Life's Ratchet: How Molecular Machines Extract Order from Chaos (38 page)

We have seen that the mechanists, from Democritus to Helmholtz, were right: Life is based on machines—on pumps and motors. What these scientists could not know is that these machines are molecular nanobots that work very differently from any machine they could have imagined. The nanomachines of life are the offspring of chaos. They are driven by chaos, and as we will see in the next chapter, they are, at least in part, designed by chaos.

Quotation courtesy of K. Eric Drexler.

I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection.

—C
HARLES
D
ARWIN

What, as hath already been said, but to increase, beyond measure, our admiration of the skill, which had been employed in the formation of such a machine? Or shall it, instead of this, all at once turn us round to an opposite conclusion, viz. that no art or skill whatever has been concerned in the business, although all other evidences of art and skill remain as they were, and this last and supreme piece of art be now added to the rest? Can this be maintained without absurdity? Yet this is atheism.

—W
ILLIAM
P
ALEY

W
ILLIAM PALEY (1743–1805) WAS AN EIGHTEENTH-century clergyman, theologian, and philosopher. His work was so greatly admired by fellow clergyman that the Church made him the subdean of St. Paul’s Cathedral and the rector of Bishopwearmouth, providing ample income for a philosophizing priest. Paley’s moral writing was surprisingly modern. He attacked slavery and the active maintenance of
poverty by the rich. He even defended the right of the poor to steal, if this was necessary to feed themselves and their families. In his natural history, Paley was a reactionary. Writing at the end of the scientific revolution, he espoused a natural philosophy that harkened back to prerevolutionary times. Yet, his writing was so persuasive that even a young Darwin became one of his admirers. What pleased his fellow churchmen was that, in their eyes, Paley destroyed the mechanical philosophy. They agreed with him that it was absurd to believe that matter can organize itself. Moreover, they concurred that belief in the self-organization of matter was akin to atheism.

The most famous passage of Paley’s writing is the beginning of his
Natural Theology
: “Suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place; we perceive . . . that its several parts are . . . put together for a purpose . . . that the watch must have had a maker: that there must have existed, . . . an artificer or artificers who formed it for [a] purpose.”

The analogy of living organisms with watches or clocks has been so persuasive that radical agnostics like La Mettrie, Christian apologists like Paley, and even twentieth-century scientists like Schrödinger have all employed this analogy to support their completely divergent points of view. The mere observation that the superficial similarity of an organism with a watch or a clock could support atheism, Christianity, and scientific mysticism should raise suspicion. Is it a good analogy at all?

To answer this question, let us ask it in a different way: Are our bodies similar to the machines we design? The answer must clearly be no. As much as Descartes or La Mettrie were impressed by the pumps, pipes, and levers that make up our body, we now know that the human body is something that emerges from the interactions of
molecules
. Of course, there are macroscopic pumps and pipes and levers in our bodies, but on their own, these cannot explain what makes us alive. Bacteria are also alive, but they have no heart, lungs, or arms. We can build a machine that contains pumps and levers, but it would not find its own food and reproduce.

If life, then, is based on molecules, it will necessarily be subject to the randomizing power of atomic motion. Chance will play an important role. And indeed, if we look at the motion of molecular machines or the mechanism
of evolution, chance is a constant companion of life. This is not the case for a watch. The last thing we want in a watch is for chance to play any role—chance is only detrimental.

Paley ridiculed chance: “What does chance ever do for us? In the human body, for instance, chance, i.e. the operation of causes without design, may produce a wen, a wart, a mole, a pimple, but never an eye. Amongst inanimate substances, a clod, a pebble, a liquid drop might be; but never was a watch, a telescope, an organized body of any kind, answering a valuable purpose by a complicated mechanism, the effect of chance. In no assignable instance hath such a thing existed without intention somewhere.” What I find interesting about this view is that he relegates a liquid drop to chance, when a liquid drop is very much the result of necessity. A pebble is, of course, part chance, but also the result of the formation of atoms from subatomic particles, the creation of heavy elements in supermassive stars and supernovas, the crystallography of complex silicate minerals, and numerous complicated geological processes, from volcanism to erosion. A wart, on the other hand, is the result of a sophisticated,
evolved
machine—a virus. Paley could not have known these things, but it shows how such deeply felt beliefs fare in the light of modern knowledge.

A watch clearly has an artificer—because a watch is a brittle design. It performs one specific task, it only works if all of its parts work, and it cannot cope with any influence of chance or chaos. In short, a watch is not really that complicated. As a matter of fact—apologies to my watchmaker father—watches are Tinkertoys compared with even the smallest organelle of a cell. On the other hand, many natural entities, which even Paley would have excluded from being designed, are vastly complex: stars, planets, mountains, volcanoes, weather patterns, and, yes, even pebbles.

Paley was similarly misguided on the topic of reproduction. He mused about the possibility of one day finding that the watch could make another watch, “similar to itself.” Would that not be proof that the creator was even more sophisticated than we thought? The watch’s ability to reproduce would only add to the complexity of the watch and would therefore make it even
more
likely that an artificer had created it. But this reasoning is flawed: If a watch could make another watch, it clearly would not need a creator. A watch would simply be the result of another watch. And if the new watch, as Paley argues, were merely “similar” to the original one,
then why couldn’t the new watch be a little bit better than the old one? Interestingly, Paley introduces chance into the argument when he says that the new watch is similar, but not identical. How similar? What determines what is the same and what is different in the offspring? What if there were millions of such watches, reproducing and exchanging information about their construction, passing every improvement to the next generation— would these watches not improve over time?

Before you object that watches don’t have babies, let me remind you that I am simply following Paley’s argument. Obviously, a watch that could reproduce itself would stop being a watch. A watch is an artifact made for an
external
purpose—to tell the time. Once the watch starts reproducing itself, it acquires an
internal
purpose—efficient reproduction. If we still had an external agent who selects watches for how well they tell time and only lets good timepieces reproduce, they would, over the generations, become better and better watches. But in the absence of an external agent, the watches would stop just being watches, because efficient reproduction would become their new raison d’être. After some time, they would radiate into many different machines—based on which could reproduce the best.

Now let’s go one step further. Nothing works in the absence of energy. A watch needs to be wound up to work. A living organism must eat. Thus, reproducing watches would need to take in energy. They would need to find ways to beat competing watches in the race to sequester enough energy to reproduce. This would require them to find new ways of making a living. Biologists call these roles
niches
. Before long, we would not recognize our watches anymore. Few would still tell time. Their wheels would now be used for digestion or locomotion. The hands and the dial would be used for attracting a suitable partner with which to exchange information. Maybe, a glow-in-the-dark hour hand would drive the opposite sex wild. This is evolution—this is life.

How do molecules evolve? Despite the histrionic debates in various American school boards, the mechanism of evolution is, as we saw in
Chapter 1
, quite obvious when contemplated with an open mind. This observation
prompted Darwin’s supporter Thomas Huxley to lament his not having thought of it first. Molecules are subjected to the same natural selection that applies to the more macroscopic parts of an organism. As a matter of fact, the evolution of proteins is a good way to see how evolution works, because there is a direct relationship between the protein’s amino acid sequence and the information encoding this sequence in DNA. Every molecular innovation—every new molecular machine that transports cargo a bit faster or makes fewer mistakes when transcribing DNA— will give an advantage to the organism it inhabits. Consequently, better molecular machinery will become more prevalent in a population. Or when conditions change, new machinery will emerge to deal with the changed conditions.

A famous example of the evolution of proteins was the 1975 discovery of a strain of
Flavobacterium
in a wastewater pond at a Japanese nylon factory. The bacteria in this pond had evolved to eat chemicals associated with nylon manufacturing—chemicals that do not exist in nature. On further investigation, researchers isolated three enzymes that had evolved inside these bacteria and that helped the bacteria break down nylon. None of these enzymes existed in
Flavobacterium
strains that were not raised in the nylon pond. How did the bacteria invent the new enzymes? Bacteria multiply very fast and exist in large numbers. Therefore, they can evolve very rapidly. In this case, the DNA replication machinery of a few
Flavobacterium
cells apparently made a mistake. The machinery read off a DNA sequence from the wrong starting point, leading to a so-called frame-shift mutation. It so happened that the resulting protein was helpful in breaking down nylon, which is helpful when you live in a pond full of the stuff. Is such serendipity really believable? Absolutely. Just consider that a human body contains 10
¹⁴
(a hundred thousand billion) bacteria. The Japanese pond must have contained much more than that. A typical time for bacteria to multiply is twenty to sixty minutes. Assuming the slower time and assuming that the nylon factory was in production ten years, the bacteria would have gone through 87,600 generations of gazillions of bacteria. Considering this enormous number of bacteria and the many generations they pass through, a rather unlikely mutation now moves into the realm of definite possibilities. But we are not done yet: The first enzyme may not have been good at digesting nylon, but a bad nylon-digesting enzyme was
certainly better than none at all. Once the bad nylon-digesting enzyme spread through the bacterial population, it evolved and improved rapidly.

The glacial, step-by-step, and somewhat unpredictable process of evolution makes it difficult for people to believe that this mechanism could have led to the sophisticated machinery of our cells. But as the above example shows, sometimes evolution happens in a few years. Remarkably, the lion’s share of the history of life (almost three-quarters of life’s history, or three billion years) consisted of the evolution of single-celled organisms. Multicellular organisms only appeared in the last billion years. Why did it take so long for multicellular life to appear? When we look at the complicated machinery of our cells, an answer suggests itself: It took billions of years of evolution to turn the first primitive enzymes into our modern sophisticated cellular machinery. Multicellular organisms became possible only when a minimum degree of efficiency and sophistication was reached. This view of life’s early evolution is supported by the observation that on a fundamental level, all multicellular animals (and all plants) are the same. Humbling as it may sound, at the nanometer scale little distinguishes a human from a fungus. The basic cellular toolkit is the same. The complexity of this kit justifies the length of time it took for it to develop. Once the toolkit was in place, evolution was free to create ever more amazing multicellular creatures, from octopi to redwood forests. In some sense, the real mystery of life lies at the molecular scale. This is where all the real work of evolution was done. The rest is icing on the cake.