When I was a kid, we learned how to classify living things. There were two
kingdoms, "Plants" and "Animals". Plants were all the ones that
photosynthesized, and Animals were all the ones that could move under
their own power.

At the time, nothing seemed excluded or on the borderline, except perhaps a
small green (photosynthesizing) protozoa called Euglena, which had flagella
and could thus move around under its own power. It bugged me that the
definitions weren't quite right, but they seemed to make everyone else happy,
and we made do with that. I don't remember exactly discussing bacteria at the
time, but I'm sure in retrospect that they were considered anumals, because
they don't photosynthesize and move around a lot.

Well, times have changed and we have learned a great deal. Life forms are now
divided into three domains: Eukarya, Bacteria, and Archaea. My best guess
at pronouncing the last is "Ar-KAY-uh", no guarantees.

Bacteria, we have learned, do not contain cell nuclei. This is definitely a
big deal. They reproduce in fundamentally different ways from higher life
forms. This revelation caused us to rethink our taxonomy, and now bacteria
and all prokaryotes (no nucleus) are separated off, while all the rest
of us, Plant and Animals alike, with our nucleated cells, are Eukaryotes,
belonging to the domain "Eukarya". Eukary is still divided into the Plant 
and Animal kingdoms.

The above is sort of background info, at least it is for me. I had picked up 
this much all along, but I was recently reading an article in Science
(23 Aug 1996 vol 273, p1043) entitled "Life's Last Domain" on the subject of
"Archaea". This third domain is made up of strange microbes. The article
is a write-up of a tour-de-force of gene sequencing, in which a very 
strange microbe named Methancoccus jannaschii, a methane producing organism
which lives near deap sea hydrothermal chimneys called "white smokers".

This organism and others like it are very primitive. The genes were 
compared to sequences from already-sequenced bacteria, Haemophilus influenzae 
and Mycoplasma genitalium. Only 44% of the genes matched. This is a remarkably
low percantage. I agree that this indicates that these organisms are markedly
different, and I accept that they are more primitive than Bacteria.

I am perplexed because the article did not leave me with a clear way to decide
whether an organism is a bacterion or an archaeon. It seemed to be based on a
quantitative study. I don't believe this is actually the case. If there were
a smooth blend of organisms between M janaschiii and familiar bacteria, then
there would be no need to create a third domain of life. I am pretty sure that
there is no such blend, and that there really are distinctions of note between
what are classified as Archaea, versus Bacteria. I would like to learn more 
about this.

Archaea are not limited to deep-sea settings, btw. 
Methanbacterium thermoautotrophicum is an archaeon that lives in compost.

Archaea are divided into "Crenarchaeota" and "Euryarchaota", but I am lost
on that distinction as well. There are a lot of methane prodicers in the
Euryarchaeota, but also halophiles and others.

Archaea, and the study of their genes in particular, may lead to some 
interesting new theories about the origin and/or early development of life 
on earth. 

17 responses total.

  I think there were five kingdoms when I was a kid (fungi was
another one, besides plant and animal), and seven levels of
classification, with kingdom at the top.  Is domain an eighth,
added above kingdom, or is it a parallel type of categorization,
outside the old 7-level system?  (In the way that "color" could
be a parallel type of categorization).  If domain is a new level,
how long has it been around, approximately?

I am not sure if "domain" is the right word for it, but it is used in this
article rather consistently, and this is a scientific journal. I believe
"domain" in this sense is now a new higher level of classification. I think
that the other 7 levels only apply to Eukarya, though. There is classifcation
of Bacteria and Archaea, but it seems to require less structure.

You are correct to note that because Fungi do not photosynthesize, they would
also have been an exception. Sorry - I forgot to mention them.
Actually they were considered 
"plants that had lost their ability to photosynthesize".

(seems a stretch to me)

The 5-grouping you remember may have come along later, but prokaryotes 
(bacteria) were not separated out from the classification into a separate
domain until after 1970, I think.

The article has a little line drawing showing the various Eukarya. 
If I am interpreting it right, there are now many more than 5 top-level
subdivisions of Eukarya. I don't know if they still call the top level
"kingdom" anymore. The list is:
Animals, Plants, Fungi, Ciliates, Flagellates, Trichomonads, Microsporidia,
Diplomonads, Slime molds, and Entamoebae. This appears to reflect a promotion
of many of the protozoa which used to make up the phylum of protozoa to the 
top level. I am not sure if I am reading this all right, though.

I've been somewhat curious about these taxonomic issues myself.

It's kind of annoying. It was a really good article on the issue of the
process of sequencing the genome, and especially on some of the surprising
things they found, or failed to find, but it left out some basic info on what
distinguishes Archaea from Bacteria. Both have free-floating DNA. Neither
have cell nuclei.

OK. I went to check out the "Tree of Life" I don't know why I didn't think
of this before. It is a very cool website, located at 

http://phylogeny.arizona.edu/tree/life.html

I did not find the answer, but I found that there are now two competing views
on how to organize the classification of living things at the highest level,

---begin copy/paste from the Tree of Life ----

Two alternative views on the relationship of the major lineages (omitting
viruses) are shown below

The "archaea tree": 

     ,=============== Eubacteria
     |
     |            ,== Euryarchaeota
=====|  ,=Archaea=|
     `==|         `== Crenarchaeota-Eocytes
        |
        `============ Eukaryotes

The "eocyte tree": 

     ,======== Eubacteria
     |
     |  ,===== Euryarchaeota
=====|  |
     `==|  ,== Crenarchaeota-Eocytes
        `==|
           `== Eukaryotes

---end copy/paste---

I am not sure what the issues are wrt these two viewpoints, but my curiosity
is now piqued even more. There were a lot of references given, so I imagine
I can find out from a book or journal if I have the time to follow up and
no answer appears here.

I also see that the correct term for the class of normal bacteria is 
Eubacteria. "Prokaryote" and "Prokarya" appear to have gone out of fashion.
Actually "Prokaryote" is arguably anything that is not a "Eukaryote".

These viewpoints have in common the fact that the Archaea are closer to
eukaryotes (people, fungi, and trees, etc.) than they are to Eubacteria.
This is totally at odds with my mental model that they were older and
more primitive than the other forms. Perhaps it was the name that 
threw me off. 

<time passes while I browse the net>

Here is a better answer. I just found it on the web. I am getting too lazy to
do real reference work, as the web makes it too easy.  From
http://monera.ncl.ac.uk/VHG/systematics/archaea.html
I found this:

---begin---
The Archaea (or Archaebacteria) are a heterogenous group of 'prokaryotes' 
which differ markedly from other prokaryotes (bacteria) in their 16S 
ribosomal RNA sequences and in other important characteristics of 
cellular composition. 
---end----

That is a bit vague, but different ribosomal RNA sequences is a major point.
While they don't have nuclei, they seem to be more similar to Eukaryotes
than to bacteria. The name means "ancient ones" but they now seem to 
be less ancient than ordinary bacteria. More like a link between bacteria and
higher forms (Eukaryotes == us).

We've been discussing these questions at home a little, but did not do
searches, so I'm glad to get some pointers here. On a more general point,
Gould's _Wonderful Life_ emphasizes that the fossil record shows many
more *phylums* than are known today. They arose, lived, and expired. The
same can certainly be true of life patterns at much earlier times. Thus,
the effort to draw "trees" of the connections between the unicellular
organisms *known today* can be frustrated by who-knows-how-many missing
unicellular "kingdoms". 

  Apparently there are two competing classification systems.  The one
I learned is from 1969, and has five kingdoms (Plantae, Animalia,
Fungi, Protista, and Monera).  A newer one was developed in 1978 that
has three kingdoms (called "domains" in srw's article: Archeobacteria,
Eubacteria, and Eukaryotae), and better reflects evolutionary history.
In the five-kingdom system, methanogens are in the Monera kingdom.

  This info is from http://gause.biology.ualberta.ca/bio108.hp/lect03.html.
The University of Alberta has lecture notes for their Biology 108 course
posted there, complete with illustrations.

This response has been erased.

One of the levels in the hierarchy is "order", if I'm not mistaken.
(Not that I have any training in these areas, but that stuck in my memory.)

Assuming we start with domain, it then goes kingdom, phylum, class, order,
family, genus, and species. Just remember, DKPCOFGS! The system is
imperfect as life isn't that orderly - there are "subs" at every level,
and a lot of organisms whose category is controversial.

  I don't think "domain" is part of that chain.  It seems to be a
synonym for "kingdom" in the three-kingdom system, and "kingdom" is
at the top of the five-kingdom system.  Also, in the five-kingdom
system, the second level of classification is phylum or division,
depending on the kingdom.  Animals have phyla, plants have divisions,
and I'm not sure about the other kingdoms.  Makes you wonder who
thought that up!!  So you just have to remember "K(P/D)COFGS".  :-)

My daughter is taking elementary biology at Pioneer, so I raised this
question with her. Well, she says she will follow *the textbook*, as she wants
to pass the course. Pretty pragmatic.

    hmmm. the mnemonic i learned for the hierarchy was "king philip, come out,
for god's sake!"...kingdom, phylum, class, order, family, genus, species.

Interesting commentary, thanks. I was primarily interested in what
distinguished archaea from bacteria, and I wouldn't mind learning more details
than I posted above. 

As a sidelight it is quite interesting to note how the classification tree
has shifted about over the years, as we have learned more and questioned some
old dogma.

Or as more information becomes available.  It's hard to distinguish
between convergent evolution and common heritage, but the DNA will
often show the difference quite conclusively.

No question. "often" is even an understatement. "Nearly always" works.

  That's probably true, though there are cases where there are such huge
gaps in current representatives of an evolutionary branch, that DNA still
can't provide all the answers.  In other words, if many of a currently
living species' evoltionary ancestors all died out millions of years ago,
you can have a problem figuring out how it's related to other species in
the same situation.

You can still get some idea of which evolutionary precursor branched
off first.  OTOH, the exact order isn't horribly important for most
purposes.

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