Methods – Page 4 – The Big Room (and the little things in it)

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.)

Well, a PHP example, anyway

Once I dove in and started messing around, I only had to fix two typos as the example I was working on seems to work correctly, at least to the extent that I’ve tested it. I now have what appears to be a working example of Geostring parsing in PHP. In this case, the example reads my feed from the Twitter website, sifts out any geostring tags it finds, then generates Google Maps links for each one found. As I write this, there are two geostring tags on that page, representing places (and times)
that I have actually been, and it seems to work.

You can take a look at the source code for the example here, or see it in action here.

Feel free to grab a copy to play with if you’d like (or write one yourself that isn’t so messy – hey, as someone who doesn’t consider himself a professional “coder”, I’m just happy that it did exactly what I wanted it to do on the first try…). You should only need to worry about two things – changing the $text_to_read, and whether or not your web server (or CLI) has fopen wrappers turned on so the script can read another web page if you use a web page as your text to parse rather than a local file.

Since generating a geostring tag is trivial, I didn’t bother trying to incorporate that into this example. If you want one, then here:

<?php
//generate a geostr tag with the most typical information only
//point not part of a track nor including heading or angle
$lat=44.027168;
$lon=-111.297892;
$elev=”1711.9m”; //could leave off the “m” and treat as float, since it defaults to “meters”
$timestamp=”20071125T123438-06″; //6 hours behind UTC

print(“geostr:$lat,$lon,$elev:$timestamp:geostr”);
//”full” version: print(“geostr:$lat,$lon,$elev:$timestamp,:,:geostr”);
//completely unnecessary, but legal
?>

As always, comments and suggestions are welcome.

The care and feeding of Saccharomyces

Let me pause now for a moment to review what I’ve learned so far:

Yeast are filthy little jerks

No, seriously. I’ve previously reviewed their promiscuous sex lives,
their sexually-transmitted diseases, and their toiletry habits. Somehow, though I still want to do more brewing, so let’s continue.

Bag of 'Parodina Yeast Chow'. I am not affiliated with Purina Mills corporation! This image is PARODY!

Yeast need to be fed particular sugars

The three major elements needed by pretty much every living thing for “food” are Carbon, Nitrogen (as reduced “amino” nitrogen), and phosphorus (as oxidized phosphate) (Reduced sulfur is also needed in small amounts for proteins). Glucose (“dextrose” or “corn sugar”), fructose, or sucrose (“table sugar”, each molecule of which is made of a molecule of glucose attached to a molecule of fructose) are all used as carbon sources by Saccharomyces yeasts. Possibly also Galactose under certain conditions[1]. Saccharomyces yeasts don’t appear to be able to use lactose (“milk sugar”, each molecule of which is made of a molecule of glucose and a molecule of galactose), so some recipes include lactose in order to ensure there is some residual “sugar” in the mix at the end, for flavor and “body”.

Yeast need reduced nitrogen (amino nitrogen or ammonia…or urea)

Aside from sugars, this seems to be possibly the most important yeast nutrient. The most
“natural” source of this nutrient would seem to be amino acids or very short peptides (2-5 amino acids long). Apparently urea (carbamide) also makes a good yeast nutrient, but:

You don’t want TOO much nitrogen available to the yeast, or there’ll be excess urea dumped back into the brew

This could combine with the ethanol to make “ethyl carbamate”, which is considered
a probable carcinogen, at least if it’s present at a high enough level. Obviously if you use urea as a
yeast nutrient, that’s only going to increase the possibility of a problem.

Saccharomyces yeasts are effectively incapable of using proteins for nutrition.

Proteins can be a source of amino nitrogen (and carbon and sulfur), but like all real microbes, yeast cells cannot just “eat” chunks of protein. They have to be broken down into very small chains of amino acids or even as individual amino acid molecules before the yeast can suck them up and use them. Saccharomyces yeasts do not appear to normally excrete protein-digesting enzymes, so by themselves they cannot make any use of protein for nutrition[3].

Yeast need oxygen

Oxygen is necessary for making certain components of the cell membrane, in addition to it’s more obvious role in respiration. Without a way to replace used up membrane components, the yeast stop reproducing and eventually fall apart and die. There seems to be some suggestion that to a certain extent one can substitute some raw membrane material for oxygen here (either as “yeast hulls” or possibly even certain of the natural waxes on some fruits).

If you give yeast oxygen, though, they consume the sugars entirely instead of making alcohol…

…or do they? Between the “Crabtree effect” (when there are high concentrations of glucose, alcohol production continues even in the presence of oxygen) and indications in scientific papers[2], it seems SMALL amounts of oxygen may not be a problem, and might very well be beneficial.

Yeast need vitamins and minerals

B1 (“Thiamine”) is commonly mentioned, though apparently the need for it varies from strain to strain. Also potentially important are Pantothenic Acid (B5), Niacin (Nicotinic Acid, Vitamin B3), Biotin, Inositol, as well as Potassium, Magnesium, and trace amounts of calcium and a few other minerals[4].

Unhealthy yeasts are more prone to make (EEK!) Off-Flavors and Off-Odors (EEK again!)

For one thing, it seems to be a general rule that you don’t want your brew sitting on the corpses of dead yeast (the “lees” of wine, or “trub” of beer), because that is a potential source of (insert dramatic music and crash of thunder here)Off-Flavors and Off-Odors. Yeast dying and falling apart is also a major source of urea being dumped into the brew, too. Some strains of yeast under certain conditions, such as insufficient pantothenic acid, may be prone to producing nasty-smelling sulfides as well.

So, in most cases what we want to do when brewing is keep our yeast as alive and happy as possible, and get them to hurry up and finish our primary fermentation before they start dying off. Coming up: My (as yet untested) plot for accomplishing this – without specialized scientific equipment or materials.

[1] Wilkinson JF: “The pathway of adaptive fermentation of galactose by yeast” Biochem J. 1949; 44(4): 460�467
[2] Nagodawithana TW, Castellano C, Steinkraus KH: “Effect of dissolved oxygen, temperature, initial cell count, and sugar concentration on the viability of Saccharomyces cerevisiae in rapid fermentations.” Appl Microbiol. 1974 Sep;28(3):383-91.
[3] Bilinski CA, Russell I, Stewart GG: “Applicability of Yeast Extracellular Proteinases in Brewing: Physiological and Biochemical Aspects.” Appl Environ Microbiol. 1987 Mar;53(3):495-499.
[4] Fugelsang KG, Edwards CG: “Wine Microbiology: Practical Applications and Procedures” 2007; Springer Science+Business Media LLC, New York; pg 17

What really counts as a “microbe”?

Just a brief pre-post before the main one I’ve got brewing now (which will be posted either later today or tomorrow).

A tapeworm: Since when does 30-36 feet long count as 'micro'??? Microbiology is the dominating topic of this particular blog, but I don’t think I’ve ever addressed what I consider to really count as “micro”biology. This isn’t necessarily an obvious topic. My old “Microbiology” book from 8 years ago, plus the textbook from last year’s “Pathogenic Microbiology” class both contained large sections discussing organisms that are visible without a microscope. Heck, the “Pathogenic Microbiology” text even had a whole section on spider and insect bites. And, tapeworms? Since when is “over 30 feet long” considered “micro”? As I like to say: It’s time for Microbiology to grow up and move out of Medicine’s basement.

So: Here are the defining features of what I consider to be a “microbe”, at least for purposes of what I tend to discuss here on the blog:

Obvious: the organism cannot be effectively examined visually without a microscope and individual organisms can virtually never be observed by the “naked eye”.
In nature, a full normal population of a microbe can and will develop from a single live cell, and isolated individual cells are reasonably commonly observed.
Microbes do not “eat”.

It’s that last point that prompted me to write this post, mainly because it’s such an important part of why microbes work and how they affect their surroundings, especially when it comes to food microbes. What I mean by “do not eat” is that they are incapable of taking large (microbially speaking) chunks of material into themselves to use. Any cell nutrient for a microbe must be in the form of small molecules, like sugars, small peptides or individual amino acids, and so on that can be easily transported across the cell membranes and through the cell wall where applicable.

The importance of this is that for a microbe to grow on a complicated substance like meat or bread (for example), they have to excrete specialized enzymes that break down the substances out in the environment into simpler components like sugars or small peptides. If a microbe cannot secrete a protein-digesting “protease” enzyme, it can be surrounded by tasty, nutritious proteins and still starve to death. If a microbe can’t secrete an amylase (starch-digesting) enzyme, it doesn’t matter that starch is made of nice yummy glucose molecules because they’re all wadded up into long chains of starch that the microbe can’t get at.

And that, finally, is important because it brings up issues of growing multiple microbes together to accomplish something. Sake, for example, is made by fermenting rice, but rice is made primarily of starch. Saccharomyces yeasts don’t make amylases, so in order to make sake, you also have to add a kind of mold (Aspergillus oryzae, one of the types of white-mold-with-little-black-specks that you may see growing on the bread you’ve left sitting around for too long). A. oryzae is also a microbe and therefore can’t “eat”, but it does produce amylase. Since the amylase is breaking down the starches outside of the cells, this means the released glucose is also available for the yeast to use.

Admittedly, my definition above isn’t perfect. On the one hand, it leaves out protozoa (like amoebae and the well-known Paramecium, both of which actually do take in “chunks” of food, but both of which most people would normally consider to be “microbes”. It also leaves IN things like mushrooms, which are not usually thought of as being “microbes” by people who aren’t microbiologists. And, of course, it leaves me with no excuse not to go and learn something about eukaryotic (“plant”) algae (as opposed to bacteria-algae, a.k.a. cyanobacteria) and diatoms. Suggestions for updating my definition may be left in the comments…

Just something that came up while I was assembling what will be the next post. Stay tuned.

Do Not Want: Celestron LDM

Back in Idaho for the moment. The trip was somewhat exhausting, but I thought a followup to The previous post on the Celestron LDM microscope was in order, as I finally got a reply back after almost two weeks.

(20080329:Quick update. I am surprised to see this post is getting more interest that I’d anticipated. I’ve added a brief summary to the end of the post to help clarify my opinion since it seems people may be interested.)

I had asked them if it was possible to replace the objective lenses (so as to be able to use an oil-immersion lens to get 1000X magnification – pretty much a neccessity for decent bacteriological work – such as examining yogurt cultures) and whether the camera could be swapped for a regular eyepiece. Larger yeast cells used in brewing might be okay in 400X, but even there it’d be nice to be able to zoom in adequately to get better detail – like watching conjugation or budding of yeast cells.

The answer:

“The answer is ‘no’ to both because of the sizes, etc. are specific to this unit.”
Email ID: ZZR-372549
Department: Technical Support
Priority:
Status: Closed

I guess there’s no point in asking about getting a darkfield condenser for it. On the plus side, they did actually give me a reply at least.

I’ve got to say I’m seriously disappointed that Celestron has evidently intentionally engineered this microscope product (and their other offerings as well, perhaps?) to Not Play Well With Others. Why else go to the trouble and additional expense of coming up with your own special specifications for the parts when standard parts are readily available?

This seems especially absurd in a product aimed at science enthusiasts, who strike me as very likely to be strongly aligned with the “Maker” attitude…at least if they’re any good at Science Enthusiasm. I think the “if you can’t open it, you don’t own it” concept meshes very well with the investigative attitude necessary for science. So, we want “internet”, and they give us “AOL” instead. A sad, sad fate for an otherwise great concept, and on this basis I must render a verdict of “Do Not Want”.

Find me a version of this product – from any vendor – which can accept standard oculars and objective lenses and I’ll sell blood plasma and beg on the street to raise money for it. (If nothing else, it’d give me an excuse to finally start up the “science begging” blog-post series I’ve been threatening for a while now…) Of course, it’d be nice to have an ordinary “real” microscope, too…this blog still doesn’t have enough pictures.
(P.S. Dear Celestron: although I doubt anybody at Celestron will ever even see my obscure blog, and in that respect my previous post’s comment about sending me one to review was just a joke. Despite this, I was sincere, so in the unlikely event that someone out there sees this post and has the authority and inclination to do so, feel free to send me one to review anyway. And a pony.)

SUMMARY (in my opinion):
Good:

VERY nice, highly desirable concept overall.
Self-contained, platform-neutral design, should work with anything that can support SD cards or USB Storage devices.
Potentially a nice field microscope? (Probably not hard to hack together a battery pack that could be used in place of the AC adapter)

Bad:

Does NOT appear suitable for bacteriological or similarly high-magnification applications
Non-standard components prevent upgrades.
Non-standard components mean vendor lock-in problems (if Celestron gets tired of making replacement parts and some kid scratches your objective lenses or cracks the viewscreen, you’re out of luck.)
Digital camera and viewscreen appear to be integral, so if the camera or viewscreen dies I’d guess the whole device becomes a useless lump.

My recommendations for Celestron or other microscope manufacturers (should any of them care about the opinion of some nerd on some obscure blog like this one):

Please, please use standard parts wherever possible – it makes your device a much safer bet for anyone thinking ahead towards possible upgrades or replacement parts.
Don’t ignore bacteriological applications.
Easily replaceable parts make for graceful failures. For example, if the camera on this model could be swapped for an ordinary ocular, the microscope would at least be usable while the camera portion was being sent in for repair or replacement.

More on the shocking life of yeasts

(Brief Update: Hello Ontario! Did I attract the attention of a Toronto homebrewing club or something? Anyway – welcome!)

I am amazed at how much depravity I uncover as I explore the mystery that is
Saccharomyces cerevisiae.

I’ve previously discussed how the filthy little beasts have drunken orgies and exchange sexually transmitted diseases with each other. Now I find out the inebriated little jerks are peeing in my beer, possibly to try to give me cancer!

No, seriously. Given enough “Free Amino Nitrogen”, for example in the form of the pirate’s favorite amino acid, like tiny little single-celled bladders, the yeast will start excreting extra nitrogen in the form of Urea all over whatever they’re growing in.

Of course, the whole time they’ve also been excreting ethanol. It turns out, under certain conditions urea (more formally known as “carbamide” nowadays) and ethanol will combine like drunken evil “Wonder Twins” to form Ethyl Carbamate.

Front Cover of the book I ran into this as I was reading through my shiny new Wine Microbiology book, which has two pages on this yeast pee byproduct. An article linked to from fark.com recently reminded me of it and prompted this post.

To be honest, this seems a lot like the acrylamide media circus (compare the two links…) that popped up back in 2002. In both of these cases, we’re talking about a substance that occurs as a natural result of the preparation process rather than some new industrial chemical, and in both cases the processes in question have been around probably since prehistory. And in both cases, the real situation seems to boil down to something like “pay attention to your preparation technique, and if you try to live entirely on a diet of overcooked French fries and dessert wines, you might be at an increased risk for cancer.” QED. Or perhaps DUH.

Other than not trying to live on a French McDonald’s� diet, there are some things you can do when you brew to limit ethyl carbamate formation. Put very simply: don’t overfertilize your grapes because that can directly lead to unnecessarily high levels of nitrogen available in your wine, and don’t leave your bottles of brew in hot conditions for long, because ethyl carbamate forms faster in hot conditions.

There, problem solved. A more detailed “ethyl carbamate preventative action manual” may be found here. Meanwhile, I’m pretty sure our favorite drunken little micro-hedonists are too busy partying and making our wines and beers to be plotting our cancerous dooms.

WANT(?)

My parents, apparently comfortable with being microbiology “enablers“, ran into a digital microscope (pictured at right) that they pointed me to. It looks pretty nifty for the price, except for one issue: it only comes with three objectives, topping out at 40X. I can find marketing materials for this microscope, but no technical information beyond what’s on the company’s website (click image to reach that). Therefore, I can’t tell if the objectives are replaceable or not. If they are, the idea of picking up an inexpensive surplus 100X oil-immersion lens and ending up with a decent microscope with which to watch the Yeast Porn and such – on a nice digital screen, no less, rather than squinting into an eyepiece – has a certain appeal to it. The fact that the digital camera takes the pictures itself and only needs a computer connection to transfer files – and not even then if you use an SD card – means that I wouldn’t have to worry about ending up with something that requires Microsoft� Windows� just to look at some microbes (or post glamour shots of them to this blog).

However, I don’t think trying to view conjugating yeast cells or, say, Lactobacillus or Gluconobacter/Acetobacter bacterial cells at 400X would be very rewarding, so an oil-immersion lens is a necessity. And don’t let the “up to 1600 Power with Digital Zoom” thing fool you – it just makes the picture bigger and blockier, not actually more detailed.

So….do I WANT, or not? I sent off an email to Celestron asking about whether I could swap out objective lenses on this model or not. I got back the form “we got your email” email – we’ll see if I get a real reply from them or not. If so, I’ll update this post.

Speaking of which – still no reply from Bristol Brewing Company. Guess they’re either just not “nerd-friendly”, or the person who handles email queries is on vacation or something.

P.S. Dear Celestron – if you were to send me an evaluation model, I’d be happy to review it here on my blog for the ~~thousands~~ ~~hundreds~~ ~~dozens~~ pairs of people who read my ~~elegant prose~~ incoherent babbling…

Where Was I?: “I’m going to have a place like this someday…”

Brewery building for the New Belgium Brewing Company in Fort Collins, CO

Quality Assurance lab at New Belgium Brewing Company, as seen through the 'employees only' door. Incidentally, did you know it’s a long way from southeastern Idaho to southeastern Texas? I made the drive last week, and I’ll be making the drive back as soon as I can get some things FINALLY done around here. On the upside, it’s kind of a fun, if long, drive other than Wyoming’s tendency towards having ridiculously high winds and roads paved with what appears to be a mixture of wet ice and motor oil. I made it down here though, but I’ve already been delayed about a week due to some issues getting inspection arranged on the home we’re trying to buy out here. But you didn’t come here to read me whining about that, did you?

On the way down, I did manage to stop at one of the two Colorado breweries mentioned in the “Wildbrews” book. New Belgium Brewing Company just happened to be only a couple of blocks away from my route through Fort Collins, so I took the opportunity to stop by and check them out.

If you’re familiar with them at all, it’s probably for their “Fat Tire” amber ale which I have seen in stores around the country, but I didn’t care about that. What I cared about is that they actually let their microbiologist (and, it turns out, their other employees too) play, and they have experimental “sour” beers in the same general style as Belgian lambics. Pictured at left is their famous one – “La Folie” (“the folly”). Well, the label on the tap for it, anyway. I’m not certain if cultures other than the standard canned strains of Saccharomyces cerevisiae are used in the initial ferment, but they then move the brew over to barrels that were previously used to age wine, and which no doubt contain a variety of traces of live lactic acid bacteria, other yeasts, and the like (their website also suggests they directly inoculate the beer with lactic acid bacteria as well). The brew sits in the barrel for up to 3 years. The result is nicely carbonated, and tastes almost sweet to me due to the pleasant tartness of the lactic acid. This particular brew is mentioned in the book. Seeing my obvious enthusiasm for the style, I was also allowed to taste a more recent concoction. “Eric’s Ale” was a lighter sour brew made with peaches which I absolutely loved. I really wish they’d had it in bottles for me to buy, but neither it nor “La Folie” were available in portable form, as far as I could tell. Guess I’ll just have to make my own. Once I finally manage to sit in one place long enough to try, dangit.

It was the Belgian Lambic-style ales that convinced me that I really do like beer after all, so long as it isn’t mass-market commercial swill (“Bladderwash”, as Leon Kania, author of “The Alaskan Bootlegger’s Bible” calls it) nor too strongly hops-flavored.

I did taste their “1554” ale – a “black ale” style that they were able to date back to at least 1554 while doing research on the style in Belgium, and several others whose names I don’t recall at the moment. One brew whose name I don’t remember was spiced with Yerba Mate – a caffeine-containing South American herb also found in Celestial Seasoning’s “Morning Thunder tea. (Ethanol is nice and all, but methylxanthines are my favorite…).

And, no, I didn’t forget their names because of drunkenness. When I say “taste” I mean I had a sip or two of each variety I sampled. They had these nifty little glasses like miniature brandy snifters for tasting. I’ll need to get me a set of those one of these days.

An unrelated bit of spiffiness about the brewery is that they seem to run the place as “green” as possible. They even go so far as to subject their brewing wastes to bacterial fermentation to produce methane, which they use to heat their water. How cool is that?

On a final, still unrelated note: there’s evidently been a fad of people selling things on eBay that have shiny surfaces, such as metal teapots. The trick is to take the picture of the item while naked, and standing such that one’s reflection is just visible in the picture of the item that appears on eBay. You know those classical shiny aluminum “Airstream” camping trailers? They had one out in the parking lot.

Photograph of New Belgium Brewing Company's 'Airstream' trailer.

Wait…I don’t see myself in that at all. Dagnabbit, standing in that freezing cold wind with everyone staring at me was a waste of time, wasn’t it…

The other “wild brew” place in Colorado is the Bristol Brewing Company in Colorado Springs. Unfortunately, the only indication I can find of their “wild” brews is a “sour beers” class they did as part of their recent “beer college” series, and a “Skull ‘n Bones” (evidently what they were calling their sour-beer series) T-shirt. As there is also no mention of brewery tours, I did send an email off to the person who appeared to be the contact for such questions, but I’ve yet to hear back. I’d love to stop by on the trip back, but the route will add a couple of hours to the overall trip. This would be well worth it if they’re doing tours, or still doing “sour” beers, or if I could even spend a few minutes chatting with their microbiologist. If not, though, I’ll just have to get on with working on it all myself.

Oh, yes, and the place in Austin that I previously mentioned was called “The Bitter End”…and it ended. Apparently a fire destroyed part of it, and now its being demolished to make way for a massive chain-hotel building. How sad.

The tasting counter and beer cooler inside the New Belgium brewery.

Grossly Oversimplified Science: Obtaining Pure Yeast Cultures

Various yeasts of the genus Saccharomyces (particularly the “Baker’s Yeast” Saccharomyces cerevisiae) represent quite possibly the most important bit of intentional microbiology that we have. We eat and drink the little critters and their byproducts in more or less every human culture that I know of, and are now getting more seriously into burning them, too.

As I’ve mentioned before, gluttony is my second most favorite deadly sin, so bread and booze microbiology is naturally of interest to me. It seemed worthwhile to look into developing my own yeast (and bacteria…but that’s for another post) stocks to brew, vint, and bake with, so I did some poking around. I dug out my copy of Rog Leistad’s “Yeast Culturing for the Homebrewer”, Peter Duncan and Bryan Acton’s “Progressive Winemaking”, a number of internet sources, and finally some scientific papers. I know, I’m a nerd.

I have so far not found much of anything about isolating yeasts from scratch – virtually everything seems to assume that you will “buy” your yeast from somewhere else, and aside from scientific papers most assume that you’re only bothering to culture your own yeast to save money by stretching the sample you bought to brew several batches before buying more yeast from “the professionals” again. This annoys me.

Unfortunately, I’m still on the road and haven’t had time to directly embark on my culture project here. I’m also having a heck of a time tonight trying to come up with a way to make the process of isolating a pure culture sound interesting to anyone besides me. Here’s the extremely abbreviated version:

Take something that’s got (in this case) yeast in it (sourdough starter, unfiltered beer, whatever)
Make up some solidified yeast food: typically this is something like a mixture of sugar, predigested milk protein, and water, mixed with agar to solidify it, and with a small amount of acid added, since the acidity helps inhibit bacteria that might contaminate the yeast culture
Take a tiny bit of the original stuff-with-yeast-in-it, and smear it thinly over the top of the solid medium.
Cover the solid medium and put it somewhere warm for a while until you can see individual spots (“colonies”) of growth

(The idea is that if done right, at some point on the solid media the “smearing” will have spread out the yeast cells far enough that you can make out the mounds of offspring that an individual yeast cell has made. Each distinguishable round spot of growth is effectively made up of millions of clones of the original single cell that started the “colony”)

Take a bit of a single colony and put it in some sterile culture media.

If everything works correctly, this gives you a “pure” culture, isolated from any other kinds of cells that may have been in the original sample. In this example, this is hopefully a brewing or bread yeast culture that you can now use to make beer, wine, bread, or fuel ethanol (the latter assuming you have permission from the Bureau of Alcohol, Tobacco, and Firearms, since it requires distillation.)

Tomorrow: Fun facts about yeast cultures.

All this week: A topic important to secular and religious people alike

It’s not midnight here yet, I’m still on time!

Hello, “Just Science 2008” subscribers and everyone else. My life is insane at the moment but dagnabbit I’m going to do my best to get at least one post up on a scientific topic every day from today (Monday, February 4th) until Friday…

Today’s post is in the form of a gedanken experiment.

First, imagine the following:

Some “entities” existing somewhere

It doesn’t matter what “entities” you are imagining, whether they are products in a market setting, or data structures in a computer program, or topics of discussion on a news broadcast. All that matters is that there can be more than one of them.

A mechanism by which these “entities” are copied (and, optionally, also sometimes removed)

Products are manufactured or recalled, data structures can be copied or deleted, additional news anchors can be added to comment on a topic or conversely may shut up about them…

At least one mechanism by which changes can occur between or during copies

Product designs can be changed, a computer program may consult a “random number” generator and use it to make small changes in the data structure, scriptwriters may alter the news anchor’s teleprompter messages…

Some aspect of the “entities” that affects the rate at which they are copied (and/or, optionally, removed).

Demand by buyers in the market results in ramping-up of production, a computer program may perform some test or comparison of a data structure and use the result to determine how many copies of it to make (or whether or not to delete it), news topics that result in more people watching are repeated more often while those that people tune out from are dropped from the schedule…

What happens to this group of “entities” over time should be obvious. Taking the example of products in a market, producers introduce a variety of products (the group of “entities” in this example) and buyers examine their characteristics and, based on which ones they like, buy some of them. The producers observe which kinds of products are selling more and make more of those, while reducing or outright eliminating the production of those that aren’t selling well. Over time, a few of the kinds of products in this group which best fit the preferences of the buyers and the ability of the producers to make them. These products will dominate the market until the preferences of the buyers or the ability of the producers to produce them change [example: a shortage in the price of a particular material needed for a popular product].

You have most likely observed this process in the “news topic” context yourself, where it tends to happen much faster as “cheap and easy” news stories are happily picked up by news agencies to broadcast until people get sick of them and tune out.

This can all, hopefully, be understood as a purely logical outcome – a conclusion that universally and necessarily follows from the premises given. There should be nothing supernatural or even surprising here, is there?

So, now that you understand why and how evolution works (if you didn’t before), I can move on. (Incidentally, the part of the example above that describes a computerized system is actually referred to as a “genetic algorithm”.)

My purpose in starting with this is because it really and truly is fundamental to the topic that I expect to spend most of this week posting about, and which has been of vital importance to human culture and intellectual development for thousands of years. This most important subject involves such notable figures as Charles Darwin,St. Thomas Aquinas, Noted American Science-guy Benjamin Franklin, New England Puritan Cotton Mather and Quaker William Penn ,Hardcore Catholics like Pope John Paul II, Hardcore Athiests like PZ Myers, even famous religious figures like Jesus.

I refer, of course, to wine (and beer and other examples of ethanol production).

Okay, here’s the background: I just graduated with my B.S. in Microbiology, and I’ve got this whole “Hillbilly Biotech”/”Do-it-yourself”/”Practical Science” kind of thing going on in my interests. That being the case, I wondered what it would take to isolate, culture, and maintain my own yeast (and bacteria – more on that later) stocks from the environment rather than buying “canned” cultures – or at least play with the “canned” yeasts to create my own stocks. As I was poking around, though, I kept running into the same attitudes – namely that it’s “too hard” to do this, and although there are a number of people who advocate re-culturing canned commercial yeasts for a short time to save money, none of them think it’s feasible to do this for more than a couple of generations, at which point we are assured that you have to go buy it again or else “mutations” will inevitably appear and scary and mysterious “off-flavors” will result and the brewing police will come and throw you in jail for deviating from the archetype of whatever pre-defined style of wine or beer you’re trying to make. Or something like that. In any case, it’s because of this fear of “mutations” that I am starting out with this “evolution”-related post: in biological evolution, various forms of alterations in the genetic material are the “changes before or during copying” in the gedanken experiment above.

I didn’t buy it when people were telling me that it was “too hard” to learn how my computer works so that I could run Linux and should instead leave deciding what my computer should do to the “professionals”, and I’m not buying the same argument about commercial yeasts, either. If I felt that way, I might as well leave the rest of the complex technology of brewing to the “professionals” too, and consign myself to “Lite Beer” and “Thunderbird” for the rest of my life.

I’ve been spending much of the last few weeks perusing books, online articles, and scientific papers on subjects related to brewing in general and brewing yeasts in particular, and this should form the bulk of this week’s post topics, of not well beyond this week. Tomorrow I intend to start in on the actual process of culturing yeasts. Meanwhile, feel free to correct my no doubt horribly over-simplified explanation of evolutionary processes in the comments.