Rocket to the Moon

The word that kept coming to mind after watching First Man was ‘audacity’. One of the key scenes accentuating this point was someone attempting to draw on the chalkboard how far the Earth is from the Moon. It was orders of magnitude further than anything attempted so far – orbiting the Earth. It was audacious!

Courage or madness, or a combination of both, must have been part of the early NASA days. One could spin it positively and call it ‘vision’. Audacious vision, no doubt. The contraptions that were built for testing – some of these things looked flimsy and highly unsafe. As an observer, I would have pegged the chances of success as very, very slim. Having visited the Air & Space museum in D.C. ten years ago, I was reminded of how small and compact the lunar landing module was. Many scenes in First Man show the shaking head-face of an astronaut as he was being rocketed into space.

I did not know much about Neil Armstrong, I suppose because he was such a private person and the movie tries to portray this with sensitivity. First Man is firstly a movie about people and relationships, and this keeps it engaging throughout – even though you know the ending of the movie historically. Those early astronauts, engineers and scientists were audacious; I’m a wimpy play-it-safe scientist compared to them.

After witnessing all those tests in flimsy contraptions, the movie shots of the huge Saturn rocket were awe-inspiring. The marvels of engineering! Given the technology at the time, those scientists and engineers seem like wizards! But marvels come in all sizes, from awe-inspiring buildings, the sun gleaming off endless glass, to my cell-phone – a pocket-sized computer in itself. Other creatures on earth are sometimes dubbed “nature’s engineers” but none come close to the insatiable wanderlust for engineering new things as humans do.

The movie briefly shows protests by the populace. Is going to the moon worth it? Aren’t the funds being wasted for a pipe-dream? Shouldn’t we be trying to tackle hunger and poverty here on this Earth? Why are we building a rocket to the moon? Think of the human lives that have been lost in this ill-fated endeavor? There’s an old replay of Kennedy saying that we are going to the moon, not because it is easy, but because it is hard. Very, very, very hard. Audaciously hard. And while the science and technology plays its role in the movie, First Man is aptly named because it’s really about what it means to be human.

It’s been a while since I’ve played the card-game Fluxx, but I do remember one of the goals: Rocket to the Moon!

Complexity: Between Order and Chaos

Is a human more complex than a water flea? If counting number of genes is your measure of complexity, the water flea is more complex. (Image of Daphnia from Wikipedia.)

How does one measure complexity? Intuitively, we feel that a more complex entity has more of ‘something’ than a less complex entity. What is that ‘something’? That’s more difficult to define.

In a 2013 paper,¹ three authors take on this problem in a paper titled What is a complex system? In the abstract, they write that “there is no concise definition of a complex system, let alone a definition on which all scientists agree.” Their paper reviews various methods used to characterize complex systems and enumerate complexity; they think the best so far is “Statistical Complexity”. This measure meshes with the idea that complexity lies between two poles: maximal order and ‘pure’ randomness.

A maximally ordered object is potentially “easy” to describe. In my thermodynamics classes, students learn the third law of thermodynamics: A perfect crystal at zero kelvin has an entropy of zero. There is only one possible arrangement for this perfect crystal. Yes, you can imagine it in your mind’s eye – rows upon rows of ordered atoms. On the other hand, picture the atoms of an ideal gas moving around in a container at some decent temperature. The movement is chaotic, especially if you try to follow one of these atoms. It zigs and zags in multiple collisions which are somewhat dependent on what all the other atoms are doing. A 24-liter container has roughly a mole of gas particles, that’s six gazillion of them (or Avogadro’s number). Keeping track of individual atoms is a nightmare, but we can easily describe their macroscopic behavior with seemingly simple quantities such as pressure and temperature – easily enumerated and seemingly ‘constant’ at least for a large number of particles. Liquids are much harder to describe than either solids or gases. Perhaps they are more complex?

Somewhere in between those two extremes, order and chaos, is where all the interesting stuff happens. Living systems, in particular, aren’t perfectly ordered systems nor are they just a random grab-bag of chemicals. Just throwing together all the molecules does nothing. They just sit. Dead. There’s something about living systems. that seems complicated and not so easily described. They’re complex! Perhaps the question “What is Life?” should be replaced with “What is Living?”

The 2013 paper throws up some considerations of complex systems. Certain common words or phrases get bandied about regularly in such discussions. Nonlinearity. Feedback loops. Robustness. Irreversibility. Non-equilibrium. Emergence. Multi-layered organization. Information. Memory. Probability. There are several equations typically involving sums and logarithms. I admit to not understanding chunks of the paper where my eyes glazed over. One phrase jumped out at me, though: coarse-graining.

Coarse-graining is what computational scientists like me do when we are trying to model larger more complex systems. We strip out microscopic features that don’t seem to make a large contribution so we can simplify the system while hopefully retaining the essentials at the length scale being studied. For example, if I was interested in the dynamics of protein motion, I might ignore protons, neutrons and electrons in atoms and chemical bonds and replace them by balls connected together with Hooke’s Law springs. That allows me to use the more tractable equations of classical mechanics rather than quantum mechanics. But if I’m interested of how that protein interacts with other molecules in a solution, I might replace the balls and springs with a blob that captures the overall electrostatic map of the protein. Yet again I have replaced a fine-grained model with a coarser-grained one.

It turns out that coarse-graining might be an approach to study (or even explain!) how complexity arises from simpler systems. I study the origin of life, perhaps the prime example that illustrates this thorny question. So I read another interesting paper from 2017 titled Coarse-graining as a downward causation mechanism.² The crux of the idea is that a certain robustness can be achieved when some aggregate measure of the microscopic properties allows for predicting the future state of the system. The trick here is that different parameters/variables are important on different length and time scales, and a system can build complexity when over time, there is an adaptation to a more robust state. A seemingly homogenous system now becomes a two-layer system allowing for some separation of variables. Further coarse-graining can then lead to a multi-layered hierarchy, possibly even with control elements.

Both the papers are mainly about ideas. While examples are drawn from multiple areas to illustrate the idea, we don’t exactly know how to measure complexity. Complex systems, are, for lack of a better word, complex! The idea of complexity being somewhere between order and chaos, and the adaptive approach of coarse-graining, may help us in the difficult task of understanding such systems. We do know that there are many, many ways to fail!

1. J. Ladyman, J. Lambert, K. Wiesner, K. Euro Jnl Phil Sci (2013) 3:33-67.

2. J. C. Flack, Phil. Trans. R. Soc. A (2017) 375:20160338.

The Wizard and the Prophet

History, Food, Science. Three of my favourite topics combined into a fascinating narrative. I can’t believe my own ignorance, having not heard of William Vogt and Norman Borlaug, the two main protagonists in Charles Mann’s fantastic book: The Wizard and the Prophet. I’m personally very pleased with the new crop of superb science-and-story books by journalists. Last month I read another superb book, The Tangled Tree, but this one made me contemplate even more – the trait of a great book!

Who is the wizard? Who is the prophet? Why are they so-named? Mann has ingeniously chosen two less well-known names (at least to me) and convincingly argued how they exemplify the archetype of today’s wizards and prophets. Vogt might be called the father of today’s environmental movement. He strongly influenced more familiar names such as Rachel Carson (Silent Spring) and Paul Erhlich (The Population Bomb). Vogt believed that humans needed to reduce consumption drastically; otherwise we would destroy the ecosystem of our planet and usher in our own doom. Vogt is the Prophet. Borlaug, on the other hand, was a key founder of the Green Revolution (earning him a Nobel prize), and believed that humans could leverage science and technology to increase resources, particularly food, to support our growing planet. Borlaug is the Wizard and his disciples are today’s technocrats.

Mann writes: “Vogt rebuked the anonymous ‘deluded’ scientists who were actually aggravating our problems. Meanwhile, Borlaug derided his opponents as ‘Luddites’. Both men are dead now, but their disciples have continued the hostilities... Wizards view the Prophets’ emphasis on cutting back as intellectually dishonest, indifferent to the poor, even racist. Following Vogt, they say, is a path toward regression, narrowness, and global poverty. Prophets sneer that the Wizards’ faith in human resourcefulness is unthinking, scientifically ignorant, even driven by greed. Following Borlaug, they say… is a recipe for what activists have come to describe as ‘ecocide’. As the name-calling has escalated, conversations about the environment have increasingly become dialogues of the deaf.”

That’s a great turn of phrase: “dialogues of the deaf”. Mann has several others. One that jumped out at me is when the role of catalysts in the Bosch-Haber process (N₂ + 3 H₂ à 2 NH₃) is discussed. Mann writes: “Catalysts are like jay-walking pedestrians who cause car accidents but walk away from the without being affected. But unlike the disruptive pedestrians, catalysts are essential to the smooth functioning of thousands of chemical processes.” And I even got a chemical equation into this blog post! It’s one I use very often in my classes because this reaction can be used to illustrate all manner of chemical principles.

I particularly enjoyed the structure of Mann’s book. Here’s what part of the Table of Contents looks like. Chapters titled “The Prophet” and “The Wizard” book-end four chapters that constitute the middle meat of the book that is themed after the Four Elements: Earth, Water, Fire, Air. The topics in discussed in each of these chapters are Food, Freshwater, Energy, Climate Change respectively. As I was reading, I kept thinking that I could structure a yearlong interdisciplinary course that allowed for interplay between the sciences, social sciences and the humanities. I’m excited enough to start re-theming my general chemistry courses along these lines!

So I’m raving about this book but I haven’t told you much about the main arguments. That’s because you have to read it for yourself! Complex questions do not have simple answers, and it’s worth the time and effort to bathe in the complexity. Mann doesn’t try to argue for one over the other. He also drops a variety of interesting tidbits along the narrative path. For example, I didn’t know that many of the largest solar energy companies are owned by petrochemical firms. That sounds counter-intuitive – why would you try to significantly develop competitive technology (because that’s what they’re doing)? You’ll have to read the book to find out – it’s one of the many “ah, that makes sense!” moments you’ll experience.

I close this post with a vignette about science in the lab and the messiness of actual fieldwork. This struck me especially since I’m a theorist by training and computational chemist in practice.

“[The] scientific enterprise studies phenomena – atoms, clouds, organisms, planets – by transferring them from the world we live in, with all of its confusion and sentiment, into a special workshop, a place where they can be reduced to abstract, measurable quantities and manipulated in a controlled manner. It discovered the laws of electricity and created antibiotics and built the atom bomb and invented X-rays and generated techniques to harvest and store energy from the sun and wind. But it is also risky…”

“The air in the scientific workshop is so clean and bracing and the results of researchers sequestering themselves inside so satisfying that they lose their bearings. They don’t want to leave the workshop. They prefer to live in its world of abstraction… worse, the findings of the workshop seem so luminous and clear, so like beacons of truth, they forget the the workshop is a special place within the world and begin to think that it is above the rest of life and should control it… [Here] lies the peril, because the people outside the workshop will come to detest and disbelieve the people within its privileged walls.”

An observant and timely warning indeed. Given its title, The Wizard and the Prophet could have been a book about magic, a topic I occasionally blog about. It’s not. But it’s a magical read and I highly, highly recommend it.

The Onion Router

Looking for a reason to stay off the internet due to privacy concerns? The last year has brought one scandal after another where data is shared, mined, sold, and used in multiple ways. Data privacy isn’t a new issue, but the ubiquitous internet cloud that provides increasing convenience comes with increasing ability to hack data. Back in the day, before I had ever heard of a modem, and was teaching myself DOS 3.0 through a book, one of the author’s maxims stuck with me: In the never-ending battle between hackers and protectors, the hackers will always eventually win. Honestly, at the time I was on the side of the hackers – trying to find out ways to circumvent protections to copy computer games.

Anyone narrating a history chooses the salient points that provide the story arc. The history of the internet has several narratives depending on what you want to emphasize. However, the ARPANET is always mentioned, at least in passing. For many, it was nerdy computer hackers, in what was to become Silicon Valley, that built the early version of the internet. The Pentagon’s involvement through its Advanced Research Projects Agency (ARPA) is downplayed. Others note the military’s role, but emphasize that a decentralized communications network was needed in the looming specter of nuclear war.

In Surveillance Valley, subtitled The Secret Military History of the Internet, journalist Yasha Levine resurrects an old story in light of new data. “The impetus was rooted… in the dark military arts of counterinsurgency and America’s fight against the perceived global spread of communism. In the 1960s, America was a global power overseeing an increasing volatile world… These were not traditional wars that involved big armies but guerilla campaigns and local rebellions, frequently fought in regions where Americans had little experience… and some argued that the only effective way [was] to develop and leverage computer-aided information technology… a sort of early warning radar for human societies: a networked computer system that watched for social and political threats and intercepted them… hardwired to be a surveillance tool from the start. No matter what we use the network for today – dating, directions, encrypted chat, email, or just reading the news – it always had a dual-use nature rooted in intelligence gathering and war.”

Levine’s narrative is engaging and chock-full of information. I had little familiarity with early events in the ‘60s through the ‘80s, and I didn’t know about the student protests during that era against the ARPANET. I had heard of Radio Free Europe but had not pieced together how it connected to the military. I learned about the 1984 Hackers’ Conference, and individuals such as Stewart Brand and Stephen Wolff. I learned about NSFNET and how it got privatized, quietly with no fanfare. Google features prominently of course. Given its behemoth size and spread, it was interesting to learn about JigSaw, one of many pieces covered by a large ‘umbrella’ corporation.

The most interesting part of the story comes at the end. Levine traces the foundation of the Tor Network, a parallel ‘dark’ network used by dissidents, spies, black-marketers, and anyone hoping to escape being tracked on the ‘open’ internet. You’ve likely heard of Tor, thanks to now well-known names such as Edward Snowden and the Dread Pirate Roberts (founder of Silk Road). What does Tor stand for? The Onion Router. Supposedly routing yourself through layers and layers make your digital tracks difficult to trace. What does this have to do with surveillance and the U.S. military? That’s one among many questions Levine poses. There might not be a single clear ‘smoking gun’ but he has built up substantial circumstantial evidence by following a key investigate rule-of-thumb: Follow the Money. It’s uncanny and disturbing to say the least. You’ll have to read his book to draw your own conclusions from his assemblage of materials.

Coincidentally, I have just finished watching the final season of The Americans. It’s one of the few series I have watched all the way to the end. I rate it excellent overall, and that’s because it brings to light – in a very real and thoughtful way – the drama of the human condition. The backdrop of the story, assimilated Russian spies in ‘80s U.S., provides not just intrigue, but allows the exploration of the human drama. Spycraft and surveillance was very different in the ‘80s than it is today. Machine learning and A.I. strategies have become increasingly dominant as the data deluge heightens. Attempts to control the flow information today are similarly prominent, as they were during the Cold War. It might be a new cold war out here as governments today attempt to build walled ‘gardens’ to control that flow. Brave New World.

Measuring Undergraduate Innovation

Can we measure the capacity of undergraduate students to be innovative? In a recent study, Selznick and Mayhew have come up with a theoretical framework, a survey tool, and some initial analysis. Here’s the title, abstract and citation.

The authors (citing others in the field) define innovation as “the generation and execution of contextually beneficial new ideas”. The educator’s challenge is how to construct a learning environment to boost this capacity in students, and concomitantly, how to assess if progress has been made. In particular, the authors wanted to provide a construct that goes beyond the typical references to “profit-motivated innovation” such as entrepreneurship and market-oriented outcomes, and find some way to measure the development of innovative capacity.

After the requisite literature review, Selznick and Mayhew, present the framework of their study. Development of an individual is conceived in three dimensions, not necessarily independent of each other. There is (1) an intrapersonal component that encompasses personal motivation, being proactive, and something called ‘self-concept’, (2) a social component encompassing networking ability, persuasive communication, teamwork; and a (3) cognitive component encompassing creativity, risk-taking, and demonstrating innovative intentions. A summary of the framework is provided below with a sample item in each sub-category. Full details of all the survey items can be found in the article.

The survey data came from ~1400 graduating seniors from six institutions (public flagship, private research-intensive, private liberal arts). However, the pre-test data was much more limited – a group of undergraduate RAs. This was used to refine the survey questions and the survey instrument as a whole, however they are not a representative sample as the authors acknowledge. The authors mention the importance of additional longitudinal studies to further test the effectiveness of the survey instrument, and of course the subsequent results might be of interest!

Here are some tentative correlations from the preliminary study. When compared to two traits in the Ten Item Personal Inventory (TIPI), extroversion and openness to new experiences, there was some correlation. It’s unclear if comparison was checked for the other eight traits. The main meat of the study utilizes “latent trait theory and polytomous item response models”. (There are further references in the paper for the interested reader; I admit I don’t completely understand them.) The main finding is that innovation capacities lined up most strongly with “two intrapersonal constructs (i.e., proactivity, self-concept) and two cognitive constructs (i.e., intentions, creative cognitions) and less related to constructs comprising the social dimension.” The authors speculate that this has something to do with “social exchanges [being] more context dependent”.

The authors suggest several implications of their work. First, it provides a potential assessment tool that is relatively quick, easy to use, (semi-)validated, and grounded in theory. It complements “the many efforts student development scholars take in bridging theory to practice”. One interesting point they bring up is that “this study shows partial evidence that creative thinking is conceptually and empirically different that critical thinking, at least to some degree… developing critical thinks may not necessarily produce innovators.” I think this is an important distinction. I also find their study both timely and interesting, and I’ll have to read a bit more about the theoretical framework and the methodology since I’m not well versed in either. It also made me think about what sorts of exercises or class activities might promote at least the cognitive constructs; I’m not sure what to do about the intrapersonal constructs yet.

Strange and Norrell

As an academic, I’m used to reading dense material, all non-fiction of course. I very rarely read dense fiction, nor did I think I would enjoy it. My strategy reading fiction is to try and finish it in one go, if possible. However, the tome that is Jonathan Strange & Mr Norrell was worth the slow savor. It builds slowly but surely to its climactic resolution yet maintains a certain mystery throughout from beginning to end. It’s also about magic.

The author, Susanna Clarke, has chosen what seems like a pseudo-nineteenth century voice for her novel. It includes some seemingly archaic words and spelling, and it also includes footnotes, perhaps harkening to a Jane Austen novel. But it also has a decidedly modern feel. The juxtaposition gives the story a sense of being both foreign yet familiar at the same time. A perturbation, perhaps, in the world we are used to.

The story opens during the Napoleonic wars at the beginning of the nineteenth century. Magic seems to have largely disappeared from Western Europe, although much of the story takes place in England. Magic used to be much more commonplace in medieval times, so it is said, and many books pay homage to tales of magic and a shadowy powerful magician-king of yesteryear known as the Raven King.

While stories about magic abound, it is much more difficult to find books that teach one how to perform magic. Such books have been hoarded slowly over the years by England’s foremost reclusive magician, Mr Norrell. There is a wider society of magicians composed of aristocratic gentlemen, but they are theoretical magicians; their knowledge is mainly about the history of magic – who did what, when, and sometimes how, although the mechanics of magic lack detail. None of these aristocrats can actually work magic. On the other hand, practical magicians of the day are scorned as lower-class hucksters, mainly performing sleight-of-hand and trickery, but without true magical ability. The reclusive Mr. Norrell seems to be the only true magician in England, but he scorns all others. There’s an air of protecting the secrets of magic, following the traditions of the alchemists of old.

In this world, magic can be difficult to perform. Spells are arcane. Looking up books in the library is a common activity for the magician. It’s all very academic. There’s a lot of studying involved. A new magical journal is started; its main use is political – a way to advance one’s views over and against opposing views. As to how exactly magic works, descriptions are sparse, but there are interesting hints – bits and pieces, so to speak, akin to florilegia. This comes up explicitly when Mr Norrell discusses a summoning spell he has devised and written down: “I have made some amendments. I have omitted the florilegium which you copied word for word from Omskirk. I have, as you know, no opinion of florilegia in general and this one seems particularly nonsensical. I have added an epitome of preservation and deliverance, and a skimmer of supplication…”

There’s an intriguing footnote on this: “Florilegium, epitome and skimmer are all terms for parts of spells. In the thirteenth and fourteenth centuries fairies in England were fond of adding to their magic, exhortation to random collections of Christian saints. Fairies were baffled by Christian doctrine, but were greatly attracted to saints, whom they saw as powerful magical beings whose patronage it was useful to have. These exhortations were called florilegia (lit. cullings or gatherings of flowers) and fairies taught them to their Christian masters. When the Protestant religion took hold in England and saints fell out of favour, florilegia degenerated into meaningless collections of magical words and bits of other spells, thrown in by the magician in the hope that some of them might take effect.”

The footnotes are fun to read. Susanna Clarke employs them differently than Mary Roach, but they’re great to read all the same.

I’m not going to reveal who Jonathan Strange is, and I’ve tried to avoid anything that would give away the plot(s). Although there sounds like a parallel between Clarke’s book and the Bartimaeus series (by Jonathan Stroud), both set in a parallel nineteenth century England that contains magic, they are very different (magical) beasts. As to which is the better novel, my vote clearly goes to Jonathan Strange & Mr Norrell.

First Week Spring 2019

In keeping up with the tradition of blogging about my first week of classes every semester, here is the Spring 2019 edition.

First, you might be wondering: It’s already February! Shouldn’t you be further along in the semester? The reason we start late is because there’s a three-week intersession where students may take intensive classes both on-campus and at study abroad sites affiliated with the institution. I’ve never taught during this January-term because I think I would be too drained when the spring semester begins, but I’ve become increasingly tempted to do so as the international opportunities have blossomed over the past five years. (New Zealand would be my top choice since I’ve yet to visit LOTR sites!)

Anyway, my first week went normally as far as I can tell. On Day One of my classes I spent some time on the big picture: In G-Chem 2, it’s all about Energy – thermodynamics, kinetics, equilibria. In P-Chem 2, it is mainly statistical thermodynamics – connecting the macroworld and the microworld. I start off with gases; we’ve covered non-ideal gases, the virial equation, the van der Waals equation and critical points (making use of the correspondence principle); this is a first taste of how physical chemists go about connecting macroscopic properties to microscopic (actually nanoscopic) properties. Next week we get into statistics and the Boltzmann equation.

My G-Chem and P-Chem classes are quite a bit larger compared to last semester. This will mean more grading overall and busier office hours, but it shouldn’t be as bad as previous years because of my new experiment with annotated self-grading. Since that process went well last semester, I’m employing it again this semester in my classes. We’ll see how it fares with the larger groups.

I have four returning research students from last semester. This week I had individual meetings with each of them to go over their projects and research trajectories for this semester. Our high-performance computing cluster was upgraded over winter break and things seem to be chugging along smoothly. Since I chose not to take on any new students (because I go on sabbatical in the upcoming academic year), I didn’t have to train any new students the past week.

What did I do most of January? I started preparing for classes and putting together my syllabi, but I also made surprisingly excellent progress on my own research project – enough to see the full shape of a manuscript. The week before classes began, I was able to make the key figures and schemes for my paper and compile some of the data tables for the manuscript (from the much larger set of raw data). I wasn’t able to work on the manuscript this past week because I was busy getting ahead on my class prep, but I should be able to make some more progress in February. The first week of classes also brings increased administrative work, all of which I was able to complete in a timely fashion.

So, hurrah to a successful first week of the new semester overall!

P.S. To see my first week adventures from last semester (with links to previous first week posts), click here.