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Microbial Data Mining

November 21, 2011

A friend of mine, a self-described “microbial supremacist” at Small Things Considered shows how animals make use of microbial odors.

How do hoverflies locate aphids–a garden pest we wish to control? The aphids secrete honeydew, which the aphid’s symbiotic bacteria ferment to various volatile compounds. These compounds attract the hoverflies to lay their eggs.

How do malaria mosquitoes locate the choice spot to bite a human? They follow an odor trail from the smelly feet, that is, the part where feet-specific microbes produce volatile compounds. Research funded by the Bill and Melinda Gates Foundation has identified ten specific microbial feet odor compounds that attract mosquitoes. The odor compounds, of course, are detected by specific receptor molecules on the neurons (similar to visual perception and cocaine receptors–sorry, couldn’t resist).

Bacteria, too, use their own “data” to adjust behavior. An elaborate system is quorum sensing, in which bacteria “count” their population by measuring the concentation of an “autoinducer” compound secreted continually by all members. Some bacteria even distinguish between counting their own, versus counting a different signal by other species. Pathogens such as Salmonella  and M. tuberculosis may do this to adjust their pathology depending on what other pathogens are present.

What are other kinds of microbial data mining?  How might this be used in science fiction?

15 Comments
  1. November 21, 2011 10:09 pm

    If you’ll pardon the personal observation, I’ve had a lifetime of torture to brood over this phenomenum–as a youth, I shared a house with four other guys–I was always complaining about the fleas–but all four laughed it off–‘If there are fleas, why weren’t they being bitten?’ After a month of this I showed my leg to a doctor who told me I had come in just in time to avoid scarlet fever and losing the leg–it had become infected. The other house-guys finally saw the fleas–after I left there, the fleas turned on all of them en masse. In the same way, I’ve stood with garden party-ers and they all agreed that the mosquitoes were ignoring all of them to go straight for me. Now I know why at last–I must have sweet feet!

    • November 22, 2011 12:02 pm

      Yes, I found the same thing with fleas; they always liked my smell best. I never cared to experiment further.

  2. alex tolley permalink
    November 21, 2011 10:16 pm

    Clearly this sort of “computation” has uses in a range of swarm type algorithms, e.g. traveling salesmen problem.

    What I think will be more interesting is engineered bacteria that will be able to doing more interesting computations, particularly detecting chemicals (explosives), linear and non-linear separation of mixed sensor data into classes (e.g. targeting cancers, indicating health, etc.).

    It does offer some way out possibilities too, since we are hosts to a lot of bacteria. What if gene engineered bacteria made it impossible for people to meet in large groups (crowd control by quorum sensing) or even the reverse? What about bacterial aphrodisiacs (stimulate the target to be receptive by releasing the appropriate brain chemicals)?

  3. Petter permalink
    November 22, 2011 5:02 am

    synthetic bacteria could be looking for several different substances simultaneously and by looking at the concentrations of the different substances, during an infection they could then locate themselves to specific parts of the body or more interestingly the brain, where they could manipulate the coulde amplify or negate the effects of specific neurotransmitters.

    nanotech/bacteria hybrids could be situated at strategic sites to monitor the flow of neurotransmitters and transmit them to a central computer and with enough of them in place that might be enough for telepathy, uploading and more.

    • November 22, 2011 12:07 pm

      Yes, it looks like bacteria have inspired nanobot–and sometimes combined with them:
      http://nanolab.me.cmu.edu/projects/swimming/

      Insects too have inspired robot designs:
      http://www.sciencedaily.com/releases/2011/10/111017214919.htm

      Where do you get the “telepathy”? Do you envision microscopic transmitters? How strong would they have to be?

      • November 22, 2011 2:12 pm

        Joan, didn’t you have chemical transmission of thought in one of your earlier books? Must telepathy be spooky action–or could it be this more prosaic version?

        • November 22, 2011 9:35 pm

          The intelligent micros in Brain Plague communicate by emitting chemicals and tasting them. I don’t recall humans doing that. My very first book, Still Forms on Foxfield, had mental communication by nuclear magnetic resonance.

  4. SFreader permalink
    November 22, 2011 10:32 am

    One of the educational networks had a fascinating story about maggot therapy (debridement) for diabetic amputees. And, according to the Wiki entry, maggots show promise as a control for some of the more problematic infections …

    http://en.wikipedia.org/wiki/Maggot_therapy

    In a 2007 preliminary trial, maggots were used successfully to treat patients whose wounds were infected with MRSA, a bacterium (Staphylococcus aureus) with resistance to most antibiotics, including methicillin. Some of these strains include flesh eating bacteria causing frequent deaths upon infection of deep tissue. Maggots clean up the already dead tissue thus preventing further infection spread.[14].

    • alex tolley permalink
      November 22, 2011 11:53 am

      We’ve apparently cycled back to discoveries made in WWI. Amazing! 😉

  5. November 22, 2011 11:55 am

    How about using the distinctive smell of geosmin (produced by strepromyces) to find water in the desert?

    http://www.bios.niu.edu/meganathan/smell_of_soil.shtml

  6. November 22, 2011 12:11 pm

    Geosmin is what they call the “spring soil” smell. I suppose humans, too, could have evolved to like the smell of spring soil because of new plant growth. We probably evolved in the savannah, a region of borderline water.

    Pheromones are interesting–post forthcoming on that.

  7. November 22, 2011 2:19 pm

    Perhaps smells are pan-global–the spring soil smell acts upon the animals as a trigger for the mating cycle–and perhaps rutting animal scents trigger (or help trigger) the growing of new shoots and buds in vegetation, which start the bees working, whose honey smell awakens the Bears in their caves, etc., etc. (?) –well, pan-continental maybe, the distances of oceans and equatorial zones confining the whole molecular-interchange to the north or south hemispheres, allowing for the opposing seasons…

    • November 22, 2011 8:37 pm

      It seems that humans are quite sensitive to geosmin. When I googled it, many of the references were how to get the geosmin out of food, because it messes up smell and taste. I found the reference to animals using this smell to track water interesting, and I wonder whether it would work for humans.

      One way I did use geosmin was to make sure a planet I wrote about smelled very different. Most of us don’t think about the fact that the “soil” smell is actually a bacterial product. Unless there’s a strong functional reason for soil bacteria to make geosmin, I suspect that the soil on alien worlds will smell very different.

  8. November 22, 2011 9:39 pm

    Yes, that’s a very good point. On Prokaryon, in The Children Star, all the soil bacteria as well as plants and animals produce “secondary products” different from those of terrestrial ecosystems; so they taste different than the most foreign habitats on Earth. So even when people have been genetically modified to consume Prokaryan food, they still can’t stand the taste. What smells like ripe fruit to a native might smell like airplane glue to a visitor.

  9. Heteromeles permalink
    November 26, 2011 9:48 pm

    New example: it’s not microbial exactly, but it’s how spider mites allegedly swipe genes from other organisms to eat more plants. Shades of the oankali!

    http://www.cbc.ca/news/technology/story/2011/11/25/science-spider-mite-genome.html

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