The New Ptolemy

The evolution of consciousness since the Enlightenment can be thought of as the progressive, and unwelcome realization of human insignificance. We inhabit this rock, spinning in infinity*, the center of nothing, outweighed in biomass by ants. God still loves us, right?

Or not…did we piss them off?

Sacrifice a goat. Sacrifice the SUV’s, whatever. Repent, ye sinners!

Where is your pride? We have enormous powers! We can change the planet’s climate with our fire. We are the Anthropocene! We can wipe species off the map with our axes. Just not the ants…

*Credit Paul Simon

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Further GRBaV Observations

A number of things we have noticed about red blotch did not really fit into the themes of prior posts but we feel bear mention.

The first, along the lines of Dr. Golino’s finding of a similar virus in a leaf from Sonoma County in 1940 is something we bumped into on the UC Master Gardener website.

Roger's Red

“Roger’s Red” apparently is a prized “cultivar” for horticulturalists. Photo credit A google search will show that this vinifera/californica hybrid first found by Roger Raiche along Palmer Creek Road west of Healdsburg in 1983 has been propagated far and wide as an ornamental.

We sent an email suggesting this be tested for GRBaV to Master Gardeners and were assured the suggestion has been sent to Rhonda Smith.

The second is just an observation we make no attempt to interpret of unusual cane reddening and subsequent abnormal growth in a miniscule subset of symptomatic vines. We have not found it  in any asymptomatic vines, and it seems randomly distributed.

IMG_0742 We first noticed it before overall leaf drop in some symptomatic vines vines that prematurely lost their basal leaves. Early basal leaf drop corresponds with the first year of symptom development to our eyes. In contrast, we find reduced abscission in fully developed gross symptomatic vines similar to that from girdling by breakage or the beetle.


This photo does not show it very well but in December we found unusual growth from these reddened canes. We could go around the vineyard to a half dozen places where red leaves were still hanging on and find growth like this from reddened canes.

The last is a quick comment on the red blotch state of affairs. Dr. Daane has been unable to get leaf hoppers to transmit blotch even at feeding levels barely sub lethal to the plants even though the virus can be assayed in their guts. The vector  remains at large. In Sonoma county researchers have had difficulty finding GRBaV negative control vines for comparison studies. Most assays performed so far have been to verify symptoms. The cost to systematically assay a vineyard remains staggering. We really have no idea the extent of this disease except as it is revealed through symptoms.

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Say Watt? Or Why I Just Love Math

Mathematics is one of the many human languages. It is written in very impressive hieroglyphics that can include multitudes of “terms”, many of which are given Greek letters. This language has been very much in fashion since the Enlightenment and in the popular imagination anything written it has an automatic aura of truth.

To decipher this language it is necessary to define the “terms”. Recently I had a go with watts.

A watt is defined as one joule per second. Very nice. We know what “1” is and our clocks tell us what a second is, but what is a joule?

A joule is the energy required to move one kilogram one meter using one newton of force.

Um, if the newton is doing the work, why do we need the joule? A supervisor, perhaps.

Will we ever know what a watt is? They just keep adding new terms.

Ok, a newton is the energy to move one kilogram one meter at the RATE of one meter per second squared.

Hooboy, we ALREADY moved that kilo a meter back when it was a joule. The crowbar we used was a newton. Now they say our crowbar was just the energy to produce a certain (and seemingly arbitrary) rate of movement across a meter. Is a definition circular if the energy to move a kilo a meter is defined by the energy to move a (presumably different) kilo a meter in the square root of a second? Why are we squaring the seconds, anyway?

We delved into this squared thing a while back. Sir Isaac just loved squares and his finding that gravity diminished (crudely) with the square if distance may be the hazy rationale for our definition of a newton. Yet our watt, if we can remember back that far, is already a rate. We are defining a rate with a rate.

So here is our evolved hieroglyphic for a watt:

1w=(1k/m/s2 moving 1k a distance of 1m)/s

w=((k/m/s2)km)/s or some such.

At least it is a precise definition, but somehow I still don’t feel I really know what a watt is, and if that is the precise definition, why didn’t they just say so to begin with?

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GRBaV, Heredity or Environment?

The burning question in the vineyard business these days is whether or not to rip out and replant Red Blotch infected vines. On the one hand, the first variant of the disease has spread at an average of maybe 4% per year at the UCD Oakville station. This might be a rate of spread that is manageable now that we are dialed into the symptoms.

On the other hand, a second variant of the disease has seemingly invaded the Oakville station from a different direction and general symptoms have spread to very nearly 100% of vineyards in Napa, Sonoma, and Mendocino counties within the last few years.

The best estimates of the latency period between infection and symptoms is 1-2 years. The average rate of vineyard replanting in Napa and Sonoma is on the order of 5%. In the seven years since GRBaV was first noticed, we might expect that 35% of the vineyards have been replanted.

All of these vineyards could potentially have been replanted infected. An equal number of additional vineyards infected by transmission from neighboring vineyards at the internal vineyard rate might bring the expected total to an aggregate 70% of vineyards possibly infected by planting and transmission since 2008. Yet if we accept the two year latency, no vines planted or vector infected this last year should be symptomatic yet. This would reduce the expected aggregate infection since 2008 to 60%.

Turning this analysis on it’s head, to reach the 100% infection of vineyards observed, it would be necessary to postulate that for four years prior to 2008 beginning in 2004 the same rates of infected planting and transmission to an aggregate infection of 40% of vineyards by 2008 went unnoticed.


Oakville station is a very small sample size and it is possible that internal rate of spread there is not representative. Yet this low rate is roughly consistent with the rate observed in a completely isolated vineyard an order of magnitude larger.

An alternate possibility is that the virus spreads more efficiently between vineyards than within. This possibility could explain edge/road effects. The vector would prefer the dust and turbulence of frequently travelled roads to the intermittent passage of machinery and workers within the rows. Then again, it could prefer ambient vegetation to vines and be a reluctant invader.

The edge/road effect is pretty ironclad, but what does it really mean?


If it means that a vector is established in ambient vegetation or an adjacent vineyard or block and efficiently colonizes the edge of a new vineyard or another block, why would it spread less efficiently within the new vineyard or block? The Napa valley is essentially grape monoculture, one giant vineyard. The areas of ambient vegetation are limited to the perimeter of the valley, a few creeks and volcanic knobs, and landscaping.  If this is what is meant by edge we should see a pattern of infection emanating from theses areas. This is not what we see. We see a pattern of infection along roads throughout the monoculture.

The very existence of this road pattern within individual vineyards and within the monoculture as a whole suggests that there is more going on than a monotonic internal rate of spread.

The following is the pattern of grossly infected vines in autumn 2014 in an isolated vineyard. An isolated vineyard can be thought of as a microcosm for Napa or Sonoma valley monoculture.

2014 Blotch


The red vines are defined as grossly symptomatic with more than 50% red canopy. The blue vines are missing in action and undoubtedly victims of trunk diseases and landslides. There are a few yellow vines shown that are really red but convey misinformation because they were transplanted or budded over.

There are three rootstocks. The light grey is 44-53, the darker grey is 99R, and the black is 1103P. A quick take is that the 44-53 is wildly symptomatic. I have written this but I hereby repent. A more careful analysis reveals that the combination of 44-53 rootstock and the CS337 clone best explains the disparity in distribution.

The vineyard provides a way to separate the variables. Most of the 44-53 rootstock was  grafted with CS337, but not all.

By Rootstock

When the data is sorted by rootstock it becomes clear that when the 44-53 is paired with CS 4 there is a drastically reduced rate of gross symptoms.

By Clone

When the data is sorted by clone it is apparent that it is not just the clone either because when the 337 clone is paired with 1103P rootstock the gross symptom rate also drops off dramatically. The 44-53 and 337 seems an unhappy pairing.

Heredity plays a role.

Environment seemingly as well.

4453 337

The image above is cropped to highlight the extent of the 44-53/337 in the vineyard. There are two areas divided by a heavily forested area and a 300′ ravine. To our eyes they are different animals. In the tradition of phylogenetics and population biology we conclude that the upper area with 34% average gross symptoms is the original source of infection. This area also shows far less edge concentration. In contrast, the lower area shows striking edge concentration.

14 15 16

The image above is of the upper portion in 2009, the image below of the lower portion swung around to a similar view attitude on the same date.

Blk 12

While the reservoir side clearly shows red leaf symptoms in October 2009, the other side does not. It should be noted that the 28 qPCR assays we have  done so far of symptomatic vines have all been positive for GRBaV and RSPaV but negative for all other viruses tested. We also performed two phytoplasma assays which were negative.

We know so little about this virus that is premature to jump to grand conclusions, but our evidence suggests that the virus spread from the reservoir side to the other side of the ravine along the roads. The notion of road dispersal is further reinforced by observations of roadside infection of wild grapes and even cultivated grapes overhanging St Helena/Spring Mountain Road.

While this road effect is by no means certain, the possibility that it is real is a very important factor in any decision to replant a vineyard. If the new vineyard cannot be protected from reinfection, the effort is pointless.

As much as we would love to believe that the distribution of GRBaV follows from grafted heredity, our information suggests that the environment is a very important factor as well.


Posted in Biology, GRBaV, Red Blotch Disease, Wine | Tagged | Leave a comment

The State of the Onion

Let’s say the way this planet works is an onion. There are many layers and they interact in ways far more complex than onion rings. Yet we have to start somewhere, and peeling back the layers of this onion can at least help us grasp the huge holes in our understanding.

Let’s start around the middle of the onion at the surface of the earth. A very significant transition takes place here between land and water on one side and air on the other. The water is confounding because it fills in low areas we might be inclined to call land if there were no water there. These low areas get quite deep and are so extensive that 70% of the planet is covered by ocean.

The ocean and the atmosphere have mirror image onion layers beginning with a mixed layer and progressing to stratified layers.

Atnosphere and Ocean

The lower image above is the ocean and the upper the atmosphere.

The Aristotelian elements, air and water have different properties, but at the interface and extending up ten kilometers in the atmosphere and down somewhat less than a kilometer down in the ocean are turbulent mixed layers. These mixed layers both transition, up and down respectively, to stratified layers that make our onion proud. The atmosphere has more layers and is more complex because gravity assures that cold materials go nowhere but down and warm materials go nowhere but up. The ocean below the “clines” is simple and incredibly stable because there is nowhere for it to go. It is constrained at the bottom by another Aristotelian element, earth.

There are generally two sorts of earth, continents and ocean basins.


This graphic by NASA shows the general layers of oceanic crust.


This graphic (credit unavailable) is a good general representation of the onion rings of sediments overlying the different sorts of igneous rocks (ocean and continental and their relative densities) and the mantle layer below. The oceanic crust is to the right and continental crust to the left.

Since we are downward bound from the middle of the onion, lets head for the center of the earth.


This graphic (credit Geopangea Research Group) is a good representation of the earth’s internal onion rings. Each layer is known from a change in velocity of seismic waves from earthquakes.

Problems with our understanding of the onion begin at the core. It has long been posited that convection within the outer core creates the earth’s magnetic field. A nice, easy answer, but it happens that Iron melts above its magnetic Curie point. Above the Curie point a material loses its magnetic properties.

Let’s just say we have no idea how the earth’s magnetic field is generated.

The seismic waves from earthquakes show us amazing things. Above the core/mantle boundary there are two very interesting extrusions.



To me they are doughboys. Credit Ritsema. One can think of them as Atlas holding up the earth. The important thing is they flatten out at the 660 km discontinuity like thunderheads hitting the stratosphere.

We have long been told that mantle convection causes the continents to move.

Dashed Conceptions

Childish conceptions like this. Credit unavailable.

The very same seismic waves that illuminate the doughboys show us this simply isn’t true.


The mantle is substantially stratified. Nothing anywhere near mid-ocean convection driving ocean floor spreading is in evidence.

Kustowski et al 2008

These sections from Kutowski et al (2008) show that the ocean ridge system is in fact a shallow feature. It is readily apparent down to 100km but vanishes as a linear feature before the 660 discontinuity and is unrecognizable in the Perovskite at 1000 km in the lower mantle. At the core/mantle boundary at 2800 km all that remains is the doughboys.

If the doughboys are feeding the ridge system at all they are doing it through tiny venturi in the Perovskite and then spreading out as massive sills. Other offset venturi through the intervening layers and the Mohorovicic (MOHO) discontinuity would then need to feed the sinuous dead end rivers of the ocean ridge system.

Doesn’t really work for me but  the raw edge of human understanding does not bear waxing pedantic. Another very serious problem is that the MOHO just below the crust marks the beginning of a low velocity ductile zone generally referred to as the “asthenosphere”. It is on this layer that crustal “plates” are supposed to be moving. Trouble is, seismic waves appear to show that continents have roots far deeper than this.


Credit NatureGeo. Continents appear to have roots that extend to 400 km near the base of the Olivine layer and the ductile material that allows their movement may be more a result of local pressure from movement forces than from a continuous ductile layer.

Let’s just say we have no idea why the continents are moving.

We are working our way backwards from the core of the onion and listing the problems with our understanding. We have reached the surface where we live and where we started. Take a deep breath of the atmosphere.

The atmospheric mixed layer, called the troposphere, is thought to have varied in average temperature within a range of six degrees for all of geological time. We happen to live in one of half a dozen glacial periods known in geological time so it is comparatively chilly out. Furthermore, the last three glacial periods including our own have been characterized by oscillations between glacial and interglacial episodes. We live towards the end of an interglacial.

We have no idea what causes glacial/interglacial fibrillations nor what causes the macro scale glacial periods to come along every few hundred million years.


This is what the descent into our current ice age, the Pleistocene, looked like.

Let’s just say we have no idea why the mixed layers of the lower atmosphere and ocean warm and cool.

The next layer of the atmosphere is the stratosphere. It’s a long way back to the first graphic so it is reiterated here.


Temperature declines steadily through the mixed layer or troposphere for a bit over 10 km and suddenly flatlines up to about 20 km  where it starts warming again and this warming accelerates through the ozone layer in the mid stratosphere. The warming continues well above the ozone to the top of the stratosphere at about 50 km where cooling resumes throughout the mesosphere to about 80 km where it flatlines and then warms in the thermosphere.

One weird onion. Strange how the speed of sound follows temperature rather than density. We ain’t done yet. There is at least another 100 km “sphere of influence” above the thermosphere.


This is a NASA image of the Van Allen ring currents, more a donut than onion rings.


In this graphic from the Chinese Academy of Sciences we reach the outer skin of our onion. Beyond the onion we get into the rest of the universe, 95% of which seems comprised of dark energy and dark matter of which we have no understanding.

So what is the state of the onion? It is just a silly metaphor to attempt to reduce head spinning complexity to something we can get our heads around, yet even at this dumbed down level our understanding utterly fails.

1. We have no idea how or even if the planet’s core produces the earth’s magnetic field evident in the “bow shock”, the flakey outer skin of our onion above. We further have no idea why it periodically and erratically switches polarity.

2. We have no idea what is causing the crust to move.

3. We have no idea what is causing changes in oceanic and atmospheric temperature nor why these changes seem limited to a range of 6 degrees  over geological time.

Generally, we are missing a lot of energy, both inside the onion and out.

Posted in Climate, Geology, LLSVP's are Doughboys, Magnetic Reversals, Moho, Oceanography, Seismic Tomography | Tagged | Leave a comment

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


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.


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.


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


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


Back down at the hut…


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.


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


South from Mt. Goddard.



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



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.




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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