across the valley. The climb begins through tuffaceous alluvial fan conglomerates with a spectacular lens of brilliant white tuff from the Long Valley caldera explosion about 750 kya. Isotopically identical ash from this explosion has been identified as far away as Sonoma county.

The black in Black Canyon comes from the Andrews member of the Campito formation and darl slaty members of the Deep Springs formation of the latest Precambrian and early Cambrian (500-530 mya) when creatures more elegant than worms and microbes were just getting started. The Deep Springs is a bit older and pre trilobite.


At some point gold bearing quartz intruded contacts between limestone and more silica rich slate beds and miners followed.



As you enter Black Canyon proper black Deep Springs slates are bedded almost level but as you progress northeastward the bedding gets contorted and twisted in three dimensions as if by a giant dough hook so much that Deep Springs sometimes appears to be intruded into the Campito. Makes you feel that our models of geology are broken down.


If there is any moral to this story it is that if you must break down, Bishop is a great place to do it.



Posted in Geography, Geology, History of Life, Mount Whitney, Paleogeography, Sierra View | Tagged , | 3 Comments

Russians R Us

So perhaps you are red headed and fancy yourself Celtic. Well, I’ve got news for you. There may have been a few red genes somewhere but the Celtic genome and culture were centered in France and characterized by brown hair and male pattern baldness.

You see, the red hair gene harks from more northerly tribes centered around the Jutland peninsula in what is now Germany. We don’t know much about them. Angles, Saxons, Jutes. All we know is that in the fifth century AD they were doing something right such that they grew out of their britches and began migrating in all directions.

Some came to England to fill the vacuum of the Roman abdication. They became known as Anglo Saxons. This is basically the reason I am writing in a language called Anglish. Many also went to Scandinavia where they became known as Vikings.

Now these red headed dudes were nothing but trouble. Bolstered by a climatic optimum they colonized Greenland and Iceland for a bit before the weather went south. They conquered half of England until their cousin Alfred held them off. They plundered France until they were given Normandy (read norsemandy). They dragged their boats between river basins and floated down, bringing their brand of plunder when you can, trade when you can’t all the way to the Black and Caspian seas and contact with the Islamic world.

This brings us to Russia as the Volga is one of these rivers. Rus is red. Pretty much.

All this was prompted by a picture of a late Russian scientist, Vladimir V. Beloussov.

Vladimir V. Beloussov

This guy could well have been one of the Irish clergy recruited to serve in Charlemagne’s bureaucracy. Insulated from the dogma of plate tectonics he developed a hypothesis that rather than subducted ocean crust distilling continents, the ocean floors are continental crust converted to basalt.

I find no reason to believe this, but now that the supposed mechanism of plate motion has been invalidated by modern seismology, everything is on the table. You have to hand it to the guy for thinking outside the box. Maybe it’s the red. Let’s hope the Russians continue to be us.

Posted in Anthropology, Geography, History, Plate Tectonics, Seismic Tomography | Tagged , , , | Leave a comment

Wild Rogue


It had been fourteen years since last running the wilderness section of the Rogue river with my two younger kids then chest high. The first June of the new millennium saw very high flows and few other boaters. The river was roaring and a bit intimidating. Bearing my wife’s stern admonitions we scouted most of the rapids. I remember waiting on the trail that follows the river for a couple of hours pondering the chaotic hydraulics on one rapid and being very relieved and fortunate to see a single raft, probably a local who knew the river well, bounce uneventfully down the middle.

We did the same and had a wonderful trip that left nothing but fond memories. I had not even got my raft in the water for last season so I  jumped at the opportunity to join a trip down the Rogue this year. Rather than a single boat with two kids, this trip had five working boats rowed by extremely competent and experienced boatmen. Rather than high flows, we had sufficient but moderate water to enjoy.

The so called fish ladder is a channel blasted for a route around Rainey Falls. I seriously doubt the fish were in need of such a ladder and suspect it was more the love of kaboom and the need for a human ladder. In June 2000 it was definitely the only game in town as a result of the high flow and this year the water was too low for the other alternatives to running the actual falls and we all wound up taking the fish ladder this time as well.

Oar boats do not do well in the fish ladder and this time we got spun around two times but when you get to the bottom with no broken oars or bones you’ve had a decent run.

At moderate flows the wild Rogue is just a read and run river with fun bouncy rapids. Upstream winds can be a problem on the flats and we were in a onshore pattern with one rainy night, but this is the Pacific Northwest after all.


Lush forests of Douglass fir, oak and madrone line canyon walls of alternating sediments and metamorphosed ocean floor that get progressively younger as you proceed down the river. The bigger rapids take place at the sutures between rock units with harder metamorphic and volcanic rock forming ledges where softer rock downstream was chewed away. For reasons we really do not understand a succession of volcanic island arcs and their eroded sediment basins piled up one after the other in the area of the Klamath and Siskiyou mountains of northern California and southern Oregon beginning two billion years ago when the single celled creatures living then were first evolving nuclei and the continents were apparently swept into a pile down at the south pole.


In Mule Creek Canyon the river cuts between two rock types but the canyon itself seems to be cut into a metamorphic basement underlying the entire complex. Mule Creek Canyon culminates in Blossom Bar rapid, the most technical on the river. At high water in 2000 we were held for a bit in a giant hole where water crashed over the top of the big boulders and pounded down on a kayak strapped across the back of the raft. This year we had difficulty crossing from the scouting eddy back into the main channel. When we finally succeeded on the third try the rapid was pretty easy, but it is very important to get out of the left side current where you must enter and cross to the center channel.

As we approached the take out, my friend Laura who is a veteran of 17 days in the Grand Canyon with me a few years ago asked me what it was about the rivers that keeps me coming back for more. It was a very good question since many senior rafters are beginning to question whether they have the strength for the hard work and the fire in their bellies to take on difficult rapids.

It’s the water. The wonderful ways it moves around the rocks and the awesome power as it falls down rapids. Our hunting and gathering forebears migrated up river canyons, camping as we do, and moving on. Some of us feel that pull and the need to follow the irresistible force of the water, to regain some sense of how to move with it like the fish we once were, and to make it a metaphor for the river we all must follow.




Posted in Geology, Metaphor, River, Rocks, Wilderness | Tagged , | Leave a comment

What Climate Sensitivity Should We Expect?

The great failing of climate science has been the inability to constrain the range of climate sensitivity to human CO2. The possible range remains from slightly negative to +5 degrees for a “doubling”. The concept emerged when the atmosphere was 350 ppm and doubling would be 700 ppm.

We are 50 ppm into the program with little warming to show for it. It is time to look for new approaches. We suggest taking a step back and evaluating what we do know and how that might help us constrain sensitivity.

Half tongue in cheek we have offered a “Dud PDO” index of sensitivity. This is not a great index because we know little about the PDO except that the most recent warming phase was a decade too short for the pattern and it hasn’t warmed since. Maybe the 1997 Niño  shot the wad for the cycle and temperatures have been languishing before a coming fall?During the last cool phase temperatures did fall fitfully for three decades.

We know that human Carbon is only about 5% of the annual Carbon cycle on earth. Elemental Carbon is not a big warming factor, but when you look at the Carbon cycle, Carbon moves through almost entirely as CO2, the accused. One can reasonably argue that our portion of the annual cycle is the outside limit of sensitivity. About half of our emissions appear to be absorbed currently (the red numbers) reducing sensitivity further to around 2.5 %.

Photo Credit: NASA

Photo Credit: NASA


All of the Carbon dioxide currently in the atmosphere represents only about 2% of the “greenhouse gasses” by weight. Humans stand accused of a bit more than 1/4 of the accumulation. However, the gasses do not resonate by weight, they do it by molecule and CO2 is twice as heavy as water, the primary greenhouse agent. For any given weight there will be twice as many resonating molecules of water as CO2. This line of reasoning sets human culpability at about .25% of the greenhouse effect.

Would that it were that simple. A significant part of the greenhouse effect is from the “top down” from incoming solar radiation and CO2 is a marginal player in these spectra.


This effect potentially divides the .25% in half again.

In the outgoing spectra CO2 occupies a prominent position.

saturated wings

But the bands in the middle of the four vertical lines are saturated by Beer’s law. The narrow columns on either side remain and may be amplified by “pressure broadening“. Pending Robert Brown’ s conclusions on the quantum quantities of the broadening effect, we offer an “energy of the photons” gauge for the importance of saturation. This energy is given by the speed of light divided by the wavelength times Planck’s constant. By tabulating the energies for each wavelength in the CO2 absorption spectrum and subtracting the portion that is saturated, we derive a 63% reduction in energy as a result of saturation.

If we keep dividing our culpability in half like this there won’t be much sensitivity left.

So how much climate sensitivity should we expect? What does it mean that we contribute 5% to a global annual cycle that has resulted in the accumulation of 120 additional ppm of a gas that in aggregate represents 1% of the resonating molecules in the atmosphere? What does it imply that whatever effect our contribution has made is heavily weighted to the outgoing spectrum which is maybe half of the greenhouse effect and perhaps half of that spectrum is saturated?

It means that unless there are feedback or emergent effects that have been conspicuously absent for the last 17 years, we have little reason to expect high climate sensitivity to a “doubling” of CO2. If we are responsible for .0625% of the current greenhouse effect and the greenhouse effect explains all of the warming since 1850 (.8 degrees), we are responsible for .05 degrees so far. Five hundredths of a degree divided by 120 ppm yields a human climate sensitivity of .0004 degrees/ppm.

Not much.



Posted in Climate, climate sensitivity, Dud PDO, Energy of Photons | Tagged | Leave a comment