November 2, 2021 | David F. Coppedge

Origin of Species by Microbes?

Moving speciation from chance variation to microbiomes still leaves it up to chance.


The theory of evolution is at a “tipping point” 160 years after Darwin, says Asia Miller at Vanderbilt University. Since Miller’s field of study involves microbiomes, this may be her “nail” in the proverb of a person who only had a hammer and saw every problem as a nail. The press release from Vanderbilt, printed by, explains how she and her co-authors do not wish to replace Darwinism but supplement it:

Vanderbilt researchers are reimagining Charles Darwin’s work by communicating how the origin of species might depend largely on the microbiome—the totality of bacteria, viruses, fungi and other organisms—living in or on a host body.

Darwin’s On the Origin of Species put forth a seminal and revolutionary thesis for the life sciences in 1859: Populations with a common ancestor evolve over time with enough change to become different species that no longer successfully interbreed. This process of descent with modification continues over time to produce lineages of new species. Darwin famously referred to the process of one species becoming two as “the mystery of mysteries.” 

The time has come for a tipping point, Miller says. They tip their glasses to Darwin. According to her view, speciation happens when parents and their offspring accumulate different microbiomes.

This work highlights how the evidence for microbiomes as agents of host speciation has essentially reached a tipping point for microbiologists, evolutionary biologists, chemists, immunologists and developmental biologists. It sets the stage for a more integrative phase of study, funding and meetings focused on host-microbe interactions shaping the origin of species.

All this tipping may make Darwin, already drunk on Darwine, feeling even more tipsy. Miller’s call for “a more integrative phase of study” presupposes that Darwin’s “seminal and revolutionary thesis” was too narrow. Evolutionists need to expand their visions of the possibilities of the Stuff Happens Law.

Their paper in PLoS Biology* puts forth the new idea:

Results from interspecific transplants of phylosymbiotic microbiomes between related host species support the hypothesis that selective pressures shape holobiont compositions and phylosymbiosis. For example, fitness (for instance, survival) in Nasonia parasitoid wasps and performance (for instance, digestibility) in Peromyscus deer mice are reduced in an evolutionary-informed manner upon exposure with increasingly different microbiomes from related host species.

These results are akin to the costs experienced upon mitochondrial introgressions among related host lineages and suggest that natural selection can drive phylosymbiotic changes within parental species that may, in turn, contribute to the evolution of deleterious interactions between hybrids and their microbiomes.

*Miller et al., “The microbiome impacts host hybridization and speciation,”PLoS Biology, October 26, 2021

What’s the purpose of their presentation?

In this perspective, we call attention to literature on the microbiology of animal hybrid hosts to equip evolutionary biologists, developmental biologists, biochemists, and microbiologists with case examples of how the microbiome sheds important light on speciation and hybridization.

Do they have numerous cases to shed light on their proposal? Admittedly, no.

Here, we survey and synthesize exemplar cases of how endosymbionts and microbial communities affect animal hybridization and vice versa. We conclude that though the number of case studies remain nascent, the wide-ranging types of animals, microbes, and isolation barriers impacted by hybridization will likely prove general and a major new phase of study that includes the microbiome as part of the functional whole contributing to reproductive isolation.

Are their case studies exemplary? No; the 8 cases they investigate (mites, wasps, flies, carp, whitefish, mice, deer and elk, horses) involve degenerative interactions (e.g., parasitism, sterility, or reproductive barriers). Not one of these cases involved the origin of a new species! It was all downhill. Darwin will never get people from bacteria that way.

All they offer is a suggestion: “microorganisms and their interactions with hosts have been put forth as an engine of novelty that may spur the origin of new species.” Thanks for the funding, NIH and NSF; your futureware is in the mail.

Problems Galore

Their hypothesis is just as naturalistic as the old Darwinism and neo-Darwinism. Unless they can account for the genetic information for eyes and wings in microbes, their ideas get swallowed into the blob called the Stuff Happens Law: the anti-science “law” that offers no explanation for things beyond chance (“stuff happens”).

If these microbiome specialists think they are doing Darwin favors, they have another think coming: a rethink. Are they ready to credit the foresight of a Creator God who (in their microbiome-centric view) endowed microbes with the ability to give new organs to animals and plants? Ask that and get laughed out of the room. Like Darwin, they envision a natural world, devoid of purpose and direction, unfolding into a pattern of unguided speciation “which Darwin viewed as grandeur, most beautiful and most wonderful.” The euphoria of evolutionists can be expressed in the maxim, “Chance is beautiful” which, being translated, means, “Anti-science is beautiful.”

Observers of science trends may see more indications of rumblings in the Darwin Camp.


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