I'm about forty percent through DBB. I wanted to bring up an interesting part of the book, which I think does show fingerprints of hyperdimensional forces.
Behe describes a key mechanism of the acquired immune system below:
Behe then describes an alternative, theoretical system which is far more simpler in structure and function:
A materialist who does not believe in intelligent design may be forgiven for asking, if there is such clear evidence of intelligence in the structure of proteins, their domains, and the signal transduction cascades that mobilize gene expression, white blood cells, etc, then why is the system evidently a lot more complex than it needs to be to get to the same ends?
If the sole purpose of that system was to simply function as it was supposed to, what exactly does the additional complexity contribute?
From a Darwinian perspective, they're not charged with coming up explanation as to how that works, since to them it's all random anyway (their challenge is of course to prove the theoretical rate of mutation and effectiveness of natural selection acting on a population actually match up with what we observe in nature, as is layed out in Genetic Entropy and Evolution 2.0.)
From the perspective of intelligent design, the appearance of extraneous complexity can also be explained by the existence of multiple purposes, as well as the possibility of multiple designers. The more features you build into a household appliance, the more complex it necessarily becomes. Of course, we have an advantage looking at appliances because, as the designers, we can infer the purpose behind certain components and features. But since the designers of life are obviously not human, the kind of purposes behind certain things are not immediately obvious to us, either because of our unfamiliarity, or because we have limited ability to comprehend certain things.
How this works back around to hyperdimensional battles is, they are chiefly through us, and through our biology. If you have two intelligent opponents attempting to outsmart one another, they're going to compete in altering an external "playing field" according to certain constraints in a sort of intelligence arms race to manipulate conditions to their advantage. For two brilliant people facing off, if the game was very simple (like Tic-tac-toe), there would be constant stalemates and both sides would be thwarted in the exercise of their abilities to achieve their ends. So the complexity of the game is expanded (say, by graduating to the game Chess or Go) to allow more effective maneuvering, novel functions, etc. to outsmart the opponent.
If you look at a fresh battlefield or, larger still, an entire war theater, you're going to see some military bases here and there, troops dispatches, logistical lines, etc, but also some crater-filled battlefields, bombed out cities, and mass graves. If a Darwinist saw this picture, they would conclude that all that assembled by random means. If we took the opposite approach and said this scene was a product of intelligence, we would be right. But a product of a single intelligence would be like a country at peace and prosperous like, say, Japan. The warzone would most likely resemble land acted upon by competing intelligences, due to evident existence of zones where competing intelligences faced off and generated entropy in the field (the destroyed parts, but also the areas near enemy lines and no-mans-lands where there is more chaos).
Another hypothesis I had about that was the idea of "military" (intelligence) budgets for each side to focus on and deal with certain challenges in the hyperdimensional warfare. Some battles are perceived as more important than others depending on which side you are on, which is a general feature of asymmetric warfare. And the battle between STO and STS is clearly asymmetric from the perspective of one side being "allowed" to violate free will, while the other cannot, but fares well anyway because it is nourished by the higher densities of the information field (instead of being fed upon by same like the STS).
To go back to the military analogy, STS is like the tyrannical military with no moral or legal scruples in how it conducts warefare, violating human rights constantly, but is also weighted down by parasitic institutions in the military that constantly take battle spoils for themselves (think military-industrial complex). STO is like a noble military which strictly adheres to the principles of defensive combat only, immaculately safeguards the lives of civilians, etc, and which has vastly superior technology. Sort of like the US vs Russia.
Behe describes a key mechanism of the acquired immune system below:
When a microscopic invader breaches the outer defenses of the body, the immune system swings into action. This happens automatically. The molecular systems of the body, like the Star Wars anti-missile system that the military once planned, are robots designed to run on autopilot. Since the defense is automated, every step has to be accounted for by some mechanism. The first problem that the automated defense system has is how to recognize an invader. Bacterial cells have to be distinguished from blood cells; viruses have to be distinguished from connective tissue. Unlike us, the immune system can’t see, so it has to rely initially on something akin to a sense of touch.
Antibodies are the “fingers” of the blind immune system—they allow it to distinguish a foreign invader from the body itself. Antibodies are formed by an aggregation of four chains of amino acids (Figure 6-1): two identical light chains, and two identical heavy chains. The heavy chains are about twice as big as the light chains. In the cell, the four chains make a complex that resembles the letter Y. Because the two heavy chains are the same and the two light chains are the same, the Y is symmetrical: if you took a knife and cut it down the middle you’d get identical halves, with one heavy and one light chain in each half. At the end of each pronged tip of the Y there is a depression (called a binding site). Lining the binding site are portions of both the light chain and the heavy chain. Binding sites come in a large variety of shapes. One antibody might have a binding site with a piece jutting up here, a hole over there, and an oily patch on the edge. A second antibody might have a positive charge on the left, a crevice in the middle, and a bump on the right.
If the shape of a binding site just happens to be exactly complementary to the shape of a molecule on the surface of an invading virus or bacterium, then the antibody will bind to that molecule. To get a feel for it, imagine a household object with a depression in it and a few knobs poking up out of the depression. My youngest daughter has a doll wagon with front and back seats—something like that will do nicely. Now take the wagon/object, go around the house, and see how many other articles will fit snugly into the depression, filling both the front seat and the back seat without leaving any spaces. If you find even one, you’re luckier than I am. Nothing in my house fit snugly in the wagon, and neither did anything in my office or laboratory. I imagine there’s some object out in the world with a shape complementary to the wagon’s, but I haven’t found it yet.
The body has a similar problem: the odds of any given antibody binding to any given invader are pretty slim. To make sure that at least one kind of antibody is available for each attacker, we make billions to trillions of them. Usually, for any particular invader, it takes 100,000 to find one antibody that works.
When bacteria invade the body, they multiply. By the time an antibody binds to a bacterium there may be many, many copies of the bug floating around. Against this Trojan horse that breeds, the body has 100,000 guns, but only one works. One handgun isn’t going to do much good against a horde; somehow reinforcements have to be brought in. There’s a way to do this, but first I have to back up and explain a bit more about where antibodies come from.
There are billions of different kinds of antibodies. Each kind of antibody is made in a separate cell. The cells that make antibodies are called B cells, which is easy to remember because they are produced in the bone marrow.2When a B cell is first born, mechanisms inside of it randomly choose one of the many antibody genes that are encoded in its DNA. That gene is said to be “turned on”; all other antibody genes are “turned off.” So the cell produces only one kind of antibody, with one kind of binding site. The next cell that’s made will in all likelihood have a different antibody gene turned on, so it will make a different protein with a different binding site. The principle, then, is one cell, one type of antibody.
Once a cell commits to making its antibody, you might think that the antibody would leave the cell so it could patrol the body. But if the contents of all B cells were dumped out into the body, there would be no way to tell which cell the antibody came from. The cell is the factory that makes the particular type of antibody; if the antibody finds a bacterium, we need to tell the cell to send us reinforcements. But with this hypothetical setup, we can’t get a message back.
Fortunately, the body is smarter than that. When a B cell first makes its antibody, the antibody anchors in the cell membrane with the prongs of the Y sticking out (Figure 6-2). The cell does this trick by using the gene for the normal antibody, and also using a little piece of a gene that codes for an oily tail on the protein. Since the membrane is oily, too, the piece sticks in the membrane. This step is critical, because now the binding site of the antibody is attached to its factory. The entire B cell factory patrols the body; when a foreign invader enters, the antibody-with-attached-cell binds.
Now we have the factory close at hand to the invaders. If the cell could be signaled to make more of the antibody, then the fight would be helped by reinforcements. Fortunately, there is a way to send a signal; unfortunately, it’s pretty convoluted. When an antibody on a B cell binds to a foreign molecule it triggers a complex mechanism to swallow the invader: in effect, the munitions factory takes a hostage. The antibody then breaks off a piece of membrane to make a little vesicle—a self-made taxicab. In this taxi, the hostage is brought into the B-cell factory. Inside the cell (still in the cab) the foreign protein is chopped up, and a piece of the foreign protein sticks to another protein (called an MHC protein). The cab then returns to the membrane of the cell. Outside the factory, along comes another cell (called a helper T cell). The helper T cell binds to the B cell, which is “presenting” the chopped-up piece of invader (the foreign fragment in the MHC protein) for the T cell’s consideration. If the fit is just right, it causes the helper T cell to secrete a substance called interleukin. Interleukin is like a message from the Department of Defense to the munitions factory. By binding to another protein on the surface of the B cell, the interleukin sets off a chain of events that sends a message to the nucleus of the B cell. The message is: grow! FIGURE 6-2 SCHEMATIC DRAWING OF A BCELL. The B cell begins to reproduce at a rapid rate. T cells continue to secrete interleukin if they are bound to a B cell. Eventually the growing B-cell factory produces a series of spinoff factories in the form of specialized cells called ‘plasma cells.’ Instead of producing a form of the antibody that sticks in the membrane, plasma cells leave off the last oily piece of the protein. Now free antibody is extruded in large amounts into the extracellular fluid. The switch is critical. If the new plasma-cell factories were like the old B-cell factory, the antibodies would all be confined to quarters and would be much less effective at inhibiting the invaders.
Could this system have evolved step-by-step? Consider the vast pool of billions to trillions of factory B cells. The process of picking the right cell out of a mixture of antibody-producing cells is called clonal selection. Clonal selection is an elegant way to mount a specific response in great numbers to a wide variety of possible foreign invaders. The process depends on a large number of steps, some of which I have not discussed yet. Leaving those aside for now, let’s ask what the minimum requirements are for a clonal selection system, and if those minimum requirements could be produced step-by-step.
The key to the system is the physical connection of the binding ability of the protein with the genetic information for the protein. Theoretically this could be accomplished by making an antibody where the tail of the Y bound to the DNA that coded for the protein. In real life, however, such a setup wouldn’t work. The protein might be connected to its genetic information, but because the cell is surrounded by a membrane, the antibody would never come in contact with the foreign material, which is floating around outside the cell. A system where both the antibody and its attached gene were exported from the cell would overcome that problem, only to run into a different one: outside the cell there would be no cellular machinery to translate the DNA message into more protein.
Anchoring the antibody in the membrane is a good solution to the problem; now the antibody can mix it up with a foreign cell and still be near its DNA. But although the antibody can bind the foreign material without floating away from the cell, it does not have direct physical contact with the DNA. Since the protein and DNA are blind, there must be a way to get a message from one to the other.
Behe then describes an alternative, theoretical system which is far more simpler in structure and function:
Just for now, for the sake of argument, let’s forget about the tortuous way that the message of binding actually gets to the B-cell nucleus (requiring the taxicab, ingestion, MHC, helper T cells, interleukin, and so on). Instead let’s imagine a simpler system where there’s only one other protein. Let’s say that when the antibody binds to a foreign molecule, something happens that attracts some other protein—a messenger to take word of a hostage to the factory nucleus. Maybe when the hostage is first found, the shape of the antibody changes, perhaps pulling up a little on the antibody’s tail. Perhaps part of the antibody’s tail sticks into the inside of the cell, which is what triggers the messenger protein. The change in the tail could cause the messenger protein to scuttle into the nucleus and bind to the DNA at a particular point. Binding to the right place on the DNA is what causes the cell to start growing and to start producing antibody without the oily tail—antibody that gets sent out of the cell to fight the invasion.
Even in such a simplified scheme, we are left with three critical ingredients: (1) the membrane-bound form of the antibody; (2) the messenger; and (3) the exported form of the antibody. If any of these components is missing, the system fails to function. If there is no antibody in the membrane, then there’s no way to connect a successful antibody that binds a foreign invader to the cell containing the genetic information. If there is no exported form of the antibody, then when the signal is received there is nothing to send out into the world to fight. If there is no messenger protein, then there is no connection between binding the membrane antibody and turning on the right gene (making the system about as useful as a doorbell whose wires had been cut).
A cell hopefully trying to evolve such a system in gradual Darwinian steps would be in a quandary. What should it do first? Secreting a little bit of antibody into the great outdoors is a waste of resources if there’s no way to tell if it’s doing any good. Ditto for making a membrane-bound antibody. And why make a messenger protein first if there is nobody to give it a message, and nobody to receive the message if it did get one? We are led inexorably to the conclusion that even this greatly simplified clonal selection could not have come about in gradual steps.
Even at this simplified level, then, all three ingredients had to evolve simultaneously. Each of these three items—the fixed antibody, the messenger protein, and the loose antibodies—had to be produced by a separate historical event, perhaps by a coordinated series of mutations changing preexisting proteins that were doing other chores into the components of the antibody system. Darwin’s small steps have become a series of wildly unlikely leaps. Yet our analysis overlooked many complexities: How does the cell switch from putting the extra oily piece on the membrane to not putting it on? The message system is fantastically more complicated then our simplified version. Ingestion of the protein, chopping it up, presenting it to the outside on an MHC protein, specific recognition of the MHC/fragment by a helper T cell, secretion of interleukin, binding of interleukin to the B cell, sending the signal that interleukin has bound into the nucleus—the prospect of devising a step-by-step pathway for the origin of the system is enough to make strong men blanch.
A materialist who does not believe in intelligent design may be forgiven for asking, if there is such clear evidence of intelligence in the structure of proteins, their domains, and the signal transduction cascades that mobilize gene expression, white blood cells, etc, then why is the system evidently a lot more complex than it needs to be to get to the same ends?
If the sole purpose of that system was to simply function as it was supposed to, what exactly does the additional complexity contribute?
From a Darwinian perspective, they're not charged with coming up explanation as to how that works, since to them it's all random anyway (their challenge is of course to prove the theoretical rate of mutation and effectiveness of natural selection acting on a population actually match up with what we observe in nature, as is layed out in Genetic Entropy and Evolution 2.0.)
From the perspective of intelligent design, the appearance of extraneous complexity can also be explained by the existence of multiple purposes, as well as the possibility of multiple designers. The more features you build into a household appliance, the more complex it necessarily becomes. Of course, we have an advantage looking at appliances because, as the designers, we can infer the purpose behind certain components and features. But since the designers of life are obviously not human, the kind of purposes behind certain things are not immediately obvious to us, either because of our unfamiliarity, or because we have limited ability to comprehend certain things.
How this works back around to hyperdimensional battles is, they are chiefly through us, and through our biology. If you have two intelligent opponents attempting to outsmart one another, they're going to compete in altering an external "playing field" according to certain constraints in a sort of intelligence arms race to manipulate conditions to their advantage. For two brilliant people facing off, if the game was very simple (like Tic-tac-toe), there would be constant stalemates and both sides would be thwarted in the exercise of their abilities to achieve their ends. So the complexity of the game is expanded (say, by graduating to the game Chess or Go) to allow more effective maneuvering, novel functions, etc. to outsmart the opponent.
If you look at a fresh battlefield or, larger still, an entire war theater, you're going to see some military bases here and there, troops dispatches, logistical lines, etc, but also some crater-filled battlefields, bombed out cities, and mass graves. If a Darwinist saw this picture, they would conclude that all that assembled by random means. If we took the opposite approach and said this scene was a product of intelligence, we would be right. But a product of a single intelligence would be like a country at peace and prosperous like, say, Japan. The warzone would most likely resemble land acted upon by competing intelligences, due to evident existence of zones where competing intelligences faced off and generated entropy in the field (the destroyed parts, but also the areas near enemy lines and no-mans-lands where there is more chaos).
Another hypothesis I had about that was the idea of "military" (intelligence) budgets for each side to focus on and deal with certain challenges in the hyperdimensional warfare. Some battles are perceived as more important than others depending on which side you are on, which is a general feature of asymmetric warfare. And the battle between STO and STS is clearly asymmetric from the perspective of one side being "allowed" to violate free will, while the other cannot, but fares well anyway because it is nourished by the higher densities of the information field (instead of being fed upon by same like the STS).
To go back to the military analogy, STS is like the tyrannical military with no moral or legal scruples in how it conducts warefare, violating human rights constantly, but is also weighted down by parasitic institutions in the military that constantly take battle spoils for themselves (think military-industrial complex). STO is like a noble military which strictly adheres to the principles of defensive combat only, immaculately safeguards the lives of civilians, etc, and which has vastly superior technology. Sort of like the US vs Russia.