The Big Room (and the little things in it) – Page 7 – Applied Empirical Naturalism on a Microbiological Scale

Since I’m sure you’re all aching to know:

According to the nutrition information on the back of the bag and some quick calculations, powdered Xanthan Gum has a density of a little over 610mg/ml (or about 10 slugs/hogshead).

I think I may be an Applied Microbiology nerd.

See, when I put dirty dishes in the sink to wash later, I often fill them up with water to soak. I didn’t see this much in Idaho, but down here in Texas I notice that if I leave them too long, the water will sometimes end up turning into a thick slime.

And here I am, wondering what kind of slime it is and if I could find a way to produce it in quantity and purify it (and then find something useful to do with it).

I’m also wondering if this delightfully simple gel electrophoresis technique might be scaled up for more production-type purposes.

This Week = No Fun, but here’s an update anyway…

Busy week with unpleasant surprises, but I ain’t dead yet. You’re probably wondering what a hot dog that’s apparently eagerly anticipating eating itself has to do with that. The answer is: nothing, but it does relate to something I have been intending to post about for a long time, but haven’t since I didn’t have access to the paper…

So, in lieu of blasting out Twitter®-style updates on my Laconica feed that nobody reads anyway (a few people no doubt see the echo of them on Twitter® itself, but I don’t know if anyone cares…), here are a couple of what-I’m-doing-now updates before I go to bed:

I just shot off an email to the webmaster (the only contact I could find who might have the relevant information) of the Institute of Brewing and Distilling, trying to get access to a classic paper published in the Journal of the Institute of Brewing and Distilling for the upcoming “On the Shoulders of Giants” carnival.

There’s no way I can afford the ~$300US that it would cost to join the group, nor even at the moment to pay the typical $30 or so that greedy paywall-imprisoned publishers charge for individual articles. However, they appear to be opening up their archives to the public, for which I think they deserve substantial praise. Still, they haven’t worked their way back to the first few decades of the 20th century yet, so I had to email and ask if there was a way to get the article in question. If not, I’ll see if there’s any way to get it through inter-library loan in time.

“Small Things Considered” asks “What Microbiological Discovery in 2008 Did You Find Especially Interesting?” Which brings us to the “self-eating” thing.

The paper on caffeine’s induction of macroautophagy (“self-eating”) in yeast (and what happens when benzoic acid is also present) finally escaped from the paywall prison in January, and I now have a copy. I at least thought it was full of interesting implications (along with some useful knowledge), so I’ll hopefully be posting about it soon.

I’m also a computer nerd

Particularly when it comes to things like Linux. I’ve been thinking of trying to do some recordings on a couple of practical subjects that interest me for “Hacker Public Radio”

And of course, I still need to do some Xanthomonas snot Xanthan Gum experiments.

I am ~~an attention-whore~~willing to listen to my readers’ interests, so if anyone has suggestions or comments feel free to post them…

The rightful place of science, and “The definition of an intoxicating beverage”

Just a brief point first: President Obama in his inaugural address promised to “restore science to its rightful place.” In traditional fashion, this prompted all manner of verbosity on blogs around the web concerning just what science’s rightful place actually is. Let me just take a moment to settle this question:

Science’s rightful place is kneeling at my feet in supplication and doing my bidding! AH, HA HA HA HA HA!!!!!

But that’s not what I came here to post about. Instead, I wanted to mention a paper I finally got my hands on. You may recall that some time back there were a few stories that popped up about what was said to be a “you can’t get drunk on beer” paper published back in the 1950’s. As usual, the people doing the reporting couldn’t be bothered to actually cite the paper in question, but I figured out which one it was. The paper is this one:
Greenberg LA:”The Definition of an Intoxicating Beverage”; Q J Stud Alcohol. 1955 Jun;16(2):316-25.

I have that paper. And I am quite disappointed in it in much the same way I was with Linus Pauling’s paper proposing a triple-helix structure for DNA. I did, though, learn some interesting things from Greenberg’s paper.

It turns out that the paper actually concerns the legal definition of “intoxication” and whether or not, based on this definition, beer should be classified as an “intoxicating beverage”. Greenberg actually raises some good points…but first, some amusement:

“The average alcohol content of American beers is 3.7 per cent[…]The strongest ale is 4.2 per cent” (page 320, paragraph 4)

Unfortunately, this isn’t quite as funny as it sounds, because the part I clipped out of that quote is where he says “by weight”. It’s still kinda funny though, since that would mean, in mass-market-bladderwash terms, that “The Strongest Ale” is Heineken.

—
This Alcohol-by-Weight-vs-Volume issue may actually be part of why American beers have a reputation for having watery, feeble beers. It evidently used to be that places like Canada were using alcohol-by-volume, while the US was using alcohol-by-weight on their labels. An otherwise-identical beer bottled in Canada would have a higher “percent alcohol” on the label than the US-bottled version, making it seem as though the American version was weaker. So, evidently it’s not really true…things like “Coors Lite” notwithstanding. (See this recent page at Fermentarium.com for more details.)
—

But back to the point of the paper…evidently as Greenberg was writing this paper half a century ago, there wasn’t a clear, quantitative scientific or legal definition for “intoxication”. He points out that you can’t just define it in terms of alcohol merely having noticeable effects on the drinker, since the magnitude of the unpleasant effects at low to moderate drinking levels aren’t really much different than that for (for undesirable effects) lack of sleep, distraction [remember all those studies saying talking on the cell-phone while driving is as bad as being drunk?], hunger and so forth. For that matter, I think we can all see the problem of trying to arrest anyone who is being relaxed and amiable for “public intoxication”.

Greenberg solves this problem by looking at the average blood-alcohol concentration of people arrested for “intoxication” (0.21% back in the 1950’s, evidently), and a couple of previous studies from the 1920’s and 1930’s, and he finally settles on 0.15% Blood Alcohol Concentration as a level he’ll use as the line for “definitely intoxicated”. He then proceeds to go through the common classes of alcohol-containing beverages to determine how easy it is for someone to consume enough to reach this BAC.

In summary – For hard liquor, and average person would have to consume 8 ounces plus one ounce per hour of drinking (for example, 9 ounces consumed over the course of one hour). That’s not a difficult quantity to fit into a typical stomach, so hard liquor is obviously an “intoxicating beverage”. Fortified wines (like Port, Madiera…or Thunderbird): about 18 ounces plus 2 ounces per hour – say, a pint and a half in about 4 hours. Still pretty easy to do. An ordinary wine (like, say, a Gewürtztraminer): 36 ounces plus 4 ounces/hour – or a 7-11 “Super Big Gulp®”-sized portion in two or three hours. Getting to be a fairly substantial amount of liquid, but still plausible.

And then there’s beer. Greenberg comes up with a figure of 80 ounces + 10 ounces/hour. That’s roughly three quarts within one hour, which is quite a bit more than the approximately 2 quarts that a human stomach can hold. He goes on to describe several controlled experiments on beer consumption and the resulting blood-alcohol concentration. By pushing one group to consume a gallon and a half of beer over a period of 8 hours, they were able to get up to an average of just under “intoxicated” (by Greenberg’s definition) at 0.13%. The rate of beer ingestion required to pass the “intoxication” threshhold was more than most test subjects could even manage. Therefore (Greenberg concludes) beer should probably not actually be classified as an “intoxicating beverage”

Now for the party-poopery: Greenberg explicitly points out that this is certainly not the same as saying that beer cannot impair a drinker’s performance or judgement, so just because you haven’t consumed anything stronger than beer it doesn’t mean you should be allowed behind the wheel of a steamroller. Nor does it mean that it’d be okay for an alcoholic to drink beer (since an alcoholic is very unlikely to stop with just beer). Furthermore, these days “intoxicated” is legally about half of the level that Greenberg is using – 0.08% in most places in the US as far as I can tell. By Greenberg’s measure, you can easily get that amount of alcohol out of a pitcher of beer consumed over an hour.

So, Greenberg isn’t crazy, and beer can still make you drunk, just as we all would expect. How disappointing. Still, it’s an interesting paper and I’m glad I dug it up.

On a related note, if I can get my hands on an old paper from the Journal of the Institute of Brewing, I may have found my selection for February’s Giant’s Shoulders blog carnival. Stay tuned, more to come…

Vindicated! Margarine is correlated with stupidity!

I’ve been saying for years that anyone who actually wants to eat margarine has something wrong with their head. Now, there’s PROOF:
“The study suggests that if children eat certain types of food their intelligence may be boosted or significantly lowered. It singles out margarine as having particularly strong links with lower IQ scores.”

It’s still not entirely clear whether margarine makes you stupid, or if instead being stupid predisposes you to eat margarine (or both). Either way, I continue to maintain that if you want to eat vegetable oil on your bread instead of good, wholesome, delightful butter – just get some herbed olive oil and a little balsamic vinegar [it’s not butter, but it’s darned good]. Don’t run it over powdered nickel while pumping it full of hydrogen gas to make it hard, color it yellow, and then use it as make-believe butter-like-food-product because if you do, you might as well make a Play-Doh® bread-like-loaf-product to put it on.

And before anyone asks – no, I’m not affiliated with the dairy industry…though if anyone in the dairy industry feels sympathetic to my current situation with my under-equipped home lab and wants to send me an old bacteriological microscope they just happen to have sitting around, I’d be willing to consider being a paid shill independent advocate in return…

“Untersuchungen über Bacterien”

Once again I’m down to the last minute, trying to juggle too many things and almost missing this month’s “Giant’s Shoulders” blog carnival. Almost.

Today we go once again all the way back to the Victorian era, to see that if you thought bacterial taxonomy was difficult now, imagine what it was like over 130 years ago:
Cohn F:”Untersuchungen über Bacterien”; Beiträge zur Biologie der Pflanzen; 1875, vol 1; pp 127-222
(Or “Researches regarding Bacteria”, in “Contributions towards the Biology of Plants”)

This paper is an overview of the problem of categorizing bacteria among the types of living things, and makes some early suggestions. I don’t think it’ll spoil too much of the punchline to point out that not only is the journal about the biology of plants, but the paper also starts out with Cohn describing how he came to work at the “plant physiological institute”. Cohn’s assertion that bacteria are definitely a form of plant actually stuck for at least another three-quarters of a century or so – I have a copy of a 1945 book on bacteriology that actually has a short discussion on why bacteria are categorized as plants rather than animals (or “animalcules”, even). That’s only part of what’s interesting about this paper, though.

Cohn discusses a number of problems with the nature of bacteria in his time. For one thing, he says there had been little real effort to even come up with a coherent scheme for classifying bacteria at that point. He does mention one previous attempt to come up with a system, but on the whole it seems everyone is just coming up with terminology on the fly – even taking Pasteur himself to task for throwing around a variety of terms related to microbes without distinguishing what the terms actually refer to. The reason for this, really, is just that figuring out pretty much anything in detail about bacteria was a seriously difficult problem at the time. Cohn explains why; how it is really impossible to make out more than general shape and size from microscopic examination, and how the lack of any detectable sexual reproduction makes it impossible to do positively identify members of the same species. In fact, even very obvious differences in appearance might not be definitive. It was suspected (and later demonstrated) that some of what appeared to be completely different fungi were actually just different life-stages of the same fungus. (Hopefully you can see the picture at upper right, with the bacteria/yeast-like growth on one tube and the obvious and very different fuzzy mold-type growth on the other. Both are actually the fungus Blastomyces dermitiditis.) Just as some of Cohn’s contemporaries considered that perhaps all molds and yeasts were really just different stages of life of the same organism, perhaps the same might also be true of bacteria?

Cohn does, after all, promote the notion of bacteria as a type of fungus. You may even remember an old word for bacteria: Schizomycetes, that is “fission-fungi” (that is, fungi that reproduce by splitting in half rather than producing spores). This makes sense if you consider that bacteria are more like plants and algae than animals, and fungi were considered to be plants that lacked chlorophyll. Although lamenting that it was not feasible to really separate out individual bacteria to determine whether they ever changed form – this was still three years before Joseph Lister actually did so – Cohn unwaveringly felt that bacteria were in fact made up of several different genera and species, and set out an early attempt at classification.

Once again, Our Friend the American Society for Microbiology hosts a translation of this paper, complete with a couple of paragraphs of more modern editorial commentary at the end. It’s well worth a look.

Unfortunately, I don’t think Ferdinand Cohn’s hairstyle is nearly as spiffy as Eduard Buchner’s cool “Colonel Sanders Guest Stars on Miami Vice” look. I think he looks kind of like a slightly-better-fed Sigmund Freud with a bad comb-over. But that’s just me.

“Geomicroblogging”? “Microgeoblogging”?

I don’t know what it should be called…but anyway, I put up a page where I can try to organize my allegedly spiffy idea . After my little “Proof of concept” experiment with audio geomicroblogging during the holidays, I’ve decided that the concept is indeed at least fun to play with. Since I’m still too poor to buy myself any really expensive toys or take a long luxury vacation, I figure I can amuse myself by trying to turn my experiment into a “real” system that someone might actually want to use. I’ve posted my current idea and plans for the first release at the link up there. I figure getting to the first basic implementation will take a few days to a few weeks, mainly depending on whether anyone but me likes the idea (if it seems interesting to anyone else, there’s a lot more reason to focus on getting it done than if it’s just a crazy idea that everyone else hates…)

Coming Soon to a Bigroom.org blog post near you!

I got a little money for Christmas, but I’m feeling quite guilty as I didn’t really have the time and money to reciprocate in advance. I also haven’t been able to figure out what to spend it on until now. Now, I have a solution for both problems.

I intend to spend it all on fermentation-related food ingredients and do some experimentation with sweet-tasting foods. Initially, in addition to flavors (spices and whatnot), I need to track down bulk quantities of:

Erythritol, which is a virtually non-caloric sugar alcohol which unlike sorbitol and so forth is not normally prone to cause gastric distress, and unlike Xylitol is not hazardous for beloved household pets. Better still, it actually is very tasty unlike that nasty hippy “Stevia” crap (which isn’t produced by fermentation anyway, as far as I know).
Food-grade Glycerol (“Glycerine”), which I hypothesize is close enough to the structure of Erythritol to mix well with it and help the erythritol dissolve (and hopefully prevent crystallization, much the same way the “corn syrup” does with sucrose).
Xanthan Gum. MMmmmmm…edible bacteria-snot. (Okay, for all that this sounds disgusting, it’s really somewhat similar to pectin, which like xanthan gum is a polysaccharide. Pectin is just fruit-snot rather than bacteria snot. Dietarily, both count as “soluble fiber”.)

There are probably other ingredients I can come up with as well. For those of you out there who are owed gifts: Chewy candies, hard candies, baked goods, and/or beverages, what’s your preference for my initial experimentation? Assuming anyone’s interested, I will probably blog my results…

Meanwhile, I’ve also been thinking about geolocation, geotagging of audio and video media, and Asterisk again. I want to take the lessons learned from my playing with the “Where Was I?” prototype and turn it into a real geolocation system, integrating with Asterisk and Laconica (which turned out to be easier to set up than I’d feared – I’ve now got my own Laconica server at http://omniblab.dogphilosophy.net/laconica, though I need to sit down and activate the IM integration (Twitter may have abandoned IM, but it reportedly works fine in Laconica).

It also turns out that you can use Asterisk with cellphones(!), at least if they have bluetooth. That’s handy to know…

Argh – too much to do, not enough time!…

Winter break over…CRAP!

Open Thread here, just to let my readers know that I haven’t forgotten you. Please post appropriately chastising comments below for not getting nearly as much done as I’d hoped during the break…

Bedtime – I’ve got Real Work™ to get back to in the morning…

Exhaustipated, but I’m home

I had to forgo the pleasures of lounging in the hotsprings, due to the excess of time it took to load up Flagella for the trip back and finish running errands. I had to get out of Idaho while the getting was good, as another storm was on the way. Still, the return trip wasn’t a total loss:

FloppyCow gazes from inside Flagella (my car) at the beer I just picked up at New Belgium Brewing Company - La Folie and Frambozen
I managed to score a couple of bottles of La Folie and a six-pack of Frambozen. FloppyCow is jealous. These brews may make a decent relaxative with which to treat my exhaustipation.

I learned a few things playing with my prototype “Where Was I? application for Asterisk. For one thing, I need a longer greeting message, so that my asterisk box will still be listening when my cellphone finally obeys me mashing on its keypad and sends the tones. For another, Suddenlink may be screwing me over on my outgoing data (I’m supposed to be getting 384k outgoing, which ought to be plenty of bandwidth, but strangely enough from outside my VOIP packets are getting completely screwed up. I need to research this to see if it’s really them.) In any case, I had fun playing with it, and now have a better idea of how to (re-)design it for regular use.

Meanwhile, though, now that the car is finally unloaded again it’s time to rest and try to remember everything else I needed/wanted to get done during the holiday break.

Oh boy. This is “bad”.

(Note the “scare quotes” around “bad” up there…)I woke up kind of late this morning, which is probably just as well as I think I really needed the sleep before I load up the car with stuff from the old house and make the ~1600 mile (about 2575km or 83.45 picoparsecs) return journey. As a bribe to myself for making this trip, there are two places I had been considering stopping for a bit on the way back. One of those two is New Belgium Brewing Company in Fort Collins, Colorado. In order to do this, though, I obviously need to arrange to be going through Fort Collins (around 8-9 hours from here) while they’re open. The thing is, there’s really not much point in stopping from my perspective unless they happen to have what I’m really interested in – their not-always-available limited-release “La Folie” (link from the image goes to the page describing it) and possibly their seasonal “Frambozen“. Last time I went by it appeared they always had some La Folie on tap at the tasting counter but not in bottles for take-out.

It turns out New Belgium is open on Saturday until 6pm. And they have both La Folie and Frambozen in bottles there right now.

The other possible stop is Lava Hot Springs, Idaho, where I find it very enjoyable to lounge in the hot springs amid all the snow. However, they open at 9am, so even if I get up really early to make it to Fort Collins before New Belgium closes, I can’t spend any time in the hot springs until 9am anyway, so I’d never make it from the Hot Springs to Fort Collins on the same day. I could, of course, lounge at the hot spring today and then hit Fort Collins tomorrow morning, stopping somewhere between Central Wyoming and Fort Collins tonight, but that could mean the return journey spanning three days rather than two.

However, the weather on this side of Idaho and Wyoming looks most passable today especially later in the afternoon when the roads have been cleared off well, and it looks like getting across the bad wind and snow on the Eastern side of the Wyoming may be safer and better tomorrow morning rather than today.

So, basically, the entire Universe (or at least that portion of it in charge of weather for this region of the country) is obviously telling me that I should take my time loading up and getting out of town, and then go ahead and stop at Lava Hot Springs for a little while to relax before continuing on to somewhere around Rawlins or so, and then resume in the morning which should just coincidentally put me going through Fort Collins in the Late-Morning to Early Afternoon time frame, when New Belgium Brewing is open.

I mean, I don’t want to stop and enjoy myself. Really, I want to be a good boy and drive back in the quickest, most efficient way possible, but who am I to thwart what is the Obvious Will of the Universe? (Supernaturalism makes some of the best excuses…)

In other news, I did manage to fix the Stupid Mistake™ in my little “Where Was I?” application for Asterisk, so now not only do the location updates happen but also the conversion of the associated voice update to MP3 for listening now happens automagically as well. I also fixed the hard time-limit, so updates shouldn’t cut off at 30 seconds like the one from Fort Collins did on the 24th. If you keep an eye on the page and everything goes well for me, you may catch an update from Lava Hot Springs later in the day. If you are especially bored (or are being paid by a Secret Government Agency or Vast International Conspiracy or Santa Claus to spy on me) I will try to do an update from there while sitting on the steps in view of the East Webcam. If so, I’ll be the tiny figure waving at the camera from the steps. If you happen to be watching at the right time, you might catch me there to gaze upon my magnificent pixellated spiffitude. Just don’t look directly at it or you may go blind…

Naturally, a live update from New Belgium Brewing Company is planned for tomorrow as well. After I return I can work on making my little application more interesting (embedded audio player, nicer presentation, maybe an embedded map, ability to come back later and attach related pictures…) and masssaged into a condition that wouldn’t be too embarassing to let others use. This “live neogeographical netcasting” thing is too much fun to keep just to myself. (I wonder how hard it would be to interface this with the Laconica microblogging system?…)

Further bulletins as events warrant…