Life is just a fancy way for water to get around.

Most narratives of the evolutionary story focus rather predominantly on the notion of competition, of natural selection, of survival of the fittest.  Granted, the forces of natural selection are ever present in a resource limited environment (such as the Earth).  Organisms must compete with each other for nutrients, shelter, and mates, and those most successful in competition will be most likely to reproduce.  It is a well worn story, and it has been extraordinarily important in overthrowing an ancient obsession with anthropomorphized deities and creation myths.  But this is the 21st century, and as we mature finally into the era of a technologically competent whole globe societal system, with an ever growing population and an ever more apparent scarcity of resources (and competence...), it becomes essential that we re-evaluate our understanding of the development and maintenance of sustainable systems (such as organisms and ecosystems), if we are to avoid out-competing each other into nuclear holocaust.

Organisms are, fundamentally, sustainable systems.  That is their very essence.  They operate under meager inputs of energy and achieve efficiencies unheard of in human engineering (leaving aside those engineers now turning to bio-mimicry - we'll get to that).  They can withstand numerous large perturbations or disturbances (relative to their size), and in many cases come out not just alive and well but stronger than before (they are anti-fragile!).  They are enduring and productive, and in the case of humans (or ecosystems), capable of immense creativity and profound transformations of the physical environment.  Is all of this merely a matter of competition and descent by natural selection?

The simple answer is: most definitely not.  I contend, along with a growing number of others (mathematicians, physicists, ecologists) that much of the natural beauty and profound capacity of living systems derive not from the arms-race of natural selection but from the inherent pattern-forming processes that underlie the dynamics of our universe.  Life on Earth is a Cosmic phenomenon, and don't you forget it!

See, living systems are first and foremost physical systems.  They are built out of molecules and ions, and are as subject to the fundamental physical laws of the universe as anything else.  If we are going to understand their profound capacities for efficiency, work, and ultimately creativity, we must take stock of some physics.  Now, the laws of physics are unreasonably simple - I am not being facetious.  There is no reason that physics should be as neat and tidy as it is, given the overwhelming complexity of the physical universe.  But, fortunately for us (perhaps necessary for us), much of it is surprisingly easy to understand.  Of course there is the further matter of carrying out detailed calculations, but that is essentially irrelevant (if you are merely interested in ideas), and is ultimately designated to a computer.

To understand the physics of living systems, we begin with a simple system, a hot cup of coffee on a table in a room-temperature environment.  What is happening to our system, the cup of coffee, and to its environment, the room?  Clearly, the temperature of the coffee is running down - heat is leaving the cup (we can usually see it, and it is usually very pretty) and entering the room.  Why is it doing that?  Well, the coffee is made up of (liquid) particles bouncing around in a cup, and the environment is made up of (gas) particles bouncing around in a room.  The coffee is hotter, so its particles are moving faster, and so it is overwhelmingly likely for some of them to bounce their way out of the cup, and into the room, but it is not nearly as likely for particles in the room to bounce into the cup.  So heat (the bouncing of particles) leaves the cup.  When the temperature of the cup reaches that of the room, the chance of a particle leaving the cup and one entering the cup are the same (since they are all going at the same speed, on average), and so we say the system has reached equilibrium.

If given the opportunity, all systems will eventually reach equilibrium.  This is entirely a matter of statistics.  At equilibrium, things are relatively boring.  But on their way to equilibrium, things are much more interesting.  Indeed, the coffee-cup heat is only a simple example.  Far more fascinating are the patterns in rivers, galaxies, neurons, and trees.  Ultimately, all of these designs
stem from a common origin in the statistics of non-equilibrium systems.  Ultimately, I contend, this is the essential character of life on Earth, which is only supplemented and encouraged by the forces of competition and natural selection.

So let's make more concrete steps from coffee mug to living system.  First of all, consider a situation in which we maintain the heat of the coffee, say by keeping it on a hot plate, and the amount of coffee, say by having a constant (very small) influx into the cup to offset evaporation.  Then the system will dissipate heat indefinitely (and display beauty indefinitely in the heat patterns!), as it will never be able to reach equilibrium, since we continue to drive it by providing more coffee and more heat.  Such a system we call a driven, dissipative, non-equilibrium system, or just a dissipative system for short.  Its driven because there is constant energy input (coffee and heat), its non-equilibrium because there are gradients present (temperature difference between coffee and room), and its dissipative because heat is constantly leaving the system.

Living systems, similarly, are driven, dissipative non-equilibrium systems.  They are driven by sunlight (ultimately) and nutrients (more generally), they are non-equilibrium because they are chalk full of gradients and structure and interesting patterns (which don't occur at equilibrium), and they are dissipative because they give off heat (the reason night vision goggles work) and excrete waste.  So they are very much like our coffee cup.  If we did in fact let the coffee cool down, to equilibrium, we might then say that our system has 'died', since it no longer displays interesting patterns.  Similarly, for an organism, if we deprive it of food (nutrients and/or sunlight), it will die, eventually reaching equilibrium, where there are no more interesting patterns (like lungs and brains and fingers and bellybuttons and eyeballs).

Now, this tendency for systems to decay to equilibrium, to dissipate gradients, and to degrade the quality of energy available to them, is known as the Second Law of Thermodynamics and is one of the hottest topics in physics, even to this day, despite it being over a hundred and fifty years old.  Essentially, the 2nd Law defines the sorts of processes we can expect to occur in the universe: a cup falls of a table and shatters into a hundred pieces, but doesn't spontaneously re-assemble into a cup; hot things cool down, but cool things don't heat up (unless you heat them); a drop of ink in a glass of water diffuses out until the concentration is equal everywhere, but doesn't spontaneously re-condense into a drop; and so on.  How is it then, in the context of a universe where gradients are always set to run down, that systems as complex as cells and organisms and ecosystems could possibly be built up?  Indeed, this is the standard argument of creationsists and religious folks who know only too little physics.

The key is driving and dissipation, as we noted above for the coffee cup.  A system which is driven and dissipative spontaneously organizes into wonderful patterns as it attempts, as best it can, to dissipate the driving energy.  The patterns that form in cigarette smoke are precisely these sorts of patterns - they emerge in the pursuit of dissipating the energy available in the form of burning tobacco.  The patterns that form in the Earth's atmosphere are similar - they emerge to facilitate the dissipation of the sun's energy into heat.  Hurricanes and tornadoes, which in and of themselves are highly structured patterns, emerge because they facilitate the destruction of many other surrounding patterns - ie. they facilitate the dissipation of gradients and the degradation of energy, in direct accord with the Second Law.  Self-organization in one place, then, emerges in order to facilitate disorganization in another.

On Earth, the primary system for dissipating the incoming sunlight energy is the water cycle.  The patterns of the atmosphere, which are many and quite formidable, exist because they facilitate the dissipation and degradation of the sun's energy.  If they weren't there, then sunlight would just bounce back into space with the same energy it had coming in.  But this is less likely, according to the Second Law, and so we have the formation of patterns in the atmosphere.

Living systems emerge as an extension of the water cycle, in its capacity to dissipate and degrade sunlight.  Life augments the ability of the water cycle to dissipate the sun's energy.  As a result, less sunlight is reflected back into space, and more heat is produced.  According to the Second Law, this is a favourable result.  So from the perspective of this analysis, Life is actually highly probable on a planet such as ours (with abundant water and carbon), as it complies directly with the Second Law of thermodynamics.  So, contrary to the argument of the creationist (which asserts that Living Systems, by containing so much structure, violate the second law), Life is actually a result of the Second law, since it facilitates the dissipation and degradation of the sun's energy on Earth.  Hence life is more favourable, thermodynamically, then no life.

So how do you like that?!  Life is just an extension of the water cycle.  Or, if you like, life is just a fancy way for water to get around!

At this point I think it is constructive to take note of the difference between Human engineering and Natural engineering.  Human's are concerned predominantly with the conversion of heat into work.  We burn liquid fuels, giving off immense amounts of heat (and patterns in the heat, but we mostly ignore these), and use that heat to drive turbines to produce electricity.  We know, however, and have known for as long as we've had the second law, that this process is fundamentally inefficient, in that one cannot convert all of the heat released into an equal amount of work (this is known as Carnot's theorem).  On the other hand, Natural engineering (if we may use such a phrase) is concerned with the exact opposite process, that of converting work into heat: sunlight comes in (work) and is dissipated as heat.  But in between, a whole myriad of processes occur which siphon off the energy of the sun and use it to drive the various cycles and reactions that constitute Life, before the energy is ultimately dissipated.  Somewhat paradoxically, energy ends up being stored in the system for an extended period of time, contributing to its highly ordered and structured dynamics and profoundly beautiful patterns.  In this way, living systems become thermodynamically favourable by adhering to the Second Law, and so are anti-fragile.  In contrast, human engineered systems are profoundly fragile - small mishaps can lead to devastating consequences.

I suspect that in the near future, we will learn to engineer society to derive all its energy needs from incoming sunlight, and to comply more directly with the second law, slowly siphoning off the energy for the myriad processes of our socio-economic system, storing it on board for extended periods of time, and finally dissipating it as heat.  In this way, we will become more thermodynamically favourable and ultimately anti-fragile.  We will become sustainable.

Metals and the Alchemy of Life

There's this awesome question about the origin of life, how it started or where it came from.  For all I really know, it could have come from anywhere; mushroom spores from another Galaxy or super advanced slug creatures laying eggs on our planet far from home.  Regardless, I think its a fun exercise to approach the problem using the constraint that life evolved wholly on Earth.  Then we are left with only the materials of the early Earth, and of course an abundance of sunlight.

The early earth had lots of water, lots of nitrogen, lots of carbon, and lots of metals.  These are the essential ingredients for life.  People often neglect the significance of metals in biological systems, but they are absolutely essential.  Your cells wouldn't get oxygen if it weren't for iron.  They wouldn't be able to communicate if it weren't for calcium.  Your brain wouldn't be able to maintain its wiring if it weren't for zinc.  Most of your proteins wouldn't function if it weren't for an arsenal of metal ions.  And so on.  But the importance of metals really derives from their relationship with electrons, that is, their knack for letting electrons flow.

Flowing electrons are behind everything in our civilization.  All electricity, technology, and power applications involve flowing electrons.  Not surprisingly, so do living organisms.  But living organisms aren't full scale conductors the way copper wires and platinum electrodes are.  They're semiconductors, like the transistors inside your computer, but based on carbon instead of silicon.

Electronic processes in the body happen in the form of 'redox' reactions, also known as REDuction-OXidation.  Your entire metabolism is a complex network of redox reactions.  A redox reaction is simply a reaction between molecules where there is a transfer of electrons.  One molecule gains electrons, one molecule loses them.  Redox.  The neat thing about them, though, is the energy associated with the electron as it hops from one molecule to another.  If you play your cards right, you might be able to harness some of this energy to do something functional with.  And that, my friends, is the secret of living systems.  It's also the secret to batteries and fuel cells, but in a less elegant manner.

So in the beginning there were places on earth that were both very wet and very dense, gel-like places with an abundance of metals and simple small molecules bumping into each other in confined regions.  Due to the heat of the early Earth and the incoming light, chemical reactions occurred that produced the first organic molecules and their combinations.  At the same time, heat, light, and heterogeneity were pumping redox reactions left, right, and center.  At some point, an organic molecule shows up that can participate in the redox reaction - it's no longer just between metals and water.

Then everything changes.  Now organic molecules are picking up and giving off electrons as they're pumped by the metals, facilitating even more reactions and molecular evolution.  They're also coupling themselves to the metal redox processes, offering an enormous space of possible pathways for electrons to flow.  This in turn increases the opportunities for other molecules to couple with the redox processes, and, potentially, to suction some of the electron's energy to do something interesting.

An explosion of couplings occur between metals and organic molecules to facilitate redox processes.  The earth is ablaze in early biochemical electronics.  Somewhere along the line a curious organic molecule shows up.  He's called RNA.  He's a chain of smaller molecules (nucleotides) that can bind to other molecules, break them, and combine them.  He can even bind other nucleotides and arrange them into a copy of himself.  He is a replicator.

Replication is certainly necessary for life, but it is not sufficient.  For a replicator to actually become something living, it must be replicating meaningful information; in particular, information that codes for the maintenance and functioning of a redox network.  Viruses and prions, two examples of replicators that are not defined as living, do not code for redox processes.  It turns out that RNA, in certain configurations, can bind to a plethora of small organic molecules.  In a sense, the region of RNA that binds the molecule also 'codes' for the molecules, and when the RNA is replicated, so too is the information for 'binding' to the molecule.  If the molecule of interest is involved in a redox process, then our RNA contains meaningful information.

RNA is awesome because it not only contains information, it acts on it.  It physically goes and binds to the molecule it codes for.  In so doing, it probably disrupts the redox process the molecule was part of.  This opens the floor for the redox process to explor other pathways, in other words to be modified by the activity of the RNA, which has done nothing more than bind a molecule that was part of the pathway.

Now here's a unique point.  If an RNA can bind to a molecule, then it isn't too much of a stretch for us to suppose that the same RNA might be able to build that molecule itself.  In fact, we've recently discovered that some modern RNA sequences do just that (well, they actually code for a protein which builds the molecule that they bind to).  So now suppose you've got an RNA which can bind to a molecule and make that same molecule.  So it can only do one or the other.  If its bound to the molecule, its not making it, and the redox pathway is broken since the molecule is unavailable.  If its not bound to the molecule, its synthesizing it, and the molecule can participate in the redox reaction.  But if it makes too much, it'll start binding to it again, and slow down the redox process.  Suddenly we have controlled feedback regulation of a metabolic circuit.  BAM! - get a bunch of those interacting, and you've got a living system.

Of course now there's all the problems of the origin of protein and DNA, their relationships with RNA, origin of the cell membrane, and so forth.  That stuff would be fun to discuss.  So too would considerations of entropy and the free energy storage of these systems.  But the key milestones have already been overcome: replicators that encode meaningful information about the construction and modulation of metabolic circuits.  That's the essential.  And I'd like to emphasize that the entire thing was built around metals and water.

It's interesting to consider our evolving relationship with metals.  As the posterchildren of material strength and functionality, they've been integral to human evolution since the beggining.  Not only do they make respiration and our bodies possible, but we organize human history into the stone age, bronze age, iron age, and so forth.  Now we are in a silicon age.  When you cosider that stone is really composed of metal (metal oxides, actually), then you realize that our history is characterized by the metals we used, which shaped everything about our lives.  This is true still today.

And especially today, with new technologies involving the curious quantum properties of metals constantly evolving, metals become an ever more significant and scarce resource.  Rare metals are used more and more frequently in high tech applications involving lasers and magnetism, powering our gadgets and our clean energy future.  They are the cornerstone of our reality.

Know your metals.  Alchemy never ends.