Sunday, 19 August 2012

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.

Sunday, 5 August 2012

Vegetable Spirits

 In "The Botany of Desire", Michael Pollan breaks down how four plants, apple, tulips, cannabis, and potatoes, have shaped and manipulated Humanity in profound ways.  In each case, we find a bivalent relationship between man and plant, showering it in praise when times are good, and condemning it when times are bad.  But in each case, bad times are the result of human overindulgence. 

Apples: apples, hailing from Kazakhstan, are normally bitter when planted straight from seed.  Only a select few of the apples might be sweet, and these have to be cloned, as they have been for hundreds of years now.  Bitter apples, however, are perfect for making cider, and hence the primary use of apples in America before the last century was as booze

Tulips: Tulips are prized, obviously for their beauty.  In the seventeenth century, tulips made a huge splash among the Dutch, driving them into what is now known as Tulip Mania.  The price of a single tulip could be as high as that of a coastal estate, or what might now be $10-15 million.  The most beautiful tulips were those with wild colorful designs on their leaves.  Such heady designs were caused, unbeknownst to the Dutch, by viruses.

Cannabis: The cannabis plant is perhaps the most pampered plant on the planet.  Though it is technically a weed, the oily resin produced by females to catch male pollen contains high concentrations of a psychoactive compound, THC, which modulates human consciousness in a (usually) desireable manner, rendering this weed highly desirable.  The plant also has a variety of medicinal effects.  By growing females only, growers put the plants into a state of sexual frustration, a whole group of sexy ladies clothed in dark greens and purples and flickers of red looking hot for a lay and finding none, causing them, in effect, to layer up in more and more sticky jewelery, those cannabinoid dense jewels that glisten on the surface of their buds.

In the late 1980s, it was discovered that there exists a receptor system in the brain that binds THC.  It was later found that there are other molecules, made by the body, that bind to these receptors.  One of these, called anandamide (taken from the Sanskrit 'ananda' = 'bliss'), is a crucial molecule in brain cell communication and has been found to play a major role in the art of updating memory - in some sense, the art of forgetting.  Sound familiar?

Potatoes: Originally cultivated in the Andes by the Inca, potatoes changed the course of history in numerous ways when they were brought to Europe.  On the one hand, they provided a dense bundle of calories that could grow in the harsher conditions of northern Europe, eradicating periodic famines that were known to occur.  On the other hand, countries like Ireland, for example, became so reliant on potatoes that they would practice mono culture, ie. growing only one crop.  So when a ship shows up one evening in the early nineteenth century with a bug that Ireland had never seen before, the country's potato stock got wiped out in a few days.  And since they were growing nothing else, they went very, very hungry

In the modern age, a similar mono-culture excersice exists with regards to potatoes (as well as many other crops, unfortunatley).  McDonalds, an enormous potato buyer, is interested in only one type of potato, the Russet Burbank.  This lone variety is monocropped consistently across the continent, often obliging the use of heavy pesticide coverage.

Farmers who choose biodiversity and organic farming practices can grow a variety of different potato types and employ natural methods to protect plants (like ladybugs).  Since they don't have to spend millions on chemical pesticides and since they can fetch higher prices for the quality of their products in the market, organic farmers are more and more able to keep up economically with their more chemically inclined competitors.

Hats off to you, organic farmer.