Showing posts with label Mentions Suki. Show all posts
Showing posts with label Mentions Suki. Show all posts

Friday, April 19, 2019

Me, Me, Me

Most of my blog posts are about the textbook Intermediate Physics for Medicine and Biology. This post, however, is all about me. IPMB makes a few appearances, but its mainly me, me, me.

OUTV Interview

I was recently featured in a Focus on Faculty interview filmed by the Oakland University TV station (OUTV). I uploaded a copy to Youtube, and you can view it here. I apologize for the hair; I was supposed to get a haircut before filming began, but I got busy. Watch for a cameo by IPMB.

OUTV interviews Brad Roth at Oakland University.
https://www.youtube.com/watch?v=IKjab7_unRA

Daughters Kathy and Stephanie with me, and with Auggie, Smokie, and Harvest.
(l-r) Daughters Kathy and Stephanie with me,
and with Auggie, Smokie, and Harvest.

Harvest

Long-time readers of this blog will remember Suki, my beloved Cocker Spaniel-Westie mix who helped explain concepts in IPMB. After her death about a year ago, my wife and I decided to get another dog. Let me introduce you to Harvest, our 65-pound Treeing Walker Coonhound. She is as lovable as Suki (though not quite as smart). We adopted her from the Making Miracles Animal Rescue. On the right is a picture of me with my daughters Kathy and Stephanie, along with Harvest and my two granddogs Auggie (the foxhound) and Smokie (the greyhound), about to start a 5k walk. We like to take them to a dog park, and as we enter yell "Release the Hounds!"

The photo of Harvest and me published in the October 2018 issue of Physics Today
The photo of Harvest and me published
in the October 2018 issue of Physics Today.
Harvest is already famous. She was featured in the October 2018 issue of Physics Today. The magazine had a selfie contest that Harvest and I entered. Unfortunately, in the magazine our location is listed incorrectly; we are actually in our home in Rochester Hills, Michigan. To the left is the selfie that appeared in Physics Today.

Harvest with the IPMB Ideal Bookshelf.

Live Action IPMB Ideal Bookshelf

The logo for the Intermediate Physics for Medicine and Biology Facebook page is a drawing of the IPMB Ideal Bookshelf. You know how Disney often makes live-action movies out of previous animated shows? (Dumbo is the most recent example.) I’ve done the same thing. Below is a photograph of the “live-action” version of IPMB's My Ideal Bookshelf. Harvest helped me with the filming, so on the right I include a photo of her on the set.

The IPMB Ideal Bookshelf, consisting of books cited in Intermediate Physics for Medicine and Biology.

How to Get Published

Below is a video (divided into two parts) of Michael Sevilla (Distinguished Professor of Chemistry at Oakland University) and me talking to a group of graduate students about how to publish their research. Enjoy!

Part 1 of a discussion about Academic Publishing: How to Get Published in a Peer Review Journal, held Nov. 15, 2013 at Oakland University and hosted by the graduate student group Grad Connection. The host is then-graduate student George Corser, and the guests are Brad Roth and Michael Sevilla.

Part 2.

Friday, February 9, 2018

Suki Roth (2002-2018)

Intermediate Physics for Medicine and Biology: Suki Roth (2002-2018)
Suki Roth (2002-2018)
Suki Roth (2002-2018).
Regular readers of this blog are familiar with my dog Suki, who I’ve mentioned in more than a dozen posts. Suki passed away this week. She was a wonderful dog and I miss her dearly.

Suki and I used to take long walks when I would listen to audio books, such as The Immortal Life of Henrietta Lacks, Musicophilia, Destiny of the Republic, Galileo’s Daughter, and First American: The Life and Times of Benjamin Franklin. This list just scratches the surface. On my Goodreads account, I have a category called “listened-to-while-dog-walking” that includes 84 books, all of which Suki and I enjoyed together. 

Me holding Suki in the forest in Michigan among the fall color.In my post about the Physics of Phoxhounds, I mentioned that a photo of Suki and me (right) was included in Barb Oakley’s book A Mind for Numbers: How to Excel at Math and Science (Even if You Flunked Algebra). Recently I learned that Barb’s book has sold over 250,000 copies, making Suki something of a celebrity.

Suki Roth next to the textbook Intermediate Physics for Medicine and Biology.Suki helped me explain concepts from Intermediate Physics for Medicine and Biology, such as age-related hearing loss and the biomechanics of fleas. Few people knew that she had this secret career in biomedical education!

Thanks to Dr. Kelly Totin, and before her Dr. Ann Callahan, and all the folks at Rochester Veterinary Hospital for taking such good care of Suki. In particular I appreciate Dr. Totin’s help during Suki’s last, difficult days. As she said near the end, her focus was on the quality of Suki’s time left rather than the quantity; an important life lesson for us all.

I’ll close with a quote from one of my favorite authors, James Herriot. In his story “The Card Over The Bed,” the dying Miss Stubbs asks Herriot, a Yorkshire vet, if she will see her pets in heaven. She was worried because she had heard claims that animals have no soul. Herriot responded “If having a soul means being able to feel love and loyalty and gratitude, then animals are better off than a lot of humans. You’ve nothing to worry about there.”

Suki Roth resting in her bed.
Suki resting.

Suki Roth with her nephew Auggie, a foxhound.
Suki with her nephew Auggie.

Suki Roth with all five editions of Intermediate Physics for Medicine and Biology.
Suki with all five editions of IPMB.

Suki Roth (right), her niece Smokie Roth (the Greyhound, center), and her nephew Auggie Roth (the Foxhound, left), about to get treats from my wife Shirley.
Suki (right), her niece Smokie (the Greyhound, center),
and her nephew Auggie (the Foxhound, left),
about to get treats from my wife Shirley.

Suki and me, 15 years ago.
Suki and me, 15 years ago.
Suki Roth as a puppy.
Young Suki

Friday, December 1, 2017

Suki Has Fleas

Suki Roth, resing in her bed.
Suki
Suki has fleas. It’s her worst infestation ever. My wife and I have battled them for about a month, and are finally gaining the upper hand by constantly vacuuming the house, washing her bedding, and giving her baths.

While I am sure you empathize with our little puppy, you are probably asking “what do Suki’s fleas have to do with Intermediate Physics for Medicine and Biology?” A lot! In Problem 47 of Chapter 2, Russ Hobbie and I ask students to determine how jumping height scales with mass. I won’t give away the answer here, but when you are asked how something scales with mass, one possible answer is that it doesn’t. In other words, if the allometric relationship is Jumping Height = C Massn, where C and n are constants, then one possible value for n is zero; jumping height is independent of mass.

Scaling: Why is Animal Size So Important? by Knut Schmidt-Nielsen, superimposed on Intermediate Physics for Medicine and Biology.
Scaling: Why is Animal
Size So Important?
by Knut Schmidt-Nielsen.
The next homework exercise, Problem 48, analyzes one of the many scaling arguments made by Knut Schmidt-Nielsen in his marvelous book Scaling: Why is Animal Size so Important? The start of Problem 48 gives away the answer to Problem 47:
Problem 48. In Problem 47, you should have found that all animals can jump to about the same height (approximately 0.6 m), independent of their mass M.
Are you skeptical that, for instance, a tiny flea can jump 60 cm (about two feet)? I can tell you from first-hand experience that those little buggers can really jump. Each evening we inspect Suki with a flea comb, and sometimes a flea jumps away before we can kill it. 

Problem 48 requires that students calculate the flea's acceleration. Again, I won’t give you the answer, but those fleas sure undergo large accelerations! If you don’t believe me, do Problem 48, or read what Knut Schmidt-Nielsen writes.
For a flea, acceleration takes place over less than 1 mm, and takeoff time is less than 1 msec. The average acceleration during takeoff must therefore exceed 200 g. It is worth a moment's reflection to think of what such high acceleration means. It means that the force on the animal is 200 times its weight (any mammal would be totally crushed under such forces), and the insect must have a skeleton and internal organs able to resist such acceleration forces.
I wonder how fleas avoid concussions?

I’m glad that our little fleabag is cleaning up her act. Suki turned 15 a few months ago, and she is the old lady of the family. But she is still up for our walks, during which I listen to audiobooks and she snoots around (that’s probably how she got the fleas). And what is her favorite book? Intermediate Physics for Medicine and Biology, of course.

Friday, November 10, 2017

Facebook

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, July 28, 2017

Suki is Going Deaf

Suki Roth, in front of a copy of Intermediate Physics for Medicine and Biology.
Suki Roth, in front of a copy of
Intermediate Physics for
Medicine and Biology.
Suki is going deaf. She has not lost all her hearing yet, but when I call her in a normal voice she does not respond. She used to jump up when she heard me get the leash for a walk, but now I have to show it to her. Before she was scared of thunderstorms, but lately she snoozes through all but the loudest rumbles. In the past she got excited when the garage door opened, but nowadays she ignores it. Suki will be 15 years old this October, so such problems are expected. Still, I’m sad to see her sink into silence.

I think my hearing is getting worse too, but slowly. My dad uses a hearing aid, and I take after him. I find myself asking “what did you say?” more often than other people do. I decided to test myself using the website http://www.animations.physics.unsw.edu.au/jw/hearing.html. Below I plot my hearing (red dots) as a function of frequency, and compare it with the normal hearing response of a young adult (solid curve) shown in Figure 13.7 of Intermediate Physics for Medicine and Biology. I normalized the two curves so they are equal at 1 kHz.
A plot of my hearing response curve: the threshold sound intensity versus freqneucy.
My hearing response curve.
My hearing appears normal except for an odd deficit around 3000-4000 Hz. Also, I may be missing some high frequencies, but the loss is not dramatic.

I didn’t follow the website’s instructions exactly. I plotted the lowest intensity tone that I could just hear. I don’t trust this test, performed on myself using a website; it is very subjective and the loudness changes in large 3 dB steps. (In case you do not have IPMB handy, Eq. 13.34 indicates that a ten-fold change in intensity corresponds to a step of 10 in decibels.) I would be interested in hearing (get it?....) if you have a similar result using this website.

Age-related hearing loss is called presbycusis. Wikipedia says it is the second most common illness in the elderly, after arthritis. Normally we lose the high frequencies as we age, which has implications for how teenagers choose ringtones.


On the above video, I could hear the 8 kHz ringtone but not the 12 kHz or higher ones. Can you? I am not sure if it is me, my computer, or the video.

I may be losing some hearing, but probably not much. (Perhaps I just don’t pay attention when my wife talks to me.) Suki, however, is in worse shape. She is the world’s best pet, and I intend to give her extra treats to make up for her lack of hearing.

Friday, January 6, 2017

Neuroskeptic

Over the Christmas break I discovered a blog written under the pen name Neuroskeptic.
Neuroskeptic is a British neuroscientist who takes a skeptical look at his own field, and beyond. His blog offers a look at the latest developments in neuroscience, psychiatry and psychology through a critical lens.
Neuroskeptic’s interests overlap topics covered in Intermediate Physics for Medicine and Biology. For instance, often Neuroskeptic writes about functional magnetic resonance imaging, a technique Russ Hobbie and I describe in Chapter 18 of IPMB.
“The term functional magnetic resonance imaging (fMRI) usually refers to a technique developed in the 1990s that allows one to study structure and function simultaneously. The basis for fMRI is inhomogeneities in the magnetic field caused by the differences in the magnetic properties of oxygenated and deoxygenated hemoglobin. No external contrast agent is required. Oxygenated hemoglobin is less paramagnetic than deoxyhemoglobin. If we make images before and after a change in the blood flow to a small region of tissue (perhaps caused by a change in its metabolic activity), the difference between the two images is due mainly to changes in the blood oxygenation. One usually sees an increase in blood flow to a region of the brain when that region is active. This BOLD contrast in the two images provides information about the metabolic state of the tissue, and therefore about the tissue function (Ogawa et al. 1990; Kwong et al. 1992).”
Neuroskeptic’s author is obviously an expert in this method, but is suspicious about some of its claims. Often he—I will use the masculine pronoun for convenience, but I have no idea about his gender—analyzes new papers in the field. For instance, in his recent New Year’s Eve blog post he writes
Earlier this year, neuroscience was shaken by the publication in PNAS of “Cluster Failure: Why fMRI Inferences for Spatial Extent have Inflated False-Positive Rates.” In this paper, Anders Eklund, Thomas E. Nichols and Hans Knutsson reported that commonly used software for analysing fMRI data produces many false-positives. But now, Boston College neuroscientist Scott D. Slotnick has criticized Eklund et al.’s alarming conclusions in a new piece in Cognitive Neuroscience. In my view, while Slotnick makes some valid points, he falls short of debunking Eklund et al.’s worrying findings.
Another area Neuroskeptic analyzes is functional electrical stimulation. In Chapter 7 of IPMB, Russ and I write
stimulating electrodes…may be used for electromyographic studies; for stimulating muscles to contract called functional electrical stimulation (Peckham and Knutson 2005); for a cochlear implant to partially restore hearing (Zeng et al.2008); deep brain stimulation for Parkinson’s disease (Perlmutterand Mink 2006); for cardiac pacing (Moses andMullin 2007); and even for defibrillation (Dosdall et al.2009). The electrodes may be inserted in cells, placed in or on a muscle, or placed on the skin.
Two recent Neuroskeptic posts (here and here) analyze a controversial method of electrical stimulation called transcranial direct current stimulation (tDCS). I share his doubts about this technique, in which week currents (about 1 mA) are applied to the scalp. In a post last August, I hinted at some of my concerns, but my suspicions continue to grow. The electric fields induced in the brain by a 1 mA current to the scalp are minuscule.

Neuroskeptic also wonders if nonionizing radiation can cause cancer, a topic covered extensively in Chapter 9 of IPMB. He writes
Does non-ionizing radiation pose a health risk? Everyone knows that ionizing radiation, like gamma rays, can cause cancer by damaging DNA. But the scientific consensus is that there is no such risk from non-ionizing radiation such as radiowaves or Wi-Fi. Yet according to a remarkable new paper from Magda Havas, the risk is real: it’s called “When Theory and Observation Collide: Can Non-Ionizing Radiation Cause Cancer?”... Non-ionizing radiation such as radiowaves and microwaves consists of photons, just like visible light, but at a lower frequency. Because the energy of a photon is proportional to its frequency, very high frequency photons (like gamma rays) have enough energy to disrupt atoms…But visible light can’t do this, and still less can microwaves or radiowaves. There’s no known mechanism by which such low-energy photons could harm living tissue – except that they can heat tissue up in high doses, but the amount of heating produced by radio and wireless devices is tiny.
Neuroskeptic is not merely a debunker. Sometimes he examines promising new methods, but always with a questioning eye. For instance, his review of a paper developing new contrast agents for MRI is fascinating.
In a new paper called “Molecular fMRI,” MIT researchers Benjamin B. Bartelle, Ali Barandov, and Alan Jasanoff discuss technological advances that could provide neuroscientists with new tools for mapping the brain.

Currently, one of the leading methods of measuring brain activity is functional MRI (fMRI)…. Recent work, however, holds out the hope that a future “molecular fMRI” could be developed to extend the power of fMRI…. Molecular fMRI would involve the use of a molecular probe, a form of “contrast agent,” which would modulate the MRI signal in response to specific conditions.
I would be interested in knowing what Neuroskeptic (I always want to type “the Neuroskeptic” but he never uses the definite article before his name, so I won’t either) thinks about claims of using the biomagnetic field as the gradient field in MRI, as I discussed in my June 2016 blog post.

Everyone has their own gimmick, and Neuroskeptic’s is that he keeps his real identity secret. Some of you are thinking: “Oh, I wish Roth would be anonymous! We hear far too much about him and his little dog Suki and his own research in this blog.” Well, sorry. It’s too late to change now, so you are stuck hearing about Suki and me in addition to learning about physics in medicine and biology. But if you want a well-written, anonymous, and sometimes dissenting view of neuroscience, read the Neuroskeptic.

Friday, May 20, 2016

Five Generations

A five generation picture of me, my daughter, my mom, my grandmother, and my great grandmother.
A five generation picture.
When my first daughter Stephanie was born, we included her in this photo of five generations. From left to right are my maternal grandmother, my great-grandmother (born 1889), my daughter Stephanie (born 1988), me, and my mom. My great grandmother lived to be over 100 years old. I remember playing poker with her when I was young; she generally won and kept the money!


A photograph of all five editions of Intermediate Physics for Medicine and Biology.
All five editions of
Intermediate Physics for Medicine and Biology.
Recently I took another five-generation photo. There now exist five generations (editions) of Intermediate Physics for Medicine and Biology. My office is one of the few places you can find all five on one bookshelf. I was coauthor on the fourth and fifth editions; the first three editions were authored by Russ Hobbie alone.

Suki with all five editions of
Intermediate Physics for Medicine and Biology.
The yellow book is the first edition of IPMB, published by John Wiley and Sons in 1978. The blue version with the yellow sine wave on the cover is the second edition, again published by Wiley in 1988. The green cover is the third edition, published by Springer with AIP Press in 1997. The blue fourth edition was published by Springer alone in 2007. Finally, the blue/purple fifth edition, again published by Springer, appeared in 2015. My dog Suki seems to like them all.

A photograph of all five editions of Intermediate Physics for Medicine and Biology.
All five editions of
Intermediate Physics for Medicine and Biology.
I have a special fondness for the first edition, which I bought for a class taught by my PhD advisor John Wikswo at Vanderbilt University in the early 1980s (price: $31.95). That is where I learned much of my biological and medical physics. When Russ was preparing the second edition, he asked John and I to create some three-dimensional figures of the electrical potential and magnetic field of a nerve axon. There figures have appeared in each subsequent edition of IPMB, and are Figs. 7.13 and 8.14 in the fifth. My third edition is pretty beat up. It is the textbook I taught out of for several years after I arrived at Oakland University. The fourth and fifth editions I know best, as I helped write them (although Russ remains the primary force behind every edition).

A photograph of all five editions of Intermediate Physics for Medicine and Biology.
All five editions of
Intermediate Physics for Medicine and Biology.
IPMB has changed over the years. The first seven chapters are the same in all versions, but Russ added chapters on charged membranes and biomagnetism in the second edition. The first edition’s chapter on signal analysis split into two in the second: one on one-dimensional signal analysis and another on two-dimensional images. The 4th edition picked up a chapter on ultrasound. The first edition’s chapter on x-rays fissioned into a chapter on how x-rays interact with tissue and a chapter on the medical uses of x-rays. Finally, the second edition introduced a chapter on magnetic resonance imaging. Early editions featured a figure on the cover. I particularly like the first edition’s electrocardiogram picture (Fig. 7.16 in the 5th edition). Russ and I planned on using a computed tomography illustration, Fig. 12.12, on the 4th edition cover, but Springer opted to use a generic cover with no figure.

A photograph of me holding all five editions of Intermediate Physics for Medicine and Biology.
Me holding all five editions of
Intermediate Physics for Medicine and Biology.
Working on revisions of IPMB has been a pleasure and an honor. But really, the five generations of IPMB is a tribute to Russ Hobbie and his vision of advancing the teaching of physics in medicine and biology, which he has pursued over nearly four decades. I hope you find the book as useful as I have.

Friday, January 15, 2016

You Can Hear About a Nickel’s Worth of Difference

In Chapter 13 of Intermediate Physics for Medicine and Biology, Russ Hobbie and I describe a logarithmic scale for sound intensity: the decibel. In general, an increase in intensity is perceived as a greater loudness (although this relationship is surprisingly complex). Is there an analogous relationship between frequency and pitch? Yes! Loudness is determined using a logarithmic scale with a base of ten, whereas pitch is measured using a logarithmic scale of base two, because a doubling of the frequency corresponds to raising the pitch by one octave. Those familiar with music are accustomed to associating different pitches with different notes in a musical scale. Most instruments are tuned using the equal tempered scale, dividing an octave into twelve equal logarithmic steps. One step, called a semitone, corresponds to the difference in pitch between, say, F and F-sharp. The fractional change of one semitone is 21/12 = 1.0595, or an increase in frequency of roughly 6%. This frequency shift is so important that it is expressed by a special unit: one semitone is equal to 100 cents. The cent is to pitch as the decibel is to loudness. Doubling the intensity corresponds to an increase of 3 dB, whereas doubling the frequency corresponds to an increase of 1200 cents.

How finely can the human ear resolve pitch? In other words, if you play two pure tones one right after the other, by how much must their frequency differ for you to notice that they are indeed different? A typical listener can detect a change of about 5 cents, leading to the rule of thumb that you can hear about a nickel’s worth of difference. Try testing your own pitch perception online here. When I tried, I could always detect a difference of 50 cents (tones of 440 and 453 Hz, presented one after another; I assume this is a control used by the testing software, because the difference is obvious). I could never detect a difference of 4 or 6 cents (440 compared to 441 or 441.5 Hz). I had inconsistent results with 8 and 11 cents (440 compared to 442 or 443 Hz); sometimes I perceived slightly different tones, and sometimes I didn’t. Ten cents is a reasonable approximation to my just noticeable difference, which confirms what I have always suspected: I have poor but not pathological pitch perception. When playing the tuba in my high school band, the director often had us “tune up” relative to a standard note, typically played by the first clarinet. I always had trouble with this task; he had to tell me if I was sharp or flat. Poor pitch perception has its advantages: you don’t need to hire a piano tuner! Pity my poor wife—my only audience, other than my dog Suki—but my wrong notes are probably more bothersome than the out-of-tune piano, so spending for a piano tuner would not help.

Humans can hear pitches from roughly 20 to 20,000 Hz. Because 210 is about 1000, humans can hear frequencies that range over roughly ten octaves, or 12,000 cents, and therefore you (but not I) can distinguish about 2400 different tones. A piano keyboard plays notes 28 to 4186 Hz, which is a little more than seven octaves, or roughly 8700 cents (87 semitones between the 88 keys). Sometimes changes in frequency are measured in millioctaves: 1 mO = 1.2 cents. Although the cent is not a metric unit, I still worry that the SI police, who insist that all things centi- are going out of fashion compared to all things milli-, will demand we start using the millioctave. I hope not.

If two tones are played at the same time, rather than one after another, you can perceive small differences in pitch using beats. Consider the triginometric identity
A  triginometric identity relating the sum of two sine waves to the beat frequency.
If frequencies A and B are similar, then their sum consists of a carrier frequency equal to the average of the two original frequencies modulated by the difference of the two frequencies. For instance, if you have a tone corresponding to concert A (440.00 Hz) and another tone out of tune with concert A by 3 cents (440.78 Hz), when played together the sound consists of a tone having frequency 440.39 Hz modulated by a sinusoid that gets louder and softer with a frequency of 0.78 Hz (or a period of 1.3 seconds). Your ear can’t tell that the pitch of the carrier tone is different from concert A, but it can detect the variation in loudness caused by the beats. You can hear beats generated online here.

If several tones have widely separated frequencies, your ear (or more properly, your brain) detects distinct notes played together; a chord. If two tones have nearly the same frequency (like in the example above), you hear a single tone with modulated amplitude; beats. For intermediate frequency differences (say, between a note an octave above concert A, 880 Hz, and a severely out-of-tune A at 897 Hz, a difference of 17 Hz or 33 cents) you hear neither a chord nor beats. Instead, your brain perceives dissonance. A London police whistle generates frequencies of 1904 and 2136 Hz, a difference of 232 Hz or more than 200 cents. It sounds annoying. Try it yourself.

The frequency ratio between a C and G (a perfect fifth) should be 3:2, which is 702 cents. However, in equal tempered tuning the shift between C and G is 700 cents. This difference of 2 cents is indistinguishable to all but the best ears. The major third is more of a problem. It should have a ratio of 5:4, or 386 cents. In the equal tempered scale, a third is 400 cents, off by 14 cents, which a good ear can hear. If all these tonal relations are different than what they would be in just intonation, then why do we use an equal tempered scale? It allows us to change keys without retuning the instrument. But we pay a price in that a major chord does not have precisely the desired 4:5:6 frequency ratio. Pythagoras must be turning over in his grave.

Both pitch perception and color vision arise from the physics of frequency detection. But the tones we hear and colors we see are determined by more than just physics. There is a lot of information processing by the brain, which leads to many fascinating and unexpected results including surprising pathologies. To completely appreciate how we perceive frequency, you also need to understand the brain.

Friday, August 15, 2014

Physics of Phoxhounds

I don’t have any grandchildren yet, but I am fortunate to have a wonderful “granddog.” This weekend, my wife and I are taking care of Auggie, the lovable foxhound that my daughter Kathy rescued from an animal shelter in Lansing, Michigan. Auggie gets along great with our Cocker-Westie mix, “Aunt Suki,” my dog-walking partner who I’ve mentioned often in this blog (here, here, here, and here).

Do dogs and physics mix? Absolutely! If you don’t believe me, then check out the website dogphysics.com. I plan to read “How To Teach Physics To Your Dog” with Auggie and Suki. According to this tee shirt foxhounds are particularly good at physics. Once we finish “How To Teach Physics To Your Dog,” we may move on to “Physics for Dogs: A Crash Course in Catching Cats, Frisbees, and Cars.” Apparently there is even a band that sings about dog physics, but I don’t know what that is all about.

Auggie is a big fan of the 4th edition of Intermediate Physics for Medicine and Biology. His favorite part is Section 7.10 (Electrical Stimulation) because there Russ Hobbie and I discuss the “dog-bone” shaped virtual cathode that arises when you stimulate cardiac tissue using a point electrode. He thinks “Auger electrons,” discussed in Sec. 17.11, are named after him. Auggie’s favorite scientist is Godfrey Hounsfield (Auggie adds a “d” to his name: “Houndsfield”), who earned a Nobel Prize for developing the first clinical computed tomography machine. And his favorite homework problem is Problem 34 in Chapter 2, about the Lotka-Volterra equations governing the population dynamics of rabbits and foxes.

How did Auggie get his name? I’m not sure, because he had the name Auggie when Kathy adopted him. I suspect it comes from an old Hanna-Barbera cartoon about Augie Doggie and Doggie Daddy. When Auggie visits, I get to play doggie [grand]daddy, and say “Augie, my son, my son” in my best Jimmy Durante voice. I’m particularly fond of the Augie doggie theme song. What is Auggie’s favorite movie? Why, The Fox and the Hound, of course.

A photograph of Brad Roth holding his dog Suki Roth in Michigan's fall color.
Me holding Suki.
Our dog Suki has some big news this week. My friend and Oakland University colleague Barb Oakley has a new book out: A Mind for Numbers: How to Excel at Math and Science (Even if You Flunked Algebra). I contributed a small sidebar to the book offering some tips for learning physics, and it includes a picture of me with Suki! Thanks to my friend Yang Xia for taking the picture. Barb is a fascinating character and author of an eclectic collection of books. I suggest Hair of the Dog: Tails from Aboard a Russian Trawler. Her amazon.com author page first gave me the idea of publishing a blog to go along with IPMB. To those of you who are interested in physics applied to medicine and biology but struggle with all the equations in IPMB, I suggest Barb's book or her MOOC Learning How to Learn.

All Creatures Great and Small, by James Herriot, superimposed on Intermediate Physics for Medicine and Biology.
All Creatures Great and Small,
by James Herriot.
James Herriot—the author of a series of wonderful books including All Creatures Great and Small, which will warm the heart of any dog-lover—loved beagles, which look similar to foxhounds, but are smaller. If you’re looking for an uplifting and enjoyable book to read on a late-summer vacation (and you have already finished IPMB), try Herriot’s books. But skip the chapters about cats (yuck).

Auggie may not be the brightest puppie in the pack, and he is too timid to be an effective watch dog, but he has a sweet and loving disposition. I think of him as a gentle soul (even if he did chew up his grandma’s shoe). Below is a picture of Auggie and his Aunt Suki, getting ready for their favorite activity: napping.

Suki Roth with the lovable foxhound Auggie, napping.
Suki and Auggie.

Friday, February 28, 2014

The Encyclopedia of Life

Although I am a champion of applying physics to biomedicine, physics has little impact on some parts of biology. For instance, much of zoology and botany consist of the identification and naming of different species: taxonomy. Not too much physics there.

A giant in the field of taxonomy is the Sweedish scientist Carl Linnaeus (1707-1778). Linnaeus developed the modern binomial nomenclature to name organisms. Two names are given (often in Latin), genus then species, both italicized with the genus capitalized and the species not. For example, the readers of this blog are Homo sapiens: genus = Homo and species = sapiens. My dog Suki is a member of Canis lupus. Her case is complicated, since the domestic dog is a subspecies of the wolf, Canis lupus familiaris, but because dogs and wolves can interbreed they are considered the same species and to keep things simple (a physicist’s goal, if not a biologist’s) I will just use Canis lupus. Hodgkin and Huxley performed their experiments on the giant axon from the squid, whose binomial name is Loligo forbesi (as reported in Hodgkin and Huxley, J. Physiol., Volume 104, Pages 176–195, 1945; in their later papers they just mention the genus Loligo, and I am not sure what species they used--they might have used several). My daughter Katherine studied yeast when an undergraduate biology major at Vanderbilt University, and the most common yeast species used by biologists is Saccharomyces cerevisiae. The nematode Caenorhabditis elegans is widely used as a model organism when studying the nervous system. You will often see its name shortened to C. elegans (such abbreviations are common in the Linnaean system). Another popular model system is the egg of the frog species Xenopus laevis. The mouse, Mus musculus, is the most common mammal used in biomedical research. I’m not enough of a biologist to know how viruses, such as the tobacco mosaic virus, fit into the binomial nomenclature.

Out of curiosity, I wondered what binomial names Russ hobbie and I mentioned in the 4th edition of Intermediate Physics for Medicine and Biology. It is surprisingly difficult to say. I can’t just search my electronic version of the book, because what keyword would I search for? I skimmed through the text and found these four; there may be others. (Brownie points to any reader who can find one I missed and report it in the comments section of this blog.)
If you want to learn more about any of these species, I suggest going to the fabulous website EOL.org. The site states
The Encyclopedia of Life (EOL) began in 2007 with the bold idea to provide “a webpage for every species.” EOL brings together trusted information from resources across the world such as museums, learned societies, expert scientists, and others into one massive database and a single, easy-to-use online portal at EOL.org.

While the idea to create an online species database had existed prior to 2007, Dr. Edward O. Wilson's 2007 TED Prize speech was the catalyst for the EOL you see today. The site went live in February 2008 to international media attention. …

Today, the Encyclopedia of Life is expanding to become a global community of collaborators and contributors serving the general public, enthusiastic amateurs, educators, students and professional scientists from around the world.

Friday, September 20, 2013

Musicophilia

Musicophilia: Tales of Music and the Brain, by Oliver Sacks, superimposed on Intermediate Physics for Medicine and Biology.
Musicophilia: Tales of
Music and the Brain,
by Oliver Sacks.
Those who know me well are aware that I spend considerable time walking my dog Suki. Usually during these walks I am listening to recorded books. Being too cheap to spend money on this habit, I borrow these recordings from the Rochester Hills Public Library. They have a impressive selection, but Suki and I have been at this for a while (she is almost 11 years old), and I have slowly worked my way through their stock of recordings in genres that I ordinarily listen to; science, history, and biography. I don’t view this as a problem, because it has forced me to sample books about topics I would not ordinarily listen to. The most recent example is Musicophilia: Tales of Music and the Brain, by Oliver Sacks. Perhaps you object that this is a science book, but I view it more as a medical book outside my normal experience. Regardless, I was pleasantly surprised to find considerable medical physics discussed.

I had listened previously to Sacks’s delightfully-titled The Man Who Mistook His Wife for a Hat, so I knew what I was getting into. In Musicophilia, Sacks discusses a variety of abnormalities in the perception of music. For instance, he begins with musical hallucinations. This is more than just having a song stuck in your head. These were examples from his clinical practice of people who had, say, suffered a brain injury and afterward would hear music in their mind that they could not distinguish from real music. They sometimes could not turn it on or off, but were stuck with it more or less continuously. Another example is people who, after a stroke, lost the ability to hear music as music. An opera sounds like someone screaming, and a symphony like pots and pans crashing onto the floor. In one case he related, this occurred to a former professional musician. It’s amazing.

Sacks describes all sorts of brain studies being done to examine these patients. There is considerable discussion of data measured using electroencephalography, magnetoencephalography, positron emission tomography, functional magnetic resonance imaging, and transcranial magnetic stimulation—all of which Russ Hobbie and I analyze in the 4th edition of Intermediate Physics for Medicine and Biology. For me, hearing these stories makes me nostalgic for my years working at the National Institutes of Health, where I used to collaborate with neurologists such as Mark Hallett (whose research is mentioned by Sacks). Hallett and his team studied all sorts of odd diseases while I was helping them develop magnetic stimulation. In this case, we physicists and engineers were not discovering new biological ideas or medical abnormalities, but we were providing the tools for others to make these discoveries. And, oh, what tools!

Sacks notes there are some patients who have lost their ability to tell which of two tones is the higher pitch (but can still hum a song). These patients are in contrast with those rare individuals with perfect or absolute pitch; they can tell what note a sound is when heard in isolation. My sister has something approaching perfect pitch. When I was in high school, I took piano lessons. Whenever I played a wrong note while practicing (which was quite often) she would call out from an adjacent room “F-sharp!” or “B-flat!” Do you know how annoying it is not only to have your mistakes pointed out for all to hear, but also to have the specific note identified precisely? Worst of all, she was always right. Some of these piano pieces she had played herself, but others she had not; she was just able to identify the pitch. I have always envied people with perfect pitch, but Sacks raises an interesting point. If people with perfect pitch hear a song played flawlessly but in the wrong key, they get all agitated and upset (he compared this to seeing a painting with all the colors wrong). I, on the other hand, would remain blissfully unaware of the problem. When I was in graduate school in Nashville, I bought a used piano from a blind fellow who refurbished pianos for a living. This particular piano was so old that he could not tighten its strings completely, so the piano was tuned about 3 steps too low (He gave me a good deal on it). The improper tuning never bothered me in the least (my sister hated that piano). However, sometimes my weakness with tonal discrimination has caused me some embarrassment. I played tuba in my high school band, and before concerts the director would have us all “tune up”. The first clarinet would play a note, and we would each play the same note in turn to make sure we were in tune. I always hated this, because I could never tell if I was sharp or flat, and the director would usually end up yelling at me in frustration “You’re flat. Flat! Push the tuning slide in!”

Sacks’s book got me to thinking about all sorts of unusual sensory perceptions. He describes people who could hear but could not perceive music, and I thought it must be like someone born without sight. But Sacks had a better analogy; imagine someone born colorblind (say, completely color blind, instead of just lacking one of three color receptors). How do you describe color to such a person? It has no meaning. How do you describe music to someone born unable to make sense of it? Then I began thinking of other odd sensory inputs, like magnetoreception and the ability to perceive the polarization of light. Humans can’t perceive these signals, but other species can. If you will let me indulge in a bit of anthropomorphization, I suspect there are some bird families who sit in their nest at night saying to each other “those humans can’t perceive magnetic fields or polarization! How to they ever get home?”

Finally, for those of you who know Suki, let me provide a quick update. Earlier this year she damaged her anterior cruciate ligament, and our walks came to an abrupt halt. After much debate (she is a small dog, and is 10 years old) we decided to have her undergo surgery. The veterinary surgeon Dr. McAbee did a marvelous job, and we are now back to our walks as if nothing ever happened.

Friday, January 6, 2012

Destiny of the Republic

Destiny of the Republic: A Tale of Madness, Medicine and the Murder of a President, by Candice Millard, superimposed on Intermediate Physics for Medicine and Biology.
Destiny of the Republic:
A Tale of Madness, Medicine
and the Murder of a President,
by Candice Millard.

Regular readers of this blog know that I am in the habit of listening to audio books while I take my dog Suki on her daily walks. My tastes lean toward science, history, and biography, and I always keep a watch out for biological or medical physics in these books. Over the Christmas break, I listened to Destiny of the Republic: A Tale of Madness, Medicine and the Murder of a President, by Candice Millard, about the assassination of President James Garfield in 1881, shot by madman Charles Guiteau.

The book tells the fascinating story of Garfield’s nomination at the Republican National Convention in 1880, back in a time when conventions were less choreographed and predictable than they are today. Garfield nominated his fellow Ohioan John Sherman (General William Tecumseh Sherman’s brother), who was running against Senator James Blaine and former president Grant. After many ballots in which no nominee obtained a majority, the delegates turned to Garfield as their compromise choice. After being chosen the Republican nominee, he defeated Democrat and former Civil War general Winfield Scott Hancock in the general election.

A few months after being sworn in, Garfield was shot by Guiteau, who had applied for a job in the new administration but had been turned down. The bullet did not kill Garfield immediately, and he lingered on for weeks. At this point, medical physics enters the story through one of the book’s subplots about the career of Alexander Graham Bell, inventor of the telephone. Millard tells the tale of how Bell set up one of his early telephones for demonstration at the 1876 Centennial Exposition, but was ignored until a chance meeting with his acquaintance, Emperor Pedro II of Brazil, who drew attention to Bell’s display. Upon hearing that the President had been shot, Bell quickly invented a metal detector with the goal of locating the bullet still lodged in Garfield’s abdomen. The detector is based on the principle of electromagnetic induction, discussed in Section 8.6 of the 4th edition of Intermediate Physics for Medicine and Biology. A changing magnetic field induces eddy currents in a nearby conductor. These eddy currents produce their own magnetic field, which is then detected. Essentially, the device monitored changes in the inductance of the metal detector caused by the bullet. Such metal detectors are now common, particularly for nonmedical uses such as searching for metal objects buried shallowly in the ground. At the time, the device was rather novel. Michael Faraday (and, independently, Joseph Henry) had discovered electromagnetic induction in 1831, and Maxwell’s equations summarizing electromagnetic theory were formulated by James Maxwell in 1861, only twenty years before Garfield’s assassination. Being a champion of medical and biological physics, I wish I could say that Bell’s invention saved the president’s life, or at least had a positive effect during his treatment. Unfortunately, it did not, in part because of interference from metal springs in the mattress Garfield laid on, but mainly because the primary physician caring for Garfield, Dr. Willard Bliss, insisted that Bell only search the right side of the body where he believed the bullet was located, when in fact it was on the unexplored left side.

Another issue discussed in the book is the development of antiseptic methods in medicine, pioneered by Joseph Lister in the 1860s. Apparently the direct damage caused by the bullet was not life-threatening, and Millard suggests that if Garfield had received no treatment whatsoever for his wounds, he would have likely survived. Unfortunately, the doctors of that era, being skeptical or hostile to Lister’s new ideas, probed Garfield’s wound with various non-sterile instruments, including their fingers. Garfield died of an infection, possibly caused by these actions.

I enjoyed Millard’s book, and came away with a greater respect for President Garfield. Bell’s metal detector was used to locate bullets in injured soldiers throughout the rest of the 19th century, until X rays became the dominant method for finding foreign objects. It is an early example of the application of electricity and magnetism to medicine.

Listen to Candice Millard speak about her book.

 Candice Millard speaking about Destiny of the Republic.
https://www.youtube.com/embed/TmebtlLULpY

Friday, April 9, 2010

Galileo's Daughter

Galileo's Daughter, by Dava Sobel, superimposed on Intermediate Physics for Medicine and Biology.
Galileo's Daughter,
by Dava Sobel.
As is my habit, I listen to recorded books when I walk my dog Suki each day. Recently, I listened to the book Galileo’s Daughter, by Dava Sobel. I was surprised how touching I found this story (like Galileo, I have two daughters). It is a biography of Galileo Galilei (1564–1642), the famous Italian scientist, but also tells the parallel story of Sister Maria Celeste (1600–1634), Galileo’s daughter who was a nun at the San Matteo convent near Florence. The book quotes Maria Celeste’s letters to Galileo, which Sobel herself translated from Italian. (Unfortunately, Galileo’s replies are lost.) Maria Celeste comes across as a loving, intelligent and extremely loyal daughter who played a central role in Galileo’s life. “She alone of Galileo’s three children mirrored his own brilliance, industry, and sensibility, and by virtue of these qualities became his confidante.”

I tend to see biological physics everywhere, and I found some in this story. Late in his life, Galileo published his final book, Two New Sciences. One of these sciences was the motion of projectiles, and the other was what we would now call the strength of materials. In the part about materials, Galileo addressed the issue of scaling in animals. I quote Sobel, who quotes Galileo:
I have sketched a bone whose natural length has been increased three times and whose thickness has been multiplied until, for a correspondingly large animal, it would perform the same function which the small bone performs for its small animal. From the figures here shown you can see how out of proportion the enlarged bone appears. Clearly then if one wishes to maintain in a great giant the same proportion of limb as that found in an ordinary man he must either find a harder and stronger material for making the bones, or he must admit a diminution of strength in comparison with men of medium stature.
Scaling: Why is Animal Size so Important? by Knut Schmidt-Nielsen, superimposed on Intermediate Physics for Medicine and Biology.
Scaling: Why is Animal
Size so Important?
by Knut Schmidt-Nielsen.
(You can find the picture of the two bones here.) This example of how the strength of bones must scale with animal size did not make it into the 4th edition of Intermediate Physics in Medicine and Biology, although I sometimes discuss it when I teach PHY 325 (Biological Physics) at Oakland University. It serves as an excellent example of how physics can constrain the structure of animals. I won’t hold it against Galileo that he didn’t get his drawing of the bones quite right; it was the 17th century after all. According to Knut Schmidt-Nielsen (Scaling: Why is Animal Size so Important)
The need for a disproportionate increase in the size of supporting bones with increasing body size was understood by Galileo Galilei (1637), who probably was the first scientist to publish a discussion of the effects of body size on the size of the skeleton. In his Dialogues [Two New Sciences was written in the form of a dialogue] he mentioned that the skeleton of a large animal must be strong enough to support the weight of the animal as it increases with the third power of the linear dimensions. Galileo used a drawing to show how a large bone is disproportionately thicker than a small bone. (Incidentally, judging from the drawing, Galileo made an arithmetical mistake. The larger bone, which is three times as long as the shorter, shows a 9-fold increase in diameter, which is a greater distortion than required. A three-fold increase in linear dimensions should give a 27-fold increase in mass, and the cross-sectional area of the bone should be increased 27-fold, and its diameter therefore by the square root of 27 (i.e., 5.2 instead of 9)).
Russ Hobbie and I discuss the issue of scaling in Chapter 2 of Intermediate Physics for Medicine and Biology. In Problem 28 of Chapter 2, we ask the reader to calculate the falling speed of animals of different sizes, taking into account air friction. The solution to the problem indicates that large animals, with their smaller surface-to-volume ratio, have a larger terminal speed (the speed of descent in steady state, once the acceleration drops to zero) than smaller animals. We end the problem with one of my favorite quotes, by J. B. S. Haldane
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, and man is broken, a horse splashes.
When listening to Galileo’s Daughter, I was surprised to hear Galileo’s own words on this same subject, which are similar and written centuries earlier.
Who does not know that a horse falling from a height of three or four braccia will break his bones, while a dog falling from the same height or a cat from eight or ten, or even more, will suffer no injury? Equally harmless would be the fall of a grasshopper from a tower or the fall of an ant from the distance of the Moon.
Of course, the climax of Galileo’s Daughter is the great scientist’s trial by the Catholic Church for publishing a book supporting the Copernican view that the earth travels around the sun. Although I was familiar with this trial, I had never read the transcript, which Sodal quotes extensively. Listening to the elderly Galileo being forced into a humiliating recantation of his scientific views almost made me nauseous.

Sobel is a fine writer. Years ago I read her most famous book, Longitude, about finding a method to measure longitude at sea. Galileo himself contributed to the solution of this problem by introducing a method based on the orbits of the moons of Jupiter, which he of course discovered. However, the longitude problem was not definitely solved until clocks that could keep time on a rolling ship were invented by John Harrison. I have also listened to Sobel’s book The Planets, which I enjoyed but, in my opinion, isn’t as good as Longitude and Galileo’s Daughter. I hope Sobel continues writing books. As soon as a new one comes out (and arrives at the Rochester Hills Public Library, because I’m too cheap to buy these audio books), Suki and I plan on taking some long walks. I can’t wait.