The Big Room (and the little things in it) – Page 8 – Applied Empirical Naturalism on a Microbiological Scale

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)?

Geotagging through Asterisk?

Between telemarketers annoying me into getting my upgrade to Asterisk 1.6 finished and the hasty long-overdue road-trip back to and from Idaho again, I’m reminded of an idea that has been fluttering around in the back of my head, not unlike a small bat in the top of a bell tower.

My vast hordes of cult-like fans always seem to want to know where I am. This is obviously an issue in a case where I’m going to be driving 1600 miles, then turning around and driving back, over the span of 4-6 days. It would be pretty easy to set up something on a web page somewhere with some kind of map. The real problem is – how do I update the map?

In some places, I could stop for a while, haul out Igor, boot up, find a public wireless network connection to the internet, and do the update that way. However, that’s time-consuming and awkward, and I want to get this trip successfully completed as quickly as I can. Plus, it’s not always easy to find public network access points, especially through the barren, windy, snowdrift-covered wastelands of Southern Wyoming where a chunk of my route will take me. I have a hypothetical solution, however…

Continue reading Geotagging through Asterisk?

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.

�ber alkoholische G�rung 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 �ber alkoholische G�rung ohne Hefezellen

Wells Fargo Bank is evil

Submissions for the next edition of The Giant’s Shoulders blog carnival are due in the next couple of days. I actually had the paper I’m doing for this one picked out last month even as I was submitting last month’s paper on Lister’s experiments with fermenting milk. I expect I’ll have this month’s written up this weekend…but first, partly as a reminder to myself, I just wanted to say Wells Fargo Bank is a greedy evil bastard.

Seriously, if Wells Fargo Bank was a cartoon character, it’d be someone resembling Snidely Whiplash. I can totally hear the corporation saying “If you don’t give me the deed to your ranch I’m gonna throw you on the railroad tracks!” and twirling its evil little moustache.

What prompts this outburst of a blog post, you ask? Well, even if you don’t ask, I’ll tell you anyway.

I got a phone call this evening. Someone from Wells Fargo Bank calling to tell me they were going to mail me something. “Why the heck”, I thought to myself, “do they need to call me to tell me they’re mailing me something? Why can’t they just mail it?” You see, apparently I may be eligible for over a million dollars of death and disability coverage! And I’ll have sixty days to look it over and it won’t cost me anything! Isn’t that great? But still….”Why do they have to call me to tell me they’re mailing me something? Why can’t they just mail it?”

Here’s why: evidently they feel they’re not getting enough “raping people’s accounts with Mystery Fees” income these days…so unless I’m mistaken, this insurance from Wells Fargo is an “opt out” thing. They’re calling because when they say “hey, we’re doing this and mailing stuff to you”, and I say “Oh, okay”….That’d mean I’d just consented to it. If I get busy or the mailing they send gets “lost” and I forget, Wells Fargo gets to automatically start extracting “insurance premium” mystery fees from my account. (No doubt if they happen to do it on a day when my account is low, they get to charge me an overdraft fee along with the insurance premium. Isn’t that great?) Maybe I’m misinterpreting this, but it sure sounded like this was what was going on from the obfuscated sales-pitch script the caller was going through.

I asked them to go ahead and cancel me before even sending out the stuff, since I already have insurance. We’ll see if they honor my request. I was, incidentally, quite cordial with the poor person who has to do this evil crap for a living in the call center. I’ve done tech support, I know what it’s like having to deal with awful crap that’s not your fault…

Anyway, just wanted to mention this in case anyone else has their bank pull this trick – and so in case I forget and they try to send me the stuff anyway, I’ll hopefully see this post again and be reminded to go through whatever obnoxious “opt-out” procedure I’ll have to deal with…

(I’m reminded of when BlockBuster slipped a tiny, folded notice, buried in a full-size envelope with some other stuff, alerting me in tiny print that they wanted to sell my information to junkmail marketers but they wouldn’t if I filled out their tiny little form and mailed it back to them. As I recall, I had to buy the stamp to mail it, too…)

Anyway, I just had to get that out there. I’ll be back to microbiology and biochemistry shortly. We shall begin with another bit of spiffy practical microbiology from the late 19th century…

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…

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