October 24, 2022 | Jerry Bergman

Origin of Eukaryotes: Still Wishing and Hoping Endosymbiosis Is True

Subsequent to the origin of life, the origin of eukaryotic cells
is admittedly the next most serious problem for evolutionists


by Jerry Bergman, PhD

Evolutionists believe that at one time, in the far distant past, “the defining characteristics of modern eukaryotic cells—the nucleus, mitochondria, cytoskeleton, cell membrane, and chloroplasts, among others—made their debut.”[1] The problem is, evolutionists admit ignorance of how that happened. [Note: Eukaryogenesis is a fancy term meaning the origin of eukaryotes.]

Most of the details of these evolutionary leaps, however, remain unsettled. Researchers do not uniformly agree on which branch of life eukaryotes sprang from, which microbial players might have contributed to the process, or on the order of specific evolutionary milestones along the way. But the recent identification of the Asgard archaea, thought to be the closest living relatives to modern eukaryotes, has enlivened discussions about eukaryogenesis.[2]

The superphylum Asgard, within the kingdom of archaea, may have enlivened discussions about eukaryogenesis, but it has not done much more. First, the problem needs to be detailed, then the potential evolutionary solution introduced.

Definitions and Issues

All living cells are divided into two major groups: prokaryotes, cells without organelles, and eukaryotes,  cells with organelles.  Prokaryotes are, by far, much simpler than eukaryotes. For this reason, evolutionists postulate that prokaryotes evolved first, and eventually, after billions of years, some prokaryotes evolved into eukaryotes.

A prokaryotic cell compared to a eukaryotic cell. Notice how comparatively simple the prokaryote’s cell is compared to the eukaryote’s cell. From Wikimedia Commons.

An enormous gap exists, however, between these two cell types. Not only is evidence lacking that eukaryotes evolved from prokaryotes, but the gap could not have been bridged by transitional forms. Natural selection would have rendered incipient organelles worse than useless until they were at least partly functional. (The origin of prokaryotes is itself a major difficulty for materialists. There is no evidence that prokaryotes evolved from non-life.)

Many secular scientists recognize these and numerous other problems with the theory that prokaryotes evolved into eukaryotes.

The Endosymbiosis Theory

Lynn Margulis (1938-2011) the main developer of the endosymbiosis theory. Historian Jan Sapp has said that “Lynn Margulis’s name is as synonymous with symbiosis as Charles Darwin’s is with evolution.” From Wikimedia Commons.

The most popular attempt to explain this wide gap was the endosymbiosis theory developed by the late biologist Lynn Margulis. Throughout her career, Margulis’ work aroused intense objection (one grant application elicited the response, “Your research is crap. Don’t ever bother to apply again.”) and her paper, “On the Origin of Mitosing Cells,” appeared only in 1967 after being rejected by fifteen journals.[3]

The endosymbiosis theory proposes that, eons ago in the unseen past, some proto-eukaryotic cells engulfed prokaryotes, and eventually the engulfed proteobacteria evolved into organelles in primitive pre-eukaryotes. After more millions of years, the last organelles existing in eukaryotes evolved by a similar means.

To show her independent mindset, it may be of interest to know that Margulis believed in conspiracy theories about the 9/11 terror attacks in New York City. She maintained that there was “overwhelming evidence that the three buildings [of the World Trade Center] collapsed by controlled demolition” evidently by our or another government. (Quote from Sagan, Dorion (ed.), Lynn Margulis: The Life and Legacy of a Scientific Rebel, Chelsea Green Publishing, White River Junction, Vermont, 2012.

Margulis’s first version of her endosymbiosis hypothesis—that mitochondria evolved from a bacteria which somehow got into another bacterial cell—was immediately recognized as problematic. The eminent University of Alberta professor Jack A. Tuszynski mocked her “lucky accident” notion in 2007:

The many contrasts between the prokaryotic and eukaryotic means of producing ATP provide strong evidence against the endosymbiosis theory. No intermediates to bridge these two systems have ever been found and arguments put forth in the theory’s support are all highly speculative. In the standard picture of eukaryote evolution, the mitochondrion was a lucky accident. It proposed that first, the ancestral cell, probably an archaebacterium, acquired the ability to engulf and digest complex molecules. At some point, however, this predatory cell didn’t fully digest its prey, and an even more successful cell resulted when an intended meal took up permanent residence and became the mitochondria.[4]

The many other major problems with this theory may lead one to conclude that it is widely accepted today only because it is the least implausible evolutionary hypothesis around—not because of empirical evidence in its favor. All other hypotheses are even far less plausible.

At least Margulis rejected Darwinian gradualism. She admitted in 2002 that “No missing links between eukaryotes and bacteria exist, either in the fossils or in life. The sudden appearance of eukaryotes… was genuinely discontinuous and not gradual.”[5]

In spite of the many problems with endosymbiosis, a news article in The Scientist this month endeavored to remain optimistic about it. In her article, “The long and winding road to eukaryotic cells,” reporter Amanda Heidt began by restating the problem in her subtitle: “Despite recent advances in the study of eukaryogenesis, much remains unresolved about the origin and evolution of the most complex domain of life.”[6]

Farther down in the article, she quoted Daniel Mills, of Ludwig-Maximilians-Universität in München, who called the origin of eukaryote cells “arguably one of the most important events in the history of life, after the origin of life itself.”[7] In an accompanying infographic, Heidt says, “A lot happened in the hundreds of millions of years separating the first and last eukaryotic common ancestors, but when and how most features arose remains a mystery.”[8]

Not deterred by the failures to fill this “enormous gap” in the eukaryogenesis story, Heidt tells how a team of researchers has recently taken a very different approach.


A New Story

In recent years, evolutionists have searched the driest places in the world on a hunch that these often unexplored areas might hold clues to the origin of eukaryotes. A team from the University of Paris went to the Atacama Desert in South America. They eventually found pockets of life—specifically cyanobacteria [formerly called blue-green algae]—that they concluded lived long before Earth resembled its current design. They argued that the microbial mats they found there “were the forests of the past,” and that scientists could use these clumps of microscopic life “as analogs of past ecosystems that certainly occurred at the time when eukaryotes first appear[ed],” team member López-García stated.[9]

A careful evaluation of these clumps of microscopic life revealed that they were complex ecological systems of several types of microbes.

Each layer of these living mats is composed of different types of microbes that rely upon one another. At the surface, where light and oxygen are plentiful, photosynthesizing cyanobacteria dominate, while just below, heterotrophs that can persist in low-oxygen environments feed on their byproducts. Deeper down, the mats become dark and smelly, the result of the sulfate reducers and methanogens that populate these oxygen-bereft zones. Here, these partnerships become even more essential, with the castoffs of one group serving as fuel for another.

Then the speculation began, as noted by my added bold italics:

These close metabolic associations between organisms, a type of symbiosis known as syntrophy, may have prefaced the evolution of complex life by creating alliances that turned permanent over time…. In this way, individuals of different microbial species could have nested within one another to create a host with one or even several symbionts. This is exactly what scientists suspect happened to form a whole new type of cell, the eukaryote, which thrived and subsequently diversified into the macroscopic array of life we see today, including humans. So-called eukaryogenesis is not defined the same way by all researchers, but broadly, the term describes an evolutionary surge toward increasing cellular complexity between 1 and 2 billion years ago. Today, at the microbial mats in the Atacama Desert and other sites throughout the world, scientists are investigating what the earliest eukaryotic cells may have looked like, the partnerships they may have struck up with other organisms, and how their molecular machinery might have functioned and evolved. … Eukaryogenesis, he adds, is “arguably one of the most important events in the history of life, after the origin of life itself.”[10]

Can these newly-discovered organisms bridge the gap between prokaryotes and eukaryotes? Aside from the admitted speculation indicated in bold italics, several problems exist with this attempt. Among them were hints that the genomes of these archaea contain the genetic code for genes that produce eukaryotic proteins! Among them were homologs for actin, a distinctly eukaryotic protein that gives cells their shape. This was found in a genome that was otherwise clearly archaeal and not eukaryotic.

Researchers eventually detected additional homologs of eukaryote-like proteins involved in everything from ubiquitin signaling to gamete fusion. This is leading them to propose that an ancient archaeon—not a bacterium or proto-eukaryote as many previously assumed—was present at the critical first step in the evolutionary process that ultimately resulted in a new type of cell.

Still Searching

As has been the trend over the past century, relatively unexplored areas of Earth are revealing more variety and complexity in the natural world. These microbes were not caught in the process of evolving. Instead, they can be described as unique micro-organisms, similar to the bacteria found thriving along with tube worms deep in the ocean when hydrothermal vents were first discovered.[11]

Evolutionists must assume that these Asgard archaeal microbes have thrived unchanged in their habitat for over a billion years. Those involved in the investigation continue clinging to a modified form of the endosymbiosis theory. Here is one statement as an example:

At some point in the past, the prokaryote host formed a partnership with an alpha-proteobacterium and permanently engulfed it, creating the mitochondrion. Researchers debate whether phagocytosis was needed to establish this relationship, but mitochondria did help power much of eukaryotes’ subsequent radiation.[12]

One scientist involved in the research admitted,

the identity of the original host in the symbiotic partnership that birthed modern eukaryotic cells remains mysterious, [and] some researchers say the evidence suggests it was an archaeon rather than a bacterium. Scientists call this host, which lived more than a billion years ago, the first eukaryotic common ancestor.[13]

To pile story on top of story, the proponents of this latest idea then claim that these microbes “are the ultimate living fossils.” By that they mean that they have hardly changed at all in a billion years. They join a long list of living fossils that defy evolution. These include horseshoe crabs, the coelacanth, the tuatara, the ginkgo tree, the koala, the hoatzin, the platypus, the nautilus, the red panda, the aardvark, the crocodile, and others.[14]

The first concern of these evolutionists ought to be, ‘How could they have lived for over a billion years without changing during such an enormous span of time?’ But if they did evolve, on the other hand, then they could tell us very little about what conditions were like allegedly a billion years ago. Either way, eukaryogenesis remains a theory in crisis.


The data from this new proposal about eukaryogenesis tell us a lot about the enormous amount of variety living on our Earth today and in the past, but do not help to explain how prokaryotes evolved into eukaryotes. The gap between those two types of cells leaves evolutionists with as big a mystery as ever.


[1] Heidt, Amanda, The long and winding road to eukaryotic cells, The Scientist, 17 October 2022.

[2] Heidt, 2022a.

[3] Margulis, Lynn, Gaia Is a Tough Bitch. Chapter 7 in The Third Culture: Beyond the Scientific Revolution by John Brockman, Simon & Schuster, New York, New York, 1995.

[4] Tuszynski, Jack A., Molecular and Cellular Biophysics, CRC Press, Boca Raton FL,  pp. 207-208, 2007.

[5] Margulis, Lynn, and Dorion Sagan, Acquiring Genomes: A Theory of the Origins of Species, Basic Books, New York, New York, p. 139, 2002.

[6] Heidt, 2022a.

[7] Heidt, 2022a. Quote by Daniel Mills, Ludwig-Maximilians-Universität München.

[8] Heidt, Amanda, Infographic: Evolutionary Leaps Leading to Modern Eukaryotes, The Scientist, 17 October 2022.

[9] Heidt, 2022a.

[10] Heidt, 2022a; emphasis added.

[11] Boutin, Chad, Two miles underground, strange bacteria are found thriving, Princeton University, 20 October 2006.

[12] Heidt, 2022a.

[13] Heidt, 2022a

[14] Nelson, Bryan, 16 Animals That Are Living Fossils, Treehugger, 5 May 2022.

Dr. Jerry Bergman has taught biology, genetics, chemistry, biochemistry, anthropology, geology, and microbiology for over 40 years at several colleges and universities including Bowling Green State University, Medical College of Ohio where he was a research associate in experimental pathology, and The University of Toledo. He is a graduate of the Medical College of Ohio, Wayne State University in Detroit, the University of Toledo, and Bowling Green State University. He has over 1,300 publications in 12 languages and 40 books and monographs. His books and textbooks that include chapters that he authored are in over 1,500 college libraries in 27 countries. So far over 80,000 copies of the 40 books and monographs that he has authored or co-authored are in print. For more articles by Dr Bergman, see his Author Profile.

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