Tag Archives: mutation

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.

How Random is Evolution?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

But there is even more to the story of evolution.

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

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

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

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

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

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

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

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

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

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

However, even in the late nineteenth century, a number of biologists noted cases in nature in which cooperation played a prominent role in evolution. In the 1880s, the Scottish biologist Patrick Geddes proposed that the reason the giant green anemone contained algal (algae) cells as well as animal cells was because of the evolution of a cooperative relationship between the two types of cells that resulted in a merger in which the alagal cells were merged into the animal flesh of the anemone. In the latter part of the twentieth century, biologist Lynn Margulis carried this concept further. Margulis argued that the most fundamental building block of advanced organisms, the cell, was the result of a merger between more primitive bacteria billions of years ago. By merging, each bacterium lent a particular biological advantage to the other, and created a more advanced life form. This theory was regarded with much skepticism at the time it was proposed, but over time it became widely accepted. The traditional picture of evolution as one in which new species diverge from older species and compete for survival has had to be supplemented with the picture of cooperative behavior and mergers. As one researcher has argued, “The classic image of evolution, the tree of life, almost always exclusively shows diverging branches; however, a banyan tree, with diverging and converging branches is best.”

More recent studies have demonstrated the remarkable level of cooperation between organisms that is the basis for human life. One study from a biologist at the University of Cambridge has proposed that human beings have as many as 145 genes that have been borrowed from bacteria, other single-celled organisms, and viruses. In addition, only about half of the human body is made up of human cells — the other half consists of trillions of microbes and quadrillions of viruses that largely live in harmony with human cells. Contrary to the popular view that microbes and viruses are threats to human beings, most of these microbes and viruses are harmless or even beneficial to humans. Microbes are essential in digesting food and synthesizing vitamins, and even the human immune system is partly built and partly operated by microbes! If, as one biologist has argued, each human being is a “society of cells,” it would be equally valid to describe a human being as a “society of cells and microbes.”

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