Tag Archives: Heisenberg

Beyond the “Mechanism” Metaphor in Biology

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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.

Materialism: There’s Nothing Solid About It!

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“[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 observer— and 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.