The Birth of the : a Personal Retrospective

Carl R. Woese Department of University of Illinois Urbana, Illinois 61801

Dedicated to Wolfram Zillig: A founder of the archaeal revolution.

Mailing address: Department of Microbiology, University of Illinois, 601 South Goodwin Ave., Urbana, IL 61801-3709. Phone (217) 333-9369. Fax (217) 244- 6697. E-mail [email protected]. Carl R. Woese

Let There Be Light My job was to determine the complete For me the moment was, I believe, the sequence of every oligonucleotide of afternoon of June 11, 1976. I had just significant length (five or more taped the film of a primary "Sanger nucleotides) in the primary pattern, pattern" to a back-lit translucent "wall" in which required the aforementioned the lab and had begun to "interpret" the "secondary" patterns. These in turn pattern in terms of the "secondary cuts" were created by removing little snippets taken from it, the corresponding films of of paper at the appropriate places in the which were lying on a huge light table corresponding original directly beneath the "primary"; the object electrophoretogram and further being to infer the sequences of all the digesting the oligonucleotide(s) therein oligonucleotides (of significant length) in (in situ) with one or a few ribonucleases the primary pattern. Except for this of different cutting specificities than that eerie lighting arrangement, the room of T1 RNAse (thereby creating sub- was fairly dark, with the only prominent fragments). These enzymatically treated features being the pattern of back-lit snippets were then individually black spots on the "primary" film and the reinserted (mashed) into a very large corresponding transluminated lines of sheet of (DEAE cellulose) paper (about black "sub-cut" spots on the "secondary" 30 of them in a line near the "bottom" of film lying below. such a sheet). Each large "secondary" sheet was then subject to one dimensional electrophoresis to resolve The spots on the "primary" film the sub-fragments in each of the thirty- represented specific oligonucleotide odd secondary digestions from one fragments into which a (radio-labeled) another. From the one or several 16S rRNA (ribosomal RNA) had been "secondary" cuts taken from a primary cut by T1 ribonuclease, then subjected spot, the exact sequence of the to a two dimensional paper oligonucleotide(s) in the corresponding electrophoretic separation, with the primary spot could (almost always) be resulting oligonucleotide "spots" deduced (Uchida et al, 1974). detected by means of X-ray film (Uchida et al., 1974). The "isopleth" pattern on "Reading" a Sanger pattern in this the film of the "Sanger pattern" (Sanger fashion was painstaking work, requiring et al, 1965) already revealed a great a good fraction of the day to work up a deal about the sequence(s) of the single "primary", something I at the time oligonucleotide(s) in the individual spots; had been doing for several days a week for instance, the length of oligo, number off and on for a long time. It was routine of uracil residues it contained (a primary work, boring, but demanding full determinant of the overall structure of concentration. [There were days when the isopleth pattern), and the C I'd walk home from work saying to (cytosine) vs. A (adenine) contents of myself: "Woese, you have destroyed the individual spots in each in an your mind again today"]. But this day isopleth (Sanger et al, 1965). [Each was special: I and were in for a oligonucleotide had but one G residue, surprise! First, however, more at its 3' end, the cut site of ribonuclease background. T1 (Sanger et al, 1965)].

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The Birth of the Archaea: a Personal Retrospective

Starting Down the Yellow Brick Road However, I differed from the whole lot of them in perceiving the nature of the I had had an abiding interest in the code as inseparable from the problem of translation process since the latter part the nature and origin of the decoding of the 1950s; first with the ribosome and mechanism. Thus, translation to me its subunits, then, starting in 1960, with was the central biological concern. It the genetic code ─ the hot topic of represented one of a new class of major molecular biology at the time. The code evolutionary problems that molecular had come into prominence on the heels probings of the cell were bringing to of Watson and Crick's two world-shaking light. Now was the time to start thinking 1953 publications. The physicist about the evolution of the cell and its George Gamow thought he could see macromolecular componentry. How this "pockets" in the double stranded evolution occurred is almost as much a structure of DNA, pockets of just the mystery today as it was four decades right size and spacing to hold and ago. But one thing was certain from the discriminate among amino acids, start: approaching these sorts of "deep" suggesting the basis for a direct universal evolutionary problems would templating mechanism upon which require a universal phylogenetic translation could be based (Watson & framework within which to work Crick, 1953; Gamow, 1954). effectively. Since no universal phylogeny then existed ─ our understanding of evolutionary Then came a thrilling but brief period relationships being effectively confined when a clique of physicists and to and animals ─ this meant molecular worked together taking on the rather large task of and competed to see who would be first determining genealogical relationships to derive the "code" from "first for the microbial world, the and principles". The prospect of theoretically single-celled eukaryotes, which, as it solving the genetic code, the "language turned out, meant determining the of life", was so seductive that cameo missing 95% or more of the "tree of appearances on the coding stage were life". A slight diversion in my research made by Feynmann and Teller (no program would be necessary ─ a doubt prompted by the charismatic diversion that lasted a good two Gamow). The decoders soon split into decades! two camps, however, those who, like A method for my madness. In 1965, Gamow, believed that the basis of the on his way to developing nucleic acid code lay in specific recognition of amino sequencing technology, Fred Sanger acids by nucleic acids, and those who, had spun off an "oligonucleotide like , believed it impossible cataloging" methodology (Sanger et al., that nucleic acids could recognize 1965). This procedure, applied to anything except other nucleic ribosomal RNA (the small subunit rRNA acids/nucleotides, which they did it turned out), was exactly what we through base pairing (F. H. C. Crick, needed to determine genealogical unpublished "Letter to the RNA Tie relationships across the entire breadth Club; see Judson, 1996). When I of the phylogenetic spectrum. It was belatedly entered the area, my intuition already apparent from DNA-rRNA sided with Gamow. hybridization studies that the sequence of a ribosomal RNA tended to be highly conserved, probably to the point that recognizable sequence similarity would

3 Carl R. Woese

extend across the full taxonomic 's search for these spectrum (Yankofsky & Spiegelman, relationships had gotten itself into. 1962). Ribosomal RNAs are obviously ubiquitous; they occur in the cell in thousands of copies; and they can be The best advice I'd solicited regarding radio-labeled and isolated with relative organism choice came from my ease. In addition, they are functionally colleague in the Microbiology about as constant as one could wish for Department at Illinois, Ralph Wolfe. By ─ they are not adaptive characters. And now I'd gotten used to last but not least, rRNAs are integral suggesting that we work on their favorite parts of a complex, integrated molecular bugs, and in this respect, Wolfe was no aggregate (genetically dispersed within different. But what he had to say was; the genome), which would make them his advice was more compelling than as insensitive as can be to the any other I had received! I can almost vicissitudes of reticulate evolution (Fox remember his words: he told me the et al, 1977a). Only technological methanogens were united as a group by problems seemed to stand in our way: a unique biochemistry that involved a growing the various organisms and set of unusual coenzymes. Yet, the doing so in a low phosphate, radioactive organisms showed no uniformity in their medium; tweaking the Sanger method to morphologies, which latter fact had fit our needs; finding needed help; and caused taxonomists initially to scatter so on. Scientists do not want to, or them throughout the various taxa in the often cannot, create all the things they 7th edition of Bergey's Manual (Breed et need in their work. In our case the chief al, 1957). [In Bergey's 8th, however, problem was the organisms required for they had all been grouped on the basis the project. Half of them at least would of their common biochemistry (Murray et be too fastidious for anyone but an al., 1974)]. Finally! here was the kind of expert to grow. Striking up phylogenetic challenge I was hoping collaborations with experts in the culture for. I longed to characterize a of particular organisms was essential. methanogen rRNA as soon as possible. But it wasn't possible ─ at least not yet. Wolfe and I had spoken in early 1974 (if Learning our way around. Coming I recall correctly), and the technology into the game as a needed for growing and radio-labeling biophysicist/molecular my the methanogens safely was not at that knowledge of bacteria and time in place. Now, back to the main bacteriologists didn't extend far beyond thread. E. coli, Bacillus, and ; and I didn't have the foggiest notion of how bacteria were related to one another. It Epiphany! was time to ask real microbiologists for help in choosing the right organisms. By the beginning of 1976 my lab had Each, of course, had a different opinion "cataloged" (generated T1 (the bacteria they themselves worked oligonucleotide lists) for roughly 30 with, that is). At that stage, I didn't know organisms, mainly "procaryotes" and a that actually there were no experts on smattering of eukaryotes. It had bacterial relationships (those above the become obvious that the two groups level, say, of and occasionally could be readily distinguished from each family, that is). And I was completely other on the basis of "oligonucleotide unaware of the bizarre state that the signatures", which were lists of

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The Birth of the Archaea: a Personal Retrospective

oligonucleotides characteristic of one of syllable monstrosity that was always the two groups to the exclusion of the shortened to "∆H", the organism's strain other. The two apposing oligonucleotide designation (Zeikus & Wolfe, 1972). signatures were remarkably distinct. [In addition, a set of "universal" oligonucleotides existed, those found in From the get-go ∆H's Sanger pattern all the rRNA catalogs we had so far was strange. First of all the two small generated]. In working up a Sanger "odd" oligos on the primary pattern that pattern for an organism, one had only to screamed out "procaryote" were "read" a small number of oligos into it absent. Intrigued by this appetizer, but before being able to smile and say: "Oh, afraid to make too much of it, I quickly that's a procaryote", or "that a euk". jumped into the "G isopleth" There were two spots on the primary (oligonucleotides that lack a uracil films of all procaryotic rRNAs that easily residue), hoping to find the first of the caught one's eye, for they contained procaryotic signature oligos, which modified nucleotides and, so, were would certainly set things back on the located at places in the Sanger pattern procaryote track! Imagine my surprise where normally there would be no when that "signature" oligo was missing oligonucleotides. These "odd oligos" as well. Not only that, but the G-isopleth allowed one to declare "procaryote" at contained the rather large 3' terminal first glance: after that, it was just a oligonucleotide of this 16S rRNA, which matter of detailing the rest of the pattern did not belong there! What was going to figure out the relationship of the new on? This methanogen rRNA was not procaryote to ones already cataloged. feeling procaryotic. The more oligos I sequenced, the less procaryotic it felt, as signature oligo after procaryotic By 1976 Wolfe and his student Bill Balch signature oligo failed to turn up. had developed a technique for growing However, a number of them were still methanogens (in pressurized serum there, as, surprisingly, were some oligos bottles) that was sterile, fast, and (most from the eukaryotic signature, and, important from our point of view), safe thankfully, quite a few of the oligos we'd enough to permit cells to be radio- considered universal in distribution. labeled (Balch & Wolfe, 1976). George What was this RNA? It was not that of a Fox, then my post-doc, had known Bill procaryote. It was not eukaryotic. Nor from a course they'd taken together at was it from Mars (because of the Woods Hole the summer before George "universals"). Then it dawned on me. arrived at Illinois. Their acquaintance Was there something out there other made it easy for George to approach Bill than procaryotes and eucaryotes ─ about a collaboration to work on perhaps a distant relative of their's that methangens ─ which George did on his no one had realized was there? Why own initiative ─ the year the Balch-Wolfe not? But the idea surely wasn't in method was being published. It was on keeping with conventional wisdom! that aforementioned day in June 1976 that I began to read the Sanger pattern produced (by my technician Linda I rushed to share my out-of-biology Magrum) from George and Bill's first experience with George, a skeptical successful methanogen rRNA prep. George Fox to be sure. George was The formal name of the organism was always skeptical. That's what made him Methanobacterium a good scientist; and because of that, thermoautotrophicum, a fourteen whatever skepticism he initially evinced

5 Carl R. Woese

quickly dissipated. "Yes", he agreed, ribosomal RNA is a non-adaptive, there probably was something else out universal character. That's what makes there: it wasn't just procaryotes and its sequence so good for tracing eukaryotes all the way down. That was organismal genealogies. It is also what a heady thought, novel enough that we makes it completely uninformative as sensed trouble in trying to convince regards the phenotypes of the other biologists of the idea. Little did we organisms whose genealogies it traces. know how much trouble there would be! Darwin had defined evolution as descent with variation. In our case there had been a long trail of descent, and, A finding like this you do not therefore, we should find a comparably immediately go out and shout about. huge amount of variation, not only You had better have all your ducks in a quantitative but qualitative. In other row and have firmer evidence than words, there had to be important would otherwise be needed. We went features characteristic of our new into fast-forward mode: by the end of the urkingdom that distinguished it sharply year (1976) we had five additional from the rest of the living world, and methanogen catalogs in hand, with there should be impressive variation more on the way. They would cover all among the in the urkingdom, as the disparate morphologies associated well. Testing these two main with the known methanogens. And sure evolutionary predictions drove our work enough, none of the new catalogs was from that point on. "procaryotic" (or eukaryotic): and they were all of a kind! The methanogens represented a new highest level There had already been a promising taxonomic grouping, which could be sign in the biochemistry of the defined by a characteristic methanogens. We now knew for sure oligonucleotide signature. [And tellingly, that methanogenesis was indeed that signature was no more extensive confined to a particular phylogenetically- than were those of the "procaryotes" or defined group of organisms and that the the eukaryotes, implying that within process utilized a set of co-enzymes whatever new taxon they represented, that apparently were found no where the methanogens were quite a highly else (Balch & Wolfe, 1979). Doubly diverged group]. Darwin had long ago good! But with their highly specific, said that there would come a day when restricted distribution these coenzymes there would be "very fairly true were going to be of no use to us in genealogical trees of each great searching for non-methanogenic kingdom of nature." Perhaps that day members of our new urkingdom. was at hand! In any case, there was lots of work still to do. The big question was then: where are the predicted other phenotypes? How Build It and They Will Come. could they be found? [As it turned out, a couple of the sought-for non- A new "urkingdom" (as we were methanogenic archaeal phenotypes lay beginning to call our new highest level unknown on our "to-do" list. phylogenetic group) would be a major Thermoplasma (which had been evolutionary find. It afforded a rare described as a mycoplasma growing opportunity to put the theory of evolution freely under hot and acid conditions) to serious predictive test. As I've said, was among the mycoplasmas tabbed for

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The Birth of the Archaea: a Personal Retrospective

rRNA characterization in a collaboration peptidoglycan; and possession of with Jack Maniloff (University of peptidoglycan-containing cell walls had Rochester), a collaboration that had come to be considered one (of the few begun in earnest in the spring of 1975 positive) unifying characteristics of (with Mycoplasma gallisepticum). And procaryotes (Stanier et al, 1963). There there were the extreme halophiles, had been no systematic examination of whose unusual obligate high salt growth bacterial walls before about 1967, conditions made them obvious although a fair number of them had candidates for the phylogeny project in been characterized on a hit-or-miss any case. I have often mused in recent basis. What Kandler had known (which times about how the history of the we didn't) was that the walls of at least archaea would have played out had one methanogen and those of some their entrance into our world been extreme halophiles did not contain through one of these other portals. No peptidoglycan (Kandler & Hippe, 1977). doubt that things would have gone very differently! What did these atypical walls imply? On Fortunately, the job of hunting for other the basis of the cell wall studies alone phenotypes that might belong to the (the lack of peptidoglycan), one could new urkingdom turned out to be easier not reliably infer much, especially infer than I imagined. Unbeknownst to that the peptidoglycan-less organisms George and me, our collaborator Ralph constituted a monophyletic grouping Wolfe had invited the well-known unto themselves. [Bacteria atypical in German microbiologist Otto Kandler to one way or another were often Urbana for a visit. [Being a molecular encountered, and sometimes they biologist, I had never heard of this lacked some property that Kandler fellow ─ or almost any other microbiologists had come to believe was well-known microbiologist, for that typical of "procaryotes". But in all such matter ─ until the day that Ralph cases, the idiosyncrasy in question had marched him into my office to hear the been passed off as adaptation to some official word from George and myself unusual environment. It would require about the new urkingdom]. According to much stronger evidence than one or two his records, Otto (as I would soon come out-of-the-blue idiosyncrasies to make a to call him) visited Urbana in January of microbiologist question a bacterium's 1977, well before publication of our procaryotic pedigree. And as we were finding. soon to find out, there were some among them who would not question that pedigree even when confronted The German Smiled. Amazingly, with strong evidence!] Kandler ─ unlike the others we'd tried to convince about what our findings meant ─ wasn't incredulous or disbelieving or Kandler had fully realized the potential anything. I think he smiled. A "third significance of the cell wall studies in the form of life" was fine with him; he had light of our rRNA molecular phylogenetic almost expected it. For some time evidence, and had immediately gone Kandler had, from his own work and that back to Germany intent upon fleshing of others, known that the walls of certain out the comparative study of cell walls ─ procaryotes were highly atypical. The and to spread the word. But his visit walls of the bacteria so far characterized had left us with a critical clue in our hunt had (almost) all contained for novel archaebacterial phenotypes: if

7 Carl R. Woese

unusual cell walls meant anything, of the cloning era (signaled by the perhaps the extreme halophiles would recent cloning in bacteria of the gene for turn out to be members of our new "far the growth hormone somatotrophin). At out" group. We were desperate to get the time, no one could see that this our hands on cultures of extreme fortuitous coincidence foretold the halophiles. coming battle over biology's future, and the coincident press releases were With the help of Jane Gibson (Cornell) tantamount to the first skirmish in the we obtained some halophile cultures ideological struggle that would pit the from the Woods Hole collection. I was forces of what would become the not about to wait for a student or a biomedical-industrial complex against collaboration to come along to grow the those representing a resurgent organisms. I donned my acid-eaten lab . Our "third form of life", which coat (which had hung on the back of my touched upon one of the deepest chords office door for over a decade) and went in human nature (i.e., where we came back to the bench. I grew the cultures from), completely wiped the press myself, turning them over to one of my release announcing the era of "Man-the- students, Kenneth Leuhrsen, for the medical-miracle" off the front pages of more exacting extraction and isolation the papers. I was overjoyed at the procedures for a radio-labeled 16S public's appreciation of our work (Fox et rRNA; and Ken's prep would as always al, 1977b; Woese & Fox, 1977b)! be given to our trusty Linda for Sanger pattern production. By late spring of 1977, a year after we'd seen our first But there were already rumblings from methanogen catalog, we were gazing at the scientific heights. On the day the a 16S rRNA catalog from the first front page of The New York Times extreme halophile. It didn't disappoint. announced our discovery of a "third form Here was the first non-methanogenic of life", my colleague Ralph Wolfe phenotype to join the group ─ and a received a telephone call from his friend, novel phenotype it indeed was. But I'm the Nobel Laureate Salvador Luria getting ahead of myself. It's time to see (whom he did not initially name), an how the public ─ and the biology upset Salvador Luria. According to establishment ─ reacted when this Wolfe, Luria told him in no uncertain strange archaeal chimera was loosed terms to publicly dissociate himself from upon their world. this scientific fakery or face the ruination of his career. In a recent recounting of the episode (Wolfe, 2001) Ralph said he Confrontation and Heresy was so humiliated he "wanted to crawl under something and hide"; but he The press release concerning the "third managed to tell Luria that supporting form of life" was set to coincide with the evidence for the claim had just been publication of the first of our two papers published in the Proceedings of the in the Proceedings of the U. S. National National Academy of Sciences (a fact Academy of Sciences, November 3rd that had appeared in the New York 1977. A telling coincidence was to Times account). Luria begrudged that occur. November 3rd just so happened he hadn't known about any publication, to be the date chosen by the then but that the journal happened to be president of the U.S. National Academy there on his desk. Fortunately, Ralph of Sciences, Philip Handler, to release left for a planned family gathering out of an official statement heralding the dawn

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The Birth of the Archaea: a Personal Retrospective

town the next day (Wolfe, 2001) and It was not simply the extreme halophiles thereby escaped further humiliation. that had the strange lipids, either: Two other recently isolated bacteria, (Darland & As you might expect, I saw the episode Brock, 1970) and Sulfolobus and its overall significance differently. acidocaldarius (Brock et al, 1972) did as How could this Luria fellow have the well (Langworthy et al, 1972; 1974). temerity to excoriate his friend and my Thomas Brock, whose laboratory had colleague like that? What pedestal was first isolated and characterized both he standing on? It appears that he had organisms, had noted the lipid blustered at Ralph something to the coincidence. And he later would say that effect that: "Everybody knows that all the unusual lipids the two shared was a bacteria are procaryotes; there can't be clear case of convergent evolution. In any such thing as a 'third form of life'"! support of that assertion Brock would Irony of ironies! As time (and the invoke the ether-linked lipids of the diligence of a particular scientific extreme halophiles: "This hypothesis is historian) have shown, the fakery lay not strengthened by the fact that in our work, but in the Halobacterium, another quite different concept itself (Sapp, 2005): it is now organism, also has lipids similar to those clear that the "procaryote" was mere of the two acidophilic thermophiles" guesswork. [More on this below]. But in (Brock, 1978). the hey-day of the procaryote, which this was, the true believers were out to pillory us for our heresy: how dare we Brock's argument doesn't make sense; proclaim that the mighty at least today it doesn't. In its time, PROCARYOTIC EMPEROR WASN'T however, it was reasonable. Like all WEARING ANY CLOTHES! biologists of that period, Brock firmly believed all bacteria to be "procaryotes". If both of the Expanding the Urkingdom thermophiles were procaryotes and they were not specifically related (as was With the halophiles came another clue ─ believed), then their common lipids, highly unusual ether-linked, idiosyncrasy has to represent branched chain lipids. In my whole convergence, independent adaptations career I'd never paid attention to lipids, to their respective extreme niches. and here we were with lipids on the From this perspective the case for brain! The fact that extreme halophiles convergent evolution is indeed possessed ether-linked lipids had been strengthened by pointing to a third published in the mid-1960s (Kates et al, prokaryotic species (the extreme 1965; Kates, 1972), but nothing much halophiles), from a still different extreme had been made of it: these strange niche, that also had similar strange lipids seemed to be just one more lipids. Brock's conventional mind set unexplainable biological idiosyncrasy. here is a wonderful example of what Microbiologists and biochemists didn't comes of unquestioned acceptance of view things evolutionarily. From a the assumption that all bacteria are genuinely biological perspective, "procaryotes" ─ all idiosyncratic however, these lipids were significant ─ characteristics then become adaptive evolutionarily significant. changes.

9 Carl R. Woese

We didn't know what kind of lipids the Tornabene (a colleague and oft-time methanogens had, and that was critical, collaborator of Langworthy's). And in for the lipids were a good candidate for short order there the answer was: a property shared by all of the methanogens have ether-linked lipids organisms in the new urkingdom. (Tornabene & Langworthy, 1979)! The Determining the lipid type of the circle had been closed. The first methanogens was essential. I archaebacterial-universal phenotypic frequently discussed with Wolfe whom property had been found. we could enlist to find the answer. Although Brock wasn't the one to approach, one of his colleagues, Tom Recently Tom L. recalled to me in Langworthy at the University of South touching detail our first contact (he has Dakota (an expert in lipid analysis), a photographic kind of memory). It was seemed to me a good bet; and it was warm that day in mid-November 1977. decided (I thought) to send cells to He had been eating lunch and reading Langworthy. an article in the latest issue of Time magazine about a "third form of life". Since there had been no mention of our Ralph then threw me a curve ball. He unpublished halophile work in the Time had come up with a different candidate, article, Tom was unaware that we knew a young Professor at Yale who was about any lipid connection. So, Tom about to join our Microbiology faculty, had his own "eureka moment", for some who was also an expert lipid chemist, of the bacteria he was working with, name of John Cronan. Ralph felt Thermoplasma and Sulfolobus, were (rightly, I had to admit) that it would be unusual enough in their properties that more collegial for us to work with they might even represent a fourth Cronan. So Ralph ordered a pellet of urkingdom; c.f. Brock quote above. He methanogen cells sent off to John for was thinking of contacting Time lipid analysis. Days went by; weeks magazine about the possibility, when went by; it seemed like more; and no the phone rang. It was Woese calling to word from Yale. Ralph finally agreed to ask him for help working with just these call Cronan up and find out what had organisms. We had decided to grow happened. It turns out that John's lab them ourselves and were seeking had done a quick, but definitive, initial cultures from Tom, which he provided screen of the methanogen for lipid type on the spot. I was not willing to wait for upon receiving the prep and then Thermoplasma rRNA to come in under dropped the project as uninteresting: the mycoplasma collaboration; it was at there was nothing new there; the the bottom of Maniloff's list, methanogen lipids were just like the halophile lipids! John had perceived the whole thing from a strictly biochemical The work on Thermoplasma went perspective. Hadn't Ralph made clear smoothly, and by the beginning of 1978 to him how critical methanogen lipids there existed a catalog defining the 2nd were to our case? major non-methanogenic archaeal phenotype. I wanted to publish this one in Nature, to give wide scientific It was back to plan A. Bill Balch was coverage to the fact that archaebacteria asked to prepare methanogens again, were now a real group (comprising at and these were sent to Tom Langworthy least two diverse organismal and another lipid biochemist, Thomas phenotypes). A manuscript had been

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The Birth of the Archaea: a Personal Retrospective

prepared accordingly and submitted. In encountered), the 16S rRNA from early June of that year a letter from Sulfolobus, the first crenarchaeon, had Nature's editor arrived, which I opened near an order of magnitude more of expectantly. Rejection! "Dear Professor them. The high levels of modified Woese ... I realize that there is nucleotides had proven true of their considerable interest in your tRNAs as well (Gupta & Woese, Archaebacterial group; nevertheless the unpublished). [A high degree of basic idea has been so well exposed modification in rRNA and tRNA, of that I am not convinced that the course, was reminiscent of eukaryotes. assignation of T. acidophilum to the Strange coincidence! It was tucked group really demands a place in away for future consideration]. Nature". Perhaps I should have expected it. Nature was a mouth-piece for molecular biology, a biology in which It was clear from the start that the organism's evolutionary history and Sulfolobus was indeed one of the the organism in its own right don't really archaebacteria: it had many of the by- count. An evolutionary finding rates now familiar archaeabacterial signature only a "so what!" with these people ─ be oligonucleotides. Yet, its catalog did not it world shaking or not. Fortunately, our fall within the grouping defined by the work on the halophiles, moving toward archaebacteria we'd already publication on a separate track was characterized. Our new urkingdom not accepted (quite rapidly, I might add) ─ only contained several disparate the only drawback being that it had been phenotypes, but was deeply divided into submitted to a journal having much less two major subgroups within itself. [This coverage than Nature had (Magrum et latter fact would become more apparent al., 1978). So at least some of the when the less informative biology community would be aware that oligonucleotide cataloging method was the archaebacteria comprised more than replaced by direct sequencing of whole one organismal phenotype. The rRNA molecules ─ and we started to Thermoplasma rRNA catalog was never present the data primarily in the form of published in its own right. phylogenetic trees rather than oligonucleotide signatures (Woese & Olsen, 1986)]. The other organism Langworthy had sent us, Sulfolobus acidocaldarius, was not being so cooperative. It would turn The Archaeal family grows. There out to be the first one of what we now began to grow ─ in good measure call the Crenarchaeota, the second of thanks to the prosylatizing and other the two archaeal kingdoms (the first now efforts of Otto Kandler in Germany ─ an goes under the name ) increasingly large coterie of "archaeo- (Woese et al, 1990). We had actually philes", each of whom approached the begun the Sulfolobus catalog a month archaebacteria from their own before starting in on Thermoplasma, but perspective. Thus by 1980 a fair it took seven months in all to bring it to amount was known about the specific fruition. The primary obstacle here was and general characteristics of the the hard-to-characterize modified archaebacteria. Notable among the oligonucleotides. Instead of having half new faces in the movement were a dozen or so modified oligonucleotides Wolfram Zillig and his associate Karl (as had the eubacteria and all Stetter, then a sort-of post-doc. archaebacteria we'd so far Wolfram, one of the Abteilung Leiters at

11 Carl R. Woese

the Martinsried Max Planck Institute, the vicinity of boiling sulfurous hot had built his career around molecular springs so often, Karl came to refer to characterizations of the DNA-dependent crenarchaeal hyperthermophiles as "the RNA polymerases. By the late '70s he organisms from hell", even naming one (by his own admission) had settled into genus Stygioglobus and at least one "the rut of refinement" with bacterial species infernus accordingly]. RNA polymerases. Somehow the word had filtered down to him about the "third form"; likely via Kandler. Immediately, It was only a matter of time before there Wolfram and Karl turned their attentions would be a formal scientific conference to the RNA polymerases of the ─ the field's initiation rite. Thanks to archaebacteria, publishing first on the strenuous efforts on the parts of novel RNA polymerase of the Wolfram and Otto, it happened sooner halobacteria ─ in the same year we rather than later. Planning began in publicly announced our own findings on 1980, with furious exchanges of letters their rRNAs (Zillig et al., 1978). This and phone calls; they also had to obtain was followed by a mid-1979 description financial support (not an easy matter). of a similar atypical RNA polymerase The meeting got scheduled for 1981 at from Sulfolobus acidocaldarius ─ on the Max Planck Institute at Martinsried- gross inspection whose subunit bei-München. The Martinsried meeting composition appeared rather eukaryote- fulfilled everyone's hopes; it covered the like (Zillig et al, 1979). We were still full spectrum of workers and work on the finishing up the 16S rRNA catalog of archaebacteria. Don't think this means Sulfolobus acidocaldarius at the time, that the number of participants was and hadn't begun to think about large; there were relatively few of us in publication, which actually occurred those days. A wonderful sharing of several years later in collaboration with knowledge and developing or expanding Wolfram, a publication now based upon of scientific relationships occurred at the a total of three different [crenarchaeal] meeting. Best of all, it gave a feeling of extreme thermophiles (Woese et al., group identity, a camaraderie, to many 1984). who attended. The archaebacteria had arrived!

Wolfram and Karl had figured out the ether-linked lipid connection for Starting in 1977 (if I'm correct) George themselves (if I'm not mistaken). Indeed and I had begun planning to write a it is to these two that we owe any strong comprehensive publication about all the emphasis that there was on the phylogeny work that had gone on in the crenarchaeal branch of the archaeal phylogeny project ─ one that would give tree in the beginning. Wolfram had also biology a little surprise! I nicknamed the deduced that when Tom Brock isolated project "Big Tree". There would be and characterized his many authors on Big Tree, reflecting the thermoacidophiles, he had probably many people who had worked on the missed a whole world of anaerobic project in my lab and all the thermoacidophiles. And here would be collaborators who had contributed the the start of his and Karl's colorful (and radio-labeled rRNA starting materials. sometimes dangerous) adventures The actual writing, however, involved hunting for hyperthermophilic archaea mainly George and myself. That proved around the globe (later carried on by difficult enough! Karl alone). [Given that he frequented

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The Birth of the Archaea: a Personal Retrospective

When dedicating our paper to him I had With the hard part over, I submitted Big read only van Niel's early work on Tree to Science on January 31, 1980 natural classification of bacteria, (eschewing Nature this time around). collaborations, first with Kluyver and With Science things went smoothly, and then with his student Stanier. Little did I the paper appeared in July of that year: know at the time what van Niel's final "The phylogeny of procaryotes", by Fox judgment on bacterial phylogenetics had et al, (1980). It was a heady been: it was "a waste of time to attempt experience, publishing a phylogenetic a natural system of classification for tree that (in outline) covered all of life, bacteria" (see Stanier et al., 1957). and said to boot that there were three, Moreover, in 1962 he and Stanier had not two, primary lineages of organisms even renounced their earlier efforts in on this planet. Before genealogical bacterial classification as something analysis had been transposed to the "neither of us cares any longer to molecular level, the best that biologists defend". Our paper apparently didn't had been able to do was make trees for change van Niel's mind, for I never animals and/or plants. Here, for the first heard from him. But what I've just said is time, was the skeleton of the full Tree of based upon what I discovered later, Life. Monumental! Reviewers' reactions from a fairly comprehensive study of van to the paper had been good. The Niel and his cohort's writings on reaction of the scientific public this time bacterial phylogeny. was good as well.

The dedication unwanted and Given the nature of our Science paper recognition ungiven. I had dedicated and the reception it received, it should "Big Tree" to C. B. van Niel (long have been nominated for "Paper of the retired), who was one of the great Year" in Science, which, indeed, it was. microbiologists of his era. He had won But the "Tree of Life" came in 2nd (as I microbiology's highest honor, the was told by "sources"). I also found out 1970 ─ an award what may have been the reason: one of given once a decade by the the judges had, apparently innocently, Royal Academy of Sciences to "the praised the work as a contribution scientist who has made outstanding "almost as important as the eucaryote- contributions to the advancement of procaryote dichotomy". "Hmm", I microbiology during the preceding ten fumed; "how can our work be almost as years". I had thought that van Niel important as something that is totally would be pleased and honored to see wrong-headed, something that has the final solution to the problem of a influenced the course of microbiology so natural bacterial classification dedicated adversely! Who is this stupid judge?" to him; for it was a problem that he, Kluyver, and Stanier (among others) had struggled with for a very long time Procaryote by Any Other Name ... without having the (molecular) technology to cope with it. [A former The more things progressed, the more student and friend of van Niel's, Robert procaryote loomed large, like a current Hungate, had offered to send him the against which no one could swim. I'd paper personally]. often reflected on why that day in June 1976 it seemed so incredible to discover a procaryote that wasn't a procaryote. The reason was obvious once I thought

13 Carl R. Woese

about it, which I ─ and it turns out every working in the early decades of the 20th other biologist ─ had never felt a need to century infer anything about the do previously. That's why we organization of a bacterial cell, much encountered such difficulty in convincing less what features were common among others of what we'd discovered. That's the organizations of all bacterial cells: why the Nobel Laureate Luria had so bacteria were a morphologically diverse scornfully rejected the three urkingdom group, and all that one had to go on as notion. Ralph Wolfe, who frequented regards their internal organizations was microbiology meetings would tell me at negative evidence: they were not (what the time about the "talk in the corridors" we now call) "eucaryotic"! None of it ─ i.e., the behind-the-scenes, clubby made sense! dismissal of the three urkingdom concept. I was itching for them to come after me in print. But none of them Although we were unaware of it at the would! It was so important to get the time (or for some time thereafter), we "procaryote" matter out in the open. were not faced with an ordinary Something was strange about this scientific situation here; it was no simple "procaryote"! case of a new, more detailed and factually supported hypothesis displacing an entrenched older one. Whatever the reason, "procaryote" had The strength of that older idea, its special significance for microbiologists. dominating, dogmatic hold on Yet, the reason couldn't be historical microbiology, implied rather more than usage of the term. "Monera" was the that. But what? Answering this preferred term for bacteria in the first question has taken me on a somewhat half of the 20th century; Schizomycetes bizarre journey that has lasted over two also being used. And I couldn't find the decades, and only recently shows signs term "procaryote" anywhere in the of coming to its end. My understanding literature before 1962 ─ and neither has had to pass through three distinct (more recently) could the historian Jan stages, each broader in scope than the Sapp (2005). “Procaryote” seemed to previous. appear out of nowhere at that point in time (Stanier & van Niel, 1962). So why were microbiologists so wedded to the First attempt: apply scientific "procaryote" that they rejected any reason. When we initially realized that suggestion of a third urkingdom without the procaryote concept was the even thinking about it? immovable object in the road to microbiology's development, I thought the matter would resolve scientifically: By the 1970s a generation of tell biologists what their "procaryote" microbiologists and biologists in general really is and they will understand. had been raised believing that Accordingly, George and I prepared a "procaryote" (term and concept) had paper entitled "The concept of cellular originally been the brain child of the evolution" (Woese & Fox, 1977a). In it protozoologist Edouard Chatton (1938; we denied the two defining tenets of Stanier & van Niel, 1962; Sapp, 2005). "procaryote", but kept the term itself, And, the recent historical analysis also hoping thereby to ameliorate the rather found no evidence for Chatton's even revolutionary change we were presenting the concept (Sapp, 2005). In proposing. The prefixes "pro-" and "eu-" any case, how could any biologist had a familiar ring to them; the notion

14

The Birth of the Archaea: a Personal Retrospective

that bacteria were separate from and It may have sounded absurd at the time older than ─ some perhaps even that archaea and eubacteria had ancestral to ─ eukaryotes was evolved the same cellular organization traditional. independently. But the absurdity actually lies not in our proposal but in the original assertion that all bacterial Our argument went: "yes", the terms cells were of a kind, had the same "procaryote" and "eukaryote" do (procaryotic) cellular organization ─ from obviously recognize distinctly different which monophyly had to follow (Stanier kinds of cellular organization, but "no", in & van Niel, 1962; Stanier et al., 1963): the case of the prokaryote a common as I’ve said, there was no way anyone in general organization does not the early, middle, or even late decades necessarily denote common ancestry for of the 20th century could have known all! Procaryote should be looked at only anything about the nature of the as a level of organization, a level distinct organization of any but the eucaryotic from that of the (higher, more complex) cell (and that was only a superficial eucaryotic cellular organization. description). Therefore, archaebacteria and In spite of what I thought was sound eubacteria can have the same general pleading, our argument had no takers; I level of organization, but have arrived at don't think that the vast majority of it independently. In other words, the (micro)biologists even bothered to procaryotic level of organization has consider it. We would have to dig evolved at least twice! deeper to get at the root of the problem.

The general principle here is that Second attempt: follow the leader. biology is a study in emergent levels of After this, I essentially went off on my increasingly complex organization. This own to try to solve the problem ─ which idea, of course, was anathema to 20th meant acquiring the perspective needed century reductionist biology; but it had to see it in historical terms. Where had currency in the 18th and 19th centuries "procaryote" come from in the first (Burkhardt, 1977). We were simply place? Microbiologists had traditionally resurrecting the notion and recasting it made a strong distinction between in modern scientific terms. bacteria and the cells of "higher forms" (see above). But none of it was taken as certain or factually supported. It was all In keeping with this general notion we just necessary speculation on the road then postulated a primitive level of to developing an understanding of organization even simpler than the bacteria. All that these early procaryotic and eucaryotic, one that had speculations really accomplished was to preceded the other two. We named it define bacteria negatively: they were not the "progenote" to signify that the as large as eucaryotic cells; and they genotype-phenotypic link at that early lacked this, that, and the other stage had yet to reach the eventual microscopically visible features so perfection, precision, and sophistication characteristic of eucaryotic cells ─ in that characterizes modern cells (Woese addition to their showing no (common) & Fox, 1977a). microscopically discernible intracellular structures of their own.

15 Carl R. Woese

Where, then, did this strongly asserted, more clearly formulating a `concept of a definitive, inflexible "procaryote" come bacterium'." (Stanier & van Niel, 1962), from? Focusing on the "procaryote's" because "... the ultimate scientific goal origin brought me directly to one, and of biological classification [i. e., a apparently only one, source, R. Y. natural, or phylogenetic classification] Stanier and his cohort. As I said above, cannot be achieved in the case of I couldn't find "procaryote" in the bacteria ..." [italics original] (Stanier et literature before 1962, when it appeared al., 1963). Only in 1962-63 does one in the classic paper of Stanier and van begin to see such a definitive, strongly Niel (1962; Sapp, 2005). It was also worded and inflexible position taken on noteworthy that, although the term the nature of bacteria. There was no "procaryote" was featured in the 2nd sound scientific reason for it either, for edition of "The Microbial World" (Stanier the “prokaryote” was founded solely et al., 1963), it was nowhere to be found upon rhetoric, with no intent or attempt in the text's 1st edition (Stanier et al., to give it a firm foundation 1957)! subsequently. The whole thing was only scientific "guesswork" (sensu Schroedinger, 1954). No terminology before 1962! Was it the same for the underlying concept? Yes; 1962 was the first time the commonality What sank matters further into of all bacterial cellular organization was strangeness was the fact that the asserted (rather than just mused microbiology community accepted this about). There had been the older, guesswork (both alien term and out-of- questioning, more speculative attitude the-blue concept) immediately and about the nature of bacteria for some overwhelmingly! No criticism, no time, but nothing like this, the self- serious discussion greeted the assured, dogmatic "procaryote" we had procaryote's debut. encountered in 1977.

[An obvious weakness in the authors' It is particularly important to know how presentation had been the lack of "procaryote" was defined in 1962, for adequate comparative evidence upon there is a tendency today to adjust the which to base the assertion of properties term at will (Judson, 1996), which is common to all bacteria ─ too few counterproductive in that it is properties and too narrow a sampling of tantamount to superficial "surgery" that bacterial taxa (Murray, 1962), which only further conceals a deeper chronic could have been remedied easily by condition. "Procaryote" rests on two doing more work, sampling a wider definitional pillars: 1) the assertion that it range of taxa. Yet no one did this or represents one of "...two different apparently saw the need to! It was as organizational patterns of cells ...", (the though microbiologists simply wanted to other being that of the eucaryotic), from make the issue go away: it was time to which it must follow: 2) that "... we can close the door and move on (Sapp, therefore safely infer a common origin 2005). for [all "procaryotes"] in the remote evolutionary past ..." (Stanier & van Niel, 1962; Stanier et al., 1963) [italics It is revealing to compare the ready and added]. The procaryote, moreover, was enthusiastic reception of the procaryote seen to provide "... our only hope of with the irate reaction that the three-

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The Birth of the Archaea: a Personal Retrospective

urkingdom archaebacterial concept microbial variety and long- and short- engendered a decade and a half later ─ term evolutionary dynamics, make for a even though the three urkingdom "tetrahedral" synthesis called concept had solid factual support, with "organism", quintessential biological more facts obviously to come. I clearly organization. needed to get to the bottom of this, to understand the diametrically opposed responses the microbiology community Within the context of his time the great had given to the two points of view. microbiologist Martinus Beijerinck appreciated bacteria in just this full sense. When in 1905 he was asked (on What I had now learned was that the occasion of being awarded the individuals could not be held responsible Leeuwenhoek Medal) to articulate his for what had happened to microbiology view of the microbial world and its study, in the middle decades of the 20th he had replied that the most effective century. They were among the few who approach to understanding had seen the problem, and they had was "... the study of tried to resolve it ─ unfortunately in the ..."; adding that wrong way! Those "responsible" were microbes represent the "... lowest limits just the lead birds in a migrating flock: of the organic world, and ... constantly shooting them down does not effect the keep before our minds the profound flock's course. There was a deeper problem of the origin of life itself." (van dynamic at work here, one that would be Iterson Jr. et al., 1946; van Niel, 1949). far more difficult to change. Here in the making was a rich, genuinely organismal picture of the microbial world. Third attempt: understand the mythology. This last insight proved critical. An intellectual tide was the key Unfortunately, Beijerinck's successors to the problem. Molecular biology, in its did not, nor did they care to, realize his insistent reductionism, lay at the heart of vision. Initially it was not technologically the issue (Woese, 2004). The feasible to do so, but doing so in any intellectual landscape was indeed being case would have meant going against restructured! Two factors were going to the new reductionist tide, which shape 20th century microbiology, the microbiology was conceptually power of molecular biology's vision and unequipped to do. Therefore, outside the weakness of microbiology's. influences, not innate tendencies, would shape the discipline.

Bacteria are organisms, not simply bags of biochemistry. Microbiology is a fortiori To Beijerinck's successor A.J. Kluyver an organismal discipline. Organisms in (and his " School") the organism in their fullness must be its study. The its own right (i.e., as a biological organism's parts are surely important, organization) meant nothing: but important in what they contribute to biochemistry was the essence (Kamp et an overall understanding; the same al., 1959). The emphasis would be on being true of the higher level uncovering the main biochemical interactions that structure microbial themes among the bacteria (Kluyver & communities, their ecologies. These, Donker, 1926) ─ and all of the nuanced together with an appreciation of variations thereupon (Kluyver, 1931)!

17 Carl R. Woese

Yet, how many of the organic had no real conceptual base compounds we know do you think would (mythology) from which to draw exist on this planet if some kind of support. And this is why the procaryote biological organization weren't around to concept (or something equivalent) was produce them (Kaufmann, 1995). [Most needed in order for the discipline to organic compounds we see in nature have an "organismal" sense of itself. are like the new elements at the high end of the periodic table in that they require "organismal intervention" to exist The "procaryote" was only scientific at appreciable levels]. After all, bacterial guesswork (as said above). But it did metabolic diversity in the last analysis is seem to give microbiology the badly not a biochemical problem; it is an needed keystone in its conceptual evolutionary one ─ a question of why foundation (its mythology). Procaryote and how such great biochemical provided an overarching, authoritative. (metabolic) diversity arose in the first and authenticating framework within place, and why certain biochemical which now to work. Yet, note that the pathways were evolutionarily singled out concept had precluded an evolutionary for (biological) amplification. By the (phylogenetic) definition of bacteria ─ in middle of the 20th century our my opinion, the only concept possible. conception of bacteria had moved from Beijerinck's multifaceted organismal one to the Delft School's disassembled one Missing the train. One needs to recall (see van Niel, 1949). here that the "procaryote" concept developed while molecular biology was providing the scientific world its first The Reason for Roots glimpse of the power that lay in molecular sequencing (Sanger & Tuppy; Every scientific discipline rests upon an 1951; Sanger & Thompson; 1953). axiomatic foundation, a scientific Zuckerkandl and Pauling (1965) were mythology, which informs it and the trumpeting the molecular approach to world as to what it is and in the process evolution; and F. H. C. Crick (1958) had charts its course. Microbiology's said: "Biologists should realize that mythology, non-organismal and almost before long we shall have a subject non-existent, reflected the Delft School which might be called `protein perspective. And that is why in 1962, in ´ ─ the study of amino acid the heyday of microbial biochemistry, sequences of proteins of an organism when all manner of new biochemicals and the comparison of them between and metabolic pathways were being species." Adding that "... these uncovered, R. Y. Stanier had said (in sequences are the most delicate introducing the "procaryote" concept): expression possible of the phenotype of "... the abiding intellectual scandal of an organism and that vast amounts of bacteriology has been the absence of a evolutionary information may be hidden clear concept of a bacterium ... the away within them." problem of defining these organisms as a group in terms of their biological organization is clearly still of great It seems highly unlikely that the vast importance, and remains unsolved" majority of microbiologists were totally (Stanier & van Niel, 1962). It was ignorant of the new molecular approach obvious that microbiology was in a state to organismal relationships, especially of disarray; it did not understand itself; it given the exquisite need the discipline

18

The Birth of the Archaea: a Personal Retrospective

had for evolutionary underpinnings. were a resonating thunderous clap that What is more likely (as discussed) is would awaken the Sleeping Giant of that a conceptually unsettled evolution! As I saw it, the discovery of microbiology wanted to rid itself of a the archaea had turned over the perspective that was not in keeping with reductionist rock, and the weakness in the reductionist tenor of the times that paradigm now lay there for all to (Woese, 2004). The procaryote see! But things didn't turn out that way. accomplished that: it papered over "... the problem of defining [bacteria] as a group in terms of their biological The evolutionary message inherent in organization ..." (Stanier & van Niel, the discovery of the archaea faded! 1962). But it had cut microbiology away Consequently, microbiology has yet to from its organismal, evolutionary roots in resolve its foundational issues. The the process. [While a considerable discipline goes on today rootless as amount of nucleic acid hybridization ever, unconcerned with microbial work was subsequently done in evolution, living in the scientific dream microbial taxonomic structure, the world of the procaryote. The evidence is work's intent was simply to improve everywhere: "procaryote" remains existing bacterial taxonomy. The grand imprinted across the discipline; challenge of a natural classification, a structuring its modes of thought; universal phylogeny for bacteria (Stanier defining its curriculum, its scope; & van Niel, 1941) had disappeared from shaping its future. One glance at how the scene!] the discipline of microbiology responded to the challenge of the archaebacteria and later to the advent of genomics will There is actually nothing surprising show you a discipline lost in its past, about this strange "procaryote period" in blown about by the capricious winds of a microbiology's history. The dynamic at society. Microbiology did not meet the work here is encountered in many challenge of the archaebacteria, nor has different fields: "the past needs to be it yet met that of genomics. forgotten because it reveals the confusion and lack of cohesion of the present!" It's just that in this case the Microbial genome sequencing began whole thing was so patently unscientific. only in 1995 (Fleischmann et al., 1995). I know from personal experience that had microbiologists (and biologists in Where Are We Going? general) perceived its significance, microbial genomics could have begun A biology that does not concern itself by the mid 1980s (Woese, 1993). with evolution is not biology! Archaea are so unlike eubacteria, and Contradicting the ill-framed reductionist we didn't (and still don't) know enough view of biology is precisely why I had about them. Genome sequencing was established the program of (molecular) the only way to bring the "third phylogenetic reconstruction in the first urkingdom" up to scientific speed place. The program's raison d'etre was (Woese, 1993). to revive the evolutionary spirit that underlies biology and had been nearly squeezed out of existence by Sadly, when microbiologists finally took reductionism. Thus, the archaea were a genomic approach, it was only indeed a splendid surprise to me: they because genomics could be used (and

19 Carl R. Woese

funds obtained for that) to attack a host become far more of a basic biological of practical problems (medical, discipline than it has ever been ─ some agricultural, environmental), problems sort of modern realization of Beijerinck's that they had been dealing with for holistic vision. Throughout the 20th decades. To the extent that microbial century, microbiology's course was genomics affected the intellectual charted by the dictates of molecular climate in microbiology at all, it did so reductionism and the practical concerns adversely; each microbial genome of a biomedically oriented society. rationalized and sequenced for a Biology itself was the low man on the different reason. No concerted program scientific totem pole; and microbiology in, no organismal rationale for, microbial the low man on its. genome sequencing even existed until quite recently. Now things must reverse. Not only must microbiology become the leading Moving horizontally. discipline, the guide, in biology; but biology itself should become the basal Many microbiologists have developed discipline of the sciences. Microbiology's interests in horizontal gene transfer lack of concern with evolution has been (HGT) over the past decade. In that the discipline's downfall in the past and HGT provides an important, if not the could remain its (and Biology’s) nemesis most important clue to the dynamic of in the future. Microbiology departments cellular evolution there would seem to today are products of historical accident, be hope in this. With a few important held together in essence by institutional exceptions, however, the microbiologist inertia. It is not a good sign that the has not seen the fundamental basic research at microbiology's evolutionary significance of HGT: most forefront is increasingly being done of the concern centers about health outside of the context of formal related matters, and a little also with the microbiology departments. particulars, cellular mechanisms involved in HGT. Nevertheless, there are very promising studies involving The future of biology lies in metagenomic approaches to microbial understanding the nature of biological community structure and dynamics organization. Microorganisms are a beginning, in which the role of HGT (and central concern here, for they are ) is absolutely central (Rachel et biology's primary window on the al., 2002; DeLong, 2005; DeLong & problem. Twentieth century biology Karl, 2005). (especially microbiology) was structure oriented, reductionist, and temporal in its view of life. The biology of today The Defining Problems of 21st must be evolutionary, holistic, and Century Microbiology (and Biology). process oriented.

The future of microbiology does not lie on the field's current path. If the status We meet 21st century biology right now quo in microbiology persists, the in terms of two grand problems: 1) the discipline is on course to become a evolution of the cell; and 2) an complete and total service discipline, understanding of the global simply bioengineering! What is needed, environment. While these two may what is essential, is that microbiology seem quite unrelated, the one as

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The Birth of the Archaea: a Personal Retrospective

fundamental as biology now gets, the other essentially applied (and of pressing concern), this is not so. At base both represent problems in biological organization. And the two will become closely joined when biology comes to study the early stages in the evolution of the cell, when horizontal gene transfer dominated the evolutionary dynamic, leading to an evolution that was essentially communal, not individual (involving distinct lineages) (Woese, 1982; 2002). Only a microbiology that embodies the spirit of biological organization, organism and evolution, will be fit to lead biology in the 21st century.

Acknowledgements My work is supported by grants from the Department of Energy, and the National Aeronautics and Space Administration.

21 Carl R. Woese

References DeLong, E. F. (2005) Microbial community Balch, W. E. & Wolfe, R. S. (1976) New genomics in the ocean. Nat Rev Microbiol. approach to the cultivation of methanogenic 3, 459-69. bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of DeLong, E.F. & Karl, D. M. (2005) Genomic Methanobacterium ruminantium in a perspectives in microbial oceanography. pressureized atmosphere. Appl Environ Nature. 2005 Sep 15;437(7057):336-42. Microbiol. 32, 781-91. Fleischmann, R. D., Adams, M. D,. White, Balch, W. E & Wolfe, R. S. (1979) Specificity O., Clayton, R. A., Kirkness, E. F., and biological distribution of coenzyme M (2- Kerlavage, A. R., Bult, C. J., Tomb, J. F., mercaptoethanesulfonic acid). J Bacteriol. Dougherty, B. A., Merrick, J..M et al. (1995) 137, 256-63. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. R. S. Breed, E. G. D. Murray & N. R Smith Science. 269, 496-512. (ed.) Bergey's manual of determinative bacteriology, 7th edition. Baltimore: Williams Fox, G. E., Pechman, K. R. & Woese, C. R. & Wilkins. 1957. (1977a) Comparative cataloging of 16S OR ribosomal RNA: molecular approach to Robert S. Breed, E.G.D. Murray, Nathan R. procaryotic systematics. Int J Syst Bacteriol Smith, and Ninety-four Contributors, 27, 44-57. Bergey's Manual of Determinative Bacteriology. Seventh Edition Baltimore: Fox, G. E., Magrum, L.J., Balch, W.E., The Williams and Wilkins Company, 1957. Wolfe, R.S. and Woese. (1977b). Classification of methanogenic bacteria by Brock, T. D., Brock, KM, Belly, RT, Weiss, 16S ribosomal RNA characterization. Proc. R. L. (1972) Sulfolobus: a new genus of Natl. Acad. Sci. USA 74, 4537-4541. sulfur-oxidizing bacteria living at low pH and high temperature. Arch Mikrobiol 84, 54-68. Fox, G. E., Stackebrandt, E., Hespell, R.B., J. Gibson, J., Maniloff, J., Dyer, T.A., Wolfe, Thomas D. Brock (1978) Thermophilic R.S., Balch, W.E., Tanner, R., Magrum, L.J., Microorganisms and Life at High Zablen, L.B., Blakemore, R., Gupta, R., Temperatures Springer-Verlag Bonen, L., Lewis, B.J., Stahl, D.A., Luehrsen, K.R., Chen, K.N., and Woese, C. Burkhardt Jr., R. W. "The `Spirit of System: R.. 1980. The phylogeny of . Lamarck and Evolutionary Biology" Harvard Science 209, 457-463. University Press, Cambridge MA 1977. Gamow, G. (1954). Possible relations Chatton, E. Titres et travaux scientifiques between deoxyribonucleic acid and protein (1906 - 1937) de Edouard Chatton (Sottano, structures. Nature 173, 318. Se\h`-0.3'\(gate, 1938). Judson, H. F. (1996) "The Eighth Day of Crick, F. H. C. 1958. The biological Creation: makers of the revolution in replication of macromolecules. In Symp. biology" Plainview, NY: Cold Spring Harbor Soc. Exptl. Biol. 12, 138-163. Laboratory Press.

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