Tuesday, January 10, 2012


First let me say that I, along with everyone else in their right mind, am a huge fan of biological research. What we are discovering about some of the mechanics of the body and the awesome detail and precision of those mechanics is fascinating and will surely lead to vast improvements in the way we are able, not to cure illness because we are never able to do that, but to better assist the body in curing itself. These discoveries, however, are based more on the use of modern optics and the dilligence of modern researchers. Very little is based on wisdom or insight. Ridiculously inflated exaagerations of what we have done, what we have discovered and predictions of what we will discover in the near future are either conscious attempts to delude, or are based on the self-delusion of the researchers themselves who do not really understand fully what is required to create what they are observing and/or who cling to a Victorian Darwinian framework which falls laughably short of being able to explain either past or present living phenomena with any depth of understanding.

Here is a quote from biologist John K. Young, who teaches at Howard University and does research on the cerebellum. I have singled him out not for his achievements in the field, he is perhaps better known as a teacher and popularizer of modern biology, but because his statements, like the following, are typical of the kinds of assumptions and belief systems that most main stream biologists operate from:

"Cells originate in the cells of the embryo. How do they differentiate from embryonic stem cells into muscle, heart, nerve and epithelial cells? How do they transform into this great variety of shape and functions?

Up until recently biology has only been able to describe how these things happen. We could see these things happening and could describe them, but we really didn't understand what was going on. Until recently biology has been a descriptive type of science, in which we give names to things but it hasn't been a really mechanistic science because we didn't know the basic mechanisms that drive these changes.

Biology in the last fifteen to twenty years has changed from a descriptive science to more of a mechanistic science. Now we are beginning to understand the nuts and bolts of life and we are beginning to understand what specific signals trigger to cause these mature cells to originate. So this makes it a very exciting time for biologists."

This, of course, is not the first time that biologists have claimed that we are at the very core, at the nuts and bolts, of life. When Watson and Crick discovered the double helix formation of the DNA molecule and when further discoveries determined that the arrangement of nucleotides along the DNA double helix determines an organism's different traits, we were then supposedly at the very 'center' of life. What Professor Young is referring to is the discovery of the functioning of protein molecules and their role in the stimulation of genes and in the operational work of the living cell and is describing these protein molecules as the 'nuts and bolts' of life.'

Modern biological research can be broken down into two broad categories. One is research on genes and one is research on proteins and the interconnection between the two. Let's first talk about genes.

The genes themselves are nucleic acids. They consist of long strings of four different nucleotides: Adenine, Cytosine, Guanine and Thymine, which themselves are relatively simple molecules. The arrangements of these four nucleotide molecules into different patterns is what causes an amazing variety of results because they are "CODED." Now what they are coded for can be argued. Obviously on a physical level they are coded for amino acids. Each arrangement of three different nucleotides (ACC, CGT or GTT for instance) codes for a specific amino acid. And when these arrangements are strung together in a certain order, they are coded for whole long strings of amino acids so that, when that code, through a whole series of utterly precise and amazingly complex processes (accomplished by the coordinated efforts of many perfectly engineered molecular machines called proteins) , is transcribed onto an MRNA molecule (about 2000 different protein molecules called transcription regulating factors and composing almost 8% of the entire genome, are involved in this transcription process alone), and then the transcribed mRNA molecule is transported from the nucleus of the cell through another entire series of utterly precise and amazingly complex series of processes (accomplished by another array of perfectly engineered molecular protein machines) to a ribosome organelle where it, through another series of utterly precise and amazingly complex processes (also accomplished by another set of perfectly engineered molecular protein machines), is translated from a string of nucleotides to a string of amino acid molecules, and when that string of amino acid molecules, through another series of utterly precise and amazingly complex processes (once again accomplished by still another set of perfectly engineered molecular protein machines) is transported to the rough endoplasmic reticulum and the Golgi apparatus where it is, through yet another series of utterly precise and amazingly complex processes, folded into the utterly precise and amazingly complex shapes of a protein molecule and carbohydrates or sugars are added in yet another series of utterly precise and amazingly complex processes (all accomplished by, you guessed it, yet another array of perfectly engineered molecular protein machines) so that the protein molecule is then complete and is then, through still another set of utterly precise and amazingly complex processes (accomplished by you know what), transported to the exact spot within the cell or the exact spot outside of the cell where it is needed to carry out its intended function. The timing of all these processes, started by the stimulation of certain protein molecules which results in the firing of certain gene sequences, is also amazingly complicated and precise, because the proteins manufactured by these genetic firings must be used when needed, and those needs are often urgent, and these proteins are often used as amalgams of two or three or several proteins that all have to be manufactured and arrive at that spot in the body where they all need to be at the exact coordinated time. All of these processes are happening many, many times simultaneously in each of the one hundred trillion cells in your body and they require, among other things, the stimulation of the exact set of base pairs of nucleotides of the three billion nucleotides in each of the one hundred trillion cells that will fire the precise gene sequence needed at that moment.

For the moment you will just have to accept the fact that all these processes are utterly precise and amazingly complex, although I will discuss later on a few examples of that precision. Yet you may safely assume their precision and complexity since it is these very processes that are being studied in molecular biology and organic chemistry departments in universities and research centers all over the world, and Nobel Prizes are given out regularly to any enormously diligent researcher who has spent many years making any kind of headway in further understanding the mechanics of these processes.

So you can say that the genes are just coded for amino acids; but when fired (actually not even when they are fired but from the moment that they 'need' to be fired) a whole series of processes, as I mentioned above, is engendered, and they also, and of huge importance in the construction of bodies and the continually changing shape of bodies and the continually changing shape of cells within the body, they produce in conjunction with the synchronous firing of many, many other genes, by manufacturing many thousands and millions of other protein molecules, a specific shape, be that the shape of an organ, a tissue, an organelle within a cell or the shape of the amalgamized combination of the proteins themselves. This shape, although engendered by the gene sequence and obviously connected to the gene sequence, has no visible, observable connection to the gene sequence. In other words, certain combinations of genes result in certain shapes, but how those shapes are formed is a mystery. All biologists can observe is how the building materials of these different shapes arrive at a certain location and when they arrive; but the shaping of an organ or an organelle, just like the shaping and reshaping of the embryonic cell mass through gestation, can be observed only in its results. In other words we can see organic molecules shaping themselves (but of course they are not doing it by themselves) into a variety of precise and wonderful shapes (wonderful because it is these very shapes that makes humans recognizable as humans and fruit flies recognizable as fruit flies) but the mechanics of how those things are being shaped, the 'shaper', or even the blue print for these shapes, is never observed.

So, although the genes can be observed to code for amino acids and in the proper sequences, to code for proteins; the firing of genes, but really beginning with the 'need' to fire certain genes, engenders a whole series of amazing processes, the mechanics of some which can be seen, and the mechanics of some of which cannot be seen. In this essay I will show how these unobservable processes are inherently unobservable, and will never be 'discovered' by the continued diligent observations of whole armies of research biologists. Also, I will show how the context in which these freshly discovered biological phenomena are viewed (not the phenomena themselves, but the context in which they are viewed) as accidental outcomes of a random and unintelligent process, is ludicrous for any number of reasons, and is clung to with the same stubbornness and rigid tenacity that the most ardent religious fundamentalists cling to any belief, regardless of all evidence to the contrary.

For now, I just want to say this about the genes and the genetic code: It's a code. It's a code! IT'S A CODE! IT'S A CODE!! IT'S A CODE!!!!! What is a code? Letters are codes. Numbers are codes. The high and low frequencies used in digital devices and computers is a code. Codes are means of transmitting ideas. The ideas do not belong to the code. The ideas belong to the transmitter of the code. In other words, when you read a novel, you don't imagine that the ideas of the novel were conceived by the letters that make up the words, do you? When you study mathematical equations, you don't imagine that the idea communicated by the equation was thought up by the numbers in the equation. And you certainly don't think that the high and low frequencies of computer code created, by themselves, Apple Computers and applications, do you? So how in the world do we come up with this idea that a code, a genetic code, does anything but communicate ideas from the being, or Being who originally conceived of the ideas being communicated through the code and originally conceived of the code as a way of communicating these ideas.

Also, for a code to be functional it must have a reader of the code. Letter codes and number codes were created long after there were human brains and human eyes to read these codes. But if we are talking about the beginning of life; if life did indeed begin with a code, then it had to also begin with the equipment necessary to read that code. The equipment required to read the code is the entire system of transcription and translation involving mRNA and tRNA nucleotides, involving scores of precisely engineered proteins with the ability to locate the needed code, with a precise signaling system that sets the entire operation in motion when a particular protein is needed, involves the copying of the code on to the mRNA, the transport of the mRNA to the precise area where it can be translated into a string of amino acids, the precise mechanisms for folding those amino acids into a functional protein, and an elaborate timing system so that the proteins manufactured will be manufactured in a sequence that will result in a synchronized and elaborately integrated organism and not just in a random pile of proteins.

If archaeologists examining an ancient ruin made the discovery that those scratches on the walls of a building were actually a code, that discovery would elevate the archaeologists' perception of the advancement and level of intelligence of the culture that once lived in that ruin. It is only modern scientists, so inculcated with Victorian Darwinian notions, that would use the discovery of a code as proof that intelligence does NOT exist in the formation of life. The basic difference between the modern scientific perception and the traditional, spiritual perception is that modern scientists believe that life and later intelligence, came about through the random interactions of matter; while the traditional, spiritual perception is that all things begin with intelligence out of which comes matter and later life forms. Intelligence, desire and will are all non-physical things, but associated in our world with physical bodies; yet they precede physical bodies, precede all of matter, and it is out of intelligence, desire and will that matter and later life forms were created. The tortured explanations of how matter began, ignoring the fact that a whole series of precise and brilliantly callibrated laws had to be in place before anything, even the Big Bang could have occurred; and the tortured explanations of how life formed from matter, explanations which run contrary to all discoveries of geologists and everything we know about environmental conditions as they were at the beginning of life on this planet (see my post 'EVOLUTION'); and the tortured explanations of how oxygen metabolizing organisms could have 'evolved' from photosynthetic organisms; and the tortured explanations of how complexly organized eukaryotic cells with whole internal systems of organelles could have 'evolved' from relatively much simpler 'prokaryotic' cells; and all the nonsense about pre-biotic pools of organic material that supposedly lay unmolested on this planet for millions upon millions of years enduring intense volcanic activity, unbearable heat and the continual bombardment of meteors; while organic molecules randomly and accidentally accumulated, a process taking, supposedly, many, many millions of years, to form the first life form, or the first molecule determined to replicate itself and desirous of replicating itself, when there is absolutely no evidence to support any of this or even a reasonable conjecture as to how any of this could have possibly happenned; all of this can be seen as a desperate attempt to continue to cling to the idea that life evolved without intelligence, or design; and what is most ludicrous is that these Victorian Darwinian ideas are clung to in the face of the discovery of the astonishing intricacy and complexity of life at the very 'simplest' level, even within a single cell; none of which could have possibly evolved by a random, hit and miss series of interactions of mindless molecules, as neo-Darwinin evolutionists would have it. To the contrary, all the evidence regarding organic materials on this planet is that they first appeared four billion or more years ago, not in tide pools of organic material, but already organized into microbes which, exactly like today's microbes, had a genetic system of transcribing and translating nucleic acids into amino acids, a system of folding proteins, a system of digestion, a system of elimination, a system of metabolism, a system of growth and reproduction, and a sensory system of responding to their environment. And that was at the very beginning, at the inception of life on this planet, or at least on the surface of this planet, which occurred exactly at the time when the temperature of the Earth had cooled down enough for there to be non-boiling water at its surface. And even hundreds of millions of years before that, there were hyperthermophilic bacteria living at or above the boiling point of water in thermal vents way below the surface of the water. These microbes could thrive in this super-hot environment because of the extra bonding of their protein molecules. So how in the world could these hyperthermophilic bacteria accumulate from random pieces of organic material when any of those pieces would break down in such an environment as fast as you could boil an egg?

And let me say that the reason I can say so emphatically that none of the amazing complexity and precision of cellular life could have possibly evolved through the supposed random hit or miss process of genetic misfires, is that any biological organism, no matter how 'simple' lives as the result of literally countless, minute and utterly precise biological processes. These are processes that are essential to life. There is no genetic code, no transcription, no translation, no folding of a protein molecule, no gestation, no growth, no mitotic division, unless thousands upon thousands of processes are simultaneously undergone with perfect synchronicity and precision. The supposed hit and miss process of evolution, (occurring supposedly whenever there is a one in one hundred million times miscopying of one nucleotide which is one part of thousands of nucleotides which make up the code for one gene), happens within the context of living organisms, but any 'misses' at the basic cellular level would mean death. Everything must proceed by hits not by misses. There could be no organisms that were trying billions of times to get transcription right. If they didn't get it right the first time, there would be no organism. There is no long line of organisms still working out 'translation.' Again, if translation didn't happen right the first time, involving awesome complexity and precision, then that blob of organic matter would never have become anything other than a blob of organic matter.

Here is Professor Young again, "Now we are beginning to understand the nuts and bolts of life and we are beginning to understand what specific signals trigger to cause these mature cells to originate."

The signals Young is referring to are certain protein molecules that have the ability to re-enter the nucleus of the cell (all proteins are manufactured outside of the nucleus) and once back within the nucleus, are able to stimulate the firing of certain genes or whole sets of genes. What I want to distinguish here is the understanding of what signals cause something and the understanding of what is going on at a deeper level. I know what signals are needed to operate my washing machine. I can put the dial at thirty minutes, can put it at the beginning of the soak cycle and then press another button to turn it on. Does that mean that I understand my washing machine? Of course not. The proof is that when the machine needs a repair, I must call a repair person whose knowledge of the machine far exceeds mine. This person understands the mechanics far more deeply than I do. Still, when I need a new washing machine, I must contact yet another person. The repair person may know how to get my original machine to function better, but he does not know how to manufacture a new machine from raw materials. Now if we are talking about a biological entity and not a washing machine, we are talking about an entity (and this may be a whole organism, a cell, an organ, a tissue, or an organelle within a cell) which undergoes enormous change within it's own span of existence. Those changes may not just be the normal ones of growing, maturing and aging, in and of themselves miraculous and miraculously complex, but they may often include the most dramatic changes of shape, size and function, which would be akin to my washing machine changing into a Mack truck, or my cell phone changing into a personal computer. What person would I call if I wanted my washing machine to grow or to metamorphazise into a truck, or to reproduce, because I felt like hearing the soothing rumble of three or four tiny washing machines in my house? Where would I find the person with that know how? So, although biologists are identifying the signals that trigger the genes that allow such amazing transformations and the construction of new biological entities, all of which is amazing, that does not mean, AT ALL, that we really understand these amazing transformations, or that we even have an inkling of understanding as to what is really going on.

Now let's talk about proteins. We usually think of proteins in relation to the food we eat, and we think of it in slabs: breasts of chicken, sides of beef, filets of fish, etc. But biologists understand that proteins function in the body on the molecular level. The number of protein molecules in the body is unfathomable. There are hundreds of thousands, perhaps millions of them in each of the one hundred trillion cells of the body and countless numbers of them in our blood and digestive fluids.

So here are some facts about protein molecules: No protein molecule (and no protein) was ever made except within a living organism by the process of genetic transcription and translation. Each protein molecule is not merely a chain of amino acids, but is folded into a particular and absolutely precise shape, often along with sugars and fats (also precisely shaped), which shape along with a precise pattern of positive and negative charges, allows the protein molecule to function. And each protein molecule is manufactured in the body to fulfill, and is designed to fulfill, a particular function. Now even though these molecules are microscopic, many of them are enormously complex. Protein molecules are each microscopic machines, and often very complicated, and always absolutely precise machines as well. Some of them function as pumps, as messengers, as escorts, as filters, as freight cars, as guards, as medical alert teams, and scores of other functions. Now you may think I am exaggerating and anthropomorphising the role of these molecules. If you think that please study anything about protein molecules. Again, their intricacy, precision, and complexity cannot be exxaggerated. And again, these molecules could not possibly have originally evolved in a hit or miss process of Darwinian evolution.

Here I have to make a distinction between the two main ways that proteins are used in the body. Proteins are used in the actual construction and continual reconstruction of the body, and proteins are used as enzymes for the daily functioning of the body to aid in such things as digestion, excretion and protection against invasion into the blood stream of harmful microbes. Scientists have seen over and over again how a 'mistake' in the genetic firing (which may or may not be a mistake at all) can cause an improvement of digestion, the ability to digest a new food source, or the ability to eliminate a new pathogen thereby protecting the body from harm. In this way, 'mistakes' in genetic firing create more resilience within a species to survive severe changes in available food sources and in the ability to survive attacks by new pathogens. These occasional 'mistakes' which are actually part of a brilliant system which makes an entire species more adaptable, is the reason that research scientists have conjectured that whole species, whole new body types, can be created eventually through an accumulation of these tiny mistakes.

Nothing could be further from the truth. Regarding the proteins involved in the structure of the body and the continual restructuring of the body as it grows, ages and as structural cells die and need to be replaced, any miss in the genetic copying of the proteins for these structures, any mistake in the transcription or translation of these genes, or in the folding of these proteins, would result in a change of shape and/or charge which would make that protein non-functional or less functional and would result in either the severe impediment to or the culmination of that organism's existence. I should note that I am not talking about the healthy mixing of genes in sexual reproduction where the offspring receives a healthy combination of two sets of healthy genes. And I am not talking about the mingling of traits that results from this genetic mixing, all of which is an utterly brilliant system for creating variety within a species and making each species more adaptable as a whole. I am talking about a 'mistake' in the genetic copying of a gene so that one of the amino acids that compose the gene is the wrong amino acid. All of these mistakes, with one exception that I will explain, causes a diminishment in the functioning of an organism if not in its death. The one exception that neo-Darwinists will harp on is the genetic 'mistake' that causes sickle cell anemia. The sickle cell mutation is common in parts of Africa where malaria is present. Inheriting a sickle cell mutation from one of the parent's genes confers resistance to malaria, so that people that have that one sickle cell gene survive at a higher rate than people that don't in malaria infested areas. Yet sickle cell is a sickness, is really a deterioration of the hemoglobin protein molecule which distributes oxygen throughout the body. People who inherit two sickle cell genes, from both parents, will have severe anemia and die in childhood. People that inherit one gene will have only a mild case of anemia and will also have only a mild case of malaria, since the malaria parasite, which operates by invading the red blood cells, is trapped within the sickled and damaged hemoglobin molecules so that the damaged hemoglobin molecule and the offending parasite are eliminated from the body. So this is one case, THE one case, where a mutation , call it 'accidental if you will, gives a survival advantage to an advanced species in a malarial area, even though it, actually, damages the normal functioning of our oxygen distribution system by damaging, not improving, the functioning of hemoglobin molecules.

And again, we are not talking, at all, about species changing or any kind of evolution. A person with sickle cell is still a person. They have not changed into a new species. They will not supplant the human race. In fact, no so called advanced species has supplanted any so called inferior species. Life on this planet began with single celled microbes and remained exclusively single celled microbes for two billion years, fully half the length of time of all life on this planet. More advanced species have certainly not supplanted microbes. In fact the 'simple' microbe, which is not simple at all, still outnumber multi-celled species by billions and trillions to one. So for two billion years there was no evolution of life on this planet, in the sense of one species 'evolving' into another. There was adaptation. Microbes, with amazing versatility, adapted to every change of heat and cold, of dryness and moisture, of changes in the chemical contents of the oceans, etc. Scientists have long known that all these amazing adaptations could not have been accomplished by the one in one hundred million 'accidental' mutation theory of neo-Darwinists. Complex changes require not just one but whole series of mutations that must happen in an absolutely precise order and must occur to precisely that one organism that has been the recipient of every step of that mutational series up to that point. And this imagined series of mutations, the chances of which are utterly and impossibly minuscule, needed to have happened not in 'endless' time, but in the context of the urgent situation of microbes being threatened by a predator, a toxin or a sudden change in environment for which they had no genetic defense.

What was discovered is that these 'primitive' microorganisms engage in something called gene swapping. What happens is that when one microorganism possesses the genetic material that enables it to manufacture an enzyme which confers resistance to a certain threat (and there is no plausible evolutionary explanation as to how that microorganism managed to have that ability in the first place), it will replicate copies of that genetic material and find another microorganism in danger of annihilation and donate this genetic material by growing pilli, or pores, which connect from one organism to another so that the endangered microorganism receives not just the enzyme, but the genetic material that will allow it to manufacture that enzyme for the rest of its life. Is there a more sophisticated survival mechanism in all of life? For this to happen it must require recognition on the part of the donor organism or the donee organism or both, of exactly what genetic material is needed; then that genetic material must be replicated in the donor and then with enormous precision the ducts or pilli must be grown to transfer this material from one organism to the other. If you can't imagine single celled microorganisms having that kind of recognition, which is a reasonable assumption since we (human beings) do not come close to having any such recognition ourselves (we just discovered that there was such a thing as genetic material about sixty years ago), then what being or Being or intelligence was there that had that recognition and was able to create such a fantastic mechanism? I remind you that this most sophisticated survival device appeared three to four billion years ago at the very beginning of so-called evolution. Please explain to me how gene swapping could have slowly 'evolved' over many, many millions of years of replication mistakes, and, even if that were possible, how could it, once evolved, function at all without a transcendent intelligence; and if not the transcendent intelligence of the microbe, than whose transcendent intelligence must be involved?

One of the things that Professor Young tries to explain in his book is how we now know how the various cells in the body are shaped. There are thousands of different types of cells in the body, all originating from seemingly identical embryonic stem cells. He attributes the shape of cells and the shape of the nucleus of cells (nuclear shapes vary widely among cells) to a system of filaments. There are nuclear filaments that maintain the shape of the cell nucleus and there are cytoplasmic filaments that maintain the shape of the entire cell. These various filaments are made from a variety of different proteins causing differences in rigidity, strength and suppleness. They are also positioned differently in different cells. But the filaments do not create the shape of the cell. They maintain the shape of the cell. In the same way that the girders of a building support the building's shape. When you are looking to design a building you hire an architect; you don't hire a girder.

Each different type of cell has a different task to accomplish in the body, and each of these has a special kind of nucleus whose shape and arrangement of genetic material is designed specifically to efficiently accomplish that purpose. Professor Young writes,

"Sperm cell nuclei are very much smaller and more arrow like in shape than most nuclei, which is in accord with their function of swimming as streamlined rockets through the fluids of the reproductive tract. They also possess a type of B lamin (lamins are proteins that compose the nuclear filaments) that is not found in any other cell. If an ordinary cell is forced to produce sperm cell laminas, its nucleus will become deformed to resemble the pointed morphology of a sperm cell nucleus."

So this is very interesting. The gene for the B lamin protein specific to the sperm cell is the code for the string of amino acids that, when delivered and folded and manufactured, will become the B lamin protein that compose the nuclear filaments of the sperm cell nucleus. But it is also, somehow, connected to a shape, the arrow like shape of the sperm nuclei. And researchers have seen this over and over again; that by isolating the protein molecule that can re-enter the nucleus and fire up a certain gene or isolating a protein molecule that can also re-enter the nucleus and block the firing of a certain gene, then that cell becomes damaged in a specific variety of ways; and by studying this damage in the weakened cell or organism that has been the recipient of such protein triggers injected into a cell that wouldn't normally produce that gene, or blocking the firing of genes that would normally be produced, and by surveying this biological destruction, biologists can pinpoint what protein molecules cause the firing of what specific genes and the suppression of which specific genes, and they can note the specific function of the proteins that that gene manufactures. In the above case we can note that there is some connection between the B lamin protein which makes up the nuclear filaments of the nucleus of a sperm cell and the arrow like shape of that sperm cell. And we know this by injecting the protein trigger for the B-lamin gene into a cell other than a sperm cell. The nucleus of that cell starts to acquire an arrow-like shape before it dies, because, of course, that cell cannot function appropriately with that kind of shape. That cell, whatever it is, has a nucleus whose shape and the location of the entry and exit pores of that nucleus and the arrangement of the genetic material within that nucleus are all designed precisely to allow that nucleus to serve the functioning of that cell in the most utterly precise and specific way. So any tinkering on a genetic level, by causing the firing of genes that wouldn't naturally fire in that cell, or at that moment in the life cycle of that cell, or the suppression of genes that would naturally fire at that moment in the life time of that cell, will seriously damage the efficiency of that cell, which damage is the very thing that biologists observe to forward their understanding of which proteins, after re-entering the nucleus, triggers the firing of which genes and what function does each of the proteins operating outside of the nucleus within the cytoplasm of the cell actually accomplish.

So in this case, and many other cases, genes are found to be connected not only to the manufacture of a certain protein but they are also connected to the generation of a certain shape. Let's look at the transformation of a lymphocyte into a plasma cell. Lymphocytes and plasma cells are part of the immune system of the body. When a foreign molecule (an antigen) is presented in precisely the right way by an antigen presenting cell to a lymphocyte, the lymphocyte is stimulated into metamorphasizing into a plasma cell. Professor Young again,

"The lymphocyte begins life as a small cell with a marginal amount of cytoplasm; as it turns into a plasma cell, the volume of the cytoplasm expands considerably and becomes filled with massive amounts of rough endoplasmic reticulum (rER) and Golgi stacks.

This is appropriate for the function of the plasma cell. Plasma cells secrete prodigious amounts of protein (180,000 molecules per hour!) at about six times the rate of other secretory cells like fibroblasts. In order to secrete so much protein, plasma cells must make appropriate adjustments to their protein-making machinery."

This is all written, of course, in the usual manner of biologists, from the unexamined perspective that the cells are doing all of this on their own. There is no conscious entity called a plasma cell that knows it is going to need to secrete a lot more protein and knows that it must make appropriate adjustments to its protein-making machinery. The cell is not saying to itself, "Gee, there's this antigen here, so I better snap to it and start producing 180,000 protein molecules every hour to combat this antigen and remove it from our system. Let's see, hmmm! I guess I'll start growing a whole bunch more cytoplasm and I'm going to need a lot of rER and Golgi stacks. Golly! I'd better get busy!"

The cell is, of course, thinking no such thing. It is not thinking at all. It could care less whether that antigen invades the body or not; whether it remains a lymphocyte or turns into a plasma cell. The cell is a mindless cog in an utterly brilliant mechanical system. You can either think that this system gradually and accidentally evolved (but that is hard to imagine, because in the millions of years of this so-called evolution, these antigens would have been having themselves a field day in this unprotected organism which wouldn't survive a day without a functional immune system) or you can think that it was, along with everything else in the body, a brilliant IDEA. And it was an idea that came from a being or Being who cared that those antigens not take over your body; that cared that your body survived, because that being cared that you continue to have the kind of experience that you have been having when that Being provided that body for you in the first place. Certainly the 'body' doesn't care if you are able to fight off an invasion of antigens; and the cells and all the almost infinite number of mechanical parts of your body don't care either. They are all synchronous parts of a fantastically elaborate machine that has been designed and synchronized to provide you with a certain experience, an experience of being alive and conscious in a particular way which is a function of the very design and synchronicity of this body. You, yourself, may care about whether or not you are invaded, but you certainly lack the knowledge to do anything about it, and probably don't even know about it until it's too late. The body and brain which are both matter, don't care, because there is nothing in matter that cares. The only other thing left that could possibly care, that could invest energy and intelligence into this process, is the creator, architect and builder of your body who has designed every part of it so that you can have a continuous experience, and the richest possible experience, including seeing, hearing, smelling, tasting, thinking, and so that you are able to want things and are able to do, in the great, great majority of cases, the things that you want to do, and you are able to figure out, ultimately, what this life is about and who you, apart from all this fantastic apparatus that you have received, really are.

But I digress. What happens mechanically in the transformation of a lymphocyte into a plasma cell is fantastically complicated, but I will try to give you a shortened version that you may be able to read without getting a headache. In response to the antigen, the lymphocyte starts producing immunoglobulin proteins at an elevated rate. Before they become proteins, however, these chains of transcribed and translated amino acids must be folded into their proper shape. This folding takes place in the rER and is aided, of course, by a number of proteins. There is a whole category of proteins that are called 'chaperone' molecules which aid in this folding process. Some of the amino acid components of the protein are hydrophobic, or water-averse. These must be chaperoned, or protected, from the watery cytoplasm during the folding process until they are safely enfolded into the inner part of the protein molecule and surrounded by hydrophilic amino acids that are not water sensitive. When too many unfolded chains of amino acids arrive in the rER there is another protein called BIP which will bind with these hydrophobic parts of the chain to protect them until chaperone proteins are available. If the rER gets too backed up, then the BIP protein binding sites get saturated which causes the BIP to dissociate from a protein on the rER membrane called inositol requiring enzyme 1 (IRE1). These liberated IRE1 protein molecules can then join with each other and are able to remove a 26 nucleotide long intron loop (intron loops are extra nucleotides attached to a gene that are usually removed within the nucleus) attached to the mRNA for another protein called the X-box binding protein (XBP). The removal of this intron loop allows the XBP to function.

Are you still with me? XBP is a DNA-binding transcription regulating factor. " When it binds to DNA, it binds to a type of DNA sequence called the X-box and stimulates the transcription of at least two dozen genes for proteins that are required for assembling the rER (these include Sec61, signal sequence receptor, signal peptide protease, signal recognition particle, a number of chaperone proteins, etc.) This leads to the synthesis of all the components of the rER and an expansion of the rER that is needed for the secretion of so much protein." (Professor Young, again).

Please bear with me. There is still more. "The XBP protein is not the only one required for the transformation of a lymphocyte into a plasma cell. BLIMP is another transcription regulating protein..... that suppresses the activation of about 250 genes that are active in lymphocytes.....So BLIMP is turned on to suppress the features of B-lymphocytes, and then XBP is turned on to activate the features of plasma cells."

This same sort of process, where one transcription factor protein that stimulates a whole host of genes and another transcription factor that suppresses a whole host of genes is probably the same basic mechanism used in many other cell transformations. The pancreas begins as a conglomeration of simple duct cells, for instance, which are later transformed into the much larger and much more active pancreatic acinar cells.

So this is another example, like the one of the gene for the B lamin proteins for sperm nuclei, which is associated with an arrow-like shape; here we have a whole host of genes manufacturing a whole host of proteins, all the materials necessary for the manufacture of rER and the Golgi apparatus, both of which are the biological equivalent of extremely precise and advanced electronic manufacturing equipment, all programmed to arrive at the right location and in the right order, but, again, how are all these materials assembled to achieve the precise shape, and integration of shapes, to make the new rER and the new Golgi apparatus functional? When the XBP binds with DNA, "This leads to the synthesis of all the components of the rER," as Professor Young says, but how are all these components, comparable to the components of an enormously complex piece of electronic equipment, assembled? How are all these various shapes and shapes within shapes achieved?

Professor Young also talks about the replacement of damaged cells. Embryonic cells divide mitotically, but as cells become more specialized they lose their ability to undergo mitosis. If those cells become damaged or just worn out with age, they must be replaced. Adult stem cells in the bone marrow, in connective tissue and in many other places in the body can be stimulated to migrate to the scene of an injury and by the same methods as above, by the stimulation of sets of genes accomplished by the release of growth factor proteins, these stem cells can quickly take on, in fact become, identical copies of the cells they are replacing. In the case of wounds in the skin, a clot is quickly formed consisting of blood platelets and clotting proteins. Platelets also transmit platelet-derived growth factor (PDGF) into the surrounding tissues. This, combined with other growth factors, allows the surrounding fibroblast cells which had been incapable of mitosis, to now mitotically divide. Again, all these explanations describe the proteins involved and the genes involved but say nothing about shape. How is it that in minor injuries, after all the new cells arrive, whether from adult stem cells or from the mitotic division of neighboring cells, that the wounded area achieves the identical shape that it had before the wound? How does the bone or the muscle or the skin surface knit together so perfectly that it is impossible to tell that there was any injury there in the first place? What is the borderline, the contour of the outer edge of that bone or muscle, or the outer edge of an organ or an organelle, or the outer edge of the entire body, for that matter, made of? How are these precise shapes being achieved over and over again? We know the mechanics of how the material gets manufactured but how is it shaped?

Now let's discuss what is perhaps the most baffling of all biological subjects, which Professor Young deals with at some length: the differentiation into all the various cells and all the various shapes of the human body from what is initially a seemingly undifferentiated mass of embryonic stem cells, in fact, from one embryonic stem cell, which is the single fertilized oocyte which, through a fantastic series of multiplications and differentiations becomes your entire body.
Here we are approaching a mystery that is so awesome that even Professor Young is forced to look up from his microscope and use a little poetry. He writes about an almost 'invisible blue print' in the cytoplasm of the egg that divides the egg into special parts. This is a blueprint of protein molecules which have the ability to re-enter the nucleus and cause the firing of certain genes or certain sets of genes, or the supression of certain genes or sets of genes. And it is this firing of certain sets of genes as opposed to others that causes the change in the shape of the cell and the nucleus and the organelles and the function of that cell.

Let's talk about this 'invisible blueprint.' First of all, the blueprint is composed of a specific arrangement of protein molecules. Those protein molecules had to be manufactured by the firing of genes in the egg prior to fertilization. What caused the firing of the genes that created the blueprint molecules? They had to be fired by a whole timing sequence which is in itself a blueprint, but a blueprint for the blueprint, if you will. That initiating blueprint, the sequence of what genes to fire and when to fire them, is not visible; it cannot be observed, and yet it must exist, and exist with absolute precision and specificity. So where is it? I will say it is in the mind of God. If you have another idea, or a more politically correct way of saying it, then I welcome it. Please let me know. Then, the protein molecules have to be held in place and in an absolutely precise place in the supposedly free floating cytoplasm of the egg. How is this done? Where are the filaments or the system of charges that hold such a structure in place? Perhaps we will find that system of charges, but what is the origin of this system? Again, I must say in the mind of God; and again I invite your interpretation. The arrangement of that blueprint has to be absolutely precise. How does each protein molecule know exactly where to go? How do the genes of the egg know exactly which genes to fire and in what sequence to produce this blue print of protein molecules? Was there yet another set of protein molecules that caused the firing of the genes that manufactured the blue print molecules? Was there a blueprint for the firing of the genes that cause the firing of the genes for the other blueprint? How far back can we go? And how is this blueprint for the blueprint held in place? All these molecules are in the supposedly free floating cytoplasm of the egg; and yet the egg is about to undergo a whole series of rapid mitotic multiplications and a whole series of folds and twists and undulations. So included in the design of this blue print which mysteriously arrives and which mysteriously holds its position, is the foreknowledge of all the twists and turns and multiplications that these embryonic cells will undergo; otherwise how would it know that that particular protein molecule in that first egg will wind up in the right position to stimulate the genes to create nerve cells or muscle cells or epithelial cells? And not just those broad categories of cells, but each of the two thousand specific types of cells that exist within these broad categories, which must be the precisely right cell to occupy each of the one hundred trillion cell positions of the human body. And to further complicate things, this initiating single cell, this fertilized oocyte, will divide and differentiate into not only the actual fetus, but into the placenta, the yolk sac, the amniotic membrane, the chorion, the embryonic villi that attach to the uterus and the entire temporary system of intra-uterine feeding and eliminating and blood supplying to that embryo until it develops the systems to do it on its own. And all of this differentiation, according to one theory, results from the placement of the right gene firing proteins and the right gene suppressing proteins in the cytoplasm of the original egg. Are we to believe that this placement happens with no intelligence, no foresight, just the happy outcome of a fortuitous series of molecular collisions? And you think it's hard to believe in God, in a creator, in a transcendental intelligence? It's so much harder not to.

And let's talk about the twists and turns and undulations of the whole embryonic mass. Each species undergoes a different set of turns and convolutions. How is this done? We are not talking about anything that happens within cells. We are talking about the shaping of the entire mass of cells. Of course that is the same thing with each organ, tissue, organelle and feauture of the body. It is not shaped from within the cell. It is not the result of genes which merely create the material that is being shaped. And it is the shape, as much if not more, than the quality of the materials, that makes the whole thing functional; and that distinguishes one species from another. There can be no other conclusion than that all these shapes are ideas and that the genes are there to supply all the physical materials needed to fulfill this shape, the contours of which already exist on some plane of energy that we have not yet detected, and these proteins engendered by genes along with sugars and fats, fill out a shape that already exists on some subtle level, in that mysterious border area between the physical and the non-physical, and is the result of a functional idea which may include new materials, or the re-combining of already existing materials, both of which include the alteration of genes or the alteration of the firing patterns of genes, and which includes shape, and shapes within that shape. And this shaping does not directly involve the genes, but is really the 'invisible blue print' which creates the contours of every cell, every organelle, every organ, every tissue and every feature of the body.

Here are some words from Richard Dawkins, one of the world's foremost front men for Darwinian thinking, who was at least at one time an extremely strident, professional atheist (one may conclude from some of his recent statements that he is now an agnostic, but he would never admit to this),

"At the end of a virtuoso origami performance; after numerous foldings-in, pushings-out, bulgings and stretchings of layers of cells; after much dynamically orchestrated differential growth of parts of the embryo at the expense of other parts; after differentiation into hundreds of chemically and physically specialized kinds of cells; when the total number of cells has reached into the trillions, the final product is a baby."

Look carefully at this statement. This professional atheist who declares a physical, observable cause for everything, makes no mention of any cause at all for all of the fantastic gymnastics, all the 'foldings, pushing's-out, bulgings and stretchings,' which are the very things that form the embryo, that allow those human shapes of human faces and arms and feet, the very things that absolutely thrill us, the parents, when we are able to glimpse them through sonograms and other devices, the very thing that makes humans humans, and chickens chickens, because every species has their own particular method of foldings and bulgings and stretchings that result in a particular species. Are the genes doing this? Is any chemical within the embryonic mass doing this? How could it? This is the entire embryonic mass moving through these 'contortions' as a whole. Certainly the genes are related to these foldings. An oocyte containing the human genome undergoes one kind of folding process; an oocyte containing a chicken genome undergoes another, quite different, folding process. But how can you say that the genome in either case is "causing" that particular type of folding. That would be like saying that the wheat and the salt at the Synder's Pretzel Factory is causing it to be folded into a pretzel; or that the metal and plastic and rubber at the Toyota Factory is causing it to become a Prius. It is true that when a new shipment of wheat and salt arrives, a whole series of activities involving loaders and unloaders and sifters and mixers and bakers and ovens and packagers is begun, but all of that activity really began with an idea in the mind of either old man Snyder or one, or several, of his designers. They are the true cause of this activity. And, of course, the same thing would be true at the Toyota factory, or any factory, even the living factory. These are all the products of ideas, and in living beings, the products of fantastically complicated, transcendentally brilliant ideas. And with living bodies, as with all creation, man-made or natural, we never see ideas directly, we just see the physical manifestations of them.

Every one reading this blog has a body, but you are not your body. Your body is your equipment. You experience the world through this body and you fulfill your desires through this body. You are not observable, neither with the naked eye or with any sort of biological equipment. You are the ground of your experience. You are consciousness; you are context, not content. You are the background within which all your experience takes place. Biology is not the study of life; it is the study of the fantastically complex and brilliantly synchronized equipment through which you experience the world in a particular way and manifest desires in a particular way. Biologists can see neither your desires nor your experience, only the physical body and brain which are the intermediaries between desire and experience. The fantastic system of genes and proteins and the signaling between the two, explains how all the materials needed for the body to survive and to respond to the desires of the being that occupies that body, are manifested. In the case of the so-called 'unconscious' processes, they are initiated not by genes, not by the firing of genes, but prior to that, by the desire of the creator to keep our bodies functioning. In the case of conscious behavior, these processes are initiated by our desires which instantaneously fire the exact combination of neurons which will set in motion a whole process of muscular contractions, of genetic firings, of protein molecular activity, which will allow us to pursue those desires. And what we desire is a certain kind of experience, for ourselves or for others: to experience feeling filled when we experience hunger; feeling satisfied when we experience thirst; feeling well rested when we experience exhaustion; feeling acknowledged when we experience being disregarded. The initiator of this activity, God's desires and our desires, and the result of this activity, our experience and God's experience, is something that is beyond the province of biology which studies the physical plane, which is the intermediary between desire and experience.

By studying living bodies, which are the intermediate phase, biologists will never get to the real cause or initiator of biological activity, or the true result of biological activity. They can only assist us in helping us, through our bodies, to get our desires met. This is a huge contribution and biologists and their research should be honored for it. When society goes astray is when we promote biologists to be 'life' experts and think that because of their years of research and their understanding of various aspects of our equipment, that they are then in a position to pontificate about life itself, about consciousness, about desire, and about the origin and meaning of life. You are life, you are boundless and unobservable, you are ultimately unchangeable and limitless, you are an intrinsic and inseparable part of the cosmic consciousness of the entire universe. Don't let anyone, even if they have won Nobel Prizes in biology, tell you otherwise.

Your comments are always welcome.

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