Virtual Colonoscopy

Ever had a colonoscopy? It’s not pleasant. A paper published this week in the New England Journal of Medicine (Volume 359, pages 1207—1217), titled “Accuracy of CT Colonography for Detection of Large Adenomas and Cancers” suggests an alternative to the traditional procedure for detecting colorectal cancer: a “virtual colonoscopy.” This X-ray technology uses Computed Tomography (CT), which Russ Hobbie and I discuss in Chapter 12 of the 4th edition of Intermediate Physics for Medicine and Biology. The NEJM article concludes that “in this study of asymptomatic adults, CT colonographic screening identified 90% of subjects with adenomas or cancers measuring 10 mm or more in diameter. These findings augment published data on the role of CT colonography in screening patients with an average risk of colorectal cancer.” To learn more about this study, see the Associated Press article by Mike Strobbe, and an article in US News and World Report.

Any X-ray procedure does have a risk associated with the radiation dose. A typical virtual colonsocopy has a dose of 5 to 10 mSv. By comparison, the yearly dose from the natural background radiation is about 3 mSv. (The sievert is a unit of dose equal to a Joule per kilogram, adjusted for its biological effectiveness. A mSv is one thousandth of a sievert.) See my December 7, 2007 entry in this blog, or Chapter 16 of the 4th edition of Intermediate Physics for Medicine and Biology, for more information about radiation safety and CT scans. Of course, any risk of radiation must be weighed against risks involved with traditional colonoscopy procedures.

Now for the bad news: You still need to “clean out your bowels” before the procedure, regardless of which method you use: traditional or virtual.

Particle Physics Rap

Today’s post (a rare non-Friday message) has nothing to do with the 4th edition of Intermediate Physics for Medicine and Biology, and nothing to do with medicine and biology at all. But if you are a physics fan, you must check out the particle physics rap at www.physicscentral.com (see the video highlight). This rap celebrates the Large Hadron Collider (LHC), which was turned on September 10, beginning what may be some of the greatest particle physics experiments ever. The rap is too delightful to miss. Enjoy.

Note added October 26: Physics central took the blog off their site, but you can still find it at youtube: http://www.youtube.com/watch?v=j50ZssEojtM. 

 Listen to a physics rap celebrating the Large Hadron Collider.
http://www.youtube.com/watch?v=j50ZssEojtM 

Switching from Physics to Biology

Physicists studying from the 4th edition of Intermediate Physics for Medicine and Biology may be interested in entering the field of biological physics. If so, I suggest reading “Switching From Physics to Biology: Physicists in Transition Help Shape Biological Theory” by Jennifer Ouellette (The Industrial Physicist, Volume 9, Pages 20–23, 2003). The article, which can be found online, begins

Many in physics chafe at the oft-quoted maxim that the 21st century is the “age of biology.” Others see the biological boom as offering unique opportunities for physicists—and not just in the traditional area of building instrumentation for experimental research. Physicists are well positioned by their training to contribute to the development of a theoretical framework in biology, a field that has matured to the point where sufficient quantitative data and sophisticated experimental tools exist to test biological theories.

For other physics-to-biology stories, see Yuh-Nung Jan’s interview in Current Biology and Chris Sander’s story told on the Sloan-Kettering Institute website. Also, here is some advice from the “Grant Doctor” published in Science. 

 Listen to Jennifer Ouellette talk about change.
https://www.youtube.com/watch?v=tGZn0IdFHp4 

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.