Animate Materials

I know how to position my next grant proposal: my area of study will be animate materials. This idea comes from reading a witty blog post by Philip Ball about the limits of our imagination when thinking about future cities, their tech and society. Many exciting things fall into the category of animate materials; you’ve likely heard of smart materials or self-healing materials. Animate might be a synonym for Life. Organisms can be smart, self-healing, and engage in a variety of other activities. All hail the self-repairing car – it just needs to be omnivorous!

I scrawled the phrase “Animate Materials” in my research-reading notes to help me remember it. Then I thought I should write a blog post because physically scrawling something on a piece of paper has less permanence than encoding it in 0’s and 1’s on a cloud server – it’s shocking how we think in the twenty-first century – the virtual having more permanence than the physical! All it will take is a major worldwide crash to see how robust our system really is.

These past several weeks I’ve been reading and thinking about the rise and role of autocatalysis in metabolic evolution, or “how does a chemical system become animate?” I even ran some preliminary calculations to test the feasibility of a new project based on a figure in a book I’m reading. So while I’m interested in the origin-of-life, a question for which it’s not so easy to get grant funding, maybe I can spin my interests into studying the fundamentals of animated materials – using biochemistry as a guide to design potentially interesting new materials from small organic molecules. I just need to work on how to make the connection compelling between the systems I really want to delve into, and the systems of interest to materials science, perhaps.

In his article, Ball thinks that in the future, materials will be protean. The reader of Harry Potter will immediately recognize the protean charm, a piece of clever magic Hermione comes up with for coded communication. (All that magic around Hogwarts disrupts the use of electronics so your cellphones won’t work.) Animate materials are by definition protean – they can change their form. The word comes from Proteus, a water-god, also known as Old Man of the Sea. The Greek protos, from which we get proton, means “first”. Its counterpart protogonos means “primordial”, which to my ears has origin-of-life connotations. It’s also where we get “protein”, fittingly so since origin-of-life research kicked off with Miller’s experiment where amino acids were synthesized from simpler substances. It seems the connection of life’s origins and animate materials are not so far as they might have first appeared!

Manual or YouTube

I recently taught myself how to use some python-based computational software as part of a new research project. This involves a combination of reading online text tutorials and the software manual, while also perusing python standard references. I did not watch a single video – it simply didn’t occur to me to do so.

Perhaps that’s because when I first learned to code, or to use software, there were no videos available. I read manuals and other people’s code, putzed around by trial-and-error, and asked someone more knowledgeable if I was still stuck. Maybe these are simply old habits carried over from yesteryear’s technology. However, if I need to fix an appliance or cook something unfamiliar, today I turn to YouTube. In yesteryear, I would read text-based manuals or cookbooks or D.I.Y.-guides. But no longer. What’s going on here?

One reason might be how I (unconsciously) separate the type of work involved. Coding and learning software are perhaps some sort of intellectual activity, not requiring manual dexterity; while fixing an appliance requires my mimicking a procedure I would otherwise be hopeless at figuring out – there’s a reason I’m a computational chemist and not an experimentalist who works in lab. There might be evolutionary reasons for how we learn or pick up biologically primary versus secondary skill sets.

Or maybe I’m biased in how I think disparately about the two types of activity. When I’m fixing an appliance, it’s always at a rudimentary novice level because I don’t do it often, have low self-confidence, avoid doing the work if possible (my wife is both more competent and patient), and would never dream of wanting handyman-D.I.Y. as a hobby or career. Learning how to use computational software, on the other hand, is part of my job-career, and I see it as a long-term investment. In contrast, D.I.Y.-fix to me is a one-time get-it-out-of-the-way activity.

This made me think about how students approach learning chemistry. A textbook, the equivalent of a text manual, is available – and I only select a textbook if I think it does a decent job. But many students use the text sparingly, and as a last resort. The first resort is YouTube. Students have shown me videos they find helpful, and often, these either resemble a repeat of something I’ve done in class, or something covered (clearly in my opinion) in the textbook. Maybe today’s generation is wired differently (I doubt it!) but maybe they think about learning chemistry the same way I think about learning D.I.Y.

If I just mimic what I see in the video, I can do what the person in the video can do – maybe that’s how the thinking goes. When I’m learning D.I.Y., I’m hoping to only do the activity once. If I have to do it a second time a few months later, I will likely have to watch the video again. The skill isn’t retained in long-term memory. To actually be good at it, I would need to practice, practice, practice. But it’s not a priority in my life to be good at D.I.Y. On the other hand, I care much more about my teaching-research activities, and so I spend time practicing and learning through more comprehensive reading materials.

Is learning chemistry an important priority for students in my classes? If I were to answer this question honestly, I would say yes for a small number, but no for most. Getting a ‘decent’ grade is the high priority, but that’s a short-term goal. Perhaps it’s not surprising that students opt for YouTube over the textbook. One might argue that the wired generation has shorter attention span; that might be true – but when my students wax about an interest or hobby, I find they can pay remarkable attention.

I brought up cooking in paragraph two and neglected to mention it subsequently. That’s because I think it might offer a bridge (at least in my life) between the two poles. I enjoy cooking, but as a fun activity – I’d never want to do it as my job. I wouldn’t even classify it as a hobby, because I don’t devote as much time and attention to it as I have in prior hobbies. The YouTube cooking video serves two purposes. It teaches me a relatively simple technique I can mimic, and what the result should look like. But it also serves as a motivational reason for me to try this new thing (yes, I have a weakness for food-porn). If I try something and like it, and I don’t think it’s too much work (yes, I’m lazy), I will repeat cooking it again shortly after the first time to solidify my learning. My repertoire has now increased.

But I’m not like the creative chefs I’ve seen on Chef’s Table. I don’t have the desire to research the intricacies of tastes, textures and aromas. I do browse cookbooks, but mainly for motivation if a photo catches my eye and the recipe doesn’t look super-complicated. And that’s okay. But perhaps I can learn a lesson by reflecting on all this. If I can help move some students to think about chemistry less as D.I.Y. to be suffered through, and more like cooking, at least in the way I experience these activities, maybe I should make a few videos where I solve a chemistry problem but highlight in some way the conceptual joy behind it. This is something I will be seriously pondering.

Chemistry in Leadership

A recent conversation with a colleague in chemical education has made me ponder once again the challenge connecting the microscopic, macroscopic, and symbolic worlds in teaching and learning chemistry – the three corners of Johnstone’s Triangle. Someone with chemistry expertise fluidly moves through this space. Am I a big picture thinker? Or am I a detailed-oriented person? I would say both! As a chemist, I must be comfortable operating in both the macro and nano realms and smoothly move between them when needed. I may be biased, but I do think that the best leaders have this ability, and that it is in short supply.

But being comfortable operating across multiple theaters ranging from grand strategy to specific tactics is not enough. The best leaders must also have the communication skills necessary to excite colleagues about a vision or a specific action. Deftly employing the needed language and symbols to convey tasks and ideas is crucial to move projects forward. It’s no longer the philosopher-king but the administrator-manager-leader that rules best.

Given the overlap in skill set, it seems to me that chemists should make good all-round leaders – at least those with a certain bent. The most famous world leader today who was trained as a chemist is German chancellor Angela Merkel – she has a PhD and is a computational chemist, which is also my area of expertise. Former British prime minister Margaret Thatcher was also trained as a chemist at the undergraduate level. I know a number of other chemists who have gone on to leadership positions in academia; there have been quite a few presidents and provosts who started out as chemistry faculty members. I wonder if chemists have been disproportionately represented in academic leadership; maybe someone should do a study, though that would be leadership in chemistry rather than chemistry in leadership.

A Google search on chemistry leadership brings up a whole range of articles titled “the chemistry of leadership” which point to that effervescent ill-defined linking of chemistry to making good connections a la “we have good chemistry!” Some of the articles are cringeworthy, especially when they try to connect leadership to actual chemistry, neuroscience or biology. Here’s some representative text: “Leadership is more than just a science, more than just an art, and more than a craft. It is based on human chemistry…” And there’s even a whole book making connections between leadership and biochemical molecules titled “Leaders Eat Last”. No, I haven’t read the book, but I found this web article describing it rather cringeworthy.

I do read books and articles on leadership. Some have clever analogies, and I’ve even previously written a blog post connecting management and thermodynamics. I suppose some readers will deem it cringeworthy. The first two paragraphs of this post might have made you cringe. Perhaps cringe-worthiness is in the eye of the beholder. And while chemistry is about connections – chemical bonds – it’s about making and breaking those connections. Chemistry is about changing or exchanging connections.

Returning to the original question: Can having chemical expertise provide one with the tools of being a capable leader in an organization or society? Perhaps. Perhaps not. The human element (cringeworthy pun intended) complicates matters. We cannot easily be reduced to homo economicus or any analogous generalization, and it keeps things messy, complex, and interesting. This past month I gave a couple of talks on my research discussing how I use quantum chemical calculations to cut through the messiness and complexity encountered in origin-of-life research. I have a slide at the end of my talk to emphasize the ultra-narrow slice of my research within a greater whole, and that it will require multiple approaches to tackle such complex questions.

Bad Assessment: Moloch Version

Today’s rabbit hole reading started with an article (might be behind a paywall) in the Chronicle of Higher Education titled “How Ed Schools Became a Bastion of Bad Ideas”, subtitled: “A tale of assessment, learning styles, and other notorious concepts.” The author is Erik Gilbert, a history professor who blogs at badassessment.org.

My own blogging on assessment has usually focused on formative and summative assessment of student learning, rather than Assessment with a capital A or capital ASS depending on who you talk to. I have participated in Assessment, and it can be potentially valuable, although I’m against the Culture of Assessment prevalent in our educational institutes mandated by administrators who claim these are mandated by accreditors and government regulators.

In an InsideHigherEd guest blog post, David Eubanks, who has been in the field for twenty years and has become increasingly skeptical with the current Practice of Assessment quotes a government report from the Department of Education related to proposed rules for accreditors:

Assessment models that employ the use of complicated rubrics and expensive tracking and reporting software further add to the cost of accreditation. The Department does not maintain that assessment regimes should be so highly prescriptive or technical that institutions or programs should feel required to hire outside consultants to maintain accreditation. Rather than a “one-size-fits-all” method for review, the Department maintains that peer reviewers should be more open to evaluating the materials an institution or program presents and considering them in the context of the institution’s mission, students served, and resources available. (Section 602.17b, pg. 104)

“Scrap the machine” is Eubank’s interpretation. There are better and more useful things to do with your time to aid student learning. (He provides examples from his institution in the post.) There is little evidence that it's helpful.

But the power of narrative is best illustrated, not in a factual report, but in a fictional story. The rabbit hole led me to Gilbert’s fable: “Stop Sacrificing Children to Moloch”. It’s a not-so-funny story about farmers trying to improve their harvest, and their interactions with a cadre of priests building up their temple complex. Moloch is an ancient Canaanite deity mentioned in the Bible, to portray the archaic-ness of the entire process. I won’t preview or summarize the fable – it should be read in its entirety.

As someone who studies complex systems, and being embedded in the ever-complexifying university in a time of belt-tightening and minimaxing, it’s perhaps not surprising how much time and energy gets sucked into the Practice of Assessment. Maybe I’m just jaded and I don’t think I can fight the juggernaut. I do think that perhaps we can learn something from the differences between formative and summative assessment as applied in our classrooms, to how Assessment should be applied at an institutional level. But it will require trust between different parties, something that’s in rather short supply and worsening over time.

Metabolic Evolution

Evolution is messy. The evolution of metabolic pathways is murky because different observations have led to different hypothetical models to explain how things work. Can these different hypotheses be tested? Possibly, at least that’s the subject of a paper titled “In Silico Evolution of Early Metabolism” (Artificial Life 2011, 17, 87-108). The authors and abstract are shown below.

Four scenarios are considered.

(1) In the backward evolution hypothesis, enzymes further downstream in extant biochemistry are evolutionarily older. This seems counter-intuitive at first glance, but makes sense because one might expect early autocatalytic cycles to deplete a chemical ‘food’ source, and therefore the system evolves to make new molecules as alternative inputs to the system.

(2) In the forward evolution hypothesis, the opposite is expected – evolutionarily older enzymes should be upstream. The idea is that evolution proceeds by building on increasingly available intermediate molecules generated from earlier catalytic steps. Demand is generated from production, so to speak.

(3) In the patchwork model, new pathways co-opt enzymes from pre-existing pathways. Perhaps a mutation results in an enzyme becoming a better fit to catalyze an alternative useful reaction. Reuse the old for the new!

(4) In the shell hypothesis, metabolism grows first from an initial autocatalytic core and new ‘shells’ are constructed around this core. Hence, you’d expect to see highly conserved ‘ancient’ enzymes in the core and newer ones appearing in successive shells.

These scenarios are not mutually exclusive. The simulations in the paper lend support to different models/hypotheses depending on the variable ‘environmental’ conditions. For example, when food is abundant, forward evolution is observed, but when food is scarce, backward evolution begins to show up.

Two of the hypotheses were first proposed by Morowitz – I’ve blogged about his book Mayonnaise and the Origin of Life, and he has come up with some pithy definitions of life. Over the years I’ve found myself increasingly persuaded by some of his foundational ideas related to prebiotic chemistry, and my current sabbatical aims to explore some of these aspects. The challenge is that biochemistry is highly evolved, and even seemingly ancient enzymes and metabolic pathways have likely undergone much refinement over the millennia, by which I mean millions and millions of years. (Why on earth is a millennium a thousand years anyway?)

We can’t replay the tape (except maybe in a boardgame!) and hypotheses and models will continue to remain speculatory. Simulations can only take us so far, and by their very nature, simulations have to be highly constrained for the calculations to be tractable. Otherwise you might be waiting millennia for a great supercomputer to come up with answer for which the question might be ill-posed.

Evolution is messy. All proposed scenarios and more are likely contributors to the twists and turns leading to the constrained molecular diversity we observe in life today. I do think that ‘omnivorous eating’ is important in the chemical origins of life. In the quest for efficiency, metabolism has become increasingly specialized. A reduction of messiness perhaps, but managing the messy will always be an issue; perhaps that gives us a clue into the evolutionary process of metabolism!