Monday, December 14, 2009

Spontaneous Organization

The market economy is a self-organizing system because it is made up of countless people who act out of their own self interest to buy and sell to other people. It is not designed and not made by a designer.



A language system such as the english language, is a self-organizing system. Each speaker of english uses english words in conversation with other english speakers. The language itself is shaped and evolves through the sum total of individual conversations and at the same time the language system as a whole shapes the way that each individual speaker uses it in conversation.



Although laws are made by governments and moral codes are often passed on from one generation to the next through formal and informal education, moral systems can also be seen as self-organizing. Our interpretation of values, social norms and rules helps to shape our everyday conduct with others. Each person's conduct in turn, is interpreted by and influences other's value systems and conduct in a vast circle of social networks. Some people's behaviour is exemplary and very influential, other's behaviour is despicable and serves as an example to be shunned.



All these human systems I am describing have emergent properties that are not reducible to a simple description of physical causes. Being an english speaker I can choose to speak eloquently or massacre the language. Either way, I am part of the english language system without being determined by it.



Consciousness is another system, in this case neurological, where the state of consciousness is an emergent property, not reducible to a physical chain of neurons firing.



The parts of consciousness interact together with the other parts: The mid-brain systems that keep us alert and awake and that help us to pay attention, the sensory systems, the motivational system that helps us to focus and prioritize, the memory systems of the cerebral cortex that help in making associations with past experience, and make experiencing into a continuous flow, the parts of the cortex dealing with language, and meaning that help to put ideas into words, the parts that allow us to visualize ideas, and the prefrontal areas of the cortex that assist us in judging and and decision-making.



Our thoughts, sensations, feelings and judgement get organized into coherent ideas and narratives spontaneously without being planned or designed. For any planning, necessarily already involves ideas and narratives, so it can't be primary.



We tend to model reality after ourselves. This is called “anthropomorphism”. At first we attribute human qualities to natural phenomena such as the weather, the sea, volcanoes, the sun and moon, and the stars. We invent mythologies to explain how these things act, as if they were people and acted according to their own purposes.



Determinism can be seen as just another form of anthropomorphism. Just as all humans make things and do things for a reason, determinism sees everything that happens as determined by previous causes. Determinism equates living things with machines as if they were designed for a reason.



According to determinism there is no free will because everything that happens is determined by antecedant causes. But does causation explain everything, and does it really determine behaviour?



Think back to the flock of sandpipers that I talked about in a previous article. The flock flies in unison, quickly manoevering around obstacles as one, and lands on the beach in unison. Where was the cause of that flock's behaviour? Was it the sum total of all the individual sandpipers' behaviour?



But didn't the behaviour of the flock as a whole influence the behaviour of each individual bird? The behaviour of the flock influenced the behaviour of the individual birds, and the individual birds influenced the behaviour of the flock. In which direction was the cause?



We're talking in circles here. If causation happens in both directions or is “circular” in what sense is it determinate?



Everything can influence us at once, and if so what is it that causes us to do what we do? Everything? Then the concept of causation and determinism itself are both meaningless.



It seems to me that self-organization can generate free will because the influence and interaction of a self-organized system can be omnidirectional.



Think of the brain. Interactions between many different parts of the brain contribute to each moment of consciousness. At the same time our conscious experience influences those interactions. What causes the experience then?



That's why we say that consciousness is an emergent phenomenon and not reducible to the firing of nerve cells. And we can say the same thing about “purpose” and “meaning”. These emerge out of living and self-organizing systems.



Purpose is more basic than meaning because it does not require consciousness. The purpose of maintaining life appears to be already part of every life-form. Meaning emerges from consciousness so it requires consciousness.



It may seem rather abstract, what I'm talking about but these are all things that science has a problem dealing with but are in the province of religion. Consciousness emerges from physical phenomena but cannot be reduced to them because it influences those phenomena. Purpose emerges from life and influences life, meaning emerges from consciousness and influences consciousness.



The key to all these phenomena is that they appear to emerge spontaneously from the bottom up in self-organizing systems, without being designed or planned. This has obvious implications for religion. But that's not my department.

Monday, December 7, 2009

Earth-House-System

I'm reading a book by Phillip Ball, called: Water, Matrix of Life. If you want to know more about water, it's fascinating and well written. I particularly like this quote of his: “Water is the agent of geological, environmental and global change. It confers fecundity on parched regions, while it's passing turns grasslands into deserts.”

Water does all this and more. But water is incredibly effective at what it does because water is a team player. Apparently there's water on the moon in the form of patches of ice, but it's inert, it doesn't do anything because it lacks the other team players. Let's introduce these other team members.

Water is a compound not an element although the Greeks and the Chinese thought it was one of the “four elements” - Earth, Air, Water and Fire. Let's run with this idea but let's assume that fire can mean all types of energy, especially the Sun. Let's use a bigger name for Air. We'll call it the Atmosphere. Let's say that “Earth” means the planet and not just a hunk of rock. Now let's add a fifth element, and call it “Life”.

Put these five elements together and they will interact spontaneously. And these interactions form the great geophysical systems of the Earth.

The Earth's surface has mountains and basins. It's lowest points are where most of the water is – in the oceans. The Earth's gravitational field is strong enough to hold all the gases: the oxygen, nitrogen, carbon dioxide, and water vapour that make up the atmosphere.

Think of Earth as a house without a switch because it runs itself. It's roof is the atmosphere. It lets vital energy from the Sun in and gives us a bit of insulation at night. Too much insulation is not good, as we see with the planet Venus, with its surface temperature of 460 *Celsius.

The Earth's got plumbing, heating, ventilation and power, mostly run by one system: the weather. But it's also got backup power from internal heat which causes plate tectonics to reconfigure the seas and continents every hundred million years or so.

It's not like a house that was designed and built, because it repairs itself. Tell me, what house that we have built repairs itself, or has lasted as long as Earth has?

As a plumbing and heating system and power system the weather is partly predictable and partly unpredictable. Sometimes we get too much water sometimes not enough. Sometimes it gets too hot, sometimes it's just right.

The weather operates under the usual physical laws. The Earth's spin causes winds to curve in the direction of rotation making cyclonic wind patterns counter-clockwise in the northern hemisphere and clockwise in the Southern Hemisphere.

The Sun's radiation heats water on Earth's surface and causes water molecules to change from liquid to gas. The water vapour can rise into the atmosphere because it contains heat from the sun.

Weather is partly predictable, we recognize the seasons, but also unpredictable, we don't know what the weather will be like a month from this day. The weather is a self-organizing system. Weather systems can last up to a week and travel thousands of kilometres.

Let's call a system: a group of parts that interact together to form a whole that is separated from the external world by a boundary.

Let's divide the world of systems into three: machines, institutions, and self-organizing systems.

Self organizing systems are systems of parts that interact via simple physical laws. The parts of the Solar system - the sun and the planets, interact by the laws of motion and gravity to form a balanced system that has maintained itself over time.

All machines are mechanical systems designed and built by humans for various goals. A house is a mechanical system that transfers heat and energy from outside and holds it inside. Houses and other machines have switches on them. When the switch is turned on, the machines start to work and when it's turned off they stop working.

What is a self-organizing system? Think of a flock of sandpipers flying low over the water – the precision and coherence of their flight. The flock swoops and glides as a unified whole as if it acts with one mind.

But each bird is acting on its own and the subtle alterations in flight that each bird makes in response to its neighbours creates an emergent unity.

Unlike machines, self-organizing systems are not deterministic. These systems have properties that emerge from the interaction of all the parts that cannot be predicted from the nature of the parts alone.


You cannot predict the weather beyond a week; Human behaviour is both predictable and unpredictable. Weather systems and large-scale human societies exhibit complex behaviour that is the hallmark of self-organizing systems.

Monday, November 30, 2009

How Water Keeps Us Alive

It's uncanny how many essential functions water serves for life processes. But perhaps the most important function is the regulation of temperature. And the amazing thing is, water acts to regulate temperature simultaneously and independently on multiple levels. On a micro sub-cellular level, a human level, a regional level, and a global level.

Life survives in a narrow temperature range that just happens to correspond with the temperature at which water is a liquid. That's not a coincidence. Life and water are tightly coupled on Earth. All of life's metabolic processes – the things that make a living organism “alive” - happen in water.

The temperature at which water is a liquid is not necessarily the temperature that's ideal for many types of chemical reactions. In some cases heat needs to be added to get a reaction underway, or a chemical reaction can produce a lot of heat in an uncontrollable chain reaction. Either way, the reaction proceeds at a temperature much too hot for life.

All biochemical reactions are catalyzed (made easier) by large convoluted protein molecules called enzymes. The key to an enzyme's function as a catalyzer of chemical reactions is its complex shape. And the key to an enzyme's shape is how the molecule twists and folds in on itself in relation to the water molecules that surround it.

Water is also necessary because it facilitates the flow of dissolved molecules that form the raw materials and the products of enzyme mediated reactions. But that's another story.

The enzymes that catalyze most biological reactions work best within a narrow range of a few degrees centering around 37 Centigrade, normal body temperature. Hotter than this and the enzymes lose their shape and cease to function. Too cold and the chemical reactions slow down too much to sustain metabolic processes.

The human body has several independent systems that work to keep the body's temperature within the narrow range necessary for life. All of these systems involve water in a crucial way and yet each uses water in a unique way.

When we are cold our circulation system shunts blood away from the extremities, where it would be more likely to lose heat to the external environment. This keeps more of the body's water within the better insulated core where it protects the vital organs.

When we are too hot our circulation system shunts more water out to the extremities where heat can be transferred out of the body. Another independent system kicks in to cool the body by secreting water in the form of sweat on the body's outer surface. On a hot sunny day the sweat on our skin evaporates cooling us off.

When we are cold another independent system come into play. We “shiver”. This is a muscular reaction that produces heat to warm the body by increasing metabolic rates and shunting blood to the large muscles of the body. Muscle cells are controlled by nerve cells, and nerve cells cannot tell muscle cells what to do without the medium of water.

So here comes the analogy. Just as water plays the major role in keeping our bodies alive it also plays the major role in keeping life on Earth alive. For it is water in all it's forms that moderates temperature on Earth's surface.

Did I already mention in a previous column that water has the second highest heat capacity of any liquid? Water retains heat. That's why we use it for radiators. But that's also why it's warmer near the ocean in winter, and cooler in the summer. Large bodies of water moderate climate, because they absorb heat and are slow to give it up.

In places far inland it's colder in the winter and hotter in the summer because these places lack the moderating influence of a large body of water. Note that the majority of the world's population lives within 50 miles of the ocean.

Water also has a huge role to play in temperature regulation via an entirely different system – the weather. Here's how it works: The Sun's radiant energy heats the surface water of the oceans. When this happens some of the surface water evaporates. It changes from it's liquid form to water vapour – a gas. In doing so it absorbs heat and cools the surface water.

Not a big deal in terms of the proportion of water that ends up in the atmosphere .001 % of Earth's total, but it's still enough to make a huge difference to the Earth's surface temperature.

The water vapour rises up into the atmosphere where it gets blown far away by the winds. The higher the water molecules rise the colder the air. Eventually the the molecules condense back to liquid and form water droplets. When this happens the latent heat of evaporation is given off into the atmosphere.

But here's the deal - where the water molecule absorbed the heat and where it gives it back can be thousands of miles apart. Thus the sun's energy powers the transfer of heat over the Earth's surface through the medium of water.

But that's not all folks. There's another couple of systems involving water in a major role that effect the Earth's surface temperature independently of the one's I just mentioned. Water freezes into ice at 0 C. Ice reflects sunlight and cools the Earth's surface. That's why during an ice age the Earth's surface gets colder.

But there's more. In the atmosphere water vapour molecules have a stronger greenhouse warming effect than carbon dioxide. This is counterbalanced both by the cooling effect of evaporation, and the fact that water molecules do not stay long in the atmosphere before gravity takes over and pulls the water down to the earth in the form of rain.

OK but there's still more. Because water, unlike most other liquids expands when it freezes, ice forms on top of liquid water and because of that ice insulates water and keeps most of it from freezing in the winter.

Used for warming and cooling, multiple independent systems involved, tightly coupled with life itself -That's Water.

Monday, November 23, 2009

Water, The Restless Creator

The cells of our body are bathed in water. It circulates throughout our bodies in our blood vessels. Water is intimately involved in all aspects of life. No other substance is as important for life.

Water is constantly moving, circulating over the Earth's surface in ocean currents, or drawn downhill to the sea by Earth's gravity, or up into the atmosphere.

Water is drawn up into the atmosphere by solar powered evaporation, it forms into clouds and falls again to Earth as rain, sometimes in the sea and sometimes on land.

When it falls on land some of it ends up as groundwater, some in lakes. But all is drawn to the sea by Earth's gravity. It is the triple actions of the Sun's radiation, the Earth's gravity, and its centrifugal motion that creates the water cycle on Earth's surface

As if to mirror what goes on on the face of the Earth, water in the form of blood is pumped and circulated throughout our bodies by our hearts. This coordinated internal flow of water provides us with food in the form of dissolved carbohydrates , dissolved oxygen, and electrolytes; It gets rid of wastes; It carries immune cells that protect us from disease, white blood cells and platelets that help to repair the body and hormones and chemical transmitters that communicate information from one organ to another.

Water is not just water. It is the universal solvent. It can hold an unbelievable amount of different molecules in solution. Water is constantly in motion, carrying things, carrying chemicals in solution, carbonic acid, which eats away at minerals and carrying sulphates, phosphates, carbonates, and oxides to the sea.

Streams and rivers carry aluminum and magnesium silicates in suspension, and carry rocks and boulders down stream , depositing sediments on the edge of the continental shelves. Over vast scales of time water recycles all the major elements of life except nitrogen.

No-one can survive without water. Not only do we have to drink it every day, but we wash in it, cook with it, clean with it, use it in manufacturing, use it in transportation, and in recreation.

Without water we wouldn't be able to make cement and even our houses would lack a foundation. It's indespensible in religion, where it signifies holiness, purity, and rebirth

Water is the mother of life. The very first living cell was born in water, All of us were conceived and gestated in water. When we are born, we are born from out of our mother's water.

We find ourselves drawn to water, and feel it's calmness, it's churning, it's raging, and it's bubbling. Houses with a water view are worth more money because of the positive psychological effect of seeing water.

But water by itself is not sufficient for life. Without the Earth in it's special relationship with the Sun, and the Earth's size and shape to hold and channel the water, life could not have existed.

What do I mean by Earth's special relationship with the Sun? We know that the Earth, unlike the rest of the planets is just the right distance away from the sun to keep most of the water on Earth in a liquid state. Not to cold to freeze everything and not too hot to boil it all away.

Water is necessary for life, but it's got to be largely in liquid form for life to have originated and for life to continue. That's because life's metabolic processes, the ways that living things get energy, all happen in liquid water.

When, cells photosynthesize it happens in water; When cells do respiration it happens in water; When cells divide it happens in water. All the molecular reactions that are necessary for life work in water and never outside it.

That doesn't mean that water isn't important to life in it's non-liquid phases. Right now 2.9 % of Earth's water is locked away in glacial ice. Over millions of years the glaciers ebb and flow creating ice ages and lowering sea levels then mysteriously stopping their advance over the Continents, retreating towards the poles and making the oceans rise during warmer times.

Water vapour is a more powerful greenhouse gas than carbon dioxide but the reason it does not play as important a role as carbon dioxide in global warming is because a water molecule only stays in the atmosphere for a matter of days, whereas a molecule of carbon dioxide can stay in the atmosphere for hundreds of years.

97% of Earth's water lies in the great oceans. Because water has one of the highest heat capacities of any substance, second only to ammonia, the Earth's oceans play an important role in moderating and regulating climate and temperature. Tune in next week when I talk about the effect of water on global temperature regulation.

Saturday, November 14, 2009

Science vs Religion

Religion and Science are two very different activities, but they are both quintessentially human endeavors.

Science is really a way of asking questions and getting answers. Scientists asks how things happen and look at antacedant causes to find the answers. But answers in science are provisional – never final. For instance, Issac Newton's Theory of Gravity was supplanted two hundred years later by Einstein's Theory of Relativity.

That's why scientific knowledge is made up of theories, not immutable decrees. Scientific knowledge is ever growing and never completed. This is different from religion where if someone adds new revelations to established scripture, it often becomes a separate religion with separate adherents, like Mormonism.

Religion, is also a way of asking questions and getting answers but it asks the question “Why?” rather than “How?” because it is really about meaning and purpose in our lives.

We are the only religious species because we don't do well if we don't have a sense of meaning and purpose in our lives. Science can also give one a sense of meaning and purpose but, because science is provisional – it doesn't give the same sense of security that religion does.

One of the reasons that science and religion conflict is because they are both about life, and life, as we have discovered, is about maintaining itself. Life is intrinsically purposive. Living creatures try to keep on living for as long as possible; They try and begat progeny; They behave purposefully.

Science has subtle problems with this because it doesn't like asking questions about purpose – that's too subjective. It would rather ask questions about physical causes.

One of the main reasons a lot of people are uneasy with scientific descriptions of life is that they sound too mechanistic and meaningless. You can get the impression from strict Darwinists, like Richard Dawkins, that life just happened to evolve purely by chance.

This offends our religious sensibilities – it certainly offends mine. Since everything about life is purposeful, I don't see how the evolution of life could all be due to chance.

But that's a religious approach, not a scientific approach. The questions: “Why does life exist?” and “Why am I here?” - that sort of thing.

I like to think that I'm here for a purpose, that the universe begat life for a purpose, that there is a meaning to life. These are concerns about my subjective experience, about my participation in life.

Science is trying to be objective, trying to approach the ideal of objectivity - which it never quite reaches, because it is provisional and never final. Science is largely uncomfortable getting mixed up in “subjective experience” But that's OK because we've got religion and our religious propensities to deal with the subjective.

We can be uneasy about mechanistic explanations of evolution and human behaviour, but some people go to the extreme of denying the existence of evolution and global warming.
When people deny that life evolved they are taking Martin Luther's extreme position that the holy scriptures trumps every other human authority, including and especially Science.

The people who wrote the Bible were not scientists, they were not really interested in the question of causes and evidence for causes. They were interested in religious questions about who we are, why we are here, why do bad things happen to us, and what happens after we die.

The people who wrote the Bible were fundamentally people. Therefore they had axes to grind, they had personal and political reasons for writing the things that they did. No living person is immune from this, especially not people who claim to be inspired by God, as recent events testify over and over again.

Whoever wrote the book of Genesis was not writing a scientific description of how life originated. He or she, was trying to get people to observe the Sabbath.

God created the world in six days and rested on the seventh. So we should observe one day in the seven day week as a holy day. That's what that story is all about. This writer had ulterior motives as do all other writers.

When scientists ask questions such as: “How old is the human species?” and “Where and how did humans originate?” , the answer from Genesis, that God created the world in six days, just doesn't cut it. It's just a way of telling people to shut up and stop asking inconvenient questions.

The evidence is all around us that life is constantly changing, that life is incredibly old, that the Earth is incredibly old, and that we, as the human race, are not all that old. We should have respect for our elders.

Monday, November 9, 2009

Eukaryotic Cells: A Symbiotic Journey

Symbiosis, is everywhere around us if we know what to look for. Lichens, those scraggly little things that grow on rocks, are half algae half fungi. Fungi and Algae are two very distant families The algae provides the ability to photosynthesize and the fungi provides the physical structure and the ability to gather nourishment from rocks. Neither of the two species that makes up the lichen can exist anymore without the other.

Coral is a creature that forms all the coral reefs in the warm waters of the oceans. Coral is both an animal and an algae. The algae is what gives coral it's colour the greens, reds, and yellows. The animal, called a polyp, is what secretes the calcium carbonate or rock hard body of the coral. If the water stays too warm for too long it kills the algae. If the algae die, the coral dies, because the animal part cannot survive without the energy it gets from the photosynthesizing algae.

The largest structure made from living creatures is the Great Barrier Reef in Australia. This is a series of coral reefs 2600 kilometers long and 344,000 square kilometers. This huge living structure is bleaching out and dying because the algae part of the coral organism cannot tolerate the warmer waters.

Trees are in symbiotic relationships with soil fungi that live on their root tips. The fungi extract minerals and chemicals from the soil and feed them to the tree and the tree is able to feed the fungi with sugars manufactured through photosynthesis in it's leaves.

Termites, which can eat wood, digest the wood with the help of specialized bacteria in their stomachs. Cows and other grass eating herbivores are able to digest the cellulose in grass because of bacteria in their stomachs. Without the bacteria, the cow would not be able to digest the grass. Without the cow, the bacteria wouldn't have access to so much fresh grass,

There are bacteria in our intestines that help us process our waste, making it easier for our intestines to absorb Vitamins B12 and K. Without these vitamins we get blood disorders. When both creatures benefit this is called symbiosis.

There is, in every cell in our body a thing called a mitochondria. Much smaller than a cell, the are about the size of a bacterial cell. The mitochondria take oxygen and sugars and join them to phosphorus creating molecules that store energy. They're like little generators inside your cell. And there can be anywhere from one to a thousand or more of these little mitochondria in each cell, especially in cells that do a lot of work like muscle cells.

In fact, mitochondria are in every type of eukaryotic cell, the type of cell that makes up just about every living thing we know about . But they do not exist in any prokaryotic cells, which is what bacteria are. That means that mitochondria originated when eukaryotic cells originated, two billion years ago, after the proportion of oxygen had increased in the atmosphere. Bacteria could live without oxygen, but eukaryotic single celled creatures with their bigger size and more complex structures couldn't have done without the extra energy that oxygen provided.

One of the most interesting things about mitochondria is that they have their own DNA. Not only that, they appear to be one of the few organelles like plastids in plants and algae, that divides by itself.

Microbiologist Lynn Margulis was not the first scientist to suggest that mitochondria and plastids were actually forms of ancient bacteria, but her version was the first to gain acceptance in the biological community. This was largely because when it became technically feasible to analyze the DNA of mitochondria and plastids separately from the cell's nucleus, scientists discovered that the DNA of these organelles was more closely related to the DNA of ancient bacteria then to the DNA in the cell's nucleus.

Something happened two billion years ago. An oxygen breathing bacteria got swallowed by or invaded a non-oxygen breathing bacteria. Instead of harming each other they benefitted each other. The new cell couldn't survive without the oxygen breathing bacteria so they too were passed on whenever the cell divided. Over time the oxygen breathing bacteria lost some of it's independence, until it too could not survive outside the cell.

All algae, all plants, all animals, all fungi, all single-celled eukaryotes came from this symbiotic combination of bacteria two billion years ago. And the evidence for this caper is in every one of our cells.

One of the reasons it took so long to accept this theory of cell symbiosis is because this didn't quite fit the Darwinian picture. Natural selection was supposed to be imperceptively gradual and stepwise. But here we have the biggest revolutionary change in biology next to the origin of life, the evolution of eukaryotic cells from procaryotic cells, occurring through the fusion of two or more types of ancient bacteria.

This wasn't a gradual series of changes in the cells' characteristics. This was a relatively sudden jump in the structure and functioning of a cell due to the joining together of two or more distinct species. It was not the slow gradual time frame that Darwin had suggested.

The evolution of dinosaurs and human beings was child's play compared to the evolution of the eukaryotic cell. And it couldn't have happened without symbiosis.

Saturday, October 31, 2009

Eukaryotic Cells: Size Matters

Every living thing is either a cell or made up of cells. The fact is, every living thing starts life as a single cell. This divides and divides again as the body is constructed cell by cell.

Lewis Thomas in his famous essay “Lives of a Cell said: “ The uniformity of the earth's life, more astonishing than its diversity, is accountable by the high probability that we derived originally from a single cell.”

The cell is the basic building block of biology. It can be all there is to an organism as many creatures are single-celled, including all bacteria. For humans and other multi-celled creatures one cell can be a tiny fraction of our body, yet each and every cell in our bodies carries our entire genetic identity.

The cells of every living thing are unique. They all contain DNA molecules, the molecules of heredity, that are unique to that particular organism and nothing else. That's why my body can detect the cells of other organisms and produce antibodies that mark these alien cells for destruction by my immune system.


It was about two billion years ago I recall, when something very important happened and a new type of cell developed from bacterial cells. This new type of cell we call Eukaryotic.

If you are old enough to remember, at that time there were no plants, no animals, only microscopic critters called bacteria. Lots and lots of bacteria, many different kinds of bacteria: bacteria that ate iron sulphate and produced sulphur and bacteria that ate sulphur and produced hydrogen sulphide, bacteria that produced methane and bacteria that ate methane. And while there was great diversity in the different metabolic processes that bacteria could do there wasn't much diversity in the size and shape of bacteria.

Why would diversity of size and shape matter? Think about what a world of nothing but bacteria would look like... We're talking soup, slime, and ooze, and PU, what a smell. Enough to literally kill you - not a particularly attractive place to raise your kids. And that was what life on Earth was like for maybe three billion years. Until eukaryotic cells came along, that is.

OK, now what does life look like? There's grass, human beings, seaweed, eagles, redwood trees, moss, elephants, sharks and whales. There's microscopic single-celled sea creatures with fantastic glass houses called diatoms, there's turtles and squids and giant clams and periwinkles. Talk about different shapes and sizes and temperments. Better than 60 degrees of slime any day.

Eukaryotic cells, which is what plants, animals, fungi, and diatoms are made of, are bigger and more complex than prokaryotic (bacterial) cells. They have more parts than bacterial cells and much more DNA, 1000 times more. Eukaryotic cells have more membranes that separate and protect all the numerous parts of the cell.

Eukaryotic cells can do more things, they can specialize and link up to other cells forming organs and entire bodies. They have structures and scaffolding that allow the cells to move about like amoeba or link together like bones, skin, nerves and muscles or layers and fibers in a tree. They can secrete shells of calcium carbonates or silicates to surround and protect themselves.

Bacteria just don't have it in themselves to do any of these things. Their masters of the slime universe but what do they do besides consuming and polluting and exchanging genetic calling cards?

Let's not be disrespectful to our elders now. After all it was out of bacteria that the eukaryotic cell evolved. And that's the amazing thing that I'd like you to contemplate, because if we're looking at the “tree of life” then bacteria aren't in the branches and they aren't part of the trunk. They are in the roots.

Charles Darwin conceived of evolution as a tree with successive species as successively smaller branches, as old species went extinct and new species came into being. New species developed by inheriting new characteristics that eventually separated them from the old species.

Darwin saw the mechanism behind the generation of new species as the competitive struggle to survive. But note: the roots of a tree don't compete with each other. They each extract nutrients from the ground and send them into the tree.

Just so, the first eukaryotic cell evolved not from bacterial competition but from bacterial cooperation. That's something that Darwin didn't anticipate. Tune in next week as I describe how this symbiosis came about.

Thursday, October 22, 2009

May the Phosphorous be With You

Phosphorous burns with desire for Oxygen. To prove its love it will even burn under water. Carbon won't do that. So it is Phosphorous that makes Oxygen potential food rather than poison. Without Phosphorous Oxygen would have remained on the dark side of life. A deadly toxin that was killing off it's photosynthetic producers. We should be thankful for this intense love affair between Phosphorous and Oxygen, for without it we wouldn't exist.

Our brains require both sugar molecules and oxygen to remain conscious. Sugar is the product of photosynthesis. Oxygen is also the product of photosynthesis. Consciousness would not be possible without photosynthesis.

Imagine that. We think we are so independent, we can understand things not seen, see things that are no longer there, and predict things that haven't happened, yet we could not do any of these things without the existence of photosynthesizers.

Oxygen has great potential, electrically speaking. And molecules with phosphorous are the key to tapping its potential. Phosphorous is essential to bone formation and basic metabolism in most animals. It forms a part of ATP, otherwise known as Adenosine triphosphate and ADP, or Adenosine diphosphate. These are the molecules that are the workhorses of “ cellular respiration”

And DNA – the molecule of heredity, is non-functional without phosphorus. Maybe it's the power of love between Oxygen and Phosphorous that has really made it possible for life to endure longer than the mountains and the continents


In cellular respiration oxygen atoms are passed from one molecule to the next in a controlled stepwise process that extracts the maximum energy from an oxygen atom and makes it available to the cell for work. It is molecules of ATP and ADP that makes this possible.

Microbiologist Lynn Margulis is the scientist who first brought to our attention the idea that oxygen played a major role in shaping the direction of early evolution.

“Whereas fermentation typically produces two molecules of ATP for every sugar molecule broken down, the respiration of the same sugar molecule utilyzing oxygen can produce as many as thirty-six.”

“With greater quantities of energy available to them cyanobacteria exploded into hundreds of different forms. They spread into greater extremes of the environment, from cold marine waters to hot freshwater springs.”

“Cyanobacteria's continuing air pollution forced other organisms to acquire the ability to use oxygen too. This set off waves of speciation and the creation of elaborate forms and life cycles among them.”

“Growing, mutating and trading genes, some bacteria producing oxygen and others removing it, they maintained the oxygen balance of the entire planet.”

Oxygen has been twenty-one percent of the atmosphere for hundreds of millions of years. This is a sign of the endurance of the balance of nature. It shows that there has been a balance between photosynthesizers and respirers for at least that long.

If oxygen was much higher than 21% then all the plants on land would burn even if they were wet. But if there was much less oxygen than 21% then all animals, including humans would asphyxiate. So as animals that need to breathe and depend on plants for food we are lucky that there is just the right proportion of oxygen in the atmosphere.

How could this be? Some lovers of certainty think that there must be an intelligent designer behind it all. On the other hand, strict Darwinists, like Richard Dawkins can't explain this as anything but a coincidence. Neither considers that new properties can emerge from the ground up. In fact, living things maintain themselves. They sometimes adapt to change by changing the environment.

When too much oxygen was produced its dark side came into play. There was massive extinctions. When new forms of life evolved to take advantage of oxygen, the new form of energy, they quickly expanded in population. A new balance was created between the creatures that produce oxygen and the creatures, like us, that consume it. All this occurred over a time scale of millions of years.

There is a parallel between oxygen and oil. We humans have changed the face of the Earth much faster than any other creature. We discovered coal and oil in the ground and developed technologies like steam, diesel, and internal combustion engines to utilize the new form of energy. This occurred over a few hundred years.

Developing transportation, agricultural and extraction technologies based on machines that run on fossil fuels allowed the human population to grow rapidly because it gave us the ability to get more resources from the ground, to grow more food, and to provide more amenities for ourselves.

The greater population led to the greater utilization of fossil fuels which in turn is leading to a greater output of carbon dioxide. It is carbon dioxide that regulates global temperature and ocean acidity. Increasing the amount of carbon dioxide in the atmosphere along with other stresses on other life forms caused by increases in human population is leading to a new major extinction event.

Many creatures will go extinct. Carbon dioxide will stabilize at some higher level until millions of years from now new life forms evolve to fill the empty niches left behind by the mass extinctions and they draw down the amount of carbon dioxide in the atmosphere once again.

The balance of nature is a metaphor, but it represents a real process. In maintaining itself life uses energy and creates pollution. Pollution is toxic to many organisms and many of them die off. New life forms evolve to take advantage of the pollution creating a balance.

 The global combination of all living creatures may keep the content of oxygen and carbon dioxide in the atmosphere in stable proportions until a new creature, in this case one that adds huge amounts of carbon dioxide, tips the entire system over.

Thursday, October 15, 2009

Oxygen: Saviour

We're the blue planet. That's us. When you're talking planets - blue is associated with life. The blue colour comes from oxygen which makes up a large portion of the weight of a water molecule. And the blue sky also comes from the element oxygen. Oxygen comprises twenty-one percent of our atmosphere.

The colour red also has to do with oxygen. Rust, gets it's red colour because it is oxidized iron. Blood gets it's red colour from the iron and oxygen in hemoglobin. The planet Mars gets it's red colour from oxidized minerals which means that Mars used to have oxygen, probably in the form of water.

Oxygen, with it's all consuming hunger for electrons, has a lot of potential energy. But it is potential for good or ill. Free oxygen has the potential to destroy biological molecules. That's why we use bleach to get out stains. Bleaching is an oxidation process. Oxygen, by grabbing electrons from other elements, weakens covalent bonds in organic molecules leading to their disintegration.

Atmospheric oxygen is the source for ozone, a molecule made up of three oxygen atoms. Ozone is a toxic pollutant, an ingredient in automobile exhaust, but it also exists in the atmosphere where it protects life on Earth from ultraviolet rays. High up in the atmosphere a layer of ozone absorbs the ultraviolet light that would otherwise harm living creatures.

Not only does ultraviolet light harm living things but for time periods of billions of years it has even greater potential for harm. The high energy content of ultraviolet light means that it has the power to break the bonds of water molecules.

Once liberated from water, hydrogen can escape Earth's gravity into space. Without protection, over billions of years, the sun's ultraviolet rays could deplete the oceans of water.

There is evidence on Mars – the famous “Canals” - that there was once water there. Now there is no water and only a thin atmosphere of carbon dioxide. No oxygen in the atmosphere. No ozone to protect against ultraviolet light. No water anymore. And without water there is no life.

No life without water and no water without life. Earth has both. Mars had only one and now has none.

Twenty years ago there was an international treaty signed to protect the ozone layer from a man-made substance called freon. Freon was used as the main coolant in virtually all refrigerators and air conditioners. The problem was that when it was released into the air , which is what happens eventually when all fridges and air conditioners are discarded, it rose high into the atmosphere where it chemically reacting with ozone - destroying it.

Sometime during the 1990's Scientists discovered a “hole” in the Ozone in the southern hemisphere. The Ozone hole has gotten smaller since countries complied with the treaty and stopped manufacturing freon, but not before it took it's toll on Australia, where the incidence of skin cancer has increased considerably.

When bacteria first existed there was no oxygen so there was no ozone to protect living things from ultraviolet rays. It took millions of years for oxygen to reach a high enough percentage for the protective ozone layer to develop. We call that a “Time-lag. In that time bacteria were on their own to develop resistance to these deadly toxins: oxygen and ultraviolet light.

Life is autopoietic, but in maintaining itself life alters the chemistry of the Earth. And when that chemistry changed from zero free oxygen to twenty-one percent free oxygen, life developed in a radical new direction.

From photosynthesis, to – “respiration” – the utilization of oxygen to supply chemical energy to life, oxygen,which was first a pollutant and a toxin, became the basis for all new forms of life.

Tune in next week when we learn who helped Oxygen turn from the “dark side” and transform into a Creator.

Wednesday, October 7, 2009

Why Bacteria Invented Sex

Bacteria are the ultimate survivors. They've been around for three and a half billion years. Longer than the continents, and all the mountain ranges on Earth. In contrast, the animal kingdom has been here only a paltry six hundred million years – one sixth of that time.

Bacteria are the simplest of creatures being as they were the first of all creatures to exist. They are single-celled. They are so small,that they are invisible to the naked eye. But they are not solitary creatures and they live in huge communities that are sometimes visible in the form of coloured blobs of slime, the kind you might see in a petri dish or on rotting food. It's easy to look down on them as disgusting and smelly but without them we would not exist.

It is bacteria, more than any other creature that has altered the face of the Earth – breaking down it's rocks, and adding to it's atmosphere gases such as carbon dioxide - which is crucial to Earth's temperature regulation, methane, and oxygen – without which we animals could not survive.

The technical name for bacterial cells is “Prokaryotes” , which refers to the fact that bacteria don't have a nucleus. All “Eukaryotic cells” - the kind of cells that we have in our bodies – have a nucleus. The nucleus contains all our genetic material wound up like the rubber strands in a golf ball only way tighter – if the DNA in the nucleus of one of your cells was unwound it would stretch to the moon and back several times.

That extra genetic material and the protective membrane means that eukaryotic cells can do more things and make up more complex multicellular organisms like us.

In contrast bacteria don't have as much genetic material. And the genes are looser, not packed as tight because they are not surrounded by a nuclear membrane.

But, bacteria have an advantage over eukaryotic cells. Bacteria are the original party animals. They love to hang out in huge numbers, and they're not so particular that they have to hang out with their own species. They love to mix and when they mingle they can easily exchange genetic material with whoever they please. They have no shame and the whole thing is over in seconds. Which means that bacterial evolution has been fantastically quicker than the evolution of eukaryotes

This bacterial promiscuity is the basis for genetic engineering, by the way. Because it's so easy to get bacteria to take on different genetic material bacteria can be given genes that will manufacture just about anything we want. That kind of stuff is just not possible for eukaryotic cells, thank God.


Technically speaking, “sex” is the exchange of genetic material between different organisms. It isn't necessarily tied to reproduction the way it is for bigger eukaryotic creatures. Bacteria aren't male and female because they pre-date reproductive sex.

It's immaculate conception. Bacteria can split all by themselves, And go on making millions of exact copies of themselves. They don't need love. But they need protection from toxins.


Ultraviolet light coming from the sun is hazardous to life. It can damage biological molecules. It damages DNA molecules,the genetic material for all forms of life. In Microcosmos, Lynn Margulis and Dorion Sagan's book about microbial evolution, the authors hypothesize about this connection: “The pressure to patch up damaged DNA or die induced the development of DNA repair systems. Sometimes instead of using healthy copies of their own genetic material, crowded bacteria borrowed DNA from their neighbours.”

“By adapting to life under harsh light the microcosm had invented sex. Though this first sex was different from the kind of sex animals are involved in, it was sex all the same...”

This was probably their most important means of evolving rapidly in the face of environmental danger. We now know why it was so easy for bacteria to aquire resistance to deadly toxins like anti-biotics. Bacterial sex takes advantage of the natural variety in the population to provide resistance to new toxins.

It's easy enough to say that bacteria should have just kept away from the sun's dangerous rays, and then they would have survived. Because if that's all they ever did they would never have developed photosynthesis and then we wouldn't exist. It's autopoieses. Life maintains itself. And life that survives over time does so because it adapts to Earth's changing environment. In next week's article we will discover how life can also change the odds for itself in a positive direction by altering the environment.

Friday, September 18, 2009

Oxygen: Destroyer

Oxygen gas is an anomoly. Earth's atmosphere should not be 21% molecular oxygen because oxygen is a very greedy element. It wants electrons badly and would much rather take those electrons by binding with elements on Earth's surface, then hanging around with other oxygen atoms in the atmosphere. As long as these elements are out there oxygen will "oxidize" them, which is what happens when iron rusts or something catches fire.

So why is there always 21% oxygen in the atmosphere? No other planet in our solar system has free oxygen in it's atmosphere (even though it's the third most abundant element in the universe). But no other planet in our solar system has liquid water and no other planet in our solar system has life. That's where the connection lies. It all hinges on a metabolic process called photosynthesis that was invented about two billion years ago by the bacterial ancestor of cyanobacteria or "bluegreen algae".

Lynn Margulis and Dorion Sagan, in their book, What is Life?, call photosynthesis: "the most important metabolic innovation in the history of the planet." Why? Because with photosynthesis life could derive energy from freely available sunlight for the first time.

The first bacteria probably lived off hydrogen sulphide bubbling up from volcanic vents under the sea. They derived their energy from catalyzing the hydrogen bonds, combining hydrogen with carbon to make simple sugars. Eventually, different kinds of bacteria evolved that were able to catalyze various non-organic substances such as iron and sulphur, then other bacteria evolved that could derive still more energy by fermenting the waste products of previous kinds of bacteria. Note that all early bacteria were "anaerobic", that is they did not use oxygen in any metabolic process.

There's a pattern here. First, an organism develops a way of getting energy from one substance. Then it grows and multiplies until it exhausts that resource. A crisis ensues which leads to the evolution of new life that is able to utilize new forms of energy, then those resources are exhausted and a new crisis ensues. Out of these series of life-crises bacteria came to invent every single metabolic process utilized by living things. Margulis and Sagan's point is that the development of photosynthesis temporarily bypassed this boom and bust process. By utilizing the energy from sunlight the ancestor of cyanobacteria was able to metabolize enough energy to split water molecules into hydrogen and oxygen, obtaining hydrogen from a virtually limitless source - the oceans - something that no bacteria before it was able to do.

But photosynthesis wasn't just a brilliant solution for bacteria, it rewrote the rule book for every single new life-form that has evolved since that time 2.5 billion years ago. Because, other than bacteria, all forms of life are either photosynthesizers themselves or they survive by eating photosynthesizers or by eating animals that eat photosynthesizers. That's what we mean by "the food chain".

Let's go back to that connection between oxygen in the atmosphere, water, and life. Because they had just liberated themselves from energy scarcity, the new kids on the block - bluegreen bacteria - were able to grow and multiply and grow and grow and grow until they had covered Earth's surface, wherever there was moisture. We're talking all the oceans and most of the surface rocks. We're talking a vast global empire of bluegreen slime.

But in the process of splitting water into hydrogen and oxygen, bluegreen bacteria gave off oxygen gas as a waste product. Thus the second type of crisis: pollution. Life multiplies up to it's limit, but in this case, because we are talking about sunlight and water as raw materials there was no imminent shortage. But there was a problem with pollution. Oxygen was created as a waste product and oxygen was toxic to bacteria in those times. In fact if sufficient atmospheric oxygen had been around at the time that life originated it wouldn't have originated. The oxygen would have burned up all the organic molecules before they had a chance to react with each other. Like I said, oxygen is greedy.

At first the oxygen pollution wasn't much of a problem, because oxygen was reacting with all the surface rocks, so it didn't stay long in the atmosphere. There are red bands of oxidized iron and other oxidized minerals in the layers of ancient rocks that date back to that time about two billion years ago. And, in fact, that's the strata of rocks that supplies us with iron ore to this day. From the rock record of oxidized iron we can read back the time it took for oxygen to get a foothold in the atmosphere - four hundred million years. But once everything was oxidized, all the oxygen that was produced by photosynthetic bacteria stayed in the atmosphere, creating a vast die-off of anaerobic bacteria.

Nowadays anaerobic bacteria are far less dominant, existing only in earth, mud, stagnant water, and in the guts of animals, all places where they are safe from the ravages of free oxygen.

This global event, when oxygen increased from one millionth to one fifth of the atmosphere was, according to Margulis and Sagan, in their book: MicroCosmos, "..by far the greatest pollution crisis the earth has ever endured." Unfortunately, there is no fossil record of this event, as bacteria, not having bones or hard shells have left very little in the way of fossils.

Since animals evolved, one and a half billion years ago, there have been five major extinction events recorded in the fossil background. These were global catastrophes, where from fifty to ninety-five percent of all species on Earth were wiped out. The most famous of these was the Jurassic-Cretaceous event sixty-five million years ago, believed to be caused by a giant meteorite striking the Earth, leading to the extinction of the dinosaurs and paving the way for warm-blooded species like birds and mammals.

We are now, as we speak, involved in the sixth (or seventh, if you include "the Oxygen Holocaust") global extinction event, an event which is predicted to lead to the extinction of more than fifty percent of all species in our lifetime. This one is due to carbon dioxide pollution and habitat destruction caused by our clever utilization of a previously unused energy source - hydrocarbons. What goes around comes around, as they say. Whether we will survive it or not, is an open question. Stay tuned.

Tuesday, September 1, 2009

The Carbon Connection

“Only connect!... Only connect the prose and the passion and both will be exalted, and human love will be seen at its height. Live in fragments no longer. Only connect...” E. M. Forster

What do we mean when we say that life is an interdependent web? Partly it's a metaphor that points to the way that living things make up of a vast network of interrelations. How are living things connected? All life-forms are made from the same types of molecules: water, proteins, carbohydrates, lipids, DNA, and RNA; All life forms metabolize energy with the help of enzymes made from amino acids; All life-forms share a common ancestor, according to Darwin's theory of evolution; All living things ultimately depend on the Sun's energy; All living things share materials and substances that are only available on Earth; All living things interact cooperatively and competitively with other living things.

All well and good, but what makes this vast and intricate global interdependence possible? If I was to pick one thing it would be the element Carbon. You may recall that I said in the previous article that each element is a kind of character. Carbon is the most extroverted sociable element there is. He is an exceptionally friendly fellow. He makes bonds with everybody and they are often strong bonds called covalent bonds that require more energy than the other two kinds of bonds to break apart. Diamonds, the hardest substance known, are made from pure carbon bonded covalently.

OK, lots of elements bond covalently, but what differentiates Carbon from everyone else is that he can't get enough of himself. Carbon loves to bond with himself and does it over and over in chains, and in rings, in two dimensional sheets and in three dimensional tetrahedons. There is literally no end to the number of carbon atoms that can join together to form chains of fantastically diverse lengths.

And Carbon is a multi-tasker extraordinaire. So while he's linking up to carbon copies of himself, he's always socializing with the other elements on the side, especially with Oxygen,Hydrogen and Nitrogen. These chains of carbons with various side links then form the backbones for literally all the molecules of life: the proteins, enzymes, carbohydrates, fats, etc... It's the incredibly complex shapes that are created by carbon bonds that are the key to life.

Life is autopoietic - it maintains itself over time. But in order to maintain itself a living organism must perform many functions , all of which require a vast variety of different kinds of molecules and only Carbon makes that possible .

But that's not all, because Carbon, in the form of carbon dioxide, is essential in regulating Earth's surface temperature and the acidity of the ocean and our bodies. These are big jobs and somebody's got to do them, or life as we know it would cease to exist. So why Carbon?

You'd think that a substance that makes up only .03% of the Earth's atmosphere would hardly be up for the job, but it's the size of the molecule that matters when it comes to the greenhouse effect. And carbon dioxide with three atoms, one Carbon and two Oxygen, is a bigger molecule than the two other main components of the atmosphere – Nitrogen and Oxygen - which each form molecules of only two atoms each. Note that water and methane, which are also bigger sized molecules are even more potent greenhouse gases than carbon dioxide but they don't remain in the atmosphere as long as carbon dioxide does, so their effect is smaller.

We think of carbon dioxide as being the bad guy because of global warming but in actual fact without carbon dioxide the Earth would be a ball of ice. It's just that our industries and transportation systems are producing too much carbon dioxide right now. But that's for another article.

When carbon dioxide dissolves in water it forms a weak solution of carbonic acid and bicarbonate which together makes it a buffer. Chemical buffers keep the pH of a solution more stable by neutralizing acids and bases, thus keeping the ocean and our blood at near constant pH. But if too much carbon dioxide is dissolved in water then it loses it's buffering quality and becomes an acid. When that happens in our blood stream we die from acidosis. The thing is, the metabolic reactions that sustain life only occur in a narrow range of temperatures and pH, so Carbon's role in regulating temperature and ocean pH is vital to life. The problem is when too much carbon gets into the atmosphere both those systems go out of whack and then we get into trouble.

When you think about it, we take Carbon for granted. Carbon has got a lot of responsibility for supporting life as we know it . We oughta give him some slack instead of making his job harder. After all, he's kinda like that guy Atlas, the one who holds up the sky in Greek mythology. Maybe somebody should write a book about him – a “green” Atlas Shrugged.

Saturday, August 29, 2009

Hydrogen: Life, the Universe, and Everything

“We are called to restore within ourselves the sense of awe and delight, to respond to matter as a mystery of ever increasing connection.” - Patriarch Bartholomew

What makes life possible? For those of you who successfully avoided Chemistry classes in high school, I'll try to make it simple by talking about four (that is, mostly four) elements. But it doesn't end there. To really understand what makes life possible you need to go all the way back to the beginning of the Universe. You think I'm kidding right? Nope.

Just about everything there is is made from countless atoms. Atoms are ridiculously small. You can't see them even in electron microscopes. There are only about one hundred kinds of atoms. Each kind is called an element and it has unique characteristics that differ from all the other elements. All the atoms of a particular element say, Hydrogen, have virtually identical chemical properties. If you've seen one, you've seen em all. And the same goes for the rest of the elements. But to reiterate, each element has a set of chemical characteristics that's unique to it and it alone. So understanding those characteristics helps to understand why those particular elements are so basic to life.

Our bodies are mostly made up of four main elements. They are, in order of abundance: Oxygen, Hydrogen, Carbon and Nitrogen. I like to think of each one of these four elements as characters in a story. Each one has it's quirks, it's own special history.

Hydrogen is really special. It's in a class by itself. It's the lightest element, the simplest element, and the most abundant element in the Universe, although wait another ten billion years and that will no longer be the case. But for now it's tops. Hydrogen is also the oldest element because all the hydrogen that exists came into existence during the Big Bang – the origin of the Universe.

Let's just stop and think about that for a moment. One of the main ingredients that makes up our bodies comes from the very origins of the Universe. Every hydrogen atom in our bodies, and believe me, there's a lot of them, is fourteen billion years old. Talk about experienced. Those hydrogen atoms have seen it all. And because hydrogen is so simple – one proton and one electron – it reacts with everything. They've had relationships with every other element many times over. Been there, done that.

Hydrogen is also the main fuel for stars. Stars like the Sun are giant furnaces that burn hydrogen giving off incredible amounts of energy that we see as light. It's the Sun's radiation, caused by the fusion of hydrogen atoms that ultimately supports all life on Earth.

Hydrogen is the building block of the universe, and all the other elements are made from it, forged in the fiery furnaces of stars. A star like our Sun, which is about 4.5 billion years old and counting, is too small and doesn't burn hot enough to create many kinds of elements. That job is reserved for supergiants, stars so big that they burn up in a matter of tens of millions of years , then explode into supernovas, explosions so awesome they can light up a whole galaxy, outshining millions of other stars. It's in the unbelievably hot core of these explosions where all the heavier elements are forged, which include the other three elements that are important to life: Oxygen, Carbon, and Nitrogen.

Life, which requires these and other heavier elements, could not exist without the death of supergiant stars. Joni Mitchell was right, we are stardust. And we have to get back to the garden too, but that's another article. And so begins a theme that I will come back to again and again: even as every living thing dies, life itself comes from death.

Thursday, August 27, 2009

What is Life?

What is life? Biology is the study of life and yet a typical modern biology text with, say, about 1200 pages will devote at most about three pages (and usually less) to answering this question . You will be hard put to find any University courses exclusively devoted to this subject. But after all, Biologists study living things, they are not philosophers.

Everyone has an intuitive feeling for what life is. We can generally tell the difference between something that is alive and something that is either dead or simply material matter. Living things move, they feel warm to the touch, and they react to stimuli. That's enough for most people. But think of a flame or a hurricane. They both move, grow, and die, they react to stimuli and give off heat but they are not alive in the same sense as you or I.

What differentiates a living thing from a flame? Like living things, a flame metabolizes. It takes energy in from the environment and processes it. A flame burns because it's reached a certain temperature and it's fed by fuel. Once the fuel is used up the flame dies. The flame does not go looking for more fuel somewhere else. But a living creature will maintain itself purposefully; it will search out food sources; it will avoid dangers and predators; it will adapt to changing circumstances; it will reproduce and thus maintain some of it's genetic characteristics even after it dies.

This ability to self-maintain is called “autopoiesis”. It's an amazing property because it has created an unbroken link between us and the very first cell. Lynn Margulis and Dorion Sagan, in their book, What is Life? capture it's essence well: “ Once autopoiesis appeared in the tiniest bacterial ancestor it was never completely lost....As sheer persistence of biochemistry “we” have never died during the passage of three billion years. Mountains and seas and even supercontinents have come and gone but we have persisted.”

How does autopoiesis come about? We have to be careful when we try to answer this question because it's all too easy to go in circles. Did the first bacterial cell create itself on purpose? And this is also the place where those of us who are impatient for certainty want to bring in God, alias - “The Intelligent Designer”.

Imagine a sandpile. A constant trickle of grains is being added to the middle of the pile. At some point just adding a single grain can cause an avalanche. Maybe a small avalanche, maybe a large avalanche. There's actually no way predict which it will be. Thus the sandpile exhibits complex behaviour. Per Bak, the Danish Physicist who came up with the sandpile model explains how it works in his book How Nature Works – The Science of Self-Organized Criticality:

“The addition of grains of sand has transformed the system from a state in which individual grains follow their own local dynamics to a critical state where the emergent dynamics are global.... It is clear that to have this average balance between the sand added to the pile say, in the center, and the sand leaving the edges, there must be communication throughout the entire system. There will occasionally be avalanches that span the whole pile. This is the self-organized critical state.”

Of course the sandpile doesn't do anything besides reach a peak and spill over it's edges but the point is that it is a simplified model that gets at the essence of emergence. It shows how complex global behaviour can emerge from the simple addition of individual parts without recourse to purpose or design. This model has been used to explain how complex systems such as living cells, human societies, and economic systems can come about from the bottom up, that is through the action of individuals alone.

Obviously autopoiesis, life's ability to self-maintain, is an emergent phenomenon. It cannot be predicted from the chemical properties of all of the molecules in a cell. But we now know that it is possible for such an emergent property to come about from the bottom up, that is from some critical state brought about by the addition of a sufficient number of certain kinds of molecules. For now how these molecules first came together is a matter of conjecture.

One of the problems with Darwin's theory of Evolution has been that although natural selection can explain the evolution of life from the first cell to all the living creatures that exist today it doesn't explain how the first cell came to be. Many critics have pointed out the fantastically small odds of such a cell ever coming to be by chance. We used to think that there were only two alternatives: chance or design. But now we see a third alternative: self-organized criticality. And this fits better with the continuing scientific project of reading universality into the world. Life is an inevitable property of a certain level of molecular organization. That is, whenever that level of organizational complexity is reached that organization will self-maintain and life will occur. The question is – what are the conditions that make autopoieses possible? This is a question I will address in my next series of articles.

Monday, August 24, 2009

What Are They Smoking Now?

It ain't easy being green, making Canadians feel badly about the Tar Sands. I could have had a comfortable job like Ben Eisen, earning a living working for the Frontier Center For Public Policy, helping Canadians feel good about themselves. ( http://timestranscript.canadaeast.com/opinion/article/767682 ) The Tar Sands may be spewing megatons of carbon dioxide into the air but it's really OK because Canada's "emission intensity" has decreased.
Gosh, I feel better already, knowing that Canada has gotten much more efficient at contributing to global warming. Let me guess.... The Frontier Center For Public Policy wouldn't be funded by any oil companies would it? Nah. After all they're at the frontier of public policy, and have nothing to do with the nasty corporate back rooms where they're pulling the strings on government energy policy.
Reminds me of a story I once heard. Remember "light cigarettes"? Not so long ago the big tobacco companies spent millions in an effective campaign to confuse the public and delay governments from regulating what has turned out to be a very carcinogenic product. During those times some marketing genius thought up the idea of "light cigarettes" - cigarettes with less nicotine and tar. The idea was that if smokers knew that tobacco caused cancer they might be enticed to smoke a product that appeared to be safer. Instead of quitting, they could feel less guilty and better about themselves by smoking something "safer". It turns out that light cigarettes were just as likely to cause cancer as ordinary cigarettes because smokers unconsciously smoked them more intensely and therefore received equivalent amounts of nicotine and tar as if they had smoked regulars.
It's no coincidence that the global warming delayers are talking about emission intensity instead of "crude indicators such as total emissions" of carbon dioxide. Why not recycle a clever idea when you don't have anything good to offer in the first place.

Sunday, August 16, 2009

Prophecy and Kairos

“From the moment when a (large scale) disaster appears inevitable and especially after it becomes a reality, it can, like every great torment, become a productive force for the religious point of view. It begins to suggest new questions and to stress old ones.”

“Dogmatized conceptions are pondered afresh in the light of events, and the faith relationship that has to stand the test of an utterly changed situation is renewed in modified form. But the new acting force is nothing less than the force of extreme despair, a despair so elemental, that it can have but one of two results: the sapping of the last will of life, or the renewal of the soul.”

I love this quote from Martin Buber, the Jewish theologian because it seems so appropriate for our times. And yet, it was not written in response to the threat of global warming, it was written seventy years ago, just after the second world war ended, a war which like the ancient Babylonian and Roman assaults on Jerusalem, threatened the very survival of Judaism. This quote comes, not from Buber's most famous work: I and Thou, but from a book called The Prophetic Faith, a book about the ancient Hebrew prophets.

Judaism is unique among the world religions in having a long historical line of major prophets – historical figures like Jeremiah who spoke truth to power at a time when there was no free press or human rights. The Hebrew word for prophet “nabi”, means “one who is called” . The nabi saw themselves as called to speak the word of God even if it was opposed to what the Hebrew kings and their subjects wanted to hear. The prophets challenged their rulers to adhere more strictly to monotheism and eschew the worship of other gods. They also protested against injustice and gross inequality. This was at a time when the Hebrew culture and religion were under direct threat of extinction from the much more powerful empires around them.

It is instructive to note the historical period when the Hebrew prophets were active. We are talking about a period of about four hundred years from the time of king David and king Solomon, to the rebuilding of Solomon's temple after the Babylonian exile. During these times the Hebrew kingdoms of Israel and Judah were declining in power and increasingly threatened by the powerful empires of the Assyrians and the Babylonians.

Eventually in 722 Bce , the kingdom of Israel was destroyed by the Assyrian army and the population scattered to the four corners of the Assyrian Empire, where they disappeared from history. That's what happened to the ten lost tribes, by the way.

Two hundred years later Judah, the remaining Hebrew kingdom was conquered by the Babylonian army. Solomon's temple was reduced to rubble and the major portion of Jerusalem's population was exiled to the capital city of Babylon.

It was during these disastrous times that the Hebrew prophets were active. The amazing thing is that with all this destruction the Jewish religion not only survived it became more resilient. In contrast, there is no Moabite, Canaanite, Egyptian, or Babylonian religion today in spite of the fact that some of these countries lasted much longer than Israel and Judah.

After Solomon's temple was rebuilt the Hebrew Bible records no more major prophets. Ezra, the Jewish leader who oversaw the rebuilding of the temple was most likely the same person who edited and redacted the Hebrew Bible into the basic form that we know today. He wove together the various writings – the historical material, and the writings of the prophets into a single work which codified Jewish monotheism. A large part of the Hebrew Bible, in fact, is devoted to the writings of the prophets, and for a very good reason. For without these prophets the Jewish religion would not have survived.

A common misperception of a prophet is of someone who predicts the future. This is not what the Hebrew prophets were doing, and if it was they would not have been able to save the Jewish religion from extinction. I think Buber has the best description of what prophecy is about: “ A true prophet does not announce an immutable decree. He speaks to the power of decision lying in the moment and in such a way that his message just touches this power.” The future is uncertain. What decisions we make now will effect our future. The role of the prophet is to point out the consequences of our present actions and the possibilities of renewal if we change our behaviour.

Today, three thousand years later, our global civilization is under threat of extinction from the very different threats of global warming and eco-catastrophes. And religion does not play the same role that it did in ancient times. Because our civilization is global, and there are many world religions no single religion has the capability to unify and preserve our cultures. Our civilization probably doesn't have one hundred years left, let alone four hundred years. The world religions are slowly responding to the new ecological threats, but the role of the prophet is now paramount and the new prophets are not necessarily religious prophets. While religion has a definite role to play in all of this it is largely scientific knowledge that feeds modern prophecy, if we keep true to Buber's definition of what prophecy is.

In the Greek language there are two concepts of time: “chronos” which refers to sequential time, and “kairos” (pronounced keros) which refers to the right time or opportune moment. According to the Protestant theologian Paul Tillich kairos refers to a crisis in history which demands a life-changing decision on the part of each person. According to Tillich, the coming of Christ is the prime Christian example.


Today global warming is our kairos. This is what Greek Orthodox Patriarch Bartholomew has said, and he elaborates in his essay: “The Orthodox Church and the Environmental Crisis”

"Our way of life is humanly and environmentally suicidal....yet the crisis is not first of all ecological. It is a crisis in the way we perceive reality and relate to our world......At a time when we have polluted the air we breathe and the water we drink, we are called to restore within ourselves the sense of awe and delight, to respond to matter as a mystery of ever increasing connection."


I can't help seeing an analogy between Patriarch Bartholomew's saying that this is a crisis in the way we perceive reality and relate to our world and the Hebrew prophets' relentless emphasis on monotheism during their prolonged crisis. The ancient Hebrew prophets saw monotheism as the key to Jewish survival. The importance of monotheism to Judaism is that it redefined the relationship between the Jewish people and the divine and it changed the way they perceived the divine. Jesus called the “Shema” from Deuteronomy the great commandment: “You shall love the Lord God with all your heart and all your soul, and all your might.” It basically sums up Judaism in one sentence.

I am not advocating monotheism as the answer to the ecological crisis. Judaism was saved from extinction because a lot of people worked hard to change the Jewish people's perception of their relationship with the divine. To love God with all your heart is to make God personally meaningful, which means that this relationship can survive regardless of whether or not there is a temple, or official priests, or the proper sacrifices. That's why Judaism could survive and grow stronger after the destruction of the temple and the exile. Our civilization will only survive if we stop perceiving nature as something we can control and start seeing ourselves as just one part of the interdependent web of life. “We are called to restore within ourselves the sense of awe and delight, to respond to matter as a mystery of ever increasing connection.” I say amen to that.