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.



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



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.