WONDER

Please consider this description of a living cell by Australian micro-biologist Michael Denton:

" Viewed down a light microscope at a magnification of some several hundred times, such as would have been possible in Darwin's time, a living cell is a relatively disappointing spectacle appearing only as an ever-changing and apparently disordered pattern of blobs and particles which, under the influence of unseen turbulent forces are continually tossed haphazardly in all directions. To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometres in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus itself would be a vast spherical chamber more than a kilometre in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell.

We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines. We would notice that the simplest of the functional components of the cell, the protein molecules, were astonishingly, complex pieces of molecular machinery, each one consisting of about three thousand atoms arranged in highly organized 3-D spatial conformation. We would wonder even more as we watched the strangely purposeful activities of these weird molecular machines, particularly when we realized that, despite all our accumulated knowledge of physics and chemistry, the task of designing one such molecular machine - that is one single functional protein molecule - would be completely beyond our capacity at present and will probably not be achieved until at least the beginning of the next century. Yet the life of the cell depends on the integrated activities of thousands, certainly tens, and probably hundreds of thousands of different protein molecules.

We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction. In fact, so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late twentieth-century technology.

What we would be witnessing would be an object resembling an immense automated factory, a factory larger than a city and carrying out almost as many unique functions as all the manufacturing activities of man on earth. However, it would be a factory which would have one capacity not equalled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours. To witness such an act at a magnification of one thousand million times would be an awe-inspiring spectacle.

To gain a more objective grasp of the level of complexity the cell represents, consider the problem of constructing an atomic model. Altogether a typical cell contains about ten million million atoms. Suppose we choose to build an exact replica to a scale one thousand million times that of the cell so that each atom of the model would be the size of a tennis ball. Constructing such a model at the rate of one atom per minute, it would take fifty million years to finish, and the object we would end up with would be the giant factory, described above, some twenty kilometres in diameter, with a volume thousands of times that of the Great Pyramid.

Copying nature, we could speed up the construction of the model by using small molecules such as amino acids and nucleotides rather than individual atoms. Since individual amino acids and nucleotides are made up of between ten and twenty atoms each, this would enable us to finish the project in less than five million years. We could also speed up the project by mass producing those components in the cell which are present in many copies. Perhaps three-quarters of the cell's mass can be accounted for by such components. But even if we could produce these very quickly we would still be faced with manufacturing a quarter of the cell's mass which consists largely of components which only occur once or twice and which would have to be constructed, therefore, on an individual basis. The complexity of the cell, like that of any complex machine, cannot be reduced to any sort of simple pattern, nor can its manufacture be reduced to a simple set of algorithms or programmes. Working continually day and night it would still be difficult to finish the model in the space of one million years."

And let me add my two cents to this astounding picture. The model that you would complete a million years later would be just that, a lifeless static model. For the cell to do its work this entire twenty kilometer structure and each of its trillions of components must be charged in specific ways, and at the level of the protein molecule, it must have an entire series of positive and negative charges and hydrophobic and hydrophilic parts all precisely shaped (at a level of precision far, far beyond our highest technical abilities) and charged in a whole series of ways: charged in a way to find other molecular components and combine with them; charged in a way to fold into a shape and maintain that most important shape, and charged in a way to be guided by other systems of charges to the precise spot in the cell where that particle must go. The pattern of charges and the movement of energy through the cell is easily as complex as the pattern of the physical particles themselves.

Also, Denton, in his discussion, uses a tennis ball to stand in for an atom. But an atom is not a ball. It is not even a 'tiny solar system' of neutrons, protons and electrons' as we once thought. Rather, it has now been revealed to be an enormously complex lattice of forces connected by a bewildering array of utterly miniscule subatomic particles including hadrons, leptons, bosons, fermions, mesons, baryons, quarks and anti-quarks, up and down quarks, top and bottom quarks, charm quarks, strange quarks, virtual quarks, valence quarks, gluons and sea quarks." Are these particles, found in every one of the ten trillion atoms in every one of the one hundred trillion cells that make up our bodies, the 'ultimate' particles? Or will even more advanced optical and chemical technology reveal these sub-atomic particles to be also, in and of themselves, vast force fields or lattices connected by whole series' of even more unfathomably minute particles?

And let me remind you again, that what we are talking about, a living cell, is a microscopic dot and thousands of these entire factories including all the complexity that we discussed above could fit on the head of a pin. Or, going another way, let's add to this model of twenty square kilometers of breath taking complexity another one hundred trillion equally complex factories all working in perfect synchronous coordination with each other; which would be a model of the one hundred trillion celled human body, your body, that thing that we lug around every day and complain about; that would, spread laterally at the height of one cell at this magnification, blanket the entire surface of the earth four thousand times over, every part of which would contain pumps and coils and conduits and memory banks and processing centers; all working in perfect harmony with each other, all engineered to an unimaginable level of precision and all there to deliver to us our ability to be conscious, to see, to hear, to smell, to taste, and to experience the world as we are so used to experiencing it, that we have taken it and the fantastic mechanisms that make it possible for granted.

My question is, "Why don't we know this?" What Michael Denton has written and I have added to is a perfectly accurate, easily intelligible, non-hyperbolic view of the cell. Why is this not taught in every introductory biology class in our schools? Why doesn't every member of our society know this information? If archaeologists found under the surface of our planet the remnants of any man made technology that even faintly resembled our biological technology, that approached the complexity and sophistication of a life form in even the feeblest way; why that would be the greatest discovery in the history of archeology. If aliens arrived here from elsewhere in the universe possessing technology that had a small fraction of the ability of the human body to replicate and to deliver consciousness and sensory awareness, thinking and memory, to the level that we enjoy it; that would again be a discovery that would have rewarded all the radio astronomers and UFO watchers, who have been waiting for such discoveries for decades, beyond their wildest dreams. Where are the poets who, inspired by this unfathomable technical magnificence, would write volumes in joyous praise to this gift of life?

To get some sense of the sophisticated mechanical nature of just one of the billions of molecular machines of the cell, consider these words, by biochemist Michael Behe, describing the workings of two protein molecules, myoglobin and hemoglobin, as they operate in our human bodies. (The non-italicized comments in parenthesis are mine.)

Myoglobin binds oxygen and stores it in muscles; it's especially abundant in the muscles of diving animals such as whales that have to endure long times between breaths. The protein chain of human myoglobin has 153 amino acids, 22 of which are positively charged, 22 negatively charged, 32 water-loving, and 57 waterfearing (oily). In eight segments of the protein chain, the amino acids are arranged so that roughly several oily ones are followed by a few water-loving ones, which are followed by several more oily ones, and so on. This arrangement allows the segment to wrap into a spiral in which one side of the helix has mostly oily amino acids and the other side mostly water-loving ones. The helical segments are stiff but the portions of the chain between the helical segments are rather flexible, allowing the helical segments to fold toward each other. Happily, separate segments can now interact and press their oily sides against each other in the interior of the now compactly folded protein, shielding them from water. (Amazingly, during the folding process 'chaperone' molecules arrive to protect the oily segments from the watery cytoplasm until the myoglobin is folded. This system of chaperone molecules protecting amino acids during the protein folding process happens not just with myoglobin but with many other proteins.) Their water-loving hydrophilic sides face outward to contact water. When all is said and done, the myoglobin chain has folded itself into the exquisitely precise form shown in Figure A.I.






FIGURE A.l

A drawing of myoglobin by the late scientific illustrator Irving Geis. The numbered balls (encased in gray shading) connected by rods are the amino acid postions of the protein. (For clarity, details of the structure of the amino acids are not shown.) The flat structure in the middle is the heme. The sphere in the center of the heme is an iron atom. The letters mark different helices and turns in the protein. The folded shape of the protein is required for it to work.

The shape of the folded myoglobin allows it to bind tightly to a small, rather flat molecule with a hole in its center. The molecule is called "heme" ...... The heme itself is rather oily and fits into an oily pocket formed by the folded myoglobin, like a hand fits into a glove. Now, the heme is also the right size, and has the right chemical groups, to tightly bind one iron atom in its central hole. When the heme fits into the myoglobin pocket, a particular amino acid (the histidine at the eighty-seventh position in the protein chain; histidine is abbreviated as "H") from the myoglobin is precisely positioned to hook onto the iron and keep the heme in place. The iron in heme can bind......to six atoms. Four of those atoms are provided by the heme itself, and one is from the myoglobin's "H". That leaves one position of the iron open to bind another atom. The open position can tightly bind oxygen when it's available. All those features combine to allow myoglobin to fulfill its assumed role as an oxygen-storage protein in muscle tissue.

Again, don't worry about remembering those technical details.....the most important point for us to notice here is that myoglobin does its job entirely through mechanistic forces-through positive charges attracting negative ones, by a pocket in the protein being exactly the right size for the heme to bind, by positioning groups such as "H" in the very place they are needed to do their jobs. Proteins such as myoglobin don't work through mysterious or novel forces, as they once were thought to do. They work through well-understood ones, like the forces by which machines in our everyday world work.........

Believe it or not, myoglobin is one of the smallest, simplest proteins of the nanobot. What's more, myoglobin works alone, which is unusual among proteins. Most proteins work in teams where each protein fits together with others in a sort of super Rubik's cube, and each has its own role to play in the team's task, much as a particular wire or gear might have its own role to play in, say, a time-keeping mechanism in a robot. To give a taste of such teamwork.... I'll briefly discuss the workings of a protein system that is related to, but somewhat more complicated than, myoglobin.

Myoglobin stores oxygen in muscle, but a different protein, called hemoglobin, transports oxygen in red blood cells from the lungs to the peripheral tissues of the body. Although in many ways it is similar to myoglobin, hemoglobin is more complex and sophistiicated. Hemoglobin is a composite of four separate protein chains, each one of which is approximately the same size and shape as myoglobin, each one of which has a heme group that can bind an oxygen molecule as myoglobin does. So hemoglobin is about four times larger than myoglobin. The four chains of hemoglobin consist of two pairs of identical chains: two "alpha" chains and two "beta" chains......The sequence of amino acids in both the alpha and beta subunits is similar to, but not identical with, the sequence of amino acids in myoglobin. When correctly folded, the four subunits of hemoglobin stick together to form a shape like a pyramid. The subunits all have regions that allow them to adhere to each other strongly and precisely, in just the right orientation so that the right amino acids are in the right positions to do the right jobs.

The task hemoglobin has to do is trickier than myoglobin's. Myoglobin simply stores oxygen in muscles, but hemoglobin transports it from one place to another. To transport oxygen, hemoglobin not only has to bind the gas in the lungs where it is plentiful, it also has to release it to the peripheral tissues where it is needed. So it won't do for hemoglobin just to bind the oxygen tightly, since it then wouldn't be able to easily let it go where it was needed. And it won't do just to bind it loosely, because then it wouldn't efficiently pick up oxygen in the lungs. Like a Frisbee-playing dog that catches, brings back, and drops the saucer at your feet, hemoglobin has to both bind and release. Hemoglobin can bind oxygen tightly in your lungs and dump it off efficiently in your fingers and toes because of a Rube-Goldberg-like arrangement of the parts of the hemoglobin subunits...... When no oxygen is bound to hemoglobin, the iron atom of each subunit is a little too fat to fit completely comfortably into the hole in the middle of the heme where it resides. However, when an oxygen molecule comes along and binds to it, for chemical reasons the iron shrinks slightly. The modest slimming allows the iron to sink perfectly into the middle of the heme. Remember that "H" that was attached to the iron in myoglobin? (I knew you would!) Well, there also is an "H" attached in hemoglobin. As the iron sinks, it physically pulls along the attached "H." The "H" itself is part of one of the helical segments of the subunit, so when the "H" moves, it pulls the whole helix along with it. Now, at the interface of the subunits of hemoglobin, where alpha and beta chains contact each other, there are several positively charged amino acids across from negatively charged ones; of course they attract each other. But when the helix is pulled away by the "H" that's attached to the sinking iron, the oppositely charged groups are pulled away from each other..... What's more, the shape of the subunits is such that when one moves, they all have to move together. So hemoglobin changes shape into a somewhat distorted pyramid when oxygen binds, and electrostatic interactions between all of the subunits of hemoglobin are broken.

That takes energy. The energy to break all those electrical attractions comes from the avid binding of the oxygen to the iron. But here's the catch. Just as only one quarter dropped into the slot of a soda machine can't release the can, the binding of just one oxygen doesn't provide enough energy to break all those interactions. Instead, several subunits must each bind oxygen almost simultaneeously to provide enough power. That only happens efficiently in a high-oxygen environment like the lungs. Conversely, when a hemooglobin that has four oxygen molecules attached to it is transported by the circulating blood from your lungs to the low-oxygen enviironment of, say, your big toe, when one of the oxygens falls off, the others aren't strong enough to keep the hemoglobin from snapping back. The electrostatic attractions between subunits reform, which yanks back the helix, which tugs up the "H," which pushes off the oxygens. As a result, the remaining several oxygens are unceremoniously dumped off, exactly where they are needed.

My point in discussing the intricacies of the relatively simple molecular machine that is hemoglobin is not to tax the reader with details. Rather, the point is to drive home the fact that the machinery of the nanobot works by intricate physical mechanisms. Robots in our everyday, large-scale world (such as, say, robots in automobile factories that help assemble cars) function only if very many exactly shaped and precisely positioned parts-nuts, bolts, levers, wires, screws-are all in place and working. If they are ever built, artificial nanobots will also have to work by excruciatingly detailed physical mechanisms. Biological nanobots must do the same. There is no respite from mechanical complexity except in idle dreams or Just- So stories.

Many molecular machines in the cell are much more complex than hemoglobin, but all work in the same mechanistic way. There are proteins that act as automatic gatekeepers, regulating the flow of small molecules or ions into and out of the cell. There are proteins that act as timing devices; others that are molecular trucks to ferry supplies to different parts of the cell; still others that act as cables and winches, pulling on cellular parts that need to be together: One of my favorites is a protein called gyrase, which can literally tie DNA into knots. In terms of our big, everyday world; gyrase is somewhat like a machine that could tie shoelaces. In developing an intuition for how such molecular machines act, a good start is to ask yourself how a shoelace-tying machine might work in our big world, or how a clock might work, or a delivery system, or a reguulated gate. As you might suspect, they all would work by mechanical principles, and none of them would be simple.

And just to add one side note, before we move off the topic of hemoglobin: Your body manufactures hemoglobin molecules to the exact specifications detailed by Behe, without one amino acid out of place or one alteration of shape, at the rate of four hundred trillion times every second!

My question again is: why isn't biology taught in this fashion, as an understanding of organic mechanics as much as an understanding of organic chemistry? Before students have any grasp of what is going on in a cell, they are required to memorize long and tedious lists of foreign sounding amino acids and nucleotides and organelles. They may learn 'where' different things take place (transcription takes place in the nucleus, translation takes place at the ribosome, etc.) but no details of 'what' actually takes place. This knowledge is more the geography of the cell rather than the working of the cell. Look again at the descriptions of the function of the myoglobin and the hemoglobin molecules by Michael Behe. It is fairly detailed (of course it could be much more detailed), but is it hard to follow? Not at all. Looking past foreign sounding words like 'heme' and 'histidine' the actual mechanics are quite simple. Each particle is either positive or negative, either water loving or water fearing, and is brittle or supple. With this highly precise but basically simple knowledge a whole new understanding and appreciation of the complexity and working of a protein molecule, which is one of the billions of tiny machines hard at work within each of your one hundred trillion cells, is easily come by. So, once again, why is this knowledge being kept under wraps? Why the big secret?

The first reason is historic. Before we had any really grasp of the mechanical nature of protein molecules and how they are energized and combined to do the cell's work, we had some understanding of what was going on in the cell chemically. With our vision limited by the magnification of the light microscope and unable to see the actual workings of the cell, we were still able to detect, chemically, what was going into a cell and what was coming out. Further, within each organelle, within the nucleus, the ribosomes, the mitochondria, etc., we could detect, again, without actually seeing them, the results of the chemical processes within them. Although the knowledge of much of these workings is now known in the rarified evirons of microbiology graduate departments, the general public still thinks of cellular activity as primarily chemical and not mechanical. Given the current state of molecular biological knowledge one would think that university departments of 'organic mechanics' should rival or surpass in their enrollments departments of organic chemistry; but they do not even exist. Ostensibly the study of organic chemistry will lead to superior treatments and medicines for a wide variety of human ailments. Shouldn't we suppose, equally, that the study of organic engineering would lead to enormous advances in our human technology that would have a wide range of benefits in every field of human endeavor?

The other reasons for this obfuscation are, I think, more insidious. Science is taught, at least at the introductory levels, in terms of what is known. Our current technology allows us to see far more than we understand. With the processes of transcription and translation, with the processes of protein folding and combining, with the manner in which these proteins move to the exact spot where they are needed and the precise timing of their manufacture and delivery, we know 'what' is going on, but we don't know, precisely, 'how' it is done. Are scientists, particularly evolutionary biologists, afraid to reveal how much is unknown? Are they concerned that our gaps in understanding of cell mechanics will be filled in by people of a spiritual persuasion who will ascribe 'supernatural' causes for these gaps? Perhaps. In my own view, I am sure that the entire workings of the cell are both guided and mechanical. Of course there are mechanisms. There are mechanisms within mechanisms, within mechanisms, within mechansisms. There are whole levels of mechanisms that have yet to be discovered or even conceived of (at least by humans). Whoever and whatever operates in the physical world has to operate within the inviolable laws of physics and chemistry. If I intend to climb a mountain I can't just wish myself to the top. I have to mechanically burn the energy and use the muscles to overcome gravity. If I want to get into my house I can't just dream myself through the door. I have to mechanically open it. Intelligence is not just dreaming. It's figuring out ways, mechanical ways, of using energy to harness natural forces to realize those dreams. The transcendent, supernatural intelligence of the cell is evident not because physical laws are avoided, but because energy is used (metabolism) in absolutely astonishing,brilliant mechanical ways to bring about replication, growth, digestion, elimination, and responsiveness to light, sound, taste and touch.

Also, the one hundred trillion cells that make up our bodies are all factories. Within each of these factories are many, many millions of protein molecules which are the mechanical apparatus, the machines, of these factories. How do you describe a machine? The same way, basically, that Michael Behe described the workings of the myoglobin and hemoglobin 'machines' in the above insertion. You explain how it is 'designed;' how energy moves through the various parts and how 'the shape' of each part, whether that shape be cylinders, or pistons or pumps or wheels or levers, as it is charged with energy, interacts with the 'shapes' of the other parts enabling the work of the machine to get done. Yet the common understanding of a cell is not as a high tech factory crammed with amazingly sophisticated and precisely shaped equipment, but as a fairly undefined, amorphous space, a kind of biological beaker or test tube in which chemical reactions take place.

My contention is that the amazing details and specificity of this molecular equipment flies in the face of neo-Darwinian evolutionary theory which contends that all this, almost endless, complexity and synchronicity, was arrived at by a random process of very rare genetic replication accidents. Also, from the Darwinian perspective, life was supposed to have evolved from simple beginnings. Yet we see breathtaking complexity within the cell, at the very beginning of life. And whatever knowledge we have now of the functioning of genes is about how genes specify different amino acids which combine into proteins. This is information about how genes determine the building materials, the chemical contents, of bodies. We know nothing, or, perhaps, next to nothing, about how genes determine the shapes that these proteins will take or how these proteins or combinations of proteins form themselves into the fantastically precise shapes and contours of ducts and membranes and tubes and processing centers and cilia and flagella; which shapes are essential to the entire mechanical functioning of the body. (Please note that I am not challenging the fact that genes specify proteins and these then form into specific shapes; but simply that we do not know how it is done.)Is it because evolutionary biologists are more comfortable talking about the chemical contents of amino acids and proteins and less so about the shapes they take, that the precision of these shapes and how integral they are to the functioning of the cell; in other words the entire mechanical design of the cell and its molecular machines, are hidden from the general public's view?

Now much of my blog does argue for the impossibility of genetic mutation and natural selection being able to produce anything resembling the complexity and coherence of even a 'simple' cell, never mind the one hundred trillion coordinated and synchronous cells of the human body. But what my opinion is is beside the point at this juncture. And Darwinian assumptions about the simplicity of cells, ideas that were popular one hundred and fifty years ago, are also beside the point. The point is: there is this fabulous design. However you think it got here, intelligently or randomly, the fact is: it actually is here. So let's not pretend it isn't.

We are all searching for common ground. We are all searching, in this increasingly crowded and inter-connected world, for a way of living in harmony and cooperation with each other. This cannot happen, I think, if there is no sense of mutual respect, and, to my mind, it is impossible to have respect for everyone if we don't have respect for ourselves. Again, however you think this fabulous equipment, that allows you to think and see and hear and respond and develop relationships and do what it is that you feel like doing; however you think it got here is beside the point. The point is that it did get here. It is here. You have it. I have it. Every person on this planet has it; and it is, regardless of who you are, or how the surface of your body is commonly regarded as to cultural standards of beauty, or how much health you enjoy or illness you suffer from; a technically awe-inspiring masterpiece.

Also we may have spiritual differences. I am absolutely clear that all this equipment, as fabulous as it is, is not me. I am that which uses this equipment and experiences life through the perspective of this equipment. I am not these amino acids and nucleotides and neurons and hemoglobin molecules that I study. I am that which uses those amino acids and nucleotides and neurons and hemoglobin molecules to experience my life. This equipment is not me; this equipment is here for me! I am grateful for this equipment. I am the recipient of this equipment. Again, you may think differently. You may think that you and the biological equipment that you are studying are one and the same thing. That you are this equipment; that you are trillions upon trillions of nucleotides and protein molecules that just happen to talk and think and see and hear. Okay, fine. That makes absolutely no sense to me, but, again, you are entitled to your opinion. But whatever your opinion is, that does not diminish one iota the breathtaking complexity and brilliance and beauty of this body/brain, whether you actually consider it to be you or to be your equipment, or whether you consider the creation of it to be intentional or some amazing accident.

Whatever the reason for the obfuscation, isn't it time to shine some light on what have been clearly the most amazing discoveries of this century and the second half of the last one? I think when everyone begins to understand at some level the magnificence that lies under our skin, then that may be the beginning of a growing self-respect and respect for others; a softening of the hierarchical nature of many of the institutions of our society and a diminishment of cruelty, injustice and abuse.

What do you think? Let me hear from you.