Saturday, March 26, 2016

The Demeaning of Life...Part V

Here’s the next installment…I would say one of the best, inspiration-wise. Most of my readers know at least the rudiments of cell biology, but here’s a look into their workings that should offer some genuine surprises. I believe this section paints a picture of Cellworld unlike any you’ve read about in books, emphasizing some things that are typically downplayed or not even mentioned. Truly amazing stuff….

V.  The Cell is Beyond Beyond Belief


Cells are the atoms of life, and life is what cells do.
                                                                            
        Franklin M. Harold, In Search of Cell History

We have learned to appreciate the complexity and perfection of the cellular mechanisms, miniaturized to the utmost at the molecular level, which reveal within the cell an unparalleled knowledge of the laws of physics and chemistry…. If we examine the accomplishments of man in his most advanced endeavours, in theory and in practice, we find that the cell has done all this long before him, with greater resourcefulness and much greater efficiency.
                   
       Albert Claude, from his 1974 Nobel Prize lecture[1]
                            
Consider another illustrative example of unconsciously life-belittling thought. (Such things are so prevalent in our culture that they go unnoticed, in the same manner that people unwittingly adopt advertising slogans as figures of speech.)  

How many times have you come across a commonly used expression: “primitive life form”? Most of us, without pause, instantly conjure vague mental images of a worm-like organism…something with very few “moving parts,” something considerably less complicated than its modern-day descendants. In the same way, single-celled creatures are persistently viewed as being simple compared to higher forms. These are grave misconceptions; each and every living form is an unbelievably elaborate entity. The simplest known self-sustaining organisms carry out around 550 distinct biochemical processes. Single-celled varieties are merely small, not simple. 

Another quick review to provide a bracing sensation of unalloyed amazement:

People commonly lack awareness of the difference in size between prokaryotes and individual eukaryotic cells.[2] A run-of-the-mill bacterium like E. coli (2 µm) is roughly a thousandth the volume of an average-sized (20 µm) eukayotic cell. This makes it somewhat easier to begin to grasp the fact that while a human body is made up of those 60 trillion—that’s 60,000,000,000,000—cells, there are significantly more prokaryotic microbes colonizing it (number-wise, primarily in the gut) than there are tissue cells. Over ten times more, ladies and gentlemen.

Also unappreciated is the sudden appearance of eukaryotes in the Cambrian period (over 500 million years ago) after three billion years of unicellarity, and the subsequent explosion of multicellular life forms with entirely new subcellular systems—facts not much less amazing or improbable than life’s beginning in terms of the difficulty of explaining how such a radical shift in forms occurred. And made even more mysterious by the question of why it took so long and, unlike so many biological innovations, occurred but once. According to molecular biologist Nick Lane, “The void between bacterial and eukaryotic cells is greater than any other in biology…. [Their origin] looks far more improbable than the evolution of multicellular organisms, or flight, sight, and intelligence. It looks like genuine contingency, as unpredictable as an asteroid impact.”

Eukaryotic cells—for the sake of brevity, what will primarily be under discussion here—are often referred to as “miniaturized factories.” This analogy doesn’t quite capture the true state of affairs; more apt would be to think of them as highly industrialized cities. (A cell’s organelles—its internal organs—are, quite literally, the factories.) But the whole thing is contained within a discrete province invisible to the human eye, with more separate components than a Boeing 747. Paradoxically, this tiny metropolis is immense: there’s room in its interior for millions of busy molecules.

To ponder the frenzied yet perfectly coordinated activity in each and every cell is an almost futile undertaking. Humans simply aren’t equipped to form mental images of what actually goes on in a cell’s liquid interior. It’s not the scale so much as how things behave in that close-packed setting; everything about it is utterly foreign.

Each cell has an enclosing plasma membrane. Structurally, it is composed of identical molecules called phospholipids, which each have a head end made of hydrophilic (“water loving”) phosphate attached to two lipid tails. Lipids, a fatty substance, are hydrophobic. In water, phospholipids will spontaneously assemble themselves into a two-layered sheet—a lipid bilayer—with the hydrophilic phosphate heads outermost and the water-repelling lipids sandwiched between. The phosphate heads are strongly attracted to one another, forming a resilient outer or intracellular membrane that instantly repairs itself if punctured or damaged. In the words of molecular biologist David Goodsell, “Each individual molecule rotates like a top, and its hydrophobic tails wag and flail. Lipids also slide rapidly past one another, always staying in the sheet, but randomly migrating sideways.”

Lipid bilayers, absolutely critical for all eukaryotic life forms, are functionally ideal in many regards. Small molecules, like oxygen and carbon dioxide, can readily cross the plasma membrane by simple diffusion while it remains impervious to larger ones thanks to the tightly entangled lipid tails. Large constituents—both waste products leaving the cell and essential materials entering—pass through by way of an array of molecular “gatekeepers.” These structures, some quite complex, operate in various ways to allow different classes of chemical substances free passage. Aquaporins, for  instance, are simpler affairs known as channels that allow water molecules to diffuse in and out of the cell. Numerous kinds of receptors, plugged straight through  the membrane, accept messages and pass them into the cell. Others, having received instructions, seize specific molecular prey in passing and drag them through the membrane into the interior. The receptors and gatekeepers imbedded in the surface of a single cell number in the tens or hundreds of thousands, held in place by the same forces that align the phospholipids. And, like phospholipids, the various gates and channels and receptors migrate freely within the confines of the membrane.

The  flexible outer membrane is stiffened by an elaborate internal cytoskeleton, which is able to maintain (or alter) a cell’s characteristic shape while continually changing.[3] It consists of a jungle-like scaffolding of compression-resistant microfilaments and tension-bearing intermediate filaments (that anchor the organelles). A third system of sturdier, hollow microtubules creates transportation and communication networks by furnishing interconnecting conduits for the orderly movement of materials and information. All three types serve multiple purposes. Microtubules and microfilaments are both continually being degraded, renewed, reattached, and re-anchored in new locations. On average, an individual microtubule lasts for only about ten seconds.

A cell’s inner matrix, or cytoplasm, is filled with a liquid—the cytosol—which is around 70% water and close to the same viscosity. Molecules move by normal diffusion through what they experience as a viscous, gel-like substance. Despite the densely crowded environs, they travel almost without restraint through the cytosol in a random walk caused by incessant collisions. Think of bullets ricocheting off one another in a space as crowded as a jar full of beans. Every second, each individual collides with vast numbers of others, the larger ones relentlessly pummeled by water molecules.

Electrons “orbit” atomic nuclei trillions of times per second; particles within the nucleus spin at rates far in excess of that figure. All the contents within a cell are continually tumbling; globular proteins rotate at perhaps a million revolutions per second.[4] It is this mad vibrational energy inherent to atoms and molecules that drives all cellular activities. Things are incessantly zipping through membranes via the aforementioned gates and channels. For example, neurons employ countless ion channels with associated pumps to manipulate the concentration of ions (charged particles, which conduct nerve impulses) and up to ten million of these crucial ions can be pumped through one in a second’s time. Everything takes place at unfathomable speed with countless things happening simultaneously in a riotous molecular tempest.

Most cellular activities are carried out by proteins. These giants of the molecular world, made up of sometimes thousands of amino acid building blocks,[5] are tightly folded into precise shapes that lend them their specific properties. This folding, an innate property, is mostly automatic—the result of individual sections being chemically attracted to or repelled by neighboring portions. The specific form of individual molecules can now be mapped with precision. Computer-assisted graphic representations are a terrific aid in conceptualizing protein complexity and the vast array of often random-appearing forms they take; some look like ornate cumulus clouds…others are symmetrical doughnut-shapes. Many are clearly modular and may have twisting side chains or knobby protrusions. Hidden in their forms are secondary structures: pleated sheets, and alpha helices. All are remarkably elaborate and bewildering to ponder.[6]

David Goodsell again: “A typical bacterium builds several thousand different types of proteins, each with a different function. Our own cells build about 30,000 different kinds, ranging in size from small…hormones like glucagon, which has only 29 amino acids, to huge proteins like titin, which has over 34,000….” Whether individually, in combination, or in teams, each of those 30,000 varieties will perform at least one (sometimes several) of roughly 100,000 specific individual tasks. A cell’s physical components are largely made up of structural proteins, while the other main category, biologically active proteins, assists with all cellular processes.

The latter include those vitally important molecules—enzymes—whose job is to speed up, or catalyze, chemical reactions. Certain extremely important reactions, if not induced by enzymes, wouldn’t move forward at all; others would literally require thousands of years. In some cases they proceed billions of times faster than if left without assistance.[7] With cells, everything has to happen at lightning speeds; any sort of carbon-based life would simply be impossible without catalysts.

An enzyme functions by randomly colliding with a specific target molecule—its  substrate. The substrate has a small region on its own surface that is chemically attracted to a complementary area on the enzyme’s (called an active site), causing them to momentarily bond. Their connection is often compared to a lock-and-key type arrangement, indicative of high specificity. This fleeting association, which causes the protein to change shape while remaining intact, simultaneously lowers the substrate’s activation energy,[8] allowing the reaction to proceed much, much faster than it would otherwise. The substrate is merely altered or splits into new substances; the reaction’s end result (product) floats off. Task complete, a catalyst automatically resumes its usual byzantine form, ready for the next customer. The ratio of catalysts to reactants is extremely small. And for an idea of their efficiency: one of the record holders in terms of speed is carbonic anhydrase: a single molecule can assemble up to one million molecules of carbonic acid per second. (The slowest enzymes require a couple of seconds to catalyze just one reaction.) The more typical rates are still amazingly fast. Understanding how catalysts work, combined with the knowledge that each substrate collides with virtually every enzyme inside the cell in little more than a second goes a long way toward giving a sense of how business proceeds in Cellworld.  

Individual proteins are fashioned into complex assemblages, actual machines, that are built by other proteins. Whether hastily fabricated at a moment’s notice or off duty, these versatile nano-machines undergo constant maintenance (as do lone protein molecules). Fabricated for specific duties, they’re quickly taken apart after the task is complete; in a typical cell, 20–40% of newly made proteins are dismantled within an hour. A number of kinds involved with regulation last for only minutes. Worn-out or damaged individuals, and those being “retired,” are reduced to their modular components for efficient recycling. This essential task is carried out by a teams of machines; smaller helpers assist the giant proteosome. Goodsell writes, “Proteosomes are voracious protein shredders, but all the protein-cutting machinery is carefully hidden away inside a barrel-shaped structure.…[T]he proteosome is able to wander freely inside the cell, and only the proper proteins are fed into its hungry maw.”

Proteins construct all the chemical needs of the cell (including, for instance, carbohydrates and lipids). They make hormones and antibodies. They are responsible for the adhesion of cells within tissues. Proteins churn out actin, the basic molecular component of self-assembling microfilaments. Also self-assembling, the hollow microtubules are made of a protein building block called tubulin.

Intriguingly, some reputable scientists consider it possible that the microtubule system could form part of a sort of cellular computer. No less than physicists Roger Penrose (better known for his work with black holes and relativity theory) and Francis Crick (co-discoverer of DNA) cite the coordinated behavior of cells as indication that they have some kind of information-processing ability. Without offering direct evidence they believe microtubules, which link all parts of the cell’s interior, would be ideal conduits for information transmission.[9]

Proteins are directly involved with other aspects of a cell’s transport system: as types of receptors embedded in both inner and outer membrane surfaces they selectively bind, in the fashion of enzymes, to targeted chemicals. The receptors release their targets after adding molecular tags so that the substance being directed elsewhere will be recognized upon arrival at its destination and permitted entry. Similarly, they also form receptors on the surface of membrane-bound cargo containers called vesicles, which are used to transport materials throughout cells. (These are hauled by molecular motors, small proteins that move by actually walking along microtubules with their relatively massive burdens in tow.) Proteins form the channels, gates, and pumps that regulate the passage of diverse types of chemicals through cell membranes.

In their role of assisting with communication, both within and between cells, these incredibly diverse molecules act as identifying markers on the cell’s surface and as messengers—traveling to specific locations where they bind with some target to elicit a chemical response. (As receptors, they both accept and pass on these messages.) The list of proteins’ absolutely indispensable roles is a long one.

Individual proteins are constructed from chains of amino acids (polypeptides) through the process of translation by one of the cell’s most remarkable machines: the ribosome. These minute factories use copied genetic information, carried from the nucleus by molecules of ribonucleic acid (RNA—specifically, a variety called messenger RNA, or mRNA). Analytical biochemist Roland Hirsch writes:

No simpler machine is known or even imagined that could carry out all of the steps in protein synthesis with such accuracy and speed. Yet no living cell can exist without the means to rapidly and continually synthesize hundreds of proteins over and over again with high fidelity to the code in its DNA. Even the formation of the ribosome itself requires a large number of synchronized steps and more than 100 proteins and 100 small RNA segments.


Ribosomes, the smallest machines known, consist of a large and small subunit that come together only when they attach themselves to a molecule of mRNA.[10] Hundreds of thousands of free-ranging ribosome subunits roam through a cell’s interior at any given time and work in teams to fabricate proteins that stay within the cell; other proteins destined to be excreted (or implanted in membranes as receptors) are assembled by ribosomes fixed in the surface of the endoplasmic reticulum—a flattish, highly folded organelle that surrounds and is actually continuous with the bilayer membrane enveloping the nucleus. ER (as it is generally known) comes in two varieties: smooth and rough. Both are so convoluted that together they comprise around half the membrane surface area in a typical animal cell. Rough ER is so called because its surface, unlike the smooth form, is copiously studded with ribosomes. (To give a sense of their abundance: about 13 million are found on the rough ER within a single human liver cell.) Smooth ER participates in a number of different metabolic processes.

Ribosomes on the rough ER’s surface extrude polypeptide chains as they are being assembled directly into its labyrinthine interior (the cisternal space) as individual free-floating amino acids are added one by one with lightning speed. Once released into the cisternal space, these partially finished proteins have other components added and a destination label affixed while molecules known as chaperones assist with what is otherwise an almost automatic folding process.[11] Other enzymes perform a quality-check, recognizing and removing improperly formed proteins before breaking them down for recycling. 

Partially formed proteins are sent to another organelle, the Golgi apparatus, where they receive further processing before being directed to their destinations. The Golgi (named for the 19th century Italian physician who discovered it) is made up of a series of flattened chambers. Unfinished proteins arrive in vesicles, which merge with the Golgi’s surface like fusing bubbles, spilling their contents inside. After each addition another vesicle, carried by some molecular motor, carries the still incomplete protein to the next chamber for further modification. The Golgi has its own quality-control system. Once complete, the finished protein is carried by one last vesicle to its final destination.

The entire process of protein formation is only one among hundreds of highly involved activities taking place in each and every type of cell. To illustrate the diversity of cell functions, Robert Wesson reports that in the human liver there are

about 500 [different] functions, including: manufacture of bile and other digestive fluids; storage, conversion, and release of carbohydrates; the storage of iron and vitamins; the regulation of fat, cholesterol, and protein metabolism; the manufacture of materials used in the coagulation of blood (some 30 substances); the removal of bacteria from the blood; and the destruction of excess hormones and many toxic substances. And almost all of these functions are performed by cells of a single type.[12]


And then there are those cellular engines, the mitochondria, which are responsible for taking the energy of digested food and converting it into an easily transported form that can be used for most cellular functions. Indeed, they supply most of the energy needs of most non-photosynthetic cells. They have two membranes: a smooth outer one and a much-convoluted inner membrane, studded by protein machinery. Mitochondria are former bacteria that had learned how to handle toxic, highly reactive oxygen in a world that had been without it (until photosynthesis arrived). They invaded—or were engulfed by—a primitive single-celled eukaryote, forming a lasting partnership. (Mitochondria were perhaps the first endosymbionts—organisms that live inside other life forms, in a mutually beneficial rather than parasitic relationship.[13])

To give an idea of their importance and ubiquity: there are hundreds of them in each cell…in some tissues with high energy demands, thousands. A typical eukaryotic cell contains about 300–400 while metabolically active varieties (found in muscle, liver, or brain tissue, for instance) contain hundreds or even some thousands of the minute organelles, occupying up to around 40% of certain cells’ volume. Up to half of a heart cell’s cytosol, for instance, is occupied by mitochondria. There are perhaps 10 million billion—a 1 followed by 16 zeros—in an adult human, making up around 10% of their weight. (A later section will deal with the amazing manner in which they carry our their primary duty. Suffice it to say that they have many roles, also being intimately involved with sex, fertility, and cellular aging.)

Inside any cell, thousands of individual processes are carried out simultaneously by hundreds of thousands of molecular machines, all attending to highly specific tasks. Countless molecules rush headlong through the cell’s crowded interior, ceaselessly colliding with structural supports, conduits, other chemical substances, and interior surfaces…until by chance they come in contact with an enzyme, or dock with one of the thousands of varieties of specific receptor sites. And things happen.

It’s a world of chaotic activity, taking place inside the 60 trillion nano-cities that make up our bodies. Right now. While we sleep. Every day until we die…at which  point that once-vibrant universe is disassembled piece by piece and, sooner or later, turned back into other living things. Atoms from long-dead people, plants, and extinct creatures without number reside inside each of us—all of them originally forged inside several generations of stars and now ceaselessly cycled through Earth’s biosphere. Small wonder that our minds revolt when asked to confront such outlandish notions.                            

But out of such chaos, order is continually seen to emerge. Most of us have been persuaded to believe that the sorts of almost miraculous things described here, awe-inspiring as they might be, are nothing more than the result of chemistry and physics operating on inert matter. Personally speaking: while I have never subscribed to a belief that some supernatural agent’s unseen hand guides what happens in the universe, it’s perfectly reasonable that a religiously inclined person should believe in a Creator-God. What I do find genuinely astonishing is that so many people—the highly intelligent and well-educated—have taken reductionist thinking to its extreme and reached the conclusion that, ultimately, life is nothing more than a vast collection of molecules randomly careening about. And, by extension, that living things are nothing more than machines.

No…it won’t do; the mechanistic view is a portrayal that serves only as versatile analogy. All organisms have machine-like qualities, have components that operate according to machine-like principles, but even the simplest of living forms are elaborate networks of hyper-complex organization with two overarching functions: to be…to be, and remain, alive. And to make more of their kind. They have numerous distinctive qualities that no machine will ever possess. If we hope to someday have a clearer understanding of life beyond how the parts work, it is imperative that some innovative model augment or extend the old—one that encompasses the true nature of nature.


     ©2016 by Tim Forsell      draft                  25 Feb 2016


[1] From his Nobel Prize lecture, Stockholm, 12 Dec 1974. Albert Claude (1899–1983) was a Belgian medical doctor and cell biologist who discovered the process of cell fractionation, which involved grinding up cells and using a centrifuge to isolate their contents. This led to his discovery of the ribosome and several major organelles.
[2] For a general perspective on size: Cells and microorganisms are considered at scales ranging between the nanometer (1 nm is one billionth of a meter) and the micro-meter (1 µm is 1000 nm—one millionth of a meter). At their widest dimensions: a water molecule is about 0.2 nm; a globular protein, 2–4 nm; a small virus, around 30 nm. The smaller bacterial species are in the range of 150–250 nm with the average-sized varieties, 1–10 µm. (The abundant gut bacteria, Escherichia coli, is 1–2 µm.) A human red blood cell, our smallest form, is about 7–8 µm. Eukaryotic animal cells on average range from 10–30 µm. The largest  (extant) single cell is an ostrich egg and motor neurons in a giraffe’s neck approach 3 meters in length.
[3] Bacteria and their kin have a simpler, rigid cell wall.
[4] “Globular,” a somewhat outdated categorization, perform many of the vital roles associated with proteins. They are often water-soluble (forming colloids) as opposed to the wholly structural fibrous proteins.
[5] Amino acids are small organic compounds composed mostly of carbon, hydrogen, oxygen, and nitrogen. There are about 500 known types but living things, for unknown reasons, employ only 20. (Actually, 22; two new ones have recently been discovered. One is known only from seven primitive prokaryotes.)
[6] “Parts…coil into helices, other segments lock into rigid rods, still others act as flexible swivels. One amino acid called cysteine binds strongly to other cysteines, forming virtual ‘spot welds’ where the chain attaches to itself. Very long amino acid chains often fold into huge wads. Parts of chains loop out, double back, cut over to the opposite side of the wad, shoot out in a great helix, then return in a straight line to the center of the wad…. In many proteins there are sequences of hydrophobic amino acids that are pushed deep inside the wad, away from the surrounding water…. Sometimes…the hardest-working part of the protein may be at the bottom of a deep pocket or cave. One enzyme, for example, is known to have a tunnel into which it pulls the substance it is to break down. Electrical charges on the outside of the tunnel attract the opposite charge on the target molecule, essentially sucking the hapless target into the tunnel. The molecule is broken apart and the pieces are ejected through another tunnel, again propelled by electrostatic charges.”
[7] Their functionality is often dependent on the presence of a single metal ion (such as iron, molybdenum, or copper) whose specific elemental properties lend themselves perfectly to catalytic roles.
[8] This is the minimum amount of energy needed to activate atoms or molecules so that they can undergo a chemical reaction.
[9] Experiments and theoretical calculations cast doubts on this idea but it remains an open question.
[10] The mRNA, like a single-stranded version of DNA, is essentially a copy—lifted from a gene—of the instructions for constructing specific proteins to the most exacting standards. It acts as a template.
[11] Rensberger describes how chaperones “grasp the new, partially folded chain and push or pull it into one particular shape. Like a sculptor modifying an unsatisfactory clay figure, the chaperones massage the amino acid chain, nudging a helix sideways or shifting a loop from this side to that.”
[12] Robert Wesson (1920–1991) was a distinguished scholar and prolific author, and fellow of the Hoover Institute, a conservative think-tank. Best known for his work in political science, he was a dilettante biologist. This fascinating book, one of the earlier popular science books (MIT Press)to openly question neo-Darwinism, is generally thought to support a creationist agenda even though the author made clear that this was not his position. It has received criticism for its many minor factual errors, many of which were due to a widely ranging subject matter and use of outdated information to support his stance. Nonetheless, it is a fascinating and entertaining book that presents many valid and thought-provoking arguments.
[13] The discovery that mitochondria, chloroplasts, and possibly other organelles were former bacterial invaders (or undigested meals) turned endosymbionts was a major clue in imagining a route to the rise of eukaryotes. But many of their features, vastly different than those of prokaryotes, are enigmatic and remain unexplained.

Sunday, March 6, 2016

The Demeaning of Life...Part IV

Another installment of my serialized work about the “meaning” of biological complexity and what it has to say about our collective understanding of the natural world. This part examines the methods we use to conceptualize our world, and some of their built-in shortcomings…the ways we limit ourselves by seeing life as a product of material processes and nothing more. Following this section I’ll take readers on a tour of the cell—a look into the inner workings of every living thing.

IV.  Materialism’s Two-Edged Sword


The problem is to construct a third view, one that sees the entire world neither as an indissoluble whole nor with the equally incorrect, but currently dominant, view that at every level the world is made up of bits and pieces that can be isolated and that have properties that can be studied in isolation.… In the end, they prevent a rich understanding of nature and prevent us from solving the problems to which science is supposed to apply itself.

             Richard Lewontin, Biology as Ideology: The Doctrine of DNA          
           
We can still offer thanks to that brilliant 17th century French mathematician René Descartes for turning the entire universe into an arena open to rational investigation. Materialistic naturalism (or materialism)—a product of the Cartesian worldview—is responsible for the basic premises of the scientific method and its inherent assumption of our world’s intelligibility. The ostentatious-sounding name simply denotes a philosophic belief that physical matter is the only reality and that everything in the universe (including thought, feeling, mind, and will) can be explained solely in terms of physical law. And, by extension, that all phenomena—being the result of purely natural causes—need no explanation involving any sort of moral, spiritual, or supernatural influence. Materialism, by way of its incomparable capacity to describe the world we experience and then make predictions through its discoveries that allow the control of nature—has made possible most of the great advances that led directly to our current way of life. From medicines and improved food crops to scanning electron microscopes and Doppler radar, science’s creative productions surround us at all times.

Very little was known about genes before the discovery of DNA confirmed their material nature. Many experimental doors were throw open once it was perceived that the double helix acted as an actual bearer of hereditary information. After that historic shift, impressive successes within the fledgling field of microbiology (thanks to brand-new technologies used to analyze and manipulate enzymes and other nucleic acids) provided confidence that unscrambling the code hidden within the physical substance of heredity would reveal evolution’s secrets. This led to an attitude of unreserved certainty that life, just like other aspects of the material universe, would eventually be explained purely on the basis of its chemical nature and molecular parts. Riding the wave, Francis Crick (a steadfast physicalist) wrote, “The ultimate aim of the modern movement in biology is to explain all biology in terms of physics and chemistry.”

Not long after its inauguration the modern Darwinian synthesis came to be recognized as the virtual foundation of biology and, to this day, remains the dominant paradigm of evolutionary thought. However, biochemical researches conducted during the last few decades, plus findings from entirely new lines of enquiry (such as the discovery of quorum sensing in bacterial consortia, whereby colonies of microbes interact socially via chemical signaling) have revealed that all  biochemical processes are far more complex than was ever imagined and sometimes—as in the case of the “behavior” of DNA repair enzymes—appear to go beyond the dictates of basic chemistry. As would be expected, molecular biologists and biochemists, long committed to a materialist stance, are unwilling to even consider that living things function by means other than straightforward chemical processes.

The institution of science features a genuine and powerful taboo against entertaining hypotheses that might open the door to any sort of supernatural explanations. However, for the same reasons our conceptions of what life is deserve a fresh look, newly revealed types of biological complexity invite a re-evaluation of the way we perceive all natural processes, including current evolutionary theory and theories of mind.

This shift is actually well underway despite a lack of media attention (which  nowadays correlates to a lack of public awareness). Currently, the Gaia hypothesis—the concept that Earth itself can be regarded as a colossal organism responding to stimuli via feedback mechanisms—has gained increasing support. Another fascinating viewpoint, which never attracted wide attention in the west, was that of Russian scientist Vladimir Vernadsky.[1] His theory is related to the Gaia hypothesis but preceded it by decades. Unlike Vernadsky’s early 20th century contemporaries, he saw life as being a geological force that had a profound effect on the world through chemically and physically altering its surface, and by transforming and transporting materials around the globe. In line with the Gaia concept, Vernadsky saw life as being a global phenomena—but more as part of a larger process. He didn’t regard it independently from other aspects of nature; it was just “living matter.” Furthermore, he pictured the entire biosphere—including both animate and inanimate matter—as being alive. By rejecting accepted principles and manners of categorizing and labeling, Vernadsky was able to formulate a new and conceptually coherent world model.

In contrast to such notions, one derivative of materialism was the cultivation of a powerful idea: that all entities are best studied and can be understood by reducing them to their parts. This is known as reductionism or reductive thinking, an essential tool in gaining empirical knowledge. How could anatomy be tackled except through the study of individual organs, their tissues, and their tissues’ cells? In biology, this time-honored approach has continually proven its worth and has been key to most advances.

However, there is currently a burgeoning movement away from reductionism in the life sciences toward a more inclusive wide-ranging “systems” approach, which a growing number of scientists regard as the way of the future. Reductionist methods serve admirably to understand, say, how circulatory systems work or nerve impulses are conducted but ultimately break down when considering all the layers of complexity in their state of seamless integration. As a sort of backlash to the long-needed reappraisal of biological thinking, reductionism has taken on a suspect standing in certain areas where its shortcomings are seen to hinder further progress (such as those fields dealing with pattern and form, or ones where intricate relationships resist quantification). Many of the criticisms leveled against reductive thinking are, in fact, directed toward what has been termed radical reductionism—the assumption that larger scale phenomena can be explained entirely by what occurs at smaller scales. (As in, Biology is nothing more than chemistry.)

One of the main limitations of reductive thinking is seen in its tendency to downplay or ignore so-called emergent properties—patterns, behaviors, or traits that can’t be deduced from either lower or higher levels of association. (The deliberate, organismic behavior of DNA helper molecules being a fine example.) Nonetheless, despite recognized limitations, reductionism will doubtless continue to occupy its central role in all scientific endeavor.

Another unforeseen spinoff of endless scientific triumphs has been an ever-increasing tendency to fragment knowledge into discrete areas of specialization. Biology professor and science journalist Rob Dunn writes of the resulting quandary:

For individuals, it has become more difficult to have a broad perspective. The scientists of each field have developed more and more specific words and concepts for their quarry. It is now difficult for a neurobiologist to understand a nephrologist and vice versa, but it is even difficult for different neurobiologists to understand each other. The average individual’s ability to understand other scientific realms has become limited…. The more divided into tiny parts a field is, the less likely some types of big discoveries become.… [V]ery few individuals are standing far enough back from what they are looking at to be able to make big conceptual breakthroughs.
       
Entirely new sub-sub-disciplines emerge continuously—such as paleomicrobiology or biogeochemistry—and the compartmentalization of knowledge leads to an overly narrow focus on complex issues (such as what can result if a scientist devotes their career to studying one facet of one variety of cell in one type of organism). This almost  inevitably results in skewed perspectives, even within someone’s own discipline. The same can happen on a larger scale; in one example pertinent to this narrative, only a century ago, the intellectual isolation of several interrelated fields led to a sort of “scientific provincialism” that created a need for the modern synthesis.

Neo-Darwinism rose to a dominant working model of evolutionary pathways by virtue of that succession of breathtaking new microbiological discoveries. Due in part to the lucid and entertaining writings of authors such as Richard Dawkins, Carl Zimmer, and Sean B. Carroll, the elegant simplicity of neo-Darwinian precepts leads scientifically literate people to believe that any unexplained mysteries of evolution have by and large already been solved…or soon will be.

Among our well-educated populace, whose image of reality is now effectively defined by science, a mind-set is often on display that could be characterized as a self-assured but naïve conviction that this worldview represents an objective description of the “real” world. Indeed: the people of any given era and culture share a generally agreed-upon overall worldview; those inhabiting a given period feel sure that their view of reality—having superseded the mistaken and antiquated beliefs of generations past—is entirely accurate. History reveals this certainty to be a recurring cultural illusion though people almost invariably ignore this truism. During a speech at Cambridge in 1923, Haldane (the foremost popularizer of science in his day) said, “Science is in its infancy, and we can foretell little of the future save that the thing that has not been is the thing that shall be; that no beliefs, no values, no institutions are safe.”

This was a prescient statement in Haldane’s time but the observation is no less true today. So…what’s our excuse? Living in the 21st century at (or near) civilization’s zenith, having seen so much, one would think we would have perceived this historical pattern and humbly acknowledge that at least some things fervently believed to be irrefutable facts will become obsolete anachronisms. Alas: History is made…and then ignored. As it has always been, our grandchildren will look back on their ancestors’ quaint and primitive ways, marvel at the hilariously crude machines, and long for simpler times.

Another thing: religion, for many educated people, has been supplanted by science as their reality-defining milieu. Faith in God has been exchanged for faith in the scientific approach to such an extent that there’s a term, in use since the mid-1800s, for what has been recognized as a philosophy or even a quasi-religion: scientism.[2] As such, it represents a wholly materialistic standpoint, insisting that only empirical methods are capable of providing accurate views of reality and that all other modes of thought, if not just plain wrong, lack substance. Those unacquainted with the nitty-gritty of actual research or how things work in academia often seem rather unaware of how messy the scientific arena can be, with incessant struggles for funding, researchers’ sometimes slipshod work, the bitter rivalries and envy—even the occasional outright frauds.

Alan Lightman, astronomy and physics researcher, put it this way: “[O]ne must distinguish between science and the practice of science. Science is an ideal, a conception of logical laws acting in the world and a set of tools for discovering those laws. By contrast, the practice of science is a human affair, complicated by all the bedraggled but marvelous psychology that makes us human.” Stephen Jay Gould further emphasizes that practitioners of science often fall prey to cultural predispositions:

Our ways of learning about the world are strongly influenced by the social preconceptions and biased modes of thinking that each scientist must apply to any problem. The stereotype of a fully rational and objective “scientific method” with individual scientists as logical (and interchangeable) robots is self-serving mythology.


The truth behind Gould’s words is exposed by another striking historic pattern: phenomena being accounted for in language linked to a particular era’s latest promising discovery or  leading technology. In times past, the biological vital force was ascribed to fire, magnetism, electricity…even radioactivity. And thus has it been the “fashion” to describe observable fact using a succession of terminology borrowed from clock making, steam power, radio technology, and electrical engineering. In the last century, life processes have been considered in terms of quantum dynamic effects, computer science, game theory and non-linear dynamics. (Presently we are undergoing a shift toward various biological topics being thought of in terms of information theory.) Recognizing the consequence of such influences reveals the subtle effect culture has on the practice of science. Tellingly, it’s impossible to even imagine what technology our next contextual aids might be borrowed from. 

In our time, there is a widely held conviction that scientists, in order to be considered scientists, are limited exclusively to materialist explanations for all phenomena. Materialistic naturalism grants no basic worth or import to nature’s rich pageantry, not  to mention the pre-eminence of mind. Disregarding the mysterious nature of life, a materialistic approach pays no heed to the reality of things beyond its reach—at the extreme end, going so far as to argue that concepts like beauty and morality are illusions serving no constructive purpose…that all living things, including humans, are the result of chance events…that life, ultimately, has no object or underlying significance.

This is the stance of well-known evolutionary scientists Jacques Monod, George C. Williams, and Richard Dawkins—each of whom has rebuked (in some instances quite harshly) those who make the cardinal error of inserting subjectivity into matters that lie within science’s domain. Their position is entirely justifiable in the context of science’s dealing exclusively with matters within reach of external verification, but not things that can only be experienced. However, those authors go beyond simply reminding their readers that science is powerless—is the wrong tool—to make judgments about concerns like morality or beauty; they unswervingly insist that the products of our minds and sense organs have no objective value per se, aside from how they might contribute to genetic success. Dawkins informs us that life “is just bytes and bytes and bytes of digital information”…that life’s sole “purpose” is for DNA to make more DNA. (Oddly, he never bothers to ask why this should be so.)

Once again: we don’t even know what life is, much less what—if any—its “purpose” might be. Even if the public isn’t aware of it, there are yet a host of unanswered questions. And others that haven’t yet been asked. Science, taken as a whole, is likely humanity’s greatest innovation and our bequest to—hopefully—a bright future (or, in the ever-astute Gould’s more incisive words, “whatever forever we allow ourselves”). Lifting us out of darker ages, the work of all those individuals, building on that of their predecessors, made our way of life possible—another oft-overlooked detail. But we still aren’t close to knowing precisely how our senses work, what dreams are for, or where memories reside. Consciousness, the greatest of all mysteries, remains a variegated enigma. Lacking humility, we persist in taking as a given our ability to perceive, evaluate, and act with consistent propriety…or restraint. Which leads to problems.

The physicist Richard Feynman, widely considered in his day to be one of the most brilliant people alive, said in an interview:

I can live with doubt and uncertainty and not knowing. I think it’s much more interesting to live not knowing than to have answers which might be wrong. I have approximate answers and possible beliefs and different degrees of certainty about different things but I’m not absolutely sure of anything and there are many things I don’t know anything about such as whether it means anything to ask why we’re here…. I don’t have to know an answer. I don’t feel frightened by not knowing things….

While it’s generally assumed that scientists are objective and impartial in their views, such intellectual bravery and humbleness as this is vanishingly rare. For Richard  Feynman (who suffered from terminal curiosity) it always came down to the pure joy of   discovery. Charles Darwin also displayed this quality in spades; he had the courage to question his own views, and openly invited others to challenge his cherished theories.

So why this tendency to feel such certainty, such resolute assurance, that the wondrous things all around us ultimately have no importance…or are of no particular consequence? Why the need for such staunch conviction? And what exactly does this say about our culture, that we denigrate life so? Even if philosophy and religion are left out of the picture entirely, individuals will still seek meaning and purpose in the world, invite beauty into their lives, and go on living by a moral code based on what they believe to be objective values. Such things are still fundamental, inescapable aspects of what it is to be human. For mystics, atheists, and rational materialists alike.

Yes, we eternally owe a debt of gratitude to those great minds that made our modern way of life possible. But, in an essay—almost a manifesto—co-written by Dorian Sagan, Lynn Margulis, and Ricardo Guerrero, we are reminded of another way:

Perhaps Descartes did not dare admit the celebratory sensuality of life’s exuberance. He negated that the will to live and grow emanating from all live beings, human and nonhuman, is declared by their simple presence. He ignored the existence of nonhuman sensuality. His legacy of denial has led to mechanistic unstated assumptions. Nearly all our scientific colleagues still seek “mechanisms” to “explain” matter, and they expect laws to emerge amenable to mathematical analysis. We demur; we should shed Descartes’ legacy that surrounds us still and replace it with a deeper understanding of life’s sentience. In [Samuel] Butler’s terms, it is time to put the life back into biology.

Promoting this way of thinking is my intent. But to take it even farther—not simply to put the life back in biology, but to replace it with a greater concept of life. While fully cognizant of the sheer unlikelihood that a non-scientist could perceive things about the natural world that have somehow been overlooked by untold numbers of highly trained professionals, I have been unable to shake this powerful conviction: There is a much deeper reality behind the way we currently perceive nature. As with DNA, our views of the way cells work shows how little we credit the power of Natural Design. 
       

     ©2016 by Tim Forsell    draft                                                                                                        
            25 Feb 2016




[1] Vladimir Ivanovich Vernadsky (1863–1945) was considered one of the founders of  both geochemistry and radiometric dating and also popularized the concept of the noösphere. “In Vernadsky’s theory of the Earth’s development, the noösphere [human and technological] is the third stage in the earth’s development, after the geosphere (inanimate matter) and the biosphere (biological life). Just as the emergence of life fundamentally transformed the geosphere, the emergence of human cognition will fundamentally transform the biosphere. In this theory, the principles of both life and cognition are essential features of the Earth’s evolution, and must have been implicit in the earth all along.… Vernadsky was an important pioneer of the scientific bases for the environmental sciences.”
[2] The term is often used pejoratively by those who insist that scientism results to an impoverished worldview.