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…

A secret message for Climate-Change Skeptics..


I admittedly find it hard to believe that such a large proportion of scientists in any field, climatology or otherwise, could actually conspire together to pull off this big of a hoax when at all other times they’re competing pretty intensely against each other for funding and attention. Heck, most of us mad scientistsGrumpy Visionaries would sooner give up our armies of Atomic Robot Zombie Clones than share credit for scientific discoveries. Still, I’m just cynical enough to believe that it’s not impossible. Even if it’s true, though, I don’t care, because something unprecedented and very important is happening right now, and there’s no way we’re likely to ever have this chance again.

To those of you reading this who agree that something needs to be done about “Climydia” (hat-tip – if I wore a hat – to Justin Jackson of “This Week in Science” for this neologism; a combination of “Climate” and “Chlamydia”, if it’s not obvious, making “Global Warming” a metaphorical embarassing but hopefully curable disease): you can stop reading now. I agree. We must do something about it. It is a serious problem and needs to be corrected. The rest of this post is for those who don’t agree. Go ahead and click away. Don’t worry, I’ll tell the deniers off, you can go read something else now. Thanks.

Continue reading A secret message for Climate-Change Skeptics..

Eggs suck.

Don’t misunderstand – I like all kinds of foods made with eggs. Eggs are tasty. They’re handy. They’re nutritious, too. Their protein is so good they are the standard against which nutritionists have historically compared other food proteins. As a bonus, a medium-sized egg contains only one-eighth the cholesterol in a single ounce of human brain (and is much less likely to give you kuru).

However, could it be possible to come up with a more inconvenient packaging scheme? This thing was obviously designed by someone that hates us. “Let’s see, we’ll make it tasty and very nutritious. But just so people don’t think we like them, we’ll make it the consistency of snot, and package it by sealing it inside a specially-made, inedible brittle container so that you have to literally smash the thing open to get at the food, ensuring that the consumer* gets nasty goo all over his or her hands, or gets shards of the container mixed in with the food, or both. That’ll show the little jerks. And if that’s not enough, we’ll also have that container extruded out of a chicken’s butt.” (For some odd reason, as I write this, I’m picturing an Evil Santa Claus giving a presentation to the Evil Elves who are about to go off and implement this idea…”Sneezy, Drippy, and Runny – you three will head up the design committee…”)

They’re not screw flies or anything, but perhaps eggs can still count as an example of “irreducible grotesqueness”. (The picture, in case it isn’t obvious, is an egg separator. The image is linked to the site where you can buy them.)

This short rant has been brought to you by I’m-Making-Too-Many-Egg-Based-Meals-Lately Industries. That, and a second test to make sure I’ve got the DNS issues that I initially had resolved now. Can you all see this? I’d be thankful if everyone who was seeing this would post a quick “yeah, I see it” in the comments so that I can get on with the real posts again.

* Am I the only one who finds it insulting to be called a “consumer”, as though I were nothing more than a gaping mouth with a wallet? Am I sitting here mouth agape like a baby bird, waiting for a “supplier” to stroll by, grab some money out of my wallet, and cough up some “product” for me to “consume”? (I contend that I am not a “consumer” but a active participant in this economy, dagnabbit!)

SHENANIGANS! Caffeine is our FRIEND!

Our new Asylum has real internet finally now and we’re getting settled in. The Houston area here is one of the most hot and humid areas of the US. All hot and sweaty. So of course I’ve been advised that my favorite psychotropic substance – 1,3,7-trimethylxanthine [“caffeine” for party-poopers who aren’t into the fancier names] – is no longer my friend, because it’s a diuretic that’ll dehydrate me, right?

NO! Shenanigans! Caffeine is our FRIEND! And that stuff about it being a diuretic? CRAP! LIES AND SLANDER!

But don’t just take my word for it. After all, humans are a bunch of freakish multicellular soft-celled eukaryotes, and I normally focus on normal organisms like bacteria, archaea, and yeasts. So, let’s ask some real human-physiology type scientists and check out their official peer-reviewed findings:

Armstrong LE, Pumerantz AC, Roti MW, Judelson DA, Watson G, Dias JC, Sokmen B, Casa DJ, Maresh CM, Lieberman H, Kellogg M: “Fluid, electrolyte, and renal indices of hydration during 11 days of controlled caffeine consumption.”; Int J Sport Nutr Exerc Metab. 2005 Jun;15(3):252-65.

“[…]The following variables were unaffected (P > 0.05) by different caffeine doses on days 1, 3, 6, 9, and 11 and were within normal clinical ranges: body mass, urine osmolality, urine specific gravity, urine color, 24-h urine volume, 24-h Na+ and K+ excretion, 24-h creatinine, blood urea nitrogen, serum Na+ and K+, serum osmolality, hematocrit, and total plasma protein. Therefore, C0, C3, and C6 exhibited no evidence of hypohydration.[…]”

Abstract on Pubmed

Armstrong LE, Casa DJ, Maresh CM, Ganio MS: “Caffeine, fluid-electrolyte balance, temperature regulation, and exercise-heat tolerance.” Exerc Sport Sci Rev. 2007 Jul;35(3):135-40.

“[…]This review, contrary to popular beliefs, proposes that caffeine consumption does not result in the following: (a) water-electrolyte imbalances or hyperthermia and (b) reduced exercise-heat tolerance.”

(Review article, apparently – Abstract on Pubmed)

Del Coso J, Estevez E, Mora-Rodriguez R: “Caffeine effects on short-term performance during prolonged exercise in the heat.” Med Sci Sports Exerc. 2008 Apr;40(4):744-51.

“[…]RESULTS: Without fluid replacement (NF and NF + CAFF), subjects were dehydrated by 3.8 +/- 0.3%[…]CONCLUSION: During prolonged exercise in the heat, caffeine ingestion (6 body weight) maintains MVC and increases PMAX despite dehydration and hyperthermia. When combined with water and carbohydrate, caffeine ingestion increases maximal leg force by increasing VA (i.e., reducing central fatigue).”

(“NF” = “No Fluid replacement” – the “dehydration” mentioned here is due to exercising in the heat, and doesn’t appear to be related to whether the test subjects consumed caffeine or not)

Abstract on Pubmed

Scott D, Rycroft JA, Aspen J, Chapman C, Brown B:”The effect of drinking tea at high altitude on hydration status and mood.” Eur J Appl Physiol. 2004 Apr;91(4):493-8. Epub 2004 Feb 11.

“[…]Several markers of hydration status were also taken immediately pre and post each condition, including measures of urine specific gravity, urine electrolyte balance (K+, Na+), and urine colour. None of these measures indicated a difference in hydration status as a result of the dietary intervention in either the control or tea condition.[…]”

(In this study, the tea was the only caffeine-containing substance involved. The study group’s caffeine came solely from the tea. The control group got no caffeine at all.)

Abstract on pubmed

Paluska SA: “Caffeine and exercise.” Curr Sports Med Rep. 2003 Aug;2(4):213-9.

“[…]It[caffeine] is relatively safe and has no known negative performance effects, nor does it cause significant dehydration or electrolyte imbalance during exercise.[…]”

Abstract on Pubmed

Grandjean AC, Reimers KJ, Bannick KE, Haven MC.: “The effect of caffeinated, non-caffeinated, caloric and non-caloric beverages on hydration.” J Am Coll Nutr. 2000 Oct;19(5):591-600.

“[…]This preliminary study found no significant differences in the effect of various combinations of beverages on hydration status of healthy adult males.[…]”

Pubmed entry – full text available

See? Oh, I know what you’re going to say next – “But, like, dude! When I drink my Venti Mocha Crappucino [note: Link goes to “Foamy the Squirrel”, who is a bit of a pottymouth, ranting about the “Tall/Grande/Venti” nonsense.  It amused me.] or a can of Jolt Ultra I have to take a major whiz a little while later! Isn’t that ‘cuz of the caffeine?” Well, no, it isn’t. It’s because you just drank a bunch of liquid. Duh.

So, you see, caffeine really is our friend. Be nice to caffeine. But don’t feed it to your yeast in the presence of benzoic acid because it’ll kill them. See? I managed to turn this into a segue back to the stuff I was talking about before the whole “buy a house in Texas” thing started interfering. Stay tuned…

Was it a mistake to buy Magellan GPS? Stay tuned…

A dead Magellan eXplorist 600 GPS unitWell, the good news is that after calling their support line and trying the three-button-reset ritual that I hadn’t known about, my Magellan eXplorist 600 is still completely dead. They did not give me any hassle about replacing the unit, they just gave me an RMA number. My dead eXplorist was sent to their “Repair” center in Fort Worth, TX this afternoon. A replacement should arrive in about a week to a week-and-a-half.

The bad news is that Magellan has discontinued the $350 eXplorist 600 (and the rest of the eXplorist line) and insists that they can only offer their newer $250 Triton 500 as a replacement. I’ll withhold judgement on whether to be ticked off at the $100 of retail value that is being lost here until I see the specifications. It looks at first glance that the basic capabilities really are pretty much the same, so it may turn out okay…except for the most important feature by far, which I originally chose the eXplorist for in the first place: documented data formats.

The Triton series GPS’s appear to use a bizarre, undocumented file format, completely different from the documented format of the Meridian and eXplorist models. This means that as of right now, a Magellan Triton owner is not permitted to work with their OWN DATA without going through a proprietary, Microsoft-Windows-only GUI package, which ironically apparently uses GPSBabel to do file conversion. GPSBabel doesn’t support the Triton formats since there is no information available on how to read and write them yet. Since I have no Microsoft Windows machines anywhere, this means the shiny new Triton 500 (which I – seriously – can’t stop thinking of now as the “Magellan Vista”) will be nothing more than a highway map that requires batteries unless their proprietary “VantagePoint” software will run under WINE.

I’m hoping that they’ve merely been busy and will soon get around to adding this units specifications to their “Interface Solutions” information. This is where the openly-published file format (and communication protocol) specifications which were highly (and rightfully) praised by the GPSBabel project are made available for the now-abandoned Meridian and eXplorist units. If the GPS data I work so hard to obtain remains locked inside the proprietary format, only accessible at the whims of Magellan and Microsoft, I’m going to be extremely peeved. If, on the other hand, GPSBabel soon gets the information necessary to add support for the Magellan Triton line, the only serious complaint I have with all this will go away. Honestly, if I can at least get enough documentation to write my own simple waypoint, track, and route reader for their Triton files I’ll be happy.

I think a real, old-fashioned letter, printed on dead tree and everything, mailed to their corporate HQ is called for…

Anybody out there have any experience dealing with Magellan corporation? I’d like to think they want to do the right thing…

I’m not a real hillbilly, but I play one on the internet…

My first “Will It Ferment” project is now in process.

See, I’m stuck with a somewhat unpredictable schedule and a need to travel frequently, cramped spaces to work in at the moment, and a streak of gustatory perversion that I just can’t help an urge to rebel against purists at the moment.

Quick bit of background on that latter statement: I’ve noticed that people seem to think there are only two-and-a-half kinds of “real” non-commercial fermented beverages. There’s beer (which is apparently defined as a strong tisane of hops, flavored by mixing it into fermented malt), there’s wine (which is always made of grapes of course), and out on the fringes of respectability is Mead (“Honey wine”) which seems to be slowly gaining some acceptance as a mildly exotic brew. The attitude is that anything else you might want to brew (say, a beer flavored and preserved with something besides hops, or a wine made out of anything but grapes) is probably some quaint “country” (i.e. hillbilly) thing for people who either live too far from civilization or are too poor to just buy a “real” beverage, or are too ignorant to know the difference. Either that, or it’s just some desperate attempt to make something to get drunk on. Might as well be making pruno.

The attitude kind of annoys me, so I’m trying to make a sort of “free person’s pruno”. I figure if the end result is as palatable as it could be, it’ll probably resemble “Zima®”.  Uh, no, I don’t expect it to be great – this is merely an experiment.  My must has an Original Specific Gravity (“O.G.”) of approximately 1.054, about the same as most lagers start out. As I write this, my gallon of must is on the stove in a stainless steel pot. I’m going to try to heat it to boiling and let it boil for a few minutes in hopes of driving off much of the benzoic acid in it, so as not to inhibit the yeast fermentation.

To your right, you should see the ingredients used in this project. Yes, those two bottles in the background are there on purpose. I’m trying to make…Mountain Dew® Wine.

Here’s the plan:

  • Last night, I took a couple of clean glass 1 Qt milk bottles, rinsed them with iodophor solution to sanitize, let them dry. Then, I put about 12 ounces of tap water (unchlorinated) into one and dumped the contents of both yeast packets you see in the picture into it to rehydrate.
  • The yeast packets were opened over a year ago – I don’t even recall what I did with the tiny amount of yeast I poured out. They’ve been sitting in the ‘fridge since then. What’s more, they had expired in December of 2006 to begin with.
  • The two yeasts (Red Star Montrachet and Red Star Flor Sherry) were both mixed into the same container in hopes that I could encourage a yeast orgy, giving me as much genetic diversity as possible from the two strains and maximizing the chance that I’d be able to get a culture which can grow in flat Mountain Dew and whatever benzoic acid (from Sodium Benzoate) might remain in it. I had read that V8 juice was actually an excellent medium for inducing yeast sporulation. Since sporulation occurs as a result of yeast cells mating, I made a huge leap of logic towards thinking the V8 might maximize my chances of getting some yeast mating going on.
  • After a few minutes to rehydrate, I dumped the 12-ounce can of V8 into the bottle and shook well. I also crushed up a children’s chewable vitamin (see bottle at lower-left) and a small portion (perhaps 1/5) of a capsule of the L-Arginine as a nitrogen source and added them as well. I then poured it back and forth between the two bottles a few times to aerate, then split the mixture between the two bottles, capped loosely, and went to bed.
  • As of this morning, fermentation was obviously occurring in the mixture, so sitting in my fridge open for over a year hadn’t killed off ALL of the cells. I opened the bottles and swirled to re-aerate, and added about a tablespoon of “corn sugar” (glucose a.k.a. dextrose) to wake the yeast cells back up. Since then, I’ve been pouring a bit of Mountain Dew right out of a third bottle into each of the yeast starter bottles every couple of hours. The amount of bubbling I see suggests to me that fermentation is still going on (and is not just from the carbonation of the Mountain Dew). Hopefully this will help the yeast culture acclimate a bit to the benzoic acid.
  • I dumped the other 2 2L bottles of Mountain Dew into a stainless steel 8-qt pot and heated to boiling, whisking with a steel whisk frequently to help get the dissolved gases to bubble out (hopefully along with some benzoic acid in the steam). At this moment, it’s up to 75°C (about 165°F) according to the thermometer I have stuck in it. It’s steaming a bit, and I can smell some of the citrusy aroma boiling off, unfortunately. I was afraid that’d happen. UPDATE: our ancient stove with one working burner seems to have trouble getting this much liquid above 200°F without cranking it up all the way and risking the bottom getting too hot. Since there’s a substantial amount of hot water vapor coming off, I’m going to hope that’s carrying away some benzoic acid and just let it start cooling down. I’ll stir it vigorously and frequently with the whisk until the temperature drops to about 160°F and then I’ll cover it for the night.
  • Meanwhile, before I go to bed, I’m going to recombine as much of the two yeast culture bottles as I can into one bottle, then rinse out the other. In that one, I’ll mix up about 12 ounces of tap water and enough corn sugar to reach a gravity of about 1.050-1.055. I’ll crush up another chewable vitamin and about half of the remaining arginine capsule into it, mix well, and warm it with a quick spin in the microwave (no exact measurements, just until it’s “obviously warm” to the touch after mixing). Then I’ll shake the V8 culture well to mix, and splash about a tablespoon’s worth into the new bottle.
  • In the morning, I’ll re-aerate the new culture and add a tablespoon of corn sugar to wake it back up, then once it’s going, I’ll start adding the now-cooled cooked flat Mountain Dew to it in small increments. Assuming it keeps going, I’ll dump in the remainder of the L-Arginine capsule, crush in one last chewable vitamin, and them combine the new culture with the rest of the cooked flat Mountain Dew in a nice plastic 2-gallon “water” container that I picked up (already rinsed with iodophor and dried). Cap it with a latex glove attached with a rubber band as described in the “Pruno” entry in Leon Kania’s “Alaskan Bootlegger’s Bible” (Click image for link) just because I thought it was the funniest airlock design I’d ever run into. Yes, I am easily amused.
  • If I’m lucky, there’ll be so much live and active yeast in the second culture at that point that the fermentation will finish quickly, because I’m driving to Texas the following day. Alternatively, I may be lucky and the remaining benzoic acid will slow the yeast down, so I can safely leave it fermenting (sitting in my sink in case of overflow while I’m gone) for the week that I’ll be gone.

If I’m UNlucky, either it won’t ferment at all (and I can then use it to try to develop a Mountain Dew Tolerant strain of yeast), or it’ll ferment but taste utterly disgusting (in which case I can use it to try to obtain some Gluconobacter strains and make Mountain Dew Vinegar), or it’ll be “infected” and will already BE Mountain Dew Vinegar, which would also be pretty funny anyway. So, other than completely unforseen results, this experiment can’t be a TOTAL waste.

[Update 20080727: Preliminary results of this perverse project may be read In this more recent post…]

I Hate You, Carl Zimmer!

Carl Zimmer wrote a book. Of course, that’s no reason to hate him, and I don’t hate him for that.

His book is all about Escherichia coli (“E.coli”). The friggin’ “Microsoft” of the biotech world. Accursed E. coli, hogging up all the print space and protocol development and sucking up electricity for -80°F freezers. I mean, come on people! You could be doing transformation of B. subtilis and related organisms instead, which form nice, sturdy endospores which you can dry out and keep in an any cool, dry place, no -80°F freezer needed! Or you could use something like Agrobacterium tumefaciens, and as a bonus be able to then transfer your nice transformed genes into plants, too! But NOOOOOooo….it’s always “E.coli, E.coli, E.coli.” DAMN YOU, E.COLI!

Of course, none of that is Carl Zimmer’s fault, either, so this is also no reason to hate him.

Now, if his book was lousy, that MIGHT be a reason to hate him, but as far as I can tell there’s no reason to think the book is lousy, so this is no reason to hate him either. In fact, that’s kind of the problem.

No, the reason I Hate Carl Zimmer is that he’s written a book about friggin’, stage-hogging E.coli…and I want it. (Well, a copy of it anyway.) It sounds like a very interesting book. I feel like a Republican who wants a copy of “The Audacity of Hope”. Or a Democrat who wants to plan a vacation to visit the George W. Bush Presidential Library. The cognitive dissonance torments me, and it’s all Carl Zimmer’s fault! CURSE YOU CARL ZIMMER!

Okay, got that out of my system. A review might follow eventually if I manage to get a copy of the book. Meanwhile, for a change of pace, anybody want to hear about my Asterisk setup? Or should I just get back to the fermentation stuff?

P.S. Here’s a bit of trivia for you: “Frig” is apparently an old-English word meaning “to wiggle”…

Make it stop!

Specifically, I think I’m getting a severe case of Noel poisoning.

One of the things I hate most about Christmas is the incessant “re-imaginings” of the same handful of accursed songs, generally done in the same awful forced pretend-emotional tone.

They’ve got “The First Noel” playing in the style of a late-1950’s/early-1960’s Disney Choir style. On a loop. For the last half hour so far.

Ugh. Make it stop…

Thank the Noodly One for headphones, Amarok, and the collection of hard bouncy techno music that happens to be on Igor here…

I’m down to the last class of the last week prior to next week’s finals, so I should have time for a real post again soon…

Libel! Blasphemy! Slander!…

Injustice! Perfidy! HUMBUG!

Periodically, someone puts up a “could you pass a grade-school science class” quiz. The one linked to the image below goes to one that I just broke down and took, purely out of curiousity. Take a look at this outrage!:

JustSayHi - Science Quiz

Oh, sure, it LOOKS good, but what you don’t see is that it only gave me a 96%, implying that I missed one (it was a short quiz)! Sure, the quiz was very much in the modern fashion for “standardized testing” (aka the “No Child Left Awake” project) where the emphasis is on memorizing stuff for a test rather than actual comprehension. So, I thought, maybe I hadn’t correctly memorized which word was correct for one of the word-memorization questions. But, no, according to the “answer sheet”, the one I supposedly got wrong was this one:

(Note: If you’re planning to actually take that quiz, do so now before you read on and I give away one of the answers…)

“How do mammals respire?”

The options were:

  • Aerobically
  • Anaerobically
  • Both aerobically and anaerobically

Come on, I may hardly ever concern myself with perverse eukaryotic systems but…never mind just “mammals”, as far as I know, all eukaryotes (animals, plants, and fungi) only possess aerobic (oxygen-requiring) respiratory systems.

However, the “answer sheet” for the quiz claims that the answer is “Both aerobically and anaerobically”.

So….they’re wrong. I’m pretty sure what what they were intending to ask, given this answer, is “what kind of metabolism do mammals have?”, in which case their answer is correct.

See, “respiration” is only one part of the cellular energy-generating system. Specifically, it’s our friend, the Electron Transport Chain, which (to grossly oversimplify) harnesses the energy of oxygen sucking electrons off the end of the chain various biochemicals to recharge molecules of ATP. That’s not the only way a cell can get ATP, though. What the quiz authors are presumably alluding to is that there are non-oxygen-requiring biochemical pathways that animal cells can take to make energy – such as the one your muscles use when they can’t get enough oxygen, which involves production of lactic acid, which in turn gets blamed for the “burn” sensation you get when you work your muscles hard.

So, the authors of this quiz are bad, bad people, besmirching my reputation and harming my precious self-esteem by giving me less than 100% on that quiz!

On a related subject: breathing causes cancer in Sprague-Dawley™ rats!

No, seriously, it’s true – try raising one group of Sprague-Dawley™ rats with air, and one group with no air, and examing both populations 150 days later. I guarantee you’ll find many more cancerous growths in the “with air” group than in the group that was denied air to breathe…

What brought this outburst on? It was this blog article. “No, It’s for Real: Aspartame Causes Cancer”, the post proclaims. They’re talking about This study(pdf). Go ahead, take a look, but in particular, look at the tables of actual data, not the paper’s abstract. In particular, take a look at Figure 1, especially “D” and “E” (showing survival rates for the different groups of Sprague-Dawley™ rats as the study progressed), and at the number of “tumor-bearing animals” in Table 2.

Notice that at around 120 days on the survival graphs, the groups with the highest percentage of members still alive were the groups receiving the most aspartame in their feed. It’s worth noting that the highest-Aspartame group there was getting roughly the equivalent of a human drinking <em>thousands</em> of cans of diet soda every day. Also note, in fairness, that both graphs seem to show little difference between the groups, so rather than assuming that Aspartame makes Sprague-Dawley™ rats live longer, I would tend to assume that there’s really not much difference.

Notice also that in terms of the percentage of Sprague-Dawley™ rats that developed one or more tumors, there were fewer of them in the group that got the equivalent of 500 mg/kg of aspartame: which scaled up to human terms means about 200-250 cans of diet soda EVERY DAY worth of aspartame.

You may be wondering why I keep mentioning Sprague-Dawley™. It’s because this is a particular commercially-bred strain of rat that’s popular with labs for this kind of thing. One point that isn’t always mentioned is this: Sprague-Dawley™ rats are known to be prone to developing cancer spontaneously. This can be handy if you’re doing studies of “borderline” carcinogens. The hope is that if something has even a tiny ability to cause cancer, you’ll be able to measure the effect in a population of critters known to get cancer at the drop of a metaphorical hat, when in a human population the incidence might be so rare that you can’t distinguish it from random chance. To my admittedly-not-big-on-the-biochemistry-of-perverse-eukaryotes mind, this study really seems to show that there’s little or no effect – and certainly no dose-dependent effect – of aspartame even on cancer-prone lab rats.

I don’t know what it is, but “artificial sweeteners”, and especially aspartame, seem to generate such passionate hatred in some people. It reminds me a great deal of people’s reactions to “genetically modified” crops. People just really want to hate it. The authors of this paper are obviously trying REALLY hard to show somehow that aspartame is a dangerous poison, despite the inconclusive-appearing actual results. Though I suppose one could argue that they showed Aspartame to be at least as much of a deadly poison as Expired JellO®.

And now that I have exposed my readers to several times the Recommended Daily Allowance of Humbug, I bid you all a good night – I have Art History and Philosophy to attend in the morning…

The Gram Stain Post to End All Gram Stain Posts

Gram stain, Gram stain, Gram stain! Bah. I think it’s time Microbiology grew up and moved out of Medicine’s basement.

Sure, the Gram stain[1] has its uses, but the procedure is grossly over-hyped. “[…]the most important stain in microbiology[…]”[2]! “[…]it is almost essential in identifying an unknown bacterium to know first whether it is Gram-positive or Gram-negative.”![3] “The Gram Stain reaction is an especially useful differentiating characteristic.[…]The Gram reaction turns out to be a property of fundamental importance for classifying bacteria phylogenetically as well as taxonomically.”![4] “[…]differentiates bacteria into two fundamental varieties of cells.”![5] “The Key to Microbiology“![6] [emphasis added…]

Bah! Sure, the Gram stain has its uses, but the hype it gets (even 125 years after its invention) is ridiculous. It’s worse than Harry Potter!

You really want to know what the Gram reaction tells you? Really? Okay, here it is:

A “Gram Positive” reaction tells you that your cells have relatively thick and intact cell walls

A “Gram Negative” reaction tells you that they don’t.

That’s it. That’s about all you can reliably infer from the Gram stain.

Previously, I put up a post describing what was my understanding of the conventional view of why the Gram stain works. Today, I’ll give you a much more detailed – and more correct – explanation of why it works as well as what its real significance is to identification of microbes. But first, a brief one-paragraph rant on why I think the Gram stain has such a hold on microbiology teaching.

I blame the fact that microbiology education is still largely in the shadow of medical technology education. When you artificially exclude the 99+% of organisms that aren’t associated with human diseases, the tiny number left do, indeed, seem to largely separate into two phylogenetic categories. Judging by what I’ve encountered thus far, it seems you get a lot of Proteobacteria (especially ?-Proteobacteria, like E.coli), which are “Gram-negative”. You also get a lot of Firmicutes (Bacillus, Streptococcus, Staphylococcus, etc.), and a couple of scattered Actinobacteria (Mycobacterium, for tuberculosis and leprosy, Corynebacterium for diptheria…). Both of these are considered “Gram-positive” (although if you use the standard procedure these days, the Mycobacteria may show no reaction at all). That’s, what, 3 phyla out of about 25 eubacterial and archael phyla? If we throw in Syphilis and Chlamydia, that’s still only 20% or so of the currently recognized prokaryotic phyla. If your microbiology classes assume everybody is training to be a medical technologist or clinical microbiologist, then the Gram stain becomes inflated in importance.

Enough of that – here’s a quick review of how the Gram stain works. Solutions of “Crystal Violet” (a purple dye) and Iodine are applied to cells fixed to a slide, where they soak in and precipitate in the cells. A “decolorizer” (usually ethanol) is applied to see if it will wash this dye precipitate out of the cells. A different, lighter-colored dye (such as safranin) is added so that the cells which DO have their dye washed out can be seen as well. In the end, “Gram positive” cells are a dark purple from the crystal violet/iodine that was not washed away, and “Gram negative” cells are not dark purple. (Usually they are pink, from the safranin, assuming that’s the dye used as the counterstain.)

Note that this does not differentiate cells into “two fundamental types” as is often claimed. You actually get four types: Groups of cells that are normally always “Gram positive”, Groups of cells that are normally always “Gram negative”, Groups of cells that are normally sometimes “Gram positive” and sometimes “Gram negative” (“Indeterminate”, or as I like to call it, “Gram-biguous”), and groups of cells that are normally NEITHER Gram-positive nor Gram-negative, like Mycoplasma, which aren’t dyed at all by the process. Incidentally, phylogenetically speaking, Mycoplasma is one of the “Gram positive” Firmicutes, just like Bacillus and Staphylococcus.

It’s kind of interesting to me that the Gram stain reaction has been such a mystery up until a century after its invention. What is it that makes “Gram positive” cells retain the dye while “Gram negative” ones don’t? Along the way, it seems like nearly every part of the bacterial cell was hypothesized to be the reason for the Gram reaction – lipids, carbohydrates, nucleic acids, “Magnesium ribonucleates”, and so forth. Davies et al, 1983, includes a table listing many of these and referencing historical papers making the claims. The fact that the reaction had something to do with the cell wall seems to go back quite a while, though the “Magnesium ribonucleates” idea doesn’t seem to have been entirely abandoned until the mid-1960’s[7]. It was also hypothesized that the “Gram positive” cells simply absorb more dye and therefore take longer to “decolorize”.

It turns out that “Gram-positive” cells actually don’t, necessarily, take up more dye than Gram negative ones. This was tested by taking a set concentration of bacterial cells and adding them to a set concentration of dye. After letting them soak, the samples were centrifuged to remove the bacteria, and the amount of dye found to be missing from the liquid was taken as the amount absorbed by the cells. They found that some Gram negative cells actually took up more dye than the Gram positives did. So much for that idea.[8]

Even relatively recently, I’ve seen it written that the bacterial cell wall, specifically, is what holds onto the stain, but even that turns out not to be true. Although the cell wall is the structure that seems to be responsible for the Gram reaction, in the late 1950’s it was demonstrated that it was not actually the staining of the cell wall that caused the reaction, but rather the ability of the cell wall to keep the decolorizer out of the cell.[9]

Apparently, the Crystal Violet/Iodine complex itself doesn’t even play a vital role. The complex apparently dissolves again more or less instantly as soon as the decolorizer touches it[10], and it’s even possible to differentiate “Gram positive” and “Gram negative” with simple stains like methylene blue or malachite green, if you’re clever about it[11]. The latter authors set up a clever test with crushed cell material, dye, and paper chromatography. They had the decolorizer soak into the paper, past a spot where dye-soaked cell material from Gram-positive and Gram-negative cells was placed, and watched for obvious differences in the amount of time it took the dye to be carried out by the decolorizer. Incidentally, my quick examination of this paper makes it look like cheaper 100% isopropyl alcohol (“rubbing alcohol”) might be slightly better than the standard 95% ethanol for Gram stains.


So, here we are at 1970 or so, and we already know that the Gram reaction is entirely based on how well the cell wall structure prevents organic solvents (like ethanol) from soaking into the cell to dissolve the dye complex. Yes, the mystery of why the Gram stain works in normal cells was largely solved by the Nixon era.
A few corners of the mystery remained, though. Why do “old” cultures of “Gram positive” cells often end up staining “Gram negative”, for example? Why do some kinds of cells seem to be sometimes Gram positive and sometimes Gram negative in the same culture? What, exactly, is really happening to the cell, deep down, during the staining process?

In 1983, the Gram Stain made the great technological leap into the 1930’s, when a variation of the technique was devised which allowed the Gram Stain to be observed by electron microscopy[12]. Using a funky platinum compound in place of iodine, the electron microscope reveals exactly where the dye complex is at any particular stage of the Gram stain process. Using this technique, it was possible to see how the decolorizer disrupts the outer membrane of classically-Gram-negative organisms and to see that the decolorizer potentially damages the cell wall and interior membrane, possibly allowing cell material to leak out (or decolorizer to get in and dissolve the dye complex). It was also seen that the dye complex permeates the entire cell, not just the cell wall.[13]

If you’ve been wondering about the sometimes-Gram-positive-sometimes-Gram-negative cells, the same technique was also used to investigate this. As suspected, it turns out that the “old cultures become Gram negative” problem is due to the cell walls breaking down as the culture ages. Bacteria are continuously, simultaneously, building up and tearing down their cell walls, in order to be able to grow and divide. As nutrients run out, the bacteria run out of material to rebuild cell walls, while the cell-wall degrading enzymes keep on chugging. Breaks in the cell wall occur, and through these breaks the decolorizer can get in and rapidly dissolve the dye. Actinobacteria can have a similar problem, but rather than only being in “old” cultures, apparently weaknesses appear briefly during cell division, and if a particular cell happens to be at this stage of growth when you stick it on a slide, heat-fix, and Gram stain it, the weakness at the septum where the division is occuring can crack and allow the decolorizer in, resulting in a “Gram negative” response even while surrounding cells of the same kind might still be “Gram positive”.[14]

This brings us to archaea and some eukaryotes (i.e. yeasts). Yeasts stain “Gram positive” normally. Although their cell walls are completely different chemically than bacterial cell walls, they are quite thick (microbially speaking). Poor, neglected Archaea seem to be all over the place in terms of Gram reaction. Since their Gram reaction doesn’t tend to correlate to any particular phylogenetic grouping[15], it seems nobody really pays much attention to their Gram stain reaction. On the other hand, and on the subject of “Gram-biguity”, I thought the investigation of Methanospirillum hungatei[16] was interesting. M.hungatei is an archaen that grows in chains. When Gram-stained, the cells on the ends of the chains are “Gram positive”, while the others have no Gram reaction at all. It turns out that the chains are covered by a sheath, and the only contact with the outside world is through thick “plugs” in the cells at the ends of the chains. These “plugs” act like thick cell walls, allowing the Gram stain dye material to soak in but excluding the decolorizer, while the sheath keeps the rest of the cells from soaking up any stain at all.

There you have it – a relatively detailed history and explanation for the Gram stain, and you didn’t even have to get through some obnoxious paywall to read it. Aren’t you lucky?

Comments, suggestions, and corrections, as always, are welcome.

[1] Gram, HC.”Ueber die isolirte Faerbung der Schizomyceten in Schnitt-und Trockenpraeparaten.” Fortschitte der Medicin. 1884 Vol. 2, pp 185-189.

[2] Popescu A, Doyle RJ. “The Gram stain after more than a century.” Biotech Histochem. 1996 May;71(3):145-51.

[3] Brock TD, Madigan MT, Martinko JM, Parker J. “Biology of Microorganisms (7th Edition).” 1994. Prentice Hall, Englewood Cliffs, NJ pg. 46

[4] ibid, pg. 715

[5] Beveridge TJ.”Use of the gram stain in microbiology.” Biotech Histochem. 2001 May;76(3):111-8.

[6] McClelland, Rosemary. “Gram’s stain: The key to microbiology – isolate identification method – Tutorial” Retrieved 20070810 from

[7] Normore WM, Umbreit WW.”Ribonucleates and the Gram stain.” J Bacteriol. 1965 Nov;90(5):1500.


[9] BARTHOLOMEW JW, FINKELSTEIN H.”Relationship of cell wall staining to gram differentiation.” J Bacteriol. 1958 Jan;75(1):77-84.


[11] Bartholomew JW, Cromwell T, Gan R.”Analysis of the Mechanism of Gram Differentiation by Use of a Filter-Paper
Chromatographic Technique.” J Bacteriol. 1965 Sep;90(3):766-77.

[12] Davies JA, Anderson GK, Beveridge TJ, Clark HC.”Chemical mechanism of the Gram stain and synthesis of a new electron-opaque marker for electron microscopy which replaces the iodine mordant of the stain.” J Bacteriol. 1983 Nov;156(2):837-45.

[13] Beveridge TJ, Davies JA.”Cellular responses of Bacillus subtilis and Escherichia coli to the Gram stain.” J Bacteriol. 1983 Nov;156(2):846-58.

[14] Beveridge TJ. “Mechanism of Gram Variability in Select Bacteria.” J Bacteriol. 1990 Mar;172(3):1609-20.

[15] Beveridge TJ, Schultze-Lam S. “The response of selected members of the archaea to the gram stain.” Microbiology. 1996 Oct;142 ( Pt 10):2887-95. (Abstract)

[16] Beveridge TJ, Sprott GD, Whippey P. “Ultrastructure, inferred porosity, and gram-staining character of Methanospirillum hungatei filament termini describe a unique cell permeability for this archaeobacterium.” J Bacteriol. 1991 Jan;173(1):130-40.