The Myth of Stasis

As one gets on a bit in years it is a comfort when customary things like the dental floss and shoes stay the same, but the sad fact is that most often they do  not and it is necessary to find available replacements with a different fit and feel.

So it seems to have been through geological time. Even a casual look at sediment sections  in cuts along the side of the road reveals that nothing ever stays the same. Yet there seems a notion among people who embrace and foster new styles of floss and shoes, that our climate should stay the same. Not.

Because we are fortunate enough to live in an interglacial period of the current ice age, the Pleistocene, and human agriculture, civilization, and technology began to flourish after it had warmed up a bit, we seem to believe we are entitled to a stable climate. It has never been thus. Civilizations have been wiped off the map when they built sand castles on the assumption that climate would endure.


Far from the garden of Eden, this is what Oxygen isotopes in ocean cores tell us about the temperature of the Pleistocene. The genus Homo  is believed to have evolved at the Pliocene/Pleistocene boundary. The real garden was before the janky Pleistocene when the climate was a bit warmer and far more stable. No wonder we naked apes are fraught with guilt and inclined to sacrifice when the fickle Edens of interglacial periods wane dry and cold.

All this is time scale of millions of years. A human life is twenty to thirty thousand days.


The “Hollowscene” is the name we have given the interglacial period we happen to live in as if it warranted classification with the Miocene, Pliocene, etc. We feel sooo special. For perspective there is evidence of agriculture in Asia about eleven thousand years ago, the first cities five thousand years ago, and the Persian  first super empire and the foundations of world religions over a millennium centered about two thousand years ago.

The graphic above is a nice piece of work from a while back that shows eight different proxies for temperature since the last glaciation and a stupid heavy “average” line. At first glance one might conclude that our proxies are completely out to lunch, out of phase, and unreliable. This is not the case. They record regional variations. The dark blue (hard to cipher at this lousy resolution) is a tropical Atlantic core. The rust color is a composite of Pacific cores and these two are the most logical segues from the worldwide composite of cores in the first graphic. The other proxies are Greenland, Kilimanjaro, and two Antarctic ice cores,  a North Atlantic core, and European pollen.

The take home message should be that the regional variations are so extreme and out of phase as to render the average meaningless in regard to living conditions.

Drought American West Cook et al 2007

We can zoom in to a particular region, the western U.S, in this graphic from Cook et al 2007. The Anasazi founded Chaco Canyon, the hub of a cultural center and an impressive series of roads in about 900 and abandoned it in about 1130.


Let’s zoom in further to something codgers alive today can remember. Everything here is back to global scale and the red temperature anomaly is the thermometer and satellite version of the average dark line panned as meaningless in the hollowscene. No actual place on earth experienced this time series as such and it is extracted from daily, seasonal, and regional variations that would render it absurd, but if we will compare temperature with other global observations, we have no choice.

It should be clear that climate like evolution, language, civilization,  culture, and political hegemony is not static on any time scale. Weather has always been crazy. We can no more hold on to some idealized climate than I can forever have my favorite dental floss.

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GRBaV, An Hypothetical Model for Disease Progression

It’s not like we really have a firm understanding why some plants typically produce brilliant red foliage before dropping their leaves and others do not. It has been suggested that anthrocyanins are produced as a sun screen as chlorophyll is pulled back, but this seems a little shaky as it is unclear why soon to be abandoned leaves would warrant this protection and it does not explain why a large number of plants, including grapes, don’t bother.

At least they are not supposed to. It has been well known for some time that certain mineral deficiencies, certain viruses, and a girdling beetle prompt red varietals to produce red leaves worthy of an autumn centerpiece, but a new player, GRBaV, has burst on to the scene in the last five years and the associated disease has progressed rapidly enough that it is becoming harder and harder to find red varietal vineyards in Napa and Sonoma counties that do not exhibit symptoms. Infected white varietals do not show any red leaf color but have the same low brix and high acidity as affected reds.

And now it is in the wild grape, vitis California. In late August we first noticed symptoms in wild grape. These vines climb high in trees and are often protected by formidable sentries of poison oak. When we finally found an accessible sample we took it to the UC Davis Oakville station. This small sample did not test positive but subsequent testing of symptomatic wild grape did test positive for GRBaV. (Dr. Sudarshana, personal communication).


Symptoms like these have proliferated since August in the wild grape.

It is easy to get the feeling that people just don’t have their arms around the magnitude of this problem. One sees symptomatic vineyards being ripped out and replanted as if there were a meaningful way to prevent reintroduction of the disease. Some vineyards replanted in 2010 are already completely reinfected.


We see the disease beginning in vines with red anthrocyanins being produced around the loci of insect damage. Mites and leafhoppers are prime suspects.


In this picture one can see typical mite stippling that has led to typical rust colored “bronzing” and then a progression to more scarlet coloration and vein reddening characteristic of red blotch.

We see a second stage where leaves develop red veins but remain yellow and fall off prematurely.


We observe a discoloration of the cane wood typical of beetle girdling but ending at nodes which beetles avoid. This suggests to us progression of the disease down the shoots from initial infection in the leaves. A downward progression is also consistent with observed “one armed” infections of cordons.


Sample 15 CS4 1103P  IMG_0760


We see the final stage as the development of gross symptoms. These symptoms of maroon leaves are associated with a unique tissue profile strongly deficient in Phosphorus and extremely elevated in Iron. Prior to symptoms the tissue profile is normal. This would seem to indicate a blockage of P uptake and Fe circulation.

Dr. Sudarshana at Davis has observed a one year latency between detection of the virus by assay and the onset of symptoms and Dr. Fuchs at Cornell has found an average two year latency. Part of the discrepancy may be in the definition of “onset of symptoms” but two strains of the virus have been identified and it could be that the western version moves more quickly to symptoms. It seems the western variety may spread more efficiently as well.

We suspect a two or three year progression between initial and gross symptoms and see a strong association of extreme gross symptoms with the 44-53 rootstock. At the gross symptom stage the plants seem to hold on to their leaves longer than in the initial stages.

If there is any good news here it is that symptomatic plants can still produce bountiful crops of grapes. The symptoms do not appear until very late in the growing season and this year they have been progressive, even accelerating after harvest.

It is clear to us that it is far too late to contain this disease. We will need to adjust viticultural and winemaking techniques and probably winemaking styles until resistant stock is found.

It seems to us that current research is bogged down with insect vectors. This would be interesting to know but current IPM and sustainable techniques forbid the complete elimination of insect populations even if this were possible. We should be aggressively looking for resistant stock, but to the best of our knowledge there is no current research on this front.

We may be witnessing the transition of red varietals to plants that do turn red in the fall.

KEF_2013_11_01_9723-Edit Maple

Maple. Photo credit KEF.

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Satellites and Thermometers

In a recent blog discussion with some unusually astute folks who are still concerned about human warming, the thread came to a dead-end at satellites and thermometers. It became clear that the real crux of the climate debate between well-studied people boils down to whether one believes the satellite or the surface temperature time series.

So what are the differences?


Here is the NASA Goddard surface index in red and the UAH satellite index in green from 1975. The surface index is from about five feet off the ground at weather stations and the satellite measures the entire lower atmosphere up to about the height of Mt. Whitney so one expects it to be generally lower and it is. They agree pretty well with no systematic discrepancies until recently.

uah giss best

Here I added triple running mean filters, linear trend lines, and the Berkeley land only data for kicks. Once again pretty much what one expects except the land data has a hotter trend and goes way out to lunch and out of phase with the others in 2010 (the data is cautioned as preliminary).


Here we zoom in to examine the systematic recent differences that begin in 2013. The trend lines are headed in different directions. Which to believe? If you look carefully at the second graphic you can see that there was only one time previously in the late eighties when the vectors diverged in sine.

There is the specter of data adjustments. They have occurred in both datasets but the surface adjustments have the disturbing habit of always cooling the past and warming the recent.

Noaa Adjustments

Here is what NOAA acknowledges.


Here is what Tony Heller finds since 2012. As you can see the changes are very small, but adding .07C to the GISS surface data would account for the divergence since 2013.

GISS rotated

One can get the idea from this crude rotation of the plot.

The issue is critical because when atmospheric warming is negligible, the atmosphere makes no contribution to ocean warming. The atmosphere cannot warm the ocean directly because IR radiation from greenhouse gasses penetrates no deeper than the micron scale skin of water surfaces and the ocean is always warmer than the atmosphere. The atmosphere can only warm the ocean by increasing in warmth itself and thereby slowing the rate of ocean cooling.

So either the atmosphere is significantly warming or it is not. Either it is contributing to ocean warming or it is not. Two sets of measurements, two different results, enormous consequences, the crux of the climate debate.





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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