New Thinking About the Origin of Life (2): Catalysts and Containers

Jeremy Sherman’s book, Neither Ghost Nor Machine: The Emergence and Nature of Selves, describes Terrence Deacon’s theory of how, from lifeless chemical reactions, self-generating arrangements of molecules might have emerged that led to the first living cells. In the previous post I summarized highlights of Sherman’s description of purpose and self-ness as the distinguishing features of not just humans but of all living things. All living cells—as selves—share three abilities: self-repair, self-protection, and self-reproduction. Ordinary chemical reactions lack all three and soon fizzle out, their components lapsing into the disorder that overtakes any reaction that cannot sustain itself long enough. What kinds of reactions could come together to meet that requirement?

Catalysts are part of the story—perhaps even the heroes. Catalysts are substances that speed up a chemical reaction without themselves being altered. Sherman compares catalysts to a wheelbarrow used “for hauling gravel over a hill. Without the wheelbarrow, it takes a lot of work to move the gravel. With it, the gravel moves more efficiently and the wheelbarrow isn’t altered in the process. Its presence therefore reduces work, haul after haul” (140).

An example of catalysts that we put to use most days is the catalytic converter built in to the exhaust pipes of our cars. The converter consists of metal plates coated with a catalyst such as aluminum oxide that converts the engine’s polluting exhaust that flows over the catalyst into carbon dioxide and water that comes out the tailpipe. The catalyst itself is never used up.

Now imagine this: chemicals A and B, helped along by catalyst X, react to form a compound. Catalyst X itself is not used up; it continues to speed the reaction as long as sufficient A and B are around. Now assume that the compound produced by this reaction is X itself, the same chemical, Catalyst X, that boosted the reaction. The result? The total amount of X—the original amount that never diminishes plus the added amount produced by the reaction—increases rapidly. This is autocatalysis (stress on tal), a sequence, a chain of reactions, in which a chemical reaction happens to produce the catalyst that stimulates the reaction itself. Autocatalysis takes many forms, with different reactions producing various compounds and catalysts, sometimes in a sequence but always coming full circle to add to the existing supply of catalyst.

Now “Imagine,” Sherman writes, “autocatalysis occurring within a container. It would look a little like a very simple cell—a chemical population explosion occurring within something like a cell membrane….Imagine that one of the autocatalytic by-products was a capsid molecule [a protein that forms a shell, usually around a virus],… yielding a container” (152). Deacon calls these proto-cells autogens—self-generators.

Still, container or not, even autocatalysis winds down when it runs out of fuel. The key to Deacon’s theory is that another reaction takes place to constrain the autocatalysis and resupply it. Moreover, this second reaction would also fail at some point were it not also constrained in turn by the renewed catalytic cycle. The second law of thermodynamics wins if a reaction or the structure of something is left to itself; things come apart, break down, disperse. But if two reactions are such that they stop each other and resupply each other before one fizzles out, the second law must come back another day.

The formation of the container is the second reaction here and the container will sooner or later break apart, perhaps after a large molecule bumps into it. When that happens, the capsid molecules that form the container will drift away, the catalysts inside the capsule will come in contact with new reactant molecules in the environment, the reactions will produce more capsid molecules which will in turn form containers around new clusters of reactants and catalysts. In this way, at this stage in their cycle, the autogen as a whole has repaired and renewed itself. The cycle seems complicated, but the following video illustrates it well.

Terrence Deacon, Origins of life, Autogen Demonstration – YouTube

A five-minute animated video about Deacon’s autogens (“autocells” in the video).

 

 

 

 

 

This cycle of closed container-open container-closed container sound far-fetched until we realize that it’s a pattern that echoes through the living world. Sherman points out that the cycle parallels that of a plant’s protected seed that opens to release an array of molecules that regenerate and arrange themselves again into plants that produce new seeds. “In a very loose parallel, a sunflower isn’t the seed phase or the plant phase but the complementary tendency to alternate between the phases. The autogen is even a little like the chicken and egg. Regardless of which comes first, we identify the pair of alternating phases as a self within a lineage of selves” (165).

Among non-living things, fires burn out, even rocks erode. But autogens are able to postpone the disorder and the dispersal that characterizes lifeless matter by building phases of reshuffling and rearrangement into their cycle. And autogens evolve, as certain varieties come to outnumber others. Some capsules become more likely to open in the presence than in the absence of  fresh reactants, improving their efficiency. Others carry around a template, an early kind of DNA, that preserves a particular sequence of, for example, a successful catalytic reaction. In such ways, “selves resist nonexistence” (193). And while autogens are not living cells, with each change that makes them better at persisting, they get closer.

 

New Thinking About the Origin of Life (1): Purposes and Selves

How does a living thing differ from a lifeless one? And how might those living characteristics have emerged from the lifeless matter that preceded them?

Jeremy Sherman’s new book, Neither Ghost Nor Machine: The Emergence and Nature of Selves discusses recent thinking on these questions, especially the work of neuroanthropologist Terrence Deacon. In this post and the next, I’ll summarize highlights.

Sherman emphasizes this difference between living and non-living things: living things have purpose, non-living entities do not. Purpose here has little to do with a person’s “sense of purpose” and it has nothing to do with divine intention. It refers instead to biological processes aimed at maintaining the state of being alive. The heart’s purpose—its function—is to pump blood. The purpose of a leaf is to produce food for the plant. We take for granted that bodies and all their parts serve functions and yet it may feel strange at first to identify purpose itself as a distinguishing biological feature of all organisms, even single-cell bacteria.

campfire (shutterstock.com)

shutterstock.com

Non-living stuff, on the other hand, has no such purpose or aim or sustaining function. A fire in the fireplace burns and gives off heat and carbon and other gasses, after which the fire, without more fuel, goes out. Sherman writes, “Most chemical reactions yield a proliferation of molecular products” but such reactions soon peter out. The reactions in living things, on the other hand, don’t fizzle out so easily. Through their biochemistry, living things “are self-regenerative in two senses: they maintain their own existence, and they produce new selves” (9).

New selves? Sherman, following Deacon, refers to organisms as selves. Applying self to an organism calls attention to the ways that even a bacterium as well as a human works to find food, defend its-self, repair its-self, and make more selves. Inanimate things aren’t selves. Left alone long enough, anything inanimate will become disorganized and break down; an ice cube left on a counter will melt and then evaporate, its molecules finally dispersing into the air. Another difference between selves and inanimate things: with selves, we can say that something—fuel, information, lower temperature—is good or bad or useful or significant for it. But, as Sherman puts it, “Nothing is ever functional, significant, or adaptive for sodium chloride, snowflakes, mountains, fried chicken, or even computers” (25).

But what about natural selection? Didn’t Darwin’s work explain how living things evolve? Yes, but natural selection doesn’t explain the first appearance of the selves that do the evolving. “To claim that natural selection explains purpose is like claiming that erosion explains mountains. Erosion…explains how mountains are passively sculpted, but not what’s sculpted. Likewise, natural selection explains how populations of selves are passively sculpted…[as] some lineages produce more offspring than others, but not how selves arise in the first place.” (9).

So, the question: what kinds of inanimate chemical reactions might have come together as stepping-stones towards purposeful, self-regenerative selves? Until now, that question has been explored in terms of possible ingredients. Chemical stews, viruses, RNA molecules, an iron-and-sulfur world have been among the candidates for starting points. But Terrence Deacon has asked instead what kinds of reactions, regardless of their ingredients, could sustain themselves long enough to avoid the terminal fizzle of most reactions? In the abstract, his answer is that you need not one but two reactions, each of which constrains the other before it can burn itself out. How? I’ll explain in my next post.

Forgiveness and the Second Law of Thermodynamics

The Second Law of Thermodynamics has always seemed depressing to me. It states that anything left to itself, without new energy to sustain its structure, will become continually more disordered. Molecules of different gasses in a container will move around until they become thoroughly intermixed. Ice cubes in a glass of water will melt. And as the sayings go, “You can’t unscramble an egg” and “Whatever can go wrong will go wrong.”

This tendency towards disorder, this inability of things to remain what they are unless  energy sustains them, is entropy. The Second Law asserts that entropy in the universe always increases. Sustainability is always in doubt. In human affairs, entropy implies that nothing worthwhile—relationships, art, satisfying work, better communities—can remain finished and stable on its own. Ugh.

But Steven Pinker takes a more generous view in a short piece written for Edge and reprinted in the Wall Street Journal in 2016.

The Second Law also implies that misfortune may be no one’s fault. The human mind naturally thinks that when bad things happen—accidents, disease, famine—someone must have wanted them to happen….[But] not only does the universe not care about our desires, but in the natural course of events it will appear to thwart them, because there are so many more ways for things to go wrong than to go right. Houses burn down, ships sink, battles are lost for the want of a horseshoe nail.

entropy (keelynet.wordpress.com)

keelynet.wordpress.com

And without a flow of economic energy, people go hungry. “Matter doesn’t spontaneously arrange itself into shelter or clothing, and living things don’t jump onto our plates to become our food. What needs to be explained is not poverty but wealth.”

I thought about conspiracy theories and entropy. For some, it may feel satisfying to account fully for a disaster by believing in the plots and actions of secret human enemies. But entropy and its agents— coincidence, irrational human impulse, materials and systems gone awry, among others—are all on stage as well, more difficult to identify, and less satisfying to blame.

Pinker’s perspective also cast a new light for me on the familiar serenity prayer: that we should try to accept what we cannot change, find the courage to change what we can, and hope that we can tell the difference between the two. The Second Law puts a foundation under that difficult first step, the acceptance of what we can’t change. It’s easier to do that when we understand that things don’t easily stay as they are in the first place–and often no one is at fault. We may do the best we can to stay healthy, so we’re reluctant to accept that our body will fail eventually for reasons beyond our control. Committees and governments may bring the benefits of social order for a while, but we can recognize how such social efforts will fall into stagnation or conflict eventually without anyone being at fault.

Entropy is sometimes described as a re-organizing and re-forming force, rather than as a dis-ordering one. An organized thing will if left to itself take on new forms, occupy more or less space, detach and reattach. If it’s the original thing that you are focused on, then indeed that thing will have “broken down.” Ice cubes melt and disappear. But a friendship may rearrange itself into a marriage, then into a divorce, then into a business partnership. Stars explode and their atoms of metals form Earth and us. Entropy, transformation, Buddhist impermanence.

But for Pinker, so disruptive is the Second Law that it defines life’s purpose. The Second Law “defines the ultimate purpose of life, mind and striving: to deploy energy and information to fight back the tide of entropy and carve out refuges of beneficial order.” Appreciating the Second Law means pursuing such purposes more consciously while understanding that, without blame, the tide always comes back in.