Tuesday, July 7, 2015

How You Consist of Trillions of Tiny Machines

Today, driven by ongoing technological innovations, the exploration of the “nanoverse,” as the realm of the minuscule is often termed, continues to gather pace. One of the field’s greatest pioneers is Paul Falkowski, a biological oceanographer who has spent much of his scientific career working at the intersection of physics, chemistry, and biology. His book Life’s Engines: How Microbes Made Earth Habitable focuses on one of the most astonishing discoveries of the twentieth century—that our cells are comprised of a series of highly sophisticated “little engines” or nanomachines that carry out life’s vital functions. It is a work full of surprises, arguing for example that all of life’s most important innovations were in existence by around 3.5 billion years ago—less than a billion years after Earth formed, and a period at which our planet was largely hostile to living things. How such mind-bending complexity could have evolved at such an early stage, and in such a hostile environment, has forced a fundamental reconsideration of the origins of life itself.

At a personal level, Falkowski’s work is also challenging. We are used to thinking of ourselves as composed of billions of cells, but Falkowski points out that we also consist of trillions of electrochemical machines that somehow coordinate their intricate activities in ways that allow our bodies and minds to function with the required reliability and precision. As we contemplate the evolution and maintenance of this complexity, wonder grows to near incredulity.

One of the most ancient of Falkowski’s biological machines is the ribosome, a combination of proteins and nucleic acids that causes protein synthesis. It is an entity so tiny that even with an electron microscope, it is hard to see it. As many as 400 million ribosomes could fit in a single period at the end of a sentence printed in The New York Review. Only with the advent of synchrotrons—machines that accelerate the movements of particles, and can be used to create very powerful X-rays—have its workings been revealed. Ribosomes use the instructions embedded in our genetic code to make complex proteins such as those found in our muscles and other organs. The manufacture of these proteins is not a straightforward process. The ribosomes have no direct contact with our DNA, so must act by reading messenger RNA, molecules that convey genetic information from the DNA. Ribosomes consist of two major complexes that work like a pair of gears: they move over the RNA, and attach amino acids to the emerging protein.

All ribosomes—whether in the most humble bacteria or in human bodies—operate at the same rate, adding just ten to twenty amino acids per second to the growing protein string. And so are our bodies built up by tiny mechanistic operations, one protein at a time, until that stupendous entity we call a human being is complete. All living things possess ribosomes, so these complex micromachines must have existed in the common ancestor of all life. Perhaps their development marks the spark of life itself. But just when they first evolved, and how they came into being, remain two of the great mysteries of science.

All machines require a source of energy to operate, and the energy to run not only ribosomes but all cellular functions comes from the same source—a universal “energy currency” molecule known as adenosine triphosphate (ATP). In animals and plants ATPis manufactured in special cellular structures known as mitochondria. The nanomachines that operate within the mitochondria are minute biological electrical motors that, in a striking parallel with their mechanical counterparts, possess rotors, stators, and rotating catalytic heads.

The ATP nanomachine is the means by which life uses electrical gradients, or the difference in ion concentration and electrical potential from one point to another, to create energy. The nanomachine is located in a membrane that separates a region of the cell with a high density of protons (hydrogen ions) from an area with a lower density. Just as in a battery, the protons pass from the area of high density into the area of lower density. But in order to do so in the cell, they must pass through the ATP nanomachine, and their flow through the minute electric motor turns its rotor counterclockwise. For every 360-degree turn the rotor makes, three molecules of ATP are created.

Living things use a great many primary energy sources to create ATP. The most primitive living entities are known as archaea. Though bacteria-like, they are a distinct group whose various members seem to have exploited almost every energy source available on the early Earth. Some, known as methanogens, cause carbon dioxide to react with hydrogen to create the electrochemical gradient required to make ATP, producing methane as a by-product. Others use ammonia, metal ions, or hydrogen gas to create the electrochemical gradient. Bacteria also use a variety of energy sources, but at some point a group of bacteria started to use sunlight to power photosynthesis. This process yielded vastly more energy than other sources, giving its possessors a huge evolutionary advantage. Falkowski has spent most of his career unraveling the deep mystery of photosynthesis and how it changed the world.

by Tim Flannery, NY Review of Books | Read more:
Image: Martin Oeggerli/Micronaut