Summer Research and Reading

Last week was an in-between week. Classes and final exams were over the previous week, and I enjoyed seeing our senior class graduate and meeting their happy families. This week, many of the students are back for summer research, so the building is starting to bustle with activity again. My research lab is being renovated this summer, and on that pretext I decided not to take on summer students. (Actually I do have one student starting today who is primarily working in a different lab this summer 75% of the time. The other 25% of the time she will continue her project in my lab from the past year. She is remarkably independent and can make good progress with little supervision.)

I took advantage of the quietness last week to outline my research plan for the summer. Having the time to slowly read through my research students’ final reports from the spring semester, I decided to focus on moving one of the exploratory student projects to the point of submitting a manuscript. I outlined the scope of the suite of molecular complexes that needed to be calculated (I’m a computational chemist) and put it on my white board – now clear of last-minute questions from students prior to final exams. I’ve been adding small flourishes to the diagram as I make progress on the project. Here’s a snapshot from today.

I have two other goals: (1) learn a new piece of potentially useful software, and decide if I want to purchase licenses for the next year, and (2) devote some time to reading broadly in my field. Starting last week I divided up my day so that research on my main project takes place in the morning. The afternoon is spent reading and learning the new software, with the last hour at work on research again. If some of the earlier computations have finished, I set up a few more calculations for the machines to crunch on while I’m away from work in the evenings. I do have the occasional administrative task or meeting to attend to, but so far this plan is working out well.

Besides reading papers directly related to my research projects, my May-June reading plan will cover three books. The first is a book I actually read through quickly over winter break: Nick Lane’s The Vital Question: Energy, Evolution and the Origins of Complex Life. The goal was to take a first pass to see if there were any crucial insights I should incorporate into my current research projects. The goal this summer is to read through it again slowly and carefully, and evaluate the grand plan put forward by Lane as he pulls together different pieces supporting his hydrothermal vent redox coupling scenario. I’m familiar with the work by Lane, and also that of Mike Russell who had predicted the existence of milder temperature alkaline vents before Lost City was discovered. Lane’s book is well-written and he always has provocative and interesting ideas. (Since discovering his excellent book Oxygen over a decade ago, I’ve kept an eye out on his writings.) I hope to write a multi-part blog presenting and analyzing some of the ideas in his book in late June or early July.

In the meantime I have just started reading A Brief History of Creation by Bill Mesler and Jim Cleaves. It begins with the ideas of Anaximander (one of those Greek philosophers), then moves on to Aristotle and the idea of Spontaneous Generation. Augustine of Hippo makes a brief appearance before we skip forward to the 17^th century featuring Francesco Redi and Antonie van Leeuwenhoek. I did not know much of the history surrounding these two men, but the authors have an engaging narrative that brings them to life! Next up, in the 18^th century, is a story of rivalry between Needham and Voltaire, with appearances by the Comte de Buffon (I still can’t get over his funny sounding title). No story would be complete without a love triangle involving a girl, a brilliant one at that – and very possibly smarter and more capable than all the men featured. That’s as far as I’ve gotten but I’m looking forward to the rest of the book. Depending how it goes, I might use it in a class in place of Genesis: The Scientific Quest for Life’s Origins by Robert Hazen. (I previously used this as supplementary reading in two classes and it worked well.)

While the books by Lane and Mesler/Cleaves are aimed at a more general audience, I’m most of the way through a more academic book, The Minimal Cell. The subtitle of the book describes its contents: The Biophysics of Cell Compartment and the Origin of Cell Functionality. Like many other specialized academic books in the sciences, it is a collection of articles by different authors. One of the editors (who also contributes to the volume) is Pier Luigi Luisi, a big name in the origin-of-life field. He has brought together an eclectic collection of scientists with expertise in different areas. The result is an interesting book but also highly technical in parts, and therefore not as accessible without background information. I struggled through parts of the book and skimmed over some areas.

Interesting things I learned from this collection of articles:

·      Cell cytoplasm is super-crowded, and this has a significant impact on the thermodynamics and kinetics of chemical reactions. Having just taught second-semester Physical Chemistry, it’s a reminder how the “dilute” approximation greatly simplifies the equations. But this is clearly not the case in the cytoplasm!

·      What is the lower limit of organism size? Given the ALH84001 controversy twenty years ago, and more recent reports of nanobacteria, this is particularly relevant to demarcating the transition from chemistry to biology. I learned about gene sizes, water content, number of copies of ribosomes and other proteins needed for minimal functionality, and differences in autotroph, heterotroph and parasitic requirements. Given certain assumptions, the limit might be ~200nm in diameter assuming a sphere.

·      The behavior of water and solutes in gels and at interfaces is very interesting. I have very little background in rheology, and I found it both fascinating and baffling. Given the size of cells and their membranes, it’s crazy how they still function while being experimentally subjected to electroporation, the patch-clamp method, and inserting microelectrodes. One author described this as disrupting the membrane using lances, swords and guns.

·      Building a minimal cell from scratch to investigate how few components are needed for the cell to “do its work” complements reductionist approaches where things were taken apart to learn how they functioned. But this may have importance beyond origin-of-life questions. A carefully engineered minimal cell could be very specific and efficient in its biosynthetic task. Furthermore its fragility outside narrow laboratory conditions also reduces potential hazards of such organisms “escaping” into the outside-world.

Reading and Research – an excellent way to spend the summer! No doubt I will also be thinking about my classes (I’m excited!) and some ideas that I have been churning on how to teach chemistry in the context of magic. I expect to be blogging about those too! I am reminded how much I appreciate the rhythm of life in academia, and count myself very fortunate to get paid for something I love doing.

Flat Time

Sherry Turkle’s Alone Together is subtitled “why we expect more from technology and less from each other”. Her narrative is divided into two parts. In the first half of the book, she discusses the rise of a variety of robots that mimic emotional connections with humans, from Tamagotchis and Furbies for the young, to Paro (a friendly seal) as a companion for the elderly. She delves into what it means to communicate and commune with another (or an "other"), and how our views of robot companions are moving from better-than-nothing to simply better. Her book was published in 2011, and the companion robots have only gotten better at the Turing test – not that we don’t intellectually recognize they are robots, but we respond to them as if they were “living” creatures.

The second half of the book is about our brave new networked world where we can immerse ourselves in living a second or third life in the cloud, siphoning away the time we spend in the present one. The virtual simulation Second Life is aptly named, and it is but one among many worlds where we can lose ourselves. As an anthropologist, Turkle conducts many interviews. A young law professor who spends the majority of his waking hours on the internet says that when he “leaves the bubble [it] makes the flat time with [his] family harder. Like it’s taking place in slow motion.” Turkle describes it as stepping out into a light that is too bright, and sadly the professor after dinner with his family “is grateful to return to the shade of his online life”.

Flat Time. Like a soda gone flat, real life seems to lack fizz – it moves at a slower pace. But on the Internet, boredom can be alleviated one click or one swipe away. Just move on to the next thing. In online action games, there is no flat time. You've got to keep moving. It reminds me of today’s action movies – the only genre that still gets me to the movie theatre for its immersive experience. When I come out, I am blinkering in the sunlight. Driving home, it seems I am driving too slowly – and maybe so is everyone else.  For a short while, the real world feels kinda blah. There aren’t fighting superheroes (I recently watched Captain America: Civil War) and the threat of an immediate crisis.

The lure of immersion is strong. Our minds are amazing! We can transport ourselves into other worlds that tickle the imagination, that trigger excitement, and that grab our interest. This weekend, I set aside five hours to immerse myself in Charlie Jane Anders’ new book All the Birds in the Sky, a coming together of the worlds of fantasy-magic and science fiction. The two main protagonists meet as kids, and then go separate ways – one has gifts of magic and is trained in a school of magic, while the other is a technological and engineering genius building devices of the future in the present. When they meet again, there is a war between science and magic. Can the two be reconciled, both people and systems? (I won’t give away the ending.)

While the premise of the book was interesting, I was disappointed by the lack of fleshing out the magical system. Regular readers of my blog know I’ve been thinking about this topic for a while. I was looking for a revelation, but I guess I will have to keep working on this. On the other hand the author, given her background, is clearly versed in the science fiction aspects, and has a strong grasp of Artificial Intelligence (AI) systems, that interestingly meshed with my recent reading of Turkle’s book. However the story is really about two quirky characters as they stumble their way through life, intimacy, and relationships, while simultaneously tethered to magic and technology. (I predict that this book will be turned into a movie or TV series in the near future.)

Turkle delves into the issue of intimacy in our new world. In the conclusion she writes “My own study of the networked life has left me thinking about intimacy – about being with people in person, hearing their voices and seeing their faces, trying to know their hearts. And it has left me thinking about solitude – the kind that refreshes and restores. Loneliness is failed solitude. To experience solitude you must be able to summon yourself by yourself; otherwise you will only know how to be lonely.”

Is this something my students today (most of who are in the traditional 18-22 age range) struggle with, more than those in the past? Turkle’s many interviews with teenagers is a very sobering aspect of the book. Having grown up with both the faster pace of technology and the ability to “hide” behind a screen, might they both crave and fear face-to-face intimacy and interactions more than those of us who did not grow up ensconced in a mobile network? After reading Turkle’s book, I noticed that when I walk through campus nowadays I hardly actually hear students talking on their cellphones. It’s all texting – convenient in more ways than one. Ten years ago, I would see and hear the students walking with the phones to their ears. Twenty years ago, students would walk together in groups while chatting in-person. But now the norm seems to be moving towards being Alone Together.

Actual relationships are messy. Human persons are involved. We can’t control the situation, and if we try, sometimes things get worse. Relating takes work. And time. And patience. Escapism has always been an option certainly further back than the theater of the Greeks. But as an avatar in an online world, our choices have multiplied exponentially. Why do the hard work of living in flat time when you can live livelier under circumstances you can control. The magic of real life has been substituted by the siren call of life in the Matrix. And as the bots become increasingly good at distracting us from the harsh realities, we will continue to cede more and more control to them, and maybe choose a life through Surrogates, as Bruce Willis and Rosamund Pike do in the movie of the same name. Flat time seems so… well, flat. Turkle’s book is a cautionary tale that should awaken us to thinking carefully about where our technology is taking our humanity.

Scopes version 2.0+

In preparation for being part of the Faith and Reason living learning community (LLC) next semester, I’ve resumed reading about issues related to science and religion. The political circus surrounding the run-up to the U.S. presidential elections motivated me to re-read The Creationists. This key book, by historian Ronald Numbers, first published back in 1992, does an excellent job tracing the strange situation that has evolved in the United States. Since much has happened in the last 25 years, I was looking for the updated (and expanded) 2006 version at the library. They didn’t have it, but they did have the e-Book Intelligently Designed: How Creationists Built the Campaign Against Evolution by Edward Caudill published in 2013.

Like the earlier classic by Numbers, Caudill traces the rise of antievolutionism, its entanglement with the rise of Fundamentalism. (This word has a narrower meaning, but has widespread colloquial use that strays from its original definition. We have a similar situation for the word Evolution.) The usual suspects are present: George McCready Price and the Genesis Flood authors Morris & Whitcomb. But with the rise of the Intelligent Design movement in the last quarter-century, the book also covers Philip Johnson, Michael Behe, and the events of the 2006 Dover Pennsylvania legal proceedings. Caudill however situates his narrative to the 1925 Scopes trial in Dayton, Tennessee. The actual events, personalities, and key moments, in the historical version are much obscured because of the popular classic 1960 movie Inherit the Wind. The movie is based on the 1955 play (of the same name written) at the height of the McCarthy proceedings.

Our LLC watched the movie the previous Fall semester. It was amusing to observe the students who seemed somewhat bored for the first 30-40 minutes – these old classics seem hokey to them – but when the trial started, you could see them put down their cellphones and start to pay attention. The scenes are quite dramatic! The historical trial pitted three-time presidential candidate William Jennings Bryan against famed American lawyer Clarence Darrow. In the movie, these characters are given different names, Matthew Harrison Brady and Henry Drummond. The stand-in for the famed acerbic journalist and critic H. L. Mencken is E. K. Hornbeck. (I think the parallels of the real and fictional names are interesting.) Brady is portrayed as a buffoon, and one gets the impression that in the battle for “reason”, that science triumphs over antiquated religion.

Who won? And is this even about winning and losing? Historically, Scopes was found guilty (of violating the Butler Act) and fined $100, which he ended up not having to pay due to a court technicality. But the aftermath was that more antievolution laws or guidelines were proposed. Did Inherit the Wind succeed in convincing the public that the folksy backward religious townspeople and their champion Brady were plain silly? The caricature might be fodder in scientific circles, but Caudill argues in his book that the Scopes trial, and in particular the flawed movie, were a watershed for many subsequent instances of Scopes version 2.0. Played out in courtrooms across the country, antievolutionists lost legally but won publicity. If anything, the simple-minded strawman ridiculing of religion had the effect of catalyzing the banding together of “creationists” (another slippery label). A parallel “science” (or perhaps pseudoscience) has developed into a multi-million dollar industry. A massive theme park, Ark Encounter, is being built in Kentucky and scheduled to open in July courtesy of Ken Ham and Answers in Genesis.

Inherit the Wind portrayed Brady and Christianity as being old-fashioned, close-minded, and stilted in reason. It is ironic to see the same strategy employed by the antievolutionist movement. The claim made is that the scientists are the close-minded ones, and not open to new possibilities at the frontier opened up by the Intelligent Design movement. The creationists may have lost in the court skirmishes, but they have fared much better on the political warfront. Caudill writes that William Jennings Bryan was not in Dayton primarily to engage in reasoning about science or faith. He was there as part of a political campaign. The event was staged for a media circus, and it certainly succeeded on that front. Scopes v2.0 plays out repeatedly as the media feels obliged to cover with “equal time” both sides of the story. That’s what you do in political media journalism. It’s not about the science.

Caudill has an excellent summary chapter if you don’t have time to read the whole book. Here is the first paragraph of Chapter 8:

“The Scopes trial was the first public performance of modern America’s science-versus-religion drama. Its high visibility and dramatic quality gave it a special place in the subsequent fight because the trial defined terms and tactics that have endured into the twenty-first century for the antievolution movement. Creationists still use Bryan’s arguments against evolution and his appeals to American myths and democratic values. His lessons in practical politics and using the press to promote one’s agenda have not been lost on the modern antievolution movement. First, putting the fight in court meant a public argument. Even without the impetus of sensation and the bizarre, news media were obligated to cover courts, much as they did legislatures, school boards, and other public bodies. Those were familiar venues, facilitating coverage and making the issue easier to follow. Second, defining belief in evolution as a test of one’s faith brought large numbers of religious people into a fight they otherwise might have ignored. Eradicating nuances helped enlist adherents, as it would in any campaign. People, by nature, will shun the effort required to sort through, perhaps to unsatisfactory conclusions, the complexities of a topic such as the impact of modernism on theology, or the place of materialistic science in one’s faith, or if science even has a place in faith.”

That last sentence is scary. If there’s something I’ve learned over the years, and I hope my students learn this as part of their education, it is that real issues bedeviling our world are complex and require nuanced discussion. There’s a lot of grey (aptly, the color of our LLC). As discussed in a previous post on Foxes and Hedgehogs, nuance requires a lot of hedging (which interestingly is what the fox does, rather than the hedge-hog). In another post a while back, I mentioned Randy Olson’s book Don’t Be Such a Scientist, where unfortunately accuracy is not the most important thing in communication; story-telling is. Many of us scientists are bad at story-telling and we throw a bunch of facts at the public as if we should obviously be believed because of our erudite data dump. Two months ago I attended a seminar where Olson had analyzed the communication of politicians past and present. Donald Trump, to his horror (and possibly to most of us academics in the audience), scored far, far better on communication than anyone else, especially on TV and video.

In his book, Caudill refers to Mencken and Darrow as elites, at least this was the company they kept back in the days of the Scopes trial. Bryan however identified with the people of Dayton, backwater as it might seem according to an elite (and certainly portrayed that way). In today’s version, academics (and scientists) are part of the new elite. There is much head-scratching and hand-wringing as to why Trump seems so popular to the “working-class white folks” even when he himself is clearly not one of them. Does Trump have policies and proposals that are realistic and practical? I would say no, but maybe that’s because I much prefer nuance to bluster. But Trump isn’t trying to convince academics or the political elite, he is running a campaign – much like Bryan did in Dayton. He might not ultimately win the presidency (Bryan did not) but he knows how to communicate to his constituency regardless of accuracy or substance.

Many op-eds hearken to the older days where one could build bridges across camps for the common good in the political arena. Today, ideology rules. We live in an “us versus them” world where the polarized battle lines are drawn as starkly as possible. (This also makes it easier for the media to write an engaging story – perhaps emphasizing the engagement, a term that is used in warfare.) Scopes version 1.0 and its descendants, thanks to Inherit the Wind, helped catalyse the drawing of battle lines between “creationists and evolutionists”. Who gets the dominant media coverage? Those willing to spout extreme (and sometimes bizarre) views.

I close this post with a sober observation by the British theologian N. T. Wright. In a chapter on politics (in his book Surprised by Scripture), he writes:

“Meanwhile the major ethical and public/political issues of our day rumble on – global debt, the ecological crisis, the new poverty in our glossy Western society, issues of gender and sex, stem cell research, euthanasia, and not least the complex questions of the Middle East – and as long as the debates are carried out in terms of fundamentalism and secularism, they will never be anything other than a shouting match. At this point, ironically, the Enlightenment dream has begun to eat its own tail, as its greatest strength – the emphasis on reason as a means to peaceful coexistence – has been undermined by its greatest weakness, the dualistic division between God and the public world, with human public discourse collapsing into spin and emotivism.”

Cosmos: 19th Century Polymath Version

I’m now 80% through Andrea Wulf’s The Invention of Nature, a broad sweeping narrative on the life, ideas, and influence of the polymath Alexander von Humboldt. Polymath isn’t a word we use nowadays. In 1834, another polymath William Whewell introduced the term ‘scientist’ when he reviewed a book by one of the most famous (and rare) women polymaths, Mary Somerville. 1834 was also the year that Humboldt, now aged 65, would begin working on his opus – Cosmos. More than a century later, Carl Sagan (I consider him a polymath too!) would be well known far wider than his scientist colleagues for his TV show of the same name. But where Sagan focused mainly on things outside planet Earth, Humboldt would attempt to encompass everything about our planet.

These days higher education news is saturated with the decline of the liberal arts and the rise of STEM and professional fields. It’s all about the job market, supposedly. As a practicing scientist, I am steeped in the practice of the ‘publishable unit’ aimed at my narrow tribe of chemists with all the accompanying jargon. Humboldt's Cosmos does the exact opposite. A blend of engaging poetic prose with very detailed science (not dumbed down for the public), it is a testament to why a holistic approach can be so compelling. Charles Darwin took the same tack in his Voyage of the Beagle, owing much to Humboldt’s earlier Personal Narrative of his journeys through South America. It’s no surprise that travel writing continues to be popular – it opens up new worlds – vibrant worlds that both immerse and delight the reader. Wulf does a masterful job in her book, and I can’t do any better than quote her.

“[In 1834] the very year that the term ‘scientist’ was first coined, heralding the beginning of the professionalization of the sciences and the hardening lines between different scientific disciplines, Humboldt began a book that did exactly the opposite. As science moved away from nature into laboratories and universities, separating itself into distinct disciplines, Humboldt created a work that brought together all that professional science was trying to keep apart.”

Twelve years later the first volume was published. Wulf describes the response: “The world was electrified… [a publisher said] he had never seen so many orders – not even when Goethe had published his masterpiece Faust. Students read Cosmos, as did scientists, artists and politicians… Poets admired it, as did musicians, with the French Romantic composer Hector Berlioz declaring Humboldt a ‘dazzling’ writer. The book was so popular among musicians, Berlioz said, that he knew one who had ‘read, re-read, pondered and understood’ Cosmos during his breaks at opera performances. In England, Queen Victoria’s husband, Prince Albert, requested a copy, while Darwin professed himself impatient for the English translation.”

“In the second volume [two years later] Humboldt took his readers on a voyage of the mind, through human history from ancient civilizations to modern times. No scientific publication had ever attempted anything similar. No scientist had written about poetry, art and gardens, and about agriculture and politics… It was also a history of science, discovery and exploration covering everything from Alexander the Great to the Arabic world, from Christopher Columbus to Isaac Newton.”

“Until this point few Americans had read Humboldt’s previous works, but Cosmos changed that, establishing him as a household name across the North American continent. Ralph Waldo Emerson was one of the first to obtain a copy… No one, Emerson said, knew more about nature than Humboldt.” Edgar Allan Poe’s last major work Eureka was a response to Cosmos as well as being dedicated to Humboldt. Wulf dedicates a whole chapter to discuss the strong influence Cosmos would have on Henry David Thoreau and his opus Walden.

It’s sad that we no longer see this sort of work, or this type of thinking. The specialization of our disciplines in the sciences has resulted in an ignorant myopia outside our narrow area of expertise. Those who branch out are few and far between. Many would say that Carl Sagan paid a price in academia for his popularization and popularity. Others attempt to fit everything to one particular framework in their field, even when it does not work (here’s an example). Science is viewed by the public as useful, but difficult and incomprehensible in its details. College level science classes are seen as a slog for students who take no delight in learning what seem to them obscure details. We teachers need to integrate the big picture much, much more – but that will mean getting out of our comfort zone, and looking over the walls of our cloister. Perhaps Humboldt can inspire us.

Free Your Mind Friday

It is Friday the Thirteenth. Did you see a black cat walk past you? Did you see the same thing a second time? Déjà vu. Maybe it is a sign that something has changed in the Matrix.

Are we living in a simulation? That’s the question I’m thinking of posing for the first meeting of a discussion group in the residence halls next semester. Once again, I will be part of the college Living Learning Community program aimed at first-year new students. (Yes, my semester hasn’t quite ended yet and I’m already excited for the next one! Last month I had a wild idea for my class final project – Imagining New Elements.) I signed up to be in the same theme as last semester, Faith and Reason. The first movie in the Matrix trilogy provides all manner of interesting fodder for discussion related to the theme. It also has great special effects (for 1999) and lots of action (my kind of movie).

I’m thinking of calling this activity “Free your mind Friday”. To check if this might work, I consulted a student who will be an RA (resident assistant) in the residence hall that will house the Faith and Reason community. She was enthusiastic (I think) and thought that Friday afternoons would work well. (The fact that she is a chemistry major and will be in my Quantum class next semester might have helped!) Part of my impetus is to have something for students who aren’t interested in off-campus partying and might want to participate in a community co-curricular activity that has an intellectual component on a Friday afternoon. Apparently Thursday evening doesn’t work as well because the non-partiers are usually studying for Friday exams or working on papers. This is why it helps to have a student consultant as a partner-in-crime. She also suggested that she could organize a movie night ahead of the discussion event – apparently because a number of students may not actually have watched the Matrix. I guess 1999 was a long time ago – although the movie is still fresh in my memory

It's not easy to get students to come to “dorm events”. When I was in college and worked as a house adviser, this wasn’t a problem because we actually just had ten people living in a house so the community was in-built. However when I had an appointment as a resident faculty member, the student RAs or staff resident coordinators would sometimes have a hard time getting students to meetings or events. And that was over ten years ago. If anything there might actually be less hanging out in community spaces today (as observed by Rebekah Nathan when she went undercover). I had mixed success – I organized some movie and documentary viewings plus discussion. Participation was scant (handful of students showed up) even though good snacks were provided. Two things I organized that worked very well, were a session on careers and graduate school (lots of seniors attended, not surprising) and the surprise hit “How to Plan a Wedding on a Budget”. Having planned my own wedding on a budget that we paid for ourselves in grad school, I was at least slightly knowledgeable in this area. The resident coordinator even brought the top tier of a wedding cake for dessert – the students loved it! (The event earned rave reviews. It was a nice contrast to Bridezilla news in pop culture at the time.)

But I digress. My wild idea to lure students to Free Your Mind Friday is for the advertising of the event too be less obvious, perhaps even intriguing – like how Neo is invited to a secret meeting with Morpheus to learn the answers to his questions. I’m thinking that in the first few weeks we could put up some cryptic signs or symbols. My suggestion was to have White Rabbit stickers posted strategically. Students who Follow the White Rabbit will be led to the meeting time and place. Clearly it should not be too cryptic otherwise no one will show up. I’m also thinking of putting posters of Morpheus in his fancy shades holding out the red pill and the blue pill without quite explaining why. Maybe intrigue will serve as a hook for students. My partner-in-crime thought that this strategy could work although we would have to flush out the details. I am no master of intrigue, so I assigned her homework this summer: (1) to think of an intrigue campaign, and (2) to watch the movie – since she wasn’t familiar with the plot of the movie and the references I was making (although she remembered the blue and red pill).

I’ve decided not to plan other topics in detail, although I’d like to do one related to whether or not a Wizarding community does exist unbeknownst to us Muggles. And then perhaps the usefulness of learning Potions, a.k.a. Chemistry!

Scientific Exploration: Extreme Edition

This week I have been reading The Invention of Nature, Andrea Wulf’s book on the remarkable polymath Alexander von Humboldt. Thirty years before Charles Darwin’s famed Voyage of the Beagle, Humboldt was trekking his way through the jungles, rivers and mountains of South America. He would visit many other places, scientific instruments in tow, and might be one of the greatest and bravest naturalists in history. Certainly there are more “things” named after him than any other scientist in history.

The breadth of Humboldt’s explorations led him to a unified view of nature – one that was intertwined and deeply interconnected even if on the surface there was much diversity. Reading his ideas of our planet as a holistic organism reminded me of Lynn Margulis and James Lovelock’s still-controversial Gaia hypothesis over 150 years later – a question for our time as the topic of climate change continues to heat up. The writing of Humboldt significantly influenced Darwin, and there are many similarities between Humboldt’s Personal Narrative and Darwin’s diary of his voyage.

Thinking about Darwin and Humboldt reminded me of how I am an armchair scientist. Literally. My work chair has armrests and I spend my time in front of a computer screen. Two actually. In contrast, Humboldt braved crocodiles and mosquitoes rowing up the Orinoco to try and determine if it shared a source with the Amazon river. As he hiked the treacherous Andes, instruments and a menagerie in tow, he tried to climb as many mountains as possible. He almost died multiple times, and when he tackled the mighty peak of Chimborazo, even his guides refused to go as far as he did. What was he trying to do? Take measurements! Humboldt was ever the consummate scientist and explorer, braving sickness and harsh conditions, and traveling treacherous roads.

Are not all scientists explorers in a sense? I’d like to think I explore the inner workings of nature, but I do it from the comfort of my climate-controlled office. I work reasonable hours, and spend my leisure time – well, leisurely. Perhaps I lack the curiosity and drive of a great scientist – one who sees himself or herself as an intrepid explorer striking out into the unknown. It must have been a visceral experience for Humboldt as he encountered nature in its rawness. I, on the other hand, have become tamed by the comforts of suburbia. I’d like to think that I do a good job conveying the excitement of science and discovery to my students, but maybe the lack of the visceral, physical experience brings about certain limitations that I can’t quite grasp. Maybe there's a certain authenticity that only comes with physicality. I’d like to think that my physically being present in the classroom helps, but maybe if you replaced with me with a video stream (albeit an interactive one), it might not make too much of a difference.

The closest I expect to get to walking in Humboldt’s shoes (which often wore out on journeys), well actually Darwin’s shoes, is probably through a boardgame. I’m looking forward to trying out the Voyage of the Beagle expansion to Robinson Crusoe. In the base game, there are several scenarios where you try to survive, explore and thrive on an island after being shipwrecked. I’ve now worked my way through five out of the six. The Beagle expansion is a campaign game that looks very daunting, but I’ll get to collect rare beasts, strange plants, and other artifacts, and if I’m lucky get them back to “civilization” where fame and fortune await. All this from the comfort of my living room! Humboldt must be turning in his grave hearing me utter such blasphemy. I suppose we enjoy different things, Humboldt and I. And that’s okay. I’m very happy being a professor and a computational chemist! When I want my nature fix, I can watch the equivalent of National Geographic.

Maybe I’ll become an armchair polymath, learning little bits about many things. Sort of like Simon Winchester, except that he is widely traveled and has covered important world events as a journalist and writer. I just write a blog based on interesting things that I read (perhaps the only thing I have in common with Bill Gates). Earlier this year I read one of Winchester’s books, The Man Who Loved China, about another polymath Joseph Needham – a biochemist who became both historian and diplomat, traveling in China during a dangerous time and unveiling its mysteries and technological advances to the “West”. In that sense, Needham shares similarities to Humboldt – they were passionate scientists who took on the Extreme Edition of Exploration. Maybe reading about them has awakened a small passion in me to do a bit more travelling. We’ll see, as the semester draws to a close.

Warning! Mimesis might occur

In our final official department faculty meeting of the semester, we went around the room sharing pedagogical and active learning approaches we had been trying out in our classes. It was both fun and inspiring to hear what others were doing. Two incidents reported by my colleagues jumped out at me. (1) A CRISPR debate in Biochem. (2) Using scratch-cards for group “quizzes” in a G-Chem lab. These two cases particularly resonated with the many examples that Mark Carnes provided in his book Minds on Fire (reviewed in this earlier blog post).

For the CRISPR debate, the class (Biochem II) considered two issues. Half the class debated the first issue: Should the human genome be edited using CRISPR technology? The other half debated CRISPR patent and intellectual property rights. My colleague set up the class in the format of a formal debate and the students were assigned specific roles (initial presentation, rebuttal, summary, etc). The structure of the debate was clearly laid out with strict time limits, and there were external judges (scientists and faculty members) present. The students represented individuals or organizations involved in the debate (that they had read about).

Like the Reacting role-playing immersion games described by Carnes, even though this was just a single session (with preparation ahead of time), the students took on their assigned roles with enthusiasm. Students from whom nary a squeak was heard all semester long voiced their opinions and arguments passionately. Some continued to debate the issue after class time was over. And they dug into researching the question! The motivation to “win” (this came up in Carnes’ many interviews with former students), and not be “clueless” in front of class, were apparent even in a single activity. I think the students might have even surprised themselves!

In the scratch-card example (G-Chem II Lab), another colleague was experimenting with team-based learning approaches that have students take a multiple-choice quiz individually and then repeat the quiz in small groups. The questions and multiple choice answers must be carefully chosen to potentially elicit different responses depending on common errors students might make. The group must come to a consensus answer. When done well, this activity can elicit good discussion and help students articulate and clarify what they think they know. (I’ve seen many examples where it has worked well, and others where it has not.) What really raised the energy in the room, I think, was the “game” aspect of having scratch cards. The physical act of having to scratch a card (like winning a lottery or a gamble) got students very passionate about the activity.

The scratch cards from IF*AT by Epstein Education were used. If the students scratch the right answer, a star appears! (Hah! College students can be motivated by stars. It’s not just for young kids.) If the answer is incorrect, there is a blank instead. This gives the students immediate feedback (and a high energy sense of anticipation as one students scratches a choice). If the group gets the answer wrong, they discuss what they would try next and why. It’s also easy to grade because you can see how many tries the group needed to get the right answer. But it’s the peer discussion that’s key! The students invested energy not just in getting the right answer but they really wanted to know why an answer might be wrong (either individually or as a group). They went beyond “did I get it right or wrong?” to “WHY did I get it right or wrong?” While this type of peer learning activity is not new, the simple use of the game-like scratch cards significantly changed the energy dynamics and ratcheted up the immersion factor (not to mention the meta-cognitive reflection).

Games, role-playing and immersion are what light minds on fire – the argument made by Carnes. But amidst his many positive examples of student engagement, he also pauses to consider potential problems with the Reacting approach. In Chapter 9 (“Teaching the Past by Getting it Wrong”), he considers a number of arguments that might undercut this approach. I encourage you to read his book if you’re interested in the details. I do however want to highlight an interesting diversion he makes to discuss Plato, Socrates, and mimesis – assimilating oneself into another self both in speech and mannerism, essentially role-playing by immersion.

In Plato’s Republic, mimesis is banned in the ideal city-state: “So if we are visited in our state by someone who has the skill to transform himself into all sorts of characters and represent all sorts of things… [we] shall tell him that he and his kind have no place in our city.” There are several arguments for this. For one, such folks provide a superficial misrepresentation (they are not “truth”). Another issue is that they lead people to unsuitable (and perhaps unseeming) activity. Carnes paraphrases the argument: “But a shoemaker who imagined himself to be a warrior [being enthralled by the performance of actors] would do neither job well. This was particularly pertinent to the ruling elite. Because their task was to rule, rulers should do nothing but rule. They should never imitate (through mimesis) actions of any other kind.”

Carnes think that this argument is “little more than a smoke screen to conceal a far more compelling danger. Namely that mimesis was psychologically too potent… Athenians, Socrates insisted, had become besotted with Homeric representation: they crowded round to see orators and actors bring [heroes and other characters] to life… The Greeks had become suckers for the reality shows of their day.” (And not much has changed in two millennia.) The utopian state should suppress or perhaps even eliminate poets and actors “because mimesis inflicts a cumulative psychological damage on audiences. Reason appeals to our best self, while representation appeals to the lower elements of the mind.” And perhaps, Carnes argues, scholars have taken this too much to heart. Academia, in its “critical detachment” might in fact be anti-mimesis – dissecting, reducing, atomizing, the subject matter until it becomes dead, dull, lifeless. I’m pretty sure that’s what at least some of my students think of chemistry. (I hope I disabuse them of such a notion.)

The kicker is that while Plato is making this philosophical argument, he clearly understands the importance of engaging his audience to make his point and ensure they would long remember his words. How does he do so? “Plato channeled the spirit and words of Socrates and had him ‘speak’ directly to readers in the first person, present tense (like Homer!).” In a classical irony, after criticizing Homeric myth and mimetic approaches, Plato, the cunning pedagogue, employs mimesis to teach his philosophical truths. Can I do the same with chemical concepts? Or will the potential distortions or representations detract from the “scientific truths”? If we’re going to immerse students in mimetic roles and game-like situations, will our classes need warning labels? Warning! Mimesis might occur!

Teaching, Research and Scholarship Part 3

Today’s post will focus on the landmark Boyer (1990) work, Scholarship Reconsidered. For earlier posts in this series, see part 1 and part 2.

Boyer’s key definitions are found early in chapter 2. As he sees it, one big problem in the academy (at least in institutions seeking to be “research active”) is that “lip service [is paid] to the trilogy of teaching, research and service, but when it comes to making judgments about professional performance, the three are rarely assigned equal merit.” That was more than twenty-five years ago, and the situation has been exacerbated. The ubiquity of “data” and being able to count things have taken pre-eminence over more qualitative measurements.

Part of the problem has to do with the narrowing of what is considered scholarship/research. Boyer writes: “Scholarship in earlier times referred to a variety of creative work… and its integrity was measured by the ability to think, communicate and learn. What we now have is a more restricted view of scholarship, one that limits it to a hierarchy of functions. Basic research has come to be viewed as the first and most essential form of scholarly activity, with other functions flowing from it.” The intensifying teaching versus research debates in higher education punditry is partly a result of the advancement-and-reward system tied to the narrow definition of what counts as scholarship.

Boyer would like to widen the categories. “Surely, scholarship means engaging in original research. But the work of the scholar also means stepping back from one’s investigation, looking for connections, building bridges between theory and practice, and communicating one’s knowledge effectively to students.” He proposes a four-fold expanded definition. He also carefully notes that these four categories do overlap with each other in practice.

The first category, the scholarship of discovery, is the most familiar to academics. This is what we think of as “basic research”. There are many good reasons to engage in such scholarship. I won’t discuss them here and Boyer does repeat the favorable arguments. The second category is the scholarship of integration. He defines this as “making connections across the disciplines, placing the specialties in larger context, illuminating data in a revealing way, often educating nonspecialists… [not] returning to the ‘gentleman scholar’ of an earlier time, nor [a] dilettante, [but] serious, disciplined work that seeks to interpret, draw together, and bring new insight to bear on original research.” Because of its close relationship and overlap with discovery scholarship, this mode is now becoming increasingly accepted as interdisciplinarity (another buzzword) has gained in popularity in recent years.

The third category, the scholarship of application, is trickier because of its overlap with that other nebulous area, “service”. Part of the problem is that service has become a catch-all term that may or may not include “serious intellectual scholarship”. Is there a clear line? The blurring of applied and basic work has led to arguments aplenty about what counts as scholarship with the two camps using different definitions to highlight and strengthen their own legitimacy. The issue of rigor in scholarship is another blurry line. What counts as being rigorous enough?

The fourth category is the scholarship of teaching. Boyer makes the point that one problem is that “teaching is often viewed as a routine function, tacked on, something almost anyone can do”, and that this is insufficient. Instead teaching is “a dynamic endeavor involving all the analogies, metaphors, and images that build bridges between the teacher’s understanding and the student’s learning.” No mention is made of the education specialists we see arising in some fields – certainly in math and science. A number of larger chemistry departments at larger institutions now have chemical education specialists. Smaller liberal arts colleges on the other hand do not, since it is an expectation that we all engage in thinking carefully about how to improve student learning. But is it rigorous? Do most of us have the time to engage it in rigorously while also steeped in trying to advance the scholarship of discovery? Perhaps that is Boyer’s point. A diversity of approaches, even within a single department, may enrich the community of learners – students and teachers alike.

I have come across Boyer’s categories often in higher education punditry so this was familiar territory. What jumped out at me in Boyer’s work was chapter 4 where he proposes the use of a creativity contract. First he sets the stage. “It flies in the face of all experience to expect a professor to engage in the same type of performance across an entire career, without a change of pace. Faculty renewal is essential. Yet, today, academic work is defined, all to frequently, in single-dimensional terms, with research and publications used as the yardstick by which success is measured. In such a climate, those who don’t publish with regularity are often considered ‘deadwood’, as if professional commitments are narrow and unchanging. Such a suffocatingly restricted view of scholarship leads frequently to burnout or plateaus of performance as faculty are expected to do essentially the same things year after year.” Amen to that.

Boyer provides a series of examples and data tables. I won’t repeat his arguments here but go straight to his suggestion. “Given personal and professional changes that occur across a lifetime, what’s needed, we believe, are career paths that provide for flexibility and change. Alternating periods of goal-seeking and reassessment should be common for all academics. Specifically, we recommend that colleges and universities develop creativity contracts – an arrangement by which faculty members define their professional goals for a three- to five-year period, possibly shifting from one principal scholarly focus to another.”

This sounds partly like my own varied trajectory, minus the actual contracts. As a new faculty member, my scholarship was mainly focused on the discovery mode. I did what “counted”, landing research grants, publishing peer-reviewed articles in my field, and involving students integrally in undergraduate research (being in a liberal arts college setting). While I made an effort to improve my teaching, this had mainly to do with learning new teaching tactics, classroom management strategies, and keeping my students relatively engaged (I hope) in learning the material. During my not-so-recent-anymore sabbatical, I got interested in more integrative approaches – so I spent my time learning much more broadly about origin of life chemistry. (The connection to my previous work was molecular self-assembly.) This led me to drill into a new specific discovery topic, which would then broaden as I started to see new web-like connections. In the midst of this, I took some time off to help start a new college, and this led me to think and read widely about the scholarship of teaching. I started to delve into research from cognitive psychology and the learning sciences. This made me think much more strategically about teaching (rather than on the small-scale tactical level). I’ve begun to integrate the teaching and research to a small extent, and am starting to visualize application ideas.

We’ll see where all this leads, but I do agree with Boyer, that my intellectual engagement has continued to be revitalized by being able to pursue my varied interests (thanks to a very supportive department). The starting of this blog was a result of broadening my ideas and intellectual framework. I’d like to continue working towards the same goal for my students!