Virus and Veins

Whether Ebola infects the blood tube walls directly or causes an immune response that damages them, one of the advanced symptoms is leakage of blood from the tubes or vessels. We know even less about the red blotch virus that is infecting our grape vines except that, like Ebola in humans, it can be found in all parts of the plant. Also like Ebola a signature symptom of red blotch is the damage to leaf veins that causes them to release red anthrocyanins, particularly on the underside of the leaf.


The analogy can only be taken so far. While neither Ebola nor Red Blotch seem to be very efficient transmitters, Red Blotch, which we propose to rename Red Vein Virus after its characteristic symptom, seems rarely fatal to the grapevine.  In fact, the late onset of the symptoms in the growing season allows bountiful grape production. It is not yet clear if the late loss of green canopy or asymptomatic processes earlier in the growing season are responsible for the slow ripening, low sugar accumulation, and high acidity in Red Vein Virus affected fruit.

A brief natural history of viruses seems worthwhile. Before life had colonized land, viruses and bacteria and  had been battling for hegemony in the oceans for billions of years. Fungi probably entered the fray about 1.5 billion years ago. The bacteria were busy building algal mats and the sort of stuff we might call slime. All the while they had to deal with these terrorists or barbarians we call viruses, yet the competition and genetic accommodation yielded advances. We may very well owe the polymerases of mitochondria which provide the energy for all more complex life, sex, and even photosynthesis to viral innovation.

At a price. Viruses are also prime suspects for mass extinctions and huge swings in ocean chemistry.

With all this in mind, how do we deal with our comparatively trivial problems today? Dr. Sudarshana of USDA and UC Davis says that Red Vein Virus is endemic to California. My suspicion is he is more right than he knows. The results are not yet back but we have found very similar symptoms in wild grape, vitis California, wild blackberry, and possibly poison oak.


Red Vein Viral symptoms in wild Grape emerged in 2014.


Suspicious symptoms in wild blackberry.

We have seen strong circumstantial evidence that Red Vein Virus is now entering vineyards from adjacent woodlands. This would be truly endemic.

We strongly suspect mites as one of the vectors, but their low mobility and strange mid vineyard cases suggest other more mobile vectors as well.

One school of thought is that Ebola is lethal because it elicits an all or nothing cytosine overreaction from the human immune system. Whether or not this is the case, we wonder if the widespread ripping out of infected vineyards may be an exaggerated “immune response” from growers. Relying on clean plant material and slow transmission of the disease may be a bad choice if reinfection from native plants joins infection from ubiquitous infected neighboring vineyards and infected roots left in the soil as agents of the disease.

We may have reached the point where the disease is truly endemic and inevitable. The better choice may be to learn to work with it until resistant stock can be developed.

Posted in Biology, Extinctions, Microbial Dark Matter, Red Blotch Disease, RGBaV | Tagged , , | Leave a comment

The Ocean Ate It

One of the arguments one hears often these days to explain the lack of lower atmospheric warming for a human generation is that the ocean is somehow absorbing the “heat” or enthalpy that Carbon dioxide is supposed to be creating in the atmosphere. This argument has a large number of failings straight away since the infra red back radiation produced by this friendly dioxide can only penetrate a few microns into the ocean surface; the oceans are extremely thermally stable and stratified with the 80m  warm mixed layer very happy to stay on top of the colder layers below; and the way our planet generally works is that the sun warms the surface (70% ocean) and the surface warms the air.

Kevin Trenberth published an absurd paper a while back (Balmaseda et al, 2013) claiming that the piling up of warm water in the western Pacific prior to an el Niño somehow injected this water deep into the ocean. Our response was that whatever mysterious energy source could force this warm water down against the thermal gradient would in itself explain the missing heat.

With the backdrop of this sort of foolishness it is a  great pleasure to be able to respond to a recent paper,  Chen and Tung (2014), whose authors actually have a clue how the planet works and have put their fingers on a mechanism that actually can transmit substantial amounts of enthalpy into the deep ocean. That mechanism is salinity and the thermo-saline sinking of super cooled and super dense salty water at the edges of sea ice where rejection of brine from the freezing process tips the density to a point where warmer water will sink.

Their analysis of this process is correct and they provide interesting evidence that enthalpy is being transmitted to at least 2000m in the north Atlantic and the Atlantic portion of what is now called the Southern ocean. Unfortunately, they have cast this impressive bit of work as yet another apology for the lack of atmospheric warming when there is no logical connection between the heat being sunk and the atmosphere. The areas where this saline subduction occurs are extremely small in relation to the surface of the planet and generally remote from the areas where air temperature is high. The atmosphere would be very hard pressed to focus enough energy on these small areas to cool itself. It seems far more likely that the energy being sunk is solar warmed surface water from the Indian and Atlantic oceans whose waters account for all of the average ocean warming since the millennium.

Almost all modern temperature data for the oceans and atmosphere are expressed as anomaly, or deviation from some baseline. There are good reasons for doing this, but in doing so one loses any sense of the relationship between absolute temperatures of the ocean and the atmosphere. By way of rebuttal, we offer here an analysis of the absolute temperatures of the water and lower atmosphere in the areas where this saline subduction is shown to occur as well as the rest of the oceans.

Proponents of human warming are very fond of citing their knowledge of the optical and physical properties of Carbon dioxide as if this tiny bit of physics alone could explain how a gas that represents less than 1% of the resonating molecules in the atmosphere and whose absorption bands are 50% saturated could accomplish such magnificent warming between 1976 to 2000 and suddenly stop. The rest of physics argues against this and among these physics is the rule that energy flows, on average, from warmer to colder bodies.

Olv2 1 2000

Here is the average absolute sea surface temperature from January 2000. You can see that in the Atlantic zone of the Southern ocean the temperature ranges from 0 to -1.7C as do the north Atlantic/Arctic waters north of Iceland. South of Iceland and northeastward to Scandinavia the Gulf Stream keeps the temperature much higher, maybe 7C.


Here is the absolute lower atmospheric temperature for January 2000. It is in Kelvin so you must subtract 272 to get C. North of Iceland and in the Southern ocean the average air temperature is -17C and south of Iceland it is about -12C. These air temperatures are 10-15C lower than the ocean below. Energy is flowing from the ocean to the atmosphere even in these saline subduction regions. Furthermore, the same relationship holds for all ocean areas with the tropical ocean temperatures being 20C higher than the atmosphere above.


Here we skip to the other extreme in the fourteen year range explored by Chen and Tung.


We are not going to bore you with 168 examples of the monthly differentials for the fourteen year period, but without exception the absolute atmospheric temperature above the saline subduction areas as well as all ocean areas has been lower than the absolute ocean surface on a monthly average basis.

If Chen and Tung will argue that the ocean heat content increases they have shown from 2000 to 2014 represent heat lost to the atmosphere they will need to show where and how this energy transfer would occur. Would it be sensible heat? Latent heat? Qnet? Would there be tunnels of energy flow masked in the monthly averages? Would a bottom layer in the lower atmosphere somehow transfer energy to the ocean in a fashion masked by the entire profile?

We do not have data to answer all of these questions, but it is very clear that the net energy flow on a planetary basis is from the ocean to the atmosphere. It is also very clear that Carbon dioxide cannot warm the ocean without also warming the atmosphere. The lower atmosphere has stopped warming. If we are to believe that increases in ocean heat content represent sequestration of atmospheric enthalpy alleged from exponential increases in human CO2, a real time mechanism for energy transfer from the atmosphere to the oceans must be shown. That effort is all the more difficult when the ocean is warmer than the atmosphere.

The ocean didn’t eat it.



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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

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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.


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