Theory of Intelligent Design, the best explanation of Origins

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Theory of Intelligent Design, the best explanation of Origins » Intelligent Design » Irreducible complexity » the best of Behes book Darwins Black box

the best of Behes book Darwins Black box

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1 the best of Behes book Darwins Black box on Sat Jul 25, 2015 8:43 am

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The best of Behe's book :  Darwins Black box

Darwins Black Box page 40:

http://reasonandscience.heavenforum.org/t2115-the-best-of-darwins-black-box#3760

So let us attempt to evolve a bicycle into a motorcycle by the gradual accumulation of mutations. Suppose that a factory produced bicycles, but that occasionally there was a mistake in manufacture. Let us further suppose that if the mistake led to an improvement in the bicycle, then the friends and neighbors of the lucky buyer would demand similar bikes, and the factory would retool to make the mutation a permanent feature. So, like biological mutations, successful mechanical mutations would reproduce and spread. If we are to keep our analogy relevant to biology, however, each change can only be a slight modification, duplication, or rearrangement of a preexisting component, and the change must improve the function of the bicycle. So if the factory mistakenly increased the size of a nut or decreased the diameter of a bolt, or added an extra wheel onto the front axle or left off the rear tire, or put a pedal on the handlebars or added extra spokes, and if any of these slight changes improved the bike ride, then the improvement would immediately be noticed by the buying public and the mutated bikes would, in true Darwinian fashion, dominate the market. Given these conditions, can we evolve a bicycle into a motorcycle? We can move in the right direction by making the seat more comfortable in small steps, the wheels bigger, and even (assuming our customers prefer the «biker» look) imitating the overall shape in various ways. But a motorcycle depends on a source of fuel, and a bicycle has nothing that can be slightly modified to become a gasoline tank. And what part of the bicycle could be duplicated to begin building a motor? Even if a lucky accident brought a lawnmower engine from a neighboring factory into the bicycle factory, the motor would have to be mounted on the bike and be connected in the right way to the drive chain. How could this be done step-by-step from bicycle parts? A factory that made bicycles simply could not produce a motorcycle by natural selection acting on variation—by «numerous, successive, slight modifications»—and in fact there is no example in history of a complex change in a product occurring in this manner.
So far we have examined the question of irreducible complexity as a challenge to step-by-step evolution. But there is another difficulty for Darwin.  If the base were made out of paper, for example, the trap would fall apart. If the hammer were too heavy, it would break the spring. If the spring were too loose, it would not move the hammer. If the holding bar were too short, it would not reach the catch. If the catch were too large, it would not release at the proper time. A simple list of components of a mousetrap is necessary, but not sufficient, to make a functioning mousetrap.

In order to be a candidate for natural selection a system must have minimal function: the ability to accomplish a task in physically realistic circumstances. A mousetrap made of unsuitable materials would not meet the criterion of minimal function, but even complex machines that do what they are supposed to do may not be of much use. To illustrate, suppose that the world's first outboard motor had been designed and was being marketed. The motor functioned smoothly— burning gasoline at a controlled rate, transmitting the force along an axle, and turning the propeller—but the propeller rotated at only one revolution per hour. This is an impressive technological feat; after all, burning gasoline in a can next to a propeller doesn't turn it at all. Nonetheless, few people would purchase such a machine, because it fails to perform at a level suitable for its purpose.

Performance can be unsuitable for either of two reasons. The first reason is that the machine does not get the job done. A couple fishing in the middle of a lake in a boat with a slow-tuming propeller would not get to the dock: random currents of the water and wind would knock their boat off course. The second reason that performance might be unsuitable is if it is less efficient than can be achieved with simpler means. No one would use an inefficient, outboard motor if they could do just as well or better with a sail.

The «simplest» self-sufficient, replicating cell has the capacity to produce thousands of different proteins and other molecules, at different times and under variable conditions. Synthesis, degradation, energy generation, replication, maintenance of cell architecture, mobility, regulation, repair, communication—all of these functions take place in virtually every cell, and each function itself requires the interaction of numerous parts. Because each cell is such an interwoven meshwork of systems, we would be repeating the mistake of Francis Hitching by asking if multicellular structures could have evolved in step-by-step Darwinian fashion. That would be like asking not whether a bicycle could evolve into a motorcycle, but whether a bicycle factory could evolve into a motorcycle factory! Evolution does not take place on the factory level; it takes place on the nut-and-bolt level.
The arguments of Dawkins and Hitching fail because they never discuss what is contained in the systems over which they are arguing. Not only is the eye exceedingly complex, but the «light-sensitive spot» with which Dawkins begins his case is itself a multicelled organ, each of whose cells makes the complexity of a motorcycle or television set NUTS AND BOLTS

Mechanical objects can't reproduce and mutate like biological systems, but hypothesizing comparable events at an imaginary factory shows that mutation and reproduction are not the main barriers to evolution of mechanical objects. It is the requirements of the structure-function relationship itself that block Darwinian-style evolution.

if it is the job of one protein to bind specifically to a second protein, then their two shapes must fit each other like a hand in a glove. If there is a positively charged amino acid on the first protein, then the second protein better have a negatively charged amino acid; otherwise, the two will not stick together. If it is the job of a protein to catalyze a chemical reaction, then the shape of the enzyme generally matches the shape of the chemical that is its target. When it binds, the enzyme has amino acids precisely positioned to cause a chemical reaction. If the shape of a wrench or a jigsaw is significantly warped, then the tool doesn't work.

The parts of an animal cell.

FROM HERE TO THERE

mitochondrion can be thought of as containing four separate sections: the space inside of the inner membrane, the inner membrane itself, the space between the inner and the outer membranes, and the outer membrane itself. Counting membranes and interior spaces, there are more than twenty different sections in a cell. The cell is a dynamic system; it continually manufactures new structures and gets rid of old material. Since the compartments of a cell are closed off, each area faces the problem of obtaining new materials.
There are two ways that it could solve the problem. First, each compartment might make all of its own supplies, like so many self-sufficient villages. Second, new materials could be centrally made and then shipped to other compartments, like a large city making blue jeans and radios to be sent to small towns. Or there might be a mixture of these two possibilities. In cells, although some compartments make some materials for themselves, the great majority of proteins are centrally made and shipped to other compartments. The shipping of proteins between compartments is a fascinating and intricate process. The details can differ depending on the destination of the protein, just as shipping details can differ depending on whether a package is headed across town or across the ocean.

In this chapter I will concentrate on the mechanisms a cell uses to get a protein to the cell's garbage disposal, the lysosome. You will see that the cell must deal with the same problems that the Centers for Disease Control encounters in shipping a vital package.

LOST IN SPACE

A new protein, freshly made in the cell, encounters many molecular machines. Some of the machines grab hold of the protein and send it along to the location it is destined to reach. In a little while I will follow a protein along one pathway from start to finish. Protein machines all have rather exotic names, however, and it is difficult for many people to picture these things in their minds if they are not used to thinking about them. So I will first use an analogy, which will take the next several pages.

The time is far in the future. Humanity has tried to explore space firsthand, but between comets, magnetic storms, and marauding  aliens, the dangers were too great. So the job has been given to mechanical space probes that have been shot out into the cosmos to explore the outer edges of our galaxy and beyond. Of course, it takes awhile to get to the edge of the galaxy, and even longer to get beyond, so the space probes have been built to be self-sufficient. They can set down on barren planets and mine for raw materials; they can manufacture brand new machines from ore; and they can capture the energy in starlight and use it to charge their batteries. The space probe is a machine, so it has to accomplish all of its tasks by painfully detailed mechanisms, not magic. One task is to
recycle old batteries; batteries go bad after awhile, so the probe makes new ones. The new batteries are made by grinding up old batteries, recovering the old components, melting them down, recasting the casing, and adding fresh chemicals. One of the machines that is used in this process is called the «battery crusher.» The space probe is shaped like a huge sphere. Inside the sphere are a number of smaller, self-contained spheres, each of which holds machinery for specialized tasks. In the biggest of the interior spheres—let's call it the «library»—are the blueprints for making all the machines in the space probe. These are not ordinary blueprints, however. They can be thought of as blueprints in braille—or perhaps as sheet music for a player piano— where physical indentations in the blueprint cause a master machine to make the machine for which the blueprint codes. One fine day the space probe senses (by some mechanism we'll ignore) that it needs to make another battery crusher and to send the newly made machine to work in the garbage treatment room, where it will help in recycling old batteries. So the process to do that is set in motion: The blueprint for the battery crusher is photocopied in the library, and the blueprint copy floats over to a window in the library (remember; there's no gravity). On the edge of the blueprint are punch holes arranged in a special pattern, which exactly matches pegs on a scanner mechanism at the window. When the blueprint hooks onto the scanner; the window door opens like the shutter of a camera. The blueprint jiggles loose of the scanner and floats out of the library into the main area of the probe. In the main area are many machines and machine parts; nuts, bolts, and wires float freely about. In this section reside many copies of what are called master machines, whose job it is to make other machines.
They do this by reading the punch holes in a blueprint, grabbing nuts, bolts, and other parts that are floating by, and mechanically assembling the machine piece by piece. The blueprint for the battery crusher, floating in the main area, quickly comes in contact with a master machine. Whirring, turning appendages on the master machine grab some nuts and bolts and start assembling the crusher. Before it assembles the body of the crusher, however, the master machine first makes a temporary «ornament» that marks the crusher as a machine that has to leave the main area.

In the main area is another machine, called a guide. The shape of the guide is exactly complementary to the shape of the ornament, and little magnets on the guide allow it to attach securely. As the guide snuggles up to the ornament it pushes down on the master machine's switch, causing the master machine to halt its construction of the crusher. On the outside of one of the interior spheres (we'll call the sphere «processing room #1») is a receiving site that has a shape complementary to part of the guide and part of the ornament. When the guide, ornament, and attached parts bump into that shaped section, the master machine's switch is flipped back on, causing construction of the crusher to resume. Right next to that shaped section is a window. When the ornament taps on the window (there's a lot of jostling going on), it activates a conveyor belt inside the processing room and the conveyor belt pulls the new battery crusher inside the processing room, leaving the master machine, blueprint, and guide on the outside.

As the crusher was being pulled through the window another machine removed the now-unnecessary ornament. Now, amazingly, construction machines embedded in the flexible walls of processing room #1 cause a section of the wall to close in on and surround some of the machines, forming a new, free-floating subroom. The remainder of the wall that was left behind smoothly seals itself. The subroom now floats a short distance through the main area before bumping into a second processing room. The subroom merges with the wall, and spills its contents into processing room #2. The battery crusher then passes through processing rooms #3 and #4 by mechanisms similar to those that took it from room #1 to room #2. It is in the processing rooms that machines receive the tags that direct them to their final destinations. An antenna is placed on the battery crusher and quickly trimmed down to make a very special configuration; the special shape of the trimmed antenna will tell other mechanisms to direct the crusher to the garbage treatment room. In the wall of the last processing room are machines («haulers») with a shape complementary to that of the trimmed antenna of the battery crusher. The crusher sticks to the haulers, and that area of the wall begins to pinch off to form a subroom. Outside the subroom is another machine (the «delivery coder») with a shape that exactly complements the shape of a machine (the «port marker») sticking out of the garbage treatment room. The sub-room hooks up to the garbage treatment room through the two complementary machines. Another machine (the «gateway») then drifts by. The gateway has a shape that is complementary to a portion of the delivery coder and the port marker. When it sticks to them the gateway punches a small hole in the garbage treatment room, and the transit sphere merges with it, dumping its contents into the disposal. The battery crusher is able to begin its work.

Perhaps by this point in the book, the reader can easily see how the transport system that sent the battery crusher to its destination is irreducibly complex. If any of its numerous components is missing, then the crusher is not delivered to the garbage treatment room. Furthermore, the delicate balance of the system must be maintained; each of the many components that interlock must do so precisely and then disengage, and each must arrive and depart at the proper times. Any single error will cause the system to fail.

The space probe itself is the cell, the library is the nucleus, the blueprint is the DNA, the copy of the blueprint is RNA, the window of the library is the nuclear pore, the master machines are ribosomes, the main area is the cytoplasm, the ornament is the signal  sequence, the battery crusher is a lysosomal hydrolase, the guide is the signal recognition particle (SRP), the receiving site is the SRP receptor, processing room 1 is the endoplasmic reticulum (ER), processing rooms 2 through 4 are the Golgi apparatus, the antenna is a complex carbohydrate, the sub-rooms are coatomer or clathrin-coated vesicles, and various proteins play the roles of the trimmer, hauler, delivery coder, port marker, and gateway. The garbage treatment room is the lysosome. Let's quickly run through a description of how a protein that is synthesized in the cytoplasm eventually finds its way to the lysosome. This will take just one paragraph. Don't worry if you rapidly forget the names and procedures of cellular transport; the purpose is simply to give you a glimpse of the cell's complexity. An RNA copy (called messenger RNA, or just mRNA) is made of the DNA gene coding for a protein that works in the cell's garbage disposal—the lysosome.  The mRNA is made in the nucleus, then floats over to a nuclear pore.

Proteins in the pore recognize a signal on the mRNA, the pore opens, and the mRNA floats into the cytoplasm. In the cytoplasm the cell's «master machines»—ribosomes—begin making  lysosomes using the information in the mRNA. The first part of the growing protein chain contains a signal sequence made of amino acids. As soon as the signal sequence forms, a signal recognition particle (SRP) grabs onto the signal and causes the ribosome to pause. The SRP and associated molecules then float over to an SRP receptor in the membrane of the endoplasmic reticulum (ER) and stick there. This simultaneously causes the ribosome to resume synthesis and a protein channel to open in the membrane. As the protein passes through the channel and into the ER, an enzyme clips off the signal sequence. Once in the ER, the  lysosome has a large, complex carbohydrate placed on it. Coatomer proteins cause a drop of the ER, containing some lysosomes  plus other proteins, to pinch off, cross over to the Golgi apparatus, and fuse with it. Some of the proteins are returned to the ER if they contain the proper signal. This happens two more times as the protein progresses through the several compartments of the Golgi. Within the Golgi an enzyme recognizes the signal patch on garbagease and places another carbohydrate group on it. A second enzyme trims the freshly attached carbohydrate, leaving behind mannose-6-phosphate (M6P). In the final compartment of the Golgi, clathrin proteins gather in a patch and begin to bud. Within the clathrin vesicle is a receptor protein that binds to M6E. The M6P receptor grabs onto the M6P of the  lysosome and pulls it on board before the vesicle buds off. On the outside of the vesicle is a v-SNARE protein that specifically recognizes a t-SNARE on the lysosome. Once docked, NSF and SNAP proteins fuse the vesicle to the lysosome. The  lysosome has now arrived at its destination and can begin the job for which it was made. The fictional space probe is so complicated it hasn't been invented yet, even in a crude way. The authentic cellular system is already in place, and every second of every day, this process happens uncounted billions of time in your body. Science is stranger than fiction.

THE DEMANDS OF THE JOB

Lysosomes travels a distance of about one ten-thousandth of an inch on its journey from the cytoplasm to the lysosome, yet it requires the services of dozens of different proteins to ensure its safe arrival. In our imaginary TV movie, the vaccine traveled perhaps a thousand miles from the Centers for Disease Control to the big city where it was needed—a trillion times farther than  lysosome traveled. But many of the requirements for transporting the vaccine were the same as those for getting the enzyme from the cytoplasm to the lysosome. The demands are imposed by the type of task to be done; they don't depend on the distance traveled, the type of vehicle used, or the materials out of which the signs are made. A current textbook distinguishes three methods that the cell uses to get proteins into compartments.1 The first, where a large gate opens or closes to regulate the passage of proteins through the membrane, is known as gated transport. This is the mechanism that regulates the flow of material such as newly-made mRNA between the nucleus and the cytoplasm (or in space-probe language, the flow of the blueprint out of the library into the main area). The second method is transmembrane transport. This occurs when a single protein is threaded through a protein channel, as when the  lysosome passed from the cytoplasm into the ER. The third way is vesicular transport, where protein cargo is loaded into containers for shipment, as happened for the trip from the Golgi (the final processing room) to the lysosome (the garbage treatment room). For our purposes the first two methods can be considered to be the same: they both use portals in a membrane that selectively allow proteins through. In the case of gated transport the portal is quite large, and proteins can pass through in their folded form. In the case of transmembrane transport the portal is smaller, and proteins must be threaded through. But in principle there is no roadblock to expanding or contracting the size of a portal, so these are equivalent. Therefore I will call both of these gated transport. What are the bare, essential requirements for gated transport? Imagine a parking garage that is reserved for persons with diplomatic license plates. In place of a human attendant the garage has a scanner that reads a barcode on the license plate, and if the barcode is correct the garage door opens. A car with diplomatic plates drives up, the scanner scans the barcode, the door opens, and the car drives in. It doesn't matter if the car drove ten feet to the garage or ten thousand miles, or whether the vehicle is a truck, jeep, or motorcycle; if the barcode is there, it can pass through. Thus three basic components are required for gated transport at the garage: an identification tag; a scanner; and a gate that is activated by the scanner. If any of these things are missing, then either the vehicle does not get in or the garage is no longer a reserved area. Because gated transport requires a minimum of three separate components to function, it is irreducibly complex. And for this reason the putative gradual, Darwinian evolution of gated transport in the cell faces massive problems. If proteins contained no signal for transport, they would not be recognized. If there were no receptor to recognize a signal or no channel to pass through, again transport would not take  place. And if the channel were open for all proteins, then the enclosed compartment would not be any different from the rest of the cell.

Vesicular transport is even more complicated than gated transport. Suppose now that, instead of the diplomats' cars entering the garage one at a time, all diplomats had to
drive their cars into the back of a large tractor-trailer truck, the truck would drive into the special garage, and the cars would drive off the truck and park. Now we need a way for the truck to recognize the proper cars, a way for the garage to recognize the truck, and a way for the cars to get out of the truck inside the garage. Such a scenario requires six separate components:
(1) an identification tag on the cars; 
(2) a truck that can carry the cars; 
(3) a scanner on the truck; 
(4) an identification tag on the truck; 
(5) a scanner on the garage; 
(6) an activatable garage gate.
 In the cell's vesicular transport system these components correspond to
mannose-6-phosphate
clathrin vesicle 
M6P receptor in the clathrin vesicle
v-SNARE
t-SNARE 
SNAP/NSF proteins.
In the absence of any of these functions, either vesicular transport cannot take place or the integrity of the destination compartment is compromised.
 Because vesicular transport requires several more componens than gated transport, it cannot develop gradually from gated transport. For example, if we had barcode stickers on the diplomats' cars, placing cars inside a truck (a vesicle to transport them) would hide the stickers, and they would fail to enter the garage. Or suppose instead that the truck had the same label that the cars had, so it could enter the garage. But we would still be missing a mechanism to get the cars on the truck, so the truck would be of no use. If some cars randomly entered the truck then, again, nondiplomats' cars would enter the garage. Returning to the world of the cell,
if a vesicle just «happened» to form there would be no mechanism for identifying the proteins that should enter it, and no way to specify its destination. Placing proteins containing address labels into an unlabeled vesicle would make the labels unavailable, and therefore would be detrimental to the organism that had a happily functioning gated transport system. Gated transport and vesicular transport are two separate mechanisms; neither helps in understanding the other.The brief sketch of the requirements for gated and vesicular transport in this chapter did not take into account many complexities of the systems. But since these only make the system more intricate, they cannot ameliorate the irreducible complexity of targeted transport.


“To a person that doesn’t feel obliged to restrict his search to unintelligent causes, the straightforward conclusion is that many of these systems were designed. They were designed not by the laws of nature, not by chance and necessity; rather, they were planned. The designer knew what the systems would look like when they were completed, then took steps to bring the systems about. Life on earth at its most fundamental level, in its most critical components, is the product of intelligent activity” (Behe, 1996, p. 193).

Gibson (1993) also concludes that it is credible to believe in special creation by an intelligent Creator. He does not mean to imply that every aspect of biblical creationism is supported by science because there are some aspects of nature that remain unexplained. However, there is no alternative theory that explains all the data.

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