Order from Chaos: OoL Version

How did life begin?

Does the Origin of Life (OoL) exemplify order from chaos?

Ancient cosmologies suggest that this is so. In the ancient Egyptian cosmos, the earth and sky are separated from chaos, thanks to gods and goddesses. The Bible book of Genesis begins the creation story with turning chaos into order, by importantly separating the different waters. (Seas were considered ‘chaotic’.) The Babylonian Enuma Elish begins with two god-oceans, Apsu and Tiamat, with conflict leading to creation of the heavens and the earth. Old maps would indicate uncharted waters where chaos reigns. There be dragons. Or Leviathans.

Being unable to experimentally test any of the ancient cosmologies, today’s priesthood of scientists tries to narrow the question. How did seemingly more complex ‘living’ things arise from seemingly simpler things? Inherent in this narrower question are two assumptions: (1) that there is some correlation between life and complexity, and (2) that there is directionality from the simpler to the more complex.

Modern-day research into the chemical origins of life gained momentum starting with the classic Miller experiment (1953). Simple chemicals (methane, ammonia, hydrogen, water) were mixed, and after sparking the mixture with an energy source, lo and behold, seven days later, more complex molecules appear! These include some of the most common amino acids – the building blocks of proteins in all systems we characterize as ‘alive’. In the last sixty years, scientists have successfully synthesized practically all the ‘building block’ molecules of life from simpler substances. Progress has also been made in connecting the building blocks to make larger and more complex systems. Simple to complex – possibly one measure of life increasing from low to higher ‘order’ and conjures up the ‘great chain of being’. (Picture below is one of many from the link.)

Synthesizing more complex ‘life’-like molecules revealed another enigma. These chemical reactions made a very, very, very wide range of molecules, many of which resemble the molecules of life; close cousins you might call them. Extant life only uses a tiny subset of these molecules and it is unclear how or why. This conundrum is known as the Prebiotic Chemist’s Nightmare. It is an embarrassment of riches in the form of a gooey brown or black tar. Somehow selectivity must be involved. Scientists are working hard to uncover the rules that govern such selectivity, or failing that, a plausible contingent pathway that may have led to the particular choices we see in life today. By ‘choosing’ just a few options among the plethora available, life brings some order to the chaos. The narrowing of choices may be one measure of order. If anything and everything goes – well, that’s just chaos.

One area where scientists have made good research progress is in making proto-cells. These cells do not contain everything that is needed for life, but they can self-assemble, divide, and perform chemical reactions. Most origin-of-life scientists agree that encapsulation, forming a boundary that keeps some chemicals inside, and other stuff outside, is an early crucial feature of proto-life. It promotes catalysis, prevents important molecules from being diluted away, and provides a basis for growth, inheritance and evolution. Boundaries. Maybe that’s what brings order to chaos. In a sense, this echoes the ancient cosmologists. By separating the realms, the chaotic ill-defined ‘void’ or sea is brought to order.

The restlessness of the sea – water in its liquid state – brings opportunities for life to flourish. All living cells contain water. The liquid juice may be gooey and viscous, but fluidity allows dynamic motion while preserving structural integrity. This is what makes the liquid phase much more interesting than the solid or the gas phase. Liquids, particularly gooey ones packed with solutes, are also much more difficult to describe in a mathematical model. The behavior of solids and gases turn out to be much easier to model and make predictions about subsequent behavior, i.e., their evolution is perhaps much less interesting. We can in fact describe gases in an orderly way, because after all the word ‘gas’ comes from chaos.

Liquids, on the other hand, operate at the edge of chaos. This is also how most of us in the field would describe life and living systems; they operate at the edge of chaos. Things could turn catastrophic and lead to widespread death, and it all balances on a knife’s edge. For example, DNA error correction mechanisms operate at this very edge, finely balanced with mutation rates and what is barely needed for the next generation to function. If the ability to evolve and diversify is one feature of life, it must operate at the edge of chaos.

So how did life begin? We still don’t know the answer, and it seems that some semblance of order is needed amidst the chaos, be it complexity, selectivity, or defining boundaries. But chaos seems to also play an important role in the richness of life. Perhaps the ancient cosmologists were on to something that we modern day scientists are just starting to glimpse.

Order From Chaos: MM version

A guest post from an avid reader of murder-mystery books. My companion “Order from chaos” on the origin-of-life will be coming up next.

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Order from chaos: The appeal of the murder mystery

Why murder? From the Golden Age mysteries of Agatha Christie, Ngaio Marsh and Josephine Tey, to the ubiquitous police procedurals on TV today, what is the fascination with homicide investigations? Public libraries today have whole sections just for “Mystery” (most of which are murders). Isn’t the name of the sub-genre of “cozy mysteries” (most of which are murders) an oxymoron?

One possible answer is that murder comes with an air of finality, a kind of certainty in an uncertain world. A tragedy has occurred; a person’s life has been ended. And yet, in the investigation, life goes on. Not for the victim, maybe, but for those around them. There is life after death. The detective and his team encounter a mass of relevant and irrelevant information. They tease out the complex web of relationships. Slowly, they sift through the debris of life and personalities, and zero in on facts. They bring these facts in line and use them to establish means, motive and opportunity. The murder investigation makes meaning out of the chaos of life and death—it is an oasis of order in a disorderly world.

That is why it is strangely comforting to observe the tidy trail of interviews of Hercule Poirot, to follow the measured progress of Inspector Parker or Alleyn or Grant or Lewis, to bask in the California sunshine with the team from The Mentalist. All detectives, like Poirot, rely on the “little grey cells”. But whether it is Father Brown, who emphasizes the psychology of the individual, or Chief Inspector Gamache of Quebec, who believes in the emotions, or Lord Peter Wimsey and Harriet Vane, who dismiss motive and insist on means—“when you know how, you know who” (see “Busman’s Honeymoon”), both the homicide detective and the private agent of inquiry go about their work with reason, method, and deliberation. They ask questions, and they reflect. They (or their underlings) follow leads, take notes, write summaries. They review the evidence. All persons are categorized, all events gathered into a timeline. Everyone is accounted for, everything has its proper place.

The thing that cannot be accounted for, the one who does not fit—that is the clue that breaks the case open. Inconsistency is what the bloodhounds are looking for. That is why the police collect (and try to break) alibis. That is how Father Brown cuts through conundrums. A murder investigation is eminently rational, even if the crime itself is not. “When you have eliminated the impossible, whatever remains, however improbable, must be the truth,” Holmes tells Watson.   

In the murder mystery, all murders are solved, even if not all killers are brought to justice. Donna Leon’s Brunetti often finds that although he may have found the proximate cause—the identity of the killer or the truth behind the murder, the moving force or unseen hand remains elusive, unpunished. The problem of evil and corruption is too pervasive. Still, by the end of the investigation, all motives and movements, jumbled truths, half-truths, and lies, have been sorted out. People’s lives have been put under a microscope, turned inside out—there is no privacy in a murder investigation, says P.D. James’ Adam Dalgliesh—and made sense of.  

By the end, we know who is guilty and who is innocent (and of what); why he said this or she said that; how someone panicked, who covered for whom, which parts were totally irrelevant. Out of the messiness of daily life, all the comings and goings have been filed, sorted, discarded—everyone’s character has been revealed, the victim has been brought back to life and laid to rest; everything now makes sense. We have lived, for awhile, in an orderly world. We have looked at the consequences of violent death (cf. newer series like Broadchurch and The Killing) and survived. Life is a puzzle, but we have the means to solve it. That is the power of the murder mystery—all wrapped up in a neat package, ready to be examined at your leisure. A way to spend some time in a world that, for once, makes sense.  

Muddling Through: The Science and Art of Administration

Public Administration Review is not a journal that I read. But somehow I muddled my way into finding a 1959 article by Charles Lindblom. Its catchy title: The Science of “Muddling Through”. (Vol. 19, No.2, pages 79-88, if you’re interested.)

How does an administrator, particularly in the complex area of policy, determine how to proceed? The issues are thorny. There are no ‘right’ answers. There are pressures left, right and center. The scientist might expect a rational approach based on fundamental principles. Find all the available data, systematically analyze everything, rank the results according to the objectives and goals, and the best solution will emerge. The problem is that, for the most part, this strategy does NOT work.

How then do administrators make decisions? Enjoying my present situation as a ‘regular’ faculty member without formal administrative duties, it can seem as if some administrative decisions are made capriciously, poorly, and sub-optimally. But having been an administrator before, I know this isn’t always the case, but sometimes it might be – or it certainly looks that way from the outside. The timing of my reading this article was uncanny, given the recent U.S. government shutdown this past weekend. Since I don’t know much about politics and public policy (I should learn more), the whole enterprise looks ridiculous.

But perhaps there is a method to the madness, even if unconsciously adopted. One might say that the administrator ‘muddles through’ the options (although hopefully not actually like Mr. Muddle.) This is the subject of Lindblom’s article. He calls it the method of successive limited comparisons, and contrasts it to the rational-comprehensive method, the latter being more familiar to scientists as the way we think decisions ought to be made. A simple moniker for each: branch and root. The characteristics of each method are laid out below by Lindblom.

The branch strategy is “continually building out from the current situation, step-by-step and by small degrees”. The root strategy is “starting from fundamentals anew each time, building on the past only as experience is embodied in a theory, and always prepared to start completely from the ground up.” Lindblom analyzes each step closely. I recommend his original article for the full analysis, but here are my highlights.

In the ideal world, values/objectives/goals are laid out, prioritized, and come before the analysis. A process is then laid out that maximizes the goals, i.e., determining what constitutes the ‘best’ policy. In reality, the goals and the analysis are closely intertwined, and therefore (paradoxically) the laying out of values/objectives/goals comes from the actual articulation of policy, but not prior to it. Furthermore “to show that a policy is mistaken one cannot offer an abstract argument that important objectives are not achieved; one must instead argue that another policy is more to be preferred.” So what makes the policy ‘good’ or ‘best’? Agreement, wherever it can be found, even if the goals and values of different constituencies are not necessarily in complete alignment.

Why might such a limited analysis be sufficient, instead of going the whole comprehensive hog? “[It] reduces the number of alternatives to be investigated and also drastically simplifies the character of the investigation of each. For it is not necessary to undertake fundamental inquiry into an alternative and its consequences; it is necessary only to study those respects in which the proposed alternative and its consequences differ from the status quo.” Furthermore, “because policies being considered are like present and past policies, the administrator can obtain information and claim some insight. Non-incremental policy proposals are therefore typically not only politically irrelevant but also unpredictable in their consequences.”

An important feature that acts as a proxy to the missing comprehensiveness is, ironically, having multiple agencies, pressure groups and watchdogs. Policies also evolve over time, as they respond to different interest groups, even strongly partisan ones. By using a limited incremental approach to policy formulation, different groups can anticipate what their rivals might do, in a sort of counter-correction. This may not lead to the ‘best’ solution in the eyes of any individual constituency, but that’s not the point. Lindblom reminds us: “Policy is not made once and for all… [it] is a process of successive approximation to some desired objectives in which what is desired itself continues to change under consideration. Making policy is at best a very rough process. [No one] knows enough about the social world to avoid repeated error in predicting the consequences of policy moves. A wise policy-maker consequently expects that his policies will achieve only part of what he hopes and at the same time will produce unanticipated consequences he would prefer to avoid. If he proceeds through a succession of incremental changes, he avoids serious lasting mistakes…”

In my limited experience as a higher education administrator at both a start-up institution and a more established one, much of what Lindblom articulates rings true in terms of how things actually work. Those experiences have been an education for me personally to step away from the model-building theory-laden world of computational chemistry research, to dealing with the social complexity of different constituencies in a varied institution with different desires, plans, values – some carefully masked and others more overt.

But one of the glaring problems that results from Lindblom’s analysis is the need for time and institutional memory. The accelerations of the 21^st century are exponentially more acute than in 1959. Leaders in higher education are increasingly coming from the outside rather than nurtured from within the institution. The gospel of Disruption as a synonym for Innovation has the loudest disciples. (The New Yorker has an excellent article where Jill Lepore takes apart the Clayton Christensen gospel.) Fear-mongering is effective today as in ages past, and sadly so is demagoguery. Leaders and educators at administrative institutes don’t want to be ‘left behind’ as technology races towards its supposed apotheosis.

As I consider new creative opportunities this year in my teaching, scholarship and yes, even administrative work, I am reminded of the value of incremental change. In some cases, I might take big steps, but in others perhaps smaller ones. Maybe age has made me a little more patient, and I’ve come to terms with ‘muddling through’ some of the less tractable issues. But the muddling can be systematic or capricious, and it’s important to recognize the difference. Lindblom addresses this when comparing theorists (root) and practitioners (branch).

“Theorists often ask the administrators… to follow the best canons of the scientific method, when the administrator knows that the best available theory will work less well than more modest incremental comparisons. Theorists do not realize that the administrator is often in fact practicing a systematic method. It would be foolish to push this explanation too far, for sometimes practical decision-makers are pursuing neither a theoretical approach nor successive comparisons, nor any other systematic method.”

Capricious, it may be. But I think I would still prefer trying to persuade a fellow human being, over generating a huge database with complicated black box algorithms run by an innovative Artificial Intelligence. Sounds like Deep-Fried Data.

Selection of other eclectic administrative musings:

·      Bagman or Crouch?

·      Managing Thermodynamics

·      Garbage Can Organizational Choice

Whither Democracy?

Three Hours.

That’s how long it will take to read The Retreat of Western Liberalism by Edward Luce. On the back cover, one of the odes exhorts: “Read this book: In the three hours it takes you will get a new, bracing and brilliant understanding of the dangers we in the democratic West now face…” However, the three-hour estimate was made by Luce himself at the end of the preface in a quid pro quo with the reader. “So I propose a pact with the reader: if you take my pledge at face value, I will try to redeem it. My guess is it will take you roughly three hours.”

The book’s title carries shades of another Edward – Gibbon’s ominous-sounding Decline and Fall of the Roman Empire. It is a monster of a tome in six volumes. Luce clocks in at 200 pages of reasonably sized print with sufficient white space. But his message is equally sobering because it deals with today rather than once-upon-a-time. His theme is nuclear, with four trite chapter titles. Fusion. Reaction. Fallout. Half Life. Another back cover ode summarizes the main thrust of the book. “What is the future of Western liberal democracy? How did it get into its current mess, and how will those origins shape its forthcoming evolution? This volume is the very best guide for starting to grapple with those questions.”

Luce takes a historical slant, as does the book I just finished reading, Simplifying Electricity. There is even a passage that strikes a similar chord, but starts with Edison rather than Franklin. “For those who still believe our age’s disruptions match what happened after 1870, ask yourself which you would first give up, your iPhone or the flush toilet? Laptop or antibiotics? If you have trouble answering those, ponder life without electricity. It is a measure of our solipsism that we take for granted what went before.” But Luce has a more ominous slant as he begins the book with a Hegel quote: “We learn from history that we do not learn from history.”

Just before the Hegel quote, the author shows the Elephant Chart (without explaining it). The chart underlies several bleak notes, with at least one on higher education. “The developing world is making most of the capital goods that are used to displace the jobs of the middle-income people in the developed world. Their work is now increasingly devoted to looking after the rich. Should we cling to the idea that sending everybody to university is a solution? Apart from the fact that the impact of education reform would take twenty or more years to be felt, the machine is almost certainly moving faster. Technology would have long since overtaken updates to the curriculum.” But then he proposes a liberal arts solution: “reviving a focus on the humanities, including basic levels of political literacy.” This is followed by a strong indictment and plea to the wealthy ‘elite’. “Ancient thinkers always thought the rich posed a greater threat to the republic than the poor: they cling on far more tenaciously to what they have. ‘No tyrant ever conquered a city because he was poor and hungry,’ said Aristotle. If nothing else, history offers us a vast early warning system.”

It took me about three hours to read Luce’s book from the comfort of my own couch this weekend. While my income and lifestyle certainly does not put me in the elite, I chose to stay at home on a cold day rather than be out supporting the Women’s March. Distraction and apathy, are the tyrant’s weapons of today. Not too different from the bread and circuses of Rome. What use is having a democracy if voices stay silent? So much for my own liberal arts training; I feel truly indicted. But will I take up the next opportunity? I don’t know yet.

Whither democracy? The Arab Spring has withered away, while a whiter democracy is the aim of provocateurs in the U.S. and Western Europe. This is the story Luce traces to the present. We are dealing with the Fallout. Content to live a Half Life. Winston Churchill supposedly said that “democracy was the worst form of government… except for all the others that have been tried.” Demos kratos could be Power of the People, or Rule of the Mob.

Luce indicts liberal elites to “resist the temptation to carry on with their comfortable lives and imagine they are doing their part by signing up to the occasional Facebook protest.” He also quotes Benjamin Franklin, not on electricity, but rather on liberty: “The price of liberty is eternal vigilance.” If a liberal democracy is not careful, it will slip imperceptibly into an illiberal democracy, and the rule of tyrants is not far behind.

Black Box Bargains

How you respond to technology relative to your date of birth (modified from a Doug Adams quote):

1. Anything that was invented before you were born is ordinary stuff and just how the world works.

2. Anything invented between when you were 15 and 35 years old is exciting and revolutionary; you can probably find a career in it.

3. Anything invented after that is devilish and against the good order of things.

The light switch is an excellent example of the first category. You “flip” the switch and voila! Let there be light! (And there was light.) Interestingly, even though I grew up in a house with light switches, I still use the phrase “turn on” and “turn off” the light. Perhaps back in the day, before the toggle switch was invented, you literally turned a knob – probably true for gas lighting pre-Edison. (I haven’t done the research to check.) In any case, most of us treat the light switch a black box, and we don’t think about what’s inside the technology. It just works.

Until it doesn’t. And that’s when you might start being a scientist and asking questions. Why isn’t the light coming on? Is it the bulb? Is it the switch?

Carl Roach, in the prologue to his book Simply Electrifying, paints a scenario. “Imagine your world without electricity: No morning alarm clock or coffee maker. No electric lights, heat, or air conditioning. No whirling electric motors. And no computers or cell phones.” Roach traces the ‘discovery’ and use of electricity; his book is subtitled The Technology that Transformed the World, from Benjamin Franklin to Elon Musk. The story begins with Franklin and his famous kite experiment, but the key (pun intended) according to Roach was a bold mind “eager and able to imagine electricity – to see the unseen.”

Seeing the unseen. It’s a way one peers into the black box of what was previously mysterious and unknown. As a chemistry teacher, that’s my everyday work: To make visible the invisible. How do those tiny things we call atoms and molecules lead to the properties of everything we can see and touch? How can we transform one thing into another? Chemical reactions are like magic in a way. Writing this, I’m reminded that my familiarity with chemistry should not blind me into blandness. The commonplace isn’t simply ordinary. And I hope my students see that delving deeper into the invisible world can be exciting, even revolutionary!

But there’s more. By examining the broad scope of history, the economist Roach, examines the roles played by fundamental science, public policy and private enterprise, transforming the power-electricity business into the complicated behemoth it is today. Why is this important? Roach writes: “History can help decision makers in business and government by leading them to take a broader view… to look across time; surely what happened yesterday influences what happens today… to look across all the factors that drive change, including those document in this book: science and technology; politics and geopolitics; regulatory policy; law and the courts; business strategy; economics… [However] if the narrative of electricity was wrongly said to begin with Edison, it would have missed the heart and soul of the original story – the science of Franklin, Faraday and Maxwell. Failing to consider that science would lead to a faulty understanding of the past as well as an inability to see the great hope of the future.”

Roach begins his book with the science, then moves on to the Edison-Westinghouse/Tesla battle. The Hoover Dam, Tennessee Valley Authority, Three Mile Island, the California Electricity Crisis and Enron, are among the topics discussed both in detail but also with a broad-angle lens. Elon Musk shows up at the end, underscoring the importance of fundamental science in technological innovation. Without exploring the black box, there can be small incremental improvements, but not a groundbreaking revolution.

When the automobile was first invented, you needed a bit of the mechanic’s knowledge if you were going to drive. If the car broke down, you likely had to fix it. When I first started driving, I learned how to diagnose simple mechanical problems – hopefully enough to get me to a mechanic’s shop if I ran into trouble. Cars ran smoother, the end-user knew less, and a specialization – the mechanic’s business – grew. The last time I brought my car into the shop, even the mechanic had to hook it up to the computer to diagnose the problem. One black box looking into another.

Thirty years ago, when there was a problem with the computer, I would open it up. Depending on the problem I might check the disk drive head. Or open up the metal box and swap card slots. I’ve even opened up an old CRT when there were monitor issues. Today, my MacBook is a black box. I’m not sure I could open it even I wanted to, at least without invalidating my warranty if I needed something fixed. Is this the black box bargain we’ve made? Give me smooth end-user technology. I don’t care what’s inside so long as it “works”. So what if there’s an algorithm that ‘streamlines’ what I see with every click on the Internet? What is an algorithm anyway? What does it mean that the net is neutral? Or not? The black box of technology is not just about physical products but encompasses systems and social structures – some so complicated that they lead to worldwide market crises – stocks, electricity, medicine.

I don’t wish for the good ole days. I’m happy to have the lights come on with the flick of a switch. But I should be a lot more circumspect about my black box bargains, particularly in the age of interconnected big data. I don’t think it’s the devil, but the devil might be in the details. Those of us in the education business are being inundated with promises of the next enterprise system Maxwell Demon that will shed light on the tiny nuances we might otherwise miss. We should rightly be suspicious, thermodynamics notwithstanding.

Bohr's Magic Wand

Apparition (from Merriam-Webster):

1.     a) an unusual or unexpected sight

b) a ghostly figure

2.     the act of becoming visible

In Harry Potter’s magical world, you need a license to apparate, at least in Great Britain. You’re not supposed to disappear like a ghost and reappear unexpectedly, scaring the jeepers out of anyone around you. How having a license changes the jeepers remains unclear.

In the real world, apparition happens all the time. We just don’t notice.

This strange phenomenon was proposed to be commonplace over a century ago by a physicist named Niels Bohr. All atoms did it. Specifically, all electrons in atoms did it. Fellow physicists were aghast at the idea. While no one accused Bohr of wizardcraft (and he has been lauded as a visionary wizard of physics over the years), he was at least accused of using a ‘magic wand’.

The tale begins in Chapter 5 of Helen Kragh’s Niels Bohr and the Quantum Atom. The chapter is appropriately titled A Magic Wand. The issue at hand is the Correspondence Principle. The accuser who was also a close collaborator, the equally visionary Arnold Sommerfeld, wrote that “Bohr has found a magic wand in his analogy principle, which without clearing up the conceptual difficulties allows him to make the results of the classical wave theory directly useful for the quantum theory.”

Before explaining what this means, first let’s agree on one thing. Quantum mechanics is strange.

The world of human beings, shiny marbles, and Amazon boxes, is the macroscopic world. Hypothetically if a marble was allowed to randomly rattle on the floor of a box (never to escape it), eventually it would explore each speck of floor space equally over a long period of time. The probability of finding the marble is equal at any spot along the floor of the box. It doesn’t matter how fast the marble is moving, or how much kinetic energy it has. This is the ‘classical’ result.

But in the micromicroscopic world, much smaller than a micron, the quantum marble behaves strangely. (See illustration below from McQuarrie’s Quantum Chemistry, the text I use when teaching Quantum.) In a one-dimensional box, at its lowest energy level (n = 1), the particle spends most of its time in the middle of the box. But at the second lowest level (n = 2), it prefers to be at the quarter or three-quarter mark, but avoids the middle and the edges. Now that’s very strange behavior. A crest indicates high probability, while a trough on the box floor indicates zero probability.

As n increases, the probabilities get more and more wiggly until you can’t tell the difference between a crest and a trough, or the wiggle for that matter. At this point, I might as well draw a straight horizontal line to represent the probability distribution – the marble can be found equally anywhere in the box, the classical result. In my Quantum class, this is where students first encounter the Correspondence Principle. It’s weird down low, but fine up high. What exactly happens in the middle, and how it happens, well, that’s magic. (The adabiatic principle is a story for another time.)

But even if you avoided Quantum, you might have learned the Bohr model of the atom in a chemistry class somewhere, sometime. For example, here’s the sodium atom with its three rings (non-elven, unfortunately) and eleven electrons.

The beauty Bohr’s work was devising a model of the atom that explained the spectral lines of hydrogen. No, the lines aren’t spectral in a ghostly sense. They come from light absorbed and emitted when the electron in a hydrogen atom changes energy levels. These energy levels are very specific. Therefore, the change in energy between lines is very specific, and hence the line colors are also very specific. In Bohr’s model the rings correspond to energy levels, with inner rings being lower energies (more stable) than outer rings (less stable).

Thus, an electron is typically most stable when located in the innermost ring. However, if it receives energy in the form of ultraviolet light at 103 nm, the electron can absorb that energy and apparate to the third ring. At some point, in a bid to become more stable, it will emit that energy to apparate back to a smaller ring. For example, moving from the third to the second ring will emit red light at 656 nm. Why do we observe this? Conservation of energy.

Here’s the kicker. Only certain orbits are allowed. (We see very specific lines rather than a continuous rainbow spectrum of color.) How then does the electron know “where to stop” when it moves between levels? It seems to know ahead of the jump where to land, and there was no mechanism to explain any of this. Both acknowledging the power of Bohr’s model and its strangeness, Kragh quotes several physicists writing at the time: “the weak side of the theory consists in the heavy sacrifices it requires at the very outset… notwithstanding its somewhat magically arithmetical character.” “I consider it horrible that this success will help the preliminary, but still completely monstrous, Bohr model on to new triumphs.”

A selection from Kramers and Holst frames the paradox clearly. “On the whole it is very difficult to understand how a hydrogen atom, where the electron makes a transition from orbit 6 to 4, can during the entire transition emit a radiation with a frequency different from that when the electron goes from orbit 6 to 5… Even from the very beginning the electron seems to arrange its conduct according to the goal of its motion and also according to future events. But such a gift is wont to be the privilege of thinking beings that can anticipate certain future occurrences. The inanimate objects of physics should observe causal laws in a more direct manner, i.e., allow their conduct to be determined by their previous states and the contemporaneous influences on them.”

This sounds very much like the three D’s of apparition. Destination, Determination, Deliberation. “One must be completely determined to reach one’s destination, and move without haste, but with deliberation.” So says Wilkie Twycross, Ministry of Magic apparition instructor, in Harry Potter and the Order of the Phoenix. In the books, apparition is sometimes accompanied by sound, ranging from a loud crack to a faint pop. However, the movies stress the visual accompaniments over sound. (Here’s a YouTube collection of such scenes.)

It seems reasonable to assume that casting a magical spell to apparate requires energy. This energy must be drawn from the surroundings. If part of the energy absorbed comes from the visible part of the electromagnetic spectrum, then we should expect to see ‘black’. When an electron absorbs energy, that specific line disappears (or goes ‘black’ in the electromagnetic spectrum). Conversely, when the electron emits energy, it releases light corresponding to the same specific lines.

So, I think many of the scenes in the movies get it right. And I like the choice of black smoke to represent the Death Eaters apparating, although the line of smoke suggests poor apparating ability, absorbing all sorts of energy en route, akin to traveling rather than disappearing and reappearing. In other instances, some bright light accompanies the apparition. I could interpret this as drawing too much energy, and then having to release some of it, particularly in the act of reappearing. The more subtle the apparition (perhaps without even a faint pop), the more the wizard or witch exerts fine control over exactly how to optimally and efficiently perform the spell. Another reason why a magic-user aspiring to the top ranks should learn some chemistry and physics!

Want more of Bohr? See here, my dear.

Thebes: A Whiff of Academia

Since I’ve always found archaeology fascinating, buying the boardgame Thebes was a no-brainer. The bonus: Playing the game gives one the ‘feel’ of academia packed into an engaging 60-90 minute experience. I have the 2007 Queen version of the game. I played it two dozen times the first couple of years, but then it tapered off to an average of one game per year. Reading about the Phaistos Disc reminded me how much I enjoyed the game and I managed to play it this past week!

Below is a combined review and session report of the game. I apologize for the fuzzy pictures. I have shaky hands and I didn’t want to slow down the game while I was snapping photos.

In Thebes you are an archaeologist at the turn of the twentieth century. The goal of the game is to earn the most victory points (VPs). The main way to do this is by digging up artifacts, but you can also earn VPs by being the foremost expert in an archaeological site, going to conferences, and putting up exhibitions of your finds. Here’s a snapshot of the board early in a three-player game.

I’m the red player with a figure in London (top left) where I have been gathering knowledge.  In the top right are the cards players collect when they visit various European cities. The bottom right quarter shows the five archaeological sites: Greece, Crete, Egypt, Palestine and Mesopotamia. The edge of the board has a 52-spot time ‘track’ representing the weeks in a year. This is one of the most innovative parts of the game: Travel and different activities take up time measured in weeks. Instead of taking turns in a ‘round’ like most other games, it is your turn if you are ‘last’ on the turn track, i.e., you’ve spent the least time up to that point.

During your turn, you either (1) visit a city and take one of the four cards available, or (2) go to an archaeological site and dig for treasure. You advance your turn marker along the track but how far it moves will depend on whether you are traveling a long distance and/or doing something that takes a long time. In the game above, I had just traveled to London so I could accumulate specific knowledge about Greece (the card with the three orange books). The clock in the top right of each card tells you how many weeks you have to spend. Cards with fewer books require less time to acquire. The card below that (the car) allows you to reduce travel time between locations. The shovel card allows you to draw an extra tile when digging for artifacts. The final card is “rumors of the people” and gives you one-time-use knowledge for Palestine (green). Each archaeological site has its own associated color.

In this game, I made a quick early rush to collect knowledge in Greece. Above you can see that I’ve accumulated 7 orange books, the most recent 3 from a visit to Berlin. Next to them is my time wheel, another innovative part of the game. I have just adjusted the wheel to indicate I have knowledge = 7 represented by the white number in blue background. The wheel then tells me how many tiles I will get to draw (in red) depending on the number of weeks I spend digging at the site (in black). For example, I can stay 7 weeks to draw 6 tiles or 10 weeks to draw 8 tiles. The more information you have, the more tiles you get to draw and the less time you need to stay.

As I was pondering whether to go to Greece during another player’s turn, 1 more orange book turned up so I grabbed it before heading to Greece. My fellow players were still gathering information so I was the first player to dig. The first player has two advantages. The minor advantage is receiving a “surface-level” treasure. You can see in the initial game board picture that each site has one circular tile. The major advantage is that you get first dibs on the treasure trove. Each site has thirty tiles: 13 tiles are artifacts that give you victory points, 2 tiles give you knowledge in other areas, and 15 tiles are “dust”. I drew nine tiles on this expedition and did quite well as you can see below. The number on the wreath tells me how valuable each treasure each, i.e., how many VPs I would earn. More than half of the tiles I drew were treasure!

Each site has a slightly different distribution of treasure. Above you can see the 6 tiles of treasure I obtained (1 surface, 5 from the dig) and a card showing the distribution of treasure value in Greece. I got the three highest valued treasures (the 6 VP city seal of Troy, a 5 VP Parthenon decoration and a 5 VP Zeus statue) along with some lower value treasure. The rectangular orange chit with an X now shows that I have dug at Greece this year and I must wait until next year before I can dig at the same location again. What happened to those dust tiles I drew? They go back into the bag! The next person who digs at Greece will have a harder time getting treasure as the ratio of dust tiles is now higher!

While I was off digging at Greece, the other two players were accumulating information mainly at the other four sites. They went on to dig at those sites before I got a chance to go. Why might you want to dig at several sites? Because exhibitions require that you have artifacts from two or three sites. Here’s another snapshot of the board in the middle of the game. You can see the three available exhibition cards below. These “small” exhibitions give you VPs if you travel to the appropriate city and you have the number and color of the artifacts indicated. I would need to dig at other sites to do an exhibition. (My competitors are digging at Crete and Mesopotamia.)

Here’s my tableau of cards after traveling around Europe mainly to gain more knowledge in different areas. (You can also see the three markers on the time track. It is the Green player’s turn.)

Below the shovel card, you can see a conference card I picked up from Wien. One conference card is only worth 1 VP, but two are worth 3 VP, three are worth 6 VP, etc. My competition had been going around to conferences while I was off at Greece. But while they were off digging, I picked up a little knowledge about Palestine (green), a chunk of knowledge about Egypt (yellow), some knowledge about Mesopotamia (blue), and sadly only a tiny bit of knowledge in Crete (purple). Sadly, there will be no Phaistos Disc for me. On the right are general knowledge cards that can contribute to any of the sites. They take longer to acquire but are well worth it!

I then quickly headed over to Egypt and was the second to dig there. While half the tiles were dust, I actually had a great haul including the 5 VP Rosetta Stone!

After that I went to Palestine. I was the third to dig so there would likely be slim pickings but a number of the higher VP treasures had not yet been found. You can see a lot of dust below but I snagged the highest possible treasure, the 7 VP Dead Sea Scrolls from Qumran! (There was a lot of joyful yelling from me and groans from my competitors at this point.) I also got a Roman coin and the Tel Dan stele.

Even though I was also the third at Mesopotamia, I had a surprisingly good haul. This allowed me to do three exhibitions (two “large” and one “small”) before the game ended as you can see in the picture below.

I had the highest haul of treasure and the most points from exhibitions at the end of the game, but I came in second. While I was doing my exhibitions, one of the other players edged me out by being the foremost expert (collecting the most books) in multiple areas. The other two players also had done four conferences apiece to my measly one.

Why do I enjoy Thebes? I get to pretend I’m an archaeologist in an era where I’m competing with others for knowledge, glory and artifacts. The game mechanics fit very well with the theme! The two nifty innovations (the time track turn order and time wheel for digs) work very well. The random draw from the bag with increasing chance of dust is very thematic! Slim pickings if you arrive late. But sometimes you get lucky and snag a treasure of high value regardless! It’s like academia. Sometimes you get lucky and hit a gold mine, and sometimes you just eat the dust. Lots of things don’t work. Like academics, I can choose to go to conferences, or I can choose to present my work at exhibitions. I can opt for a narrow strategy of focusing on just a couple of areas, or I can try to diversify. I didn’t show you all the cards but there are also “research assistant” cards. You can hire R.A.s to help with your dig. (One of my friends who was a grad student in geophysics at the time called them ‘lackeys’ probably because that’s what it feels like when you’re out in the field.)

All this is packed into an immersive 60-90 minute experience with nice game components and even a chart that tells you what all the treasures are! The game designer, Peter Prinz, did a fantastic job. So if you enjoy the theme or would like to experience a whiff of academia, I highly recommend Thebes.

Creating Symbols

The Phaistos Disc remains an enigma. Discovered in 1908 at an archaeological Minoan palace-site on the island of Crete, the clay disc comprises 241 ‘tokens’ made up of 45 distinct ‘signs’ or symbols. While there have been suggestions that the disc might be a more recent forgery-hoax, archaeologists have generally accepted it as a Minoan bronze age artifact. But no one knows what it means. Is it some sort of code? Is there a written message? Without more examples that show the same symbols in other contexts, we may never know.

In the final chapter of The Writing Revolution, Amalia Gnanadesikan mentions that the disc might be the first typewritten document! So it’s possible that some form of movable type was used centuries before the Chinese or the Europeans. (Interestingly, there is a slight discrepancy with Wikipedia as Gnanadesikan mentions 242 characters and 46 ‘punches’. I haven’t done the research to resolve this.) In any case, I knew I had seen the Phaistos Disc in one of my boardgames. I looked in Thebes, and sure enough, it was one of the archaeological treasures you can dig up in Crete. I really should play Thebes again; it’s been a while!

But back to the book. In my previous post, I mentioned three early chapters I had read. Now that I’ve finished the book, I will highlight several later chapters that got me thinking about the choices and trade-offs in designing a set of symbols to store and convey information. Writing is closely tied to its technology, from the wedge-shapes of cuneiform to the constraint of the Roman alphabet typewriter, and the digital era’s diversity of fonts and symbols created by Unicode. There are many more spoken languages than written ones. For many around the world, being literate also means experiencing the dissonance of diglossia. The read-write ‘formal’ language can be distinctly different than its colloquial ‘informal’ oral use. This is true even for English, although much less pronounced than, say, for Arabic.

In Chapter 10, The Empire of Sanskrit, the author writes: “With startling speed, the literary use of Sanskrit – in a form now known as Classical Sanskrit – swept the subcontinent… To sponsor a work of Sanskrit grammar was a status symbol no self-respecting ruler would want to forego. No longer confined to brahminic liturgy, Sanskrit was used by all literary people, regardless of their caste, native language, or religion. [It] was the language of literature, of kingship, of scholarly inquiry, and of education... even in the Dravidian South… written Tamil was almost entirely eclipsed by Sanskrit. [The written was] increasingly formalized and removed from anyone’s actual spoken language. Here was diglossia with a vengeance: anyone who wanted to become literate had to learn a special language.”

The most amusing chapter in the book is Greek Serendipity. The author indulges in a fictional tale of how Greek translated and mutated (or transmutated!) Phoenician with dollops of confusion and error to give us the Greek alphabet. The novel creation: Vowels in the alphabet! The author suspects that “the Greek alphabet was created by an illiterate, not someone at home with writing Phoenician… [because] the changes made… were exactly those that a native speaker of Greek would make as mistakes.”

The author then makes an illuminating point (which wowed me!): “Creativity is rare in the history of writing, the more so among peoples with well-established literacy. Writing is so conservative in its influences that once one truly knows how to read and write it is virtually impossible to think of doing it any other way… Generally speaking, only uneducated barbarians have their own scripts. Fortunately, the Greeks at the time fit the description.” It looks like yesterday’s barbarians became today’s literati judging by the subsequent literary and intellectual output of classical Greece – still revered today in core canonic curricula in the liberal arts.

But then further mutations take place! After Greek became the language of Christianized Byzantium, the emperor received a request for someone to teach a Slavic prince and his people who had recently embraced the Christian faith. A monk named Cyril, knowledgeable in languages, but who had misgivings about the request was asked to carry out the task. “If he tried to teach an illiterate people, how quickly would his words get mutated by the oral tradition, laying the Slavs open to heresy, and himself to accusations thereof? He would go, he said, only if he could set down what he was teaching in an alphabet. Permission was granted.” The original script that Cyril designed was probably not what we refer to as Cyrillic today which derived from an attempt to mesh the Greek and Slavonic alphabets. The Cyrillic alphabet today enjoys widespread use having been also adapted to many non-Slavic languages. But there’s a catch, as Gnanadesikan points out. “The [adaptation] is therefore quite clumsy, not at all the elegant one-phoneme/one-letter system that Cyril intended. But Cyrillic is now one of the scripts of civilization, and poor alphabetic design is the price many languages have had to pay for a share in civilization.”

That last phrase is haunting. Maladapted design is a price one pays for advances in civilization. Is there a better way?

In the majority of cases, a single written version constrains the expression of many spoken languages. But in rare cases, the opposite occurs. This brings us to the interesting chapter on Japanese: Three Scripts are Better than One. The Japanese literati first learned the Chinese language and accompanying script. But there were significant difficulties with adapting the Chinese (kanji) script to writing in the Japanese language: syntax, inflections, name pronunciations, honorifics, etc. Interestingly, it was poetry that finally led to the significant development of a new script. This further evolved into the hiragana and katakana scripts, a result of parallel developing cultures among aristocratic women on the one hand, and Buddhist (male) monks on the other hand. Because of the functional differences in all three scripts, today’s Japanese is an interesting combination. (Below is the word for Japanese written in the three scripts.

A showcase of elegant design comes from an unprecedented moment in history. In another fascinating chapter, the author traces Korean back to King Sejong’s One-Man Renaissance. A scholar literate in Chinese, he revitalized an academy by inviting the participation of elite scholars (apparently also instituting academic sabbaticals!) to further his renaissance. Confucian teaching was compiled. Meteorological and geographic surveys were commissioned. Technology was invented to increase food production. A calendar was invented. A medical school was opened. But “Sejong was repeatedly stymied by the fact that his subjects couldn’t read. How could they learn about advances in technology? How could they benefit from moral philosophy?” And thus in stealth, knowing his literati would oppose the idea, he set about creating a new script that “matched the Korean language and could be easily learned by everyday people.” Sure enough, when he was done, the academy was concerned about endangering political relationships with China, lead to cultural illiteracy and lower standards, and asking “why would the king of a self-respecting country want to imitate barbarians?” However, history has vindicated King Sejong and the script he invented is “a wonder of simplicity and linguistic insight.” As with the evolution of the Japanese scripts, the author details the massive undertaking required by Sejong in “systematically analyzing the phonology of his language… from scratch”.

The elegance of the Korean script could have been lost with the invention of the typewriter. Having read engaging descriptions of languages and evolving scripts around the world, I was particularly impressed by how Gnanadesikan closes her book. The final chapter is titled The Alphabet Meets the Machine. After tracing the different technologies of writing, we get to the invention of the typewriter. Whether or not the Phaistos disc is the world’s oldest typewritten document, the 1873 Remington typewriter was clearly “an alphabetic machine”. And just as writing in longhand had served administrative purposes for millennia, “typing made bureaucracy, administration, and commerce run more smoothly. In the newly global economy that came in the wake of colonialism and saw the growth of new multinational corporations, the result was to advantage those nations whose scripts fit easily onto a typewriter keyboard.” Korean, not so much.

Thankfully, the new technology of computer word processing came along as “an equalizing force for the world’s scripts, undoing some of the damage done by the typewriter.” You can pretty much get to any major script with the appropriate software installation. But perhaps something has been lost with the formal encoding of all scripts, electronically or otherwise. The Japanese thought that “handwriting is a window to the soul”. Unique individuality has been replaced with a typeset font. Although today’s word processors have many fonts to choose from along with an accompanying array of accompanying accents and emojis, they are typeset nevertheless.

Doomsayers have been predicting the death (or dearth) of reading and writing, as audiovisual communication technology gains prominence. Last century, we had the radio and television. The opening of this century has brought us YouTube and Instagram. But in the closing paragraphs, the author makes another insightful point. Reacting to the latest “Report: text messaging harms written language”, she responds: “Written text is not just a cheap substitute for speech, and it never has been. It was invented as an information technology, and while it ended up being an alternative way to express language, it is not recorded speech. Its beauty is that it is actually much less than speech.” While some things are certainly lost in translation, “text can be transmitted with much lower bandwidth than speech… It also takes less time to process it. Writing may take time and effort, but (silent) reading is very fast… The more the world relies on rapid access to information, the more it will rely on the written word.” Or at least it will rely on the efficient encoding of symbols. By digitizing the written word into Unicode, you can take advantage of search capabilities enhanced by gobs of data in the cloud.

But let me re-emphasize: Writing is about creating a set of symbols to represent, store and transmit information efficiently. The set of designs (the ‘language’) can be both creative and flexible, but could end up being haphazard and cumbersome. In reality, all languages have some of the good, the bad and the ugly.

This last chapter made me think about the language of chemistry and its symbols. There were various alchemical signs (see above) to represent chemical symbols through the years. When John Dalton revitalized atomic theory, he conceived a series of symbols (see below) to represent the atoms of each element. Combining these atomic symbols allowed the scientist to represent the composition of each substance with reference to its elemental entities. However, it was still a cumbersome system to use. 

 The translation of Dalton’s elemental symbols into the elemental symbols in our modern periodic table was undertaken by the Swedish chemist, J. J. Berzelius. The compact form in which we chemists write our chemical formulae owes a great debt of gratitude to Berzelius. While my introductory level students might disagree with me, I think the system is elegant and it’s hard for me to imagine a better one. But perhaps it is because I am acculturated into the chemicaliterati. (Hah! I just invented a new compound word.) This accords well with Gnanadesikan’s earlier statement that “writing is so conservative in its influences that once one truly knows how to read and write it is virtually impossible to think of doing it any other way.” It’s a good thing Berzelius used the Roman script, easily typeset for the typist-and-typewriter to churn out a formal chemistry article suitable for publication. I shudder to think how chemical communication might be hampered by a more cumbersome symbolic representation. Even then, it takes time for the students to become facile with chemistry’s symbolic language and pictorial representations.

As teachers, we think the visual structures of molecules aids in learning how to see the unseen. But if we wanted to encode the information for search and research, we need a language that a computer program could exploit. The number of molecules far exceeds the number of words in any language, even if you just built them from the four main elements of organic chemistry: CHON. How do you translate complex non-linear chemical structures into a linear language? We currently have two scripts: SMILES and InChi. (I’m using SMILES in a data-related project because I find it intuitive and easier to work with.) Are these optimally designed? I don’t know, but reading The Writing Revolution motivates me to take a second-look at the intricacies of the code.

This has been a very long blog post, probably the longest I’ve written so far. It took me 4-5 hours just to write a draft of the text (not counting reading, thinking and editing) over several days. It probably took you 5-10 minutes to read if you made it from beginning to end. Hopefully I’ve conveyed something interesting that at least tickled your brain. It probably took me 6-8 hours to read The Writing Revolution (mainly in 20-30 minute chunks over two weeks so I could slowly savor and digest the information). I don’t know how long it took Gnanadesikan to write the book, but I’m sure glad she did. My roughly 4 pages of text are mere quick finger-food appetizers compared to the sumptuous feast of her 300-page book; I highly recommend reading the book in full if you found any of this (or the previous post) interesting. Even as a non-expert, I found the book very readable and engaging.

P.S. This book reminded me:

·      That I enjoy and get so much more out of reading meatier material, and I should spend more time doing so rather than going for the more popular but fluffier stuff.

·      That languages, reading and writing are fascinating!

·      To think more deeply and creatively about my own field of chemistry. (I have some ideas!)

·      Who Berzelius is and how much he and others contributed to the chemical vocabulary we take for granted today.

·      That I should play (the boardgames) Thebes and History of the World soon. (The latter represents the ebb and flow of civilizations, but I think would partly mirror the evolution and spread of languages.)