Phylogeny or Classification: What is the Tree of Life about?
The Tree of Life project is about organismal diversity and the phylogeny that generated it. It is not about classification. A clear distinction between the concepts of phylogeny and classification is critical for understanding the nature of the project.
Throughout much of history of systematics (the study of organismal diversity), people have been preoccupied with naming and classifying organisms. This is understandable, given the number of species out there, and the need for names for the species and groups of species, so that we may talk about them. But recently more researchers are focusing, not on the names of organisms, but on understanding the origin of their diversity. The phylogeny or evolutionary tree that generated current diversity is a critical part of our understanding of the history of a group of organisms. This knowledge forms the core of the science of systematics. Modern systematics seeks to learn about this history.
In spite of this change in the nature of systematics, you will often find chapters on organismal diversity in introductory biology textbooks labelled "Classification". This is an odd thing, for of course all fields of endeavor (not just systematics) have their own "Classification" of the objects and concepts in that field. Why doesn't a chapter called "Classification" refer to the naming system we use for cell types, or molecules? Systematics has been so indelibly equated with the naming system systematics uses that we introduce our students to organismal diversity through nomenclature rather than the scientific study of organismal diversity.
Such chapters in textbooks should be called "Phylogeny" or "Organismal Diversity" rather than "Classification". Calling "Phylogeny" by the name "classification" confuses and (in the eyes of many) demeans phylogenetic biology in the same way calling "molecular biology" by the name "classification" would.
This is not to deny the importance of classification: we couldn't possibly talk about organismal diversity if we didn't give names of organisms. In the Tree of Life project, the names we use for organisms reflect the names used in current classifications of organismal diversity. The Tree of Life must use classifications, but it is not about classification.
Of course, there is in general a correspondence between the classification and our ideas about phylogeny. Most researchers feel that the groups we give names to in our classifications should correspond to single branches or clades on the phylogeny: if we wish to talk about the history of a group, it is easier to do so if the named entities are cohesive portions of that history.