I want to address one particular point in that article.
For decades enzymologists have recognized that certain enzymes are catalytically perfect—meaning that they process reactant molecules as rapidly as these molecules can reach them by diffusion.  That hinted at a principle of physical perfection in biology, but no one anticipated its breadth until recently.The point of the article is that some things in biology are "perfect" but this presents a problem for "Darwinism." According to the "scientists" at the Biologic Institute. perfection is beyond the reach of a "Darwinian mechanism." The fact that we observe perfection in biology is evidence for design.
ERV picked up on this theme in a 2009 posting: Having your Ford Pinto and Crashing it Too. That posting seemed to concede the point that enzymes are perfect.
That's the issue I want to discuss.
There's no such thing as a perfect enzyme. It's true that there are enzymes whose rate is so fast that it is only limited by the rate of diffusion of substrates into the active site. The diffusion-controlled rate is about 108 or 109 M-1 s-1. Several enzymes have second order rate constants (kcat/Km) that are close to this maximum rate.
Many textbooks claim that these enzymes have attained "catalytic perfection." For example, here's what Voet & Voet (4th edition) say (page 490) ...
Some Enzymes Have Attained Catalytic Perfection
Thus, enzymes with such values of kcat/Km must catalyze a reaction every time they encounter a substrate molecule. ... several enzymes ... have achieved this state of virtual catalytic perfection.
The "Perfect" Enzyme?There are also many enzymes that occasionally catalyze incorrect reactions. For example, several amino acid synthetases have appreciable rates of incorrectly attaching the wrong amino acid to a given tRNA molecule. The error rate of the DNA replication complex is well known, it's responsible for most mutations. I suspect there are very few enzymes that are so specific that they never make mistakes.
Much of our understanding of the mechanism of triose phosphate isomerase (TPI) comes from the lab of Jeremy Knowles at Harvard University (Cambridge, MA, USA). He points out that the enzyme has achieved catalytic perfection because the overall rate of the reaction is limited only by the rate of diffusion of substrate into the active site. TPI can’t work any faster than this!
This has led many people to declare that TPI is the “perfect enzyme” because it has evolved to be so efficient. However, as Knowles and his coworkers have explained, the “perfect enzyme” isn’t necessarily one that has evolved the maximum reaction rate. Most enzymes are not under selective pressure to increase their rate of reaction because they are part of a metabolic pathway that meets the cell’s needs at less than optimal rates.
Even if it would be beneficial to increase the overall flux in a pathway (i.e., produce more of the end product per second), an individual enzyme need only keep up with the slowest enzyme in the pathway in order to achieve “perfection.” The slowest enzyme might be catalyzing a very complicated reaction and might be very efficient. In this case, there will be no selective pressure on the other enzymes to evolve faster mechanisms and they are all “perfect enzymes.”
In all species, triose phosphate isomerase is part of the gluconeogenesis pathway leading to the synthesis of glucose. In most species, it also plays a role in the reverse pathway where glucose is degraded (glycolysis). The enzyme is very ancient, and all versions—bacterial and eukaryotic—have achieved catalytic perfection. The two enzymes on either side of the reaction pathway, aldolase and glyceraldehyde 3-phosphate dehydrogenase (Section 11.2), are much slower. Thus, it is by no means obvious why TPI works as fast as it does.
The important point to keep in mind is that the vast majority of enzymes have not evolved catalytic perfection because their in vivo rates are “perfectly” adequate for the needs of the cell.
I think we should stop talking about "perfect" enzymes. Not only does it encourage the Intelligent Design Creationists, it's also scientifically misleading if you want students to understand biochemistry from an evolutionary perspective.
[See also: Fixing Carbon: Building a Better Rubisco and Finding the "perfect" enzyme]