1IntroductionToolbox at the Physical–Life Science Interface

1.1 Motivation for Biophysics

There are distinct scientific challenges that lie right at the interface between what we now refer to as the life sciences and the physical sciences. These challenges are as fundamental as any that one can think of in science; they come down to this simple and deceptively innocuous question:

What is life?

The distinction between physics and biology as separate scientific disciplines is a relatively modern invention, though the metaphysical debate as to what is alive and what is not and the existence of vitality and of the concept of the soul go back as far as historical records can attest. The identification of a precise period of divergence between the disciplines of physics and biology is a matter of debate perhaps better suited for learned historians of science, though as a naïve observer I suspect it to be not a very valuable exercise. Developments in scientific paradigms are often only identified several years after they have occurred, through the kaleidoscope of historical hindsight of events of which the protagonists of the day were blissfully unaware. So, defining an absolute line in time inevitably suffers the dangers of having a perspective from the modern age.

That being said, the nineteenth century certainly witnessed key developments in the physical understanding of the nature of thermodynamics through giants such as Carnot, Kelvin, Joule, and then later Boltzmann and Gibbs and in electromagnetism and light largely through the genius efforts of James Clerk Maxwell (Maxwell, 1873), which today still appear as core components of any undergraduate physics degree. Similarly, the publication of On the Origin of the Species by Charles Darwin (Darwin, 1859) sparked a scientific and sociological debate that was centered around living things and the principle of selective environmental pressures resulting in dynamic evolutionary change, which is one of the key principles taught in modern biology university courses. Although these events do not define the explicit invention of modern physics and biology as academic subjects, they are interesting exemplars that at least encourage us to think about the question.

An interesting interdisciplinary historical quirk is that the grandson of Charles Darwin, also called Charles (Galton) Darwin, was a renowned physicist of his time who made important contributions toward our fundamental understanding of the angular momentum of light, which is only now coming full circle, so to speak, back toward biological questions in being utilized as a probe to monitor a variety of molecular machines that operate via twisting motions (which we will discuss in Chapter 6). It is not really a relevant fact. But it is interesting.

However, the distinctions between the biology and physics disciplines today are often a little contrived. More importantly though, they are often not terribly helpful. It is a tragedy that the majority of high-school-level science students still need to make relatively early choices about whether they wish to specialize primarily in the area of physical/mathematical biased science/engineering or instead in the life sciences. This approach inevitably results in demarcated structures within our higher education factories, faculties of physics, schools of biology, etc., which potentially serve to propagate the distinction further.

Fundamentally, the laws of physics apply to all things, including biological systems, so the need for a core distinction, one might argue, is an intellectual distraction. This distinction between physics and biology also stands out as an historical anomaly. Key developments in the understanding of the natural world by the ancient civilizations of Babylonia and Egypt made no such distinction, neither did Greek or Roman or Arab natural philosophers nor did even the Renaissance thinkers and Restoration experimentalists in the fifteenth to seventeenth centuries, who ultimately gave birth to the concept of “science” being fundamentally concerned with formulating hypotheses and then falsifying them through observation. Isaac Newton, viewed by many as the fountain from which the waters of modern physics flow, made an interesting reference in the final page of his opus Principia Mathematica:

And now we might add something concerning a certain most subtle Spirit which pervades and lies hid in all gross bodies; by force and action of which Spirit the particles of bodies mutually attract one another at near distance, and cohere, if contagious; and electric bodies operate at greater distances, as well repelling as attracting the neighbouring corpuscles; and light is emitted, reflected, refracted, inflected, and heats bodies; and all sensation is excited, and the members of animal bodies move at the command of the will, namely, by the vibrations of this Spirit, mutually propagated along the solid filaments of the nerves, from the outward organs of sense to the brain, and from the brain into the muscles. But these are things that cannot be explained in few words, nor are we furnished with that sufficiency of experiments which is required, to an accurate determination and demonstration of the laws by which this electric and elastic Spirit operates.

This perhaps suggests, with a significant creative interpretation from our modern era, a picture of combined physical forces of mechanics and electric fields, which are responsible for biological properties. Or perhaps not. Again, maybe this is not relevant. Sorry. But it’s still very interesting.

We should try to not let disciplinary labels get in the way of progress. The point is that the physical science method has been tremendously successful on a wide range of nonliving problems all the way from nuclei to atoms to solid state to astrophysics. The fundamental theories of quantum mechanics, thermodynamics, electromagnetism, mechanics, optics, etc., are immensely powerful. On the other hand, these theories can sometimes appear to be relatively toothless when it comes to life sciences: for example, a system as small as a cell or as large as an ecosystem. The fact that these objects are emergent from the process of evolution is a fundamental difference. They may be comprehensible, but then again they may not be, depending on whether 4 billion years of life on Earth as we know it is sufficient or not to reach an “evolutionary steady state.” So, the very nature of what we are trying to understand, and our likely success in doing so, could be very different in the study of the life sciences. That is the point underpinning the quote at the start of this chapter “physics does not equal biology.” We are not trying to make any point about what we call the activities of these disciplines. But it is a point about the nature of the objects under study as described earlier.

“Biophysics” in its current form is a true multidisciplinary science. A minimal definition of biophysics is this: it is what biophysicists do. Say this and you are guaranteed a titter of laughs at a conference. But it’s as good a definition as any. And the activities of biophysicists use information not only from physics and biology but also from chemistry, mathematics, engineering, and computer science, to address questions that fundamentally relate to how living organisms actually function. The modern reblurring of the lines between biology and physics started around the middle of twentieth century, at a time when several researchers trained originally from a background of the physical sciences made significant advances toward the development of what we now call molecular biology. Biophysics as a new discipline was shaped significantly from the combined successes of physiology and structural biology at around the same time. The former involved, for example, the pioneering work of Alan Hodgkin and Andrew Huxley, which revealed how the fundamental mechanism of conduction of sensory signals in nerves is achieved (Hodgkin and Huxley, 1952). The latter applied emerging physics tools to study the scattering of x-rays from crystals made of biological molecules, first exemplified in the work, from the 1930s onward, of one of the great women of modern science, Dorothy Hodgkin (née Crowfoot), in her determination of the structures of a number of biologically important small molecules, including cholesterol, penicillin, and vitamin B12, but then later on much larger molecules called proteins, first shown on one found in muscles called myoglobin (Kendrew et al., 1958).

Hodgkin and Huxley’s seminal paper, at the time of my writing this sentence, has been cited over 16,000 times and deserves its place as one of the pioneering publications of modern biophysics. To some biomathematicians and physiologists, this might seem controversial, since they may claim this paper as one from their own fields, especially since neither Hodgkin nor Huxley necessarily identified as being a “physicist” (their respective areas of primary expertise were biochemistry and physiology, respectively). But with the wisdom of historical hindsight, it is clear that their work sits very much at the cutting-edge interdisciplinary interface between biology and physics.

The beauty of this exemplar study, in particular, is that it used multiple biophysical tools to solve a challenging biological question. It investigated the fundamental properties of electrical nerve conduction by reducing the problem to being one of the ion channels in cell membranes (Figure 1.1a) that could be characterized by experimental measurements using biophysical technology of time-resolved voltage signals by electrodes placed inside and outside the nerve fiber during a stimulated nerve conduction (Figure 1.1b). But these experimental signals could then be modeled using the physics of electrical circuitry (Figure 1.1c), for example, by modeling the electric current due to ions flowing through an ion channel in the cell membrane as being equivalent to a resistor in a standard electrical circuit, with a voltage applied across it, which is equivalent to the voltage across the cell membrane, that is, the difference in electrical potential per unit charge between the inside of the cell and the outside of the cell, denoted by V_m, and the cell membrane acting as a dielectric, thus functioning as a capacitor (discussed in Chapter 2), here of capacitance per unit area C_m. In its simplest form, the electric current flow I across the cell membrane can be modeled mathematically as simply

where I_i is the electric current flow through the actual ion channel. This model can be easily expanded using multiple sets of differential equations to account for multiple different ion channels (Figure 1.1d), and this also fits the experimental observations very well.

However, the point here of these two approaches is that they illustrate not just the achievements of new biological insight made with physical science experimental tools and that they were both coupled closely to advances in methods of physical science analysis techniques, in the case of nerve conduction to a coupled series of analytical differential equations called the “Hodgkin–Huxley model,” which describes the physics of the propagation of information in the nerves via electrical conduction of sodium and potassium ions across the nerves’ outer electrically insulating membranes, an electric phenomenon known by biologists as the “action potential.” X-ray crystallography, the analysis concerned with building mathematical tools that could in essence generate the inverse of the x-ray scatter pattern produced by protein crystals to reveal the underlying spatial coordinates of the constituent atoms in the protein molecule, is a process involving Fourier transformation coupled with additional mathematical techniques for resolving the phase relationship between the individual scattering components. This tight coupling in the life sciences between analytical and experimental physical science tools is far from unique; rather, it is a general rule.

But, paradoxically, a key challenge for modern biophysics has been, in the same manner in which it is difficult for the child to emerge from the shadows of an achieving parent, to break free from the enormous successes made through the application of structural biology methods, in particular, over half a century ago. Structural biology, in its ability to render atomic level detail of the molecular machinery of living organisms, has led to enormous insight in our understanding of the way that biological molecules operate and interact with each other. However, what structural biology in its existing form cannot offer is any direct information about the dynamic process in living cells. This is a core weakness since biological processes are anything but static. Everything in biology is dynamic; it is just a matter of over what time scale. However, dynamic processes are something that single-molecule tools can now address exquisitely well. The wind’s direction is already beginning to change with a greater investment in functional imaging tools of novel techniques of light microscopy in particular, some of which may indeed develop into new methods of dynamic structural biology themselves.

The benefits of providing new insight into life through the bridging of physics and biology are substantial. Robust quantitation through physical science offers a precise route into reductionist inference of life, namely, being able to address questions concerning the real underlying mechanisms of natural processes, how tissues are made up of cells and the cells from molecules, and how these all work together to bring about something we call a living organism. The absence of quantifying the components of life precisely, both in space and in time, makes the process of reducing biological phenomena to core processes that we can understand quite challenging, especially in light of the complexity of even the simplest organism. And quantifying physical parameters precisely is one thing in particular that physics does very well.

One of the most cited achievements of biophysics is that of the determination of the structure of the biological molecule called “deoxyribonucleic acid” (DNA), which in the 1950s was resolved through an exquisite combination of biology and physics expertise, in that it required challenging biochemical techniques to purify DNA and then form near-perfect crystalline fibers, and then applying innovative physical science x-ray crystallography tools on these DNA fibers followed by a bespoke physical science analysis to infer the double-helical structure of DNA. But there are also lesser known but equally important examples in which physical science tools that initially had no intended application in the life sciences were eventually utilized for such and which today are very tightly coupled with biology research but decoupled from their original invention.

For example, there is small-angle x-ray scattering (SAXS). SAXS was a physical science tool developed in the 1980s for the investigation of material properties of, originally, nonbiological composites at the nanometer length scale, in which a sample’s elastic scattering of x-rays is recorded at very low angles (typically ≲10°). However, this technique found later application in the investigation of some natural polymers that are made by living cells, for example, the large sugar molecule, starch, that is made by plants. These days, SAXS has grown into a very powerful tool for investigating the mesoscopic periodic length scale features over a range of typically ∼5–150 nm (a “nm” or nanometer is 1000 million times smaller than a meter) of several different biological filamentous/polymeric structures and in fact is largely viewed now as being primarily a biophysical technique.

1.2 What Do We Mean by a “Toolbox?”

There are some notable differences between the core strategy of scientific research between physics and biology. Research in the life sciences, in its modern form, is very much optimized toward hypothesis-driven research. This means, in essence, setting out theories as models of scientific phenomena and constructing empirical investigations that can falsify these hypotheses (for interested readers in this basic area of the scientific method, see Popper, 1963), though can never actually prove them. To many scientists, this approach is simply what science is all about and is simply what separates science from pseudoscience. But a potential issue lies in investigating the phenomena that are currently undertheorized, to the extent that one can ask key scientific questions that are testable; but this is not necessarily the same as a “hypothesis” that a biologist might construct, which often involves an elaborate existing theory from that particular area of the life sciences. Many of these undertheorized areas are relevant to physics research, involving fundamental physical phenomena as opposed to the “fine-tuning” details of different aspects of testable existing model, and might better be described as exploratory-driven research. I mention this here simply to forewarn the reader of the differences in perception of what constitutes “good science” by some biologists and some physicists, since this, hopefully, will assist in a better genuine communication of scientific concepts and research between the two sciences.

A key challenge to finding answers in the biological sciences is the trick of knowing the right questions to ask. Physical science techniques applied to the life sciences, whether experimental or analytical, have often arisen from the need to address highly focused and specific questions. However, these techniques in general have capabilities to address a range of different questions in biology, not necessarily related to the biological systems of the original questions. As such, new emerging questions can be addressed by applying a repertoire of dynamically emerging physical tools, and this repertoire of physical science tools is essentially a “toolbox.” But as any master craftsman knows, of key importance with any toolbox is knowing which are the best tools for the job in hand.

Not only knowing what are the right questions to ask but also knowing what are the best modern physical science tools to address these questions can, in all but exceptional cases, be difficult to address simultaneously. The former is the realm of the expert biologist in an often highly focused area of the life sciences, whereas the latter lies within the expertise of the physical scientist, engineer, or mathematician who has a professionally critical knowledge of the techniques that could be applied. A more efficient approach, which has been demonstrated in numerous exemplar case studies across the world, is to engage in a well-balanced collaborative research between biologists and physical scientists. This strategy, however, is far from a smooth path to navigate. There are not insignificant cultural, language, and skill differences between these two broad areas of science, as well as potential political challenges in determining who is actually “driving” the research. The strategy is decoupled from the approach of a biologist who generates a list of questions they wants to address and asks the physical scientist to find the best tool, as it is from the physical scientist who makes less than robust efforts to explain the tools to the biologist in ways that do not demand a grasp of advanced mathematics.

In an ideal world, the interaction between biologists and physicists would be a genuinely dialectical process that could involve, as an example, the biologist explaining the background to their questions and the physical scientist engaging the biologist in the science behind their techniques that ultimately may not only alter the choice of tools to use from the toolbox but also may change the biological questions that are actually asked in light of what specific tasks the tools can, and cannot, perform. It is not rocket science. It is a simple manifestation of respect for the expertise of others.

However, a key challenge for the physical scientist is to encourage the expert biologist to be bold and think “big”—what are the really difficult questions that often are the elephants in the room that do not get addressed during a typical grant proposal? This freedom of scientific thought can be genuinely infectious to tackling difficult biological questions once started. One cannot simply cut and paste physics onto biology, that’s not how it works. But it is possible to inspire people to think beyond their comfort zones, and in doing so achieve something much higher.

For example, what drives the development of tools to add to the physical sciences toolbox? Thinking on the theme of hypothesis-driven versus exploratory research, the development of new tools is often driven by exploration. This, in turn, then leads to a greater space over which to develop hypotheses. An interesting contemporary example of this is the terahertz spectroscopy, which we will discuss in Chapter 5. The original conception of the terahertz spectroscopy had no biological hypothesis behind it but stemmed from the scientific exploration into the states of condensed matter; however, it is now emerging as a method that can inspire biological hypotheses, that is, do certain biomolecules inside cell membranes convey biological information using quantum mechanical (QM) processes?

Another important word of warning, for which the reader should be duly cautious, is the differences between these physical science tools and the tools that someone embarking on a DIY project may utilize. Physical science tools for investigating challenging biological questions are often expensive, challenging to use, and require sometimes significant levels of expertise to operate. They are thus decoupled from a relatively simple hammer for fixing fence posts or a cheap screwdriver used for assembling flat-pack furniture.

However, provided one is appropriately mindful of these differences, the concept of a suite of physical science tools that can be applied to investigate the complexities of life sciences is useful in steering the reader into learning a sufficient background of the science and applications of these techniques to inform their choices of using them further. This is not to say that this book will allow you to instantly become an expert in their use, but rather might offer sufficient details to know which tools might, or might not, be relevant for particular problems, thus permitting you to explore these tools further directly with the experts in these appropriate areas.

1.3 Makeup of the Subsequent Chapters in This Book

Although much of the book describes experimental biophysical tools, a substantial portion is dedicated to theoretical biophysics tools. Naturally, this is an enormous area of research that crosses into the field of applied mathematics. Since students of the physical sciences have often a broad spectrum of abilities and interests in math, these theoretical tools may be of interest to somewhat differing extents. However, what I have included here are at least the key theoretical techniques and methods of relevance to biophysics, as I see them, so that the more theoretically inclined student can develop these further with more advanced texts as appropriate, and the less theoretically inclined student at least has a good grounding in the core methods to model biophysical systems and equations of relevance that actually work.

In Chapter 2, an orientation is provided for physical scientists by explaining the key basic concepts in biology. For more advanced treatments, the reader is referred to appropriate texts in the reference list. But, again, at least this biological orientation gives physical sciences readers the bare bones knowledge to properly understand the biological context of the techniques described in the rest of this book, without having to juggle textbooks.

Chapters 3 through 6 are themed into different experimental biophysics techniques. These are categorized on the basis of the following:

1.4 Once More, Unto the Breach

I will not bore you with the political challenges of the collaborative process between physics and biology, such as who drives and leads the research, where you do the research, the orders of authors’ names on a research paper, and where the next grant is coming from, those kinds of things. I have theories, yes, but to expound on them requires the structure of a nearby public house, and in the absence of such I will move on.

But I will say this.

Let your scientific nose do the leading, constantly and fervently.

Question dogma. Always question dogma.

Be curious about the natural world. Endlessly curious. Keep on asking questions.

And when you think you have found the answer, well… think again….

Enjoy this book. Please let me know if you have or haven’t. I’ll aim to make it better the next time.

1.5 Summary Points

• We can treat physical science techniques applied to biology problems as a “toolbox,” but we must be mindful that these tools are often hard to use and expensive.
• Physical scientists might wish to help biologists to think of the big questions and can consider building established balanced, long-term, dialectical collaborations as an alternative to providing transient technical support services.
• Relentless progress on producing new physical science tools emerges, which then can offer different biological insights, but many old tools can still provide powerful details.

Questions

• 1.1 One criticism by some physical scientists in liaising with biologists, at the risk of propagating a stereotype, is that biologists just “don’t have the math!” Do you think this is true? Is it actually possible to convey complex mathematical ideas without, for example, writing down an equation?
• 1.2 Some biologists complain, at the risk of propagating a stereotype, that physical scientists simply do not have a good appreciation of the complexities of biology and lack the required knowledge of basic biological and chemical details to help them to understand even the simplest processes inside living cells. Do you think this is correct? Is there anything that physical scientists could do to improve this hypothetical situation?
• 1.3 Ernest Rutherford, described by many as the father of nuclear of physics, suggested famously that “all science is either physics or stamp collecting.” Discuss how modern biology is stamp collecting. Then think again, and discuss how modern biology is more than just stamp collecting.
• 1.4 I’ve suggested that there is no such thing as a dumb question. But do you agree? In terms of biophysics and the physics of life, are there some things which are so obvious that any questions concerning them really are stupid?

References