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Section 1: Introduction

Biology is complicated, really, really complicated. This should not surprise you if you think that ultimately the laws of physics explain how the world works, because biological activity is far beyond the usual realm of simple physical phenomena. It is easy to simply turn away from a true physical explanation of biological phenomena as simply hopeless. Perhaps it is hopelessly complex at some level of detail. The ghosts of biological "stamp collecting" are still alive and well and for a good reason.

Figure 1: A population of slime-mold cells forms an aggregate in response to a signaling molecule.

Source: © Courtesy of BioMed Central Ltc. From: Maddelena Arigoni et al. "A novel Dictyostelium RasGEF required for chemotaxis and development," BMC Cell Biology, 7 December 2005. More info

However, it is possible that in spite of the seemingly hopeless complexity of biology, there are certain emergent properties that arise in ways that we can understand quantitatively. An emergent property is an unexpected collective phenomenon that arises from a system consisting of interacting parts. You could call the phenomenon of life itself an emergent property. Certainly no one would expect to see living systems arise directly from the fundamental laws of quantum mechanics and the Standard Model that have been discussed in the first seven units of this course.

The danger is that this concept of "emergent properties" is just some philosophical musing with no real deeper physics content, and it may be true that the emergent properties of life viewed "bottom up" are simply too complex in origin to understand at a quantitative level. It may not be possible to derive how emergent properties arise from microscopic physics. In his book A Different Universe: Reinventing Physics from the Bottom Down, the physicist Robert Laughlin compares the local movement of air molecules around an airplane wing to the large-scale turbulent hydrodynamic flow of air around the airfoil that gives rise to lift. Molecular motion is clearly the province of microscopic physics and statistical mechanics, while turbulent flow is an emergent effect. As Laughlin puts it, if he were to discover that Boeing Aircraft began worrying about how the movement of air molecules collectively generates hydrodynamics, it would be time to divest himself of Boeing stock. Perhaps the same should have been said when banks started hiring theoretical physicists to run stock trading code.

In biology, we have a much greater problem than with the airplane, because the air molecules can be described pretty well with the elegant ideas of statistical mechanics. So, while it is a long stretch to derive the emergence of turbulence from atomic motion, no one would say it is impossible, just very hard.

Colored smoke marks the hydrodynamic flow around an aircraft, an emergent phenomenon.

Figure 2: Colored smoke marks the hydrodynamic flow around an aircraft, an emergent phenomenon.

Source: © NASA Langley Research Center (NASA-LaRC). More info

In biology, even the fundamentals at the bottom may be impossibly hard for physics to model adequately in the sense of having predictive power to show the pathways of emergent behavior. A classic example is the signaling that coordinates the collective aggregation of the slime-mold Dictyostelium cells in response to the signaling molecule cyclic AMP (cAMP). In the movie shown in Figure 1, the individual Dictyostelium cells signal to each other, and the cells stream to form a fruiting body in an emergent process called "chemotaxis." This fairly simple-looking yet spectacular process is a favorite of physicists and still not well understood after 100 years of work.

So, perhaps in a foolhardy manner, we will move forward to see how physics, in the discipline known as biological physics, can attack some of the greatest puzzles of them all. We will have to deal with the emergence of collective phenomena from an underlying complex set of interacting entities, like our Dictyostelium cells. But that seems still within the province of physics: really hard, but physics. But there are deeper questions that seem to almost be beyond physics.

Are there emergent physics rules in life?

The amazing array of knowledge in previous units contains little inkling of the complex, varied phenomena of life. Life is an astonishingly emergent property of matter, full-blown in its complexity today, some billions of years after it started out in presumably some very simple form. Although we have many physical ways to describe a living organism, quantifying its state of aliveness using the laws of physics seems a hopeless task. So, all our tools and ideas would seem to fail at the most basic level of describing what life is.

Biology has other incredible emergent behaviors that you can hardly anticipate from what you have learned so far. British physicist Paul Dirac famously said that, "The fundamental laws necessary for the mathematical treatment of a large part of physics and the whole of chemistry are thus completely known, and the difficulty lies only in the fact that application of these laws leads to equations that are too complex to be solved." Our question is: Is the biological physics of the emergent properties of life simply a matter of impossible complexity, or are there organizing principles that only appear at a higher level than the baseline quantum mechanics?

So far, we have talked about the emergent nature of life itself. The next astonishing emergent behavior we'll consider is the evolution of living organisms to ever-higher complexity over billions of years. It is strange enough that life developed at all out of inanimate matter, in apparent conflict with the Second Law of Thermodynamics. The original ur-cell, improbable as it is, proceeded to evolve to ever-greater levels of complexity, ultimately arriving at Homo sapiens several million years ago. Thanks to Darwin and Wallace and their concept of selection of the fittest, we have a rather vague hand-waving idea of how this has happened. But the quantitative modeling of evolution as an emergent property remains in its infancy.

The building blocks of evolution

Molecules of life: RNA (left) and DNA (right).

Figure 3: Molecules of life: RNA (left) and DNA (right).

Source: © Wikimedia Commons, Creative Commons Attribution-Share Alike 3.0 license. Author: Sponk, 23 March 2010. More info

Modeling evolution is a difficult task; but nevertheless, we can try. So let's start at the top and work down. Physicists believe (and it is somewhat more of a belief than a proven fact) that all life began with some ur-cell and that life evolved from that ur-cell into the remarkable complexity of living organisms we have today, including Homo sapiens. We will never know what path this evolution took. But the remarkable unity of life (common genetic code, common basic proteins, and common basic biological pathways) would indicate that, at its core, the phenomenon of life has been locked in to a basic set of physical modes and has not deviated from this basic set. At that core, lies a very long linear polymer, deoxyribonucleic acid (or DNA), which encodes the basic self-assembly information and control information. A related molecule, ribonucleic acid (RNA), has a different chemical group at one particular position, and that profoundly changes the three-dimensional structure that RNA takes in space and its chemical behavior.

Although evolution has played with the information content of DNA, its basic core content, in terms of how its constituent molecules form a string of pairs, has not obviously changed. And while there is a general relationship between the complexity of an organism and the length of its DNA that encodes the complexity, some decidedly simpler organisms than Homo sapiens have considerably longer genomes. So, from an information perspective, we really don't have any iron-clad way to go from genome to organismal complexity, nor do we understand how the complexity evolved. Ultimately, of course, life is matter. But, it is the evolution of information that really lies at the unknown heart of biological physics, and we can't avoid it.

The emergence of the mind in living systems

Player C is trying to determine which player—A or B—is a computer and which is human.

Figure 4: Player C is trying to determine which player—A or B—is a computer and which is human.

Source: © Wikimedia Commons, Public Domain. Author: Bilby, 25 March 2008. More info

Biology possesses even deeper emergent phenomena than the evolution of complexity. The writer and readers of this document are sentient beings with senses of identity and self and consciousness. Presumably, the laws of physics can explain the emergent behavior of consciousness, which certainly extends down from Homo sapiens into the "lower" forms of life (although those lower forms of life might object to that appellation). Perhaps the hardest and most impossible question in all of biological physics is: What is the physical basis behind consciousness? Unfortunately, that quest quickly veers into the realm of the philosophical and pure speculation; some would say it isn't even a legitimate physics question at all.

There is even an argument as to whether "machines," now considered to be computers running a program, will ever be able to show the same kind of intelligence that living systems such as human beings possess. Traditional reductionist physicists, I would imagine, simply view the human mind as some sort of a vastly complicated computational machine. But it is far from clear if this view is correct. The mathematician Alan Turing, not only invented the Turing machine, the grandfather of all computers, but he also asked a curious question: Can machines think? To a physicist, that is a strange question for it implies that maybe the minds of living organisms somehow have emergent properties that are different from what a manmade computing machine could have. The answer to Turing's question rages on, and that tells us that biology has very deep questions still to be answered.