Pope Misguided the XXXXXXXXIX Preaches Crusade Against Carbon

In an action that betrays all the more clearly the religious roots of the Carbon crusade, the Pope continues a long and sorry tradition of involving the church in matters best left to science and individual conscience. From Galileo a harmless gas the church has an unimaginably dismal record in matters of science. Even flipping a coin on each issue would have produced a better result. After all this time he might have learned…

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Lamarc Col, Muir Pass, Mt. solomons, Charybdis, Mt. Goddard, Echo Col, December, 1976

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We had fallen in love with the moonscape of Muir Pass and the improbable hut there while hiking the John Muir Trail in 1966. No vegetation besides hardy buckwheats and lichen can be seen in any direction from this 11,955′ pass that divides the San Joaquin and Kings rivers. We resolved then and there that we simply must see this surreal place in the winter and made three attempts to ski in during the early 70’s college Christmas vacations that were thwarted by inadequate equipment and planning, bad weather, and deep snow with companions unequal to the raw wild in roughly that order.

74-12.18 Humphries Basin Camp

We set up this camp in Humphries Basin in December, 1974 with a notion to follow the “Bishop Loop” route to Muir Pass.

Scott Lambert and I were bad assed Orinda kids and we planned another try in December, 1976, but this was the apex of the drought and there was little snow. We carried our skis over Lamarc Col, stayed several days at the Muir Hut and climbed Mt. Solomons, Charybdis, and Mt. Goddard before carrying our skis out over Echo Col. It would have been very foolish to venture out there without skis.

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The first night we camped high on Bishop Creek.

76-12_2 Sunrise on the Ice Bishop Creek

We reached Muir Pass mid-day our second day and I climbed Mt. Solomons behind the hut the first evening we were there.

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I was rewarded with this view to the south and Charybdis.

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And this view to the north of Wanda Lake and the upper San Joaquin drainage we had followed up.

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Back down at the hut…

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The moonscape, Wanda Lake, and Mt. McGee were very much the experience we had first imagined a decade earlier. The next morning we set out across the Ionian Basin to climb Mt. Goddard.

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The ice was two feet thick but it boomed like cannon under our weight.

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South from Mt. Goddard.

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North.

The next day I climbed Charybdis and found this view of Mt. Goddard to the north.

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Approaching the metamorphic weakness that allows Echo Col on the way out.

Ultimately this trip was about the ice, the lessons of cold with little snow.

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The culmination of a decade long dream nearly forty years ago, and an unforgettable lesson in the beauty and complexity of the planet we live on.

 

 

 

 

 

 

 

 

 

 

 

 

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GRBaV, The Vector, Which Mite It Be?

At a recent UC extension course, “Current Issues in Vineyard Health”, an impressive group of researchers presented their work. Dr. Brian Bahder revealed evidence of a second variant of GRBaV, commonly called red blotch virus, that seems to have invaded a block at the UC Oakville Station from a different direction. He also reported finding both variants in wild blackberry, adding that prolific bush to wild grape as natural reservoirs of the disease. Perhaps poison oak will be next?

The tone of the presenters at this course was very skeptical of a paper by Dr. Bahder’s old colleague and fellow doctoral candidate at Washington State, Dr. Poojari, (et. al 3013) which reported evidence that the Virginia Leafhopper could transmit the virus. What Dr. Poojari did was let Virginia hoppers feed on infected plants and then move them to uninfected plants. His result was that an identical virus was transmitted to the uninfected plant. Seems pretty solid, but I have heard suspicions of contamination of the supposedly uninfected sample. Dr. Bahder found at a Davis increase block that was fairly crawling with Virginia hoppers that little or no transmission seemed to be taking place, but at the Oakville Station where the Virginian has not yet arrived significant transmission is well documented. Even in Washington the Virginia hoppers seem not to be transmitting the virus in the field.

Obviously  transmission of blotch is taking place out of the range of the Virginia hopper. Still, Dr. Bahder’s picture of  blackberry looked pretty well hopper chewed to my eye. Unless  Dr. Poojari’s receptor vines were contaminated, his work shows at very least that hoppers are biochemically capable of transmitting the virus.

Vector relationships are complex and usually specific. They involve interactions between the viral coat proteins and proteins in the vector’s digestive tract. The virus must survive in the vector at least long enough for the vector to move to another plant. Relationships seem to range from short-term persistence in the mouth of the vector to “circulative” virulence where the virus takes a ride through the insect and into its salivary to long-term arrangements where the virus reproduces in the vector .

We don’t even have the first clue about much of this stuff in the case of blotch, but those of us with more than an academic interest get an automatic license to think. We live and bleed with the enormous financial consequences of this disease, and so can be forgiven an abductive thought experiment.

Let’s list the few things we think we know about the disease in rough order of certainty:

1. There are at least two variants and one may be more recent.

2. A substantially similar virus has been documented in a grape leaf collected in Sonoma  County in 1940.

3. Blackberry and wild grape harbor the virus, possibly by transmission from vineyards.

4. Koch’s postulates seem to have been fulfilled.

5. One or two year latency has been reported between detectable titers and symptoms.

6. Symptoms appear to have increased exponentially in the last season.

7. There appears to be an edge effect resulting from transmission from neighboring vineyards and woodlands.

8. There appears (to me anyway) to be a road effect of transmission by machinery, dust, or tissue.

What sort of vector could do all of this?

Let’s start out with the known vectors of Geminiviridae. Not that this list should be exclusive, but vector relationships are often conserved.

drawing.png

One can see from this after Hogenhout et al 2008 that the list of suspects is rather small and that whiteflies and leafhoppers do all the known damage with the lone exception of one case of a treehopper, a similar insect in the same family as the leafhopper. But there is a problem  because GRBaV coat proteins are very different from the four genera above and may eventually become its own genus.

Blotchcoat vector

This graphic by Dr. Fuchs shows that GRBaV coat proteins hark back to the family of all Gemini virus genera. This family is believed to have evolved in Africa from algal plasmids before the breakup of Pangea and New World Geminiviridae seem to lost the Old World retinue of “satellite” molecules by evolution in isolation.

Begomovirus Proteins Flourescing in a Whitefly

These images by Dr. Monica Gotz show Begomovirid proteins fluorescing in the gut of a whitefly.

All things considered, what little we know of Geminivirid vectors is not much help. I have heard verbally from someone who ought to know that white flies have been considered and rejected as GRBaV vectors, and the UC groups seem not at all salubrious about leafhoppers, in spite of having vacuumed them up for testing last season. Furthermore, most plant virus vector specificity is at the genus level. As Dr. Fuchs has shown, GRBaV coat proteins hark back to the family level. This may well mean all bets are off regarding potential blotch vectors.

The known vectors (hoppers and whiteflies), besides being contradicted by some research and current opinion, seem unable to explain “road effects”. They are both leaf feeders that tend to be in population decline at harvest. Furthermore, they are both adapted to dispersal by flight. They are readily visible and produce choking clouds when disturbed. One simply does not see them on harvested grapes or grape trucks. Whiteflies have sluggish instars and hoppers do not even undergo true metamorphosis with the larval stages looking remarkably like an adult.

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Trilobite looking whitefly instars credit Shetlar at Oregon State University.

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Grape leafhopper instars and an adult by Martin Rice at Iowa State.

Although sluggish instars of mealy bugs which vector leafroll virus  are known to become unlikely aviators by climbing shoot tips to launch into the wind, mealy bug adults have no ability to fly. For whiteflies and hoppers flight by adults is a vastly more efficient means of dispersal.

If not whiteflies or hoppers, what?

Sharpshooters are in the same family as leafhoppers and they have long feeding tubes able to reach into the xylem of plants. They are known vectors of bacteria, but not of viruses, and they have been shown to “hand off” Pierce’s Disease bacteria to common leafhoppers in grapes. Word has it they are being looked at, but sharpshooters are big and obvious, and absent a “hand off” to a more ubiquitous insect, they just don’t seem do have the population density or distribution in Sanapanoma to explain the rapid spread of bloch symptoms.

Blue Green Sharpshooter

Blue Green Sharpshooter UC IPM online.

Cixids are another bunch of hoppy little guys in the Cicade family with leafhoppers and sharpshooters. They are known to vector the “bois noir” phytoplasma disease of grapes in Europe and a proteobacterium disease of beets. Rhonda Smith of UC extension in Sonoma County reportedly pulled in the EGVM traps to look at Cixids. Cixids are also leaf feeders which tend to spike in population early in the season.

Cixiid

Cixiid by Ian Boyd

Speaking of phytoplasmas, a leafhopper is known to vector the phytoplasma responsible for “flavescence dore” which is spreading across Europe. The symptoms of this disease are remarkably similar to blotch. We ran broad spectrum phytoplasma qPCR assays on some blotch positive vines and they came back negative.

What about mites? They are about the only vectors left unless you want to get into fungi or pollen.

Nobody seems to be considering the Acari. There are three (barely) visible web spinning mites, Pacific, Two Spotted, and Willamette that are grapevine nuisances. None of them is a known vector of anything. Pacific and Willamette seem somewhat antagonistic since sulfur sprays commonly used in the early season to control fungus, and to which all mites seem susceptible to some degree, skew their relative populations, and generally delay their population spikes until after sulfur is discontinued. Even with the sulfur delay, populations of these mites fall to very low levels by harvest.

There is a parallel universe of biological dark matter in the form of invisible mites.

11Chuck images

This amazing micrograph by D. Walter shows microscopic broad mites catching a ride on a white fly. Microscopic mites also infest bee colonies.

The Eriophid mites are present in our grapevines and are known virus vectors. Erineum mites, “strains” of which attack buds and cause leaf curl in addition to the well known “fools phylloxera” erinea galls on leaves, are microscopic but are very sensitive to sulfur. Dr. Monica Cooper of UC Extension Napa and Dr. Vaughn Walton at OSU have studied these by putting double sided scotch tape around canes to catch them. At least in Oregon there is also a microscopic “rust” mite, Calepitrimerus, which joins the three “strains” of Colomerus Erineum mites and likely a host of microscopic predatory mites as invisible armies marching up and down our vines.

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This from Dr. Walton shows a micrograph of an Eriophid mite and an illustration of where they winter over in the buds and scales. Eriophid mites are known to vector Secovirus in black currents and peaches, and Potyvirus in wheat etc., and in figs.

There is another microscopic Acarid, Brevipalpus, which may be among us. This notorious mite with worldwide tropical and subtropical distribution is an infamous vector of Rhabdovirus. This plant version of rabies affects eggplant, coffee, passion fruit, and Orchids among commercial plants. Brevipalpus is also known to vector Bromovirus in cucumber,  Potyvirus in dasheen, and so many unknown viruses that en entire category, Brevipalpus Transmitted Viruses or BTV has been proposed. The most well known BTV is Citrus Leprosis Virus. Dr. Childers (personal communication) has found Brevipalpus californicus  on grape vines in the Central Valley.

Brevipalpus

Micrograph from Kitajima et al 2010. Microscopic mites as vectors can explain all of the known and supposed features of the spread of GRBaV. They are readily airborne and easily spread by wind and mechanical turbulence. They are spread by larger insects, birds, deer, and human workers. They explain both edge effects and road effects. They peak in population at harvest. They can explain how a truckload of grapes could infect a wild grape along a road miles from any vineyard. They have both the population and distribution to explain the rapid spread of symptoms.

In the end we are left with a virus whose coat proteins hark back to the Permian. A virus which has existed in Sonoma County since at least 1940, yet whose current symptoms have exploded in the last six years to nearly every vineyard in Napa and Sonoma counties. A virus whose current symptoms may result from the work of vectors two years ago.

A new vector relationship seems very likely. This new vector need not necessarily be a known Geminivirid vector, and in fact the known vectors and their ilk have been marginalized as suspects by recent research. The large, easy to see suspects are being exhausted. We may need to look to the microscopic dark matter of the Acari, they just mite be it.

 

 

 

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Hold and Haul, The Surprising Result of a Careful Analysis of Sustainability

The purpose of this investigation is to evaluate the “sustainability” in terms of fossil energy use between localized wastewater treatment at a sewage treatment facility and “hold and haul” trucking to the EBMUD cogeneration facility in Oakland for a new American Canyon winery.

According to the EPA typical wastewater treatment energy consumption is 1200 KWh/million gallons or .0012KWh/gallon. There are 40.7 KWh in a gallon of diesel when the two are equilibrated in joules. We therefore multiply to find that a wastewater facility typically uses .04884 (let’s just say .05) equivalent gallons of diesel to treat a gallon of wastewater

The 64 mile round trip to EBMUD from American Canyon @ 5 mpg uses 13 gallons of diesel. Divided by the 5000 gallons in the truck this yields .0026 gallons diesel/gallon wastewater delivered to EBMUD.

Right away it is clear that local wastewater treatment requires nearly twenty times more diesel equivalent energy than hauling to EBMUD.

The comparison is not quite fair because only about half of California electricity is produced by burning fossil fuels. The other half is more sustainable, although “unspecified” sources and the question of nuclear sustainability might make this a substantial exaggeration.

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In an abundance of generosity we will just say that half of California’s electricity is sustainable and divide the .05 gallon diesel to gallon wastewater at a treatment plant in half. At .025 gallons diesel per treated gallon local wastewater treatment uses only about ten times more fossil energy than hauling to EBMUD.

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Nothing is simple. California produces most of the unsustainable half of its electricity from natural gas. To make this equivalent to the diesel burned in the truck to EBMUD this natural gas must be adjusted first by the conversion efficiency to KWh and second for the relative joule content (.67) of natural gas to diesel.

We accomplish this by first dividing the .025 gallons first by the relative energy content .67 to yield .037 and this result by the conversion efficiency .32 to yield .117 diesel equivalent gallons to treat a gallon of wastewater at a typical local plant.

The analysis thus far has compared local treatment with just the transportation to EBMUD as if there were no energy used to treat it at EBMUD. Surprisingly, not only is this justified, but EBMUD actually produces 20% more energy from the wastewater by cogeneration than the processing consumes.

Thus we must take our .117 adjusted diesel gallons to process a gallon of wastewater at a local plant and multiply it by 1.2 to yield EBMUD equivalent gallons, yielding .14 gallons.

We conclude that the .14 equivalent gallons of diesel to process wastewater locally compared to the .0026 gallons used to haul it to EBMUD reveals that local processing would require fifty times more fossil fuel that Hauling to EBMUD. We therefore further conclude that hold and haul is fifty times more sustainable in terms of fossil energy use.

 

 

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The end of the Hollowscene

The concept of the Holocene epoch is a 19th century notion developed when the preceding “ice age” was thought of as a monolithic block of ice extending back to the end of the Pliocene. In this context it made sense to classify the current warmer condition as a new epoch. We have since learned that rather than being a solid block of ice the Pleistocene has been a period of wild swings between glacial periods and interglacial periods like our own, and that several prior interglacial periods have been warmer than our current interglacial so far.

Iceindex

One can easily see from the graphic above that to classify our current interglacial as an epoch in a league with the Pliocene, which began near the left edge of the graphic as the warmer yet Miocene ended, is simply absurd. The absurdity is further exponentially compounded by the recent suggestion of an “Anthropocene”, presumably beginning in 1850. This notion is propounded by zealots who ascribe far more influence to human activity than any evidence supports. We therefore declare the “Misanthroposcene” and the “Hollowscene” null and void.

Sorry y’all, but we are still very much in the Pleistocene. Tell you what, since our interglacial has not been properly named, we propose the Anthropic interglacial, and will refer to it thus henceforth.

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GRBaV, A Null Hypothesis

As one contemplates the panoramas of red vineyards and walks rows to find disturbingly few completely asymptomatic plants, it is easy to consider a null hypothesis suggested by early notions that red blotch has been around a long time masked by similar symptoms in other viruses, and Dr. Golino’s recent finding that a substantially similar virus existed in Sonoma County in 1940.

A null hypothesis could be that the virus has been here latent in every plant forever and the near universal expression of symptoms this year is the result of unknown cyclic or environmental factors.

This possibility cannot be completely ruled out, but a number of observations about the current outbreak argue against it.

1. Dr. Sudarshana has documented the spread of the virus to plants that previously tested negative at the U.C. Oakville field station.

2. The pronounced edge effect. There is no reason to expect an edge effect unless a new strain or vector relationship has developed.

3. The existence of “one armed” symptoms on cordoned vines. One would expect a widely distributed latent infection to be evenly expressed in the plant.

We present here possible evidence of symptom evolution in an isolated mountain vineyard block. If our interpretation is correct, this evidence would further argue against the null hypothesis.

Google Earth imagery lacked the resolution for any detailed analysis until about 2008 when a significant resolution upgrade seems to have occurred. The usefulness of this imagery is also limited because the photography needs to happen during the symptomatic stages of red blotch which in most vineyards is from September to November. Such photography took place on October 24, 2009.

The resolution is still far less than ideal. Close examination reveals pixelation on the order of ten feet which represents two vines in this vineyard. Additional uncertainty of one position is introduced by the way AutoCAD allocates points along a polyline that extends around corners as this block was counted. In the strictest sense this data could be written off as statistically meaningless. Nevertheless, photons tell no lies. When an otherwise green vineyard registers red and purple areas and appropriate margins of error are incorporated, it may well be possible to derive significant results. In our opinion we are not to the stage of this investigation where any evidence can be ignored unless it is demonstrably wrong.

Below are three pictures of the Oakville Field Station 10-24-09. The first, a native image, shows a gross infection, possibly with several viruses, and a progressive infection in neighboring vineyards.

Ok 10 09 base annotated

The second image is saturated in Picassa and more detail of the surrounding vineyards and hints of infection within the Station can be found.

Ok 10 09 saturated

The third image is boosted with high dynamic range which becomes granular but polarizes green and red. This clearly shows edge effects. It is difficult to separate “edge” effects from “road” effects as edges are nearly always roads.

Ok 10 09 hdr

Moving to a remote mountain vineyard using a base image similarly enhanced from the same day, October 24, 2009, we show the block suspected of being ground zero. We find no apparent edge effect in play. This block is CS337 on 44-53 rootstock. The rootstock was thermally sterilized and propagated on site from cuttings procured in Oregon about the turn of the millennium. The 337 from numerous sources was field grafted. The partial block above and to the right also showing symptoms is CS4 on 44-53. The asymptomatic partial block to the right is CS4 on 1103P and remains one of the least symptomatic blocks today.

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This year we marked the vines we judged to be grossly symptomatic defined as over 50% red. Here they are superimposed over the same image as 5′ diameter circles in accordance with vineyard spacing. There is a slide in the middle where vines were removed. Once again we find no edge effect.

Gross 141516 2014

When the less symptomatic vines are removed (it should be noted that it is very difficult to find completely asymptomatic vines in this block), we find a poor correspondence between the grossly symptomatic vines this year and those from 2009. Although symptoms are progressive and great caution must be exercised comparing different seasons and mapping dates, we feel that this at least leaves open the possibility that vines develop resistance over time.

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There are no surviving tissue samples so there is no way to be certain the symptoms from 2009 were GRBaV, but all qPCR assays from this block and the entire vineyard to date indicate the presence of only GRBaV and RSPaV.

We take this analysis one step further with a look at dead and missing vines.

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The slide and the sorry row where machinery was moved in are apparent, but again we find poor correspondence with vines symptomatic in 2009. We find therefore no evidence of increased mortality.

We must constantly remember that our minds are wired to find patterns and conclusions from insufficient information. Yet it strikes us that edge and/or road effects are key to understanding the recent explosion of symptoms in Northern California. Other blocks in this vineyard show striking edge/road effects and even indication of infection from adjacent woodland.

We had been watching the wild grapes for a couple years and in  August 2014 noticed red leaf symptoms in wild grapes on the St. Helena Road in a location miles from any vineyard. Careful (but not rigorous) examination of this and many subsequent wild grape symptoms, which have also exploded in the last year, suggest that the source of infection is the road. Vines remote from the road are initially asymptomatic and infections always seem to begin at the road.

Some time ago Dr. Golino demonstrated that wild grapes harbor leafroll virus and we took a poorly collected sample of these new red leaf symptoms to Mike Anderson at the Oakville Field Station. Subsequent work showed that GRBaV is indeed present in wild grapes.

What remains haunting to us about the location of our first observation in wild grape is its remoteness, yet trucks from the vineyard discussed above and others have passed beneath this spot overhanging the road for years. If our intuition serves us, at least one vector must be capable of riding considerable distances on harvested grapes or machinery.

When nearly every vineyard seems suddenly symptomatic, and when nearly every vine seems to show some level of symptoms, it is easy to consider a null hypothesis that the disease has always been latent and that drought stress or some other environmental variable is causing the current expression of symptoms. This hypothesis cannot be completely ruled out, but considerable evidence argues against it.

 

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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.

Iceindex

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.

Holocene_Temperature_Variations_Rev

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.

dT

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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