WANT – Page 2 – The Big Room (and the little things in it)

Obscure scientific papers, Mad Science, Travel, and other randomness

First – an amazingly astute observation that I’m ashamed to have not previously noticed myself (click image to go to it’s original site and see it full-size…):

I’m proud to say that I think testing Mad Hypotheses is great, and will continue to try to be a Mad Scientist. And a “Dirty Old Man” someday, but that’s a whole separate issue.

Second – I am really loving the perks of my new job – namely access to the college library system. I had previously mentioned (see last couple of paragraphs) a certain article that I wanted to get my hands on:

Greenberg LA:”The Definition of an Intoxicating Beverage”;Q J Stud Alcohol. 1955 Jun;16(2):316-25

Not only does the medical library have copies of a Czechoslovakian microbiology journal, the main library had a set of this old journal, too. I have my bedtime reading for tonight…

Thirdly – Another Giant’s Shoulders carnival has come and gone. I now believe that Eduard Buchner had hit upon not only a useful truth of living systems, but also a nifty alternative “mad scientist” hairstyle. Now I need to come up with one for next month. It’s been getting me thinking, though. That blog carnival is intended for “Classic” papers. Implied is that the papers are somehow important to the development of some scientific field or other. I’d like to see a variation on the “old papers” theme focussing on random old papers (where “old” might mean a few years or decades, depending on the subject) that people have found useful or interesting. Stuff that isn’t necessarily ground-breaking and has perhaps been forgotten or lost to obscurity but still has useful things to teach us. Naturally, I’m thinking especially Microbiology (and especially Microbiology other than Medicine) and Food Science. The Carnival could be called something like “Second Chance Science” or something of the sort. Just a thought.

Fourth – speaking of “Microbiology Other Than Medicine” and Food Science, apparently The National Academies of Science want to know what scientific topics people most want to read about. As usual, “microbiology” appears to have been relegated in their breakdown to merely a subset of either medicine/diseases, “biology”, and perhaps a small subset of “energy” and “Feeding the World” (no, seriously). The survey includes space to tell them what they’re missing – I heartily encourage anyone who cares to make sure you take the survey, and mention industrial and environmental microbiology and food science as subjects they shouldn’t continue to neglect.

And, finally – next week I need to make a very-long-overdue run back up to Idaho to grab some things from the old house and make sure it’s still standing, the water’s really turned off, nothing unnecessary is running, etc. 1600 miles of driving each way. Ugh. Anybody got any good recommendations for things to listen to on the trip? Other than having a chance to finally grab some things that I am missing, maybe I’ll at least have a chance to visit New Belgium Brewing Company again, since my route goes right past it. So long as I’m not driving by on Christmas day (when I assume they’ll be closed) I may have a chance.

Nerd Reading Spasm!

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

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

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

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

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

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

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

Continue reading Nerd Reading Spasm!

Stir-Fried Random Ep 03: All I Want for Christmas Is…

Thanksgiving = Shopping, evidently. Anyway, since this is about the time of year when the vast population of my devoted fans around the world begin demanding to shower me with gifts and asking what kinds of gifts they should give me…this episode of Stir-Fried Random has some suggestions. Enough suggestions, in fact, that I didn’t even have room to include a Nerd Word, Emprical Observation of the Week, or Microbiology Microlecture. Therefore, while this episode will probably be slightly less interesting to the microbiology and computer-nerd focussed listeners, it should be of special interest to members of my immediate family, secret admirers, cultists who worship me as a living embodiment of divine spiffitude, and agents of the NSA, FBI, CIA, USDA, and Federal Department of Blog Enforcement who are busily profiling me. There is some other stuff though – please give it a listen, pass copies along to your friends, play it over the Public Announcement system at school, turn it into a techno-dance remix video on YouTube®, whatever.

As usual, direct download links for mp3 and ogg versions, plus <audio> tag support for those with really new browsers to listen in place, and embedded Flash-based mp3 player for everyone else who wants to listen in the browser instead of downloading and singing along during your commute or whatever.
(UPDATE 20081126: I’ve REMOVED the embedded player for now – it seems it ignores me when I tell it to wait until it’s told to before it starts playing. Autoplay annoys the heck out of me, and this seems to insist on it. The embedded player will remain gone until I get it to behave properly. Meanwhile, you can double-click or “right-click -> save as:” on the ogg or mp3 download link to get the audio files to listen to. Apologies to anyone ambushed by the unwanted auto-playing of the sound…)

Show Notes:
Continue reading Stir-Fried Random Ep 03: All I Want for Christmas Is…

Double-Ewe Tea Eff: “Modified Food Starch”

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

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

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

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

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

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

Anybody got a good reference on industrial food processes?…

[1] 21CFR172.892

Lake-spanking map and pictures

Lake Conroe has been persistently naughty. Since nobody else seemed to be taking responsibility for its misbehavior, we took matters into our own hands yesterday and gave it a good spanking. I paddled it until I got blisters.

I think this will need to be done much more often, since I don’t think the lake has learned its lesson yet. On the other hand, I learned a few – interactive photo-map and details below…

Continue reading Lake-spanking map and pictures

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

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

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

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

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

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

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

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

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

I finally got to Bristol Brewing Company…

Signage in front of the Bristol Brewing Company After spotting the company’s mention in Jeff Sparrow’s “Wildbrews“, I’ve been wanting to visit Bristol Brewing Company, particularly since they may be the only such brewery using local yeasts and bacteria that they isolated themselves from their local environment.

Since we’re moving from Southeastern Idaho to Southeastern Texas, I’ve been going back and forth between the two location. It just so happens that along with New Belgium Brewing Company, Bristol Brewing is actually right along a convenient route between the two locations. (Let’s see if I can figure out how to work the Google Maps plugin):

How’s that look? How does it work? (Those of you reading this on the RSS feed: The interactive map only appears on the website, it would seem. Please check it out here.) I made the KML file myself…

Bristol Brewing is a cozy little brewpub, and the people there are encouragingly helpful. They were in the middle of bottling, so there were no tours. Also, there were not currently any of the skull-‘n-bones beers available. However, I did get an educational series of tastes of their current brews on tap (thank you to the employee I spent most of the time talking to whose name I’ve embarrassingly forgotten, but who I believe was Tad Davis judging from the photos on the web site). I also lucked out and their microbiologist, Ken Andrews, happened to be there. I asked about their native Colorado brewing flora. Turns out Bristol Brewing isn’t quite as bold as I originally thought. They’re still doing their primary fermentation with “normal” brewing yeasts. What they’ve done is inoculated some wine barrels with the locally-isolated yeasts and bacteria, and they use the barrels for a secondary fermentation and aging instead. Much safer if you have to worry about having a drinkable product at the end, and of course it makes me feel like more of a crazed rebel for wanting to isolate my own local bugs for the main fermentation. So, a great visit overall.

Incidentally, it seems they’ll be tapping a new Skull-‘n-Bones brew in a couple of weeks, at 5pm on Tuesday, May 27th (2008). It sounds like they’ll probably have some available for a few days before it all disappears, so I’m hoping my return to Texas can be timed such that I can swing by and at least get a taste.

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”…

WANT: “Teamaker” hops

Just a brief “aw, crap, has it really been over two weeks since my last post?” post, really, but I thought this was interesting.

It would seem that there’s a variety of hops that’s been registered recently known as the “Teamaker” variety. It’s got all the magic bacteria-stopping power of a hops plant, but composed of almost entirely the non-bitter component. I’m not sure how hard it would be for me to get them to send me a plant or two to evaluate it’s usefulness for yeast cultivation (as an anti-firmicutes antibiotic) and for controlling the growth of bacteria in fermented foods and drinks…

House-hunting (“Yep, these are house droppings all right. Fresh ones too…” [everybody’s seen that Monty Python bit, right?]) in southeast Texas and the related travel (both in the area here and between here and the other abode in southeastern Idaho) is eating my life at the moment, but I’ll try not to neglect the blog so much.

More to follow.

Fermentation: not just for alcohol

What does gluconic acid taste like, anyway?

Well, that was an interesting reminder. I’m tracking “fermentation” on Twitter, and caught a random reference to an interesting fermented beverage being made in Germany. The “reminder” I drew from this serendipitous reference was that “fermentation” doesn’t necessarily mean alcoholic fermentation.

“Fermentation” seems to be slightly tricky to define accurately. Most definitions seem to directly mention alcohol production from sugar, but this is only an example and not a definition. I’ve also seen the term used to mean simply “to grow a culture of microorganisms” (because the tank they are grown in can be referred to as a “fermentor”.)

Properly speaking, fermentation is what you get when you have microbes growing under conditions where the elelectrons that get sucked away from “food” molecules like sugars ends up on another, simpler carbon compound rather than something like oxygen, and therefore fermentation is implicitly anaerobic although that’s not the same as saying that fermentation cannot happen in the presence of oxygen (e.g. the Crabtree Effect, and of course fermentation of ethanol to vinegar requires oxygen). The end product is generally assumed to be organic acids (like acetic acid [vinegar]) or alcohols, and carbon dioxide. So, making beer and wine is fermentation. Making vinegar is fermentation. Making yogurt (lactic acid) is fermentation. Citric acid can be made by fermentation of glucose by Aspergillus molds, as can malic (apple) acid (see US Pat#3063910). You can make tartaric (grape) acid from glucose by fermentation as well (see US Pat#2314831).

I am familiar with the flavors of all of those products. One I’ve never directly tasted is gluconic acid, which is the main product of the fermentation process used to make “BIONADE�” (it seems to be written in all-caps everywhere).

According to their English-language page discussing their process – linked from the image at right, click to view – they are starting with malt, just as one would for beer, but instead of Saccharomyces yeasts, they are fermenting this wort-like liquid with “acid bacteria”. I’m going to hazard a guess that the bacterium in question is a strain of Gluconobacter oxydans or one of its close relatives. This group of bacteria is in the Acetobacteraceae family of bacteria which is involved in turning your wine into vinegar. It would appear that under the right conditions, the enzyme Glucose Oxidase (EC 1.1.3.4) produced by G.oxydans converts glucose to a compound which reacts with water to form gluconic acid. BIONADE� then adds flavor extracts and juices to the filtered fermentation product, carbonates it, and bottles it.

Not being familiar with the flavor of gluconic acid, I’m aching to get my hands on some of this stuff and try it.

For another example of a relatively non-alcoholic fermented beverage, see also Kombucha, which is essentially sweetened tea fermented by acetic-acid bacteria and non-Saccharomyces yeasts…which I also have yet to taste.

geostr:50.4600,10.2208:200804110105-06:geostr (at least if Google Maps interpretation of the address I could find at the moment is correct, and assuming the information I dug up and my interpretation of it is correct, this should be the approximate location of the brewery responsible for BIONADE� production.)