Theoretical physics and the 'grey areas' of biology

Mikhail Tikhonov uses tools inspired by physics to re-examine some of the fundamental assumptions of biology.

In 1916, microbiologists discovered a bacterium, dubbed Methanobacillus omelianskii, that fed on ethanol and produced methane. For decades, scientists studied it in labs, puzzled by its unique metabolism but confident that it was a single organism. In the fifty years after its discovery, M. omelianskii was studied more thoroughly than any other methane-producing organism, but not until 1967 did researchers discover its true nature: M. omelianskii was actually a mixture of two organisms that are as far from each other on the evolutionary tree as humans are from E. coli.

Tikhanov

“They depend on each other so much in their metabolism that they were very hard to separate and cultivate separately, and they don't look that different under a microscope,” explained Mikhail Tikhonov, assistant professor of physics in Arts & Sciences. Tikhonov uses tools of theoretical physics to study ecology and evolution, reexamining some of the fundamental assumptions of biology. For him, the saga of M. omelianskii demonstrates that the dividing line between organisms is blurrier than we typically think.

“Textbooks start from the assumption that living matter is made of organisms, and organisms come in different species,” he said. “None of that really is true. Species at some deep fundamental level are not defined, and not definable.”

Scientists have long grappled with this grey area, and Tikhonov believes that applying theoretical physics to the problem can offer surprising insights. His research runs counter to everyday experience in our macroscopic world, where a cat and a mouse are clearly distinct organisms belonging to different species. But in many ways, when it comes to the microscopic scale, biology defies our intuition.

Take the microbiome, the community of microorganisms that inhabit living things all the way from plants to people. Research increasingly shows that the composition of the microbiome carries significant consequences for the health of the host organism.

“We now know that a cat is not even a cat,” Tikhonov said. “It's an ecosystem, an entire ecosystem with bacteria. Take away the bacteria, and the cat gets sick.”

This presents a conundrum for scientists working within the framework of current biological theories. “When you're looking at some system, you first need to decide whether this is an organism or an ecosystem,” Tikhonov explained. “If it's an organism, you use the language of evolution, and if it's an ecosystem, you use the language of ecology. They're distinct in fundamental ways. For example, an organism is a ‘replicator’: It makes more of itself and seeks to maximize its fitness. Ecosystems do absolutely no such thing.”

“Species at some deep fundamental level are not defined, and not definable.”

In an approach inspired by physics, Tikhonov seeks to bridge the gap between the languages of ecology and evolution using simplified “toy” models. These models might allow him to frame the interactions of species competing for resources in the same mathematical language as the mechanisms by which an organism regulates its physiology. In these toy models, at least, ecology and evolution appear mathematically equivalent.

One idea that Tikhonov applies in his work comes from solid-state physics. An ideal crystal can be thought of as perfectly structured, a lattice where each unit looks identical to the next. But real-life crystals contain defects, such as an occasional nitrogen atom in a lattice of carbon atoms. One approach to creating theoretical models of crystals is to start with a perfect crystal and view the defects as perturbations of it. Another approach is to start with an “anti-crystal,” a solid completely lacking structure, and add in structure bit by bit.

Viewing the categorization of organisms into species as an abstract mathematical space, Tikhonov can apply the same technique to ecology. On the totally structured, crystalline side of the spectrum lies the traditional model of well-defined, mutually exclusive species. On the totally unstructured, “anti-crystalline” side is a model where the notion of species does not exist at all. According to Tikhonov, the truth lies somewhere in the middle, like a crystal with numerous defects.

Tikhonov also studies emergent simplicity, the phenomenon that under certain circumstances, predicting the behavior of a large number of interacting species can be easier than predicting the behavior of only two or three.

In his toy models, he has observed significant qualitative differences in the behavior of ecosystems as more and more species are added, much as ice behaves differently than liquid water. Physicists call this a phase transition. Biologists have studied emergent simplicity for decades, but the connection to phase transitions offers the potential of a new approach to the study of ecosystems.

By studying biology with a physicist’s perspective, Tikhonov hopes to shed more light on the ways that traditional biological theories limit the questions that researchers ask.

By studying biology with a physicist’s perspective, Tikhonov hopes to shed more light on the ways that traditional biological theories limit the questions that researchers ask. In quantum mechanics, particle-wave duality—the idea that an object can be a particle and a wave simultaneously—doesn’t allow scientists to count particles better, but rather enables them to ask new questions. For Tikhonov, the same holds true in his biological research.

“The goal is absolutely not to count organisms better. I have zero interest in trying to make precise when I should count it as one organism or two or 1.7. I think that's the wrong question.”

In most cases, considering organisms and species as discrete is an excellent approximation. But in the history of physics, the revolutionary insights of quantum mechanics and relativity were discovered only because scientists kept prodding at minor inconsistencies that their current theories couldn’t explain. That’s why Tikhonov believes his toy models can help guide future research.

“These toy worlds force you to come up with new questions because the familiar questions by construction are no longer defined,” he said. “And these new questions can be useful in the real world.”

Studying how imbalances in the human gut microbiome can lead to disease, predicting how at-risk ecosystems will respond to the effects of climate change, tracing how germs develop resistance to antibiotics—all these areas of research will benefit from a more sophisticated understanding of ecology and evolution. And Tikhonov envisions that physics will play a central role.

“I deeply believe that theoretical physics is a method that is very much applicable to this frontier of knowledge.”