Saturday, February 8, 2014

Classifying Life

Humans, by nature, seem to like order: distinct entities with names that fit neatly together in relationships that make sense, like in filing cabinets and family trees. It makes sense that if humans classify everything in their own lives, they would want to do something similar with the life that surrounds them. We are a "botanic garden" and that very name involves a classification of life ("plants"). When you explore a botanic garden, you find that initial classification broken down further into more specific groups (family, genus, species) that are often indicated on display labels in front of individual plants. So how did this classification come about and how exactly does one go about classifying life, starting at the most general level?

I suspect if we were asked to organize and classify living creatures, most of us would do what was done prior to the 18th century: divide all life up first into "vegetative life" and "animal life" based on mobility and how organisms look overall. Vegetative life would include creatures like plants, algae, and fungi, while animal life would include mammals, humans, birds, fish, reptiles, insects, etc.

So where do we put this guy?  #classificationconundrums (Seriously, this is real: photo from

This first division of life into Vegetative and Animal was used by Carl Linnaeus in the early 1700s when he set out to create a comprehensive classification and naming system for life on earth. One might say the classification of life first became a science at this time. He developed a hierarchical system for classification in which Vegetative and Animal were "kingdoms" with subcategories that started out general and became more and more specific (i.e. phylum, class, order, family, genus, species). His system was based mostly on reproductive characteristics, which were more reliable and accurate than using overall physical appearance and mobility as main considerations.

Carl Linnaeus' landmark work on the classification of life, Systema Naturae.

Linnaeus did a lot for the science of classification (known as "taxonomy"), but a huge amount of life, which for the most part cannot be seen with the naked eye, went unclassified in his work, even though Antonie van Leeuwenhoek discovered microorganisms in the mid- to late-1600s with the help of the advanced (at the time) microscopes he developed. Finally in 1866, a man named Ernst Haeckel took these creatures into consideration by classifying life first into three kingdoms as either Plants, Animals, or Protists (single-celled organisms and simple multicellular organisms that did not seem to fit well as either a Plant or an Animal). This was another step in the right direction, but there was still much to learn about these tiniest of life forms, which were to make a disproportionately large splash in taxonomy.

Amoebas are single-celled organisms that wound up classified as can understand the dilemma of trying to decide how to classify this sort of creature.

In the 1800s, taxonomists began to arrange life into "family trees" to reflect relationships, based on the view that all life shares a single ancestor and differentiated over time into separate species, which was not really something considered prior to 1859, when Darwin's "Origin of Species" was published.

Here's an early "tree of life" done by Haeckel. Note the three main divisions of life.

When creating these "trees," the first division of life reflected the earliest presumed differentiations, which were usually determined to be the most fundamental differences. As we mentioned earlier, the most fundamental differences in life were thought to be between plants and animals (and later, protists), but in the late 20th century, classification systems experienced dramatic restructuring based on cellular and genetic analysis of life, which was previously impossible due to technological limitations. Scientists began realizing that the differences between plants and animals were much less fundamental than originally thought, relative to other life forms on earth. Plants and animals are actually quite similar on the fundamental levels of cell makeup and genetic structure / coding:

Taxonomists today think that the difference between life with cells having DNA in a nucleus and membrane-bound organelles (specialized structures found in cells of plants, animals, and fungi) and life with free-floating DNA and no membrane-bound organelles are the most fundamental meaningful differences in life, also thought to have occurred very far back in time. We call these two forms of life prokaryotic life and eukaryotic life. Because of this, notable taxonomists like Carl Woese now think that the first division of life should be made into domains like Bacteria, Archaea, and Eukarya, which would be a level above kingdoms (plants, animals, protists, fungi, etc.), which were previously considered to be the most general classifications of life.

A diagram of Woese's three-domain classification, showing how plants, animals, and fungi are actually "close relatives" when compared to some of the other life found on earth, most of which is not readily visible.

Bacteria and Archaea do not reproduce sexually and are both single-celled prokaryotes, but they have enough significant differences in very fundamental areas (membrane structure and genetic structure, makeup, and coding) to warrant splitting into two domains. Prokaryotic life is believed to have begun on earth from 3.5 to 2.7 billion years ago, developing in the earth's early inhospitable conditions. Since the conditions of early earth are hypothesized to have been quite extreme, it is likely that organisms much like today's Archaea, which live in extreme environments such as underwater hydrothermal vents, oil deposits, and volcanic hot springs, were first to exist. Bacteria are also ancient; Cyanobacteria are the first life forms we have evidence for in the fossil record. It is the only prokaryote that uses photosynthesis to produce food and it forms the basis of most of the aquatic food chain along with algae. While it is generally agreed that prokaryotic life was the first life on earth, it is not certain if Bacteria or Archaea came first.

Archaea form the basis of deep sea hydrothermal vents, using the chemical compounds from the vents for energy.

Cyanobacteria can also tolerate some extreme conditions; they are responsible for the psychedelic colors (except the blue) of the Grand Prismatic Spring in Yellowstone National Park.

Eukaryotes appeared 2.1 to 1.6 billion years ago and may have developed when certain prokaryotic cells were "eaten" by others and rather than being digested, were put to use by the cell. These became the membrane-bound organelles like chloroplasts and mitochondria found in eukaryotic cells. Somewhere along the line, single-celled eukaryotes began to work together as groups to make multicellular organisms, eventually becoming many of the easily visible organisms we are most familiar with. It's amazing to think that "I" am actually trillions of specialized cells working together. It's not until we progress very far up the "tree of life" that we encounter humans, who are out on the tip of a far branch as relative newcomers to the planet and only a single species among thousands. Here's a beautiful diagram called the Hillis Plot, which is basically a modern "tree of life" in circle form, with humanity's position indicated in the upper-left-hand corner:

It's incredible to think that only a single species among so many thousands has had such a disproportionate impact on the planet...

...and in such a small span of time: in the "hour" of the earth's existence, humans have been around for 0.1 seconds.

I hope you've gained an appreciation of just how difficult it is to classify life, and we've only been considering the most general categories, which should be the easiest! Now just imagine making the thousands of further distinctions and categorizations in the "tree of life" on the levels of phylum, class, order, family, genus, and species that you see in the Hillis Plot... I can assure you it doesn't get easier. Classification and naming of life is certainly not cut and dry, and as much as we humans dislike disorder and chaos, life seems to resist the organized classification we would like to make for it. All that I've brought up in this post is really only the tip of the iceberg and there's good reason to believe the classification of life we currently have will look quite different a hundred years from now. Indeed, taxonomists are starting to transition from the idea of life and its history as a "tree," seeing it now more as a chronological "web" for reasons such as horizontal gene transfer.

Who knew life could be so complicated and that those two apparently innocuous questions posed in the first paragraph would require such an explanation... Go grab some ice for your brain, as I'm sure it's pretty sore after reading this post!

Sometime later, after you've recovered, I hope to discuss the classification of plants in particular and why it's so important, now that we've seen where they fit into the larger framework of natural life.

Rick Hederstrom (domain: Eukarya, kingdom: Animalia, phylum: Chordata, class: Mammalia, order: Primates, family: Hominidae, genus: Homo, species: sapiens)
Associate Director

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