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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