Knowing the archaea is your living reminder to keep learning
Step by step, you made your way through the foundation articles on this website. You now have a basic introduction to all the kingdoms of life: bacteria, protoctists, fungi, animals and plants. You can see something of their wealth and power. You've read many stories of their interrelationships, their creativity and their cooperation.
When you look around your neighbourhood, are you now seeing those different living beings from every kingdom? Do you notice them in the media: the papers, magazines, television and film?
At the same time, you are also getting a glimpse of some of the processes used by evolution itself. Remember the different components of the two great cell types, the prokaryote and eukaryote? An ancient symbiosis resulted in the creation of the eukaryote cells from the smaller prokaryotes.
But before you get to comfortable with this “just so” story, remember to include the archaea ( pronounced "ar KEE a")
The archaea are unicells first found in the 1970’s in places where no life was expected: in hot springs, deep sea vents, the guts of termites and salt pans. At first they were labeled “extremophiles”: lovers of difficult environments. How could they survive such temperatures, the lack of oxygen or such saltiness and acidity? How did they grow using sulphur or nitrogen? And imagine living beings creating methane?
(Take a moment and view this website about archaea in the hot springs in Siberia.)
New millennium sees revolution in thinking about life
By 2000, archaea were found everywhere else too: in the oceans, in soils of every kind and in the guts of other animals including humans. They appear to be ancient inhabitants of the earth. They share many features with bacteria such as loosely organized DNA and growth by division. They have extra rings of DNA (plasmids) and happily share genes with other unicells as do bacteria.
But they have unusual features that make them stand apart from not only bacteria but all the other kingdoms too. Their cell membranes are chemically different. And their ribosomes, the structures that work the DNA and produce proteins, are of a type unique to themselves alone.
Then some features of the archaea seem like those of all eukaryotes. In fact, some of the similarities, which are based on the molecular analysis of proteins, have the specialists thinking that the archaea and eukaryotes are as related as sisters.
The puzzle about the archaea seems to be “where do they fit?” Answering this is a major debate in biology right now. Understanding what’s involved will shake you out of what you have always heard. You won’t see the world in the same way ever again.
The power in knowing about the kingdoms of life is the power that comes with explanation. And you know how a good explanation influences just about everything in your life.
Here's how the debate is going. One one hand, one way to sort all living beings is to put a high value on a single subunit of one molecule called the 30S subunit of the ribosome. Remember ribosomes are those parts of a cell that "read" the DNA and build molecules according to that information.
Since ribosomes are a necessity, they are always part of every single cell. They are also largely unchanged generation after generation, in species after species. Except for this one subunit. In all living beings, this one molecular detail seems to vary and only in one of three shapes.
One shape is used by all the eukaryotes. Another is used by all the prokaryotes. And another is used by the archaea. So, is all of life to be divided into groups according to three main cell types rather than two? Is this a feature so characteristic that we should create a new classification for it? Shall the three cell types be classified as three domains, within which we should rearrange all the kingdoms?
The other side of the debate
But there is another side to this debate. If we are sorting life, how about considering not only the molecular biology but also all fossil records and life-histories too. Nature, with all its processes of selection, works on living beings, throughout each life cycle, on each individual.
These histories are vital in understanding each living being. Isn’t it important the archaea and bacteria are both unicells with similar life cycles? Isn't it important that they can also share genes easily? Shouldn’t this type of information be central to any classification system? Isn't it more meaningful to put the Archaea as a group inside the kingdom of Bacteria?
Well, let's look a bit deeper into this. If you consider again how symbiosis works, you can imagine how the archaea and the bacteria could BOTH have contributed to the evolution of the eukaryotes. In particular, specialists think the archaea seem to have contributed to the development of the nucleus of the eukaryote.
This nucleus is so unlike the nucleus of the bacteria. The DNA is tightly organized and bound up with membranes. This larger, different nucleus is a feature shared by the kingdoms of protoctists, fungi, animals and plants but not bacteria. How can a classification system best show these relationships?
Two personalities in the great debate: Woese and Margulis
Mapping these relationships is the crux. Carl Woese, a cell biologist, emphasizes the absolute importance of the three ribosome subunits. He suggests that this information is the key to everything. He believes all the kingdoms should be placed in three great domains, based on these cell types: Archaea, Prokaryote and Eukaryote.This interview with Woese goes into more detail.
Lynn Margulis, a microbiologist, insists on the integrity of living beings as whole organisms. She also values the role of symbiosis and suggests that this powerful process happened again and again. Some of the steps once taken may be long buried from view. Try as we might, we may not find molecular traces. She does not believe that molecular data alone should dictate classification.
So Margulis suggests a different classification system. This one includes the small bacteria and archaea, with their ability to trade genes with each other, in one major group called the prokarya. The other groups, all with their larger cells, their membrane bound nucleus, are under the heading of eukarya. Here would be the protoctists, fungi, plants and animals. This interview with Margulis explains her ideas in more detail.
What they agree on and wonder about
Although Woese and Margulis differ, they agree that the origins of living beings probably involve more than a single common ancestor. In fact, there is likely to be a suite of very diverse ancestors. Some may have died out and only left traces of their existence in the cells of today’s living beings.
Both Woese and Margulis also consider that viruses should fit in the classification somewhere. Viruses can be seen as traces of living beings. They are leftovers after their ancestors economized to such an extent that they didn't even need cells anymore to exist. A virus is simply a package containing DNA. The virus infects a cell by entering it and using their DNA to hijack the cell's living systems, forcing it to produce what the virus needs.
There is also the other mystery: how to classify prions? Prions are infectious material made of proteins. They manage without any DNA. These prions are found in animals wherever there is mad cow disease or scrapie. The prions found in fungi are even more mysterious: whether they cause a disease in fungus or are helpful is quite uncertain at this point in time.
Shaking up everything you know
Knowing about the archaea, you now find that how you thought about the kingdoms and everything else is not set in stone. It’s actually fluid. But you know something of the controversies. You can see that using kingdoms or domains or prokarya/eukarya are all useful labels in their own way for now. They tell you something about how the living beings being classified. But they also tell you a lot about the ideas of the people who use one system over the others.
Who knows where this is all heading? There could be a big shake up when something else is discovered and once more, someone suggests how to re-organize everything.
The value of knowing the kingdoms
Meanwhile, you have to swim with all the inconsistencies and the contradictions. You've got to keep learning. Whatever the arguments, there are still basic cell types. There still are whole groups of living beings with strong similarities in how they live and reproduce. Each of these contrasts with other groups.
The "kingdoms" are still very useful ideas for a lot of purposes, especially for introductions. They are like training wheels, so you can get up and riding with the basics of biology. Being able to see the different groups of life for what they are is an enormously valuable skill.
Take a moment and look at this short summary of the history of classification. In days to come, this website will post more articles about these classifications, the diagrams, their history and uses. Once you know the basics about the kingdoms, you're ready to take on next level of discussions and debates.
Now for the Tangle
All the groups are so tangled together that there really is no way to separate living beings into a hierarchy or ranking system. What can make any group more important than another?
Sometimes, as with the bacteria, it can really hard to identify separate stable species. There are specialists who say that bacteria really don't exist as species at all, not like species as we animals know them.
Sometimes, it is really hard to pinpoint what is an "individual". What does that word mean? What is the individual when fungi and algae combine and create lichens? What is a bluebottle, this animal made up of communal zooids? And what is this animal and algae combination called coral?
Classification can seem so pointless! Why bother with it? But its very limitations are useful in an unexpected way.
When you can see the tangle for exactly what it is, you get a rather humble quick glimpse of something. It's all beyond words. There, through the corner of your eye, you can see a bit of both the truth and the mystery of life.
It’s worth repeating:
Knowing the Archaea is your living reminder to keep learning
We welcome your comments! What do you think?
Here is a challenge. Right in your local neighbourhood, “adopt” a kingdom or a domain or any member in these groups. Tell us -- which one do you choose? What more do you want to know about them?
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