Monday we published a paper in the journal BIO-Complexity that demonstrates that enzymes can't evolve genuinely new functions by unguided means. We argue that design by a very sophisticated intelligent agent is the best explanation for their origin. I want to take some time to lay out our argument against evolution and for intelligent design. It's important, because it reveals the logical fallacy in most evolutionary thinking.

Just to give an example of the evolutionary thinking of ID critics, here is a quote from one of the references in our paper (Kherhonsky et al (2006) "Enzyme promiscuity: Evolutionary and mechanistic aspects." Current Opinion in Chemical Biology 10:498-508).
An oft-forgotten essence of Darwinian processes is that they occur gradually, while maintaining organism fitness throughout. Consequently, a reasonable assumption is that, ever since the emergence of the primordial living forms, very little novelty has evolved at the molecular level. Rather, existing genes were modified, or 'tinkered with', to generate new protein structures and functions that are related to those of their ancestors. Unlike 'out of the blue' scenarios advocated by the 'intelligent design' school, 'tinkering' scenarios depend on the availability of evolutionary starting points. The hypothesis that the broad specificity, or promiscuous functions, of existing enzymes provide these starting points was first formalized by Jensen in a review that has inspired many. Jensen proposed that, in contrast to modern enzymes, primitive enzymes possessed very broad specificities. This catalytic versatility enabled fewer enzymes to perform the multitude of functions that was necessary to maintain ancestral organisms. Duplication of genes and divergence led to specialized genes and increased metabolic efficiency. Since Jensen, the structures of >30,000 proteins, and the sequences of hundreds of thousands, have taught us that these processes led to the creation of enzyme families and superfamilies. The vestiges of these divergence processes are the scaffold and active site architecture shared by all family members.
To summarize, the key points of that evolutionary argument are:
  1. Evolution is true. That is, enzymes have evolved new functions by a process of random mutation and natural selection.
  2. Modern enzymes can't evolve genuinely new functions by random mutation and natural selection but can only tinker with existing functions.
  3. Therefore, ancient enzymes must have been different, capable of carrying out a broad range of enzyme activities.
  4. Those enzymes underwent duplication and diverged from one another, becoming specialized.
  5. How do we know this happened? Because we now see a broad array of specialized enzymes. Evolution is the explanation.
This begs the question of whether evolution is true. It is a circular argument unsubstantiated by the evidence and unfalsifiable. No one can know what ancient enzymes actually looked like, and whether they really had such broad catalytic specificities.

In contrast, our argument is as follows:
  1. Is evolution true? Test case: do enzymes evolve by a process of natural selection and random mutation?
  2. Modern enzymes are the only thing we can test.
  3. No one knows if ancient enzymes were different. They are lost in the deep past, so claims with regard to their promiscuity or ability to evolve are hypothetical and unfalsifiable.
  4. Modern enzymes can't evolve new functions, based on our own experiments.
  5. We haven't tested the universe of modern enzymes, so our result is qualified, but the nine most similar enzymes did not change function.
  6. Our estimate for the likely waiting time for an enzyme to evolve a new function is at least 10^15 years.
  7. Therefore evolution of enzymes is likely to be impossible.
  8. Given the sophistication of enzymes and the way they work together, intelligent design is the best explanation for the origin and current diversity of modern enzymes.
You can read the argument in more detail in our paper.

Notice both arguments agree that modern enzymes can't evolve genuinely new functions. The difference is in the conclusion reached. The evolutionary argument assumes what it concludes - it's a snake swallowing its tail, and goes nowhere.

In contrast, our argument relies on the uniformitarian principle that underlies all science. What is true for modern enzymes was true for ancient ones as well.

From Wikipedia:
"Uniformitarianism is the assumption that the same natural laws and processes that operate in the universe now have always operated in the universe in the past and apply everywhere in the universe. It has included the gradualistic concept that "the present is the key to the past" and is functioning at the same rates. Uniformitarianism has been a key principle of geology and virtually all fields of science."
Gradualism has since been discarded in geology and paleontology, and it is not part of our argument. But the part about processes having always operated in the same way does apply: the evolutionary mechanism has always functioned in the same way, with the same limits, and enzymes have always functioned in the same way, with specific, not promiscuous, catalytic activities.

Now here's the point: anyone who wants to make a special case for the non-uniformitarian origin of enzymes (or animal groups) has created a special category to protect the idea that evolution is true. That idea is apparently untouchable. Any hypothesis about the deep past is accepted if it allows an evolutionary explanation for current diversity, and avoids problems with difficult facts. As a consequence, papers on the origin of life, protein evolution, the origin of animal form, and human origins are full of speculation masked as supporting argument, or even as statements of fact. But the problem remains. If you start with the assumption that evolution is true, and view all evidence through those glasses, you won't even notice that your argument chases its tail.