Joint Adventures

The cells in our bodies are constantly being replaced naturally. Like the Ship of Theseus, am I still me? I feel like it’s the same me but with inevitable deteriorating physical capabilities as I age. I hope I retain my mental acuity, but there may come a point where I don’t recognize others or even myself. We consider aging a natural course of events although we don’t know exactly why our bodies have a clock that winds down towards eventual death. But thanks to doctors, scientists, engineers and inventors, there are artificial replacements for the wear-and-tear.

 

Which body parts can be replaced and what can they be replaced with? This is the question prompting Mary Roach’s latest book, Replaceable You. I’ve enjoyed several other books by Roach, who deftly combines humor, fearlessness, all while she teaches you some very interesting facts about the limitations of being humans and possibly how to get around them. She also somehow gains entry into surprising places and manages to get people to divulge interesting information that is unexpected. With words, she also capably paints a picture of the sights, sounds, and smells of wherever she happens to be.

 

Today’s blog post is on Chapter 8, “Joint Ventures”, subtitled “woodworking without wood”. As a reader, I feel I’m transported by Mary’s Adventures. To give you a taste of her writing, here’s how the chapter begins: “The third hip replacement of the morning looks very much like the second and first. The patient and the whole operating table are covered with surgical drapes, resembling not so much a person having surgery as a small vehicle under a tarp. A surgeon stands alongside, holding a metal instrument in a hole in the patient’s side. The hole – the incision – is held open by a circular plastic retractor the size of an automobile gas cap. From where I stand, six feet back, this is all I can see. Hip replacement has the visual drama of a visit to a Chevron station.”

 

The next paragraph begins in an arresting way: “It’s the sounds that undo you. The whine of the bone saw as the surgeon cuts…” I’ll stop describing here, but you can bet that Roach makes plenty of comparisons to a woodworking shop. But there’s a major difference as Roach goes on to describe: “A (wood) cabinet has no immune system. It doesn’t throw up defenses against building materials it perceives as hostile invaders. It doesn’t die under siege from bacteria that gained a foothold on a piece of inlaid metal or plastic. In other words, the surgeon’s skill can take you only so far. It’s the material guys you’re depending on for a lasting, complication-free build.”

 

My aging mother has had both hips replaced in the last three years. I’m glad for the significant pain reduction that has resulted, and the efficiency of modern medicine. I don’t recall exactly what materials were used, but Roach takes me through the history of such joint replacement starting in 1938 when stainless steel was used for both stem and socket cup. Titanium and other alloys eventually replaced this, but metal-on-metal wear and tear can result in debris that leads to inflammation. Ceramics (metal-oxides) can reduce the wear but their underlying brittleness can be a problem in a high-impact situation. Teflon was used at some point, but there were problems; compact polyethylene has proved better. And so it goes in the evolution of materials. The challenge, as Roach notes, is that “you can’t know for certain how a material will perform or react until you put it into a patient and watch what happens for five, even ten, years. Yet the time required by the FDA to establish the safety of a new medical devices is often shorter.” Worse, there’s a “minor changes” loophole that can avoid clinical trials.

 

Ivory turns out to work surprisingly well. We know this from a surgeon in Burma who managed to persuade a local ivory carver to fashion “knob-topped stems to push inside people’s bones, where no one would even see them. It was like trying to hire Georgia O’Keeffe to paint the janitor’s closet.” No wonder most of the artisans turned him down. The surgeon performed hundreds of successful surgeries with only a two percent failure rate, which is an astoundingly successful rate, given this was in the mid-twentieth century. Part of why is the low infection rate with ivory even without antibiotics. There’s a tricky balance at play: Ivory is very smooth providing fewer nooks and crevices for bacteria to invade, but modern materials are also intentionally made porous to encourage bone growth. You want the bone to grow in before bacteria can proliferate. I also learned that an exception comes from dental implants because saliva and possibly our gum tissue seem to have natural antibiotics because the mouth is literally a cesspool. The stringent “clean” practices in joint replacement surgery have evolved significantly to reduce infection rates, and Roach gives credit to those who painstakingly tested different protocols.

 

I haven’t named any of the people Roach discusses as she sets up her joint-replacement learning adventure. That’s because Roach has some very funny bits about the name coincidences; you can get your hands on her book and read them laughing out loud for your own enjoyment. Her acknowledgements section is also hilarious, where she thanks all these people who said “yes” to her invading their workspaces and pestering them with questions. You might also want to know about all those other body parts you might want to replace and where we are with the technology. Let’s just say I was surprised at the very wide range of stuff discussed in Replaceable You. You might be surprised too!

All About Maxwell

I am halfway through The Man Who Changed Everything, a biography of James Clerk Maxwell, written by Basil Mahon. As a physical chemist, I know something about Maxwell’s scientific achievements. The Maxwell-Boltzmann distribution shows up in multiple places because chemistry is about the movement of zillions of tiny particles, meaning you have to apply statistical methods to bridge the microscopic world to macroscopic phenomena that we large lumbering humans observe. Maxwell’s 1873 paper titled “Molecules” is marvelous, showcasing his lucid writing and insightful though; I have on occasion assigned it to first-year undergraduates along with light annotations to help them read along. I mentioned this in my very first blog post!

 

What I didn’t know much about, and am delighted to learn from Mahon’s book, is who James Clerk Maxwell was as a person. I learned about his rural upbringing that made him initially stick out as a weirdo in a more urban school, and how his geniality, generosity and genius eventually won over his classmates. While his mother had passed away in his early life, he had a loving extended family, and in his early twenties, he devoted much of his time to caring for his ailing father. He was beloved by his friends, an occasional prankster, liked to exercise, and wrote poetry. Given his fame for conjuring mathematical relationships of physical phenomena, I was surprised to learn that he frequently made lots of math mistakes in his derivations, but his scientific intuition was brilliant and almost always on the mark. A famous contemporary scientist said: “He is a genius, but one has to check his calculations.”

 

Maxwell was also a devout Christian but did not get sucked in to the many debates pitting science against religion. In declining to join an eminent society discussing such matters, he replied: “I think that the results which each man arrives at in his attempts to harmonise his science with this Christianity ought not to be regarded as having any significance except to the man himself, and to him only for a time, and should not receive the stamp of a society. For it is in the nature of science, especially those branches of science which are spreading into unknown regions, to be completely changing.” Maxwell’s views on the relationship between theory and experiment in science are also immensely quotable, for example: “I have no reason to believe that the human intellect is able to weave a system of physics out of its own resources without experimental labour. Whenever the attempt has been made it has resulted in an unnatural and self-contradictory mass of rubbish.”

 

I confess that I never took a physics course in college or beyond. How I became a professor who teaches physical chemistry still amazes me. My weak physics background, and perhaps lack of effort to improve my mediocre mathematical ability, means that I don’t really understand Maxwell’s famous equations although I do have the gist of its broader impact. I was heartened to read that Maxwell made great effort to find physical analogies to explain seemingly mysterious phenomena such as lines of force. Even now, I find it challenging to think through the lens of a field approach, and I use Maxwell’s ideas of fluid flow as a crutch to think about flux. Maxwell’s analogy of potential difference and hydrostatic pressure is also helpful; I use it when I teach electrochemistry in General Chemistry. (In fact, I will use it in my class tomorrow morning!)

 

What jumped out at me in reading the account of Maxwell’s struggle to derive a mathematical framework for Faraday’s lines of force was the ability to bring together insights from one area of physics to solve another. The jumping off point was a discovery by William Thomson (later Lord Kelvin) who found that the equations for the strength of electrostatic force looked similar to those describing the rate of steady heat flow. This seems odd: why would static equations resemble dynamic ones? But Maxwell made it work by imagining the flow of an “ideal” weightless incompressible fluid through pipes. I’m presently covering kinetics in my Physical Chemistry, and was looking ahead at my lecture on molecular collision theory. With Maxwell in my mind, one of the equations looked suspiciously familiar. I flipped back to a lecture I had given in the second week of the semester on the Lennard-Jones potential energy curve (for two-body molecular interactions), and sure enough, the mathematical expression for the static temporary dipole attraction looked analogous to the rate equation in collision theory. Wow!

 

I was impressed to read about the breadth of problems Maxwell tackled. His work on optics and colour vision culminating in his famous colour triangle is brilliant. He even devised spectacles for those with red-green colour-blindness. I did not know that Maxwell won a prestigious award for deriving mathematical equations to describe the conditions of stability of Saturn’s rings. When tackling the possibility that the rings are a fluid rather than a solid, he showed they would break up into smaller entities. But how would a hodgepodge of particles maintain an orbit? Maxwell showed that such rings vibrate in different ways and could be stable at low enough average densities. When he considered multiple rings, “he found that some arrangements were stable but others were not: for certain ratios of the radii the vibrations would build up and destroy the rings.” This sounds like the remarkable Bohr orbits of quantum mechanics where the electron orbiting the nucleus is treated as a standing wave to be stable.

 

Another surprising thing I learned was that despite his lucid and clear writing, Maxwell’s success in classroom teaching was mixed. Mahon writes: “For all his talents, he never mastered the technical part of teaching. He would prepare a lesson beautifully, do fine for a time while he stuck to his script, and then fly into analogies and metaphors which were intended to help the students but more often than not mystified them. He was not expert on the blackboard, where he made algebraic slips which took time to find and correct. And yet the students liked him and some found him truly inspiring… It seems paradoxical [for] such a fine scientific writer… as he believed fervently in the value of good education… Appreciating that people learn in different ways, he may have tried too hard to bring in helpful illustrations and analogies, confusing his audience with a welter of rapidly changing images… And perhaps he was too much of an idealist. All good teachers aim, as he did, to teach people to think for themselves, but most also recognize that all some students want is to gain a second-hand smattering of the subject so they can pass exams, and make a specific effort to help them succeed in this limited ambition. Maxwell never did.”

 

Those are sobering words for me as an educator who is also very excited about imparting chemistry to my students. I certainly try to give metaphors and analogies which I hope are helpful. Given my theoretical bent (a product of both my training and my interests), I have noticed that I now spend more time trying to impress upon my students the key frameworks on which my discipline builds its foundations. And I do this unprompted; it’s not in my lecture notes. It’s almost as if, like Maxwell, I can’t help myself. I feel compelled to make those connections to the broader edifice of how chemists think about the world. One progresses from novice to expert by first glimpsing and then progressively seeing more clearly the abstract categories that undergird chemical knowledge. I pontificate more than I used to. When I first started teaching, I couldn’t see some of the hidden frameworks; my focus was getting the students through the material in a systematic way that allowed them to (hopefully) provide them the basics to solve chemical problems on an exam to prove they understood what I was trying to teach. I am still aware that the majority of students in my classes are interested in the “second-hand smattering of the subject so they can pass exams”, and make efforts to help them along, but I also want to truly inspire the minority to see the beauty and depth of chemistry. Maxwell cannot help me resolve this tension, but I am inspired by his efforts. I look forward to sinking my teeth into the second half of his biography!

Biochemistry Mishmash

I am slowly working my way through The Natural Selection of the Chemical Elements by Williams and Frausto da Silva. It’s not the easiest book to read, but it approaches issues of biochemistry from an inorganic and evolutionary lens that I find helpful. I used one of their books in a class three years ago because our library had a digital copy.

 

Today’s post is a mishmash of thoughts sparked by my reading of chapters 11-13 touching on the evolutionary organization of cells and the roles of different chemical substances. Since I study the chemical origins of life, I filter what I’m learning through that particular lens. From that perspective, the book’s contents are idiosyncratic and generates more questions than it answers. But it gives me much to mull about.

 

Since the authors have a background in inorganic chemistry, the function of metal ions features prominently. The big change to the chemical environment is a redox shift from reducing to oxidizing conditions. We have plenty of O₂ in our atmosphere today, but this was not so on the Hadean Earth. The progressive oxidation led to a decrease in the availability of some substances, particularly Fe(II) and sulfides, but led to the increase in others, with newcomers such as Zn and Cu becoming available, alongside a shift to complexity, symbiosis, and eventual multicellularity.

 

The final paragraph of chapter 13 begins: “The conclusion we have reached is that multicellular development was bound to increase in complexity as newly available elements were incorporated but could only do so by coexistence with simpler forms. Complexity is eventually self-defeating and the escape from this dilemma is only possible with an ecosystem of the simple and the complex.” Biochemistry is a tinker, so the first sentence is not surprising. There is a mishmash of systems layered upon more primitive ones, palimpsests sometimes peeking through. The second sentence is provocative. Is it true? I don’t know. But we do know that complex systems open the possibility of catastrophic system failure.

 

Things that jumped out of me:

(1) The evolution of life is all about kinetic traps. “Energized” molecules quickly dissipate energy in their thermodynamic progress towards the equilibrium state. But to get a system going that allows for control, kinetic traps are essential, as is the evolution of catalysts. Before central control emerged, persistence is about being trapped long enough or often enough.

(2) Vesicles and other compartments within the cell have chemical environments that can be very different from the cytoplasm and use messenger systems similar to the “outside” of a cell, calcium-based systems for example.

(3) The rates of phosphate versus thioester hydrolysis can vary greatly over different pH and temperature. This may be a clue to a takeover of energy transduction from a thioester world to the modern one primarily using phosphate esters.

(4) The assertion the DNA codes qualitatively for proteins, but not quantitatively, is interesting. The quantitative aspects that require control and regulation were previously “set” by more primitive cells. Since I think a primitive metabolism is prior to nucleic acid coded information, this makes sense to me.

 

Things I need to ponder more: Why is negative feedback more prevalent in the evolution of living systems? Does it arise because living systems are thermodynamically semi-closed? I regularly tell my students in G-Chem II and P-Chem II that we study equilibrium thermodynamics because we can construct a model and its accompanying equations for closed systems. I contrast this to the non-equilibrium thermodynamics of open systems and use life as an example of staying alive by avoiding the equilibrium state. But an enclosed cell that tries to maintain some level of homeostasis along with growth and repair isn’t completely open. It’s very finicky about what goes in and what goes out, and what concentrations are maintained inside.

 

The authors also reminded me about the distinction between control and regulation: “Control acts at the level of metabolism and one part of it is concerned with the use of proteins including catalysts but not with their productions… Regulation acts at the level of gene and… was little altered from that in anaerobes by the development of multicellular organism…” From my slant, this suggests that control precedes regulation, at least on a local level. A protometabolic system evolves to control matter and energy. How? By tinkering! Why? I don’t know but it reminds me of the dictum: “What persists, persists. What does not, does not.”

Square Integrable

I am reading about the extraordinary math and science contributions of John von Neumann in Ananyo Bhattacharya’s book The Man from the Future. I definitely get the feeling that von Neumann was indeed a rare genius. I also got the feeling that maybe I should have persevered in learning more math when I was younger. If so, not only would I have a better appreciation of von Neumann’s achievements, I would also be able to tackle some interesting problems in my research that require mathematically modeling beyond my current abilities. Feynman’s quote notwithstanding, I would like to better understand quantum mechanics since I use it heavily in my research.

 

Today’s blog post is about Chapter 3 of Bhattacharya’s engaging book. The chapter is titled “The Quantum Evangelist” and leverages the author’s physics background. While I know a number of facts about the history of the development of quantum mechanics, I learned a lot more about von Neumann’s contributions and the context surrounding his work. Reading this chapter gave me a better idea of the conceptual differences between Heisenberg’s matrix mechanics and Schrodinger’s wave mechanics. The connections to set theory in mathematics (and Hilbert’s program of systematization) helped clarify the context. Quoting the author: “An atom has an infinite number of orbits… so Heisenberg’s matrices must also be of infinite size to represent all possible transitions between them. The members of such a matrix can… be lined up with a list of the counting numbers – they are ‘countably’ infinite. Schrodinger’s formulation, on the other hand, yielded wave functions describing… an uncountably infinite number of possibilities. An electron that is not bound to an atom… could be literally anywhere.”

 

I now have a better appreciation of Dirac’s “ingenious trick to merge the ‘discrete’ space of Heisenberg’s matrices and the ‘continuous’ space of Schrodinger’s waves” with the delta function. Bhattacharya describes it as a “salami slicer, cutting up the wavefunction into ultra-thin slivers in space”. While Hilbert space still feels fuzzy to me and I don’t quite comprehend it, I can dimly see where square-integrable functions come from. When I teach quantum chemistry, I tell students about this important property and its practical uses along with Born’s probability postulate, I had never talked about their mathematical basis (because I didn’t understand it myself).

 

Where does von Neumann come into the story? Given his mathematical talents, he realized that square integrable functions “can be represented by an infinite series of orthogonal functions, sets of mathematical independent functions that can be added together to make any other… How much of each function is required is indicated by their coefficients... [which] were exactly the elements that appear in the state matrix.” In my class, I invoke orthogonality from a consequence of Hermitian operators. I discuss the importance of having linearly independent functions and spaces (e.g. Cartesian space or polar coordinates) conceptually but my students still struggle to think about it. Linear algebra is not a pre-requisite for my class and most students haven’t taken it. Neither have I for that matter. Until reading this chapter, I had not realized the connection between square integrable wavefunctions and orthogonality. In my class, when we get to multi-electron multi-atom systems, I introduce students to manipulating linear combinations of functions that sum up (invoking the principle of superposition) to get better results when solving the Schrodinger equation. They learn that the sum of the squares of the coefficients must add up to one, but I hadn’t made the connection to square-integrability.

 

There is plenty more in the chapter about the weirder aspects of quantum mechanics, wavefunction collapse, hidden variable theory, pilot waves, Bell inequalities, and Many Worlds. But what really stood out to me was where square integrable functions come from (as part of Hilbert space) and how they connected to orthogonal component wavefunctions. All these connections were a revelation to me, and I’d been teaching for a quarter of a century! How little I know. How much more to learn. This reminds me that I should get back to Beyond Weird by Philip Ball.

Are you You?

Getting a new phone this month meant moving from thumb authentication to face authentication. It seems to work pretty seamlessly when I pick up my phone – the devices are getting smarter. Also, this month I’ve noticed Gmail regularly Captcha-asking for additional authentication to prove I’m not a bot. Is agentic A.I. causing more issues? I don’t know. But it made me think about how verifying my identity has changed over my lifetime.

 

Everything was done manually when I was young. No computers or internet. I don’t remember how I was verified when I first entered primary school. How did the school and teachers know I was not an impostor? In my most recent videochat with my mother (a former schoolteacher, long retired), I asked her and she told me about the systems they would use. My first major verification that I vaguely recall was the primary school national exams. Apparently, the government sent us letters with an entry slip and a unique number; and this allowed me to take my exams where I think I had to carefully write the unique number on all my exam papers. I vaguely remember teachers drilling us to do this. And while I don’t recall exactly, I think our own teachers were also the ones who verified us because we’d been in their classes for a whole year.

 

After the age of twelve, when I had secondary school examinations, we all had to bring in our identity cards, and place them on the corner of our desks for each exam. Each of us had a specific desk that had our name on it, and the invigilators who were not our teachers, walked around (clipboard in hand) to verify each of us via the identity cards. I still experience this process when I’m at the airport, visiting the bank in person, checking in to a hotel, picking up my badge at a conference, or any other situation where I need to verify who I am because the verifiers don’t know me and wouldn’t recognize my face. If you lived in a small village and never had to leave, everyone knows everyone and verification is easy. But in an era of urbanization, global travel, and not knowing your neighbors, verification becomes trickier.

 

The age of the internet has made authentication even more challenging. Are you who you say you are? How does the system know? There are logins, passwords, two-factor authentications, additional questions for information unique to you, and now voice and face verification. These are going to get more stringent as A.I. makes it easier to “fake” more characteristics. We’ll be increasingly up the wazoo in verification.

 

“Authenticating” is the title of the second chapter in Brian Christian’s The Most Human Human which details his experience as a confederate in an annual Turing Test competition. He’s trying to prove he’s the human against an A.I. competitor. The chapter opens with a story about a man with phonagnosia. He cannot recognize anyone’s voice and growing up had assumed his voice was distinctive because everyone else recognized his voice but he couldn’t recognize anyone else’s which made phone calls an interesting case of guess-the-identity for him. He couldn’t voice-verify. In another vignette, someone easily breaks into the email account of a public figure simply by selecting “I forgot my password” and then verifying information based on internet searches.

 

The meat of this book chapter, however, is about what might be unique between a human conversationalist and a chatbot. Many of the successful chatbots in the early competitions were able to steer the conversation to avoid the tricky out-of-book situation, which is a reasonably strategy when the conversations are timed in a speed-dating like format. Successful bots typically had a single programmer devoted to developing the bot’s personality so that it would seem like a single coherent individual. The bot felt like a singular You. Today’s A.I. large language models however were developed with the opposite philosophy: use weighted statistics from millions of disembodied conversations. Apparently, this is why A.I. translators are weak on long literary novels which require a singular coherent voice throughout, but do just fine on shorter snippets.

 

When you’re conversing with a chatbot today, you’re conversing with a multitude of voices averaged into a response. Your interlocutor is Legion for they are many. They contain multitudes. You are no longer talking to an individual but a host of ghosts. I’ve never had an extended conversation with a chatbot (I have better things to do with my time), and my queries have usually been specific and chemistry-related; I dabble in exploring if chatbots can help my students gain a better understanding of chemistry. So I don’t personally know if I would ever feel that a chatbot feels like a friendly human; I know some of my students do enjoy their chatbot chats. And it may be that sufficient familiarity and multiple chats provides its own authentication, for better or worse, now that chatbots can access their memory store of their personal conversation from you and draw from it. I suppose this is what Personalization is all about. At some point the chatbot might feel like a You. But that’s because of you.

Out of Book

In The Most Human Human, Brian Christian muses about his experience playing a “confederate” during the 2009 Loebner prize. It’s an annual Turing Test competition where entrants have designed artificial intelligence computer chatbots to mimic a human. A judge has a five-minute conversation over a computer terminal with a chatbot or an actual human being, and then has to decide which is which. As a “confederate” Brian is one of the humans. The chatbot that best fools the judges into thinking it’s a human is dubbed “The Most Human Computer”. The human that best convinces the judges of his or her humanity is “The most human human”.

 

Chapter 5 of Brian’s book, titled “Out of Book”, refers to where chess games at interesting. Chess openings and endings are often scripted. Over time a database builds up on effective opening moves and their variants. The same is true at the endgame where few pieces remain on the board and a brute-force analysis can determine who the winner will be. The Book refers to this wealth of knowledge in chess openings and endgames. It’s the midgame where things gets interesting, when players are forced into out-of-Book situations. Computer chess programs are loaded with The Book. All decent programs have them. What might make a program superior to others is how it handles the out-of-Book midgame. What makes a chess player a grandmaster is being able to successfully navigate the midgame.

 

At the novice level, memorizing more openings and endgames and practicing them a lot, often leads to victory over someone with a less prodigious memory. You get into a superior position by standing on the shoulders of the grandmaster giants who have gone before, and the game is about who blunders first by playing a known inferior move from the database. You don’t really need to understand the why behind the moves; you just need to execute them in the correct sequence. At the mastery level for humans, understanding the why is crucial to know when to effectively get out-of-Book and try to outplay your opponent with ingenuity. The challenge in playing against today’s computers is that they can store a huge Book and shrink the space between opening and ending. You might lose to a computer program before even getting out-of-Book.

 

All this makes me thinks of A.I. use in education. The majority of my students use chatbots to help them complete homework assignments and study for exams. They think it helps their learning, and that may be true some of the time, but I suspect it also leads to a dose of self-deception. They think they know something but when exam time comes (with no book or chatbot to consult), they don’t perform well. My exam questions should be no surprise based on what we cover in class and the study guides I provide, and the academically strong students have no problem doing well.

 

In contrast, I see a mishmash of nonsense written by the students who have no clue what’s going on.  They don’t know what they don’t know. If they made the effort to memorize the worked examples and explanations in class, they might do a tad better on the exams, but that’s not what’s happening. Instead, they cut-and-paste a question to pose to a chatbot, and read the answer thinking they understand it. Compounding the issue is that if you have little understanding of the subject matter, you are unable to tell if the chatbot answer is correct, wrong, or not-even-wrong. Large Language Model chatbots are designed to sound plausible. Their prodigious memory means they are likely to string together words that sound like the right answer. Maybe it is, maybe it isn’t, maybe it’s simply misleading and neither here-nor-there.

 

A.I. is hailed as a potential disruptor and savior of education. Its champions are the tech companies trotting out deals to hook the young early in the hopes that they will shell out money for premium access later. Schools and universities are stirred into a frenzy by FOMO vibes and guilt-tripped about not preparing their students for the upcoming A.I. revolution. You’ve gotta be able to access The Book. Everyone’s doing it! But like the novice chess players who consult a book to advance their moves without understanding the deeper reasons, novice chemistry students consult an A.I. chatbot and now think they have advanced their understanding of the subject matter.

 

I think that A.I. coupled with knowledge-expertise can be an excellent tool for discovery and pushing the frontiers of knowledge. There lies the out-of-Book realm, ripe for discovery. For novices, though, chatbot education only provides a shallow and self-deceptive “learning”. If the world is headed towards an idiocracy, this might not matter. What pains me is that the bifurcation between the haves and have-nots will continue to expand, and it may devolve into total anarchy or a totalitarian state of affairs.

 

Interspersed with the stories of computer chess, Brian concludes his chapter by thinking about the conversations between humans. There’s an opening and closing, mostly scripted, and a potential interesting middle where two people might learn something new about each other and themselves. In a brief chat with a stranger or an acquaintance, one might never stray out-of-Book. Many top chatbots in the Loebner prize were able to steer the conversation to stay in The Book, banal yet effective. It encouraged me to think about getting out-of-Book and become a better conversationalist. Maybe I can try out some new surprising out-of-Book lines with my students and make a better connection this new year!

PJ Adventures

This winter break, I read the first five books of Percy Jackson & the Olympians penned by Rick Riordan. It was one of my thoughtful students who recommended I read them; he thought I would enjoy the creativity of infusing Greek myth and magic into modern day life. PJ&O is suitably found in the Young Adult section of my local library. Each book is a romp; the action moves quickly and punctuated with plenty of humor.

 

I’d read a fair bit of Greek mythology and was familiar with the Labours of Heracles and The Odyssey, two key sources of the myriad characters that show up in PJ&O. But they show up in surprising circumstances and often in disguise. I also see many similarities to the Harry Potter series with a young protagonist, discovering his true identity and abilities, being thrown into adventures alongside his close friends. In each book, the kid grows a year older, as a prophecy looms towards its fulfilment. There’s an antagonist who is slowly gaining power and trying to resurrect himself.

 

There are several types of beings in PJ&O. Ordinary mortals having ordinary physical characteristics normally do not perceive magic because of the Mist, more about that later. Gods can change form and present themselves in different ways; they seem to have some physicality and can be hurt by magical weapons. Demi-gods are the offspring of gods and mortals and seem to have the physicality of mortals but special characteristics depending on who their god-parent is. Percy, the son of Poseidon, can manipulate water. Monsters cannot be perceived by most ordinary mortals and their true form is hidden by the Mist. They turn into dust when slain with magical weapons and can be re-formed at a later time.

 

Are the gods and monsters made of different physical elements? It’s unclear. They certainly interact with earth and water. But at least some of them can change shape and form, so maybe it’s a different underlying physicality. The books hint that belief in the gods seems to sustain their existence. There are ordinary mortals who can perceive the world of myth and see through the Mist. How and why is also unclear. Is there a color of magic that can only be seen by some? Few are born with the ability and it’s unclear how such a trait arises and whether it can be passed down genetically. The scientist in me is curious about such details, but the stories skip right to the action. You suspend belief and go with the flow. At least that’s what Percy does as he blunders through one adventure after another.

 

The Mist is interesting. Is it a matter of physical perception or is it that mortal brains can only interpret what is physically familiar and therefore cannot perceive the magic. If you saw something so stupendous it defied belief, your mind might rationalize it into something that fits into your world view. The alternative is to go mad, a not-unreasonable possibility. There is no Magical Squad that goes around obliviating the memories of otherworldly sights in PJ&O. Ultimately, like any good fictional story successfully immerses you into its supernatural world so that the physical oddities aren’t as important. The themes of friendship, loyalty, love, truth, anchor the story and that seems to be what most of us mortals care about. The abstract takes precedence over the physical surface, and those of us constantly sweating the physical details are the odd ones out among mere mortals.

Thermodynamic Warfare

Sometimes you just need an equation. Even if you’re writing a “popular” book where equations are discouraged. No, I’m not talking about E = mc² that shows up just to be associated with someone famous.

 

Karen Lloyd, the author of Intraterrestials is a superbly engaging writer. Her book is littered with well-chosen metaphors and analogies to explain how scientists study organisms hiding away deep in the subsurface of our planet. But I appreciate that the professor in her wants to teach her readers something useful and profound. She chose the Gibbs Free Energy equation:

 

I explain this equation every year to my G-Chem 2 students when we discuss thermodynamics. Lloyd does so with much more flair. In chapter 6 (“Breathing Rocks”) she opens with her life-harrowing yet exhilarating experience of sampling for microbes at a volcano caldera in Chile. After the scenario of physical heat and motion (get your samples quick so you don’t die!), she launches into the heat and motion associated with thermodynamics. She explains the Gibbs equation with colorful examples such as roller coasters and hand warmers. I could quote her for several paragraphs, but instead, I recommend you read her book in full. It’s a page-turner!

 

The crux is that subsurface organisms, unable to get their energy from the sun (like photosynthetic organisms) or eat food they can metabolize with oxygen (like most of us do) respire by breathing rocks. They eke out a low-energy lifestyle turning carbon dioxide (from carbonate rocks) into biomass with the help of nitrogen and sulfur compounds, also found in minerals. Such chemical reactions typically have a small negative delta-G, so you can’t get much energy from them, but they are still energetically “downhill” and thus favorable.

 

But things get even weirder when there’s competition for resources. In chapter 7 (“Life on the Edge”), Lloyd sets up the discussion with another vignette in the cold of Svalbard, Norway, where she is cutting sediment cores dug up for her research. While doing so, she ponders life in the cold Arctic with tremendously varying sunlight. And now I have to quote her: “But intraterrestials don’t care about sunlight or cold. They care about delta-G.” And unlike our familiar surface microbes that “secrete deadly antibotics, hoard nutrients, and grow ultrafast to get ahead” and beat out the competition, subsurface microbes have an additional weapon: “If one microbe’s delta-G is better than another one’s then the first microbe can asphyxiate the second.”

 

I was delighted that Lloyd chose sulfate-breathing microbes to illustrate her point since I’m studying the role of sulfur at the origin of life in competing autocatalytic cycles. She delves into the equation, now focusing on how delta-G can be modulated by Q, the reaction quotient. It’s counterproductive for them to grow big fast because that decreases sulfate diffusion in their cellular bodies. Releasing antibotics is also bad because it would kill symbiotic species in addition to its direct competitors. Molecular hydrogen is a required “food”; you can’t stop your competitors from getting it, but you can hoard enough so that you still have a borderline negative delta-G, while forcing the delta-G of your competitors to turn positive (“uphill”, energetically unfavorable) so their metabolism no longer yields energy and they die.

 

Lloyd writes: “Like a shipwrecked sailor dying of dehydration while surrounded by water, these microbes expire with their food right in front of them. Sulfate reducers win because they take the whole system to the bitter edge of their own thermodynamic capabilities, which pushes everyone else off the cliff.” Ugh. That’s war. But then as the amount of sulfate reduces, the sulfate reducers now face extinction. As they die off, their competitors (often methanogens) can access more hydrogen once again and a revolution takes place.

 

Life gets weirder still. Some microbes (methanogens!) can reverse their food and waste as delta-G switches, so they can keep eking energy. Others ferment; in Lloyd’s words: “takes one slice out of the pie and puts the rest back into the fridge for others to eat later. It’s very polite. Because of this restrained eating, fermentation ends up being one of the lowest-energy processes known to support life.” The low-energy living of intraterrestials suggests that they might live a long, long time without reproducing. It’s immortality of a sort, though not the one we might desire.

 

Reading Lloyd’s book rejuvenated my excitement about my research projects. It also reminded me that I want to be a better teacher and communicator. While this was a library book, I will be purchasing my own copy because it deserves re-reading, and I still need to delve into the scientific papers listed in the references!

 

Hydrothermal Conditions

I’ve been conflating hydrothermal vents and fields. I realized this after reading Chapter 3 of David Deamer’s Assembling Life. Most of us who study the origins of life are familiar with the hypothesis that life on Earth may have begun in submarine hydrothermal vents. The initial discovery in 1977, that life was teeming deep in the ocean bed where the water was locally hot around magma-driven minerals was a surprise! The heat and the minerals both act as energy sources (thermal and redox-chemical respectively). Since living organisms crave energy, they congregated to form a local ecosystem.

 

There are two types of hydrothermal vents. The first to be discovered were dubbed “black smokers” because that’s what the sulfide minerals look like under the very harsh conditions where temperatures could reach 400 Celcius. Water remains as a liquid because 2km deep in the ocean the pressure is approximately 300 atmospheres. The vent fluid is also quite acidic (pH 2-4) which can drive certain types of chemical reactions. Black smokers are transient, lasting up to a few hundred years before they collapse and reappear elsewhere along the mid-ocean ridge where the crust is thinner and underlying magma can break through.

 

Origin-of-life researchers have been more enthusiastic about “white smokers” because that’s what the carbonate minerals look like under the not-as-harsh conditions. Water temperatures might be 50-90 Celcius, and the vent fluid is alkaline (pH 9-11) which also drives chemical reactions. These vents can last thousands of years, perhaps longer, and are not associated with volcanic activity. Their existence was predicted before they were discovered in 2000, and the most famous of these, Lost City, is sometimes referred to as a hydrothermal field, which confuses things and likely contributed to my conflating vent and field. Abiotic chemical reactions at these minerals under these conditions can generate methane and molecular hydrogen, important precursors for prebiotic chemistry experiments. Scientists have set up experiments mimicking these alkaline vents and produced some key molecules that may be the building blocks of organic life.

 

Deamer distinguishes hydrothermal fields from vents in the following way. In the submarine vents, there is only one interface: mineral-seawater. Fields on the other hand have exposure to the atmosphere. Instead of being deep in the ocean, they are terrestrial in origin. In the aftermath of a volcanic eruption, the minerals slowly transform such that eventually rainwater collects to form pools. Hot springs and geysers at Yellowstone National Park are an example of such fields. There are three interfaces: mineral-water, mineral-atmosphere, and atmosphere-water. Crucially, the water initially derives from freshwater and although this will dissolve some of the minerals, the ionic strength of the solution is much lower than in seawater. This is critical if you want to form cellular structures from lipid molecules. The high Ca²⁺ and Mg²⁺ content in seawater inhibits the self-assembly of micelles and vesicles.

 

Another important feature of such pools is that the acidic water (pH 4-5) of hydrothermal fields also dissolves apatite (calcium phosphate), the same mineral that makes up your tooth enamel. Phosphate is a key constituent of living systems: it’s in your DNA backbone, it’s crucial in the energy transducing molecule ATP, and it’s also use as a biochemical tag in proteins. In neutral or alkaline pH, phosphate precipitates into a solid and is not available for chemistry in an aqueous solution; this is known as the “phosphate problem” in the origin of life. Sulfur compounds likely contribute to the acidity in hydrothermal field solutions, which is why I’m studying them.

 

Terrestrial pools of water have two other attractive features. Since they are not as deep, photosynthesis can play a role. By this I mean that an appropriate mix of molecules that can absorb solar photons that penetrate through the atmosphere provides an additional energy source of driving chemistry. There’s even a pigment-world hypothesis of the origin of life that makes this center-stage. Secondly, a shallow pool potentially allows for wet-dry cycling. This is important because as water evaporates, it concentrates the potential reactants in solution. In particular, evaporating conditions drive the assembly of polymers. If you’re deep in an ocean with lots of water, hydrolysis reigns and water chops up any short polymers back into smaller fragments. The wet-dry cycling of a shallower pool, on the other hand, allows polymers to form and re-form polymers, and a complex mixture could begin to “select” for the most robust ones.

 

Did life on Earth begin in hydrothermal fields (as opposed to vents)? I don’t know. Deamer makes an attractive case for the fields. But it’s a messy complex system and designing good experiments that allow you to extract good data is not easy. I’m thankful to Deamer for making the distinction between vents and fields explicit and I expect to use his definition in the future.

Hermione's Helping Hand

I’m on vacation and was inspired to re-read the Harry Potter series. This seemed like an appropriate time given that today, July 31, is Harry Potter’s birthday. Also, in a recent family conversation about the re-telling of fairy tales, we mused about the different experiences you might have with an “updated” fairy tale, or one that takes a different perspective from an original source, depending on whether you had read the original version. I remember back in 2001 talking to a friend who had watched the first Harry Potter movie in the cinema, but who had not read the books beforehand. Being from a different country, he had also not been exposed to the Western canon of fairy tales. He enjoyed the movie, but found it a bit disjointed, and was confused what some scenes were about.

 

So, I wondered what it would feel like to re-read the books with some of these thoughts in mind. I have to admit that the first book is not as good as I remembered. That being said, every fresh re-reading rewires how one thinks about the text so perhaps all this is not surprising. I found the text clunky in some parts, possibly because I have not read any fiction catering to eleven-year olds in a while. Another thing I noticed this time around is how much guiding the author uses to set up a future scene. Is it a helping hand for younger readers? I don’t know.

 

My reading is also coloured by my profession as an educator. I’m constantly noticing what may be “teachable moments”. This time around, Hermione’s nagging, her drawing up study schedules for Harry and Ron, her checking of their work, made me wonder if students today need more Hermiones. It may not seem cool, but having a friend and peer want you to do well academically and makes the effort to help, even when it seems like being a nag, might be a good thing. That sort of helping hand might not be welcome, but in this case, Ron and Harry greatly benefit from it. Once Harry gets on the Quidditch team and his timetable gets tight, it’s Hermione’s strategies that gets him through the end of the year and final exams.

 

The title of today’s post comes from Book 6. In that instance, the beneficiary is Ron, but the help is particularly un-Hermione-esque. And throughout the books, the influence runs both ways. I’d like to think that Ron and Harry learn good study habits with Hermione’s help, but this aspect isn’t emphasized. If Hermione wasn’t there to nag them, would Ron and Harry be diligent in their classes? Rather when Hermione decides to stray from her straight-laced approach and become more “rebellious”, this is what’s celebrated. I’m not sure what the lesson is here. (For example, I previously blogged about Hermione organizing an illegal study group.)

 

Finally, an observation made by my sister after she had read the books has stuck with me. One of Hermione’s roles is to help provide information to the reader. In the first book, Hermione does so by quoting books she has read such as Hogwarts, A History. This keeps the story moving along without being bogged down. Need a factoid to keep things going? The Hermione character provides a way to insert knowledge. Other characters in the book also do this, but none as much as Hermione. Her helping hand is integral to the books!

On Not Reading

To read or not to read. That is the question. Even if you don’t read a book, in no way does it prevent you from talking about it. Or if you feel obligated to skim, ten minutes might be enough. It might even be preferable for you not to read if you are a book critic. This advice sounds positively blasphemous if you love reading and talking about books. But it does come packaged in a witty and humorous book by Pierre Bayard, aptly titled How to Talk About Books You Haven’t Read.

 

I’ve written about many books on this blog. I assure you I’ve read all of them. I even read most of Bayard’s but I did skip a few chapters and skimmed others. I think the author would be proud of me. On the one hand, the book made me think that literary criticism is an absolutely vacuous activity. On the other hand, Bayard emphasizes the non-static nature of a book. Read or not, it provides a jumping point to talk about opinions, ideas, musings, speculations, and engage in other human-like activities. It seems apt that books, read or unread, can promote the idealism of the humanities. Or it might just be a load of rubbish.

 

Ideas are two-faced. Janus-like. That was my biggest takeaway from Bayard’s musings. Two people can have completely different ideas when encountering some reading material, especially if they differ greatly in their backgrounds. There’s a most amusing chapter cherry-picking conversations that an anthropologist has with the Tiv tribe in Africa where she tries to tell them (or perhaps sell them) on the universal human tale of Hamlet. The Tiv may disagree with the typical literature interpretations you might encounter in a college classroom but they interact with the story nevertheless as they ridicule its tropes. I have never read Hamlet although I know enough of the story to quote from it.

 

The other interesting idea comes in the very first chapter with quotes from a book that I hadn’t heard of, The Man Without Qualities by Robert Musil. In it, there is a most peculiar librarian who pointedly never reads any book in the library other the table of contents so that the book can be situated with other books it is related to. An exasperated patron wants to know why. The librarian says that were he to read the actual book, he might “lose perspective”. That sounds preposterous but it turns out the librarian in fact loves all books, so much so, that “incites him to remain prudently on their periphery, for fear that too pronounced an interest in one of them might cause him to neglect the others.” By taking a step back and having a more expansive view, it is the dynamic relationship between books that is more important than one book’s particular content. It’s holistic knowledge by taking preservation of the whole to the extreme.

 

Most books have not been read by most people. And if you do read a book, you begin to forget the moment you start reading. I find this to be more and more true as I’ve aged. I retain the gist of books, stories, TV shows, movies, but I’ve forgotten the details. If enough time has passed, I can’t even tell you the gist. I could consult my blog to reacquaint myself with what I thought of it back when I read it the first time, but a second reading might induce a different response. I’m a different person now than when I first read the book and may interact with it differently as my constellation of ideas has shifted over time. But I don’t think I will ever be like Musil’s librarian. I love the pleasure of reading a book even if it means I miss out on others. Or even re-reading. Since skimming Bayard’s book, I have a hankering to re-read the Harry Potter series. Fresh eyes might provide more fodder for my blog!

In Search of Nothing

Nature abhors a vacuum. At least on the surface of Planet Earth which supports a gaseous atmosphere at a pressure of 760 mm Hg. How did we know this number? One of Galileo’s students, Torricelli, turned a tube of mercury upside down into a bowl of mercury. As long as the tube is more than 760mm long, there will be a gap of nothing at the top. It’s not an air gap. It’s a gap of Nothing.

 

Toricelli was actually looking for the mystical aether, the sacred material breathed by the gods, the fifth element, the quintessence. Supposedly it “allowed light from the stars to propagate” and was “also holding planets in their orbits”. I’m learning about this history reading through Mark Miodownik’s It’s a Gas. Toricelli had finally isolated the aether, a quest of the alchemists, some of whom thought it associated with the philosopher’s stone that would balance the four humours and cure all illnesses. Perhaps it could even prevent death. No wonder that Voldemort coveted it.

 

The trick to creating vacuum is to pump out all the air molecules from a closed container. That container must be truly air-tight. No leaks! Miodownik writes: “We take the accuracy and intricacy of screws, gaskets and valves for granted today. In the seventeenth century such precision engineering was just beginning.” What shot vacuum to fame was the famous demonstration at Magdeburg by Otto von Guericke. He didn’t use the chemical techniques of the alchemists. He just used mechanics to make an airtight pump. Once the air was pumped out of two hemispheres cupped into a sphere not held together by any other means, two teams of eight horses each could not pull the hemispheres apart.

 

What are the properties of Nothing? Now that scientists could reliably make it. They could start running tests. No living thing survived. (Oxygen was yet to be discovered.) Sound does not travel through vacuum, although light does, and magnetism is unaffected. Turns out that metal wires will glow hot in an enclosed vacuum tube when a voltage is applied, and  Voila! Electric lighting is invented! Even if the wire breaks, you can sometimes get electricity to flow. (Electrons leap across but they didn’t know that yet!) This led to vacuum tubes. And now you have TV. Once you’ve mastered manufacturing silicon chips in vacuum conditions, you now have computers and all manner of smart devices. Who would have anticipated that Nothing would be so important!

 

Miodownik also relates the now-familiar story of the discovery of the noble or inert gases. They upended Mendeleev’s Periodic Table. It took painstaking evidence to show that they existed. They weren’t just Nothing even though they seemed to have no chemical reactivity. How were the noble gases discovered? Rayleigh was unhappy with the imperfections of the masses of the chemical elements. They almost followed a beautiful mathematical pattern, but not quite, and so he decided to measure their masses again with high precision. This is much harder than it sounds. You needed to create a vacuum in a flask and weigh it, then pipe the gas in and weigh it again. But the pressure, temperature, and humidity of the room can affect this measurement. You needed to more than triple-check everything. Most scientists didn’t believe Rayleigh, even after Ramsay provided an independent confirmation. Eventually argon was joined by helium, neon, krypton and radon. Chemistry’s 1904 Nobel Prize went to Ramsay for his discoveries. And eventually scientists and engineers found uses for all these gases that at first glance did Nothing!