Special Issue of RNA Biology Dedicated to Carl Woese
Landes Bioscience, publisher of the journal RNA Biology, has dedicated their entire March 2014 issue to articles on Carl Woese. Below is the table of contents of the article, or visit the journal's website for this issue here.
March 2014, Volume 11, Issue 3, Table of Contents
A special issue in memoriam of Carl Woese
Introduction to special Carl Woese issue in RNA Biology
Robin R Gutell
Carl Woese: A structural biologist’s perspective
Peter B Moore
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.
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.
Molecular phylogenetics before sequences: Oligonucleotide catalogs as k-mer spectra
Mark A Ragan, Guillaume Bernard and Cheong Xin Chan
From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbial evolution.
Constraint and opportunity in genome innovation
James A Shapiro
The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.
Carl Woese's vision of cellular evolution and the domains of life
Eugene V Koonin
In a series of conceptual articles published around the millennium, Carl Woese emphasized that evolution of cells is the central problem of evolutionary biology, that the three-domain ribosomal tree of life is an essential framework for reconstructing cellular evolution, and that the evolutionary dynamics of functionally distinct cellular systems are fundamentally different, with the information processing systems “crystallizing” earlier than operational systems.
From Woese to Wired: The unexpected payoffs of basic research
Fundamental observations about nature sometimes take a circuitous and utterly unpredictable course from bright idea to demonstrably practical impact. The tale of how Carl Woese’s basic insights about microbial diversity eventually contributed to the emergence of a new field of science with numerous potential applications is just such a story.
Carl Woese, Dick Young, and the roots of astrobiology
John D Rummel
The beginning of the space age in the late 1950s gave rise to innovative and interdisciplinary research concepts and perspectives, including the concept of “exobiology” as a way to approach the fundamental aspects of biology through a study of life outside of the Earth, if it existed. This concept was embodied by NASA into its formal Exobiology Program and into the philosophy of the program both before and after the Viking missions that were launched to Mars to search for signs of life in 1975.
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.
Organelle evolution, fragmented rRNAs, and Carl
Michael W Gray
I am honored to have been asked to contribute to this memorial issue, although I cannot claim to have known Carl Woese well. Carl’s insights and the discoveries that his research group made over the years certainly stimulated my own research program, and at several points early on, interactions with him were pivotal in my career. Here I comment on these personal dealings with Carl and emphasize his influence in two areas of long-standing interest in my lab: organelle evolution and rRNA evolution.
Remembering Carl Woese
Kenneth R Luehrsen
Woese on the received view of evolution
As part of his attempt to reconstruct the earliest phase of the evolution of life on Earth, Woese produced a compelling critique of the received view of evolution from the 20th century. This paper explicitly articulates two related features of that critique that are fundamental but the first of which has not been sufficiently clearly recognized in the context of evolutionary theorizing.
Secondary structure adventures with Carl Woese
Harry F Noller
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.
A backward view from 16S rRNA to archaea to the universal tree of life to progenotes: Reminiscences of Carl Woese
Roger A Garrett
I first became aware of Carl Woese in the mid-1970s when he and George Fox criticized a few of the 16S rRNA oligonucleotide sequences emerging from Strasbourg in the 10–12 y RNA sequencing project of the first 16S rRNA from Escherichia coli, some of which we were using for assembling RNA binding sites of ribosomal proteins. When I realized that they were attempting to sequence 16S rRNAs from a range of bacteria to classify them phylogenetically, I seriously questioned their sanity.
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.
History and impact of RDP: A legacy from Carl Woese to microbiology
James R Cole and James M Tiedje
The Ribosomal Database Project (RDP) grew out of Carl Woese’s vision of how rRNA comparative methods could transform biology. First at the University of Illinois Urbana-Champaign, and later at Michigan State University’s Center for Microbial Ecology, the project has grown from a few hundred to several million rRNA gene sequences. In the years since Woese started the RDP, publications describing the database and related tools have been cited over 11 000 times in journals spanning a wide range of disciplines.
Casting a long shadow in the classroom: An educator’s perspective of the contributions of Carl Woese
Mark O Martin
“What does one do when the giants pass away?” remarked a very famous microbiologist to me, soon after the death of Carl Woese in late 2012. I teach microbiology and introductory cell and molecular biology at a small undergraduate institution; Woese’s example and contributions have long been part of every class I teach, and with good reason. Thus, I didn’t know quite what to say to my colleague at first; I was still mentally processing the event.
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.
Ten lessons with Carl Woese about RNA and comparative analysis
Robin R Gutell
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.
Memories of Carl from an improbable friend
Harris A Lewin