The Winter Ocean

This is a bit of an odd piece.  It’s simultaneously a highly personal piece about the experience of depression and an explanation of seasons in the temperate coastal ocean, framed by the geology of the local Del Mar and Torrey formations, which form the backbone of the described beach. 

I’m including it partly because of that and also because depression is both horrifyingly common in our society and yet still poorly understood.  It’s hard to understand from the outside (unless you’ve been there before) just how the world distorts itself for the depressed person, leading to the all-too-common idea that they’re just feeling down rather than the gray loss of all emotion that a true depressive is likely to feel. 

More recent research has found that depression itself can literally reshape the brain as well as twist one’s experience of reality, illustrating that biology is not as reductionist as we’d like to think and that it is not in fact only genes and molecules, but interactions with the environment as well.  The human brain is fortunately fairly plastic, so much of this damage can be repaired through therapy – but it is never really “fixed” so much as controlled, much like other, more obviously physical illnesses like diabetes or hypothyroid.

This piece dates back to January 2007, when I had just finished my Master’s degree and was in the middle of having the total nervous breakdown I’d been staving off for the latter half of my graduate school career.


It’s New Year’s Day in Southern California, bright and sunny and clear and cold, and to top it off I’m standing on a beach a few miles north of San Diego, being buffeted by a remorseless ocean wind.

The beach looks different than just about any other time I’ve been; the parking lot is closed off, and it’s difficult to tell if it’s started to erode after they began trying to renovate it, or before. The beach carries the hallmarks of winter storms: shells and other debris left high on a beach made primarily of cobbles. While gentle summer waves push sand onshore, harsh winter waves drag it back offshore, leaving a jagged beach of very different character. Sand dragged offshore exposes tidal channels carved into the soft grey claystones of the Del Mar formation – longitudinal bars carved by the endless push-pull of the tidal current. The tide is currently low, and the others are heading across the slippery rocks to access the tidepools. The ocean will be coming in soon, so I follow the others out.

The Solana Beach tidepools are an interesting anomaly – not to say that tidepools are uncommon, and they do tend to form in soft sandstones and claystones such as these. However, the rocks exposed here are fossiliferous. Nut-shaped Eocene oysters stand out in contrast to the gnarled Recent specimens clinging on top of them, and burrowing mussels dig into the claystones and fossil shells. Tumbled blocks of Torrey Sandstone provide hiding places for brittle stars and octopus on their lower surface, while their upper surface is decorated with the winding burrows called Thalassinoides, standing out in smooth relief and oxidized a rusty red. Farther out both formations are covered with too much sea life and too much seaweed to really make out the fossils, as competition is fierce for hard surfaces to encrust. Were the summer beach sands to bury the rocks for more than a season, should sediments come down the rivers in sufficient quantity to bury the coast and to lithify, the eroded surface of the Del Mar and Torrey formations would create a picture-perfect disconformity: rocks that remain horizontal, but are missing approximately 33 million years’ worth of time.

The ocean is blue-grey and has been lashed by the same storms that stripped the sand from the beach. Out there there’s nothing to erode, but the falling temperatures at the surface have reduced the density differences in the water column. Where the summer ocean is layered, with warm sunlit water floating atop the cold deep water like an oil slick, the winter ocean is cold from top to bottom and much easier to stir. Deep and shallow waters mix, and dissolved nutrients from the depths replenish the depleted stocks at the surface. Spring and summer plankton lie dormant in the surface waters, and the eggs of last year’s fish and copepods drift. There’s plenty of drifting life in the ocean to feed the riot of mouths waiting at the tidepools and rocky reefs closer to shore, but it isn’t quite like spring and summer when the coastal waters explode in the green and gold of diatoms and dinoflagellates. The effect is more like a winter field lying fallow, waiting for the warmth of spring.

I point out a few fossils here and there (force of habit). I point out the cross-bedding exposed in the sandy cliffs where beach currents once pushed ripples across a shallow seafloor, oxidized a blood-red in the orange cliff wall. The blibs and blebs in the Del Mar claystones that are burrows, if you erode the sediment down to cut through them at odd angles. Things I’ve been shown before, had explained to me, was taught what to say by real geologists, real paleontologists. I don’t trust myself enough anymore to identify rocks on my own, since training in field identification and other such staples of the field were somewhat lacking in my education (there’s only so much time in the day, or in the three years alotted for a Master’s degree). Explainations about the living animals are easier, since I had a full undergraduate education in biology – but most of it was at a smaller scale, animals cut in cross section and placed on a glass slide, or soaked in ethanol until they turned pastel colors. Study of the living web of the tidepools would have mostly been the purview of a different department, the next floor up at my alma mater. Very few people in my department studied animals in the whole. Most of my education of macrobiology was the 101-type classes, the ones with over a hundred students, the ones that we had to get out of the way to gain access to the real classes. A glance at the biology research listings at UCR reveals a similar pattern: life cut down the the quick and studied at the smallest scales.

Sometimes I remember why I fled the field of biology.

Unfortunately, doing so seems to have landed me a degree in a field I’m trained pretty poorly in. I’m still not sure what to do with either skill set, as they seem to be pretty mutually exclusive: trained on the one hand for soft-rock geology (field mapping – sedimentary geology; stratigraphy; quantitative biostratigraphy) and on the other for molecular and subcellular biology (molecular and genetic lab techniques; transmission electron microscopy; light microscopy). Supposedly with a Master’s Degree I’m more employable than I would have been even with a PhD, but it doesn’t feel like it; tell the truth, I’m looking back at what I was originally taught to do over the last several years and getting the sort of feeling one gets when they graduate with a degree in Underwater Basket Weaving. Namely – the hell am I supposed to do with this?

But I suppose it doesn’t matter at the moment. All I’ve wanted to do for the last year is to hide, to give up, to let go – but I’m too stubborn for that, for starters, plus I tend to have an overdeveloped sense of obligation. So I finished, and it doesn’t feel like an accomplishment, or even like an ending. Just a sudden cessation, brittle as ice. And now that I’ve had the chance, all I’ve done is hide away from the world, curled up in shame, and wanting to forget that either the past or the future exists. Tired of worrying or caring about either.

Blank as the winter ocean.

Waiting for the sun.

Green Planet

Green planet began life as a post I was going to put up on Suburbivore to talk something about the science of food production, specifically soils and how plants evolved.  However, once it was finished it didn’t fit the blog topic, and I didn’t think I could make it fit without monkeying around with it until it was about something very different.  As a result it ended up languishing on my hard drive for a while before finding its way here.

I’ve taught introductory geology courses before, and this was always one of my favorite parts of the program, where I tie together what I know about planetary astronomy and how rocky planets develop with the history of life on Earth to explain why Earth is such an anomaly in the Solar System.  Sometimes I wonder if I’d stop seeing so many claims that the Earth was made for man (which drive me bananas) if more people understood how much Earth is both like and unlike other rocky planets we’ve observed, and why.


It is a peculiar chauvinism of our species that we named our planet “Earth” when, by all rights, we probably should have named it “Ocean.” This oddity has been noted in the past by better writers than I , where they comment on the fact that 70% of our planet is covered by water and only about 30% is available as dry land.  I would go a step further and argue that our world should perhaps most rightfully been named “Life” – for the world as we know it would not be possible without life, and would indeed be a very alien place to those of us used to the modern green and blue Earth.

However, it wasn’t animal life that most changed the world into the one we have now.  We are most emotionally invested in the forms life most like ourselves, and we therefore pay the most attention to warm-blooded animals, particularly large ones.  This homeothermic chauvinism can be seen, for example, by the very different levels of outrage over the wearing of fur versus the use of insecticides.  In general, if we are averse to the poison, it is not for the sake of the insects but because it affects other mammals or birds (if not ourselves!).  But while insects are alien and “other” to us, plants represent a step still further away on the tree of life, often viewed more as a form of living scenery than as organisms in their own right.  If we deign to notice plants, it is in their usefulness to us – the food they produce that we can eat; the aesthetic value of the leaves and flowers they bear; or the spiritual calmness of the forests they create, sheltered under towering trees and spreading leaves.  Bacteria and archaea, if they impinge on our consciousness at all, are swept into the catch-all category of “germs” and become things to be annihilated with the increasingly omnipresent triclosan and hand sanitizers.

But plants are more than just food factories and living carpets for our lawns, and the bacteria and archaea – both kingdoms in their own right – are more than just the seeds of disease.  Together they created the very air we breathe, and the earth beneath our feet.

Part One: Prologue

Our world was born without an atmosphere nearly 5.6 billion years ago, for as a small planet Earth does not have the gravitational grip to hold onto the light gases that were most common in the vortex of gases available as the solar system formed.  Only larger planets could retain these early, primary atmospheres of hydrogen and helium, so the outer giant planets alone held onto them, growing large enough to keep even flighty hydrogen from escaping due to the cooler temperatures present farther away from the nascent Sun.

We acquired an atmosphere later, after the planet had cooled from an initial molten state driven by constant impacts with the dust and debris left behind from early planetary formation.  Now a different type of impact introduced the materials that the great planets of the outer solar system had used to grow so large: water, methane, ethane, and carbon dioxide, the inorganic and organic ices that could only solidify in the cold dark of  the outer solar system, far from the Sun.  Additional gases were released from their mineral prison in the interior of the Earth as began to experience volcanic activity with a heat and violence unmatched by any modern natural disaster.  From these starting materials were born our primordial oceans and a secondary atmosphere wholly alien to us today, but actually more characteristic of small rocky planets of our type.  The dominant gases would have been carbon dioxide, nitrogen, and argon (about 95%, 3%, and 2% respectively, based on the current atmosphere of Venus and Mars1), with other gases making up tiny fractions of the remainder.  Oxygen is present in the atmospheres of both of these planets, and would likely have also have been present as part of Earth’s primordial atmosphere.  There is not much, however, and it is likely that any oxygen available close to the surface would probably have been rapidly consumed by rusting minerals exposed on the rocky surface, like the interactions that produced the red surface of Mars1.

Oxygen is not produced in great quantities through normal planetary processes like those described above; it takes life to do that, and life is much older on our planet than we are used to normally thinking.  There are some possible hints (quite controversial) that life arose 5 billion years ago2, but life was definitively present by at least 3.5 billion years ago as tiny, bacterial things1.  It then proceeded to spend the next two billion years doing nothing terribly interesting, at least based on the fossil record.

The problem, of course, is that a bacteria is a bacteria is a bacteria, and they have very strong selective pressures to stay small and morphologically similar to each other2.  Internally, of course, they are more free to diversify and have done so: bacteria and their distant cousins the archaea, ancient ancestors of our own multicelluar life, have developed incredibly diverse strategies for surviving and producing energy from the environment.  They live in the scalding heat of geothermal pools, the freezing interstices between granules of glacial ice, and can generate energy from sulfur and iron.  One group of them long ago seems to have developed a method for generating energy by using the energy of sunlight to split water, and it is this group that would transform the world: the cyanobacteria or “blue-green algae”, the descendents of which are present in the cells of every green living thing.  Photosynthesis evolved only once on our planet, and it was the cyanobacteria that managed to do it2.

Part Two: Air

Some 2.4 billion years ago, give or take a few million (it is difficult to determine exact dates in rocks so old), Earth’s atmosphere began to change to more closely resemble our modern one in what is now referred to as the Great Oxygenation Event.  Levels of carbon dioxide fell, leaving nitrogen behind as the most common element in our atmosphere, as it is today.  Oxygen levels rose.  Cyanobacteria are an old group, and biomarkers that indicate their presence were found in rocks that predate this event, some 2.71 billion years ago6.  So what changed?

Here is where the narrative gets fuzzy, in no small part because it is difficult to exactly tell the ages of rocks and correlate them across continents in the absence of distinctive and recognizable fossils (fossils are present in such rocks, of course; but as I said before, most bacteria tend to look very much alike).  The current going theory is that large-scale glaciations spread multiple times across the early Earth, possibly reaching down to the equator, with the ice only driven back by the release of trapped methane gases from beneath the seafloor3,4.Even smaller-scale glaciations, however, could have been the key.  They would have scraped dust and sediment from the exposed continents and washed them into the sea, providing a means of burying the bodies of early cyanobacteria so that they  could not react with the oxygen they had produced in life to rot.  As more and more carbon was buried, less and less of it was exposed to the amounts of oxygen that the survivors were producing to generate their food, and so more of it was free to build up in the atmosphere2.

This poisonous gas would have smothered most of the early life originally present on Earth, but bacteria are nothing if not resourceful (a generational span of minutes will do that) and some of them, the purple bacteria or proteobacteria, appear to have learned how to utilize this new toxic by-product in their own metabolism to help break down food.  Much as the cyanobacteria are the original progenitors of all chloroplasts, the tiny green parts inside plant cells that allow them to photosynthesize, the proteobacteria are the ancestors of our modern mitochondria, the tiny cellular machinery that forces us to breathe oxygen in order to break down our food for energy.  Ricksettia prowazekii, an obligate parasite from this portion of the bacterial family tree and the infectious agent behind typhus, is one of the closest living cousins to the tiny endosymbionts living in our cells5.

The buildup of oxygen is recorded in the rocks in a series of iron deposits known as banded iron formations (BIFs) found throughout the world and even today still mined as our primary source of iron ore.  They are remnants of great stores iron that were once dissolved in Earth’s oceans during its early anoxic years, most of them converting to an insoluble form and settling to the seafloor as oxygen built up during the great periods of glaciation that swept the early Earth6.  Our great railroads from the turn of the previous century, and the bodies of our cars even today, are built from the fossils of the turnover of our atmosphere.

Oxygen in our atmosphere had a second side-effect besides giving us sweet cars and transcontinental railroads, billions of years later.  Oxygen high in the atmosphere interacts with the ultraviolet radiation produced by our sun and present in sunlight, creating a layer of ozone that subsequently absorbs incoming UV radiation before it can reach the Earth’s surface.  Life could exist sheltered in the deep oceans because water absorbs UV radiation very quickly, protecting aquatic life and its DNA from the damaging energy of full sun exposure.  The development of an ozone layer would allow life to spread into shallow water and to emerge from the sea in time, to reshape the land as it had the sky2,7.

Part Three: Earth

We don’t give dirt a lot of thought despite having named our planet after it, but much like our atmosphere it’s actually quite unique in the solar system.  The surface of our moon provides a current example of what Earth’s early surface probably looked like before the advent of soils.  Igneous rocks would have formed from volcanic activity much as today, forming great solid sheets of magma, and impacting comets and asteroids would have blasted great craters out and let the dust and debris settle on the surface to form regolith, the pure inorganic sediment that makes up the surface of the moon and Mars.

Soil is quite different.  Regolith is only powdered rock of varying degrees of fineness, but soil contains regolith and more: the clays, sheetlike silicate minerals that only appear after the rise of the earliest land life8, and humus, an organic component made from decomposing plant or animal matter.  As the cyanobacteria began to conquer the land, sheltered inside the cells of multicellular plants, the types of chemical interactions required to produce both could finally occur.  Living plants or even simple cyanobacterial colonies produce organic acids that they excrete onto the surfaces that they live on, and it is thought that these are part of the chemistry required to convert igneous minerals into clays.  As these early plants died they would have broken down through the actions of the ever-present, ever-busy bacteria, leaving behind a carbon component in the sediment that would allow the formation of soils.  The structure of clays attracts organic acids to them and traps water, allowing such chemical interactions to continue underground as more plants die and more soil forms above them.

And so soils build up across the land over time, the speed at which they do determined by temperature, water availability, and the presence, ultimately, of life.  The formation of soils would later allow larger plants to grow, the great coal-measure swamps and their kind, moving ever farther from the water’s edges to conquer the sterile stone of the continental interiors, allowing the buildup of oxygen in the atmosphere to even well above modern levels.  Although these levels would ultimately fall at the close of the Permian, driving the greatest extinction ever seen on this planet1, the stage was set some 360 million years ago for the Earth as we know it today: green land, blue skies, and enough oxygen for a modern organism to breathe.

So remember this, as you tend your garden soil or water your houseplants: the world as we know it today is actually very unusual, and the plants that we care for are descendants of pioneers, the first terraformers, the life that took a plain rocky planet and reshaped it into a haven for – and ultimately built by – life.  While Earth was not made specifically for life, life made the modern Earth and, in doing so, fit itself to the changes it wrought on the planet in a positive feedback loop of change and adaptation.

They say Earth is truly a blue planet due to the extent of its oceans.  I say it is a green one due to the presence of, and the changes made by, life.


  1. Morrison, D. and T. Owen.  2003.  The Planetary System. 3rd edition.  San Francisco: Addison Wesley.
  2. Lane, N. 2009.  Life Ascending: The Ten Great Inventions of Evolution.  New York: W.W. Norton and Company.
  3. Hoffman, P.F. and D.P. Schrag.  2002.  “The snowball Earth hypothesis: testing the limits of global change.”  In: Terra Nova 14(3): 129-155.
  4. Kennedy, M.J., N. Christie-Blick and L.E. Sohl.  2001.  “Are Proterozoic cap carbonates and isotopic excursions a record of gas hydrate destabilization following Earth’s coldest intervals?”  In: Geology 29: 443-446.
  5. Gray, M.W.  1998.  “Ricksettia, typhus and the mitochondrial connection.”  In: Nature 396 (12 November 1998): 109-110.
  6. Basta, F.F., A. E. Maurice, L. Fontboté and P.-Y. Favarger.  2011.  “Petrology and geochemistry of the banded iron formation (BIF) of Wadi Karim and Um Anab, Eastern Desert, Egypt: Implications for the origin of Neoproterozoic BIF.”  In: Precambrian Research 187 (3-4): 277-292.
  7. Barley, M.E., A. Bekker, and B. Krapež.  2005.  Late Archean to Early Paleoproterozoic global tectonics, environmental change and the rise of atmospheric oxygen.  In: Earth and Planetary Science Letters 238(1-2): 156-171.
  8. 7. Berkner, L.V., and L.C. Marshall.  1965.  “On the Origin and Rise of Oxygen Concentration in Earth’s Atmosphere.”  In: Journal of Atmospheric Sciences 22: 225-261.
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