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

 

Are Human Beings Just Atoms?

In a previous essay on materialism, I discussed the bizarre nature of phenomena on the subatomic level, in which particles have no definite position in space until they are observed. Referencing the works of several physicists and philosophers, I put forth the view that reality consists not of tiny, solid objects but rather bundles of properties and qualities that emerge from potentiality to actuality. In this view, when one breaks down reality into smaller and smaller parts, one does not reach the fundamental units of matter; rather, one is gradually unbundling properties and qualities until the smallest objects no longer even have a definite position in space!

Why is this important? One reason is that the enormous prestige and accomplishments of science have sometimes led us down the wrong path in properly describing and interpreting reality. Science excels at advancing our knowledge of how things work, by breaking down wholes into component parts and manipulating those parts into better arrangements that benefit humanity. This is how we got modern medicine, computers, air conditioning, automobiles, and space travel. However, science sometimes falls short in properly describing and interpreting reality, precisely because it focuses more on the parts than the wholes.

This defect in science becomes particularly glaring when certain scientists attempt to describe what human beings are like. All too often there is a tendency to reduce humans to their component parts, whether these parts are chemical elements (atoms), chemical compounds (molecules), or the much larger molecules known as genes. However, while these component parts make up human beings, there are properties and qualities in human beings that cannot be adequately described in terms of these parts.

Marcelo Gleiser, a physicist at Dartmouth College, argues that “life is the property of a complex network of biochemical reactions . . . a kind of hungry chemistry that is able to duplicate itself.” Biologist Richard Dawkins claims that humans are “just gene machines,” and “living organisms and their bodies are best seen as machines programmed by the genes to propagate those very same genes,” though he qualifies his statement by noting that “there is a very great deal of complication, and indeed beauty in being a gene machine.” Philosopher Daniel Dennett claims that human beings are “moist robots” and the human mind is a collection of computer-like information processes which happen to take place in carbon-based rather than silicon-based hardware.

Now it is true that human beings are composed of atoms that are the basis of chemicals and molecules, that are the basis of chemical compounds, such as genes. The issue, however, is whether describing the parts that compose a human being is the same as describing the whole human being. Yes, human beings are composed of atoms of oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorous. But these atoms can be found in many, many places throughout the universe, in varying quantities and combinations, and they do not have human qualities unless and until they are organized in just the right way. Likewise, genes are ubiquitous in life forms ranging from mammals to lizards to plants to bacteria. Even viruses have genes, though most scientists argue that viruses are not true life forms because they need a host to reproduce. Nevertheless, while human beings share a very few properties and qualities with bacteria and viruses, humans clearly have many properties and qualities that the lower life forms do not.

In fact, recognizing the very difference between life and death can be lost by excessive focus on atoms and molecules. Consider the following: an emergency room doctor treats a patient suffering from a heart attack. Despite the physician’s best efforts, despite all of the doctor’s training and knowledge, the patient dies on the table. So what is the difference between the patient that has died and the patient as he was several hours ago? The quantity and types of atoms composing the body are approximately the same as when the patient was alive. So what has changed? Obviously, the properties and qualities expressed by the organization of the atoms in the human being has changed. The heart no longer supplies blood to the rest of the body, the lungs no longer supply oxygen, the brain no longer has electrical activity, the human being no longer has the ability to run or walk or jump or talk or think or love. Atoms have to be organized in an extremely precise manner in order for these properties and qualities to emerge, and this organization has been lost. So if we are really going to accurately describe what a human being is, we have to refer not just to the atoms, but to the overall organization or form.

The issue of form is what separates the ancient Greek philosophers Democritus and Plato. Both philosophers believed that the universe and everything in it was composed of atoms; but Democritus thought that nothing existed but atoms and the void (space), whereas Plato believed that atoms were arranged by a creator, who, being essentially good, used ideal forms as a blueprint. Contrary to the views of Judaism, Christianity, and Islam, however, Plato believed that the creator was not omnipotent, and was forced to work with imperfect matter to do the best job possible, which is why most created objects and life forms were imperfect and fell short of the ideal forms.

Democritus would no doubt dismiss Plato’s ideal forms as being unreal — after all, forms are not something solid, so how can anything that is not solid, not made of material, exist at all? But as I’ve pointed out, the atoms that compose the human body are found everywhere, whereas actual, living human beings have these same atoms organized in a precise, particular form. In other words, in order to understand anything, it is not enough to break it down into parts and study the parts; one has to look at the whole. The properties and qualities of a living human being, as a whole, definitely do exist, or we would not know how to distinguish a living human being from a dead human being or any other existing thing composed of the same atoms.

The debate between Democritus and Plato points to a difference in ways of knowing that persist to this day: analytic knowledge and holistic knowledge. Analytic knowledge is pursued by science and reason; holistic knowledge is pursued by religion, art, and the humanities. The prestige of science and its technological accomplishments has elevated analytic understanding above all other forms of knowledge, but we remain lost without holistic understanding.

What precisely is “analytic knowledge”? The word “analyze” means “to study or determine the nature and relationship of the parts (of something) by analysis.” Synonyms for “analyze” include “break down,” “cut,” “deconstruct,” and “dissect.” In fact, the word “analysis” is derived from the New Latin word analyein, meaning “to break up.” Analysis is an extremely valuable tool and is responsible for human progress in all sorts of areas. But the knowledge derived from analysis is primarily a description and guide to how things work. It reduces knowledge of the whole to knowledge of the parts, which is fine if you want to take something apart and put it back together. But the knowledge of how things work is not the same as the knowledge of what things are as a whole, what qualities and properties they have, and the value of those qualities and properties. This latter knowledge is holistic knowledge.

The word “holism,” based on the ancient Greek word for “whole” (holos), was coined in the early twentieth century in order to promote the view that all systems, living or not, should be viewed as wholes and not just as a collection of parts or the sum of parts. It’s no accident that the words “whole,” “heal,” healthy,” and “holy” are linguistically related. The problems of sickness, malnutrition, and injury were well-known to the ancients, and it was natural for them to see these problems as a disturbance to the whole human being, rendering a person incomplete and missing certain vital functions. Wholeness was an ideal end, which made wholeness sacred (holy) as well. (For an extended discussion of analytic/reductionist knowledge vs. holistic knowledge, see this post.)

Holistic knowledge is not just about ideal physical health. It’s about ideal forms in all aspects, including the qualities we associate with human beings we admire: wisdom, strength, beauty, courage, love, kindness. As mistaken as religions have been in understanding natural causation, it is the devotion to ideal forms that is really the essence of religion. The ancient Greeks worshipped excellence, as embodied in their gods; Confucians were devoted to family ties and duties; the Jews submitted themselves to the laws of the one God; Christians devoted themselves to the love of God, embodied in Christ.

Holistic knowledge provides no guidance as to how to conduct surgery or build a computer or launch a rocket; but it does provide insight into the ethics of medicine, the desirability or hazards of certain types of technology, and the proper ends of human beings. All too often, contemporary secular societies expect new technologies to improve human lives and pay no heed to ideal human forms, on the assumption that ideal forms are a fantasy. Then we are shocked when the new technologies are abused and not only bring out the worst in human nature but enhance the power of the worst.

Materialism: There’s Nothing Solid About It!

[I]n truth there are only atoms and the void.” – Democritus

In the ancient Greek transition from mythos to logos, stories about the world and human lives being shaped by gods and goddesses gradually came to be replaced by new explanations from philosophers. Among these philosophers were the “atomists,” including Leucippus and Democritus. Later, the Roman philosopher and poet Lucretius expounded an atomist view of the universe. The atomists were regarded as being among the first atheists and the first materialists — if they did acknowledge the existence of the gods (probably due to public pressures), they argued that the gods had no active influence on the world. Although the atomists’ understanding of the atom was primitive and far from our modern scientific understanding — they did not possess particle accelerators, after all — they were remarkably farsighted about the actual workings of nature. To this day, the symbol of the American Atheists is a depiction of the atom:

However, the ancient atomists’ conception of how the universe is constructed, with solid particles of matter combining to make complex organizational structures, has become problematic given the findings of atomic physics in the past hundred years. Increasingly, scientists have found that reality consists not of solid matter, but of organizational principles and qualities that give us the impression of solidity. And while this new view does not restore the Greek gods to prominence, it does raise questions about how we ought to understand and interpret reality.

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Leucippus and Democritus lived in the fifth century BC. While it is difficult to disentangle their views because of gaps in the historical record, both philosophers argued that all existence was ultimately based on tiny, indestructible particles (“atoms”) and empty space. While not explicitly denying the existence of the gods, the philosophy of Leucippus and Democritus made it clear that the gods had no significant role in the creation or maintenance of the universe. Rather, atoms existed eternally and moved randomly in empty space, until they collided and began to form larger units, leading to the growth of stars and planets and various life forms. The differences between types of matter, such as iron, water, and air were due to differences in the atoms that composed this matter. Atoms could join with each other because of a variety of hooks or sockets in the atoms that allowed for attachments.

Hundreds of years later, the Roman philosopher Lucretius expanded upon atomist theory in his poem De rerum natura (On the Nature of Things). Lucretius explained that the universe consisted of an infinite number of atoms moving and combining under the influence of laws and random chance, not the decisions of gods. Lucretius also denied the existence of an afterlife, and argued that human beings should not fear death. Although Lucretius was not explicitly atheistic, his work was perceived by Christians in the Middle Ages as being essentially atheistic in outlook and was denounced for that reason.

Not all of the ancient philosophers, even those most committed to reason, accepted the atomist view of existence. It is reported that Plato hated Democritus and wished that his books be burned. Plato did accept that there were different types of matter composing the world, but posited that the particles were perfect triangles, brought together in various combinations. In addition, these triangles were guided by a cosmic intelligence, and were not colliding randomly without purpose. For Plato, the ultimate reality was the Good, and the things we saw all around us were shadows of perfect, ideal forms that were the blueprint for the less-perfect existing things.

For two thousand years after Democritus, atomism as a worldview remained a minority viewpoint — after all, religion was still an important institution in societies, and no one had yet seen or confirmed the existence of atoms. But by the nineteenth century, advances in science had accumulated to the point at which atomism became increasingly popular as a view of reality. No longer was there a need for God or gods to explain nature and existence; atoms and laws were all that were needed. The philosophy of materialism — the view that matter is the fundamental substance in nature and that all things, including mental aspects and consciousness, are results of material interactions — became increasingly prevalent. The political-economic ideology of communism, which at one time ruled one-third of the world’s population, was rooted in materialism. In fact, Karl Marx wrote his doctoral dissertation on Democritus’ philosophy of nature, and Vladimir Lenin authored a philosophical book on materialism, including chapters on physics, that was mandatory reading in the higher education system of the Soviet Union.

As physicists conducted increasingly sophisticated experiments on the smallest parts of nature, however, certain results began to challenge the view that atoms were solid particles of matter. For one thing, it was found that atoms themselves were not solid throughout but consisted of electrons orbiting around an extremely small nucleus of protons and neutrons. The nucleus of an atom is actually 100,000 times smaller than the entire atom, even though the nucleus contains almost the entire mass of the atom. As one article has put it, “if the nucleus were the size of a peanut, the atom would be about the size of a baseball stadium.” For that reason, some have concluded that all “solid” objects in the universe, including human beings, are actually about 99.9999999 percent empty space, because of the empty space in the atoms! Others respond that in fact it is not “empty space” in the atom, but rather a “field” or “wave function” — and here it gets confusing.

In fact, subatomic particles do not have a precise location in space; they behave like a fuzzy wave until they interact with an observerand then the wave “collapses” into a particle. The bizarreness of this activity confounded the brightest scientists in the world, and to this day, there are arguments among scientists about what is “really” going on at the subatomic level.

The currently dominant interpretation of subatomic physics, known as the “Copenhagen interpretation,” was developed by the physicists Werner Heisenberg and Niels Bohr in the 1920s. Heisenberg subsequently wrote a book, Physics and Philosophy to explain how atomic physics changed our interpretation of reality. According to Heisenberg, the traditional scientific view of material objects and particles existing objectively, whether we observe them or not, could no longer be upheld. Rather than existing as solid objects, subatomic particles existed as “probability waves” — in Heisenberg’s words, “something standing in the middle between the idea of an event and the actual event, a strange kind of physical reality just in the middle between possibility and reality.” (Physics and Philosophy, p. 41 — page numbers are taken from the 1999 edition published by Prometheus books). According to Heisenberg:

The probability function does . . . not describe a certain event but, at least during the process of observation, a whole ensemble of possible events. The observation itself changes the probability function discontinuously; it selects of all possible events the actual one that has taken place. . . Therefore, the transition from the ‘possible’ to the ‘actual’ takes place during the act of observation. If we want to describe what happens in an atomic event, we have to realize that the word ‘happens’ can apply only to the observation, not to the state of affairs between two observations. It applies to the physical, not the psychical act of observation, and we may say that the transition from the ‘possible’ to the ‘actual’ takes place as soon as the interaction of the object with the measuring device, and thereby with the rest of the world, has come into play. (pp. 54-55)

Later in his book, Heisenberg writes: “If one wants to give an accurate description of the elementary particle — and here the emphasis is on the word ‘accurate’ — the only thing that can be written down as a description is a probability function.” (p. 70) Moreover,

In the experiments about atomic events we have to do with things and facts, with phenomena that are just as real as any phenomena in daily life. But the atoms or the elementary particles themselves are not as real; they form a world of potentialities or possibilities rather than one of things or facts. (p. 186)

This sounds downright crazy to most people. The idea that the solid objects of our everyday experience are made up not of smaller solid parts but of probabilities and potentialities seems bizarre. However, Heisenberg noted that observed events at the subatomic level did seem to fit the interpretation of reality given by the Greek philosopher Aristotle over 2000 years ago. According to Aristotle, reality was a combination of matter and form, but matter was not a set of solid particles but rather potential, an indefinite possibility or power that became real only when it was combined with form to make actual existing things. (pp. 147-49) To provide some rough analogies: a supply of wood can potentially be a table or a chair or a house — but it must be combined with the right form to become actually a table or a chair or a house. Likewise, a block of marble is potentially a statue of a man or a woman or an animal, but only when a sculptor shapes the marble into that particular form does the statue become actual. In other words, actuality (reality) equals potential plus form.

According to Heisenberg, Aristotle’s concept of potential was roughly equivalent to the concept of “energy” in modern physics, and “matter” was energy combined with form.

All the elementary particles are made of the same substance, which we may call energy or universal matter; they are just different forms in which the matter can appear.

If we compare this situation with the Aristotelian concepts of matter and form, we can say that the matter of Aristotle, which is mere ‘potential,’ should be compared to our concept of energy, which gets into ‘actuality’ by means of the form, when the elementary particle is created. (p. 160)

In fact, all modern physicists agree that matter is simply a form of energy (and vice versa). In the earliest stages of the universe, matter emerged out of energy, and that is how we got atoms in the first place. There is nothing inherently “solid” about energy, but energy can be transformed into particles, and particles can be transformed back into energy. According to Heisenberg, “Energy is in fact the substance from which all elementary particles, all atoms and therefore all things are made. . . .” (p. 63)

So what exactly is energy? Oddly enough, physicists have a hard time stating exactly what energy is. Energy is usually defined as the “capacity to do work” or the “capacity to cause movement,” but these definitions remain somewhat vague, and there is no specific mechanism or form that physicists can point to in order to describe energy. Gottfried Leibniz, who developed the first formula for measuring energy, referred to energy as vis viva or “living force,” a concept which is anthropomorphic and nearly theological.  In fact, there are so many different types of energy and so many different ways to measure these types of energy that many physicists are inclined to the view that energy is not a substance but just a mathematical abstraction. According to the great American physicist Richard Feynman, “It is important to realize that in physics today, we have no knowledge of what energy ‘is.’ We do not have a picture that energy comes in little blobs of a definite amount. It is not that way. It is an abstract thing in that it does not tell us the mechanism or the reason for the various formulas.” The only reason physicists know that energy exists is that they have performed numerous experiments over the years and have found that however energy is measured, the amount of energy in an isolated system always remains the same — energy can only be transformed, it can neither be created nor destroyed. Energy in itself has no form, and there is no such thing as “pure energy.” Oh, and energy is relative too — you have to specify the frame of reference when measuring energy, because the position and movement of the observer matters. For example, if you move toward a photon, its energy in that frame of reference will be greater; if you move away from a photon, its energy will be less.

In fact, the melding of relativity theory with quantum physics has further undermined materialism and our common sense notions of what it is to be “real.”  A 2013 article in Scientific American by Dr. Meinard Kuhlmann of Bielefeld University in Germany, “What is Real,” lays out some of these paradoxes of existence at the subatomic level. For example, scientists can create a vacuum in the laboratory, but when a Geiger counter is connected to the vacuum container, it will detect matter. In addition, a vacuum will contain no particles according to an observer at rest, but will contain many particles from the perspective of an accelerating observer! Kuhlmann concludes: “If the number of particles is observer-dependent, then it seems incoherent to assume that particles are basic. We can accept many features to be observer-dependent but not the fact of how many basic building blocks there are.”

So, if the smallest parts of reality are not tiny material objects, but potentialities and probabilities, which vary according to the observer, then how do we get what appears to be solid material objects, from rocks to mountains to trees to houses and cars? According to Kuhlmann, some philosophers and scientists say that we need to think about reality as consisting entirely of relations. In this view, subatomic particles have no definite position in space until they are observed because determining position in space requires a relation between an observer and observed. Position is mere potential until there is a relation. You may have heard of the old puzzle, “If a tree falls in a forest, and no one is around to hear it, does it make a sound?” The answer usually given is that sound requires a perceiver who can hear, and it makes no sense to talk about “sound” without an observer with functional ears. In the past, scientists believed that if objects were broken down into their smallest parts, we would discover the foundation of reality; but in the new view, when you break down larger objects into their smallest parts, you are gradually taking apart the relations that compose the object, until what you have left is potential. It is the relations between subatomic particles and observers that give us solidity.

Another interpretation Kuhlmann discusses is that the fundamental basis of reality is bundles of properties. In this view, reality consists not of objects or things, but of properties such as shape, mass, color, position, velocity, spin, etc. We think of things as being fundamentally real and properties as being attributes of things. But in this new view, properties are fundamentally real and “things” are what we get when properties are bundled together in certain ways. For example, we recognize a red rubber ball as being a red rubber ball because our years of experience and learning in our culture have given us the conceptual category of “red rubber ball.” An infant does not have this conceptual category, but merely sees the properties: the roundness of the shape, the color red, the elasticity of the rubber. As the infant grows up, he or she learns that this bundle of properties constitutes the “thing” known as a red rubber ball; but it is the properties that are fundamental, not the thing. So when scientists break down objects into smaller and smaller pieces in their particle accelerators, they are gradually taking apart the bundles of properties until the particles no longer even have a definite position in space!

So whether we thing of reality as consisting of relations or bundles of properties, there is nothing “solid” underlying everything.  Reality consists of properties or qualities that emerge out of potential, and then bundle together in certain ways. Over time, some bundles or relations come apart, and new bundles or relations emerge. Finally, in the evolution of life, there is an explosion of new bundles of properties, with some bundles containing a staggering degree of organizational complexity, built incrementally over millions of years. The proper interpretation of this organizational complexity will be discussed in a subsequent post.