Editing Carl Woese (section)

==Work and discoveries==
=== Early work on the genetic code ===
Woese turned his attention to the [[genetic code]] while setting up his lab at [[General Electric]]'s [[GE Global Research|Knolls Laboratory]] in the fall of 1960.<ref name="sapp2009"/> Interest among physicists and molecular biologists had begun to coalesce around deciphering the correspondence between the twenty [[amino acids]] and the four letter alphabet of [[Nucleobase|nucleic acid bases]] in the decade following [[James D. Watson]], [[Francis Crick]], and [[Rosalind Franklin]]'s discovery of the structure of DNA in 1953.<ref name="pnas2012"/> Woese published a series of papers on the topic. In one, he deduced a correspondence table between what was then known as "soluble RNA" and DNA based upon their respective [[base pair]] ratios.<ref name="woese1961ratio">{{Cite journal 
| doi = 10.1038/189920a0 
| last1 = Woese | first1 = C. R. 
| author-link1 = Carl Woese
| title = Composition of various ribonucleic acid fractions from micro-organisms of different deoxyribonucleic acid composition 
| journal = Nature 
| volume = 189 
| issue = 4768 
| pages = 920–921 
| year = 1961 
| pmid = 13786175
|bibcode = 1961Natur.189..920W | s2cid = 4201322 }}</ref> He then re-evaluated experimental data associated with the hypothesis that viruses used one base, rather than a triplet, to encode each amino acid, and suggested 18 codons, correctly predicting one for [[proline]].<ref name="sapp2009"/><ref name="woese1961viruses">{{Cite journal 
| doi = 10.1038/190697a0 
| last1 = Woese | first1 = C. R. 
| author-link1 = Carl Woese
| title = Coding ratio for the ribonucleic acid viruses 
| journal = Nature 
| volume = 190 
| issue = 4777 
| pages = 697–698 
| year = 1961 
| pmid = 13786174
|bibcode = 1961Natur.190..697W | s2cid = 4221490 }}</ref> Other work established the mechanistic basis of protein translation, but in Woese's view, largely overlooked the genetic code's evolutionary origins as an afterthought.<ref name="pnas2012"/>

In 1962, Woese spent several months as a visiting researcher at the [[Pasteur Institute]] in [[Paris]], a locus of intense activity on the molecular biology of gene expression and gene regulation.<ref name="sapp2009"/> While in Paris, he met [[Sol Spiegelman]], who invited Woese to visit the [[University of Illinois]] after hearing his research goals; at this visit Spiegelman offered Woese a position with immediate [[tenure]] beginning in the fall of 1964.<ref name="sapp2009"/> With the freedom to patiently pursue more speculative threads of inquiry outside the mainstream of biological research, Woese began to consider the genetic code in evolutionary terms, asking how the codon assignments and their translation into an amino acid sequence might have evolved.<ref name="sapp2009"/><ref name="woese1964">{{Cite journal | last1 = Woese | first1 = C. R. | author-link1 = Carl Woese| last2 = Hinegardner | first2 = R. T. | last3 = Engelberg | first3 = J. | doi = 10.1126/science.144.3621.1030 | title = Universality in the Genetic Code | journal = Science | volume = 144 | issue = 3621 | pages = 1030–1031 | year = 1964 | pmid =  14137944|bibcode = 1964Sci...144.1030W | doi-access =  }}</ref>

=== Discovery of the third domain ===
For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their [[biochemistry]], [[morphology (biology)|morphology]] and [[metabolism]]. In a highly influential 1962 paper, [[Roger Stanier]] and [[C. B. van Niel]] first established the division of cellular organization into [[prokaryote]]s and [[eukaryote]]s, defining prokaryotes as those organisms lacking a [[cell nucleus]].<ref name=stanier1962>{{Cite journal | doi = 10.1007/BF00425185 | last1 = Stanier | first1 = R. Y. | author-link1 = Roger Stanier| last2 = Van Niel | first2 = C. B. | author-link2 = C. B. van Niel| title = The concept of a bacterium | journal = Archiv für Mikrobiologie | volume = 42 | pages = 17–35 | year = 1962 | issue = 1 | pmid = 13916221| bibcode = 1962ArMic..42...17S | s2cid = 29859498 }}</ref><ref name=pace2009>{{Cite journal | last1 = Pace | first1 = N. R. | author-link1 = Norman R. Pace| title = Problems with "Procaryote" | doi = 10.1128/JB.01224-08 | journal = Journal of Bacteriology | volume = 191 | issue = 7 | pages = 2008–2010; discussion 2010 | year = 2009 | pmid =  19168605| pmc =2655486 }}</ref> Adapted from [[Édouard Chatton]]'s generalization, Stanier and Van Niel's concept was quickly accepted as the most important distinction among organisms; yet they were nevertheless skeptical of microbiologists' attempts to construct a natural [[phylogenetic]] classification of bacteria.<ref name=sapp2005>{{Cite journal | last1 = Sapp | first1 = J. | author-link1 = Jan Sapp| title = The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology | doi = 10.1128/MMBR.69.2.292-305.2005 | journal = Microbiology and Molecular Biology Reviews | volume = 69 | issue = 2 | pages = 292–305 | year = 2005 | pmid =  15944457| pmc =1197417 }}</ref> However, it became generally assumed that all life shared a common prokaryotic (implied by the [[Greek language|Greek]] root πρό (pro-), before, in front of) ancestor.<ref name="pace2009" /><ref name=oren2010>{{Cite book| chapter = Concepts About Phylogeny of Microorganisms–an Historical Perspective| publisher = Caister Academic Press| isbn = 9781904455677| pages = 1–22|editor1=Aharon Oren |editor2=R. Thane Papke 
| last = Oren| first = Aharon| title = Molecular Phylogeny of Microorganisms| location = Norfolk, UK| date = 2010-07-01| chapter-url = https://books.google.com/books?id=a5t9DYZ-wccC&q=concepts+Aharon+Oren+phylogeny&pg=PR7}}</ref>

In 1977, Woese and [[George E. Fox]] experimentally disproved this universally held hypothesis about the basic structure of the [[tree of life (biology)|tree of life]].<ref name="pace2011pnas" /> Woese and Fox discovered a kind of microbial life which they called the “archaebacteria” ([[Archaea]]).<ref name="woese1977" /> They reported that the archaebacteria comprised "a third kingdom" of life as distinct from bacteria as plants and animals.<ref name="woese1977" /> Having defined Archaea as a new "urkingdom" (later [[domain (biology)|domain]]) which were neither bacteria nor eukaryotes, Woese redrew the [[Taxonomy (biology)|taxonomic]] tree. His [[three-domain system]], based on phylogenetic relationships rather than obvious morphological similarities, divided life into 23 main divisions, incorporated within three domains: [[Bacteria]], [[Archaea]], and [[Eukaryote|Eucarya]].<ref name="Woese_1990" />

[[File:PhylogeneticTree, Woese 1990.PNG|thumb|left|450px|Phylogenetic tree based on Woese et al. rRNA analysis. The vertical line at bottom represents the [[last universal common ancestor]] (LUCA).<ref name="Woese_1990"/>]]

Acceptance of the validity of Woese's phylogenetically valid classification was a slow process. Prominent biologists including [[Salvador Luria]] and [[Ernst Mayr]] objected to his division of the prokaryotes.<ref>{{Cite journal | title = Two empires or three?| doi = 10.1073/pnas.95.17.9720| volume = 95
| issue = 17| pages = 9720–9723| last = Mayr| first = Ernst| author-link = Ernst Mayr| journal = Proceedings of the National Academy of Sciences |year = 1998| bibcode=1998PNAS...95.9720M| pmid=9707542| pmc=33883| doi-access = free}}</ref><ref name="sapp2007">{{Cite journal| title = The structure of microbial evolutionary theory| doi = 10.1016/j.shpsc.2007.09.011| pmid = 18053933|  volume = 38| issue = 4| pages = 780–95 | last = Sapp| first = Jan A.| author-link = Jan Sapp| journal = Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences |date=December 2007}}</ref> Not all criticism of him was restricted to the scientific level. A decade of labor-intensive [[oligonucleotide]] cataloging left him with a reputation as "a crank," and Woese would go on to be dubbed as "Microbiology's Scarred Revolutionary" by a news article printed in the journal ''[[science (journal)|Science]]''.<ref name="morell1997">{{Cite journal| title = Microbiology's scarred revolutionary| doi = 10.1126/science.276.5313.699| issn = 0036-8075| volume = 276| issue = 5313| pages = 699–702| last = Morell| first = V.| journal = Science| date = 1997-05-02| pmid = 9157549| s2cid = 84866217}}</ref> The growing body of supporting data led the [[scientific community]] to accept the Archaea by the mid-1980s.<ref name="sapp2009"/> Today, few scientists cling to the idea of a unified Prokarya.

Woese's work on Archaea is also significant in its implications for the search for life on other planets. Before the discovery by Woese and Fox, scientists thought that Archaea were extreme organisms that evolved from the microorganisms more familiar to us. Now, most believe they are ancient, and may have robust evolutionary connections to the first organisms on Earth.<ref>{{Cite journal| title = Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes| doi = 10.1098/rspb.2010.1427| volume = 278| issue = 1708| pages = 1009–1018| last = Kelly| first = S.|author2=B. Wickstead |author3=K. Gull | journal = Proceedings of the Royal Society B: Biological Sciences| date = 2010-09-29 | pmid=20880885 | pmc=3049024}}</ref> Organisms similar to those archaea that exist in extreme environments may have developed on other planets, some of which harbor conditions conducive to [[extremophile]] life.<ref name="stetter2006">{{Cite journal| title = Hyperthermophiles in the history of life| doi = 10.1098/rstb.2006.1907| volume = 361| issue = 1474| pages = 1837–1843| last = Stetter| first = Karl O. | journal = Philosophical Transactions of the Royal Society B: Biological Sciences| date = 2006-10-29| pmc = 1664684| pmid=17008222}}</ref>

Notably, Woese's elucidation of the [[Tree of life (biology)|tree of life]] shows the overwhelming diversity of microbial lineages: single-celled organisms represent the vast majority of the biosphere's genetic, metabolic, and ecologic niche diversity.<ref name=woese2006prok>{{Cite book | last1 = Woese | first1 = C. R. | chapter = How We Do, Don’t and Should Look at Bacteria and Bacteriology | title = The Prokaryotes | pages = 3–4 | year = 2006 | isbn = 978-0-387-25476-0 | doi = 10.1007/0-387-30741-9_1}}</ref> As microbes are crucial for many [[biogeochemical cycle]]s and to the continued function of the biosphere, Woese's efforts to clarify the evolution and diversity of microbes provided an invaluable service to [[ecologists]] and [[conservationists]]. It was a major contribution to the theory of [[evolution]] and to our knowledge of the history of life.<ref name=pnas2012>{{cite journal | doi = 10.1073/pnas.1120749109 | issn = 1091-6490 | volume = 109 | issue = 4 | pages = 1019–1021 | last = Nair | first = Prashant | title = Woese and Fox: Life, rearranged | journal = Proceedings of the National Academy of Sciences | date = 2012-01-17 | bibcode=  2012PNAS..109.1019N | pmid=22308527 | pmc=3268309| doi-access = free }}</ref>

Woese wrote, "My evolutionary concerns center on the bacteria and the archaea, whose evolutions cover most of the planet's 4.5-billion-year history. Using ribosomal RNA sequence as an evolutionary measure, my laboratory has reconstructed the phylogeny of both groups, and thereby provided a phylogenetically valid system of classification for prokaryotes. The discovery of the archaea was in fact a product of these studies".<ref name=mcb />

=== Evolution of primary cell types ===
Woese also speculated about an era of rapid evolution in which considerable [[horizontal gene transfer]] occurred between organisms.<ref name="pace2011pnas">{{Cite journal
| title = Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life
| doi = 10.1073/pnas.1109716109
| issn = 1091-6490 
| volume = 109
| issue = 4
| pages = 1011–1018
| last1 = Pace
| first1 = Norman R.
| author-link1 = Norman R. Pace
| first2 = Jan 
| last2 = Sapp
| author-link2 = Jan Sapp
| first3 = Nigel
| last3 = Goldenfeld
| journal = Proceedings of the National Academy of Sciences
| date = 2012-01-24
|bibcode = 2012PNAS..109.1011P
| pmid=22308526
| pmc=3268332| doi-access = free
}}</ref><ref name="woese2002cells">{{Cite journal
| title = On the evolution of cells
| doi = 10.1073/pnas.132266999
| volume = 99
| issue = 13
| pages = 8742–8747
| last = Woese
| first = Carl R.
| journal = Proceedings of the National Academy of Sciences of the United States of America
| date = 2002-06-25
| pmid = 12077305
| pmc = 124369
| bibcode = 2002PNAS...99.8742W
| doi-access = free
}}</ref> First described by Woese and Fox in a 1977 paper and explored further with microbiologist [[Jane Gibson]] in a 1980 paper, these organisms, or ''[[Progenote|progenotes]]'', were imagined as protocells with very low complexity due to their error-prone translation apparatus ("noisy genetic transmission channel"), which produced high mutation rates that limited the specificity of cellular interaction and the size of the genome.<ref>{{Cite journal 
| last1 = Woese | first1 = C. R. 
| last2 = Fox | first2 = G. E. 
| title = The concept of cellular evolution 
| journal = Journal of Molecular Evolution 
| volume = 10 
| issue = 1 
| pages = 1–6 
| year = 1977 
| pmid = 903983
 | doi=10.1007/bf01796132
| bibcode = 1977JMolE..10....1W| s2cid = 24613906 
}}</ref><ref>{{Cite journal|last1=Woese|first1=Carl R.|last2=Gibson|first2=Jane|last3=Fox|first3=George E.|date=January 1980|title=Do genealogical patterns in purple photosynthetic bacteria reflect interspecific gene transfer?|url=https://www.nature.com/articles/283212a0|journal=Nature|language=en|volume=283|issue=5743|pages=212–214|doi=10.1038/283212a0|pmid=6243180|bibcode=1980Natur.283..212W|s2cid=4243875|issn=1476-4687}}</ref> This early translation apparatus would have produced a group of structurally similar, functionally equivalent proteins, rather than a single protein.<ref name="pace2011pnas"/> Furthermore, because of this reduced specificity, all cellular components were susceptible to horizontal gene transfer, and rapid evolution occurred at the level of the ecosystem.<ref name="woese2002cells"/><ref name="buchanan2010">{{Cite news|title=Evolution, but not as we know it|last=Buchanan|first=Mark|date=2010-01-23|work=New Scientist|issue=2744|volume=205|pages=34–37|issn=0262-4079}}</ref>

The transition to modern cells (the "[[Darwinian threshold|Darwinian Threshold]]") occurred when organisms evolved translation mechanisms with modern levels of fidelity: improved performance allowed cellular organization to reach a level of complexity and connectedness that made genes from other organisms much less able to displace an individual's own genes.<ref name="woese2002cells"/>

In later years, Woese's work concentrated on genomic analysis to elucidate the significance of horizontal gene transfer (HGT) for evolution.<ref name="woese2005hgt">{{Cite book
| title = Microbial Phylogeny and Evolution:Concepts and Controversies: Concepts and Controversies
| chapter = Evolving biological organization
| publisher = Oxford University Press
| pages = 99–117
|editor1= Jan Sapp
| last = Woese
| first = Carl R.
| author-link = Carl Woese
| access-date = 2013-01-04
| year = 2005
| isbn = 9780198037774
| chapter-url = https://books.google.com/books?id=SMvLpiK-fgsC&q=Evolving+Biological+Organization&pg=PA99
}}</ref> He worked on detailed analyses of the phylogenies of the aminoacyl-tRNA synthetases and on the effect of horizontal gene transfer on the distribution of those key enzymes among organisms.<ref name="woese2008">{{Cite journal 
| last1 = Woese | first1 = C. R. 
| author-link1 = Carl Woese
| last2 = Olsen | first2 = G. J. 
| last3 = Ibba | first3 = M. 
| last4 = Söll | first4 = D. 
| title = Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process 
| journal = Microbiology and Molecular Biology Reviews 
| volume = 64 
| issue = 1 
| pages = 202–236 
| year = 2000 
| pmid = 10704480 
| pmc = 98992
| doi = 10.1128/MMBR.64.1.202-236.2000
}}</ref> The goal of the research was to explain how the primary cell types (the archaeal, eubacterial, and eukaryotic) evolved from an ancestral state in the [[RNA world]].<ref name=mcb />