Ambien Ramblings

Me: "I'm happy I'm not in the state one-one-prime."

Pat: "What's that?"

Me: "That's where I don't know what I'm doing and the next adjacent state is an oscillation parameter of the first."

 --  A conversation I had with Pat after taking an Ambien.

Pat just found a notebook where she recorded our conversation.  Too busy these days to write, through I have lots of material to report.  Next time...

Errors and Creativity

In any deep and complex endeavor, it is easy to make mistakes.  Even after intense scrutiny, errors in logic and reasoning can be difficult to catch.  However, when properly harnessed, errors can lead to new and interesting ideas.

Recently, a bright junior colleague made a mistake in a calculation, and I am sure that he was down on himself over the whole thing;  so, I wrote him the following email (which I have modified slightly for you).  After rereading it, I thought it would be good general advice to all students who are struggling with work at the boundaries of the unknown where mistakes are common.

Dear Student,

Do not be hard on yourself about such errors.  We all make them.  When you have been around long enough to have made all the simple errors, you move on to the more complex ones.  As you mature, you will make these transitions over and over again.  The two of us are similar in the sense that we perhaps make more errors than the average physicist.  This can become a strength if you use it to your advantage.
 
I believe that the tendency to make mistakes is associated with creativity. Mistakes take us into new territories that others may never imagine.  Often, it's a mistake that leads me in new directions that brings me into uncharted domains.  When my colleagues question me about how I ever even thought of doing X, I can't explain it.  Now that I think about it, I should answer that it was a string of errors that led me to X.  These random meanderings avoid the huge walls that block the straighter paths.

The key is to work hard and tirelessly in the pursuit of entertaining lots of new ideas, be slow to publish so that you can catch your mistakes before they become public, and allow yourself times of unrestrained creativity but temper those times with disciplined thought.  And most importantly, do not get caught up in mathematics without thinking about the physical consequences.  It is the physics that is the most fulfilling and the best guide through your intellectual hardships.

Should I get back on Statins?

Next week, I need to make a decision that may strongly impact my health a decade or two down the road.   The million dollar question, "should I get back on statins?" given that a high fat diet worked for me in the past but is a bit slow to lower my risk factor this time around.  This is a long post so for the short summary, you can skip to the end (Section 4).

1. Background - 1996 to 2012

a. Experts were saying that a high fat diet would not result in weight loss, but would raise cholesterol

A short digression will explain how I got to this point.  In 1996, I started the Atkins diet to combat my growing bulge.  At the time, I was warned not to do it because (1) Eating lots of fat can't make you lose weight; and (2) My cholesterol would rise and I would certainly dye of a heart attack.  My doctor also cautioned me about these issues; but, being an open-minded and intelligent individual, he suggested that my cholesterol be monitored periodically.  He also informed me that the best medical advice of the day was that the ratio of total cholesterol to HDL, called the risk factor, should be below 5 -- but the lower the better.

b. The experts were wrong.  My weight plummeted and my health improved while I was eating lots of fat

A couple months after I started the diet, the ratio tested at almost 8 (see green points on the plot to the right) -- so huge that I was truly concerned.  My cholesterol from a year before was inching up to 5, so 8 was a huge increase.  Since my weight was literally dropping exponentially, as you can see from the red points in the diagram to the right, I decided to wait another 3 months (Atkins stated that the cholesterol in his patients dropped in the long term).  The reading was 6 and then three months later, 4, and six months after that down to almost 3.  So, the critics were wrong.  My weight and cholesterol remained low for over 6 years.  As an added benefit, I felt great; my skin cleared to the sheen of a baby's butt, my weekly migraines disappeared, indigestion was gone, blood pressure plummeted, insomnia was cured, and I was full of energy.  I may be confusing correlation with causation; but, all these effects correlated with my weight loss and risk factor decrease.  The bottom line is that getting over 75% of my calories from fat and about 20% from protein did not make me unhealthy according to the metrics used by the medical profession.

c. The diet was tasty and easy to maintain for more than 6 years

The diet was not difficult to maintain because the food was tasty and enjoyable, and I never felt hungry.  What killed my "healthy" lifestyle was traveling overseas.  In Europe, the "healthy foods" and "exercise" did me in.  My wife and I spent a large fraction of one delightful summer in Belgium.  We had no car so we biked or walked everywhere; yet, I gained over 10 pounds.  A few more years of traveling overseas and my weight and cholesterol slowly crept up; so, I eventually took statins and decided that my health was protected, so I went back to eating pasta, bread, fruit, vegetables, and of course meat.  By the time we got back from our trip to Italy last summer, I was nearing my peak weight of 1996, so I decided to once again go on the Atkins diet for good.

2. The present - Summer of 2012 to Now

I started the Atkins diet for the second time at the end of the summer of 2012.  The data appears to the left (the black points represent my weight).  Over the first two weeks of the diet, my weight hovered between 205 and 210.  Back in 1996, I had lost about 10 pounds in the same time interval (for comparison, blue curve from my 1996 data superimposed in the recent data.)

Internet searches revealed articles that claimed statins were responsible for all kinds of evils, from fog brain to fatigue to increased blood sugar to muscle pain.  I had experienced all these same symptoms to varying degrees.  However, these articles did not offer proof.  They were based on lots of anecdotal evidence.  It is not unreasonable for people to experience all these symptoms as they age, and since statins are prescribed to older people, one could easily confuse correlation with causation.

a. Is Ezetimibe/Simvastatin the Culprit?

I was taking Ezetimibe/Simvastatin for my cholesterol, and it did a good job of lowering it to an acceptable level.  Just as I was getting frustrated with my lack of success on my diet, I also read articles suggesting that while Ezetimibe/Simvastatin does indeed reduce cholesterol, some studies showed that this particular combination (ezetimibe is a cholesterol absorption inhibitor and simvastatin a statin that inhibits HMG-CoA) was no better in outcome than a simple statin.  And since statins alone did not lower my cholesterol, I wondered whether I was really being protected from heart disease.

b. Testing the hypothesis that Ezetimibe/Simvastatin interferes with weight loss

While I could not determine the efficacy of the Ezetimibe/Simvastatinin in protecting me from heart disease, I could test its effect on weight loss.  On day 19, I stopped taking my medication and the weight began to consistently drop.  I accept that this may have been a coincidence, but I noticed improvements in my overall well-being - again a subjective observation.

I regularly play floor hockey year round and ice hockey in the winter.  Since starting my Ezetimibe/Simvastatinin prescription, I felt a general degeneration of physical stamina.  After sprinting for 10 seconds, I was exhausted, and needed to rest for longer and longer periods of time between shifts. More depressing was the unpleasant exhaustion I experienced for at least 12 hours after playing.  The nature of my fatigue was not the good feeling after a workout.  It was a diseased feeling.  Hard to explain, but I attributed it to getting older.  Remember, correlation does not imply causation, so I had no reason to believe that Ezetimibe/Simvastatinin was to blame.

About two years after starting to take my medication, I had an unexpected hit of fog brain.  It was very distressing and it resulted in a lasting general fuzziness of my senses.  I was concerned enough to visit my doctor, who did various tests including an MRI of my head.  Nothing showed up.  Again, I attributed this to aging.

After I stopped taking Ezetimibe/Simvastatinin this year, my energy and stamina returned.  I can now sprint in multiple bursts in a shift without fatigue and I once again feel blissful fatigue after each game, which fades after just a couple hours.  The improvements are so extreme that I am certain that the effect is real. And its been this way consistently for five months.  It's harder to say whether or not the termination of medication has impacted my occasional bouts of fog brain. On this front, I would say the results are inconclusive.

c.  Effects of high fat diet on cholesterol

In my diet of 1996, my cholesterol drop lagged my weight loss by about 6 months.  In reading many books on the topic, and even mentioned in Atkins book from the early 70s, the first phase of an Atkins diets is associated with a cholesterol increase due to cholesterol entering the blood stream as fat is metabolized.  Once weight loss levels off, cholesterol drops.  This is indeed what I observed, with more than a factor of 2 drop in my risk factor.

To track my results this time around, I am monitoring my blood (glucose, ketones, triglycerides, HDL, LDL, etc.) on a weekly basis.  My experiment is complicated by the fact that I stopped taking medication during the diet and then only later started doing blood tests.  In the newer figure above, the horizontal dashed red line represents my risk factor (total cholesterol/HDL) when on medication and the red points show my measurements after getting off the meds.  There is a clear increase in risk factor over time, though with sawtooth features.  The horizontal solid red line is the danger level, and I am in very high territory, though not as high as during the initial phase of my 1996 diet.

Because I have changed both my diet and my medications, there is no clear way to deconvolute the two.  However, there is one striking feature;  my weight plateaued between about day 40 and 90, followed by a precipitous increase in the rate of weight loss.  In contrast, the 1996 data shows a steep and steady drop.    Could the plateau be due to my metabolism making an adjustment to me stopping the medication, and I am finally in the state of rapid fat loss, thus the increase in risk factor?  Did the medication change the equilibrium point of my metabolism to a more unfavorable level? Or am I just becoming old?

d. Cholesterol is not the whole story - the size of LDL particles

New research has shown that LDL comes in a distribution of sizes.  The tiny particles are the ones that lodge themselves in the arteries, while the big fluffy ones do no damage.  Sadly, there is no such test available in my area.  However, studies show that the triglyceride/HDL ratio is a proxy for the LDL particle size and levels below 2 are good.  The green squares show my data and the horizontal green line labels a ratio of 2.  In this regard, my numbers during my 2012 are good.

3. The Science

The issue of diet has been highly politicized and much of the research is not science.  I recommend that readers check out the books by Gary Taubs to understand how our society has become so averse to fat even in the face of contrary evidence. There have been many criticisms of his book that he selectively chooses data that supports his views and ignores the other data. To some extent this is true.  However, his explanations ring true based on my experiences.  The problem is that counter arguments also make sense, so how is the patient to decide the best course of action?
 
My intention is to study the scientific literature to develop an understanding of the ideal healthy lifestyle.  Sadly, this is a daunting task given the huge number of studies.  Also, given the complexity of the human body, variations between individuals, and the difficulty in doing clean studies, it is likely that no single strategy exists that applies to all individuals.  If this is the case, it is foolish to come up with a one-size fits all recommendation, yet that is how patients are treated.

a. How can we judge the truth of the matter?

 Here are the facts.

1. Double blind studies are the hallmark of research that involves people but are not are clearly not possible to implement in diet research.  My own study is not blind at all, and therefore not reliable as a test of any hypothesis, though it does confirm that increasing fat intake and decreasing carbohydrates has resulted in weight loss (1996 data and 2012 data), and based on the 1996 diet, cholesterol drops too.  So, high fat diets can do some good, but are there downsides?
2. Epidemiological Observational Studies (EOS) observe diets of large populations in search of correlations between diet and health (this can include whole countries or studies such as the huge one of doctors and nurses who periodically respond to questionnaires). These can be used to generate hypotheses but do not constitute proof of causation.  Other studies are needed to prove anything.  Unfortunately, such studies are often deemed to constitute proof.  EOS studies have good statistics but do not prove anything.
3. Controlled studies, in which individuals are fed strict diets under researcher supervision, or are taught to independently continue with the diet with frequent monitoring are the best comprise.  The degree of intervention required necessarily limits such studies to smaller groups of individuals and therefore have sparser statistics.
4. Studies on one individual, such as mine, give lots of data but suffer from bias and lack of statistics. This approach gives indicators that can be used by the individual to make medical decisions.  It is satisfying when an N=1 experiment correlates with larger studies.  Indeed, my weight loss dats from 1996 is much cleaner than the data in the literature analyzing the Atkins diet.

There are certain statements that can be definitively tested even in small studies.  For example, the statement that people can't loose weight on low carb diets is falsified by evidence to the contrary.  Controlled studies show that some people loose lots of weight on this diet.  Similarly, eating lots of fat does not guarantee that you will have high cholesterol.  We must also acknowledge that there are populations that eat high carbohydrate diets who are healthy, so it would be false to state that such diets always lead to poor health.  However, this observation does not prove that carbohydrates make you healthy.  The problem always comes down to generalizations.  I need to make a decision about me, and what happens in the case of the average population is of no help.

4 What should I do?

Here is the sequence of events:

A. Historically, when I went on low fat diets (including a vegetarian diet), I

1. never lost weight
2. was always hungry
3. suffered from idigestion
4. couldn't sleep
5. had chronic migraines
6. felt miserable

B. On a high fat diet,

1. I lost weight dramatically
2. My cholesterol risk factor dropped by more than a factor of 2
3. The diet was tasty, I ate as much as I wanted and was never hungry
4. Many of my other indicators of health got better
5. I felt great

 C. I slowly drifted off of the high fat diet due to

1. overseas travel were it was impossible to get enough fatty foods
2. pressure to conform when dining out
3. constant bombardment by the media and the medical establishment of the evils of fat
4. slowly losing faith in the wisdom of staying on a low fat diet given all the persistent voices to the contrary

D. After abandoning the diet

1. I tried to stay away from processed carbohydrates and eat less fatty meats
2. my weight drifted upwards
3. my cholesterol got high enough to require a prescription
4. I was prescribed Lipator(R) but it did not lower my cholesterol
5. Vytorin(R) 10/12 dramatically lowered my cholesterol
6. while on Vytorin(R) for 5 years

• I became extremely fatigued after exercise
• my blood pressure increased
• I developed fog brain
• my weight increased to almost its 1996 peak

E. After going back on the diet

1. My weight loss was stalled until I stopped taking Vytorin(R)
2. My weight is now dropping fast
3. My cholesterol levels started rising after going off the Vytorin(R)
4. My fatigue after exercise is gone
5. My doctor is urging me back onto statin

So, should I go back on statins?  I am seeing my doctor on the 12/17/12, and will then have a blood test.  I want to develop talking points with him to bring up the pertinent questions and I also want to have a decision tree ready before we talk so that I can make choices without emotion.

Here is what I am thinking:

1. I do not do well when eating carbs, so my only alternative is to eat lots of fat.  Since I need to continue eating fat, I need to better understand if it is having a negative affect on my health based of my higher cholesterol and C-reactive protein numbers during my recent diet. My CRP was up a few months ago, but still below the recommended value.
   
2. If statins decrease my cholesterol and my C responsive protein (two purported risk factors for heart disease - though a causal link is not definitively established), then I would gladly take statins if they cause no other ill effects.
3. Statins alone did not lower my cholesterol but the combination drug did.  However, it has been shown that the outcomes (i.e. disease or death) for the combination drug is no better than for statins alone.  So will a statin really help me if it does not decrease my cholesterol or CRP?
4. Given that the combination drug reduces my ability to exercise, and may have other side effects, I prefer to avoid them.
5. Given that statins have been shown to have positive outcomes, perhaps acting as anti-inflammatory agents, then maybe I should take them even if they do not lower cholesterol and then check my CRP and decide later if I should quit.
6. What if there are other systemic effects of statins?  Will they interfere with my insulin response and unravel my positive response to the high-fat diet?  Could this lead to an increased chance of diabetes? Given my data, the combination drug seemed to have had an adverse effect.  Are plain statins better?
7. Sometimes no action is better than action if the benefits are not well defined and the risks unknown. If statins will not help with my chances of decreasing heart disease risk, perhaps I should not take them given the potential risks.
8. Large scale drug tests do not take into account individual variability.  What in my medical history can be used to make a more informed decision?

 My plans for now are to go ahead with a blood test next week.  If my numbers are getting better, I'll probably hold out for another 3 months then plan another visit to my physician.  This is the simplest outcome given the fact that I expect a 6 month lag between starting the diet and stabilization of my cholesterol levels.  The complication is that the combination drug may have delayed this effect.  If  my lipid panel is the same or getting worse, should I stay the course to give my diet a chance, or should I take the statins and risk them making me worse off in the long run by interfering with my diet?

There are clearly no clear-cut answers. What do you think?

How do We Know a Black Hole Lives at the Milky Way's Center?

People often wonder how science can get a handle on out-of-this-world things like the properties of the universe many light years away or the small-scale structure of space-time itself.  In 2005, I presented the distinguished faculty address to give my audience a sense of how this is done.  The title of my talk was, "From Black Holes to the Internet:  How We Use The Scientific Method To Understand the Mysteries of Things Unseen."  It was a very enjoyable hour with lots of wonderful audience participation.  Here I summarize one part of my talk on "how we know" that there is a black hole in the center of our galaxy.

Science often proceeds by taking small steps that together build a general understanding. Here I outline how experiments on the earth along with observations of our universe can lead to an amazing understanding of the natural world.

The outline below shows how simple experiments on the earth's surface can be used to detect a massive black hole at the center of our galaxy, the Milky Way.

1.  Establish Newton's Theory of Gravity by measuring forces between hanging masses here on earth.
2. Use Newton's Theory of Gravity to determine the mass of the earth and check if it is consistent with what we know about the earth's composition and size.
3. Predict the orbital shape and period of the moon based on the earth's mass. It is found that the calculated period is consistent with the measured one and the shape of the orbit is accurately predicted (ellipse with the earth at the focus). This evidence suggests that gravity acts on lunar distances.
4. From the orbits of the planets, the mass of the sun is determined. Every planetary orbit gives the same solar mass (with the sun at the focus of every ellipse), so gravity appears to work even on these larger scales. Furthermore, the density of the sun that is determined from its mass is consistent with what we know of the sun's composition from independent spectroscopic measurements.
5. The orbital properties of all bodies in the solar system obey Newton's Theory of Gravity with impeccable precision. This includes comets, asteroids, moons, satellites, and space ships.
6. Mercury's orbit is found to deviate ever so slightly from Newton's predictions. This irks physicists until Einstein formulates the General Theory of Relativity in 1918 which fully accounts for the small deviation. It turns out that Newton's Theory of Gravity is a special case of General Relativity, which predicts the possibility of the existence of black holes.
7. Telescopes that view infrared light are able to penetrate the dust that obscures the center of the Milky Way to visible light to see stars at our galaxy's center.
8. Astronomers measure the orbits of these stars over more than a decade. As predicted by Newton, the orbits of the stars are perfect ellipses. The foci of these ellipses all coincide with an invisible object.
9. Using the orbital data, the calculated mass of the dark object is almost 4 million solar masses.
10. Some of the stars get very close to the dark object, so an upper limit of the object's size is determined from the distance of closest approach.
11. The dark object's mass and density fall in the range predicted by general relativity for a black hole.

The infrared observations of stellar orbits as described above do not prove the existence of a galactic black hole; but provide strong evidence. There are other independent measurements that all point to a black hole (see below). When the pieces of the puzzle are assembled, the picture that emerges is one of a huge black hole at the galactic center.

Incidentally, such massive black holes are found at the centers of other galaxies and even globular clusters. Since evidence of smaller black holes are routinely "observed" in binary star systems, it becomes clear that black holes are out there.

This journey illustrates something fundamental about nature, and about the breadth of physical laws. Richard Feynman said it best, "Nature uses only the longest threads to weave her patterns, so that each small piece of her fabric reveals the organization of the entire tapestry."

A youtube video shows the motions of the stars around the central black hole that comes from direct telescopic observations.  The data covers over a decade of observations. A more dramatic version can be seen here.

Scientists are slow to accept a new idea or theory unless there are multiple pieces of supporting evidence.

The case for black holes is bolstered by X-ray observations of the hot gas surrounding the galactic black hole at the heart of our Milky Way. The observed X-ray spectrum can be used to determine the gas temperature using the same principles that betray the temperature of glowing orange embers in our fireplaces.

If the gas is to remain stationary, the inward gravitational tug of the black hole must be balanced by the outward pressure of the gas. The calculation is simple enough for a high school physics student, requiring only Newton's Universal Law of Gravity (see below) and the gas laws.

This simple calculation leads to a black hole mass of about 3.4 billion suns, in agreement with the observations of stellar orbits.

Newton's Universal Law of Gravity

Newton's universal law of gravity states that the force of attraction between two objects is proportional to the product of the two masses and inversely proportional to the square of the distance between their centers. The constant of proportionality is G.

G can be determined be measuring the forces between masses that are measured with a torsion balance. This is a common experiment done in most physics departments by students, and even in high schools.

 

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Kepler's Laws (1571 - 1630) Kepler's laws follow from Newton's theory of gravity.   Kepler's Laws state that: Planets travel in elliptical orbits with the sun at one of the foci (shown above). Equal areas are swept in equal times (see diagram below). The time it takes to complete one orbit is proportional to d3/2 All objects in our solar system are observed to obey Kepler's Laws, and therefore confirm Newton's more general theory. Einstein's Theory of General Relativity is the most general theory that makes small corrections to the orbit of Mercury and is required to make the GPS system work. But don't believe the authorities. Anyone can observe the motion of Jupiter's moons to determine the mass of the gas giant. I took the photo below of Jupiter and three of its moons.

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 Cutting Through the Dust

Raleigh found that the degree of scattering is proportional to the inverse of the fourth power of the wavelength of light. Blue light has a shorter wavelength than red light, so is more strongly scattered. Rayleigh scattering explains why the sky is blue.

Yellow fog lights work on the same principle. When white light is filtered to remove the blue light, what remains is green and red, which appears yellow. The longer wavelengths pass further through the fog and the scattered glare from the blue light is eliminated, making it easier to see.

The infrared range of the spectrum is made from light of even longer wavelengths, allowing telescopes to see through the muck. Special detectors are used to image the light. The image below is of the center of the Milky Way, taken by researchers at Max-Planck Intitut fur extraterrestrische Physik.

What I expect of my PhD students

Every graduate student needs to be aware of expectations.  Each adviser is unique and operates on different principles.  A small number view their students as a pair of hands to do the dirty work.  In the old days, some advisers expected their grad students to mow their lawn and do housework. A friend of mine from grad school had an old-school adviser who had him come to his place on the weekend for services.  However, most faculty members by that time had already moved into the modern era and this kind of despicable practice is no longer tolerated.

It is important that each student have an understanding of what they are getting into when they join a research group. Here I will explain what I expect.

My highest principle is thinking of a graduate student as a junior-colleague-to-be.  Even the best students start out incapable of doing real research.  They are clumsy in the lab and need lots of hard work to sharpen their analytical skills.  As such, my first criterion is that they be good students who like to learn.  That doesn't mean that they need to be straight-A students.  In fact, many A students make poor researchers because they lack creativity.

On the topic of classes, I believe that the more the better.  I encourage students who are in the middle of their research phase to take classes.  Ironically, the students themselves resist because they feel it interferes with research.  Even some of my colleagues prefer that their students not take courses that are not of direct help to the research at hand.  I strongly disagree with this premise. The process of learning new things sows new ideas.  I myself enjoy learning because these new nuggets of knowledge invariably get incorporated into my research, which leads to totally new and wonderful directions.

Principle 1.  Always keep learning from classes, reading the literature, and just thinking about crazy ideas.  If you feel yourself to be leaving your comfort zone, you are on the right track.  I expect my students to never stop learning and to be constantly pushing themselves.

An important part of being a PhD scientist is independence.  Grants, which support research activities, expect results.  Many advisers thus give their students a very short leash.  The end result is bad for the student's independence.  I prefer to give the student a specific assignment, and let her and him work on it for a year or so without giving them a detailed map of how to get there.  However, I do give lots of course corrections and teach them things they need to know along the way (or send them to the literature) if their struggles are based on missing information.

I once had a PhD student who complained that I seemed to be giving another student lots of attention while neglecting him.  I treat PhD and masters degrees differently.  The individual with a masters degree needs skills to survive in industry, while a PhD scientist is required to come up with new ideas and find ways to tackle a new problem.  Having said that, some of my best and independent students happened to be masters students who were quite capable of getting a PhD.

Principle 2. Learn to be self reliant early on in your research.  Read the literature and talk to others to gain the skills you need to do your work, but don't wait for someone to tell you what to do with those skills.  Constantly try new things in the lab or with paper and pencil to both sharpen your skills and generate new ideas.  You will make lots of mistakes along the way when not given step-by-step instructions, but making these mistakes and getting through them are the most important part of the experience.

I do not yell at my students, ever.  I may tell them when I am displeased with research performance, but if a student does not perform, (s)he will not get a degree.  Passing the Prelim and being in a research group is no guarantee of success.   I disagree with the idea espoused by the administration that we need to help the students along so that we increase our graduation rate.  Graduating a PhD without the proper skills and talents serves nobody.  A PhD degree is not a ticket to a good job.  It's the skills that the individual has mastered and the ability to think independently that makes him or her valuable to society.  A huge pool of unemployed physicists is not what we want to be generating.

It takes lots of hard work and perseverance to finish a PhD degree.  People often ask me how many hours they should work.  My answer is all the time.  If you are not excited by your work and don't enjoy thinking about physics beyond your area of expertise, then you're in the wrong field.  Academic jobs are tough to get, and real research jobs in industry are rare.  However, PhD physicists have lots of success in engineering jobs, which are more plentiful.  If you like to tinker, then engineering may be an excellent way to earn a good living while having fun.

A PhD degree should not only be a guarantee of skills, but of work effort and perseverance.

Principle 3.  Approach your research with a passion.  The benefit of enjoying your work, aside form the direct rush of endorphins, is that you will put in the time required to do a good job.

One of the most important attributes is perseverance.  Watching Star Trek, or other sci-fi shows/movies gives one the impression that scientists apply skills to very easily solve problems.  This is not the case unless a student is super lucky.  I have a long list of stories on the same theme;  students who would spend months trying to get an experiment to run, only to have to start from scratch to try a different approach.  Aside from being good problem solvers, the PhD degree is an imprimatur of a person that does not give up.

In my PhD work, I had spent quite some time building an experiment on a 5' x 10' table optical table, which was filled with all sorts of laser sources and optics, resembling a Borg city.  Each step in the process often required a step backwards.  After completing the construction of the experiment, it still didn't work.  I then figured out the reason, tore the experiment apart and rebuilt the whole thing on another optical table with another laser.  Luckily, it ended up working.  Only then could I start taking the data that was the topic of my thesis.

Principle 4. Don't give up.  When something doesn't work, don't shy away from the problem.  Work twice as hard.  This will serve you well in all aspects of your lives.  When I was a new faculty member, aware of the importance of getting grants, I would write two new proposals for every one that did not get funded.  After my first two years, I built a healthy portfolio of projects.

Many people do not recognize the creativity behind science.  Creativity is part of choosing a scientific problem to study, helps in problem solving, and leads to interesting new science.

Principle 5.  Be creative.  Always think about neat implications of what you are doing or find new ways of looking at old problems.  This skill is particularity important in the career of young scientists who want to make it to the next level.

Principle 6.  Be meticulously careful in your work. Do not publish sloppy results, which will come back to haunt you, and always apply the highest standards to yourself.  You should be more critical of your own work than I am of you as your  adviser.  On the flip side, do not let this attitude prevent you from finishing a project.  In the end, we can never be sure if we are right, and there will always be a mistake somewhere.  If a paper is perfect, it is not science.  When working in the unknown, there are always huge dark shadows in the areas not exposed by your searchlight.

Principle 7.  Be honest with others, but especially with yourself.  Many very good scientists have fallen into the trap of fooling themselves into believing in something that is false.  Consider cold fusion, N-rays. etc.  Design experiments that are resistant to experimenter bias.  Also, do not try to make data fit your adviser's expectations.  I need to know when an experiment contradicts my viewpoint.  And it goes without saying that you should never fudge data in any way or plagiarize the work of others.

Principle 8. Impress me.  When you graduate, I need to make an honest assessment of your strengths and weaknesses in the letter of recommendation, which will determine your success on the job market.  Follow all of the above principles.  Do not come to my office to ask what you should do next.  Tell me the issues you are having, your line of reasoning, possible explanations, and engage me in debate about the possibilities.  You should act as a junior colleague.  Don't worry about offending me.  I am more interested in getting at the truth than being right.  However, that does not give you the right to be caustic.

What I have posted above mentions nothing of the content of the work, which is of central importance.  A short post cannot cover the nuances.  To zeroth-order approximation, I expect the student to add a new piece of physics to the body of knowledge.  This could be a theory that helps us understand a phenomenon or the discovery of a new phenomena.  Fitting data to a mathematical expression is not enough.  The parameters of the theory must have meaning that is independently testable, be interpretable in terms of fundamental processes, and make predictions well beyond the domain of the original results that generated the theory.  Perhaps I will write more on the topic later.

If you approach everything in life with a passion, it will be a fulfilling one.   When you take a break from physics, make it count.  While I may seem one-dimensional in this post, I do find time for other activities.  Though I am not good at it, I play ice hockey with a passion.  I enjoy playing the piano and writing.  Taking a break from work is, in a sense, work.  During times of alternate activities, things percolate in the brain.  I have had the most profound revelations while driving my car in the middle of nowhere or playing the piano.  So, don't hesitate to take a break with intense activities.

I have to run now.  After I finish packing, I will take a short walk around San Diego, then I have to catch a plane back to Pullman.  Until then, get excited about physics.

Perhaps this time it may be right - taking a big chance

I wrote a while back how Shiva's measurements gave 0.29eV as the binding energies in our polymer/dye material (with an experimental uncertainty of 0.02 eV) which is responsible for forming domains that are at the heart of our theory of self-hearing .  I tried to figure out what interactions between molecules and polymer would give this energy and came up with a possibility.  But because I read the data tables incorrectly, I wrongly thought I had solved the problem.

When preparing my talk for SPIE a couple days ago, I drew the PMMA polymer chain with a molecule drawing program and added a few DO11 tautomer molecules to see where they would fit.  Miraculously, as a plopped the DO11 molecules on the page, I immediately saw that the NH from the DO11 tautomer cozies up to one oxygen in the PMMA polymer chain while the OH group naturally attaches itself to another oxygen in the chain, as shown above.  And he energy?  You got it; the sum of the two hydrogen bound energies is 0.30eV, a match.  The table below shows the energies of four types of hydrogen bonds.




There are always other possibilities that we have not yet considered, but this smells right.  Perhaps we are onto something.  Future experimentalists will allow us to test this hypothesis and zero in on what is going on when a molecule self heals.

This project has been one huge puzzle, were each new experiment presents to us a new piece.  It reminds me of how the discovers of the structure of DNA (Crick, Watson, and Wilson  ) pieced together cardboard cutouts of molecules to guess its molecular structure, and confirmed their results using x-ray scattering data from  Rosalind Franklin.  Incidentally, the story behind Franklin's contributions to the discovery of DNA and not being recognized  at the time makes for interesting reading.  I also recommend readers to check out Schrodinger's guess as the structure of DNA using simple physics principles.  The title of his very thin but fascinating book is

"What Is Life?: with 'Mind and Matter' and 'Autobiographical Sketches'"

I can imagine the thrill of discovery experienced by Crick, Wason, Wilson, and Farklin.  From little cardboard pieces and an "X" on a piece of film from an x-ray scattering experiment (shown above), they revolutionized our understanding of the workings of DNA.  Ironically, the forces that hold together the double helix reside in the hydrogen bond, the very forces that seem to be at work in our molecule/polymer system.

I am preparing my talks this morning, and plan to go on a limb proposing stating that the interaction between a DO11 molecule and a polymer chain  through hydrogen bonding underpins the phenomena of self healing.  I am not a chemist and have a naive view of the intricacies of how molecules interact.  But, I hope that my bold proposal will result in good feedback form my audience that will help us fine tune our models of the mechanisms of self healing.

I have been very excited in recent months by all of the discoveries that we are making.   Even if they end up being wrong, the process of the search for the truth is exhilarating.  Gotta run.  Too much to do.  And again, sorry for the typos!

Even teeny weeny discoveries are great fun

This morning, in the process of editing a paper, I made a small discovery. We have developed a new mathematical framework for determining the properties of quantum graphs in terms of the properties of the pieces. This work provides simple identities on the pieces that will allow us to determine general principles form the ground up rather than having to calculate the properties of the full graph.

I have to run because my wife is calling me to lunch.

Here is my email to my collaborators.

Your introduction to edge states was perfect. I liked the physical approach that leads to the formalism. In fact, its clarity was instrumental in allowing me to make a minor discovery (see below).

With regards to the paper, EDGE STATES ARE WONDERFUL! I am taking a break for lunch now, but FYI, I have been working soley on the appendix because I have done what I think is a really neat calculation which uses the power of the edge state. If you recall, in the past, we used the fact that the sum over all of the edges yields the full sum rule. However, it turns out that there are sum rules on each edge! The edge state formalism has allowed me to do this very easily. The result is given by Equation A20 of the geometry. I have pretty much dropped everything to work on this, but I will need to get back to preparing my talks for SPIE since I still have lots to do.

I suggest the following. I still need to reread the appendix because I was making changes while calculating -- never a good thing in terms of introducing typos. I will work on this after lunch. In the meantime, please check the appendix and let me know if I made any errors. The result is so logical that it seams right. I will then alternate between working on my talks and working on the paper.

Most likely, I will not go in to work today so that I can finish the paper in time to be posted on the archives tonight. Even these small discoveries are great fun.