Molecular Brainstorming

The Emerging Theory of Neutral Constructive Evolution

by by Eli Scheer

illustration by by Diane Zhou

When you think about evolution, perhaps Darwin’s finches come to mind—and along with them, the idea that adaptations propagate in a species based on their ‘selective advantage,’ allowing only the fittest organisms to survive long enough to pass on their genes to the next generation. Darwin’s theory of natural selection, having withstood rigorous testing for over 150 years, remains the bedrock of modern evolutionary biology. However, as we delve deeper into biology on the smallest level, we may get a gut feeling that it cannot capture the richness of molecular mechanisms that gave rise to all life around us today. After all, natural selection does not decide the fitness of individual molecules, but rather the organism as a whole. Inside an organism, natural selection couldn’t care less how a particular process is carried out, so long as it works. Over millions of years, organisms can become highly adapted to their environments, but on the molecular level, proteins often have multiple subparts that each carry out specific functions, making these molecules more closely resemble Rube Goldberg machines than a simple lever.

Constructive neutral evolution
But how and why does such staggering molecular complexity arise? Over recent years, a theory known as ‘constructive neutral evolution’ has gained traction for its ability to explain how high-probability genetic changes can cause more complex protein structures to evolve. Gene duplication, a relatively common genetic event, can increase the number of genes that code for a specific protein, even if the protein structure itself does not change. This opens the door for mutations to accrue in these genes, since there is a greater buffer against complete loss of function with two genes encoding for a protein in the place of one. These mutations can, however, create mutual dependencies between the protein molecules for which they encode, increasing the number of necessary molecular actors to carry out a particular task. This process constructs molecular complexity without necessarily conferring a positive or negative selective advantage on the organism as a whole. The mutual dependencies made through constructive neutral evolution are thought to act as a ratchet for complexity, meaning that it is much harder to become less complex than more complex over time.

This is all fine as a theory, but it wasn’t until earlier this year that a group of researchers led by Dr. Joseph W. Thornton at the University of Oregon, used a stunningly direct method to show experimentally how exactly neutral constructive evolution works. The article, which appeared in Nature, had an equally direct title: “Evolution of increased complexity in a molecular machine.” Dr. Thornton, a self-described molecular archaeologist, tries to understand molecular evolution through statistical inference of ancient protein structures followed by direct experimentation on those inferred structures in the context of the modern organism. Using an alignment of modern protein sequences from distantly related species and known phylogenetic trees, which show the divergence of different organisms over time, the researchers can infer the ancient protein sequence with a high degree of confidence. They then simply synthesize this protein by reverse engineering its DNA sequence and introducing that sequence transgenically into the organism of interest (yes, that is possible now!). This allows them to test the ancient protein’s function in a modern context with or without historical mutations that caused it to evolve. Dr. Thornton calls his approach ‘the functional synthesis’ because it pairs “the reductionist culture of molecular biology...with the historical realism of evolutionary biology.”

Fungus among us 
In their article, the researchers began from the observation that a protein found in all eukaryotes (all organisms with nuclei, comprising all life except for bacteria) called a V-ATPase, which performs the critical function of acidifying specific subcellular components, has a markedly more complicated structure in fungi than in animals or plants. In fungi, V-ATPase is composed of three smaller proteins, whereas in animals and plants it is made up of only two. Following their approach, they reconstructed the sequence of the V-ATPase protein as it existed in the most recent common ancestor of fungi, plants, and animals. They were able to infer both the protein sequence of this ancient protein and its structure, which was composed of only two smaller proteins, similar to the two-component V-ATPase system in animals and plants.

When the researchers resurrected this ancient two-component system into mutant yeast strains lacking the modern V-ATPase, they observed that it could functionally substitute for the modern protein. So if a two-component V-ATPase functions essentially the same way as a three-component one, why would evolution spend 800 million years making this more complicated protein? In the case of the fungal V-ATPase, the researchers showed that a gene duplication in one of the two subunits in the ancient V-ATPase molecule was followed by complementary mutations in each of these ‘daughter’ genes, which resulted in these two protein molecules needing each other to do the task where one protein had once sufficed. These two subunits, in addition to the one subunit that remained unchanged, yielded a three-component system, a more complex arrangement that worked no better or worse than the original arangment. This is the perfect validation of neutral constructive evolution!

Don't need intelligence to be complex 
Thornton’s research was hailed by the evolutionary biology community for its directness and for its ability to undermine one of the biggest arguments of intelligent design proponents, the so-called problem of "irreducible complexity." Michael Behe, the biochemistry professor at Lehigh University who coined the term, uses the same observation of molecular complexity to argue that modern-day complex molecules could not have arisen from simpler ones in the past because their function only arises when all of the parts are put together in the current arrangement. Instead, he claims, such machinery must have been “designed” by an intelligent being. But we don’t need to start a culture war over such a trivial argument: we can see from research like Thornton’s that complexity can arise through high-probability genetic events like gene duplication and point mutations, which increase the number of molecular actors involved in any given process. And since a three-component molecule works as well as a two-component one for a fungal V-ATPase, it would seem that in this case, the complexity is indeed reducible. In the theory of neutral constructive evolution, we have a biochemical rationale for molecular complexity that complicates our previously held notion that evolution acts only to economize and simplify biological designs. It may in fact be just as important for the process of evolution to increase complexity to provide enough raw material that can be later honed by natural selection. This phenomenon, known as exaptation, can find adaptive uses for structures made purely through the random molecular jumble of evolutionary history. A notable example of this also comes from Thornton’s lab, who showed that hormone receptors evolved before they ever interacted with a hormone molecule. This was a fortuitous interaction: it enabled the animal endocrine system as we know it today, which plays a role in growth, metabolisim and human moods.

ELI SCHEER B’12.5 can arise through high probability genetic events.