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We Don’t Know What We’re Missing

I enjoyed this article in Science about looking for hidden types of life. There are, of course, plenty of microorganisms that can’t be cultured (this has been known for a long time). And there are plenty of odd DNA sequences that are pulled out of environmental samples, corresponding to undescribed bacteria and archaea.
But what about things that we’re not even seeing through those techniques?

Undiscovered life, if it exists, is either absent at the locations of existing environmental surveys or is missed by current approaches. There are reasons to believe that current approaches may indeed miss taxa, particularly if they are very different from those that have so far been characterized. The “universal” primers used to detect 16S rRNA genes from bacteria and archaea in environmental samples can miss major lineages because of primer mismatches (5). Similarly, the selection of specific single cells from environmental samples for genome sequencing has been based on rRNA gene identity, thus also relying on these universal primers. Organisms whose 16S rRNA genes are not recognized by the primers would not be detected using this approach. Past explorations of available metagenomic data sets have focused on the discovery of matches to the known genes and genomes—an analysis that is naturally biased against uncovering completely novel life. Finally, although we may soon have petabases of metagenomic sequence data, samples have been collected from only a minute fraction of Earth’s countless different environments.
Recognizing these limitations, it is reasonable to speculate that undiscovered and highly divergent branches of life may exist, possibly represented by domains whose marker genes differ extensively from those of the bacterial and archaeal branches on the tree of life.

The authors speculate that even the hypothetical “RNA world” organisms from the beginning of living systems might still be found in remote, protected environments (deep rocks, etc.) It’s just that our current methods of detection are likely to miss them, even if they’re present. I look forward to seeing where this goes, and what implications this work may have for chemical biology and synthetic biology. I also like the way that these studies may prove useful in identifying and confirming extraterrestrial organisms. The day when we have some of those to argue about is, I think, closer than many might think.

10 comments on “We Don’t Know What We’re Missing”

  1. matt says:

    I wonder if you’d care to comment on this:
    Short version: on earth, basalt is not found in sedimentary layers, because water attacks/reacts with/dissolves the iron/magnesium/calcium in basalt. By the time it’s laid down in sediments, those elements have been transformed or carried off.
    On Mars, nearly every rock closely examined appears to be sedimentary, very many of which are basaltic in composition.
    Seems like physical chemistry might shed some light on this. Reaction conditions under less than 1 atm of non-standard atmospheric gas aren’t hard to reproduce, nor are cold temperatures. Nor the effects of strongly oxidizing or strongly reducing environments.
    Nor should it be hard to consider other possible compounds that might be liquid at ranges of temperatures found on Mars, and rule in/out their presence there in large quantities.
    Reduced settling and changes in composition sorting due to 1/3 gravity are a bit harder to whip up in the lab. As are geological time-scale reactions. 🙂
    It’s a puzzle, and although there’s the danger that Dunning Kruger will strike, and chemists will go stomping in like Andy Grove to pharmaceuticals, I think there’s some room for consideration.
    The most interesting thing, to me, is like these off-the-beaten-path RNA, it makes us rethink all those assumptions we constantly use. We are standing on the shoulders of giants, as Newton said, and occasionally situations are so different they make us hop off those shoulders and go back to ground level. Very humbling, but illuminating at the same time.

  2. Anonymous says:

    The discovery of a fourth domain of life is definitely one of these “free Nobel to whomever pulls this off” topics (it’ll nab a Chemistry, mark my words, for no other reason than to tick off the chemists).
    I’m not expecting it anytime soon, but it sure would make one hell of a splash, and it’s still more likely than these room-temperature superconductors.

  3. dearieme says:

    Physicists have “dark matter”; why shouldn’t biologists have “dark life”? Especially since the latter won’t just be trying to excuse a mistaken calculation.

  4. Pedantic Spaker says:

    Cairns-Smith actually proposed that the first lifeforms were clay crystals, which our current techniques would certainly not recognise as life. I remember reading that tests with “hypo” crystals yielded negative results regarding heredity, in that the inheritance of crystal defects was not sufficiently faithful, but clay minerals may be better, iirc; and if clay crystals can exhibit heredity, it may be that clay life is all around us.
    If they were too accessible, they would likely be replicators rather than reproducers (for the same reason RNA-world replicators can only be found “in remote, protected environments” if they still exist at all), but they could incorporate organic components if sufficiently sheltered and it may even be possible in principle to have an almost wholly inorganic organism.

  5. Simple biologist says:

    @ comment 3.
    Discovery of third domain was never deemed wofthy of Nobel. Not even after extensive and long campaign by microbiogists.
    New microbial domains tend to have no connection to 1st world diseases or cancer, ie. snooze button at Arlanska and Royal academy.

  6. Anonymous says:

    But think of all these weird metabolites that they would have! Clearly some of these could show anti-cancer activity.

  7. anonymous says:

    what’s the difference between a “replicator” and a “reproducer”?

  8. tangent says:

    @6 “tend to have no connection to 1st world diseases or cancer”
    It’s really quite something how the archaea will live in every absurd environment running every wacky metabolism, and they live in our flora, but they never seem to act as pathogens. Not one clear pathogen in the whole kingdom. (Have any exceptions been found?) I’ve heard some theories, but none seem like enough to cover the whole mindblowingness of it.
    Business now open for wild theories about how we just don’t know what they’re causing. Cancer? Erectile dysfunction? Aging?

  9. sepisp says:

    I’m going to rain on your parade here, and say that the article was profoundly uninformative and almost unscientific. In principle I can go and proclaim that “hairy giants, made of ice and apostrophes, and with ears made of polyurethane, may inhabit Lake Vostok”. That is technically a good scientific hypothesis, since it’s specific, falsifiable and testable. Yet, think, why would it appear unscientific? I’m not going to give answers here, just think about it.
    DNA/RNA is a red herring. Sure, current quick screening methods rely on it, but bacterial life was discovered before DNA, and the *effects* of bacterial life were discovered before the bacteria. To make any claim of “alien Earth life” there should be some sort of evidence that would suggest it should exists. So far, there is none. None as in not seen anywhere ever, not even seriously claimed.
    That doesn’t answer the question of why there is only one type of life. One possible reason there is only one type of life is that the current bacteria wept out all competitors. We did that to mammoths and North American megafauna.

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