Microbiology’s Scarred Revolutionary^(PDF), Carl Woese (pron.: /ˈwoʊz/), a biophysicist and evolutionary microbiologist whose discovery 35 years ago of a “third domain” of life in the vast realm of microorganisms altered scientific understanding of evolution, died at the beginning of this at his home in Urbana, Ill. He was 84.

Carl R. Woese (1928–2012)

WF Doolittle. Published 2013 in Current Biology. http://dx.doi.org/10.1016/j.cub.2013.01.057

Carl Woese died two days before this year began, in Urbana, Illinois, his academic home for nearly fifty years. Without the far-reaching ideas and prodigious datasets generated by Woese and his protégés, enthusiastic colleagues and hordes of more distant admirers, all of biology, but most especially microbiology and cellular evolution, would be immeasurably the poorer. Lynn Margulis, who died little more than a year before, once termed this cohort of evolutionary investigators “Woese’s Army”, and indeed Carl’s following has that sort of character. If we sought reasons to endorse a “Great Man Theory” of (scientific) history and progress, we could find no better exemplar.

Credit: (Doolittle, 2013)

This is the classic paper explaining Woese’s career and his struggle to change how we see phylogeny and evolution:

Microbiology’s Scarred Revolutionary

V Morell. Published 1997 in Science DOI: 10.1126/science.276.5313.699

Carl Woese started a scientific revolution–and paid a price. Twenty years ago, the University of Illinois evolutionist announced that the Archaea–a group of one-celled organisms–are so different from all other living things, including bacteria, that they belong in a separate domain of life. Far from being just one of life’s five major kingdoms, microbes are actually two of its three broad domains: Bacteria, Archaea, and Eukarya (which includes all multicellular organisms, from plants to people). The stunning implication: Most life is one celled, and all Eukarya are but a twig on what amounts to a great microbial tree. It took years for other biologists to accept this transformation of the tree of life.

“Imagine walking out in the countryside and not being able to tell a snake from a cow from a mouse from a blade of grass, that’s been the level of our ignorance.”-Woese

Carl Woese’s distinguished career was dominated by his idea that divisions between different kinds of living organisms could be better defined by their small subunit ribosomal RNA^{(smaller bottom piece here)}  sequences than by their morphology, biochemistry, outer membrane, or even necessarily the most basic of divisions like multicellularity or the presence of cellular organelles. Indeed, seeing life through this much clearer lens, he was able to show that the microbes known as Archaea are at least as different from Bacteria as they are from Eukaryotes like plants, animals and us, a finding he presented here to much controversy and derision:

Phylogenetic structure of the prokaryotic domain: the primary kingdoms.

CR Woese & GE Fox. Published 1977  in PNAS USA.

A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the eurkaryotes, now represented in the cytoplasmic component of eukaryotic cells.

He fought for his perspective eloquently and decisively here:

Bacterial evolution.

CR Woese. Published 1987 in Microbiological Reviews

A revolution is occurring in biology: perhaps it is better characterized as a revolution within a revolution. I am, of course, referring to the impact that the increasingly rapid capacity to sequence nucleic acids is having on a science that has already been radically transformed by molecular approaches and concepts. While the impact is currently greatest in genetics and applied areas such as medicine and biotechnology, its most profound and lasting effect will be on our perception of evolution and its relationship to the rest of biology. The cell is basically an historical document, and gaining the capacity to read it (by the sequencing of genes) cannot but drastically alter the way we look at all of biology. No discipline within biology will be more changed by this revolution than microbiology, for until the advent of molecular sequencing, bacterial evolution was not a subject that could be approached experimentally. With any novel scientific departure it is important to understand the historical setting in which it arises-the paradigm it will change. Old prejudices tend to inhibit, distort, or otherwise shape new ideas, and historical analysis helps to eliminate much of the negative impact of the status quo. Such analysis is particularly important in the present instance since microbiologists do not deal with evolutionary considerations as a matter of course and so tend not to appreciate them. Therefore, I begin this discussion with a brief look at how the relationship between microbiology and evolution (i.e., the lack thereof) developed.

And presented it again thirteen years later, but this time as core scientific dogma:

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

CR Woese, O Kandler & ML Wheelis. Published 1990 in PNAS USA. doi: 10.1073/pnas.87.12.4576

Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems–i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy–reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a “domain.” Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.

“Today, whenever a student of biology opens their textbook what they see first is a blown up image of the tripartite tree of life – a small tribute to a man and a discovery that changed our view of nature forever.“

Credit: http://en.wikipedia.org/wiki/Phylogenetic_tree

If you guys want to get a visceral sense of how we use this man’s work today here is an unpublished sequence of the DNA that encodes for a 16s ribosome fragment made from a PCR^{(helpful animation)}  reaction with universal primers a strain one of my old students isolated from soil. For reference this is a few hours work and about a hundred bucks worth of reagents and sequencing costs.

attgaacgctggcggcaggcctaacacatgcaagtcgagcggatgagaagagcttgctcttcgattcagcggcggacgggtga
cttcgggccttgcgctatcagatgagcctaggtcggattagctagttggtgaggtaatggctcaccaaggcgacgatccgtaactggtctgag
agggtgatcagtcacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattggacaatgggcgaaagcctga
tccagccatgccgcgtgtgtgaagaaggtcnnnnnnnnnnnnnnnnnnnnnnngaagggcattaacctaatacgttagtgttttga
cgttaccgacagaataagcaccggctaactctgtgccagcagccgcggtaatacagagggtgcaagcgttaatcggaattactgggcgtaa
agcgcgcgtaggtggtttgttaagttggatgtgaaagccccaggctcaacctgggaactgcatccaaaactggcaagctagagtacggtag
agggtggtggaatttcctgtgtagcggtgaaatgcgtagatataggaaggaacaccagtggcgaaggcgaccacctggactgatactgac
actgaggtgcgaaagcgtggggagcaaacaggattagataccctggtagtccacgccgtaaacgatgtcaactagccgttggaatccttga
gattttagtgnnnngctaacgcattaagttgaccgcctggggagtacgnccgcaaggttaaaactcaaatgaattgacgggggcccgcac
aagcggtggagcatgtggtttaattcgaagcaacgcgaagaaccttaccaggccttgacatgcagagaactttccagagatggattggtgc
cttcgggaactctgacacaggtgctgcatggctgtcgtcagctcgtgtcgnagatgttgggttaagtcccgtaacgagcgcaacccttgtcct
tagttaccagcacgttatggtgggcactctaaggagactgccggtgacaaaccggaggaaggtggggatgacgtcaagtcatcatggccct
tacggcctgggctacacacgtgctacaatggtcggtacagagggttgccaagccgcgaggtggagctaatctcacaaaaccgatcgtagtc
cggatcgcagtctgcaactcgactgcgtgaagtcggaatcgctagtaatcgcgaatcagaatgtcgcggtgaatacgttcccgggcct

You can compare it to all of the other 16s ribosomal RNA sequences that have ever been published, as of less than a month ago, here at the Ribosomal Database Project. Just paste the sequence into the box, click the isolates only option, and hit submit. It will tell you exactly what the bacteria is down to the genus and if you click on [view selectable matches] it will tell you individual identified bacteria it is most similar to (by the S_ab score, which is a statistical measure of similarity).

In the 1960s while Carl Woese was originally doing his thing, he had none of these simple techniques that can be done by bleary eyed undergrads. He sequenced the RNA fragments themselves directly using an old, delicate, and incredibly tedious technique known as oligonucleotide cataloging. For starters he was working with RNA, which means that at every step he needed to beware of the RNA degrading enzymes that exist everywhere, are secreted from our pores, and aerosolized on our breath. However the method itself involves using an enzyme that cuts at every g molecule (guanine) and then each of these fragments (only 6 to 20 nucleotides long) would be sliced into smaller fragments with other enzymes that recognized other nucleosides. All of this was then run out on radiolabelling gels would separate everything purely by size creating a massive puzzle that is near impossible to tease apart by hand if you even get that far. Naturally, Woese was one of two or three people on the planet crazy enough to learn how to do something this mad. How arcane the necessary technique was was a large part of why so few of the older fuddyduddies believed him or cared until the mid 80s, before the few remaining doubters had to finally concede with the sequencing revolution of the 90s.

“It’s clear to me that if you wiped all multicellular life-forms off the face of the earth, microbial life might shift a tiny bit, if microbial life were to disappear, that would be it — instant death for the planet.”-Woese