Fossils, Microbes, and King Kong

Seeing may not always mean believing, but it helps. Especially when the object is big, important, and embedded in a good story. People who might otherwise doubt the reality of dinosaurs nonetheless have the bones and the movies to help persuade them.  As do those who may still doubt our descent from apes. The story of King King may not convince them, but it makes an argument: the giant reptiles are followed by the giant ape who succumbs to a woman and to the modern city. Popular culture loves fossils, giants, and a tragic romance

The trouble is that what we think of as fossils—old bones, mosquitoes trapped in amber, hardened bits of plants—date back no more than 600 million years. That leaves three billion more years before that, six times further into the past, with no familiar evidence to vouch for it. For there were no animals or plants during those billions. There were only microbes, single cells reproducing, clumping together sometimes, like their descendants today in our gut. Little wonder that those eons are never the backdrop for any saga of the bacteria and archaea, No bones from which to reconstruct giants, no fossils to serve as relics to fire the imagination.

Or almost none.

Stromatolites in Australia, probably looking much as they did 3.5 billion years ago. (

U Microfossils from 3.5 billion years ago (








Start by searching for the oldest rocks. Try Australia, Greenland, or South Africa to find the ones that formed four billion years ago. Slice them thin, put them under a microscope, look for microfossils, tiny creatures’ cell walls that have mineralized into tough material. And look for chemical smears of carbon or the products of the earliest photosynthesis.

Elsewhere look for petrified stromatolites, the layered habitats of colonies of bacteria that filtered sea water for nutrients as far back as 3.5 billion years.

Or look for bands of rust in ancient rocks. Such rust means iron and oxygen, abundant oxygen given off by bacteria as a waste product, enough of it two billion years ago to poison the atmosphere for bacteria that couldn’t tolerate it and then make it a necessity for those microbes that could.

banded iron (

Banded iron (







But could the tiny remains and the odd colors and chemicals that you might find, ancient though they are, actually become the stuff of museum exhibits and monster movies? Could they find their place in popular culture as both entertainment and subtle education, as dinosaurs and apes have?

I think so. It’s not difficult to imagine exhibits of interactive, oversized ancient microbes. Or Hollywood dramas about invasive bacteria from a billion years ago, defeated in the nick of time by oxygen saturation while the heroic Caltech professor of Biogeochemistry (an actual field) explains that the godzillas of 200 million years ago were softies compared to the early microbes that thrived in volcanic vents.

Then our sense of the marvels of our ancestors would reach back through the full history of life.

The Pioneers: Archaea and Bacteria

For many years I shared the common belief that living things fall into three or four basic categories. Besides plants and animals, there are, I thought, one or two others groups that consisted of creatures too small to see, with names that varied over the years—Bacteria, Protists, Prokaryotes.

phylogenetic tree wikipedia

In this evolutionary genetic tree, animals and plants, in the upper right corner, are not the main limbs.         (Wikipedia)

Today there are still three categories, called Domains, but they are all too small to see. The only familiar name is Bacteria. Plants and animals are now small print in another Domain called Eukaryotes (you-CARRY-oats), meaning cells with a nucleus.

The third Domain is the Archaea. Archaea are like Bacteria in that they have no nucleus and are simpler, smaller and older than Eukaryotes. I’ve known so little about Archaea that I wasn’t even sure how to say the word. Either AR-kee-ah or ar-KY-a is acceptable. That noun is plural; the singular is AR-kee-on, an Archaeon, sounding faintly of Star Wars.

So how are these Archaea so different from Bacteria that they get their own subdivision? Biologist Carl Woese in 1977 argued they are indeed a different form of life. He showed that in much of their chemical make-up and their genetic sequencing, Archaea not only are distinct from Bacteria but are in some ways closer relatives than Bacteria to the Eukaryotic cells that form plants and animals.

I’ll describe a few features that Archaea and Bacteria have in common and then some features that are unique to Archaea. The information, from Wikipedia and elsewhere, is quite specialized and my renderings of it are admittedly general and selective.

Both Archaea and Bacteria are small, unstructured, and simple compared to the Eukaryotes that came after them. But one achievement they both share has been to try out nearly every possible chemical or environmental source to get their energy. Sunshine, salty water, temperatures ranging from volcanic to polar, even radioactive settings—varieties of Bacteria and especially Archaea have found ways to draw energy from, and live off of, these and many other environments.

Another similarity is that Archaea and Bacteria don’t reproduce sexually; two cells don’t mingle their genes to form a new individual that is slightly different from the parents. Instead, individual cells just multiply themselves by two and then divide to form identical clones. But despite their reproductive sameness, they had—and have—a different trick for switching up their DNA. A Bacterium or Archaeon can pump some of its DNA into another cell. Or a cell can just pick up a bit of DNA floating near it. No merging, no swapping, just fresh ingredients. It’s one reason that antibiotic-resistant bacteria in hospitals can spread their immunity to other bacteria so quickly.

archaea hot springs yellowstone nationa park (

Archaea at home in a Yellowstone hot spring.       (

This gene-sharing is called lateral gene transfer, and it has an interesting feature. It doesn’t have to take place between members of the same species. For animals and plants, sexual reproduction, to be productive, almost always takes place within one species. But DNA can be transferred from any Bacterium or Archaeon to any other variety in those Domains if the conditions are right. If plants and animals could do that, the mind boggles. You might see squirrels transferring some of their DNA into dandelions. Or vice-versa. Such promiscuity makes it easier, I think, to imagine how Bacteria and Archaea have evolved in so many different kinds and colors in so many different environments.

Despite their similarities, though, Archaea are distinct from Bacteria in notable ways. Archaea were first discovered in extreme settings where Bacteria fear to tread: geysers, intensely salty water, even thermal vents at 251 degrees F, the hottest place any organism has been found living. Another feature is that, while some varieties of both Archaea and Bacteria get their energy from light, Archaea do it their own way, through a process unrelated to the photosynthesis that Bacteria passed on to plants. Importantly, too, only Archaea produce methane, essential to organic decomposition. Finally, while many Bacteria can make us sick—think Lyme, Cholera, Syphilis—Archaea may be nicer; no pathogenic Archaea have been discovered, so far.

Archaea and Bacteria had the Earth to themselves for well over a billion years. Then about 2 billion years ago, Eukaryotes appeared, evolving from their single-celled predecessors but larger and internally more developed. By then, Archaea, like Bacteria, had carried out much of the groundwork for living, pioneering what it takes to survive in different conditions, experimenting with energy sources, trying out each other’s genetic parts.

And they succeeded. They didn’t fade away after the sophisticated Eukaryotes began evolving into countless large species. Today, the total mass of Archaea and Bacteria on earth is at least equal to the mass of all the plants, animals and other organisms together. They got the basics right.