By Sara Frueh

Paleontologist and National Academy of Sciences member Neil Shubin discusses the twists and turns of evolution, the ancient viruses we carry, and our deep links to the rest of life

While reading an autobiography of the late playwright Lillian Hellman, paleontologist Neil Shubin ran across a line that — though it referred to something else entirely — struck him as a perfect nutshell of current thinking about the evolution of life on Earth: “Nothing, of course, ever begins when you think it does.”

In other words, the changes that enabled pivotal moments in evolution — like fish starting to walk on land, or birds taking to the air — began long before those milestones, and for other purposes, explained Shubin.  

“If you think that lungs evolved as animals were about to walk on land, or feathers came about as animals were about to fly, and other inventions came about during great revolutions, you’d be in really good company,” he said. “You’d also be 100 percent wrong.”

Paleontologists have known this for over a century, and recent work with fossils and in genetics has shed further light on these transitions, explained Shubin, who spoke at a recent webinar hosted by The Science & Entertainment Exchange, a program of the National Academy of Sciences.

“When you collect fossils, when you look at genes, you find unbelievable surprises in the record of the history of life.”  

‘Using old inventions in new ways’

In over 40 years of investigating evolution, Shubin has led expeditions on all seven continents to collect fossils of ancient fish and other creatures. His lab at the University of Chicago studies those fossils, as well as DNA and the evolution of genomes, to piece together the great transitions in the history of living things. 

One of those shifts happened about 375 million years ago, when fish began to walk on land — a change that required multiple new physical features, including limbs, lungs, and necks, Shubin said. 

But research has shown that these characteristics weren’t new at all — each had evolved far earlier for different reasons. “These features were already there,” said Shubin. “It was repurposing them, changing their function, exploiting opportunities for allowing them to live on land when the need arises.”

For example, lungs had emerged earlier to allow fish to gulp air from the water’s surface in situations where oxygen levels were too low to let them breathe through their gills.  And in the Canadian Arctic, Shubin and his team discovered Tiktaalik roseae, an ancient fish with limbs: When they cracked open the fish’s fin, they found bones corresponding to an upper arm, a forearm, a wrist, even stubs of fingers. “Every invention that was necessary for animals to walk on land actually arose in fish living in aquatic ecosystems.”

Similarly, the features that birds needed to fly — such as feathers and hollow bones and specialized lungs — first arose to serve other functions in dinosaurs living on land. For example, feathers evolved presumably to regulate dinosaurs’ body temperature, and possibly for coloration and courtship displays.

“It was using old inventions in new ways, for new purposes,” said Shubin. “That’s what evolution is about.”

The legacy of ancient viruses

Shubin described another example of repurposing, one that involves an evolutionary surprise revealed by recent work in genetics: Ancient viruses, after invading the bodies of our distant ancestors, got incorporated into the human genome. “Almost 10 percent of our genome is a graveyard for ancient viral infections,” he said.

One early virus appears to have been repurposed by the human genome and harnessed for different ends, Shubin explained, describing the discovery of neurobiologist Jason Shepherd, who studies the genetic and physiological basis of memory.

Shepherd’s work focused on a gene called Arc, which is involved in memory. Mice who have a mutation in Arc can solve a maze but can’t remember their solution the next day. Humans who have a mutation in the gene experience a range of cognitive deficits.

As he examined the proteins made by Arc with a microscope, Shepherd realized their appearance was identical to an image he’d seen before: human immunodeficiency virus (HIV), the virus that causes AIDS. As it turns out, the sequence and structure of Arc and its proteins contain the classic signature of a virus similar to HIV, said Shubin. Just as the protein clumps on HIV help move genetic material from cell to cell, Arc acts in a similar way, but for a different function.

Shepherd and his colleagues hypothesize that sometime in the distant past — several hundred million years ago — a virus invaded the DNA of one of our distant ancestors. “Instead of causing an infection, it was domesticated, and it was repurposed for a new use,” said Shubin.

Life’s shared toolkit

As the human body develops from embryo to adult, our genes turn on and off, guiding where limbs and organs and vertebrae are placed and defining the structure of our bodies, said Shubin. Other creatures have versions of these genes too.

“The basic toolkit that builds the bodies of creatures like us and mice is shared with worms, flies, and fish,” said Shubin. “All of the tools that are used to build our bodies originally arose in flies and other creatures … We have deep connections to the rest of life on the planet.” 

These connections are enabling scientific and medical discoveries that are ultimately likely to help humans, Shubin explained. During the past several decades, Nobel Prizes in medicine and physiology have been awarded to scientists who have studied flies, mice, and tiny worms to understand how genes turn on and off in health and disease.

“I’d like to think that as we discover cures to everything that ails us, from Alzheimer’s to different cancers, that the breakthroughs that will extend and enrich our lives, will in some way be based on the knowledge of flies, worms, and in some cases even fish,” said Shubin. “I can’t imagine a more powerful or more beautiful statement on the importance of our evolution and our shared connection to the rest of the species on the planet than that.”

Watch the full discussion. The event was part of a weekly series launched in April 2020 by The Science & Entertainment Exchange, a program of the National Academy of Sciences that connects entertainment industry professionals in Hollywood with the STEM community. Support for this series is provided by the Howard Hughes Medical Institute and the Alfred P. Sloan Foundation.