phylogenetic lineage, as Woese had recently proposed (Barnabas et al. 1982).
However, later genome sequencing showed that these two lineages share many
closely related genes separate from their bacterial analogs, suggesting the cytoplasmic aspect of eukaryotes might have arisen from an archaeal ancestor (Spang et al.
2015). It is sad to realize that Dayhoff passed away shortly after that article was
published. Had she lived to pursue this apparent discrepancy in her and Woese’s
findings, perhaps she might have spearheaded analyses that would have discovered
the link between archaeal and eukaryotic evolution earlier and so have led to greater
insights about this important question than we now have. She was already showing
an interest in this question as evidenced by a posthumous article about bacterial and
eukaryotic evolution (Hunt et al. 1984).
Those interested in microbial evolution now had a method, nucleic acid sequence
comparisons, to read Darwin’s “written pedigrees.” Consequently, Darwin’s dream
had been realized:
The time will come I believe, though I shall not live to see it, when we shall have very fairly
true genealogical trees of each great kingdom of nature. (Darwin Correspondence Project
Letter no. 2143 2020b)
2.8 Macromolecular Sequencing Revives Darwinian
Influences
The stage was now set to bring Darwinian ideas and principles back to the study of
bacterial evolution. Except for a scattering of efforts using various protein sequences
and the speculative articles about the evolution of microbial processes mentioned
above, major advancement in the field at this time was largely through the efforts of
Carl Woese (Fig. 2.9).
Woese was by training a biophysicist. While at Yale and the General Electric
Research Laboratory, he became interested in the nature of the genetic code (Woese
1962) and, after moving to the Department of Microbiology at the University of
Illinois, the evolution of the code (Woese 1965). This naturally led to interest in its
decoding by translation, both prebiotic (Woese 1968a) and biotic (Woese 1968b).
His interest in the evolution of the translation apparatus led him to examine 5S
rRNA sequences, basing this on the work of Zukerkandl and Pauling and Fitch and
Margoliash cited above, among others (Sogin et al. 1972). Complete sequencing of
rRNAs was impossible, but he realized that oligomer cataloging, as described above,
might suffice. He was familiar with this technique as his departmental colleague,
Saul Spiegelman, in 1968 set up Sanger’s system of RNA fingerprinting for use in
his studies of RNA viruses (Sapp 1979). Woese found that this method allowed him
to detect relationships at least to the level of intra-family relations. This study already
challenged existing phylogenetic schemes, suggesting that the Pseudomonadaceae
family was misplaced. Interestingly, the article concludes by saying that this method
is simple and could be used by any laboratory interested in studying bacterial
phylogeny. It does not seem to have convinced anyone as virtually no labs did
40
K. M. Noll
However, later genome sequencing showed that these two lineages share many
closely related genes separate from their bacterial analogs, suggesting the cytoplasmic aspect of eukaryotes might have arisen from an archaeal ancestor (Spang et al.
2015). It is sad to realize that Dayhoff passed away shortly after that article was
published. Had she lived to pursue this apparent discrepancy in her and Woese’s
findings, perhaps she might have spearheaded analyses that would have discovered
the link between archaeal and eukaryotic evolution earlier and so have led to greater
insights about this important question than we now have. She was already showing
an interest in this question as evidenced by a posthumous article about bacterial and
eukaryotic evolution (Hunt et al. 1984).
Those interested in microbial evolution now had a method, nucleic acid sequence
comparisons, to read Darwin’s “written pedigrees.” Consequently, Darwin’s dream
had been realized:
The time will come I believe, though I shall not live to see it, when we shall have very fairly
true genealogical trees of each great kingdom of nature. (Darwin Correspondence Project
Letter no. 2143 2020b)
2.8 Macromolecular Sequencing Revives Darwinian
Influences
The stage was now set to bring Darwinian ideas and principles back to the study of
bacterial evolution. Except for a scattering of efforts using various protein sequences
and the speculative articles about the evolution of microbial processes mentioned
above, major advancement in the field at this time was largely through the efforts of
Carl Woese (Fig. 2.9).
Woese was by training a biophysicist. While at Yale and the General Electric
Research Laboratory, he became interested in the nature of the genetic code (Woese
1962) and, after moving to the Department of Microbiology at the University of
Illinois, the evolution of the code (Woese 1965). This naturally led to interest in its
decoding by translation, both prebiotic (Woese 1968a) and biotic (Woese 1968b).
His interest in the evolution of the translation apparatus led him to examine 5S
rRNA sequences, basing this on the work of Zukerkandl and Pauling and Fitch and
Margoliash cited above, among others (Sogin et al. 1972). Complete sequencing of
rRNAs was impossible, but he realized that oligomer cataloging, as described above,
might suffice. He was familiar with this technique as his departmental colleague,
Saul Spiegelman, in 1968 set up Sanger’s system of RNA fingerprinting for use in
his studies of RNA viruses (Sapp 1979). Woese found that this method allowed him
to detect relationships at least to the level of intra-family relations. This study already
challenged existing phylogenetic schemes, suggesting that the Pseudomonadaceae
family was misplaced. Interestingly, the article concludes by saying that this method
is simple and could be used by any laboratory interested in studying bacterial
phylogeny. It does not seem to have convinced anyone as virtually no labs did
40
K. M. Noll