"Look at life from our perspective, and you eukaryotes will soon cease giving yourselves such airs. . . . you newcomers on the block, you eukaryotes, you barely distinguishable congregations of a monotonously narrow parish, you are little more than fancy froth on the surface of bacterial life. Why the very cells that build you are themselves colonies of bacteria, replaying the same old tricks we bacteria discovered a billion years ago. We were here before you arrived, and we shall be here after you are gone." *


Welcome to the world that bacteria have built; maintaining us, they nourish for us, and recycle necessary, but scarce, materials from your ancestors to you and for your children and all our descendents to reuse.

Without them we are nothing, with them we survive better because without them we would perish.

notes: on the Life sciences: revolutions in learning
Lynn Margulis, Symbiotic Planet, A New Look at Evolution, (New York, Basic Books, 1998).


 "Symbioses are like flashes of evolutionary lightening."


Coral reef

 1 Symbiosis Everywhere

 2 Against Orthodoxy

 3 Individuality by incorporation

 4 the Name of the Vine

 5 Life from Scum

6 Sex Legacy

 7 Ashore

 8 Gaia

A Coral reef is comprised of many different species, whose members are creatures which actually are animals that have algae or protoctista living in their flesh, this is referred to scientifically as endosymbiosis.


five     Three Domains of life


 "As a species we cling to the familiar comforting conformities of the mainstream.

However,'convention' penetrates more deeply then we tend to admit. Even if we lack a proper name for and knowledge of the history of any specific philosophy or thought style, all of us are embedded in our own safe 'reality.' Our outlooks shape what we see and how we know. Any idea we conceive as fact of truth is integrated into an entire style of thought , of which we are usually unaware."

Pp. 2-3.


"Call the cultural constraints 'trained incapacities,' thought collectives,'social constructions of reality.' "

p. 3.

"Like those of everyone else, the scientists hidden assumption affect his or her behavior, unwittingly directing thought."

p. 3.

Symbiosis, "our lack of awareness of its prevalence."

 "symbionts are not obvious, but they are omnipresent"
"we are symbionts on a symbiotic planet."

 "Physical contact is a nonnegotiable requisite."

p. 5.

Ivan E., Wallin, he believed that "new species arise though symbiosis."


fruit flies bread in progressively warmer temperatures, eventually became distinct form the parent or originating species.

p. 7

"That turned out to have something to do with a parasite." !

 "Symbioses are like flashes of evolutionary lightening."

p. 8.

Platymonas, single celled green algae in worms on the coast of France, Brittany

p. 9.

"we animals, all thirty million species of us, emanate from the microcosm. The microbial world, the source and well spring of soil and air, informs our own survival."

p. 10.

chlorella, Ophrydium balls of jelly embedding green chlorella algae

 Kefir is symbiotic -- 25 different kinds of bacteria and yeast

2 : Against orthodoxy

p. 13.

her collegiate training was at the University:

"I adored Crow's general genetics course: it changed my life."
The superb science of the University of Chicago...

"Human and other animal consciousness, as well as other types of biological beauty and complexity are properties of our coevolving, pointillist bacterial ancestry."

 "cellular inter living,... produced everything from spring-green blooms, to warm, wet mammalian bodies..."

p. 20.

"All beings alive today are equally evolved."

p. 20.

"The findings of the importance of symbiosis in evolution have forced us torevise the earlier nucleocentric view of evolution as a bloody struggle of animals."

pp. 19-20.

"...symbiosis, beginning as an uneasy alliance of distinct life-forms, may underlie the origin of major evolutionary novelty."

p. 20.

"The genes in other words are not necessarily in the nucleus."

These genes are also in some organelles

 "the mitochondria contain their own genes."

p. 22.

At the University of Chicago, "We where taught how, through science, we could go about to answering important philosophical questions."

What are we?
Of what are we and the universe made?
Where do we come from?
How do we work?
p. 23.

"a set of methods that are honest, open, accessible, and energetic seems hardly to exist in the 'technological fix' mentality of today."
p. 23.

"Realization that the emphasis on connecting genetics to chemistry had unnecessarily given scientists too narrow a perspective , one overly focused on the nucleus, was my jumping off point."
p. 25.

plastids and mitochondria apparently had there own peculiar genes outside of the cell nucleus.
p. 25.

"Genetics ... Still seemed to me to be the key to evolutionary history."
p. 27.

hard to distinguish blue green bacterium embedded in cells and chloroplast, based on function and behavior.

 Serial endosymbiosis theory and Symbiogenesis
p. 29.

SET Serial endosymbiosis Theory.
p. 31.

3 : "Individuality by incorporation."

coined in 1873, by German botanist, Anton deBary, living together of very different kinds of organisms.
p. 33.

Sym + biosis [Latin: with + living] ; living with or living together
the existence of two distinct species of organisms in such a manner that the genetic success of one is tied to the genetic success of the other.

examples of symbiosis:

type of Being, producing species + consuming species

lichens, algae + fungus
corals, zooxanthelae algae + animal polyp
legumes, cyanobacter root nodules + plants
rhododendron, mycorrhizae fungus + forest trees (plants)
termites, gut bacteria + other gut bacteria

Not a special case in biology but an obvious successful pattern.

Question: Did bacteria build plants, animals and fungus in order to best survive extreme conditions, competition for scarce resources , or to establish new territories in which to thrive?

Spirochetes become undulipodia (motile bacteria become an organelle to move cytoplasm)
p. 35.

Cyanobacteria are relatives of chloroplast
p. 36.

mitochondria are relatives of oxygen breathing bacteria
p. 38.


4 : The name of the Vine

 "names of living beings seem harmless enough."
taxonomy defined as the means used to separate one thing from another in an agreed upon classification system.

p. 51.


 "...such trees are idealized representations of the past. In reality the tree of life often grows in on itself."

tangled bank
Anastomosis, branches forming nets"

p. 52.

Ivan Wallin's 1920s suggestion that chloroplasts and mitochondria "originated as symbiotic bacteria."

p. 53.

17th century origin of bacteria classified as "animalcules"

 "Language can confuse and deceive."

p. 55.

"Most bacteria a no more harmful than air..."

"Wallin's colleagues confused the map with the territory."
p. 55.

The idea of plants, animals, and germs "this idea is as dangerous as it is prevalent"
p. 56.

Ernst Haeckel (1800s) added protists to Anton van Leeuwenhoek's animalcules (1600s)
p. 57.

Linnean system, late 1700s, had focused on sexual organs to distinguish one species from another, one genus from another and one order from another.
p. 58.

Ernst Haeckel's championing of evolution.
He established Monera as the phyla for radiolarians and foraminiferans, or the radially symmetrical forms of life he found in the sea.
pp. 59-60.

Herbert Copeland
took the term (1860) "protoctista" and in 1956 subdivided the Monera kingdom
p. 60.

Whittaker at Cornell refined Copeland's separation in 1959.five

Five kingdom system: protists animals

p. 61.

"All protoctists evolved from bacterial symbiosis."

p. 62.

protoctista gave rise to plants, animals and fungus.

  / Zoomastigotes -----> Animals
Protoctista Chlorophytes --------------> Plants
  \ Chytrids ----------------> Fungi


p. 63.

"viruses today spread genes among bacteria and human and other cells."

p. 64.


Prokarya versus eukarya as major divisions in the five kingdoms or three domains.

p. 64.

Carl Woese three domain system:

(RNA based, RNA for building ribosomes differ)

The domains are: five animals

The reproductive strategies of each grouping differ remarkably:

p. 65-66.

ribosomes are the place in the cell where transfer RNA inserts a cloned form of DNA from the nuclei and the place in the cell where proteins are constructed from the available amino acids.

"The move toward evolution based taxonomic classification systems has taken hold."

p. 68.

5: Life from Scum

seashore mats -- photosynthetic bacteria in worms, such that the worms lose their capacity to use their mouths, originally used for eating.

"These colorful seaside expanses, called 'microbial mats,' enchant me – a living landscape just where the sea meets and rolls back and forth over the land" 

"death is part of life."

p. 69-70.

"The properties of minimal bacterial life, first life, can be inferred by several approaches."

1) comparatively – what do all living things have in common?
p. 70.

2) paleobiology – microfossils in rocks of particular ages.
3) attempt (in the lab) to remake a cell
4) the bacterial cell, "today's minimal unit of life,...is where we must begin."
5) "Prelife, with a suitable source of energy, inside a greasy membrane, grew chemically complex."


Harold J. Morowitz "amusing book on mayonnaise."
p. 71.

3.5 billion year old rock from South Africa, Swaziland, oldest bacterial evidence.
p. 72.

How rare are the events associated with life on Earth?
Event Age percent ratio of duration
Big Bang singularity, 20,000 million years ago 100%  
Earth formed 4,600 million years ago 23% > 1:5
life established 3,500 million years ago 17.5% > 1:6

6. Sex Legacy

"when bacteria wildly reproduce they need no sex to do it. The bacterial sex that responds to certain environmental contingencies is occasional."

p. 88.

Sexual processes, the merger of attracted beings, probably originated as did the early symbiosis."

"meiotic sex began long after bacterial sex as abortive cannibalism in certain protists."

"Symbiogenesis is far more splendid than sex as a generator of evolutionary novelty."

p. 89.

Sex here emerges as a kind of median or medial along a spectrum of intimacy from proximate to distant cohabitation
living together   living apart
  <-------- Sex -------->  
(touching)   (remoteness)
intimacy   separation

"programmed death is a nonnegotiable consequence of the sexual mode of life."
"is linked intimately with the imperative of plants and animals to die."
p. 90.

"Animals, all of them, an essential 30 million species belonging to nearly forty phyla, revert to a single-cell protist -like stage in each generation ....Mortality is the price they pay..."
p. 91.

The Cambrian, (Preston Cloud)

"All animals are aerobes."
p. 95.

female sex, parthenogenesis.
p. 99.

"Abortive cannibalism in single celled protoctists resulted in a truce called sex."
p. 100.

stressed conditions encourage protists to eat anything and everything.
p. 101.

7. Ashore

Star Trek is a depauperate (plantless, bacterial less, machino/macho) sort of science fiction.

"Ecosystem services"
"An ecosystem is the smallest unit that recycles the biologically important elements."

p. 105.

Carbon and Nitrogen cycles given as examples of essential nutrients

"I prefer the idea that Earth is a network of ecosystems (as a set of communities) over any personification of Mother Gaia."

p. 106.

"The material and energy needs of organisms in any ecosystem are met by recycling all the scarce chemical compounds required for life maintenance."

p. 106.

Land dwellers may owe their hold on dry ground to specific symbioses between plants and fungi."

"Plant roots and fungi grow together into bumps on roots called mycorrhizae."

p. 107.

fungal fusion to explain the coevolution of green plants, 450 million years ago

p. 107.

lichens symbiotic associations of algae, fungi, bacteria.

p. 108.

"animated water", after Vernadsky, the capacity of plants to pump water

90% of plants have mycorrhizae associated with their roots.

p. 110.

8. Gaia

 "What has emerged is the mathematical outline of an overlap between natural selection and global temperature regulation."

"global temperature regulation is a paradigmatic example of Gaian regulation."

stabilization of temperature is a product of the daisy world models.

p. 127.

SET diagram of the phylogeny of Moneran descendents:

Prokaryotic organisms:

 Archaebacteria, Eubacteria, & Cyanobacteria

Eukaryotic organisms:
all algae (red, green, brown
cilliates, slime mold
water molds

root mycorrhizae

Animalia animals
snails, mollusks
fish, birds, reptiles

Plantae plants
flowering plants

pp. 31, 129.

"We people are just like our planet mates. We cannot put an end to nature; we can only pose a threat to ourselves."

p. 128.

SET means Serial Endosymbiosis Theory.

classifications of all eubacteria -- The eubacteria are more complex, and common, than the archaebacteria. It is the eubacteria that most people are talking about when they say bacteria, because they live in more neutral conditions. They can be found everywhere around us – in our bodies, our food, etc. There are four phyla of bacteria, some of which are divided into subgroups.



Proteobacteria is one of the largest phyla of all the bacteria. Many are gram-negative. They are divided into several subgroups, such as enteric bacteria, chemoautotrophs, and nitrogen-fixing bacteria. The enteric bacteria live mainly in intestinal tracts, like E. Coli. The chemoautotrophs oxidize chemicals in minerals to obtain energy. The nitrogen-fixing bacteria are essential to many ecosystems – one type converts the unusable nitrogen in the atmosphere to ammonia, the form plants can use most easily.

Cyanobacteria are photosynthetic, like plants, which means that they use the sun’s energy to make food for themselves. They are thought to be the second organisms in existence, because they give off oxygen as a byproduct. This allowed aerobic organisms (ones that need oxygen to survive) to develop. They are found in the water and were once thought to be blue-green algae (however, they lack a membrane-bound nucleus and chloroplasts).

Spirochetes are [ gram-negative -- a gram stain is a technique for classifying bacteria ], spiral-shaped, and heterotrophic. Some of them live in the presence of oxygen, others don’t. They may be parasitic, living symbiotically (where two organisms live off each other), or free-living. One type of spirochete causes syphilis.

Gram-positive bacteria are not all gram-positive, despite the same. They are grouped together due to other similarities. This phylum includes the strain of streptococcus bacteria that causes strep throat. It also includes the bacteria that produces yogurt, by growing and fermenting in milk (producing lactic acid). These bacteria also produce many of our antibiotics.

Welcome to the world that bacteria have built for us, maintain for us, and recycle necessary, but scarce materials for you, your children and all our descendents to reuse. With them we live better, because without bacteria we would all perish.


1 Symbiosis Everywhere

  2 Against Orthodoxy  
  3 Individuality by incorporation  
  4 the Name of the Vine  
  5 Life from Scum  
  6 Sex Legacy  
  7 Ashore  
  8 Gaia  

Richard Dawkins, The Ancestor's Tale. (Boston: Houghton Mifflin, 2005), p 558.