Monday, March 06, 2006
Behe's Box and Huxley's Horse Part Two
Albert Einstein said time and time again, "God does not play dice" in reference to the Universe and the sciences. Some like to believe that he was perhaps a believer, but good biographies say otherwise. He was not willing to believe in a personal God, but rather a God who could be found in the design of all things.
Dr. Thomas Torrance writes in Einstein and God: "Einstein regularly read the Bible, Old and New Testaments alike (which he continued to do throughout his life). He was taught the rudiments of Hebrew, but never mastered it, and he avoided the course for the traditional Bar-Mitzwa. He revelled in mathematics and music, especially in playing the violin, but recoiled from rigid orthodox rites such as those regarding kosher food, 3 compulsory rules, and Talmudic ways of thought. He began to develop a distrust of all authority, including biblical and religious authority. He had an unusually independent attitude of mind, critical but not sceptical, which was accentuated by his resentment against the authoritarian discipline of his German schoolmasters. This led him to give up his uncritical religious fervour in order to liberate himself from what he spoke of as "the only personal", but without becoming atheistic or hostile to religion."
Einstein, like many scientists down through the ages, expected to find order at the heart of every system he studied. Scientists have used logic in their scientific methods and have expected to find logic at the end of the roads they travel.
"This saying, now engraved above a fireplace of the faculty lounge of the Mathematics Department in Princeton, is the translation of Raffiniert ist der Herr Gott, aber boshaft is Er Nicht. 51 By that Einstein said he meant "Nature hides her secret because of her essential loftiness, but not by means of ruse." 52 It was, like the other sayings, often repeated, not always in the same words. I prefer the stronger form: Raffiniert is der Herr God, aber hinterlistig ist Er nicht, which suggests that while God is subtle he is not wily or artful, he is deep but not devious–he does not deceive us or play tricks with us.
If "God does not wear his heart on his sleeve" is meant to express the idea that the secrets of nature cannot be read off its phenomenal surface, "God is deep but not devious" expresses the complexity and subtlety yet ultimate simplicity and reliability of the universe. That is to say, the immanent order hidden behind the intricate and often baffling complex of connections which we find in the universe is essentially trustworthy, for in spite of all that might appear to the contrary when we come up against sets of events for which there seems to be no rational explanation, the universe is not arbitrary or evil, but unitary and trustworthy in its intelligibility." - Einstein and God By Thomas Torrance
Einstein did not believe in a personal God, but he did believe in design. He trusted in a natural and logical order to the Universe and that trust helped him advance the cause of science.
Darwinists are scientists of a different nature. Darwinists fly in the face of several scientific principles. They gnash their teeth when we say that Macroevolution does not make sense in the light of the second law of Thermodynamics, even though it is true. They also don't like the fact that, unlike most of science, Darwinism expects that the statistical laws of probability are not bent, not just broken, but completely ignored when considering the idea that millions of different varieties of living creatures made up of millions and billions of components have all developed without plan or design by chance, helped by the operation of natural selection. Much whistling in the dark past the grave of their logic ensues while they try to explain away complexity issues.
Consider the book by Lehigh Professor of Biochemistry Michael J. Behe, “Darwin’s Black Box.” In the book, he explains the concept of “Irreducible Complexity”:
"By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.”
Behe uses a simple mousetrap as an example of an IC system, merely to explain what he means by IC. I have since seen scientists go to great lengths to try to prove that a mousetrap is NOT irreducibly complex! But Behe simply wanted the term understood, and when he also used an example of a Rube Goldberg contraption it certainly made the point.
“Darwin’s Black Box” looks at five systems as examples of IC systems, where a gradual evolution to the current system would not happen, since anything taken from one of these systems would not allow it to function and therefore would not be naturally selected. All five of the systems are immensely complex. To give you an idea, the flagellum of a bacteria:
Bacterial Motility “Flagella consist of a hollow, rigid cylinder composed of a protein called flagellin, which forms a filament anchored to the cell by a curved structure called the hook, which is attached to the basal body. Flagellae are, in effect, rotary motors comprising a number of proteinaceous rings embedded in the cell wall. These molecular motors are powered by the phosporylation cascade responsible for generating energy within the cell. In action, the filament rotates at speeds from 200 to more than 1,000 revolutions per second, driving the rotation of the flagellum. The organization of these structures is quite different from that of eukaryotic flagella. The direction of rotation determines the movement of the cell. Anticlockwise rotation of monotrichious polar flagella thrusts the cell forward with the flagellum trailing behind. Peritrichous cells operate in the same way.” - (University of Leicester course notes on Bacterial Motility.)
” …some scientists have called the bacterial flagella the most efficient machine in the universe with its:1) self assembly and repair; 2) water-cooled rotary engine; 3) proton motive force drive system; 4) forward and reverse gears; 5) operating speeds of 6,000 to 17,000 rpm; 6) direction reversing capability within 1/4 of a turn; and7) it's hard-wired signal transduction system with short-term memory." (Access Research Network).
"The human body contains a large number of bacteria, most of them performing tasks that are useful or even essential to human survival. Those that are expected to be present, and that under normal circumstances do not cause disease, are termed normal flora.
Overall, there are about ten times as many bacteria as human cells in the body, 1 quadrillion (10 to the 15th) versus 100 trillion (10 to the 14th), with bacterial cells being much smaller than human cells. Though normal flora are found on all surfaces exposed to the environment (on the skin and eyes, in the mouth, nose, small intestine, and colon), the vast majority of bacteria live in the large intestine. It is estimated that 500-1000 different species of bacteria live in a human.
Bacteria that move do so in one of four ways. Most bacteria that move can only wander randomly though the media they occupy by twitching. Others can control their buoyancy. Some of these have tiny gas-bags (vacuoles) which can inflate to let the bacterium sink or float.Other species have flagella, which beat like whips to drive the bacterium along. Flagella may be arrayed around the cell of the bacteria and these can move in unison, so send the bacteria in a particular direction. Other, called spirochetes, can move in a corkscrew-like motion associated with their shape. They have spiral flagella wrapped around themselves and this modifies their shape so they can adopt the twisting motion. Many members of the latter three groups can move in a particular direction, according to stimuli they receive. This movement is called taxis." (answers.com)
FLAGELLA-Some bacteria swim in viscous liquid environments by using helical propellers called flagella. Such bacteria boast a marvelous swimming device, the flagellum, which has no counterpart in more complex cells. In 1973 it was discovered that some bacteria swim by rotating their flagella. So the bacterial flagellum acts as a rotary propellor -- in contrast to the cilium, which acts more like an oar.
CILIA-Cilia are hairlike organelles on the surfaces of many animal and lower plant cells that serve to move fluid over the cell's surface or to "row" single cells through a fluid. In humans, epithelial cells lining the respiratory tract each have about 200 cilia that beat in synchrony to sweep mucus towards the throat for elimination. A cilium consists of a membrane-coated bundle of fibers called an axoneme. An axoneme contains a ring of 9 double microtubules surrounding two central single microtubules. Each outer doublet consists of a ring of 13 filaments (subfiber A) fused to an assembly of 10 filaments (subfiber B). The filaments of the microtubules are composed of two proteins called alpha and beta tubulin. The 11 microtubules forming an axoneme are held together by three types of connectors: subfibers A are joined to the central microtubules by radial spokes; adjacent outer doublets are joined by linkers that consist of a highly elastic protein called nexin; and the central microtubules are joined by a connecting bridge. Finally, every subfiber A bears two arms, an inner arm and an outer arm, both containing the protein dynein.
Now, let us sit back, review the workings of the cilium, and consider what it implies. Cilia are composed of at least a half dozen proteins: alpha-tubulin, beta-tubulin, dynein, nexin, spoke protein, and a central bridge protein. These combine to perform one task, ciliary motion, and all of these proteins must be present for the cilium to function. If the tubulins are absent, then there are no filaments to slide; if the dynein is missing, then the cilium remains rigid and motionless; if nexin or the other connecting proteins are missing, then the axoneme falls apart when the filaments slide.
What we see in the cilium, then, is not just profound complexity, but also irreducible complexity on the molecular scale. Recall that by "irreducible complexity" we mean an apparatus that requires several distinct components for the whole to work. The mousetrap must have a base, hammer, spring, catch, and holding bar, all working together, in order to function. Similarly, the cilium, as it is constituted, must have the sliding filaments, connecting proteins, and motor proteins for function to occur. In the absence of any one of those components, the apparatus is useless.
The structure of a flagellum is quite different from that of a cilium. The flagellum is a long, hairlike filament embedded in the cell membrane. The external filament consists of a single type of protein, called "flagellin." The flagellin filament is the paddle surface that contacts the the liquid during swimming. At the end of the flagellin filament near the surface of the cell, there is a bulge in the thickness of the flagellum. It is here that the filament attaches to the rotor drive. The attachment material is comprised of something called "hook protein." The filament of a bacterial flagellum, unlike a cilium, contains no motor protein; if it is broken off, the filament just floats stiffly in the water. Therefore the motor that rotates the filament-propellor must be located somewhere else. Experiments have demonstrated that it is located at the base of the flagellum, where electron microscopy shows several ring structures occur. The rotary nature of the flagellum has clear, unavoidable consequences ...for evolutionary scientists.
The bacterial flagellum is a nanomachine made of about 30 different proteins, each of them in multiple copies ranging from a few to tens of thousands. (All but one of the proteins are unique to the motor and are not found in any other living system. From whence, then were these protein parts co-opted?) It is constructed by self-assembly of these large numbers of proteins, each into a different part that exerts a different function, such as a rotary motor, bushing, drive shaft, rotation-switch regulator, universal joint, helical propeller, and rotary promoter for self-assembly.
Flagellar proteins are synthesized within the cell body and transported through a long, narrow central channel in the flagellum to its distal (outer) end, where they self-assemble to construct complex nano-scale structures efficiently, with the help of the flagellar cap as the assembly promoter. The rotary motor, with a diameter of only 30 to 40 nm, drives the rotation of the flagellum at around 300 Hz, at a power level of 10-16 W with energy conversion efficiency close to 100 %.
The structural designs and functional mechanisms to be revealed in the complex machinery of the bacterial flagellum could provide many novel technologies that would become a basis for future nanotechnology, from which we should be able to find many uses. Yes, modern engineers are studying the DESIGN of these motors to apply the technology to today’s solutions!
MICROTUBULES IN FLAGELLA AND CILIUM - Cilia are short and numerous. They provide force parallel to the plasma membrane, like oars on a canoe. Flagella are long and few in number and provide force perpendicular to the plasma membrane. Both cilia and flagella are extensions of the plasma membrane. They contain a ring of nine fused pairs, microtubules, with an unfused pair of microtubules in the center of the ring.This pattern is produced by a centriole located just beneath the plasma membrane. Two members of each triplet on the centriole give rise to the pairs of microtubules in the cilium or flagellium.
Experiments have indicated that ciliary motion results from the chemically-powered "walking" of the dynein arms on one microtubule up the neighboring subfiber B of a second microtubule so that the two microtubules slide past each other. However, the protein cross-links between microtubules in an intact cilium prevent neighboring microtubules from sliding past each other by more than a short distance. These cross-links, therefore, convert the dynein-induced sliding motion to a bending motion of the entire axoneme.
What does irreducible complexity have to do with Darwinian evolution? Evolution by mutation and natural selection must proceed by one slight, functional improvement at a time. So how can it build an irreducibly complex propeller motor one step at a time if the motor can't propel at all until all of its parts are in place? It can't. Something else built it.
Even if all the protein parts were somehow available to make a flagellar motor during the evolution of life, the parts would need to be assembled in the correct temporal sequence similar to the way an automobile is assembled in factory. Yet, to choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions. Arguably, this system is itself irreducibly complex. In any case, the co-option argument tacitly presupposes the need for the very thing it seeks to explain: a functionally interdependent system of proteins.
In summary, as biochemists have begun to examine apparently simple structures like cilia and flagella, they have discovered staggering complexity, with dozens or even hundreds of precisely tailored parts. It is very likely that many of the parts we have not considered here are required for any cilium to function in a cell. As the number of required parts increases, the difficulty of gradually putting the system together skyrockets, and the likelihood of indirect scenarios plummets. Darwin looks more and more forlorn. New research on the roles of the auxiliary proteins cannot simplify the irreducibly complex system. The intransigence of the problem cannot be alleviated; it will only get worse. Darwinian theory has given no explanation for the cilium or flagellum. The overwhelming complexity of the swimming systems push us to think it may never give an explanation.
It was a shock to people of the nineteenth century when they discovered, from observations science had made, that many features of the biological world could be ascribed to the elegant principle of natural selection. It is a shock to us in the twentieth century to discover, from observations science has made, that the fundamental mechanisms of life cannot be ascribed to natural selection, and therefore were designed. But we must deal with our shock as best we can and go on. The theory of undirected evolution should already be dead.
Other examples of irreducible complexity abound, including aspects of protein transport, blood clotting, closed circular DNA, electron transport, telomeres, photosynthesis, transcription regulation, and much more. Examples of irreducible complexity can be found on virtually every page of a biochemistry textbook.
CONCLUSION: It is important to realize that we are not inferring design from what we do not know, but from what we do know. We are not inferring design to account for a black box, but to account for an open box. A man from a primitive culture who sees an automobile might guess that it was powered by the wind or by an antelope hidden under the car, but when he opens up the hood and sees the engine he immediately realizes that it was designed. In the same way biochemistry has opened up the cell to examine what makes it run and we see that it, too, was designed.
Credit for most of the last several paragraphs from Darwin's Black Box by Michael Behe.