In his seminal book, The Origin of Species, Charles Darwin proposed the theory of descent with modification by means of natural selection, a postulate he supported with considerable evidence from myriad observations and exhaustive experimentation. Darwin’s powerful insights can be summarized as follows:
Offspring vary from their parents. Some of the variances are heritable. Only a fraction of the total offspring of any organism survives to themselves reproduce. Those heritable variances that are advantageous to an organism are “selected for” by the environment and those that are disadvantageous are “deleted” by the environment. This differential survival is known as natural selection. The accumulation over time of the differences that survive is descent with modification .
Ironically, one of the insights Darwin does not propose in The Origin of Species is how species arose in the first place and how new species originate. In other words, the Origin is mute on speciation and, therefore, the underlying engine of biodiversity. There is a quip attributed to Australian biologist George Miklos that, “the origin of species was precisely what Darwin’s book was not about.”
Natural selection is not innovative, meaning it does not create new life forms. Rather, it is an editor, selecting from the variety of previously created life forms. One of the keys to understanding evolution lies in understanding the phenomenon of speciation, the underlying cause of variation that results in the creation of new species.
Many neo-Darwinists have argued that the variation acted upon by natural selection leading to the origins of new species is caused by mutation. In fact, the notion of mutation as the major driver of biodiversity has become the prevailing wisdom.
Although mutation does contribute to variation within species, there is no evidence in the literature that this author has seen that mutation leads to new species. Scientists have induced mutations in various species in the laboratory for years. Some of these induced mutations have been passed along to offspring, demonstrating that mutations are indeed heritable. Yet no scientist has been successful in creating a new species in the laboratory by inducing mutation in an existing species .
In addition, researchers have found no evidence in the fossil record of gradual speciation as a result of cumulative mutation. To the contrary, the preponderance of evidence supports “punctuated equilibrium”. Punctuated equilibrium is an argument put forth by Paleontologists Stephen Jay Gould and Niles Eldredge which counters the gradual view of evolution with evidence from the fossil record illustrating long periods of small variation in species without direction (the “equilibrium” part) and the sudden appearance of new species (the “punctuated” part) .
Eldredge studied Cambrian Period trilobites, preserved in sediment in Morocco and upstate New York, looking for gradual transitions from one species to the next. However, he did not discover evidence supporting the trend of a slow transition from one species to another. Instead, he found evidence that one species would persist with minor variations for hundreds of thousands of years and fossils of another species would suddenly appear on the scene, accumulating modest variations of its own for hundreds of thousands or a million years. There are no fossil records of “transitional” or “intermediate” forms showing gradual evolutionary change between species. Richard Fortey, a paleontologist at the Natural History Museum in London, later reconfirmed Eldredge’s conclusions concerning trilobites. Similar discontinuities in the fossil record have been observed in snails, clams, Devonian fish, and dinosaurs. It is not that the fossil record has holes. The sedimentary rocks containing the Cambrian trilobite fossils are continuous, as are the fossil records of the other organisms. It appears it is evolution that is discontinuous.
In addition to the lack of evidence supporting mutation as the cause of variation leading to speciation, more often than not mutation is deleterious. Hermann J. Muller, the Nobel laureate, showed that X-rays are mutagenic in fruit flies. He also pointed out that 99.9% of the mutations are negative and do not get selected for . So while mutation clearly plays a role in evolution, and it may be a major reason for variation within a species, it is not the driving force of speciation.
Fortunately there is an alternative hypothesis for the cause of variation underlying the creation of new species, and therefore, the engine of biodiversity. This compelling hypothesis is “the acquisition of genomes”. Specifically, the hypothesis involves genome acquisition as a result of symbiogenesis – long-term symbiosis leading to evolutionary change.
There is ample evidence supporting the hypothesis that speciation, and in turn biodiversity, stems largely from genomic acquisition. The protagonist of this gigantic creative activity turns out to be a midget in stature – the microbe. To borrow a phrase from Darwin, there is grandeur in this view.
One of the modern day champions of the theory of genomic acquisition is Lynn Margulis, a biologist at the University of Massachusetts, Amherst, who against considerable opposition early in her career proposed and defended the endosymbiont theory of mitochondria and chloroplasts, which is now subscribed to by many biologists and supported by overwhelming evidence.
According to the endosymbiont theory, eukaryotes did not evolve from a prokaryotic ancestor that accumulated mutations over time until it gradually arrived at the structural level of a eukaryotic cell. Rather, the origin of eukaryotic cells can be traced to a symbiotic relationship, a prolonged physical association between two or more different types of organisms, among prokaryotes . Over time this consortia of prokaryotes became stable and resulted in symbiogenesis – symbiosis that led to evolutionary change.
The idea that the eukaryotic cell is comprised of a group of microorganisms was originally proposed by Russian biologist Konstantin Merezhkovsky early in the twentieth century. Merezhovsky was not widely read because most scientists in the West did not read Russian. The literature of the Russian botanists was later translated but their revolutionary evolutionary thinking did not take root, probably because papers penned by Russian botanists of a bygone era are just not sexy . The idea was put forth independently by American biologist Ivan Wallin, in the 1920s. In 1981, Margulis proposed the theory of endosymbiosis that now enjoys support by many in the biological community.
So, symbiosis is responsible for producing eukaryotic life from bacteria (at least the mitochondria and chloroplasts). Since all non-bacterial life is eukaryotic, animals, plants, fungi, and protoctists all can trace their origins to symbiogenesis. However, the contribution of genomic acquisition to variation did not end with the evolution of the first nucleated cell. In fact, the evidence suggests the appearance of eukaryotes was just the beginning of novelty created by symbiogenesis.
Many biologists do not subscribe to the bacterial nature of eukaryotes. Instead, some believe that eukaryotes evolved from archaebacteria without resorting to symbiogenesis. Radhi Gupta, a biochemist at McMaster University Medical School in Hamilton, Ontario, argues otherwise. He claims that all eukaryotes, even those lacking mitochondria or chloroplasts, are chimeras, a reference to the mythical beast with the body of a goat and the head of a lion. Gupta compared the protein sequences of hundreds of different bacteria with those of certain protists. He discovered that the eukaryotic cells contained some protein sequences similar to those found in archaebacteria and others similar to those found in eubacteria . Thus, it is plausible that Gupta’s chimera was formed from the merger of two symbionts, a eubacteria and an archaebacteria.
There are other fascinating examples supporting the Îchimericâ nature of eukaryotes and their creation from genomic M&A. G.A. Dubinina discovered the species Theodendron latens was in fact not a single species but rather a bacterial consortium of a Desulfobacter and a Spirochaeta . Dennis Searcy looked at his own red blood cells for evidence that eukaryotic cells retain their prokaryotic ancestry. His hypothesis is that the first eukaryote was likely a bacterial consortium of a Thermoplasma that produced hydrogen sulfide and a Spirochaeta. He was looking to see if the cytoplasm in red blood cells retained its prokaryotic ability to metabolize sulfur. He chose red blood cells for purity of experiment since they lack mitochondria (as well as nuclei and cell walls). He found that even though there was no reason to expect it, red blood cells did generate hydrogen sulfide when given elemental sulfur. He replicated the experiment successfully with plants, fungi, and protoctists.
Recently, researchers from Canada and Brazil built a mathematical model using Volterra-Hamilton Systems to test the evolutionary theory of Carl Woese, a microbiologist from the University of Illinois at Urbana-Champaign, who has proposed a theory of horizontal gene transfer, against Margulis’ theory. The researchers evaluated the scientists’ predictions and compared them to the output from their model. They found Woese’s theory suffered from instability in its chemical exchange processes, which is required for evolution to occur. They found no such shortcoming in Margulis’ theory. While this author does not purport to have vetted the mathematics of the research, it is an interesting “simulation” brick in the edifice of observational evidence being erected in support of the theory of genomic acquisition.
Lichens, coral reefs, and dairy cows are macroscopic examples of life forms made up of consortia of species living in long-term, stable, symbiotic relationships that have effectively become individuals through merger. Lichens, one of the toughest living “organisms”, are in reality intimate collaborations between fungi and algae. Corals contain photosynthetic algae within their tissues that provide it with nutrients. A menagerie of microbes makes their home in the stomachs of cows, keeping them alive by digesting the cellulose of grass they injest.  Closer to home, as a result of the human genome project, scientists have learned that approximately two hundred and fifty of the genes of Homo sapiens come from bacteria. 
There are extreme reactions to the logical conclusion to which this theory leads. One reaction can be given voice by Nobel Prize winner Christian de Duve who has said of Margulis: “she does not hesitate to speak of the “spirochetal nature of intellect.” Spirochetes, it may be recalled, are corkscrew-shaped bacteria among which are found the agents of syphilis and Lyme disease.” 
The other reaction is embodied in the words of Lewis Thomas, who reflected: “Mitochondria are stable and responsible lodgers, and I choose to trust them. But what of the other little animals, similarly situated in my cells, sorting and balancing me, clustering me together? I like to think that they work in my interest, that each breath they draw they draw for me, but perhaps it is they who walk through the park in the early morning, sensing my senses, listening to my music, thinking my thoughts.” 
They might be giants, de Duve and Thomas, but there is a giant gulf between the views they give voice to regarding the origins of species. In the end, the weight of the evidence, as always, will point us to the right answer. Currently, it seems there is a paucity of evidence supporting mutation as the cause of speciation, and while far from conclusive, there is a growing body of observational and experimental evidence stacking up in favor of symbiogenesis as the major driver of speciation and, therefore, biodiversity.
1 Charles Darwin, The Origin of Species (London: Signet Classic, 2003).
2 Lynn Margulis and Dorian Sagan, Acquiring Genomes: a theory of the origins of species (New York: Basic Books, 2002) 11-12.
3 Niles Eldredge, Fossils: the evolution and extinction of species (New Jersey: Princeton University Press, 1991) 32-60.
4 Richard Fortey, Trilobite!: eyewitness to evolution (New York: Alfred A. Knopf, 2000).
5 Margulis and Sagan, 11-12.
6 Neil A. Campbell and Jane B. Reece, Biology: sixth edition (San Francisco: Benjamin Cummings, 2002) 549-551.
7 Margulis and Sagan, 97-98.
8 Ibid, 153-157.
9 Ibid, 145-150.
10 Ibid, 150-153.
11 P.L Antonelli, L. Bevilacqua, S.F. Rutz, ãTheories and models in symbiogenesis,ä Nonlinear Analysis: Real World Applications 2003.
12 Richard Fortey, Life: a natural history of the first four billion years of life on earth (New York: Vintage Books, 1999) 60-63
13 Margulis and Sagan, Dorian, 76.
14 Christian de Duve, Life Evolving: molecules, mind, and meaning (Oxford, U.K.: Oxford University Press, 2002) 118.
15 Lewis Thomas, The Lives of a Cell: notes of a biology watcher (New York: Penguin Books, 1974) 4.