Friday, February 12, 2016

Perspectives on Working at the Physics-Biology Interface

The cover of the journal Physical Biology, containing the special issue Perspectives on Working at the Physics-Biology Interface, by Howard Berg and Krastan Blagoev.
Physical Biology.
A few weeks ago, I wrote that “I’ve always been fascinated by physicists who move into biology, and I collect stories about scientists who have made this transition successfully.” Imagine my delight when I discovered a special issue of the journal Physical Biology about “Perspectives on Working at the Physics-Biology Interface.” Howard Berg and Krastan Blagoev collected many stories about physicists working in biology. In their introductory editorial, they write
Physics is analytical, heavily dependent on mathematical equations; biology is more descriptive, heavily dependent on historical facts. There is a cultural gap. In physics, a theorist who can interpret others' experimental results is revered. In biology, such a person is suspect: ideas are thought cheap, facts dear.

But cultures can change. As problems in physics have become more difficult and more expensive to solve, or have been solved and thus are less interesting, physicists have begun to explore more complex areas of endeavor, including biology. Biologists, on the other hand, have begun to appreciate the benefits of thinking more quantitatively about their data. We thought it would be of interest to hear from physicists who have negotiated this cultural gap. What did they find challenging about biology, and how did they manage to begin work in such a different field? What advice might they have for younger practitioners of the art? One of us (HCB) moved long ago from work on hydrogen masers to studies of the motile behavior of bacteria. His trajectory is given in an interview published in Current Biology [1].

Some of our contributors have been involved with biophysics since their PhD, several were trained in condensed-matter theory, and others in nuclear or high-energy particle physics. Their interests range from the structure of proteins, RNA, or natural products, to cognitive or social abilities of bacteria, to emergent properties of complex or active media, or to the behavior of immune systems or neural networks. They all have interesting points of view, some subdued, others outspoken. We hope you enjoy the mix. Our hope is that with this issue we are able to capture the situation at the beginning of the 21st Century and to follow with another issue of this kind in ten years time.
Below I list all the papers in this special issue, along with their abstracts. I hope readers of Intermediate Physics for Medicine and Biology will find them as inspiring as I did.

The emergence of a new kind of biology by Harold J Morowitz

“It is happily no longer axiomatic that a biophysicist is a physiologist who can fix his own amplifier. Fortunately, physicists are still drifting into biology and bringing new ideas. Please dear colleagues, do take the time to learn biochemistry.” Harold Morowitz provides a personal perspective on working at the interface between the physical and biological sciences.

Two cultures? Experiences at the physics-biology interface by John J Hopfield

“I didn’t really think of this as moving into biology, but rather as exploring another venue in which to do physics.” John Hopfield provides a personal perspective on working on the border between physical and biological sciences.

A Perspective: Robert B Laughlin by Robert B Laughlin

Despite their cultural differences, physics and biology are destined to interact with each other more in the future. The reason is that modern physics is fundamentally about codification of emergent law, and life is the greatest of all emergent phenomena.

Ask not what physics can do for biology—ask what biology can do for physics by Hans Frauenfelder

Stan Ulam, the famous mathematician, said once to Hans Frauenfelder: “Ask not what Physics can do for biology, ask what biology can do for physics.” The interaction between biologists and physicists is a two-way street. Biology reveals the secrets of complex systems, physics provides the physical tools and the theoretical concepts to understand the complexity. The perspective gives a personal view of the path to some of the physical concepts that are relevant for biology and physics (Frauenfelder et al 1999 Rev. Mod. Phys. 71 S419–S442). Schrödinger's book (Schrödinger 1944 What is Life? (Cambridge: Cambridge University Press)), loved by physicists and hated by eminent biologists (Dronamraju 1999 Genetics 153 1071–6), still shows how a great physicist looked at biology well before the first protein structure was known.

Universal relations in the self-assembly of proteins and RNA by D Thirumalai

Concepts rooted in physics are becoming increasingly important in biology as we transition to an era in which quantitative descriptions of all processes from molecular to cellular level are needed. In this perspective I discuss two unexpected findings of universal behavior, uncommon in biology, in the self-assembly of proteins and RNA. These findings, which are surprising, reveal that physics ideas applied to biological problems, ranging from folding to gene expression to cellular movement and communication between cells, might lead to discovery of universal principles operating in adoptable living systems.

Physics transforming the life sciences by José N Onuchic

Biological physics is clearly becoming one of the leading sciences of the 21st century. This field involves the cross-fertilization of ideas and methods from biology and biochemistry on the one hand and the physics of complex and far from equilibrium systems on the other. Here I want to discuss how biological physics is a new area of physics and not simply applications of known physics to biological problems. I will focus in particular on the new advances in theoretical physics that are already flourishing today. They will become central pieces in the creation of this new frontier of science.

Research at the interface of physics and biology: bridging the two fields by Kamal Shukla

I firmly believe that interaction between physics and biology is not only natural, but inevitable. Kamal Shukla provides a personal perspective on working at the interface between the physical and biological sciences.

Let’s not forget plants by Athene Donald

“Many physicists see the interface with biology as an exciting place to be.” Athene Donald provides a personal perspective on working at the interface between the physical and biological sciences.

My encounters with bacteria—learning about communication, cooperation and choice by Eshel Ben-Jacob

My journey into the physics of living systems began with the most fundamental organisms on Earth, bacteria, that three decades ago were perceived as solitary, primitive creatures of limited capabilities. A decade later this notion had faded away and bacteria came to be recognized as the smart beasts they are, engaging in intricate social life through a sophisticated chemical language. Acting jointly, these tiny organisms can sense the environment, process information, solve problems and make decisions so as to thrive in harsh environments. The bacterial power of cooperation manifests in their ability to develop large colonies of astonishing complexity. The number of bacteria in a colony can amount to many billions, yet they exchange 'chemical tweets' that reach each and every one of them so they all know what they're all doing, each cell being both actor and spectator in the bacterial Game of Life. I share my encounters with bacteria, what I learned about the secrets of their social life and wisdom of the crowd, and why and how, starting as a theoretical physicist, I found myself studying social intelligence of bacteria. The story ends with a bacteria guide to cyber-war on cancer.

Working together at the interface of physics and biology by Bonnie L Bassler and Ned S Wingreen

Good communication, whether it is between quorum-sensing bacteria or the different scientists studying those critters, is the key to a successful interdisciplinary collaboration, Bonnie Bassler and Ned Wingreen provide a personal perspective on working at the interface between the physical and biological sciences.

Learning physics of living systems from Dictyostelium by Herbert Levine

Unlike a new generation of scientists that are being trained directly to work on the physics of living systems, most of us more senior members of the community had to find our way from other research areas. We all have our own stories as to how we made this transition. Here, I describe how a chance encounter with the eukaryotic microorganism Dictyostelium discoideum led to a decades-long research project and taught me valuable lessons about how physics and biology can be mutually supportive disciplines.

Letting the cat out of the bag: a personal journey in Biophysics by Carlos J Bustamante

When the author arrived in Berkeley, in the mid 1970s, to study Biophysics he soon felt as if he was engaging himself in a somewhat marginal activity. Biology was then entering another of its cyclical periods of annotation that was to culminate with the human genome project. Two decades later, however, at the end of this process, it had become clear that two main tasks were acquiring a central importance in biological research: a renewed push for a quantitative, precise description of biological systems at the molecular level, and efforts towards an integrated understanding of the operation, control, and coordination of cellular processes. Today, these have become two of the most fertile research areas in Biophysics.

A theoretical physicist’s journey into biology: from quarks and strings to cells and whales by Geoffrey B West

Biology will almost certainly be the predominant science of the twenty-first century but, for it to become successfully so, it will need to embrace some of the quantitative, analytic, predictive culture that has made physics so successful. This includes the search for underlying principles, systemic thinking at all scales, the development of coarse-grained models, and closer ongoing collaboration between theorists and experimentalists. This article presents a personal, slightly provocative, perspective of a theoretical physicist working in close collaboration with biologists at the interface between the physical and biological sciences.

Understanding immunology: fun at an intersection of the physical, life, and clinical sciences by Arup K Chakraborty

Understanding how the immune system works is a grand challenge in science with myriad direct implications for improving human health. The immune system protects us from infectious pathogens and cancer, and maintains a harmonious steady state with essential microbiota in our gut. Vaccination, the medical procedure that has saved more lives than any other, involves manipulating the immune system. Unfortunately, the immune system can also go awry to cause autoimmune diseases. Immune responses are the product of stochastic collective dynamic processes involving many interacting components. These processes span multiple scales of length and time. Thus, statistical mechanics has much to contribute to immunology, and the oeuvre of biological physics will be further enriched if the number of physical scientists interested in immunology continues to increase. I describe how I got interested in immunology and provide a glimpse of my experiences working on immunology using approaches from statistical mechanics and collaborating closely with immunologists.

Rejoice in the hubris: useful things biologists could do for physicists by Robert H Austin

Political correctness urges us to state how wonderful it is to work with biologists and how, just as the lion will someday lie down with the lamb, so will interdisciplinary work, where biologists and physicists are mixed together in light, airy buildings designed to force socialization, give rise to wonderful new science. But it has been said that the only drive in human nature stronger than the sex drive is the drive to censor and suppress, and so I claim that it is OK for physicists and biologists to maintain a wary distance from each other, so that neither one censors or suppresses the wild ideas of the other.
One of my favorite quotes is from Morowitz’s paper: “Like many physicists, Gamov was impatient with biochemical nomenclature and for adenine, thymine, guanine, and cytosine he substituted hearts, spades, clubs, and diamonds.” Many of the papers reinforce the need for tight collaborations with biologists, and the need to learn some biology. I agree with that view, but it was nevertheless a guilty delight to read Robert Austin’s article, in which the old physics hubris takes center stage. Read it, but don’t tell anyone that you did.

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