Category Archives: biology

The Joy of the Circle

I didn’t like to fly. I kept waiting for the bumps to stop. Regardless, the supple machine continued to bob and thrash like a trout in the rapids. A few rows forward, a child began to cry. Between the two of us, adults read their magazines and played video games on their phones. No doubt, they recalled that flying was safe. The statistics were incontrovertible. And in theory, the engineers knew exactly how the air would flow and how the engines would perform. Why should a passenger worry?

Yet no one had predicted the rolls and soft spots in the atmosphere over which we presently skipped. No one really knew what fury of heat and pressure swirled in the engine at that moment. Flying was inherently dangerous. The little boy up front knew it because he didn’t believe in theories yet. He knew what happened when a glass fell off the counter. He knew what happened when a stick, flexing like the wings were, bent too far. I knew it because I habitually did dangerous things and tried to make them safe. I had faith in statistics, but I also knew that sometimes, only one little thing had to go wrong. In the chaos of fluids which sustained our flight, if the one little thing did go wrong, we were all lost without hope of recovery.

The boy’s naiveté could be forgiven, as could the adults’ ignorant confidence, but what about my fatalism? I had better have a reason for getting on this flight, hadn’t I? My children had no one else to care for them. Countless, unimagined opportunities awaited back on the ground at home. What did I have to say for myself and my self-conscious gamble with extinction?

All I could come up with was et tu quoque. I had seen a Wyoming toad once. It was at night, at a rest stop, in the middle of Summer. Its species was endangered, yet this toad made no excuse of the fact. It followed a line of ants down the middle of the sidewalk beneath the streetlights, lapping up the insects one after the next. My six year old son crouched over the little amphibian, delighted. It would never have a better friend and ally, but it couldn’t have known. All it could have known was that the shape looming over it had not struck yet, and that the ants were right there. The toad was gambling with extinction, and a critic might have called it selfish.

But the toad could have responded. If it believed in theories, it could have claimed that it was simply a disciple of Yamamoto Tsunetomo, obeying his dictum:

Even if one’s head were to be suddenly cut off, he should be able to do one more action with certainty.

Or it could have called upon Nietzsche in its defense, claiming that it didn’t pursue ants, but rather:

…a becoming that knows no satiety, no disgust, no weariness: this, my Dionysian world of the eternally self-creating, the eternally self-destroying, this mystery world of the twofold voluptuous delight, my “beyond good and evil”, without goal, unless the joy of the circle is itself a goal…

The toad’s response was better though, because it didn’t believe in theories. Its defense was: a warm night and an Eldorado of ants. Mine would be the same. How else would I defend even my love for my children? No set of laws bound us to each other, only a chance (in theory) arrangement in space and time. Yet it was a chance that went straight to the bone, no question. I had no better answer for the feeling that had gotten me strapped in this chair, bouncing through the sky to an uncertain fate. It was a feeling for a stranger, I’d have to admit if pressed. But it wasn’t composed of what I knew about her, anymore than my love for my children was composed of what I knew about them. It was a chance arrangement in space and time. It was nothing I chose, but it went straight to the bone, no question. Like the toad, I’d risk every calamity with open eyes. I took a breath, shook my head, and stopped waiting for the bumps to stop.

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Is a Virus Alive?

life, living matter and, as such, matter that shows certain attributes that include responsiveness, growth, metabolism, energy transformation, and reproduction. – Encyclopedia Brittanica

Close enough, and encompassing the generally accepted criteria: responsiveness, reproduction, metabolism and adaptation. My older son asked the question about viruses the other day. I have been looking forward to this question. It means that he is prepared to understand some things about life which are important. It is a tricky question if considered from the wrong viewpoint. A virus displays some of the characteristics which define a living organism. It can respond to stimuli, attaching to the proper cells and injecting its genetic material through the cell membrane when it makes contact. It can replicate. It can adapt to avoid a host immune response. But it does not have the capacity to metabolize. It cannot, in other words, run its own show. It is entirely dependent on its host organism in that respect. Nor is the virus alone on the gray borders of life. Certain families of bacteria lack some essential metabolic processes which would make them autonomous. They must live inside another cell, and depend on their host’s metabolism to survive. Yet, they too can reproduce, adapt, and respond to stimuli in their environment. Because they have a membrane which is active, biologists are prone to give obligate intracellular bacteria, like mycoplasma and Rickettsia, a break. Most biologists are less charitable when it comes to prions. Prions are mis-folded proteins which replicate by somehow inducing their own conformal change in normally folded proteins with which they come in contact. Prions can reproduce, but they cannot metabolize. They cannot adapt much (although they have managed to pass from cows to humans), but they can respond to their environment, albeit in a very limited way. Still, the difference between the prion and the obligate intracellular bacterium would seem to be one of magnitude rather than quality. Differences in their classification reflect a little bit of membrane chauvinism on the part of biologists. The same prejudice is evident in the gray zone at the other end of the complexity scale. By our criteria for life, is a male angler fish alive? The fish can survive for a short period of time independently, but it cannot carry on its own metabolic processes independently for the long-term. It must rely on a female angler fish. It must quickly sniff out a female and attach itself to her, permanently. The male fish spends most of its existence as a tissue of the female angler fish’s body; its brief, free swimming existence is a transitional aberration. Its ability to adapt is extremely limited. Its existence can be mapped on an algorithm only barely more complex than the one which describes a prion’s lifestyle. So what does differentiate the male angler fish from a mycoplasma bacterium, a virus, or even a prion? A few extra membranes make the only difference. Even our own status as living things is at risk if we apply our criteria strictly. We can certainly reproduce, just like the viruses, obligate intracellular bacteria, prions, and angler fish. But it is questionable whether or not we can independently metabolize. We actually rely on hereditary intracellular symbionts for our primary metabolic process. Without these symbionts, our mitochondria, we could live only minutes on the metabolic processes encoded by our own genetic material. So, we can hardly be blamed for fudging our criteria. We certainly want to call ourselves alive. Since it looks and acts alive, we want to call the male angler fish alive. For practical purposes, we also want to call Rickettsia and mycoplasma alive, as well as viruses from time to time. As for the prions, it is often more convenient to view them as sophisticated toxins rather than living things. And that’s the upshot of my son’s question. The issue of whether or not a virus is alive is only confusing if we consider “life” an actual, efficacious thing. But life is just a category. When we look out across the terrible landscape of things, we see phenomena which cluster about each other by dint of their shared heritage. Our account of our cluster is biology, and our criteria for life provide the outline for our biological stories. This is correct viewpoint on the question of life, and what is alive. But this is not the popular viewpoint. The popular viewpoint attempts to preserve life as a thing, as vital essence or emergent property. Unfortunately, the popular viewpoint is not feasible. It leads inexorably back to the original question rephrased, “where is the life in a thing to be found?” In the end, we find that the essence or the emergent property is explained by the operational mechanisms and properties of the thing in question, but it in turn, explains nothing about the thing; it just notes where that particular thing lies on the vast, terrible landscape of things. Despite its glaring inadequacy, the popular viewpoint remains popular because it seems to save us from losing an idea that we don’t feel comfortable losing. But we don’t need to worry, becoming a category doesn’t vitiate life. We have the things which the category marks clustered around us after all, even if it’s only according to our viewpoint. We can’t escape life anymore than we can climb out of our skins. So, the answer to the question? Sure, a virus is alive – as long as you can explain why.

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The Word from the Land of Absolute Relativism

“Look at all this shit!”
He waved the stack of envelopes at me.
“Look at this one.”
He held up the letter on top. It was from another hospital and marked, ‘Important: Do Not Discard’.
“These are the ones you have to be careful to discard.”
He threw it in the wastebasket, and followed it with the rest of the unexamined mail. I was far enough into my training not to be shocked by this sort of thing. I’d weathered surgeon’s tirades and soaked up jaded, callous humor in the emergency room. Still, my experience with this psychiatrist had me believing for years afterwards that, in his specialty, like sought like.
“This kind of clutter is the enemy,” he continued, opening the top drawer in his desk.
He scooped out a handful of keys.
“Look at these! I don’t know what this is for,” he said, holding up a sturdy door key. Into the bin it went.
He tossed a few more, then dumped the remainder back in the drawer with an expression of disgust.
“We’ve wasted enough time,” he declared, “better show me the case.”
I handed him the chart, with my history on top. He lingered on the assessment at the bottom of the page. Residents sometimes began to sweat when attending physicians paused too long in their documentation review. I did not in this case, because the assessment was not mine in the first place; the patient brought her diagnosis with her from the last admission. He grunted and moved on to the ancillary notes, containing the comments from psychiatric nurses who had evaluated the patient.
“Jesus Christ! Did you read this?”
Now I began to sweat. I hadn’t read the nurse’s notes. He handed me the chart with a shake of his head. I’d gotten lucky; the question was rhetorical. Curiosity displaced my anxiety and I began to read with interest. Immediately, I realized what he was on about.
At the bottom of the page, several of the nurses (a cabal?) postulated that dark forces were at work in the patient’s life. The assessment dwelt upon the young lady’s practice of witchcraft, not as an expression of alienation in a personality dangerously adrift, but as an activity with sinister efficacy. I looked up at him as I finished reading.
“How can we hope to do anything for the patients when we’re up against this kind of stupidity from the staff? Borderline,” he stated, returning to my assessment, “Do you really believe that?”
I shrugged. She had the black nail-polish sign, which every trainee knew was pathognomonic for borderline personality disorder.
“There are some people that fit the bill, but mostly the term is an epithet applied to people who we don’t like because they are frustrating. It’s the DSM used as a cudgel, and it justifies our bringing these people into the institution when their community becomes too frustrated with their behaviors. They come in for a few days or a few weeks until they’ve cooled off, then they go back out with the same problems, to the same problems. So this kind of inpatient treatment is like firing into the tree line: it’s good for keeping the enemy’s head down, but it’s not good for hitting anything.”
His words were familiar in structure and reference. At home that evening, I poured through my memory and my boxes of books, and I eventually placed them. They recalled an image from Heart of Darkness.

Once, I remember, we came upon a man-of-war anchored off the coast. There wasn’t even a shed there, and she was shelling the bush. It appears the French had one of their wars going on thereabouts. Her ensign dropped limp like a rag; the muzzles of the long six-inch guns stuck out all over the low hull; the greasy, slimy swell swung her up lazily and let her down, swaying her thin masts. In the empty immensity of earth, sky and water, there she was, incomprehensible, firing into a continent. Pop, would go one of the six-inch guns; a small flame would dart and vanish, a little white smoke would disappear, a tiny projectile would give a feeble screech – and nothing happened. Nothing could happen. There was a touch of insanity in the proceeding, a sense of lugubrious drollery in the sight; and it was not dissipated by somebody on board assuring me earnestly there was a camp of natives – he called them enemies! – hidden out of sight somewhere.

The image stuck and grew stronger over the years until I ceased to see my preceptor as chief among madmen and came to see him as Marlow on the boat. He was the lone relativist in a wilderness of absolutists who considered borderline personality more than a label on a charge sheet (it is that at least, for the Diagnostic and Statistical Manual which codified the term is a tool intended to itemize mental illness for billing). For his fellow wardens of the institution, there existed a borderline personality fact about certain people, caused by borderline personality pathologies and amenable, potentially, to borderline personality treatments. He saw them firing into a continent. He did not, of course, live in the land of absolute relativism, where everything is an onion made of layer upon layer of motives and relations with no pertinent core. He believed in borderline personality as a country over yonder. It recognized certain commonalities, but those commonalities arose in the villages. They accrued; they did not come down from on high.
He cared about how seriously the nurses, psychologists and patients took diagnoses, not because relativism was true. He cared because absolutes did not obtain. Worse, absolutes destroyed. On occasion, bullets fired into the tree line did hit something, and that something was an enemy by definition. Over his career, he’d seen victory declared over schizophrenia and the state institutions emptied onto the street. He’d seen the profession take a pass on intractable diagnoses, like personality disorders. He’d heard from his predecessors about neurosurgical solutions considered quite successful in their time. It wasn’t that relativism was true, it was just that truth didn’t work that way. It wasn’t diagnosis-friendly, and the truth about psychology all the less so.

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Vitrification

Autumn is a season for reflection. The humors slow. We are reminded of mortality, as the life around us shuts down. The maudlin huddle under blankets and hide from the change. Happy fatalists jump in the leaves and ignore it. We shouldn’t contrive a situation where certainty is ours and we wait for the change with eyes shut tight. We ought to be thinking about life instead of death, but not in the fatalists’ way. Out in the cold, in crevices and under bark, tiny creatures illustrate a better way as they face the real crux, the exposure.
As the nights cool, substances like the stored reserves of hibernating animals accumulate in the tissues of certain insects. But rather than providing energy through a long sleep, these substances will embalm their creator. If the rate of transition allows, water in the animal’s body will become an amorphous solid, a glassy ice. Glass spares all the containing structures in the body from lacerating crystals which destroy cell membranes and organs when the other form of ice takes hold. We are familiar with this process because, with less reflection than the insects, we bring the dilemma of a frozen state to our own, furry kinsmen. Motivated at once by fatalistic optimism (in the method) and insecurity (in the act itself), people have taken advantage of vitrification to postpone the development of human and animal embryos in anticipation of more favorable conditions.
In every case, resuscitation is not guaranteed. Some of the vitrified wild animals are clearly doomed. They don’t have enough of the embalming substances in their cells, or have too much water on board. Some are victims of circumstance, as the rate and depth of temperature change affects survival, all else being equal. The insects can’t bank on their potential. For all they know, when the frost takes them, they are dead. That’s all we know too. We freeze many embryos because we can’t know what’s going to happen to any one of them, only what tends to happen to a population. Life is like that. It is fuzzy on the edges, where things like viruses, self-replicating proteins, frozen beetles, and frozen embryos lie in wait to rob us of our reassuring, formal picture.
Worse, when the frozen, the ones that do survive, come back to life, it is through a completely generic influence. Heat does it. The atoms in a particular space vibrate a little faster and the bug resumes its life. The embryo begins to grow again, and barring any further mishaps, becomes a lamb or a human infant, depending on what came before it. The potentials of the process, like those of the form, fade into the landscape. Odds don’t mean much for the frozen individuals. The relationship of the odds to the individual demonstrates that the forms and processes of life aren’t special. We can’t have precious life and its illusion of prescience to hide beneath. We want it instinctively though, because it protects us from the vista tugging at our tails. Nor does the landscape recede if we write it off to fate. If we look down from our preoccupations, we see the individuals poised on vertiginous points of space and time. The location is special, but not cozy. It’s a spot of massive focus and alien potential. The view down is disturbing, but it is more accurate, and more immense than our mythology or our philosophy, if we can take it in.

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