Evolutionary biology and the beauty of confirming hypotheses with data and experiments

Two groundbreaking new studies provide important evidence for key theories about the evolution of humans and the interplay between viral RNA and our own cells, offering a glimpse of how science evaluates competing ideas and a potential window into the nature of all life on Earth.

Last month, a groundbreaking new study in Proceedings of the Natural Academy of Sciences looked at the role of increased meat consumption in human evolution.  Many had long assumed that eating meat, which offers more protein and a much higher calorie count than fruits and vegetables, was essential to our upright bodies and bigger brains.  Some took this to mean that “meat made us human” almost literally.  The new study, however, found something different and, to many, unexpected.  The researchers analyzed existing data from already excavated archeological sites in an attempt to determine how much meat our ancestors ate and at what point in our history.  Previously, researchers found what is known as “butchery marks” on animal bones at these sites, signs that humans were using tools to cut meat as long as 2.6 million years ago.  Around 2 million years ago, the quantity of these signs exploded along with the emergence of Homo erectus, an immediate forebear to our own species, Homo sapiens.  This timing was seen as causation, not coincidence, leading to the idea that H. erectus evolved thanks to consuming a lot of meat.

Briana Pobiner, one of the authors of the study and a paleoanthropologist at the Smithsonian Museum of Natural History, was herself a proponent of the theory.  “I have definitely been a ‘meat made us human’ hypothesis purveyor,” she told the science and technology site, Inverse.  When she and her team actually looked at the data from these 59 East African sites dated between 2.6 and 1.2 million years ago, however, they didn’t find the linear or even geometric increase in meat consumption we would expect if one was driving the other.  Instead, they found no pattern at all.  Meat eating appears to fluctuate irregularly over this period with no direct connection to underlying evolutionary trends, even after controlling for the size of the site and potential bias in the methodology.  “At times when you have bigger fossil samples, you’re more likely to get evidence for meat-eating,” Ms. Pobiner noted, but overall she was “totally surprised by the results,” concluding that “There may be more than one factor involved in these big changes in our evolutionary history.”

Personally, I applaud and admire the study, but didn’t find these results surprising because I’ve been an adherent of a competing theory for more than 10 years.  Richard Wrangham’s Catching Fire: How Cooking Made Us Human proposed a different, and in my opinion more compelling idea.   Mr. Wrangham reasoned that even some of nature’s most successful hunters fail more often than they succeed.  For example, a pride of lions is believed to kill their prey only about 30% of the time.  Even Africa’s most successful hunters, the wild cape hunting dogs, only achieve an 80% success rate.  We cannot say for sure where early humans would rank, but assuming they were somewhere around average, they would fail to obtain food over 50% of the time.  Moreover, hunting takes a massive amount of time and energy, and an early human hunter returning from a failed trip would still need to consume enough calories and nutrients to survive and prosper, their big brains being the equivalent of a gas guzzling V8 engine.  Where would those calories come from?

Mr. Wrangham looked at our nearest cousins, the great apes, who are primarily plant eaters, and found they spent a huge amount of their time eating.  Mountain gorillas, for example, spend about half of their waking hours consuming plants.  Chimpanzees also spend approximately four hours a day finding and eating fruit, then another one to two hours feeding on young leaves.  Both species have far more sedentary and less energy intensive lifestyles than our ancestors, who are believed to have ranged far and wide to find food, even forgetting the demands of their larger brains.  What was a hunter returning from a failed trip to do?  There simply wouldn’t have been enough hours in the day to spend six hours eating raw vegetables to keep up their energy level.  Therefore, Mr. Wrangham concluded that something else was needed to enable humans to hunt and scavenge in the first place.  He proposed that we had to learn a primitive art of cooking first, because cooking food greatly increases the nutritional value by breaking down the plant or animal fibers, and allowing the digestive tract to extract far more calories per ounce.  This hypothetical failed hunter might not dine on steak every night, but cooked fruits and vegetables would enable him to survive to hunt another day, whereas raw food would not.

Of course, more research is needed, but it seems that Ms. Pobiner’s study at least indirectly supports Mr. Wrangham’s hypothesis that cooking came first, hunting second in human evolutionary history.  (I say indirectly because the study didn’t definitely look at cooking practices, though many of the sites were large and sophisticated for the time period and assuming they had fire at these locations seems reasonable.)  This is the beauty of science in action:  Scientists propose ideas that can be measured and tested in the real world, compared to the actual findings of studies and other experiments.  The leading hypotheses are those with the most support and the least contradictions to real world events.  When someone says science or praises science, this process is generally what they are referring to, seeking the truth by proposing ideas and constantly comparing them to the data.

Moreover, this process applies to both the large and the small, even the microscopic.  Scientists have long been aware of a process called “horizontal gene transfer” that allows bacteria to rapidly swap DNA using viruses as a medium.  The process is straightforward to describe:  A virus copies a portion of DNA from one bacteria, then inserts it into another.  In bacteria, the process is also highly effective, allowing them to evolve much faster than normal replication.  Thanks to horizontal gene transfer, a beneficial DNA sequence can rapidly propagate through an existing population, rather than waiting on the far lengthier reproductive process.  This process is so successful, it’s estimated that as much as 20% of the DNA in a common E. coli bacteria, present in all of our stomachs, has been inserted by viruses at some point.  Horizontal gene transfer also has the added benefit of being able to copy and insert long pieces of DNA, as opposed to the traditional step-by-step process of evolution where the rate is barely measurable, some 10 to the negative sixth or even ninth power per nucleotide per generation, making it both faster and potentially more effective.

The process itself is reasonably well studied in bacteria.  Scientists have identified multiple different mechanisms and methodologies, from transformation to conjugation. The details don’t need to concern us here, except these studies have been focused almost exclusively on bacteria and their other prokaryotic cousins, the archaea.  This is because DNA in these organisms is free floating in the cell, easily enabling viruses to pick up and move sequences.  The application of horizontal gene transfer to the far more complicated and secure eukaryotic cells with their DNA bound up tightly in a nucleus has always been a tantalizing proposition.  Could the direct ancestors of our own cells have benefited?  Could even multicellular animals somehow take advantage of this evolutionary hack?  The possibility certainly seemed real, the potential practically limitless, but no one really knew for sure, perhaps until now.

Scientists at the Department of Botany at the University of British Columbia in Vancouver, Canada, and the Department of Zoology at the University of Oxford in the United Kingdom studied 201 eukaryotic cells and 108,842 viruses.  They’re conclusion?  Horizontal gene transfer occurs in more complex cells, and that it has provided functional, evolutionary benefits, the same as in bacteria.  The team based their study on complex, yet well established computer analyses known as phylogenetics to understand the evolutionary development and the diversification of different species of cells and other organisms.  Dr. Nicholas A.T. Irwin, the first author of the study, explained to Medical News Today, “One of the important factors that allowed us to conduct this analysis was the enormous amount of genomic data that has now become available from eukaryotes, viruses, and prokaryotes (including bacteria and archaea). These new resources have resulted from major DNA sequencing efforts trying to understand the diversity of genomes across the tree of life.”  “Having a large diversity of high-quality genomic datasets was crucial, as it allowed us to infer which species were participating in these gene transfers,” he added.

First, the researchers compared the DNA between the eukaryotic cells and the RNA and the viruses to identify genes shared in common.  These common genes were considered candidates for either transfer from the eukaryotic cell to the virus or from the virus to the eukaryotic cell.  They found instances of both types of transfers, though viruses seemed to take on about twice as much genetic material as the cells.  The reasons for this difference are not entirely clear, but are likely the result of evolutionary processes after the transfer, meaning the virus benefitted more on average from the eukaryotic genes than the eukaryotes did from the viral.

Finally, they compared the transferred genes to the broader genetic tree of life, a catalog of the hundreds of thousands of different genomes we’ve mapped over the past 40 years, encompassing everything from a sea sponge to a human, to determine when these transfers occurred in our evolutionary history.  If a gene was present across a broad range of modern organisms, it was inserted before those organisms became separate species.  If it was distinct to a single species, it was inserted after.  Dr. Irwin explained, “If we observed a viral gene in a human genome, we would predict that the gene was acquired after humans speciated from other primates. In contrast, if a viral gene was present in all animals, say from sponges to chimps, we would infer that gene to have been derived in the last common ancestor of animals.”

Ultimately, they found two critical functions in humans that could have been derived from viral DNA.  Genes for the production of hyaluronic acid, used in the fluids of eyes and joints, acting as a cushion and lubricant, and genes for the development of the placenta, one of the things that makes us mammals in the first place.  They also found evidence that genes in the mitochondrial DNA of certain human-adapted parasites that can cause sleeping sickness and other diseases originally came from viruses.  Of course, these results are preliminary and Dr. Irwin himself cautioned, “there are different ways to interpret these patterns, but we base our interpretations on the assumption that gaining a gene through gene transfer is more difficult and unlikely than losing a transferred gene.”  At the same time, he said “I also think this study has interesting implications for how we view viruses. Similar to how the discovery and characterization of the microbiome changed our view of bacteria, I think that revealing the influence that viruses have had on the evolution of life could encourage more nuanced thoughts about the importance of viruses in nature.”

To this, I would also add another interesting implication:  This study appears to provide support for another long standing evolutionary hypothesis, the evolution of evolvability.  This is the difficult to prove belief that natural selection does more than create life forms uniquely adapted to survive and reproduce.  It also favors those that are more adaptable over all and more capable of changing quickly in response to changes in the environment or other conditions.  This may seem like a self-evident proposition, but it is uniquely difficult to prove when, generally speaking, we can only observe an organism as it is currently adapted to a specific environment.  Rarely, can we consider what that same organism might look or behave like should the environment suddenly change, making how adaptable an organism is almost impossible to measure directly.  We can, however, find evidence elsewhere.  Horizontal gene transfer is an example of the kind of evidence we can expect:  If even complex organisms like mammals can benefit from genes inserted by viruses, a process that Darwin himself wouldn’t have been able to conceive in his day, it seems reasonable to continue pursuing the belief that life has evolved to evolve.

Interestingly, Darwin might not have been able to conceive of it, but there is a sense that evolutionary science is coming full circle back to some of his original thinking.  The neo-Darwinian synthesis that took hold in the mid-20th century after genes were discovered assumed that organisms were selected based on their ability to replicate their own DNA, replacing Darwin’s hazy concept of heredity and the physical and reproductive fitness.  This was seen as a slow, mechanical process, essentially a shuffling of a deck of genetic cards every generation. Since then, however, we’ve learned that an organism’s DNA is only part of the story and the actual processes that underlie the building of a body are far more complex and intertwined, as if the deck itself can change and be influenced by outside forces.  DNA is not merely stored in the cell nucleus.  Organelles like mitochondria have their own that is passed down outside the fusion of the genetic material in the sperm and the egg.  Horizontal gene transfer is also separate from normal reproduction, the genes passed down after they are inserted.  Other new studies suggest that proteins surrounding our DNA help mitigate mutations in essential sections, while allowing them more frequently in others.  The result is a far more complex and dynamic picture, one where the phenotype, that is our physical form, is constructed through a process driven by our genes, but influenced by a multitude of other factors we are just beginning to understand, much less prove by experiment. The one thing we are learning for sure: The underpinnings of life are capable of capable of changing far faster than we ever thought possible, enabling rapid adaptation and endless variety while preserving essential systems.

This takes us directly back to the true beauty of science:  Ideas are proposed and tested.  The best ideas are preserved and passed down, the same as evolution itself.

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