The Maker Shed is Moderately Awesome

I’ve got two blog posts that I want to get done this weekend. This is one of them.

I’m something of a fan of MAKE magazine and its related websites and such, being a frustrated “Maker” and all. “Frustrated” because although I have a strong urge to make things, I seem to have a gross oversupply of chores and issues constantly popping up to keep me from getting much done. Still, I try, despite the efforts of the Dog and five (insert mild profanity here) cats (I seem to have been declared the household “Stuff that goes into and comes out of nonhuman mammal companions technician”), and living space that thinks it’s necessary to demonstrate how entropy works on a constant basis. MAKE’s slogan is “If you can’t open it, you don’t own it”, which I so passionately agree with that I wish they were a political party so I could vote for them.

Anyway…MAKE magazine recently posted a poll asking for opinions on the magazine, the website, and so on. The way the poll was structured didn’t really let me address what I really like and dislike about the site, so I thought I’d post it here in case anyone besides me is interested.

But first, some praise: part of the poll was asking about the online store they run – The Maker Shed. I filled in the poll just a day or so before I went and ordered something from it, so I couldn’t give any opinion of it at the time. Having now gotten what I ordered, I have to say the store seems to be moderately awesome.

One of my complaints about the MAKE franchise is that it often seems to be made entirely of Arduino™ electronics, Arts-and-crafts (e.g. knitted things), and baking-soda-volcano sorts of projects for children. In truth it’s not that bad, but I would personally like to see “less Arduino™, more ‘Bioreactor’” – they actually published a “Bio-hacking“-themed issue a while back, so there’s hope. I bring this up because what they had at the Maker Shed that I bought was microbiological staining supplies (not actually the kit pictured above, but they didn’t have pictures of individual bottles of what I got). I put in my order online expecting it to be shipped the next business day, and was pleasantly surprised to find an “okay, you’re order’s been shipped” notice in my email within an hour or two. The stuff even arrived by that weekend (i.e. today), hopefully leaving me time to use it for my planned second blog post of the weekend. So, definitely fast service at the Maker Shed.

There are a few annoyances I have with the MAKE franchise, though:

  • Their “pod®casts” appear to all be videos (no audio-only podcasts at all)
  • I’d actually really like to have actual no-video-required audio shows that I could listen to on my 2½-hour daily commute. Not all of us want to (or can!) sit and stare at computer and/or “iPod®” video screens but still would like regular infusions of MAKE-related news and information.

  • The videos appear to be all presented in proprietary Apple® formats or proprietary Flash on youtube.
  • This isn’t a major technical problem for me – Mplayer handles the files just fine. However, given that Apple’s preferred formats are all heavily patent-encumbered and proprietary and therefore not really legally usable for “making” video without special paid-for permission from Apple® corporation, it seems an odd choice for the “If you can’t open it you don’t own it” folks. Perhaps they’re just paranoid that Steve Jobs is lurking just on the other side of the bay, waiting for an excuse to come up there and kick their butts if they aren’t pro-Apple® enough? In any case, I’m kind of surprised they seem to have no interest at all in legally-free, amateur-multimedia-maker friendly formats like Vorbis and Theora.

  • Where are the “Food and Drink” issues of MAKE?!?!? (And I don’t mean an Arduino®-controlled Lego® motorized model of a carnivorous cupcake or something, I mean actual edible food and potable brews. Not that “Killer Lego Robot Cupcake” wouldn’t be kind of neat….)
  • There’s enough “kids stuff” to split off into its own publication
  • Or so I believe, anyway. They already split the arts-and-crafts stuff off into its own CRAFT magazine. If they also split off the “make a paper plate toy” stuff to “Make: Kids” (Wait, “making kids” sounds like some kind of pornographic euphemism. Make that “Kids: Make”) there’d be more room for the more hardcore stuff (and a higher chance of more stuff I’m personally interested in).

  • It doesn’t seem like you can log in to comment on the Make blog without an account somewhere else (I USED to have a login directly on the site from when it first started, but that login no longer seems to work and the login screen implies the need to login through some other site’s service. Time to look up how to set up my own OpenID server…)
  • The Maker Faire always seems like it’s awesome but I can never go.
  • This isn’t really MAKE’s fault, unless they’re part of the secret cabal that conspires to keep me from having enough wealth and leisure time to attend things like this.

  • I can’t get this dang cat to quit jumping on my lap while I’m trying to type.
  • Okay, this has nothing to do with MAKE, but it’s annoying me right now.

There – now I’ve gotten it out of my system and out here where if anybody actually cares they can see it. Just some stuff that there was no way to convey in the survey. Otherwise I highly recommend MAKE magazine and its associated online material. The world needs more Makers and they’re doing some spiffy stuff to help in Sebastopol these days.

Now then, if all goes well I should have another post tomorrow with some pretty pictures of soap. Stay tuned…

“Stir-Fried Stochasticity” podcast: pilot episode

Cornelia the Happy Mutt with a tennis ballI’m still not sure I know why I have a desire to push recordings of my voice onto a more or less innocent worldwide population, but I do. And now I have a real theme to wrap an attempt at a podcast (or as I prefer – “oggcast”) around: scientific papers.

I finally got annoyed at press-release-based science stories one too many times, and thought to myself “why does almost nobody who does these stories at least cite the dang thing so I can go look it up and see what’s really in it, if they can’t be bothered to actually read and report on it themselves rather than just the press-release?” The story in question was the recent one about how babies understand dog-language (or something like that). Since I consider the dog to be a philosophical role-model, I wanted to read the actual paper and see if it was as silly as the headlines made it sound or (as I suspected) less flashy but more solid…but even “Science Daily” didn’t cite it.

Finally talking myself out of putting off doing audio recording, I tracked down the original paper, read it, and whipped out a rough show discussing what I found in the paper. I had fun doing it, so I’d like to turn it into a series.

I’ve put up a utilitarian page at http://bigroom.org/stirfry with both a built-in <audio> tag interface and direct-download links for both Ogg Vorbis and MP3 versions.

I’m still deciding exactly how I’m going to decide on the papers to cover – should I pick obscure, forgotten ones that almost nobody else would ever read again without me stumbling on them and talking about them? Classic papers? Papers related to recent news stories like this one? All of the above? Depending on how long I end up trying to make the episodes, perhaps starting with some kind of scientific question and then reporting on a selection of papers I dig up to address the question, or just a selection of papers on the same subject? I’ve already gotten a request for an episode on the theme of prokaryotic extracellular polysaccharides…

The rate at which I can convince myself to try to crank these out (and improve their quality) is directly proportional to how much interest there might be out there in them, so please don’t hesitate to let me know if you think this might be interesting. Please don’t let me slack off! Also, feel free to correct me if I’m wrong about anything I mention in the show or the attached show notes.

If you don’t want to comment here, you can also email me at epicanis at bigroom.org.

Thank you, and good night…

Nerd Reading Spasm!

Did I mention the place I work has some amazingly spiffy perks for a nerd like me?

Last night, I was poking around pubmed looking for references to yeast and erythritol (namely, do yeast interact with it, and will they metabolize it?) I found precisely one relevant reference. From 1975. In a Czechoslavokian microbiology journal. A no-longer-existent Czechoslovakian microbiology journal. Even though it was a journal published in English, I didn’t figure I’d be able to find the article I was looking for. It did turn out that the greedy (insert long string of profanity here) anti-open-access “SpringerLink®” Netherlands organization has an electronic copy of the article…which I can get limited access to for a short time for a mere $34.00. Not going to happen, obviously.

Just in case the college had a subscription that would let me get to the article at no extra cost, I checked. No such luck. But…

…The campus medical science library just two buildings over from where I work has dead-tree editions of essentially the entire journal! Im name des Nudelmonster! Instead of paying $34.00, I got a photocopy of the article for about $0.50. Bonus: As I had hoped, the article[1] reports that erythritol is not metabolized by yeasts, although it is taken up to a small extent. That means I can add erythritol (or xylitol or sorbitol or whatever) to must or wort, and it’ll still be there when the yeast finish, leaving the resulting beverage still sweet. Hooray!

Plus, I was also able to get access to an electronic copy of a review of the uses of poly-?-glutamate[2], which I was bemoaning not having access to over on an interesting Small Things Considered post recently.

Speaking of reading, one thing I really could use are any worthwhile books on the general subject of applied/industrial microbiology, bioprocess engineering, fermentation, and so on. “Worthwhile” here means practical texts that are A)primarily about microbiological processes (as opposed to, say, bioengineering of plants) B)Reasonably technical, and C)Either “not very old” or “very old indeed” (I collect old science books).

I’m not a fan of Amazon.com’s abuses of the patent system, but I’m in a hurry since it’s past my bedtime already. Therefore, purely as a sampling of the kinds of books that sounded interesting to me, here is a selection in more or less random order of books that came up in a quick search on amazon.com. Anybody out there have any other suggestions?

Continue reading Nerd Reading Spasm!

Stir-Fried Random Ep 02:Sex, Violence, and Cinnamon Bears, y’all!

Only about five more days until the next “Giant’s Shoulders” blog carnival. I still need to pick a paper. ARGH!
(UPDATE 20081126: I’ve removed the embedded flash player – it seems to ignore me when I explicitly tell it NOT to automatically start playing rather than waiting until you intentionally hit “play”. Sorry for anyone annoyed by the autoplay. The embedded player will not return until I solve this.)

Meanwhile, here’s this week’s episode of “Stir-Fried Random”, weighing in at a MASSIVE 12 WHOLE MINUTES or so. As before, there’s an “<audio>” tag pointing directly at the Ogg Vorbis audio for those of you running a beta of the Firefox 3.1 series, a recent version of Opera, or (I believe) the current Safari on a system with the Ogg Vorbis Quicktime component installed. There is also the usual embedded Flash®-based mp3 player and direct download links for both versions.

Somebody please let me know if I’m making a fool of myself here… Anyway, here are the show notes:
Continue reading Stir-Fried Random Ep 02:Sex, Violence, and Cinnamon Bears, y’all!

FoodTV’s new “Food Detectives” show…

That’s all I can stands, I can’t stands no more! I had intended to try to come up with another post for this month’s “The Giant’s Shoulders” anthology, but I’ve just encountered such an appalling concentration of disappointing un-science that I cannot restrain myself any further. Guess I’ll have to settle for one post in the anthology this month.

FoodTV’s new “Food Detectives” show sounded so promising. I thought to myself “‘MythBusters’ meets ‘Good Eats’!?!? That would be pure, refined, pharmaceutical-grade WIN!” Then I saw their premier episode. The “experiments” appeared blatantly and badly staged, and in some cases shockingly badly designed. For example, their “experiment” with refrigerator deodorants involved showing a guy sticking his face into a ‘fridge allegedly full of smelly stuff and filming him making faces while they timed how long he pretended to be willing to keep his face in there.

Continue reading FoodTV’s new “Food Detectives” show…

“Ueber die isolirte Faerbung der Schizomyceten in Schnitt- und Trockenpraeparaten”

The Giant’s Shoulders blog carnival is coming up in two days, and I just realized I still haven’t gotten a post up for it yet. So, here it is.

I put up some quick reviews of several classic microbiology-methods papers for the previous edition of this blog carnival, but didn’t actually get around to putting up the one for what is almost certainly the most well-known microbiology technique: “The Gram Stain”. So, this post is about it:

Gram HC: “Ueber die isolirte Faerbung der Schizomyceten in Schnitt- und Trockenpraeparaten”; Fortschritte der Medicin; 1884; vol 2, pp 185-189

That’s “Regarding the Isolational(?) Coloring of Schizomycetes in Cut- [i.e. tissue sections] and Dried Preparations” in “Medical Progress”. The translation hosted by the American Society for Microbiology uses the word “Differential” where I’ve put “Isolational” – which is probably not quite right either but it’ll have to do for now – but I’ll get to that in a moment.

If you’ve ever been exposed to microbiology labwork before, you’ve almost certainly done or at least watched a procedure referred to as a “Gram stain”. In brief, you smear your sample with bacteria on a glass slide and bake it on, then you dump some purple stuff on it, them some brown stuff, then you rinse it briefly with alcohol, then you dump on some pink stuff, and then rinse it in water and look at it under a microscope. Bacteria that stay the original dark purple-blue color of the original purple/brown stuff are considered “Gram Positive”, and those that don’t instead appear the pink color of the last stain, and are considered “Gram Negative”. Many textbook authors and microbiology instructors will breathlessly proclaim that the Gram Stain reveals two “fundamental” categories of bacteria, but I’ll spare you my rant about that.

Properly speaking, this isn’t actually Gram’s stain, as described in his original paper. The modern variations that we’re all taught in microbiology class were developed later, and I believe they are nowadays based mainly on Victor Burke’s 1922 paper on the subject[1].

Regarding the title of the paper: “schizomycete” is what they used to call most kinds of bacteria. “Mycete” meaning “fungus”, as bacteria were assumed to be “plants without chlorophyll” just like molds and mushrooms, and “Schizo-” meaning “split in two”, since bacteria reproduce by splitting into two cells rather than by producing spores like “other” fungi. I say “most” because things like cyanobacteria (“blue-green algae”) or Green Sulfur Bacteria would have been referred to as “Schizophyta” (“fission-plants”). What Gram was originally trying to do wasn’t to differentiate one kind of bacteria from another, either, but to make it easy to tell bacteria from from the nuclei of cells in bacteria-infected tissue.

For that matter, Gram was really metaphorically standing on the shoulders of Koch and Erhlich, as he was building on their technique for staining “tubercle bacteria” – that is, tuberculosis-causing members of the genus Mycobacterium. Gram mentions that you need to stain this type of bacteria for the “usual” 12-24 hours to make this work, incidentally, as opposed to a few minutes for other “schizomycetes”. This suggests that you are expected to have some idea of what you’re going to find before you use the stain, as opposed to the modern implementation which is supposed to tell you something about what kind of bacteria you’re finding.

Still, Gram does report that some bacteria take the stain and some don’t, giving us a preview of the “differential” character of the modern version. He specifically notes typhoid and some causes of bronchial pneumonia fail to hold the stain. Given that Typhoid Fever is caused by a strain of the “Gram-negative” butt-bacter Salmonella enterica, and there are a number of “Gram negative” bacteria as well as “Gram positive” that can cause pneumonia, this makes sense. He also does mention the use of Bismarck Brown R a.k.a. Vesuvine as a counterstain in order to make the nuclei of the infected cells brown in contrast to the dark blue of the infectious bacteria in the tissue.

For much of the century-and-a-quarter since Gram’s publication, the question of why the Gram stain works was thoroughly investigated, and even today I occasionally hear or read assertions to the effect that the Gram Stain isn’t well understood. I disagree with this just as I think its importance to bacterial identification is grossly overblown, and if you want to know why, I have a previous post all about why the Gram stain works and how we know. You may or may not also be interested in an older post regarding whether or not “acid-fast” bacteria like the ones that cause tuberculosis (which don’t stain at all when using the modern version of the Gram stain) are “Gram Positive” or not. As always, if you spot any errors or have any questions, please let me know…

[1] Burke V: “Notes on the Gram Stain with Description of a New Method.” J Bacteriol. 1922 Mar;7(2):159-82.

“Antibiotic Susceptibility Testing by a Standardized Single-Disk Method”

Okay, one last post in the Classic Science Papers challenge before my time’s up:

Bauer AW, Kirby WM, Sherris JC, Turck M :”Antibiotic susceptibility testing by a standardized single disk method.” Am J Clin Pathol. 1966 Apr;45(4):493-6.

Petri dishes containing bacteria, showing inhibition of growth by certain substancesThe “Kirby-Bauer” antibiotic susceptibility test is another standard method that you should cover in microbiology class. The method involves getting a pure culture of the bacteria you want to treat, and then growing it in a petri dish. By putting paper disks soaked with various anti-bacterial substances, you can identify which ones are most effective at killing (or at least stopping) the bacteria in question – for example if you’re trying to figure out what kind of antibiotic to give to the guy coughing up some unknown plague in your doctor’s office… The anti-bacterial substance that the paper is soaked in slowly diffuses into the area around it on the petri dish, getting more dilute the further it gets from the paper. You can then estimate how powerfully anti-bacterial the stuff is by how far from the paper the bacteria stop growing.

The authors here didn’t invent this trick. Not all antibiotic-susceptibility tests are “Kirby-Bauer” tests (the blurry picture there is of an experiment I did involving the beer ingredient hops, and is not a Kirby-Bauer test. Click the picture to go to my “Beer Cures Anthrax” post from long ago…). What this paper describes is a method that finally standardized this test. Instead of having to use multiple paper disks with different amounts of the same substance, the “Kirby-Bauer” test prescribes specific concentrations of each antibiotic, and specific nutrient agar formulations, and so forth, so that determining which antibiotic your mystery bug is best treated with can be done in a way that gives consistent results regardless of who is performing the test.

The method is regularly updated to account for new antibiotics, but is still referred to as the “Kirby-Bauer” antibiotic susceptibility test to this day. Incidentally, the American Society for Microbiology kindly hosts a reprint of this paper as a .pdf file, so you can read it yourself if you’d like.

(UPDATE 20110328: new URL for the reprint of the paper. Thanks, Alex S!)

“A simplified method of staining endospores”

One more for the “classic papers” challenge:

Schaeffer AB, Fulton MD: “A Simplified Method of Staining Endospores”; 1933; Science; 77; pg 194

If you take a microbiology lab, this is the endospore staining technique (or “technic” as they used to spell it) that you’ll practice. This is a nice, simple, one-page paper. Alice B. Schaeffer and co-author Mac Donald Fulton describe a few of the other variations on endospore staining techniques, then describe how they’ve further simplified what they felt was previously the simplest one, described by a Mr. Wirtz in 1908.

“Endospores” are a sort of “escape pod” for certain specific kinds of bacteria. Unlike spores formed by yeasts and molds, these are not reproductive – each bacterium only produces one thick-coated spore, into which it shoves it’s genetic material and a few vital enzymes to get itself going again later when the spore finds itself in favorable conditions.

Since only a few kinds of bacteria produce these endospores, if you see endospores in your unknown bacterial culture it goes a long way towards helping to identify the bacterial species, so having a simple method for staining your bacteria so that endospores are obvious under a microscope is helpful. (Of course, these days most of us would rather just get a 16s rDNA sequence with PCR, but never mind that for now…)

Endospore stain under a microscope (via Wikipedia)Evidently, Wirtz’s original method involved using Osmium Tetraoxide (“osmic acid”) to stick the bacteria to the slide before staining. Not only is that stuff poisonous, it’s also expensive. I found a site selling sealed glass ampoules containing 1 gram each of this stuff for $35.00 each. Schaeffer and Fulton’s method does away with this in favor of much cheaper and easier heat-fixing (just as is done with the Gram stain and others). They use the dye “Malachite Green” for the initial stain, and steam-heat the dye-covered bacterial slide a few times to sort of “cook” the dye into the thick-walled endospores if they are there. Rinsing then washes the dye out of everything but the endospores, and a light red dye (safranin) is added as a counterstain. The end result is that under the microscope you’ll see light-red bacteria. If any of them form endospores, you’ll be able to see them as smaller green dots – sometimes still bulging inside of bacterial cells, sometimes floating around freely having escaped from the now-empty bacterial cell.

The “Schaeffer-Fulton Endospore Stain” is pretty easy to do, though the occasionally messy steambath part can be annoying. The method is pretty resistant to errors, so it’s not too hard to get good results even if you’ve never done it before.

Incidentally, you can buy Malachite Green at many pet stores – it’s still used as a treatment for “ick” (Ichthyophthirius infestation) in tropical fish.

Hmmm…still a couple of hours before it’s not longer May – Perhaps I can throw in one last post before time’s up…

“They laughed at me! But I’ll show them all! AH, HAHAHAHA!”

Another T-shirt to add to my list of T-shirts I want.

I’m spending more hours shoveling my way through the books and papers and crap we’ve got up here at House v1.0, since if all goes well I’ll be making a brief run back down to Southeast Texas so we can sign the papers for House v2.0 down there, at which point we’ll be able to start actually moving. I sure hope this one goes through. Not only is it our third attempt to buy a house down there, but I’ve already identified a convenient location to build my “Intentional Food Microbiology” brewlab in it.

Since there’s no way I can afford to buy a -80°F freezer, I have an obvious interest in alternate means of preserving the yeast, mold, and bacterial cultures that I want to keep. To me, drying seems like the most desirable method when it’s feasible, since dried cultures should require the least amount of maintenance. After a several-month delay, I’ve finally gotten around to getting back in touch with the archivist at Brewer’s Digest to see about getting an old article on the viability of dried yeast cultures[1].

Speaking of old but useful scientific papers, there’s an extremely nifty challenge going on through the month of May (deadline: May 31st) over at “Skulls in the Stars” blog: find a classic scientific paper, read it, and blog about it.

“My “challenge”, for those sciencebloggers who choose to accept it, is this: read and research an old, classic scientific paper and write a blog post about it. I recommend choosing something pre- World War II, as that was the era of hand-crafted, “in your basement”-style science. There’s a lot to learn not only about the ingenuity of researchers in an era when materials were not readily available, but also about the problems and concerns of scientists of that era, often things we take for granted now!”

I think this is a brilliant idea – the classic papers often seem to be forgotten and often explain things that people seem to take for granted these days. I already mentioned my post about the Gram Stain (original paper published in 1884), though that post really talks more about what has happened with the Gram Stain over the last 125 years rather than only being about the original paper. There are a couple of other classic microbiology papers that I’m going to try to get to if I have time before the May 31st deadline arrives.

I also need to get some yeast activated and get my must processed – I’m hoping a brief boil will reduce the amount of a yeast-inhibiting substance in it. I’ll post more detail after I get it going.

[1] Wickerham LJ, AND Flickinger MH:”Viability of yeast preserved two years by
the lyophile process.” 1946; Brewers Digest, 21, 55-59; 65.