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-whorewilling 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”

Advocates for the repeal of prohibition carrying 'We Want Beer' signs

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…

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.

Xanthomonas campestris growing in a petri dish and exuding slimeI 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!…

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…

Phone-in Geolocation: almost working…

It’s a hasty and rather brittle thing, but I seem to have the asterisk side of the equation functioning at a minimal level, including recording audio to go with the latitude and longitude that I dial in when I call. Aside from the beautification and cleanup to make it more intuitive, all I need to do is test the “convert the recording to mp3” call and whip up a quick frontend to display the data. Then all of you loyal fans (and/or secret conspirators) can follow along on my long but hasty journey complete with audio. Aren’t you lucky? (Don’t answer that…) If my schedule works out well enough, I may even be able to do a travelogue update from New Belgium Brewing Company along the way.

The basic process is that I whip out my trusty cellphone, call home, and dial the appropriate extension. I then key in my latitude and longitude, and then record up to a five minute bit of audio to go with it. The script then sticks the latitude, longitude, and timestamp (local to the server) at the end of a comma-separated text file and will then invoke a background process of LAME to convert the file to mp3 for online listening. I’m probably only going to have time for a really simple web interface for the moment since I’ve got to hit the road by lunchtime tomorrow after some work in the morning, but once I’m back from this trip I’ll hopefully have a chance to spiff it up.

UPDATE 20081223:If you’re bored, and you watch http://omniblab.dogphilosophy.net/where you MIGHT see an update or to show up during the day, assuming everything works. Unfortunately I won’t actually know if it worked until tonight when I stop for the evening and get online to check it out…

ANOTHER UPDATE 20081223 (late): Now that I’ve stopped for the evening, I’ve fixed the stupid last-minute typo that was keeping the page from working. The audio isn’t automatically being converted to mp3, so until I get time to figure that out the audio parts of the updates won’t show up until I have time to log in and start the conversion by hand. Hopefully be able to fix that (and spiff up the display page) in a day or two.

Any questions, comments, or suggestions (or requests)?

Über alkoholische Gärung ohne Hefezellen

In my last submission to “The Giants’ Shoulders” blog carnival, we saw how the famous surgeon Dr. Joseph Lister deftly demonstrated definitively that fermentation processes were caused by live microbes rather than some sort of mysterious soluble substance that just happened to be associated with microbes. In today’s episode, we will see how Eduard Buchner definitely demonstrated that fermentation was caused by a soluble substance that was associated with microbes, and no microbes are actually needed.

Better still…they’re both right. “Wait…what?” Read on, O Seeker of Microbiological Knowledge, and be enlightened by this month’s entry: Continue reading Über alkoholische Gärung ohne Hefezellen

Saccharomyces cerevisiae – Shameless Libertine!

I’ve been wondering about starting my own little yeast-breeding operation. I haven’t yet figured out where you can by the necessary teeny, tiny yeast-sized versions of the Implements of Extremely Impolite Probing that breeders of other species use, but even before that, I need to understand yeast reproduction better in the first place.

I had gotten an impression from some of the stuff that I’d read in a Genetics textbook and online that yeasts were normally haploid, and only became diploid briefly during mating (you see, when an “?” haploid yeast cell and an “a” haploid yeast cell fall in love, sometimes they’ll…). On the other hand, while reading a review of yeast virology[1], the author explicitly wrote that yeast cells are normally diploid. How to resolve this issue? Plus, I was wondering how, if I happened to have a pure culture of a haploid yeast, how could I tell if it was “a” or “?”?

I recently realized that there was one Dr. Bryk in the department where I work who specifically researches yeast chromosomes…so I asked her…

Continue reading Saccharomyces cerevisiae – Shameless Libertine!

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!

“Top Ten Favorite Microbes” proto-meme…

Dr. Joseph over on the “(It’s a…) Micro World (…after all)” blog posted a list of his ten favorite microbes. After showing up in the comments of his post and being a wiseass about E.coli and Gram staining, the least I can do is participate here. Besides, it’s a great idea. Therefore here are ten of my current favorite microbes:

Continue reading “Top Ten Favorite Microbes” proto-meme…