Stigma, The Scarlet Letter, and The Red Blotch

In the highly competitive business of marketing wine, consumer perception is everything and nobody wants to admit their vineyards have problems. This fear has slowed research into the habits of a virus now known to cause Red Blotch Disease. It is not such a good name because it often causes red veins more than red blotches and absent nutrient deficiencies and other stresses, infected vines may have no more severe symptoms than pale green leaves with red veins more apparent on the underside of the leaf.

Underside redening veins

Individual canes and cordon arms can be symptomatic while the rest of the vine remains healthier.


The retail cost of assays to positively identify the virus approaches $500 and the cost to test every vine in a vineyard is prohibitive to anyone but the USDA, but they have done this in the UC Davis Oakville field station and some cooperating private vineyards with the caveat that the locations remain secret. The result is that they have watched the disease move through the vineyard from areas of complete infection to adjacent vines in a shotgun fashion. Fortunately, reddening of the veins distinguishes the disease from other read leaf symptoms enough that at least crude diagnoses can be made on the fly.


In the image above Red Blotch has jumped the road from a generally infected block on the left to form a beachhead patch  in a clean block on the right. There seems to be a significant edge effect to the spread of the disease that lead us to propose the highway hypothesis.


Infection above may have come from vineyard below which was ripped out and replanted.


This vineyard is speckled with a concentration along the edge.

Dr. Poojari at Washington State University let Virginia leafhoppers chew on Red Blotch leaves for three days and moved them to uninfected vines, showing that at least in greenhouse conditions Virginia leafhoppers can transmit the disease.

We do not yet have Virginia leafhoppers in Sanapanoma, but like the Virginians our local hoppers overwinter in weeds and wooded areas and migrate back to the vines each year. One east coast hopper does not even overwinter in the northern regions and makes an annual migration of hundreds of miles to chew on northern grapes.

Pruners beginning at the edges with infected shears and mites are other possible explanations for the edge effect.

The stigma has resulted in many vineyards being ripped out and this is epidemic in Carneros right now. Driving around it is easy to see that nearly half of the older vineyards in Napa and Sonoma are infected. Some vineyards have dropped all the fruit on infected vines. As long as the new Scarlet Letter is the letter R, expect to see many more uprooted vines soon.

The Oakville field station seems to be doing a very good job of managing the disease and aside from the stigma it may well be possible to produce excellent wine from infected vines. If a way can be found to preserve the flavors in these vines, a reduction in brix might be a benefit by reducing the high alcohol content introduced to winemaking by phylloxera resistant rootstocks.








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GRBaV, The Highway Hypothesis

On our highways fossil energy propels nearly incessant rivers of iron and plastic machines at velocities approaching one hundred feet per second. These machines produce billowing vortices of dust, microbes, micronutrients, and exhaust chemicals in the surrounding atmosphere as they pass. These billowing vortices are nearly invisible on paved roads but are readily apparent from the higher dust content on dirt roads in the vineyards.

It has been well-known for a long time that dust in orchards and vineyards fosters mites and dust suppression has been long advised. This year has been a bad mite year and anyone paying attention can see mite damage beginning at vineyard row ends near highways and progressing in. If you practice a bit, you can begin to distinguish mite damage from other red symptoms because it typically produces a more bronze than red coloration that reads duller from a distance.

Mite Damage

The bronze patch in this roadside vineyard is mite damage.

Working in the Northern California wine country, business and habits carry me widely and last year it seemed red vines were cropping up on highway row ends. Whether because these high profile red plants were deemed unsightly, or because the owners were wise, many of these plants were removed and replaced. No farmer would replace a vine for mite damage.

RGBaV typically produces a brighter and more translucent red coloration that progresses from the veins of the leaf like these wild grape leaves photographed on the St. Helena road.

Maybe RGB

To the best of my knowledge RGBaV has not yet been identified in Vitis californica and I had been watching for symptoms for a couple of years. This was the first red coloration of any kind I had seen in wild grape and I took samples to the UCD Oakville field station where it will be assayed for the presence of the virus.

If this test proves positive, it will be interesting because there are no neighboring vineyards and this plant and another on the St. Helena side are right on the road.

The natural world we live in is far more complex than we care to believe, and we must avoid jumping to hasty conclusions. We offer here only a hypothesis based on a few observations that will need far more testing, but it is possible this circular virus is taking a ride down the turbulent rivers of air pumped along by our cars.

Posted in Biology, Ecology, Red Blotch Disease, RGBaV, Wine | Tagged , , | 1 Comment


It happens I have an extremely goofy dog. Teasing him as he thrust his legs in the air as if doing some high hurdle in reverse lying on his back on the couch, he looked over upside down and winked at me. He probably thinks me goofy as I exercise horrid approximations of yoga postures.

It became suddenly clear that a wink is a gesture of trust. I winked back. He winked again…

Wink Dog

This is not my dog, but you get the idea. Seems likely to mean, ” I can take my eyes off you, for you are my friend.” Of course, humans can construe anything and we can spin winks cynically, but that is our problem. Dogs just don’t do that.

Wink Human

Posted in Animal Behavior, Anthropology, Biology, Body Language | Tagged , | Leave a comment

Aftershocks Implicate Unusual Fault System in American Canyon Quake

California can be thought of as a ice flow where multiple independent blocks with different inherent buoyancies are at times pressed together, pulled apart, and slid past each other. The M 6.1 American Canyon quake did not take place on any of the major fault systems we are taught to fear. Some early speculation was voiced that it was on the West Napa fault, but the pattern of aftershocks implicates an unusual fault system that extends along the crest of the Mayacamas mountains.



Here is the epicenter and immediate aftershocks on a geological map of Napa County. The magenta line is a hypothesized southern extension of the Mayacamas ridge fault.

Update, USGS has revised the epicenter and streamed in a large number of “aftershocks”. They consider an interesting swarm of subsensory quakes up by Clearlake to be aftershocks. Whether these should be considered a separate event is debatable.

Rev Aftershocks



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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