In The Design Matrix, I explain how the process of gene duplication, conventionally taken as a ‘brute given,’ is actually a mechanism of front-loading evolution given that it can carry designs far into the future. Now we have evidence that gene duplication, in the correct context, actually functions as a nudge for the evolution of increased complexity:
“In all organisms, genes get duplicated every so often, for reasons we don’t fully understand,” Fernandez said.
As I said, gene duplication is viewed as a brute given. The reason genes get duplicated every so often is that such dynamics are embedded into the architecture of life to facilitate the evolution of life.
“When working efficiently, natural selection eliminates many of these duplicates, which are called ‘paralogs.’ In our earlier work, we saw that an unusual number of gene duplicates had survived in the human genome, which makes sense given selection inefficiency in humans.”
In other words, natural selection typically behaves as a process that opposes gene duplication. To unleash the full potential of this process, we need to push the blind watchmaker off to the sidelines as “inefficient.” How so? By having gene duplication occur in small populations:
Lynch said one aspect of Fernandez’s research that is potentially groundbreaking is the observed tendency of proteins to evolve a more open structure in complex organisms.
“This observation fits with the general theory that large organisms with relatively small population sizes — compared to microbes — are subject to the vagaries of random genetic drift and hence the accumulation of very mildly deleterious mutations,” Lynch said.
In principle, he said, the accumulation of such mutations may encourage a slight breakdown in protein stability. This, in turn, opens the door to interactions with other proteins that can return a measure of that lost stability.
“These are the potential roots for the emergence of novel protein-protein interactions, which are the hallmark of evolution in complex, multicellular species,” Lynch said. “In other words, the origins of some key aspects of the evolution of complexity may have their origins in completely nonadaptive processes.”
This research shows how a feedback loop might emerge that nudges evolution toward a state of higher complexity. As organisms become more complex, their population sizes become smaller, natural selection becomes more inefficient, and thus gene duplication adds more complexity, making natural selection even more inefficient.
Fernandez said the research reveals how increasingly specialized proteins can evolve. He drew an analogy to a business that hires two delivery drivers that initially cover the same parts of town but eventually specialize to deliver only to specific neighborhoods.
“Eventually, even if times become tough, you cannot lay off either of them because they each became so specialized that your company needs them both,” he said.
The more simple a creature is, the fewer specialized proteins it possesses. Humans and other higher-order mammals need many specialized proteins to build the specialized tissues in their skin, skeleton and organs. Even more specialized proteins are needed to maintain and regulate them. This complexity requires that the duplicates of the original jack-of-all-trades gene be retained, but this does not happen unless selection is inefficient.
Once again, it is becoming more clear that evolution is dependent on dynamics that are intrinsic to life and its design.