Uprooting a “Bad Design” Argument

In spite of recent claims, the enzyme rubisco is optimally designed

A few years ago I delivered a lecture to faculty and students at the University of North Florida as part of their weekly science seminar series. During the Q&A session, one of the biology faculty members challenged me to account for bad designs in nature. One example he raised was the enzyme rubisco.

Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) is the most abundant protein in nature. It plays a central role in photosynthesis and has primary importance in ecosystems. Despite its significance, Rubisco has acquired a reputation among biochemists as an inefficient, wasteful enzyme, the type of system evolution would generate, not a Creator.

This enzyme catalyzes the addition of carbon dioxide to the 5-carbon sugar ribulose 1,5-bisphosphate. The first step in the so-called dark reactions of photosynthesis, this chemical transformation sustains virtually every life-form in Earth’s surface biosphere. However, the carbon fixation reaction proceeds slowly and inefficiently. Rubisco is error prone, sometimes confusing molecular oxygen for carbon dioxide, thus, further compounding this inefficiency. When rubisco makes this mistake, oxygen combines with ribulose 1,5-bisphosphate to form unwanted compounds. This undesired process detracts from the carbon fixation reaction, causing waste and necessitating many more copies of rubisco than would be otherwise required if this enzyme operated with greater efficiency.

Biologists, like the one I encountered at the University of North Florida, frequently point to seemingly faulty designs in nature, like rubisco, as evidence for evolution. Why would an all-powerful, all-knowing, all-good Creator produce poorly designed systems—especially when they are so critical for sustaining life on the planet? Evolution, on the other hand, would be expected to produce marginal designs that are just good enough.

This inefficiency has prompted some biochemists to focus their efforts on developing genetically engineered plants with novel forms of rubisco that operate with greater efficacy than those found in nature. The hope is that these genetically modified plants would boost food production around the world.

But the complexity of rubisco has presented this research effort with difficulties. The protein consists of eight large and eight small subunits. The proper assembly of these subunits is difficult to achieve in the test tube. Likewise, genetically modified variants also face this problem, thus, hampering efforts to evaluate them for improved efficiency and selectivity.

A research team from Germany recently developed a means to effectively reconstitute rubisco in the laboratory.1 In a commentary on this work, biologist R. John Ellis takes the opportunity to deride rubisco, referring to it as a “superb example of unintelligent design.” Once again a challenge to the case for the Creator based on rubisco’s bad design.2

But as I discuss in The Cell’s Design, work done in 2006, has changed the way biochemists view this enzyme.3 Rubisco’s slow turnover and struggles to discriminate between molecular oxygen and carbon dioxide stem from the featureless, nonpolar nature of both gases. In other words, rubisco’s confusion between oxygen and carbon dioxide is not due to a faulty design, but rather results from the inherent chemical nature of these two gases. To overcome this confusion, this enzyme slows down the carbon fixation reaction. Rubisco faces a trade-off between rate of reaction and discrimination between carbon dioxide and molecular oxygen. Rubisco is not poorly designed at all.

The biochemists that discovered this trade-off commented, “Despite appearing sluggish and confused, most Rubiscos may be near-optimally adapted to their different gaseous and thermal environments. If so, genetic manipulation can be expected to achieve only modest improvements in the efficiency of Rubisco and plant growth.”4

In response to Ellis’ commentary, two agricultural scientists from Denmark maintain that the efficiency of rubisco has no bearing on crop yields, further undermining the view that this protein is poorly designed.5 They point out that increased crop production relates to larger leaves that capture more energy and prevent weeds from growing by creating more shade near the tree. They also note that crop physiologists have known for a long time that respiration and photorespiration do not detract from crop production. In fact, they assert that increasing the rate of photosynthesis—which would result if the efficiency of rubisco was increased—would reduce, not increase, crop yields. This counterintuitive effect stems from the fact that increased photosynthesis would consume a greater amount of energy because of higher respiration costs and higher demand for proteins to sustain the increased photosynthetic activity.

Rubisco no longer deserves its reputation as a poorly designed product of evolutionary processes, thus, uprooting another so-called example of a bad design. 


1. Cuimin Liu et al., “Coupled Chaperone Action in Folding and Assembly of Hexadecameric Rubisco,” Nature 463 (2010): 197–204.

2. R. John Ellis, “Tackling Unintelligent Design,” Nature 463 (2010): 164–65.

3. Guillaume G. B. Tcherkez et al., Proceedings of the National Academy of Sciences, USA 103 (2006): 7246–51.

4. Ibid.

5. John R. Porter and Bernd Wollenweber, “The Rubisco Enzyme and Agricultural Productivity,” Nature 463 (2010): 876.