Scaling Up

One enduring challenge in chemical synthesis is scaling up. You may have discovered how to make a particular compound that is important commercially, but the protocol used in the lab may not pan out on a larger industrial scale. Scaling up is also a challenge in non-chemical business ventures, and this is the subject of John List’s The Voltage Effect. The book’s title comes from electrical circuits where the driving force to move electrons in a circuit – the potential energy difference measured by the voltage – can be higher or lower than expected.

 

The first half of the book covers the five problems that can prevent what seems like a good business idea from scaling up, i.e., they cause a voltage drop. These are: (1) false positives usually due to a non-representative data set when testing, (2) not knowing your audience or how to broaden it, (3) whether your innovative source is dependent on certain individual people, or processes, or products, (4) unforeseen spillover effects, and (5) sheer cost of scaling up. Like any business book, there are memorable anecdotes. The author provides a good mix of academic research and notable vignettes from his time in industry.

 

I wouldn’t say anything jumped out at me that I hadn’t read before, but it made me think about whether teaching and learning can be scaled up. The author (having worked at both Lyft and Uber as chief economist) makes the point that digital things can be scaled up easily; we have the technology to quickly and easily copy 0’s and 1’s! But Baumol’s cost disease applies to human beings with expertise if scaling up for mass production. So, it depends on whether you need the person-to-person direct transmission. I suppose some things can be learned through a digital device, but other things are not so easy. There may also be an issue of quality degradation – how important it is will depend on many factors. If you need expert human teachers, scaling up will be a huge problem because the supply is limited. I’d like to think my expertise both in chemistry and in teaching is irreplaceable, but perhaps that’s not true depending on one’s end-goal.

 

The second half of the book provides four “secrets” to increasing the voltage of your undertaking. These are (1) having the appropriate incentives that can scale, (2) keeping the margins in mind – an economic way of approaching certain problems, (3) knowing when to quit, and (4) the scaling of that nebulous, undefinable thing known as workplace “culture”. The incentives discussion is mostly common sense, while marginal thinking isn’t. The latter is well-worth learning, in my opinion, although I can’t say I’m great at it yet – I learned the hard way why it’s important. The most interesting chapter was the one on knowing when to quit. It made me think about significant points in my own life where I faced challenging forks in the road – do I pursue something or do I let it go as a sunk cost?

 

One annoying part about the book is that it feels like the author’s vignettes shout out how clever he and his colleagues are in figuring out things that would scale and things that wouldn’t. I don’t know if that was his intent, but if felt like being exposed to resume padding and self-promotion. He does have interesting vignettes because of his varied experience, and I was reminded that those experiences can be very useful in thinking outside the box. Having spent most of my working life in academia my thinking is likely overly insular and I should at least consider branching out if the right opportunity comes along. I’m good at saying “no” when I should be better at saying “yes” because I like to protect my own time. But maybe I’m just afraid of change and challenging myself. That reminder is one positive aspect of reading The Voltage Effect.

Plotting a Taboo

I finally finished my re-read of the Harry Potter series. It took a month to work my way through all seven books but it was enjoyable, and the last two books are simply excellent! Today’s post will focus on one small aspect of the final book: the Taboo.

 

As Voldemort and his minions take over the Ministry of Magic, to hunt down their opponents, they enchant the name ‘Voldemort’ with a Taboo. If someone were to say the name out loud, their location will be betrayed, and the bad guys will apparate (teleport) to the location to capture or eliminate the good guys who have formed the resistance. It’s a clever strategy because no one would say Voldemort’s name by mistake. His followers call him ‘the Dark Lord’. Everyone else calls him ‘You-Know-Who’, and only those who oppose him dare call him Voldemort.

 

Instead of Hermione who usually has the role of explaining things, it’s Ron that breaks the news to Harry: “… the name’s been jinxed… that’s how they track people! Using his name breaks protective enchantments, it causes some kind of magical disturbance – it’s how they found us in Tottenham Court Road… anyone who says it is trackable – quick-and-easy way to find Order [of the Phoenix] members.”

 

Back in the third book, we encountered a GPS-like tracker, the Marauder’s Map. In that case, it’s as if everyone carried a tracker with them and as long as they were in known locations of Hogwarts, they would be observable on the Map. The Room of Requirement, presumably unplottable, does not show up and anyone in it cannot be tracked. It takes a while for Harry to puzzle this out in the sixth book in his vain search for Malfoy. In the seventh book, Hermione and Ron disappear from the Map because they have gone down into the Chamber of Secrets to destroy a Horcrux. So maybe the tracker analogy isn’t as accurate. The Map is more akin to a Security Room that has cameras showing all known locations and can tag (using some sort of facial recognition?) everyone in its view. I applaud the Map’s creators for their nifty magic which has its counterpart in today’s I-Spy technology.

 

The Taboo works something like that. The technological equivalent is a mass of satellites or cellphone towers covering all plot-able ground, that can receive signals from anyone carrying an appropriate device. But instead of an actual device, the signals received are sound waves. And if a pattern of soundwaves – Voldemort’s spoken name – is detected, an alert is sent to the bad guys that they’ve likely found a member of the resistance. For a while, our three heroes avoid using his name because of Ron’s insistence that it is bad luck even before they’ve found out about the Taboo. An exception to this was when they were in Grimmauld Place and Voldemort’s name was spoken freely. But because the old Black residence was unplottable, it seems the Taboo wasn’t triggered. I suspect the same would apply to the Room of Requirement.

 

Technologically, if the government was hunting for a fugitive, and had satellites or cell-phone towers gathering huge amounts of data, the strategy would be to find some signature that will lead to pinpointing the fugitive. This would require sifting through huge amounts of data. You want the identifying signature to be simple but unique. The Taboo is well-chosen in that regard. Perhaps this says something about the limits of magic. Coming up with a spell that will automatically allow you to find a particular individual wherever they are must be very challenging – although it can be done in a limited space as proved by the Marauder’s Map. Could a larger scale Map be conjured? I don’t know. But given what some countries are doing now with their technology to essentially spy on anyone within their borders, it’s already happening in our world. How can one make themselves unplottable in this new world? I don’t know, but the battle between surveillance and privacy from it rages on.

Chemical Economics of Life

One challenge for the theory of evolution: it needs to encompass both creativity and predictivity. Creativity, because new species come into being, never having been observed before. Predictivity, because underlying causal mechanisms come into play as organisms with certain traits are selected for instead of their less adaptable relatives. In addition, biological arguments often invoke the notion of ‘function’ – which is an overlying rather than an underlying cause hierarchically. Biochemical arguments, excising macroscopic ecology from the picture, attempt to explain the function in terms of ‘structure’ to emphasize underlying causes.

 

In his treatise, Jeffrey Wicken incorporates thermodynamics and information to broaden the theory of evolution beyond the neo-Darwinian. Chapter 12 of his book is titled “The Economics of Selection”. How do organisms grow and reproduce? By funneling energy through themselves and degrading it to build new structures. Why do they so? Well, to grow and reproduce. Note the chicken-and-egg argument I just made with the how and why questions, which has led to the idea of biological relativity – no particular level within the hierarchy can be easily singled out as the primary cause.

 

The economic currency here is energy. In our neighborhood of the solar system, an energy gradient exists between the sun (shooting out photons) and the ‘coldness’ of the vacuum of space. In between sit the planets, full of matter and some (okay, one) with the potential for supporting living organisms. Translating the energy gradient in chemical terms, Wicken writes: “As energy penetration increased the free energy of the emerging biosphere, it built into it proximate free energy gradients that could be exploitatively tapped. These involve both sources with high-energy electrons and oxidative sinks for accepting those electrons. The fundamental economic boundaries of a system are set by its source-sink relationships and the kinetic mechanisms at its disposal for exploiting them.”

 

My chemistry students will hopefully recognize that some sort of redox reaction must be involved. Electrons are moving from a source (the reducing agent) to the sink (the oxidizing agent). Hydrogen is the prototypical reducing agent. Oxygen is the prototypical oxidizing agent. Using handwaving (or bookkeeping) arguments involving ‘oxidation numbers’, students learn in introductory chemistry that hydrogen transfers its electron to oxygen and H₂O is formed from elemental hydrogen and oxygen. The formation of water is energetically very favorable – there’s a gradient from the higher (potential) energy reactants, H₂ and O₂, to the lower (potential) energy product H₂O. More subtly, and I emphasize this point in my upper division P-Chem thermodynamics class, O₂ is the “high-energy” species from the perspective of the relative ‘strengths’ of chemical bonds. And why is carbon central to life? I’d say it’s along for the ride thanks to its ability to expand chemical space to create new structures. This notion of expanding chemical space will be important to Wicken’s thermodynamic argument.

 

While our present atmosphere has lots of free O₂, and heterotrophic organisms (we can’t make our own food, we have to eat it!) utilize O₂ for metabolism, this was not so at life’s origin on our planet. Oxygen was locked into both minerals (many ores are metal oxides) and carbon (as carbon dioxide in the gas phase, bicarbonate in aqueous solution, and carbonate both dissolved and in ionic solids). The reason why we have lots of O₂ today is because, at some point in the distant past, photosynthesis was ‘invented’ thereby allowing autotrophic organisms (that make their own food) to directly utilize the sun’s high-energy photons to reduce CO₂ essentially by adding hydrogen to it. That’s why living organisms are full of compounds containing carbon, hydrogen, and oxygen. Carbohydrates and lipids are in this category. (Proteins and nucleic acids also contain some nitrogen, sulfur and phosphorus.)

 

As pathways to utilize energy emerge, there will be competition. This is where thermoeconomics comes in. Wicken writes: “Competition among thermodynamic flow patterns expresses itself in ecosystem dynamics by imposing a condition of selection on community structures that in turn imposes selective conditions on adaptive strategies of populations. No community organization is uniquely able to process the energy made available by a given abiotic matrix. Any community is but one of many alternative solutions to the business of energy processing, and is therefore in competition with these alternative solutions.”

 

And how do we expect evolution to proceed in this case? Here’s what Wicken has to say: “Since the biosphere is a closed system, and since irreversible flows of energy through closed systems require cyclic movements of matter… ultimately all [autocatalytic pathways] must contribute to the cyclic movement of matter through the biosphere. As open systems, organisms fulfill their thermodynamic destinies by fitting into higher-order systems that express greater degrees of closure. The ecosystem, with its community structure for processing energy, is the first level of cyclic closure – cycling scarce nutrients and unidirectionally processing others, such as carbon and oxygen, which are in greater supply. Then come systems of ecosystems, in which the outflow of one is utilized as input by another. The biosphere as a whole is the ultimate unit of cyclic closure.”

 

This makes sense to me as a physical chemist. Using the language of thermodynamics allows us to deal with macroscopic-level variables without being bogged down by microscopic causal explanations. We just need to follow the energy trail! Wicken’s distinguishing the fates of C and O (and implicitly H, the most abundant element in the universe) from N, S, P, and trace metals is, I find, a refreshing way to look at the interplay of the different elements in chemistry. That’s why we have a nitrogen cycle! Cycles are fundamental to life.

 

But there’s more. Wicken writes: “Yet ecosystems are quite vulnerable thermodynamically to invasive dissipative modes – whether nurtured within the relational structure of the community or by endogenously generated parasites.” There’s a reason why life is dynamic: the second law of thermodynamics. Entropy must continue to increase in the biosphere (approximated as a closed thermodynamic system) if it is not stuck in chemical equilibrium ‘death’. This thermodynamic vulnerability of an ecosystem is a feature, not a bug, in the evolution of life. I expect this principle of vulnerability to be dominant at life’s origins, before the establishment of complex control mechanisms in organisms to stay alive.

 

As an ecosystem matures, the flows change. Wicken argues: “That mature ecosystems have lower specific dissipations [i.e., lower specific entropy production] than immature ones (higher biomass/throughput ratios) reflects the selective premium on using resources efficiently. That evolution occurs under conditions of limited resources means that it occurs under economic boundaries with limiting kinetic means of degrading energy.” What this means is that in the early immature stage, there tend to be multiple kinetically accessible pathways to dissipate energy. New pathways (the “invasive modes”) continue to emerge, essentially to expand the energy economy. But gobbling up resources leads to shortages, leading to the selection of more efficient routes – and the closing down of some pathways. This interplay leads to specialization and mutualism. Wicken writes: “In ecosystem development, founder populations of energy-intensive generalists give way to more complexly organized communities of interacting specialist populations that get more biomass for their energy dollar.” This also applies to a complex multicellular organism such as humans! Wicken argues that our natural life span corresponds to the decreasing specific entropy production from early stages of the zygote to eventual death of the organism.

 

Wicken subdivides this into three stages: (1) “In early development, an organism’s high dissipative rate and low efficiency provide thermodynamic force for the generation of organization according to its coded information.” (2) “Maturation is accompanied by decreasing specific dissipation as body size peaks and organizational networks reach their full, mutualistic complexification.” (3) “The decline of the dissipation during the aging process expresses a gradual yielding of homeostatic function… systematic losses of the behavioral and metabolic plasticity that allow organisms to accommodate environmental stresses.”

 

But why do organisms eventually lose homeostatic ability? Why can’t we stay immortal keeping ourselves at steady state and away from equilibrium? Why is death built into life? Wicken writes: “The wearout of energy-processing pathways inheres to organisms by virtue of their particular condition of closure, which is to information rather than energy.” We’ll need to unpack this statement. First, the environment surrounding an organism is ever-changing. To maintain itself, an organism needs to buffer itself against many of these changes. An energy-inefficient generalist (with lower information content) has a variety of mechanisms it can employ to respond to external perturbations. An energy-efficient specialist within a mutualist community (with higher information content) has fewer response mechanisms. Don’t forget that specializing and mutualism is to some extent inevitable because of the second law. Wicken writes: “Since success in the competition for energy flows is predicated on current adaptive payoff rather than the future stabilization of community structures, the survival-reproductive fruits of minimizing metabolic and behavioral burdens make the trend toward increasingly specialization inexorable… This essential conflict between adaptive commitment and environmental change mandates eventual extinction for most species.”

 

So on the one hand, thermodynamics drives the opening up of chemical space and encourages a diversity of structures to form. The more different kinds or types, the higher the entropy produced. And entropy must be produced for anything to proceed. Otherwise you’re stuck in chemical equilibrium – the stasis of death (or I suppose an unchanging immortality). You’re down in the (potential energy) well and there’s nowhere to go. But as you open up the chemical space and increase in complexity, specialization and mutualism kick in for increased efficiency in a climate of ever-changing resources. But specialization is also an eventual death-knell in a dynamic environment. All those command-and-control systems that emerged allowing an organism to grow (and possibly reproduce) become limiting because they are selected here-and-now and not for the future. We’re all short-termers at heart. To build robustness for the long-term requires an efficiency trade-off, and the possibility of losing the fight for resources in the here-and-now. A Catch-22.

 

Why are we in this situation? Here’s Wicken’s overaching view: “The driving force [for this evolutionary trend, in both the organic and socioeconomic realms, has been the fact that energy resources have existed in excess of their mechanisms of utilization. Evolution has been more kinetically than energetically limited. Prior to the emergence of technology, this kinetic limitation was guaranteed. Relatively small fractions of influx in solar radiation are autotrophically fixed. Of that fraction, not all can be heterotrophically utilized – the residue sinking into fossil fuel. Socioeconomic evolution has powerfully accentuated the trend toward the invention of kinetic mechanisms to create new patterns of dissipation. Econodynamics is inescapably evolutionary in this way. A caveat is that these dynamics have promoted the evolution of more highly dissipative economies by exploiting the fossil fuels that resulted from eons of surplus production of autotrophic fixation. As future socioeconomic evolution becomes more energy-limited, selection for efficiencies will inevitably reverse the historical relationship between organizational complexity and dissipation.” Humans – we’ve really changed things on Planet Earth!

 

I close this long meandering blog with closing thoughts by Wicken on the relationship between parts and the whole: “The whole is not exactly more than the sum of its parts, since parts are relationally constituted by the wholes in which they evolved… The organic world consists of just such mutually constituting part-whole relationships between individuals and higher-order flow patterns. The success of any whole is predicated on the coordination of its parts; conversely, adaptive strategies of parts are conditioned by the requirement that they participate in higher-order webs of processing energy. The information content of an ecosystem expresses this hierarchically codefining relationship between part and whole.”

Flourish & Blotts

After being less-than-impressed with the storyline of the third Fantastic Beasts movie, I felt motivated to re-read the Harry Potter series. My last re-read was 2.5 years ago before the pandemic. I’ve now finished the first three books. This time around, I felt that the writing in the first book seemed weaker and the characters more caricatured. It felt like an old-school children’s book in more ways than one. For the first time, I felt that the second book was stronger than the first, and I was less annoyed by Lockhart. Maybe I need to change my ranking of the books. The third book is still superb!

 

Today’s post will focus on things that jumped out at me in one chapter of Chamber of Secrets. “Flourish & Blotts” is the chapter title and also where Hogwarts students buy their school textbooks for the new term. Early in the chapter, we read of Arthur Weasley asking Harry all about Muggle life. Plugs and the postal service are mentioned, and Arthur thinks it astounding how Muggles have adapted to live without magic with their ingenious inventions that save time. The harnessing of electricity allows us to create devices that certainly seem magical to our forebears, and one can come up with numerous examples. It makes sense to me that if magic rides on electromagnetic radiation, electricity is the appropriate rival.

 

I hadn’t thought much about the postal service, but seeing it mentioned made me think about the advantages and disadvantages of Owl Post. For one thing, you need an owl. And it needs to be healthy enough to fly. When your owl is away, you have to wait for its return. I suppose you could go to the Owl Post Office if you don’t own an owl. How do owls locate a recipient? There must be some sort of owl-data-sharing system to improve delivery efficiency. If owls didn’t communicate with each other, I suspect deliveries would take much longer unless owls had some sort of way to “know” how to find the recipient. Can a non-owl extract information from the owl network for spying purposes? I don’t know. There is no mention of anyone attempting it.

 

In the same chapter, we read that Lockhart has assigned his seven books not just to Harry’s second-year Defense of the Dark Arts class, but to all levels. (Ginny in her first-year and the Weasley twins in their fourth-year get assigned the same books.) Clearly Lockhart isn’t a good teacher, nor has he followed any prescribed curriculum where what you learn in an earlier year scaffolds the material for subsequent years. Quirrell, in Harry’s First Year, at least assigns what seems like a standard textbook. Lupin, in Harry’s Third Year, seems to be using a standard textbook that at least contains a bestiary and he designs a practical curriculum. Snape makes reference to what students should be able to tackle in their first years when he jumps ahead to discuss werewolves later in the textbook. The Standard Book of Spells seems to have levels for each year, presumably from introductory to advanced. Reading all this made me think about how one designs and scaffolds a magical curriculum. I’ve previously speculated that Lumos should be the first spell learned.

 

To get to Diagon Alley, the Weasley family travels by Floo Powder. Harry messes it up his first time, although I don’t think it’s entirely his fault. This made me think of the various transportation methods in the magical world: Floo Powder using a fireplace network, Portkeys for one-time point-to-point travel, Apparating (including side-on), broomsticks, an enchanted vehicle (flying car or motorcycle, for example), or just plain superman-type flying. Some are teleporter-like while others require traversing at some relative speed. I’d love to have a teleporter-like mode of travel. But I’m not sure our Muggle ingenuity can get us to that point – there are some significant physical limitations.

 

When Harry lands in Knockturn Alley by mistake, and spies on the Malfoys in a shop devoted to Dark Magic objects, we read about the “Hand of Glory”. When you insert a candle, it gives light only to the holder. I suppose our Muggle equivalent is night-vision goggles. Although our night-vision technology basically tries to capture the slivers of visible light available possibly coupled with collecting light at the edges of the visible, for example in the infra-red. The Hand of Glory sounds like it illuminates the visible but only to the holder of the object. It isn’t placed over the eyes, so how exactly it would do so is unclear.

 

I was pleased that so many questions tickled my brain while reading “Flourish & Blotts”. What a wonderful name for a bookstore! And now onwards to the fourth book which is also the pivotal turning point in the series.

 

P.S. For my last read of Chamber of Secrets, I blogged about what might have been if Harry was in Slytherin.

Thermodynamic Driving Forces

In my previous post on Jeffrey Wicken’s Evolution, Thermodynamics, and Information, I discussed how he distinguishes machines from organisms. Today, I will focus on Chapter 5 of the book: “Thermodynamic Driving Forces”.

 

Wicken doesn’t like the expression “driving forces” because “it suggests some kind of external propulsion – which is not what the teleomatic directive of the Second Law to randomize matter and energy in quantum space is about.” But he admits that “the metaphor has value, since there is an internal propulsion to the emergence and evolution of life”. Note his mention of randomizing matter and energy; I’ll get to that momentarily.

 

As in previous chapters, Wicken is concise in his definitions and tells you where he is going upfront: “Evolution is about variation, the constraints under which it occurs, and its selection according to ecological success. We will be discussing the physical basis for the variation-constraint-selection triad…” So, let’s proceed with some thermodynamics.

 

For anything to proceed according to the Second Law, you need an energy source that can be utilized, and a sink to dissipate the energy (or as Wicken says, “to receive its entropic waste”). For energy to flow from higher to lower potential, there needs to be “[energy] charging of the prebiosphere to higher levels”. Once this charging is achieved, the dissipation of that energy generates molecular complexity. Carbon chemistry is particularly facile for molecular diversity.

 

What’s the best source? Photons. Concentrated packets of energy. Matter (atoms and molecules) can absorb the photon energy and become “energized” so to speak by having an electron excited energetically. Its potential energy has increased. It could release that energy by emitting a photon of the same wavelength, but more interestingly it could dissipate the energy via different pathways. It could dissipate it by making a new chemical bond between two atoms – an exothermic reaction that releases energy as heat (non-utilizable entropic waste). By forming chemical bonds, matter becomes more structured.

 

But Wicken goes further and argues that for this structuring to lead to complexification, requires that “the properties of the elements involved in the structure not be sufficient to determine that structure.” This is particularly interesting because it suggests that for complex matter to form, you need to be able to access multiple diverse structures and that there is uncertainty as to which subset of structures is actually formed. Physics and chemistry constrains those possibilities but if there is still room to play after those constraints, complexification is not only possible but it is expected according to the Second Law. Wicken says “complexity requires structure; but it also requires options”.

 

And now the crux of Wicken’s argument: “The physical basis for information is complexity. Complexity makes available different possibilities for functional interconnections. Organization can’t itself be quantified, since it reflects how well a system operates with respect to some desired output, rather than a physical property. One can, however quantify the complexity of an organization. A major evolutionary trend has been toward increased organizational complexity. The question is, does this trend result simply from selective pressures that provide ecological space for complex systems? Or is there a drive toward complexity operating in evolution independently of natural selection? Both are involved in evolution; but it is in prebiotic evolution that the drive toward complexity can be seen most clearly apart from selection, preparing the scene for life’s emergence. The operation of this drive depended on certain conditions of closure to which the prebiosphere was subject.”

 

Wicken defines information mathematically using a simple equation that mirrors Boltzmann’s entropy equation. He then divides up this “macroscopic” information into three parts: energetic (a function of internal energy), thermal, and configurational. The latter two are the “negative entropy” terms that can be calculated from statistical mechanics. The changes to the thermal contribution relate to structuring (“the movement of thermal energy from practically continuous translational modes to much less densely spaced vibrational modes”) and can be quantified.

 

Now let’s get back to dissipation. Wicken divides these into two categories: “energy-randomization” and “matter randomization”. Energy-randomization is driven by forming chemical bonds. This reduces internal energy (and its informational counterpart). Wicken states: “The result of these associations has been to reduce the number of discrete chemical entities in the biosphere and to increase their average sizes and complexities.” Where does this energy go? It is dissipated thermally.

 

Matter-randomization is the more interesting case. Essentially the more different kinds of molecules you can form, the more you can dissipate configurational information (or produce configurational entropy). Wicken uses some simple kinetic arguments to show that this must be a crucial player in any chemical reaction trying to move towards equilibrium: “Matter-randomizing considerations therefore promote all reactions through some compositional range, and reciprocally assure that no reaction can proceed entirely to completion.”

 

Once he has done this, Wicken can now track the information from all three parts through the various scenarios of prebiotic chemistry. Forming the diverse molecular building blocks of life is possible because this process dissipates configurational information. But after the divergent step comes the convergent step of forming biopolymers and other aggregates driven by the formation of chemical bonds. Wicken then discusses the constraints in play and what drives the process forward in connection with the Second Law. I feel that I’m grasping the mere edges of his argument, but I think he’s on to something compelling. I’m also biased my own research project of mapping the energetic space of proto-metabolism so I’m predisposed to his matter-randomization arguments. But I’ll need to ponder this a little longer before I can translate a Wicken-type analysis to a model system for which I have data.

How and Why

A decade ago, I read Jeffrey Wicken’s Evolution, Thermodynamics, and Information. I should say I tried to read it, but didn’t understand it. Now I’m trying again, and with some Ganti and Rosen under my belt, it’s making more sense. Like Ganti and Rosen, Wicken’s ideas were outside of the mainstream. The trio are pioneers – not understood during their time – but they’ve paved the way to a more comprehensive view of what it means to be a living system, and given us glimpses of what it might mean to transition from non-life to life.

 

Wicken’s goal is to bring together the three strands of thermodynamics, evolution, and information. Each area has its own historical development. They might make reference to each other, or more often cause confusion perhaps because we don’t quite understand any of the three well enough to forge deep connections among them. Wicken begins with the distinction between operation and genesis – essentially how and why. The two can be separated cleanly for machines: One can explain the cause and effect processes as the machine proceeds through its mechanism of operation. As to the purpose of the machine – its genesis – a reason for its existence and why it was built is external to the machine itself.

 

For an organism, on the other hand, operation and genesis are not so easily separable. We kinda sorta talk about them separately (yet in parallel), but how they intertwine is a trickier business. Wicken’s one-sentence summary: “It is characteristic of natural organizations from organisms to societies that their existences are inseparable from their operations as informed dissipative structures.” There’s a lot packed into that sentence because it adds three new pieces to the story in the last three words: information, dissipation, structure.

 

How do we even begin to untangle this? Wicken’s approach is to follow the energy flow. For that, one has to begin with thermodynamics. He will expand on this in detail, but here’s his pithy encapsulation: “All irreversible processes result from the disequilibrium brought about by cosmic expansion, between potential and kinetic forms of energy. Energy flows occurring under the impress of this disequilibrium have predictive consequences with respect to the overall form of evolution.” This will involve things I’ve mentioned before in a previous blog post: The disequilibrium comes because radiant energy from the sun hits our planet, and thanks to carbon chemistry, this energy is dissipated as heat because outer space is cold! Energy flows from source to sink with life in-between to dissipate it.

 

But the sun’s rays also fall on other planets and moons and there’s no life there that we know of – so we need to figure out how and why the environmental constraints of planet Earth allowed for the evolution of life. Thus is born a research program. I like Wicken’s description: “Research programs are conceptual spaces in which theories are nurtured, examined, and given room to grow. They can therefore only be as good as their metaphysical suppositions, which must be carefully spelled out. So too must language, terms, and definitions.” Wicken will do this throughout his book, but here’s his research program in his own words: “… to provide unifying principles for evolution – from the prebiotic generation of molecular complexity through the self-organization of living systems through their phylogenetic diversification.”

 

In discussing reductionism, Wicken writes: “Whenever one attempts to explain a phenomenon in terms of something else, it is with the presumption that the ‘something else’ is more general, more basic than the phenomenon at hand. Bringing one discipline into the explanatory orbit of the other is theory reduction… Those who believe that living systems can be explained exhaustively in terms of present physics and chemistry are ontological reductionists. Ontological reductionism has little to recommend it biologically. Organisms are organized wholes, not sums of molecular parts. The most conspicuous triumphs in the application of reductionist methodology… biochemistry and molecular biology – disciplines whose major foci have concerned the study of parts and processes or organisms in isolation from organizational settings… a willingness to whittle down the richness of the organic world to one of nuts and bolts.”

 

And this is why Wicken wants to bring in thermodynamics: “A virtue of the thermodynamic approach is that it does not lend itself to talking about chemical parts. Thermodynamics is a science of systems, dealing more with processes than static elements… Life can’t however be reduced to thermodynamics…” The second law of thermodynamics is often quoted by proponents and antagonists of the theory of biological evolution, and the common understanding of entropy relates it to order and disorder. Wicken wants to carefully define his terms and makes a distinction between order and organization. Order has to do with how. Organization has to do with why. Here is how he describes it:

 

“Organisms are not only systems of very high potential energies compared with equilibrium systems of the same composition; they are also extremely ordered, low-entropy systems. Low entropy is of itself of little biological concern [e.g. inorganic crystals are highly ordered]… Organization involves function, and the physical sciences don’t deal with function… Organized systems are characterized by structural relationships that require information for their specification… When we talk about a ‘well-organized system we are referring to how effectively it carries out certain activities, rather than to specific structural factors internal to the system. Yet, function depends on the existence of structural factors, and quantification requires that organization be looked at from their vantage point… Degree of organization would then be measured by the degree of constraint, by the extent to which interactions between components limit their individual degrees of freedom.”

 

That last sentence is essentially the thesis of Terence Deacon’s Incomplete Nature, except Wicken is both clearer and more concise despite his book being 35 years older. Wicken carefully defines constraints, and ties them to function and information. Two properties of constraints: degree and complexity. This allows him to distinguish machines and organisms: “Machines are organized for external functions, which means that their operations can be kept distinct from their existences. This allows machines to be equilibrium organizations: there is no need for them to degrade free energy to maintain themselves. This is not the case with organisms…”

 

Wicken continues: “There are two ways in which the elements of a physical system can be arranged nonrandomly. One is according to internal patterns or statistical biases; the second is according to functional considerations. The former expresses order, the latter organization and functional information. That biological organization is ordered as well as information-rich expresses a unique feature of living systems that that the machine world does not share… But at the molecular level, order and informational-richness stand in mutual opposition: order requires pattern, periodicity, or a reduction of combinatorial options; informational capacity decreases as these are imposed.” (Wicken defines order in terms of information compressibility, and complexity as “the measure of information required to uniquely specify the elemental relationships of structured systems.”)

 

Entropy lies at the heart of quantifying order and information. But like other very general concepts such as Energy and Life, it is tricky to define. Wicken distinguishes Boltzmann entropy from Shannon entropy, and discusses why they are sometimes conflated even though there are significant differences in how they are defined. (They share equations that look similar.) This provides a way to quantify the ‘how’ in terms of statistics and probability calculations, but the ‘why’ remains elusive. Wicken writes: “Information content depends on complexity but is not coextensive with it.” He will attempt to connect the how and why, but that’s the subject of a future blog post.

Space-filling

After watching the third Fantastic Beasts movie, and realizing how little of the previous movies I remembered, I decided to go back and watch them. The fantastic beasts are more interesting and plentiful, especially in the first movie. This time around, I found myself pondering the space-filling serpent. According to the Harry Potter Fandom Wiki, it is called an Occamy (and shown in the picture below from the wiki). The ability to grow or shrink to fill space is ‘choranaptyxism’, an invented word in the Wizarding World pulled from the Greek words for ‘space’ and ‘unfolding’. Why not use Latin instead of Greek?

 

Why does the beast grow or fill to shrink its space? I don’t know. Why doesn’t it do so when living in Newt Scamander’s garden of beasts? I don’t know either. Why does Newt ask for a teapot to trap it – shouldn’t any other container do? Possibly, it’s unclear. Maybe Newt says this in the heat of the moment to allow his comrades to focus on a solution. How does this beast change its size to fit its container? I don’t know, but I have speculated on what atomic-level forces might be affected as matter is enlarged or shrunk (it is more problematic than it looks). Then again, this is a fantastic magical beast so maybe the rules of ‘normal’ matter don’t apply as when you cast an Engorgio spell to make a spider larger (to Ron Weasley’s horror) or if (Marvel Comics) Ant-Man shrinks.

 

In an introductory chemistry class, students are taught that gases “take the shape of their container”. The size of the gas particles does not change. Rather, because of their constant motion, the particles whiz around to “fill” the container in their never-ceasing movement. Matter isn’t being resized as the container size changes. The pressure of the gas rises or falls proportionally as the volume of the container is decreased or increased respectively, provided the temperature remains constant (Boyle’s Law).

 

Also in introductory chemistry class, students learn different ‘models’ to represent molecules, one of which is called the space-filling model. This model is sort of like a gas-filled container except that (1) instead of gas particles, electrons are the constantly moving entities, and (2) there isn’t actually a boundary per se – the negatively-charged electrons stay relatively close to the positively-charged nucleus because of electrostatic attraction. The space-filling model comes into play because the electron ‘clouds’ on two different molecules cannot substantially penetrate each other because of the Pauli Exclusion Principle. Were molecules to meet in motion, they would bounce off each other, never passing through each other like ghosts.

 

This reminded me of a vignette in Tom McLeish’s book. Robert Grosseteste was a thirteenth century cleric who became Bishop of Lincoln in 1235. He incorporated what we would today call ‘science’ into his theological thoughts. One thing that puzzled him was the ‘solidity’ of matter. (It’s surprising that students today aren’t puzzled – it is strange!) McLeish writes: “If [Pauli Principle repulsion] were not the case then solid or liquid matter as we know it could not exist – all matter would simply pass through itself… think of a simple version of an atomic picture in which the atoms are really point-like particles – since this is the picture faithful to the ancient Greek atoms – the indivisible ones. At first it seems as if this might be a promising route to explain the matter we experience in terms of its hidden, and simpler, substructure… but in this case classical atomism doesn’t work. If we stay with the idea of point-like particles then solidity simply does not appear.”

 

Why don’t we just give up the idea of point-like particles and use ‘hard spheres’? This isn’t as easy as it looks because it still begs the question as why you have hard spheres. For that matter, classical mechanics (the stuff one learns in physics class) is predicated on using point-charges that give us beautiful and simple equations we can use! Without explaining the ‘bulk’ of atoms, we’re stuck in a circular argument spiraling into infinitesimal point-sized particles (which don’t exist). We had to wait until quantum mechanics to figure out Pauli repulsion – a good seven hundred years after Grosseteste became a bishop.

 

Grosseteste’s idea (in De luce) was to use light as a sort-of explanation. McLeish writes: “… light, unlike atoms, does possess a natural ‘extension’ – open a shutter and it streams in to fill the dusty air beyond uniformly and immediately. If matter cannot of itself (simple and without dimension) fill space, then maybe the operation of light on matter might endow the tiny particles with extension by carrying them, or somehow extendedness into them. Actually, [Grosseteste] is very careful to say that this source of corporality might not actually be light itself, but if not then something very like it… Remarkably, Grosseteste’s insight turns out to be more or less correct… light is space-filling in that it is a wave… the quantum waviness of matter allows it to be solid, and prevents my falling through the chair I am sitting on.”

 

Taking this a step further, Grosseteste “makes an extraordinary leap of imagination: he attempts to apply his theory of local matter to the structure of the universe as a whole. Beginning with a flash of light, the entire universe is filled and expanded by its self-propagation until it has reached huge dimensions. Solidifying in its exterior shell, re-reradiated light from this shell of ‘perfected matter’ then concentrates matter back towards the center, leaving the successive planetary shells in its wake, and the unrefined elements of fire, air, water and earth at the center.” It’s clever. Grosseteste comes up with a ‘Let There Be Light’ creation of Aristotle’s cosmos. As an aside, Grosseteste was also interested in how matter might manifest in different Aristotelian ‘accidental’ forms – because he was interested in how one might explain Catholic theology’s concept of transsubtantation – the bread becomes the ‘body’ of Jesus Christ in some participatory way even though it still looks and tastes like bread to the eater.

 

Is there a creative explanation for the space-filling serpent in the magical world of Fantastic Beasts? I don’t know. I’d love to get my hands on a standard Hogwarts textbook: Magical Theory by Adalbert Waffling might be one. Or maybe Newt’s textbook. But I have a feeling that the explanation will leave me wanting. Or I need to ghostwrite the book with an infusion of the magic of quantum mechanics. Quantum mechanics isn’t astrology, but sometimes feels like it. (That book has been written.) So as you’re sitting on your chair reading this, take a moment to ponder why you don’t fall through it. The weirdness of quantum mechanics that gives rise to the space-filling model of molecules gives us solidity!