Friday, July 25, 2008

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 as:

"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 Fourth 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!", which 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.

Friday, July 18, 2008

Max Delbruck

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.

Friday, July 11, 2008

Georg Charles von Hevesy

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 1930's 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.

Friday, July 4, 2008

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.

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 cannot 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."

For a guide to some of the lore of numerical computing, I recommend two delightful books by Forman Acton:
Numerical Methods that Work (Spectrum), 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!"

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, 4th Edition (Biological and Medical Physics, Biomedical Engineering) 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."