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Dec 30 2012

So long, and thanks for all the Archaea

Biologist Carl Woese has died of pancreatic cancer at age 84:

Carl and his colleagues wrote two papers published in 1977 that overturned a universally held assumption about the basic structure of the tree of life. They reported that the microbes now known as Archaea were as distinct from bacteria as plants and animals are. Prior to this finding, scientists had grouped Archaea together with bacteria, and asserted that the tree of life had two main branches – the bacteria (which they called prokarya), and everything else (the eukarya). The new discovery added Archaea as a third main branch of the evolutionary family tree.

Woese was one of those guys who overturned a paradigm  and became a founder of the succeeding paradigm. And he lived long enough to see the “dogma” he helped establish start to be undermined by new information, like recent suggestions that the common ancestor of all eukaryotes was likely Archaean, thus suggesting that having two main branches of life really does work as a model.

If there’s a better definition of success in a scientific career, I don’t know it.

43 comments

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  1. 1
    Wes

    like recent suggestions that the common ancestor of all eukaryotes was likely Archaean

    Just out of curiosity, does this include the ancestors of endosymbiotic organelles like mitochondria or chloroplasts? I’ve always been confused by how if endosymbiosis is true, should certain organelles be part of the classification scheme?

  2. 2
    Stacy

    Thanks for the information, Chris. RIP Carl Woese.

    suggestions that the common ancestor of all eukaryotes was likely Archaean, thus suggesting that having two main branches of life really does work as a model

    –But in this one Archaeans would be classed with eukaryotes instead of prokaryotes?

  3. 3
    mythbri

    Rita Levi-Montalcini also died today, at age 103. Stealth science and speaking truth to power ftw. Impressive woman.

    http://www.msnbc.msn.com/id/50324234/ns/technology_and_science-science/

  4. 4
    Andrew G.

    Just out of curiosity, does this include the ancestors of endosymbiotic organelles like mitochondria or chloroplasts?

    Mitochondria and chloroplasts are clearly bacteria in origin, not archaea; we can even identify their approximate relationship to other bacteria.

  5. 5
    rorschach

    Just out of curiosity, does this include the ancestors of endosymbiotic organelles like mitochondria or chloroplasts?

    IIRC, mitochondria shared a common ancestor with today’s Rickettsia bacterium around 600 million years ago.

  6. 6
    Amphiox

    But in this one Archaeans would be classed with eukaryotes instead of prokaryotes?

    More accurately, it is eukaryotes classed within the Archaea!

    IIRC, mitochondria shared a common ancestor with today’s Rickettsia bacterium around 600 million years ago.

    That date seems suspiciously recent to me, though. The earliest trace evidence of eukaryotes is over a billion years old, and there are even presumably mitochondria-possessing multicellular forms around by 600 million years ago.

  7. 7
    chigau (違う)

    Damn.
    I’m not going to understand a word of this thread.

  8. 8
    John Morales

    chigau, the Old Ones are not yet dead, but wait unsuspected deep benearth the Earth.

  9. 9
    Nathaniel Frein

    I love threads like this. I understand, like, every third word.

    Wonderfully humbling.

  10. 10
    chigau (違う)

    JM
    That’s just what I’m talking about.

  11. 11
    Stacy

    More accurately, it is eukaryotes classed within the Archaea!

    Cool.

  12. 12
    zekehoskin

    Okay. Assume that eukaryotes arose by archaea engulfing bacteria and then developing a nucleus, or vice versa? And the oxygenating atmosphere happened afterwards, when pre-algae got their chloroplasts working, or before, or during?

  13. 13
    Reptile Dysfunction

    Sad news about Dr. Woese. Pancreatic cancer got my
    mother & two of her brothers & I expect that’s the way
    I’ll go out, also. Wasn’t the Great Oxygenation supposed
    to have happened over a billion years ago?

  14. 14
    Nick Gotts

    The earliest trace evidence of eukaryotes is over a billion years old – Amphiox

    There’s still a lot of dispute about the date of eukaryotic origins, with paleontologists generally favouring older dates (1800-2700 Mya) and many molecular clock analyses suggesting dates around 1000 Mya, but the article linked to re-analyses molecular evidence, reaching results in conformity with the paleontological dates.

    Assume that eukaryotes arose by archaea engulfing bacteria and then developing a nucleus, or vice versa? – zekehoskin

    All claims for eukaryotes without mitochondria seem to have been refuted (in some cases, the mitochondria have degenerated), and Nick Lane, in Power, Sex, Suicide: Mitochondria and the Meaning of Life, and Life Ascending argues that the mitochondrial endosymbiosis was essential to the development of eukaryotic genetic complexity and the formation of the nucleus.

  15. 15
    carlie

    One of my colleagues took a couple of classes from Woese in the 60s, and has always spoken admirably of him. Said he was a good person as well as a great scientist.

  16. 16
    MikeG

    Man, that is sad. We just named a new piece of equipment after him.

  17. 17
    carlie

    MikeG – you have a Woesenator???

  18. 18
    lpetrich

    The oldest unambiguous eukaryote is Bangiomorpha pubescens, a 1.2-billion-year-old red alga that closely resembles present-day ones like Bangia. Red algae (Rhodophyta) have some distinctive features, and that’s what that identification was based on.
    -
    So these events had already happened by then:
    Acquisition of mitochondria
    Acquisition of chloroplasts
    Separation of red algae from other Archaeplastida
    Separation of Bangia-like red algae from other red algae

  19. 19
    Nicole Glynn

    I think this post just told me how dated my science textbooks were growing up. I went through school in the 90′s and was taught that there were the two branches, eukarya and prokarya – no mention of Archaea was ever made.

  20. 20
    lpetrich

    Coexisting with Bangiomorpha was lots of “acritarchs”, microscopic organic non-mineral structures. The earlier ones tend to be close to spherical, while after about 1 billion years ago, they start getting lots of spines and the like. They also had faster fossil-species turnover by then.

  21. 21
    MikeG

    Carlie, we name most of our equipment. It’s a thermal cycler, and joins Rosalind and Francis in our pcr duties. Oddly enough, though, we can’t seem to amplify any archea from out newest samples, even when we use Carl. We’re even using the primers Woese designed. Ah, the joys of research. Are we doing it wrong or have we found the one place on Earth without archea?

  22. 22
    yubal

    For the endosymbiont topics. Keep in mind that they not necessarily had to leave decedents. More like distant cousins of forms with living decedents.

    Also keep in mind that there is no plausible reason that this could have happened only once. Like ambiogenesis could as well have occured several times. We don’t see much evidence in the genetic record but the genetic record is written only by the victors.

  23. 23
    MikeG

    And in memory of Carl, I make an offering to Tpyos.

  24. 24
    jaxkayaker

    Nicole: the Archaea are prokaryotes, so they would be part of the Prokarya.

    As to undermining Woese’s paradigm by accruing evidence that the common ancestor of eukaryotes was archaean, I thought that had long been the situation, not a recent development. I thought that recent evidence suggested that Archaea shouldn’t be considered a branch separate from Bacteria.

    Also, IIRC, oxygenation of the atmosphere was attributed to cyanobacteria.

  25. 25
    tomfrog

    In the very unlikely case of anyone not getting the reference in the title of this post (I know, I should have more faith —hum— in Human kind), here’s the intro of the Hitchhiker’s Guide To The Galaxy and its “So Long, and Thanks For All The Fish” song.

  26. 26
    ChasCPeterson

    recent suggestions that the common ancestor of all eukaryotes was likely Archaean

    c’mon, man. You can’t post something like this without a link; that’s not cool.

    recent evidence suggested that Archaea shouldn’t be considered a branch separate from Bacteria.

    ditto.

  27. 27
    Glen Davidson

    Nicole: the Archaea are prokaryotes, so they would be part of the Prokarya.

    “Prokaryote” isn’t a taxonomic term, and some have suggested that it should be abandoned.

    However, most think it’s a useful term for eukaryotes like ourselves to refer to “the rest,” the non-eukaryotes. That’s a junk drawer term, though, useful without telling us all that much beyond the fact that you don’t mean the eukaryotes.

    Glen Davidson

  28. 28
    Bronze Dog

    Well, I’ve learned something new.

    Popped over to ‘kipedia to look at a labeled tree of life to see how they related. When I went to school, the books tended to emphasize five “kingdoms”: Animals, plants, fungi, protists, and I think it was something like “monerans” for bacteria and viruses, which struck me as odd, even back then, since I knew viruses were especially oddball, being non-cellular and later, often RNA-based. In other words, it was a “junk drawer term.” Among bacteria, I think they even divided it into eukaryotic and prokaryotic subgroups, with the presence or absence of the nucleus being the big distinction. Guess I should find out more about the cellular biochemistry distinctions between the groups, sometime.

    I guess the five kingdom thing I got in school continues to show how egotistical we are about multicellularity since on the Archaea page’s tree, four of those five kingdoms are on a single major branch, while the “monerans” would cover everything else.

  29. 29
    Chris Clarke

    Chas:

    recent suggestions that the common ancestor of all eukaryotes was likely Archaean

    c’mon, man. You can’t post something like this without a link; that’s not cool.

    Yeah, I know. I spent about twenty minutes looking for the piece I’d seen within the last three weeks without success, and then decided I was being rude to my (new batch of) houseguests so I just posted.

    I’ll keep looking and maybe make a post out of it. In the meantime, it’s as jaxkayaker suggested: the suspicion that Eukarya is a daughter clade to Archaea (at least in some calculations) isn’t really news, as evidenced by this for example. Depending, of course, on whether you define Eukarya as merely the descendants of the original heterotroph that ate the other guys.

  30. 30
    Chris Clarke

    Oh, and there’s this little goodie from September.

  31. 31
    Amphiox

    With respect to the discrepancies between published molecular dates and fossil record dates, one of the things about molecular dating as a technique is that it needs to be calibrated with the fossil record. As the fossil record starts to get increasingly sparse after you get past 600 million years or so, the potential error in molecular dating starts to increase significantly as the dates determined get further and further away from the nearest reliable calibration date.

    For anything dating older than 500 million years I am generally inclined to believe the fossil dates over molecular dating if there is a discrepancy, and if it is a date for which there are no fossils, one must remain healthily skeptical with respect to the overall range of error for the molecular date.

  32. 32
    ChasCPeterson

    Let’s level the playing field with some background:
    ‘eukaryote’ refers to organisms that have a nucleus. All nuclei are similar complex structures and have therefore long been regarded as homologous (i.e. all eukaryotes share a common ancestor that was a eukaryote; nuclei evolved only once afawct), and al kinds of moleculr-phylogeny studies confirm this: Domain Eukarya is monophyletic.
    It used to be thought that a few basal groups of extant eukaryotes lacked mitochondria because their lineages had branched off from the rest of the eukaryotes before the evolution of mitochondria (which happened by endosymbiosis of a–prokaryotic–bacterium). However, genetic and in some cases morphological traces of mitochodria have since been identified in these groups, so the ur-eukaryote probably had mitochondria too; the order of evolution of nuclei and mitochodria is therefore uncertain. (Plastids evolved later, maybe a couple of times independently from bacteria and then by various endo-endosymbioses within eukaryotes.)

    ‘prokaryote’ refers to organisms without a nucleus; their DNA is not encolsed within a membrane and there are no membrane-bound organelles inside the cell. Woese’s contribution was to show that there were actually two very different groups of organisms with prokaryotic cells. This was based on molecular sequence comparisons of ribosomal RNA, and even then similarities between archaean and eukaryotic rRNA were noted. Therefore it’s long been suspected that the domains Archaea and Eukarya were (slightly) more closely related than either was to the Bacteria. That assumes all three are monphyletic. It would also be possible for the eukaryotes to be nested somewhere within the (other) Archaea.

    But there are lots of controversies about all this, and this part of one of the OP links explains the complications, involving known and hypothesized horizontal gene-swapping, endosymbioses, and transdomain cell-fusions…’kipedia summarizes:

    The leading hypothesis is that the ancestor of the eukaryotes diverged early from the Archaea, and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this explains various genetic similarities but runs into difficulties explaining cell structure.

    …and that’s current as of 2008.

  33. 33
    Tethys

    I love threads like this. Latin terms, and fossils, and wonderful science links abounding, oh scrabous joy! Thanks Chas for the background.

    Ipetrich

    The oldest unambiguous eukaryote is Bangiomorpha pubescens, a 1.2-billion-year-old red alga

    I’m guessing the key word here is unambiguous because Grypania spiralis is classified as an eukaryote and it is 2.11 billion years old.

  34. 34
    Chris Clarke

    Yes, thanks for the background, Chas, which I happily concede would have been best covered in the original post.

  35. 35
    zekehoskin

    I suppose it’s conceivable that eukaryotes already existed before some common ancestor of rickettsia and mitochondria replaced what they were using up till then, but I’d need a lot of evidence to buy it. Likewise a DNA-transferring virus infecting all the mitochondria until the survivors had something that would look like common ancestry. When I did my MSc in biophysics back in the early seventies, we turned out to have no notion what we were looking at. This is fun!

  36. 36
    Stacy

    When I went to school, the books tended to emphasize five “kingdoms”: Animals, plants, fungi, protists, and I think it was something like “monerans” for bacteria and viruses

    Ha! When I went to school, sonny, there were 3 kingdoms–Animals, plants and “protists.” There were no domains, the Archaea hadn’t been discovered, and nobody mentioned “clades.”

    (Also we had to walk 12 miles in the snow to get to biology class. Both ways.)

    ~~~

    Double-checking I find that by 1969-1970, when I was introduced to taxonomy in Jr. High (which is as far as my formal education in the subject goes,) they distinguised between plants and fungi, and there were several 4-kingdom schemes. I remember being taught only 3….

    I love this stuff. Learning the relationships between living things. The classifications change so quickly, as our knowledge grows day by day.

  37. 37
    Stacy

    I meant, uphill. Both ways. Never mind.

  38. 38
    xenithrys

    Chris: here’s a link to a blog summary, which has a link to the paper. http://phenomena.nationalgeographic.com/2012/12/20/redrawing-the-tree-of-life/

  39. 39
    ChasCPeterson

    aha; thanks xenithrys. (I should have remembered that post since I see I commented on it!)

    So this new info suggests that eukaryotes are nested within the archaeans instead of basal to them. Two Domains with eukaryotes as specialized archaeans instead of a separate and equal branch.

    cool.

  40. 40
    Noah Rahman

    Obviously the conceptualization and fleshing out of archaea was a tremendous contribution. However, I am afraid he lent his name to some rather dodgy science coming out of U of I towards the end. Some of you are no doubt familiar with Prigoginism. I’ll not rehash it (unproven dissipative far-from-equilibrium structures).

    All I can add now though is whatever type of Kool-Aid Nigel Goldenfeld and Carl Woese were drinking must be the same as Prigogine’s, viz. http://www.annualreviews.org/doi/abs/10.1146/annurev-conmatphys-062910-140509, also http://www.uncommondescent.com/intelligent-design/goldenfeld-and-woese-paradigm-busting-even-more-with-added-goodies-for-id-front-loaders/ (extra bonus: arXiv version of the supremely condescending first link)

    Woese is well known to you all, but Goldenfeld is the author of a well regarded renormalization (mathematical technique in statistical physics) textbook and was formerly a postdoc at UCSB where my teachers used the book and regarded him highly. Was this just late stage intellectual syphilis? I mean some of the biological phenomena are interesting, but if I were a biologist I have to admit the unnecessary references to condensed matter quadrivia might turn me off, as well as the tone.

    And especially when there are better explanations for speciation without resorting to statistical mechanical woo even more pernicious than quantum, namely: http://genomebiology.com/2012/13/11/R107/abstract

  41. 41
    Noah Rahman

    NB: Specifically, Goldenfeld and Woese purported to invoke condensed matter physics techniques to treat the problem of horizontal gene transfer (as cited in one of the other comments above), by treating the discrete so-called fitness landscape as continuous and proceeding to apply statistical mechanical techniques on the resulting differential equations.

  42. 42
    Noah Rahman

    I apologize for the remarks above about disease. That post was copied from something written before Woese passed away and I didn’t check it thoroughly. The tone of that arXiv paper was just so condescending that several months ago when I wrote that I wasn’t very kindly disposed towards him.

  43. 43
    David Marjanović

    IIRC, mitochondria shared a common ancestor with today’s Rickettsia bacterium around 600 million years ago.

    Give or take a few zeroes. Well, give.

    eukaryotes arose by archaea engulfing bacteria and then developing a nucleus

    Apparently; the nucleus has been suggested to provide protection against transposable introns, and introns come from mitochondria.

    And the oxygenating atmosphere happened afterwards, when pre-algae got their chloroplasts working, or before, or during?

    Probably all of the above; chloroplasts are endosymbiotic cyanobacteria, and cyanobacteria (“blue-green algae”) were probably doing photosynthesis long before the first eukaryote showed up.

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