Timstories

Friday, April 13, 2018

Piute Log...Ten Years Ago Today 1993

1 Aug (Sun) Today happens to be the tenth anniversary of the day I first came here. Wow. But spent it in bed, mostly. [Had injured my back the day before, carrying a heavy log I’d cut to be my new hitchrail.] Up at six, tweaked and temporarily disabled. Had planned a celebratory climb up Tower Peak today but instead took Advil, read books, napped and…accomplished nothing whatsoever. I was pretty glum all day, ate little, and will probably go to bed before it’s even quite dark. Sooooo, not much in the way of festivity but a fine opportunity to tell the story of my first day here at Piute, back in 1983. ◦◦◦◦◦ Ten years ago, today I was hanging out on Movie Flat in the Alabama Hills [outside Lone Pine] and had been “camping” there since early March, living out of my Toyota pickup with the little shell that I’d turned into a mini-camper and was essentially money-free. But I was rock climbing on all those picturesque boulder outcrops, taking daily strolls and scrambling up peaks every week or so (a number of them the local fourteeners). ◦◦◦◦◦ I’d turned twenty-five three weeks previously…quarter of a century old. Waking up each morning at sunrise I’d sit up and look out my camper window at the glowing face of Mt. Whitney lit up deep orange or red, full of anticipation for another day. In order to feed myself and pay for gas I was hustling jobs—cleaning windows, digging ditches (yes, well, digging electric-line trenches for an old man in town), fixing little-old-ladies’ fences and scrubbing grime off their kitchen walls with ammonia-soaked rags. There were days when the entirety of my monetary assets wouldn’t buy me a loaf of bread and on those days I went to town and found some work. ◦◦◦◦◦ In exchange for meals I was also washing dishes and helping out part-time in a little café where, within days, I met “Lucky” Lorenzo Stowell. Turned out that this guy—a strapping, tanned man who looked about forty (he was forty-eight) with bushy black hair and beard—worked for the Forest Service and had just returned to the states from Ecuador prior to starting his seasonal job up north. In the interim, he was staying with his friend Robert—the guy who owned the café. So, over a couple of weeks, I became friends with this certified lunatic who ended up being my boss for eight years and who also became my mentor, friend, and brother-in-arms. ◦◦◦◦◦ As a matter of fact, the day we met, it was around lunchtime. I happened to be washing dishes just a few yards away and was barely aware of this loud, animated talker at the counter speaking to a softer-spoken man whose voice I didn’t even notice—just some random stranger who had evidently just asked the loud one what he did for a living. (Lorenzo, I soon learned, would happily talk to anyone who’d stand still.) I wasn’t paying attention but whoever this guy was, he talked very loudly. And when I overheard him say “I work for the Forest Service…I’m the Wilderness Foreman up in Bridgeport,” I instantly toweled off my hands and sweaty brow, walked right over to him, stuck out my hand and (I remember this clearly) said these words: “Hi! I’m Tim. You need to hire me.” The bearded madman turned to face me, glanced down at my extended hand, leaned back on his stool, shook said hand while looking me over, and said, (I also remember the exact words) “Oh yeah? Well, what can you do? People who work for me have to be wilderness fanatics.” We talked just a bit more, and later, because—by chance—we ended up being neighbors for the next two weeks or so. He was staying at Robert’s leased property on the lower slopes of Lone Pine Peak, right at the very foot of the Sierra front just a couple of mountains over from Whitney. (Fabulous place, another story.) By this time I’d moved into the old barn there and Lorenzo was staying in a tiny trailer less than a hundred yards away. I’d visit him the evenings and we’d drink his cheap red jug-wine while he mesmerized me with incredible stories told in a fashion I’d never heard before. He was really animated, a genuine raconteur who spoke in different voices representing a bunch of made-up characters he peppered his tales with. He didn’t talk about himself or delve into what he thought about things—he mostly told stories and spun yarns. Lorenzo and I quickly became friends. But he told me right off there was no way he could hire me. (For one thing, I didn’t have a college degree.) ◦◦◦◦◦ But then: that spring there were serious flash floods all over the Sierra—runoff from the previous winter’s massive snowpack—and one hot July day, I showed up at the café and Robert told me Lorenzo had called for me. Turns out he’d just had a bunch of FEMA money dropped in his lap for emergency trail repair—enough to hire a two-person contract “trail crew.” When I called back he told me to get an application, fill it out, tell all sorts of lies about my experience (I had none) and…he told me what to bid. “I’ve got $6000 to hire two guys for ten weeks. So you have to bid $3000—any more, you won’t get it. Three thousand. Exactly.” I remarked that, so far as I knew, it was illegal to tell potential government contractors what to bid. He laughed. Don’t recall any reply but this was merely the first of many crimes Lorenzo committed while I worked for him. ◦◦◦◦◦ In short, I got hired along with “Big Jim” Kohman, who at the time was working for Lorenzo as a volunteer just to be doing something new and different. Jim, 6’5”, was very mild-mannered and agreeable, calm, and he had a taste for the ironic and absurd—the ideal workmate. I drove up from Lone Pine on the July 31^st and we all met up that evening at Wheeler Guard Station [Forest Service housing facility, formerly a fire station, near the Sonora Pass junction along Highway 395] as arranged. I walked in and there were those two, Lorenzo gabbing away. Shaking Jim’s hand, I grinned…knew instantly that we’d get along fine. (He was the Piute ranger in ’85, ’86, and most of 1987 while I was up Robinson Creek. We’re still friends; now he’s a carpenter and lives in Santa Cruz.) ◦◦◦◦◦ I remember nothing of the next morning. I’m sure there was frenzied last-minute packing. Our first assignment was to walk to a distant backcountry station Lorenzo called “Piute” where the ranger-in-residence—I’ll call him “Kelly”—would put us to work for the next ten days and show us how to do “trailwork.” We were to deliver a note from Lorenzo (I still have it) that starts out, “Dear Kelly, please work the piss outa these two guys.” ◦◦◦◦◦ We drove to Leavitt Meadows Campground and parked at the metal bridge. Get this: I was carrying my old Kelty Tioga frame pack, ten days worth of food and clothes, sleeping bag, personal gear, my own tent & stove & fuel; a couple of books. My pack, I recall, weighed more than Jim’s—it was an honest sixty pounds if not a little more. Definitely the heaviest load I’d ever carried. In addition, we’d each been issued a fire shovel, long-handled brush loppers, a doublebit axe, and a pulaski [firefighter’s tool, like a doublebit axe but with one side of the head an adze for grubbing]. I strapped the axe and loppers on the pack and carried the pulaski and shovel in either hand. (This was now an immense load…probably close to seventy-five pounds.) ◦◦◦◦◦ The trip was an up & down, eleven mile hike on a hot day; generally following the river but much of it away from water. My hiking boots at the time were really crummy and they scrunched my toes so, not far into our ordeal, I switched to my Nike running shoes. We’d been instructed to “rock” the trail [remove loose stones from the trail tread] on the way in but we gave up on this after a few miles. ◦◦◦◦◦ Every step was an effort. I’d never gone out for ten days before; never carried a pack anything near so heavy…plus all those tools! (Later that day, learned that this was a sort of hazing—once at the cabin, we found a bountiful cache of all the tools we’d carried in.) The hike went on and on and on. My eyes were glued to the trail after the first mile or so and I remember few details aside from the heat, the sagebrushy smells, the view of imposing Tower Peak in the distance (which I climbed just a few days later with Kelly). ◦◦◦◦◦ Big Jim was hurting, too, and for the same reasons. His size fifteen feet were crammed into the largest boots he’d been able to find—size fourteens. (He ended up badly blistered.) We marched, then plodded, then staggered…tiny steps, burning thighs, aching shoulders and hips rubbed raw under the straps. Farther along the slog, we began to take many breaks. With a pack station near the trailhead, this trail had constant livestock traffic and was consequently pounded to fine sand and dust. Long stretches were much like walking on a beach (a complaint I later fielded countless times from disgruntled backpackers). ◦◦◦◦◦ Back then, all the trail signs came out of a Forest Service regional sign shop in Salt Lake City and they still had mileages. [Mileage on trail signs was gradually phased out in Wilderness Areas.] We came to one that completely demoralized us: it said that we’d come six miles from Leavitt Meadows and had six miles to go to Upper Piute Meadows. We’d only come half way?! No!! Groan! What we didn’t know was that this notorious sign was way off: it should’ve read seven miles back to the trailhead, four to Piute Meadows…and it was eleven miles in, not twelve. So we’d actually gone about two-thirds of the way. At the time, we were both seriously deflated. ◦◦◦◦◦ Eventually, we reached the flats along the meandering river in Lower Piute Meadows. Then that final, cruel climb, which just about finished us off. But then: glimpses of dramatic peaks through the trees…a barbwire stock fence and gate…lodgepole pine thicket leading down to a languidly slow-flowing West Walker River. (We’d left the drier mixed forest some miles back and had finally entered the alpine zone—it now felt like we were in the real high-country.) As we dropped down to the river crossing the view opened up into a truly stunning, National Park-caliber vista. This happened suddenly and most dramatically: dead ahead was the Sierra crest and Yosemite Park boundary, only a few miles away. Hawksbeak Peak dominated the skyline—craggy, with classically pointed summit (and still largely snow-covered after the monumental winter). We took our shoes off to wade across a partially submerged log bridge. Final tottering steps up to the cabin which proved to be the quaintest old-timey log cabin imaginable, perched on a knoll just above the most gorgeous mile-long meadow I’d ever seen, buried deep in this glacier-carved valley. The cabin had a giant, roofed porch of laid stone. (A good covered porch is maybe the most important feature of a house, sez I.) ◦◦◦◦◦ The ranger wasn’t home so we had awhile to take all this in. And I vividly recall these, my first impressions: dripping sweat, clothes drenched, I heaved my pack off and leaned it against the porch railing—my feet, hips, shoulders, thighs, back were fried. I put both hands on that thick log rail, leaned forward, surveying the scene. The delightful sensation of a gentle breeze cooling my sweat-soaked T-shirt, the sensation of sudden lightness, almost floating. And this gen-u-ine, real live log cabin (I’d never been in a log cabin)—somebody’s home!—in a place that felt like heaven…a haven, a sanctuary, in an ideal mountain setting. It was, flat out, the finest “scene” I’d ever run into and I felt awed at the idea that someone actually got to live and work at a place like this. To live there. I distinctly recall thinking, “This right here, this is it, Tim. This is the best place…ever. It doesn’t get any better.” And I said to myself (actually, this was more of a feeling, a certainty) Whatever it takes—however long it takes—you’re going to live here some day. Never had I wanted anything so badly, and never since. It was a powerful feeling, the way life-changing decisions usually are. ◦◦◦◦◦ The ranger, who I’m calling Kelly for reasons I’ll explain shortly, showed up before my sweat had dried. He was a red-haired Irish crazyperson; loud, brassy, dogmatic, naturally wired. Of course, I felt awed by him. He invited us inside after unlocking and swinging open a metal-grated outer door. I quickly took in the rustic bunks and table, shaft of light illuminating dust in the somewhat dark space, ladder leading to an open half-loft…funky antique wood stove…two bunks made of peeled logs and boards with stained, ancient-looking cotton-batting mattresses…tools hanging from nails on one wall, axes & shovels & sledgehammers in the corner…old aluminum coffee pot and cast-iron skillets. I was enchanted and, although I’ve undoubtedly romanticized this day in my mind, I’ve been telling people for years that when I saw this place that first time I felt like I’d finally come home. ◦◦◦◦◦ It took five summers to get the job, after two rangers had moved on. Kelly looked to be a lifer but two years later he committed a grave error. He’d just come out of the woods and drove to the Forest Service office in Bridgeport where he was overheard on the phone after calling a friend in Berkeley to put in an order for a bag of weed (According to the office gossip, these immortal words: “Send me an ounce! I need it, BAD!”) It was a Saturday and he thought he was alone but, with his always-loud voice, several people in other rooms heard him clearly. This naturally blew up into a big scandal and Kelly had to go. So big Jim took over in 1985, which suddenly opened up a spot for me to take the Robinson Creek position after my summer as a volunteer (1984, the year after our ten-week trails gig). Then, end of August 1987, Jim had had enough of the remoteness and solitude and was ready to move on himself. I was more than keen and spent a few weeks up at the cabin to end my third ranger season. ◦◦◦◦◦ Ten years on, I love this place as much as ever though no doubt I’ve grown somewhat jaded about things that were once pure magic—after all, “it’s just a job.” (No, not really….) But still, nightly, I sit on the porch (if the bugs are bad or if it’s wet) or down in the meadow on my little folding chair for the big view, and feel thrilled to be here watching the last light crawl up the peaks at sunset or the moon coming over the ridge. This place is my home, my sanctuary; the setting for my moods and contemplations. I live with horses and cats, my “neighbors” are wild animals. Despite the insecurities and built-in temporary-seasonal nature of the job [wilderness ranger positions are classed as “temporary seasonal”], I could never hope to find one finer or better suited to my personality and quite specific needs. This is my true place, my ecological niche—to live a simple, solitary life of toil and sweat on the mountain. I am the steward (Lorenzo always emphasized this) of a discrete chunk of land, a “country,” in the sense we wilderness-types use: Piute Country. I have a relationship with this land and am part of its web of life. No one, literally no one—ever—knows this place better than me. I could never have made it here except for my parents and Robert Frickel and Lorenzo Stowell. I thank them all. Nor could I have pulled this off without good luck, near perfect timing, and patience. To be able to stay here—live this sort of life and keep coming back—I’ve had to give up a lot of things most people (that is, modern American-type folk) consider essential. Not only have the so-called sacrifices been worth it, they’ve shown me how little we truly need. “The man is richest whose pleasures are the cheapest.” (Thoreau) Security is an illusion. And I’ll probably pay for my decisions later in life when I’m broke-down and poor. But, meanwhile, I’ve been showered with grace and good fortune. They’ve been heaped upon me. I’ve seen things, done things, and had way more fun than ‘most ev’rybody. Thanks for everything! The good and the bad!

Copied inside the cover of this volume of Piute Log:

From the day I first set foot in interior Alaska, and more specifically on Richardson Hill, I knew I was home. Something in me identified with that landscape. I had come, let’s say, to the dream place. Not exactly, of course, for there never was an exact place, but here was something so close to it that I could accept it at once. I think such a recognition must be rare, and I was extremely fortunate to have it happen in the way that it did. Such a purity of feeling, of joy and of being in the right place, I have not often felt since.

John Haines, from Living Off the Country

I ended up spending sixteen full seasons stationed at the Piute Meadows cabin over a twenty-one year stretch. After 1988, I missed only one—1998—when I was a full-time packer for three Toiyabe Forest trail crews. My last, 2003, was the year a new supervisor took over, a man who proved to be the-boss-from-hell (everybody gets at least one…). The following spring, when I received my re-hire packet, it came with a new job description: there were to be no more rangers stationed in specific areas, no more use of livestock, no more basecamps even. It couldn’t have been more obvious that I was being asked to leave. It almost broke my heart and I never went back, never will. But, things usually work out for the best—this departure set me up for my almost-but-not-quite-as-good gig at Crooked Creek, in the White Mountains, where I met Dylan, married, and started a whole new phase.

Sunday, April 8, 2018

The Demeaning of Life...Chapter 7. Why Does Everything Have to Be So...Complicated?

Interviewer: What do you mean by functional complexity?

Schützenberger: It is impossible to grasp the phenomenon of life without that concept, the two words each expressing a crucial idea. The laboratory biologists’ normal and unforced vernacular is almost always couched in functional terms: the function of an eye, the function of an enzyme, or a ribosome, or the fruit fly’s antennae. Functional language matches up perfectly with biological reality. Physiologists see this better than anyone else. Within their world, everything is a matter of function, the various systems that they study [are] all characterized in…functional terms. At the level of molecular biology, functionality may seem to pose certain conceptual problems, perhaps because the very notion of an organ has disappeared when biological relationships are specified in biochemical terms. But appearances are misleading. Certain functions remain even in the absence of an organ or organ systems. Complexity is also a crucial concept. Even among unicellular organisms, [there] are processes of unbelievable complexity and subtlety. Organisms present themselves to us as a complex ensemble of functional interrelationships.

Marcel-Paul Schützenberger, interview (1996)[1]

The simplicity and tidiness of the mechanistic worldview has proved ideal for textbooks and an ever-increasing number of publications written for laypeople, a genre with the unfortunate name “pop science” (short for “popular science”). In the not-too-distant past, serious scientists were discouraged from publishing their findings outside of respected scholarly journals. Not only is this no longer the case, but some scientists forego publishing their findings in technical journals and present them in book form, using language accessible to laymen. The result has been a tremendous leap in the scientific literacy of an interested and voraciously curious public. Likewise, modern science writers routinely cite other popular works in their bibliographies. By explaining complicated matters in clear, non-technical language and simplifying challenging material, cutting-edge scientific topics are made available to the masses as never before.

No author consciously intends to restrict readers’ awareness of nature’s complexities (which, indeed, usually require at least some explanatory simplification for the sake of intelligibility). Still, widely read books on an array of biological topics often portray not only the more esoteric but “normal” life processes in an overly simplistic fashion, glossing over subtleties or skipping complicated explanations. This is often necessary to preserve narrative flow; it is altogether too easy to get diverted or bogged down in details. But the sort of oversimplification I wish to draw attention to does not always benefit a technically fluent audience. Then again, in many cases this tendency toward simplification and generalization may be an unavoidable consequence of trying to reach readers with broad ranges of knowledge.

In truth: without exception, everything relating to living matter is staggeringly complicated. Educators abridge descriptions of life-processes to bring such matters within intellectual reach. Often, this abbreviation is just a matter of condensing large amounts of information into manageable form. But an author who promotes the idea that nature operates by “simple” rules is, consciously or otherwise, advancing a mechanistic stance—one that aims to smooth out nature’s often tortuous pathways.

Take any generalized written account of, say, mitosis. Readers will often be fore-warned that the subject of cellular division is both extremely involved and highly technical. Following this brief disclaimer, multiple layers of mentally numbing intricacy are not merely be downplayed—typically, they will not even be alluded to again. Nor will the collective causal effects conferred by such complexity even be touched upon as a gentle reminder that can impart valuable perspective. Incurious readers seldom think to ask tough questions, having (literally) been schooled to assume that the entire train of events takes place automatically and is not particularly noteworthy to begin with.

Another important issue is the habitual time lag in imparting the latest information. When fresh data or exciting findings appear—information that might bring to light new details and add nuance to some biological model—there is typically a lengthy delay in their conveyance. Many people still rely on books and magazines as their preferred choice when it comes to learning about things. Especially for lay audiences, the imparting of important new information in printed form can sometimes be held back for years. (Indeed, presenting up to date facts and ideas that readers may not have heard about is a major impetus behind this work.) Another obstacle in providing the public with advanced information can be traced to textbooks; many are revised repeatedly and distributed as new editions without antiquated details being checked for truthfulness and retired when appropriate; a good deal of superseded or downright false material is disseminated in this fashion.[2] Finally, the broad range of factual veracity found online has created a real impediment to finding accurate, reliable information. Hopefully, this serious problem will somehow be mitigated in coming years.

Long after it should have become universally recognized that cells are far more complicated than was previously imagined, they continue to depicted in ways that make light of their extraordinary intricacy. Researchers continue to unravel our most tangled riddles and many biologists believe that, sooner or later, various lingering unknowns will be settled. Meanwhile, thanks to the wondrous qualities of what I call acute bio-complexity seldom receiving a fitting level of emphasis in textbooks and works of pop science, our “scientifically engaged” public has ended up with a flawed and inadequate view of how living things operate. (This, partly a result of a tendency to deliberately dumb-down media and internet renderings.) The true wonders of nature merit highlighting when appropriate; acute bio-complexity is an attribute of life that deserves to be kept in mind continuously.

Here are two passages from an excellent book about the cell and current (circa 1996) biochemical research by Boyce Rensberger—at that time, science writer for The Washington Post—which are illustrative of this effectively trivialized approach:

The discovery of self-assembly explains many events in cells that once seemed utterly mysterious. It is akin to learning that the steel skeleton of a building will assemble spontaneously once a load of girders is dumped at a construction site. The genes cause a load of protein molecules to be synthesized in the cell, but the proteins, needing no further control, spontaneously assemble themselves into larger structures. The plan of the final result is implicit in the structure of the components.

To back up this assertion, he then cites two classic examples of structural self-assembly: the case of microtubules (which spontaneously form when molecules of tubulin—a protein synthesized in all cells—join together in a uniform spiral pattern) and the self-ordering of phospholipids into the bilayer membranes common to all eukaryotic cells. Rensberger promotes a sense that such auto-assemblage is marvelous, yes, but simply the result of an opportune coincidence of chemical properties.

Still, Rensberger’s descriptions are a bit misleading (given that the two key processes are far from entirely automatic and, additionally, the components have to first be fabricated within the cell). As for microtubules: a number of specialized protein machines assist with the construction of new (and degradation of old) tubules along with their attachment to organelles or the cell wall. In the case of lipid bilayers, thanks to the powerful chemical self-attraction of lipids in an aqueous solution, they readily assemble into sheets or vesicles. However, cellular membranes are actually constructed piecemeal by the endoplasmic reticulum, then further processed in the golgi and, finally, are transported in vesicular form to fuse with some targeted portion of the membrane.

In the second excerpt, Rensberger again de-emphasizes complexity in favor of fostering an impression of straightforward simplicity:

Amazingly enough, some of the regulatory DNA sequences are not situated near the gene they control. They may be hundreds or tens of thousands of bases away. And yet, if the right regulatory proteins don’t bind to them, the gene won’t be expressed. How can this be? How can the gene or the RNA polymerase “know” whether certain proteins have grabbed onto the DNA strand…? Simple. DNA is flexible. It simply forms a loop in itself, bringing the distant regulatory protein into contact with other proteins on the promoter. In the case of the beta hemoglobin gene, there are several regulators…that speed up the gene-activation rate to varying degrees and some that slow it down to varying degrees. Somehow they work it out among themselves how often the gene should be allowed to express itself.

My intention is not to denigrate Rensberger’s excellent book—still one of the best overall accounts of cellular life. These two examples are merely representative of the cavalier language and rhetoric sometimes used to explain such phenomena. Many contemporary books about these types of subjects are peppered with similar instances; when some involved process requiring multiple steps and coordinated assistance is described, the whole affair is frequently put across in a fashion that deftly underplays its elaborate nature. (A later chapter will examine this issue in more detail.) What Rensberger has just described here describes only one step in a remarkably complex process involving thousands of molecular helpers. And there is nothing simple about any of it.

Unquestionably, individual molecular interactions are events involving straight-forward chemical and electrical attractions (or repulsions). The occasional use of superlatives like “amazing” and “wondrous” in books like Rensberger’s Life Itself (or any biology textbook) merely allude to the uncanny ways in which inanimate molecules behave. The reader is routinely assured that such things happen automatically and according to the types of rationally ordered but non-intentional activity under discussion here. (Often times this disclaimer is accompanied by a comment reminding the reader that there are no mysterious agencies involved, so strange can these happenings seem to non-scientists). Unquestionably, some of the complicated issues discussed here have by now been explained in some measure. Some have not. But answers to many of my own pointed questions are not to be found in typical popular science books. The kind of information I seek is more likely located in the plethora of scholarly literature found in scientific journals (published at a rate of some thousands per day).

One thing I have observed while reading technical papers—a noticeable pattern: various molecular participants arrive on the scene of some reaction to play a part in a key process with no word of where they came from, how they were manufactured, or what regulatory agency was involved in their appearance. Such tangential information may have been deemed non-essential or beyond the subject matter’s scope. Perhaps it is unknown. But the absence often strikes me as intentional; things simply “show up.”

And show up they do…. In their frenetic comings and goings, molecules display a sort of purposefulness that only higher-level organisms are thought to enjoy. Are their coordinated actions, taken together, purely mechanical? Microbiologist James Shapiro writes about “the growing realization that cells have molecular computing networks which process information about internal operations and about the external environment to make decisions controlling growth, movement, and differentiation”:

Bacterial and yeast cells have molecules that monitor the status of the genome and activate cellular responses when damaged DNA accumulates. The surveillance molecules do this by modifying transcription factors so that appropriate repair functions are synthesized. These inducible DNA damage response systems…include so-called “checkpoint” functions that act to arrest cell division until the repair process has been completed…. One can characterize this surveillance/inducible repair/checkpoint system as a molecular computation network demonstrating biologically useful properties of self-awareness and decision-making.

This is not a conventional portrayal of mindless molecules at work. Recall that, in the second excerpt from Life Itself, Rensberger wrote of these regulatory enzymes: “Somehow they work it out among themselves.” Obviously, Rensberger did not intend to allege truly purposive action being displayed in using this offhand way of explaining the solution to an arcane problem, but simply sought to carry on with his narrative. In the course of my research, though, never have I seen so much as a hint of there being anything out of the ordinary about the way protein machines bustle about in what are described as resolute teams, with individual members making crucial decisions.

Returning to my original statement regarding the nature of life: it possesses its own form of intelligence and a quality of self-directedness that is displayed by all organisms—even manifesting at the molecular level. It would be a mistake to equate this kind of willful discernment with its human analogue. Nonetheless, these traits are called to mind as it becomes ever more obvious that living things operate according to singular types of molecular organization—with involvements that go well beyond the ordinary chaotic collisions that cause things to proceed in cell-world. And behind all such activity there is often an element suggestive of intent.

In fact, enzymes display intelligence-mimicking behavior in the form of a functional property called allostery, made possible by an enzyme’s capacity to change shape such that an active site can no longer bind with its substrate (as discussed in Chapter 5.)

Say a particular enzyme’s job is to catalyze a reaction that produces a chemical whose concentration causes problems, maybe even a fatal toxicity, when exceeding certain limits. How does it “know” when to stop? Answer: the catalyzed reaction’s product (or, if the reaction results in more than one product, one of them) also serves as a control molecule. When this product’s concentration reaches a certain level, it begins binding to a second active site on the enzyme, changing the enzyme’s shape so that the substrate is no longer able to dock, thus halting production of the chemical in question. This is what is known as a negative feedback loop,[3] a vital feature exhibited throughout nature from the nano-scale to the planetary (where, for instance, forms of self-correcting regulation are seen at work in the carbon and hydrological cycles).

Allostery forms the basis of regulation in cells. Physicist-turned-microbiologist Peter Hoffman adds extra perspective on the intricacy of these regulatory systems:

There are more complicated schemes that involve vast networks of interacting enzymes. The product of one enzyme may act as the control molecule for another enzyme, either enhancing or inhibiting its activity. The product of this second enzyme may again control the first enzyme, forming a two-enzyme feedback loop…or the product may influence a third enzyme, which influences a fourth, and so on. Complicated schemes of feedback loops and mutual enhancement or inhibition provide the computing power that makes living cells seem intelligent.

This dual-functionality of proteins—their ability to both carry out reactions and adjust results to some necessary end—is a crucial feature in the regulation of cellular metabolism. Allosteric enzyme activity is essential to prevent the chemical chaos that would result if not delicately tuned to a cell’s strict requirements. Jacques Monod, who discovered the phenomenon in Paris in the early 1960s while working with François Jacob on bacterial cell metabolism, felt the significance of allostery to be so indispensable that called it “the second secret of life.” (The “first” being the genetic code itself.) Horace Judson, in The Eighth Day of Creation, offers this:

Allosteric proteins were relays, mediating interactions between compounds which themselves had no chemical affinity, and by that regulating the flux of energy and materials through the major system, while themselves requiring little energy. The gratuity [“the freedom from any chemical or structural necessity in the relation between the substrate of an enzyme and the other small molecules that prompted or inhibited its activity”] of allosteric reactions all but transcended chemistry, to give molecular evolution a practically limitless field for biological elaboration.

These are all attributes whose subtlety deserves more emphasis whenever cellular functions are under discussion. Instead, we find a marked tendency to de-emphasize the sophistication of features such as auto-regulation. By the same token, it is not only the subtlety and phenomenally clever quality of all these things that boggles and bewilders, but the way (despite their being completely entangled) these activities are so precisely coordinated. This “higher order” of interaction is what has such weighty implications: this is where the impression of intelligence and intentionality is grounded.

Whenever I read descriptions of highly involved matters such as allosteric feedback loops imediately followed by assurances of their simply resulting from predictable, ordinary molecular interactions, such guarantees sound hollow and forced. This leaves me further convinced that life’s creative impetus is the agency behind such beyond-belief sophistication. While attempting to always keep in mind the risky proposition of relying on an emotional response to things one finds intellectually difficult to accept, I continually find myself dubious and forever questioning accepted narratives. For an example of my thought-train: regarding mitosis, How do all the molecular players involved gather and position themselves at the outset? Is there an overall strategy? How do they know exactly when to perform their assignments, avoid interfering with other teammates, and recognize when to cease and desist? How do they all make it to the game on time? What “master gene” calls them to their tasks? What controls those master genes? How did such an elaborate system come to be in the first place?

And I hear the committed materialist’s answer: Yes, yes, yes…we know how each of these things take place: it’s all by gene-controlled chemical signals…markers, couriers, vesicular transport. Regulatory genes. Allosteric proteins. The subtlest details are being worked out even now; these automatic processes are well-understood, at least in general outline. It’s all chemistry!

About those “upper-echelon proteins:” whether self-regulating or controlled by genes—the ones that initiate and direct the actions of whole assemblages of nano-scale machines—how do they discharge their responsibilities? What orders them up and accounts for all the functions carried out during their vital, higher-level tasks? How are the actions of allosteric enzymes coordinated with those of genes, when neither has controlling influence over the other?

And now, one last example that underscores yet another aspect of these profound, multifaceted interactions. During the various stages of mitosis, including DNA replication, genes remain dormant. (In the case of Homo sapiens, for some hours.) Hence, all instructions relevant to cell division have to be issued beforehand; all the suites of enzymes and protein machinery involved have to be synthesized, tagged for recognition, and somehow programmed in advance. Many of these will need to be repaired or replaced—perhaps several times—while they wait. Once provided with final marching orders, though, all these soldierly nanomachines rejoin other troops careening about the cell, killing time until a molecular bugler sounds the call.

Andreas Wagner, specialist in the new field of computational biology, provides an answer (of sorts) to all these quandries and seeming bottlenecks. (This elucidation is likely about as straightforward as can be achieved using plain language.) He writes:

The answer lies in regulation…. And what regulates the regulators? Simple: more regulators…. And what about these regulators, how are they regulated? Through other regulators. All these regulators often form daisy chains, regulation cascades….[This] would seem enough complexity…but alas, regulation can get much more complicated: Regulators form not just linear chains but complex…circuits where regulators regulate each other…. Each [activates or represses] a gene [and] can twiddle the knobs of other genes—up to hundreds—outside the circuit…. Inside a cell these influences create a symphony of mutual activation and repression, where each instrument in the orchestra of genes responds to the melodic cues of others with its own notes, until the circuit reaches an equilibrium—like a polyphonic closing chord—where the expression of circuit genes no longer changes and their mutual influences have reached a balance.[4]

Wagner’s portrayal of symphonic regulation provides an apt context for the asking of three Big Questions that draw near the heart of what I have termed Natural Design: At what point do all these circles close? What is the nature of these highest levels of organization and control? Can something be identified that, ultimately, is “in charge”? Whatever it is, whatever might be considered the “conductor,” appears to operate by way of a multilayered complexity that is beyond normal means of description. Or is perhaps not within reach of our imagination. This…thing…is rooted in the underlying character of life. An overarching executive “directing principle” need not operate by way of some centralized agency, after all. This, a natural way for humans to conceptualize the matter, simply reflects our limited intellectual and imaginative capabilities.

Immanuel Kant, whose thoughts on these particular concerns are still pertinent, believed the whole subject inaccessible to causal explanation. As he urged, we might be better served by simply taking life’s nature as a given and let biology proceed from that starting point. There is, after all, precedence for his stance: this being essentially the way physicists treat matter, time, and the elemental forces—core principles matter not subject to further elucidation. For instance, there is no point in even asking why protons and electrons bear charge. They just do. Case closed.

But, given what we now know about cellular regulation, it is feasible to conceive that life and all its processes in their entirety are synchronized, modulated, and controlled by one colossal network of self-regulating feedback loops. There is no conductor; while biologists have long known this, it is a only in recent years that we finally have the means and proper framework to finally begin to piece together scenarios that can encompass systems of the sort of complexity found throughout nature.

One matter that probably should have been addressed earlier in this discourse: the functionality, the “behavior,” of atoms and molecules—though amazing—is always straightforward and wholly foreseeable. Every electron in the universe is absolutely identical. (The same is true of all the subatomic particles.) Atoms of specific elements vary in the number of neutrons and electrons they carry but individuals of the different forms are identical. Each form has distinct properties and acts upon other atoms in ways that may vary with conditions, but each form is eternally the same. In this sense there is no mystery whatsoever in the way chemical substances interact; indeed, few things are more predictable. The speed and fidelity of enzyme/substrate interactions, for instance, is automatic and unvarying. Mistakes made during the replication of DNA are remarkably rare because of the reliability and constancy of the participants’ actions. It is this level of uniform consistency that makes life possible…and its possibility so extraordinary. What I doggedly contend to be beyond normal chemistry is the essential nature of those myriad interactive systems and their extreme degrees of coordination.

Protein form is yet another issue, each specific type having presumably evolved step by step in Darwinian fashion (based on selection for functionality). It is known that individual amino acids can be substituted through time with no adverse effect on the protein’s performance. On the other hand, a single missing or misplaced amino acid can be catastrophic, resulting in sickness or death. Their crucial folding process, as discussed previously, is based on particular properties belonging to the different amino acids and takes place semi-automatically (though often requiring assistance from chaperones) depending on the charge of the different species or their chemical rapport with water molecules. They vary tremendously in size: hormones like glucagon, which has only 29 amino acids, to huge proteins like titin, which has over 34,000.

In any case, we would benefit from there being a suite of exclusive descriptive words to capture different aspects of nature’s daunting complexity, this being one of its most distinctive and fundamental characteristics. While it should be standard custom throughout the study of nature to routinely reference this complexity as a subtending biological theme, this would only result in excessive qualification. Which, unfortunately, would serve to further burden the communication of information that is already terribly involved at the outset. In fact, the exacting approach required in describing multifaceted natural processes has always presented conceptual and descriptive challenges, given that the capacity to sustain awareness of many things interacting simultaneously is a gift few are endowed with. Still, such awareness—even an approximation—is crucial in the effort to understand life at its deepest levels. Fortunately, sophisticated digital visual aids are proving to be a tremendous tool and will only improve over time.

At present, though, many individuals (including leading experts in their fields) often create an impression of not being fully awake to this crucial truth: in biological systems, at all scales and each level of organization, different types of the attribute Marcel-Paul Schützenberger termed functional complexity are in operation. And at each organizational stratum, new structures or regularities appear: that property known as emergence. Each stratum employs its own logic. And each calls for its own manner of describing relationships between parts or processes that often are not even present at levels above or below. In fact, life could be said to be an emergent property arising from a consortium of emergent properties.

After some reflection, few people would likely find anything smacking of falsehood in these claims. Recognizing emergentism as an essential feature of all life processes has become accepted truth. Still, I continually observe in others an apparent inability to grasp the subtext beneath nature’s profound intricacy. There is perhaps an unconscious resistance to the idea that this ineffable quality has pivotal meaning on its own. Acute biological complexity is rooted in one of life’s most distinguishing traits: the capacity of its productions to be both self-governed and harmoniously organized. This shadowy, indefinable quality fails to explain things but provides support for collectively reassessing emergent properties—a movement already well underway.

[1] Marcel-Paul Schützenberger (1920–1996) was a member of the French Academy of Sciences, a medical doctor, mathematician, and according one contributor to a memoriam in The Electronic Journal of Combinatorics (Volume 3, Issue 1), Herbert Wilf, Schützenberger “was interested in (and therefore passionately interested in) the many flaws in the Darwinian theory as it is commonly presented…. [He] became one of the first distinguished scientists in the world to point out that a theory of evolution that depends on uniformly randomly occurring mutations cannot be the truth because the number of mutations needed to create the speciation that we observe, and the time that would be needed for those mutations to have happened by chance, exceed by thousands of orders of magnitude the time that has been available.”

[2] Paleontologist Simon Conway Morris referred to such information being “still routinely cited…in that zoo of good intentions, the undergraduate textbook.” A classic example is the formerly ubiquitous embryo drawings by Ernst Haeckel illustrating his long-discredited “biogenic law” with its tongue-twisting axiom, “ontogeny recapitulates phylogeny,” found in generation after generation of biology texts. Only 30 years after Haeckel produced the compelling drawings (around the turn of the twentieth century) his biogenic law had been refuted, yet they continued to be reprinted for decades.

[3] Negative feedback occurs in a system or process when some function of its output is “fed back” in such a way as to reduce the effect of perturbations and help maintain a state of equilibrium. The classic example is the effect of a heater’s thermostat.

[4] While remaining true in spirit, this excerpt is a significant reduction of Wagner’s much lengthier account.

Sunday, March 18, 2018

Piute Log...Kingfisher Surprise 1995

28 Sep (Thu) Last day at Piute! Up at five, only 28° on the porch. (I’m actually writing this down in Lone Pine a couple days later.) ◦◦◦◦◦ Got ready to go. By the roaring stove and lantern-light I tried to catch up as much as possible in this log. I’d gotten a lot done yesterday but there were still many loose ends and the unending final this’n’thats. Nonetheless, an easy time of it. Unhurried but full of urgency…autumn personified, change in the air. A final sweeping of the floor, a closing of doors. Anticipation and nostalgia wrapped up together. All in all, a mood hard to describe. Spent part of my last hour out in the meadow, kicking down shit piles so the grass’ll grow easier next spring. ◦◦◦◦◦ I locked both doors and said goodbye to Piute and, as usual, didn’t look back. (Mostly because I was trying to get the horses in line and didn’t have a chance.) Did cast a last look over my shoulder at Hawksbeak and breathed a little thanks. Just past the gate, not even noted at the time, the first part of a strange occurrence. ◦◦◦◦◦ Had just gone through the gate and was getting my horses slowed down and into their rhythm. The silence disappeared all of a sudden when I heard a kingfisher’s call from down in the river gorge—that shrill, sorta metallic cackle. I’ve always been fond of these strange, secretive birds. They’re so different. Odd, maybe, that we only have the one member of a family that’s more common in other parts of the world. They’re exceptionally alert birds and always leave a perch when they see you so it’s hard to get good looks. Had noticed earlier this season that they haven’t been flying past the cabin much this year and then had the quirky thought that it was somewhat odd that I’d never found one of their feathers. And that I would like to. (The wing feathers would be very pretty.) [I collected feathers, something I’d been doing for many years.] “I could find one today! Think I’ll find one on the trail! Or, at least, a hawk feather…or something.” That was the “thought” I heard in my mind. ◦◦◦◦◦ This wasn’t the usual internal dialogue—my own voice talking inside my head; rather, it was sort of a drawn-out feeling, more of a wordless sentiment somewhat like in a dream. But there was a distinct sureness to the intuition that I’d find a feather and it felt just like other times when I’d “known” I’d find an arrowhead or some such thing. But I didn’t find a feather by the trail and didn’t even think about it again and never would’ve except…. ◦◦◦◦◦ When I got home to Lone Pine on Friday evening (the next day), Diane was still at work. In the dusk, I moved all my stuff into the shack and, among other things, cleared the kitchen table before starting to prepare supper. In the dim light of the kerosene lantern I noticed several small wing feathers sitting on the windowsill by the kitchen table. I only glanced at them in the poor light but had the passing thought, Hmmm…looks like from a woodpecker. Still hadn’t checked them out the next morning when we had breakfast. Diane said, “Oh, did you see these? I found ‘em. D’you know what they belonged to?” Picked one up and looked at it for about five seconds before I suddenly realized what it was. And something else was trying to come up to the surface. Then I remembered. Amazing! I was just thinking about finding one of these myself! Diane asked again, “Do you know what it is?”and I replied, “Yeah, actually…it’s from a belted kingfisher. One of the primaries [the long “flight feathers”]. “How do you ‘know’ that? Just by looking at it?” Like lots of people, Diane found this particular talent of mine fairly esoteric. “Hard to explain. I just know. For one, I can tell what size bird it was. And, this steel-blue color? That’s the real giveaway. There’s no other bird in the US with this color. It could only be a kingfisher. Amazing, though—I was just thinking a couple of days ago when I was riding out…heard a kingfisher right after leaving the cabin and wished I could find one of their feathers ‘cause I never had before. Where’d you find these? Diane laughed and said, “By the trail. The day I left the cabin [two days before me]. I dunno…a few miles down.”…. ”You…found these by the trail?”….”Yeah. If I hadn’t, you probably woulda spotted ‘em yourself as you rode by.” Well. ◦◦◦◦◦ So: back to Thursday. I had a lovely ride out, slow for old Val’s sake. (Greta recently informed me he’s “only” twenty-three.) Saw no visitors, no otters, few birds. Heard the solitaires singing, staking out their winter territories. Checked out some old scenes in new ways but spent much time thinking. The aspens are still green—only a few branches starting to go yellow. This is the first season I’ve come on after the aspens had already leafed out and the first I’ve left before they’d dropped their golden load. Made me sad to think of what I missed and will miss. ◦◦◦◦◦ Unloaded on the road at the truck and trailer and didn’t even go over to say bye to the pack station folk. It was after sunset and I still had much to do. Dropped the horses at Wheeler, said goodbye to them as well. To the warehouse, got all my stuff unloaded by flashlight, took a shower, and finally started dinner (a can of soup) at nine. I’d been going steady for 14 hours.