Life From Parts and Silos


When we think about the world and how it is composed, we tend to think of it in parts and silos. In other sections, we have looked at what science can tell us about the fundamental structure of the world. Quantum Mechanics is the field that gives us the best account of this, as far as we know.

What we find when we look into the quantum regime, is that parts are not always easy to define, in the way we might think. Some systems, behave as if the spacelike separated 1parts, are actually somehow connected in a non-physical or non-local way. This is called entanglement, and it is at the heart of what makes the quantum seem so strange to us.

You might think that as long as we focus on the world, at human scale, and ignore the strange happenings of subatomic particles, that we should be able to go back to easily defining parts and silos. It turns out that this is not necessarily the case.

At the scale of human experience, we have many areas wherein the hierarchy of parts, doesn’t always make sense. Further, we have several issues where the very concept of parts becomes murky at best, and downright mystifying in some instances.

Life From Parts and Silos

What Parts Create Life?

In 1944 Erwin Schrödinger published a book titled “What is Life?” (The Physical Aspect of the Living Cell). Many years prior to the discovery of DNA, Schrödinger conjectured that life was a system that consumed what he called “negentropy” to maintain itself, and used an “aperiodic crystal” to store and transfer information about itself. He was shockingly on the mark, especially when you consider that his day job was inventing quantum mechanics, and threatening cats with superposition. Schrödinger was a genius who thought out of the box, and was even prescient well beyond his field of expertise, and yet the essence of life, still eluded him.

NASA has teams of biologists and engineers pondering the question of what life is, and how they can detect it, with probes on other planets.

When it comes to life, it seems the most common definitions we tend to produce, are evermore refined lists of parts. We might say that life is based on DNA, or RNA, so those are parts of life we can look for. We might say that life is about CHNOPS, not the cheap airplane booze, but Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous, and Sulfur. These are six of the most important elements we find correlated with life on earth. So, is that life itself? Only the most alien observer devoid of a soul, metaphorically speaking, would claim that it is. That said, we can clearly assert that though no list of chemicals seems to be life itself, there are many kinds of parts that seem to go along with life. What should we make of that?

Does Life Create a Special Kind of Whole, from Separate Parts?

It seems that what we find with life, is that the structures that matter most, are not made of matter, themselves. They are not so much the physical parts, but the dynamic relations between them.

There is an interesting way to consider life, which is more through the lens of “Structural Realism”. James Ladyman has been a proponent for this kind of approach, in terms of the metaphysics of science etc. (particularly a brand known as OSR or Ontic Structural Realism). Here I am referring to a more general sense of structural realism, that, whether ultimately true or not, may be helpful in reformulating the way we think about life and its origins.

The basic premise is that what really matters and what is actually the most “real”, are in some sense the structural regularities, rather than any of the individual parts. This is a kind of thinking that is being applied to some puzzling questions in the foundations of science, such as in quantum mechanics. One might ask if an approach based less on parts, and more on structured regularities, might also be helpful when thinking about life.

To be clear, this not to say that life is quantum, or that quantum is equal to life, even though we do see quantum effects used in bird migration and in photosynthesis, for example. What I’m suggesting is more in the sense of taking an approach that views the structure of observed regularities, to be something more “real”, than we might ordinarily think. Something distinct from the parts, but no less “ontic”.

When viewed from that perspective, life becomes more about a dynamic pattern, that creates the relationships between the inert parts. To put it another way, it may be impossible to find or define life in terms of parts, and yet we can be confident that we will find certain kinds of relationships between parts, wherever the dance of life arises.

It could be that by focusing on DNA, or cells, or hemoglobin, or amino acids, that we might be missing something essential. We could lose sight of the strong hints that the essence of life, seems to be that it takes parts, and involves them in a dynamic dance, that makes them function as a whole.

The seeming whole of the body, is really, in some sense, a biological shadow, of the real thing, which is the dance between the parts. In other words, we may be looking for static parts, all the while the only parts that matter are the dynamics themselves.

There are several new lines of inquiry, and research programs, that have emerged in recent years, for thinking about the question of life, and the wholeness of systems more generally. Next we look at one such example, that can help to get a sense of these issues.

Assembly Theory

One of the most promising developments, in the quest to define life, is known as Assembly Theory. This new approach to life and complexity, is spearheaded by Sarah Walker of Arizona State University (a physicist turned Astro biologist) and Lee Cronin from the University of Glasgow (a chemist, coder, and roboticist). Together with their research teams in the United States and Europe, they have started to point their finger at a particular way of viewing the questions of life, that may turn out to be invaluable.


The basic idea is that each form in the universe, that is not fundamental, must in some sense be assembled. As far as we know, particles, like electrons, are treated as excitations of a fundamental quantum field. This means that in effect they don’t require any “assembly”. In contrast, something like a dolphin, does not seem to pop out of the vacuum fully formed, on a regular basis. If it did, SeaWorld would be in trouble, and we would need to have inflatable pools blanketing the earth, to catch poor flipper, if he should ever spontaneously materialize over your driveway.

Obviously, dolphins popping out of nowhere isn’t what we observe, but this goes to a serious point. Everything we do observe, that cannot essentially pop out of the vacuum, must be assembled, and it is this process of assembly, particularly regarding complex forms, that begins to shed some light on at least a corner of life’s mysteries.

Assembly Path

If an electron needs no assembly, but a dolphin presumably needs tremendous amounts of assembly, how does the universe know how to assemble a dolphin?

There is something subtle in that question to pay attention to. Notice that here I am not asking, how “life” assembles a dolphin, or how “DNA” assembles a dolphin, but rather we are zooming all the way out, dropping a number of standard assumptions, and just asking the general question. How do complex forms come to be assembled in the universe, repeatedly, where the second law of thermodynamics tells us that disorder is increasing asymmetrically, in the direction we call “the future”?

The intuition of Assembly Theory, is that there are often many paths to get from some starting state, to the fully assembled form. Some forms will not have that much difference between the paths that can assemble it. A hydrogen atom, for example, consists of one proton and one electron. It is the simplest atom in the periodic table of elements, and the most abundant element in the universe. Nature seems to assemble hydrogen incredibly easily, and so it’s everywhere. For something like hydrogen, we don’t learn much from its assembly path. Said another way, the assembly path to hydrogen is so simple that it would be virtually impossible to distinguish hydrogen “assembled” by the early universe, v hydrogen “assembled” in a university laboratory.

In contrast, when we think of the case of the dolphin, we are dealing with a form of such incredible complexity, that it’s assembly seems to require an entirely different kind of explanation than hydrogen. Such an explanation may, even, require some new view of physics, that fits what we know, and yet also extends the operation of the universe in novel ways.

Combinatorial Space

Combinatorial space is an abstract way of thinking of all the possible combinations, as if they were laid out in space. In this way, we can talk about regions of combinatorial space like regions of a country. We can talk about distance between combinations, like having to take difference routes and vehicles, to get from your couch to the coast of France.

Assembly Theory, is a way of rigorously quantifying and evaluating the paths through combinatorial space, that can result in the assembly of the relevant form.

What becomes crucial, is the recognition that very complex forms such as dolphins, and babies, and even planes etc., are at places in combinatorial space, that are seemingly impossible to reach randomly. Random generation of complex forms, is made even more implausible when you consider forms such as plants and animals, that are produced with high degrees of repetition and regularity, at least from the human scale experience.

So, this suggests that when we see forms above a certain level of complexity, there are likely to be many paths to assembly, that are unimaginably sinuous and labyrinthine. In contrast, there may be other paths that are radically more efficient and straightforward.

Though not directly a part of assembly theory, we can use cellular automata to demonstrate something stunning that assembly theory seems to be honing in on. If you do a search for rule 30, or rule 110 cellular automata, you will find two excellent examples of the point I’m speaking to now. The basic idea, is that a system such as a rule 30 cellular automata, generates forms that are so incredibly complex and random, relative to the minimal rule set. In a way, it doesn’t seem “fair” in the sense of being plausible, that such a minimal program could “assemble”, such a complex form.

The insight, here, is that there are many ways to code all kinds of rules for different programs, that could generate output similar to a rule 30 or rule 110 cellular automata. The crucial point is that the overwhelming number of those other programs would be so much longer and less efficient, compared to what the minuscule rule 30 or rule 110 programs can already generate.

So, the takeaway is that there are some programs that generate seemingly radical complexity from minuscule inputs. This gets to the heart of what Lee and Sarah are pointing to, in the world of biology, outside digital computing.

One of the suggestions of Assembly Theory, is that the regular production of forms, i.e., combinations, above a certain complexity, requires something akin to “life”, to find those most efficient paths to assembly, and to repeatedly assemble complex forms.

Chemical Space

There appears to be an inseparable connection between life and chemistry. For the first time, perhaps, Assembly Theory seems to put the connection between life and chemistry in more of a natural context. Here the connection is treated less as an intrinsic aspect of life itself, and more as a scale that allows for the first major combinatorial explosion. If you think of starting at the scale of electrons and quarks, there are not many combinations that can be made. We have less than 120 distinct atoms in the periodic table of elements. Sure, there are many other isotopes that can be created by changing the number of neutrons in the nucleus, but that still is nothing like the dramatic expansion of options, that comes when you start putting separate atoms together.

Chemistry is the scale at which we deal with combinations of atoms, which form molecules. Stuart Kauffman has a saying that “history enters the picture, above the level of atoms”. What he means by this, is that up to the scale of atoms, nature can randomly create much of what we see without much difficulty. Some heavier elements, such as iron, will take several generations of stars to produce, but even that is no big deal to a vast universe with all the time in the world.

What becomes striking, is how radically the space of possible combinations expands, as soon as you go above the scale of single atoms. Just as a quick example, there are bio molecules with 200,000 separate atoms. Imagine that all the universe did, every second since the Big Bang, was to take the six CHNOPS elements (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), and create 1 new combination every second. This would be 6 elements to the 200,000 slots in the molecule. That number is so astronomically massive, that the universe would not even have scratched the surface of exploring that combinatorial space, even millions of years from now.

So, this changes how we think about life and chemistry in some sense. Life, in this case, is not really seen as a byproduct of chemistry, as it usually is. Instead, chemistry is seen as the grounds for enabling the expansion and exploration, of much larger combinatorial spaces. In this way, it makes chemistry more separate from life in principle, while also explaining why life and chemistry seem to go hand in hand, in practice. In short, it is not about the chemicals themselves, but about the expansion of combinatorial space they facilitate, above the level of atoms.

Counterfactually, one can suggest that if our universe had different constraints, life would appear much differently as well. We could have a physics wherein the fine structure constant was different. Maybe there could have been different kinds of bonds that could form between subatomic particles etc. In those cases, we might expect to see signs of life, not at the same scale as in our universe. We might instead see life at much larger or much smaller scales. The key insight is that it would be about the scale that allows for the right kind of combinatorial explosion, rather than any particular substance.

The chemist, Lee Cronin, has created a robotic laboratory and a computer language called “Chemputation” that allows for the automatic translation of code into chemistry. By doing this, Lee and his collaborators are allowing us to explore chemical space in a radically different way. For the first time it really allows us to start operating on the information embodied by the chemistry, rather than being stuck having to always deal with the properties of the chemicals, as the primary leverage point for intervention.

In many ways, this is a new kind of telescope or microscope. Telescopes helped us to see the distant stars and planets. Microscopes helped us to see the world of microbes and viruses, hiding in plain sight. These examples show that there are often other ways of “seeing” the world, that provide new answers and prompt new questions.

It was hard to ask questions about the cosmos when all we could see was the moon. Eventually, all that looking up at the sky, through ever increasingly powerful telescopes, lead to putting a man on the moon in 1969. Eventually, we even sent our “eyes” to the cosmos, in the form of the Hubble and more recent, James Web telescopes. It’s hard to treat and prevent the spread of disease, when all you can see are the human scale symptoms. Only once we started to really peer into the micro world and tinker around at that scale, did we gain a true appreciation, for what causes disease and how to treat and prevent it.

Almost no two scientists will agree on their definitions of life. That said, one sentiment that would probably garner near universal agreement, is that we’ve been looking in the same places for a long time, and still haven’t found the essence of life. It could be that phenomena such as life, which tend to involve astronomical complexity and information processing, cannot be “seen” with the tools we have, either theoretical, instrumental, or analytic. Life itself may be a kind of phenomena, that ironically is far beyond the scale at which humans experience their own lives. We may be like ancient people thinking that evil spirits spoil food, and make people sick, instead of microbes and viruses. So often, we do not know what we cannot see.

It’s possible that one of the first steps to actually answering these profound questions about life and how it assembles parts into wholes, is to start “seeing” life, more as it really is, and less in the mold of our human centered narratives. One analogy that I am fond of using, is to say that I think what we call “life” might actually be like the “shadows” on that wall in “Platos Cave”. We see the shapes and the movement of life, but we may be chained, as it were, and unable to see directly. We might be tethered to a particular scale of time and space and energy and computation etc., that until now, has precluded us from ever actually “seeing” “life” itself.

So, a striking conclusion that one may come to regarding questions about the essence and origin of life is the following: Maybe the deepest reason we can’t explain the origin of life, or define it with clarity, is that we have literally never even “seen”, life, on its terms. So, how would we expect to describe something we’ve never truly witnessed?

Closing Thoughts

Perhaps we have never even “seen” life, but have only glimpsed its shadow. This may sound preposterous. Surely, you might say, ‘but I am life, how can you say that I haven’t seen what I am?”. Well, seeing what we are, and what really exists, tends to be a constant struggle, not just for the sciences, but also for matters belonging squarely within the domain of the human experience.

If you genuinely believe you know precisely what you are, or even who you are for that matter, there is an excellent chance you’re an absolute sage, or a typically self deceptive human, like the rest of us.

To cast this in a more clear light, obviously our ancestors stretching back through time, all were “life”, and yet prior to sometime around 1953, they had no idea what DNA was. So, in one sense, of course they knew what life was because they were participating in the dance of life. On the other hand, of course they didn’t know what life was, if they did not even know the double helix form, of nucleotide rungs, between sugar-phosphate rails, twisted beautifully like a spiral staircase, that form we call DNA. Prior to the invention of the microscope and the discovery of the microbes and viruses and cells, our ancestors had absolutely no idea how so many core aspects of life and biology could function. There are so many other examples I could list, but hopefully, you get the point.

There is a saying / aphorism attributed to Lucretius, that goes something like this. Everyman thinks the tallest mountain that CAN exist, is the tallest mountain HE has seen. I emphasized some words to draw attention to how much our perception of the world is driven by personal narratives. So, often we find ourselves in the same role as the foolish man described by Lucretius.

When we speak about the origins of life, are we not just doing a modern version, of deciding how tall mountains can be, based on only the mountains we have seen? Are we not deciding that life must be DNA, and cells, and metabolism, just because those are the “mountains” that science, in our era, has enabled us to see? Surely, we are doing this collectively, even if just to some degree. If, that is the case, as it has been throughout all known human history, then what seems ludicrous at first, becomes almost entailed just by the logic.

We are only now arriving into an age where computation, artificial intelligence, robotics, physics, mathematics, philosophy, biology, etc., are getting to a point of maturity, that allows them to connect. Finally, we can start combining them in interesting ways, to ask some very different kinds of questions. Perhaps questions about Assembly Theory are a step in that direction.

Maybe we really need new tools and methodologies and philosophies, to even be able to peer at life in its native space. A space which, paradoxically, may not be the physical space of the human experience, but may be the combinatorial space where Sarah and Lee, are just beginning to explore, in an automated and scalable way. I for one, can’t wait to see what new “mountains” they find on the road to assembling life.

  1. Spacelike separated, means that two events are so distant in space, that an influence would have to travel faster than light, in order for one event to causally effect the other. Timelike separation means events are close enough for influences to connect them below light speed. Lightlike separation means that an influence traveling precisely at the speed of light “c”, could causally connect both events, but not an influence slower than c. ↩︎