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Woese once said of himself and his work that when a wise man points out the moon, only a fool looks at the finger. Let us all be fools if just for a moment .
January 2, 2013 7:29 AM   Subscribe

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

Imagine walking out in the countryside and not being able to tell a snake from a cow from a mouse from a blade of grass, that’s been the level of our ignorance.”-Woese
Carl Woese's distinguished career was dominated by his idea that divisions between different kinds of living organisms could be better defined by their small subunit ribosomal RNA(smaller bottom piece here) sequences than by their morphology, biochemistry, outer membrane, or even necessarily the most basic of divisions like multicellularity or the presence of cellular organelles. Indeed, seeing life through this much clearer lens, he was able to show that the microbes known as Archaea are at least as different from Bacteria as they are from Eukaryotes like plants and animals, a finding he presented here to much controversy and derision:
Woese, Carl R.; George E. Fox (1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms.(PDF)". Proceedings of the National Academy of Sciences of the United States of America 74 (11): 5088–5090
A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the eurkaryotes, now represented in the cytoplasmic component of eukaryotic cells.
Fought for eloquently here:
Woese, Carl R. (1987-06-01). "Bacterial evolution.(PDF)". Microbiological Reviews 51 (2): 221–271
A revolution is occurring in biology: perhaps it is better characterized as a revolution within a revolution. I am, of course, referring to the impact that the increasingly rapid capacity to sequence nucleic acids is having on a science that has already been radically transformed by molecular approaches and concepts. While the impact is currently greatest in genetics and applied areas such as medicine and biotechnology, its most profound and lasting effect will be on our perception of evolution and its relationship to the rest of biology. The cell is basically an historical document, and gaining the capacity to read it (by the sequencing of genes) cannot but drastically alter the way we look at all of biology. No discipline within biology will be more changed by this revolution than microbiology, for until the advent of molecular sequencing, bacterial evolution was not a subject that could be approached experimentally. With any novel scientific departure it is important to understand the historical setting in which it arises-the paradigm it will change. Old prejudices tend to inhibit, distort, or otherwise shape new ideas, and historical analysis helps to eliminate much of the negative impact of the status quo. Stch analysis is particularly importaht in the present instance since microbiologists do not deal with evolutionary considerations as a matter of course and so tend not to appreciate them. Therefore, I begin this discussion with a brief look at how the relationship between microbiology and evolution (i.e., the lack thereof) developed.
And presented again thirteen years later, this time as core scientific dogma:
Woese, C R; O Kandler, M L Wheelis (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.(PDF)". Proceedings of the National Academy of Sciences of the United States of America 87 (12): 4576–4579.
Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.
It’s clear to me that if you wiped all multicellular life-forms off the face of the earth, microbial life might shift a tiny bit, if microbial life were to disappear, that would be it — instant death for the planet.”-Woese
Later in life he became something of an elder statesman of evolutionary microbiology publishing the occasional review:
Woese, Carl R.; Nigel Goldenfeld (2009). "How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis". Microbiology and Molecular Biology Reviews 73 (1): 14–21.
In this commentary, we provide a personal overview of the conceptual history of microbiology and molecular biology over the course of the last hundred years, emphasizing the relationship of these fields to the problem of evolution. We argue that despite their apparent success, all three reached an impasse that arose from the influence of dogmatic or overly narrow perspectives. Finally, we describe how recent developments in microbiology are realizing Beijerinck's vision of a field that is fully integrated with molecular biology, microbial ecology, thereby challenging and extending current thinking in evolution.
Today, whenever a student of biology opens their textbook what they see first is a blown up image of the tripartite tree of lifea small tribute to a man and a discovery that changed our view of nature forever."
posted by Blasdelb (26 comments total) 22 users marked this as a favorite

 
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posted by motorcycles are jets at 7:38 AM on January 2, 2013


Nice post! This is my favourite quotation from Woese, from a longer piece about him a few years back:
According to Miller and several other colleagues, Woese has survived the stresses of scientific controversy by keeping his sense of humor intact. Ask him what he does in his “spare time” for recreation, he growls: “I drink beer!” Then, hooting with laughter: “Really, I sit at home and drink beer! It's the cheapest way I can get drunk—and I get drunk so I can have ideas and write [scientific] papers better.
The relationships among microbes are a lot more complicated than the canonical 16S tree would suggest, but there is no question that his work was a sea change from the uncertainty and despair that characterized the 1950s and 1960s.
posted by aeolicus at 7:56 AM on January 2, 2013 [2 favorites]


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posted by OmieWise at 8:02 AM on January 2, 2013


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posted by CBrachyrhynchos at 8:05 AM on January 2, 2013


I graduated from high school in 1995, so we only had kingdoms when I took biology. I love teaching my students about our constantly evolving understanding of life and how it evolved, and telling them that Archaea was not even mentioned when I was in high school fascinates the younger ones (the non-traditional students, many older than me, just smile knowingly). I haven't invoked Woese's name in the past, but maybe I will this spring. Thanks for the fascinating post.
posted by hydropsyche at 8:11 AM on January 2, 2013 [1 favorite]


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plus an ! for being awesome.
posted by Kid Charlemagne at 8:21 AM on January 2, 2013


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posted by DevilsAdvocate at 8:50 AM on January 2, 2013


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Nobel prize richly deserved. Hope he gets it soon. Oh, wait...
posted by Mental Wimp at 8:58 AM on January 2, 2013


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

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

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

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

How arcane the necessary technique was was a large part of why so few of the older fuddyduddies believed him or cared until the mid 80s, before the few remaining doubters had to finally shut up with the sequencing revolution of the 90s.
posted by Blasdelb at 9:09 AM on January 2, 2013 [9 favorites]


Aw. I do molecular biology and was specialized in microbial diversity as an undergrad, and I had sort of hoped to meet him someday. It's crazy to think we still use the same techniques; the 18S nuclear ribosomal rDNA (homologous to the 16S, but in Eukarya) is still the very first gene I sequence for any organism I am trying to identify or trace the evolutionary history of. The gene has limitations (two of the organisms I work with have greatly distorted rDNA sequences for unknown reasons, making it fairly useless for them) but it's still very valuable.

It's usually better for Bacteria and Archaea than the Eukarya (for one thing it's fairly immune to horizontal gene transfer, which is a huge problem for following the evolution of protein-coding genes in the prokaryotic domains).
posted by Mitrovarr at 9:19 AM on January 2, 2013 [3 favorites]


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posted by Amplify at 9:19 AM on January 2, 2013


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posted by Westringia F. at 9:31 AM on January 2, 2013


I am at a loss for words, so instead I'll quote Nigel Goldenfeld's statement from the UIUC obit:
"Beginning as an outsider, he turned a field that was primarily subjective into an experimental science, with wide-ranging and practical implications for microbiology, ecology and even medicine that are still being worked out.

"The largely untold story of the intellectual struggle he endured, and his years of hard, painstaking work have been a model of how scientific discoveries get made and a source of inspiration to all those whose lives he directly touched, be they scientists, educators, students or laypeople."
posted by Westringia F. at 9:51 AM on January 2, 2013 [2 favorites]


Blasdelb: And presented again thirteen years later, this time as core scientific dogma:
Blasdelb, it's a fabulous post (and eulogy), and although I understand the metaphorical usage of "dogma" here, ... science does not, and by definition, cannot, have dogma.

I'm not saying it isn't treated dogmatically - I've known many, many brilliant scientists who treat certain solidly established principles as unshakeable and absolute fact, but that which requires faith in the face of contrary evidence is not science.

If Carl Woese's life shows us anything, it is that great scientists are willing to throw any prior belief out the window, if the facts point in another direction.
posted by IAmBroom at 9:53 AM on January 2, 2013 [1 favorite]


While there is Oppenheimer's great quote, that Woese actually uses in the last review he published [FULL TEXT]*:
There must be no barriers for freedom of inquiry. There is no place for dogma in science. The scientist is free, and must be free to ask any question, to doubt any assertion, to seek for any evidence, to correct any errors.
—J. Robert Oppenheimer, The Open Mind, p. 114 (1955)
there is a partially facetious sense of the word coined by Jim Watson that is still used in biology, especially referring to Central Dogma, which underlies everything.
*Woese, Carl R.; Nigel Goldenfeld (2009). "How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis". Microbiology and Molecular Biology Reviews 73 (1): 14–21.
In this commentary, we provide a personal overview of the conceptual history of microbiology and molecular biology over the course of the last hundred years, emphasizing the relationship of these fields to the problem of evolution. We argue that despite their apparent success, all three reached an impasse that arose from the influence of dogmatic or overly narrow perspectives. Finally, we describe how recent developments in microbiology are realizing Beijerinck's vision of a field that is fully integrated with molecular biology, microbial ecology, thereby challenging and extending current thinking in evolution.
posted by Blasdelb at 10:24 AM on January 2, 2013 [3 favorites]


Great post as usual, Blasdelb. At least Woese lived long enough to see his ideas acknowledged, even if not from the people he wanted.

As for dogma, I have hardly any biological training, but if you used "dogma" in a scientific conversation with me I would immediately think of biology's Central Dogma. We learned it (under that name) in high school biology. And from what I've read, it looks like it is being challenged, hence the whole field of Epigenetics.
posted by benito.strauss at 10:45 AM on January 2, 2013


And from what I've read, it looks like it is being challenged, hence the whole field of Epigenetics.

"DNA makes RNA makes protein regulates DNA."

I know, too simplistic, but closing that loop is the essence, as I understand it.
posted by Mental Wimp at 10:51 AM on January 2, 2013


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posted by cromagnon at 10:59 AM on January 2, 2013


The Central Dogma is one of the many things in science that is pretty much always true except for the times it isn't. Epigenetics, which is a horrible word that really means nothing by meaning everything, doesn't actually challenge Central Dogma so much as explain it. The basic idea is that DNA makes RNA makes protein, and from the beginning it was obvious that the proteins that were figured to mediate the whole process (We now know that RNAs are also at least equivalently involved) need to get information somehow about how much RNA to make from DNA and how much protein to make from RNA. It is however directly challenged by the lifestyles of Eukaryotic retroviruses and temperate RNA bacteriophages that store their genetic information as RNA, reverse transcribe it into DNA, which they then use to make RNA, which then makes protein.

In terms of Woese's work, any phylogenetic tree (except for this one) is just about the most foolish thing in science you could possibly get a tattoo of. However, it is a pretty safe bet that even when we hopefully have a yet more nuanced understanding of the evolution of life and LUCAS, it will only be able to see so far by standing on the shoulders of Woese's model and those that came before as if they were giants. Ala Bernard of Chartes: nanos gigantum humeris insidentes.

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posted by Blasdelb at 11:13 AM on January 2, 2013 [1 favorite]


The Wikipedia Central Dogma page has a good discussion on the topic and Crick's poor choice of words. A prof I knew once said the only truism in biology is that "everything's gotta eat something".

Great post. Woese is a great example to point to when someone claims there are no new frontiers left.

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posted by benzenedream at 11:20 AM on January 2, 2013 [1 favorite]


"DNA makes RNA makes protein regulates DNA."

That makes complete sense. I'm just pointing out that neither my (30 year old) high school biology class, nor the simple diagram in the Wikipedia page include that flow.
posted by benito.strauss at 11:42 AM on January 2, 2013


The revolutions in microbiology and paleobiology during my lifetime are things I keep pointing out to evolution deniers and saying, "Look! Evolutionary biology has gone through two scientific revolutions in my lifetime (and arguably is on the verge of another with epigenetics and synthetic biology). If you think you have the evidence, bring it!"
posted by CBrachyrhynchos at 1:29 PM on January 2, 2013 [4 favorites]


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posted by lalochezia at 4:16 PM on January 2, 2013


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posted by genehack at 8:20 PM on January 3, 2013


Thank you for posting about Carl Woese. He recently co-published this paper on treating biology as a physics problem. I can't say I fully comprehend it, but it is obvious that there is some serious thinking going on there and it was put into perspective how very far we still have to go in understanding what this thing called Life is. Carl Woese was a very admirable human being.
posted by surfgator at 12:47 PM on January 4, 2013 [1 favorite]


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posted by cnanderson at 12:48 PM on January 4, 2013


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