Download A New Way of Classifying Life?

A New Way of Classifying
Life?
_.
_.
_.
_.
_.
_.
_.
_.
_.
The Evolutionary Family Tree
Kingdoms Crumble
Enter the Domain of "Domains"
Bigger Questions
An Attempt at Answers
The Modern Cell
Further Reading
Internet Sites
Keywords
We all have ancestors: great-grandparents, great-great
grandparents, great-great-great grandparents, and so on. But have
you ever thought about your universal ancestor? For many years,
scientists have wondered what type of cell gave rise to the diverse
world of living organisms that inhabit Earth. From what type of
cell could both humans and bacteria have evolved?
The Evolutionary Family Tree
Perhaps an easier question is: How are human cells and bacteria
related? For years scientists have been classifying organisms
(categorizing them into groups based on similarities and
differences) and trying to determine their evolutionary histories.
One popular classification system, the five kingdom system,
divided all species that live or once lived into 5 groups called
kingdoms: Animals, Plants, Fungi, Protists (single-celled
organisms such as amoebae and euglena), and Monera (bacteria).
Using similarities and differences in form and structure, scientists,
after initially assigning organisms to one of these 5 kingdoms,
have then subdivided the kingdoms into phyla, classes, orders,
families, genera, species, with each succeeding category signifying
a greater level of similarity. For instance, human beings are
classified as follows:
Kingdom
Animals
Phylum
Chordates
Class
Mammals
Order
Primates
Family
Anthropoids
Genus
Homo
Species
Homo sapiens
Series of branches, called phylogenetic trees, are used to depict
how kingdoms divide into their subdivisions. Each branching
supposedly represents a refinement in the process of evolution.
Kingdoms Crumble
With the advent of techniques for sequencing genetic information
(such as DNA and RNA), scientists have focused on classifying
organisms based on similarities and differences in genetic material,
rather than morphological differences (such as physical structures
and functions). Ribonucleic acid, or RNA, is the genetic material
that helps a cell translate the deoxyribonucleic acid, or DNA, code
into structural and functional proteins. RNA is unlike DNA in that
RNA is a single-stranded molecule, while DNA exists as a double
helix. However, RNA is similar to DNA in that it is a chain of
molecules, each consisting of a sugar, a phosphate group, and a
base. Also like DNA, the RNA bases come in different varieties,
and the sequence of bases forms a code on the RNA strand that is
translated into proteins.
Comparison of RNA sequences of the broad spectrum of living
things revealed flaws in the five kingdom system. The Kingdom
Monera consists of two types of unrelated bacteria that evolved
separately. All of the organisms in the four other kingdoms
evolved from one or the other of these types of bacteria and are
thus not really separate from the Kingdom Monera, but are a subset
of part of that kingdom.
Enter the Domain of "Domains"
In the early 1990s, a microbiology professor at the University of
Illinois named Carl Woese devised a new classification system in
which all organisms are assigned to one of three Domains:
Eubacteria, Archaea, and Eukarya. A common ancestor first gave
rise to two different lineages of prokaryotic organisms (organisms
whose cells lack a membrane-bound nucleus and other cell parts).
One lineage evolved to become the many types of Eubacteria or
"true bacteria." The other lineage spilt into Archaea, a group that
includes bacteria known as extremophiles that live in extreme
climates, and Eukaryota, the group that includes animals, fungi,
plants, and protists (organisms called eukaryotes which have true
membrane-bound nuclei). Eubacteria and Archaea were classified
in the single Kingdom of Monera in the five kingdom system.
Woese based his findings on the similarities and differences
between a specific type of RNA found in all living things. Not
many molecules are common to every type of life, but rRNA, or
ribosomal RNA, is a molecule common to all life because of its
central role in a major metabolic process. Ribosomes are the
microscopic cell parts where proteins are made according to
instructions encoded in the base sequence of DNA. Each ribosome
is comprised of two subunits—one small and one large. The
subunits have different functions, and each is built of structural
protein and nucleic acid (ribosomal RNA). Woese sequenced the
rRNA of the small ribosomal subunits of many organisms and
classified organisms based on the similarities in their rRNA.
Bigger Questions
Not all scientists have embraced Woese's classification system.
Many biology textbooks still use the five-kingdom system, and
while most microbiologists have accepted the newer system, most
botanists and zoologists are more reluctant to But whatever
classification system is used, there still exists the question of the
origin of all of Earth's diversity.
Charles Darwin, the famous evolutionist, proposed the Doctrine of
Common Descent, the theory that all of Earth's species descended
from one primordial form. This primordial form was the universal
ancestor from which all life supposedly evolved and is represented
as the root of the phylogenetic tree. The question then arises, what
was this primordial form like? Was it a full-fledged cell?
An Attempt at Answers
Recently, Carl Woese has challenged the assertion that there was
just one primordial form. He says there were many life forms
existing as a community, none of which were like what we call
"cells" today. Eubacteria, Archaea, and Eukaryotes are very
different in how they replicate, or make copies of their DNA when
their cells divide. But many similarities exist in their translation
and transcription processes (how the sequence of DNA, the
hereditary material, is used as a code by RNA for the production of
proteins in the ribosomes). This leads scientists like Woese to
assume that before the three domains of organisms existed, the
cell-like common ancestors contained RNA as their only genetic
material. DNA and DNA replication evolved much later.
According to Woese, these cell-like forms evolved by a means
known as lateral or horizontal gene transmission (HGT). When we
commonly talk of evolution, we are referring to vertical gene
transmission. When parents pass on their genetic material to
offspring via sexual reproduction, the offspring inherit half of the
maternal genes and half of the paternal genes, leading to novel
genetic combinations. Novel combinations can also arise if
mutations occur in the parent's gametes. Either way, novel gene
combinations are produced when organisms pass down genetic
information vertically from one generation to the next. When these
combinations are subjected to selective pressures, vertical
evolution occurs.
Horizontal gene transmission occurs when organisms within the
same generation swap genetic material. The primordial cell-like
forms that gave rise to the three domains of organisms were so
simple in structure and metabolic processes and their genetic
material was so similar that they were able to directly exchange
genetic material with one another. Even today, some bacteria can
exchange DNA by this means. Woese asserts that the only way for
these primitive common ancestors to have evolved into the
complex full-fledged cells that make up the three domains of life,
was for HGT to have occurred, because only then could the
unprecedented variety and novelty required for cellular evolution
be generated. Because HGT allows a group of primitive beings to
swap genetic material within generations, evolution occurs
simultaneously and rapidly.
The Modern Cell
Eventually, different environmental features exerted different
selective pressures on the community of cell-like forms, causing
them to differentiate. As they became more and more differentiated
and complex, they were no longer able to swap genetic material
with each other.
Woese theorizes that the level of complexity achieved by the
common ancestors that impeded HGT was the development of
gene translation, the process by which the genetic code is
translated by RNA into proteins. Woese attributes the development
of translation as the transition from mere cell-like beings to fullfledged modern cells. He likens the development of translation to
the invention of human language, which separated human beings
from other primates; both human language and translation involve
allowing biological systems to represent themselves in symbolic
forms.
For Woese, it is this point in the history of life, the development of
HGT-impeding translation, that is represented by the root of the
phylogenetic tree. This marked the arrival of genetic material
transferable only vertically from parent cell to daughter cell, not
horizontally.
The root of the phylogenetic tree was not the end of HGT as we
know it. Woese says that the first branching of the tree represents
the origin of the Eubacteria lineage. At this point, there was still a
community of cell-like forms evolving via HGT that became able
to translate proteins and produced the Archaea and Eukarya
lineages.
Further Reading
"The Universal Ancestor." Carl Woese. Proceedings of the
National Academy of Sciences, June 1998, page 6854.
Internet Sites
"On the Evolution of Cells." (www.pnas.org/ cgi/ doi/ 10.1073/
pnas.132266999) An online abstract of Woese's paper about the
evolution of cellular organization.
"Microbial Evolution and Diversity: An Interview With Carl
Woese." (www.hbcollege.com/ lifesci/ bioweb/ depts/ interviews/
woese.html) An interview with Carl Woese covering topics in
microbiology.
Keywords
phylogeny, phylogenetic tree, Carl Woese, Archaea, Eukarya,
Eubacteria