The Tree of Life

This is part 5 of a series. For part 4, click here.

Two hundred years ago, Charles Darwin, set out to discover whether different species were uniquely different, or not.

Most Western philosophies in those days were derived from religious teachings, so most scientists assumed that all the various species had been created at the same time. As such, each species must be fundamentally unique.

But Darwin set all those philosophical pins tumbling when he proved (correctly) that all species are related to one another.

Hilariously, some people objected because it implied that human beings were related to monkeys (since proven true with DNA). In fact, it’s probably the most famous aspect of Darwin’s theory of evolution.

Yet the fact that his theory postulated (again, later proven true with DNA) that human beings are related to trees was, and still is, largely forgotten, yet it’s far more important than our similarity to apes.

We are all related.

Human beings use the exact same gene sequence to digest sugars as a tree does. We both inherited it from our common ancestor.

Atropos, Clotho, and Lachesis

In fact, every single animal, tree, bird, fish, reptile, insect, tree, bush, plant, and fungus that you’ve ever eaten, seen, heard, or touched in your life is closely related to human beings.

If the Tree of Life was first planted three billion years ago, then every life form that exists on the macroscopic (big) level is a tender young shoot emerging from the topmost branch.

All of us – every single fish, person, and banana – are fundamentally different from the microscopic world.

And it’s not just about the physical scale, either.

Whereas all of us in Big Land are, biologically, nearly identical, there are vast differences between different life forms on the microscopic level.

There’s still some debate, but we generally think of the first three branchings of the Tree of Life as domains.

The names of those domains are Archaea, Eukaryotes, and Bacteria.

A tiny, tiny, tiny subset of eukaryotes eventually became multicellular and then grew to enormous size.

That’s what we all are in the Big World – eukaryotes.

A simplified Tree of Life.  Archaea are green. We’re in red. Bacteria, the dominant life form, are in blue.

Archaea are extremely interesting but, unfortunately, fairly irrelevant to our tale, so we’ll have to table that discussion for another time.

Anyway, it’s the last domain that needs discussing, Bacteria. Because a wholescale misunderstanding of bacteria plays a key role in the events leading up to World War 3.

A Disrespectful Bully

Frankly, bacteria are as different a form of life from us as any sci-fi space alien could ever be.

The fact that they’re an entirely different domain of life means that they’re far, far older than us and have a far more diverse and unique genetic history.

If we are the tiny rosebuds on the top branch of the Tree of Life, then bacteria are the sold, wide base.

Despite the fact that bacteria are microscopic, they are so numerous that, collectively, their combined weight is equal to our (macroscopic life) combined weight.

Bacteria are everywhere and in everything.

They are our ancient grandfathers who shepherded us into this world back when we were just single-cell creatures ourselves.

We’ve spent our entire existence on Planet Earth in their presence, and we depend on them for our survival even today.

If all the bacteria departed from your body, you’d fall down dead.

And one tiny, tiny, subset of bacteria converts sugar into lactic acid as part of their normal way of life.

This is what the revered Louis Pasteur deemed a “disease-causing organism.” And he’s both the “father” of immunology as well as the co-author of the Germ Theory of Disease.

Blind as a Bat

One of the weirdest mysteries in Western science occurred in 1676.

Using a brand-new microscope, Antonie van Leeuwenhoek carefully documented microorganisms and then published his findings in the Royal Society (of London).

Although he didn’t know it, Leeuwenhoek was looking at bacteria (he called them “animacules” or “little animals”).

Yet despite this amazing breakthrough, no one ever bothered to look for microorganisms again for more than a hundred years, instead, preferring to focus on crap like the influence of the stars, the balance of the four humors, witchcraft, and “bad air.”

As we learned in Part 5 of this series, scientists began using the word “virus” to describe any unseen (i.e. microscopic) disease-causing organisms.

By the 1800s, when Pasteur and Darwin were working, scientists had begun to prefer using the word “bacteria” for the organisms that they could see under their microscopes.

So when Pasteur was killing off microorganisms in milk, he thought of it as killing “evil” bacteria, which was biologically correct.

But when he was examining how fermentation works in bread, he also thought of yeast as being bacteria, which isn’t correct. Yeast is actually a fungus, so it’s more closely related to us than it is to bacteria.

In fact, neither Louis Pasteur nor his contemporary rival Robert Koch ever figured out which microorganisms were bacteria and which weren’t.

As far as they were concerned, all microorganisms were bacteria, which completely crippled any scientific understanding of viruses (which we shall discuss later on).

Heil Heinrich

Robert Koch does deserve credit for going much farther than Pasteur in determining the individual cause of an infectious disease rather than just saying “kill them all” indiscriminately to all microorganisms, but he only climbed halfway up the mountain before giving up.

I kinda, sorta, figured out what causes infectious diseases

Koch’s breakthrough was developing his so-called postulates or guideposts for identifying infectious diseases.

After all, how can you really be sure that a tiny microorganism is actually responsible for causing diseases in a macroscopic organism like a person?

In simplified terms, here are Koch’s four original methods to determine whether or not a microorganism is to blame for a disease:

  1. A sick person has the microorganism inside them while a healthy person does not.
  2. Someone needs to isolate and identify the microorganism.
  3. The isolated microorganism should then make a healthy person sick when it’s injected into them.
  4. The second person who got sick also needs to have the microorganisms inside them isolated and identified as being the original microorganisms, proving that they, too, became infected from the same agent.

Unfortunately, even during Koch’s own research trials, these postulates or guideposts were shown to be useless.

Cholera, a disease which Koch studied intensively, is not caused by bacteria, and plenty of healthy people have cholera microorganisms inside them and never get sick.

Furthermore, it is virtually impossible or absolutely impossible to isolate many microorganisms. For instance, tuberculosis, a bacteria, something Koch also studied, takes a really long time (weeks) to isolate.

Even worse, sometimes when you successfully manage to isolate a microorganism from a genuinely sick person and then inject it into a healthy person, that doesn’t always cause the healthy person to get sick.

And the final nail in Koch’s Postulates coffin is that plenty of microorganisms mutate or evolve so rapidly that, even if you do get that second person sick, the microorganism you find inside them may be completely different from the microorganism that you found in the first person.

In other words, all four of Koch’s Postulates are quite unscientific in determining whether or not a microorganism is causing a specific disease.

Despite this, the postulates continue to be used as the foundation of the Germ Theory of Disease, an orthodox belief in Western science today.


Not that modern immunologists, microbiologists, and public health specialists haven’t tried to tweak Koch’s postulates to get them to fit the evidence.

Today, if you’re studying microbiology or infectious diseases, you’ll probably learn an updated version of Koch’s postulates that go something like this:

  1. Most, but not all, people who are sick with a disease should have a microorganism present that can be detected with a PCR test (which thusly identifies the microorganism via its DNA).
  2. Healthy people should have fewer of those microorganisms inside them than sick people do.
  3. When a sick person recovers and gets healthy, the quantity of those microorganisms inside them should go down.
  4. If you find a microorganism’s DNA in a healthy person and then they later get sick, that probably means the microorganism caused it.
  5. The microorganism at fault for a disease should act like similar, known microorganisms.
  6. If possible, the microorganism should be isolated and then tested on a healthy person, and the healthy person should get sick.

In other words, the theory is still pretty loosey-goosey.

After all, it says that some people might be sick with a disease and not have the microorganism (which “causes it”) present.

And some people might be healthy but have the microorganism (which “causes” disease) present.

And some microorganisms might act much differently than their close cousins.

And many times, it’s either impossible to isolate the microorganism or too much amplification with a PCR test will cause false-positive results, meaning you can’t always be sure that a person that you think has the microorganism actually does.

And if all of that weren’t bad enough, some diseases thought to be caused by microorganisms (such as cervical cancer caused by papillomaviruses) don’t follow the pattern at all.

In other words, there’s no definitive way to tell if a specific microorganism causes a specific disease or not.

At best, it’s just a case of “probably.”

The Germ Theory of Disease

If Koch had been right, that certain microorganisms definitely cause disease, then his co-authorship of the Germ Theory of Disease (GTOD) might stand up to scrutiny.

Unfortunately, it doesn’t.

The germ theory states that certain “germs” (originally all referred to as either “viruses” or “bacteria” but later expanded to also be microsporidia, bacteria, fungi, viruses, prions, etc.) encounter a healthy organism (like a person), invade that organism, and this always causes a disease.

This “invasion” process is known as an “infection,” and the diseases that are indisputably and undeniably caused by these invaders are called “infectious diseases,” according to the GTOD.

The GTOD also coined the phrase “the immune system,” in which an organism like a human being strives to always be in a pure, healthy, uninfected state and so employs a series of weapons to protect that purity. These weapons are collectively known as the “immune system.”

As such, all germs are evil while the immune system is a holy force for good.

Yet what Koch, Pasteur, and all of the other co-authors of the GTOD didn’t realize is that the concept of a separate, “pure” human being who is then “contaminated” with infectious germs is pure bunkum.

That is why Pasteur, Koch, and the others focused so much time on trying to exterminate microorganisms. Because why not? Those microorganisms are disease-causing germs!

But not only were Koch and the others unable to devise a way to prove that a single disease was definitively caused by a “germ,” they were completely wrong about how we, in the big world, interact with microorganisms.

A Pound of Bacteria

Bacteria are essential for our survival in a number of ways, including their role in processing Vitamin B12.

But they’re also part of us. Every adult human being has at least one pound (400 grams) of bacteria inside them and probably much more.

Bacteria are in every “nook and cranny” of our bodies and play vital roles in both our digestive and “immune” systems.

Bacteria are in our saliva, on our skin, inside our eyes, and in our intestines.  For every cell in our body that’s ours (has human DNA), there are between three and 10 bacteria.

In other words, we are vastly outnumbered in our own body by bacteria.

And the vast, vast majority of these bacteria-human interactions are positive for both parties.

Furthermore, bacteria also play an important role in helping plants uptake nutrients from the soil as well as nitrogen from the air. And since we depend on these plants for food, bacteria also feed us as well.

Every breath you’ve ever taken has been loaded with bacteria. Every bite of food you’ve eaten contained millions and millions of bacteria. Bacteria are us and we are bacteria.

Instead of a “pure” and “immune” human body being “infected” by germs, the truth is that human beings are in an ancient, symbiotic relationship with bacteria and other microorganisms.

Hygiene to the Rescue

At first, though, it’s easy to see why the GTOD and Pasteur’s ideas about exterminating “germs” to stop infectious diseases became so popular.

That’s because, starting in the 1800s, scientists modernized the concept of hygiene.

Originally referring to the daughter of Asclepius (master of the Snake Juice) who would clean and bandage wounds, the concept of hygiene was expanded to refer to anything that killed germs.

If a microorganism got you sick, then the way to deal with it was to kill it, or, in other words, make it hygienic.

And since hygiene was at an all-time low in Western industrialized countries in the 19th and early 20th century, applying the principles of the GTOD did, indeed, make vast inroads into eradicating some infectious diseases.

Illnesses that are nearly forgotten today such as typhoid, scarlet fever, trench foot, and puerperal fever were successfully combated with improved hygiene, and it’s likely that millions of lives were saved.

Lister’s Lung

Furthermore, post-surgical infection rates dropped dramatically when GTOD hygiene practices were adopted.

One highly influential doctor in the modern hygiene movement was Joseph Lister, a British surgeon who was a huge fan of Louis Pasteur’s work.

As such, Lister began spraying carbolic acid (a disgusting, nasty substance derived from coal tar) absolutely everywhere before, during, and after every surgery on the theory that it would kill all the “germs” present.

Although he could barely see through the “carbolic fog” (as one assistant called it), he found that many more of his patients were surviving their operations.  And while surgical procedures and hygiene products are much more refined nowadays, some still do use carbolic acid as an effective way to kill microorganisms (aka “germs”).

And just as diseased milk from mistreated cows could be pasteurized and thus rendered safe, so too did GOTD-based hygiene procedures reduce the transmission rate of some infectious diseases among people living in filthy, substandard conditions.

Improving hygiene definitely saved human (and bovine) lives, but what no one realized was that this GTOD-influenced hygiene would one day cause millions of people to get sick and die from completely new diseases.

And the first casualty, if you will, of this GTOD-induced mania for hygiene was polio, one of the most terrifying illnesses of the 20th century, something we shall cover in the next installment.

You can read the next part by clicking here.

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