The Need To Create

Needless to say, churches abound in Rome. The most awesome one is of course St. Peter’s Basilica. Awesome, literally: built during the period of counter-reformation, its very purpose is to showcase the papal power. It is “the building designed to awe”, writes Lonely Planet Rome. It certainly lives up to its purpose, with masters’ strokes of genius embedded in its inception: Bramanate laid the initial ground work; Michelangelo put in it the dome; Bernini’s gave it the baldachin. Beside the architectural wonders, it has perhaps the most elaborately decorated church interior, with paintings, frescoes, sculptures, ceiling and pilaster decorations. Its pure artistic beauty is breathtaking, even for non-believers. For believers, there are also masses conducted inside the praying area every day. If feeling connected with something bigger than oneself (a.k.a. the god) is the purpose of the mass, it is certainly a great place to do so.

Speaking of mass, as a non-believer, I was not allowed to sit in any of the masses inside the church. But I got a perfect chance to blend in: the New Year Mass conducted by the Pope in the St. Peter’s square. There was a huge crowd, mostly local Italian. The pope addressed the crowd from a window in a building north of the square, and the crowd listened. But obvious I couldn’t understand a single word, so I looked up his speech on the web (link, at least I think it is this one). The content of the mass is about slavery in today’s world—child labor and human trafficking, a very up-to-date topic (with numerous biblical references, of course). I guess it explains the church’s enduring popularity: It has provided moral guidance for millions for over two thousand years.

St. Peter’s Basilica is only one part of the Vatican city. The other part permitted for tourists is the Vatican Museum. The crowning jewel of the museum and “the heart of the Vatican” is the Sistine Chapel, which is most famous for Michelangelo’s paintings of stories from the Book of Genesis on the ceilings and the Last Judgment on the wall. I was slightly taken aback when the audio guide announced matter-of-factly that these paintings is the story of human history. Then I figured, well, if the brainwashing doesn’t happen here, where else?

So I had this random thought while staring at the Last Judgment: I found all those who are going to hell are dark and have twisted body, and all those who are in the heaven are full of light and have very muscular bodies. Visible physical beauty, as the narration of the audio guide claims, is an expression of virtue and hope. It then came to my mind that who actually go to heaven? In his Divine Comedy (which I only read the introduction and the first a few chapters), Dante put Socrates, Plato, and Aristotle in Limbo, the outside circle of hell, so I cannot help but wonder where Confucius might end up. Well, my conclusion was not flattery to the Chinese philosopher, to put it mildly. Perhaps Nietzsche said it better, “In heaven, all the interesting people are missing.”

Wandering among the ancient ruins in Roman Forum and Palatino, gazing at the marvelous ceiling of the Sistine Chapel, and transfixed by the monumental Colosseum, I felt connected with Rome’s rich and glamorous past. With the help of some self-indulgent imagination, I can easily picture myself walking with senators of the Roman Republic along Via Sacra, or watching Michelangelo painting his masterpiece, or hearing ten thousand people cheering at gladiators slaying beasts. These illusions of grandeur easily swelled me with a sense of self-importance; it is dangerous, for mental health, among many other things. A quick read of Roman history (and the history of Italy) made me realize the disproportionately large number of Roman emperors who became insane or mad (literally, not figuratively) and how those who tried to emulate their glory often ended up on the wrong side of history. Mortal danger indeed.

So, to keep those grandiose thoughts in check, I will first write about the trivialities of my trip in Rome.

Toilets are hard to find in Rome. It is a real challenge. Public toilets are often located near main tourist attractions. The entrance fee is anywhere from fifty cents to one euro. Toilets inside museums are free. But sometimes, the queues are long, and it is not uncommon for the gents’ and ladies’ toilets to be in one room. The labels of the public toilets around St. Peter’s Basilica and St. Angelo’s Castle are not easily seen. You may have to ask the police or local workers where the toilets are. Restaurants’ toilets are only for customers, and the cleanness of the toilets is positively correlated with the price of the restaurants. Bars that sell sandwiches and pizza usually don’t have toilets. However, I once wandered into the pedestrian shopping districts near Pantheon and found a pay toilet inside an ice cream and cookie shop. All in all, the touristy places in Rome are small enough to walk but large enough for the unprepared to test the elasticity of his/her bladder. I wish google map has labels for public toilets.

Food can be expensive. It should go without saying that one should only buy things after looking at their price. But following common sense hasn’t been my strong suite. The first morning in Rome, I had a 21-euro breakfast; the food was excellent, but it was definitely overpriced. I wouldn’t have had the meal there if I had seen the menu with price before ordering. The cheapest way to eat, according to Lonely Planet, is to buy sandwiches or pizzas at bars and eat on the go. One sandwich or one slide of pizza is around 2 to 4 euros. I did just that when wandering aimlessly in the city and when I visit the Roman Forum, the Palatino, and the Colosseum.

Navigation is a piece of cake with google map at hand. Paper maps are good to have too, especially when the smartphone battery is running low.

Trains in Italy are usually crowded, often run late, and always need reservations. On my way to Milan, the train was late for 30 mins, I almost missed the connecting train to Rome. And the train to Rome was late for half an hour as well. I met a couple from Alberta on the train to Milan, and they told me that trains in Italy are usually delayed. One also has to look for the platform number inside the train station. Reservation has to be made in advance, even with train passes like Eurorail pass. It took ten euro for my trains within Italy and eleven euro for my international trains into and out of Italy. The reservation can be done either on the web or at the self service machines in train stations (in theory). I didn’t make the reservation for trains back to Stuttgart. I regretted the decision after seeing the long long queue in front of the ticket office in Rome train station (and in Florence too). My reservation from Milan to Basel somehow cannot be printed out at the self-service machine, so I had to join the queue.

Electric adapter. Unique Italian. German adapter won’t work.

Queues for Vatican Museum and St Peter’s Basilica are long. I booked tickets for the museum online beforehand, and on my first day of the museum visit when I saw the queue, I felt that was the smartest decision I have made for a long time. St. Peter ‘s Basilica, however, has no online booking system. The entrance is free. But one day in the early morning around nine o’clock, I got in without queuing.

Lastly, freshly squeezed orange juice is a must. Almost every bar has a machine for it. I saw the bar attendants squeezing the juice with the machine several times; it takes about four to five oranges to make one glass of juice. The taste of freshness is addictive.

“What is to give light must endure burning.” – Viktor Frankl

Viktor Frankl, Austrian psychiatrist and concentration camp survivor, wrote the book in nine days, just a few months after he was freed. The book is divided into two main parts. The first part is about his experience in concentration camps and his interpretation of those experiences as a psychiatrist. The second part is about logotheraphy, a school of psychotherapy he founded partially based on his experience in the concentration camps. The main idea of the book is that the main motivational force in a person’s life is the “will for meaning”. This “will for meaning” is in contrast to the “will for pleasure” in the psychoanalysis of Sigmund Freud, or the “will for power” in the psychology of Alfred Adler.

Frankl states that one can find meaning in one’s life through three ways: (1) by work; (2) by experiencing beauty, truth, art, and nature or by loving someone; and (3) “by the attitude we take toward unavoidable suffering”. In the concentration camps, he kept his will for life by reconstituting his lost manuscript, by imagining giving lectures about lives in concentration camps, and by thinking about his wife and the possibility of seeing her again. His experience and his observation of others in the concentration camps validated the key idea behind logotheraphy. He wrote:

“We who lived in concentration camps can remember the men who walked through the huts comforting others, giving away their last piece of bread. They may have been few in number, but they offer sufficient proof that everything can be taken from a man but one thing: the last of the human freedoms— to choose one’s attitude in any given set of circumstances, to choose one’s own way.”

This idea that one always has the freedom to choose his/her response in a given situation is the reason why Frankl believe everyone is ultimately responsible for his/her own life. To quote again:

“A human being is not one thing among others; things determine each other, but man is ultimately self-determining. What he becomes— within the limits of endowment and environment— he has made out of himself. In the concentration camps, for example, in this living laboratory and on this testing ground, we watched and witnessed some of our comrades behave like swine while others behaved like saints. Man has both potentialities within himself; which one is actualized depends on decisions but not on conditions.”

Just as there are specific music that suits specific moods, there are specific books that suit specific age. This is the book that would a bit too emotionally heavy to read in any early age of my life. Now seems to be a good time to read this book.

Again, some of the amazing quotes from the book:

On humor: “Humor was another of the soul’s weapons in the fight for self-preservation. It is well known that humor, more than anything else in the human make-up, can afford an aloofness and an ability to rise above any situation, even if only for a few seconds.”

On emotion: “Emotion, which is suffering, ceases to be suffering as soon as we form a clear and precise picture of it.”

On curiosity: “Cold curiosity predominated even in Auschwitz, somehow detaching the mind from its surroundings, which came to be regarded with a kind of objectivity. At that time one cultivated this state of mind as a means of protection.”

On duality of human nature: “Life in a concentration camp tore open the human soul and exposed its depths. Is it surprising that in those depths we again found only human qualities which in their very nature were a mixture of good and evil? The rift dividing good from evil, which goes through all human beings, reaches into the lowest depths and becomes apparent even on the bottom of the abyss which is laid open by the concentration camp.”

PS. The idea that one has the freedom to choose his/her response in a given situation is the key idea behind Stephen Covey’s Habit 1 being proactive. To Stephen Covey, a given situation (the stimulus) can encompass not only present environments and conditions, but also past experiences. One can proactively re-scripting oneself according true principles. That is a whole new level of proactivity.

Last Friday was Bio-inspired Adaptive Materials Symposium. It covered topics ranging from 3D printing to building designs to robotics. The great variety of topics reflects various approaches to research by the speakers.

Some research  are more real-life problem-oriented. For example, Jeff Karp’s work on designing cardiac devices for infants and biodegradable adhesives. Or George Whitesides’ work on soft robotics.

Some research are more question-oriented.  For example, Peter Vukusic’s work on structural color in biology.

Some researchers pick a material to study. For example, Fiorenzo Omenetto’s work on silk.

Some research have a generic method. Given the theme of the symposium, the method is bio-inspiration and biomimetics.  The need for bio-inspiration come from the fact that our previous training, knowledge, and experience consciously or unconsciously limit our thought and idea-creation processes.

The variety itself is inspiring already. Which one works the best? Is there a best one?  What are the advantages and disadvantages for each approach? For any given project, how to combine two or more approaches to maximize the strength of each approach?

Taking this course is a response to what I realized previous term: I need a proper introduction to equilibrium statistical mechanics. The lecturer, Girma Hailu, followed the textbook Thermal Physics by Charles Kittel very closely, almost religiously. His style is energetic, and his approach is very helpful in guiding students to read through the textbook, which is a classic.

The central concept is entropy. I had wondered why using logarithm in the expression of entropy, and hence one of the most enlightening moment for me is to read the follow:

“The use of logarithm is a mathematical convenience: it is easier to write 10^20, than exp(10^20), and it is more natural for two systems to speak of σ1 + σ2, than of g1g2. “

All the other major concepts follow readily from very simple considerations. For example, temperature is the partial derivative of entropy over energy and gives criteria for energy transfer/equilibrium of systems in thermal contact. Chemical potential is the partial derivative of entropy over number of particles and gives criteria for material transfer/equilibrium of systems in thermal and diffusive contact. Gibbs distribution and Boltzmann distribution followed again from simple applications of chemical potential in a two state system and its classical limit.

Taking this course is an effort to brush up my maths. The lectures by Eli Tziperman are very well organized, and he always gave road maps at the beginning of lectures so that we always have the big pictures  in mind (before getting lost in mathematical details).

The course covers mostly partial differential equations, from the standard 2nd order PDE like diffusion, wave, and Laplace equations, to 1st order PDE and method of characteristics, to Greens function method, to variational methods, perturbation methods, and some nonlinear PDE. It sounded silly, but when he finished Greens functions, I started to realize why mathematics is field of research.

One of the difficulties in learning maths on one’s own is that it is hard to choose which textbooks to use. Three main textbooks for this course are Carrier & Pearson’s Partial Differential Equations – Theory & Technique; Greenberg’s Advanced Engineering Mathematics, 2nd Ed; and Zauderer’s Partial Differential Equations of Applied Mathematics. I found Greenberg’s book delightful to read.

Greenberg’s book not only teaches maths, but also how to think about maths and physics. One of his most enlightening comments is quoted below:

On classification of PDEs: “Why do we classify so extensively? Because the most general differential equation is far too difficult for us to deal with. The most reasonable program, then, is to break the set of all possible differential equations into various categories and to try to develop theory and solution strategies that are tailored to the specific nature of a given category. Historically, however, the early work on differential equations – by such mathematicians as Leonhard Euler (1707-1783), Jakob (James) Bernoulli (1654-1705) and his brother Johann (John) ( 1667 – 1748), Joseph-Louis Lagrange (l736- 18l3), Alexis-Claude Clairaut ( 1713- 1765), and Jean le Rond d’Alembert ( 1717- 1783) – generally involved attempts at solving specific equations rather than the development of a general theory.”

In the language of my college maths teacher, one needs to see both the forest and the tree.

I sat in this course because I want to learn nonequilibrium statistical mechanics. I had a decent taste of the topic I wanted to hear, and much more.

The course began with review of thermodynamics and equilibrium statistical mechanics, and their applications in polymers (biomolecules) and phase transition (DNA helix-coil transition). It then dived in stochastic chemical kinetics (enzymes dynamics) and biological engines before finally reaching the topic of nonequilibrium mechanics, which covers Langevin equation, fluctuation and dissipation theorem, Smoluchowski equation and Kramer’s theory, and chemical master equations. The course ended with a survey of microscopy and spectroscopy techniques,  and brief introduction to electron transfers and gene expressions in living cells.  As you can tell, the range of topics is enormous.

A self-professed conceptual person, Prof. Xie provides just enough mathematical details to wet one’s appetite. But because all the equations are presented through Powerpoint slides, the pace of the lectures is fast. In this sense, the whole course is a big survey course on topics related to single molecule biophysics. Frankly, the course isn’t for everyone, except if you know what you are looking for.

 

Another academic year, four more courses. This year, I audited Fluid Dynamics by Mahadevan, and Frontier in Biophysics by Sunney Xie in the fall, and Thermophysics by Girma Hailu and Physical Mathematics II by Eli Tziperman in the spring. Every one of them is a rewarding experience.

This is the second time I audited Maha’s fluid dynamics class. A year and half ago, when I first  sat in Maha’s class, I was playing catch-up on required maths all the time. By the time he reached the full form of Navier-Stokes equation, which was about six weeks into the semester, my mind was already stuffed and could not take in any more. This time around, the situation got much better. In addition, I had a study buddy with whom I discussed homework problems, and the discussion helped understanding enormously.

Maha covered a wide range of topics in the class: dimensional analysis, kinematics, derivation of Navier-Stokes equations, Stokes’ flows, lubrication theory, surface tension, waves, instability, and boundary layer theory. The textbook he uses is Elementary Fluid Dynamics by D.J. Acheson, although he often digresses in lectures. The class emphasizes intuitive understanding, and Maha often uses dimensional analysis to guide the intuition before any formal analysis.

One quote he likes to repeat is “All models are wrong, but some are useful”. It is by George Box, a statistician. Being a fervent quote collector, I looked it up. Pithy it sounds, it is not like those witty single standalone quotes; there is actually a book about it. One may gain some understanding about George Box’s idea on model-building on this wikiquote page. I quote a few to illustrate the key idea.

A mechanistic model has the following advantages:
1. It contributes to our scientific understanding of the phenomenon under study.
2. It usually provides a better basis for extrapolation (at least to conditions worthy of further experimental investigation if not through the entire range of all input variables).
3. It tends to be parsimonious (i.e, frugal) in the use of parameters and to provide better estimates of the response

Remember that all models are wrong; the practical question is how wrong do they have to be to not be useful.

In fact, the longer one ponders these quotes, the wider one would find their applicability. Not just mechanical models, but all physical models are wrong, really. But we often confuse models with reality. The question “is light particle or wave?” is not just a false dilemma but a completely wrong question. The correctly phrased question is “should be light be modeled as particle or as wave?” As another example, the molecular description of all the reactions in organic and inorganic chemistry are based on molecular structures, which are in fact only models, albeit very good ones. They are much less quantitative than models of particles or waves, and much less powerful for use to predict or extrapolate than the models of lights. Still, they are useful within a certain extent.

In a way, the insight that “all models are wrong, but some are useful” is a liberating idea. It frees one from the constant worry of constructing a “wrong” model, and makes one bolder in attempting to build something useful.