Magicians, Mutants, Midichlorians

This semester I’m trying to sit in on a colleague’s special topics course on Interdisciplinarity in the sciences. I say “trying” because at some points during the semester I will probably get so busy that I might have to forego this luxury. Anyway, this past week the course was about getting students to think about Energy from the perspective of biology, chemistry, physics and mathematics. Thermodynamics is one of the main topics of my General Chemistry and Physical Chemistry classes, so it will be fun to see the synergies!

One of the exercises had students working in small groups to come up with consensus terms that described energy from these different perspectives. My colleague then showed results from similar exercises he has done with faculty groups. I was particularly intrigued that the largest diversity of terms came from the chemists, although it’s possible that biochemists in the mix significantly enlarged the terminology. As a chemist, I feel that my field has no grand narrative. Physics has the standard model and Biology has evolution. You might think that the periodic table was a unifying narrative, but having delved into it from my perspective, I see the elements in their grainy particularity – individualistic elements that try to defy attempts at herding them into groups. (I really should elaborate on that in a future post!)

Today’s post is my attempt to weave together an interdisciplinary narrative that spans science, science-fiction and story-telling – just for the fun of it! I have blogged about a number of these themes, but in an attempt to keep the prose flowing I will not reference them in the paragraphs below. If you’re interested in seeing some of these earlier ideas, three examples are here, here and here. And now I present my unedited speculative story on Energy!

M-Theory from the theoretical physicist’s perspective is an attempt to unify the different strands of string theory. The quest is no less than understanding the deep unifying principles behind matter, energy, and existence. If indeed the foundations of the natural universe are based on vibrating membranes and strings, it would be indeed music to the ears. Even after many years, my favorite creation story remains the Ainulindale from J. R. R. Tolkien. It would be poetic justice indeed if creation was sung into existence by supernatural beings in melodies that weave harmony and discord into a fantastic tapestry, the end of which is yet hidden from the mind of men.

I propose a new M-Theory that unites three worlds: Magicians from fantasy literature, Mutants from the comic universe of superheroes, and Midichlorians from the movie juggernaut that is Star Wars. Where do these supernatural powers come from? How can they exist in humanoid beings? What is the link between the miraculous and the mundane? I propose humble beings, found in great numbers in our very cells: Mitochondria.

If there is a thread to biological evolution stretching eons back into chemical evolution, it may lie in the laws of thermodynamics. An expanding universe requires the dispersion of energy from a Big Bang, and the parallel way such dispersion is achieved is through an expanding diversity as chemical space is explored. “Be fruitful and multiply!” It is an injunction that touches on the most efficient way to satisfy the second law of thermodynamics in a cooling universe – the evolution of chemical structures in hypercyclic systems through energy transduction. Who can better capture the energy as it streams through, animating organisms that stretch out the dissipation of energy across time and space.

Chemical energy in deep vents across redox potentials might have been the birthplace of primitive assemblies, but the streaming of electromagnetic radiation – a boon from the heavens – led to species that would harvest the power of the sun. A poison becomes life-giving as organisms adapt to an oxygenated environment. As one organism swallowed another, a new symbiosis emerged. Mitochondria! A better, more efficient way to transduce energy – converting it into forms that allow specialization, complexity, and the rise of a new multicellular organism.

For many an era, these energy powerhouses lived within the organism, but then emerged Man – a creature that would extend his reach of energy by building a cyborgian future. Smoke would rise as stone-coal dead feed the needs of the living. Water, Light, the harnessing of Electricity, and splitting the atom, would further extend the energy-producing capabilities of this new creature. Man’s energy sources reached far outside his body. Nature had never before been manipulated as quickly, and the Second Law was pleased by evermore consuming and dissipating its currency, Energy! Corporations and countries, organizations of men, jostled for control of the new currency – therein lies the power.

But there arose a new Man. One who would not be as dependent on the external structures carefully built and organized to serve the complex corporate organism. One who had the energy to manipulate the natural world from within. The new man had different names in different worlds. Magicians, they were called, in some forgotten realms. Mutants, others were called, in dystopian realms. Midichlorians, would infuse a rare few, in a galaxy far, far away. These tiny symbionts would be the clue to find the one capable of wielding a force of power, to throw energy across space and time.

The lowly Mitochondria would be key to supplying the enhanced energy needs of one whose acts would seem supernatural. Who is the Magician, but one who is able to channel energy through the electromagnetic spectrum and move collections of atoms into new configurations? Who is the Mutant, but one whose enhanced biochemistry allows for rapid healing, super-speed, and prodigious strength? Midichlorians are the new evolved Mitochondria. Harnessing energy requires energy, and the price of thermodynamics must still be paid.

It is said that life on earth uses barely 1% of the energy available today. Could we evolve mitochondria that could enhance our metabolism? If so, might we be capable of seemingly supernatural acts? Is this perhaps the link between the miraculous and the mundane? Could a broader M-Theory link the brotherhood of magicians, mutants and midichlorians, to the mitochondria of mere man?

Pantelligent

There’s a frying pan that apparently transforms you into a gourmet cook. At least, that’s the story of one of the founders behind Pantelligent. For $199 (according to an old issue of Time magazine), the snazzily-advertised product “guides you step-by-step in real-time ensuring a perfect dish every time”. As a scientist, perhaps it’s not surprising that I clicked first on the “How It Works” webpage.

One claim is “precise temperature control on the stove top”. What this actually means is that it gives you a real-time readout of the temperature at the surface of your pan where it is in touch with the food you are cooking. Unless you have a very fancy stove-top that’s linked up to your pan, and your fancy burner can adjust the temperature very finely and very quickly, what you have is a good sensor (patent-pending). Is it worth $199? Well, let’s see what else is on offer.

The selling point seems to be the mobile app that is linked to the sensor (via Bluetooth). There are pre-loaded recipes that hand-hold you all the way through the cooking portion. Voice instructions mean you don’t have to be reading a recipe book for the next step while your food is burning on the stove. And you might get consistency with this approach, perhaps even robotic consistency. Is that a worthy goal? Perhaps for some people. I personally like the experimentation that comes with non-Pantelligent cooking. There’s an excitement to cooking – serendipity in discovery and having a bit of skin in the game (because you could mess up), perhaps not high stakes on your steaks. (Couldn’t resist the bad pun.)

Another claim: “An interactive algorithm keeps your food in the optimal temperature range from start to finish ensuring a perfect dish every time.” I’m skeptical. Not about whether there’s an algorithm, but how useful it will be if you’re a novice cook and don’t know the personal quirks of your stove-top well. If you aren’t a novice cook, you’ve probably already learned to spot the appropriate signs. The shimmer of the oil, the golden-brown of the garlic (okay, stir-frying with garlic is my stock-in-trade), the crackle as you stir ingredients around, and the right combination of smoke and sizzle that tells you whether some liquid is needed. Could Pantelligent teach you to be a better cook? Yes, but only if you make use of your observation skills and not just rely on the sensor-fed talking-app.

What Pantelligent got me thinking about this week, is not so much cooking, but the notion of Temperature. I suppose it’s because I’m teaching thermodynamics in both General Chemistry and Physical Chemistry. I decided to spend a few minutes this week in class discussing the connection between temperature and the average speed of a collection of molecules. Since I’m teaching chemistry classes, one of my goals is that the students learn how to connect notions in the macroscopic world (such as temperature) with what might be happening in the microscopic or even nanoscopic world. We briefly talked about how liquid (mercury or alcohol) thermometers worked, but did not have time to delve into solid-state devices and thermocouples (probably what Pantelligent uses).

I also started planning some lessons in my head surrounding the notion of temperature. What is temperature? How can it be measured? How precise and accurate are the measurements? What are the limitations to such measurements? Why should we care? What does it mean to have an absolute zero on a scale that you may not be able to reach? Why does life cluster around a narrow range of temperatures? I would like such an investigation to be conceptually rich, beyond the 5 minutes here and there, that I will inject into class discussions. Now that I think about it more, I could probably plan a whole scientific inquiry block on temperature. Unfortunately, I don’t have time to incorporate such a plan into either one of those classes this semester. But I will probably put together a stand-alone lesson plan that I can use when I’m visiting a chemistry class at a different institution. (I sometimes get invited to be a guest lecturer in a college or high school chemistry class.) I’ve found these visits to be a good motivator to build up engaging activities for students. In fact, I almost always incorporate them into my classes the following year.

I could even use Pantelligent to spark some interesting class discussion. Besides thinking about the engineering and how it might be improved perhaps more cheaply, students could critique the two graphs on the website (shown below). Even though I feel no inclination to buy their product, what I like about Pantelligent, is that it made me think! This means that I can see ways to incorporate it into my class to get the students thinking. I had a similar experience (once again from magazine browsing) with Float Therapy. It allowed me to combine an exercise both in scientific inquiry and in quantitative reasoning into my non-majors course last semester. Besides discussing the potential validity of “advertised” benefits, I had students come up with a cheap bathtub design – that, among other things, also required temperature control!)

Letting the Unconscious Work for You

I am enjoying reading Richard Nisbett’s Mindware: Tools for Smart Thinking. I’m halfway through, and since I’ve read a number of popular cognitive science books the last several years, much that is written is familiar. The book reminds me of Daniel Kahneman’s Thinking Fast and Slow. Many of the same “classic” examples are used to illustrate the main point, although Nisbett’s prose is breezier and less technical. Each chapter ends with a Summing Up section that recaps the main points, but is also written in an advice-giving style for the reader looking for how the science can translate into thinking tips! This makes the book accessible to a wide audience.

The book is divided into six parts. (I’m in the middle of Part 3 which deals with statistical inference.) Today’s post will be about Part 1 (“Thinking about Thought”), in particular Chapter 3 (“The Rational Unconscious”). Nisbett opens the chapter discussing the fact that “although it feels as if we have access to the to the workings of our minds, for the most part we don’t. But we’re quite agile in coming up with explanations for our judgments and behavior that bear no resemblance to the correct explanation.” We, humans, are constantly trying to make sense of the world around us – and we’re very good at finding patterns, even those that are not there, to weave together a narrative. Nisbett argues that sometimes choices that engage the conscious can be suboptimal, if one doesn’t allow the unconscious to play its part. This is because the conscious “tends to focus exclusively on features that can be verbally described” while the unconscious covers both the verbal and non-verbal.

There are many experiments showing that the unconscious perceives much more than the conscious (that we are aware of). One example Nisbett provides came from a Dutch study where students try to determine the best apartment to rent given several options. There were objective criteria that could be used to rank the apartments by desirability. Students were placed in three groups. After seeing the apartments, they (1) had to make an immediate decision, or (2) were given some time to deliberate on their choices, or (3) were given the same amount of time as the second group, but “weren’t able to process it consciously because they had to work on a very difficult task” (presumably cognitively). Group 3 came out clear winners over Group 2 (who could not even do better than Group 1).

What can the unconscious do better than the conscious? Learning complex patterns is one category (and Nisbett provides examples) although sometimes we make up patterns than are not there, ascribing “a collection of events that are utterly random [to] have been caused by some agent such as another person”. Problem solving is another example. I even experienced it firsthand just this morning. I do the New York Times crossword puzzle daily. On weekdays, I usually work on the puzzle in the evening. Perhaps my brain is tired from the day’s work. On weekends, I do it over breakfast. Yesterday (Friday) evening, I barely completed half the puzzle before I got stuck – making no progress after a certain point. So I gave up. This morning, however, as I looked at the puzzle over breakfast, I was very quickly able to solve it to completion. This isn’t the first time I’ve had this experience, and I often take a break when I get stuck, do something else, and then come back to the puzzle an hour or two later.

Midway through the chapter, Nisbett poses the question: “Why do we have conscious minds anyway?” This is an interesting question that he doesn’t quite answer. He does provide examples that show how the conscious and unconscious problem-solve using different rules. We are able to verbalize the process for the conscious, but we still don’t understand how the unconscious works. One example provided is playing the game of chess. Newbies “move the pieces around without being able to tell you what rules, if any they are following” but they are apparently following the “duffer strategy”. If effort is made to improve by learning chess strategy, players becomes “conscious” and can articulate why they are doing what they are doing. But then once a certain level of expertise is reached, it becomes more difficult once again to articulate strategy. Nisbett explains: “This is partly because they no longer have conscious representation of many of the rules they learned as an intermediate player and partly because they have induced unconsciously the strategies that made them masters or grandmasters.”

All this reminds me of the wonderful Pixar animated movie Inside Out. If you have not seen it, and you find thinking about thinking interesting, go watch it! While the personal storyline was interesting and engaging, I found myself thinking hard about how the brain, the conscious, the unconscious, the emotions, and thinking, were represented. In a recent conversation, where an old memory was triggered, my spouse even described it as a “memory ball being drudged up”. When the human protagonist goes to sleep, interesting things happen. The “Train of Thought” stops, although there is still plenty of activity. There are workers (bean-shaped, perhaps resembling proteins) deciding on which memories to dump or move to different storage areas. A whole crazy cast of characters makes up mash-up movies for the dream world. Abstract thought changes the dimensions – perhaps leading to different solutions! One of the best parts is how you get ditties or jingles stuck in your head that crop up at the most ridiculous random times. I might have to watch the movie again now that I’m thinking more about thinking!

What advice does Nisbett have in his Summing Up section? I will just highlight one item: “You have to help the unconscious help you.” Nisbett argues that consciousness is “essential for identifying the elements of a problem, and for producing a rough sketch of what a solution would look like.” Without this “draft”, you can’t actually make your way towards the solution. After waking up from sleep, “consciousness is necessary for checking and elaborating on conclusions reached by the unconscious mind”. Nisbett’s advice to teachers is not waiting to the last minute to prepare discussion questions for class, simply because they are of lower quality compared to those one comes up with after mulling things over them (both consciously and unconsciously) for several days. His advice to students: “Question: When is the right time to begin working on a term paper due the last day of class? Answer: The first day of class.”

As Nisbett concludes: “The most important thing I have to tell you – in this whole book – is that you should never fail to take advantage of the free labor of the unconscious mind.” Hence: “If you’re not making progress on a problem, drop it and turn to something else.” I’d like to think that my best blog posts come after mulling over something for a stretch, and then having the story tumble out as I type the words. But perhaps I’m imposing a pattern that isn’t there. In any case, it’s interesting to be on the carousel thinking about thinking!

Fantastic Beasts: Chimeras everywhere!

Not so long ago, in a galaxy not far away at all, I was in the cinema watching a slew of previews before the feature presentation. One of these previews was Fantastic Beasts (and where to find them), the latest movie in the Harry Potter franchise. I have not read the stand-alone book, although it sounds similar to a middle ages bestiary that added tidbits to the series. Very little was revealed in the preview: A wizard travels to New York with a briefcase of magical creatures and some (or all?) of them escape. Eddie Redmayne, who did a great job portraying Stephen Hawking in “The Theory of Everything”, plays Newt Scamander in his younger days before he became the author of a best-selling bestiary. Apparently he’s also a Hufflepuff!

While the name Scamander may be familiar as a Trojan warrior in the Iliad (thanks, liberal arts education), with the first name Newt it brings up the image of a salamander. I wonder if that was intentional. Several of the names in Rowling’s series evoke certain characteristics of the owner of said name, the moment you read it without knowing anything about the character. Severus Snape sounds sneaky, and Draco Malfoy certainly sounds up to no good, and the name Slytherin clearly sounds like the bad house to be in. Even more so are textbook authors. Let’s see the list from the first Harry Potter book.

·      The Standard Book of Spells by Miranda Goshawk

·      A History of Magic by Bathilda Bagshot

·      Magical Theory by Adalbert Waffling

·      A Beginner’s Guide to Transfiguration by Emeric Switch

·      One Thousand Magical Herbs and Fungi by Phyllida Spore

·      Magical Drafts and Potions by Arsenius Jigger

·      Fantastic Beasts and Where to Find Them by Newt Scamander

·      The Dark Forces: A Guide to Self-Protection by Quentin Trimble

When I read this list, the first two did not conjure anything noteworthy in my mind. However the next five clearly do. Magical Theory sounds addled with a lot of waffling. Potions sounds like a lot of jiggering with dangerous chemicals. The Herbology and Transfiguration authors clearly sound as if they were born to the task or so aptly named at birth. I think a more likely possibility is that they were writing under pseudonyms, pen-names, or even assumed names given their fame in a particular area. Alchemists and others in the medieval world often invoked the names of more famous people to bolster their own work, in what would look like as reverse plagiarism in the college classroom today. This is where Newt Scamander and his book first get mentioned. (Why is this a textbook for Harry? He doesn’t take Care of Magical Creatures until third year.) As to the final book on the list, the name Trimble sounds like “tremble”, and is quickly reinforced when Quirrell is first introduced as the teacher.

But back to salamanders. As amphibians, they have a dual-nature related to land and sea (or to terrestrial and aquatic environments). The ancient Maya ascribed special significance to “boundary-breaking” creatures, as I learned in a recent visit to a museum exhibit on the Maya (coincidentally the day before I saw the Fantastic Beasts preview, both of which inspired this blog post). From the blurry photo I took below, you can see that bats, diving birds, and crocodiles are among the list of creatures. So is the jaguar, which features prominently in the duality of day and night, life and death. Down through the ages, across many cultures, there seems to be a fascination with creatures that seem to span two realms. They are sometimes referred to as chimera, or having a chimeric nature.

The Chimera is first mentioned in the Iliad (thanks, Wikipedia) – a lion-headed, goat-bodied, snake-tailed, fire-breathing creature. In the Harry Potter world, the salamander is a fire-breathing lizard, related to what you might find in a medieval bestiary. (Note: If you had an amphibious, flying, fire-breathing salamander, you could span all four elements of the ancient world.) This dangerous and fantastic beast is finally defeated by Pegasus, the winged horse, yet another example of a chimeric creature! In the third Harry Potter book, we are introduced to the Hippogriff, half-eagle and half-horse, one of whom plays a prominent part in the tale. Thestrals show up in the fifth book, winged skeletal-looking horses that seem to have some connection between the realms of the living and the dead.

Lest you think that such beasts are only found in the imagination, but are only as real as the fabled unicorn, it turns out our natural world is full of chimeric creatures. Without a symbiotic lifestyle with our gut bacteria (that outnumber us easily by cell count), we might not do a good job turning our chomped food into useful energy to do work, building biomass, and ridding ourselves of toxins. One could argue that a symbiont isn’t a true chimera, but if you take a closer look at bacteria more generally, they turn out to be strange. We are used to thinking of families of related creatures having similar characteristics that are inherited vertically through genetics – this is what we observe in “larger” organisms such as bats, birds, crocodiles, salamanders, and even ourselves. Bacteria however can swap genes through horizontal gene transfer. They look like tiny monsters combining parts from other creatures – chimera, in essence. This actually makes it difficult to construct a phylogenetic “tree of life” because life history is getting erased. That hasn’t stopped scientists from trying to determine what the Last Universal Common Ancestor (LUCA) looked like, but it is not going to be easy.

What is even more puzzling perhaps is what the first eukaryote, much more “complex” than prokaryotic bacteria, might have looked like. Every eukaryotic cell in our body betrays a strange chimeric origin – genes from archaea and bacteria. Not just from one type, but from an assortment of them (at least given our present assigned groupings). Even the way we pass our genes to our descendants is chimeric. While the nuclear genome is primarily assembled from the coming together of the male and female gametes, the mitochondrial genome comes from our mothers. There seems to be close interplay between the two genomes: their differential rates of evolution, how apoptosis works, and the fact that the biochemical constituents of our respiratory chain are encoded by both genomes. Our bioenergetic core, what powers us to stay alive, is chimeric in nature. We are chimera!

Does our chimeric nature extend beyond the physical realm? This is perhaps a religious or philosophical question that we cannot test scientifically (at least through the natural sciences as currently conceived). Do humans have a non-physical soul or spirit intertwined with our physical nature? Is this why we seem to be capable of abstract thought and imagine fantastic beasts such as unicorns? We can conceive of such creatures even though, as far we know, there are no natural physical examples. We have built and immersed ourselves in virtual worlds where fantastic beasts can be found, coded in bits and bytes.

Near the end of Harry Potter and the Deathly Hallows, while Harry is physically lying down in the forest and having a “conversation” with Dumbledore, he asks: “Is this real? Or has this been happening inside my head?” Dumbledore beams at Harry and replies: “Of course it is happening inside your head, Harry, but why on earth should that mean that it is not real?”

Being on the Block

I had the pleasure of visiting Quest University, located 50 miles north of Vancouver in British Columbia, Canada. Quest is among a handful of new colleges aiming to attract students through a new innovative curriculum steeped in the liberal arts. Students start with a foundational curriculum in their first two years, at the end of which they develop the outline or the idea of a Question. (You can see examples on the university’s website.) The next two years are spent on a Concentration – exploring a series of courses for the student to delve into his or her Question. The student co-designs this roadmap with a faculty mentor. What is often referred to as the “capstone” in higher education lingo manifests itself as the Keystone at Quest. A student’s Keystone presentation represents the culmination of a two-year exploration called the Question. (If you didn’t notice it before, these terms force you to look at the link between the words “quest” and “question”.) There are no majors at Quest, nor are there traditional departments.

There’s a lot more I could write about Quest: flat faculty hierarchy with no tenure system, fully residential experience, engaged students, and the development of its curriculum (at least what I could glean from a very short visit, beyond what you might find on the website). However I want to concentrate on just one aspect of the curriculum: The Block System. Quest is not the only institution that uses the block system. I first learned that such a system existed when I was a postdoc and I met several graduate students who went to Colorado College, a pioneer of the block system. Traditional institutions also have a flavor of the block system – in summer of intersession intensive courses. So do professional programs. Intensive classes aren’t novel in this regard, rather it’s having your entire college experience taking only one class at a time in an intensive format that distinguishes Quest and Colorado College from many of their peers.

First, a description of Quest’s system. (You can find all this on their website too.) To graduate a student needs to complete 32 blocks, or an average of 8 blocks per year. There are three terms (Fall, Spring, Summer) each with 4 blocks. So technically a student could graduate in slightly under 3 years by taking 4 blocks every term consecutively. No one actually does this – it is way too intense! The median is currently 4 years (i.e. an average of 8 blocks per year) although the time-to-completion seems to be creeping up. In my discussion with students, they found that in addition to summers off, they also liked a month off every now and then. So while many students still take 4 blocks in the Fall and 4 blocks in the Spring, a number of students are starting to spread out their intense workload. (This is akin to what a typical college student might do at an institution that offers 4-credit-hour courses rather than the more common 3.) Full-time faculty teach six blocks per year, akin to a liberal arts college with a 3/3 load.

A block is 3.5 weeks long, and typically includes 54 contact hours (or an average of 3 contact hours per weekday). Then there is a 4-day break before the next block. The student only takes one class during the block. According to the faculty I talked to, students are typically expected to work 4-6 hours per day on course material outside of class. That’s pretty intense, but it’s not uncommon. What is uncommon is doing this four times in a row during a semester. Even summer terms at traditional institutions stretch from 4-6 weeks with a slightly lower intensity – and a student wouldn’t take more than two in a row (because after that summer is over).

Although the academic work is challenging and intense, my conversation with the students seemed to indicate that they thought the academic piece was generally manageable. The trouble seemed to be balancing this with their other interests and co-curricular activities and not be completely tired out. (I only had lunch with 6-8 students, all very engaged, so that’s a rather small sample size. My conversations with faculty and staff seem to indicate that the students I met were not atypical.) A number of students did indicate that every now and then, they would choose to “take a block off” (i.e. to enroll in 3 rather than 4 blocks in a semester). December and January were the most popular months to do this. If you plan ahead, according to the students, there was no impact on tuition.

I asked the students what happens if someone gets very sick for several days during a block. (I also asked the faculty this question but you really want to hear it from the students directly.) Most of them said that typically you’d have to “drop the block”. There is a mechanism by which to do this and certain procedures that the student would need to follow that would allow them to make-up a block in the coming summer. There was some stress surrounding this – since it might mess up the student’s plan. Students indicated that some professors were willing to work with the student if not too many days were missed, and others would not. It depended on the course and the instructor. The students cited small class sizes and good relationships with professors, and that they would at least have a conversation with the instructor.

How intense is it for the professor? What I garnered from my conversations with faculty is that it can be a bit of a shock to the system the first time around, but after that you get used to it. There seems also to be quite a bit of flexibility in how to schedule your class. As long as there are rooms available (this did not seem to be a huge problem in general), the registrar would entertain varied configurations. Some faculty would divide up their class into a morning session and afternoon session to give themselves a break. I would probably do this if I taught in the block system. I find myself drained of energy after a lecture-discussion class. Some of my colleagues seem okay with back-to-back classes; I never do this. The one exception is the 4-hour chemistry lab. The pace and intensity is much more manageable in the lab course. I do walk around a lot and make many observations. When necessary I have a quick discussion with the students to keep them on the right track, or to get them to think a little more deeply about why they’re doing what they’re doing. But I try not to interrupt the flow of a student unless they’re having some downtime (waiting for a calibration for example), in which case I take the opportunity for some light banter.

Scheduling can still be a tricky business. I had some great conversations with the registrar and the chief academic officer. Since I have some experience scheduling and working closely with a registrar’s office (I ran one for a short period while I helped hire a new registrar), it was interesting to compare and contrast the issues surrounding scheduling in a block system versus a traditional system. I think the block system is a little easier from a registrar-viewpoint, but that’s probably because Quest is still small. The larger the institution, the more complex the moving parts. I won’t go into details of the analysis here since I’d like to keep this post light and readable. I will just point out that student stress is high during the 1-2 day add-drop period at the beginning of a block. In a traditional system, this is spaced out over a couple of weeks at most institutions. In a block system, if you’re only taking one class, and you drop – you’re done for that block. Thus choosing a class is much more high stakes. My sense was that the registration part of the block system can be quite stressful for students.

The biggest advantage of the block system, in my opinion as an educator, is that you can design the class for maximum learning impact. You’re not constrained by a system that forces you to teach in three 1-hour slots or two 90-minute slots per week. You’re not forced to vacate a classroom after the hour is up. Students in fact stay on after official class hours to continue working together. Having the larger block of time also, in my opinion, facilitates group work and other active learning pedagogies. I wonder if the reason why many of us who still have a substantial “lecture” part to our classes do so in part because of its efficiency in “communicating content” when you’re constrained by the class time. I feel deep learning in group work is leveraged when you have more time. It’s hard to get beyond just quick surface discussion when you have five minutes here and ten minutes there. Not to mention, students are fully immersed in your class – they aren’t taking any others simultaneously.

For classes that have a field component – this spans the sciences, social sciences, and humanities – the block class is a boon! Want to take your students to an ecological field site? No problem. It’s the only class they are taking so there are no academic scheduling conflicts. The same applies for a visit to a museum or an art gallery. Perhaps an urban studies field trip into the nearby metropolis (this would be Vancouver in the case of Quest) would really enhance the educational experience of the student. You could even take the students to an off-site location for the entire block. This is rare, but possible. (There is a fund for “field trips” and a faculty committee administers this.) Since faculty autonomy is very high at Quest, one can imagine that classes are structured in rather varied ways. As the institution approaches its current maximum capacity (they’re not quite there yet), constraints will start to be felt simply from an operational point of view. But at the moment, there is a lot of freedom to design a class they way you think is best as an instructor, for maximal educational impact to the student. What a wonderful quest for an institution!

The Hunt for Vulcan

Science, philosophy and history are marvelously woven into Thomas Levenson’s new book, The Hunt for Vulcan … and how Albert Einstein Destroyed a Planet, Discovered Relativity, and Deciphered the Universe. The book opens with Newton’s Laws and the discovery of the planet Neptune. Riding on his success with Neptune, the upstart celestial mechanic Urbain-Jean-Joseph Le Verrier, predicted the existence of Vulcan, a body closer to the sun than Mercury that would explain part of the perihelion shift unaccounted for. Ultimately no evidence of Vulcan is found, nor is evidence needed once Einstein has had his say on the matter.

Levenson first lays the groundwork leading up to Newton’s Laws of motion. The story begins with Edmond Halley (of Halley’s comet fame) and the discovery of what seemed like an inverse square law in explaining the motion of planets around the sun. Halley seeks out Newton to help explain the behavior of orbiting objects grounded in mathematics. His nine-page response to Halley, “On the Motion of Bodies in an Orbit” turned out to be of great significance. Levenson writes that “Newton hadn’t just solved a single problem in planetary dynamics. Rather, Halley grasped, his friend had sketched something much greater, a newly rigorous science of motion of potentially universal scope.” Newton’s subsequent Principia was broad in scope covering, well, everything to do with how things moved. It certainly seemed to work with all known objects at the time at least when measured to some degree of imprecision.

With the discovery of Uranus via observation by William Herschel in 1781, the task of calculating its approximate orbit went to the brilliant mathematician Pierre-Simon Laplace. The problem is that when you add a new object to the system, it will affect and be affected by the motion of everything else. That the mathematics is highly complex and ugly is an understatement. Add to that, with more precise measurements in astronomy, differences between an idealized calculation and actual observations become magnified. But even after all that, Newton’s Laws and the power of mathematics continue to triumph, and bring into harmony what had seemed disparate in the motions of Jupiter and Saturn. If you could account for all the moving objects, you could perfectly know their future and past – at least as portrayed by Laplace in his great work, Celestial Mechanics.

The nineteenth century is where things get interesting. Better and more precise observations and the accumulation of more data begin to suggest potential problems. Mercury starts to misbehave, but Uranus is the big bad boy looking for a solution. Could Newton’s Laws be wrong? Levenson shines in bringing to light how the “scientific method” plays out historically, and laying out the philosophical conundrums surrounding what to do when there seems to be a conflict between theory and experiment. Here’s a different question: Maybe Newton’s Laws aren’t wrong but take on slightly different characteristics at different length scales? Uranus is so far out there – maybe there is an additional factor that does not make much of a difference at closer distances, but starts to be important farther out (or farther in – in the case of Mercury). Or maybe there are other superceding descriptions at different length scales, quantum mechanics for example (but that would take another century to figure out). Or maybe different forces have different strengths at different length scales – certainly classical electrostatics can be compared with gravitation.

But what if Newton’s Laws did not need any modification? What if there was some other orbiting body further out that was causing Uranus to “deviate” from its ideal calculated path given the presence of Jupiter, Saturn and the Sun. (The rocky planets closer to the sun have very little effect.) Le Verrier was not the first to make this suggestion, but he had the audacity and mathematical prowess to calculate how this other body might move based on the data from Uranus’ motion. The historical tale is full of twists and turns, and Levenson describes them engagingly (so if you’re interested, go read his book!). Let me just reveal that after Le Verrier had predicted where exactly to look in the night sky for this new object, none of the French astronomers did so. Nor did the English. A young German astronomer however did. And he saw a new planet! They named it Neptune (after lots of wrangling of course).

Newton’s Laws continue to reign supreme. What should we do about misbehaving Mercury? Maybe the same strategy will work. The now very famous Le Verrier does the calculations and makes a prediction of where to look. This "planet" even has an appropriate name – Vulcan. Why hadn’t anyone seen it before? Maybe because it is hidden in the sun’s glare and the only chance of catching it might be “during a total eclipse of the sun” according to Le Verrier. The story has its own twists and turns, but now both professional and amateur astronomers looking for a chance at fame and glory turn to the skies. Here’s the catch. Some of them “see” something “new”, but many others do not. Was their equipment not good enough? Did the weather conditions at different sites play a role? Is the object seen indeed new or is it an older known star?

When you are the limits of precision in measurement, imagination can start to play a role in interpretation. Given my interest in origin-of-life research, this reminds me of the controversies surrounding the Allan Hills meteorite controversy in 1996 and whether there were microfossils, and the more recent spat between Brasier and Schopf with regard to the Apex chert in the 2000s. In an interlude, Levenson provides contemporary examples in particle physics and Big Bang cosmology. He sets the stage by discussing the interplay between scientific theory and experiment/observation. (I’m quoting him below.)

“No shows are hardly alien to science. Theories predict. That’s their job. Ever since Newton and his co-conspirators consummated their revolutionary program of subjecting nature to mathematics, this has come to mean that particular solutions to systems of equations can be interpreted as physical phenomena. If a given mathematical representation hasn’t yet matched up with some phenomenon in the real world, that’s what’s called a prediction. From the theory of Uranus, Neptune; from the theory of Mercury, what, if not Vulcan?”

“Long gaps between prediction and observation always raise the question: what finally persuades science – scientists – to abandon a once successful idea? When do you take “no” for an answer?”

Indeed. When? We now know from many examples, that if scientists had followed a monolithic scientific “method”, we would not have made anywhere close to as much progress. (“Set the dials with the right question, pour data in to the funnel, and pluck knowledge from the other end. And, most important: when that outcome fails to match reality, then you go back to the beginning, work the dials into some new configuration, try again.”) Levenson’s book highlights the dilemma and the fuzziness in philosophy of science – it's one of the best parts of his book.

The tale closes with Albert Einstein, lone genius working in a patent office in Switzerland. Newton’s theory finally bends, literally, as does space-time, with the powerful tour de force that is General Relativity. The repercussions of the theory are bizarre, and science is indeed stranger than science-fiction. Two groups make observations during the 1919 eclipse. The group at Sobral confirms Newton’s Laws stand unmodified, while the group at Principe measures what Einstein predicts. We hear the triumphant story of Arthur Eddington’s confirmatory expedition, as if, the aha moment was figured out through the telescope. History turns out to be both more complicated and more interesting.

As I was preparing an overview talk of origin-of-life research this week, I was reminded of a lone German patent lawyer working quietly for years on an idea that would rival the mainstream view. Gunter Wachtershauser is not a household name since the conclusion to his theory is still an open question. As described by Robert Hazen, in his very readable and engaging Genesis: The Scientific Quest for Life’s Origins, “Wachtershauser, a chemist by training but a Munich patent attorney by day, erected a sweeping theory of organic evolution in which minerals – mostly iron and nickel sulfides, which abound at deep sea volcanic vents – provided catalytic energy-rich surfaces for the synthesis and assembly of life.”

I don’t expect this complex problem to be solved anytime soon (otherwise I would have switched fields). Wachtershauser’s out-of-the-box thinking has led to a new generation of scientists working to combine the best parts of multiple theories to understand the riddle of life. It has also highlighted the importance of interdisciplinary research. Biology, Chemistry, Geoscience, Physics (and a good dose of math) must come together and scientists must combine their expertise if they are to make headway. Will we find the smoking gun signal to life? Can we imagine what life’s solution might be? Will we see what we want to see? Will a fundamental scientific law be challenged? In a heady and exciting time, it’s important to remember the lessons of history.

Procrastination (and Community)

After an excellent twelve days of essentially zero work, I made it back to the office at 7:45am today. The new semester hasn’t officially started yet, but when it does, I’ll have to get in earlier since I’m slotted to teach the 8am section of second semester General Chemistry. The goal for this week is to make headway in things I procrastinated from doing end of last semester. It was nice to have a smooth, relaxing end partly because of my procrastination. I have no regrets after a good break.

The main item on my plate is to finish a research manuscript, or at least get it into good shape before classes begin. Last semester I wrote the abstract, half the introduction sans references, and half the methods section with references. The bulk of the paper, the results and discussion sections, are looming. My student has compiled some tables of results, but I will need to make some choices as to what goes into the main manuscript, and what goes into the supplementary material. She’s also started making a few figures, and chances are I will have to make some too. The undergraduate working on this project is very capable, but she’s only a sophomore and doesn’t have as much experience (this is her first project). In any case, I always double-check data before it goes out. Target submission: end of January.

But I’ve been avoiding making headway on the manuscript last semester, and today was no different. I always have difficulty motivating myself to write up research results. For me, it feels "unproductive", because the research is completed and I already know the story. So this morning I managed to distract myself by responding to some e-mail from the last couple of weeks, chat with colleagues and wish them a happy new year, write a recommendation letter for a student (due in three weeks), and catch up on some journal article reading in my research area of interest but not closely related to my actual projects. After lunch with another colleague, and more chatting about teaching and pedagogy, and “cleaning my desk” one more time, I had finally run out of excuses. So at 2pm, I downloaded the latest update of EndNote (my final bit of procrastination) and got to work. I made minor modifications to the text of the abstract and introduction but what I really accomplished was hunting down some papers I had read a while back and putting in the references in the introduction. Two hours later, I decided that was enough for the day, and I’ll make more progress tomorrow. The important thing was to actually start. Once I do that, it gets easier.

Over the break I was watching DVDS of the TV series Community. It’s about a bunch of quirky friends who form a study group at a community college. The characters are colorful, the adventures are wild, the college-wide laser tag and blanket forts are way over the top, and there are a bunch of crazy people who do silly things. Granted, this is TV, and I don’t think actual college students behave like this. I certainly didn’t get the same vibe reading Rebekah Nathan’s book. But it did make me think about how much students procrastinate. This study group spends practically no time studying (although there are many dioramas built as class projects) and it’s all about wacky interpersonal relationships. After all, the show is called “Community”, and it is a laugh-out loud comedy. It reminds me why I avoided study groups when I was a college student – you didn’t get very much done. Yes, I would ask friends who were classmates if I was really stuck on something, but we wouldn’t have scheduled study group sessions.

However, building community is important (as described in my last post). So the time I took to shoot the breeze with people is a good thing to do, even if I did procrastinate. It’s not always about cranking out the manuscripts. I think I’m willing to sacrifice some potential “productivity” for good community. And I make good use of procrastination. By having a larger project that I try to avoid doing, I get a bunch of other stuff done. It works well, until you really do need to finish that larger project. To get that accomplished I have an even larger pie-in-the-sky project (with no deadline) where I’ve made hardly any progress.

Goal for tomorrow: More writing. But it’s okay to work on a few other things too! And no, writing this blog is NOT used to procrastinate from work. I keep my work time separate from my non-work time, and almost never write this blog when I’m at work. Okay, there was the one time I was proctoring a final exam, and yes, I was procrastinating from something else I could have been doing! And maybe try to make it in 5 minutes earlier so I can ease into waking up earlier.

Managers: A Thermodynamic Need for Complexity?

Since getting into academic administration, I have tried to learn more about how to be a better leader and manager (and no, the two are not synonymous, although they are equally important). As an academic, I’ve mostly learned by reading so that’s what I started to do. The most important thing I’ve learned from my reading is the importance of good and careful observational skills. Not just observing by watching body language, but carefully listening and reading of e-mails/memos. This past week I stumbled upon randsinrepose.com, the musings of a manager in the tech world, himself a former software engineer. It’s funny and entertaining, but also contains great observations and nuggets from his practical experience.

Since I’m also preparing for classes this upcoming semester, where I will be teaching statistical thermodynamics (P-Chem 2 for my students) and second semester General Chemistry (covering introductory thermodynamics), the article that caught my eye was Entropy Crushers. In this article, the author (Rands) explains why project managers are crucial and important when an organization grows in complexity. You don’t need them in a small start-up, but as the organization grows so does the chaos. Thus, a good and capable project manager acts as an “Entropy Crusher” to keep production moving along as efficiently as possible. There are of course bad project managers and pointy-haired bosses.

Rands’ definition of a good manager: “A good project manager is one who elegantly and deftly handles information. They know what structured meetings need to exist to gather information; they artfully understand how to gather additional essential information in the hallways; and they instinctively manage to move that gathered information to the right people and the right teams at the right time.” He goes on to address the main concerns of software engineers with the introduction of project managers or their equivalent, since engineers are often suspicious (often with good reason) with these middle-men. Do they actually do any work? The author pulls no punches: “The irony of the arrival of crap project managers is that you’re effectively punishing inefficiency with useless bureaucracy, which, wait for it, creates more inefficiency.”

In some ways university faculty resemble engineers in tech companies. (In other ways they are not.) You’ve got a group of highly skilled people with cutting-edge expertise (at least research-wise) in their area of specialty. They are independent-minded, sometimes lacking in social graces, and have beat out significant competition to land a coveted faculty position, so sometimes they come with an ego. To run a department consisting of these folks smoothly, so they can get their best work done, requires good leadership and management skills. Otherwise you end up with dysfunctional departments, where time and energy is sucked up into some black hole, and you will have trouble hiring capable people who will happily go somewhere else.

There are many qualities one can list in a good manager, and some are listed in Rands’ definition. I’d like to point out one more before I launch into some thermodynamics. In my experience, one of the most important elements is trust. If you’re a designated leader or manager in a department who is not trusted by its members, there will be trouble aplenty (to put it mildly). Hence, building trust is key for a new manager, especially if coming from the outside. In my current department, where I’m a known quantity, the trust was built up over the years before I became chair. When I worked in a new start-up institution for a short stint, trust was built by meeting regularly with people both within and outside my area, listening very carefully, and figuring out how the organization really functioned.

But since I’m a science geek, let’s briefly discuss entropy. First, it is not chaos. It has to do with counting and chunking. But for the purposes of today’s post, a useful working definition is that entropy is what drives chemistry by allowing the dissipation of heat. Here’s my geeky allusion to being a good manager. You avoid getting into a situation where pent-up energy, built over time, leads to the explosion blowing everything apart. This is chemistry – just not the type you desire, if you’re trying to run a complex organization. It’s a great way to get to thermodynamic equilibrium or chemistry death where nothing useful will happen subsequently.

There’s another way that you can utilize entropy to drive chemistry – through a series of steps that dissipates the heat proportionately over time. Our cells do this by (geek alert!) coupling endergonic and exergonic reactions. That’s how biomass and complexity can be built up while taking advantage of the second law of thermodynamics. Proteins, acting as catalysts, allow our cells to take this route and avoid the pent-up energy approach. I suspect that the solution to the puzzle of the origin of life lies in how molecules in an appropriate environment start to take different roles. Some will act as catalysts, and in doing so will build up complexity so as to better dissipate heat according to the second law. Entropy, far from leading to chaos, can drive the evolution to complexity. (It can also lead to explosive death.) But those catalysts are needed! That perhaps is the role of the good manager. The role of catalysts sounds very much like the definition Rands provided. I’d say they are not so much entropy crushers but entropy leakers!