Background: Carl Woese, a microbiologist, has been conducting research in the area of microbial biodiversity and believes that

there are two domains of bacteria that are as different from each other as they are from the eukaryotes. Ernst Mayr, a biologist at Harvard, published a taxonomic argument challenging Woeses perspective. Many other scientists have also questioned Woeses well-known theories. To name a few, Lynn Margulis, Dr. Peter Antonelli, and Dr. Solange Rutz have expressed their doubtw. The debate about number of domains continues to the present day. Proposal: Single-celled organisms should be classified into three domains: Eukarya, Bacteria, and Archaea. Issues:
Issue Stability in the Chemical Exchange Pros Woese did not account for stability in the chemical exchange. He grossly underestimated the sophistication of the first organisms. - Therefore, Woese proved that the domains should be split into Archaea, Bacteria, and Eukarya. Cons Antonelli and Rutz showed that the chemical production necessary to support Woese's theory is not dependable and not conducive to the formation of multicellular organisms By using the Volterra-Hamilton mathematical model, Antonelli was able to show that Woeses theory about multicellular organisms developing from many different bacteria was false Biology is centered on multicellular organisms and their evolutions; direct observations and phenotypes. These observations show that there is simply too much alike phenotypically, and where their structures are now to be considered for separate domains. - Based off of mathematical simulations considering the early earth conditions, the two domain theory of bacteria that rises from interaction of multiple ancient bacteria, is not supported. -This is because Woese does not take into account stability of chemical exchange processes of many bacteria interacting, and therefore cannot assume these multifaceted interactions will hold.

Nature of Biology

- Biology of molecules, of genes and their inferred histories, as well as the evolutionary process show enough differences to create a three domain system.

Mathematical Models

- Mathematical models do not take into account a variety of factors. For example, inferred histories, evolutionary processes and likelihood of certain evolutionary pathways occurring (based on later evolutionary trends). - Mathematical models are also inaccurate because they do not take into account biochemical process differences. So the three domain system is still plausible. -Woese used the phylogenetic tree to prove that Archaebacteria should be its own domain - The phylogenetic trees were constructed from data obtained through comparative analysis from rRNA results and eventually proving that Archaebacteria should be classified separately.

Phylogenetic Trees

- Mayr and supporter of his claim believe that classification is based on two simple rules and the results of this classification show that Archaea and bacteria should not be separated domains - Mayr came to this conclusion by using the two rules of looking at only genealogy and similarity.

Default

Its the traditional system and as the title

The dichotomy system has never been truly tested.

Taxonomy

suggests default view of classification that dates back to many of the great biological minds of the 1900s. Without assumptions it is often impossible to move forward with the development of theory or scientific inquiry in a certain direction.

Scientists have never questioned whether certain traits of one Archaea are shared by the rest

Assumptions

In coming up with a new domain, Archaebacteria, Woese assumes that both they and the eukaryotes arose independently from his hypothetical universal ancestor of life. He also assumed the they were equal if not less similar to prokaryotes than to eukaryotes. Both assumptions have been refuted. Mayr believes that diversity and magnitude are essential to properly classify two different organisms States that there are only 175 different Archaebacteria compared to the 10,000 types of bacteria that have been named Mayr argues that with this diversity and population discrepancy, Archaea and Bacteria should be classified into one domain.

Biological Classification

The supporters of the three-domain idea argue that the experimentation of the theory of Prokaryotes and Eukaryotes was impossible. They also stated that the proper way to classify species was to have conceptual and explanatory power. These powers were applied sufficiently to the Archaea and Bacteria classification. Therefore, the three domain system should be used.

Microbial Diversity

- Morphological and physiological diversity that they encountered among bacteria readily led them intuitively to consider that the various major bacterial groups are of polyphyletic origin. -In short, there is just too much diversity to keep everything in one domain. Originally the amount of diversity overwhelmed biologists who unable to obtain an analyze all the data needed to make an accurate conclusion had simply postulated the all bacteria were of a single origin. Based on DNA analysis Archaea possess genes and several metabolic pathways that are more closely related to eukaryotes. Specifically, the RNA polymerases between Bacteria and Archaea are fundamentally different. Woese argues that many cases now are known in which a bacterial metabolic gene occurs in one or a few Archaea or vice versa. Woese implies that later gene transfer rarely occurs between Archaea and bacteria and therefore should be classified separately. - Woese advocates the idea that there is a

- With recent phylogenetic developments, Microbial diversity has been found to contain hundreds of interconnected phylogenetic branches,. At the moment this unprecedented genetic diversity makes it difficult if not impossible to discern between the proposed Eukarya and Archaea.

Gene Irregularity

Gene sequence similarity

Two genes of the Archaebacteria have been sequenced and compared to gene sequences of bacteria and eukaryotes. The results were consistently the same with the sequences being 42% similar to bacteria compared to 13% similar to eukaryotes.

Phenotypic

- Mayr states in his writings that phenotypes are

Difference

large enough phenotypic difference to sufficiently classify Archaea and bacteria separately. - In addition, Woese believes that even the nature of which Mayr perceives biology is flawed and therefore, the phenotypic differences dont play a large role in determining the separation of Archaea from bacteria. - The habitat is major factor that influences the behavior and habits of an animal, especially Having three domains will allow the DNA of organisms to be organized and more specifically organized during classification. Ancestors should be used to classify organisms because it will be easier on part of the scientist to classify different organisms.

the object of selection and should be the main aspect looked at when studying evolution - With this point of view, Mayr argues that there is little to no difference between the phenotypes of Archaebacteria and bacteria. - The phenotypic difference between bacteria and eukaryotes on the other, hand is extremely large.

Habitat

- This will cause more discrepancies between scientists of different nationalities.

Molecular Difference

The DNA of different organisms between different domains will be greatly varied, and may cause discrepancies.

Ancestor

This may cause discrepancies between different scientists who may not all agree on the same ancestor for a certain species.

Conclusion Based upon the issues previously discussed, I side with Woese in there exist three domains; Bacteria, Eukarya, and Archaea. Morphological, physiological, and phenotypic diversity is just too great for prokaryotes to be one domain. In addition, studies of gene transfer and phylogenetics using genetic mapping point towards the early multifaceted interactions between a number of early bacteria, which led to the distinction of two different prokaryotic domains. Using conceptual and explanatory reasoning, the three domain system of life is the only feasible option there to explain the genetic diversity observed.