Friday, October 12, 2018

A Trick to Generate Exam Problems

Intermediate Physics for Medicine and Biology.
Intermediate Physics for Medicine and Biology.
When teaching a class based on Intermediate Physics for Medicine and Biology, instructors need to write problems for their exams. My goal in this post is to explain a trick for creating good exam problems. 

One of my favorite homework problems in IPMB is from Chapter 4.
Problem 37. The goal of this problem is to estimate how large a cell living in an oxygenated medium can be before it is limited by oxygen transport. Assume the extracellular space is well stirred with uniform oxygen concentration C0. The cell is a sphere of radius R. Inside the cell oxygen is consumed at a rate Q molecule m−3 s−1. The diffusion constant for oxygen in the cell is D.
(a) Calculate the concentration of oxygen in the cell in the steady state.
(b) Assume that if the cell is to survive the oxygen concentration at the center of the cell cannot become negative. Use this constraint to estimate the maximum size of the cell.
(c) Calculate the maximum size of a cell for C0 = 8 mol m−3, D = 2 x 10−9 m2 s−1, Q = 0.1 mol m−3 s−1. (This value of Q is typical of protozoa; the value of C0 is for air and is roughly the same as the oxygen concentration in blood.)
Homework problems for Chapter 4 in Intermediate Physics for Medicine and Biology.
Homework problems for Chapter 4 in Intermediate Physics for Medicine and Biology.
I usually work this problem in class. Not only does the student practice solving the steady-state diffusion equation, but also she estimates the maximum size of a cell from some basic properties of oxygen. In the Solution Manual—available to instructors only (email us)—we explain the purpose of each problem in a preamble. Here is what the solution manual says about Problem 37:
This important “toy model” considers the maximum size of a spherical cell before its core dies from lack of oxygen. One goal of biological physics is to show how physics constrains evolution. In this case, the physics of diffusion limits how large an animal can be before needing a circulatory system to move oxygen around.
How do you create an exam problem on this subject? Here's the trick: Do Problem 37 in class and then put a question on the exam identical to Problem 37 except “sphere” is replaced by “cylinder”. The problem is only slightly changed; just enough to determine if the student is solving the problem from first principles or merely memorizing. In addition, nerve and muscle fibers are cylindrical, so the revised problem may provide an even better model for those cells. Depending on the mathematical abilities of your students, you may need to provide students with the Laplacian in cylindrical coordinates. (If the exam is open book then they can find the Laplacian in Appendix L).

Here's a second example: Chapter 1 considers viscous flow in a tube; Poiseuille flow. On the exam, ask the student to analyze viscous flow between two stationary plates.
Section 1.17
Problem 36 ½. Consider fluid flow between two stationary plates driven by a pressure gradient. The pressure varies in the x direction with constant gradient dp/dx, the plates are located at y = +L and y = -L, and the system is uniform in the z direction with width H. The fluid has viscosity η.

(a) Draw a picture the geometry.
(b) Consider a rectangular box of fluid centered at the origin and derive a differential equation like Eq. 1.35 governing the velocity vx(y).

(c) Solve this differential equation to determine vx(y), analogous to Eq. 1.37. Assume a no-slip boundary condition at the surface of each plate. Plot vx(y) versus y.

(d) Integrate the volume fluence and find the total flow i. How does i depend on the plate separation, 2L? How does this compare to the case of flow in a tube?
An interesting feature of this example is that i depends on the third power of L, whereas for a tube it depends on the fourth power of the radius. Encourage the student to wonder why.

Third example: A problem in Chapter 7 compares three different functions describing the strength-duration curve for electrical stimulation. On your exam, have the students analyze a fourth case.
Section 7.10

Problem 46 ½. Problem 46 analyzes three possible functions that could describe the strength-duration curve, relating the threshold current strength required for neural excitation, i, to the stimulus pulse duration, t. Consider the function i = A/tan-1(t/B). Derive expressions for the rheobase iR and chronaxie tC in terms of A and B. Write the function in the form used in Problem 46. Plot i versus t.
And still more: Problem 32 in Chapter 8 examines magnetic stimulation of a nerve axon using an applied electric field Ei(x) = E0 a2/(x2 + a2). Give a similar problem on your exam but use a different electric field, such as Ei(x) = E0 exp(-x2/a2).

And yet another: Chapter 10 examines the onset of cardiac fibrillation and chaos. The action potential duration APD is related to the diastolic interval (time from the end of the previous action potential to the start of the following one) DI by the restitution curve. Have the student repeat Problem 41 but using a different restitution curve: APDi+1 = 300 DIi/(DIi + 100).

Final example: Problem 36 in Chapter 9 asks the student to calculate the electrical potential inside and outside a spherical cell in the presence of a uniform electric field (Figure 9.19). On your exam, make the sphere into a cylinder.

I think you get the point. On an exam, repeat one the of homework problems in IPMB, but with a twist. Change the problem slightly, using a new function or a modified geometry. You will be able to test the knowledge and understanding of the student without springing any big surprises on the exam. Many problems in IPMB that could be modified in this way.

Warning: This trick doesn't always work. For instance, in Chapter 1 if you try to analyze fluid flow perpendicular to a stationary object, you run into difficulties when you change the sphere of Problem 46 into a cylinder, The cylindrical version of this problem has no solution! The lack of a solution for low Reynolds number flow around a cylinder is known as Stokes' Paradox. In that case, you're just going to have to think up your own exam question.

Friday, October 5, 2018

A Bidomain Model for the Extracellular Potential and Magnetic Field of Cardiac Tissue

My research notebooks from graduate school.
My research notebooks from graduate school.
In graduate school, I worked with John Wikswo measuring the magnetic field of a nerve axon. We isolated a crayfish axon and threaded it through a wire-wound ferrite-core toroid immersed in saline. As the action currents propagated by, they produced a changing magnetic field that induced a signal in the toroid by Faraday induction. Ampere’s law tells us that the signal is proportional to the net current through the toroid, which is the sum of the intracellular current and the fraction of the current in the saline that passes through the toroid, called the return current.

For my PhD dissertation, Wikswo had me make similar measurements on strands of cardiac tissue, such as a papillary muscle. The instrumentation was the same as for the nerve, but the interpretation was different. Now the signal had three sources: the intracellular current, the return current in the saline, and extracellular current passing through the interstitial space within the muscle called the "interstitial return current." Initially neither Wikswo nor I knew how to calculate the interstitial return current, so we were not sure how to interpret our results. As I planned these experiments, I recorded my thoughts in my research notebook. The July 26, 1984 entry stressed that "Understanding this point [the role of interstitial return currents] will be central to my research and deserves much thought."

Excerpt from the July 26, 1984 entry in my Notebook 8, page 64.
When working on nerves, I had studied articles by Robert Plonsey and John Clark, in which they calculated the extracellular potential in the saline from the measured voltage across the axon's membrane: the transmembrane potential. I was impressed by this calculation, which involved Fourier transforms and Bessel functions (see Chapter 7, Problem 30, in Intermediate Physics for Medicine and Biology). I had used their result to calculate the magnetic field around an axon (see Chapter 8, Problem 16 in IPMB), so I set out to extend their analysis again to include interstitial return currents.

Page 1 of Notebook 9, from Sept 13, 1984.
Page 1 of Notebook 9, from Sept 13, 1984.
The key was to use the then-new bidomain model, which accounts for currents in both the intracellular and interstitial spaces. The crucial advance came in September 1984 after I read a copy of Les Tung's PhD dissertation that Wikswo had loaned me. After four days of intense work, I had solved the problem. My results looked a lot like those of Clark and Plonsey, except for a few strategically placed additional factors and extra terms.
Excerpt from Notebook 9, page 13, the Sept 16, 1984 entry.
First page of Roth and Wikswo (1986) IEEE Trans. Biomed. Eng., 33:467-469.
First page of Roth and Wikswo (1986).
Wikswo and I published these results as a brief communication in the IEEE Transactions on Biomedical Engineering.
Roth, B. J. and J. P. Wikswo, Jr., 1986, A bidomain model for the extracellular potential and magnetic field of cardiac tissue. IEEE Trans. Biomed. Eng., 33:467-469.

Abstract—In this brief communication, a bidomain volume conductor model is developed to represent cardiac muscle strands, enabling the magnetic field and extracellular potential to be calculated from the cardiac transmembrane potential. The model accounts for all action currents, including the interstitial current between the cardiac cells, and thereby allows quantitative interpretation of magnetic measurements of cardiac muscle.
Rather than explain the calculation in all its gory detail, I will ask you to solve it in a new homework problem.
Section 7.9
Problem 31½. A cylindrical strand of cardiac tissue, of radius a, is immersed in a saline bath. Cardiac tissue is a bidomain with anisotropic intracellular and interstitial conductivities σir, σiz, σor, and σoz, and saline is a monodomain volume conductor with isotropic conductivity σe. The intracellular and interstitial potentials are Vi and Vo, and the saline potential is Ve.
a) Write the bidomain equations, Eqs. 7.44a and 7.44b, for Vi and Vo in cylindrical coordinates (r,z). Add the two equations.
b) Assume Vi = σiz/(σiz+σoz) [A I0(kλr) + (σoz/σiz) Vm] sin(kz) and Vo = σiz/(σiz+σoz) [A I0(kλr) - Vm] sin(kz) where λ2 = (σiz+σoz)/(σir+σor). Verify that Vi - Vo equals the transmembrane potential Vm sin(kz). Show that Vi and Vo obey the equation derived in part a). I0(x) is the modified Bessel function of the first kind of order zero, which obeys the modified Bessel equation d2y/dx2 + (1/x) dy/dx = y. Assume Vm is independent of r.
c) Write Laplace’s equation (Eq. 7.38) in cylindrical coordinates. Assume Ve = B K0(kr) sin(kz). Show that Ve satisfies Laplace’s equation. K0(x) is the modified Bessel function of the second kind of order zero, which obeys the modified Bessel equation.
d) At r = a, the boundary conditions are Vo = Ve and σirVi/∂r + σorVo/∂r = σeVe/∂r. Determine A and B. You may need the Bessel function identities dI0/dx = I1 and dK0/dx = - K1, where I1(x) and K1(x) are modified Bessel functions of order one.
In the problem above, I assumed the potentials vary sinusoidally with z, but any waveform can be expressed as a superposition of sines and cosines (Fourier analysis) so this is not as restrictive as it seems.

In part b), I assumed the transmembrane potential was not a function of r. There is little data supporting this assumption, but I was stuck without it. Another assumption I could have used was equal anisotropy ratios, but I didn’t want to do that (and initially I didn't realize it provided an alternative path to the solution).

The calculation of the magnetic field is not included in the new problem; it requires differentiating Vi, Vo, and Ve to find the current density, and then integrating the current to find the magnetic field via Ampere’s law. You can find the details in our IEEE TBME communication.

Some of you might be thinking “this is a nice homework problem, but how did you get those weird expressions for the intracellular and interstitial potentials used in part b)”? Our article gives some insight, and my notebook provides more. Basically I started with Clark and Plonsey's result, used ideas from Tung's dissertation, and then played with the math (trial and error) until I had a solution that obeyed the bidomain equations. Some might call that a strange way to do science, but it worked for me.

I was very proud of this calculation (and still am). It played a role in the development of the bidomain model, which is now considered the state-of-the-art model for simulating the heart during defibrillation.

Wikswo and I carried out experiments on guinea pig papillary muscles to test the calculation, but the cardiac data was not as clean and definitive as our nerve data. We published it as a chapter in Cell Interactions and Gap Junctions (1989). The cardiac work made up most of my PhD dissertation. Vanderbilt let me include our three-page IEEE TBME communication as an appendix. It's the most important three pages in the dissertation.

Coda: While browsing through my old research notebooks, I found this gem passed from Prof. Wikswo to his earnest but naive graduate student, who dutifully wrote it down in his research notebook for posterity.

Excerpt from Notebook 10, Page 62, January 3, 1985.
Excerpt from Notebook 10, Page 62.

Friday, September 28, 2018

Steven Strogatz Lectures on Youtube

Nonlinear Dynaics and Chaos, by Steven Strogatz
Nonlinear Dynamics and Chaos.
Previously (here, here, and here), I've written about Steven Strogatz, Professor of Applied Mathematics at Cornell University. Strogatz wrote one of my favorite textbooks: Nonlinear Dynamics and Chaos. Russ Hobbie and I cite it in Chapter 10 of Intermediate Physics for Medicine and Biology.

Nowadays students rarely read textbooks; they prefer watching videos. Well, I have good news. Strogatz taught a course based on his book, and his lectures are posted on YouTube. You can learn chaos straight from the horse’s mouth. You better get started: there are over 24 hours of video (all embedded below).

The second edition of Nonlinear Dynaics and Chaos, by Steven Strogatz
The 2nd Edition of Nonlinear Dynamics and Chaos.
Strogatz is an enormously successful mathematician. According to Google Scholar, his 1998 article with Duncan WattsCollective Dynamics of “Small-World” Networks (Nature, Volume 393, Pages 440-442)—has been cited over 35,000 times! His textbook has over ten thousand citations. (To put this in perspective, IPMB has 392.) He won the Lewis Thomas Prize for Writing about Science, tweets at @stevenstrogatz, and is buddies with M*A*S*H star and science communicator Alan Alda. In IPMB, Russ and I cite the first edition of Nonlinear Dynamics and Chaos, but Strogatz published a second edition in 2015.


1. Introduction and Overview

2. One Dimensional Systems

3. Overdamped Bead on a Rotating Hoop

4. Model of Insect Outbreak

5. Two Dimensional Nonlinear Systems

6. Two Dimensional Nonlinear Systems Fixed Points

7. Conservative Systems

8. Index Theory and Introduction to Limit Cycles

9. Testing for Closed Orbits

10. Van der Pol Oscillator

11. Averaging Theory for Weakly Nonlinear Oscillators

12. Bifurcations in Two Dimensional Systems

13. Hopf Bifurcations in Aeroelastic Instabilities and Chemical Oscillators

14. Global Bifurcations of Cycles

 15. Chaotic Waterwheel

16. Waterwheel Equations and Lorenz Equations

17. Chaos in the Lorenz Equations

18. Strange Attractor for the Lorenz Equations

19. One Dimensional Maps

20. Universal Aspects of Period Doubling

21. Feigenbaum's Renormalization Analysis of Period Doubling

22. Renormalization: Function Space and a Hands-on Calculation

23. Fractals and the Geometry of Strange Attractors

24. Henon Map

25. Using Chaos to Send Secret Messages

Friday, September 21, 2018

Quick Calculus

In Intermediate Physics for Medicine and Biology, Russ Hobbie and I assume the reader knows calculus. Some readers, however, have weak or rusty math skills. Is there an easy way to learn what is needed?

Quick Calculus is a self-teaching guide written by Daniel Klepner and Norman Ramsey
Quick Calculus.
Yes! Quick Calculus is a self-teaching guide written by Daniel Klepner and Norman Ramsey. Their preface states:
Before you plunge into Quick Calculus, perhaps we ought to tell you what it is supposed to do. Quick Calculus should teach you the elementary techniques of differential and integral calculus with a minimum of wasted effort on your part; it is designed for you to study by yourself. Since the best way for anyone to learn calculus is to work problems, we have included many problems in this book. You will always see the solution to your problem as soon as you have finished it, and what you do next will depend on your answer. A correct answer generally sends you to new material, while an incorrect answer sends you to further explanations and perhaps another problem.
The book covers nearly all the calculus needed in IPMB.
  • Chapter One reviews functions and graphs, emphasizing trigonometry, exponentials, and logarithms.
  • Chapter Two discusses differentiation—including the product rule and the chain rule—and maximum/minimum problems.
  • Chapter Three analyzes integration, both definite and indefinite, and covers techniques such as change of variable, integration by parts, and multiple integrals.
  • Chapter Four summarizes all the results in a few pages.
Math Book useful for Intermediate Physics for Medicine and Biology
Math Books Useful for IPMB.
The only calculus in IPMB that Quick Calculus doesn’t teach is vector calculus; for that you should consult Div, Grad, Curl and All That. Used Math covers more ground than Quick Calculus, but it is a handbook rather than a self-teaching guide.

Quick Calculus has several virtues. It is clearly written, it emphasizes understanding math visually with lots of plots, and it focuses on utilitarian techniques without distracting rigor. If you want to understand math at a fundamental level, you should take a real calculus class. If you want to brush up on what's needed to get through IPMB, use Quick Calculus.

One disadvantage is that Quick Calculus is old. The second edition—the most recent one I am aware of—was published in 1985. It might be difficult to purchase, although Amazon seems to have copies for sale. The authors make quaint comments about "readers who have an electronic calculator," as opposed to slide rules I suppose. I also found several typos, which might frustrate readers using the book for self-study.

A sample from Quick Calculus
A sample from Quick Calculus.
The format is unusual. The text is divided into approximately half-page “frames,” and the reader is guided from one frame to the next. Someone should put this book online, because it would lend itself to an interactive online format. Rather than explain how the book is organized, I've taken Section 1.17 of IPMB and rewritten it in the style of Quick Calculus (see below). In my opinion, if all of Intermediate Physics for Medicine and Biology were organized like this it would be tedious. What do you think?

Friday, September 14, 2018

Gulliver was a Bad Biologist

Gulliver's Travels
Gulliver's Travels by Jonathan Swift.
Most of my reading is nonfiction, but recently I read Jonathan Swift’s Gulliver’s Travels. The story describes Englishman Lemuel Gulliver's journeys to exotic lands, including Lilliput inhabited by tiny people, and Brobdingnag where giants live. Swift was a delightful and funny writer, but Florence Moog claims Gulliver was a Bad Biologist (Scientific American, Volume 179, November 1948, Pages 52-55). The problem is scaling, which Russ Hobbie and I discuss in Chapter 2 of Intermediate Physics for Medicine and Biology. The properties of animals change as they get bigger or smaller; you can’t just scale people up or down and expect them to function correctly. As Moog writes “for a student of comparative biology Gulliver’s book may serve as an unpremeditated textbook on biological absurdities.”

Gulliver was a Bad Biologist
Gulliver was a Bad Biologist, by Florence Moog.
Moog’s first example was the 60-foot tall Brobdingnagians. She notes that because their mass increases as the cube of their height, supporting their body would “necessitate a truly ponderous skeleton” (A point I’ve discussed before in this blog when contemplating elephants). The giants would need thick stubby legs and fat bones.

Gulliver's Travels Title Page
Title Page of Gulliver's Travels.
Moog then considers the six-inch-tall Lilliputians. “If the Brobdingnagians were too big to exist, the mouse-sized Lilliputians were too small to be human.” She explains that smaller animals have a higher specific metabolic rate (that is, rate per unit mass) than larger animals. “Gulliver … failed to realize that the creatures of his invention would have spent the larger part of their time stuffing themselves with food.”

Why was I reading Gulliver’s Travels? Blame Neil deGrasse Tyson. The Public Broadcasting System is sponsoring the Great American Read this summer, where we vote for our favorite of one hundred famous books. In their Launch Special, various celebrities select their personal favorite, and Tyson—one of the few scientists featured on the special—chose Gulliver. Apparently he hasn't studied Chapter 2 of IPMB. Regular readers of this blog know that I am a fan of Isaac Asimov, and I have been voting for his Foundation Series twice a day (once using the Firefox browser, and once using Safari) all summer.

Neil deGrasse Tyson likes Gulliver's Travels
Neil deGrasse Tyson discussing Gulliver's Travels.
Maybe Tyson has a point. Moog concludes that “after all, we must not be too hard on Gulliver for failing to understand the biological conditions that made him a man—and an implausible liar. His talents … were in the psychological realm.” His satirical story provides great insight into human behavior.

Friday, September 7, 2018

Microwave Weapons are Prime Suspect in Ills of U.S. Embassy Workers

Last Saturday, The New York Times published an article by Pulitzer Prize-winning science writer William Broad with the headline Microwave Weapons are Prime Suspect in Ills of U.S. Embassy Workers.
“Doctors and scientists say microwave strikes may have caused sonic delusions and very real brain damage among embassy staff and family members.”
The article has made quite a splash; I even heard about it on the news.

This topic is relevant to Intermediate Physics for Medicine and Biology, so I'll address it in this post. I hesitate, however, because the science is uncertain and the topic of electromagnetic effects on health is fraught with conspiracy theories and voodoo science. Yet, the issue has more than academic importance; U.S.-Cuban relations suffered because of these unexplained health effects. So, reluctantly, I wade in.

I begin with a report from last March in the prestigious Journal of the American Medical Association (JAMA) by Swanson et al. about Neurological Manifestations Among US Government Personnel Reporting Directional Audible and Sensory Phenomena in Havana, Cuba (Volume 319, Pages 1125-1133).
  • Question: Are there neurological manifestations associated with reports of audible and sensory phenomena among US government personnel in Havana, Cuba? 
  • Findings: In this case series of 21 individuals exposed to directional audible and sensory phenomena, a constellation of acute and persistent signs and symptoms were identified, in the absence of an associated history of blunt head trauma. Following exposure, patients experienced cognitive, vestibular, and oculomotor dysfunction, along with auditory symptoms, sleep abnormalities, and headache. 
  • Meaning: The unique circumstances of these patients and the consistency of the clinical manifestations raised concern for a novel mechanism of a possible acquired brain injury from a directional exposure of undetermined etiology.
The article's claim of cognitive dysfunction has been hotly debated. A post in the blog Neuroskeptic was….er….skeptical. It concludes
“Overall … the JAMA paper is pretty weak. Clearly, something has happened to make these 21 people experience so many unpleasant symptoms, but at present I don’t think we can rule out the possibility that the cause is psychological in nature.”
Last week's New York Times article was triggered by the recently proposed hypothesis that microwaves are responsible for these health issues. Russ Hobbie and I discuss the biological effects of electric and magnetic fields in Section 9.10 of IPMB. We focus on the potential of microwaves to induce tumors, and conclude that nonthermal mechanisms are implausible. In other words, radiofrequency fields can heat tissue—just like in your microwave oven—but they don’t cause cancer. The hypothesis touted in the Times article, however, is a thermal mechanism: a thermoelastic pressure wave sensed as sound by part of the inner ear called the cochlea.

Hearing induced by microwaves has been studied for years, and is known as the “Frey effect” after Allen Frey, who first reported it. A 2007 article in the journal Health Physics by James Lin and Zhangwei Wang (Volume 92, Pages 621-628) describes this phenomenon.
Hearing of Microwave Pulses by Humans and Animals: Effects, Mechanism, and Thresholds

The hearing of microwave pulses is a unique exception to the airborne or bone-conducted sound energy normally encountered in human auditory perception. The hearing apparatus commonly responds to airborne or bone-conducted acoustic or sound pressure waves in the audible frequency range. But the hearing of microwave pulses involves electromagnetic waves whose frequency ranges from hundreds of MHz to tens of GHz. Since electromagnetic waves (e.g., light) are seen but not heard, the report of auditory perception of microwave pulses was at once astonishing and intriguing. Moreover, it stood in sharp contrast to the responses associated with continuous-wave microwave radiation. Experimental and theoretical studies have shown that the microwave auditory phenomenon does not arise from an interaction of microwave pulses directly with the auditory nerves or neurons along the auditory neurophysiological pathways of the central nervous system. Instead, the microwave pulse, upon absorption by soft tissues in the head, launches a thermoelastic wave of acoustic pressure that travels by bone conduction to the inner ear. There, it activates the cochlear receptors via the same process involved for normal hearing. Aside from tissue heating, microwave auditory effect is the most widely accepted biological effect of microwave radiation with a known mechanism of interaction: the thermoelastic theory. The phenomenon, mechanism, power requirement, pressure amplitude, and auditory thresholds of microwave hearing are discussed in this paper. A specific emphasis is placed on human exposures to wireless communication fields and magnetic resonance imaging (MRI) coils.
Their introduction gives some useful numbers.
The microwave auditory phenomenon or microwave hearing effect pertains to the hearing of short-pulse, modulated microwave energy at high peak power by humans and laboratory animals (Frey 1961, 1962; Guy et al.1975a, b; Lin 1978, 1980, 2004). The effect can arise, for example, at an incident energy density threshold of 400 mJ m-2 for a single, 10-µs-wide pulse of 2,450 MHz microwave energy, incident on the head of a human subject (Guy et al. 1975a, b; Lin 1978). It has been shown to occur at a specific absorption rate (SAR) threshold of 1.6 kW kg-1 for a single 10-µs-wide pulse of 2,450 MHz microwave energy. A single microwave pulse can be perceived as an acoustic click or knocking sound, and a train of microwave pulses to the head can be sensed as an audible tune, with a pitch corresponding to the pulse repetition rate (Lin 1978).
The temperature increase caused by such a microwave pulse is rapid (microseconds) and tiny (microdegrees Celsius), and the associated pressure is small (tenths of a Pascal, or equivalently millionths of an atmosphere). People can hear these sounds because the cochlea is so sensitive.

One reason that microwaves might be a more plausible mechanism than sound waves for the apparent embassy attacks is acoustic impedance, discussed in Chapter 13 of IPMB. Air and water have very different impedances. When a sound wave impinges on a person, most of the acoustic energy is lost by reflection, and little (perhaps one part in a thousand) enters the fluid-filled body. Animals have evolved elaborate structures in the middle ear to mitigate this acoustic mismatch. However, a pressure wave caused by microwave heating originates inside the ear. No energy is lost by sound reflecting from the air-tissue interface.

I am no expert on thermoeleastic effects, but it seems plausible that they could be responsible for the perception of sound by embassy workers in Cuba. By modifying the shape and frequency of the microwave pulses, you might even induce sounds more distinct than vague clicks. However, I don’t know how you get from little noises to brain damage and cognitive dysfunction. My brain isn't damaged by listening to clicky sounds. Either there is more to this that I don’t understand, or—as neuroskeptic speculates—the rest of the cause is “psychological in nature.”

Right now, our country could use a hard-nosed scientist or engineer expert in the bioeffects of microwave radiation to look into this problem. Where have you gone John Moulder and Ken Foster? We need you!

Friday, August 31, 2018

Interface between Physics and Biology: Training a New Generation of Creative Bilingual Scientists

The journal Trends in Cell Biology publishes a type of article called “Scientific Life”. The journal website states:
Interface between Physics and Biology: Training a New Generation of Creative Bilingual Scientists by Daniel Riveline and Karsten Kruse
Scientific Life articles are short pieces that aim to discuss important issues pertaining to the scientific community or the advancement of science. The content of these articles could range from focused topics such as an unusual career path, to more broad topics such as education and training policies, ethics, publishing, funding, etc. These articles should be aimed at a broad audience and written in a journalistic style and are also intended to be provocative and to stimulate debate.
In June 2017, Daniel Riveline and Karsten Kruse published a Scientific Life article that's particularly relevant to Intermediate Physics for Medicine and Biology.
Interface between Physics and Biology: Training a New Generation of Creative Bilingual Scientists

Daniel Riveline and Karsten Kruse

Whereas physics seeks for universal laws underlying natural phenomena, biology accounts for complexity and specificity of molecular details. Contemporary biological physics requires people capable of working at this interface. New programs prepare scientists who transform respective disciplinary views into innovative approaches for solving outstanding problems in the life sciences.
Riveline and Kruse highlight two physicists who contributed to biology: Hermann von Helmholtz and Max Delbrück. Then they ask: how do we train scientists like these?
This necessity for a thorough understanding of physics concepts and a broad knowledge of genuine biology to make contributions in the spirit of Helmholtz and Delbrück calls for a new way of training the coming generation in this interdisciplinary field.
They conclude
We need translators who are able to rephrase a specific biological phenomenon in the language of physics and vice versa.
I like this idea of "translators," and I believe that Intermediate Physics for Medicine and Biology helps train them. In Section 1.2 of IPMB, Russ Hobbie and I express our view of how to translate between physics and biology.
Biologists and physicists tend to make models differently (Blagoev et al. 2013). Biologists are used to dealing with complexity and diversity in biological systems. Physicists seek to explain as many phenomena with as few overarching principles as possible. Modeling a process is second nature to physicists. They willingly ignore some features of the biological system while seeking these principles. It takes experience and practice to decide what can be simplified and what can not.
IPMB's way of preparing students to work at the interface between physics and biology is to analyze examples that capture some important biological idea using simple mathematical tools: toy models. We stress that
In many cases, simple models are developed in the homework problems at the end of each chapter. Working these problems will provide practice in the art of modeling.
Do your homework! Those problems are the most important part of the book.

Riveline and Kruse conclude that training scientists at the intersection of physics and biology is crucial.
Scientific, educational, and administrative challenges abound in this endeavor to form upcoming generations of scientists at the interface between physics and biology, but we anticipate that the gain in quality for this interdisciplinary field will benefit science in general and throughout the world. The need for such scientists appears to be essential to answer the new challenges in biology.
I concur.

Friday, August 24, 2018

Baring the Sole: The Rise and Fall of the Shoe-Fitting Fluoroscope

A homework problem in Intermediate Physics for Medicine and Biology asks the student to estimate the dose experienced by customers exposed to x-rays when buying shoes.
A homework problem in Chapter 16 of Intermediate Physics for Medicine and Biology asks the student to estimate the dose experienced by customers exposed to x-rays when buying shoes.
Problem 8. During the 1930s and 1940s it was popular to have an x-ray fluoroscope unit in shoe stores to show children and their parents that shoes were properly fit. These marvellous units were operated by people who had no concept of radiation safety and aimed a beam of x-rays upward through the feet and right at the reproductive organs of the children! A typical unit had an x-ray tube operating at 50 kVp with a current of 5 mA.
(a) What is the radiation yield for 50-keV electrons on tungsten? How much photon energy is produced with a 5-mA beam in a 30-s exposure?
(b) Assume that the x-rays are radiated uniformly in all directions (this is not a good assumption) and that the x-rays are all at an energy of 30 keV. (This is a very poor assumption.) Use the appropriate values for striated muscle to estimate the dose to the gonads if they are at a distance of 50 cm from the x-ray tube. Your answer will be an overestimate. Actual doses to the feet were typically 0.014–0.16 Gy. Doses to the gonads would be less because of 1/r2. Two of the early articles pointing out the danger are Hempelmann (1949) and Williams (1949).
To learn more about using x-rays to fit shoes, see the wonderfully titled article “Baring the Sole: The Rise and Fall of the Shoe-Fitting Fluoroscope” (Isis, 91:260-282, 2000) by Jacalyn Duffin and Charles Hayter. The abstract states
One of the most conspicuous nonmedical uses of the x-ray was the shoe-fitting fluoroscope. It allowed visualization of the bones and soft tissues of the foot inside a shoe, purportedly increasing the accuracy of shoe fitting and thereby enhancing sales. From the mid 1920s to the 1950s, shoe-fitting fluoroscopes were a prominent feature of shoe stores in North America and Europe. Despite the widespread distribution and popularity of these machines, few have studied their history. In this essay we trace the origin, technology, applications, and significance of the shoe-fitting fluoroscope in Britain, Canada, and the United States. Our sources include medical and industrial literature, oral and written testimony of shoe retailers, newspapers, magazines, and government reports on the uses and dangers of these machines. The public response to shoe-fitting fluoroscopes changed from initial enthusiasm and trust to suspicion and fear, in conjunction with shifting cultural attitudes to radiation technologies.
Why use x-rays to size loafers? Duffin and Hayter claim “the shoe-fitting fluoroscope was nothing more nor less than an elaborate form of advertising designed to sell shoes.” They say that the device was “aimed especially at mothers…the fluoroscope became yet another instrument of experts’ advice about ‘scientific motherhood.’” These fluoroscopes were rather fancy: “Like an altar to commerce, it became a featured part of the décor in high-class stores, situated on a specially lit and often elevated ‘fitting platform’…Whether in a traditional mahogany finish or art deco shapes and colors, the design responded to the demands of interior decorating.” But these x-ray sources were dangerous. “Store personnel and the adult and child customers were at risk of stunted growth, dermatitis, cataracts, malignancy, and sterility.” The papers by Louis Hempelmann and Charles Williams were the turning point.
“In 1949, two landmark articles on the hazards of shoe-fitting fluoroscopes appeared in the 1 September issue of the New England Journal of Medicine. The first, by Charles R. Williams of the Harvard School of Public Health, contained actual measurements of the high and inconsistent radiation outputs of twelve operating machines. The second, by L. H. Hemplemann [sic], also of Harvard, described the dangers of the uncontrolled use of shoe-fitting fluoroscopes, including interference with foot development in children and radiation damage to the skin and bone marrow.”
A shoe fluoroscope displayed at the US National Museum of Health and Medicine
A shoe fluoroscope displayed at the US National Museum of Health and Medicine. This machine was manufactured by Adrian Shoe Fitter, Inc. circa 1938 and used in a Washington, D.C. shoe store. From Wikipedia.
We don't have much evidence indicating how this exposure affected people's health. It was not lethal like that suffered by the Radium Girls who painted luminous dials using radium-based paint, but everyone buys shoes so millions of people were exposed. The risk of widespread low-dose radiation is difficult to assess, especially years latter.

By the early 1960s the fad was over. I was born in 1960. Yikes! I just missed getting zapped. Did you?

Friday, August 17, 2018

Scientific Babel

Intermediate Physics for Medicine and Biology, and this blog, are written in English. As far as I am aware, no one has ever translated the book into another language. A few of you may be reading the blog using a program like Google translate, but I doubt it. English is now the universal language of science, so anyone interested in science blogs can probably read what I write.

How did English become so dominant? That story is told in Scientific Babel: How Science was Done Before and After Global English, by Michael Gordin. Much of the book is summarized by the illustration below, adapted from Gordin’s Figure 1.
Percentage of the global scientific literature for several languages versus time.
Percentage of the global scientific literature for several languages versus time. Adapted from Fig. 0.1 in Scientific Babel, by Michael Gordin.
In his introduction, Gordin writes:
“English is dominant in science today, and we can even say roughly how much. Sociolinguists have been collecting data for the past several decades on the proportions of the world scientific literature that are published in various tongues, which reveal a consistent pattern. Fig. 0.1 exhibits striking features, and most of the chapters of this book—after an introductory chapter about Latin—move across the same years that are plotted here. In each chapter, I focus on a language or set of languages in order to highlight the lived experience of scientists, and those features are sometimes obscured as well as revealed by these curves. Starting from the most recent end of this figure and walking back, we can begin to uncover elements of the largely invisible story. The most obvious and startling aspect of this graph is the dramatic rise of English beginning from a low point at 1910. The situation is actually even more dramatic than it appears from this graph, for these are percentages of scientific publication—slices of a pie, if you will—and that pie is not static. On the contrary, scientific publication exploded across this period, which means that even in the period from 1940 to 1970 when English seems mostly flat, it is actually a constant percentage of an exponentially growing baseline. By the 1990s, we witness a significant ramp-up on top of an increasingly massive foundation: waves on top of deluges on top of tsunamis of scientific English. This is, in my view, the broadest single transformation in the history of modern science, and we have no history of it. That is where the book will end, with a cluster of chapters focusing on the phenomenon of global scientific English, the way speakers of other once dominant languages (principally French and German) adjusted to the change, preceded by how Anglophones in the Cold War confronted another prominent feature of the midpoint of the graph (1935-1965): the dramatic growth of scientific Russian.

But on second glance, one of the most interesting aspects of this figure is how much of it is not about English, how the story of scientific language correlates with, but does not slavishly follow, the trajectory of globalization. Knowledge and power are bedfellows; they are not twins. Simply swinging our gaze leftward across the graph sets aside the juggernaut of English and allows other, overshadowed aspects of these curves (such as the rise of Russian) to come to the fore. Before Russian, in the period 1910 to 1945, the central feature of the graph is no longer English but the prominent rise and decline of German as a scientific language. German, according to this figure, was the only language ever to overtake English since 1880, and during that era a scientist would have had excellent grounds to conclude that German was well poised to dominate scientific communication. The story of the twentieth century, which from the point of view of the history of globalization is ever-rising English, from the perspective of scientific languages might be better reformulated as the decline of German. That decline started, one can see, before the advent of the Nazi regime in 1933, and one of the main arguments of this book is that the aftermath of World War I was central in cementing both the collapse of scientific German and the ballistic ascent of English. We can move further left still, and in the period from 1880 to 1910 we see an almost equal partition of publications, hovering around 30% apiece for English, French, and German, a set I will call the 'triumvirate.' (The existence of the triumvirate is simply observed as a fact in this book; I do not propose to trace the history of its emergence.) French underwent a monotonic decline throughout the twentieth century; one gets the impression (although the data is lacking) that this decline began before our curve does, but to participants in the scientific community at the beginning of our modern story, it appeared stable. My narrative for this earlier period comes in two forms: the emergence of Russian, with a minor peak in the late nineteenth century, as the first new language to threaten to seriously destabilize the triumvirate; and the countervailing alternative (never broadly popular but still quite revealing in microcosm) to replace the multilingual scientific communication system with one conducted in a constructed language such as Esperanto. Long before all of this data, all of these transformations, there was Latin, and that is where the book properly begins.

For all the visual power of the graph, most of this book pushes against its most straightforward reading: the seemingly inexorable rise of English. Behind the graph lie a million stories, and it is history's task to uncover them….”
I am not skilled with languages. In fact, one of my favorite jokes is to brag that “between my wife and I, we know five languages!” My wife Shirley speaks Mandarin Chinese, Fukienese (another dialect of Chinese), Tagalog (the language of the Philippines), Spanish, and English. The punchline, of course, is that I know only English.

We scientists who grew up speaking English are lucky; we don’t need to learn a foreign language to read modern scientific papers. This isn't fair, but that's the way it is. I tell my international graduate students that they must learn to write English well, or their careers will suffer. Scientists are judged by their journal articles and grant proposals, and both are documents written in English. I review many papers for journals, and I complain obnoxiously in my critique if the manuscript's English is not clear. Pity the poor soul who has me as their referee.

Although I don’t speak any foreign languages, that doesn't mean I have never studied any. In high school I took three years of Latin. I translated sections of Caeser’s Gallic Wars and Cicero’s speeches against Catiline, but slowly and always with my Latin-English dictionary at my side. I never could simply read Latin; I would laboriously translate Latin into English, and then read the English to figure out what the text was talking about. Although my Latin was never fluent, I did learn much about Roman culture. In my junior year of high school, I had the top score in a statewide Junior Classical League exam about Roman history. I love Isaac Asimov's science fiction and popularizations, but the first books by Asimov that I read were histories: his two volume set The Roman Republic and The Roman Empire.

I ought to know German, because my dad's side of the family all immigrated from Germany. But that was two generations back, and there is little of the old country in our family gatherings. I tried to master French before Shirley and I visited Paris. I learned just enough to buy breakfast: "Bonjour Madam," "Trois Croissant," "Merci." All went well as long as no one asked me a question.

In college I expected to have a language requirement, and my plan was to take Russian. I started college in 1978, and the figure above explains how at that time Russian was the logical second language for an English-speaking physics student. Ultimately, the University of Kansas accepted FORTRAN as my foreign language, ending any chance of my becoming bilingual.

For those of you interested in how English became the language of science, I recommend Scientific Babel. For those of you interested in how the title of Intermediate Physics for Medicine and Biology is written in various languages, see below (found using Google Translate). Enjoy!

Friday, August 10, 2018


Intermediate Physics for Medicine and Biology
Intermediate Physics for Medicine and Biology.
This week I spent three days in Las Vegas.

I know you’ll be shocked...shocked! hear there is gambling going on in Vegas. If you want to improve your odds of winning, you need to understand probability. Russ Hobbie and I discuss probability in Intermediate Physics for Medicine and Biology. The most engaging way to introduce the subject is through analyzing games of chance. I like to choose a game that is complicated enough to be interesting, but simple enough to explain in one class. A particularly useful game for teaching probability is craps.

The rules: Throw two dice. If you role a seven or eleven you win. If you role a two, three, or twelve you lose. If you role anything else you keep rolling until you either “make your point” (get the same number that you originally rolled) and win, or “crap out” (roll a seven) and lose.

Two laws are critical for any probability calculation.
  1. For independent events, the probability of both event A and event B occurring is the product of the individual probabilities: P(A and B) = P(A) P(B).
  2. For mutually exclusive events, the probability of either event A or event B occurring is the sum of the individual probabilities: P(A or B) = P(A) + P(B).
Snake eyes
Snake Eyes.
For instance, if you roll a single die, the probability of getting a one is 1/6. If you roll two dice (independent events), the probability of getting a one on the first die and a one on the second (snake eyes) is (1/6) (1/6) = 1/36. If you roll just one die, the probability of getting either a one or a two (mutually exclusive events) is 1/6 + 1/6 = 1/3. Sometimes these laws operate together. For instance, what are the odds of rolling a seven with two dice? There are six ways to do it: roll a one on the first die and a six on the second die (1,6), or (2,5), or (3,4), or (4,3), or (5,2), or (6,1). Each way has a probability of 1/36 (the two dice are independent) and the six ways are mutually exclusive, so the probability of a seven is 1/36 + 1/36 + 1/36 + 1/36 + 1/36 + 1/36 = 6/36 = 1/6.

Now let's analyze craps. The probability of winning immediately is 6/36 for a seven plus 2/36 for an eleven (a five and a six, or a six and a five), for a total of 8/36 = 2/9 = 22%. The probability of losing immediately is 1/36 for a two, plus 2/36 for a three, plus 1/36 for a twelve (boxcars), for a total of 4/36 = 1/9 = 11%. The probability of continuing to roll is….we could work it out, but the sum of the probabilities must equal 1 so a shortcut is to just calculate 1 – 2/9 – 1/9 = 6/9 = 2/3 = 67%.

The case when you continue rolling gets interesting. For each additional roll, you have three possibilities:
  1. Make you point and win with probability a
  2. Crap out and lose with probability b, or 
  3. Roll again with probability c.
What is the probability that, if you keep rolling, you make your point before crapping out? You could make your point on the first additional roll with probability a; you could roll once and then roll again and make your point on the second additional roll with probability ca; you could have three additional rolls and make your point on the third one with probability cca, etc. The total probability of making your point is a + ca + cca + … = a (1 + c + c2 + …). But the quantity in parentheses is the geometric series, and can be evaluated in closed form: 1 + c + c2 + … = 1/(1 - c). The probability of making your point is therefore a/(1 - c). We know that one of the three outcomes must occur, so a + b + c = 1 and the odds of making your point can be expressed equivalently as a/(a + b). If your original roll was a four, then a = 3/36. The chance of getting a seven is b = 6/36. So, a/(a + b) = 3/9 = 1/3 or 33%. If your original roll was a five, then a = 4/36 and the odds of making your point is 4/10 = 40%. If your original roll was a six, the likelihood of making your point is 5/11 = 45%. You can work out the probabilities for 8, 9, and 10, but you’ll find they are the same as for 6, 5, and 4.

Now we have all we need to determine the probability of winning at craps. We have a 2/9 chance of rolling a seven or eleven immediately, plus a 3/36 chance of rolling a four originally followed by the odds of making your point of 1/3, plus…I will just show it as an equation.

P(winning) = 2/9 + 2 [ (3/36) (1/3) + (4/36) (4/10) + (5/36) (5/11) ] = 49.3 % .

The probability of losing would be difficult to work out from first principles, but we can take the easy route and calculate P(losing) = 1 – P(winning) = 50.7 %.

The chance of winning is almost even, but not quite. The odds are stacked slightly against you. If you play long enough, you will almost certainly lose on average. That is how casinos in Las Vegas make their money. The odds are close enough to 50-50 that players have a decent chance of coming out ahead after a few games, which makes them willing to play. But when averaged over thousands of players every day, the casino always wins.

Lady Luck, by Warren Weaver
Lady Luck, by Warren Weaver.
I hope this analysis helps you better understand probability. Once you master the basic rules, you can calculate other quantities more relevant to biological physics, such as temperature, entropy, and the Boltzmann factor (for more, see Chapter 3 of IPMB). When I teach statistical thermodynamics or quantum mechanics, I analyze craps on the first day of class. I arrive early and kneel in a corner of the room, throwing dice against the wall. As students come in, I invite them over for a game. It's a little creepy, but by the time class begins the students know the rules and are ready to start calculating. If you want to learn more about probability (including a nice description of craps), I recommend Lady Luck by Warren Weaver.

I stayed away from the craps table in Vegas. The game is fast paced and there are complicated side bets you can make along the way that we did not consider. Instead, I opted for blackjack, where I turned $20 into $60 and then quit. I did not play the slot machines, which are random number generators with flashing lights, bells, and whistles attached. I am told they have worse odds than blackjack or craps.

The trip to Las Vegas was an adventure. My daughter Stephanie turned 30 on the trip (happy birthday!) and acted as our tour guide. We stuffed ourselves at one of the buffets, wandered about Caesar’s Palace, and saw the dancing fountains in front of the Bellagio. The show Tenors of Rock at Harrah's was fantastic. We did some other stuff too, but let’s not go into that (What Happens in Vegas stays in Vegas).

A giant flamingo at the Flamingo
A giant flamingo at the Flamingo.
The High Roller Observation Wheel
The High Roller Observation Wheel.
Two Pina Coladas, one for each hand
Two Pina Coladas, one for each hand.