The writings of science make frequent use of the metaphor of “mechanism.” The universe is conceived as a mechanism, life is a mechanism, and even human consciousness has been described as a type of mechanism. If a phenomenon is not an outcome of a mechanism, then it is random. Nearly everything science says about the universe and life falls into the two categories of mechanism and random chance.

The use of the mechanism metaphor is something most of us hardly ever notice. Science, allegedly, is all about literal truth and precise descriptions. Metaphors are for poetry and literature. But in fact mathematics and science use metaphors. Our understandings of quantity, space, and time are based on metaphors derived from our bodily experiences, as George Lakoff and Rafael Nunez have pointed out in their book Where Mathematics Comes From: How the Embodied Mind Brings Mathematics into Being  Theodore L. Brown, a professor emeritus of chemistry at the University of Illinois at Urbana-Champaign, has provided numerous examples of scientific metaphors in his book, Making Truth: Metaphor in Science. Among these are the “billiard ball” and “plum pudding” models of the atom, as well as the “energy landscape” of protein folding. Scientists envision cells as “factories” that accept inputs and produce goods. The genetic structure of DNA is described as having a “code” or “language.” The term “chaperone proteins” was invented to describe proteins that have the job of assisting other proteins to fold correctly.

What I wish to do in this essay is closely examine the use of the mechanism metaphor in science. I will argue that this metaphor has been extremely useful in advancing our knowledge of the natural world, but its overuse as a descriptive and predictive model has led us down the wrong path to fully understanding reality — in particular, understanding the actual nature of life.

____________________________

Thousands of years ago, human beings attributed the actions of natural phenomena to spirits or gods. A particular river or spring or even tree could have its own spirit or minor god. Many humans also believed that they themselves possessed a spirit or soul which occupied the body, gave the body life and motion and intelligence, and then departed when the body died. According to the Bible, Genesis 2:7, when God created Adam from the dust of the ground, God “breathed into his nostrils the breath of life; and man became a living soul.” Knowing very little of biology and human anatomy, early humans were inclined to think that spirit/breath gave life to material bodies; and when human bodies no longer breathed, they were dead, so presumably the “spirit” went someplace else. The ancient Hebrews also saw a role for blood in giving life, which is why they regarded blood as sacred. Thus, the Hebrews placed many restrictions on the consumption and handling of blood when they slaughtered animals for sacrifice and food. These views about the spiritual aspects of breath and blood are also the historical basis of “vitalism,” the theory that life consists of more than material parts, and must somehow be based on a vital principle, spark, or force, in addition to matter. 

The problem with the vitalist outlook is that it did not appreciably advance our knowledge of nature and the human body.  The idea of a vital principle or force was too vague and could not be tested or measured or even observed. Of course, humans did not have microscopes thousands of years ago, so we could not see cells and bacteria, much less atoms.

By the 17th century, thinkers such as Thomas Hobbes and Rene Descartes proposed that the universe and even life forms were types of mechanisms, consisting of many parts that interacted in such a way as to result in predictable patterns. The universe was often analogized to a clock. (The first mechanical clock was developed around 1300 A.D., but water clocks, based on the regulated flow of water, have been in use for thousands of years.) The great French scientist Pierre-Simon Laplace was an enthusiast for the mechanist viewpoint and even argued that the universe could be regarded as completely determined from its beginnings:

We may regard the present state of the universe as the effect of the past and the cause of the future. An intellect which at any given moment knew all of the forces that animate nature and the mutual positions of the beings that compose it, if this intellect were vast enough to submit the data to analysis, could condense into a single formula the movement of the greatest bodies of the universe and that of the lightest atom; for such an intellect nothing could be uncertain and the future just like the past would be present before its eyes. (A Philosophical Essay on Probabilities, Chapter Two)

Laplace’s radical determinism was not embraced by all scientists, but it was a common view among many scientists. Later, as the science of biology developed, it was argued that the evolution of life was not as determined as the motion of the planets. Rather, random genetic mutations resulted in new life forms and “natural selection” determined that fit life forms flourished and reproduced, while unfit forms died out. In this view, physical mechanisms combined with random chance explained evolution.

The astounding advances in physics and biology in the past centuries certainly seem to justify the mechanism metaphor. Reality does seem to consist of various parts that interact in predictable cause-and-effect patterns. We can predict the motions of objects in space, and build technologies that send objects in the right direction and speed to the right target. We can also methodically trace illnesses to a dysfunction in one or more parts of the body, and this dysfunction can often be treated by medicine or surgery.

But have we been overusing the mechanism metaphor? Does reality consist of nothing but determined and predictable cause-and-effect patterns with an element of random chance mixed in?

I believe that we can shed some light on this subject by first examining what mechanisms are — literally — and then examine what resemblances and differences there are between mechanisms and the actual universe, between mechanisms and actual life.

____________________

Even in ancient times, human beings created mechanisms, from clocks to catapults to cranes to odometers. The Antikythera mechanism of ancient Greece, constructed around 100 B.C., was a sophisticated mechanism with over 30 gears that was able to predict astronomical motions and is considered to be one of the earliest computers. Below is a photo of a fragment of the mechanism, discovered in an ocean shipwreck in 1901:

Over subsequent centuries, human civilization created steam engines, propeller-driven ships, automobiles, airplanes, digital watches, computers, robots, nuclear reactors, and spaceships.

So what do most or all of these mechanisms have in common?

1. Regularity and Predictability. Mechanisms have to be reliable. They have to do exactly what you want every time. Clocks can’t run fast, then run slow; automobiles can’t unilaterally change direction or speed; nuclear reactors can’t overheat on a whim; computers have to give the right answer every time. 
2. Precision. The parts that make up a mechanism must fit together and move together in precise ways, or breakdown, or even disaster, will result. Engineering tolerances are typically measured in millimeters.
3. Stability and Durability. Mechanisms are often made of metal, and for good reason. Metal can endure extreme forces and temperatures, and, if properly maintained, can last for many decades. Metal can slightly expand and contract depending on temperature, and metals can have some flexibility when needed, but metallic constructions are mostly stable in shape and size. 
4. Unfree/Determined. Mechanisms are built by humans for human purposes. When you manage the controls of a mechanism correctly, the results are predictable. If you get into your car and decide to drive north, you will drive north. The car will not dispute you or override your commands, unless it is programmed to override your commands, in which case it is simply following a different set of instructions. The car has no will of its own. Human beings would not build mechanisms if such mechanisms acted according to their own wills. The idea of a self-willing mechanism is prolific in science fiction, but not in science.
5. They do not grow. Mechanisms do not become larger over time or change their basic structure like living organisms. This would be contrary to the principle of durability/stability. Mechanisms are made for a purpose, and if there is a new purpose, a new mechanism will be made.
6. They do not reproduce. Mechanisms do not have the power of reproduction. If you put a mechanism into a resource-rich environment, it will not consume energy and materials and give birth to new mechanisms. Only life has this power. (A partial exception can be made in the case of  computer “viruses,” which are lines of code programmed to duplicate themselves, but the “viruses” are not autonomous — they do the bidding of the programmer.)
7. Random events lead to the universal degradation of mechanisms, not improvement. According to neo-Darwinism, random mutations in the genes of organisms are what is responsible for evolution; in most cases, mutations are harmful, but in some cases, they lead to improvement, leading to new and more complex organisms, ultimately culminating in human beings. So what kind of random mutations (changes) lead to improved mechanisms? None, really. Mechanisms change over time with random events, but these events lead to degradation of mechanisms, not improvement. Rust sets in, different parts break, electric connections fail, lubricating fluids leak. If you leave a set of carefully-preserved World War One biplanes out in a field, without human intervention, they will not eventually evolve into jet planes and rocket ships. They will just break down. Likewise, electric toasters will not evolve into supercomputers, no matter how many millions of years you wait. Of course, organisms also degrade and die, but they have the power of reproduction, which continues the population and creates opportunities for improvement.

There is one hypothetical mechanism that, if constructed, could mimic actual organisms: a self-replicating machine. Such a machine could conceivably contain plans within itself to gather materials and energy from its environment and use these materials and energy to construct copies of itself, growing exponentially in numbers as more and more machines reproduce themselves. Such machines could even be programmed to “mutate,” creating variations in its descendants. However, no such mechanism has yet been produced. Meanwhile, primitive single-celled life forms on earth have been successfully reproducing for four billion years.

Now, let’s compare mechanisms to life forms. What are the characteristics of life?

1. Adaptability/Flexibility. The story of life on earth is a story of adaptability and flexibility. The earliest life forms, single cells, apparently arose in hydrothermal vents deep in the ocean. Later, some of these early forms evolved into multi-cellular creatures, which spread throughout the oceans. After 3.5 billion years, fish emerged, and then much later, the first land creatures. Over time, life adapted to different environments: sea, land, rivers, caves, air; and also to different climates, from the steamiest jungles to frozen environments. 
2. Creativity/Diversification. Life is not only adaptive, it is highly creative and branches into the most diverse forms over time. Today, there are millions of species. Even in the deepest parts of the ocean, life forms thrive in an environment with pressures that would crush most life forms. There are bacteria that can live in water at or near the boiling point. The tardigrade can survive the cold, hostile vacuum of space. The bacteria Deinococcus radiodurans is able to survive extreme forms of radiation by means of one of the most efficient DNA repair capabilities ever seen. Now it’s true that among actual mechanisms there is also a great variety; but these mechanisms are not self-created, they are created by humans and retain their forms unless specifically modified by humans.
3. Drives toward cooperation / symbiosis. Traditional Darwinist views of evolution see life as competition and “survival of the fittest.” However, more recent theorists of evolution point to the strong role of cooperation in the emergence and survival of advanced life forms. Biologist Lynn Margulis has argued that the most fundamental building block of advanced organisms, the cell, was the result of a merger between more primitive bacteria billions of years ago. By merging, each bacterium lent a particular biological advantage to the other, and created a more advanced life form. This theory was regarded with much skepticism at the time it was proposed, but over time it became widely accepted.  Today, only about half of the human body is made up of human cells — the other half consists of trillions of microbes and quadrillions of viruses that largely live in harmony with human cells. Contrary to the popular view that microbes and viruses are threats to human beings, most of these microbes and viruses are harmless or even beneficial to humans. Microbes are essential in digesting food and synthesizing vitamins, and even the human immune system is partly built and partly operated by microbes!  By contrast, the parts of a mechanism don’t naturally come together to form the mechanism; they are forced together by their manufacturer.
4. Growth. Life is characterized by growth. All life forms begin with either a single cell, or the merger of two cells, after which a process of repeated division begins. In multicellular organisms, the initial cell eventually becomes an embryo; and when that embryo is born, becoming an independent life form, it continues to grow. In some species, that life form develops into an animal that can weigh hundreds or even thousands of pounds. This, from a microscopic cell! No existing mechanism is capable of that kind of growth.
5. Reproduction. Mechanisms eventually disintegrate, and life forms die. But life forms have the capability of reproducing and making copies of themselves, carrying on the line. In an environment with adequate natural resources, the number of life forms can grow exponentially. Mechanisms have not mastered that trick.
6. Free will/choice. Mechanisms are either under direct human control, are programmed to do certain things, or perform in a regular pattern, such as a clock. Life forms, in their natural settings, are free and have their own purposes. There are some regular patterns — sleep cycles, mating seasons, winter migration. But the day-to-day movements and activities of life forms are largely unpredictable. They make spur-of-the-moment decisions on where to search for food, where to find shelter, whether to fight or flee from predators, and which mate is most acceptable. In fact, the issue of mate choice is one of the most intriguing illustrations of free will in life forms — there is evidence that species may select mates for beauty over actual fitness, and human egg cells even play a role in selecting which sperm cells will be allowed to penetrate them.
7. Able to gather energy from its environment. Mechanisms require energy to work, and they acquire such energy from wound springs or weights (in clocks), electrical outlets, batteries, or fuel. These sources of energy are provided by humans in one way or another. But life forms are forced to acquire energy on their own, and even the most primitive life forms mastered this feat billions of years ago. Plants get their energy from the sun, and animals get their energy from plants or other animals. It’s true that some mechanisms, such as space probes, can operate on their own for many years while drawing energy from solar panels. But these panels were invented and produced by humans, not by mechanisms.
8. Self-organizing. Mechanisms are built, but life forms are self-organizing. Small components join other small components, forming a larger organization; this larger organization gathers together more components. There is a gradual growth and differentiation of functions — digestion, breathing, brain and nervous system, mobility, immune function. Now this process is very, very slow: evolution takes place over hundreds of millions of years. But mechanisms are not capable of self-organization. 
9. Capacity for healing and self-repair. When mechanisms are broken, or not working at full potential, a human being intervenes to fix the mechanism. When organisms are injured or infected, they can self-repair by initiating multiple processes, either simultaneously or in stages: immune cells fight invaders; blood cells clot in open wounds to stop bleeding; dead tissues and cells are removed by other cells; and growth hormones are released to begin the process of building new tissue. As healing nears completion, cells originally sent to repair the wound are removed or modified. Now self-repair is not always adequate, and organisms die all the time from injury or infection. But they would die much sooner, and probably a species would not persist at all, without the means of self-repair. Even the existing medications and surgery that modern science has developed largely work with and supplement the body’s healing capacities — after all, surgery would be unlikely to work in most cases without the body’s means of self-repair after the surgeon completes cutting and sewing.

______________________

The mechanism metaphor served a very useful purpose in the history of science, by spurring humanity to uncover the cause-and-effect patterns responsible for the motions of stars and planets and the biological functions of life. We can now send spacecraft to planets; we can create new chemicals to improve our lives; we now know that illness is the result of a breakdown in the relationship between the parts of a living organism; and we are getting better and better in figuring out which human parts need medication or repair, so that lifespans and general health can be extended.

But if we are seeking the broadest possible understanding of what life is, and not just the biological functions of life, we must abandon the mechanism metaphor as inadequate and even deceptive. I believe the mechanism metaphor misses several major characteristics of life:

1. Change. Whether it is growth, reproduction, adaptation, diversification, or self-repair, life is characterized by change, by plasticity, flexibility, and malleability. 
2. Self-Driven Progress. There is clearly an overall improvement in life forms over time. Changes in species may take place over millions or billions of years, but even so, the differences between a single-celled animal and contemporary multicellular creatures are astonishingly large. It is not just a question of “complexity,” but of capability. Mammals, reptiles, and birds have senses, mobility, and intelligence that single-celled creatures do not have.
3. Autonomy and freedom. Although some scientists are inclined to think of living creatures, including humans, as “gene machines,” life forms can’t be easily analogized to pre-programmed machines. Certainly, life forms have goals that they pursue — but the pursuit of these goals in an often hostile environment requires numerous spur-of-the-moment decisions that do not lead to the predictable outcomes we expect of mechanisms.

Robert Pirsig, author of Zen and the Art of Motorcycle Maintenance, argues in Lila that the fundamental nature of life is its ability to move away from mechanistic patterns, and science has overlooked this fact because scientists consider it their job to look for mechanisms:

Mechanisms are the enemy of life. The more static and unyielding the mechanisms are, the more life works to evade them or overcome them. The law of gravity, for example, is perhaps the most ruthlessly static pattern of order in the universe. So, correspondingly, there is no single living thing that does not thumb its nose at that law day in and day out. One could almost define life as the organized disobedience of the law of gravity. One could show that the degree to which an organism disobeys this law is a measure of its degree of evolution. Thus, while the simple protozoa just barely get around on their cilia, earthworms manage to control their distance and direction, birds fly into the sky, and man goes all the way to the moon. . . .  This would explain why patterns of life [in evolution] do not change solely in accord with causative ‘mechanisms’ or ‘programs’ or blind operations of physical laws. They do not just change valuelessly. They change in ways that evade, override and circumvent these laws. The patterns of life are constantly evolving in response to something ‘better’ than that which these laws have to offer. (Lila, 1991 hardcover edition, p. 143)

But if the “mechanism” metaphor is inadequate, what are some alternative conceptualizations and metaphors that can retain the previous advances of science while deepening our understanding and helping us make new discoveries? I will discuss this issue in the next post.

Next: Beyond the “Mechanism” Metaphor in Biology