Monday, March 04, 2013

A Sample Size Of One and The Search For Life (part 3)

Living things have had it rough. We presently live among a measly 5% of the total number of different types of living things that have ever been. But even at 5% the numbers are staggering --an estimated 8.7 million different species alive, right now --a billion species or more, for all time. And amazingly every one, past and present, is running the same chemical machinery deep down inside. The chemical compounds that stored the genetic code of dinosaurs, also does yours and mine. The basic machinery is so precisely matched that pieces of DNA are completely interchangeable, across species (of even remote ancestry) and function perfectly well. No hiccups, no barriers, no mistakes. Carl Sagan once reflected, “Any tree, could read my DNA”. More to the point, any organism could read any other organism’s DNA. There is no fundamental restriction to this most essential of observations. 

Life is one thing, one event, one instance, playing out over and over again, in “endless forms, most beautiful and most wonderful"1. The fact that life is, at its core, the same for all is not happenstance. As we are quickly learning, the early Universe is (and continues to be) primed for life, our life. The pieces of the molecular machinery that drives our cells is universal –they are found everywhere. It is no coincidence that life is constructed of the same building blocks --they are easily made and in great abundance. They are readily available to be assembled into the larger polymers needed for life to emerge. How does this fact, coupled with our understanding of the characteristics and requirements for life, allow us to make predictions about life elsewhere?

It helps to recognize that there is a very short list of elementary particles that make up everything in the Universe. And those particles come together to form a finite number of elements. And the stability required to make monomers that can assemble into large polymers is further limited to just one atom, carbon. Life is carbon based, not just because it is convenient but because nothing else will do the trick. There are no alternatives (sorry silicon-based life form fans). Large, stable polymers, built on skeletons of carbon, are an essential ingredient for any living systems. There is simply no other way to endow enough complexity into a system to make life emerge without them.

One type of essential carbon compound is protein. Proteins are unique in the world of chemistry. They do something no other molecule is capable of doing. They behave. They move, adjust, act, react, turn, flip, grab, hold, hook, spin, open, close, etc. Every blob in this video, showing the process of DNA replication,  is a protein. It is impossible to watch and not think of them as well rehearsed; coordinating their behavior to achieve a task --as if they were alive. These proteins are performing just a single dance in the larger performance that makes your cells come alive. DNA replication is a universal process; every cell in every organism performs this activity whenever it divides, and the proteins that orchestrate it do so for all life, since day one (or very nearly so).

Just how do proteins perform these incredible feats? Their trick is in their shape. Proteins are build as strings of amino acids and after they are made, then fold and twist into 3D shapes, looking a little like a tangled extension cord. From their shape emerges their function, their behavior. Protein strings can fold into an infinite number of shapes. Most have no interesting biological function (at least, for life here on this planet), but some do. Their shapes are the result of the interactions of the different amino acids and their position in the chain. Change the sequence and you change the shape. Since the proteins of Earthly life uses 20 different amino acids, there are more possible sequences, and therefore shapes and functions, than there are total number of atoms in the Universe! DNA replication only uses about a dozen.

As remarkable are proteins are, surely there must be another way to build molecules of sufficient complexity and variability get life going. Is there any reason to suspect that all life, everywhere, would use the same building blocks?

The ubiquity of the building blocks themselves is compellingly suggestive of the likely use  of proteins in life throughout the Universe. Amino acids are everywhere. If life needs molecules like proteins, why not simply use proteins. The probability of another prebiotic system stumbling upon a novel chemistry to substitute the molecular complexity of proteins, while simultaneously missing the available building blocks to make proteins, must be incalculably low. Prebiotic chemistry is simple chemistry. The first “living” chemical pathways would have appropriated the material that was on hand, or could be easily synthesized. In a Universe filled with amino acid precursors, it is highly unlikely that anything else would have won. Life everywhere must have co-opted what was available.

Encoding protein information to ensure persistence across generations while simultaneously allowing for variations in amino acid sequences for selection to take hold, requires a molecule that works like DNA works. This line of reasoning is entirely anthropocentric (or should it be DNApocentric?), but considering that, like amino acids, nucleic acids are everywhere, the arguments for their incorporation into the machinery of life are equivalent as for proteins. In this case some flexibility is allowed. We know, for example, that proteins can perform double duty, encoding their own sequences or directing their own replication. We also know that nucleic acids can catalyze their own replication without the need for proteins to orchestrate it. Either way, these molecules work alone or in concert, but they are the ones that work. There is nothing else available.

Once you establish the common chemistry of life throughout the Universe, the next steps are to establish the common characteristics that chemistry produces and to then establish the range at which those characteristics can exist and persist. This is the where and what to look for.

-End of part 3 (part 4)

1 Darwin, Charles (1859), On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (Full image view 1st ed.), London: John Murray, pp. 502, retrieved 2013-03-04

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