Thursday, November 5, 2009


In this post I question some of the assumptions of both Darwinian evolutionists and intelligent designers. Intelligent designers are not to be confused with creationists. Creationists are people that refuse to consider any ideas or conjectures, no matter how they were arrived at, that are in conflict with the account of creation as found in the biblical Book of Genesis. Intelligent designers are people, often scientists, who reject Darwinian evolution as an explanation for the origin and development of life because they feel that it fails, as a theory, to explain the bewildering complexity and coherence of life forms. Perhaps the population of creationists is dwindling as more progress is made in biological research, but with the use of modern instrumentation, including electron microscopes, X-ray crystallography and DNA micro arrays, and the fantastic complexity of life that is revealed at it's most minute and 'simple' level, the ranks of intelligent designers, as opposed to creationists, are swelling.

Just as people tend to confuse and conflate creationists with intelligent designers, there is much confusion and conflation regarding the theory of Darwinian evolution itself. There are really, as microbiologist Michael Behe, the 'father' of intelligent design explains, three separate yet related Darwinian notions. The first is the theory of common descent which states that all life forms have evolved from the same original ancestor. There is seemingly a lot of proof for this part of the theory, including many similarities of structures and function in all life at the molecular level and within phyla or kingdoms or species, a remarkable similarity of structure and function at the level of visible organs and traits. From the perspective of modern science, including intelligent designers, this is powerful evidence for a common ancestor. And it does seem like a fairly reasonable assumption: if we have hair and an ape has hair and a raccoon has hair; then at some point in the very distant past, there was probably an ancestor of all three of ours that had hair. As I say, intelligent designers have no quarrel with this aspect of evolutionary theory, although I do, and will discuss this later on.

A second notion of evolutionary theory is natural selection, which is basically this: If there are a variety of species and a variety of different individuals within a species, then those species and those individuals that are more fit, that are better adapted to their environment, will survive more readily than those individuals and species that are not as well adapted. Over time the better adapted individuals will replace the more poorly adapted ones and will dominate that species, just as the better adapted species will dominate other species. Natural selection, for the most part, is also not really argued among intelligent designers. It is obviously true, but perhaps, more complicated than originally thought. The qualities that make an individual member of a species better adapted are often other than the obvious qualities of stronger and faster. Sometimes species and individual members of species survive because they are better able to float below the radar of predators. Sometimes they are better able to cooperate among themselves to get their needs met, and function better in groups. And so on. Also, as the environment keeps changing, it favors certain individuals over others and certain species over others. As the weather gets hotter then colder, then hotter, different species and different individuals within species are favored. The same is true for cyclical changes in humid vs. dry environments, warmer vs. colder ocean water, and many chemical changes; more saline vs. less, more oxygenated vs. less, more carbonized vs. less, etc. Once the basic conditions on this planet stabilized and the atmosphere became oxygenated, all indications are that environmental changes have been cyclical rather than linear. It's hard to imagine a linear evolutionary path being naturally selected by cyclical changes in the environment.

It should be noted that both of these first two aspects of evolutionary theory, common descent and natural selection, have no power what so ever to explain how anything originally got here or how anything gets more complicated once it is here. The first part alludes to a common ancestor, but from where and how did this ancestor arrive? The second deals with selection not creation. Natural selection can cull from existing types, but how do those types find their existence in the first place?

Let me just mention a word about natural selection and its limitations. Selection, natural or otherwise, is just that; a selection from existing types. If you eat at a restaurant, you select different things on the menu. You do not create the menu. You are the diner, not the chef. Now if, over time, no one selects certain dishes, and the chef or the owner is throwing out this uneaten food every night, this will put a very strong pressure on them to eliminate this dish from the menu. Also if, over time, not only are certain dishes not selected, but the entire restaurant is not selected and the customer base is dwindling, that will put pressure on the chef or the owner to come up with some new dishes and, over time, either the menu will change or the restaurant will disappear; but, again, while the selection process may pressure the chef to create new dishes, the selectors (the customers) never actually create these dishes. That is always the province of the chef or the owner. And it should be noted that if the chef or the owner lack the creativity and intelligence to come up with appealing new dishes or a new way of presenting those dishes or some change that will make their restaurant more attractive to customers, then the whole restaurant will dissappear. So, in terms of restaurants at least, their survival is contingent on the intelligence and creativity of chefs or owners to respond to the pressures of selection. Selective pressures, by themselves, create nothing.

In the theory of evolution, then, who is the chef? The only explanation for the creation of new species, new forms, new body plans and for the increase in complexity of these forms and plans in Darwinian evolution is through the avenue of blind, accidental and fortuitous mutations. Although Darwin had no way of knowing it in his day, these mutations take place, according to modern science, by an accident in the genetic copying of genes during the process of replication. Genetic sequences are long strings of nucleic acid molecules, or nucleotides, which are coded for specific amino acids. In our cells, a long series of coded nucleic acids is transcribed within the nucleus onto an RNA molecule which transports this code outside of the nucleus of the cell to a ribosome where it is translated to a corresponding long series of amino acids that, when linked together and folded, form a protein. A genetic copying accident can result in a change in a nucleic acid, which can result in a change in the amino acid that that nucleic acid is coded for. These accidental changes are very rare (about one 'mistake' in one hundred million copies) and are almost always either deleterious, and damage the mechanisms of the cell and the workings of the body; or neutral and have no visible effect at the level of either the cell or the organism; still, extremely rarely, there is a very, very rare mutation that, according to the theory, causes an improvement in the workings of the cell, that increases the survivability of the cell and the organism of which this cell is a part; and future generations will favor this positive change and in this way the organism will improve and eventually, over a very, very long time, undergo radical change.

This part, the random mutation part, is the one that most bothers intelligent designers. It just does not seem, to intelligent designers, to be a process that occurs frequently enough to deliver anything like the amazing variety and complexity of life forms that we find today. So the math does not work. Also you would expect from this sort of change a very gradual yet very consistent change among organisms so that not only would every organism be linked in very gradual clear steps to every other organism, but that these changes should have taken place at consistent, regular and frequent intervals in our history. Yet, simple observation tells us that there are no such links. Each mammal is very much a mammal and not to be confused with a bird or an insect; just as every insect is very much an insect and not to be confused with a reptile or a fish. Not just on the outside of their bodies, but each has a completely distinctive internal form of organization; there is clearly a mammalian way of organizing internal organs, a mammalian kind of digestive, reproductive and nervous system, and there are very clear and distinct avian and insectivore forms of internal organization. Also, historically, there is absolutely no evidence of this gradual, relentless change of species. In fact, quite the opposite is the case. All evidence points to the first cells appearing suddenly, about four billion years ago, at the moment that conditions on this planet supported their survival (when the surface of the Earth became cool enough to have non-boiling water). There are no traces of organic tide pools (the so-called pre-biotic soup), no traces of any organic material at all prior to the appearance of these photosynthetic, metabolizing, digesting, growing and environment sensing bacteria. Then, for two billion years after that, fully half of the entire history of life on Earth, there was absolutely no evolutionary change, in the sense of life forms changing their basic structure or complexity. Four billion years ago there were bacteria and only bacteria; and two billion years later there were bacteria and only bacteria. Now among these bacteria there were all sorts of adaptations, so that bacteria were able to thrive in all kinds of environmental conditions: extreme heat, extreme cold, high acid, high base, little water, etc. If by evolution one means adaptation, then, yes evolution was taking place. But what we commonly think of as evolution is the evolving of one species from another; of a change of shape, body plan and basic structure. In that sense of evolutionary change, for two billion years there was none.

While we're on the subject, it's important to distinguish between evolution and adaptation. If you follow traditional evolutionary thinking, these processes of change, which would have taken many, many centuries where life forms were in a kind of awkward transition; where new organs or forms were gradually taking shape, but not yet functional as they awaited the next in a series of almost impossibly rare mutations to complete their formation; these transitional forms would not be adaptive at all. In fact, they would be the very opposite of adaptive. They would be using a lot of metabolized energy to sustain equipment that was in some stage of incompletion and not yet functional. That would put them at a clear competitive disadvantage to those creatures who were not taking this terrifying evolutionary journey, and whose every organ and every calorie of metabolized energy was being used to assist in their present time survival. Clearly the most adaptive of all creatures is the single celled bacteria. They can survive in every nook and cranny of this planet and they outnumber us more complicated creatures by the trillions. If any creatures actually left the adaptive comfort of being bacteria to venture into this almost endless process of accumulated fortuitous mutations, they would be risking their survival, not securing it. Evolution, then, is the opposite of adaptation.

Much of the confusion around evolution and the vehemence on both sides of the argument, stems from the failure to distinguish between two aspects of a living organism. A living organism both produces chemicals and builds the factory where these chemicals are produced. One mutation, or a change of one amino acid, in the chemicals that a body produces to protect itself and help it digest, can make a marked improvement. One, or two sequential mutations, can confer protection from certain pathogens and allow the members of a certain species that have that mutation to thrive and replace the members of the same species that are vulnerable to that pathogen. The same is true with digestive fluids. One or two sequential amino acid changes may allow an individual member of a species to digest and use the energy of a food source that is toxic or unusable to the other members. Again, that mutation, that one or two sequence amino acid change, would confer a distinct advantage in a particular environment, and the individuals that had that mutational advantage would thrive and dominate the population of the species that were exposed to that pathogen or that food source.

There is no argument in terms of mutations being able to alter body chemicals and chemically confer advantages and disadvantages. (Although there is a strong disagreement about how this amazing system that requires genetic replication, transcription and translation, metabolism and digestion, and immune system protection from pathogens, and was brilliant enough to have variation within species and include these occasional mutations to enhance the survivability of a species; how all of this technical brilliance arrived here in the first place. Yes, there is a very big difference, not about the functioning, but about the origin of this whole system.)

The bigger area of disagreement lies in the area of mutation of the genes involved in the construction of the chemical factory itself. It is in the construction of bodies and their biological systems that we enter a world of absolutely fantastic complexity. As opposed to the manufacture of enzymes, bodies are not created with the simplicity of one genetic sequence doing this, and one genetic sequence doing that. Genes involved in the construction of bodies are fired in enormously complex sequences, and each gene sequence, which, really, produces one building material used in the construction of this factory, is combined with other gene sequences to make amalgams of other proteins for other materials, and the same gene is used in many different parts and at many different times in the construction of the body. Everything is amazingly intertwined, and does not just depend on the genome, but on the firing patterns that initiate the process of transcription and translation, of protein synthesis.

Let's think about the power of these firing patterns for a minute. In our own body, the same genome, depending on which genes are fired, produces our fetal body, our child body, our adult body and our senior body. With no change in the genome, different firing patterns produce our brain cells, nerve cells, blood cells and muscle cells. The same genome produces both the caterpillar and the butterfly. And the breathtaking biological journey of the butterfly is merely a walk to the corner store when compared to the biological odysey of some creatures like the liver fluke. Follow the journey of the liver fluke with, of course, one unchanging genome, as it is described by molecular biologist Michael Denton:

" The adult lives in the intestine of a sheep. After the eggs are laid they pass with the faeces onto the ground. The eggs hatch, giving rise to small ciliated larvae which can swim about in water. If the larvae are lucky they find a pond snail: they must do this to survive, for the snail is the vehicle for the next stage in the life of the liver fluke. Having found a snail the larvae finds its way into the pulmonary chamber or lung. Here it loses its cilia and its size increases. At this stage it is known as a sporocyst. While in this condition it buds off germinal cells into its body cavity which develop into a second type of larvae known as rediae. These are oval in shape, possessing a mouth and stomach and a pair of protuberances which they use to move about. The rediae eventually leave the sporocyst, entering the tissue of the snail, after which they develop into yet another larval form known as cercariae which appear superficially to resemble a tadpole. Using their long tails these tadpole-like larvae work their way through and eventually out of the snail and onto blades of grass, where each larva sheds its tail and encases itself in a sheath. Eventually they are eaten by a sheep Inside the sheep they find their way to the liver where they develop sexual organs and mature into the adult state. They finally leave the sheep's liver and migrate to the intestine where they mate and so complete their extraordinary life cycle."

This entire odyssey, I remind you, is done with no change in the genetic make up of the liver fluke. At this juncture, you must wonder if there is not some level of organization that is higher than the genome. We have been taught to look at the genome as an ultimate cause. But is it possible that the genome, itself, could be a a result of something else; a higher order of organization than the genes themselves?

I had an interesting correspondence with a molecular biologist recently. I will respect his request that I not publish any of his e-mails on this blog, but I do want to summarize one part of our communication. We were discussing gene transcription. To begin the process of protein synthesis, the desired strand of genetic code (nucleic acids, or nucleotides, that codes for that particular protein) must be transcribed onto an mRNA molecule which then transports this message to another part of the cell where it is translated into a corresponding chain of amino acids and then into a protein. I was wondering how the molecules that form the mRNA find that exact spot in the DNA (three billion nucleotides long in the case of human DNA) which is coded for the desired protein. He said, basically, that science has not yet figured out all the mechanisms, but for one thing, the DNA is folded differently in different cells, so that the pieces of code that are frequently used in a particular cell (like the codes for adrenal cortical hormone in adrenal gland cells and the codes for manufacturing saliva in salivary gland cells, etc.) are always located on the most exposed surface of the nucleosome so the molecules do not have to search through anywhere near three billion nucleic acid molecules. Here again is another indication of a higher order of organization than the genome itself. If there is a fantastically complex pattern of gene foldings, so that genes in different cells are folded differently, exposing the codes most used by that particular cell to the outside surface of the nucleosome; isn't this another powerful suggestion that there is a level of organization higher than the genome itself? How could the same genome determine a whole variety of different folding patterns for itself?

I told him that I thought all these microbiological processes were guided. He very adamantly insisted that they were not; that he was certain that there were mechanisms at every step, although many of these mechanisms had not yet been discovered, that explain how all these processes are accomplished within the cell according to known laws of chemistry and physics without any guidance. But I have no argument with mechanisms and understand that all these reactions must occur following inviolable physical laws. Guidance occurs not by violating physical laws but by marshaling the energy to overcome physical forces. For instance if we humans guide anything, and we do that all the time, we do it not by violating physical laws but by mechanically overcoming them to get what we want. Let me explain:

One of the ways that scientists use to describe how proteins come together, or how a molecule of a protein will find the corresponding molecule of a nucleic acid, is by using the image of a lock and key. Each protein molecule has a complex three dimensional shape. Proteins bind when, among other things, their shapes correspond with each other and 'fit,' like a key fitting into a lock.

Let's suppose that a group of aliens arrived on this planet that just did not get human beings at all and thought that we were completely and totally automated machines. Now there are some scientists who claim to think that way also. Steve Pinker and Richard Dawkins,for instance, who claim to be complete materialists, who claim that we and all of life is entirely mechanical. The thing is that although they talk that talk, they never walk that walk. Regardless of what they say, they still treat people as living beings, as creatures possessing will (who do what they want to do) and creatures capable of experiencing things. Even the worst slave drivers or Nazi concentration camp guards, realized that the people they were torturing and coercing had will and were capable of experience. Even if you want to, you cannot torture a rock. Torture implies the capacity of experience in the tortured. To get people to perform onerous labor for no reward, the slave driver knows he must coerce them. That means that he must make the punishment for refusing to do what the slave driver wants much worse than the actual doing it. The slave does what he is asked, not because he has no will or desires, but because he wants the severe punishment for not doing it less than he wants the pain and discomfort of doing it. You do not have to coerce a machine to do its work. You just turn it on.

So, aside from these intellectuals who theorize one way but behave in another, let's imagine that there were aliens, the Gonks, who landed here and really believed that we were not living beings with will and the capacity to experience, but that we were merely machines. Now the Gonks did not come to torture us (again, how could you torture a machine). They were just here to study us. And one of the things they studied was our doors, and how we got in and out of them. To that end they did comprehensive studies (they were as scientifically advanced as they were socially retarded, and could detect every minute physical detail with their non-invasive scientific instruments, but could notice nothing about mood, feeling or behavior with their naked eyes.) So they saw that when a human machine had to get through a door it focussed its two round electric cameras (eyes) on the door which sent a signal to its two stilt appendages (legs) which started propelling the machine toward the door (walking). To accomplish this on a cellular level they saw that a certain amount of metabolic energy was used to fire many thousands of neurons, setting off many thousands of chains of electrical impulses, and many expansions and contractions of leg and foot muscles. Then, as the door was approached a small brittle instrument (key) was removed by one of the hanging upper appendages (arms) from a sac located just below the waist (pocket). With the aid of the two electric cameras the brittle instrument was brought to the precise spot where there was a slit in the outside surface of the door (lock). This again was accomplished by many contractions and expansions of muscles at the part of this appendage closest to the trunk (biceps and triceps) but especially with the smaller appendages that descended at the end of the larger one (fingers). This small brittle instrument was then pushed into this slit opening and every shape of the brittle instrument matched, exactly the shapes of the cavity it was entering. More energy was applied through those lower appendages to turn the instrument which was connected to a horizontal rod. As one of the upper appendages turned the instrument the rod was released, and with the help of the cameras, the other upper appendage was moved to a round protuberance below the slit (knob) which was turned by the contraction of several muscles in these descending appendages. Then, when all the obstacles to the door opening were removed, the door then opened and the machine continued through the door on its two stilts and accessed its fuel (food). The Gonks continued these observations and calculations until they were satisfied that everything, in terms of the amount of energy metabolized, the balancing of electrical charges and the skeletal and muscular mechanics fit their physical, chemical and thermo-dynamic formulas.

So, you see, if you study our behavior 'scientifically' you would also see no guidance. That is because WE, the part of us that wills, that wants to do things and that experiences things, is not visible. As fellow human beings we can recognize what is willful in each other and, to some degree, what each other is experiencing, by the way those experiences and that will affects our body and our behavior. So we know that someone opens a door because they "want" to go inside, and that wanting is what marshals all these microscopic and macroscopic activities that the Gonks so diligently studied. But we cannot observe our wanting, or our objectives, or our purposes directly. All our willful activity is guided, but we can only observe directly the physical, electrical and chemical results of that guidance.

The same thing holds true, of course, for our man-made machines. If the Gonks chose to study any of our machines, they would see that they too, complied with all their formulas. Man-made machines are obviously guided and purposeful, but, as with our willful activity, those purposes cannot be directly observed. The purpose of the machine and the idea of the machine first existed in the mind of the inventor before it was committed to a plan on paper or on a computer screen and before that inventor marshaled the forces and the materials to manifest his idea on the physical plane. Steve Pinker babbles about 'killing the ghost in the machine,' so why can't he tell me the weight of the 'idea' that gave birth to the machine and the measurements of the will that marshaled the forces and the materials to build it?

If all our willful activity and our machines are obviously guided, what about our involuntary, non-willful activity: things like growth, replication, digestion, circulation, etc. My point is that whether or not all these activities are guided, the fact that you cannot directly observe that guidance, and the fact that all these activities conform with the basic laws of physics and chemistry, have no bearing on whether they are guided or not.

Let's get back to mutations. Putting aside the very serious considerations that there doesn't seem to be any way that enough of these extremely rare fortuitous mutations could have taken place to deliver the astonishing complexity and variety of current life forms and that historical evidence (the fossil record) leads us in a very different direction, is there something else; a very basic problem in our understanding of the construction of living bodies and our understanding of the gene itself that would make such an accidental, mutational development logically impossible? It seems to me that there are two logical problems with our understanding of mutations; one of which you may have heard of before and one of which is brand new to this post (at least I hope it is).

The first logical objection to mutations as the pathway for evolutionary change and development is the problem of coherent complexity. If we want to talk about the body as a machine, it is an enormously complex one, certainly far beyond the complexity of any man made machine. But if we take a comparatively simple machine, like say a pocket watch; all the various parts of the watch are coherent, in that they are all precisely designed to fit with each other in a way that delivers the desired result (accurate time). What possible accidental change (or even purposeful change, for that matter) in one individual part of the watch could bring about any improvement? The first thing that would happen if you change the shape of any part is that the watch would stop. It is possible that an identically shaped part of a different material could bring about an improvement(say a more durable metal part replacing a plastic part) but proteins don't work that way. All proteins are three dimensional. Any change in any amino acid part of a protein creates a change in shape. If that altered protein is substituted for another in a system of great coherent complexity, then the system, rather than improving, breaks down. It is impossible to imagine a watch changing step by step into a better watch, or a television changing step by step into a better television. Any major improvement may borrow some ideas from earlier models, but the actual construction would have to start from the beginning and not be tagged on at the end. Here are Michael Behe's words:

Some systems seem very difficult to form by such successive modifications—I call them irreducibly complex. An everyday example of an irreducibly complex system is the humble mousetrap. It consists of (1) a flat wooden platform or base; (2) a metal hammer, which crushes the mouse; (3) a spring with extended ends to power the hammer; (4) a catch that releases the spring; and (5) a metal bar that connects to the catch and holds the hammer back. You can’t catch a mouse with just a platform, then add a spring and catch a few more mice, then add a holding bar and catch a few more. All the pieces have to be in place before you catch any mice.

Natural selection can only choose among systems that are already working so irreducibly complex biological systems pose a powerful challenge to Darwinian theory.Irreducibly complex systems appear very unlikely to be produced by numerous, successive, slight modifications of prior systems, because any precursor that was missing a crucial part could not function. Natural selection can only choose among systems that are already working, so the existence in nature of irreducibly complex biological systems poses a powerful challenge to Darwinian theory. We frequently observe such systems in cell organelles, in which the removal of one element would cause the whole system to cease functioning. The flagella of bacteria are a good example. They are outboard motors that bacterial cells can use for self-propulsion. They have a long, whip like propeller that is rotated by a molecular motor. The propeller is attached to the motor by a universal joint. The motor is held in place by proteins that act as a stator. Other proteins act as bushing material to allow the drive shaft to penetrate the bacterial membrane. Dozens of different kinds of proteins are necessary for a working flagellum. In the absence of almost any of them, the flagellum does not work or cannot even be built by the cell.
Molecular machines are designed. Biochemistry textbooks and journal articles describe the workings of some of the many living molecular machines within our cells, but they offer very little information about how these systems supposedly evolved by natural selection. Many scientists frankly admit their bewilderment about how they may have originated, but refuse to entertain the obvious hypothesis: that perhaps molecular machines appear to look designed because they really are designed.

Advances in science provide new reasons for recognizing design.I am hopeful that the scientific community will eventually admit the possibility of intelligent design, even if that acceptance is discreet and muted. My reason for optimism is the advance of science itself, which almost every day uncovers new intricacies in nature, fresh reasons for recognizing the design inherent in life and the universe.**

Now this was excerpted from an article that appeared in Natural History Magazine, a magazine with a clear anti-design bias. Therefore to refute Behe, they must have searched carefully for the best rebuttal to his argument that they could find. Here's what they came up with, excerpted from a rebuttal argument to Behe by biologist Kenneth R. Miller:

Parts of a supposedly irreducibly complex machine may have different, but still useful, functions. Ironically, Behe’s own example, the mousetrap, shows what’s wrong with this idea. Take away two parts (the catch and the metal bar), and you may not have a mousetrap but you do have a three-part machine that makes a fully functional tie clip or paper clip. Take away the spring, and you have a two-part key chain. The catch of some mousetraps could be used as a fishhook, and the wooden base as a paperweight; useful applications of other parts include everything from toothpicks to nutcrackers and clipboard holders. The point, which science has long understood, is that bits and pieces of supposedly irreducibly complex machines may have different — but still useful — functions.

Evolution produces complex biochemical machines.Behe’s contention that each and every piece of a machine, mechanical or biochemical, must be assembled in its final form before anything useful can emerge is just plain wrong. Evolution produces complex biochemical machines by copying, modifying, and combining proteins previously used for other functions. Looking for examples? The systems in Behe’s essay will do just fine.

Natural selection favors an organism’s parts for different functions.He writes that in the absence of “almost any” of its parts, the bacterial flagellum “does not work.” But guess what? A small group of proteins from the flagellum does work without the rest of the machine — it’s used by many bacteria as a device for injecting poisons into other cells. Although the function performed by this small part when working alone is different, it nonetheless can be favored by natural selection.

Is that the refutation of Behe? This silliness misses Behe's point entirely. Yes, someone could use my stomach for a wine sac; could use my intestines to tie down luggage to the roof of a car, and play castanets with my teeth. That someone would, of course, not be me, because I, no longer having a stomach or intestines would be long dead. Behe's whole point is that there must be a continuous biological function. If any organism along the way uses its digestive system to play music, tie luggage or for any other purpose, what, in the world are they going to digest with? The point is that the digestive system, or the locomotion system, or the circulation system has to change increment by increment while still being a working digestive, locomotion or circulating system. How was this organism metabolizing before it 'learned' to metabolize? How was it eliminating before it 'learned' to eliminate? Unlike when we remodel our home and move out to a hotel for a month while new plumbing and new wiring is installed; biologically we couldn't have moved into a primordial hotel for fifty million years while our body was developing new nervous and digestive systems. Moving out is what we call death, the end of the line, biologically, evolutionarily, or otherwise. However long these evolutionary processes were supposed to take, all the basic biological processes must have been continuously functional throughout the entire process; and not only functional, but functional at a level of efficiency that enabled them to compete with other organisms that were not going through the radical upheaval of a process of evolution.

The second logical objection to mutations as the engine of structural changes in living bodies is actually the thesis of this post. (Were you wondering when I was going to get around to the thesis?) While intelligent designers make convincing arguments of math, history and coherent complexity, their assumption is always that if there were a way to explain how that many coherent mutations could have accumulated (which there is not) then that would convince us of the validity of Darwinian evolution. These arguments still miss the mark. The visible genome, as we see it and measure it, cannot, by itself, account for the entire construction of a living body, so mutations, or changes in the genome, cannot account, by themselves, for changes in that construction.

To make my point I would like you to think about the construction of man-made machines (by the way, if there is a reasonable gender neutral way of saying 'man-made' please let me know. I've come up with a few, but they all sound ridiculous.) How do you create a machine? Machines begin, like all man-made things begin, with a desire. You want to be able to do something, or accomplish something that you are not able to do. This unsatisfied desire creates a kind of stirring, a restlessness. You think about what you want and the obstacles that you must overcome to get what you want. Out of this restlessness comes the idea for a machine. Once you commit to actually manifesting this machine on a physical plain, you inevitably encounter other obstacles which require further ideas to overcome them. So the manifestation of a machine is usually the result of several 'hmmmm' moments as you run into obstacles, followed by several 'aha' moments as you come up with ideas to overcome these obstacles.

Beyond the kind of energy that you choose to operate your machine (mechanical, electrical, thermal, etc.)the idea for a machine consists of two parts. The first part is choosing or, if necessary, inventing, the materials that you need that have the right characteristics (the right strength or suppleness or rigidity or porousness, etc.) and the second is the shape that these materials must be formed into to direct the energy to its desired result. So the idea consists of materials and shapes. And finally you need a plan. The plan is the actual logistics of accumulating the materials you need in the right amounts and the right order to get the job done, and then the method of shaping these materials to achieve the exact contours that you need to get the desired results.

At this point I wanted to show you a video of the construction of a large building using time lapse photography. Please excuse my technical ineptness, but you will just have to imagine such a video. You have probably seen one at sometime. You see bulldozers excavating a hole in the ground; cranes arriving, and the building growing from the ground up, a process that probably took many months, if not years, consolidated to the span of a minute or two.So please make believe that you just watched such a video. Thanks.

Everything that is being constructed is the physicalization of first an idea, which consists of the materials and the shape of the building, and further a plan to get these materials in the right order to the job site and to shape these various materials to the exact size as indicated by the plan. Of course, you cannot see the plan on the video, but obviously the workers and the foremen were following these plans at every step of the construction. And, of course, the idea, itself, can never be directly observed. It existed solely in the mind of the architect before it was committed to paper or to a computer screen. I don't want to belabor the point, but I do have to emphasize that the building could not be built without both a method for delivering the right materials, in the right order, and a specific design of the shape of the building with a means of achieving that shape.

So if you go back to the video (that you were supposed to have just seen), you see that bulldozers arrived first to dig a hole for the foundation and then cranes arrived to move heavy materials into place. If the cranes got there before the bulldozers that would create an inefficient logistical nightmare. The cement must come before the iron girders which must come before the dry wall which must come before the office furniture, etc. Everything must arrive and leave the construction area in sequence. Suppliers must be notified in time so that they can manufacture the materials and deliver them to the site when they are needed. And everything has to take place according to not just a plan of sequence but a plan of shape. The bulldoze drivers need to know how big and how deep to make the hole. The steel workers need to know the outer dimensions of the building, etc. The materials and the shape that these materials take is dictated by the plan which is the first stage of physicalization of a non-physical idea in the mind of the architect.

Biological machines also consist of various materials and shapes. Biological machines are necessarily more complicated than man made machines because a living body not only constructs these various machines, but also manufactures the materials out of which these machines are made. There are macroscopic machines that we are all familiar with, like hearts and kidneys and livers and lungs and there are microscopic machines within individual cells. A microscopic cellular machine that has been studied intensively over the last several years is the flagellum. A flagellum is a kind of outboard motor which allows a bacterium to move about in a liquid medium. Here is an excerpt of Michael Behe's description of the construction of the flagellum from his book, The Edge of Evolution:

Just as the outboard motor of a motorboat in our everyday world consists of a large number of parts (propeller, spark plugs, and so on), so does the molecular outboard motor. The flagellum has dozens of protein parts that do the particular jobs necessary for the complex system to work. Those dozens of proteins are coded by dozens of genes in a bacterial cell. The genes are grouped into fourteen bunches called "operons." Next to each operon in the DNA are control signals. The control signals themselves fall into three categories we'll call class 1, class 2, and class 3. The genes for proteins that have to be made first in the construction process have class 1 control signals, those genes that go second have class 2 signals, and so on.

Most of the time, a bacterial cell isn't building a flagellum, because it already has one. However, after cell division a new cell has to start the construction program. To begin, the DNA control regions for class 1 genes mechanically "sense" that the time has come and switch on class 1 genes. There is just one operon in class 1, which contains just two genes. The genes code for two protein chains, which, like the alpha and beta chains of hemoglobin, stick to each other to make a single functioning protein complex. That protein is neither a part of the flagellum nor a part of the construction machinery. Rather, it's akin to the foreman of a project, who has to tell the other workers what to do. Let's call it the "boss" protein.

The boss protein binds specifically to the DNA control regions of the seven class 2 operons, mechanically turning them on. Class 2 genes code for the proteins that make up the foundation of the flagellum (plus some helper proteins), just as you'd expect in bottom up construction. One class 2 gene, however, isn't part of the foundation. It's another control protein. Let's call it the "subboss" protein. The subboss protein binds to the DNA control region of class 3 genes, which comprise proteins that make the outer parts of the flagellum. So each class of genes contains the gene for a protein that will turn on the next class.

But that's not all. Clever as that part is, the control system is much more finely tuned than just the cascading control proteins. For years researchers knew that if the genes for any of a score of protein parts in class 2-the ones that made up the foundation of the flagellum-were experimentally broken in the lab, the genes for the outer parts of the flagellum would remain switched off. But how could so many genes all control later construction?

Class 3 contains a gene for a protein that binds tightly to the subbboss protein, inactivating it. Let's call that the "checkpoint" protein. Why turn on the sub boss only to immediately inactivate it with the checkpoint protein? Later in the construction project, a clever maneuver gets rid of the checkpoint protein. The flagellum not only is an elegant outboard motor, but also contains a complex pump in its foundation, which actively extrudes class 3 protein parts to form the outer portion of the structure.

Here's the elegant trick. When the pump in the foundation of the flagellum is completed and running, one of the first proteins to be extruded is the checkpoint protein. Getting rid of the checkpoint protein releases the subboss protein to bind to the control regions of class 3 operons, switching on the genes for the outer portion of the flagellum. So the completion of the first part of the flagellum is directly linked to the switching on of the genes to make the final parts of the flagellum.

In just the past few years a group of Israeli scientists has developed clever new laboratory techniques to analyze in even finer detail the control exerted by DNA control elements on the construction of the flagellum. By successively joining the control elements to the gene for a protein that can be detected by its fluorescence, the scientists showed that, even within classes 2 and 3, the control elements switch the genes on in the order that they are needed for construction. Within class 2, the genes needed for the bottom of the foundation are switched on before the genes for the top of the foundation, and within class 3, genes for the bottom of the top are activated before genes for the top of the top.

The same group of scientists has examined DNA control elements for other cellular systems and discovered similar elegance there. When they studied cellular biochemical pathways for making amino acids, they discovered what is called "just-in-time" organization, where a protein is made as close to the time it's needed as possible:

Mathematical analysis suggests that this "just-in-time" transcription program is optimal under constraints of rapidly reaching a production goal with minimal total enzyme production. Our findings suggest that metabolic regulation networks are designed to generate precision promoter timing and activity programs that can be understood using the engineering principles of production pipelines.

What does all this jargon mean? Simply put, the more closely we examine the cell, the more elegant and sophisticated we discover it to be. Complex, functional structures such as the cilium(tiny hairlike organelles that can help a single celled creature move through a liquid medium, or help larger creatures move material through internal ducts) and flagellum are just the beginning. They demand intricate construction machinery and control programs to build them. Without those support systems, the final structures wouldn't be possible. The bacterial flagellum contains several dozen protein parts. The cilium, which so far has resisted investigation of its DNA control program, has several hundred. There is every reason to think that the control of its construction will have to be much more intricate than that of the flagellum.

Control of construction projects and other activities in the cell is difficult for scientists to investigate, because "control" is not a physical object like a particular molecule that can be isolated in a test tube. It's a matter of timing and arrangement. The upshot is that even now in the twenty-first century-more than fifty years after the double helical shape of DNA was discovered by Watson and Crick, and decades after the first X-ray crystal structures of proteins were elucidated-science is still discovering fundamental new mechanisms by which the operation of the cell is controlled.

Recently-some sixty-five years after George Beadle and Edward Tatum proposed the classic definition of a gene as a region of DNA that codes for an enzyme-an issue of the journal Nature ran a feature with the remarkable title "What Is a Gene?" The gist of the article was that the control systems that affect when, where, and how much of a particular protein is made are becoming so complex, and their distribution in the DNA so widespread, that the very concept of a "gene" as a discrete region of DNA is no longer adequate. Marvels the writer, "The picture these studies paint is one of mind-boggling complexity."

The discovery of 'control' elements in the DNA supposedly make the creation of new biological structures through accidental mutations more feasible,since the mutation of just a few 'control' genes can alter the firing and replication patterns of many sub-genes; but consider these words by molecular biologist Jonathon Wells:

"Natural selection works only within established species.Darwin’s finches and many other organisms provide evidence that natural selection can modify existing features — but only within established species. Breeders of domestic plants and animals have been doing the same thing with artificial selection for centuries. But where is the evidence that selection produces new features in new species?

Major evolutionary changes require anatomical as well as biochemical changes.New features require new variations. In the modern version of Darwin’s theory, these come from DNA mutations. Most DNA mutations are harmful and are thus eliminated by natural selection. A few, however, are advantageous — such as mutations that increase antibiotic resistance in bacteria and pesticide resistance in plants and animals. Antibiotic and pesticide resistance are often cited as evidence that DNA mutations provide the raw materials for evolution, but they affect only chemical processes. Major evolutionary changes would require mutations that produce advantageous anatomical changes as well.

The four-winged fruit fly is an....“icon of evolution." Normal fruit flies have two wings and two “balancers” — tiny structures behind the wings that help stabilize the insect in flight. In the 1970s, geneticists discovered that a combination of three mutations in a single gene produces flies in which the balancers develop into normal-looking wings. The resulting four-winged fruit fly is sometimes used to illustrate how mutations can produce the sorts of anatomical changes that Darwin’s theory needs.

This fly does not provide evidence for evolution. The extra wings are not new structures, only duplications of existing ones. Furthermore, the extra wings lack muscles and are therefore worse than useless. The four-winged fruit fly is severely handicapped — like a small plane with extra wings dangling from its tail. As is the case with all other anatomical mutations studied so far, those in the four-winged fruit fly cannot provide raw materials for evolution."

How could only three mutations in a single gene change the balancers into normal 'looking' wings? Because these genes are part of a whole series of 'control' genes. Control genes, like hox genes, realisator genes, gap genes and pair-rules genes are genes that, once fired, signal the firing of a whole series of other genes which results in the manufacture of a whole series of proteins. These control genes have supposedly given fresh new evidence of how accidental mutations could create new anatomical structures leading to brand new organisms. But as Weller points out they do nothing more than rearrange existing structures, and in the case of mutations of these genes, lead, not to an advancement, but to a horrible deformity in which a poor organism has 'extra' structures but not all the other connections (musculature, nerve connections, brain connections, adjustments in support mechanisms and equilibrium) to make these extra structures functional. What is becoming increasingly clear is that an organism is not an accidental chance amalgam of individual genes, but a functional whole and any major change in one area requires changes and adjustments throughout.

Going back to the example of building construction, these regulator genes act as supply agents for construction materials. If I were in charge of the construction of a building, there are many suppliers that I would have to call in the proper sequence and with the proper timing so that all the materials I would need would arrive at the right time at the construction site. Suppose there was a supply agent for building foundations. In other words, all I would have to do is contact him and he, in turn, would see to it that all the bulldozers, the cement mixers, the gravel, the re-enforcing bars, the lumber for the wooden cement troughs, in other words everything that was needed for the foundation and in the proper amounts, would be there at the construction site at the exact right time that they were needed. And, perhaps, going one better than that, suppose when that foundation supply agent was nearing the end of his check list, that he would contact the wall supply agent, who, in turn, would make sure that all the supplies necessary for the walls would arrive in sequence, and he, in turn, toward the end of his work would contact the roofing supply agent. In this way, with just one initial signal, my call to the first supply agent, the entire sequence of needed materials for the first excavation all the way to the last interior decoration would be guaranteed to arrive when and where they are needed. Please notice that all of this still says nothing about the actual constructing, the actual shaping and design of the building. For that I need builders, and even if I had automated builders, they would still need to have a plan, a design to follow so that all these materials could be fashioned into the required shape to make the entire building work.

My point is that as complicated as the manufacture of proteins and their timing and their delivery to the exact construction sites are, all of that still says nothing about how these proteins are shaped into the precise shapes that allow elegant structures like the flagellum to function. As was said earlier in discussing the video of the building construction, we need both the proper materials, their delivery to the proper construction sites and, of course, the plan from which the building is shaped. Where is the plan that determines not the materials, but the shape of biological machines? Now don't confuse the shapes of the protein molecules themselves with the contours of whatever it is that the protein molecules are building. Protein molecules can bind with other protein molecules to make amalgams of proteins, which have a very specific and unique shape, but these are only the building blocks of biological construction. They no more determine the shapes and contours of organs and organelles than the shape of bricks determines the shape of brick houses, or the shape of grains of sand determines the shape of sand castles. The analogy of Lego-pieces is often used to illustrate in a simple way how proteins inter-lock. But if the inter-locking mechanism of the Lego toy were only capable of creating one shape, how many Lego games would be sold? The whole point of the Lego game is that with a few hundred identically shaped pieces, with the same inter-locking system, one can create many, many shapes. How many more varieties of shapes would be possible with identical protein molecules that number not in the hundreds but in the thousands and millions and billions? And it is the shape as much or more than the material that creates the functionality of any machine, man made or biological.

Let's go back to Michael Behe's words. In his fairly detailed description of the construction of both the cilium and the flagellum, there is not a word of explanation regarding shape. All of Behe's description regards how the genetic sequencing determines how the various proteins arrive at the construction site in the proper amounts and in the proper order. The flagellum construction begins with a base of three rings. Each of these rings is composed of different proteins, and each has about twenty-six copies of their particular protein. But why a ring? Why not a line, or an oval, or a squiggle, or a rectangle, all of which shapes could be achieved with any of these proteins? The flagellum would not work with any other shape as its base. But who knows this? Not the protein molecules, and certainly not the genes which merely allow their code to be copied at a certain moment, which moment they do not directly determine. Perhaps there is some, as yet unknown mechanism; perhaps there is a circular ring of charges complementary to the charges of the protein molecules of the first ring at the cell wall. But what would be the origin of this ring of charges if they do exist? Certainly it would not be any part of the gene code for the ring proteins. It would have to have been established by a previous gene (if there is anything to sequential genetic evolution). Does that mean that the arrival of genes creating the proteins for the flagellum which supposedly happened by 'accidental' mutations was preceded by genes that prepared the way for this circular form? If that is the case, what is the origin for that circular set of charges in the cell wall? And what is the genetic antecedent for that? Are we saying that genes have foreknowledge of future mutations and pave the way for them by building charging patterns to determine their shapes? How can genes have foreknowledge of mutations if mutations are accidental, and how can genes have knowledge of anything if they are simply submicroscopic strings of nucleic acids?

The cilium is a hairlike shape. The method of construction is called IFT. These are raft-like proteins that travel up and down the sides of the cilia carrying new protein building materials in the construction phase and carrying replacement proteins in the maintenance phase after the cilium is constructed. On the way down from the tip of the cilium, these IFT rafts remove no longer needed construction equipment and during the mature life of the cilium, the IFT remove used up proteins that have been replaced by fresh ones. The length of the cilia in relation to the rest of the cell body is crucial to its efficacy. Although Michael Behe explains in great detail how all the protein material arrives there, he says this regarding the actual length and breadth of the cilium, "Apparently some as-yet-unknown switching mechanism senses how much material the cilium needs at any particular moment and changes the proportion of freight cars (rafts) between 'cargo-capable' amd 'cargo-incapable' as the need arises.'

The protein motor that powers the IFT rafts to the tip of the cilium (kinesin) is different than the protein motor that powers the raft on the way back (dynein). Behe writes, "Exactly what causes IFT to shift from kinesin-powered transport to dynein transport at the tip of the cilium remains unknown." But that shift, those rafts reversing direction, is what creates the tip. The exact spot where those IFT reverse direction determines the length of the cilia. What is it that the IFT are bumping up against that causes it to change direction? How does the cilia know exactly how long it needs to be? And what, if anything, does this have to do with genes?

So we see with the flagellum and the cilium, although much has been written about their various protein components, their genetic antecedents and how they are transcribed, translated, folded and delivered to the construction site at the precise time that they are needed, nothing is written and nothing is known about how they actually achieve the exquisite and exquisitely precise shape of cilium and flagellum, which shapes are the essential factors that enables them to do their work, that enables them, in fact, to be, cilium and flagellum.

If the shaping of these microscopic features of single celled creatures cannot be explained by any genetic mechanism, then how could they have 'evolved.' In the case of the first flagellum ring, the exact same twenty-six proteins could form any shape. If, accidentally, they formed a ring some billions of generations ago, there is nothing in the genetic sequence to distinguish those twenty-six proteins that formed a ring from those many, many sets of twenty-six that did not. And there is nothing, directly in the genetic sequence that can guarantee the replication of that ring once it was accidentally achieved. As I've said before, shape, any shape, although specified by a genetic sequence is not created by a genetic sequence. Something else is at work, and that something else is the true creative power and intelligence behind the construction of living beings. It is the shapes and the fact that all these shapes are functional that is truly wondrous. When we see pictures of the developing human embryo, there are changes in the protein materials, of course, but it is the changes in shape, the emergence of that human face and human hands and feet and a whole raft of exquisite and exquisitely functioning internal organs from a seemingly non-descript collection of cells, that really astonishes us. The genome provides the necessary materials in the right sequences, but it is the shaper that creates the human being. Without the shaper all that would be created is an undifferentiated mass of proteins.

One of the main, if not the main 'proof' of evolution is the repetitive patterns of shapes found throughout the plant and animal kingdom. This has led evolutionists to conclude that these commonly shaped traits are homologous; that they have evolved from the same genetic origin. But on further inspection, many of these seemingly homologous forms are manufactured by different genes following different embryonic pathways. In other words, the same shapes repeated over and over, but with different materials and different means of manufacture. What does this remind us of from our own world of man-made manufacture? We see, for instance, wheels made from rubber, from plastic, from iron and wood. We see them appearing in all different kinds of mechanical settings; all with the same basic shape and serving the same basic purpose, but used and manufactured in many different ways. Why is this? Because the wheel is an idea, and machines are created by combining existing ideas in novel ways.

What I am saying is that the genome is really an idea for a machine and the construction of that machine, and each gene is an idea of how to build a smaller sub-machine within that larger machine. The idea for a machine consists of two parts: the appropriate materials and the shape that these materials should take. What we have been able to observe regarding genes is the material part; how genes specify proteins. What can only be observed by its results is the idea of shape. We see the proteins manufactured from a genetic code being delivered in the right sequence to a construction site, and then we see those protein molecules assuming an exquisite and exquisitely precise shape. But the plan for that shape cannot be seen. Only the results of that plan can be seen.

Is there an actual, measurable plan? Some say there is: an energy body, or an astral body that exists prior to the physical body. This astral body is, supposedly, a subtle pattern of positive and negative charges that is the plan for all the ideas of shapes and shapes within shapes connected to that genome. The growing body of multiplying protein molecules expands along the contours of this astral body, positive to negative and negative to positive. I am not arguing, at the moment, about whether this is true or not; or if further research and more delicate instrumentation will reveal the existence of this astral body. But whether it is true or not, the next question would be: how did that astral body, or that "plan" get there? How does an idea on the non-physical plane, in the universal mind, suddenly translate into a physical body, with or without the intermediary of an energy body?

Does it seem a little too 'metaphysical' or too weird to you that an idea could 'magically' translate into a physical reality? But look at anything and everything that you ever created. Didn't that creation originally start as an idea? an idea that has no measurable, physical reality; just like the idea for the design of a building in the mind of the architect? But, you say, that idea did have a physical reality, an electro-magnetic reality, caused by the firing of neurons in my brain. But whatever idea you have, whatever thought or conception, on any topic and any laguage, verbal or non-verbal, it is associated with the firing of neurons of identical construction which yields a flow of electrons of identical voltage and deposits of identical chemicals. And that is true if these ideas or conceptions are taking place in your brain or my brain. How to explain the amazing sameness of these electrical and chemical responses with the amazing variety of conceptual stimuli? Isn't it clear then that neuron firings may be caused by an idea, may be used as a device to record our ideas, but that they are not the ideas themselves? That we have a thought, or an idea which leads to the firing of a pattern of neurons which leads to the stimulus of muscles and speech, which leads to further thoughts and actions, which leads, ultimately, to the actual manifestation of these ideas on paper or canvas or wood or clay? Isn't this basically the same process as a cosmic idea manifesting into an electrical pattern of form (astral body) manifesting into an actual physical body?

In the last fifty years science has uncovered an enormous amount of information about the chemical development of life, but nothing about the development of shape. How could the genome possibly explain, for instance, the enormously complex and constantly changing shapes and shapes within shapes of the developing human fetus? The genome of the initial fertilized egg is identical with the genome in every one of the one hundred trillion cells of the adult body. Through embryonic development the genome is replicated first millions, then billions and then trillions of times over, identically. Yet in each part of the body a different shape is created, and shapes within shapes, and all these shapes are constantly changing and are responsible for the functioning of all the various organs and their perfectly coordinated activities. Doesn't this obviously tell us that their is a central control, an over arching plan that is somehow connected to the genome, but that is not created or controlled by the genome?

As I said earlier, the idea for a machine comes out of a desire to accomplish something and a knowledge of the obstacles that must be overcome in order to accomplish that. The idea consists of two parts : the appropriate materials needed and the form that these materials must take to direct the energy to accomplish the desired task. A gene involved in the construction of a living body is an idea. The visible part of this idea is the manufacture and delivery of the appropriate materials (proteins) in the right sequence (firing pattern). The part that we do not see directly, but can only see the results of, is the idea of shape. As new proteins are manufactured and delivered to a construction site, they fill out a shape; a shape that already exists in the mind of God, or, if you prefer, in the cosmic consciousness.

Sometimes evolutionary change requires no change in the genome at all. Witness all the various incarnations of the liver fluke, all done by firing different genes with different patterns within the same genome. All that means is that many, many dramatic changes of shape can be wrought using different arrangements of the same materials. But sometimes a new idea will require a new material, and then a gene must be added. But a new gene involved in the construction of a living body can never be just added on. It's much, much more complicated than that. It must have it's own new delivery system and must be integrated into the firing patterns of many firing sequences with its own set of control genes and its own method of being delivered to various construction sites. The entire organism must be adjusted to accommodate this new gene and new structure, including adjustments in nerve and muscle connections, in sense of equilibrium, in the whole real estate of the brain since a new area must be set up to process information coming from this new structure and going to this new structure, etc., etc. For humans it would be an amazing,impossible, overwhelming endeavor. For God, or the Cosmic Consciousness, it may just be what She does.

Are there any hmmmm moments followed by aha moments when the Universal Mind is creating new structures and, possibly, adding new genes? Who knows? Perhaps that intelligence is out of time and space and already has the solution of any environmental problem before it actually occurs. Perhaps it is all foreseen. I like to think of it otherwise. I like to think of it as the Universe's loving game. As organisms continue in this process they get more and more complex and as they do the number of options of things that can be done, by building on all the existing structures (all the previous ideas) gets narrower and narrower. But coming up with an amazing solution that involves microscopic adjustments in gene sequences, firing patterns, metabolism, equilibrium, nerve and brain function, and still results in a completely integrated being that is actually more equipped, more able to deal with its environment in new and interesting ways, a creature that has more options than previously, is, it seems to me, a loving challenge worthy of the transcendent intelligence of the Universal Mind.

Going back to the hapless, isolated accidental mutation, and again I remind you that I am not talking about a mutation in the gene of a chemical that the body produces, but a mutation in a gene involved in the construction of the body itself; it should now be clear that such an accident could never result in anything but damage to the existing structures. There is no new integration, no new plan, no new firing pattern, and no idea. It is just a change in a chemical, or in the case of the accidental replication of a control gene, it may be the replication of a whole extra form, or extra idea (although it would never mean the creation of a 'new' idea). But that isolated extra 'idea' like the four winged fruit fly, would be just that: not a new idea but an isolated, disconnected useless repetition of an already existing idea, separate from all the myriad interwoven ideas that make up a complex living organism.


Please comment. Your thoughts are always welcome.

Tuesday, September 29, 2009


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.


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 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.