Sunday, May 20, 2018

The Demeaning of Life...Chapter 13: The Fitness of the Environment

Note: This was to have been chapter 9 in my sequence of postings. Due to (yet another) major rearrangement of chapters, this is now chapter 13.

The great and fruitful ideas which Darwin brought to the attention of the whole world have long since been incorporated into human thought. Not the least important among them is the new scientific concept of fitness, as it emerges from the discussion of natural selection…. [But] it has been the habit of biologists since Darwin to consider only the adaptations of the living organism to the environment. For them, in fact, the environment…has been an independent variable, and it has not entered into any of the modern speculations to consider if by chance the material universe also may be subjected to laws which are in the largest sense important in organic evolution. Yet fitness there must be, in environment as well as in the organism.

   Lawrence Henderson,The Fitness of the Environment (1913)

Lawrence J. Henderson was a professor of biological chemistry at Harvard in the early 1900s. He entered Harvard College in 1894 at the tender age of sixteen (not particularly unusual in those days), graduated from Harvard Medical School with an M.D. eight years later, and spent his entire professional career there until his death in 1942. Henderson was one of the founders of Harvard Medical School’s Department of Physical Chemistry. Notably, he was responsible for establishing the history of science as a discipline—a first at any university in the United States—and taught the initial course starting in 1911. He was most known for his work in blood chemistry. Later in his career, Henderson published works on philosophical and sociological topics.

Henderson struck many as being cold and pompous. He was notorious for his manner of writing (and speaking) in a convoluted, circuitous fashion and was known, according to a friend, for making “passionate and intolerant assertions and suffered fools not at all.” While highly regarded by his students and peers, such qualities may account in part for Henderson’s not being known widely today. Be that as it may, he was decidedly forward-thinking in advocating a systems-level approach in his methodology. Everett Mendelsohn writes, 

In spite of the several fields in which Henderson worked, a number of commentators, his contemporaries, and later analysts noted a markedly similar approach in many of his endeavors…. His focus was on organization and system: the organism, the universe, and society. John Parascandola, the author of a doctoral dissertation and several important articles on Henderson, put it succinctly: “The emphasis in his work was always on the need to examine whole systems and to avoid the error of assuming that the whole was merely the sum of its parts.”

In addition, Henderson is considered an early advocate of what is now known as the concept of cosmic fine-tuning—the notion that our entire universe, including physical constants at the heart of mathematical equations defining it, are biased to favor life.   Accordingly, there is a renewed interest in Henderson’s ideas. His influential book The Fitness of the Environment, first published in 1913, ends with these words:

The properties of matter and the course of cosmic evolution are now seen to be intimately related to the structure of the living being and to its activities; they become, therefore, far more important in biology than has been previously suspected. For the whole evolutionary process, both cosmic and organic, is one, and the biologist may now rightly regard the universe in its very essence is biocentric. 

By the early 1900s, life’s chemical nature was beginning to be well understood. Henderson’s early work, begun in 1905, centered around neutrality regulation—how an organism achieves and maintains a state of equilibrium between acids and bases within its body (that is, a neutral pH balance).[1] Maintaining that balance in physiological fluids is imperative: when pH varies from some norm by even a small amount, enzymes cease functioning and proteins begin to break down. The results are catastrophic; in humans, for instance, death occurs in just minutes if blood pH exceeds certain limits.

In order to regulate acid levels in their bodies, all air-breathing terrestrial organisms employ a carbon dioxide–bicarbonate buffering system. A buffer consists of weak acids and their corresponding bases, which act together to minimize changes in pH by reversibly capturing or releasing ions. Here is a brief description of the process in the context of human physiology: 

Recall that during cellular respiration, CO₂ and hydrogen ions (H) are produced in abundance. As waste, CO₂ is excreted and excess hydrogen ions—which acidify their cellular environs—have to somehow be removed. Most of the CO₂ generated by respiration diffuses into the bloodstream where, along with HO, it is taken up by hemoglobin (the oxygen-carrying element in blood) in red blood cells and converted to carbonic acid (HCO). While this reaction occurs spontaneously, it is greatly accelerated by the enzyme carbonic anhydrase, a multipurpose catalyst that greatly speeds what is otherwise a slow reaction. Carbonic acid is unstable; most of it spontaneously dissociates into bicarbonate (HCOˉ) and hydrogen ions. Hemoglobin also takes up much of the excess H⁺ (thereby preventing excessive acidification) and releases bicarbonate into the bloodstream, which carries it to the lungs. In the lungs, carbonic anhydrase reverses the reaction. The resulting HCO₃ again dissociates—this time into CO₂ and water—and the carbon dioxide is exhaled.

As mentioned, a small amount of carbonic acid remains in the bloodstream without becoming ionized, along with some H⁺ and significant amounts of bicarbonate. If, through some physiological change, blood becomes more acidic due to an increase of H⁺ it is neutralized by H⁺ bonding with HCOˉ, reforming carbonic acid. Or, if blood pH rises, carbonic acid dissociates and in doing so releases H⁺ until blood pH returns to equilibrium. These reversible reactions happen automatically and, with impressive efficiency, maintain a vitally important state of chemical balance, or homeostasis, in the blood at all times.[2]   

While studying the bicarbonate buffering systemHenderson noticed that its effectiveness depended to a large extent on several critical substances’ natural chemical properties—particularly those of carbonic acid and CO₂. Carbon dioxide being a gas made its excretion as a waste product a simple matter. He wrote,

Needless to say…carbonic acid is also of great importance in many physiological processes, chiefly perhaps in excretion. In the course of a day a man of average size produces…nearly two pounds of carbon dioxide. All this must be rapidly removed from the body. It is difficult to imagine by what elaborate chemical and physical devices the body could rid itself of such enormous quantities of material were it not for the fact that, in the blood, the acid can circulate partly free and, in the lungs…[it] can escape into air which is charged with but little of the gas. Were carbon dioxide not gaseous, its excretion would be the greatest of physiological tasks; were it not freely soluble, a host of the most universal…physiological processes would be impossible. 

Carbon dioxide is unusual in other ways: it is one of the few oxides[3] that is a gas at ambient temperatures.[4] It is exceptionally water soluble (having twenty times oxygen’s solubility) and whenever air is in contact with water, carbon dioxide will dissolve until its concentration is equal in both substrates. This quality makes CO₂ a consummate vehicle for spreading carbon around the globe via both the hydrosphere and atmosphere.

Over time, Henderson increasingly noted that the element carbon’s many fortuitous properties lent it the appearance of being tailor-made for a central role in all life processes—indeed, in making life possible. Carbon is unique in being the only element that can form multiple covalent bonds—not only with other elements but, crucially, with itself.[5] Carbon bonds (importantly, neither too strong nor too weak) enable the formation of countless organic macromolecules such as fatty acids, proteins, sugars, and a wide array of hydrocarbons. Over 20 million organic compounds have been described thus far, and they continue to be discovered at a furious rate—a rate amounting to hundreds of new ones added daily, many of them through being isolated from plant tissues. There is virtually no limit to the number that could potentially exist, due to carbon’s ability to form long-chain molecules of great length.

Organic compounds are matchlessly suited for use by living things thanks to other equally fortuitous qualities. One important attribute of (most) carbon compounds is the relative mildness of their chemical properties. Organic acids—DNA for instance—are not violently reactive in the fashion of their inorganic counterparts (highly corrosive substances such as nitric acid). Nor are the organic bases highly corrosive. This mildness is due in part to carbon being a relatively inert element prone to sharing electrons rather than gaining or losing them in reactions (in the fashion of a highly reactive element like oxygen). Additionally, carbon compounds have a characteristic known as metastability. Metastable compounds readily release energy in the course of reactions but are durable enough to not break down over time unless subjected to heat, radiation, or the activity of enzymes. The metastability of organic substances happens to be best exploited at temperatures neatly bracketed within the range of ambient temperatures found on Earth. 

No other element comes close to being as impeccably suited for life’s needs. Put another way: for living things to exist on other planets, an element with carbon’s qualities and capabilities would have to be readily available. As for the possibility of alien life-forms being based on the interaction of several non-carbon elements: there is no combination of elements could begin to match carbon’s accommodating versatility. Any attempt to envision a functional alternative to carbon-based chemistry encounters a succession of compounding problems. Similarly, efforts to design an alternative biochemical system—particularly if it includes being capable of self-replication—almost immediately run into insurmountable dilemmas. These are due in part to the necessity of satisfying a number of stringent (and often mutually incompatible) criteria. Carbon-based organic chemistry has serendipitously avoided all such problems. 

What are the options? A standard response is the “life-as-we-know-it” argument: life on other worlds may be in some form we can barely even imagine. Still, other-life will have to possess the means to store and process large amounts of information. Science fiction writers with solid backgrounds in astrophysics have envisioned life forms flourishing in what would normally be considered unlikely environments (for instance, as electromagnetic circuit-life whizzing about inside neutron stars or floating in the atmosphere of a gas giant planet). While such possibilities can never be categorically ruled out, in all likelihood otherworld life forms will be made of atoms. If not carbon, what else might do? Silicon is a sci fi favorite as an alternative basis for alien life. This is no random choice; silicon and carbon share certain chemical properties, each having the same configuration of electrons in their outermost orbital shells—a feature that lends seemingly unrelated elements a tendency to exhibit similar chemical behavior. Both carbon and silicon readily form compounds, bonding with many other elements. But unlike carbon, silicon cannot form the host of complex, metastable compounds likely required by any organism, regardless of type. Silicon is incapable of bonding with itself and thus form long chain molecules. (It is for this reason that silicon chemistry is much less diverse). There can be no equivalent to proteins based on silicon, nor any of the other essential biomolecules. Silicon’s oxide form, SiO₂ (otherwise known as the mineral quartz), is one of Earth’s least soluble but most abundant substances. A frequently used quip: “Silicon is good for making rocks, not life.” 

Then there are those other elements that form compounds crucial to life—the key players being hydrogen, oxygen, nitrogen, sulfur, phosphorus, calcium, sodium, and ions of several other metals. These elements all prove to be ideally suited for their roles and, it is interesting to note, their relative abundance in the cosmos closely mirrors (in most cases) their abundance within living things. Whether or not this curious fact has any significance is impossible to say.

Though found in living things in typically minute quantities relative to non-metal-bearing substances, a number of metallic ions are of crucial importance and it is no exaggeration to say that life would be impossible without them. On the far left side of the periodic table are the alkali metals sodium and potassium. Located to their right are the alkaline earth metals calcium and magnesium. The remainder of the left half of the table consists of the rare earth metals and, farther right, the transitional metals. (The members of each group share correspondences in properties such as conductivity, reactivity, and what sort of compounds they form.) 

The alkali metals, sodium and potassium are essential ingredients in a host of basic life processes.Representing the alkaline earth metals are calcium, with its ability to convey chemical information at great speed (as in the triggering of muscle contractions and transmitting nerve impulses) and magnesium, whose unrivaled light-absorption capacity makes it ideal for photosynthesis. 

Among the transitional metals there is iron—a key component of hemoglobin, that all-important carrier of oxygen in the bloodstream; copper, with its oxygen-binding capabilities exploited in the electron transport chain; and cobalt, an ingredient of vitamin B₁₂. Proteins involved with switching genes off and on contain zinc, as does that absolutely vital catalyst, carbonic anhydrase. Another transitional metal essential to life is molybdenum, a component of enzymes involved in nitrogen fixation. Given their importance, it may be surprising to learn that many enzymes containing metal ions are built around a single atom. In Lawrence’s time, the crucial role of metals was not yet fully understood or appreciated. But we now know that, as is the case with carbon, they are ideally fit for their roles.

Similarly, as was made clear in the discussion of carbon chemistry, many types of molecular compounds are seen to be supremely fit for their chemical tasks: the sugars and polysaccharides, lipids, and phosphates. The nucleotides, ideal vehicles for storing information. And proteins, with their myriad forms and capabilities, including their all-important role as catalysts. (This, as well as the dual function of being able to carry out their own tasks while simultaneously self-regulating them without assistance from intermediaries—recall the discussion of allostery, Chapter 7). 

And lastly: that tasteless, odorless, and colorless naturally occurring fluid, dihydrogen monoxide (otherwise known as water), the most abundant chemical compound in the universe and sole earthly substance occurring in liquid, solid and gaseous phases. Henderson meticulously demonstrated how each of water’s physical properties make it ideally fit for life’s needs and requirements. He provided abundant evidence showing that water is supremely fit, not only for maintaining global climatic stability, but also in its role as a veritable matrix for all living matter. And that water is not only fit in many of its highly unusual (even unique) qualities but in virtually all of them. 

Perhaps water’s most striking trait is that it is one of the few substances that expands instead of contracting as it freezes (becoming less dense). This is why ice floats. Crucially, if ice were denser than liquid HO, lakes and oceans would freeze from the bottom up and most of our planet’s bodies of water would remain permanently frozen.   

An important property of water is its thermal capacity or specific heat.[6] Water’s is higher than that of most fluids. One obvious affect of water’s specific heat is the tendency of large bodies of water to maintain nearly constant temperatures; were it less, seasonal differences would be far more extreme. Also, the effectiveness of ocean currents (such as the Gulf Stream) to transfer vast amounts of warm water from the tropics to polar regions would be far less. This would in turn exacerbate low latitude and high latitude temperature variances, resulting in more extreme weather patterns. Ocean currents are responsible for the generation of winds and their subsequent conveyance of water vapor—a major factor in the global distribution of water as rainfall. Changing the value of water’s specific heat, up or down, would dramatically affect Earth’s climate.

Working to help moderate temperature fluctuations in tandem with specific heat is the quality of latent heat. When steam condenses (or when ice freezes), heat is released. Upon evaporation (or melting), liquid water absorbs heat from the environment. Water’s latent heat of freezing and latent heat of vaporization are among the extremes of any fluid at temperatures encountered on Earth.[7] This means that an unusually large amount of energy is involved in either raising or lowering the temperature of a body of water. This quality makes it easier for bigger organisms to maintain ideal body temperatures, since animal cells are predominantly water by weight. Mammals sweat to take advantage of water’s latent heat of vaporization as a means to remove excess heat, a serious physiological challenge. (The same is true for plants, achieving essentially the same result via the process of transpiration.) Another benefit of water’s high latent heat of vaporization is that it lends sea ice and glaciers a resistance to melting, a factor that helps balance equatorial heating and slows the warming of seawater by direct sunlight.

Then there is water’s thermal conductivity—its capacity to “conduct,” or transfer heat. While far lower than most metals and many other solid materials, the thermal conductivity of HO is highest among known liquids (and far higher than most). On the other hand, the thermal conductivity of both snow and ice are low. The insulative properties of ice help prevent further heat loss from oceans and lakes. Snow, an even better insulator, helps limit the melting of sea ice and glaciers. In addition, snow’s pristine whiteness makes it a first-rate reflector of sunlight, further slowing ice melt.

Taken together, these unusual properties lend water its ability to act as a buffer—moderating Earth’s overall climate, shielding the planet from rapid or intense temperature fluctuations. Without the unique thermal properties of HO, Earth’s surface would be subject to far more violent and severe weather events. Regional climates would be radically different, with extremes of dryness or wetness and humidity, heat and cold.

Water  is an extremely versatile solvent. With the important exception of lipids and other hydrocarbons, most chemicals, if only to a slight extent, will dissolve in it. At the same time, water is not too chemically reactive. Individual molecules have a weak magnetic polarity giving water molecules a boomerang-like shape with the slightly negatively charged oxygen nuclei at the apex. This bi-polarity results from oxygen having a somewhat stronger pull on electrons than hydrogen, such that the shared electrons tend to spend more time around the oxygen nucleus. As a consequence, the slightly positive net charge in the region of the hydrogen nuclei, being attracted to other oxygens, forms ever-shifting short chains of water molecules bound by supple hydrogen bonds.[8] (This is what accounts for water’s fluidity in its liquid state.) Water’s being electrically polar is but one more feature that makes water an ideal liquid medium for all essential activities within cells. As previously discussed, water’s chemical aversion to lipids is crucial in the formation and maintenance of biological membranes and the activity of catalysts.

Another property: surface tension, a measure of a liquid surface’s resistance to being stretched or broken.[9] This quality is responsible for drawing water up through the soil to reach plants’ roots and assisting its rise to the tops of tall trees. Water is crucial for soil development; its high surface tension draws water into cracks and fissures in rocks, helping leach out chemicals. In addition, when surface water freezes and expands, the weathering process is accelerated through enlarging cracks and crevices and breaking down rock, which increases surface area, thus allowing more chemicals vital to life to be freed up. And because water has low viscosity compared to most fluids, rain and melting snow further the rapid transport and distribution of these materials via streams and rivers. In this way, nutrients essential to sea-life are made available.

In fact, water’s viscosity is an ideal balance. Were it lower, cells would be unable to withstand forces and loads they are regularly subjected to and delicate cellular structures would not likely survive normal buffeting. Were water’s viscosity significantly higher, many aquatic organisms would likely not exist. The movement of mobile organelles and large molecules through a cell’s cytoplasm would be hindered to the point that physiological processes, normally carried out at fantastic speeds, would no longer proceed. On the other hand, water’s low viscosity is ideal for the diffusion of critical materials on a cellular scale. (The rapid diffusion of small molecules over short distances is a fundamental process for all cells and microorganisms.) 

At the end of his lengthy treatment of this wondrous substance, Henderson, in ponderous style, wrote:

In no case do the advantages which [water’s] properties confer seem to be trivial; commonly they are of the greatest moment; and I cannot doubt, even after allowances have been made for the probability of occasional fallacies in the development of an argument which, though simple, is beset with many pitfalls, that they are decisive. Water, of its very nature…is fit, with a fitness no less marvelous and varied than that fitness of the organism which has been won by the process of adaptation in the course of organic evolution…. If doubts remain, let a search be made for any other substance which, however slightly, can claim to rival water as the milieu of simple organisms, as the milieu intérior of all living things, or in any other of the countless physiological functions which it performs either automatically or as a result of adaptation. 

The innate capabilities of the elements, the host of bio-friendly substances they form in combination, the suitability of Earth’s many distinctive features—indeed, the universe’s—all work together harmoniously to make life both possible and actual. (Later chapters will take up these matters in detail.) The significance of these facts—and their implications—were not fully appreciated until surprisingly recent times. A major reason for this can be traced to Darwin’s original conception of the basis for his theory, with its emphasis on nature’s unrelenting brutality as opposed to its “gentler” aspects. This point of view is changing, though the process has been a slow one. 


      ©2018 by Tim Forsell     draft                        14 Apr 2018


[1]The pH scale measures the relative acid/base (H⁺/OHˉ ion) concentration in a solution. It is a logarithmic scale (based on powers of 10) ranging from 0 to 14, with 7 being neutral; anything under 7 is an acidic solution, and anything over 7 is basic. A fluid with pH 3 is thus ten times, not twice, as acidic as one with a pH of 4. Representative examples: stomach acids are pH 2, household bleach about pH 12. Pure water is pH 7 (neutral) and human blood is maintained at a steady 7.4. 
[2]Homeostasis refers collectively to a self-regulating process (by way of feedback loops, for instance) used by living things to adjust to conditions and maintain physiological stability.
[3]Oxides are two-element compounds containing oxygen. Other gaseous oxides include carbon monoxide (CO) and several forms of nitrogenic oxides including “laughing gas” (NO) and several components of air pollution.
[4]Ambient temperatures, as used here, refers to the range of environmental temperatures typically encountered on Earth.
[5]Covalent bonds are the result of two substances sharing electrons in order to achieve chemical stability through having their outermost orbital shells filled. 
[6]For all substances, specific heat expressed in terms of calories, the amount of heat required to raise the temperature of some quantity of water by one degree celsius. (A calorie is defined as the amount of heat rquired to raise the temperature of one gram of water by 1°C.) Among ordinary liquids, only ammonia has a higher specific heat than water.
[7]At Earth’s ambient temperatures, water’s latent heat of evaporation is greater than any liquid. Its latent heat of freezing is exceeded only by ammonia. 
[8]Hydrogen bonds between individual H₂O molecules are around one twentieth as strong as the molecule’s covalent bonds.
[9]Excluding mercury, water has the highest surface tension of all common fluids at ambient temperatures.

Sunday, April 22, 2018

The Demeaning of Life...Chapter 8. Brief Detour Into the World of "What Makes Cells Go"

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]

Another installment of “Things We All Should Know About Life,” this one another brief synopsis of the methods cells employ to make life-sustaining energy available in usable forms. Respiration, phosphorylation…photosynthesis, chemiosmosis. These matters are so technical, so abstruse, that to even attempt such an abbreviated picture might well be counterproductive. But these most basic of metabolic processes are not merely representative of how living things work: they are the stuff of life’s true essence. This chapter’s aim is not an attempt to describe or explain these arcane inner workings so much as to lend a sense of the means and methods, the thrifty efficiency and harmonious balancing acts. I have attempted to distill this narrative down to its bare rudiments. This is rich food—the terminology and details will bewilder those unfamiliar with such matters. (For others, those with a semester of organic chemistry or advanced biology some-where in their past, this will perhaps dredge up some painful memories.) Let this account serve as another illustration of the remarkably effective ways and means that life has devised to cope with the bare necessities of subsistence. There is a profound beauty here…an exhibition of nature’s innate genius.[2]
Plants, some algae, and certain kinds of single-celled organisms manufacture their own energy sources using sunlight through the process of photosynthesis and are thus known as photoautotrophs. Their ability to harness “free” solar energy is the backbone that upholds all biological activity.
A much rarer life form produces its own nutrients without benefit of light, carbon, or oxygen. These ancient microbial organisms—called chemoautotrophs—use energy extracted from substances such as hydrogen sulfide, ammonia, or methane by way of anaerobic reactions (that is, in the absence of oxygen). These inorganic geochemical reactions originated with early life forms but are still widely employed by various types of bacteria and primitive bacteria-like microorganisms belonging to a group known as the Archaea, which live in hot springs and even within solid rock. All other organisms—the heterotrophs—are either directly or indirectly dependent on substances produced by photoautotrophs for their sustenance. 
There are two distinct approaches heterotrophs use to derive the energy needed for all their metabolic requirements. Both are based on the transference of electrons during chemical reactions. (In point of fact, all life processes at all levels—cell, organism, ecosystem, biosphere—are driven by the exchange of electrons.) What follows describes metabolic pathways used by eukaryotic organisms.
One of the approaches, employed by the majority of living things, is a form of oxidative metabolism called cellular respiration. In short, cellular respiration consists of exploiting oxygen (a powerful reactant) to break down organic substances, converting them into forms the cell can use. The complete process takes place in three interconnected stages: glycolysis, the citric acid cycle,[3] and the electron transport chain. Each is carried out in a series of enzyme-assisted intermediate steps. This measured strategy ensures that energy is released in small increments in a form that can be stored for later use. (Were the organic fuels oxidized in an unregulated fashion, most of the released energy would be lost to the environment as heat. This is what metabolism is: controlled combustion.) 
A second method—not nearly as effective as respiration—is fermentation, which consists of the partial breakdown of sugars in the absence of oxygen. Fermentation was the principal form of metabolism before the rise of oxygen in the atmosphere. As a means of extracting energy from food, cellular respiration is up to sixteen times more efficient. The energy efficiency of oxidative metabolism is what made multicellularity feasible and, along with the advent of nucleated cells, led to the complexification of life. 
The central figure in bioenergetics is adenosine triphosphate (ATP), a chemically stable substance unequaled in its facility to hold in store energy for future use, much like a minuscule battery.[4] ATP is frequently called the universal energy currency since all known types of life use it to power their metabolic functions. In fact, every recognized variety of cell has been found to contain ATP. Eukaryotic cells make the most of its energy storage capacity, producing large quantities when a rich food source like glucose is available. ATP’s stored potential is liberated by the removal of a single phosphate group, which releases energy and temporarily converts the molecule to adenosine diphosphate (ADP). This form, akin to a depleted battery, is then sent back to the mitochondria for “recharging.” Once there, another phosphate group is added, making it ready for re-use. One molecule of glucose can be converted to between 30 and 32 molecules of ATP. It is produced at astonishing rates: by one estimate, a single cell uses somewhere around ten million (10) molecules per second. At any given moment, our bodies contain only about 60 grams of ATP but the quantity produced, consumed, and replenished in one day’s time amounts to between sixty and a hundred kilograms (132–220 lbs).

Cells get their energy needs through byproducts of the breakdown of organic  matter including proteins, fats, starches…even indigestible substances like cellulose. Many of these substances must first be converted to one or another of the numerous forms of fatty acids and sugars.[5] Foremost among the latter is the six-carbon sugar glucose, a major energy source for most cells. Glucose (CH₁₂O) is a key ingredient in the chemistry of living things. It enters the cell by way of membrane-spanning transport proteins called glucose ports whose binding sites, upon making contact with a molecule of glucose, alter the shape of the protein such that it bodily pivots downward, in effect dragging the glucose through the cell membrane and releasing it into the cytosol.

During glycolysis (the initial stage of respiration), freshly delivered glucose is reduced to two molecules of the three-carbon compound pyruvate. As a preliminary stage, glycolysis liberates less than 25% of the glucose’s potential energy in its reduction to pyruvate. This happens one molecule at a time in the cytosol, in ten separate steps, each of which is assisted by a specific enzyme. The first five steps require energy input (in the form of ATP) but the final five conclude with a significant net energy gain. Pyruvate then passes into the mitochondrial interior space (the matrix) by way of transport proteins similar to glucose ports.

Inside the matrix, pyruvate is reduced in three further steps to acetyl CoA,[6] where this two-carbon compound enters the citric acid cycle. In the course of the citric acid cycle’s eight steps (which are steered by 18 different enzymes and coenzymes), carbon and oxygen are removed as waste products while hydrogen atoms are stripped of electrons. Upon entering the rotation, acetyl CoA is joined to oxaloacetate (the result of the step 8) to produce citrate. Subsequent steps convert citrate back to oxaloacetate and it is oxaloacetate’s eventual regeneration that makes the entire, remarkably energy-efficient process a “cycle.”

During the course of cellular respiration, numerous enzymes (assisted by coenzymes) strip electrons and hydrogen ions[7] from glucose and several other organic intermediates. These are passed to the crucial “carrier molecules,” primarily nicotinamide adenine dinucleotide (NAD+), eventually to be used in the production of ATP. During key steps in both glycolysis and the citric acid cycle, each molecule of NAD+ receives two electrons and one H ion from enzymes. It is this reduced form of NAD+, called NADH, that shuttles its ionic cargo to a series of elaborate catalytic “complexes” embedded in the surface of a mitochondrion’s inner membrane. The entire collection of coordinated nano-scale machinery comprises an electron transport chain. Nick Lane offers further perspective on this remarkable assemblage:

[T]he respiratory chain is organized into four gigantic molecular complexes…. Each complex is millions of times the size of a carbon atom, but even so they are barely visible down the electron microscope. The individual complexes are composed of numerous proteins, coenzymes, and cytochromes…. Curiously, mitochondrial genes encode some of the proteins, while nuclear genes encode others, so the complexes are an amalgam encoded by two separate genomes. There are tens of thousands of complete respiratory chains embedded in the inner membrane of a single mitochondrion.

The protein complexes pass through the membrane but are not physically connected. (Nor are the individual elements of each chain.) Electrons are dispatched from one to the next in line by other types of carrier molecules such that the chains act as minuscule wires. Through a sequence of redox reactions, each step oscillates between a  reduced state and an oxidized state. This scenario is typically represented in terms of a vertical drop: energy being gradually passed on in a downhill “cascade” to successive constituents, each of which has a greater electrochemical affinity for electrons. The exchanges occur spontaneously. At certain junctures, Hions are ejected into the intermembrane space (the area between a mitochondrion’s inner and outer membranes). In the electron transport chain’s final step, an oxygen molecule (O) receives a pair of electrons and also picks up two Hions from the aqueous solution, forming a single molecule of water. Water, along with COproduced during glycolysis and the citric acid cycle, are cellular respiration’s waste byproducts.

Useful energy is released at several steps in the respiratory chain but cells need energy in a stable, transportable form that can be redistributed to various locations, to be used for a wide variety of tasks. Here is where ATP enters my abbreviated portrayal.

A further independent element in the respiratory chain is another membrane-embedded complex called ATP synthase (ATPase for short). Recall that the energy released at each step in the respiratory chain is accompanied at several points by the physical expulsion of H ions across the mitochondrial inner membrane into the intermembrane space. This results in a concentration gradient across the membrane “dam.” Since hydrogen ions bear a positive charge, an electric gradient (in the form of electrochemical potential energy) results as well. The pressure created by this potential is called the proton-motive force; this is what lends ATPase its ability to manufacture ATP. This absolutely vital process is known as chemiosmosis.

Hydrogen ions held within the intermembrane space enter the ATPase complex. The almost beyond-belief sophistication of this matchless nanomachine is sometimes cited by creationists as proof of the existence of God. Nick Lane describes how it works:

ATPase is a marvelous example of nature’s nanotechnology: it works as a rotary motor, and as such is the smallest known machine, constructed from tiny moving protein parts. It has two main components, a drive shaft, which is plugged straight through the membrane from one side to the other, and a rotating head, which is attached to the drive shaft…. The pressure of the proton reservoir on the outside of the membrane forces protons through the drive shaft to rotate the head; for each three protons that pass through the drive shaft, the head cranks by 120°…. There are three binding sites on the head, and these are where the ATP is assembled. Each time the head rotates, the tensions exerted force chemical bonds to form or break. The first site binds ADP; the next crank of the head attaches the phosphate onto the ADP to form ATP; and the third releases the ATP.

The regeneration of ATP through chemiosmosis concludes the process of oxidative phosphorylation (so called because the addition of phosphate to ADP is the final result of a transfer of electrons to oxygen). The enzyme ATP-ADP translocase, abundantly implanted throughout the inner mitochondrial membrane, is responsible for catalyzing the shuttling of those molecules into and out of the matrix. Their flows are said to be coupled (in that ATP does not exit unless ADP enters—and vice versa). ATP, once released into the cytosol, is available for immediate use.

And there you have it. The entirety of the process of respiration, vastly more complex than this brief sketch suggests, is what powers almost all living things. (Prokaryotes, lacking mitochondria to manufacture energy-bearing ATP, follow a somewhat different path: respiration takes place within the cytoplasm, where suites of enzymes and carrier molecules are on hand at all times.) As a metabolic system, cellular respiration is unrivaled, and—from all indications—has undergone but slight modification since its establishment. To draw a parallel: it is as if one of the very first iterations of the internal combustion engine was still in use today, because the original design worked so flawlessly and with such reliability that the Model T engine was never improved upon. But this analogy is faulty in the sense that cars and trucks have been around for little over a century—not for hundreds of millions of years. (Not to mention that they break down with annoying regularity.)

Photosynthesis is an impeccably matched counterpart to oxidative metabolism—each process making use of the other’s waste products to produce energy via an elaborate series of redox reactions. Photosynthesis uses the energy of captured sunlight to make energy-rich sugars. This is made possible by that remarkable substance, chlorophyll, which has the ability to transform solar photons into energized electrons.[8] Chlorophyll is a medium-sized molecule centered around a single atom of magnesium and possessing a long hydrocarbon tail. Once “excited” by photons, grouped chlorophyll atoms initiate a series of enzyme-mediated reactions. These take place via an electron transport chain similar to the one found in cellular respiration, ultimately resulting in the production of sugars. More to the point: photosynthesis converts water and CO (one end-product of respiration) to oxygen and reduced carbon compounds—both of which happen to be required for respiration to proceed. In turn, respiration consumes reduced carbon compounds—mostly sugars—converting them to CO (essential for photosynthesis) and water. Photosynthesis, then, is essentially the reverse of cellular respiration and it is these two entwined processes that together turned a dead planet green. And once greened, Earth’s surface was soon teeming with life.
 By one estimate, each year more than 100 billion metric tons of carbon are incorporated into living organisms through photosynthetic activity. The amount of energy thus sequestered equals around six times the power consumed annually by humanity. Most prokaryotes and virtually all animals live off the products of photosynthesis, either directly or indirectly (as in the case of carnivorous animals that prey on herbivores.) Even chemoautotrophs living around deep-ocean vents are obliquely dependent on sunlight since some of them make use of photosynthetically derived oxygen dissolved in seawater or bits of organic material drifting down from the surface. The exquisite balance of this relationship powers all living things in a mutually beneficial association; it epitomizes the way life always finds ways to satisfy its needs. As is so often the case in nature, there is a paradoxical quality to life’s ways: convoluted and circuitous, they are at the same time artfully straightforward in their thrifty efficiency. 
Photosynthesis takes place inside organelles called chloroplasts. Indicative of their once-independent origins, chloroplasts (like mitochondria) have their own DNA and ribosomes. And, similar to mitochondria, their membranes are studded with ATP synthase complexes that pump protons across an inner membrane to manufacture ATP.
 Photosynthetic prokaryotes, chief among them being the cyanobacteria (formerly known as blue-green algae), have chloroplasts embedded in their plasma membrane. Chloroplasts are born primarily in the leaves of green plants but also in the tissues of stems and unripened fruit. There are around 500,000 chloroplasts contained in a bit of leaf tissue with a surface area of one square millimeter. Chloroplasts are capable of movement: in low light conditions, they orient themselves in sheets to maximize surface area but, under intense light, will seek shelter or align themselves edge-on to the Sun to avoid photooxidative damage. Like mitochondria, chloroplasts are bound by both an inner and outer membrane. Their fluid-filled interior is called the stroma. Suspended in the stroma are interconnected stacks of flattened disks called thylakoids whose outer casing, the thylakoid membrane, holds chlorophyll and various protein complexes and is the actual site of photosynthesis. The individual disk-shaped structures have a fluid-filled interior called the thylakoid space where H ions are kept in reserve. 
Photosynthesis happens in two stages: the light reactions and the Calvin cycle. 

The initial phase revolves around a pair of elaborate molecular light-harvesting elements known as photosystems I and II.[9] The process begins in clusters of up to several hundred individual chlorophyll molecules embedded in a protein complex. When excited by photons, this assemblage functions as an energy-focusing “antenna.” A discrete region in each complex—the reaction center—delivers photoexcited electrons to a specialized molecule called the primary electron acceptor. This is the first step in a photosynthetic version of cellular respiration’s electron transport chain. The first photosystem shunts electrons to the second via this redox reaction chain, providing energy for the chemiosmotic synthesis of ATP during its course. The next photosystem, which gathers energy from light of a slightly longer wavelength, repeats the process: photoexcited electrons are driven from a second reaction center to another primary electron acceptor, which then passes them on via the iron-containing protein ferredoxin to a final enzyme complex. In this terminal reaction, the carrier molecule NADP+ is converted to its reduced form, NADPH.[10]

During an early phase of the light reactions, water molecules were split, releasing H ions into the thylakoid space and O to the atmosphere (as waste). This same water-splitting reaction was the source of two electrons and one proton later used to reduce each molecule of NADP+ to NADPH. Note that energized electrons carried by NADPH, the main reducing agent in chloroplasts, supply the  energy needed to power the second stage of photosynthesis—not sunlight.

This second stage—the Calvin cycle—takes place in the stroma and is similar to the citric acid cycle in that participating components are regenerated after molecules enter and leave the rotation. In the conversion of CO into sugars, the Calvin cycle draws on both ATP and energy from electrons held by NADPH (each produced during the light-dependent reactions). NADP+ is fed back into the photosystems where, as a contributor to the electron transport chain, it is converted back to NADPH. Most of the electron carrying molecules and protein complexes are very similar to those involved in cellular respiration. Chemiosmosis proceeds along similar lines: protons from the electron transport chain are released into the thylakoid space, where there can be a thousand-fold difference in proton concentration on either side of the membrane. This proton concentration gradient drives Hions through ATPase complexes into the stroma. By using the mechanical energy provided by the rotating ATPase shaft to add phosphates to ADP, fresh supplies of ATP are generated.

Photosynthesis is considered to be the single most complex biological process, yet is known to have been fully operative in DNA-bearing, self-replicating organisms at least 3.5 billion years ago—very early in life’s history. This well-established fact is one of the most powerful bits of evidence supporting the Natural Design construct. Biology students, throughout their educations, are taught that this utterly indispensable system, including its seamlessly intertwined association with cellular respiration, is in effect a fortunate “accident” of chemical interactions. Students are repeatedly assured that “somehow” (no one really knows how), the photosynthetic process, along with all its extraordinarily sophisticated molecular machinery, simply “came together,” “one step at a time.” This is the position espoused in virtually all biological literature. As I have asserted more than once, a time will come when young students will be astonished to learn that, as late as the 21st century, such antiquated ideas were still believed.

More to the point: from a position that recognizes life’s innate capacity to craft ingenious, energetically frugal solutions to each of its needs, the notion that these sophisticated solutions arose in some providential (but in the end chance) fashion seems positively ludicrous. Metabolism entails a number of discrete, integrated systems—all acting in unison with neat efficiency, each one subject to elaborate regulatory schemes. Even in their most primitive states, the various systems would have been unable to function below a certain level of complexity. It is difficult to envision how these wonderful biological solutions could have originated. No one has yet seriously attempted to recreate likely pathways in anything more than rough outline; earnest attempts by leading experts are openly admitted to be based on pure surmise. And all such conjectures tend to set aside the thorniest obstacles, relying instead on high-octane optimism.

Given the scientific climate of our time, it is much to ask of any well-educated non-creationist that they stand aside, take in a view of life in all its totality, and see that ultra-complex processes such as photosynthesis and respiration did not simply “come about” through gradual selection over the course of eons. And as I have repeatedly emphasized, we have not yet plumbed how it is that all these things function so flawlessly, nor, in some cases, even precisely how they work. Some of the most ornate processes are understood down to the finest details while their origins remain a complete mystery. So, yes, it is folly to assert that these processes arose in stepwise fashion through the selection of chance alterations to amino acid sequences—something more was driving the courses of development. It is folly, particularly in light of the fact that hundreds of millions of years ago microbes employed many of the same processes that they use today. In other words, most of the bugs and kinks had already been worked out when life was still in its infancy. Some organizing principle was assisting in the coordination of endless mutually-dependent associations. With its assistance, subtle lawful influences helped craft the endless array of protein machines with their myriad specialized capabilities.

 I call this organizing principle Natural Design. It is an inherent and irreducible feature of nature. But it has no name…is certainly not a “thing.” It is not a force, nor is it a process. While scientifically inappropriate, the words that come closest to encapsulating the spirit of what Natural Design represents might be “ineffable influence.” The picture I have been painting all along shows a vibrant, living world that exists by virtue of an exquisite capacity to organize layers upon layers of complexity into one colossal network called the biosphere. (This topic will be the focus of Chapters 10 and 11.) But first, a look at the way Earth, and all the matter and materials that makes up its countless environments, has been found to be an absolutely ideal medium for life.   


©2018 by Tim Forsell     draft                        23 Feb 2018


[1]From his Nobel Prize lecture, Stockholm, 12 Dec. Quoted in “Cell Traffic,” Calder, 122–23. 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] A little basic chemistry to help illuminate some key details: Bonds between atoms carry an innate potential energy. The potential energy held within chemical bonds, and their resistance to being broken, vary depending upon which elements are involved. The energy released when bonds are broken in the course of chemical reactions can be captured and stored by living things, then put to use to perform work. (In physics, “work” refers to the performance of some task requiring an input of energy.) For this reason, biologists typically do not speak of energy being “generated.” Properly speaking, once liberated by a reaction, energy is conserved by being transferred to special molecules that can release this stored energy on demand. In any reaction, however, energy is lost in the form of heat due to entropy. Many important chemical reactions are based on the exchange of electrons when bonds are broken. These are known as redox (or oxidation-reduction reactions) because they occur in tandem. In a redox reaction, the substance that gives up electrons is said to have been oxidized while the substance receiving those electrons has been reduced. Another way of expressing these roles is to say that the electron “donor” is the reducing agent  while the electron “acceptor” is the oxidizing agent. For example, oxygen is one of the most potent oxidizing agents because, chemically speaking, it has a powerful “hunger” for electrons.
[3] Currently the favored name for the Krebs Cycle (feared by biology students everywhere, such is its daunting complexity).
[4] So named because a single molecule has three phosphate groups attached in line. Energetically, ATP is likened to a “coiled spring;” its phosphate groups (PO₄ˉ), being of like charge, repel one another. This makes it relatively difficult to make ATP but easy to break it apart. This is accomplished in a process that removes one of the phosphates—an energy releasing reaction.
[5] A component of lipids, fatty acids are long-chain hydrocarbons capped on one end by a carboxyl group (COOH). Sugars, rich in high energy bonds, are compounds which typically have chemical formulas based on some multiple of CH₂O.
[6] CoA stands for coenzyme A. Coenzymes are electron-carrying molecules required for the proper functioning of enzymes involved in cellular respiration.
[7] A hydrogen atom consists of a single proton and an electron. Hydrogen ions are solitary protons (designated H⁺).
[8] Chlorophyll is a type of pigment. By definition, pigments are substances that absorb visible light. Different kinds absorb light of differing frequencies; those frequencies not absorbed are reflected. Chlorophyll absorbs light in the red and blue parts of the visible light spectrum and reflects light with wavelengths in the green range, hence its apparent color.
[9] The light reactions actually commence with photosystem II. (This is so because photosystem I was still unknown when photosystem II was discovered.)
[10] NADP+ is similar to NAD+ (the energy-bearing molecule from cellular respiration) but with the addition of a phosphate group.