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Trying to Pin Down the Meaning of “Species”

E. coli
E. coli Bacteria Colorized scanning electron micrograph of Escherichia coli, grown in culture and adhered to a cover slip.

[Originally published in 2014 as Meaning of Species]

Greek philosophers are thought to be the first to classify animals and plants, each class having similar attributes. While the story behind the term species (Greek εἶδος) began with Plato, defining the meaning of species continues to be controversial.

Building on Plato, Aristotle used genus (γένος) and species as philosophical categories. A genus was a category, and a species was a subcategory of a genus. At the time, the two terms were just as often applied to inanimate things as to living ones. Then, as of now, the term has continued looking for a definition.

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Charles Darwin agonized over the longstanding problem of the term. In The Origin of Species, Darwin wrote,

… of the term species. No one definition has satisfied all naturalists.

However, for Darwin, similarities are a distinguishing factor of species. As Darwin explains:

I look at the term species as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other.

Biologist Ernst Mayr advanced today’s widely recognized modern unifying meaning of species in the 1940s, declaring:

Species are groups of interbreeding natural populations that are reproductively isolated from other such groups.”

Mayr’s definition is independent of observed similar features. The platypus epitomizes the value of Ernt’s definition of species; this duck-billed oddity resembles a mammal, a bird, and a reptile all in one species.

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In an 1860 letter to Charles Lyell, Darwin lamented that “I quite agree with you on the strange and inexplicable fact of Ornithorhynchus [platypus].” The evolutionary path of the platypus from a common ancestor was simply a “strange and inexplicable” phenomenon from the perspective of Darwin’s “Tree of Life” theory.

Six years later, Alfred Russel Wallace anticipated Mayr’s theory. In an 1866 letter to Darwin, Wallace wrote:

If you “know varieties that will not blend or intermix, but produce offspring quite like either parent”,—is not that the very physiological test of a species which is wanting for the complete proof of the “origin of species”?


Award-winning science writer Carl Zimmer, in his National Geographic article “The Zoo in the Mouth,” highlights this tension between reality and theory in defining the meaning of species. According to Zimmer, “These definitions work tolerably well for animals and plants. But they’ve turned out to be pretty lousy for microbes.”

As challenging as the platypus is within a natural selection paradigm, microbes fair worse. In the early twentieth century, scientists classified microbes based on known anatomical and biological functions. By the mid-century, scientists increasingly attempted to incorporate genetics in the analysis of species classification of microbes. For the evolution industry, though, the difficulty increased exponentially.

“The diversity of microbes turned out to be mind-bogglingly exuberant,” Zimmer laments. “Microbes that had been considered almost identical before the age of DNA turned out to be more genetically different from each other than maple trees and penguins.” Microbes are massively complex — the genetics of microbes is “mind-boggling.”

As an example, Zimmer uses a gram-negative bacterium Escherichia coli (E. coli): “A single species — E. coli — turned out to contain multitudes, from beneficial bacteria that can heal a baby’s dysfunctional gut to all sorts of pathogens that make us sick in frightfully different ways.” In different ways for sure: this year alone, the CDC identified two epidemics caused by E. coli – one linked to clover sprouts and one to ground beef.

Unlike plants and animals, microbes do not pass DNA on to the next generation. “They are constantly swapping genes with each other, with little respect for any so-called species barrier,” Zimmer explained. “Scientists sometimes try to represent this gene traffic by drawing a web of life instead of a tree of life.”Even in single-cell organisms, replacing the tree of life with a web concept undermines Darwin’s tree of life theory.

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For Zimmer,

Trying to fit microbes into a definition of species based on animals and plants is a bit like trying to herd a flock of flamingos into a school bus.

“The situation is such a mess that some microbiologists have given up on species altogether,” Zimmer continues. In 2012, geneticist W. Ford Doolittle of Dalhousie University reflected on the dilemma of species in the article “How Bacterial Species Form and Why They Don’t Exist” published in Current Biology. In the words of Doolittle:

”Two processes suggested to drive bacterial speciation — periodic selection and recombination — are generally thought to be mutually opposed. Recent work shows that data taken as evidence supporting the former may be explained by the latter, raising further problems for the idea of bacterial ‘species’.”

DNA Sequences

Scientists have been stumbling through a labyrinth of DNA and RNA sequencing techniques to classify microbes into species. Even oligotyping, a highly advanced sequencing technique, has failed to distinguish genetic differences not only between but within species.

A research team headed by A. Murat Eren (Meren) of the Center for Comparative Molecular Biology and Evolution in Cambridge, Massachusetts, in a report “Oligotyping analysis of the human oral microbe,” underscores this evolutionary problem even in the microbes commonly inhabiting the human mouth.

In the same bacteria phylum of Firmicutes, one of the most abundant microorganisms in the human mouth, oligotypes were found to vary not only among individuals but between different oral sites. “We discovered closely related oligotypes, sometimes differing by as little as a single nucleotide, that showed dramatically different distributions among oral sites and among individuals,” Meren reports.

Meren continues,

We also detected potentially pathogenic taxa in high abundance in individual samples. Numerous oligotypes were preferentially located in plaque, others in keratinized gingiva or buccal mucosa, and some oligotypes were characteristic of habitat groupings such as throat, tonsils, tongue dorsum, hard palate, and saliva. The differing habitat distributions of closely related oligotypes suggest a level of ecological and functional biodiversity not previously recognized.”

Meaning of Species Mystery Continues

Contrary to expectations following the discovery of DNA, genetics has failed to define any species — the same DNA sequences are found in distinctly different species. Even in the simplest of organisms, “Scientists [have] found that a single so-called species contained several distinct oligotypes,” Zimmer notes. Genetic oligotypes are not a distinguishing factor between microbe species. Rather than clarifying the essence of a species, DNA and RNA sequencing is compounding the meaning and mystery of species.

“It [once] seemed as though life could be disassembled and reassembled like a child’s blocks,” noted Italian geneticist Giuseppe Sermonti. “Some people then placed their faith in the omnipotence of biology and the prospect — it seemed only a matter of time — of being able to put life together and change it in a test tube.” Genetic scientific evidence, even in single-cell organisms, continues only to intensify Darwin’s Dilemma.

In the words of Sermonti, “Science has taken on the great wager … and lost.” Twenty-first-century evidence is reexamining the definition of species Darwin had distantly dedicated his life to destroy. As Darwin explained:

Generally, the term includes the unknown element [mystery] of a distinct act of creation.


Scientific evidence of unique distinctiveness is compatible with the Genesis account of creation, not evolution.

Richard William Nelson profile 2013

Written by Richard William Nelson

Richard William Nelson earned a Doctor of Pharmacy degree from the University of Southern California following graduation from the University of California, Irvine, with a Bachelor of Science degree in biochemistry. For more than a decade Dr. Nelson has been writing and speaking on the scientific merits of biological evolution. Dr. Nelson has spoken nationally and internationally to audiences in churches, schools, universities, and community organizations. As the author of the book entitled Darwin, Then and Now, The Most Amazing Story in the History of Science using more than 1,000 documented references, Dr. Nelson advocates using the scientific method to assess the merits of the theory of evolution.

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