Ghostly Material

Potions for Muggles is four years old today. Hurrah!

Did you know that chemists have detected a ghostly trilobite? The ghost of an extinct creature? That would make the news. Turns out the ghostly impression only resembles a trilobite, but it’s still cool and interesting – at least to a quantum mechanic. Here’s a link to the short article in Chemical & Engineering News and the corresponding picture below. 

In preparation for Halloween, I decided to read the third book in the Dresden Files series titled Grave Peril since it highlights ghosts! Harry Dresden the protagonist is a wizard who runs his own detective agency. The novels are written in the first person from Dresden’s point of view, and they occasionally explain the world of magic and, in this book, ghosts and the spirit world. Here is Dresden’s description of ghosts.

“Ghosts are beings that live in the spirit world. They’re impressions left by a personality at the moment of death. They aren’t like people, or sentient spirits… Ghosts don’t usually inhabit a construct – a magical body. They’re just energy. They don’t leave any physical traces behind… Usually they aren’t visible, but they can make a body out of ectoplasm and manifest in the real world when they want to, if they’re strong enough… They can throw things around and stack furniture. There have been documented incidents of ghosts blotting out the sun for a while, causing minor earthquakes, all sorts of stuff – but it isn’t ever random. There’s always some purpose to it, something related to their deaths.”

The ‘imprint’ part is similar to the description in the Harry Potter books, but there are other differences, for example how ghosts can take on some physical manifestation. I find the ‘pure energy’ definition interesting – massless photons or electromagnetic (EM) radiation perhaps? Or maybe neutrinos, also known as ghostly particles. In Grave Peril, the boundary between the spirit world (where ghost reside with stronger definition) and the human-material world is weakened. There is some traveling back and forth between the two. Interestingly, when Dresden travels into the spirit world (the “Nevernever”) the description sounds very much like the Upside Down in Stranger Things. There is even a scene where Dresden and his knightly companion in the Nevernever notice energy emanations from living souls in the adjoining human-material world, much like what happens in Stranger Things when such a boundary is weakened.

How does the material world interact with the ghostly world? Grave Peril provides two examples. In one case, Dresden is grappling with the physical manifestation of a Nightmare. They tumble down a slope into water and we can read his thoughts. “You ever hear the Legend of Sleepy Hollow? Remember the part with poor old Ichabod riding like blazes for the covered bridge and safety? Running water grounds magical energies. Creatures of the Nevernever, spirit bodies, cannot cross it without losing the energy required to keep those bodies here.” When they hit the water, the Nightmare’s body begins to melt away “like sugar in water”. Reminds me of the Wicked Witch of the West melting when splashed with water by Dorothy in the Wizard of Oz. But the wicked witch wasn’t a ghost. Why would the physical manifestation of a ghost melt in water? Unclear. Maybe the author was thinking of the analogy that easily dissolvable materials might not be as solid as they seem. My G-Chem students should be able to pipe up at this point and discuss why low-charge ionic compounds (salts) fall into this category.

The second example is much more interesting. Dresden carries a sack of “ghost dust” in an attempt to trap a ghost. But not Ghostbusters-style. Here’s how he describes it. “The whole point of the ghost dust was that it was something extra-real, that it was heavy and inert and locked spiritual matter into place when it touched it. Even inside its bag it had become a sudden stress in the Nevernever… felt like it weighed thirty or forty pounds.” When asked what the dust is made of, Dresden replies “depleted uranium”. I don’t know about the vague-ish terms “extra-real” or “spiritual matter” but depleted uranium is simply lead (plumbum), element symbol Pb in the periodic table). My G-Chem students should be able to pipe up about lead being a very dense material that can stop penetrative radioactivity from beta-particles (electrons being shot out from a nucleus) and gamma rays (high energy EM radiation). So if ghosts are “pure energy” of the EM radiation variety, then all this seems fitting.

There’s a neat paragraph echoing my thoughts on why potions are needed in the magical world for complicated magic such as healing or turning yourself into someone else (think Polyjuice potion). Dresden gets healed magically by a frenemy, but there’s a big But. “If you think I should have been happy about getting a nasty cut closed up, then you probably don’t realize the implications. Working magic directly on a human body is difficult. It’s very difficult. Conjuring up forces, like my shield, or elemental manifestations like the fire or wind is a snap compared to the complexity and power required to change someone’s hair a different color – or to cause the cells on either side of an injury to fuse back together, closing it.”

Other than those tidbits, Grave Peril reads much like the first two books. While I found the first novel both interesting and novel, the second book was less interesting overall. The same is true of this third book. It feels like more of the same, but at a more frantic pace. I found myself skimming some parts – not a good sign for holding my attention. There are a couple of clever uses of ghosts towards the story climax, but they’re spoilers. There are also a few other minor interests in passing: an allusion to dreams akin to creating a “bubble in the Nevernever”, and a brief statement about magic and language. “Magic is a lot like language: it’s all about stringing things together, linking one thing with another, one idea with another. After you establish links, then you pour power into them and make something happen.” Sounds a lot like teaching and learning. Making links between ideas. Then maybe some brainpower is exerted, and something happens. Learning and magic. Both mysterious!

Mid-semester Group Meeting

It can be challenging to find a time when classes are in session for my entire research group to meet. Partly this is because I restrict the possible times to be between 8am-5pm Monday through Friday. I’m not going to ask the students to come back in the evenings or on weekends (some of them live off campus), and I’m not interested in doing so myself either. Hence, getting schedules to mesh can be tricky. Students are typically taking five classes per semester, and have two 4-hour lab sessions per week if they’re majoring in chemistry or biochemistry. I have sophomores, juniors and seniors – all with different class schedules. Not to mention my schedule is also busy with classes, office hours and meetings.

This is why I hold my training sessions a couple of days before classes begin for new students joining my group. It helps them to be productive once the actual semester begins and they get busy. A student doing research for one unit during the semester commits to 4-5 hours per week. For two units during the semester, the commitment is 8-10 hours per week. Most students only sign up for one unit because they have such busy schedules and lives.

Day-to-day computational chemistry research is also, for the most part, a solitary endeavor. My philosophy is for each of my students to have their own independent project, and they plug away at it in bits and bites during the semester. Schedules rarely overlap so it’s not often I will find more than one student in my lab at any given time during the semester. There are no safety issues akin to experimental labs where you need to have a buddy system. And unless the student requires using the graphical user interface for building molecules or analysis, some of their work can be done remotely. The students enjoy this flexibility, and like me, they find that the most efficient way to do computational work is to do a little bit most days rather than find a single 4-5 hour block. You don’t have to babysit your calculations (unlike a reaction in organic lab) so after setting up and making sure your calculation hasn’t crashed early on due to a setup problem, you can come back and check on it later.

During the summer, the students work full-time on research. We have regular group meetings where they present their work. I also have “theory” sessions spread over several weeks of the summer where I teach them some of the nuts and bolts of computational chemistry. For the students, it’s like auditing a no-credit mini-class. No problem sets or exams, although there is reading. They don’t have other classes between 8am-4pm Monday through Friday, and neither do I, so it’s easy to schedule times for all those things. (When I train students before the semester begins I do cram in a little bit of theory in the full two-day session.)

Before the new semester begins, I work with my students to set up individual one-on-one weekly meetings so that we can check on research progress. However, in the lead-up to this semester I realized that there was some time on Friday afternoons that would occasionally work for all of us during the semester. None of my students had Friday afternoon labs, and only one had class until 2:30pm on Fridays. So before the semester began, we made plans to meet twice during the semester for ‘group meeting’. Why not more often? During the semester, a student only working 4-5 hours per week on research doesn’t actually make that much weekly progress so there wouldn’t be much to present. (In contrast, during the summer we have weekly meetings.) Three of my students were new to the group, so they’d only have had 28-35 hours of research done by group meeting time.

We had our mid-semester group meeting yesterday afternoon. I had prepped the students ahead of time with what I was expecting from them: a 6-to-10-minute presentation with 1-2 minutes of introduction, 4-6 minutes of results, and 1-2 minutes of “what I’m working on now” and future directions. For the two sophomores, it was the first time they were using ChemDraw; it’s an intuitive program and they did a good job drawing structures without me having to teach them how to do so. They were just learning arrow-pushing in organic chemistry, and while these were not included in their presentations yesterday, they remarked about it when a senior presented her work with color-coded arrows to show where nucleophiles were attacking and what made a good leaving group. At the end of last semester, when they were still first-years, I pitched doing research as complementing some of what they would be seeing in organic chemistry. (My group is studying small molecule reactions related to prebiotic chemistry.)

At the beginning of our group meeting, we drew lots to see who would go first. I groaned when I drew number 1, and the students laughed. A good way to break the tension! I did my presentation old-school with the whiteboard and reaction schemes drawn on paper. My students all used PowerPoint. We also discussed the pros and cons of both approaches. There was some Q&A after each presentation but I tried not to ask too many questions, and the students asked between 0-1 questions each, i.e., not many. One challenge is that projects can be quite different from each other so a student might feel inhibited about asking questions, or maybe because it was the first group meeting for a number of them. Overall, though, I have a good crop of students this semester and they all did a decent job on their presentations, even the first-timers! It's been a while since I've done mid-semester group meeting, but I was reminded that I should make more of an effort to make sure it happens!

Factfulness

If I was teaching a class on quantitative reasoning, I’d encourage, maybe even require, my students to read Factfulness. Hans Rosling, a medical doctor with significant experience in public health internationally, weaves in personal anecdotes with stark statistics, and employs a direct yet conversational tone in his book (in collaboration with his son and daughter-in-law). The book is subtitled “Ten Reasons We’re Wrong About the World – and Why Things are Better Than You Think”. There’s even a nifty graphic with key phrases to remind you of his main points – they make sense after you’ve read the book.

Each and every one of Rosling’s ten takeaways is important. I already discuss #3 (the Straight Line Instinct) in my classes when we’re analyzing data and trying to reach some sort of tentative conclusion or make a prediction. His approach of dividing up different socio-economic conditions into four broad levels, using a GDP per capita income that doubles in each advancing level, is genius both as a rule-of-thumb and also as something that’s easy and clear to communicate. Layering this with population numbers by country and region in color-coded ‘bubble’ charts allows you to see broad trends without losing granularity. I recommend visiting the Gapminder website to explore the data.

Today’s post will highlight two of the ten that jumped out at me.

In the Fear Instinct (#4), there is an eye-opening section on terrorism. Rosling writes: “If there’s one group of people who have fully understood the power of the fear instinct, it’s not journalists. It’s terrorists. The clue is in their name. Fear is what they aim for. … Terrorism is one of the exceptions to the global trends discussed in chapter 2 on negativity. It is getting worse. So are you right to be very scared of it? Well, first of all it accounted for 0.05 percent of all deaths in the world in 2016, so probably not. Second, it depends where you live.”

And now you really want to know what he’s going to say next. I recommend reading the book in full. The data is eye-popping and not what I expected given mass media coverage and the proclamations of populist politicians. Interestingly, Rosling doesn’t lay the blame of the fear instinct at the feet of the media – he recognizes why some things are story-worthy from that perspective, others less so, even if he disagrees with the priorities of mass media. He acknowledges the fact and moves on to practically how you or I should deal with hearing such things day in, day out. He also carefully distinguishes fear and danger. “Fear can be useful, but only if it is directed at the right things. The fear instinct is a terrible guide for understanding the world. It makes us give our attention to the unlikely dangers that we are most afraid of, and neglect what is actually most risky… Something frightening poses a perceived risk. Something dangerous poses a real risk.” System 1 takes over when our adrenaline is pumping and drowns out System 2.

The Blame Instinct (#9), according to Rosling, is “the instinct to find a clear, simple reason why something bad has happened.” Sounds like the scientific method to me. Students like things to be clean and simple, and get frustrated when the actual ‘answer’ turns out to be more complicated, convoluted and conditional. “We like to believe that [bad] things happen because someone [with bad intentions] wanted them to… [it] makes us exaggerate the importance of individuals or of particular groups… it steals our focus as we obsess about someone to blame, then blocks our learning because once we have decided who to punch in the face we stop looking for explanations elsewhere. This undermines our ability to solve the problem, or prevent it from happening again…” Did you enjoy Rosling’s to-the-point prose? Maybe it’s the Swede in him. I’ve now made a blanket attribution of his writing style to his nationality. Maybe that’s my Generalization Instinct (#6) kicking in.

I have to agree with Rosling when he writes: “The same instinct is triggered when things go well. ‘Claim’ comes just as easily as ‘blame.’ When something goes well, we are very quick to give the credit to an individual or a simple cause, when again it is usually more complicated.” One very sad example that Rosling provides is the many deaths from “rickety rubber rafts” carrying refugees across the Mediterranean Sea trying to reach Europe. Why aren’t they traveling on proper ferries or on planes or overland? The first few reasons I could think of (before reading the book) aren’t the primary problem, and things turn out to be more complicated. Rosling tries to get at the heart of systems-thinking, and how interlocking parts make a bunch of issues cascade non-independently. It’s a tangled mess. Rosling’s advice: (1) “Look for causes, not villains.” (2) “Look for systems, not heroes.”

Overall, of the many books I’ve read, Factfulness feels like it has made an immediate impact in how I think – at least for now while it’s fresh in my memory. Over time, I might revert back to a lazier more instinctual mode that has habitually built up over time. That’s why this is a book worth keeping and revisiting every so often. Overcoming those instincts is challenging. Rosling recognizes this and tries in his small way to help. I highly recommend his book.

Connecting the Liberal Arts

It’s my fault that my students have been thinking about the liberal arts and what having a liberal education might mean for them. In addition to the Open Classroom last week, involving first-year students in my general chemistry class and throughout the Living Learning Community, I also had the students (just) in my class read and discuss an article by William Cronon. Here’s a snapshot of the title, abstract and citation.

Cronon begins the article by discussing why the terms “liberal arts” or “liberal education” are confusing in this day and age. What was true in 1988 when this article was written is still true 30 years later. My students found his definitions and distinctions helpful; several of them commented that before setting foot on our college campus they didn’t really know what a liberal arts education meant, beyond it being ‘holistic’ and having to take different classes outside of your major of interest. They heard a bit more about it during orientation, and I discussed it in my first meeting with them at the beginning of the fall semester as we talked about why the college has a core curriculum.

The article then provides a very brief two-paragraph history of the liberal arts from medieval times to the present day. I like his apt description of what the liberal arts looks like to students (and sometimes to faculty, staff and administrators) – lists! Cronon writes: “[we] offer plenty of complicated lists with which we try to identify the courses and distribution requirements that constitute a liberal education.” There are “curricular tables and credit formulas” that are unique to each institution but there are also many similarities in what constitutes a ‘core’. However, “no matter how deliberately [curriculum requirements] have been hammered out in committee meetings, it’s not clear what these carefully and articulated requirements have to do with human freedom.”

Recognizing the irony of his approach, Cronon comes up with his list of what a liberal education might look like. The question: “How does one recognize liberally educated people?” To see his list of ten things, you’ll have to read the article in full. I will just highlight a few that jumped out to the students and me. (I gave students prompt questions for discussions along with the article ahead of time, and they came to class prepared!)

They listen and they hear. Cronon makes the point that it is hard work to really listen carefully to someone and pay full attention. Students resonated with this. I thought this was interesting given the ultra-distracting technological culture that we live in. Students, often glued to their cellphones, also recognize this. I have my students take a seven-day timelog to learn where their time goes, and one student said she didn’t realize how often and how much time she would spend being distracted by her phone, and took concrete steps to tackle the problem. (Kudos to her!)

They respect rigor not so much for its own sake but as a way of seeking truth. Several students expressed how they now thought, after reading Cronon’s article, that a liberal education has a lot to do with learning how to learn – being a life-long learner. Hurrah! I had this as a point to bring up, but they came up with it. Students also commented how they didn’t like the idea of “rigor for its own sake”. I should have tried to tease out this train of thought, but since the students were on a roll – and I had prefaced the discussion with the fact that I should not be doing most of the talking – I didn’t interrupt the flow of conversation and let it move on.

They nurture and empower the people around them. My first-year students are young and idealistic – good for them! It’s a reminder to my jaded older self that this is something I should pay attention to. This point also brought home student observations that Cronon’s list had nothing to do with curricular distribution requirements. This led to a discussion of how one could well graduate having fulfilled the core curriculum, but not actually imbibing what it means to have a liberal education. I think a student commented that “your education is what you make of it” and there was talk about how they were responsible for making their own personal connections to the liberal arts and their goals in life. I was very pleased by this discussion!

They practice humility, tolerance, and self-criticism. This was the one that jumped out at me, because I feel that this day and age lionizes individual branding and self-promotion. Perhaps the rise of the thought leader falls into this category? I can’t do better than using Cronon’s own words: “This is another way of saying that they can understand the power of other people’s dreams and nightmares as well as their own. They have the intellectual range and emotional generosity to step outside their own experiences and prejudices, thereby opening themselves to perspectives different from their own.”

Cronon closes with two caveats on his own article. Firstly, students should not expect, having taken their core curriculum courses, to have been liberally educated. He writes: “A liberal education is not something any of us ever achieve; it’s not a state. Rather it is a way of living in the face of our own ignorance…” Secondly, his list can be misinterpreted to stress individualistic self-improvement. Cronon turns the focus on the community of learners. “In the act of making us free, it also binds us to the communities that gave us our freedom in the first place…” With an allusion to the idea of (the Greek’s) agape love, Cronon argues that “liberal education nurtures human freedom in the service of human community”. His take-home mnemonic for all this? Only Connect… (from E. M. Forster’s Howard’s End).

The Ideas Industry

In Daniel Drezner’s new book, The Ideas Industry, the ‘marketplace of ideas’ that might resemble an old-fashioned bazaar has evolved to become a modern money-funneling industrial juggernaut. The main argument in the book is that this industry “rewards thought leaders more than public intellectuals” for three reasons:

·      erosion of trust in prestigious institutions and professions

·      polarization of American society

·      growth in economic inequality

First, we need to define the two groups of people who peddle their wares. Drezner refers to public intellectuals as “professional secondhand dealers in ideas” (quoting Hayek), and their main function is to be critical of bad ideas. Drezner’s examples come from the world of public policy, one of his areas of expertise. Public intellectuals are particularly important “in democratic discourse, exposing shibboleths masquerading as accepted wisdom [and] point out when an emperor has no clothes.” Without such individuals, “it becomes that much easier for politicians or charlatans to advance an idea into the public consciousness, regardless of its intrinsic merits…”

The rising challengers are the thought leaders. Drezner describes the thought leader as “an intellectual evangelist”. They “develop their own singular lens to explain the world [and they] know one big thing and believe that their important idea will change the world.” Drezner compares these two groups to Berlin-esque foxes and hedgehogs, a distinction I’ve discussed in an earlier post. Drezner summarizes the two in the following way. “The former are skeptics; the latter are true believers… A public intellectual is ready, willing, and able to tell you everything that is wrong with everyone else’s worldview. A thought leader is desperate to tell you everything that is right about his own creed.”

Why are thought leaders (or hedgehogs) popular in this day and age? Drezner attempts to link this, oddly enough, to psychological factors and possibly intellectual laziness, however he is unclear as to why this is the case. He writes:

“The rise of thought leaders plays into how human beings are hard-wired to process ideas. A stylistic element that matters greatly for success in the modern Ideas Industry is confidence… human beings prefer confident predictions over probabilistic ones, even though all of the empirical evidence says that the latter approach yields better predictions and more resilient ideas… Thought leaders excel and public intellectuals suffer in projecting the supreme confidence that their ideas are absolutely correct. This confidence is cognitively satisfying to audiences; even critics of thought leaders acknowledge the seductiveness of their sales pitch.”

Are these assertions true? Do we value style over substance more so today than in the yesteryear? Is there something about the situation in the twenty-first century that makes this so? If trust in previously hallowed institutions is eroding, shouldn’t we be more distrustful of any confident hawker of ideas? Apparently not. Maybe once you stop listening to the established sources, you get lost among the cacophony of ideas. Perhaps it becomes more difficult to distinguish style over substance. A new upstart, gunning for recognition, needs to be loud and confident-sounding. I might call it arrogant. Someone else might call it charismatic. Has charisma become the leading requirement for leadership positions? I happen to think that integrity is a much more important characteristic; but I get the sense that this isn’t what gets one the kudos and the position of top dog. Sad, but likely true.

What else did I learn from Drezner’s book?

In a previous post, I highlighted the role of consulting firms in business fads. Drezner echoes the same concerns, but links the rise in private sector consulting to the same reasons why a thought leader might gain more traction than a public intellectual. McKinsey comes up in numerous examples, if I was name-dropping.  Drezner writes: “Thought leaders from the private sector are increasingly prevalent in prestigious conferences… Stylistically, the private sector is far better at conveying ideas than university professors or think tank fellows… excels at finding the one number, metric, or chart that will capture the attention of the audience… easier to understand and carry more heuristic punch. This does not mean that these ideas are necessarily correct…”

Being for-profit has further advantages. Drezner is preaching to my choir here; this is why I’ve become increasingly skeptical with such organizations. “[The] implicit inference that audiences draw… if someone is willing to pay for their services, they must have value… the proprietary information they gather and provide for their clients allows access to information that more traditional public intellectuals lack [and therefore] a decided edge in presenting arguments about how the world works… proprietary information also gives the private sector a justifiable excuse for opacity. Neither consultants nor tech firms will divulge all their data or methodologies, for fear of exposing their customers to unwarranted scrutiny. This obviously makes it easier for public audiences to cast a skeptical eye at their analysis and allege conflicts of interest. At the same time, however, it makes it impossible for outside observers to falsify their arguments.”

Another interesting analysis in the book: The challenges of being a thought leader and trying to maintain ‘top dog’ status. His examples are Fareed Zakaria, Niall Ferguson and Thomas Friedman. Competition is stiff, and staying on top is akin to running the hamster wheel. As the global economy becomes more interconnected, a superstar economy has emerged in the Ideas Industry. Drezner writes: “Becoming a thought leader now is almost like making it as an entertainer or entrepreneur. The rewards at the top are lucrative… enticing enough to warp the incentives of new entrants into the Ideas Industry…” and quoting Justin Fox: “the result is an intellectual environment that seems to increasingly reward the superficial, and keeps rewarding those who make it into the magic circle of top-flight speakers even if they don’t have anything new or interesting to say.” Drezner also reflects on his own role in the Ideas Industry and the challenges of navigating between the roles of thought leader and public intellectual, as he has his feet and fingers in both worlds.

Drezner is a good writer and his prose is quotable, hence the many examples I have included in this blog post. As to his thesis, I find his examples interesting, but the theoretical framework seems elusive. The best quote comes in a section discussing Clayton Christensen’s gospel of innovative disruption and subsequent challenges by Jill Lepore and Andrew King/Baljir Baatartogokh. The best quote is by King: “A theory is like a weed. Unless it is pruned back by empirical testing, it will grow to fill any void.” That’s something I can relate to as a scientist and theorist.

Definitions of Life and Rhetoric

As part of our new core curriculum, the college is trying to infuse ‘integration’ into a student’s first-year courses. The first-year living learning communities (LLCs) have been co-opted as a vehicle to emphasize the liberal arts and introduce the notion of how different academic disciplines can ‘integrate’ in a holistic manner. The underlying idea is that knowledge is inter-connected and different knowledge areas enhance each other in conversation, dialogue and collaboration. If all this sounds buzzword-y, yes, it is also accompanied by lots of promotion that hopes to make it buzz-worthy.

How this takes shape in the fall semester is through ‘open classrooms’. The faculty members teaching in each LLC put together a session aimed at showing how disciplines integrate with other disciplines within some broader theme. These broad themes are vague sounding evocations that can easily encompass any specific discipline. Examples include words such as ‘cultivate’ or ‘innovate’. My LLC is ‘illuminate’ and I’ve themed my first semester general chemistry course “Hidden in plain sight: Elucidating the Secret Structure of Matter”. A chunk of the course material involves the interaction of light and matter, so I can easily fit the theme within my standard operating procedures for teaching the class. For example, yesterday we discussed how x-rays are used to elucidate the structure of crystalline solids.

My LLC decided that our open classrooms would involve two faculty members bringing their disciplinary expertise together – we’re showing an example of integration! By luck or design we have an equal number of faculties from the humanities and the STEM fields; I was paired with a colleague trained in Rhetoric who thinks deeply about how words communicate, define, argue, persuade, etc. She has projects in collaboration with scientists related to how certain concepts are used and communicated. I was going to incorporate my research interests in the chemical origins of life. We planned an hour-long session that engaged 40-50 students this past week. Here’s what we did.

I started off the session by having students look through a list of definitions for Life. To keep this tractable, we just considered 20 definitions. As a starting point, I had students work individually to indicate which of the definitions they thought came from a Biologist, Chemist, Physicist, Non-Scientist, or Other (with their own category). I also asked them to guess which one definition was pulled from a dictionary and which one came from a NASA panel. (I talked about the implications of having an agreed upon NASA definition when designing missions to Mars and beyond.)

In case you wanted to enjoy the experience, here they are.

1. Life is a power, force or property of a special and peculiar kind, temporarily influencing matter and its ordinary force, but entirely different from, and in no way correlated with, any of these.

2. It is the particular manner of composition of the materials and processes, their spatial and temporal organization which constitute what we call life.

3. Life seems to be orderly and lawful behavior of matter, not based exclusively on its tendency to go over from order to disorder, but based partly on existing order that is kept up.

4. Life is an open system that is self-replicating, self-regulating, and feeds on energy from the environment.

5. Any system capable of replication and mutation is alive.

6. Life is a potentially self-perpetuating system of linked organic reactions, catalyzed stepwise and almost isothermally by complex and specific organic catalysts which are themselves produced by the system.

7. Living organisms are distinguished by their specified complexity.

8. We regard as alive any population of entities which has the properties of multiplication, heredity and variation.

9. Life is the property of plants and animals which makes it possible for them to take in food, get energy from it, grow, adapt themselves to their surrounding and reproduce their kind. It is the quality that distinguishes an animal or plant from inorganic matter.

10. The most conspicuous attribute of biological organization is its complexity. The physical problem of the origin of life can be reduced to the question: “Is there a mechanism of which complexity can be generated in a regular, reproducible way?”

11. Life is an expected, collectively self-organized property of catalytic polymers.

12. Life is the ability to communicate.

13. Life is a self-sustained chemical system capable of undergoing Darwinian evolution.

14. Life is defined as a material system that can acquire, store, process, and use information to organize its activities.

15. Life is a system capable of (1) self-organization, (2) self-replication, (3) evolution through mutation, (4) metabolism, and (5) concentrative encapsulation.

16. Life is what the scientific establishment, probably after some healthy disagreement, will accept as life.

17. Life is a set of symbiotically-linked molecular engines, permanently operating out of equilibrium, in an open flow of energy and matter, although recycling a great deal of their own chemical components.

18. Life is a system which has subjectivity.

19. Life is the symphony of dynamic and highly integrated algorithmic processes which yields homeostatic metabolism, development, growth, and reproduction.

20. It’s alive if it can die.

I then had the students think-pair-share for a few minutes and then called on different pairs to tell me what they discussed and why. I had instructed them to pick out definitions they found interesting where they differed from their neighbor in their individual answers. Students got to think and discuss how they would distinguish biology, chemistry and physics, from each other, and perhaps from something outside those categories. I gave a few ‘answers’ along the way as part of the discussion, but not all, so as to keep everyone engaged. I then told the students a brief story about how one might think about the overlap between disciplines. Here’s the slide I showed.

I talked about how I’m a physical chemist, sitting at the boundary between chemistry and physics, and how someone else might define himself or herself as a chemical physicist. The two communities have their own journals – the Journal of Physical Chemistry published by the American Chemical Society, and the Journal of Chemical Physics published by the American Physical Society. I talked about biochemistry and chemical biology. There’s biophysics, but no physical biology as a field (as far as I’m aware). One of the 20 definitions was by Nobel-prize winner Manfred Eigen, a giant in the field, who is identified as a biophysical chemist. I then closed my section by discussing the usefulness and limits of definitions and whether or not there was a ‘hard’ boundary between Life and Non-Life, and made an allusion to the importance of rhetoric in how one thinks about this question.

My colleague in Rhetoric discussed the unity-diversity of knowledge starting from ancient Greece, how the liberal arts were defined and represented in the middle ages, and how disciplinary structures arose as we moved into the modern eras. There was a cool activity where students looked at different visual representations of the liberal arts (literacy levels were low) in medieval times and had students think about what was being represented in the artwork. She talked about the role and uses of rhetoric, conversation and dialogue – how the sciences and humanities have diverged to think about language and definitions differently. Finally, she brought things back to thinking about the definition of life.

I very much enjoyed participating and co-leading the open classroom discussion, and I hope the students found it interesting and enlightening. I think we accomplished our goal of discussing the liberal arts, the unity and diversity of knowledge, and showed some examples of how different disciplines interact with each other!

*Select answers: #3 is from Erwin Schrodinger, eminent physicist, who wrote a book What is Life? in 1944. #9 is from the Webster dictionary. #10 is from Manfred Eigen. #13 is the NASA panel definition from 1994.

Fool Moon

With a title like Fool Moon, you can likely guess who the denizens might be in the second book of the Dresden Files series by Jim Butcher.

Similarly, you can likely guess who the denizens might be in the second book of the (vampire) Twilight Series with the title New Moon.

If you haven’t guessed it by now, yes, werewolves show up prominently in the story. Harry Dresden, the main protagonist, learns that there are several kinds of werewolves with different origins. I found the subject mildly interesting, at least in terms of the division between internal transformation through one’s own magic versus external transformations with a talisman or some other magical source. Other than that, there wasn’t much I learned about the theory of magic in Dresden’s world except for what distinguishes non-verbal spells from spoken incantations, and what it feels like to cast a non-verbal spell without a focusing agent.

More on that in a moment, but first a detour into Harry Potter’s world of magic. In the sixth book, Harry Potter and the Half-Blood Prince, non-verbal spells come up for the first time. The scene is Snape’s N.E.W.T. level Defense of the Dark Arts classroom. Snape begins the lesson: “… you are, I believe novices in the use of nonverbal spells. What is the advantage of a non-verbal spell?”

Hermione, the fount of knowledge, replies: “Your adversary has no warning about what kind of magic you’re about to perform, which gives you a split-second advantage.” Snape dismissively agrees and elaborates. “Not all wizards can do this, of course; it is a question of concentration and mind power which some… lack.” Snape is sneering at Harry while saying this after Occlumency-Legilimency lessons the previous year. (For a connection between Legilimency and fMRI, see here.)

However, a wand is still needed to perform that magic with a non-verbal spell. Without a wand, the wizard is essentially powerless when it comes to spellcasting. Thus, the frequent use of expelliarmus to disarm the wizard by removing the wand from their hands. I’ve speculated on the wand as a conduit of power in a previous post. It is possible to do magic without a wand, although somewhat uncontrollably. Harry does this as a child before he attends Hogwarts especially in periods of high stress.

In Fool Moon, Harry Dresden finds himself in a wand-less situation. He’s without his staff, and after being shot, and beat up earlier in the day, Dresden is at present being strangled by a much stronger assailant. The one thing I like about these novels is that they are all written from Dresden’s point of view – so you get to see what he’s thinking and how he works magic. Here are the relevant passages (in italics).

I stopped trying to struggle against the man who was choking me. Instead, I grabbed his wrist and prepared to do something foolish…

Magic is a kind of energy. It is given shape by human thoughts and emotions, by imagination. Thoughts define that shape – and words help to define those thoughts. That’s why wizards usually use words to help them with their spells. Words provide a sort of insulation as the energy of magic burns through a spell caster’s mind. If you use words that you’re too familiar with, words that are so close to your thoughts that you have trouble separating thought from word, that insulation is very thin. So most wizards use words from ancient languages they don’t know very well, or else they make up nonsense words and mentally attach their meanings to a particular effect. That way, a wizard’s mind has an extra layer of protection against magical energies coursing through it.

But you can work magic without words, without insulation for your mind. If you’re not afraid of it hurting a little…

Two things happened. First, a rush of blinding thought, brilliant and wild and jangling, went through my head. My eyes swam with color, my ears with phantom sound. My senses were assaulted with a myriad of impressions: the sharp scent of the earth and dry leaves, … dozens of others I couldn’t identify. They were a side effect of the energy rushing through my head.

The second thing that happened was a surge of electricity gathered from the air round me to my fingertips, gripped on my attacker’s wrist, and surged up through his arm and into his body…

There are several interesting things in this account. For one, magic is classified as a kind of energy – and Dresden’s constant fouling up of electrical devices suggests electromagnetic radiation as a conduit of magical energy. Being able to use one’s mind to focus on shaping the spell is crucial, as I’ve speculated before about the nature of spellcasting. Words, according to Dresden help provide insulation to one’s mind and therefore it is better not to use words in one’s normal everyday spoken language. Perhaps this is why Latin and other portmanteau language combos were chosen in Harry Potter? You also get to see what casting a spell feels like. The main effect seems to be heightened senses, a reasonable side-effect when one is focused, in a stressful situation, and ‘time seems to slow down’ such that you notice every little thing. The book also portrays the limits and use of energy in spellcasting. When Dresden runs out of energy, he has problems effecting magic.

Other than that, Fool Moon has the same noir detective feel as the first book. Overall, I found it a little less interesting. Perhaps the novelty has worn off, and that’s always the challenge with sequels.

The Periodic Table: It's Kinky!

This past week my general chemistry class has covered electronic configurations, the development of the periodic table, and how certain atomic properties trend across the periodic table.

The periodic table has an organizational beauty. Unless you stare at the nitty-gritty.

The periodic table is powerful. In broad hand-waving sweeps. But the details are devilish.

If you look closely enough, the elements in the periodic table (excepting the hydrogen atom with its single electron) are idiosyncratic. Each is unique. Probed closely enough, the elements seem an unruly bunch, artificially constrained by a man-made construct. But there’s no doubt that the organizing principles in our modern periodic table are powerful and useful. That’s what I try to tell students.

The most useful broad division is to divide the elements into metals, non-metals and noble gases as I’ve illustrated below. Hydrogen (H) is considered a non-metal in this regard. The ‘metalloids’ can be treated as non-metals for the arguments made below. Note that we are considering the behavior of the elemental substances as they are found in nature at ambient temperatures and pressures.

Using these divisions, and ignoring subtleties for the moment, we can now broadly describe four broad groups of compounds. The noble gases do not form chemical bonds and remain stable as atoms. All other elements are unstable as atoms, so they combine with other atoms to become more stable. There are three possible combinations. Metals + Metals, Non-Metals + Non-Metals, Metals + Non-Metals. 

This gives rise broadly to three ‘types’ of compounds: metallic, covalent, ionic, respectively. Each of these types broadly have the same properties as shown below. 

That’s a very powerful organizing principle. With the periodic table’s help, I can start to predict the properties of different combinations of elements to form new and interesting compounds. At least broadly.

Why are the metals on the left and towards the bottom? Why are the non-metals on the right and towards the top? And why are the noble gases in the rightmost column? This is actually a tricky question. The defining property of a metal is probably its ability to conduct electricity as a pure element under ambient conditions. Why do metals conduct electricity? In chemistry class parlance, they have mobile charged particles, in this case electrons that can ‘freely’ move across the entire substance – from one atom to the next, and the next, and so on. But we are talking about the bulk property of a substance with gazillions of atoms ‘connected’ or chemically bonded in some way. The periodic table, on the other hand, is organized based on atomic properties. A single metal atom does NOT conduct electricity.

Stage left. Enter Ionization Energy.

The Ionization Energy (I.E.) is the energy required to remove an electron completely away from the influence of the atom’s nucleus, thus turning the atom into an ion. The first I.E. is the energy required to remove the electron that’s easiest to pull off. Remarkably the periodic table is arranged in such a way that the (first) I.E. increases going up a column and across a row. Thus, you could say that I.E. increases along a diagonal from the bottom left (lowest I.E.) to top right (highest I.E.). (Students in my class learn how to explain this trend.)

At this point, you could hand-wave an analogy. Metals should have low I.E.; they give up electrons more easily, requiring less energy, and that’s why you have mobile electrons and electrical conductivity. Notice how I slid from an atomic property to a bulk property. I explicitly tell the students I’m doing this in class. Now, it turns out that because we’ve covered the photoelectric effect in class two weeks prior, and I’ve hammered the point home that the work function of a metal (the energy required to eject an electron from an irradiated metal surface) is closely related to, but not exactly the same as I.E. because one is a bulk property and the other is an atomic property. My students have also compared these two numbers for the same element and see that the work function is smaller in magnitude compared to the atomic I.E.

Based on the I.E. trend, you should expect to see the diagonal separating metals and non-metals. Wow, that’s nice! Perhaps, not just coincidental. Furthermore, I.E. values give us ‘hard’ numbers allowing us to make quantitative predictions. They turn out to be very useful in a variety of contexts, including predicting what sorts of ionic compounds will form and what their most likely chemical formulae will be. Powerful stuff!

The companion to I.E. is the Electron Affinity (E.A.). It is the energy change when an electron (from far, far away) is added to a nucleus to form an ion. On the far right, the noble gases have zero or energetically unfavorable E.A., and that’s often used as an argument as to why they’re noble – it costs gobs of energy to give up an electron, there is no advantage in receiving an electron, so they’re already stable as they are. No close companions needed. The E.A. trends across the rest of the periodic table, however, are not so clean. 

You might expect that, excluding the noble gases, the bottom left should have the least energetically favorable E.A. and the top right the most energetically favorable E.A., since the definition of E.A. is kinda sorta* opposite to I.E. And you kinda sorta see that, except it’s not so clear. If you look at the actual values (picture below from the current G-Chem textbook we’re using), it looks like there’s all sorts of idiosyncracy going on at first glance. 

Plotting out these numbers (for the main group elements) below makes things a little clearer. Note that my axis has a minus sign in the name (–EA₁). You can see that the halogens (F, Cl, Br, I, At) do have the most favorable E.A., and that favorability increases across a row in the periodic table, but there is no clear trend down a column. There are also a bunch of zeroes contributing to the jaggedness of the graph. That’s because these unfavorable E.A. values can’t be easily measured. I would say there are kinks all over the place. There is some trend across a row but it’s kinky. Our current textbook doesn’t even try to graphically represent it (although some textbooks do).

But textbooks do display visual representations for I.E. because the trend is much cleaner. Here’s the one from our current textbook (in 3D-bar format). What a beautiful looking chart!

Except that if you look closely, you can see the kinks. I’ve plotted the appropriate graph below for the main group elements. The trends are still apparent. I.E. increases up a row and across a column in the periodic table.

It also becomes clearer that the kinks also follow a trend. Kinky-ness is trendy? I use the word ‘kink’ in class because the line actually looks like it has kinks. (I didn’t learn that the word has other shades of meaning until a number of years after I had been using the word and it became a habit.) The current textbook avoids such words and refers to the kinks as ‘anomalies’.

In a standard college-level G-Chem class, we delve into why the kinks are there. The standard argument for Kink #1 makes use of pictures such as the one shown below for why you see the I.E. of B is lower than Be, but then we’re back on track with C following the general trend. Kink #2 relies on Hund’s rule to explain why the I.E. of O is lower than N, but then we’re back on track with F following the general trend. My students have already been drilled about all orbital energies being pulled down as nuclear charge increases, so none of this is particularly complicated at this point in class. Orbitals are used in both these arguments (although I don’t think this one case justifies the teaching of orbitals in G-Chem).

The way I think about E.A. is that it’s kinda, sorta like the zeroth I.E. (with the opposite sign). I tell my students that if this analogy helps them, then great. If not, they can still memorize the standard definition. When you think about it this way, you can see why the magnitudes are smaller relative to the first I.E., and that the kinks kinda, sorta appear in the same places, but shifted by one. For a less jagged E.A. graph, you can potentially estimate what the unfavorable E.A. values are from quantum calculations. CCCBDB at NIST has these values. With the appropriate scales, the E.A. trend across a row (taking into account the minus sign) now looks somewhat like an I.E. trend across a row.

We could save ourselves the trouble in general chemistry and skip the kinks. After all, unless the student is a chemistry major, or someone who takes inorganic chemistry just for kicks (or kinks), these anomalies don’t come up when describing common examples of structure and reactivity. But on the other hand, it was seeing some of this strangeness in introductory chemistry and learning that there were deeper explanations for such anomalies, that lured me into chemistry. I was taking organic chemistry and a sophomore-level inorganic chemistry class when I realized that chemistry was by far the most interesting subject I was studying. And yes, learning about orbitals helped push me to major in chemistry. I saw the beauty and symmetry of molecules and their orbitals, and at the same time witnessing their power in predicting chemical stability and reactivity. I’ve also come to appreciate the beautiful, idiosyncratic, unique, unruly, elements, displayed in a powerful and useful artifact, discreetly holding its secrets, and waiting to be stumbled upon in joyful discovery!

*Hopefully you’ve seen why ‘kinda sorta’ (kind of, sort of) broad, hand-waving arguments are made all over the place in introductory chemistry classes after reading this post.

P.S. Except for the two pictures I explicitly mentioned as coming from the textbook, I made all the rest in PowerPoint.