Biocurious

While surfing the internet one evening, I stumbled upon a fascinating website that will interest readers of the 4th edition of Intermediate Physics for Medicine and Biology. It is called “Biocurious, a biophysics blog.”

Biocurious is a weblog about biology (and physics, grad school, and miscellenaeous other things!) through the eyes of physicists.

As best I can tell, Biocurious is maintained entirely by two graduate students, Andre Brown of the University of Pennsylvania and Philip Johnson of the University of Toronto. The blog is interesting, well-written, and provides insight into the interface between physics and biology, as well as the lifestyle of biological physics grad students. One enjoyable feature of this site is the “molecule of the month” (from the protein data bank), and another is the extended list of other related blogs, which I have only begun to explore. I particularly like their header image, a picture by David Goodsell of a macrophage and bacterium at a magnification of 2,000,000.

Nice blog, Andre and Philip.

PHY 325

This fall, I am teaching PHY 325, Biological Physics, at Oakland University. Of course, the textbook is the 4th edition of Intermediate Physics for Medicine and Biology. You can follow along on the class website, which includes the syllabus, homework assignments, exams, interesting links, and a section called “hot news” that keeps track of up-to-date news for the class, including homework due dates, exam information, etc. We’ll cover the first ten chapters of the book.

Class starts on Wednesday, September 3, at 8 A.M. sharp (I’I'mm a morning person, and I guess the students will have to put up with waking early this semester, too). Welcome to all my PHY 325 students, including premed students, physics majors, and students in the new Engineering Biology program at Oakland.

Still More From The Preface

From the Preface.

The Fourth Edition [of Intermediate Physics for Medicine and Biology] follows the tradition of earlier editions. The book now has a second author: Bradley J. Roth of Oakland University. Both of us have enjoyed this collaboration immensely. We have added a chapter on sound and ultrasound, deleting or shortening topics elsewhere, in order to keep the book only slightly longer than the Third Edition. Some of the deleted material is available at the book’s website: https://sites.google.com/view/hobbieroth.

The Fourth Edition has 44% more end-of-chapter problems than the Third Edition; most highlight biological applications of the physical principles. Many of the problems extend the material in the text. A solutions manual is available to those teaching the course. Instructors can use it as a reference or provide selected solutions to their students. The solutions manual makes it much easier for an instructor to guide an independent-study student. Information about the Solutions Manual is available at the book’s website...

Biophysics is a very broad subject. Nearly every branch of physics has something to contribute, and the boundaries between physics and engineering are blurred. Each chapter could be much longer; we have attempted to provide the essential physical tools. Molecular biophysics has been almost completely ignored: excellent texts already exist, and this is not our area of expertise. This book has become long enough.

We would appreciate receiving any corrections or suggestions for improving the book.

Powers of Ten

Powers of Ten,
by Philip and Phylis Morrison,
and the Office of Charles and Ray Eames.

One of my favorite books is Powers of Ten by Philip Morrison, Phylis Morrison, and the Office of Charles and Ray Eames. The authors describe their book in a section called “Advice to the Reader.”

The core of this book is the scenes on the forty-two right-hand pages that follow. By themselves, they present a visual model of our current knowledge of the universe, showing along one straight line both the large and the small. Each image stands against a black background, a little reminiscent of a darkened theater. Across from every black-framed page is a page of text and picture, a pause at each step along the journey to examine detail, evidence, or the history of knowledge.

The step from one scene to its neighbor is always made a tenfold change: The edge of each square represents a length ten times longer or shorter than that of its two neighbors. The small central square frames the scene next inward.

Stephen Jay Gould said of the book “The effect is stunning and teaches more about the size of things than any turgid treatise could.”

Powers of Ten was based on an earlier film by the Office of Charles and Ray Eames of the same title, which can be viewed on YouTube. The film is based on an earlier book, Cosmic View: The Universe in Forty Jumps, by the Dutch educator Kees Boeke.

Powers if Ten.

https://www.youtube.com/watch?v=55Gpm1Q0abk

As I discussed in the October 12, 2007 entry in this blog, Russ Hobbie and I added a section on Distances and Sizes to the 4th edition of Intermediate Physics for Medicine and Biology, motivated in part by Powers of Ten. We find the ability to imagine the relative sizes of biological objects to be crucial for understanding life.

You don't have to buy Powers of Ten to enjoy it (although your money will be well spent if you do). At a website based on the book you can view many of the pictures and find other interesting items. For instance, thumbnail pictures at each power of ten have been collected into a poster, so you can view the different scales of the universe all at once. And Nickelodeon Magazine has even turned these pictures into a child's “Powers of Ten Game.”

Charles and Ray Eames were best known not as scientists or science educators, but as designers. Just recently, the United States Postal Service issues a series of stamps highlighting their work. Philip Morrison was a well-known and respected MIT physicist.

On Being The Right Size

On Being the Right Size,
by J. B. S. Haldane.

Problem 28 of Chapter 2 in the 4th edition of Intermediate Physics for Medicine and Biology asks the student to calculate the terminal speed of a spherical animal falling under the influence of gravity and air friction. After solving the problem, the student finds that large animals fall faster because the gravitational force increases with volume (as radius cubed) while the frictional force increases with surface area (as radius squared). At the end of the problem, Hobbie and I quote J. B. S. Haldane (1892–1964) from his essay “On Being The Right Size.”

You can drop a mouse down a thousand-yard mine shaft; and arriving at the bottom, it gets a slight shock and walks away. A rat is killed, a man is broken, and a horse splashes.

Haldane’s essay addresses the general topic of scaling, which we discuss in Chapter 2. Another excerpt from “On Being The Right Size” provides insight into how scaling affects body shape.

Consider a giant man sixty feet high—about the height of Giant Pope and Giant Pagan in the illustrated Pilgrim’s Progress of my childhood. These monsters were not only ten times as high as Christian, but ten times as wide and ten times as thick, so that their total weight was a thousand times his, or about eighty to ninety tons. Unfortunately the cross-sections of their bones were only a hundred times those of Christian, so that every square inch of giant bone had to support ten times the weight borne by a square inch of human bone. As the human thigh-bone breaks under about ten times the human weight, Pope and Pagan would have broken their thighs every time they took a step. This was doubtless why they were sitting down in the picture I remember. But it lessons one’s respect for Christian and Jack the Giant Killer.

According to Wikipedia, the normal-sized Christian is “the protagonist in the First Part [of John Bunyan’s Pilgrim’s Progress], whose journey to the Celestial City is the plot of the story.” I’ve found a picture of Pope and Pagan (sitting, of course), but I don’t know if it’s the one Haldane grew up with.

The copy of On Being The Right Size and Other Essays in the Oakland University library contains an introduction by John Maynard Smith, in which he describes Haldane.

As a scientist, Haldane will be remembered for his contribution to the theory of evolution. Today, Darwin’s theory of natural selection and Mendel’s theory of genetics are so intimately joined together in “neo-Darwinism” that is hard to image that, after the rediscovery of Mendel’s laws in 1900, the two theories were seen as rivals. Haldane, together with R. A. Fisher and Sewell Wright, showed that they were compatible, and developed the theory of population genetics which still underpins all serious thinking about evolution. However, although it is not hard to identify Haldane’s major contributions to science, he is in other respects somewhat difficult to classify. A liberal individualist, he was best known as a leading communist and contributor of a weekly article to the Daily Worker. A double first in classics and mathematics at Oxford, he made his name in biochemistry and genetics. A captain of the Black Watch who admitted to rather enjoying the First World War, he spent the end part of his life in India writing in defense of non-violence.

A Dozen of My Favorite New Homework Problems

The 4th edition of Intermediate Physics for Medicine and Biology contains 44% more homework problems than did the 3rd Edition. What are some of these new problems about? Here are a dozen of my favorites:

Chapter 1, Problem 25: Poisson’s ratio

Chapter 4, Problem 22: MRI Diffusion Tensor Imaging

Chapter 4, Problem 23: The effect of buffers on the intracellular diffusion of calcium

Chapter 5, Problem 6: Osmotic pressure in articular cartilage

Chapter 5, Problem 17: Countercurrent heat exchangers

Chapter 7, Problem 30: Clark and Plonsey’s calculation of the intracellular and extracellular potential of a nerve axon

Chapter 8, Problem 17: The magnetic field produced by a planar action potential wave front in anisotropic cardiac tissue

Chapter 9, Problem 9: An analytical solution to the nonlinear Poisson-Boltzmann equation

Chapter 10, Problem 37: Ventricular fibrillation of the heart, chaos, and action potential restitution

Chapter 10, Problem 39: A cellular automata model for cardiac arrhythmias

Chapter 12, Problem 23: Analytical example of how to calculate an image from its projection using the method of reconstruction by Fourier transform

Chapter 18, Problem 18: The “magic angle” in MRI

Many of these twelve problems are more difficult than average for our book, but undergraduate physics majors should be able to handle them all. Often we introduce new concepts in the problems. For instance, Poisson’s ratio is never discussed in the text, but other biomechanics topics are, and Problem 25 of Chapter 1 introduces Poisson’s ratio by relating it to concepts we introduced previously.

If you want to get the most out of the 4th edition of Intermediate Physics for Medicine and Biology, work the problems. Otherwise, you may miss some new and fascinating applications of physics to the biomedical sciences.

PhysicsCentral

The American Institute of Physics has a website for the public called PhysicsCentral (http://www.physicscentral.com). The purpose of the site is to help you “learn how your world works.” According to the July 2008 issue of the APS News, the site was redesigned recently to include podcasts and vodcasts, blogs and RSS feeds, and other interactive new features. The website describes its mission.

The American Physical Society represents some 45,000 physicists, and most of our work centers on scientific meetings and publications—the primary ways that physicists communicate with each other. With PhysicsCentral, we communicate the excitement and importance of physics to everyone. We invite you to visit our site every week to find out how physics is part of your world. We’ll answer your questions on how things work and keep you informed with daily updates on physics in the news. We'll describe the latest research and the people who are doing it and, if you want more, where to go on the web. So stick with us. It’s a big, interesting world out there, and we look forward to showing you around.

Of particular interest to readers of the 4th edition of Intermediate Physics for Medicine and Biology is the Biology and Medicine Section of the site. Here you can find fascinating stories about medical and biological physicists, concise descriptions about the frontiers of research, and beautiful pictures. For instance, the current featured story is “The Theory of Everything...Everything Alive!” that describes the work of physicist Geoffrey West on scaling, a topic discussed in Chapter 2 of Intermediate Physics for Medicine and Biology. Students at all levels will find much to inspire and interest them. Take a look at what all the excitement is about, and have fun.

Max Delbruck, Biological Physicist

Niels Bohr's Times:
In Physics, Philosophy, and Polity,
by Abraham Pais.

Last week, I discussed the book Niels Bohr's Times: In Physics, Philosophy, and Polity by Abraham Pais. In particular, I summarized Pais’s view that Bohr played a key role in the development of nuclear medicine through his collaboration with Georg Charles von Hevesy. This week, I address another contribution of Bohr to biological physics through his influence on Max Delbruck.

Bohr had some unorthodox views about biology that were motivated by his idea of “complementarity” in quantum mechanics. Even Pais admits Bohr’s “thoughts on biology have not borne fruit,” which is a polite way to put it. But Delbruck, then a young physicist, wrote “I am perhaps the only one of his associates of those days who took [Bohr] so seriously that it determined [my] career, changing over into biology to find out whether indeed there was anything to this point of view.” Pais writes

Delbruck’s professional switch was Bohr’s greatest contribution to biology. In an obituary of Delbruck it has been written: “Odd though these views [expressed in Bohr’s lecture ‘Light and Life’] may seem to us now, in retrospect, this lecture confirmed Max’s decision to turn to biology... It is fair to say that with Max, Bohr found his most influential philosophical disciple outside the domain of physics, in that through Max, Bohr provided one of the intellectual fountainheads for the development of 20th century biology...”

[Delbruck’s] celebrated work on bacteriophages (viruses that infect bacteria) began after his move to Cal Tech in 1937, where he became professor of biology in 1946. It is worthy of note that, in the 1963 meeting at Copenhagen commemorating the 50th anniversary of Bohr’s first papers on atomic constitution, only one paper on complementarity was presented—by Delbruck, on biology. He received the Nobel Prize in 1969.

Delbruck, a German native, spent the years during World War II with the Department of Physics at Vanderbilt University in Nashville, Tennessee (where I later obtained my PhD). While at Vanderbilt, Delbruck collaborated with Salvadore Luria on an experiment using bacteriophages to show that mutations in viruses are random rather than directed events. The American Physical Society has named its prize in biological physics the Max Delbruck Prize for his work on genetics.

Why do I discuss Bohr, Hevesy and Delbruck in a blog about the 4th edition of Intermediate Physics for Medicine and Biology? Because they represent classic examples of how physics and physicists can make fundamental and lasting contributions to medicine and biology. And that is the whole point of the book.

Georg Charles von Hevesy

Niels Bohr’s Times:
In Physics, Philosophy, and Polity,
by Abraham Pais.

Recently I finished reading the biography Niels Bohr’s Times: In Physics, Philosophy, and Polity, by Abraham Pais. It is an excellent book, but not quite as good as Pais’s masterpiece, Subtle Is the Lord: The Science and the Life of Albert Einstein. Although I was familiar with Bohr’s research in atomic and nuclear physics, I was surprised to discover his pioneering role (perhaps more as a fund raiser, administrator, and mentor than researcher) in medical and biological physics.

Much of this research was in collaboration with Georg Charles von Hevesy (1885–1966). Pais writes “The work of Hevesy in the 1930s at Bohr’s institute made isotope tracers methods flourish. And so Bohr became the godfather, and Hevesy the father, of nuclear medicine.” Hevesy was a Hungarian of Jewish descent who was a professor in Germany in the 1930s until “he left Freiburg because of his disgust with the Nazi regime.” In 1934 he joined Bohr in Copenhagen. Hevesy began using heavy radioactive isotopes to study the uptake and loss of elements. In Pais’s words, Hevesy made

the first application anywhere of tracers in the life sciences... This led Hevesy to tracer research... on the resorption, distribution, and excretion of labeled bismuth compounds administered to rats, the first use of tracers in the study of animal metabolism...

In 1948 Hevesy wrote: “During our early work with natural radioisotopes as indicators, we often mentioned what an attractive place that Fairyland must be where radioactive isotopes of all elements are available. This utopia became reality almost in a single stroke, when the Joliot-Curies made their most important discovery of artificial radioactivity [man-made radioactive isotopes]. The path was thus paved for investigation of the fate of the atoms of the common constituents of the animal and plant organisms...”

Hevesy was 50 years old in 1935 when he turned his attention to applications of induced radioactivity. That year marks the beginning of the most important phase in his scientific career. [An inspiring thought to this 47-year-old writer.] From then on he very rarely published anything in physics; nearly all his further oeuvre, over 200 papers, deal with tracers in biology. That work was more influential than anything he had done before...

Hevesy certainly added to the life in Copenhagen. There is the story of the radioactive cat that had jumped out of a window of the institute for theoretical physics and was retrieved only after hours of hunting for it in the nearby park, when saliva tests on about a dozen captured cats showed one of them to be radioactive...

In 1944 Hevesy was awarded the 1943 Nobel Prize in chemistry “for his work on the use of isotopes as tracers in the study of chemical processes...”

In the post-war period the development of nuclear reactors provided for vastly enlarged production of radioisotopes. This in turn made possible much wider application of the tracer method in medicine. In hospitals all over the world one now finds special departments for nuclear medicine, a discipline which unquestionably was founded by Hevesy. Also from that period dates the use of numerous biological tracers with half-lives much longer that that of the popular P-32, notably the carbon isotope C-14 discovered in 1940.

Chapter 17 of the 4th edition of Intermediate Physics for Medicine and Biology discusses nuclear medicine, and the work of those “special departments for nuclear medicine.” Pais’s excellent biography makes clear that these important medical applications arose from the pioneering work of Neils Bohr and Georg Charles von Hevesy. Next week: the story continues, with more on Neils Bohr’s impact on biological physics.

Numerical Computing

My research involves computer simulations, so I spend a lot of time implementing numerical algorithms. I view a numerical technique as a tool for solving a problem, not as something intrinsically interesting itself. But as a numerical modeler it pays to become familiar with your tools, so I have.

The first question is which programming language to use? I use FORTRAN, and I’m sure that makes me a dinosaur in the eyes of many. But FORTRAN is still common among physicists, and has served me well since I first learned it as a senior in high school. If you look in the solution manual for the 4th edition of Intermediate Physics for Medicine and Biology, you will find a few programs written in FORTRAN. Russ Hobbie humored me by letting me write these in FORTRAN rather than C, although C appears in the textbook itself.

Numerical Recipes:
The Art of Scientific Computing,
by Press et al.

I tend to avoid software like Matlab, Mathematica, and Maple as being to “black-boxy.” I like to tinker with the guts of my program, and often you can’t do that with high-level software packages. Perhaps younger scientists disagree. I do use Matlab for graphics.

When I face a numerical problem that is new to me, the first place I look is Numerical Recipes: The Art of Scientific Computing, by Press, Teukolsky, Vetterling, and Flannery . The copy on my bookshelf is the 2nd edition of Numerical Recipes in FORTRAN 77: The Art of Scientific Computing. In the preface Press et al. write

We call this book “Numerical Recipes” for several reasons. In one sense, the book is indeed a “cookbook” on numerical computation. However there is an important distinction between a cookbook and a restaurant menu. The latter presents choices among complete dishes in each of which the individual flavors are blended and disguised. The former—and this book—reveals the individual ingredients and explains how they are prepared and combined.

Numerical Methods That Work,
by Forman Acton.

For a guide to some of the lore of numerical computing, I recommend two delightful books by Forman Acton: Numerical Methods that Work, and Real Computing Made Real: Preventing Errors in Scientific and Engineering Calculations. In Real Computing, Acton writes

This book addresses errors of the third kind. You’ve never heard of them? But you've made them; we all make them every time we write a computer program to solve a physical problem.

Errors of the first kind are grammatical—we write things that aren’t in our programming language. The compiler finds them.

Errors of the second kind are our mistakes in programming the algorithms we sought to use. They include n−1 errors, inversions of logical tests, overwriting array limits (in Fortran) and a lot of other little technical mistakes that just don’t happen to be ungrammatical. We have to find them.

Then, Mirabile visu, the program runs—and even gives the correct answers to the two test problems we happen to have already solved.

Errors of the third kind are the ones we haven’t found yet. They show up only for as-yet-untested input values—often for quite limited ranges of these parameters. They include (but are not limited to) loss of significant digits, iterative instabilities, degenerative inefficiences in algorithms and convergence to extraneous roots or previously docile equations. Since some of these errors occur only for limited combinations of parameters inputs they may never disturb our results; more likely some of them will creep into our answers, but so quietly that we don't notice them—until our bridge has collapsed!

Real Computing Made Real,
by Forman Acton.

In the rest of the book, Acton serves up a feast of tricks, tips, and techniques. Even if you don’t particularly like numerical methods, you will enjoy these books. Readers of Intermediate Physics for Medicine and Biology will find them useful when trying to write a computer program to solve the Hodgkin and Huxley equations or implement the Fourier method for computed tomography.

I end with a quote from Acton’s book that he attributes to Richard Hamming. It is one of my favorite quotes, and one I believe is worth repeating:

The purpose of computing is insight, not numbers.