Published in


Is Your Vision of the Evolutionary Tree Stuck in the 19th Century?

From Charles Darwin to Lynn Margulis, reestablishing the truth about the living realm

Image from

Darwin’s observations and analyses published in On the Origin of Species were brilliant and opened the door to a whole new vision of the history of life on our planet. It changed humanity’s vision of species being static to acknowledging they are dynamic — they emerge, evolve, and go extinct.

However, in Darwin’s time, microbiology as such didn’t exist. Ok, Antoni van Leeuwenhoek had already observed animalcules nearly two centuries before, but he had been largely ignored. Bacteriology started to become a thing only after Louis Pasteur, at the break of the 20th century, when the term microbe was coined. In 1923, David Bergey established a reference guide of bacteria, a tool still edited and used by most microbiologists today.

Thus, Darwin could not apprehend in his time the major importance of microbes in the evolution of life. He could not observe them and could not reserve them the right space on the Tree of Life. Our current vision has remained stuck 160 years behind, dominated by animals, and placing egocentric Homo sapiens at the top.

This is a problem because it does not reflect reality, and because it does not enable humanity to grasp the importance and potential of microbes in our past, present, and future.

A consortium of high-ranked scientists laid out the problem very well in The urgent need for microbiology literacy in society in 2019:

“Knowledge of relevant microbial activities, how they impact our lives, and how they may be harnessed for the benefit of humankind — microbiology literacy — is lacking in the general population, and in the subsets thereof that constitute the decision-makers.

It is indispensable for informed personal decisions, as well as for policy development in government and business, and for knowledgeable input of societal stakeholders in such policymaking.”

The actual Origin of Species

As wonderfully related by Lynn Margulis and Dorion Sagan in Microcosmos, 4 billion years of microbial evolution, the beginning of life was a progressive association of stable organic molecules giving rise to autopoietic microorganisms — organisms able to self-preserve and self-replicate, who then invented all the metabolic machines there were to invent (for more, Falkowski’s Life’s Engines focuses on these R&D achievements).

Consider that the first microorganism is thought to date back to roughly 3,7 billion years ago. Its little name is Luca, for Last Universal Common Ancestor. From this first living being, bacteria’s ability to exchange genetic material horizontally and to divide & conquer very rapidly led them to colonize every corner of Earth and to change it deeply. Cyanobacteria developed the capacity to use hydrogen from water, releasing oxygen as a waste product. Indeed, oxygen is highly oxidant, causing mutations and damaging cells — toxic for the whole living realm.

The rising levels of atmospheric O2 led to a huge biologic crisis, with all organisms unfit to escape the toxic compound to die. But, as happens with biological crises (comfort zone, anyone?), the presence of O2 kick-started the selection of innovations that would drive the rest of evolution on Earth for billions of years to come: flagella to move away, mitochondria to breathe (burn organic molecules into CO2 and water) and produce up to 36 of the energy molecule (ATP), while fermentation produced only 2.

The planet was a world of diversifying bacteria for almost the first 2–3 billion years of life on Earth. The first multicellular organism, a sort of ball-forming cluster of mobile bacteria, is dated 1 billion years ago. That means a rough 70% of the time life’s even existed, it only existed as unicellular bacteria.

Illustration of the timeline of the evolution of Life, by Author

What happened next is absolutely fascinating, and represents the life struggle of Lynn Margulis. Her theory was completely rejected and she wrestled all her life with society’s ego. Her research could not get funding, her papers could not get editors. Studying eukaryotic cells — those cells you are made of, plants are made of, fungi are made of: cells with a nucleus — and their organelles, she emitted three hypotheses, subsequently validated, that would change the vision of the tree of life forever:

1. The endosymbiosis theory: mitochondria are bacteria that infected bigger bacteria

In the primordial soup, bacteria swam about, surrounded by bacteria. Starving, they would prey on each other and infect each other all the time. The bacterium that recently invented breathing (remember, that capacity not only to survive when exposed to oxygen but to make the most of it to yield a ton of energy) must have penetrated and infected many other bacteria, such as Thermoplasma. Killing thousands. Think Covid-19 pandemic in primordial oceans. But when it was so aggressive as to kill its host, it would die away with it. So those less aggressive, which could find a balance, started to spread more and live in harmony with their host. They started to be domesticated, tolerated. They even became beneficial, providing a generous supply of ATP. Today, your cells contain a few hundred mitochondria, which still look like bacteria and replicate like bacteria.

The inside of the cell, image from Digizyme, annotated by Author

2. Another endosymbiosis, through ingestion this time: cyanobacteria becoming chloroplasts

About a hundred million years after the installation of mitochondria in the heart of their hosts, a new type of organism was about to join them in the cozy cytoplasm of such cells. A famished proto-eukaryote ingested a sort of cyanobacterium, photosynthetic blue-green plastid, which happened to resist digestion. Once in the host, this ancestor of Prochloron could still capture light and remain active.

It produced energy through photosynthesis and gave rise to chloroplasts, the organelle present in all plants and responsible for photosynthesis. This new symbiosis generated the whole kingdom of plants. Today, it is cyanobacteria and their offspring in the form of plants that supply the biosphere with oxygen.

“From a planetary point of view, mammal’s main role seems to be fertilizing plants and carrying mitochondria”. Lynn Margulis.

3. From flagella to motility, to sexuality and nervous systems

One of the major billion-dollar-patent innovations of the primordial oceans was motility. It gave the chance to get closer to food sources and crawl away from the wrong places, predators, and toxic oxygen. It happened thanks to the development of flagella by the group named Spirochetes. Flagella are a tail attached to the cell wall by a mechanism in a circular structure called 9+2, that spins. The agitation propels the cell forward.

Why is this important? Because this structure is found across the living realm and could not have evolved separately in protists, plants, and animals. Thus, the infiltration of spirochetes in other cells would, similarly to mitochondria’s ancestors, have caused widespread infection and death, and in some cases, the internalization of a structure that would then prove useful.

The inside of the eukaryotic cell is teaming with movement like a city. Organelles circulate on pre-determined routes, physically embodied by the microtubule (see illustration above). This road enables the division of genetic material from mother cells to daughter cells in eukaryotes. This was necessary for mitosis and meiosis, the two eukaryotic cells division types, explaining the invention of sexuality.

Axons and dendrites in the brain are also composed of microtubules called neurotubules. The role of such cells is to send and receive signals: the tubules could be like a cellular whip to vehiculate thought.

Think about it

After the invention of mitochondria, chloroplasts, and mobility, the rest of life’s evolution was just details. The insides and functions of our cells are almost the same. The genetic homology between you and the worm C. elegans is 83%. See how the tree of life on the top is wrong, now? What it really looks like now that molecular biology got involved, is this.

If you liked this article, I encourage you to read the tale of the beginning of life, Microcosmos, and to watch the 3 min video developed by Harvard — The Inner Life of the Cell. It is pure poetry to see the busy and adventurous whereabouts of protein in the cell, all seemingly driven by their purpose. And at the end of the day, we are here, alive. A miracle.



Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store
Nina Vinot

Nina Vinot

My Education is in Biology, Agronomy and Nutrition My Career is in Health-Promoting Bacteria My Passion is to Benefit Life, Happiness and the Planet