(06-23-2009 12:21 PM)UofL07 Wrote:  

(06-23-2009 09:48 AM)DrTorch Wrote:  I realize you had some long posts that I just skimmed, but you give yourself far too much credit. You merely cite a few topics in biology, and expect that to serve as unquestioned "evidence."

So you skim the post without actually reading any of the links and then complain about the evidence? That is not only an illogical argument but it also show that no matter what information I post, you will simply ignore it.

(06-22-2009 10:40 AM)DrTorch Wrote:  Not that the concept of "irreducible complexity" doesn't hold some validity...in fact it is quite compelling, and it's ironic that biologists of all people don't accept it.

Biologist and most scientists don't accept it because it is an argument from ignorance (also know as an appeal to ignorance or negative evidence). Irreducible complexity (IC) is a logical fallacy because its basic premise (biological systems are 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) assumes that evolution must compose these parts to create a working system (one way progression), ignoring the simpler process of subtracting parts from a less efficient system until the irreducibly complex one remains (two way progression).

Michael Behe was the first to propose "irreducible complexity". His basic logical assumption was as follows.

(P1) Direct, gradual evolution proceeds only by stepwise addition of parts.
(P2) By definition, an irreducibly complex system lacking a part is nonfunctional.
© Therefore, all possible direct gradual evolutionary precursors to an irreducibly complex system must be nonfunctional.

The problem with Behe's logical construct is that the first premise is false:evolution is not constrained to adding parts. For instance, evolution can also change or remove parts (pretty simple, eh?). In contrast, Behe's irreducible complexity is restricted to only reversing the addition of parts. This is why irreducible complexity cannot tell us anything useful about how a structure did or did not evolve.

Let's use an example from nature to show why IC is a simple concept.

Pentachlorophenol (PCP) is a highly toxic chemical, not known to occur naturally, that has been used as a wood preservative since the 1930's. It is now recognized as a dangerous pollutant that we need to dispose of. But how?

Evolution to the rescue! A few soil bacteria have already worked out a way to break it down and even eat it. And conveniently for us, they do it in an irreducibly complex way. The best known of these bacteria is called Sphingomonas chlorophenolica (also called Sphingobium chlorophenolicum).

The PCP molecule is a six carbon ring with five chlorine atoms and one hydroxyl (OH) group attached. The chlorines and the ring structure are both problems for bacteria. S. chlorophenolica uses three enzymes in succession to break it down, as follows: the first one replaces one chlorine with OH. The resulting compound is toxic, but not quite as bad as PCP itself. The second enzyme is able to act on this compound to replace two chlorines, one after the other, with hydrogen atoms. The resulting compound, while still bad, is much easier to deal with, and the third enzyme is able to break the ring open. At this point, what is left of PCP is well on its way to being food for the bacterium.

All three enzymes are required, so we have IC. How could this IC system have evolved? First of all, bacteria of this type could already metabolize some milder chlorophenols which occur naturally in small amounts. In fact the first and third enzymes were used for this. As a result the cell is triggered to produce them in the presence of chlorophenols. The second enzyme (called PcpC) is the most interesting one; the cell produces it in sufficient quantity to be effective all the time instead of just when it is needed in its normal metabolic role. Thanks to this unusual situation PcpC is available when it is needed to help eat PCP.

The inefficient regulation of PcpC is evidently the key to the whole process. So far as biologists can tell, a recent mutation that changed the deployment of this enzyme is what made PCP degradation possible for this bacterium. It also happens that both PcpC and the first enzyme in the process are now slightly optimized for dealing with PCP; they handle it better than the corresponding enzymes in strains of S. chlorophenolica that use PcpC only in its normal role, but not nearly as well as would be expected for an old, well adapted system. These factors, combined with the fact that PCP is not known to occur naturally, make a strong circumstantial case that this system has evolved very recently.

The chemistry and probable evolution of this system are explained in much greater detail in Shelly Copley's article "Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach" in Trends in Biochemical Sciences. I've provided the citation below.

Copley SD. (2000). Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends in Biochemical Sciences, 25(6):261-265.

There are two things to remember about IC; particularly when it is used to support the argument for Intelligent Design.

1) Irreducible complexity is claimed to indicate (but does not) that certain systems could not have evolved gradually. However, jumping from there to the conclusion that those systems were designed is an argument from incredulity (an assertion that because one personally finds a premise unlikely or unbelievable that another preferred but unproven/unscientific premise is automatically true). There is nothing about irreducibly complex systems that is positive evidence for design.

2) Irreducible complexity actually suggests a lack of design. For critical applications, such as keeping an organism alive, you do not want systems that will fail if any one part fails (i.e. think of a Rube Golderg experiment) You want systems that are robust.