The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree

Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.

Remembering Otto Kandler (1920-2017) and his contributions

After a brief prologue on Otto Kandler's life, we describe briefly his pioneering work on photosynthesis (photophosphorylation and the carbon cycle) and his key participation in the discovery of the concept of three forms of life (Archaea, Prokarya, and Eukarya). With Otto Kandler's passing, both the international photosynthesis and microbiology communities have lost an internationally unique, eminent, and respected researcher and teacher who exhibited a rare vibrancy and style.

Ten lessons with Carl Woese about RNA and comparative analysis

A few years before I started my graduate studies, Carl Woese was establishing a collaboration with his friend, colleague, and my PhD advisor, Harry Noller. Carl was introducing comparative methods to Harry's lab to determine the secondary structure for the 16S and 23S rRNAs. In addition to an experimental project that had minimal to no success, I was attempting to predict an RNA secondary structure from a single sequence. I determined after a few months that the complexity of RNA folding was much greater than ever anticipated. Ten lessons were learned about the dynamics of RNA folding, the comparative methods used to accurately predict the RNAs secondary structure and the beginnings of its tertiary structure, the use of comparative methods to reveal much more than ever anticipated about RNA structure, other applications beyond RNA structure, and the lessons about the process of scientific discovery.

Looking in the right direction: Carl Woese and evolutionary biology

Carl Woese is known to the scientific community primarily through his landmark contributions to microbiology, in particular, his discovery of the third Domain of Life, which came to be known as the Archaea. While it is well known how he made this discovery, through the techniques he developed based on his studies of rRNA, the reasons why he was driven in this scientific direction, and what he saw as the principle outcome of his discovery--it was not the Archaea!--are not so widely appreciated. In this essay, I discuss his vision of evolution, one which transcends population genetics, and which has ramifications not only for our understanding of the origin of life on Earth and elsewhere, but also for our understanding of biology as a novel class of complex dynamical systems.

Secondary structure adventures with Carl Woese

Not long after my arrival at UCSC as an assistant professor, I came across Carl Woese's paper “Molecular Mechanics of Translation: A Reciprocating Ratchet Mechanism.”¹ In the days before the crystal structure of tRNA was known, Fuller and Hodgson² had proposed two alternative conformations for its anticodon loop; one was stacked on the 3′ side (as later found in the crystal structure) and the other on the 5′ side. In an ingenious and elegant model, Woese proposed that the conformation of the loop flips between Fuller and Hodgson's 5′- and 3′-stacked forms during protein synthesis, changing the local direction of the mRNA such that the identities of the tRNA binding sites alternated between binding aminoacyl-tRNA and peptidyl-tRNA. The model predicted that there are no A and P sites, only two binding sites whose identities changed following translation of each codon, and that there would be no translocation of tRNAs in the usual sense—only binding and release. I met Carl in person the following year when he presented a seminar on his ratchet model in Santa Cruz. He was chatting in my colleague Ralph Hinegardner's office in what Carl termed a “Little Jack Horner appointment” (the visitor sits and listens to his host describing “What a good boy am I”). He was of compact stature, and bore a striking resemblance to Oskar Werner in Truffaut's film “Jules and Jim.” He projected the impression of a New-Age guru—a shiny black amulet suspended over the front of his black turtleneck sweater and a crown of prematurely white hair. Ralph asked me to explain to Carl what we were doing with ribosomes. I quickly summarized our early experiments that were pointing to a functional role for 16S rRNA. Carl regarded me silently, with a penetrating stare. He then turned to Ralph and said, in an ominous low voice, “I'm going to have some more tanks made as soon as I get back.” Carl's beautiful model was, unfortunately, wrong—it was simpler and more elegant than the complex mechanism that Nature actually uses. Unyielding, Carl railed against the A-site-P-site model at every opportunity,^3,4 and although we ended up enjoying a long, intense, and fruitful collaboration, and became close, life-long friends, I finally gave up trying to describe to him our biochemical and crystallographic results on the A, P, and E sites.

Early days with Carl

Science is all about making discoveries. That’s it! It was my good fortune and Carl’s good fortune to share an experiment that produced an unexpected result. In the 1960s, Carl became interested in the classification of bacteria with the ultimate goal of defining the relatedness of bacterial groups as well as events in the evolution of these organisms. He proposed to do this by studying the sequence of monomers in proteins or nucleic acids. Study of the sequence of amino acids in conserved proteins had severe limitations and could not serve Carl’s purpose. However, the publication by Sanger of a technique for analysis of RNA caught Carl’s attention. His previous experiments with the ribosome had convinced him that this organelle was of very ancient origin; it had only one role in the cell and so was “insulated” from the vast phenotypic variations of bacterial cells.

Carl Woese in Schenectady: the forgotten years

Many of the authors of these short pieces (who were invited to contribute by Robin Gutell) have already written or spoken about Carl Woese since he died at the end of December 2012. My own thoughts were published in PNAS on February 26, 2013. Still saddened by Carl’s death, I re-read what I wrote at that moment. The article was OK, although it was not strong enough for what Carl taught us: he deserved better. I’d like us to admire what Carl did over 50 years (which is a given), and to admire even more the way he did it. While Carl’s accomplishments were huge, his intense dedication to the ideas that consumed him was even more impressive.

Life is translation

Evolutionary origin of translation represents one of the key questions that Carl Woese addressed in his work. Here we give a personal account of his results in this area and the effect they have had on the field.

Carl Woese: a structural biologist's perspective

Not long after Carl Woese died, I received a message from Robin Gutell asking if I would contribute an article to this issue of RNA Biology. While my admiration for Carl’s contributions to biology knows no bounds, I did not know him well personally. For that reason I advised Robin to strike my name off the list of contributors and replace it with that of someone who is better qualified than I am, but he persisted, and here we are. I guess Robin thought it would be useful to hear from one of those who admired Carl from afar.

The naïve outsider might find it surprising that a structural biologist like me, who worries about the minutia of the three-dimensional structures of biological macromolecules, would ever have had anything in common with a big-picture, evolutionary biologist like Carl, but I did. What we shared was an interest in the structures of RNAs, especially rRNAs.