Friday, November 24, 2017

Top Ten Journal Articles Cited in IPMB

The cover of Intermediate Physics for Medicine and Biology.
Russ Hobbie and I cite many articles in Intermediate Physics for Medicine and Biology. In the introduction to an early edition of IPMB, Russ wrote:
I also hope that research workers in biology and medicine will find it a useful reference to brush up on the physics they need or to find a few pointers to the current literature in a number of areas of biophysics. (The bibliography in each chapter is by no means exhaustive; however, the references should lead you quickly into a field.)
Below is a list of my favorite dozen articles cited in IPMB. I am only considering those published in journals; books and book chapters are another story. This is not a list of the most important papers, nor the best written papers, nor the most cited papers. These are my personal favorites. Let’s count’em down to number one!

12. Barker AT, Jalinous R, Freeston IL (1985) Non-invasive magnetic stimulation of the human cortex. Lancet 1(8437):1106–1107
This paper founded the field of transcranial magnetic stimulation, which is a topic I worked on when at the National Institutes of Health in the 1990s. See here for more about Tony Barker. The Lancet is one of England’s top medical journals; think of it as a British version of The New England Journal of Medicine.
11. Lubin JH (1999) Response to Cohen’s comments on the Lubin rejoinder. Health Phys 77(3):330–332
Russ and I cite a back-and-forth series of letters and replies by Bernard Cohen and Jay Lubin regarding the health effects of low levels of radiation. Although these authors address a serious issue and each has a strong opinion, my impression is that they had a little fun with this exchange, at least when making up the titles. Health Physics is the official journal of the Health Physics Society.
10. Mermin ND (1994) Stirling’s formula! Am J Phys 52: 362–365.
I am cheating a little bit with this paper. It wasn’t cited in one of the list of references found at the end of each chapter in IPMB, but rather in a footnote of Appendix I. I included it because David Mermin is my favorite writer of physics, and I couldn’t bear to leave him off the list. Also, the article appeared in my favorite journal, the American Journal of Physics. Finally, the title contains an exclamation point (a subtle pun)!
9. Foster KR, Moulder JE (2013) Wi-Fi and health: review of current status and research. Health Phys 105(6):561–575
Ken Foster and John Moulder have been fighting the good fight for years, debunking pseudoscience about the biological effects of weak electric and magnetic fields. This 2013 paper, published in Health Physics, honors their body of work. We need more from these two.
8. West GB, Brown JH, Enquist BJ (1999) The fourth dimension of life: fractal geometry and allometric scaling of organisms. Science 284:1677–1679.
One of my favorite chapters in IPMB, Chapter 2, is about the exponential function. It discusses Kleiber’s law: metabolic rate scales as mass to the ¾ power. Why ¾? This is a long-standing and fundamental question in biology. Geoffrey West and his collaborators offer a possible explanation. The paper was published in Science, the academic journal of the American Association for the Advancement of Science. It is perhaps the most famous scientific journal.
7. Glide-Hurst CK, Maidment ADA, Orton CG (2010) Point/counterpoint: Ultrasonography is soon likely to become a viable alternative to x-ray mammography for breast cancer screening. Med Phys 37:4526–4529
The journal Medical Physics publishes a Point/Counterpoint article ever month, where prominent medical physicists debate a controversial issue. They are fun to read and a great teaching tool. Carri Glide-Hurst is a medical physicist working at Henry Ford Hospital in Detroit and is the mentor for an Oakland University graduate student, so she gets points for being part of the home team.
6. Hämäläinen M, Hari R, Ilmoniemi RJ, Knuutila J, Lounasmaa OV (1993) Magnetoencephalography—theory, instrumentation, and applications to noninvasive studies of the working human brain. Rev Mod Phys 65(2):413–497
This review article on magnetoencephography by a group of Finnish scientists is so good that I still refer students to it even though it is nearly 25 years old.
5. Clark J, Plonsey R (1968) The extracellular potential field of a single active nerve fiber in a volume conductor. Biophys J 8:842–864
John Clark and Robert Plonsey’s paper on the extracellular potential of a nerve axon influenced my work as a graduate student. Plonsey was a giant in the field of bioelectricity, Clark was his graduate student, and the Biophysical Journal is one of the top scientific journals publishing papers at the intersection of physics and biology.
4. Hobbie RK (1973) The electrocardiogram as an example of electrostatics. Am J Phys 41:824–831
This is one of several articles Russ published about medical and biological physics, which ultimately led to his writing IPMB.
3. Basser PJ, Mattiello J, LeBihan D (1994) MR diffusion tensor spectroscopy and imaging. Biophys J 66:259–267
In this paper Peter Basser and his coworkers invented MRI Diffusion Tensor Imaging. Peter’s office was just down the hall from mine when we both worked at the National Institutes of Health, and I can remember the morning he brought in a chunk of pork to do the experiments described in this article. I also knew James Mattiello at NIH; he was one of the first graduates of the Oakland University Medical Physics PhD Program.
2. Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117:500–544
Every semester I give this classic paper to the students in my Biological Physics class, and we go through it figure by figure when studying Chapter 6 in IPMB. It is truly a Nobel Prize quality paper.
1. Purcell EM (1977) Life at low Reynolds number. Am J Phys 45:3–11
This article is a gem: Wonderfully written by a Nobel Prize winner, charming hand-drawn figures, and published in my favorite journal.

Friday, November 17, 2017

William Bialek, Winner of the 2018 Max Delbruck Prize in Biological Physcis

William Bialek is this year’s winner of the American Physical Society’s 2018 Max Delbruck Prize in Biological Physics “for the application of general theoretical principles of physics and information theory to help understand and predict how biological systems function across a variety of scales, form molecules and cells, to brains and animal collectives.”

Biophysics: Searching for Principles, by William Bialek, superimposed on Intermediate Physics for Medicine and Biology.
Searching for Principles,
by William Bialek.
Bialek is author of the textbook Biophysics: Searching for Principles. When preparing this blog post, I checked out this book from the Oakland University Library and glanced through it. It is different from Intermediate Physics for Medicine and Biology in many ways. For instance, it is a graduate text, aimed at grad students in physics, whereas IPMB is targeted at undergraduates who have had a year of introductory physics and a year of calculus. Biophysics emphasizes events at the molecular scale, while in the preface to IPMB Russ Hobbie and I write “molecular biophysics has been almost completely ignored: excellent texts already exist, and this is not our area of expertise.” One of those excellent texts would be Bialek's Biophysics.

I particularly enjoyed Bialek’s introduction, which is a readable and personal account of his experiences at the intersection of physics and biology. At one point he lists a series of questions that anyone interested in applying physics to biology should think about:
  • Where is the boundary between physics and biology?
  • Is biophysics really physics or just the application of methods from physics to the problems of biology?
  • My biologist friends tell me that “theoretical biology” is nonsense [Yikes!], so what would theoretical physicists be doing if they got interested in this field?
  • In the interaction between physics and biology, what happens to chemistry?
  • How much biology do I need to know to make progress?
  • Why do physicists and biologists seem to be speaking such different languages?
  • Can I be interested in biological problems and still be a physicist, or do I have to become a biologist?
The entire introduction (indeed, the entire book) is an attempt to answer these questions. If you don’t have access to the book, you could read his similarly themed article available on the physics archive: “Perspectives on Theory at the Interface of Physics and Biology.”

Like IPMB, Bialek’s book has many homework problems. Readers of this blog know that I enjoy reducing biological and medical physics principles down to homework problems, so this footnote from Bialek’s introduction resonated with me:
“In some sections I found it difficult to formulate manageable problems. I worry that this reflects poorly on my understanding.”
For those of you who prefer video over text, below is a three-part interview with Bialek from the International Centre for Theoretical Physics

Also, here is a video of Bialek giving the 2017 Buhl Lecture “The Physics of Life: How Much Can We Calculate?”


Friday, November 10, 2017


The logo for the Intermediate Physics for Medicine and Biology Facebook page.
The Intermediate Physics for Medicine and Biology Facebook Group has now reached 150 members.

Yes, IPMB has a Facebook group. I use it to circulate blog posts every Friday morning, but I occasionally share other posts of interest to readers of IPMB. The group photo is my Ideal Bookshelf picture highlighting books about physics applied to medicine and biology.

Group members include my family (including my dog Suki Roth, who has her own Facebook Page) and former students. But members I don’t know come from countries all over the world, including:
In particular, many members are from India and Pakistan.

I am amazed and delighted to have members from all over the world. I don’t know if universities teach classes based on IPMB in all these places, or if people just stumble upon the group.

The IPMB Facebook group welcomes everyone interested in physics applied to medicine and biology. I am delighted to have you. And for those who are not yet members, just go to Facebook, search for “Intermediate Physics for Medicine and Biology,” and click “Join Group.” Let’s push for 200 members!

Friday, November 3, 2017

Countercurrent Transport of Oxygen in the Gills of a Fish

In Section 5.8 of Intermediate Physics for Medicine and Biology, Russ Hobbie and I discuss countercurrent transport.
The countercurrent principle is found in the renal tubules (Hall 2011, p. 309; Patton et al. 1989, p. 1081), in the villi of the small intestine (Patton et al., 1989, p. 915), and in the lamellae of fish gills (Schmidt-Nielsen 1971, p. 45). The principle is also used to conserve heat in the extremities—such as people’s arms and legs, whale flippers, or the leg of a duck. If a vein returning from an extremity runs closely parallel to the artery feeding the extremity, the blood in the artery will be cooled and the blood in the vein warmed. As a result, the temperature of the extremity will be lower and the heat loss to the surroundings will be reduced.
In a homework problem, Russ and I ask the student to analyze a countercurrent heat exchanger. In this blog post, I present a new exercise studying countercurrent oxygen exchange in fish gills.
Problem 19 ½. Fish use countercurrent transport to increase uptake of oxygen in their gills. Consider a capillary extending from x = 0 to x = L, with blood flowing in the positive x direction. Blood entering the capillary has a low oxygen concentration that we take as zero. Seawater flowing outside the capillary has an oxygen concentration of [O2] where it enters the gill. Consider the case when |ain|=|aout|=a in Eq. 5.24. The goal is to calculate the oxygen concentration in the blood, Cin, and the oxygen concentration in the seawater, Cout, as functions of x, and in particular to determine the blood oxygen concentration at the end of the gill where it reenters the fish's body, Cin(L).

a) Consider the case when the seawater flows in the same direction as the blood. Draw a picture illustrating this case. Derive expressions for Cin(L) and Cout(x) in terms of [O2], a, and L. Plot qualitatively Cin(x) and Cout(x) versus x when aL is greater than 1. 

b) Now consider the case of countercurrent transport, when the seawater flows in the opposite direction as the blood. Draw a picture, derive expressions, and make plots.

c) Which case results in the highest oxygen concentration in the blood when it leaves the gill and enters the fish’s body?

d) Explain why countercurrent transport is so effective using words instead of equations.
How Animals Work, by Knut Schmidt=Nielsen, superimposed on Intermediate Physics for Medicine and BIology.
How Animals Work,
by Knut Schmidt=Nielsen.
The solution is given at the bottom of this blog post. You can probably guess that countercurrent transport is more efficient for absorbing oxygen. In one of my favorite books, How Animals Work, Knut Schmidt-Nielsen describes countercurrent transport in the fish gill. His description would be an excellent answer to part d) of the new homework problem.
In the lamellae of the fish gill, water and blood flow in opposite directions (figure 27). As a consequence, the blood, just as it is about to leave the gill, encounters the incoming water which still has all its oxygen; that is, the oxygen tension of the blood will approach that of the water before any oxygen has been removed. At the other end of the lamellae, the water that is about to exit encounters venous blood, so that, even though much oxygen has already been removed from the water, more can still be taken from it by the blood. As a result of this arrangement, fish may extract as much as 80 to 90% of the oxygen in the water, an efficiency which could not easily be achieved without a countercurrent flow.

The solution to a new homework problem about countercurrent transport of oxygen in the gills of a fish, for the book Intermediate Physics for Medicine and Biology.