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Mobile Germ Sensor

A thing that can be built into mobile phones
 
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A long time ago, centuries, we all know the stories of how we didn’t have the hygiene we today have, because germs hadn’t been discovered, because we didn’t have the apparatus to see them. Operations would turn out badly because of infection, and nobody knew why, it was just one of those mysteries.

Then optics allowed things both small and near to be seen. And also large and far away, but never mind about that for now. Microbes could be seen to exist, and their effects could be studied and predicted. Soon, the beer and wine that people had been brewing for centuries could now be brewed in reality because yeast was finally understood. Operations would have a higher success rate because doctors would wash their hands beforehand, now that germs were understood to exist even if you couldn’t see them with the naked eye.

The public opinion soon swung around to fear the unseen in a totally new way — there really were germs around, too small to see. There was even a widespread “fly scare” [look, down there] which increased the general fear of every surface around.

Today, despite our modern enlightenment thinking, we have just as much a misunderstood fear of the unseen. We think germs are everywhere, and they are all harmful, and we must never allow food to come near surfaces or planes that may have come near carriers that may have come near germs. Or we assume the floor is comprised entirely of germs, and that if something goes near the floor on its way to our mouth, it will kill us.

We simply don’t know what may be there, unless we carry around a microscope, and with the exception of a large portion of people on the half bakery, probably nobody actually does carry a microscope around.

I propose a simple invention. A germ sensor that can be integrated into a phone, so that people can indeed carry a “microscope” around. Not just a microscope, but an analysing one, that can tell you not what germs there are (who cares) but what the real danger is. Otherwise, we’re back to guesswork and assumption and a (now enlightened) irrational fear of everything. I would imagine the germ sensor might be mostly optical imaging but could alternatively be based on acoustic snapshots, or even a combination, to identify such small things.

Ian Tindale, Apr 08 2016

The great fly scare http://soipa.it/riv...=publication_detail
[Ian Tindale, Apr 08 2016]

The hygiene hypothesis https://en.wikipedi.../Hygiene_hypothesis
There likely is such a thing as too germ-free [CraigD, Apr 14 2016]

[link]






       The higher-resolution a phone camera, the more that "zooming" an image is possible, resulting in the effect of magnification. So, all the phone really needs is a high- enough resolution camera to directly image germs.
Vernon, Apr 08 2016
  

       This is a great idea, except it's all wrong. Microscopy is about the worst imaginable tool for detecting bacteria, let alone identifying them.   

       What's needed is a little portable PCR machine and a few other gubbins. These things exist already, but are not really aimed at the average consumer.
MaxwellBuchanan, Apr 08 2016
  

       You could replace it with a box with a red LED with the words, "if LED is lit, bacteria are near this device" Always on.
Voice, Apr 08 2016
  

       //The higher-resolution a phone camera, the more that "zooming" an image is possible, resulting in the effect of magnification. So, all the phone really needs is a high- enough resolution camera to directly image germs.//   

       No.   

       //Microscopy is about the worst imaginable tool for detecting bacteria//   

       Yes.   

       The problems with imaging bacteria are multiple and insurmountable. If you google "Bacteria" and look at the image search results, you will see diagrams, cartoons and false-colorized images that look all 3D and cool. The problem with those is they were not made using a light microscope they used electrons. There is a total absence of cool light microscopy images like you may see with mammalian cells.   

       The key to problem 1 is in the name. Microscope. You can only effectively image down to the micrometre range. You can't just keep zooming in. Eventually, you run into the Rayleigh limit. Light is too big. The smallest visible light photons have a wavelength around 400nm, or 0.4 micrometers for simplicity. Your effective resolution, is governed by the size of light, you can tell two points apart if they are separated by more than about half the wavelength of the light you are using. So about 0.2 micrometers for violet, and about 0.4 for red.   

       Your average bacterium, if there is such a thing, is about 1-2 micrometres long. So, if you really push it, you may be able to get a 3x9 pixel image of the bacterium you want to look at. To get this image, you have to do a lot of things. If you think that getting a non-wobbly image of your dog at the end of the garden is hard... not wobbling by a single nanometre is VERY much more difficult. You also need a pretty remarkable lens. It needs huge curvature to get the magnification you need, that curvature has to be accurate to beyond the nanometre scale, how they do it is very much in the realm of industrial secrets. Despite the huge curvature needed, the side of the lens facing the sample must be VERY flat. Then, because light travelling through different substances bends differently depending on its color, you need an additional corrective lens behind the first. Then, because different parts of the image have passed through different thicknesses of lens, you need to correct for that. Why do you need the lens? well, because the amount of light coming off one bacterium is basically 0, in regular room light you're looking at 1-100 photons per minute. You need a GREAT lens to get about 15% of them. It's ok though, those lenses are very much baked, I have a used one that i can let you have at the bargain price of $45k. So you get the image, what would it look like? Nothing.   

       Here's problem 2. Cells, of pretty much every kind, are bags of water. There's simply not enough optically interesting stuff in a 1 micrometer thick bag of water to generate enough contrast, worse, remember the number of photons? If you just set up a microscope to look at hulking great mammalian cells in white light (light is transmitted, through the sample into the lens), you MAY see the nucleus, a few vesicles and with a trained eye some of the outline. Microscopy has relied on ways of generating contrast. So, you flood a sample with a dye that stains DNA. Your 3x9 pixel image may have a couple of pixels darker than the other. That's not the best analytical information.   

       Now, can someone tell me why an electron microscope is called an electron microscope? when it's exclusively used to image at the nanometre range. I'm off to vandalize a sign...
bs0u0155, Apr 08 2016
  

       As you hint, optical techniques are probably not useful here. Unless there we forgo the prospect of capturing and identifying one single small organism, and instead go for populations. I suspect the acoustic footprint or fingerprint or signature would enable detection and differentiation of enough of a population to have an effect on us, without necessarily being able to resolve a single one.   

       The main aim of this is to demonstrate that there is / might be / probably isn’t a situation where actual germs are actually there, over there, on that area of the surface, and it will / might / won’t harm us if we look at it / touch it and then touch our face / shove it up our arse.
Ian Tindale, Apr 08 2016
  

       [bs0u0155], germs were discovered long before electron microscopes existed. That means light-focusing microscopes were good enough to at least see them (which is what I thought could be done with a high-enough resolution CCD camera), even if identifying them beyond basic shape takes an e-scope. I don't challenge your statement that good-resolution imaging of germs won't be possible with a mere CCD camera. But simply noticing they are there....
Vernon, Apr 08 2016
  

       //I suspect the acoustic footprint or fingerprint //   

       Yes, the acoustic footprint would do it. Most species of bacteria (especially the gram-negatives) produce distinct ultrasonic frequencies as the bonds forming their cell walls are broken and remade. A group in Japan has shown that the frequency and timing of these sounds can be used to identify bacteria down to the genus and sometimes down to the species.   

       So you could probably do this with a phone if it had a very good microphone. Or at least you could if what I had written above was not complete bollocks, which of course it is.
MaxwellBuchanan, Apr 08 2016
  

       The way to do this is for the app to guess, based on image / color analysis, what type of germs are likely there. This is mostly to keep things consistent so a given surface (like your hand) is not proposed to have some different germ each time you look. Bacteria of a given type all look the same and so one would then use stock footage.   

       There would be an option to click through and see what the likely origin of a particular germ is: dog feces, human feces, cat feces, mucus from infected animal glands, moldy meat, etc. A further click through would have images of persons suffering from the diseases caused by that particular germ and an opportunity to purchase specific countermeasures.
bungston, Apr 08 2016
  

       //good-resolution imaging of germs won't be possible with a mere CCD camera.//   

       The camera isn't the problem. In fact we have a snazzy new super resolution microscope which pulls a few tricks to get down to the 20 nm kind of resolution. It has a very fast and sensitive camera, but we only use 1/4 of the sensor at a time, so only 512x512 pixels. Its trivial to expand the image to the whole sensor, but all you're doing is spreading the same light thinner. You gain no more information, because down at the pointy end there is no more information.   

       //even if identifying them beyond basic shape takes an e- scope.//   

       Ah, but no! Those contrast tricks we pull get pretty fancy. Initially, people found that some bacteria stain purple, some don't. Now we can do all sorts of things with fluorescent antibodies and so on. Way easier to just do the DNA stuff though.
bs0u0155, Apr 08 2016
  

       //Bacteria of a given type all look the same//   

       Indeed they very do. For example, Yersinia pestis looks identical to Yersinia ruckeri. The only difference is that one is bubonic plague whereas another only bothers some species of fish.   

       Or take E. coli (where are italics when one needs them??). Your gut is absolutely swarming with gazillions of them. But E. coli O157:H7 has a fair chance of killing you stone dead.   

       Still, this is a brilliant idea if we can get around the two problems of light microscopy being useless and appearance being irrelevant.
MaxwellBuchanan, Apr 08 2016
  

       Easiest thing to detect is moisture, in my opinion. An old saw suggests that all fungi need to grow is dark and damp, and my understanding of other microorganisms suggests the same conditions apply to them.   

       Two things:   

       1. A phone would probably detect its own presence first and most strongly.   

       2. An accurate device to detect ribosomes would at least tell you if an object has been exposed to a living being, to wit, and is contaminated.
reensure, Apr 09 2016
  

       "An accurate device to detect ribosomes" would be rather elaborate. Better to simply test for bacterial rDNA, which is abundant and very tractable to analysis.
MaxwellBuchanan, Apr 09 2016
  

       That's okay, Maxwell, but I think easier to detect if people have been there in order to guarantee that germs are there.   

       Ribosomes are a common contaminant to both domains
reensure, Apr 09 2016
  

       How about an app that just screams "Germs ! Germs everywhere ! Trillions of them ! Everywhere you look, germs ! You're all going to die ! "   

       That would neatly cover the known facts.
8th of 7, Apr 09 2016
  

       //Ribosomes are a common contaminant to both domains//   

       I think you mean rDNA. Ribosomes themselves would be pointlessly difficult to detect (or tell me how you planned to do it). rRNA is also abundant and fairly easy to detect, but any sane person would opt for rDNA.
MaxwellBuchanan, Apr 09 2016
  

       // any sane person //   

       This is the halfbakery ....
8th of 7, Apr 09 2016
  

       Disclaimer: nothing I say should be construed to be my effort to prove my sanity. :0p   

       I understand you're a microbiologist, Max, so freely point out my errors; but, how I'd proceed is use a molecular sieve followed by rna differentiation. Finding a ratio of protein to bacterial rna suggests a path to characterizing any microorganisms; maybe if sensitive enough one could differentiate riboswitches from Rho proteins, for example.
reensure, Apr 12 2016
  

       But just being aware of the presence of bacteria doesn't tell you anything. 90% of the cells in the human body are bacteria cells rather than human cells and, mostly, they're nice, beneficial bacteria.
hippo, Apr 13 2016
  

       That’s just it. Detecting actual microbes is not what this peripheral or transducer should spend its time doing. Discriminating actual danger (from microbes) is.   

       The issue is that there are people and there’s the other sort of people. One sort will lay a sandwich down on any surface, pick it up and eat it, and whatever drops out onto the floor goes back into the sandwich, if it doesn’t go into the mouth first along the way. The other sort would be convinced there’s dangerous germs just there on that surface, immediately under the sandwich, and now the germs have walked over onto the sandwich. The floor contains germs just waiting. The outer bags of anything that was bought in a shop, then went outside to get to be brought home, are now covered in germs, including from all the other people at the shop. The outer bags must not touch each other or more “inner” food. Letting bare food touch one of those outer bags is lethal.   

       My point is, where are these alleged germs. Obviously there are them, and they can cause harm, but really, are they absolutely everywhere all the time no matter what? In which case we may as well give up and take no special measures. Or can I point out that it was okay to put the biscuit down on that surface, because I know for a fact that there were no harmful microbes at that particular spot at that particular time, but had I put it down 3.5cm over to the left, well, that’s a different matter, there was a harmful colony of bacteria there at that time just as it happens.   

       We need the proof. Proof against mindless paranoid fear of the unseen. It’s as bad as fearing the wrath of invisible gods all over again, you see. Technology should be able to define and discriminate and allay, for us.
Ian Tindale, Apr 13 2016
  

       But this approach will create an environment which applies an evolutionary pressure to bacteria to select for bacteria which are dangerous but closely resemble 'good' bacteria.
hippo, Apr 13 2016
  

       » Which in turn drives evolutionary pressure toward Android / iOS developers of IoT stuff to evolve cleverer discrimination and clue finding means, probably involving google. Obviously humans won’t keep up so our first step would be to develop manufacturing robots that can, using hyper-technology, do the research, development, prototyping, assembling, mineral mining, logistics, making, design improvement, marketing and banking, all by themselves, in a perpetual arms race to the bottom of the peak of development of the war between harmful invisible germs, and beneficial invisible manufacturers.
Ian Tindale, Apr 13 2016
  

       This is, of course, assuming, as you imply, that, harmful bacteria (or other sorts of camels) have an advantageous payoff from harming humans in the first place. I’m not sure there’s an equilibrium there. I’d posit that the thriving or otherwise of colonies of harmful bacteria versus beneficial bacteria is not directly mechanically linked to the well being of passing nearby humans.   

       If there were a direct causal relationship between the more the betterment of a colony of harmful bacteria linked to the more the worsenment of a casual passer-by, then maybe.
Ian Tindale, Apr 13 2016
  

       //how I'd proceed is use a molecular sieve followed by rna differentiation. Finding a ratio of protein to bacterial rna suggests a path to characterizing any microorganisms; maybe if sensitive enough one could differentiate riboswitches from Rho proteins, for example.//   

       Horribly, horribly difficult. The world is full of protein (and somewhat less full of RNA, since it's fragile stuff).   

       Ribosomal DNA is present in multiple copies per bacterium; is relatively stable and easy to detect; and can easily be analysed in detail to distinguish bacterial species if needs be. Plenty of modern diagnostics rely on this. (In fact, I'm currently working on a fast assay for neonatal meningitis, which has to be able to detect 1-2 individual bacteria in a small sample of CSF; it uses bacterial rDNA for exactly this reason.)
MaxwellBuchanan, Apr 13 2016
  

       :) nice stuff, slow and tricky if one goes about decreasing chemical activity, elution, PCR, and all that.   

       Do you take a different approach, like spectroscopy or cross linking antibodies?
reensure, Apr 13 2016
  

       You mean me, for the meningitis stuff? It relies on a two-stage PCR (which can detect single DNA molecules pretty well), targetted at the conserved regions of bacterial ribosomal DNA. The clever bit is the way we eliminate contaminants in the system - and believe me, there is bacterial DNA in **everything**, even ultra-pure reagents.   

       I should add that my test is only aimed at giving a fast yes/no for bacteria - in a neonate, the most important thing is to know if there are *any* bacteria in the spinal fluid: you can worry about what sort they are later. If there are definitely no bacteria, you can send the mother and baby home; otherwise you have to keep the baby in for 2-4 days on precautionary broad- spectrum antibiotics.
MaxwellBuchanan, Apr 13 2016
  

       Doesn't taking a CSF sample risk infecting said neonate?
notexactly, Apr 13 2016
  

       Risk of infection vs. risk of misdiagnosed/untreated meningitis ?
8th of 7, Apr 13 2016
  

       //Doesn't taking a CSF sample risk infecting said neonate?// Not if it's done properly - apparently the risk of infection is negligible. Also, skin- borne bacteria don't appear in the CSF samples, which implies that they don't get carried in on the needle. I've not seen them taking the samples, but it's considered a low enough risk that it's done routinely for babies that seem off-colour or have a high chance of being infected.   

       At the moment, the CSF samples are cultured for 48 hours to see if any bugs grow, which means precautionary antibiotics and a hospital stay in the meantime. By the time the culture results come back, the kid's probably OK anyway. And only a small fraction of "positive" samples are culturable anyway, either because the bugs just don't like growing in culture, or because the mother has been dosed up on antibiotics before the birth as a preventative, and any bacteria in the kid's CSF are almost-but-not-quite dead.   

       The main aim of my test is to be able to send home the definitely- uninfected babies immediately; so it has to have a very low false- negative rate but can afford to have a modest false-positive rate (since the procedure then will be the same as if there was no test - i.e. treat).
MaxwellBuchanan, Apr 13 2016
  

       Clinics here have been using fast MRSA and Influenza A screens here for a while - just to throw ab/ics at bugs with a degree of sensitivity. Getting babies out of the hospital before they contract any MDR cooties is paramount. Cool work, Maxwell!
reensure, Apr 13 2016
  

       //fast MRSA and Influenza A screens//   

       Yep - most testing now is moving from culture over to PCR and/or antibody-type screens. The problem in my case is that (a) there may be, literally, only one or two bacteria in a relatively large (200µl) sample and (b) because we're testing for *any* bacterium (since many different ones can cause neonatal meningitis), we're vulnerable to contaminants by *any* bacterial DNA. Even ultra-pure, sterile reagents have significant amounts of bacterial DNA on or in them.
MaxwellBuchanan, Apr 13 2016
  

       //one or two bacteria in a relatively large (200µl) sample//   

       Why such a small sample? I'm not sure how much is a lot in neonatal cases, but instead of taking a small volume, why not ignore all the irrelevant salty water? You could use a standard needle/syringe with a tiny intermediate bit of plumbing, pull 500ul, push back through a one way valve with a bacteria-binding filter. Rinse and repeat for a couple of ml. Also, why are DNA-free solutions difficult? I have a total nightmare of a time keeping Ca2+ in the nM, but EVERYTHING is contaminated with Ca2+ (when you think about it, the Himalaya is just a very large Ca2+ contamination issue) and it's essentially indestructible.
bs0u0155, Apr 13 2016
  

       What about ethyl methane sulfinate as an alkylating agent and potent mutagen; or a repressor protein that would block the operating cells?
hippo, Apr 14 2016
  

       Well, it wouldn't obstruct replication but it does give rise to an error in replication so that the newly formed DNA strand carries a mutation and you've got a virus.
8th of 7, Apr 14 2016
  

       So I shouldn’t put my biscuits there?
Ian Tindale, Apr 14 2016
  

       Only if you're happy for them to burn twice as bright, but half as long.
8th of 7, Apr 14 2016
  

       //Why such a small sample?// The standard collection is 5 drops (each about 30-50µl) into the collection vial, and usually 2 vials.   

       I agree, you could re-inject the fluid via a filter to recover the bacteria, but then it becomes a rather different procedure, as far as the doctors are concerned. It's very difficult to get clinicians to change what they do, because they are at the sharp end of things, so to speak. There may also be some difference in regulation (for instance, a re-injection system may come under a different category of "medical device"). It would be useful, but it's got to be proven useful and has to be tested to hell and back first.
MaxwellBuchanan, Apr 14 2016
  

       Maybe with the right nanotech beads a microdialysis catheter could provide both a few millimeters surface area for an RNA footprint and draw essentially no CSF. I don't know how, but thinking it out suggests to me optical fiber and fluorescent "wells" lit by, I don't know ... photon kinetics or chemical kinases?
reensure, Apr 16 2016
  

       How about Raman spectroscopy?
notexactly, May 19 2019
  

       nice, electron nanoscopy.   

       The more bacteria, the higher chance of some bad. But still, it has to be on negative volatile molecular species, the more common the better. I have a cellphone that reacts nicely to too much meths, especially when I'm cleaning splashed paint.   

       Aside: Would a dog do?
wjt, May 19 2019
  

       Do what?
Ian Tindale, May 19 2019
  

       Do what dogs do.
8th of 7, May 19 2019
  

       That is, be mobile germ sensors... and roll in them.
wjt, May 20 2019
  

       Better than children, which are self-propelled disease incubators.
8th of 7, May 20 2019
  

       How else is the generation barrier broken?
wjt, May 21 2019
  
      
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