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What's the Matter?

Periodic Table of Elements

This is the third in a series of musings on the framework of my beliefs encouraged by conversations over campfires in Florida one winter. The dominant creation myth among my fellows was that in the beginning, God created the heavens and the earth. The earth was deemed to be initially formless and empty, with darkness over the surface of the deep, and the spirit of God more or less hovering over the waters. With the Hebrew word "yhi 'or", God then said, “Let there be light,” and there was light. God then separated the light from the darkness, calling the former day and the latter night. Excited by His first day's success, God went on to provide a vault to separate water underneath the vault from water above calling the vault sky. With His next wave of hand He said “Let the water under the sky be gathered to one place and called seas, and let dry ground appear and be called land.”

Warming to His work, God then said, “Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds.” God then said “Let there be lights in the vault of the sky to separate the day from the night, and let them serve as signs to mark sacred times, and days and years." God made two great lights—the greater light to govern the day and the lesser light to govern the night and He also made the stars. Next God said, “Let the water teem with living creatures, and let birds fly above the earth across the vault of the sky.” And God said, “Let the land produce living creatures according to their kinds: the livestock, the creatures that move along the ground, and the wild animals, each according to its kind.” He then encouraged all these living creations to be fruitful and increase in number. Finally, still unsatisfied with the role assignments, God said, “Let us make mankind in our image, in our likeness, so that they may rule over the fish in the sea and the birds in the sky, over the livestock and all the wild animals, and over all the creatures that move along the ground.”

Occam's razor is a principle that generally recommends that, from among competing hypotheses, selecting the one that makes the fewest new assumptions usually provides the correct one, and that the simplest explanation will be the most plausible until evidence is presented to prove it false. I cannot prove the theological creation myth to be false but in my musings on cosmology, I spent some time trying to present an alternative explanation for primordial nucleosynthesis during the first 10-6 seconds after the Big Bang. Later, when I was closely examining my own brain, I introduced a whole set of nano-ants called neurons, microtubules, Microtubule Associated Proteins (MAPs), calcium ions, and even a catalyst called Calmodulin-Dependent Protein Kinase II (CaMKII) without explaining how all of these complex creatures evolved from our primordial soup of four primary forces acting though the gauge bosons to impose their intentions upon nucleons, quark collections, leptons, et al.

What's the Purpose

In my own life I have tried to achieve a degree of awareness by seeking answers about life by exploring the past. and by constantly trying to avail myself of advanced intelligence. The entity that was here before there was a here was introduced in the earlier musing as a Void. and I tried to elaborate on it as pure, infinite, conscious energy. According to superstring theory, this ten dimensional infinity of conscious energy, surrounded the essence of the energy's DNA, an essence which gave it what I then called an all consuming desire to share as its everlasting, unimaginable fulfillment. In a sort of intellectually childish way, I then hypothesized the problem of this Void as requiring a Receiver of its desire to share. And so this vast all-consuming conscious energy created another consciousness to receive its energy.

Let's think of this second consciousness, this creation, as our multiverse (Physical Matter Reality) vessel collapsed from the original ten dimensions in accordance with the electromagnetic spectrum; first into a bundle of six color dimensions and then into the single dimension of our muliverse's initial singularity. This multiverse vessel has but a filtered subset of the energies available to the original ten dimensional void and so its wavelengths are longer and weaker, therefore imposing certain limitations on the vessel's biological crew members like me. So at least as of the time of this writing, we sentient and non-sentient passengers face the threat of dying every day. Add disease, pain, hunger, hatred, injury, loneliness, and sorrow until we arrive at lives of quiet desperation occasionally interrupted by delusions of grandeur.

The PMR vessel did the only thing it was capable of doing--it shunted its creator's flow of energy and in doing so, it shrank to a singular point of existence that we later came to call the "Big Bang", a sudden expression of a singularity of inconceivable energy containing protons, neutrons, electrons--all injected into the vacuum of space. Cause and effect were born. The event that shattered the PMR vessel and expanded the physical universe also gave order to the upper dimensional void so that the flow of energy might be veiled from the observational perspective of the receiver. The upper dimension achieved everlasting fulfillment and the PMR is the arena where that fulfillment had to be earned., the collective immortal soul in its unified state prior to the Big Bang. The Biblical echo of the six days of creation may be an encryption of the Big Bang singularity's intemediate six dimensional state becoming our PMR vessel's unified soul. The physical world is the lucid holographic dream where fulfillment must be earned.

As validated by quantum physics, time had no meaning in the initiating ten dimensional void which preceded the Big Bang. In the void all of the past is known as well as what will happen in the future. This musing and its writing were always known and what is occurring here at my keyboard has already occurred numerous times before, all with varying results but similar outcomes in what quantum theorists call a multiverse. Each choice that we make in life, theoretically creates its own universe. I am here because I have survived all of the choices that I have made to date. I am hopeful of surviving this moment so that my consciousness can continue into a multiverse where I survive. Everything that follows has already occurred numerous times before, all with varying results but similar outcomes. In the end, I never make it out alive, but I will extend my consciousness for as long as I can so that I can observe the continued attempts at survival of my .species.

During the dull winter months this year I took a course called "Neuroscience of Vision" in which I learned that images are constructed in our brain based on electrical signals from our eyes so that everything we perceive as matter, is also an electrical signal interpreted by our brain. The human brain is designed to interpret electrical signals sent from our five senses. How then do we know an external world even exists? What if our perceptions are originating from another source, the same source responsible for our dreams? According to quantum physics, matter doesn't even exist; the material world is simply an illusion, an electrical signal perceived by the brain to convince the soul that the universe is real.

When we examine the inner workings of an atom, we see that it is about 99.99 percent empty space. So why is it that we cannot simply walk through a wall made up of these airy atoms. The reason is electrons. Electrons are tiny, but they pack a strong negative charge. These electrons are continuously moving around the circumference of the atom at the speed of light, repelling each other. It's there repelling charge that prevents us from walking through walls. We go through our entire lives without having touched anything including our beloveds. When we stand, the electrons in our shoes repel the electrons in the floor, levitating us about a millionth of a centimeter.

So everything that surrounds us, everything that we perceive as matter, is simply an electrical signal. The human brain is designed to interpret electrical signals sent from our five senses so how do we know that an external world even exists. What if our perceptions are originating from another source, the same source responsible for our dreams? It may be that the past is gone and the future exists only as a probability distribution, a potentiallity of the possible things that can happen.

Quantum theory, however, insists that the past, present, and future all co-exist simultaneously. Since the past determines the future, everything that has happened since the Big Bang was predetermined, that everything that could possibly happen has already happened so that time is totally dependent upon the observer.

At the beginning of this musing on the purpose of life I held forth on the frequencies of the originating ten dimensions and how their wavelengths or vibrations corresponded to different colors of the electromagnetic spectrum. In an earlier, more romantic and more religious period of my life, I had the thought that there might be an eleventh dimension exiled from the ten, a dimension associated with darkness, which I then defined as absense of light. The darkness feeds off the slow, dense vibrations generated by negative energies: fear, ego, lust, greed, hatred, and violence.

It seemed to me at the time that this radically alternative reality was threatening to bring chaos to the physical world. It seemed driven by a fear-based dicotomy, dictated by a minority controlling the masses through their desire for the accumulation of matter. This negative elite seemed to be creating fiefdoms that were destabilizing the natural order of things. By unknowingly feeding the darkness, they were generating randum shifts that have self-organized into higher complexities, creating chaos. These idol worshippers of our time seemed to be starting wars to preserve the status quo. I began to develop a fear that not all of the PMR multiverses were following converging or parallel tracks and that my experiential track had deviated substantially from the norm. Humanity seemed to have shifted its collective consciousness toward self-destruction. Unless something happened soon to divert it, the train would derail and take our species with it.

Post Primordial Nucleosynthesis


Our best description of the atom is that 'something unknown to us is doing we don't know what'. This does not seem like a particularly illuminating theory and in someways reads something like 'The slithy tove did gyre and gymbal in the wabe".

Sir Arthur Eddington

Sometime between the first few millennia and a million years after the Big Bang—the exact moment cannot be pinned down much better since the process was gradual—the charged elementary particles of matter began clustering into atoms. Their own electromagnetic forces pulled them together, sporadically at first and then more frequently. The weakening radiation could no longer break them apart as quickly as they combined. In effect, the authority of radiation had subsided as the previously charged matter (“plasma”) gradually became neutralized, a physical state over which radiation has little leverage. Matter had, in a sense, managed to overthrow the cosmic fireball while emerging as the principal constituent of our Physical Matter Reality (PMR).

The emergence of organized matter from chaotic radiation was a preeminent change in the history of the PMR. The Radiation Era had naturally and inevitably given way to the Matter Era. Some scientists regard it as the greatest change that ever occurred. The onset of the Matter Era saw the widespread creation of atoms; they were literally everywhere. The influence of radiation had grown so weak that it could no longer prevent the attachment of hadron and lepton elementary particles that had survived annihilation. Hydrogen atoms were the first type of element to form, requiring only that a single negatively charged electron be electromagnetically linked to a single positively charged proton. Copious amounts of hydrogen were thereby made in the early PMR, and it is for this reason that we regard hydrogen as the common elemental ancestor of all material things. Hydrogen (and its isotope, deuterium) was not the only kind of atom fashioned during this era. Before all the electrons and protons were swept up into hydrogen, atoms of the second simplest element, helium, began to form.

When we peer into the darkness and the void, when we peer as deeply as our primitive tools allow, we descend into a realm of the "jiffy"--which defines the travel time of light across the diameter of our proton ancestor, or one billion-trillionth of a second. Within this space, far below the realm of everyday human experience, invisible lines of force--lines of interconnected quarks and gluons--stretch out of nothingness, contracting, gyrating, and creating the spherical field of an equally transparent proton.

If we try to examine a single proton of hydrogen and then pull back further still until we retreat to the electron shell of the hydrogen atom, the proton in its nucleus is, when scaled against the electron's spherical, ghostly orbital shell, no larger than a sport utility vehicle scaled against the sphere of Earth. And this, too, is a ghostly and empty, yet forceful realm. To continue drawing backward reveals the outermost shells of other atoms interlinked by electrons--which manifest, self contradictorily and simultaneously and almost everywhere at once, as waves and particles ....bound electron shell to electron shell.

Heavy nuclei originate when two or more light nuclei fuse together. They do so by means of a dual process. First, a heavy nucleus of an atom is created whenever lighter ones collide violently enough to stick and fuse. Second, the newly formed positively charged nucleus then attracts a requisite number of negatively charged electrons, thereby yielding a neutral, albeit heavier, atom. In the case of helium production, a temperature of at least 107 K is needed to thrust two hydrogen nuclei (protons) into one another. Each proton boasts a positive charge and at lower temperatures they would simply repel like identical poles of magnets. This minimum temperature ensures that the hydrogen nuclei collide with ample vigor to pierce the natural electromagnetic barrier that prevents them from interacting under ordinary circumstances. For a split second, the colliding particles enter the extremely small operating range of the Strong Nuclear Force. Once within ~10-12 cm of one another, the two hydrogen nuclei no longer repel. Instead, the attractive Weak Nuclear Force seizes control, slamming them together ferociously and uniting them instantaneously into a heavier nucleus.

Thereafter, in the later stages of the Matter Era, pairs of electrons were electromagnetically attracted to each helium nucleus, thus fabricating neutral helium atoms. Given the rapid rate at which most models suggest the PMR expanded and cooled, only so much of the hydrogen could have been transformed into helium, leaving about a dozen hydrogen atoms for every one helium atom. That’s a helium abundance of nearly 10% by number, or 25% by mass. Since helium is chemically inert, there’s no easy way to change it into something else once it exists; helium atoms cannot even "hide" within other substances, like molecules, since helium doesn't easily combine with any other elements.

By contrast, elements heavier than helium could not have been appreciably produced in the early PMR. (Nuclei of the third element—lithium—squeezed through the bottleneck, but only in smattering amounts fully a billion times less than helium.) The elements interesting to biochemistry; the oxygen and nitrogen in the air we breathe, as well as the copper and silver in the coins in our pockets were not made in the aftermath of the initial bang. Fusion of heavy elements, including all the way up to iron and uranium, for example, requires temperatures much higher than 107 K. Such syntheses also require lots of helium atoms. The trouble here is that, even though helium production was in high gear during those first few years, both the density and temperature were quickly falling. Theoretical calculations suggest that, by the time there were sufficient helium atoms to interact with one another to manufacture heavier elements, the cosmic temperature had dipped below the threshold value needed for the mutual penetration of doubly charged helium nuclei. That threshold value is ~108 K, for it takes even greater violence for multiply charged nuclei to collide, stick, and fuse. The PMR was still hot, but not quite hot enough anymore to make the heavies.

The CNO Cycle

CNO CycleThe CNO cycle (for carbon–nitrogen–oxygen) is one of two sets of fusion reactions by which stars convert hydrogen to helium, the other being the proton–proton chain. Unlike the proton–proton chain reaction, the CNO cycle is a catalytic cycle. Theoretical models show that the CNO cycle is the dominant source of energy in stars more massive than about 1.3 times the mass of the Sun. The proton–proton chain is more important in stars the mass of the Sun or less. In the CNO cycle portrayed above, four protons fuse, using carbon, nitrogen and oxygen isotopes as a catalyst, to produce one alpha particle, two positrons and two electron neutrinos. Although there are various paths and catalysts involved in the CNO cycles, simply speaking all these cycles have the same net result. The positrons will almost instantly annihilate with electrons, releasing energy in the form of gamma rays. The neutrinos escape from the star carrying away some energy. The carbon, nitrogen, and oxygen isotopes are in effect one nucleus that goes through a number of transformations in an endless loop.

Star FormationCalcium is produced by a process called silicon burning which is a very brief sequence of nuclear fusion reactions that occur in massive stars with a minimum of about 8–11 solar masses. Silicon burning is the final stage of fusion for massive stars that have run out of the fuels that power them for their long lives in the main sequence on the Hertzsprung-Russell diagram. It follows the previous stages of hydrogen, helium (the triple-alpha process), carbon, neon and oxygen burning processes. Silicon burning begins when gravitational contraction raises the star’s core temperature to 2.7–3.5 billion kelvins (GK). The exact temperature depends on mass. When a star has completed the silicon-burning phase, no further fusion is possible. The star catastrophically collapses and may explode in what is known as a Type II supernova.

So in the beginning, there was hydrogen--and not very much of anything else. Even today there are more than 9,200 more atoms of hydrogen spread throughout the universe than there are atoms of carbon or silicon. As we look around, our spectrographs and telescopes reveal, in the dust of exploded suns, that the iron running in our veins, the oxygen in our lungs, and the silicon upon which we stand came about, as it were, from fusion-based waste products in the hearts of dying stars. We can track the universal accumulation rates of the heavy elements backward along the stream of time and see that 7 billion years ago the formation of rocky, Earth-like worlds was unlikely, 9 billion years ago exceedingly impossible, and 11 to 12 billion years ago next of kin to impossible.

There was a time, inevitable and far, far in our past, when our remotest ancestors were mere hydrogen nuclei--protons. When infinitely curved and infinitely dense space-time had unraveled into a universe that, though newly born, was by our standards already ancient, an entire system of stars and Jupitor-like brown dwarfs could be scoured for all the elements heavier than helium, and we would have failed to find enough material to fashion a single, fist sized rock. We had only the miracle of a universe that was running down slowly, unavoidably, into matter: a miracle in which submicroscopic cracks in the universe gave way to frozen energy--which was, stated another way, matter. But from the lights in the heavens, we might have guessed that these were enough, and almost never would the universe be quite so simple again. Life was inevitable. The lights in the heavens--the stars--would have told us so.

The Genesis Stone

Allende MeteoriteSome 5 billion years later, the lives and deaths of stars had fused hydrogen nuclei into helium nuclei, helium into carbon, oxygen, neon,magnesium, silicon and iron. The collapse of stars into supernovae had produced, and then scattered, an entire spectrum of elements both heavier and lighter than iron. Some of those elements were injected into our solar system almost at the moment of its formation, to judge from a careful reading of radioactive decay products in the Allende Meteorite, sometimes called the "Genesis Stone." Salt veins and chemically produced proteins, along with precursors to chlorophyll and hemoglobin (complex organic molecules called porphyrins, different from any porphyrins on Earth), tell us that somewhere between the molten core and the outer surface of the asteroid parent bodies there existed, for a half-billion years or so, (until the nickel-iron cores froze), warm wet zones in which the early solar system, in diverse places, was trying to make life. From atoms and empty space...From the dust of the stars...

From such beginnings, it is possible to believe that the phenomenon we call life is but the most likely outcome of some very common elements, if stirred together and kept warm enough and wet enough for long enough. From such humble beginnings, it is possible to believe that someone, somewhere over on the far side of the galactic core, is gazing into the sky in our direction, and asking the same questions that we ask. We are the dust of the universe, trying to understand where it is going and whence it came--sometimes through theology, sometimes through science, sometimes through a combination of both. We are the dust of the universe, trying to understand itself.


By 4 billion B.C.E., a day on Earth is as few as ten hours long and the Moon orbits thousands of miles nearer. The smaller member of this double planet system is almost within the Roche limit, which means that Earth's crust--the solid surface of the planet--undergoes tidal variations. In the heavens, the Earth-facing hemisphere of the Moon is erupting entire seas of basaltic lava--which is exactly what protocell descendents, 4 billion years hence, will name the lava fields: Sea of Tranquility...Sea of Serenity...Ocean of Storms. The lunar eruption will continue for another 700 million years.

Earth is next of kin to chaos. Carbon diverges into two distinct destinies, depending on where it ends up. 4 billion years later and 300 miles underfoot of every protocell descendant's cities, carbon will be able to accumulate in only one form: diamonds. One of the most abundant elements in the world will become one of the most common gemstones in the earth. At this level lie truckloads and shiploads of diamonds--most of them dirty brown or (when favorably contaminated with nitrogen) canary yellow, some ranging beyond the diameter of a man's fist, and as clear as water from a mountain spring. The only truly rare diamonds, occasionally enhanced by the steady decay of uranium and thorium, are brilliant green or blue, sapphire pink, or wine red. The protocell descendants will treasure diamonds, in part, because only rarely do the carbon crystals rise to the planetary surface through the deepest and narrowest of volcanic wounds. High above the diamond beds, where the pressures are, relatively speaking, indistinguishable from the high vacuum of outer space, carbon can bond freely with hydrogen, oxygen, nitrogen, sulfur, and phosphorus to form DNA molecules passing from generation to generation across billions of years and prove themselves no less resilient than diamonds.

The Protocell Era, from which simple organic compounds shall emerge as living cells with an elaborate genetic machinery, is probablyProtocell already more than a quarter billion years old in 4.5 billion B.C.E. The first "useful" proteins, those that by sheer chance have appeared on or in pre-living bubbles of organic sludge and are able to induce reactions that add to their bulk, invariably prolong the survival of individual protocells. The life span of a protocell is thus directly related to the complexity and effectiveness of its metabolism; and time, the destroyer, sees to it that most protocells and their descendents run down and eventually fall apart, dispersing their contents for future absorption by other protocells. Those bubbles graced with the ability to absorb molecules from their surroundings--and to capture energy and direct it toward the knitting together of absorbed molecules into substances that can promote the survival not only of the bubbles but also of their daughter bubbles--shall be (or have already become) ancestors of the first true life-forms to populate the seas.

What the protocells require, if such compounds as hemoglobin, chlorophyll, and brain proteins are to be evolved, is something akin to a team of carpenters (RNA) and a set of blueprints (DNA), to be passed on to each daughter protocell, guaranteeing that it is able to construct the same enzymes needed for all of the reactions important for the parent's survival. What they require is the ultimate parasite; the living gene. Many years later a protocell descendant would see, at the cradle of life, an "RNA world," in which the dominant route to the construction of genetic machinery capable of bridging protein and nucleic acids is the emergence of simple "prototype generator RNAs": circular molecules only a dozen base pairs long that are able to specify only four simple classes of amino acids. This protocell descendant would demonstrate, mathematically and chemically how simple proteins and prototype transfer RNAs could be bond assembled from a single, randomly generated RNA molecule. From this point forward, Darwinian selection enters the picture, fashioning the raw material of variation by preserving those systems that work best under prevailing conditions of the day.

We live in a universe where studying the fusion of hydrogen atoms, by stars, into the heavier elements from which plants and eyelashes are made, becomes the sincerest form of ancestor worship. Heavy element accumulation rates, plotted during the 13.8 billion years since the Big Bang, suggest that there was a specific "instant" during which life could begin on the surface of Earth-like planets. The indications are that Earth formed at the "instant" Earth-like worlds could begin to form (give or take about 300 million years). We were not necessarily the first habitable solar system to arise in the galaxy, but we were certainly present at the starting gate, some 4.5 billion years ago. In a universe where the emergence of intelligent life can be measured as a function of time, the rise and fall of civilizations on this planet take on an added significance, if indeed we are one of the oldest worlds around, one of the newest and brightest creatures around--and alone in the night or very nearly so.

Chemistry to Biology

BiologyChemistry concerns itself with how electron sharing binds atoms into molecules. I never studied high school chemistry so I hardly know how to begin, but since my focus is on biochemistry I should be able to simplify things by working with only the six elements that make up 99% of Living Organisms. A chemist investigating the composition of living organisms comes away with two conclusions. First, even the simplest cell is an exceedingly large mixture containing thousands of different molecules, whose proportions remain essentially invariant generation after generation. Second, from the chemical viewpoint, rabbits and grass are very much alike, and their molecular constituents comprise but a tiny fraction of the structures known to chemistry. All cells contain virtually the same set of small molecules -- amino acids -- sugars, sugar phosphates, nucleotides, dicarbolic acids, perhaps a hundred in all, dissolved in water, which makes up as much as nine tenths of the total mass. Potassium ions always serve as the chief intracellular electrolyte, even though sodium ions predominate in the environment. All their macromolecules are made to the same plan. The myriad of known proteins are all constructed from a common set of twenty amino acids, linked into unbranched chains by a coupling called the Peptide Bond. A common set of five nucleotides accounts for all the many molecules of RNA and DNA, except for a sixth nucleotide found only in a handful of viruses. Diversity among the lipids and carbohydrates is somewhat greater, but the repertoire is quite limited.

So my next definition must distinguish the living from the non-living in some sensible way. Much of the chemical business revolves around energy. The characteristic activities of living things -- their growth, movements, the very maintenance of their structure and integrity -- depend upon input of energy from the environment. That is one of the chief functions of the metabolic web, for chemical substances serve as carriers for energy as well as matter. Like a flame or an eddy, an organism is not an object so much as a process, sustained by the continuous passage through it of both matter and energy. In addition, living things are generated autonomously, not by external sources, and what they generate is their own kind. Like begets like. Biological heredity is quite unlike the point-by-point transfer carried out by a copying machine. Instead, characteristics are transmitted from parent to offspring by a program or recipe that embodies instructions for producing the next generation. The process is extremely accurate, yet subject to occasional errors that account for the variation in every natural population.

There is always a higher degree of organization in living organisms. Even the simplest unicellular creatures display levels of regularity and complexity that exceed by orders of magnitude anything found in the mineral realm. A bacterial cell consists of more than 3 hundred million molecules (not counting water), several thousand different kinds of molecules, and requires some 2,000 genes for its specification. There is nothing random about this assemblage, which reproduces itself with constant composition and form generation after generation. A cell constitutes a unitary whole, a unit of life in another and deeper sense like the legs and leaves of higher organisms, its molecular constituents have functions. Whether they function individually, as most enzymes do, or as components of a larger sub-assembly such as a ribosome, molecules are parts of an integrated system, and in that capacity can be said to serve the activities of the cell as a whole. As with any hierarchical system, each constituent is at once an entity in itself and a part of a larger design; to appreciate its nature, one must examine it from both perspectives.

Any organism that is made up of distinct parts, and that reproduces by heredity with variation, must evolve parts that promote the organism's survival and multiplication. Their structure and function will alter over time, tracking changes in both the internal and the external environment. The reason is that an individual organism's reproductive success must be affected by environmental factors, and natural selection will favor the better adapted over the less well adapted. Adaptive behavior is seen throughout the living world, not only at the level of the legs and leaves but also at that of enzyme proteins and cellular organelles. Physiology and evolution are both central to the grammar of life.

The elements in living organisms are Hydrogen (H), Oxygen (O), Nitrogen (N), Carbon (C), Calcium (Ca), and Phosphorus (P) and the only thing special about them is that they are easily available and suitable to the task. To further introduce terms I have already started to use, I will declare that an Element is matter composed of atoms that all have the same atomic number (protons). Atoms, in turn, are the smallest component of an element that still has properties of the element, consisting of a positively charged nucleus surrounded by a charged cloud of electrons. As I explained in my cosmology musings, the positive "+" charge of the proton in the nucleus and the "-" charges of the electrons strongly attract each other by filling the space around themselves with countless millions of other tiny particles called Gluons that have only the most ephemeral existence. These ephemeral gluons are called Force Carriers or mediators and they come into existence only briefly and are gone only to be replaced by another one thrown out by the parent particle. A Proton is a particle in the atomic nucleus with a positive charge of +1 and an atomic mass number of 1 Dalton. The Neutron is a non-charged nuclear particle with the same mass as the proton. The Electron is a negatively charged particle (-1) with a mass 1/1837 of that of a proton. An Isotope is an atom with the same number of protons and electrons, but different numbers of neutrons. A Molecule is two or more atoms linked by a chemical bond. Molecules can contain different types of bonds. If atoms are sharing electrons, then the bond between them is covalent. If an atom gives up an electron to another atom, then they have an ionic bond.

Covalent bonds Methane Molecule
Methane has four covalent bonds between Carbon (C) and Hydrogen (H). The figure at right shows the methane molecule in four different views. Notice how these different views represent the atoms and their bonds differently. Electronegativity refers to the tendency for atoms to bind electrons. Oxygen (O) with an electronegativity of 3.5 has a strong affinity. Hydrogen (H) and Carbon (C) each have lower affinities. A bond between C and H will have nearly equal sharing of electrons. Oxygen and hydrogen form a highly polar bond because of the much stronger affinity for electrons by O.

ElectronsElectrons are outside the nucleus, and determine properties of the atom. Chemical reactions involve sharing or exchanging electrons. Electrons move about the nucleus in atomic orbitals. Absorption of energy can cause an electron to move up to a higher energy level. The atom is stable when the outermost energy level of most atoms has eight electrons. Electrons can be transferred carrying energy to another molecule. The Hydrogen (H) atom can carry electrons for transferring energy. Oxygen (O) has a strong affinity for electrons. Redox is a reaction transfer of electrons from one molecule (oxidized) to another (reduced). Stability can be achieved by adding, losing, or sharing electrons. Sharing electrons leads to the formation of covalent bonds. Bonds contain energy, and require energy to be broken. Bond energy (expressed as kcal/mole) is the energy required to break a bond. For example, an H-H bond requires 104 kcal/mole to break.

I always hated subjects that required definitions and rules on the first day of class and I will try to do better from here on. I earlier Eukaryotedecided to focus on just the six chemical elements associated with living things and now I am going to further simplify by paying attention only to the eukaryote which is is an living organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried. Most eukaryotic cells also contain other membrane-bound organelles such as mitochondria, chloroplasts and the Golgi apparatus. All species of large complex organisms are eukaryotes, including animals, plants and fungi.

Cell division in eukaryotes involves separating the duplicated chromosomes, through movements directed by microtubules. There are two types of division processes. In Mitosis, one cell divides to produce two genetically identical cells. In Meiosis, which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.

Like everybody else it is not immediately obvious to me just how a stream of energy in the form of heat and radiation, impinging on the primordial soup of the inorganic earth could generate higher forms of molecular and structural organization. Setting aside the particulars of chemistry that account for the formation of this molecule or that, the reason that the flow of energy through a system organizes that system is that the buildup of complexity promotes entropy production and energy dissipation. The more efficient a given system, the greater the share of energy flux and chemical resources that it can command. Reaction cycles are a case in point. Consider a particular molecule, X, that absorbs light, and is thereby converted to another molecule, Y, with concurrent degradation of the light energy to heat. No such process can long continue unless a pathway exists that regenerates X from Y. Systems that "discover" such a cycle can persist, those that do not will soon cease to operate; thermodynamics favors the cycle even though it may require several linked steps, so long as the cycle as a whole dissipates energy. Structural complexity, likewise, may be energetically favored. Biochemistry knows many instances in which small elements associate spontaneously into a larger complex. this entails a local increase in order but proceeds without any increase in energy if the aggregation results in an increase in entropy (disorder) for the system as a whole. A case in point is the spontaneous formation of spherical lipid bilayer vesicles from free phospholipid molecules. The devil, as usual, is in the details but the general principle holds: energy dissipation mandated by the second law supplies a driving force for the local generation of chemical and physical complexity. Energy does not determine the particulars, but it can supply an ultimate cause for the emergence of structure on the lifeless earth. Whereas the universe is steadily running downhill in the case of depleting thermodynamic potential, it is also running uphill in building structure. The two are coupled through the second law of thermodynamics.


EntropySo even without a presiding architect, the inexorable working of the second law may well be the background to the proliferation and diversification of life. What are mutations, chromosome rearrangements, and other mishaps that disrupt the precise propagation of living order, but consequences of that randomizing tendency mandated by the second law? Not only variation, but natural selection as well, manifests the second law. Natural selection does not evaluate organisms in pure culture, but operates on communities or ecosystems composed of many kinds of organisms evolving together. Every ecosystem can be regarded as an energy transformer, trapping radiant energy in the form of biomass and gradually degrading it to heat. As this transformation proceeds, the ecosystem makes available niches within which particular organisms can flourish and multiply according to their capacity to acquire a share of that energy stream. Natural selection favors those organisms that are most effective in channeling the flux of energy through themselves and, concurrently, in increasing the flux of energy through the ecosystem as a whole. Selection, in this view, operates hierarchically on many levels: not only on individual organisms struggling selfishly for immediate advantage, but also on populations (species) and the communities in which they participate. Thanks to its roots in thermodynamics, the general course of evolution becomes predictable: there is a tendency for energy flow (and for life) to expand into any niche, provided there is a mechanistic path; it will diversify, radiate, speciate; and it will tend to produce structures that are increasingly complex. The manifold faces of life appear as features to be expected, not as implausible marvels that must be explained.

This assertion that selection acts hierarchically on levels both lower and higher than the classical individuals (on genes, for instance, and on species), makes a lot of sense to me. Individuals end up being the proximate carriers of structural information, but that information includes the survival strategy of a species, whose ecologically contexted history is impressed into adaptive strategies of gene carriers. The most general units of selection are not individuals, but informed patterns of thermodynamic flow, of which organisms, populations and ecosystems are all exemplifications. Around the campfires in Florida I listened to the glorifications of that hero of popular American culture, the self made man whether he be Donald Trump, or Douglas Mac Arthur, or Harry Truman dropping the big one on the Japanese. I admit to having been churlish in not joining into this worship of yesterday's heroes and the virtues and rewards of intelligence, hard work, and good fortune. But common sense and hope for the future demands that we acknowledge the hero's circumstances, including the society that cherishes free enterprise, political liberty and rule of law. Would our hero have been equally successful had he been born in a peasant hut in an Indian village? Our new heroes will rise from our new fabric and will perhaps allow us to escape our primitive tendencies to attempt the annihilation of one another at the drop of a rhetorical hat.

Biochemistry to Neurobiology

Human NeuronI am now going to further narrow my biochemical interest to the interior of one kind of eukaryote, a human neuron and its membranic contacts with other cells for the preservation of memory, and the origin of the specialized elements of its interior which serve the cell as a sort of army of automaton nano-ants. The areas shown in yellow above are the microtubules (MT) which serve as a sort of cyto-architecture for the cell and the areas shown in red are the axons. Microtubules are self-assembling polymers of the peanut-shaped protein dimer tubulin, each tubulin dimer (110,000 atomic mass units) being composed of an alpha and beta monomer. Like actin, both α- and β-tubulin are encoded by small families of related genes. In addition, a third type of tubulin (γ-tubulin) is specifically localized to the centrosome, where it plays a critical role in initiating microtubule assembly. Thirteen linear tubulin chains ('protofilaments') align side-to-side to form hollow microtubule cylinders (25 nanometers diameter) with two types of hexagonal lattices. The diagram below gives names to many of the structures in the nerve cell that I am not going to pay any more attention to so that I can focus on a few kinase enzymes that modify other proteins by chemically adding phosphate groups to them (phosphorylation). Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins. The human genome contains about 500 protein kinase genes and they constitute about 2% of all human genes.

EnzymesWhen I first began to look at the functions going on inside a nerve cell it looked as though anything that could possibly be going on was going on. Closer inspection corrected that false impression: in actuality, cellular metabolism is highly selective and quite purposeful. Each reaction is mediated by a particular enzyme whose function is to enable that reaction to proceed at a high rate, often with extreme specificity and with minimum formation of useless by-products. Step by simple step, the cell's complement of enzymes break down foodstuffs, turns them into metabolites and then into cell constituents, and harnesses the energy of some reactions to drive others. Enzymes select the channels through which matter and energy flow. They can be studied as single molecules and often are, but they derive their meaning from being part of a larger whole, the metabolic web.

How enzymes perform their catalytic feats, greater by many orders of magnitude from those of inorganic catalysts, has long been one of the central questions in biochemistry. The heart of the matter is the specific, intimate, and tight binding of the substrate (or substrates) to the enzyme. Proteins (and virtually all enzymes are proteins) are not shapeless blobs, but sculptured objects equipped with crannies and cavities that admit particular molecules, while excluding others. Binding commonly entails changes in the configurations of both substrate and enzyme, inducing stresses and strains that contribute to the mechanism of catalysis. Besides, the catalytic site is tailored, as it were, to its particular task, linking its structure to its function.

The genome of E. coli encodes approximately 4,000 proteins, that of yeast 6,000; it takes 50,000 to make a man. What do they all do? Many proteins are enzymes, but by no means all. Some proteins serve as the building blocks of structural scaffolding. Some make tracks for the movement of organelles itself mediated by motor proteins. Proteins act as receptors for signals from within the cell or from the outer world; they transport nutrients, waste products and viruses across membranes. Proteins also commonly modulate the activities of other proteins, or of genes. The general principle is that, except for the storage and transmission of genetic information and the construction of compartments, almost all the cells do is done by proteins.

The explanation for the functional versatility of proteins is not chemical as much as physical. Amino acid chains can fold into a variety of shapes, globular and fibrous, each determined by the sequence of amino acids that make up the protein in question. As they fold, each generates a unique contour with its own pattern of structural features: rods and hinges, platforms and channels, holes and crevices. Moreover, proteins are flexible and dynamic constructs that commonly change shape when they interact with Ligands or with each other. The range of stable configurations that amino acids chains can assume is wider than that of other classes of macromolecules, nucleic acids in particular; and their flexibility permits all sorts of mechanical actions demanded of molecular machines.

Myoglobin With an Onboard Ligand I couldn't resist this great picture of a ligand (orange) within a protective myoglobin (blue) womb. A ligand that can bind to a receptor, alter the function of the receptor and trigger a physiological response is called an agonist for that receptor. Agonist binding to a receptor can be characterized both in terms of how much physiological response can be triggered and in terms of the concentration of the agonist that is required to produce the physiological response. High-affinity ligand binding implies that a relatively low concentration of a ligand is adequate to maximally occupy a ligand-binding site and trigger a physiological response. Low-affinity binding implies that a relatively high concentration of a ligand is required before the binding site is maximally occupied and the maximum physiological response to the ligand is achieved.

DNA to RNA to Amino Acid CodonsWe learned in high school that genes determine the structure of proteins because the sequence of bases in DNA designates the sequence of amino acids in the corresponding protein. We speak of this as a transfer of "information," a specific order of symbols, from DNA to protein. Generally speaking, the identity and function of a protein is specified entirely by its amino acid sequence; the linear amino acid chain folds up spontaneously into a particular three-dimensional shape, upon which that protein's function then depends. In bacteria, the sequence of amino acids can be mapped point by point upon the sequence of nucleotides in the corresponding gene. Eukaryotic genes are more complex, containing stretches of DNA that do not encode amino acid sequences. These inserts are excised when the information carried by the gene is expressed; their function is still debatable. The set of rules that specify which sequence of bases specifies each of the standard suite of twenty amino acids is known as the genetic code. It is a non-overlapping triplet code: three consecutive bases specify each amino acid and it is one of the universal commonalities of living organisms. The above Table of Codons that specifies which triplets stand for each of the twenty amino acids has no known theoretical basis, and had to be worked out by experiment.

DNA to ProteinI thought that I would stop narrowing my area of interest at the eukaryotic protein kinases which are enzymes that belong to a very extensive family of proteins that share a conserved catalytic core. There are a number of conserved regions in the catalytic domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a glycine-rich stretch of residues in the vicinity of a lysine amino acid, which has been shown to be involved in ATP binding. In the central part of the catalytic domain, there is a conserved aspartic acid, which is important for the catalytic activity of the enzyme.

Molecular History

Molecular HistoryWe have seen that the molecules of life make up a minute fraction of the organic substances known to chemists; why these and not others? The most plausible hypothesis holds that the twenty amino acids and the five nucleotides, ADP and NADH and the rest of the core metabolites, were part of the endowment of that ancestral cell line from which all contemporary organisms descend. Of this origin only the faintest vestiges survive; but macromolecules preserve in their very structure a record of their evolution. In the mid-sixties, when the amino acid sequences of proteins first became available, it was realized that the sequences of whale hemoglobin and porpoise hemoglobin were almost identical, while that of horse hemoglobin was considerably different. In general, the more distant the relationship between the parent organisms, the more numerous are the differences in sequence, suggesting that all vertebrate hemoglobins are descended by progressive modification from an ancestral form of hemoglobin. Unexpectedly it turned out that differences accumulate at an approximately constant rate, such that the extent of the differences can serve as a measure of the time elapsed since any two proteins diverged from their common ancestor. One can use macromolecules as markers to track the evolution of organisms, supplementing the notoriously patchy evidence of the fossil record; alternatively, one can trace descent with modification of related proteins, such as those that mediate the uptake of metabolites.

The new molecular technology, particularly the development of methods for rapidly sequencing of minute quantities of proteins or nucleic acids, have transformed the stodgy sciences of taxonomy and phylogeny. We can now examine evolution at the molecular level, where genetic variations arise, and in consequence the history of life is accessible as never before. That the ancestry of humans diverged from that of the great apes a mere 5 to 5 million years ago is now a staple of the textbooks, but was decided as an outrageous heresy when Allen Wilson first inferred it from amino acid sequences three decades ago. Now the controversy swirls over DNA sequences: the small mitochondrial DNAs diverge so quickly that they can be used to track recent revolutionary events, such as the emergence and dispersal of modern humans, which appears to have begun as little as 200,000 years ago. At the opposite extreme, ribosomal RNAs are strictly conserved, they evolve so slowly as to preserve relationships that go back billions of years. Contemporary bacterial phylogeny is based very largely on ribosomal RNA sequences. This approach also underpins the profound discovery that all living organisms can be subsumed under three domains: Eubacteria, Archaea and Eukarya. The same methods now make it possible to classify bacteria that cannot be cultured and have never been see by any microscopist, among them some that branch off at the very base of the tree of life. No whole genomes tumble like ninepins before the assault of the robotic sequencers.

The postulate of a single universal ancestor, its biblical overtones notwithstanding, rests on a solid foundation of fact. All organisms share a considerable amount of basic molecular and organizational features that cannot be explained as a consequence of chemical necessity. ATP and pyridine nucleotide coenzymes, DNA and RNA, proteins constructed from a standard suite of amino acids, ribosomes, ion trans locating ATPases, lipid membranes and many more. The most compelling argument comes from the discovery that all extant organisms employ the same genetic code. In the absence of good chemical reasons why CUU should spell leucine while CCU spell proline, the only persuasive explanation is that the code as we know it was already a feature of the last common ancestor, and has been retained ever since because mutations that alter codon assignment are apt to be lethal. This cannot be strictly true because some variations have been found in codon usage by mitochondria and protists, but there are reasons to set these aside as special cases that do not fundamentally challenge the universality of the code.

The Tree of Life

Tree of LifeThe cornerstone of all current research and reflection is the universal tree of life, based on the comparison of ribosomal RNAs from hundreds of organisms. In a highly abstract manner, the tree encapsulates the whole history of life. It displays three great stems, two prokaryotic and one Eukaryotic, that diverge from a common ancestor early in evolution and remain separate thereafter. The earliest divergence (the "root" of the tree) divided the primordial prokaryotic world in two: Eukarya, which arose somewhat later, are distinctly but specifically related to to the Archaea. Contemporary organisms represent the tips of the branches from the central stems, some very ancient and others relatively recent; unfortunately there is no simple relationship between evolutionary distance and the passage of time, and therefore the universal tree has no intrinsic time scale.

The first Calcium-Dependent Protein Kinase (CDPK) activities were reported in pea shoot membranes more than 30 years ago. In 1987 researchers provided the first biochemical evidence that soybean CDPKs are calmodulin independent. The first CDPK DNA clones were isolated in 1991. CDPKs have now been identified throughout the plant kingdom from green algae to angiosperms. Other than plants, CDPKs are found only in some protozoans, and are notably absent from the sequenced eukaryotic genomes of yeast, worms, flies, mice and humans. However, the PK domains of CDPKs are highly homologous to the mammalian multifunctional Calmodulin-Dependent PKs (CaMKII), suggesting a common evolutionary origin. Analysis of the Arabidopsis genome sequence indicates the presence of 34 CDPK genes. Information available from other genomic sequencing and extensive expressed sequence tag (EST) projects also indicates the presence of multigene families of CDPKs in other plants, including soybean, tomato, rice, and maize. These Introns shared between protist and plant CDPKs presumably originated before the divergence of plants from Alveolates. Additionally, the calmodulin-like domains of protist CDPKs have intron positions in common with animal and fungal calmodulin genes. These results, together with the presence of a highly conserved phase zero intron located precisely at the beginning of the calmodulin-like domain, suggest that the ancestral CDPK gene could have originated from the fusion of protein kinase and calmodulin genes facilitated by recombination of ancient introns.


IntronAn intron is a section of DNA within a gene that doesn't actually code for anything. Introns and exons are interspersed throughout a gene, although there are some human genes without any introns. When a gene is copied into Messenger RNA (mRNA), both introns and exons are faithfully copied, but all the introns are cut out before the final mRNA transcript is made. Less complex organisms such as yeast tend not to have introns. The function of introns, if any, is unknown, although geneticists now wonder whether the splicing together of exons required by the presence of introns allows the human genome to generate more complexity than its mere 30,000 genes would suggest.

Introns were first discovered in protein-coding genes of adenovirus, and were subsequently identified in genes encoding transfer RNA and ribosomal RNA genes. Introns are now known to occur within a wide variety of genes throughout organisms and viruses within all of the biological kingdoms. The frequency of introns within different genomes is observed to vary widely across the spectrum of biological organisms. For example, introns are extremely common within the nuclear genome of higher vertebrates (e.g. humans and mice), where protein-coding genes almost always contain multiple introns, while introns are rare within the nuclear genes of some eukaryotic microorganisms, for example baker's yeast (Saccharomyces cerevisiae). In contrast, the mitochondrial genomes of vertebrates are entirely devoid of introns, while those of eukaryotic microorganisms may contain many introns. Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.

Finally I limited my study to one CaMKII kinase because of its association with Long-Term Potentiation (LTP) in the CA1 region of the hippocampus that has been the primary model by which to study the cellular and molecular basis of memory. Calcium/calmodulin-dependent protein kinase II (CaMKII) is necessary for LTP induction, is persistently activated by stimuli that elicit LTP, and can, by itself, enhance the efficacy of synaptic transmission. The analysis of CaMKII autophosphorylation and dephosphorylation indicates that this kinase could serve as a molecular switch that is capable of long-term memory storage. Consistent with such a role, mutations that prevent persistent activation of CaMKII block LTP, experience-dependent plasticity and behavioral memory. These results make CaMKII a leading candidate in the search for the molecular basis of memory.

The AMPA receptor (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor is also known as an AMPAR. This AMPAR, or (quisqualate receptor) is a non-NMDA-type ionotropic transmembrane receptor for glutamate that mediates fast synaptic transmission in the central nervous system. AMPARs are found in many parts of the brain and are the most commonly found receptor in the nervous system. The AMPA receptor GluA2 (GluR2) tetramer was the first and currently only glutamate receptor ion channel to be crystallized. PSD- 95, a scaffolding molecule enriched at glutamatergic synapses, has a key role in modulation of clustering of several neurotransmitter receptors, adhesion molecules, ion channels, cytoskeletal elements and signaling molecules at postsynaptic sites

The NMDA receptor (NMDAR), a glutamate receptor, is the predominant molecular device for controlling synaptic plasticity and memory function. The NMDAR is a specific type of ionotropic glutamate receptor. NMDA (N-methyl-D-aspartate) is the name of a selective agonist that binds to NMDA receptors but not to other glutamate receptors. Activation of NMDA receptors results in the opening of an ion channel that is nonselective to locations with an equilibrium potential near 0 mV. A unique property of the NMDA receptor is its voltage-dependent activation, a result of ion channel block by extracellular Mg2+ ions. This allows the flow of Na+ and small amounts of Ca2+ ions into the cell and K+ out of the cell to be voltage-dependent. Calcium flux through NMDARs is thought be critical in synaptic plasticity, a cellular mechanism for learning and memory. The NMDA receptor is distinct in two ways: first, it is both ligand-gated and voltage-dependent; second, it requires co-activation by two ligands: glutamate and glycine.

Matter Conclusion

In the beginning was the Logos says the gospel of St. John. Goethe's Faust, that prototypic modern man and scientist, thought Lifeotherwise: in the beginning was the Deed. Rephrased just a little, scientists still divide into those who seek the origin of life in information and those who look to enegetics. How is it that nature generates organized material systems to which terms such as adaptation, function and purpose can be applied. Life seems to have originated from a positive feedback loop of chemical reactions where the products of reactions went on to react further, eventually building an evolving organism. Amino acids are ligands for transition metals, meaning that they form reactive complexes with these metals. As chemical reactions formed more of these ligands, an autocatalytic feedback system eventually developed, then as the mixture of cyanide and carbon monoxide was exhaled from a volcano into the sea, it cooled rapidly, providing the chemical conditions for these biological ingredients to react. This, in turn, served as a wellspring of life, the thermodynamic drive of energy dissipation, creating mounting levels of structural order for natural selection to winnow. All known living things belong to a single tribe, related by composition, function and descent. The way of the cell is also the way of all flesh, ourselves included.

Life is a material phenomenon, grounded in chemistry and physics. Life designates a quality, or property, of certain complex dynamic systems that persist by channeling through themselves streams of matter, energy and information. They have the unique capacity to reproduce themselves indefinitely, and arise on a millennial time-scale by the interplay of variation and selection that underlies biological evolution. As I tried to show in my Wetware musings, even the human mind and consciousness emerge from a set of quantum reductions that we do not fully understand. We know of no evidence for the existence of vital forces unique to living organisms, and there erratic history gives no reason to believe that life's journey is directed toward a final destination in pursuit of a plan or purpose. I life is the creation of some cosmic mind or will, it has taken care to hide all of the material traces of its intervention. One can argue that so long as we confine our inquiries to the material side of life, material answers are all that we can expect; that they do not warrant the assumption that there are no other questions to be asked, with altogether different answers. Science alone may not be sufficient o make sense of the world, but I feel that science is privileged; for of all the ways of questioning nature, science alone holds the promise of objective knowledge.

In Florida, I came upon an unexpected spiritual malaise that I later found was not localized. We take pride in our superior understanding and our masterful technology, but it is plain that these were purchased at a substantial cost in human self-esteem. Not so long ago, Western man saw himself as God's own handiwork, dwelling upon the very pivot of creation. Contemporary humanity lives in much reduced circumstances, stuck on a small planet circling a middle-sized star, one among billions in an unremarkable galaxy, and there are billions more galaxies out there. The findings of biologists cut even closer to the bone. They compel us to admit that we humans, like all other organisms, are transient, constellations of jostling molecules, brought forth by a mindless game of chance devoid of plan or intent. For anyone who takes science seriously, it becomes even harder to believe that behind the appearances abides a cosmic mind that is even remotely comprehensible to us, or one that has the slightest concern for human welfare, personal or collective. In the absence of such a transcendent presence, many of the premises of civilization lose their historical moorings: that human life is sacred, that we can know right from wrong, that we are here for some purpose and that our little lives have larger meaning. We cannot go home again. But it is not at all self-evident that, absent a belief in powers greater than ourselves, a decent and civilized society can be sustained for long. The ancient covenant is in pieces: man knows at last that he is alone in the universe's unfeeling immensity, out of which he emerged only by chance. His destiny is nowhere spelled out, nor is his duty.

For better or for worse, mankind makes itself, and no one who wanders the globe can fail to be impressed by the sheer variety of choices that the human race has made. As our numbers and powers continue to mount, conflicts are certain to arise between all sorts of time-honored practices and beliefs (those of the West no less than those of Asia and Africa) and new necessities forced on us by science and technology. If a livable world is to emerge from the race between sanity and catastrophe, we shall have to come to terms with the limits of our small planet; science must play a much larger role in shaping public policy than it does at present, particularly in matters of population and environment. But we must also find secular (or at least tolerant) soil in which to re-root those civilized values that sages have proclaimed time and time again, usually in the name of one god or another.

For those of us who have outworn the ancient covenants between man and his gods, the search for meaning necessarily becomes personal rather than tribal. This, too, is hardly a strange road, for it has been trodden for centuries by Epicureans and Stoics, by Buddhists, Sufis, and all manner of free thinkers and many thoughtful moderns, including scientists, travel it today. I do not feel diminished by the dicovery that we are all part of a vast biotic enterprise that brought forth consciousness, understanding and morality from mindless chemistry. The great tree of life does not command my worship, but it surely evokes reverence and awe; and I would surrender the dominion of ownership for the responsibilities of stewardship.

Top of Page

Musings Index

And Then Iran

Another 9/11 Anniversary


How Did Here Get Here?

Chase's 7th Birthday

The Fabric of Reality

A Clockwork Orange

Epistomology Strand

The Grand Inquisitor

Consumerism Versus Genocide

Art for Art's Sake

Edvard Munch

Vasili Kandinsky

Ernst Ludwig Kirchner

Piet Mondrian

Kasemir Malevich

Rene Magritte

Salvador Dali

Evolutionary Strand

Information Theory Strand

Traversable Wormholes

Awareness Communicated

The Mother Singularity

Mimetic Theory

The Standard Model

Thought and Symbol

The Schwarzschild Radius

Symbolic Technologies

Dark Things

Fukuyama on Transhumanism

Are We There Yet?

A Transhumanist Manifesto

The Arrows of Time

A Quantum Telescope


The Road to Reason

Persistence of Memes

Now What?

Instantiated Consciousness


Evolution of God


The Rise of Yahweh

Semitic Origins


Galileo's Commandment

The Relevancy of Science

The Bible

The Quran

Marketing God

Adam and Eve

Cain and Abel

Noah and the Ark

Procreation Management

Machining a New Soul

The Human Codon Alphabet

Symbiotic Colony

The Moist Robot

Bottom Up Genealogy

The Genetic Revolution

The Nanotechnology Revolution

The Robotic Revolution

Universal Information Processing

Memetic Matryoshka

Holonomic Brain Theory

Introduction to Wetware

Seeing in a Quantum World

Thinking In the Quantum World

What's the Matter?

What's the Purpose?

Post Primordial Nucleosynthesis

The CNO Cycle

The Genesis Stone


Chemistry to Biochemistry



Biochemistry to Neurobiology

Molecular History

Under the Tree of Life

Matter Conclusion


A Mind in a Cloud


From the Other Side

Marcel Duchamp

Pablo Picasso

Echos of Ray Bradbury



Formative Books

Herculaneum's Library

Roman Public Libraries



Religious Pluralism


Diagnostic Irregularities

Quantum Decohesion

Quantum Free Will

Three Wise Men

Pattern Recognition