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.”

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.

Animals as Gardeners

Yesterday, in my General Chemistry class, we discussed using bond energies to calculate the change in enthalpy of a chemical reaction. Breaking bonds is endothermic and requires energy input into the system. Conversely, making bonds is exothermic and energy is released from the system. Chemical reactions almost always involve both the making and breaking of bonds. Therefore, whether the overall chemical reaction will be endothermic or exothermic will depend on whether the bonds being broken are stronger (or weaker) than the bonds being formed.

 

One example I showed was ATP hydrolysis. The reaction is marginally exothermic. Even though the same types of bonds were being made and broken, the bond energies are slightly different in different chemical structures. That’s the beauty of chemistry – a subtle interplay between structure and energetics! The purpose of this example was to counter the conceptually wrong mind-worm students acquire where they tell me that “breaking bonds releases energy”. This usually comes from a simplified misunderstanding of something they hear in a biology class.

 

Towards the end of class, I couldn’t resist connecting bond energies to the origin of carbon-based life on Earth. The students had previously worked a problem on the strength of the O–H bond in water and the corresponding wavelength of a photon that matched the bond energy. Referring to the solar spectrum and ultraviolet light, I speculated about how adenine may have been important as a photon absorber prior to its role in the universal energy transduction of living systems. I mused about water-splitting, the invention of photosynthesis and suitable molecular pigments (conjugated pi-systems!) that may have arisen through chemical evolution. I didn’t say anything about such pigments dissipating thermal energy and seemingly “wasting” it.

 

This brings us to today’s question: Why do animals exist on Planet Earth?

 

This morning, I went down a rabbit-hole reading several articles by Karo Michaelian. It all started with “The Pigment World: Life’s Origins as Photo-Dissipating Pigments” (Life 2024, 14, 912). He makes the provocative claim that animals essentially “provide a specialized gardening service to the plants and cyanobacteria, catalyzing their absorption and dissipation of sunlight in the presence of water, promoting photon dissipation, the water cycle, and entropy production.” That’s a mouthful. We’ll break it down momentarily, but essentially the claim is that animals help to move molecules around, spreading them far and wide so that more and more photons can be absorbed and that energy dissipated. It’s the second law of thermodynamics in action at the level of the biosphere. And what’s the stuff we’re moving around? Pigment molecules!

 

It's an interesting argument. He begins with the argument that many leaves absorb photons in the ultraviolet and visible range before dropping off significantly at the infrared boundary. Leaves look green to us because red and blue light are absorbed more than green. Photosynthesis however only makes use of a narrow regime of red light, yet leaves strongly absorb in the ultraviolet and in the (blue) visible range. Plants evolved to absorb photons which are hardly absorbed by water, and apparently “fill even small photon niches left by water over all incident wavelengths”. That’s rather curious. Also, the albedo in life-rich ecosystems (jungles and forests) is considerably lower than in sandy deserts which reflect much more of the incident light. Additionally, “the albedo of water bodies is also reduced by a concentrated surface microlayer of cyanobacteria”. What happens to this absorbed energy? It is converted to heat – essentially chopping up a smaller number of high-energy photons into a large number of low-energy photons. It’s the second law of thermodynamics: energy is being dissipated and entropy increases mightily!

 

The evolution of these absorbing pigments in plants may have been primarily to increase transpiration. Photosynthesis is a secondary player in this regard. That’s a shocker to me. I’ve always considered the oxygenating of the atmosphere via photosynthesis to be a driver for the complexity of life – which it is – but I hadn’t thought of it as a byproduct to mostly increase heat dissipation via transpiration. In the first week of class, I told students about water’s high heat capacity and its suitability as a calorimeter. In a couple of weeks after we get through entropy, we’ll be looking at the change in enthalpy and entropy of vaporization as liquid water turns into gas. Water is an excellent dissipator that helps drive the second law of thermodynamics, but does so if there’s more of it in Earth’s water cycle. Transpiration puts more water into the cycle!

 

What do animals do? They help disperse the pollen or seed of plants. They help bring nutrients to plants through poo or death. As heterotrophs disperse organic matter, they disperse the pigment molecules. More opportunities for absorbing photons. More dissipation to high entropy heat. We animals are the gardeners, helping the second law to roll along. Humans in particular have come up with alternative ways to tap photons with inorganic materials, but that’s a recent phenomenon. The organic pigments have been at it far longer than we have. All this makes me wonder if the reason why photosynthesis is so inefficient is because life isn’t optimizing for capturing energy from photons in that way; rather it is optimizing for seemingly wasteful heat dissipation. The second law rules!

 

The tropics are rife with life. Is it because they receive the most photons? Why are there so many insects there? They’re a key part of the gardening crew. Why are there larger animals further away from the equator? The gardening crew is mostly about seed dispersal and larger creatures roam far and wide to stay alive in a less energy-rich environment. Michaelian argues that his proposal cuts to the heart of the source of evolution – the second law, a physical imperative. It cuts through the Gordian knot of biological relativity. It gets around the problem of extending the ecosystem to include more and more of its environment until it becomes an organism of sample size one where Darwinian evolution becomes nonsense. It’s an intriguing argument.

 

A linchpin of the argument is the chemical evolution of pigment molecules that absorb well in the UV-C range eventually transforming into the “broadband pigment world of today”. A specific detailed example looks at the oligomerization of HCN into adenine (C₅H₅N₅) and relies on physics-based arguments about the dissipative process after a UV-C photon is absorbed. In particular, it hinges on the photoexcited pigment rapidly reach the conical intersection that shunts it towards a particular product. There is some hand-waving about how this opens up producing a broader spectrum of molecules capable of absorbing a larger range of wavelengths in the uv-vis range. Analogies are made to how thermal convection cells arise as forces come into “balance”. Stationary states, autocatalytic cycles, and other such features are invoked. And finally, once the ozone layer built up, access to UV-C is now much reduced and therefore we’re unlikely to see life originate again from scratch on our planet. (Also, the heterotrophs will chomp up anything they can!)

 

The final kicker? If UV-C is crucial to the origin and evolution of carbon-based life, then you’re unlikely to see life evolve on systems powered by M-type red dwarf stars. That’s not good news for astrobiologists who have become increasingly interested in such systems as providing suitable cradles for life. UV-C, primarily thought of as destroyer now also takes on the role of creator – Brahma and Shiva, two-in-one, with Vishnu in between as preserver while the photon flux from our sun lasts.

 

The bottom-line of how the second law and chemistry intersect? In Michaelian’s words (from a different article): “All material will dissipatively structure, depending on the strength of the atomic bonding and appropriate wavelength region.” Funny how a first-day class exercise of connecting bond energies to photon energies might turn out to be the foundation of everything we see in our solar system be it on our living planet or our seemingly dead neighbors. I haven’t yet wrapped my head around all of this. In the meantime, I’ll just keep on being a gardener and cultivator of my students’ understanding of chemistry and its wonders. And I won’t look at a plant in the same way again!

Fuzzy Meaning

Sometimes it’s good to revisit a paper I read a while back but did not appreciate. For today’s post, that paper is “The Meaning of Biological Information” (Koonin, E. V. Phil. Trans. R. Soc. A 374: 20150065, DOI: 10.1098/rsta.2015.0065). It’s not earth-shattering, but it more than meets the eye on my second read.

 

Koonin first distinguishes coming up with an equation to calculate information from the one used to calculate Shannon entropy. Then he (correctly in my opinion) emphasizes that what constitutes information is in the eye of the beholder. Where is this information stored? The genome. No surprises there. I’d argue it’s not just the genome but the entire cell, but that’s a discussion for another day. What type of information does the genome store? What does biology want to behold? Koonin says “information about the environment, allowing the organism to predict and exploit environmental changes”. I say Amen. He goes on to say “another key part is about the (nearly) universal aspects of cellular and organismal design”. Okay, I say. But I’d say the cell is responsible for this although the genome plays a tightly coupled role in the business of living.

 

The next important observation Koonin makes is that animals and plants, the so-called ‘higher-complexity’ organisms have “the highest total information content but are also entropic genomes with a low biological information density”. Thus, prokaryotes are more information-dense. They have to be because selection is stringent for survival if you’re a bacterium or archaeum. Complex multicellular organisms on the other hand are only subject to “weak purifying selection and the high intensity of genetic drift preclude efficient purging of meaningless sequences and conversely allow proliferation of such sequence, in particular, various mobile elements”. But meaning is also in the eye of the beholder, and the question is what these mobile elements represent.

 

Koonin is going to endow such sequences with “fuzzy meaning”. Why are they fuzzy? These elements in the genome can be endowed with meaning at some point down the road evolutionary as they are transcribed. And some of them certainly are, not to make a distinct protein, but as some sort of regulatory element. This is where my limited knowledge of biochemistry hinders me from a fuller understanding. I know regulation is crucial in the living cells of extant life but I can’t quite comprehend its dizzying complexity – wheels within wheels turning every which way. Koonin helps clarify why these mobile elements might be important: “the sequences with fuzzy meaning form the material basis of plasticity from which functional molecules, primarily but not exclusively, regulators of various processes, are continuously recruited to assume better meaning.” And if you need information about changing environments around you to survive or thrive, the fitter organisms will have some plasticity as their back pocket ace.

 

What we thought of previously as junk DNA isn’t quite junk. But neither do we know exactly what it is for. It has the potential to be a useful adaptation. One example Koonin gives: “genes from selfish elements are often recruited by host organisms such that the specific activity of the encoded protein is modified and appropriated for host function”. The example I’m thinking about is how organisms coopt a poisonous molecule into a messenger molecule over time. That’s a big chunk of secondary metabolism in plants and insects, and likely many other organisms. There’s an arms race with different species employing poisons and protections. Many of the molecules we hear about that are chemically poisonous are found naturally in our body: cyanides, peroxides, hydrogen sulfide, and more. Koonin’s arguments make more sense to me now that I understand a bit more biochemistry, having forced myself to teach it last year.

 

To calculate information or ‘meaning’ in a genome, Koonin defines it as calculating the differences that could arise by comparing “an alignment of homologous sequences”. Thus, information density is relative, not absolute. I’ve been struggling to think about how to export this idea to the prebiotic molecules that I study. This is pre-genome so there’s nothing to align. But perhaps the (closed) autocatalytic set is analogous to the genome. Certainly we’d want to catalog the identities of the molecules and look at their diversity. But we’d also likely need an analog component to track concentrations of each molecule. I haven’t quite wrapped my mind around how to do this yet. It’s still fuzzy for me. And perhaps fuzzy meaning is the appropriate term to use here.

Astrobiology Frontiers

Mars gets a lot of press as the frontier in the search for extraterrestrial life on another orb. We Earthers have landed a bunch of probes, taken lots of pictures, and performed some in situ chemical analysis. We don’t know whether life existed once on Mars, although the working hypothesis is that early Mars was quite hospitable to life. The present red and rocky desert isn’t; but maybe life clings to existence in the subsurface. We have some very interesting and largely unexplored subsurface life right here on planet Earth.

 

In her recent book The Secret Life of the Universe, Nathalie Cabrol, director of the Carl Sagan Center at the SETI institute helped me broaden my frontier as to what’s interesting and potentially investigable in addition to Mars. She addresses the “veil of secrecy” of Venus and discusses possible habitable scenarios. I learned about new missions on the slate from NASA and ESA. She covers Mars, of course. But then she spends some time discussing Titan, Europa, Enceladus, Callisto and Ganymede. They’re all different, and each is uniquely interesting. I had previously heard or read about the first three as being interesting sites for finding life, but not the latter two.

 

But her book goes further afield. Ceres turns out to be quite interesting; it has geological seismic activity and possibly a liquid briny ocean beneath the ice. Pluto has “mountainous and glacial” terrain, and its partner Charon may have had a subsurface liquid ocean, I’m guessing made up of nitrogen and possibly ammonia (based on Pluto’s glaciers). I was previously under the impression that only planets in the “Goldilocks zone” of habitability where you were about the right distance from your sun to support liquid water were possible candidates for life. But Cabrol opened my gaze further afield. There could be very interesting and unique activity on a planet on a moon due to many factors, some of which might be conducive to complex chemistry arising.

 

One chapter is titled “Visions of Tatooine and Mordor”. Cabrol classifies the different exoplanets (over 5,500 and counting) into five categories, and then picks out specific examples of interest to astrobiologists. Kepler-16b is Tatooine – it has two suns. The gas giant Bespin could be Cloud City. And the ocean-world Kepler-22b could be Kamino. The interesting TRAPPIST system is also discussed. Cabrol discusses these many interesting orbs in the context of the Drake equation. Our ever-growing knowledge and discovery of so many planets, coupled with the possibility of the habitable zone being widened beyond the traditional Goldilocks parameters, suggests that E.T.’s existence is that much more likely.

 

I was particularly struck by her suggestion that “explaining the origin of life might not be enough to define it”. We’re blinkered by life-as-we-know-it, and it’s very difficult to imagine how else life might manifest. As to what it means to demonstrate the tasks of living, it may also be that “what life does is not what life is”. More questions, few answers. But it made me excited about potentially offering a course in astrochemistry. I’m certainly no expert, but it would be a great way to motivate myself to learn the material!

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.

How Life Works

In college, I thought biology was interesting, but tedious with lots of facts to memorize. I was also doing poorly at experimental lab work. Cells died under watch and I couldn’t get the data I needed. Some of my lab partners were flaky. It wasn’t the most positive experience. At the same time, I was finding both organic and inorganic chemistry intellectually stimulating! It was a no-brainer. I chose to major in chemistry.

 

Thirty years later, I wonder what younger self was thinking. Biology is fascinating and remarkable! My segue into biology began when I got interested in learning more about the chemistry of the origin of life – a complex self-assembly problem. Before long, I started to read more papers in biochemistry and molecular biology. More recently, I’ve begun to appreciate the importance of systems biology and ecological thinking. To complement the scientific articles, I’ve also been reading more big-picture books that straddle into the philosophy of biology. My most recent foray is Philip Ball’s How Life Works, subtitled “A User’s Guide to the New Biology”. 

 

The New Biology isn’t all that new. Rather it’s a shift in perspective to a more holistic view. The discovery of the DNA double-helix set biology on a path that privileged genetics over other areas. This led to significant advances in our knowledge of biology, but it also revealed the dearth of what we know about how life works. Genes turn out to be a part of the story, but not the most important part. Nature is both more complex and subtle. Today’s post will be about things that jumped out at me in two chapters from Ball’s book, “Networks” (Chapter 5) and “Agency” (Chapter 9).

 

Ten years ago, I was a fly-on-the-wall of a back-and-forth argument among several biologists about the ENCODE project. I was surprised at the vehemence of folks who thought the project was one of the most worthwhile and important things to be doing, and others who thought it was useless bunk and a waste of resources. The inner workings of the cell are not just about DNA, but RNA (all sorts of different kinds), proteins, and a bunch of other biomolecules ‘talking’ to each other, and somehow in that glorious mess doing the business of living. Ball goes through that story, and I appreciate seeing the big picture now, which I didn’t see then. We also didn’t know as much then – the growth in new biological information has been tremendous over the last decade.

 

I’m amazed by how all the different biomolecules interact with each other to do their thing. Not just one thing. Many things. Many different kinds of things. And it all looks like chaos! Molecules bump into each other, form transient complexes, and dissociate. Ball goes into detail discussing gene regulation and transcription, homing in on topologically associating domains (TADs). He calls them “ephemeral committees”. It’s as if “chromatin is a building with several floors (compartments), each with many rooms (TADs) containing separate committees. The committees have much the same membership in different cell types… molecules that are inclined to gather together. But exactly where they gather… varies between one cell and the next.”

 

It gets more complicated: TADS aren’t a “Lego-like assemblage of many molecules… like assigning everyone in a committee a specific place at the table and being unable to begin the meeting until all are correctly seated… it would take hours to get all the molecular members together in the same room and seated in the right place before any decision can be made. And this assumes that some members don’t drift away in the meantime, as perpetually restless molecules are apt to do.” Turns out the actual time spent is about six seconds, so “the committee needs to be very flexible. There might be no seating plan, nor any requirement that all members are present, so long as they have a quorum. The process may be literally rather fluid.”

 

The cell is not a factory running in what seems like organized lockstep; it’s a disorganized zoo with enclosures that are not totally enclosed. Ball highlights the potential importance of disordered proteins: “their propensity to form many indiscriminate and transient interactions with other molecules, seem to be ideally suited for promoting condensates.” I briefly discussed disordered domains in proteins when teaching biochemistry for the first time last semester, but I don’t think I really appreciate it due to my lack of knowledge. Further it highlights the incongruity between “digitally precise information [encoded] in the sequences of DNA, RNA, and proteins” that are then utilized in a “hazy environment… like telling each committee member exactly who may they talk to and what they may say, only to then create extremely lax rules about who comes to the meetings, how long they stay, and so on.”

 

Ball, however, sees an opportunity for this messiness: it’s what you need for a system to be robust instead of fragile. Ball compares it to a committee sufficiently diverse to include experts in specific areas, but also generalists, and mavens who are “good at connecting others and reconciling their points of view”. If you need “reliable generic decisions amid a tremendous diversity of experience and circumstance… lots of details [must] be weighed, filtered and integrated.” It comes down to information management and “not a concentration but a dispersal of power”. Those mavens? Their equivalent chemical skill is molecular promiscuity and leveraging combinatorial “fuzzy” logic. That’s why a “cell’s wiring can’t be compared to a complex electronic [computer] circuit”. Cell logic is wet and sloppy and needs to be!

 

Living seems to be an emergent process. Ball calls this causal emergence, and recapitulates the notion of biological relativity; no particular level of causality is privileged. The reductionist claims that all “macroscale causation is fully reducible to microscale causation”. The emergentist disagrees. One common thread in examples of causal emergence is noise reduction: “independence of the outcome on random fluctuations or chance events at the microscopic level”. The genetic algorithms and neural nets instantiated by 0’s and 1’s in a computer circuit are not like this – in fact we design them with high precision so the parts “don’t go wandering randomly out of place. But molecules do!” Ball compares the causal emergence we observe in living systems to human language, in which “meaning and indeed causal power… increase as we go up the scale from letter (or phonemes) to words, sentence, paragraphs… Zoom in on a text’s component characters and you lose all meaning.” But there’s more. Causal emergence leads to causal spreading, and Ball thinks that’s a key to how multicellularity emerged. The genomic expansion seems to be mostly in the regulatory elements. I admit that I don’t quite understand enough of the biology to grasp all this.

 

That brings us to agency. Ball’s definition: “the agent itself acts as a genuine cause of change: agents act on their own behalf.” Even in the chemistry classroom, I often use the language of agency when referring to a molecule: it wants to do something, it is attracted to something, it sees something in a neighboring molecule, it tries to lower its energy any way it can, it needs to pick up an electron, it is stable and “happy”. In the next breath, I warn my students about getting carried away with anthromorphizing molecules. Similar language is used in biology. I appreciated a footnote Ball provides from the philosopher Annie Crawford that “scientists who… consider their metaphors to be merely decorative additions that can be abstracted away from the meaning seem not to have thought very deeply about the nature of language… metaphors do real conceptual work.” I’ve become much more cognizant of this as my reading has branched into such philosophical realms.

 

Ball prefaces all this with a detailed discussion of Maxwell’s demon in the context of thermodynamics. This was familiar territory to me – an argument about the interconvertibility between information and thermodynamics. Ball then makes some intriguing and lucid statements (backed up by examples): “an organism can make use of the environment by becoming correlated with it… implying that they share information in common… such correlations become established in the process of evolutionary adaptation… [they] may also be engendered through learning from experience… it is shared information that helps the organism stay out of equilibrium… tailor its behavior to extract work from fluctuations in its surroundings… Life can then be considered as a computation that aims to optimize the acquisition, storage, and use of such meaningful information. And life turns out to be extremely good at it… The best computers today are far, far more wasteful of energy than [the Landauer] limit [apparently six orders of magnitudes more, compared to one order of magnitude in cells]… biology seems to take great care not to overthink the problem of survival.”

 

Mind blown.

 

Ball says that “having a mind is a good adaptive strategy for an organism that experiences a very complex environment”. The alternative of trying to “equip the organism with a suitable automated response for every stimulus it is likely to encounter”. That might work for something with limited functionality, but to be robust in a complex environment requires… well, you can see the challenges with automated-driving cars, and even then they only have a very limited function in the grand scheme of things. It’s amazing what our human minds can do. Ball thinks that it’s okay to bring the language of purpose back into evolutionary biology. He thinks the reason why biologists are uncomfortable is because biology “can’t deal systematically with agency and so has to infuse it into entities as a kind of magical capability… that arguments about human free will persist (often rather tediously) because we lack any account of how agency arises.”

 

It's clear I don’t really understand biology. Perhaps, like quantum mechanics, no one does. But I appreciate Ball provocatively pushing me to think both broader and deeper to do so. I think I understand a lot of chemistry, but maybe deep down I really don’t. The wonderful thing about being a teacher is that every now and then I have a small panic when I anticipate a profound question a student might ask in class (the reality rarely happens) and do a quick frenzied search about some conceptual underpinning. Inevitably, I learn that the concept is both complex and subtle; then I come up with a good-enough arm-wave explanation which I rarely have to use. But it’s the asking of deeper questions that matter, so I’m glad that I continue to ask them! How Life Works is thought-provoking in such a way that I will be re-reading it, just like Ball's book on quantum mechanics.

Theory of Learning and Evolution

I recently read three papers by Vanchurin (and colleagues) that builds a theory of learning and illustrates its generality in reference to machine learning, biological evolution, and the (presumably physico-chemical) origin of life. Math is involved, and I found some parts can be difficult to follow. But the writing is clear and the progression of the argument methodical. Today’s blog will only focus on one of these, the most conceptual of the three: “Toward a theory of evolution as multi-level learning.” (PNAS 2022, DOI: 10.1073/pnas.2120037119). I will be quoting the paper often my paraphrases will be clumsier than their clear prose.

 

What drives evolution in biology? Essentially, “solving optimization problems, which entails conflicts or trade-offs between optimization criteria at different levels or scales, leading to frustrated states…” There are three important pieces here: (1) optimization, (2) an interplay of distinct timescales in a hierarchical system, and (3) non-ergodicity that arises from competing interactions (the “frustrated states”).

 

The paper begins with seven basic principles. The first, and most important, is the existence of a “loss function of time-dependent variables that is minimized during evolution”. To stay alive is to solve an optimization problem. There needs to be some sort of learning that comes from an organism interacting with its environment. And when you’re dealing with the open unknown, the best solutions we know of involve “implementation of a stochastic learning algorithm”. Thus, learning and evolution are “optimization by trial and error”.

 

The next three principles, still very general, cover the following:

·      There’s a “hierarchy of scales”, each of which has its own “dynamical variables that change on different temporal scales”.

·      These timescales are distinct.

·      The faster-changing variables can be statistically defined by the slower-changing ones. (In thermodynamics, we can use macroscopic parameters to encompass the cacophony of the microscopic world.) This is known as Renormalization.

 

The final three principles are more specific to the living systems of Planet Earth, a sample size of one. “Evolving systems have the capacity to recruit additional variables that can be utilized to sustain the system and the ability to exclude variables that could destabilize the system.” Replication plays a key role in this process but requires the sequestering of “information-processing units”. Finally, there is two-way information flow between the slower-moving information units and the faster-changing data-collecting parts that interact with the environment. This, essentially, is learning how to stay alive.

 

What follows is an exposition of ten “basic phenomenological features of life” which the authors link to their theory of learning. I won’t go into these one-by-one, but rather pick out the concepts that I thought noteworthy. Let me preface this by commenting on the existence of a multiscale ‘situation’. It’s physico-chemical. The universe, and by extension Planet Earth, is made up of a mixture of multiple substances, which consists of molecules, which consists of atoms connected by vibrating bonds. Everything is in motion – it’s a dynamical system – but the timescales of motion are vastly different. Chemical bond vibrations are in the pico to femtosecond range. Molecules diffusing and colliding may be in the micro to nanosecond range. Nerves might pulse in a tenth of a second. I measure my time usage in minutes.

 

The inevitability of multiple distinct timescales is that different processes will ‘compete’ leading to frustrated states. But in addition to temporal frustration, there is also spatial frustration. This leads to a balance of sorts – an equilibrium, so to speak, but one that is semi-stable and may shift as the environment changes. Living systems that sequester their slow-changing informational systems that provide some organismal stability must continually receive and adapt to information being relayed from faster-changing ‘detector’ systems that interact directly with the environment. But neither of the two is privileged. It’s hard for us to think about this because we’re used to linear thinking of cause followed by effect. The lines of communication go both ways – a complex system where separation of the parts leads to death. You can’t separate the function of an organism from its genesis.

 

As to trial-and-error learning, the problem is it guarantees “neither finding the globally optimal solution nor retention of the optimal configuration when and if it is found. Rather stochastic optimization tends to rapidly find local optima and keeps the system in their vicinity”. Frustrated competing variables keep things that way. Not a necessarily bad thing since the environment will change. That’s why “biological evolution comprises numerous deleterious changes, comparatively rare beneficial changes and common neutral changes” that explain genetic drift, according to the authors. The diversity of local optima that arise from nonergodicity is why “evolution pushes organisms to explore and occupy all available niches and try all possible strategies”. We should expect a “diversity of solutions”.

 

Why do parasites show up? Diversity means that entities will arise that “scavenge information from the host” and “minimize their direct interface with the environment”. This may lead to symbiosis, but it might not. Competing imperatives are always in play. Why is there cell-programmed-death? There is an overall loss function to be minimized (the first principle!) and in a multicellular system, the tug-of-war between different scales could well result in reducing system failure by having individual cells (that have naturally accumulated problems – thanks, entropy) die off for the greater good.

 

To illustrate all this, the authors set up a (learning) neural network that has variables in different timescales. Some are ‘trainable’, others are not. There’s a logic to how they assign organismal versus environmental variables, and also how they divide the slower-changing variables into ones where changing them can be deleterious, neutral or adaptable. I won’t go into the math. Their conclusion: “slow variables determine the rules of the game, and changing these rules depending on the results of some particular games would be detrimental for the organism”, so it’s better to have “temporally stable rules” rather than an unconstrained optimization. But in the background, some of these rules can change. And as optimization continuously occurs dynamically, an environmental change may lead to a successful adaptation. Or it may lead to system failure.

 

Most important to me were the crucial setup of a system containing within it processes with distinct timescales, the inevitability of frustration, the role of renormalization, and determining what an appropriate loss function should be. The chemical systems I study (for which I build thermodynamic and kinetic maps) are likely too small. I’ve used the maximization of free energy reduction as the function to optimize, but perhaps I need to broaden or subdivide this into several mini-loss-functions. One of the papers that I didn’t discuss today goes into thermodynamics at a more general level and tries to connect it to the origin-of-life. They’re at a very abstract level, and the question is whether I can use their framework and fill in the details. It’s what keeps research interesting!

Poison to Protection

If you’re paranoid of being poisoned, one possibility is to build immunity. Folklore suggests one king Mithridates of Pontus did just that. He’d take small doses of arsenic amongst other poisons and build up to larger doses, all while fighting Pompey and the Roman empire. An internet search for “arsenic eaters” will lead you to several articles about the famed Styrian arsenic eaters, a small community of Austrian peasants who were tested by consuming arsenic on food and seemed not to suffer any ill effects.

 

If you’re interested in the history, there is a very readable and relatively short article available on JSTOR by John Parascandola: “Pharmacology and Folkore: The Arsenic Eaters of Styria” (Pharmacy in History, 2015, vol. 57, no.1-2, pp. 3-16). I learned that arsenic was considered a possible medicine and cosmetic. I suppose that in low doses it would kill pathogenic bacteria and other microbes that might cause skin blemishes. I learned that the “Styrian defense” was used in murder trials: claiming that the victim regularly consumed arsenic, and perhaps took too much in a fatal dose. I learned that some indigenous populations in the Andes had an arsenic-metabolizing gene, likely from long-term generational exposure to higher arsenic concentrations in the water. And folklore-wise, I learned about a legend of “poison maidens” from India – assassins who could kill you with a kiss, having been “fed poisonous plants and venomous snakes form infancy, becoming immune…”

 

Since I’m interested in the origin of life, and I taught a special topics class on “Metals and Biochemistry” last spring semester, I now pay attention to chemical evolution arguments on why certain substances arrived “later” on the scene. New signaling pathways came into play as eukaryotes and multicellularity came into the story of life on Earth. Why is Mg²⁺ mainly internal and associated with phosphates and nucleic acids, while Ca²⁺ is mainly involved in extracellular signaling? Why are zinc and copper latecomers in various enzymes, nickel and iron are early, and molybdenum shows up somewhere in between? One of the reference books I used in class was The Biological Chemistry of the Elements by R. J. P. Williams and J. J. R. Frausto da Silva. So, I decided to read selections from their companion book, The Natural Selection of the Chemical Elements.

 

While skimming the book, I started to be intrigued by the idea that certain substances that were poisonous and deleterious to early organisms, eventually became incorporated into living systems. This popped up throughout the book, but comes together in the final summary chapter in a section (16.3) on “The environment and evolution”. The authors pose the question: “Did the change in environment drive the evolution or was there just random searching?” They provide a compromise answer in two parts: “(1) a poison, of necessity, gives rise to protection from it; (2) a protection can give rise to functional use so as to increase survival.”

 

Here's my summary of their argument using quotes from the text: “The protection against the poison involves at first greater production of the protein system most useful in handling this poison…” Inorganic poisons result in “sequestration and rejection” by pumping out the bad stuff. Organic poisons are destroyed by enzymes. “Thus, a poison increases the turnover of certain RNA (and proteins) and therefore of exposure of local regions of DNA.” This “exposed” DNA is “more liable to mutation, [thus] selection could drive improved protection… [locally] within that short section of the code… with little effect elsewhere on the DNA. The step from protection to functional use follows the same pattern since protection involves handling the elements and requires knowledge of poisons within the cell. The obvious step is to make the poison an extracellular messenger or part of an enzyme.”

 

As I’ve studied autocatalytic cycles to understand how proto-metabolism arises, I had mainly focused on what substances are favorably incorporated and why. I’ve thought about evolution and system expansion from the point of view of protometabolites acting as catalysts, crummy at first but with increased selection better catalysts persist. I had considered molecular parasites – things that reduce the stoichiometric factor to maintain autocatalysis – but I hadn’t thought about the role of molecular poisons. What if certain nitrogenous compounds were initially “poisonous” in some way (as many are still today)? Perhaps some of these compounds, as they were recognized as such, were then turned into messenger-type molecules which catalyze other reactions to allow system expansion? This is an interesting idea fomenting at the edges of my thought process. I’m not quite sure whether this idea will lead to something concrete I can test, but I’m now reciting the mantra “poison to protection”. And now I get to do more research!

Command Copy

Moving animals do a funny thing. I call it Command Copy. In Chapter 12 of An Immense World, Ed Yong explains: “When an animal decides to move, its nervous system issues a motor command – a set of neural signals that tell its muscles what to do. But on its way to the muscles, this command is duplicated. The copy heads to the sensory systems, which uses it to simulate the consequences of the intended movement. When the movement actually occurs, the senses have already predicted the self-produced signals that they are about to experience. And by comparing that prediction against reality, they can work out which signals are actually coming from the outside world and react to them appropriately. All of this happens unconsciously, and while it isn’t intuitive, it is central to our experience of the world.”

 

This is also why you can’t tickle yourself. Unless you have certain types of schizophrenia that may also predispose you to ‘hearing’ voices and ‘seeing’ delusions. It’s possible that in these cases, something goes wrong with the copy command or with the sensory apparatus. There are two types, as Yong explains: exafference refers to signals from the external world, while reafference refers to signals from the organisms’ own actions; “think of them as other-produced and self-produced”. The crux is that “these signals are the same from the point of view of the sense organs”. Apparently, Command Copy is how pretty much all organisms resolve this dilemma, which is a rather interesting fact.

 

Most of us humans are conscious of the act of making predictions. Our brain seems to have evolved to be an advanced-prediction organ. Consciousness seems to be built, or at least follow analogous rules to Command Copy. One might argue that sensing one’s environment and being able to react in a life-saving way to it (eat food! avoid poison!) is the basis of building a life-form that ‘survives’. To sense one’s environment, it must be able to distinguish self from non-self (the environment). It’s why we think of the simplest organism as a cell with a boundary – a cell membrane at the very least. (These ‘simple’ organisms are biochemically complex when you zoom in and try to elucidate its inner workings.)

 

While organisms have receptors that can respond to single photons or single molecules, by and large organisms react to analog rather than digital signals. Only when a certain threshold concentration of molecules has been ‘detected’ is a response elicited. While response to photon seems digital in that very first detection step, it is almost always coupled to an analog chemical (molecular) signal. Why is this? I’m not sure exactly, but I think it has to do with scale. To complexify, which inevitably involves a division of labor so that different molecular machines carry out different tasks, one has to increase in size. To maintain a certain semblance of stability (to ‘persist’ and not die or be dissembled), you can’t be so sensitive that a single stray molecule or photon disrupts your entire existence. By becoming multiscale, you buffer yourself against such indignities. But by becoming complex, you run the risk of system failure – hard to diagnose because complexity ties things together in circular Gordian knots.

 

As an origins of life researcher who studies protometabolism, this idea of Command Copy is fundamental to autocatalysis. There needs to be stoichiometric increase to grow in size and scale, a necessary ingredient for complexity (and survival). Hence, I’ve been examining reactions that do this at a simpler molecular level in a few steps. And what is exciting to me is that baked into these simple autocatalytic cycles is the potential (perhaps inevitable if an energy source and molecular food sources are available) to expand towards complexity. Command Copy in a sense is the heart of it all, although I’m still struggling to map my chemical level ideas to organismal level responses that Yong describes. There’s likely a continuum that connects these, and it’s what keeps me intrigued with research and the quest for answers to difficult questions!

 

P.S. An Immense World has been a marvelous catalyst for encouraging me to think deeper thoughts. Here are my previous blog posts on Yong’s book.

·      Magnetoreception

·      Body Electrolytic

·      Umwelt