Entries in Science (6)
Would You Say a Few Words?

Last Friday (May 10, 2013) I was asked, by our campus president, to “say a few words” at the grand opening of the College of Marin’s new Science-Math-Nursing building. After being introduced by the president, here is what I said:
Thank you very much, President Coon.
Good afternoon, everyone. It is wonderful to see all of you here today on this very special occasion.
You know, I was here back in late 2009 when we broke ground for this new facility, and I’m almost sure I remember one of the speakers observing “what a great day this is for the College of Marin.” Well, I must admit: I think this is an even greater day as we celebrate the official opening of our new science math nursing facility.
The building that stands behind me is an amazing space to sharpen our focus on student learning and student success here at the college.
We do talk a lot about student success these days. And rightfully so. I believe that there are a whole range of factors that contribute to student success, and surely a positive learning environment has to rank near the top.
Among the factors of a positive learning environment, I believe, are instructors who are knowledgeable in their content areas, skilled at communicating with others, facilitating student learning, and able to do it in caring and supportive ways. We have a cadre of highly-skilled full-time and part-time instructors in this building who do all of that very well.
Another very important part of a positive learning environment - and I guess I’m talking a little bit about my philosophy of education here - is the physical space where that learning takes place. With the availability of this new science math nursing building, we now have a first-rate facility comprised of classrooms and labs that are firmly situated in the 21st century. We are very lucky. Our already outstanding programs in the sciences, in math, and in nursing have gotten a very big boost with the creation of this building. I would like to thank the citizens of Marin County for extending their vote of confidence in us and in voting for the resources to make this space a reality.
My most sincere thanks to you all.
[For a collection of my photos taken during the construction phase of the Science-Math-Nursing building, click here.]
Doctoring in the Western World

Please note:
This long essay (it’s at least four times optimum blog-post length) makes my personal case against the “medical establishment.” I do not take on the insurance companies here, though, but rather the doctors who provide front-line health care for us all.
Although I deal at length with the PSA blood test in the discussion below, I totally omit mention of the controversy currently raging about this procedure.
Caveat lector: this post would likely merit an “R” rating near the end...
I’m one of those old geezers for whom the TV commercials advertising such products as Flomax and Proscar are made: I have an enlarged prostate [benign prostatic hyperplasia (BPH)]. BPH is characterized by a number of urinary symptoms, one of the most obvious being the number of times I have to get up during the night to relieve myself. (For a list of other symptoms, click here.)
As I have monitored my condition over the last 12 years, with the assistance of various urologists in the cities I have lived, I have regularly (at least every six months) undergone the blood test for prostate specific antigen (PSA), the front-line screening protocol for prostate cancer. During this time, as my prostate has grown in size, my PSA has risen slowly, steadily, but not dangerously. I keep track of the results by means of an Excel spreadsheet and graph, and even furnish my doctors with a least-squares plot of these data at every appointment. At one point, back in late 2002, there was an unusual spike in the one of the readings, and I was advised to have a prostate biopsy. This procedure is a very invasive and uncomfortable one, but I went ahead, in early 2003, and did it anyway. After eight full days anxiously waiting, I finally was informed that the result was negative. Since that time I have simply continued to monitor the slow, steady, predictable rise of my PSA level.
Well: except that that all changed recently. In both January and March of this year, my PSA tests have yielded significantly higher readings – data that do not fit neatly within the paradigm of my least-squares analysis. After the January result, my urologist reacted as I did: one test alone means nothing. Let’s wait a bit (a few weeks) and do it over again.
And that’s what we did, though the second test in March indicated a slightly elevated level compared to the January number. It was at this point that he stated that it was time for concern and said, “you know where we go from here.” He meant a biopsy, of course, and I declined, indicating that I wanted to wait for one more blood (PSA) test before undergoing that procedure again.
However, he was very insistent that we do a biopsy, and I was just as opinionated that it was not yet time. I told him that I had one more hypothesis to test out before I would submit to the procedure. Simply put, my theory is: my PSA number is inflated due to a new dietary supplement I had started taking. Last October (over two months prior to the January blood test), I began a product called ArthroZyme, advertised as an anti-inflammatory agent, to see if it would help me out with the chronic muscle pain that has plagued me for the last few years. The active ingredient in this product is a proteolytic enzyme called serratiopeptidase. And, as it turns out, PSA itself is itself a proteolytic enzyme. I believe it is much more than coincidental that immediately after I began taking a proteolytic enzyme supplement I start testing differently for a specific proteolytic enzyme. I believe the two phenomena are connected and that this is the simplest possible, and most likely, explanation. I contend that this hypothesis is one that merits serious consideration, and that I should, therefore, simply stop taking the supplement and re-test.
As it turned out, I was only able to leave the urologist’s office in early April after hearing the strongest language he could muster that I was making a mistake and the he strongly recommended this test. NOW.
Of course, I don’t think I’m being at all unreasonable.
- I’m the guy, after all, who was told, by TWO doctors, in no uncertain terms, one night in an emergency room, that he had bladder cancer. But I didn’t, as the cystoscopy (now there’s an invasive procedure), performed a couple of days later in a doctor’s office, conclusively demonstrated.
- I’m the one who submitted to a biopsy back in 2003 on the basis of a PSA spike. And I didn’t have cancer, then, either.
- I’m the one who has been totally discounted by my primary care physician, to the point of being told that my body aches and pains were “psychiatric” in origin and that the supplements I take (and rely on) couldn’t possibly be doing me any good.
- And, I’m the person who was kept waiting for a half hour in a neurologist’s office after having experienced the intake nurse botch the explanation of my test results – only to finally talk to the doctor and learn that the (MRI) result in question was inconsequential.
In short, my trust of most medical professionals is exceptionally low, based on a history of negative experiences, how I’ve been treated by said “professionals,” and the inability of so-called “Western medicine” to get a cancer diagnosis right or to provide any kind of explanation for what’s going on with my chronic pain.
In the urologist’s office, I had to ultimately, assertively, take charge of the meeting and say, “look, this is how it’s going to be: I’m stopping the supplement and we’re going to re-test in a few weeks.” I took away with me a lab order for the blood test and an appointment card for early June.
THEN: last week I showed up for a previously-scheduled appointment with my primary care physician. After a very cursory greeting, he immediately launched into a lecture on how irresponsible he thought I was being by ignoring the urologist’s advice. In fact, he went directly to his computer screen and read to me, word-for-word, the report forwarded to him from my urologist. The write-up was clearly written to make certain that there was no doubt that I was ignoring sound medical advice, but the most irritating and distressing element of the exercise was that he read it to me with an intentional and highly-exaggerated condescending attitude. He was clearly trying to shame me into changing my mind by giving me the message of (a) how stupidly, (b) how crazy, or (c) how both, I was behaving.
“Interesting,” I said. And then I showed him the latest PSA graph, the supplement bottle containing the proteolytic enzyme I had stopped taking, and offered my explanation. I indicated to him that I was merely applying the well-known principle of Occam’s Razor: “The simplest explanation for a phenomenon is most likely the correct explanation.”
To which he, again, with an air of annoying superiority, replied, “that would be fine, except that what you offer is NOT an explanation at all, and you’re taking unnecessary chances with your life.”
I had experienced this kind of situation with him before, of course. The first true break in our relationship came about when he labeled my physical symptoms as likely “psychiatric” in nature. During the appointment at which that language was used, I let it go; I confronted him on his condescending behavior the next time I saw him, however. And he apologized at that time.
He apparently really doesn’t get it, though. Now the same kind of attitude was being exhibited over my PSA result. I sat silent for a half minute or so, took a deep breath, and then said,
“Look, I really don’t think this relationship is working out. I have much different expectations of physician behavior than you have been able to provide. Some of the qualities I expect from you are clear communication, respect, decency, dignity, honesty, and support. I resent your snobbish, superior, condescending attitude and your assumption that you know what’s “right” for me. Let me tell you, I’ve spent a lifetime becoming an expert not only on my body, but on knowing my inner self...and believe me, the numbers you have cataloged away in your little computer there are not me. I know me. You don’t. Not at all. And, you’re apparently exceptionally reluctant to allow me the freedom to make decisions about this body myself. I think it’s best to part ways, and I’m wondering if there’s any physician you know of that would be open-minded enough to take on a patient who knows what self-care is and is seeking a doctor who will serve as a consultant to that self-care.”
And I wasn’t done yet...
“Look” (I said yet again; I was repeating myself), “I’ve got the lab order for the PSA test right here in this folder. And I’ve got my next appointment with the urologist scheduled. I’ve got time scheduled away from work in June for a trip, but the plans are soft. I can easily change them and stay here and be available for a biopsy. I’m testing a hypothesis. A reasonable one, I think, but I know I could be wrong. I’ve got the plans all laid out. I’m taking care of myself. What the fuck is your problem?!”
This guy, taken in tandem with the urologist a couple of weeks earlier, had obviously struck a nerve with me: pushed my buttons big time. I immediately started reflecting on all the pre-med students I had competed with in math and science classes in college – along with my complete and utter disdain for them at the time. They were all about their course grades and med-school admission. They were exceptionally good memorizers of content, but, generally speaking, amazingly poor critical thinkers. They always got A’s, but I always got a higher A, especially in those courses that really meant something: organic chemistry, physical chemistry, etc. I pretty much kicked their collective butts. Pre-med? HA!
During my time in my primary care doc’s office, I became angry, resentful, (defensive, of course), and as assertive as I’d ever had to be in that kind of environment. I was appalled that I hadn’t changed doctors when he had labeled me a nut case the year before.
He ultimately apologized. Again. He said that he did listen to me and support me. And he said that he really didn’t know of anyone that practiced medicine any differently than he did...that everyone he knew was as skeptical of dietary supplements as he was, and suspicious of patients who experimented with unproven “natural” substances who sometimes ascribed to them “magical properties.”
I left the appointment by reiterating that I had a plan, that I was sticking to it, and that, despite his insinuations, I was neither stupid nor crazy. I said, simply, I knew how to take care of myself, and I was doing just that.
Now: could I be wrong about all this? Could I be merely delaying the inevitable cancer diagnosis by insisting on testing my theory? Might I simply be afraid of undergoing a painful, invasive procedure? Might I be terrified that I really do have prostate cancer?
The answers to the above: YES, of course. To any or all of them. But, it seems to me that I have a legitimate theory, one that I’m entitled to test out. The blood will be drawn next week and we’ll soon see if the PSA level drops. Or not.
Could I die? Well, yes. We’re all going to die, right? Have I put my life at risk by testing out a reasonable hypothesis? I rather doubt it, but, as I remind the doctors, it is my life to risk. In the matter of my body, I get to choose. Pure and simple, I get the final word here. It’s my body. It’s my choice.
Dear Doctor: If you are unable to partner with your patients in their care, then you have little business doing your business. Go be an auto mechanic, where the computer diagnostics these days are amazing, and quite often accurate, I’m told. Or, at least, do something else. And, for sure, if you can’t treat me with any more dignity, respect, or support than you’ve been able to muster so far: please go fuck yourself.
Soundtrack Suggestion
I told the witch doctor I was in love with you
I told the witch doctor I was in love with you
And then the witch doctor, he told me what to do
He said that ....
Ooo eee, ooo ah ah ting tang
Walla walla, bing bang
Ooo eee, ooo ah ah ting tang
Walla walla, bing bang...
Ooo eee, ooo ah ah ting tang
Walla walla, bing bang
Ooo eee, ooo ah ah ting tang
Walla walla, bing bang
(“Witch Doctor” – David Seville)

I need to be honest: my theory was wrong. I still think the hypothesis had merit, and that I was right in testing it out, but after stopping the supplement for two months, my PSA remained the same. I have now consented to a prostate biopsy, presently scheduled for June 22.
Stay tuned.

Greetings!
(Sorry about this group email, but it’s most efficient in getting the word out to those of you I promised the news right away...)
Yes, the news is good: the biopsy (just performed yesterday) is negative. No cancer!
After a terrible day yesterday (this procedure is way not fun), I woke up this morning with the pain gone and an optimistic attitude. I had this sense that I would get the news today (it was promised by Wednesday, tomorrow), and that it would be good. My intuition was right on, it seems. The doctor called at 1:40 p.m. and I do not have to see him again for another six months...what a relief!
Thanks for all your kind words and loving support. It (you) made a huge difference for me!
-jim






Maximum Multiplicity

On an episode of the TV program Curb Your Enthusiasm (HBO) I watched recently, Larry David took off on one of his famous stream-of-consciousness digressions – this time about his preference and tendency to use stalls, rather than urinals, when visiting public restrooms.
Interestingly enough (or maybe not), his admission stimulated some electrical impulses and activity in my warped brain that led me to think of Hund’s Rule of Maximum Multiplicity – a topic you must remember from general chemistry class. Of course, this postulate is often referred to as “the bus-seat rule.”
Hund’s Rule describes the process of populating atomic orbitals with electrons – specifically the way those electrons are arranged – as atomic number increases. Quite simply, the rule stipulates that if two electrons have two spaces (i.e., orbitals) to occupy, then they would rather occupy one orbital each rather than “pair up” and occupy just one orbital.
So, for example, take the case of the element Boron which has three “p” orbitals but just one electron in that particular energy level. For argument’s sake, let’s say that that lone electron occupies the p(x) orbital. The next element on the periodic table, Carbon, has the same number of p orbitals (but one more electron than Boron) with one electron in each of the p(x) and p(y) orbitals. And Nitrogen, the next element in line, has three electrons in this energy level, one in each of the p(x), p(y), and p(z) orbitals. Can you visualize this at all? Electrons are distributing themselves among the p orbitals much as passengers on a bus: nobody sits next to someone else unless and until they really have to. So, in the case of Oxygen, yet the next element under consideration, the configuration would have two electrons in p(x) and one each in the other two orbitals. (The two electrons in p(x) are said to be a “lone pair.”)
So, you’re probably wondering where I’m going with this? (If you’re still reading, that is). What does Larry David’s use of stalls have to do with Hund’s Rule and electrons?
Well, actually, hardly anything. It’s just that I’ve been thinking about bathroom behavior myself (remember I’m talkin’ Larry David not Larry Craig kinda stuff here!)…given that last summer, in some of the buildings on campus, new urinals were installed. Our urinals are supposedly the latest in “green” technology – as they are waterless devices that don’t use H2O to flush with. They actually don’t flush: all in all, not a bad idea to conserve water, and the campus is making points in the community for its conservation efforts.
The thing is, the urinals have been installed with no privacy dividers between them. When you’re standing there doing your business, it’s sort of like lining up at a public trough. And, for me, that’s not the most comfortable situation in the world. What’s the deal here, anyway? We’re already conserving 2.5 million gallons of water per year (!) …do we really have to give up our privacy rights too?
So: this is where the bus-seat rule comes into play. With no dividers between the urinals (hence no privacy) and, I think, many of us modern men having similar reservations about the public-trough concept, what we do is situate ourselves as far apart as possible when we’re in the restroom doing our thing. For example, I’ll walk in and I’m the only one in there. I’ll take the urinal that’s next to the partition separating the sink and the urinal sections. The next guy comes in and will take the urinal that’s tenth (out of ten) in line…around the corner a little bit. If a third person comes in, he’ll take one of the urinals approximately midway between us. And so on.
Given this, doesn’t it seem that our bathroom behavior is a little like seating on a bus or electrons in orbitals? Or, I guess, even other types of human behavior. For example, a blogger named Vishy, in a post from early 2005, observed that Hund’s Rule can also apply to seating ourselves in a cafeteria or taking the elevator.
Not that keeping your distance from others is such a bad thing. Sometimes there are certain activities that are just plain better when performed alone. Hund tells us that the pairing of electrons is an unfavorable process where energy must be expended in order to make it occur. I suggest that the closeness of humans, in some situations, is not the greatest of things either… with there being energetic, emotional and social barriers to making it (i.e., the closeness) happen.
Me? I support the practice of privacy dividers in our public restrooms or, in their absence, maximum multiplicity.



The Science Fair Experience

The 2006 Mt. Hood Science Expo (MHSE, our own regional science fair) is now history (well, except for the residual paperwork and escorting the winners to Indianapolis in May). Although the number of actual entries that showed up turned out to be rather modest (around 60), from the feedback I’ve received so far, the event was a rousing success. As with any large get-together of human beings, there were periodic crises that arose throughout the day; all were quickly and efficiently resolved by one or another of us, though.
My army of helpers was both large in number and hugely talented. An inner circle of us wore “Board of Directors” on our name tags…we were the primary planners and implementers. Then, we had professional-level judges who took off from their real jobs and gave us an entire day’s worth of time to talk with student participants and to assess their projects. Further, we recruited a very impressive showing of other volunteers, who did everything from covering the gym floor with a protective mat, to setting-up, tearing-down and carrying the tables. This kind of undertaking takes, at various points, significant amounts intellectual, emotional and physical energy. My jobs were mostly intellectual and emotional, leading me to a point of utter fatigue at the end of the day yesterday. Luckily, I had volunteers who carried on even after the awards ceremony to attend to the cleanup tasks. Some even showed up at the gym at 6:30 a.m. this morning to complete the job!
We had quite the range of projects. At the top end, we had students who just flat out “knew their stuff,” had done real science, and presented it in a way that the judges could understand and fairly evaluate. It was obvious that these kids were bright, articulate, and headed on their way to someplace significant in life. Wow, what a bunch! Of course, we had some projects on the other end of the spectrum as well. As the day wore on, and it became increasingly obvious that they were not really competitive, I realized I was feeling a little sorry for them. However, during my orientation speech to everybody at the beginning of the day, I had indicated that their science-fair experience was likely to be an intellectually-stimulating and growth-producing one whatever the outcome of their projects. I’m betting that if they didn’t understand me in the morning, some may have caught on to my meaning by the end of the day.
Even though a small core of us were dealing with a research-ethics dilemma as late as 5:00 p.m. — one that decided the last category winner — we still began the awards ceremony only a couple minutes late, a little after 6:00 p.m. That part of the program went quickly and smoothly as well (sigh…if only our Master of Ceremonies was a tad more familiar with some of the names!), so we were actually done ahead of the anticipated schedule.
I am hugely, immensely, beyond-belief indebted to several core people that were my MHSE team. This list includes, but is not limited to: Heather Ohana, Rachelle Ham, Valory Thatcher, Melissa Gonzales McNeal, Doug McCarty, Jack Brook, Jack Fassel, Tom Worcester, Stephanie Jones, and Jill Parisher. Original Board of Directors Member Michael Russell, who found the need to take leave of his responsibilities midway through our planning activities because of family issues, was with us in spirit yesterday, I'm sure. His father died during this last week, and the memorial service was scheduled at the same time as our awards ceremony last night. Michael, our hearts were with you, even though our bodies were not.
Near the end of the day, right before the awards ceremony began, Jill relayed a little story to me that almost brought me to tears. She indicated that she’d been talking the day over with one of the judges who very frequently works these regional fairs, and who had done several in the last few years. Her report to me was that judge said that this was the best-run regional fair he had ever experienced. The flow to our day was well planned-out, and it appeared that the organizers had basically thought of everything to make this a positive experience for everyone.
We tried. And I think we pulled it off. We done good, gang!




Why Study Science?

[What follows is an edited version of an email I sent to the science faculty at the college today. The task at hand is, quite simply, to propose a small number of goals for the study of the natural sciences.]
In my humble opinion, this is important stuff. By identifying and articulating goals for the natural sciences we are saying who we are. Do we know who we are? If we don’t, or if our answer keeps changing, isn’t it valuable to engage in thinking about this every so often? And shouldn’t we be publicly proclaiming who we are and what we do by identifying our goals?
I found myself reacting, initially, to one of the proposed goals in the email we received from one of our members, i.e., demonstrate application of the scientific method to real world. I would hope that we could eliminate from consideration a goal that uses such a pedestrian term as the “real world.” This, to me, connotes that there is, indeed, a discreet, identifiable, knowable, and objective “reality” — a concept entirely at odds with most everything we can infer from the field of quantum physics. We have come a long way in the manner in which we define our physical world, from a “scientific” viewpoint, just in the time I have been alive. When I was an undergraduate chemistry student, the only application of the Heisenberg Uncertainty Principle that I knew of referred to the position and momentum of an electron: the better we were able to determine the position, the less we knew about its momentum. I’m sure we still teach that. However, in more recent times, Heisenberg is cited widely in all areas of inquiry, namely that we now assume the mere observation of a phenomenon fundamentally changes it. That brings me back to “what is the ‘real world’ anyway?”
I initially became an organic chemist because it was, at that time, my way of “knowing the world.” My experience of the universe had a lot more to do with chemical kinetics and reaction mechanisms of carbon-based molecules than it did with anything having to do with human beings. I was darn good at what I did back then, publishing several articles as a grad student, but one of the reasons I moved on to explore other things in my life, is that I truly believed that there was more than one way of knowing the world and I wanted to continue “knowing” as much, and in as many ways, as I could. People had always fascinated me, and I eventually moved on from researching reaction mechanisms to inquiring about individual-, group- and organizational-dynamics.
Which brings us to “knowing.” The primary epistemological question is: what does it mean to know? (or: what is knowledge?) This is the question of continuing, and endless, philosophical debate. A question that fascinates me. Do you have an answer to what it means “to know” something? Were you, like me, attracted to science because you wanted to know, inquire, research, explore?
If so, shouldn’t we be saying something in our goals for the natural sciences that speaks directly to why and how we inquire into our physical universe (note I didn't say “reality”). What else we should be identifying as goals, I’m not entirely sure ... so I don’t really have a definitive set of goal statements that would replace the ones we received. I do know there is language out there, proposed by other science departments, that probably more closely match my world view, however.
For example, the General Education Core Curriculum of the State of Illinois, states that the purpose for studying science is to:
● develop students’ understanding of the methods of scientific inquiry, including the formulation and testing of hypotheses;
● familiarize students with selected scientific principles in the physical and life sciences;
● enable students to make informed decisions about personal and societal issues.
OK, well, maybe this is enough of a monologue for today! (I think there was a point to all of this.) I would like you all to participate. I would like for us to examine who we are as scientists. And I would like to translate all of that into goals for the sciences that we feel comfortable with in our public declaration.
I welcome your thoughts, ideas, opinions, and competing views...



