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, one or two others groups with names that varied over the years—Bacteria, Protists, Prokaryotes— consisted of creatures too small to see.

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 all refer to types of cells. The only familiar name is Bacteria. Plants and animals are now small dots in the huge Domain of 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 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 of living things? 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 possible 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 (earth-chronicles.com)

Archaea at home in a Yellowstone hot spring.       (earth-chronicles.com)

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, successful sexual reproduction 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 extremely hostile environments 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.

Is DNA Alive?

No, it’s not alive…mostly. The only sense in which a DNA molecule is a living thing is that it makes copies of itself, although it can’t even do that on its own. Otherwise, DNA fails all the tests: it doesn’t process anything in order to maintain its state, it doesn’t grow and develop, so it has no energized activity that starts or ends—in other words, it’s not born and it doesn’t die.

Somewhere along the line in reading general science I picked up the impression, even though I think I knew better, that DNA strands are alive. They are such vital keys to living organisms, and I read so many descriptions of what DNA does and of “selfish” genes, that although I knew they were blueprints of a sort, they came to seem like living blueprints.

DNA and seed (kew.org)

DNA and seed
(kew.org)

One image that took shape in the back of my mind was that DNA was a kind of seed, and seeds, I thought, are alive. But no, seeds are not fully alive either. They are not active and, until they germinate, they don’t change or develop. (Another familiar item that may seem alive but that doesn’t meet all the criteria are viruses. Viruses are bundles of DNA that become active only when they are inside a cell, at which point they take over the cell and give us the flu.)

It shouldn’t be surprising that some familiar biological components do not, by themselves, meet all the criteria for the complex condition we call “being alive.” Still, surprised I was about DNA. Perhaps because we humans are so fully aware that we are alive, it is easy to think that there must be a fully living seed or even a soul at the root. It is almost more than we can imagine that the liveliness we feel is the product of a complexity of non-living parts. It’s an astounding thing.

Steven Pinker on Emotions and Genes

Steven Pinker’s How the Mind Works might well be subtitled “And the emotions too.” It’s one terrific book. It offers a barrage of insights and connections about humans and evolution that can feel intoxicating. It stirs up the nature-nurture controversy with a blender. It does not see you as you almost certainly see yourself. And it is often very funny.

Despite the book’s title, Pinker talks more about emotions than about the mind itself. He sees them working together. The mind, he says, is computational: it processes information. Much of this information comes from the body’s biological systems. Emotions are units, modules, that use this bodily information to take direct steps—fear, anger, hunger, lust, egotism, empathy—that will promote survival and reproduction.

Humans, Pinker writes, are not, as we often believe, divided into thoughts and feelings that work against each other.

The emotions are adaptations, well-engineered software modules that work in harmony with the intellect and are indispensable to the functioning of the whole mind. The problem with the emotions is not that they are untamed forces or vestiges of our animal past; it is that they were designed to propagate copies of the genes that built them rather than to promote happiness, wisdom, or moral values. We often call an act ‘emotional’ when it is harmful to the social group, damaging to the actor’s happiness in the long run, uncontrollable and impervious to persuasion, or a product of self-delusion. Sad to say, these outcomes are not malfunctions but precisely what we would expect from well-engineered emotions. (Kindle location 7688)

So the good news is that our seemingly perverse emotional moments do not mean that something is wrong with us. But the not-so-good news is that our emotional acts are more deeply engrained in us than our well-meaning searches for happiness, wisdom, and virtue.

So are we doomed by the genes that build these emotional responses, responses that often mean we get  carried away just when we want to stay cool and collected? Pinker addresses this issue often, here in a discussion of love:

The confusion comes from thinking of people’s genes as their true self, and the motives of their genes as their deepest, truest, unconscious motives. From there it’s easy to draw the cynical and incorrect moral that all love is hypocritical. That confuses the real motives of the person with the metaphorical motives of the genes. Genes are not puppetmasters; they acted as the recipe for making the brain and body and then got out of the way. (8342)

I like the recipe metaphor. As I take it, genes are like the list of the ingredients and the steps for making a cake, but the flavor and texture of the cake itself is quite different from that sheet of instructions.

A human

A human “cake” and his genetic “recipe”
(images.nationalgeographic.com)

But if the genes have built emotions to keep us alive, doesn’t that mean those emotions are quite inflexible? Yes and no. Our own emotional core might not change much in our life time, but in species-time, the story is different.

Might the software for the emotions be burned so deeply into the brain that organisms are condemned to feel as their remote ancestors did? The evidence says no; the emotions are easy to reprogram. Emotional repertoires vary wildly among animals depending on their species, sex, and age. Within the mammals we find the lion and lamb. Even within dogs (a single species) a few millennia of selective breeding have given us pit bulls and Saint Bernards. (7721)

Pinker, in conclusion, tells us about ourselves in ways we may have difficulty recognizing. Modules and systems fine-tuned to an ancient past may seem non-human and even anti-human. But it’s not so difficult to absorb how science depicts the machinery of our emotions at the same time that we are inquiring thoughtfully about the meanings of our lives. Or, to put it another way, we can come to understand our recipe while we ponder what it is like to be the cake.

For more on the man, the book, and the debate, here is a lively and helpful article.