Carbon Starved Planet

We owe the title of this book to Ferdinand Engelbeen, who wrote the words in one of many blog discussions some years ago. Ferdinand’s words resonated instantly as a title for the book we had been working on for several years.

We decided to serialize excerpts from the book on this blog. Chapter 1 follows.


Thirteen point seven billion years ago there was a great flash of light, at first there were only quarks and stuff but within a couple minutes there was Hydrogen the primal proton, which begat Helium within another minute. A bit of Lithium and Beryllium were spawned in the next few minutes, but it was ten thousand years before first Boron and Carbon and the rest of the heavier elements were born in the explosions of supernovae.
It may seem like heresy, but this is just our cosmology in scientific clothes. The names might have seemed funny but the concepts would have made perfect sense in ancient Rome or Egypt.
“In the midst of Nun, Atum released his divine energy to create Shu, who begets the other gods of the pantheon.”
So went the cosmology of Heliopolis, inscribed 4500 years ago in Egypt. Let’s just take a look at the similarities. Nun could be either the baryon soup of photons, neutrons, electrons and quarks; or just the unfathomable nothingness that precedes all cosmology. Atum is Hydrogen, and Shu is Helium who eventually begets all the other gods of the pantheon.
The Periodic Table is our pantheon, and Carbon is the sixth elemental being. But Carbon is a very special element. Enormous powers are vested in its ability to cling to itself in a double bond, to catenate into long strings, and to form covalent bonds with many other atoms. An entire branch of chemistry, organic chemistry, is devoted to it and a typical animal is nearly twenty percent Carbon by weight.
Being element six, Carbon is the second lightest of the elements that had to wait ten thousand years to be formed in supernovae. It is the second in line for formation and it can be found in certain meteors that strike the earth. When your body is sixty-five percent water, which is three times heavier than Carbon, and the lesser constituents like Calcium (20), and Phosphorus (15) are more than twice as heavy; being nearly twenty per cent by weight doesn’t really indicate the prevalence of Carbon in your body.
Soot, charcoal, graphite, grapheme, diamond.


These images by Michael Strock show some of the forms Carbon can take. DNA is made possible by Carbon’s ability to form long strings.
So Carbon is the element of life, but more than just as a building block. Carbon is essential in life processes that take place within and between organisms. Carbon dioxide in the air and water is used by photosynthesizing creatures to create the sugars that fuel the machinery of primary productivity. This primary productivity is then consumed by Oxygen burners like us who reverse the process and gain energy by burning sugars, producing Carbon dioxide. Plants do this as well, of course. That is why they go to the trouble of making the sugars, but they produce a wild abundance. This sustainable and ever renewing cycle is the real magic of life on this planet. You could build fantastic creatures by whatever chemistry you like, but if their metabolic processes are a one way street, they will deplete essential resources and die off in wild swings. When other organisms use a reverse metabolism that renews the resource, a balance can be achieved and the wild swings stabilized within an acceptable range.
On our planet Carbon is an arbiter of the cycle. It goes Carbon dioxide to carbohydrate and back again. Call it the cycle of life. We will see that the balance has not always been well maintained and that particularly after extinction events, there have in fact been wild swings before things settled down.


NASA has found Carbon “buckminsterfullerines” many times bigger than our moon. More than half of all naturally occurring chemicals contain Carbon.
The life on our planet has found a way to take this dirty soot and make a different kind of diamond. Not a hard clear rock that will burn in the air to Carbon dioxide, but a complex evolving system with myriad forms that is remarkably and sustainably balanced. A system that hinges between alternating forms of element number six in our cosmology. Carbon is so essential to life that when its availability is reduced, we have a Carbon Starved Planet.

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The Fourth of July and the Gophernator

The fourth of July is a bad day for gophers where we live. While the rest of the United States is busy creating gunpowder explosions in the atmosphere, we celebrate with fuel/air explosions underground. These are not as visually attractive as pyrotechnics but they have practical value and it is deeply satisfying retribution to these rodent terrorists..

Gophernator is a trade mark of a company that makes an appliance that uses a torch handle as a mixing valve, a battery powered igniter, and a ball valve and automatic check valve as redundant features to prevent the explosion from climbing back up the hoses into the tanks and killing the operator and anything else within, say, a hundred yards. This would be an entirely unacceptable win for the gophers.

While laws and association regulations simply could not specifically anticipate such a device, one can be sure that powers that be would find ample general language to prohibit them if they hit the radar. I got mine some time ago just after the company reorganized with the automatic check valve feature following a lawsuit from the heirs of someone who forgot to shut the ball valve.

Initially I blasted with joyous abandon and had succeeded in driving the scurrilous rodents off my two acres. The kill rate is low, particularly for a beginning user, but the satisfaction is enormous, and the surviving gophers definitely leave. I began to get queries from my neighbors, “you been doing some shootin’?”.

It became clear when once friendly neighbors began to look down and spit on the ground that my shock and awe strategy was not going to fly and I was going to have to pick my battles with the rodents. I learned that they hate the taste of 2-4-D on their favorite weeds. I learned to trap them. I tried using a motorized plumber’s snake to find their catacombs. I learned to locate their main tunnels and be sure they were nearby before blasting them. Kill rate way up. Number of blasts way down.

Still, I was developing a reputation as the unibomber. One neighbor called the sheriff to complain of the noises and was told it was hunting season on adjacent fields.

Perhaps I should explain that my reputation was long since tainted by my use of a roofing torch to start mesquite in my barbecue. This is also moderately noisy and produces impressive sparks in the night, but the Fire Marshall ruled that while I was no longer allowed to use it on weeds, there was no regulation to prevent my use as a barbecue starter.

One day I set off the mother of all gopher blasts. My best explanation is that gopher tunnels has somehow tapped methane from a nearby wetland. The earth trembled. Perhaps a quarter of an acre levitated. After I had trundled the rig away a posse of neighbors showed up. The war on gophers is far too important to confess a secret weapon. It was impossible for them to know it was on my property and not on adjacent open fields or vineyards beyond where propane cannon are used for birds. After some arm waving and reference to hunting they left, but not before one neighbor looked at me knowingly and said with masterful understatement, “That was NOOO shotgun!”

So this is why all that remains of my shock and awe joyous blasting takes place during the fusillades of the fourth of July.

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The other 90 (or 95) Percent

We think of ourselves as finely tuned orchestras of cells. We have brain cells to make us smart, liver cells to buffer our indulgences, and immune cells to fight off invaders.

These cells are US. They have our uniquely human DNA. They are rather large cells as cells go, and wherever we go, they go.

Well, we are crusty critters. Our guts and skin are barnacled reefs of bacteria like the micrograph below (credit unavailable).

Gut Bacteria

Turns out between the reefs and the plankton floating in our body fluids only about ten percent of the cells that go where we go are human. The big ones are human. Those bacteria are tiny little guys that rack up big numbers. They might amount to a couple quarts of our total volume.

Do we own them? Do we want to? The other 90 percent of our biome, the microbial dark matter, is small compared to us.

We think of ourselves as denizens of a rational universe that obeys physical laws our brilliant predecessors have discovered. It is an harmonic music of spheres with finely tuned motions we can predict with astonishing accuracy.

Well, there is this problem with “dark” energy and matter that together comprise an unlit 95 percent of the universe. It does not go where we go. We go where it goes. it is very, very…Very large compared to us and our toy music box of understanding.

Between owning merely 10 percent of the cell nuclei in and about our bodies and understanding merely 5 percent of the universe, microbial (and other) dark matter and energy seemingly leave us in Plato’s cave.

The other 90 (or 95) percent gives us crusty critters plenty of food for thought.

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How Big is the Carbon Cycle?

Just google it and you will finds dozens of Carbon cycle illustrations. Most are cartoons, but half a dozen good ones can be filtered out. Mostly they agree in round numbers. The following by the IPCC is clearly the best:



Carbon Cycle IPCC

Most models are focused on human changes to the cycle and these are usually shown in red. The real significance of human changes must be gauged by the size of human Carbon in relation the entire cycle.

The sizes of the fluxes and reservoir sizes is really very uncertain and it is remarkable that there is as much agreement between models as there is. We became interested in using Carbon isotope ratios to constrain the cycle. This has proved very challenging and very illuminating. Perhaps the best measured parameter we have is the decline in 13C heavy Carbon in relation to lighter 12C in the atmosphere. We expected it would be fairly easy to factor (presumably) known isotope ratios of the fluxes and derive the measured slightly less than -.02 per year change. Months later we have not yet succeeded.

When you add up all the yearly fluxes it is clear that over a thousand GtC is in constant motion. A Gt (or a Pg) is the weight of a cubic kilometer of water. That’s a lot of Carbon. Well over 300 GtC cycles in and out of the atmosphere. There is a tendency to think of closely balanced input and output fluxes as net fluxes, but the isotopic fractionations are different for every flux.

Humans currently put about 9 GtC into the atmosphere every year. It is effectively a one way input as it takes a very long time for the Carbon we pull from the ground to be replaced. Microorganisms in the soil put about 60 CtC in the atmosphere every year and this is also effectively a one way input as the yearly return flow is only a small fraction of a Gt.

You can see that human input is less than 3% of the atmospheric cycle and less than 1% of the planetary cycle.

Our work with integrating isotopes shows that current conceptions like the image above are wrong. What are shown as nearly balanced input and output fluxes will need to be far more skewed, and in all likelihood, the Carbon cycle will get bigger.

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Dark Energy, Plasma, and the Whedefugawe Effect

Early in the twentieth century, even as emergent nationalism made the world pregnant with a half century of mechanized war, the greatest advances in physics since Isaac Newton were taking place. Relativity and quantum redefined the universe as a dance of electrons around mass composed of a seemingly endless parade of sub, further, and even further sub particles.

Energy and mass became convertible by the imponderable square of the speed of photons (light) in the famous relativity equation. Yet the continuing subdivision of the atom, conceived in ancient Greece as the ultimate, irreducible thing, has spared the electron. It remains fundamental to us.

On a roll and feeling swell we moved to a “theory of everything”. Congruence has been achieved in this theory with the unfortunate exception of gravity. This property of mass eludes our constructions.

What price congruence? Not only gravity, but 95% of the “stuff” of the universe in the form “dark” energy and matter escapes our model. Perhaps we pay too much for our mathematically consistent cosmology. We may have successfully modeled only a microcosm, a sub universal particle, if you will.


Those who have dedicated themselves to the morasses of equations believe they detect “strings”. From what lyre do they hark? Physics has hit the wall when quantum uncertainty tells us that we must fundamentally change what we see to observe it, and therefore “create” what we observe.

Even our trusty electrons are weird. Carver Mead stretches them to any length, even a mile long, in a super-cooled super-conducting field. They do plasma too. Like lightning or arc welding. Ionized (read electronized) gas fields with little or no net charge. What if dark energy and dark matter were a plasma?

Engineering is the art of marginalizing what is not understood to levels that do not disrupt the application. Typically this is done by organizing components in specific patterns that minimize chaotic (not understood) effects. So it is with the models we make. We can have a “theory of everything” if we marginalize gravity.

Our models of evolving systems struggle with initial and boundary conditions. Initial solutions require consistent values at single points, and boundary solutions at binary points. In the words of the Wolfram Reference:

 The final step, in which the particular solution is obtained using the initial or boundary values, involves mostly algebraic operations, and is similar for IVPs and for BVPs.

IVPs and BVPs for linear differential equations are solved rather easily since the final algebraic step involves the solution of linear equations.

…it is not always possible to complete the final algebraic step for nonlinear problems.”

Pretty much sums it up. We are left wondering if we are at the initiation or at the boundary or whatever lies between.

The whedefugawe effect. It remains the essence of the human condition.

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Doubling the Carbon Cycle

In the last post we had set out to model geological isotope excursions and found that our conception of the current Carbon cycle is so messed up that any venture into deep time hopeless. Specifically, when d13C values are integrated into the fluxes the atmosphere goes negative d13C way faster than the observed rate.

To correct this irregularity either light Carbon atmospheric inputs must be reduced or heavy Carbon increased. We chose to try to balance the books by increasing heavy Carbon input from the ocean mixed layer.

Carbon Cycle Balanced

Not only was the original model based on consensus values out of tune isotopically, it was out of mass balance as well, growing at over 60 GtC per year. We have chosen to modify the scarlet values to harmonize the atmospheric isotopic trend with the observed rate and to limit atmospheric growth to a bit over the human contribution.

Hunky dory, but we now have a 450 Gt Carbon cycle compared with the 210 Gt consensus cycle we began with. We have doubled the Carbon cycle.

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Cycling the Isotopes

We have long been interested in Carbon isotope “excursions” and took a notion to integrate isotope ratios into a simple box model of the Carbon cycle with an eye to replicating these excursions. The initial result was surprising and it became apparent we will need to adjust our conception of the Carbon cycle to match measured values of atmospheric isotopic change before we venture into geological time.

Carbon Model

Each box has its name, the supposed reservoir size, and the observed 13C variance from the PDB standard. Fluxes are shown as appendages of the boxes with an indication of the direction and the supposed rate in Gt/year. The atmosphere is unique in that it communicates with all the other reservoirs. The input from the mantle to the atmosphere by way of volcanism is ignored as it currently seems very small.


We then set up calculations for the relationship of each reservoir with the atmosphere to derive the isotopic change in one year. The result was very surprising. It showed the atmosphere going -3.8 PDB, a very substantial excursion, in one year. We have measurements atmospheric 13C since 1978 and ice core data before that which generally agree that the atmosphere is actually moving more like -.02 per year, two orders of magnitude less.

The isotopes are telling us that our notion of the Carbon cycle is wrong.

When you step back and think about this all the reservoirs are much more negative than the atmosphere except the ocean. Either we are grossly overestimating the inputs from negative sources or we are grossly underestimating the input from the ocean.

We examine here the possibility that we are underestimating the ocean.

We have two boxes for the ocean, the mixed layer and the deep ocean. At +.5  it would take an enormous flux from the deep ocean to get the atmosphere back to -.02 per year. The deep ocean is isolated from the atmosphere by the mixed layer except for small areas of upwelling and deep water formation that amount to maybe 10% of the ocean surface. The mixed layer is in direct contact with the atmosphere over 60% of the planet even after subtracting the areas of deep water communication. At +2 it seems a much better bet for balancing the books.

We confess to adding a box “Swamp” to the model to explicitly deal with biogenic methane which has been measured as low as -100 PDB. This stuff is glub glubbing up from wetlands and much is released from coal mining and oil production. The consensus might be that it amounts to little more than half a Gt/year, but with its staggering negative PDB values we feel it must be included when isotopes are integrated into the cycle.

We initially had it at 10 Gt and realizing that would be controversial reduced it to 2 Gt at a PDB value of -50. We feel this is defensible.

The bottom line it that after reducing Swamp and holding everything else the same it takes 262 Gt/yr input from the mixed layer to get the atmosphere to -.02/yr. The response is very sensitive. For example 265 Gt knocks the atmospheric response down to -.0005. The 262 Gt is about five times the reputed rate, but not an impossible number.

It should be mentioned that evaporation filters isotopes in the same direction as biological filtration. See:

The only way evaporative enrichment can occur is if light (-PDB) Carbon is exported to the atmosphere along with the vapor. This may be a force supporting the measured 7 uatm pressure disequilibrium in favor of the atmosphere over the ocean surface. According to Kevin Trenberth some 4000 Gt of water evaporates from the ocean surface each year. This evaporation factor works against our efforts to balance the isotope ratios, even as it supports the notion of a greater flux.


Realistically, our understanding of the Carbon cycle is very poor and all of the fluxes and reservoir sizes should have error bars the size if the values themselves. Integrating isotope ratios offers a new way to constrain the possibilities.

Posted in Carbon Cycle, Carbon Dioxide Loves to Swim, Climate | Tagged | 1 Comment