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.

 

Breath: Divine Gas In a Smart Body

The word breath most often refers to the air we pull in to and pump out of our lungs (or to the action of doing so) as in “Take a deep breath.” But we also give the same word loftier qualities in phrases such as “the breath of life” and in practices like yoga that view the breath as a source of health and peace. Other traditions and languages also have words for breath in both these ordinary and spiritual senses, such as Latin spiritus, Hebrew ruach, and Chinese qi.

breath spirit (soundofheart.org)

soundofheart.org

But what about the breathing body itself? Unless we are wheezing or short of breath, we usually take the smooth coordination of our lungs, diaphragm, membranes, and blood cells as unremarkable. But let’s refocus our wonderment for a moment. The air is, when you come down to it, just a mix of gasses, but our body’s ingenious respiration of them is a process to appreciate.

We breathe in air because it contains one gas that we must have: oxygen. We know that. Less familiar, though, is the step-down system that has evolved to make the most of the fact that, like all gasses, oxygen spreads out from wherever there is more of it to where there is less of it. Thanks to this step-down dispersal and our flowing  blood, we move oxygen from the air outside of us to every cell that is waiting for it, all several trillion—that’s 000,000,000,000—of them.

Why oxygen? Its electrons are arranged in such a way that it interacts eagerly and often with other elements. It’s a potent extrovert. The body’s cells may get their nourishment from food molecules but not unless they also have oxygen handy to break those molecules down. That would be like our eating dinner without any acid in our stomach to digest it. No nourishment. Without oxygen, cells go hungry.

But a little oxygen goes a long way. The numbers surprised me. Only about twenty percent of the air that we breathe is oxygen. The rest is nitrogen and a percent or two of other gasses. And of that twenty percent of oxygen that we inhale, we actually use only about a quarter of it. The rest goes out again. Our inhalation is twenty percent oxygen; we exhale fifteen percent.

Once it is in our lungs, oxygen must get across the lung’s membrane to the blood stream that will move it around the body. The amount of oxygen in the lung might not seem like much, but it is more than remains in the oxygen-depleted blood that is returning towards the lungs through the veins. So the new oxygen steps down across the thin membrane to the empty hemoglobin molecules in the blood cells for the ride to the rest of the body.

As this convoy of oxygenated blood flows near, say, a finger, the oxygen detaches from the hemoglobin, steps down once more across a membrane to a cell itself, and goes to work on the food particles. In the process, extrovert that it is, oxygen combines to form unusable carbon dioxide, crosses the cell membrane back out to some empty passing hemoglobin that just dropped off new oxygen elsewhere, rides the vein back to the lungs, gets off again, and is exhaled back out to air. Like riding the bus you took to work back home at the end of the day.

I argue for the wonderment of a distribution system that pulls in air-borne oxygen in an endless rhythm, arranges for it to disperse itself across strategic membranes, loads it on to the blood for transport to a million million cells that it will help nourish, after which it returns the way it came in. Our stunning respiration makes oxygen look good—even divine.

 

Cyanobacteria: R-E-S-P-E-C-T

We owe cyanobacteria our respect. And they might deserve our fullest gratitude as well if it weren’t for one nasty trait.

For starters, if we are to believe that our elders deserve respect, cyanobacteria certainly qualify. They date back 3.5 billion years, almost to the earliest signs of life. But they are not only old. They are interesting, they seem uncomplicated, and they are powerful and successful. They are single-celled, though many live connected to each other in colonies and filaments. They are primitive; unlike the cells of younger species, they have no nucleus. And they have not only survived all this time; they have thrived. Their species number at least two thousand that have been described and at least twice that number in total. Most are blue-green—“cyan”—but their various pigments also account for the colors of pink flamingoes and the Red Sea.

cyanobacteria (https-::i.kinja-img.com:gawker-media:image)

(gawker)

Cyanobacteria gave us oxygen—and continue to do so. For the first two billion years after the earth’s formation 4.5 billion years ago, the atmosphere contained almost no oxygen. But the blue-green pigment in cyanobacteria is a mix of green chlorophyll and a blue pigment both of which turn sunlight and carbon dioxide into sugary energy for the cell. Oxygen is the waste product—and early cyanobacteria produced so much of it for so long that it accumulated in the atmosphere and eventually supported larger, more complex cells, including ours.

Just as important, atmospheric oxygen spawned an ozone layer that reduced the lethal levels of the sun’s ultraviolet radiation. It’s that filtering that allowed early plant and animal life to finally move on to land after three billion years in the water.

Cyanobacteria made plants themselves possible by becoming part of them. Some other early bacteria engulfed cyanobacteria and then, because of cyanobacteria’s efficient energy production, turned them into one of the pieces of organic machinery enclosed within a plant’s cell. We see them today as the greenery of plants—the chloroplasts—that power them and keep them reaching for the sun.

Cyanobacteria are handy with another gas in addition to oxygen. They convert nitrogen in the atmosphere into a form that plants and animals need for such building blocks as proteins and DNA. Natural nitrogen fertilizer.

pond scum wikipedia

(Wikipedia)

Cyanobacteria often go by the name of blue-green algae. But they’re not algae. Algae is an informal term for many water-borne organisms that contain  chlorophyll but lack stems, roots, or leaves. Seaweed is algae. Cyanobacteria are bacteria—simple cells, often strung together, without nuclei.

As for that one nasty trait, cyanobacteria can kill you. Especially in freshwater ponds and lakes, blooms of cyanobacteria looking like blue-green paint slicks may be toxic to nerve and liver systems, depending on the species. The poisons may work their way into the food chain, pets may eat them, water-skiers may absorb them. The result can be respiratory failure, Parkinson’s, ALS. Not often, but too often. Respect.

Reading about cyanobacteria on the Internet, you get a glimpse of a life-form from an inconceivably ancient world that is woven throughout the air, water, and soil of our own time. We are in their debt for the breath we take, the food we eat, for our living on solid ground.  We stand on their countless, tiny shoulders.