Canadian professors' new book explores regeneration of microbial communities

A biologist and a philosopher have collaborated on a new book that looks at how microbial communities regenerate--and why.

At a time in history when microbial communities are being changed or wiped out by antibiotic use, climate changes, or human or natural disasters, the book provides some guidelines for reconstituting what is beneficial in these microbial communities.

The authors are S. Andrew Inkpen, an assistant professor of philosophy at Mount Allison University in New Brunswick, and W. Ford Doolittle, professor emeritus at Dalhousie University in Halifax, Nova Scotia.

The book, published by the University of Chicago Press in July, is titled Can Microbial Communities Regenerate? Uniting Ecology and Evolutionary Biology. It is part of a series on "Convening Science: Discovery at the Marine Biological Laboratory," in Woods Hole, Massachusetts. It is available in hardcover and in paperback.

A philosophical inquiry

Current Science Daily asked Doolittle to discuss the ideas in the book. An evolutionary and molecular biologist, he is a member of the U.S. National Academy of Sciences, and a fellow of the Royal Society of Canada and the Norwegian Academy of Science and Letters.

Doolittle summarized the thrust of the book.

"The main idea is a philosophical one," he said. "Are the regeneration of planaria, hydra or salamanders, of their parts or even as wholes, only metaphorically `the same' as the regeneration of a forest after a fire? Or of our gut microbiome after antibiotics?" 

[Planaria, hydra, and salamanders are organisms that can regrow missing parts.]

"We conclude that using the same word is problematic," Doolittle added. "There is no mechanistic sameness. If, and only if, on the other hand we imagine that both have the same `purpose'–the restoration of a former state--we might be able to say that there is a sameness. Both might have been “selected for. But to do that, we need to reconfigure what we mean by natural selection." 

He emphasized that the title of the book, including the idea of uniting ecology and evolutionary biology, "says it all."

Doolittle advocates the term teleonomy, the purpose brought about by natural selection, in place of teleology, purpose brought about by human or divine intervention.

As to how a biologist and a philosopher came together, Doolittle said Inkpen was his postdoctoral student. 

"I’ve been hiring PhDs in philosophy for the last five or so years. Andrew has a job as professor of philosophy at Mount Allison University--a superb liberal arts college in New Brunswick--and is a team leader for a regeneration project run out of the Marine Biological Lab at Woods Hole. He recruited me and we wrote the book, very much 50/50."

A provocative challenge

Doolittle talked about the philosophical implications of regeneration as he and his co-author conceive it.

We think the philosophical implications are "large," he said. 

"Most evolutionary thinking nowadays entails that natural selection is all about differential reproduction, and the trouble with ecosystems like forests is that they do not reproduce as ecosystems," he added. But much of current scientific activity addresses communities --ecosystems--and how they behave, evolutionarily. 

"Richard Dawkins’ The Selfish Gene and what the philosopher David Hull generalized Dawkins’ ideas to, is the better way to go," Doolittle said. "We are hoping to catalyze a transformation in how scientists think about selection."

(Doolittle isn't a stranger to controversy, having challenged ideas such as James Lovelock's Gaia theory or the metaphor of a "Tree of Life," or the use of function in biology.)

Ideas to ponder

For a nonspecialist, especially someone concerned with conservation of large communities, such as boreal forests, or preserving a small ecosystem or microbiome, the Inkpen and Doolittle book offers new ways of looking at solving these problems and at the concepts involved.

For example, consider a new way to look at what is an organism.

Doolittle said, "In our, and what I consider most evolutionary biologists, view, organisms have integrated parts with a common `purpose,' because there is reproduction of the whole unit. Ecosystems are not like that, so they can’t be ‘organisms’ – unless we change the meaning of that word.”

The authors highlight how we might reconceive of the interconnectedness of living systems, and how knowledge gained from one living system can be applied to another, especially concerning disease treatment

One example the authors offer from medicine is how to engineer a microbial community in the biome after antibiotic use to fight an infection. Fecal transplants, prebiotics and probiotics are some of the possibilities. They stress that the engineering efforts here are "functional," not replicating exactly what was lost, but creating a community that provides the same function for the individual.

The book stresses the need to preserve natural systems because we need to understand their secrets for future possible use. It concludes with a plea for environmental preservation of large and small species, noting, "We do wrong when we destroy them."

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S. Andrew Inkpen & W. Ford Doolittle, Can Microbial Communities Regenerate?: Uniting Ecology and Evolutionary Biology, Chicago University Press, 2022, 136 pp., ISBN 9780226820354