Category: Double-Ewe Tea Eff (WTF)

That’s “What The [Heck]”.
(“But ‘Heck’ doesn’t begin with ‘F’!” No. No it doesn’t.)

Amateur Soap Microbiology and my new Friend

I thought soap was supposed to be *clean*!

lumpy yellow microbial colonies growing on the soap inside of a hand-soap dispenser
People usually assume soap gets rid of funky microbes that might grow on things, so I was very amused several months ago when I spotted something growing on top of the soap in one of the household hand-soap dispensers. As of today, it looks as pictured at left. That lumpy yellow and brown mass atop the the soap looked to me like some sort of soap-sodden mold, and have been saving the dispenser specifically in the hopes that someday I’d have a microscope and could take a look at it. Meanwhile, the mass spread, and slowly started releasing some kind of yellow pigment into the soap.

Incidentally, I kind of doubt this indicates some sort of failure on the part of the manufacturer of the soap. I don’t recall for certain, but I think I may have opened the dispenser at one point to transfer some of the soap to another nearly-empty dispenser. When the mass started growing originally, it was a single spot, which suggests a single spore or speck of dust floating in and landing on the surface. Hey, it happens. Anyway, I’ve therefore blanked out the name of the manufacturer since I don’t think they really have anything to do with this.

VWR VistaVision Microscope
This mysterious growth upon my soap remained mysterious until today. Thanks to the Minister of Domestic Affairs and VWR (who managed to find me a really good deal), I finally got to actually get a close look at that lumpy mass. Meet my new friend Minnie (pictured at right). I could gaze into those eyes for hours. I couldn’t afford a darkfield condenser, and I sure as heck couldn’t afford to upgrade to phase-contrast gear, but I can add either one later if the opportunity presents itself. I also can’t afford the overpriced proprietary digital camera attachments either, though working around that is a whole other project. Until I identify an affordable model that plays well with Linux or work out how to modify a webcam into an ocular attachment,
I’ll have to settle for a trick…

It turns out if you take a digital camera and set it for close-up photos, you can actually stick the camera lens right up to the eyepiece and often get a serviceable picture.. Now, I had to subject the pictures I got today to moderately heavy processing to bring out the detail a bit better, but at least part of that is just me working on learning how to optimize the camera settings for this kind of use.

Equipped with some surplus slides and cover-slips donated by a kind professor who had some extra packages, I opened up the soap container and smeared a little of the yellow crud on a couple of them. One I just slapped a coverslip on for direct observation – the other I smeared over a slide and let dry with the intention of staining using the tiny, previously-unused vial of methylene blue left over from a very old plastic toy microscope. While the latter dried, I took a look at the wet mount hoping to finally see the mold mycelia that I had been expecting…

There wasn’t enough contrast to bother trying to get a photo, but it was obvious at 400x that what I was looking at was bacteria, not mold. Nerdly joy at learning something by looking in the microscope that I wouldn’t have otherwise known ensued, along with happiness as I realized this meant I had a perfect excuse to dig out my recent shipment from the Maker Shed – materials for doing a “Gram Stain”. Incidentally, the “Maker Shed” had the supplies on the way to me within hours of my ordering it, and they have lots and lots of cool stuff. I highly recommend it. Anyway, I got to do a “Gram Stain” for the first time in a couple of years (and the first time ever outside of a school lab). Want to see?

Mystery Microbe, I see you!

Gram-stained bacteria
Here it is – the nasty yellow goo that infected my bottle of hand-soap. My staining technique was a little off since I’m out of practice – the way I interpret the results is that what I’ve got here is neither a member of the Firmicutes (i.e. “Gram positive”) nor – probably – Actinobacteria. I really can’t guess at more than that, though. I think the few “Gram-positive”-looking cells there are artifacts of insufficient decolorization. I know I still had a surplus of the purple “Crystal Violet” stain still on the slide at the end. (How did I know? I’ll show you at the end…). The irregular bluish bits towards the bottom are, I believe, just bits of stuff from the soap itself.

Meanwhile, this pretty much satisfies my curiousity about the Mystery Soap-Infecting Microbe. There’s certainly a lot more I could investigate, but my developing Hillbilly Biotech lab is really intended to support my interest in intentional food microbiology and perhaps evenutally some small-scale non-food industrial microbiology. I have some remaining curiousity about the yellow pigment and whether or not it might be useful for something, but I’m doubting there is any food or beverage I might want to grow this stuff in and therefore don’t have much use for it. Still, I’ll keep the bottle around for a while before I throw it out in case I think of something fun to do with it. If I end up being really interested in the identity of the bug growing on it, I should be able to find a liquid that I can grow a big mess of it in, then run it through a simple DNA extraction process. Then all I need to do is find someone who can supply PCR primers, a thermocycler, and sequencing services cheap. It might sound like I’m being facetious, but I wouldn’t be surprised these days if I manage to find somewhere that’d do it for $20/sample or less. I may eventually do this will the Mystery Soap Bug anyway, since I hope to be running through this process with cultures of sourdough, yogurt, cheese, vinegar, and brewing microbes that I develop myself. For now, though, it’s just nice to be playing with microbiology equipment again. And now fully independently! Wheeeeeeee!!!!!!

Yes, I’m a nerd. And proud of it!

What’s next?

Now that I finally have a microscope, I no longer have any excuse for not getting to work on the rest of my Hillbilly Biotech lab. Just this weekend I was pricing out Hillbilly Autoclaves. I picked up a cheap air pump and air stone
for potentially building an aerobic bubble-column fermenter (for quick growth of yeast starters or a working model of a “Fring’s Acetator®”-style vinegar generator. I still want to build an ozone generator for sanitization and to get a pH meter. I’d like to also get my hands on some wheat, barley, and rye seeds to sanitize, sprout, and grow here as the first stage of developing a truly local sourdough culture, plus arrange to have several pounds of plain flour irradiated to sterilize it.

I’m also like summer to be over. Yes, I’m writing this in Winter, but it’s not until later in the summer to autumn that locally-grown fruits will start becoming available, and locally grown fruits ought to be an ideal source of local brewing and baking yeasts and bacteria. Finally, I’d like to find a wealthy patron (or matron, I’m no sexist…) who would sponsor me so I could just pursue food-microbe bioprospecting and research full-time…

Oh, yes, and I need to get around to finishing Episode 4 of my little podcast project, especially since episode 4’s topic is a fundamental microbiology technique.

Comments welcome below – thanks for reading!

Oh, and as a reward for getting all the way to the end, here’s a picture that I thought was pretty – crystals of “Crystal Violet” and iodine. I told you I had too much left on the slide…
Crystallized dye left on the slide

A cheap techno-toy concept to distract me from my woes…

A DataMatrix barcode with a 'secret' message...It’s been a relatively awful month here, to tell the truth, but we’re still hanging on so far. Hopefully things will improve soon. In the meantime, I’m having as much fun as I can get away with without spending any real money. Mining old patents for interesting gadgets and ideas, for example…did you know that Google has a US Patent search? And unlike the USPTO, you can actually get a PDF of old patents, not just try to view them as “TIFF” images in a plugin that you may or may not have for your browser and may or may not even work if you do…However, my quest for old designs for industrial brewing equipment and ozone generators is not the subject of this particular post.

One thing I find I like to do for fun with my computer is sort of the opposite of what most people seem to do for fun with their computers. Most people seem to treat their computers as grossly overpriced video-game devices, whose main purpose is to connect people to fake worlds to interact with. “Computer games”. Bah. Humbug. The computer is the game, boys and girls. I like to instead find ways to connect my computer to the real world. I suppose that’s where I get my interest in neogeography, and Asterisk, and home automation (which I’ve only dabbled with but still fascinates me), and so forth.

My latest discovery of a cheap real-world/computer interface is barcodes.

More specifically, I’ve discovered that there’s finally a working project that lets me read and write Data Matrix barcodes. I ran into the project when it was mentioned in the
“New Projects” section of the March 2009 “Linux Journal” (you won’t be able to actually read the article at the link unless you’re either a subscriber, or you wait until they finally open it to the public, though you might also find a copy of the magazine at the bookstore). The actual project in question is libdmtx, and they provide some basic software for generating and, more importantly, decoding these barcodes, which means I can finally actually play with them myself.

There’s an irritating “functional fixedness” issue with these barcodes. There’s an implicit assumption that they are only for one of two things – either they are for inventory tracking (i.e. they encode serial numbers or some proprietary equivalent), which renders them essentially meaningless for anyone but the entity doing the tracking, or they may be used like the QRCode barcodes popular in Japan, which are usually assumed to be used specifically to encode a company’s website URL for “consumers” to decode with their cellphone cameras. Again: Humbug! “Consumers” can go conjugate themselves. “Consumers” are the screwups who made it possible to destroy the world economy, pollute the planet, and make vampire crap a popular “mainstream” genre. No, it’s time we paid a little less attention to catering to “consumers” and gave some love to “participants” instead.

See, both Data Matrix and QRCode barcodes can encode up to a kilobyte or so worth of any kind of data, which might then be stuck in just about any kind of place where someone might see it and take a picture of it (either for immediate decoding or for later).

If this sounds familiar to you, it may be that you remember hearing about a “Hobo Code“, which wandering homeless folks might use to encode visual messages for others with small pictograms. The catch is that since in that context you have to be able to keep the entire “dictionary” of what each symbol means in your head, you’re kind of limited to a small number of specific messages. On the other hand, one ought to be able to hypothetically cram a couple of SMS/”Twitter”-sized messages into a pattern of dots not much bigger than a postage stamp…or conversely stomped out on a giant scale in a wheat field like an especially nerdy “crop circle” just in time for Google Maps’ latest satellite imagery update.

I happened to be at an office-supply store today and was kind of surprised at the variety of things are now available to be shoved through a laser printer. Not only greeting cards and mailing labels, but a variety of self-adhesive and even refrigerator-magnet sheets. I saw they even had blank bumper stickers. Never mind serial numbers and “consumers” websites – you could stick all kinds of messages in all kinds of places with this.

A tip or warning for future diners at a restaurant (“Ask for ‘Chef Special #3’, it’s not on the menu but it’s great!” or “be nice to the waitress or the chef will spit in your food” for example) might be encoded on a small sticker or card and hidden underneath the table. You might encode your personal website URL or just a friendly greeting to be stuck to the inside cover of a Bookscrossing book along with it’s ID number. You might encode a time and place for a meeting as a geostring on printed on little magnetic squares to for members of the Secret Society (or Linux Users’ Group?) that you belong to, or to be included as an “album art” image in the metadata of a geolocated sound or video recording. You might compose original short poems or haiku and leave them in random business-card racks for the bemusement of technically-inclined strangers…

I think the stress must be getting to me, because it’s usually about this point in my thought processes that in a corner of my brain a voice pipes up, saying “What the hell’s wrong with you? This doesn’t sound like you at all! You’re starting to sound like one of those artsy-fartsy techno neo-hippies that gather at things like Burning Man or guest-post at BoingBoing, babbling about nerdy art projects and ‘culture’!”. Then another corner pipes up with “Hey, it might be kind of fun to go to Burning Man one of these years”, and then another pops up with “I like pie!” and everything erupts in chaos. Next thing I know, some indeterminate amount of time has gone by without me noticing and I suddenly realize I’m dangling from a rope over a highway wearing nothing but a pair of SpiderMan™ underpants and a thick coating of cocoa butter, still clutching a handful of LED “Throwies” and looking down at the nice folks offering me a nice warm jacket with extra-long wraparound sleeves…

But I feel MUCH better now…

Am I insane, or can any of you think of other uses for this? Or is that not an “or” question?…

Wells Fargo Bank is evil

Submissions for the next edition of The Giant’s Shoulders blog carnival are due in the next couple of days. I actually had the paper I’m doing for this one picked out last month even as I was submitting last month’s paper on Lister’s experiments with fermenting milk. I expect I’ll have this month’s written up this weekend…but first, partly as a reminder to myself, I just wanted to say Wells Fargo Bank is a greedy evil bastard.

Seriously, if Wells Fargo Bank was a cartoon character, it’d be someone resembling Snidely Whiplash. I can totally hear the corporation saying “If you don’t give me the deed to your ranch I’m gonna throw you on the railroad tracks!” and twirling its evil little moustache.

What prompts this outburst of a blog post, you ask? Well, even if you don’t ask, I’ll tell you anyway.

I got a phone call this evening. Someone from Wells Fargo Bank calling to tell me they were going to mail me something. “Why the heck”, I thought to myself, “do they need to call me to tell me they’re mailing me something? Why can’t they just mail it?” You see, apparently I may be eligible for over a million dollars of death and disability coverage! And I’ll have sixty days to look it over and it won’t cost me anything! Isn’t that great? But still….”Why do they have to call me to tell me they’re mailing me something? Why can’t they just mail it?”

Here’s why: evidently they feel they’re not getting enough “raping people’s accounts with Mystery Fees” income these days…so unless I’m mistaken, this insurance from Wells Fargo is an “opt out” thing. They’re calling because when they say “hey, we’re doing this and mailing stuff to you”, and I say “Oh, okay”….That’d mean I’d just consented to it. If I get busy or the mailing they send gets “lost” and I forget, Wells Fargo gets to automatically start extracting “insurance premium” mystery fees from my account. (No doubt if they happen to do it on a day when my account is low, they get to charge me an overdraft fee along with the insurance premium. Isn’t that great?) Maybe I’m misinterpreting this, but it sure sounded like this was what was going on from the obfuscated sales-pitch script the caller was going through.

I asked them to go ahead and cancel me before even sending out the stuff, since I already have insurance. We’ll see if they honor my request. I was, incidentally, quite cordial with the poor person who has to do this evil crap for a living in the call center. I’ve done tech support, I know what it’s like having to deal with awful crap that’s not your fault…

Anyway, just wanted to mention this in case anyone else has their bank pull this trick – and so in case I forget and they try to send me the stuff anyway, I’ll hopefully see this post again and be reminded to go through whatever obnoxious “opt-out” procedure I’ll have to deal with…

(I’m reminded of when BlockBuster slipped a tiny, folded notice, buried in a full-size envelope with some other stuff, alerting me in tiny print that they wanted to sell my information to junkmail marketers but they wouldn’t if I filled out their tiny little form and mailed it back to them. As I recall, I had to buy the stamp to mail it, too…)

Anyway, I just had to get that out there. I’ll be back to microbiology and biochemistry shortly. We shall begin with another bit of spiffy practical microbiology from the late 19th century…

Double-Ewe Tea Eff: “Modified Food Starch”

A small package of 'Cinnamon Bears' candyOne of my projects is to appease one of my weaknesses. As I’ve probably mentioned before, “Gluttony” is my second-most-favorite deadly sin. If you’ve been listening to “Stir-Fried Random” (new episode coming shortly, I promise) and reading the blog recently, you can probably tell that among my large collection of “a peculiar fondess for [whatever]” attributes that I possess is one for “Cinnamon Bears“. While they’re not too bad as far as candy goes, they’re still not good for me. Plus, like any candy they can get to be kind of expensive. (Dear Amazon.com: The package plainly says “2/$100“. You’re selling these in groups of 12. Now, I only carried my calculation out to 3 significant figures, but I estimate that this should cost $6.00. Not “$6.85”. Plus $7.90 for shipping. $14.75 for $6.00 worth of convenience-store candy is just stupid.)

Anyway…I’ve gotten my grubby paws on a small bag of erythritol, which is effectively a calorie-free sugar alcohol produced from a regular sugar by a natural fermentation process. All I should need is one or more thickening agents and some oil of cassia and/or other flavors and I should be able to come up with a recipe for my own pig-out-all-I-want, even-better-than-mass-market cinnamon bears. Food is one of the few areas that I seem to have any natural artistic talent with, so I ought to be able to handle this.

A bulk bag of 'Modified Food Starch'The trick is going to be getting the right texture. I’ve found recipes online that use gelatin or pectin. The store-bought product, though, uses “Modified Food Starch”. How exactly do they “modify” the food starch? I vaguely recalled that it was an acid-treatment process that partially breaks up the long glucose polymers, but I wasn’t sure. As any modern nerd would do, I decided to ask My Friend, The Internet.

Most places seem to be vague about what exactly the “modification” is, but it became quickly obvious that there were multiple treatments that result in “Modified Food Starch”. Ah, but I was in luck! The Food and Drug Administration actually has a specific entry[1] in the Code of Federal Regulations, which can always be counted on to definitive. So, I went and looked at good old Title 21, Volume 3 of the Code of Federal Regulations and…WTF?!?!?

They list a bewildering array of chemical and enzymatic treatments that all get lumped into “Modified Food Starch” (or “Food Starch-modified” as they quaintly put it).

I guess my happy new box of “Corn Starch” will have to remain unmodified for the time being. At least until I can figure out how to produce my own ?-amylase [without spitting, that is]. I also have unflavored gelatin and pectin at my disposal here, so I’ll come up with something.

Anybody got a good reference on industrial food processes?…

[1] 21CFR172.892