Enzyme Convergence Taxes Evolutionary Paradigm

Enzyme Convergence Taxes Evolutionary Paradigm

No one likes to pay taxes. Though necessary for our government to operate, they still represent an unpleasant financial burden.

Similarly, widespread convergence observed in the biological and biochemical realms burdens evolutionary biologists. And new work by scientists from the University of California, San Francisco (UCSF), further taxes the evolutionary paradigm.1

From an evolutionary perspective, convergence describes scenarios in which it appears that natural processes generated identical (or nearly identical) anatomical, physiological, or behavioral traits in unrelated organisms (e.g., echolocation in dolphins and bats). Convergence can even occur in the molecular realm, manifesting as the independent, repeated origin of biomolecules and biochemical systems.

As I discussed in The Cell’s Design and in this article on plant convergence, quite a few scientists do not expect convergence to be commonplace because evolutionary processes are historically contingent. Evolutionary biologist Richard Lenski recently confirmed this expectation through the Long-term Evolution Experiment (LTEE) conducted in his lab at Michigan State University. Lenski and his team have directly observed historical contingency at work in populations of the bacterium E. coil. (For more on the LTEE, see previous articles on bacteria evolution and the LTEE research.)

In spite of the historically contingent nature of the evolutionary process, convergence appears to be widespread at the organismal and biochemical levels. And as the scientists from UCSF describe in a recent paper, biochemical convergence is even more extensive than anyone thought.

Evolutionary biologists recognize five different types of biochemical convergence.2

  1. Functional convergence describes the independent origin on more than one occasion of biochemical functionality.
  2. Mechanistic convergence refers to the multiple independent emergences of biochemical processes that use the same chemical mechanisms.
  3. Structural convergence results when two or more biomolecules adopt independently the same three-dimensional structure.
  4. Sequence convergence occurs when either proteins or regions of DNA arise separately, yet have identical amino acid or nucleotide sequences, respectively.
  5. Systemic convergence describes the independent emergence of identical biochemical systems.

The UCSF researchers sought to determine the relationship between functional and mechanistic convergence in enzymes. They examined 95 functionally convergent enzyme pairs, focusing specifically on the set of chemical bond changes that take place during the course of enzyme catalysis.

They discovered that, while the functions of the enzymes were the same, the overall reactions mediated by the enzymes were similar in only 44 percent of the pairs and, of those, 33 percent employed the same chemical mechanism. This result means that functional and mechanistic convergence can overlap, but they remain distinct types of biochemical convergence. From an evolutionary perspective, it also appears that a large number of enzymes evolved independently multiple times to use the same reaction sequence! This result is truly surprising.

This survey represents important insight into protein structure and function. It should help biochemists do a better job of classifying enzymes. Additionally, it provides biotechnologists with insights beneficial to protein engineering and the design of novel enzymes. On the other hand, this work also creates problems for the evolutionary paradigm simply because evolution shouldn’t repeat.

It is these types of problems that make me skeptical of the evolutionary paradigm. The red flags are up. It’s time for an audit.

  1. Daniel E. Almonacid et al., “Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function,” PLoS Computational Biology 6 (2010): e10007000. Doi:10.1371/journal/pcbi.1000700
  2. Russell F. Doolittle, “Convergent Evolution: The Need to Be Explicit,” Trends in Biochemical Sciences 19 (January 1994): 15–18