New Year’s Day will soon be upon us. That means it’s time to come up with a few resolutions. Any commitment to lose weight won’t last long. Maybe, I’ll read through the book of Proverbs in 2015. More wisdom would be good.

The advice Solomon imparts stemmed from his experience and time spent in careful reflection. Divine insight also undergirds Proverbs. In fact, Solomon thought the wisdom reflected in Proverbs is the same wisdom the LORD exercised when He created the heavens and the earth (Proverbs 8:22–30).

Based on Proverbs 8 (and other passages), I would expect God’s wisdom to be manifested in the created order. The Creator’s fingerprints—so evident in nature—should not only reflect the work of intelligent agency, but also display undeniable wisdom. Without question, biochemical systems bear the hallmarks of both.¹

When I began studying biochemistry as a graduate student, one of the things that most impressed me was the cleverness of the cell’s chemical systems. I could cite countless examples of biochemical sagacity, but for now I will focus on two recent studies (see here and here). Each relates to the amino acid composition of proteins.²

Cost Effective Amino Acid Sequences

Biochemists have long had interest in the relationship between amino acid sequence and protein structure and function. Proteins exhibit a great diversity of amino acid compositions and sequences. Biochemists believe this assortment is necessary to support the wide range of operations requisite for life.

And yet making proteins costs the cell energy and chemical resources. Some of the expense stems from the process of assembling protein chains. Cellular machinery links together amino acids to produce proteins. Each linkage requires energy. So does the production of the amino acids themselves. The cell synthesizes each of the twenty different amino acids used to assemble proteins via its own series of chemical reactions, which biochemists call a metabolic pathway. Some amino acids are easy to make, requiring minimal energy and chemical resources. Others are more expensive.

Ideally, cells need to minimize the cost of making proteins. There are thousands of proteins found in the cell at any one moment in time. If too many of these proteins are comprised of expensive amino acids, the cell won’t be able to harvest enough energy to generate the proteins needed to carry out all of its activities. This is bad news for the cell’s survival. Think of a business that sells its products for a loss. Eventually, the business will have to shut down if it can’t make a profit on what it produces. However, least-costly proteins lack the chemical diversity needed to carry out life’s necessary operations. To continue with the business analogy, think of a merchant who manufactures useless products that no one wants to buy.

Researchers from Argentina recently discovered how cells work around this conundrum. Based on modeling studies, the scientists showed that proteins found in nature are comprised of least-costly amino acids that simultaneously allow for maximal sequence diversity (and hence, function).³  In other words, proteins are optimized to balance competing interests of functionality and metabolic costs.

Optimization reflects the work of intelligent agency, evincing the Creator’s handiwork. Yet, as a biochemist, I am even more impressed with the elegant molecular logic that underlies the amino acid compositions of proteins. In principle, many different amino acid sequences can be used to achieve the same protein function. Yet the ones the cell employs are the most cost effective.

Making Proteins to Make Amino Acids to Make More Proteins

The availability of amino acids poses another biochemical conundrum, particularly for single-celled organisms such as bacteria. Proteins mediate each of the chemical reactions comprising the biosynthetic pathways used to produce amino acids. To put it another way, proteins make the amino acids that the cell’s machinery, in turn, uses to make proteins.

So what happens when cells face a shortage of a particular amino acid? Usually, the cells will ramp up production of the specific proteins needed to replenish the amino acid in short supply. But if that amino acid is required to make the proteins that make it, things come to a standstill.

By way of analogy, it is the same problem a manufacturing facility would face if it used an assembly line to manufacture widgets and the machines on the assembly line required widgets for their operation. If there were a worldwide shortage of widgets (and demand for the widgets kept increasing), there would be no way to ramp up production of widgets by adding more assembly lines because widgets would be needed to build the machines that make widgets. The only way around this stalemate would be to design manufacturing hardware that didn’t require widgets to make widgets—and this is exactly what cells do.

Investigators from UC Berkeley have discovered that the proteins that take part in the biosynthetic route that manufacture a specific amino acid make limited use of that amino acid in their compositional make up.⁴ In this way, when a particular amino acid is in short supply, the cell’s machinery can still make the proteins that synthesize the amino acid in demand. Again, as a biochemist, I can’t help but to marvel at the elegance and wisdom of this design.

In my experience, most biochemists (whether believers or skeptics) are taken with the elegant molecular wisdom that defines the architecture and operation of biochemical systems. The cleverness of the cell’s chemical systems convinced me that a Creator must be responsible for life. To think otherwise would be folly.

I don’t believe in Santa Claus—but if he and his reindeer landed on my roof one Christmas Eve, I just might change my mind. As the old adage goes, “Seeing is believing.”

Evolutionary biologists often make use of this maxim to argue that biological evolution is a fact. They point out that we can see evolution happening right before our eyes and this should be all the proof of biological evolution that anyone needs. One recent example of evolution in action was reported in Science.¹ Collaborators representing a number of American institutions observed green (or Carolina) anole lizards, located on islands off Florida’s coast, evolving over the span of 15 years (about 20 generations) in response to an invasion of brown (or Cuban) anoles.

Both lizards occupy the same ecological niche, but in the early 1990s, researchers observed green anoles perching higher up in trees when confronted with growing brown anole numbers. To determine if the invasion was the direct cause for this change in habitat, the researchers studied six islands occupied by green anoles only. They measured the lizards’ perch height and then released brown anoles on three islands, with the remaining three serving as control sites.

The researchers observed that as brown anole numbers increased, the green anoles’ average perch height increased. On the other hand, no change in perch height was observed on the control sites. The researchers discovered that on all three test sites the toe pads of the green anoles became larger as perch height increased. The bigger toe pads made it possible for the green anoles to perch higher up in the trees. This adaptation was due to genetic changes in the green anoles, not to developmental plasticity. According to Yoel Stuart, lead author of the study, “We did predict that we’d see a change, but the degree and quickness with which they evolved was surprising.”²

In many respects, this is a remarkable piece of scientific work. It helps alleviate a frustration evolutionary biologists often experience. It is difficult for these scientists to directly test the theoretical framework of biological evolution because direction observation (let alone monitoring) of evolutionary changes is rare. In the absence of direct observation, evolutionary ideas are debated based on theoretical analysis and inferences drawn from various comparative studies—but the ideas can never be experimentally confirmed or rejected.

The rapid evolution of the green anoles represents a rare opportunity to test a hypothesis advanced in the 1950s by famous evolutionary biologist E. O. Wilson. He suggested that when two closely related species co-occur and compete for resources, evolutionary divergence will result. The green anole study confirms Wilson’s hypothesis.

I often find that such studies raise concerns for Christians. After all, if seeing is believing, then how can we deny the reality of biological evolution when we can observe evolution happening before our eyes? And if evolution is a fact, does it eliminate the need for a Creator to explain the origin and history of life?

Not necessarily. We must distinguish between evolutionary change (driven by genetic variation filtered, iteratively, by selection) and the evolutionary paradigm, which argues that this mechanism is sufficient to explain life’s origin, history, and diversity. Just because evolutionary change is observed, or even inferred, doesn’t mean that the evolutionary paradigm has been established. To see how my argument plays out, think of evolutionary changes as falling into one of five categories.

1. Microevolution refers to changes happening within a species. A textbook example would be peppered moths changing wing color in response to rising pollution levels in the UK.
2. Speciation describes the scenario in which one species can give rise to a closely related sister species. A classic example is the evolution of the finches on the Galapagos Islands from an ancestral finch species that arrived to this archipelago from South America. Upon arrival, the ancestral finch evolved into a variety of species that vary primarily in body size and beak size and shape.
   These two types of evolutionary changes have been observed repeatedly and, in my opinion, are noncontroversial. The change in the green anoles falls between the categories of microevolution and speciation.
3. Microbial evolution refers to transformations in viruses, bacteria, archaea, and single-celled eukaryotes—such as the acquisition of antibiotic resistance in bacteria, the ability of viruses to hop from one host to another (e.g., SARS and HIV), and the emergence of drug-resistant strains of the malaria parasites. Microbial evolution would also include horizontal gene transfer between microbes that accounts for the evolution of pathogenic bacteria from nonpathogenic strains (e.g., E. coli O157:H7). Again, I don’t find microbial evolution particularly controversial.
4. Macroevolution includes putative changes that require that evolutionary processes have genuine creative potential. Examples would include humans evolving from a primate ancestor, whales evolving from a terrestrial wolf-like mammal, and birds evolving from theropods. Whether or not macroevolution has occurred defines the creation-evolution controversy. I am skeptical that macroevolution is a real process that has shaped life’s history. (To read representative articles that explain my skepticism, go here, here, and here.)
5. Chemical evolution refers to the processes that presumably generated the initial life-forms. According to this model, chemical selection transformed a complex chemical mixture of simple compounds into protocellular entities that evolved to yield the first true cells. (I would refer readers to Origins of Life, a book I coauthored with Hugh Ross, for a detailed rationale for my skepticism about chemical evolution.)

For the evolutionary paradigm to be true, macroevolution and chemical evolution must be unequivocally established. And they simply haven’t been. Thus, seeing shouldn’t necessarily lead to believing. We have to be careful about interpreting what we experience.