Friday, June 5, 2009

See Spot Run

[This is a science-fiction fantasy. Or is it a science-science fantasy?]

Life is like the big red spot on Jupiter. No; I am not kidding. Back forty, fifty years ago, in the seventies and sixties, the scientific consensus was stolidly mechanical. Life was chemical in character. The organic chemicals were being synthesized in labs. It was held then that in due time science would combine them in a tube and life would come wiggling out. That ambition hasn’t been jettisoned exactly; biochemists haven’t simply thrown up their hands and decided that life is some kind of hologrammatical whatsit that cannot be explained; chemistry is still very much in the saddle; but the mood has changed. An excellent, widely-used textbook, its second edition published in 1972, Biology Today, begins with the question, “What is life?” David Kirk, the author, does not provide an answer in so many words. The whole text is the answer. Today’s science would say that life is a dissipative structure like—well, like the big red spot on Jupiter.

The big red spot on Jupiter is a storm of extraordinary size and stability several times the size of the earth. It has been in continuous existence certainly since we have had telescopes powerful enough to resolve Jupiter well enough for us to see the red spot run. The powerful circulation of Jupiter’s atmosphere has constituted the red spot and keeps it organized. The red spot is a structure of gases kept coherent by a flow of energy.

Apply a shock to an open system—say a river. The river, in its downward rush, flows in a state of disequilibrium. When you shock such a system, you can cause matter to organize itself.

Lets put a big boulder into the middle of a shallow, fast-flowing brook. The boulder compresses water between the bank and itself. Turbulence. If the water keeps on flowing, with the same force as before, vortices will form. They will retain their shapes while the water keeps flowing. Turbulence is water’s way of shedding, dissipating an excess of energy. Water forms a vortex—another dissipative structure.

A Russian-born Belgian physicist, Ilya Prigo­gine, coined this phrase. He won the Nobel Prize for his discovery in 1980. He took an interest in a certain phenomenon. The first person to observe it had been Henri Bénard early in the twentieth century. Convection currents in a thin film of water, heated from below and cooled from the top, cause the liquid to display more or less hexagonal shapes. Cool water, descending, collides with hot water, rising. Like people in a narrow corridor, they move apart, squeeze past each other. Geometric shapes are formed as a consequence. Two Russian scientists, Boris Belousov and Anatol Zhabotinsky, later produced lovely circular formations by reacting malonic acid, bromate, and cerium ions with sulfuric acid in a shallow dish at a critical temperature. As the temperature changes, life-like shapes proliferate.

Matter today is said to be self-organizing under certain circumstances, and self-organization is a crucial concept in modern theories of life’s origin. Someone naïve—take me, for instance—might say that matter just behaves in certain ways. Matter just displays various forms, some regular, others not so. If anything is organizing the Belousov-Zhabotinsky reaction, it is energy acting on the fixed characteristics of the chemicals in question.

If I naively accept a mechanical explanation of reality, a phrase like self-organizing makes me sit up. I associate “self” with a living entity, preferably one capable of awareness. I feel proprietary about the word. But modern science has taken the self unto itself. It has either introduced it into matter or has abstracted it from matter’s inherent behavior. At the level of logic, this amounts to the assertion that matter is alive, and here we mean ordinary stuff like metals and minerals.

Someone reading this might say, “Cool it. Don’t get hysterical. They just use the phrase in a metaphorical, descriptive sort of way.” The truth is that the concept of self-organization, derived from studying minerals, is being applied to life, is, in fact, being used as an explanation of life. The sequence of events is the following. Self-organization of matter appears in certain processes that create what we have already seen as “dissipative structures.” Life processes are said to be special cases of such structures at the chemical level.

The extension of this logic is that life is a very complex form of dissipative structures self-organized to remember their complexity and to replicate it. These structures also have a tropism toward increasing complexity. Therefore matter, complexly arranged, is life, and life is information. That seems rather appropriate—in the Information Age. How complexity managed to emerge spontaneously is not yet clear—but dissipative structures are suspected. Why the universe might want to complexify is not addressed by any theory of science—and maybe rightly so.
Let’s go into this a little more.

Ilya Prigogine won his Nobel Prize because he developed the theoretical framework and mathematical description of open systems in high states of disequilibrium. Systems like that can change under the stimulus of increased energy flow, and, within certain parameters, a higher order of organization appears. Higher order, in this as in other contexts, means that the relationships between the participating particles become more complex; they have more discernible structure. When such changes occur and order appears, the system loses energy faster or, if you prefer, its entropy grows more rapidly. To remain in existence, dissipative structures must have a flow of energy to maintain them. This flow need not be uniform in intensity but must be continuous—and it must remain within a certain range. If we put a raging fire under the Belousov-Zhabotinsky dish, the pretty circles disappear. From this has come the notion that, under certain circumstances, an increase in entropy can result in the creation of a higher order, such as life.

The best way to picture dissipative structures is as a Canadian lumberjack up on a wet log in a river. He has to keep flailing his arms and moving his legs like mad to stay upright on the whirling log—a situation far from equilibrium. His own energy provides this entertaining scene’s tentative, suspenseful permanence. If he flags, if he grows weary, entropy will claim the victory. He has to make more and more of it to stay afloat.

From pretty circles in a lab dish to the simplest kind of living cell is quite a long ways, actually—what one might call a reach. Prigogine’s discovery is a suggestion, a mere hint, of how life might have come about. He showed that dissipative structures exist at the chemical level too, not just in gross forms like turbulence. A cell, even the simplest kind, is an organized whole of many distinct parts. It exists by constantly consuming nutrient and making waste. To be sure, some cells have mechanisms for going dormant when food is a little short, but that’s already an even higher form of order. Cells behave, in the gross, like dissipative structures in the heated dish.

But, still, it’s a reach. To get a glimpse of the difference, jump in the car, go down to the CVS Pharmacy and buy two bottles of soap bubbles. Take the kids into the backyard. Wait until one of them has produced a really nice one. Watch it persist, watch it float in the air. That soap bubble is like those Belousov-Zhabotinsky circles in the dish. Now let us say that you live in Detroit. Imagine that you’re rich enough to hire a pilot and a helicopter, and now take Edward and Kimberly up, high, high above the city, high enough so that you can see most of it stretching away into the distance. You’ll see highways and rivers and vast structures; some rise to right respectable heights; others blur into regular formations where people wash their cars—but they are too small to see. Find the parks, the factory districts, the old airport, now enveloped by development. Behold Detroit—behold the cell. This is not a poetic fancy, not an exaggeration. A single cell is as complex as a city. Thus it’s a very long reach indeed from the soap bubble to the metropolis, but the awesome differences in complexity—between circles in a dish and a living cell—are quite comparable.

The city resembles the eukaryotic cells, those that make up animals and plants. They have downtowns. A karyon is the Greek word for “kernel,” by which Biology means the nucleus where most of DNA is stored. Prokaryots, like bacteria, do not have nuclei. They’re simpler. Their DNA just floats about in a curled-up clump. Ours are housed in their own district and, from time to time, they get packaged tightly. “Pro” means “before.” Bacteria are living things with bodies as they were before the nucleus came to be, ah, self-organized? One meaning of the Greek word “Eu” means “true.” We have true nuclei, not just a single filament of DNA.

Now while we’re still playing with perspectives, picture yourself as a creature formed of about 60 trillion Detroits. After all of your exertions and expenditures, entertaining son and daughter, you crash on the couch to watch the football game with a nice cool one in your fist. After about the third one or so, you start to feel like a right dissipated structure. And the Lions are losing again.

Just in case you wondered, Jupiter’s big red spot is 15,400 miles in diameter. Vast though Jupiter is, 318 times the size of the earth, its day is a mere 10 hours long. This incredibly rapid rotation is what gives the spot its energy. The spot is rockin’, you might say. It seems to have a back and forth motion as it circles the planet, now speeding up, now slowing down. It also rotates about its own center in an anti-clockwise manner. Vast masses of material gush up from its center and geyser up, out over Jupiter’s topmost clouds by about five miles. Then the stuff spills out toward the edges of the spot. The spot seems to form a stupendous cyclone. Vast Jovian storms might be raining blobs of frozen ammonia down, the particles eventually plunging into an ocean of liquid hydrogen.

We zoom in and we zoom out. Tiny things become enormous up close to the eye. Monsters like the planet Jupiter become bright points of light by night. The cell is virtually invisible. Let’s zoom in and look at cells. It’s fair to say that cells are life. The most common and abundant form of life is one-celled animals; more easily seen instances of life—fields of grain, drum majorettes, or elephants—are vast empires of cells.

The fundamental, irreducible facts about our friends, the cells, are five in number. (1) They are enclosed in a membrane that is selectively permeable to chemicals in both directions. (2) Cells hold all the molecules they need to maintain processes inside the membrane. (3) They hold chemical templates as well as chemical tools with which to use these; and the templates can recreate precisely all the chemical components of the cell. (4) Cells are able to extract energy from their contents and to use it for all needed functions. Finally, (5) they can reproduce themselves by division so that, after this action, each successor is fully equipped to carry on, as before. This is, of course, a radically simplified description. It’s also missing a vital ingredient—no pun intended.

Our model of the cosmos will tend to influence how we see the cell. As resolute mechanists we’ll tend to concentrate on the chemical panorama. We behold inside the cell nothing we cannot also see outside it. Chemical reactions are taking place. As the tired termite said, “Everything is wood.” Everything is chemistry inside the cell.

The templates that code for protein are themselves just strings of nucleic acids. The mechanisms that read these templates are sugars. Chemical conditions trigger everything that happens. Suitable nutrients touch the cell’s fatty outer wall; the wall opens to let them in; but the wall opens because it feels a chemical prod. The food itself is just more molecules. When reactions need a catalyst to happen, and most do, enzymes rush to help—but they are drawn by chemical attraction. After the reaction is completed, they detach again moved by chemical indifference. See you around. Let’s have lunch.

Seek as we might for an active agency, we just don’t see it. We’re looking at a New Age collective, everybody trying hard not to be boss. Chemicals are just doing their own thing. We look searchingly at the templates, the DNA, thinking that they must be managing this process. The DNA turns out to be the most stable and passive component in the cell. It’s just a reference book—albeit a chemical one.

As little Alices in Wonderland, in our tiny little space suits, we swim about inside the cell’s murky ooze and watch gigantic things, like huge worms and boulders made up of matzo balls, being assembled or broken apart. We see corridors of tall things flailing like upside-down rags in a car wash, and huge blobs of marshmallow-like things are pushed in one direction only as these washrags seemingly randomly wave. But where’s the manager? What does the cell want?

Our group now splits up into factions, the Mechanists and the Dynamists, let’s say. As Dynamists we point out that the cell is busy maintaining itself by breaking down sugar glucose into carbon dioxide and water. It has a function of self-maintenance. When it isn’t feeding on glucose, it is replacing its own components.

Mechanists respond and say that this is just a dissipative structure self-organized in response to its disequilibrium and the flow of energy.

“What flow?” we ask. We say that that’s rather an exaggeration. So is the use of the word disequilibrium. The general picture here is orderly homeostasis. One of us has been counting. She says that it took 140 separate, distinct, highly catalyzed reactions to break down one molecule of glucose.

The chief mechanist sneers and says: “Didn’t you know that dissipative structures are autocatalytic? When we said ‘dissipative structure,’ that’s what we meant, exactly that.”

His chief assistant hits her palmpad, curses, and says: “Darn it, the memory is full.”

We confer. It seems that she has been counting too. Her palmpad’s memory filled up because she has been noting down the different kinds of activities going on in here, all simultaneously. Breaking down the glucose into harmless CO2 and water was just one of many, and part of that straightforward process turns out to have been more complicated than just 140 steps. Along the way a little bit of the glucose has been trapped and stored in little energy packets for use in other work, a kind of tax.

The chief mechanist, who’s also the most learned, explains that the packet is ATP, adenosine triphosphate. He holds forth about the complex chemistry of ATP and we see additional very complex reactions in addition to the 140 steps.

Our discussion back and forth eventually pauses for a moment. Somebody then breaks the silence.

“Hey. What about reproduction? Where does that come in? Why does a dissipative structure break apart precisely in two—dividing all the household goods in exactly equal halves? And I mean exactly. How does that square with whatever? What’s the chemistry of that?”

We’re discussing that, noting that the cell first grows bigger. It has to divide to maintain its own equilibrium, perhaps. Perhaps that’s the explanation. But then someone brings up cells that reproduce by budding. A little pocket appears on the cell’s wall and starts bulging out. Half of the hereditary stuff then clumps together and migrates to the bud as if catching a ride out of town. Sure enough, after a while, the bud breaks off and swims away.

“It might all be chemistry,” someone says, “but, baby, this thing is getting out of hand.”

Well, yes. It’s life, you see. It seems to have a mind of its own.

It’s time to leave the cell and enter the capsule which will restore us to our normal size. The Mechanists and Dynamists now separate, all but two. One of these happens to be Adam, the other one Eve. They met for the first time on this expedition, seem to feel a certain je ne sais quoi. They’ve been getting quite a bit of ribbing from the rest of us. Our two expeditions are housed at the Hot Springs Hilton. Those two decided to have dinner together at the Hot Springs Steak House down the street.

We’re at Hot Springs Alpha because in recent years consensus has been growing that life first originated in submarine hot springs, the process powered by the heat of lava. Fractures high up in those springs provided, perhaps, the ideal environment where organic chemicals might meet and combine under perfect chemical and physical conditions, heat and pressure being just right, and the clay walls of the fractures providing catalytic functions.

Eve excuses herself to freshen up a little. “I’ll meet you at the steak house in about half,” she says, giving Adam a smile.

Adam goes on a walk. Science really does excite him. He ponders the five facts about the cell and realizes that the most important fact is missing. All these reactions are going on, but they are coordinated, concerted, and seem to operate toward a single end. Reproduction. The wall around the cell does not strike him as adequate explanation. Or is it? The same reactions, he assumes, might have been going on in that hot spring fracture—but, of course, in that chaotic environment, they would meet catastrophic ends. The cell wall unites them, holds them in, produces the unity of a common context.

No, dammit, that’s not it. Or is it? He recalls his undergraduate studies, his first exposure to biochemistry. A professor—he can still see Dr. Bonds—explained that bacteria can divide every 20 minutes. And if sufficient nutrient were present—and room enough to hold all the bacteria—a single cell could produce, by division, a biomass greater than the earth in just two days.

His father, hearing about that, had laughed in that weird way he had, and said, sarcastically: “Be fruitful and multiply and fill the earth.”

His father had a love-hate relationship with God; that’s why he had named his first son Adam.

But Adam’s thoughts are straying towards Eve. She is a Dynamist. She believes that complexity is just information. Now he is rather drawn toward that theory. The really weird thing about those chemicals, inside that skin, is not only that they reproduce but that they have a memory. That’s what DNA is, after all. Adam remembers a paradox.

Long chains of polynucleotides, like DNA, cannot be produced without the presence of enzymes acting as catalysts; enzymes are complex proteins. But complex proteins cannot be produced without long strands of polynucleotides to code for them. The chicken and egg problem is alive and well at the cellular level. Once you have both, no problem. Adam remembers theoretical models trying to get around this problem. Something had to code for the proteins before the proteins could catalyze reactions to make the DNA.

Here, too, you have dualism, Adam notes. There are those who say that replication came before a wall enclosed the cells. Others maintain the opposite. Both explanations have major problems.

Over breakfast this morning, he and Even talked about that, and at one point, emphasizing a point she was making, she had reached out and touched his arm. That had distracted him, just then. Come to think of it, it distracted him now, just remembering that. Talk about memory.

As best as Adam can recall, she said that current theory asserted that metabolism came before replication; that the cell was initially full of a kind of chemical soup but without any DNA yet. But that replication had to begin almost immediately after the cell was formed to avoid chemical catastrophes—and by that time chemical evolution would have had to have evolved far enough so that the cell had mechanisms for maintaining not only its insides but also the fatty walls that ringed it all about.

She had emphasized that chemical evolution came before cellular. She had argued with great heat that complex chemicals could be said to carry information, that their very form held, as it were, a memory of how they had come about.

She had talked about a riot, a dance of chemicals, a great urge to increase their complexity and also, somehow, to remember how they had come about.

It was sheer mysticism, of course, Adam now thinks, good Mechanist that he is. Does information mean something, just by itself? But if Eve believed that, he intended to listen her out. He had a very strong urge to understand what she was all about. They might have to spend quite a bit of time together over that.

Well! There she is. Adam stops, waits for her to join him at a point halfway between the Hilton and the Steakhouse. She is coming with such speed and momentum, Adam and Eve almost collide.

Over dinner they talk about the problem once again, the paradox of life’s formation.

Adam keeps saying, in many different ways, that he has no problem believing that chemical reactions could take place inside a layered wall of fatty acids known as phospholipids. But from that to a self-replicating cell—he doesn’t want to use the word reproduction, just now—that, he says, is something of a leap.

They get sidetracked just talking about the wall of the cell. It is made of a hydrophilic layer on the outside, in contact with water, and a hydrophobic layer on the inside. A structure like that, once formed in water, will tend to curl around itself to make a sphere, the hydrophobic stuff trying to get away from the water.

“Don’t you know,” Eve says, “hydro means water and philic means loving.”

As if he didn’t know that. He gives her a long look. Her eyes are shining. There is a moment of silence. Then they’re both speaking at the same time. Then they’re laughing.

They eat and have some wine. Somehow the business of nutrition takes care of itself as they range far and wide over the vast field of chemistry, frequently pausing to examine chemical bonds, and not just simple kinds but strong ones, double bonds.

They also talk about complexity and information. And exchange some information. His goes into her memory, hers into his. He tells her about his father’s love-hate relationship with God.

“If Dad could’ve been there today,” he says, “down in that cell, he would have said that it was chaos—and the explanation for it all might have been God’s Spirit moving over the waters.”

Then Adam laughs, quite unaware that he laughs just like his father. His cells seem to remember how his father laughed. They’re replicating that laugh.

Eve says: “You’ve got the cutest laugh. Did you know that? Did you?”

She is a little tipsy too.

They go on a walk. This region is quite mountainous. They walk high up, find a lookout point. The hotel, the restaurant, are far below. The moon shines between two mountain peaks. He reaches down and takes her hand in his.

She doesn’t seem to mind.

The mystery of life’s origin has yet to yield to the probing of science. Cellular complexity appears like an accomplished fact. The processes that lead to it can only be inferred. A fundamental something keeps us from seeing precisely, mechanically, where the play of chemicals suddenly jells into a reproductive intentionality, complete with a sophisticated system of storing information, using it, and a powerful drive to preserve it and to combine it with other information to reach higher levels of complexity yet. The agency behind this process is invisible. Cell division, including the precise manner in which the DNA strands separate, transcend mechanism even if we manage to explain the chemical processes involved.

At the same time, and this is equally true, what science tells us about the early environment, before cellular life took hold, looks very much like life itself, only less coherent. Chemicals of ever greater complexity are forming. If life really did begin in deep hot springs beneath the primordial ocean, back when the atmosphere was hydrogen, methane, ammonia, and nitrogen and quite lethal to life as we now know it, life seems to have sprung up right out of the center of the earth.

We see a continuum. There are viruses, for instance, which are classified neither as life nor as mere chemicals. They have features of both. They carry information, do not metabolize, and cannot reproduce outside of cells. There are some bacteria that engage in a strange sort of quasi-reproduction, almost sexual in nature. They exchange some bits of DNA. Talking, you might say. And viruses are inanimate bits of information too.

On the other hand—will our wave-like motion never end?—we also see a kind of sudden qualitative change in the chemical cosmos when the cell appears and with it a fundamentally new order. It appears, as best we can tell, when the cell walls form and, instantly, the code of life appears inside them. This also seems to take place at a certain fixed time in the earth’s history and then once for all. If life is still being synthesized today, we have no evidence of it.

The cell is an active seeker of energy. It’s difficult to see it as merely a complex response to energy. It’s not entirely obvious who is the victim here. The cell might be a dissipative structure, but once you see it whaling away at sugar, the mood of the scene seems to change.

Elements, minerals might join in autocatalytic reactions at the bottom of the shallow dish; they might form structures of high order; but they don’t reproduce.

Crystal structures propagate, but not like cells.

If we had just one kind of cell instead of many different kinds—and even in the beginning, we had at least two kinds, bacteria and archea—if we could put the chemicals into a reactor, turn on the heat, shake up the broth, and see them moving about, then perhaps we would know more. Maybe. Thus far we haven’t come close.

The argument here is not to claim that cell life isn’t matter or that our scientific synthesizers will never succeed. They might. Let us suppose they did. If the life that they created behaved as life does now, would we be further ahead?

Cell life may be matter, but it is matter as our scissors are metal. There is something here we do not see.

Theories of complexity and information do not serve to explain, but assigning emergent properties to complexity might arise from an intuition. Complexity may simply be an inkblot in which we’re vaguely seeing something else. But what is that something else? All we see is Spot—and spot is running, running. But where are you going, Spot? What draws you on?

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