Beyond the “Mechanism” Metaphor in Biology

In a previous post, I discussed the frequent use of the “mechanism” metaphor in the sciences. I argued that while this metaphor was useful in spurring research into cause-and-effect patterns in physical and biological entities, it was inadequate as a descriptive model for what the universe and life is like. In particular, the “mechanism” metaphor is unable to capture the reality of change, the evidence of self-driven progress, and the autonomy and freedom of life forms.

I don’t think it’s possible to abandon metaphors altogether in science, including the mechanism metaphor. But I do think that if we are to more fully understand the nature of life, in all its forms, we must supplement the mechanism metaphor with other, additional conceptualizations and metaphors that illustrate dynamic processes.

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David Bohm (1917-1992), one of the most prominent physicists of the 20th century, once remarked upon a puzzling development in the sciences: While 19th century classical physics operated according to the view that the universe was a mechanism, research into quantum physics in the 20th century demonstrated that the behavior of particles at the subatomic level was not nearly as deterministic as the behavior of larger objects, but rather was probabilistic. Nevertheless, while physicists adjusted to this new reality, the science of biology was increasingly adopting the metaphor of mechanism to study life. Remarked Bohm:

 It does seem odd . . . that just when physics is thus moving away from mechanism, biology and psychology are moving closer to it. If this trend continues, it may well be that scientists will be regarding  living and intelligent beings as mechanical, while they suppose that inanimate matter is too complex and subtle to fit into the limited categories of mechanism. But of course, in the long run, such a point of view cannot stand up to critical analysis. For since DNA and other molecules studied by the biologist are constituted of electrons, protons, neutrons, etc., it follows that they too are capable of behaving in a far more complex and subtle way than can be described in terms of mechanical concepts. (Source: David Bohm, “Some Remarks on the Notion of Order,” in Towards a Theoretical Biology, Vol. 2: Sketches, ed. C.H. Waddington, Chicago: Aldine Publishing, p. 34.)

According to Bohm, biology had to overcome, or at least supplement, the mechanism metaphor if it was to advance. It was not enough to state that anything outside mechanical processes was “random,” for the concept of randomness was too ill-defined to constitute an adequate description of phenomena that did not fit into the mechanism metaphor. For one thing, noted Bohm, the word “random” was often used to denote “disorder,” when in fact it was impossible for a phenomenon to have no order whatsoever. Nor did unpredictability imply randomness — Bohm pointed out that the notes of a musical composition are not predictable, but nonetheless have a precise order when considered in totality. (Ibid., p. 20)

Bohm’s alternative conceptualization was that of an open order, that is, an order that consisted of multiple potential sub-orders or outcomes. For example, if you roll a single die once, there are six possible outcomes and each outcome is equally likely. But the die is not disordered; in fact, it is a precisely ordered system, with equal length dimensions on all sides of the cube and a weight equally distributed throughout the cube. (This issue is discussed in How Random is Evolution?) However, unlike the roll of a die, life is both open to new possibilities and capable of retaining previous outcomes, resulting in increasingly complex orders, orders that are nonetheless still open to change.

Although we are inclined to think of reality as composed of “things,” Bohm argued that the fundamental reality of the universe was not “things” but change: “All is process. That is to say, there is no thing in the universe. Things, objects, entities, are abstractions of what is relatively constant from a process of movement and transformation. They are like the shapes that children like to see in the clouds . . . .” (“Further Remarks on Order,” Ibid., p. 42) The British biologist C.H. Waddington, commenting on Bohm, proposed another metaphor, borrowed from the ancient Judeo-Christian sectarian movement known as Gnosticism:

‘Things’ are essentially eggs — pregnant with God-knows-what. You look at them and they appear simple enough, with a bland definite shape, rather impenetrable. You glance away for a bit and when you look back what you find is that they have turned into a fluffy yellow chick, actively running about and all set to get imprinted on you if you will give it half a chance. Unsettling, even perhaps a bit sinister. But one strand of Gnostic thought asserted that _everything_ is like that. (C.H. Waddington, “The Practical Consequences of Metaphysical Beliefs on a Biologist’s Work,” Ibid., p. 73)

Bohm adds that although the mechanism metaphor is apt to make one think of nature as an engineer or the work of an engineer (i.e., the universe as a “clock”), it could be more useful to think of nature as an artist. Bohm compares nature to a young child beginning to draw. Such a child attempting to draw a rectangle for the first time is apt to end up with a drawing that resembles random or nearly-random lines. Over time however, the child gathers visual impressions and instructions from parents, teachers, books, and toys of what shapes are and what a rectangle is; over time, with growth and practice, the child learns to draw a reasonably good rectangle. (Bohm, “Further Remarks on Order, Ibid., pp. 48-50) It is an order that appears to be the outcome of randomness, but in fact emerges from an open order of multiple possibilities.

 

The American microbiologist Carl. W. Woese (1928-2012), who achieved honors and awards for his discovery of a third domain of life, the “archaea,” also rejected the use of mechanist perspectives in biology. In an article calling for a “new biology,” Woese argued that biology borrowed too much from physics, focusing on the smallest parts of nature while lacking a holistic perspective:

Let’s stop looking at the organism purely as a molecular machine. The machine metaphor certainly provides insights, but these come at the price of overlooking much of what biology is. Machines are not made of parts that continually turn over, renew. The organism is. Machines are stable and accurate because they are designed and built to be so. The stability of an organism lies in resilience, the homeostatic capacity to reestablish itself. While a machine is a mere collection of parts, some sort of “sense of the whole” inheres in the organism, a quality that becomes particularly apparent in phenomena such as regeneration in amphibians and certain invertebrates and in the homeorhesis exhibited by developing embryos.

If they are not machines, then what are organisms? A metaphor far more to my liking is this. Imagine a child playing in a woodland stream, poking a stick into an eddy in the flowing current, thereby disrupting it. But the eddy quickly reforms. The child disperses it again. Again it reforms, and the fascinating game goes on. There you have it! Organisms are resilient patterns in a turbulent flow—patterns in an energy flow. A simple flow metaphor, of course, fails to capture much of what the organism is. None of our representations of organism capture it in its entirety. But the flow metaphor does begin to show us the organism’s (and biology’s) essence. And it is becoming increasingly clear that to understand living systems in any deep sense, we must come to see them not materialistically, as machines, but as (stable) complex, dynamic organization. (“A New Biology for a New Century,” Microbiology and Molecular Biology Reviews, June 2004, pp. 175-6)

A swirling pattern of water is perhaps not entirely satisfactory as a metaphoric conceptualization of life, but it does point to an aspect of reality that the mechanism metaphor does not satisfactorily capture: the ability of life to adapt.

Woese proposes another metaphor to describe what life was like in the very early stages of evolution, when primitive single-celled organisms were all that existed: a community. In this stage, cellular organization was minimal, and many important functions evolved separately and imperfectly in different cellular organisms. However, these organisms could evolve by exchanging genes, in a process called Horizontal Gene Transfer (HGT). This was the primary factor in very early evolution, not random mutation. According to Woese:

The world of primitive cells feels like a vast sea, or field, of cosmopolitan genes flowing into and out of the evolving cellular (and other) entities. Because of the high level of HGT [horizontal gene transfer], evolution at this stage would in essence be communal, not individual. The community of primitive evolving biological entities as a whole as well as the surrounding field of cosmopolitan genes participates in a collective reticulate [i.e., networked] evolution. (Ibid., p. 182)

It was only later that this loose community of cells increased their interactions to the point at which a phase transition took place, in which evolution became less communal and the vertical inheritance of relatively well-developed organisms became the main form of evolutionary descent. But horizontal gene transfer still continued after this transition, and continues to this day. (Ibid., pp. 182-84) It’s hard to see how these interactions resemble any kind of mechanism.

Tree of life showing vertical and horizontal gene transfers.

Source:  Horizontal gene transfer – Wikipedia

 

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So let’s return to the question of “vitalism,” the old theory that there was something special responsible for life: a soul, spirit, force, or substance. The old theories of vitalism have been abandoned on the grounds that no one has been able to observe, identify, or measure a soul, spirit, etc. However, the dissatisfaction of many biologists with the “mechanist” outlook has led to a new conception of vitalism, one in which the essence of life is not in a mysterious substance or force but in the organization of matter and energy, and the processes that occur under this organization. (See Sebastian Normandin and Charles T. Wolfe, eds., Vitalism and the Scientific Image in Post-Enlightenment Life Science, 1800-2010, p. 2n4, 69, 277, 294 )

As Woese wrote, organisms are “resilient patterns . . . in an energy flow.” In a previous essay, I pointed to the work of the great physicist Werner Heisenberg, who noted that matter and energy are essentially interchangeable and that the universe itself began as a great burst of energy, much of which gradually evolved into different forms of matter over time. According to Heisenberg, “Energy is in fact the substance from which all elementary particles, all atoms and therefore all things are made. . . .” (Physics and Philosophy, p. 63)

Now energy itself is not a personal being, and while energy can move things, it’s problematic to equate any moving matter as a kind of life. But is it not the case that once a particular configuration of energy/matter rises to a certain level, organized under a unified consciousness with a free will, then that configuration of energy/matter constitutes a spirit or soul? In this view, there is no vitalist “substance” that gives life to matter — it is simply a matter of energy/matter reaching a certain level of organization capable of (at least minimal) consciousness and free will.

In this view, when ancient peoples thought that breath was the spirit of life and blood was the sacred source of life, they were not that far off the mark. Oxygen is needed by (most) life forms to process the energy in food. Without the continual flow of oxygen from our environment into our body, we die. (Indeed, brain damage will occur after only three minutes without oxygen.) And blood delivers the oxygen and nutrients to the cells that compose our body. Both breath and blood maintain the flow of energy that is essential to life. It’s all a matter of organized energy/matter, with billions of smaller actors and activities working together to form a unified conscious being.

The Metaphor of “Mechanism” in Science

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.

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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.

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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.

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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

 

How Random is Evolution?

Man is the product of causes which had no prevision of the end they were achieving . . . his origin, his growth, his hopes and fears, his loves and his beliefs, are but the outcome of accidental collocations of atoms. . . .” – Bertrand Russell

In high school or college, you were probably taught that human life evolved from lower life forms, and that evolution was a process in which random mutations in DNA, the genetic code, led to the development of new life forms. Most mutations are harmful to an organism, but some mutations confer an advantage to an organism, and that organism is able to flourish and pass down its genes to subsequent generations –hence, “survival of the fittest.”

Many people reject the theory of evolution because it seemingly removes the role of God in the creation of life and of human beings and suggests that the universe is highly disordered. But all available evidence suggests that life did evolve, that the world and all of its life was not created in six days, as the Bible asserted. Does this mean that human life is an accident, that there is no larger intelligence or purpose to the universe?

I will argue that although evolution does indeed suggest that the traditional Biblical view of life’s origins are incorrect, people have the wrong impression of (1) what randomness in evolution means and (2) how large the role of randomness is in evolution. While it is true that individual micro-events in evolution can be random, these events are part of a larger system, and this system can be highly ordered even if particular micro-events are random. Moreover, recent research in evolution indicates that in addition to random mutation, organisms can respond to environmental factors by changing in a manner that is purposive, not random, in a direction that increases their ability to thrive.

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So what does it mean to say that something is “random”? According to the Merriam-Webster dictionary, “random” means “a haphazard course,” “lacking a definite plan, purpose, or pattern.” Synonyms for “random” include the words “aimless,” “arbitrary,” and “slapdash.” It is easy to see why when people are told that evolutionary change is a random process, that many reject the idea outright. This is not necessarily a matter of unthinking religious prejudice. Anyone who has examined nature and the biology of animals and human beings can’t help but be impressed by how enormously complex and precisely ordered these systems are. The fact of the matter is that it is extraordinarily difficult to build and maintain life; death and nonexistence is relatively easy. But what does it mean to lack “a definite plan, purpose, or pattern”? I contend that this definition, insofar as it applies to evolution, only refers to the particular micro-events of evolution when considered in isolation and not the broader outcome or the sum of the events.

Let me illustrate what I mean by presenting an ordinary and well-known case of randomness: rolling a single die. A die is a cube with six sides and a number, 1-6, on each side. The outcome of any roll of the die is random and unpredictable; if you roll a die once, the outcome will be unpredictable. If you roll a die multiple times, each outcome, as well as the particular sequence of outcomes, will be unpredictable. But if you look at the broader, long-term outcome after 1000 rolls, you will see this pattern: an approximately equal number of ones, twos, threes, fours, fives, and sixes will come up, and the average value of all events will be 3.5.

Why is this? Because the die itself is a highly-precise ordered system. Each die must have equally sided lengths on all sides and an equal distribution of density/weight throughout in order to make the outcome truly unpredictable, otherwise a gambler who knows the design of the die may have an edge. One die manufacturer brags, “With tolerances less than one-third the thickness of a human hair, nothing is left to chance.” [!] In fact, a common method of cheating with dice is to shave one or more sides or insert a weight into one end of the die. This results in a system that is also precisely ordered, but in a way that makes certain outcomes more likely. After a thousand rolls of the die, one or more outcomes will come up more frequently, and this pattern will stand out suspiciously. But the person who cheated by tilting the odds in one direction may have already escaped with his or her winnings.

If you look at how casinos make money, it is precisely by structuring the rules of each game to give the edge to the casino that allows them to make a profit in the long run. The precise outcome of each particular game is not known with certainty, the particular sequence of outcomes is not known, and the balance sheet of the casino at the end of the night cannot be predicted. But there is definitely a pattern: in the long run, the sum of events results in the casino winning and making a profit, while the players as a group will lose money. When casinos go out of business, it is generally because they can’t attract enough customers, not because they lose too many games.

The ability to calculate the sum of a sequence of random events is the basis of the so-called “Monte Carlo” method in mathematics. Basically, the Monte Carlo method involves setting certain parameters, selecting random inputs until the number of inputs is quite large, and then calculating the final result. It’s like throwing darts at a dartboard repeatedly and examining the pattern of holes. One can use this method with 30,000 randomly plotted points to calculate the value of pi to within 0.07 percent.

So if randomness can exist within a highly precise order, what is the larger order within which the random mutations of evolution operate? One aspect of this order is the bonding preferences of atoms, which are responsible not only for shaping how organisms arise, but how organisms eventually develop into astonishingly complex and wondrous forms. Without atomic bonds, structures would fall apart as quickly as they came together, preventing any evolutionary advances. The bonding preferences of atoms shape the parameters of development and result in molecular structures (DNA, RNA, and proteins) that retain a memory or blueprint, so that evolutionary change is incremental. The incremental development of organisms allows for the growth of biological forms that are eventually capable of running at great speeds, flying long distances, swimming underwater, forming societies, using tools, and, in the case of humans, building technical devices of enormous sophistication.

The fact of incremental change that builds upon previous advances is a feature of evolution that makes it more than a random process. This is illustrated by biologist Richard Dawkins’ “weasel program,” a computer simulation of how evolution works by combining random micro-events with the retaining of previous structures so that over time a highly sophisticated order can develop. The weasel program is based on the “infinite monkey theorem,” the fanciful proposal that an infinite number of monkeys with an infinite number of typewriters would eventually produce the works of Shakespeare. This theorem has been used to illustrate how order could conceivably emerge from random and mindless processes. What Dawkins did, however, was write a computer program to write just one sentence from Shakespeare’s Hamlet: “Methinks it is like a weasel.” Dawkins structured the computer program to begin with a single random sentence, reproduce this sentence repeatedly, but add random errors (“mutations”) in each “generation.” If the new sentence was at least somewhat closer to the target phrase “Methinks it is like a weasel,” that sentence became the new parent sentence. In this way, subsequent generations would gradually assume the form of the correct sentence. For example:

Generation 01: WDLTMNLT DTJBKWIRZREZLMQCO P
Generation 02: WDLTMNLT DTJBSWIRZREZLMQCO P
Generation 10: MDLDMNLS ITJISWHRZREZ MECS P
Generation 20: MELDINLS IT ISWPRKE Z WECSEL
Generation 30: METHINGS IT ISWLIKE B WECSEL
Generation 40: METHINKS IT IS LIKE I WEASEL
Generation 43: METHINKS IT IS LIKE A WEASEL

The Weasel program is a great example of how random change can produce order over time, BUT only under highly structured conditions, with a defined goal and a retaining of those steps toward that goal. Without these conditions, a computer program randomly selecting letters would be unlikely to produce the phrase “Methinks it is like a weasel” in the lifetime of the universe, according to Dawkins!

It is the retaining of most evolutionary advances, while allowing a small degree of randomness, that allows evolution to produce increasingly complex life forms. Reproduction has some random elements in it, but is actually remarkably precise and effective in producing offspring at least roughly similar to their parents. It is not the case that a female human is equally as likely to give birth to a dog, a pig, or a chicken as to give birth to a human. It would be very strange indeed if evolution was that random!

But there is even more to the story of evolution.

Recent research in biology has indicated that there are factors in nature that tend to push development in certain directions favorable to an organism’s flourishing. Even if you imagine evolution in nature as a huge casino, with a lot of random events, scientists have discovered that the players are strategizing: they are increasing or decreasing their level of gambling in response to environmental conditions, shaving the dice to obtain more favorable outcomes, and cooperating with each other to cheat the casino!

For example, it is now recognized among biologists that a number of microorganisms are capable to some extent of controlling their rate of mutation, increasing the rate of mutation during times of environmental challenge and stress, and suppressing the rate of mutation during times of peace and abundance. As a result of accelerated mutations, certain bacteria can acquire the ability to utilize new sources of nutrition, overcoming the threat of extinction arising from the depletion of its original food source. In other words, in response to feedback from the environment, organisms can decide to try to preserve as much of their genome as they can or experiment wildly in the hope of finding a solution to new environmental challenges.

The organism known as the octopus (a cephalopod) has a different strategy: it actively suppresses mutation in DNA and prefers to recode its RNA in response to environmental challenges. For example, octopi in the icy waters of the Antarctic recode their RNA in order to keep their nerves firing in cold water. This response is not random but directly adaptive. RNA recoding in octopi and other cephalopods is particularly prevalent in proteins responsible for the nervous system, and it is believed by scientists that this may explain why octopi are among the most intelligent creatures on Earth.

The cephalopods are somewhat unusual creatures, but there is evidence that other organisms can also adapt in a nonrandom fashion to their environment by employing molecular factors that suppress or activate the expression of certain genes — the study of these molecular factors is known as “epigenetics.” For example, every cell in a human fetus has the same DNA, but this DNA can develop into heart tissue, brain tissue, skin, liver, etc., depending on which genes are expressed and which genes are suppressed. The molecular factors responsible for gene expression are largely proteins, and these epigenetic factors can result in heritable changes in response to environmental conditions that are definitely not random.

The water flea, for example, can come in different variations, despite the same DNA, in response to the environmental conditions of the mother flea. If the mother flea experienced a large predator threat, the children of that flea would develop a spiny helmet for protection; otherwise the children would develop normal helmet-less heads. Studies have found that in other creatures, a particular diet can turn certain genes on or off, modifying offspring without changing DNA. In one study, mice that exercised not only enhanced their brain function, their children had enhanced brain function as well, though the effect only lasted one generation if exercise stopped. The Mexican cave fish once had eyes, but in its new dark environment, epigenetics has been responsible for turning off the genes responsible for eye development; its original DNA has been unchanged. (The hypothesized reason for this is that organisms tend to discard traits that are not needed in order to conserve energy.)

Recent studies of human beings have uncovered epigenetic adaptations that have allowed humans to flourish in such varied environments as deserts, jungles, and polar ice. The Oromo people of Ethiopia, recent settlers to the highlands of that country, have had epigenetic changes to their immune system to cope with new microbiological threats. Other populations in Africa have genetic mutations that have the twin effect of protecting against malaria but causing sickle cell anemia — recently it has been found that these mutations are being silenced in the face of declining malarial threats.  Increasingly, scientists are recognizing the large role of epigenetics in the evolution of human beings:

By encouraging the variations and adaptability of our species, epigenetic mechanisms for controlling gene expression have ensured that humanity could survive and thrive in any number of environments. Epigenetics is a significant part of the reason our species has become so adaptable, a trait that is often thought to distinguish us from what we often think of as lesser-evolved and developed animals that we inhabit this earth with. Indeed, it can be argued that epigenetics is responsible for, and provided our species with, the tools that truly made us unique in our ability to conquer any habitat and adapt to almost any climate. (Bioscience Horizons, 1 January 2017)

In fact, despite the hopes of scientists everywhere that the DNA sequencing of the human genome would provide a comprehensive biological explanation of human traits, it has been found that epigenetics may play a larger role in the complexity of human beings than the number of genes. According to one researcher, “[W]e found out that the human genome is probably not as complex and doesn’t have as many genes as plants do. So that, then, made us really question, ‘Well, if the genome has less genes in this species versus this species, and we’re more complex potentially, what’s going on here?'”

One additional nonrandom factor in evolution should be noted: the role of cooperation between organisms, which may even lead to biological mergers that create a new organism. Traditionally, evolution has been thought of primarily as random changes in organisms followed by a struggle for existence between competing organisms. It is a dark view of life. But increasingly, biologists have discovered that cooperation between organisms, known as symbiosis, also plays a role in the evolution of life, including the evolution of human beings.

Why was the role of cooperation in evolution overlooked until relatively recently? A number of biologists have argued that the society and culture of Darwin’s time played a significant role in shaping his theory — in particular, Adam Smith’s book The Wealth of Nations. In Smith’s view, the basic unit of economics was the self-interested individual on the marketplace, who bought and sold goods without any central planner overseeing his activities. Darwin essentially adopted this view and applied it to biological organisms: as businesses competed on the marketplace and flourished or died depending on how efficient they were, so too did organisms struggle against each other, with only the fittest surviving.

However, even in the late nineteenth century, a number of biologists noted cases in nature in which cooperation played a prominent role in evolution. In the 1880s, the Scottish biologist Patrick Geddes proposed that the reason the giant green anemone contained algal (algae) cells as well as animal cells was because of the evolution of a cooperative relationship between the two types of cells that resulted in a merger in which the alagal cells were merged into the animal flesh of the anemone. In the latter part of the twentieth century, biologist Lynn Margulis carried this concept further. Margulis 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. The traditional picture of evolution as one in which new species diverge from older species and compete for survival has had to be supplemented with the picture of cooperative behavior and mergers. As one researcher has argued, “The classic image of evolution, the tree of life, almost always exclusively shows diverging branches; however, a banyan tree, with diverging and converging branches is best.”

More recent studies have demonstrated the remarkable level of cooperation between organisms that is the basis for human life. One study from a biologist at the University of Cambridge has proposed that human beings have as many as 145 genes that have been borrowed from bacteria, other single-celled organisms, and viruses. In addition, 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! If, as one biologist has argued, each human being is a “society of cells,” it would be equally valid to describe a human being as a “society of cells and microbes.”

Is there randomness in evolution? Certainly. But the randomness is limited in scope, it takes place within a larger order which preserves incremental gains, and it provides the experimentation and diversity organisms need to meet new challenges and new environments. Alongside this randomness are epigenetic adaptations that turn genes on or off in response to environmental influences and the cooperative relations of symbiosis, which can build larger and more complex organisms. These additional facts do not prove the existence of a creator-God that oversees all of creation down to the most minute detail; but they do suggest a purposive order within which an astonishing variety of life forms can emerge and grow.

 

How Powerful is God?

In a previous post, we discussed the non-omnipotent God of process theology as a possible explanation for the twin facts that the universe appears to be fine-tuned for life and yet evolution is extremely slow and life precarious.  The problem with process theology, however, is that God appears to be extremely weak.  Is the concept of a non-omnipotent God worthwhile?

One response to this criticism is that portraying God as weak simply because the universe was not instantaneously and perfectly constructed for life is to misconstrue what the meaning of “weak” is.  The mere fact that the universe, consisting of a least 10,000,000,000,000,000,000,000 stars, was created out of nothingness and has lasted over 13 billion years does not seem to indicate weakness.

Another response would be that the very gradual incrementalism of evolution may be a necessary component of a fantastically complex system that cannot tolerate errors that would threaten to destroy the system.  That is, the various physical laws and numerical constants that underlie the order of the universe exist in such an intricate relationship that a violation of a law in one particular case or sudden change in one of the constants would cause the universe to self-destruct, in the same way that a computer program may crash if a single line of code is incorrect or is incompatible with the other lines of code.

In fact, a number of physicists have explicitly described the universe as a type of computer, in the sense that the order of the universe is based on the processing of information in the form of the physical laws and constants.  Of course, the chief difference between the universe and a computer is that we can live with a computer crashing occasionally — we cannot live with the universe crashing even once.  Thus the fact that the universe, while not immortal, never seems to crash, indicates that gradual evolution may be necessary.  Perhaps instability on the micro level of the universe (an asteroid occasionally crashing into a planet with life) is the price to be paid for stability on the macro level.

Alternatively, we can conceptualize the order behind the universe as a type of mind, “mind” being defined broadly as any system for processing information.  We can posit three types of mind in the historical development of the universe: cosmic mind (God), biological mind (human/animal mind), and electronic mind (computer).

Cosmic mind can be thought of as pure spirit, or pure information, if you will.  Cosmic mind can create matter and a stable foundation for the universe, but once matter is created, the influence of spirit on matter is relatively weak.  That is, there is a division between the world of spirit and the world of matter that is difficult to bridge.  Biological mind does not know everything cosmic mind does and it is limited in time and space, but biological mind can more efficiently act on matter, since it is part of the world of matter.  Electronic mind (computer) is a creation of biological mind but processes larger amounts of information more quickly, assisting biological mind in the manipulation of matter.

As a result, the evolution of the universe began very slowly, but has recently accelerated as a result of incremental improvements to mind.  According to Stephen Hawking,

The process of biological evolution was very slow at first. It took two and a half billion years, to evolve from the earliest cells to multi-cell animals, and another billion years to evolve through fish and reptiles, to mammals. But then evolution seemed to have speeded up. It only took about a hundred million years, to develop from the early mammals to us. . . . [W]ith the human race, evolution reached a critical stage, comparable in importance with the development of DNA. This was the development of language, and particularly written language. It meant that information can be passed on, from generation to generation, other than genetically, through DNA. . . .  [W]e are now entering a new phase, of what might be called, self designed evolution, in which we will be able to change and improve our DNA. . . . If this race manages to redesign itself, to reduce or eliminate the risk of self-destruction, it will probably spread out, and colonise other planets and stars.  (“Life in the Universe“)

According to physicist Freeman Dyson (Disturbing the Universe), even if interstellar spacecraft achieve only one percent of the speed of light, a speed within the possibility of present-day technology, the Milky Way galaxy could be colonized end-to-end in ten million years –  a very long time from an individual human’s perspective, but a remarkably short time in the history of evolution, considering it took 2.5 billion years simply to make the transition from single-celled life forms to multi-celled creatures.

So cosmic mind can be very powerful in the long run, but patience is required!

Physical Laws and the Mind of God

The American philosopher of science Charles Sanders Peirce once wrote that the physical laws of the universe were the expression of an evolving cosmic mind.  As he put it, physical laws were the outcome of a mind become habitual: “matter is effete mind, inveterate habits becoming physical laws.”  However, he notes that the cosmic mind is not merely habitual, but has a powerful element of indeterminacy and spontaneity, which is why the universe continues to evolve and to produce life.  The evolution of the universe, in Peirce’s view, is the gradual crystallization of mind.

There is much merit to Peirce’s idea — rather than seeing the physical laws of the universe as separate entities that pop out of nowhere and have no unifying foundation, Peirce’s concept expresses the underlying unity and order of the universe, which is still developing even as the human mind itself develops.

One criticism of conceptualizing the physical laws of the universe as being part of a cosmic mind is that physical laws by their nature have an unvarying determinism and regularity that contradicts the notion of a conscious being capable of thinking, planning, and exercising free will in order to shape events.  But the physical laws of the universe are really only part of the universal order.  On the large, astronomical scale certainly, there is determinism and regularity; but on the very small, subatomic scale, there is a high degree of indeterminism and unpredictability; and life forms have the freedom to partially evade or escape the bounds of physical determinism.  In this conception, determinism and regularity provide a foundation of order on which freedom and creativity can flourish.  One can analogize this conception with the human mind, in which many essential functions of the brain (control of breathing, heart rate, sensation) occur mostly or entirely without conscious planning or control in the lower part of the brain (the “brainstem”), while higher thought processes are conducted on top of this primitive foundational order.

Granted, there are limits to employing the metaphor of “mind” to the cosmic order, as there are with any metaphor.  But metaphors are often a necessary tool to describe things that simply can’t be communicated with literal precision.  Even the most rigorous and skeptical of scientists cannot do without metaphors.  The “physical laws” of the universe is itself a metaphor; the “Big Bang” is a metaphor; and the “selfish gene” is a metaphor.