Transition Week

Final Exams for the spring semester concluded last week. I got my grading done and submitted final grades. Teaching-wise it was a much lighter semester compared to last fall when I taught biochemistry for the first time. In the spring I had two small classes: P-Chem II and the honors section of G-Chem II. With only a dozen students in each class, there was much less grading to do! I also feel that I do a better job helping students puzzle over the material in class and answering their questions when there are fewer students and my attention is not spread too widely.

 

Summer research will commence full swing starting on Monday. I had a grant funded so I will be onboarding a new crew of five undergraduates. Some of the students have just finished G-Chem, some have just finished O-Chem, none have taken P-Chem yet, and all will be new to computational research. The research students I had this past spring semester have either just graduated (this past weekend) or have other summer plans lined up. This will be the first time in a while I have had so many new students join my lab without any experienced ones present to help as guides. I’ve been updating my research guides and crib-sheets to help orient my new students. This morning I worked on detailing the training schedule for the first two days. After that students will be assigned their individual projects.

 

I am also making a software transition. This was rather annoying at first. My current software vendor essentially doubled the license renewal price; after some frustrating back-and-forth I was able to negotiate it down partially, but that was still not enough. I was particularly annoyed because I had told them the previous year what my budget would be (written into my grant) according to what I had been paying the last several years with minor increases for inflation. Thus began a hunt for new software which meant getting trial licenses and testing things out to make sure I had continuity. I found some suitable packages that will expand my research methodology options so I now see this as an opportunity. And it fit my budget.

 

The transition will still be frustrating. For most of the summer, my students will be able to get their computations done on the old software that I’m very familiar with. The very tail end is when my present licenses run out, and that’s when the group will have to make the transition. I will have a month overlap between the old and new software licenses which will give me time to write up new protocols and orientation guides. Then my pitch to the students will be that they are helping me test new protocols! And for anyone who wants to continue research with me during the semester, they’ll have to learn the new software anyway, so it’s better to do it during the summer. Once classes get started, things get busy.

 

So unlike other transition weeks in past years, this one is busier than usual. In the final two weeks of the spring semester, as finals were looming while I was busy testing out new software, it felt overwhelming. But because much of the administrative paperwork was figured out last week, this week has felt more calm. Also, I can work from home this week which saves me the commuting time! I’m no longer frazzled, and I’m working on tuning my mindset to make the most out of summer research!

Agent Causation

What is an organism and how does it differ from a machine? We have this vague idea that it has something to do with self-agency and made out of “soft” (organic) matter rather than “hard” inorganic matter. Is there downward causation? I’ve read a fair amount of philosophy and science on this question, much of which I’ve found challenging to understand. Thus, it was refreshing to read Potter and Mitchell’s lucid article “Naturalising Agent Causation” (Entropy 2022, 24, 472. DOI:10.3390/e24040472). Maybe it was having this groundwork, or maybe the authors were just clearer in their exposition, but I found it easier to read.

 

Their opening questions: “When an organism acts in the world, is it right to say that the organism caused the effect? Or is that simply a useful metaphor or a convenient level of description? Perhaps the more accurate statement is that some biochemical pathway or neural activity within the organism caused the effect… is it right to think of organisms as agents capable of action?” On the first day of my biochemistry class, we talked about definitions of living systems and I joked that to study of biochemistry is to take “life” out of biology via reductionist methodology. Probably many biologists do the same thing unless they operate on the organism or systems-level, even though there is a shift to more holistic approaches.

 

The authors begin with definitions. I’ve chosen this statement to represent their thesis: “To justify agent causation, systems need to exhibit a causal power that irreducibly inheres at the level of the whole system while still maintaining that the causal power is instantiated in, or realized by, the system’s physical constituents.” Essentially, non-reductive and obeys physicalism. But to distinguish their conceptual framework from its detractors, the authors discuss vertical reductionism (every macroscopic description is “fixed” by a microscropic description), horizontal reductionism (attributing causation to a subset of the system), and external determinism (“the environment wholly determines the system’s actions”).

 

Their counter-argument is to propose eight criteria to exist as a causative agent. The first three (thermodynamic autonomy, persistence, endogenous activity) are familiar. I was reminded of the importance of having physical boundaries between system and environment. While I drum into students the importance of the conceptual separation when introducing thermodynamic model, sometimes we get lost in the math and forget that there are physico-chemical boundaries. Persistence ties into thermodynamic autonomy because an organism needs to constantly extract energy from the environment, even while this persistence is dynamic rather than static. But the organism has to actively do so.

 

The other five criteria are a little trickier. Holistic integration argues against reductionism, and reminds us scientists not to be overly enamored with our methodology. When we isolate a small part of a system to probe its workings in detail, that act of isolation is also a blinder. And the more we learn, the more complex things get as we scope outwards. As students in biochemistry class complain: why is it so complicated? Low-level indeterminacy relates to the quantum level, but only to set up the next criterion, multiple realisability: many microstates might lead to a single microstate and there seems to be all sorts of coarse-graining taking place as intervening layers complexify the system (as a means of regulation and control). The historicity criterion reminds scientists that we can move beyond asking how to asking why; and the agent-level normativity criterion argues for the importance of meaning.

 

But meaning, like beauty, is in the eye of the beholder. Thus, receiving and processing information must be integral to an organism. The authors do a nice job connecting signal reception from the external environment to a discussion on chemotaxis in bacteria and neural signals in “higher” organisms, to the historic evolution to the abstract processing of information, to the response (or non-response) of the organism. The middle part where physical signals are coarse-grained and manifested abstractly in some sort of network, which informs a response, is not only critical but cannot be cleanly separated from its beginning (the stimulus) to the end (the response). Hence, the organism coheres as an individual agent in its own right.

 

I end by quoting parts of their addendum (“The Reductive Instinct”) on why this is so challenging both for me as a scientist and my students, the budding scientists, to grasp. In science, there is “a slippage from methodological into theoretical reductionism… [we] employ experimental techniques that powerfully manipulate individual components and measure so specific outcomes while attempting to hold as much of the background activity of the system constant… This approach naturally lends itself to thinking that an organism’s components truly act in isolation from each other… [but] just because it is possible and often useful [as an approach]… does not mean that these elements actually work separately or have truly isolatable causal efficacy [normatively]”. While I haven’t fully figured out if their argument works philosophically (there might be some sleight-of-hand), I found their framework helpful, and more importantly their article was lucid and one that I can introduce to students. That’s a major plus in my book.

BS Jobs

My department is converting its BA degree to a BS. Ostensibly it will help our students in the job market. This is not what today’s post is about.

 

Instead, I will be discussing the anthropologist David Graeber’s book Bullshit Jobs. It’s short, engagingly written, and manages to be both amusing and depressing at the same time. If you aren’t already cynical about Dilbert-esque BS jobs in management and administration, Graeber’s work will convert you. He has testimonial after testimonial from a wide swath of people explaining why they are in BS jobs. But first we have to ask: What is a BS job?

 

Graeber works through some definitions before settling on: “a form of paid employment that is so completely pointless, unnecessary, or pernicious that even the employee cannot justify its existence even though, as part of the conditions of employment, the employee feels obliged to pretend that this is not the case.” His book came about because of a punchy article he wrote back in 2013 which resonated with many people who just needed an outlet to fess up to the despair they felt in their BS jobs. In 2015 someone bought a bunch of ads that ran in subway trains quoting from his article. Graeber lists them.

 

·      Huge swathes of people spend their days performing tasks they secretly believe do not really need to be performed.

·      It’s as if someone were out there making up pointless jobs for the sake of keeping us all working.

·      The moral and spiritual damage that comes from this situation is profound. It is a scar across our collective soul. Yet virtually no one talks about it.

·      How can one even begin to speak of dignity in labor when one secretly feels one’s job should not exist.

 

Graeber names the financial industry, telemarketers, PR consultants, and middle management as being riddled with BS jobs. He also tackles head-on the assumption that BS jobs are mostly found in the bloated government and civil service, and provides many examples where this is simply not true. While you might think that it would be anathema to  the money-making private sector to squash out any such inefficiencies, the reality might even be the opposite. Graeber pulls numbers from Ginsberg’s Fall of the Faculty to show that middle management has grown much faster in private universities compared to public ones. As an anthropologist, he also provides the intriguing suggestion that what we are seeing today is essentially feudalism dressed in new clothes. A subheading reads: “how managerial feudalism manifests itself in the creative industries through an endless multiplication of intermediary executive ranks”. I find his analogy compelling. When there are monies to disburse, layers of bureaucracy start to develop to siphon off the goods. Extractive measures are everywhere, not just in struggling poor nation-states.

 

Why are BS jobs proliferating and why are they so difficult to get rid of? Graeber suggests three levels of analysis: the individual, the socio-economic, and the culture-political. It’s an iron triangle, and the three parts self-reinforce in an interlocking system. And thanks to globalization, the phenomenon is now global. Honestly, I don’t know how we could transition into a system that is sane. Because humans are prone to greed and doing one’s utmost to maintain one’s advantages (personal, familial, or tribal), it would take a mighty upheaval to dislodge the system. Graeber doesn’t provide solutions although he thinks that Universal Basic Income might go some way to alleviating the problem. What is particularly sad is when Graeber shows one example after another that “caring” professions tend to be valued less: those that do the most useful work to society have the worst wages. Moral and spiritual damage indeed.

 

All this made me reflect on my job. I’m certainly making less than I would have if I had gone into industry (science research) where starting salaries were easily 50% higher than mine. A number of my grad school labmates went into the financial industry – investment banking – where they easily make multiples of what I am earning. Computationally-trained quants were all the rage back then. They still are now, and that proves Graeber’s point even though his book was written before the present rise of A.I.

 

Is the tuition my students are paying to attend my (private) college worth it? Yes, our classes are small (average of 25 students) – but for the amount they are paying per class (over $100 per hour), they could be getting private one-on-one tutoring with a PhD-level expert like myself. Back in my home country, before I went to graduate school (and even before college), I tutored one-on-one for cash. It was relatively easy money, and I had a knack for teaching. If I think about my salary as a professor and divide it by the number of students I teach per year, I’m probably earning less than $20 per hour per student, but since I’m teaching a class of students, I might be earning $500 per hour per class session. That’s not bad, I suppose. I’m getting a relatively good deal, but maybe the students aren’t. But at least they’re not in 400-person G-Chem classes like in the nearby R1 university.

 

My college, like many others, has grown significantly in middle management. Is that what is siphoning much of the students’ tuition? Administration seems to be about keeping the masses happy. It’s a sort of feudalism except that the guild of university professors is no longer run by the professors but by managers. I honestly find many of the administrative staff at my university pleasant to work with and helpful. I don’t know if they feel they are in BS jobs. More likely they think they are doing a helpful service. I sometimes feel I’m partly in a BS job – my students could learn chemistry without me, but they would need substantial self-discipline and spend a whole lot more time struggling over the material to be proficient. People used to learn chemistry through “distance education”. They can still learn through many asynchronous options today.

 

Maybe the teaching part of my job isn’t BS, but many of the “service” tasks could be. And surely the increasing box-checking administrative tasks are BS. Every year it gets more frustrating and I find myself increasingly unconvinced by the administration’s argument that it’s because of government regulations or auditing requirements. Even my research is likely BS. I have the luxury of wanting to know more about the chemical origins of life – which isn’t going to solve the world’s problems. I even feel bad that I have external grant funding to do this. And yes, I was annoyed by all the extra administrative tasks that came with it. All in the name of accountability, so to speak. Through Graeber’s lens, the BS looks more apparent. Perhaps I am in a BS job after all.

Before Boltzmann

On the last day of class, I touched on some big picture things in my P-Chem class on Statistical Thermodynamics and Kinetics. But after class, while sitting in my office, I started to ponder the conceptual strangeness of entropy before Ludwig Boltzmann’s statistical interpretation.

 

Sadi Carnot had laid the foundations for the theory of heat. At the time, heat was considered a ‘weightless fluid’ called caloric. This fluid spontaneously flowed from hot to cold, down a temperature gradient (the Zeroth Law of Thermodynamics). Carnot devised the heat engine model, and laid the foundations for conservation of energy (First Law of Thermodynamics) by examining the conservation of heat in the ideal cyclic process of the model. The caloric theory of heat turns out to be wrong, and Robert Mayer was instrumental in figuring out that energy (a hard-to-define word) was conserved. Mayer actually called it the conservation of force. William Thomson (Lord Kelvin) came up with ‘energy’. It’s not surprising that all this was confusing to the scientists of the day.

 

It was Rudolf Clausius that extended Carnot’s early ideas but he needed to introduce ‘entropy’ as a partner to energy. Arguments about the conservation of heat (energy) only applied to reversible processes, but we observe many other physical and chemical processes that seem to go in one direction. Entropy is crucial because for a process that proceeds irreversibly, this quantity called entropy increases, at least in an isolated system (Second Law of Thermodynamics), although how fast it would proceed was controlled by kinetics. Clausius connected entropy to heat and temperature mathematically, but could not take the step that Boltzmann did, partly because in the mid-nineteenth century, many scientists did not believe in the existence of tiny molecules that no one could see.

 

Why the Second Law is obeyed was rather mysterious. It was as if there was some hidden variable in nature that commanded that entropy must increase for anything to proceed over time and not get stuck in equilibrium. Not that scientists couldn’t posit strange abstract ideas like a weightless fluid or the luminiferous ether of space. But it’s like invoking magic. Something must be transferring. Something must be facilitating movement. But we have no idea what that something is. Is it even a thing? Invoking entropy was like invoking magic, but not uncommon for scientists positing interesting new ideas. There was a mathematical framework for calculating entropy, but no one knew what it was. We have a better idea now, but like any large cross-cutting concept, it’s hard to provide a succinct definition, and we have to rely on multiple examples to illustrate entropy. One idea is that entropy says something about the quality of energy.

 

By embracing the molecular hypothesis, Boltzmann was able to make a powerful argument that brought the statistical to thermodynamics. It’s how I approach the teaching of thermodynamics to students in my chemistry classes. Why does the Second Law do what it does? Sheer probability. When there are six-gazillions (or moles) of molecules, the most probable distributions far outweigh any seemingly ‘ordered’ macroscopic structures. That’s why entropy is often associated with disorder – a helpful analogy although occasionally misleading. We need Mack and Mike to help us think about what’s actually going on, and we have Boltzmann to thank for that point of view. 

Data Scraping

Six months from now, Potions for Muggles will be ten years old. When I started blogging, I didn’t think I would keep it up as long I as have. There were multiple occasions when I felt like throwing in the towel, but then after a week or two I would find something interesting I wanted to write about so that I could search for it should the need arise. I guess I wrote my blog so I could retrieve my own thoughts.

 

Several weeks ago I was talking to students in my P-Chem class about A.I., machine learning and data scraping. We were learning some python for P-Chem and I had told the students that ChatGPT is a good place to get snippets of code for whatever you were trying to do. With a little understanding of scripting you could modify the code for the specific task you wanted to carry out. That led to me pontificating about data scrapers and why I thought that large language models are starting to plateau. The amount of data needed for a substantial improvement is exponential. Much of the free data has been scraped. I’m sure that deep-pocketed tech companies will be willing to spend money for paywall data and there’s likely to be an arms race. I also mused on the potential problems of having an A.I. generate data to train another A.I.

 

All this made me think that my blog has likely been scraped several times over. I suppose I could scrape my own blog to train an A.I. that will spout aphorisms or make proclamations in my (written) voice. After I’m dead and gone, someone could still consult the oracle of me that has survived as an interlocutor bot. Personally, I’m not sure I’m all that interesting to talk to. That being said, I do think that I’ve shared some interesting ideas on my blog that are not my intellectual property – that’s what one should expect with a public facing free blog. I have considered stopping this blog. Why give away my good ideas for free to data scrapers? And maybe I will at some point. If this turns out to be my last blog post, then I guess that’s what I decided to do. For now.

 

Humans are fickle. I’m no exception. Also, our memories fade and reorganize over time. That’s not a bad thing. Our brains repackage our thoughts and ideas every time we access them. A large language model generating text is a re-packager of sorts. It’s an intelligence of sorts. My ideas are a molecular drop in a mole of data. Likely insignificant to a data scraping operation. I suppose I still get more out of my blog than a tech company would, and if someone wanted my ideas, they’d actually have to read through and understand my writing. Perhaps that was the whole point of writing my thoughts in the first place.

Star Wars Day

While teaching remotely during the pandemic, I tried to mix things up in my classes. Thus, on May 4, I did a Star Wars day lecture in my G-Chem class. It was an excuse to talk about several things: (1) that living systems try to stay away from thermodynamic equilibrium, (2) my research into the chemistry of the origin of life, (3) the search for life on Mars, and (4) how E.T. might phone home via the hydrogen 21-cm line. That’s an eclectic mix of topics.

 

I’ve kept up the tradition in my G-Chem II class the last several years, making small changes every year. I did so again yesterday, the Friday just before Star Wars Day. I think it was well-received and students participated in answering my questions which I had pitched as reviewing the topics for the semester. I now introduce the class as a connection between equilibrium thermodynamics (which takes up most of the semester) and the last few classes that cover electrochemistry and redox reactions.

 

We begin with a reminder of isolated, closed, and open thermodynamic systems. We talk about equilibrium being thermodynamic death: when there’s no longer any Gibbs free energy to access, organisms can’t extract chemical energy to do work! Then we talk about the oxidation of sugars into CO₂ and H₂O as a placard for catabolism. Students remind each other what enthalpy and entropy signify in a chemical reaction. When I ask them where the sugars come from, we then discuss the reverse reductive reaction: photosynthesis. Students dredge from their memory how to determine oxidation numbers of carbon so they can identify the redox reactions.

 

I then ask them why anabolism might take place if the reaction of CO₂ and H₂O to form glucose and O₂ is so thermodynamically unfavorable? That gets us into discussing photons as “low entropy” concentrated packets of energy, as in contrast to dispersed heat that cannot be recovered. Then I segue to how on early Mars (or Earth), CO₂ might react with H₂ (both exergonic and endergonic) to synthesize formaldehyde. This allows me to introduce the formose reaction and autocatalysis. We compare the pitiful energy extraction from anaerobic metabolism versus aerobic metabolism. I show them graphs depicting the rise of O₂ on Earth and the evolution of manganese-catalysts in photosystem II. Finally, we get to humans burning hydrocarbons for even more energy!

 

Communicating with alien life now takes up only a small portion of class time. We discuss the dominance of hydrogen in elemental abundance. Students are reminded of the emission spectra and electronic transitions. I remind them of electron spin and introduce the 21-cm wavelength associated with that transition. We discuss how an Earth scientist might communicate with an alien scientist by trying to find unitless quantities such as pi or the fine-structure constant embedded in the hydrogen spectrum.

 

Then I tell them about the movie “Contact”. It’s old and none of them have watched it (although I encourage them). I then tell them about the SETI message beamed out from the Arecibo telescope. I also show them pictures of the now destroyed telescope and tell them it’s not because James Bond had to foil a terrorist incident (GoldenEye). We briefly talk about why you might not want to communicate with aliens, and I mentioned The Three Body Problem. (One of my students had watched the first season. I haven’t yet.) I end with the Chibolton “reply” crop-circle which is always jaw-dropping because students have never heard of it; I suppose it’s good that none of them are into weird alien conspiracy theories, or at least no one has admitted it yet.

 

Another Star Wars day come and gone. I had fun! Hopefully the students enjoyed it too. On Monday we dive into redox and electrochemistry.