Fred Transplant: Success!

A Gram-stained view of yeasts and bacteria in a sourdough culture named 'Fred'.

I had to do a Fred Transplant last week. A grey fuzzy mold had taken up residence in on the sides of the jar above Fred’s liquid culture, so I set up a fresh container with fresh water and flour, and dipped a spoon down the center of Fred to the bottom, pulling up just a tiny amount of the stuff in there. Then I mixed it into the fresh stuff and covered it with plastic wrap (instead of a paper towel this time.)

Fred smells like Swiss Cheese Feet right now, but he’s obviously still growing, as you can see from last night’s “Gram Stain” microscopy. The slightly blurry light-red-brown lumps are, I believe, yeast cells, possibly Saccharomyces boulardii, since I dumped a capsule of supposedly-still-viable “probiotic” yeast of that species into Fred previously. I have no idea who the bacteria are in here at the moment. I did also see a small number of longer, thinner bacterial cells in there (presumably Lactobacillus) though most of them are the ones you see here.

Meanwhile, I’m about to dig out the still-unused Hillbilly Autoclave and try it out on the media I’m mixing up to try to obtain a culture of genuine wild “native flora” vinegar/kombucha yeast-and-bacteria to play with from the local wildflowers that are just now getting into full bloom.

My starting recipe goes something like this: I mix up about 2 Liters of distilled water with about 100g of glucose (“Dextrose”/”Corn Sugar”), 100g of sucrose, 500mg of L-Arginine, and enough phosphoric acid to drop the pH down to about 5.5 to 6.0. That is intended to be then poured into small “canning” jars in about 100ml amounts and pressure-cooked for at least 15 minutes to sufficiently sterilize and seal them. Meanwhile, a single generic-brand children’s chewable vitamin is crushed up and dumped into a 4-oz bottle of cheap vodka and well shaken.

Then when it comes time to go bioprospecting, I’ll pop open the jar of acidic sugar solution and add about 5ml of the cheap-vitamin-vodka to it to give me about 2% ethanol, and then go find some flowers to cut off and dump into the jars, which will be loosely covered with foil (to let air in but keep dust out) and put in a nice quiet cupboard to grow for a few days.

Hypothetically, the only things that are likely to grow in that will be microorganisms associated with vinegar-making. At some point I’ll also make up a batch of sweet black tea and see if I get a kombucha-like culture going in it, and make up some solid media to try to isolate individual microbes from it.

Microscopy Preview

Intentional food microbiology:
Various yogurt bacteria floating amid milk protein and fat globules

UNintentional food microbiology:
Wet-mount photomicrograph showing mold mycelia and a mass that kind of looks like large spore cases or something

I still don’t feel like I got nearly enough productive stuff done this weekend, but I did manage to do a bit of microscopy – plus demonstrating to myself that I still remember how to do a “Gram stain”. Real Post with explanation and more pictures to follow Real Soon Now…

Cookies as an antidote for Yule Poisoning

(Oops, quick edit: the references on erythritol toxicity – or rather lack thereof – are now actually included…)

Crowds, Crass Commercialism, and Crappy Christmas Choruses give me a nasty case of Yule Poisoning, and I’m sure I’m not the only one.

I spent the afternoon/evening prepping for and performing some cookie experiments again, and I feel much better. Yes, my cookies are that good.

I had a request for Peanut Butter cookies, so I figured I’d do some experimenting with that tonight. In fact, while I was braving the Christmas Consumption Crowds to get my supplies, I happened upon an ingredient that I decided I had to try as a variant.

(The picture, incidentally, is someone ELSE’S peanut butter cookies – “diekatrin” on Flickr – click photo to go to the Flickr page – I still haven’t quite gotten the hang of getting decent photos of my own food yet.)

My initial peanut-butter cookie recipe came out too dry and not sweet enough, but I think adding 50-75g of honey should solve that. That’s not the most successful experiment of the evening though. That’s reserved for the following recipe for…Sunflowerseedbutter cookies.
(Suitably pompous name pending, as soon as I test version 2.0 of the recipe, which will substitute bread flour for the “all-purpose” flour)

(Pompous Name Pending) Sunflowerseedbutter Cookies

Materials and Methods

Powdery stuff

  • 190g “All Purpose”(Around 1 cup) “All Purpose” Flour
  • 3g NaHCO3 (1/2 tsp)
  • 1-1.5g (1/4 tsp) “Baking Powder”
  • 2g (1/4tsp) NaCl
  • 750mg Xanthomonas campestris exopolysaccharide (~1/4 tsp “Xanthan Gum”)

“Wet” stuff and sugars:

  • 150g honey
  • 100g Erythritol
  • 4g glycerol (about 5ml)
  • 50ml double-strength black tea
  • 140g Sunflower Seed Butter (about 1/2c)
  • 60g unsalted butter
  • Contents of 1 Gallus gallus egg, 50-55g (approx 60g with shell… aka “large”)
  • 5ml Vanilla Extract

The “dry” goods were mixed in one container, while in a separate container, the “wet” goods and the sugars were mixed in another. The dry material was then blended carefully into the wet material in a large steel mixing bowl using an electric hand-held mixer until completely homogenized.

Once homogenized, the dough was spread out in the bowl and chilled at ~18°C(O°F) for approximately five minutes to enhance firmness.

The dough was then measured onto a “non-stick” baking sheet in approximately 30ml roughly-hemispherical aliquots using a small disher, and then pressed down with a fork to approximately half their original height. A few shelled, roasted sunflower seeds were pressed into the surface of each to make distinguishing them from peanutbutter cookies easier.

The cookies were than baked at 190°C (~375°F) for approximately 18 minutes, then slid onto a “non-stick” wire cooling rack at Standard Temperature and Pressure until equilibrated with the temperature of the kitchen.


The experimenter believes this batch of cookies emerged a bit too soft – actually sliding them off of the baking sheet to the rack distorted them, and they still appeared (in the words of the experimenter) “squishy”. Once equilibrated with room temperature, the cookies had a texture more in line with what would be expected from a normal “soft cookie”. The flavor was judged to be superb by the experimenter, who happens to like the flavor of sunflower seeds.


The use of erythritol makes this a “reduced calorie” and “reduced-sugar” recipe, though not entirely sugarless or “diabetic safe” necessarily, due to the use of honey. Erythritol is a sugar alcohol like sorbitol, mannitol, xylitol, or glycerol (“glycerine”), all of which are often used as low-glycemic substitutes for sucrose or other sugars. Sugar alcohols can often cause digestive discomfort, however, because they are poorly absorbed by human digestive tracts, leaving them to be digested by gas-producing gut microbes. Erythritol is unique in that it appears to be well-absorbed by humans, and yet is not metabolized by humans to any substantial degree and is safely filtered out by the kidneys and excreted in urine[1]. Being unmetabilized by humans, it is theoretically “zero calorie”, though the US FDA mandates a calculation of 0.2 calories per gram (compare to 4 calories per gram for sucrose). Unlike xylitol, erythritol is also safe for dogs[2] and ferrets[Sorry, can’t find the citation for this one at the moment…], for whom xylitol can induce fatal insulin shock and/or liver damage. Erythritol, unlike glycerol or sucrose (“table sugar”), is not appreciably hygroscopic, though, so adjustments must be made to recipes using it to avoid an overly dry result.

Glycerol (sold as “Glycerine”, which can be found in cake-making supplies as an ingredient used to keep cake frosting moist) closely resembles erythritol in structure, being (to oversimplify) a one-carbon-shorter version of the same molecule. In addition to hopefully helping to prevent drying out of the cookies, this was included here in the hopes that it would also help the erythritol dissolve. Previous informal testing (unpublished results) appears to support this hypothesis.

Honey was used as a second sweetener so as to include a “real” sugar and to help counter-balance the lack of hygroscopicity of the erythritol. The experimenter also notes that he believes mixing sweeteners tends to provide a better-tasting sweetness than relying entirely on one sweetener, particularly when including less sweet “sugar substitutes” in the mix. Honey was also chosen to provide additional moisture, as a previous batch of peanut-butter cookies (the recipe from which this recipe for sunflower-seed butter is derived) using ordinary sugar and “brown sugar” had turned out excessively dry.

“Xanthan gum” is a polysaccharide (as are cornstarch and pectin, for example) produced by a natural fermentation process from the γ-Proteobacterium Xanthomonas campestris. Along with a wide variety of exotic industrial uses (such as oil-well drilling “mud”), Xanthan gum is also used as a safe food ingredient to help hold water and keep soft foods from being too runny. It helps protect ice-cream from becoming grainy during possibly partial thaw-and-refreeze cycles during shipping and storage. It’s also used to hold “gluten-free” doughs together, which is nice for people who may be allergic to gluten proteins but who still would like to eat bread…

As far as the potentially excessive softness of the cookie, the experimenter believes that substituting bread flour for “all-purpose” flour and baking for up to 20 minutes should solve the softness problem, resulting in a chewier texture which the experimenter believes will be more appropriate.

The experimenter also notes that a second batch of the same recipe, cooked for approximately 20 minutes at ~205°C (~400°F) were nearly burned, though they did come out firmer but drier in texture. The flavor was still judged superb, other than the slight burnt note. Subsequent versions of this recipe will revert back to the original 190°C cooking temperature.

Obviously, further research is needed to determine the correct modifications to achieve perfect texture, and of course, to broaden the sample size of of the taste-testing group, and the experimenter should be given a sizable grant and a nobel prize for this research. Well, a grant at least.

Or at least some praise or something. Or a cookie, except that the experimenter obviously already has some.

[1] Munro IC, Berndt WO, Borzelleca JF, Flamm G, Lynch BS, Kennepohl E, Bär EA, Modderman J:”Erythritol: an interpretive summary of biochemical, metabolic, toxicological and clinical data.”;Food Chem Toxicol. 1998 Dec;36(12):1139-74.
[2]Dean I, Jackson F, Greenough RJ:”Chronic (1-year) oral toxicity study of erythritol in dogs.”;Regul Toxicol Pharmacol. 1996 Oct;24(2 Pt 2):S254-60.

Dangit, I’m out of time. I was going to try out some crazy ideas with my Ginger Cookie recipe, too, and see if I can develop a Kombucha culture from scratch. Guess that’ll have to wait, because it’s bedtime now. Back to work in the morning…

Magical Miracle Elixir: “better than bleach”. Secret ingredient? Bleach.

The Los Angeles Times published a bewilderingly hyped article today about an electrolytic device that makes “miracle” liquid. The article describes what actually is a kind of nifty gadget that uses an electrical current and a couple of semi-permeable membranes to generate (separately but simultaneously) a “degreaser” and a “sanitizer” out of ordinary salt and tapwater. They say that not only can you use one output to clean your dishes, the other one is “10 times more effective than bleach in killing bacteria”(insert a long string of exclamation points there). I just have one thing to say about that:


Continue reading Magical Miracle Elixir: “better than bleach”. Secret ingredient? Bleach.

Sophic Suds

A beer-colored, sepia-tone-like picture of glass of beer overlooking a valley
(Image: “When Beer Ruled the Earth” – you should really click through and read the caption that goes with it…)

A fundamental aspect of my personal philosophy is this: If you cannot play with something, you have not mastered it, and if you do not play with it, you will not master it.

I can sit here and read for hours, but it’s time I actually put my hands on some brewing again. I have a pound each of wheat and amber dried malt extract, an ounce of a low-bitterness (~2.9% alpha-acids) pellet hops, a packet of medium-attenuation dried beer yeast, two 39 millihogshead plastic containers that I can use as fermenters, an early-20th-century hand-cranked blower/bellows, a hot glue gun, a gallon of pineapple juice, some air-line tubing, a cabinet full of spices (including, of course, ginger), at least one small room air-filter, several pounds of honey, perhaps half a cup of granular erythritol, glycerol, a whole mess of glass bottles and bottlecaps, a variety of high-caffeine black tea bags, miscellaneous kitchen implements, a couple of copper-coated scouring pads, a selection of two-liter PETE bottles, iodophor concentrate, a hydrometer, a somewhat overstressed and twisted mind, a wife, four cats, and a dog. What shall I make?

I’m thinking I should aim for a mildly sweet brew with a ginger bite, perhaps adding a bit of tea or pepper if the sweetness needs balancing – but of course part of the goal of the exercise here will be to try to adapt to whatever I’m getting along the way…


What shall I do?!?

Colored nigiri rice colored and shaped like 'Marshmallow Peeps'Since natural forces have not (yet) secured a replacement job for my Minister of Domestic Affairs, I’m forced to appeal to the supernatural and assume that the Spirits are angry with me for not yet having performed the appropriate Devouring Of The Soft Pink Bunnies ritual this year…so I’m devouring a package of pink “Peeps” bunnies. No doubt good fortune will finally swiftly follow…

Meanwhile, I’m poking around in patents and scientific papers, pondering a few different possible topics for the next post:

  • More on the “Nathan System” of brewing, with reference to patents and the intended purpose thereof (and pondering how to construct a homebrew-scale “Hillbilly Biotech™” version thereof)
  • Fermented foods and beverages review and request for ones I haven’t heard of yet
  • Bad poetry
  • The previously mentioned paper on getting yeast cells to eat themselves to death
  • A post composed mainly of photographs of myself with no clothes
  • The current collection of quasi-random scientific publications I’m wading through for fun
  • Some computer-related nerdity
  • Anything else

Please place your suggestions in the comments, I beg of you. Even if they are just long strings of profane threats of violence should I elect to post on [insert forbidden topic here].

“Improvements in the Fermentation and Maturation of Beers”

Judging by my webserver’s logs, almost nobody actually bothers to click through the blog-carnival host’s site to read my Giant’s Shoulders” posts. This could be due to a secret conspiracy involving famous bloggers and several shadowy government agencies. I suppose, though, that there’s a chance that simply nobody but me is that interested in non-medical microbiology. Well…today’s post is an attempt to disprove that concept, for what aspect of non-medical microbiology could be more universally appealing than beer?

Unfortunately, in the middle of trying to assemble this posting, I see the February host has decided to put the carnival up a day early, undercutting my experiment. See, I told you it was a conspiracy! I suspect the Secret Cabal of Popular Bloggers was getting pressure from the Trilateral Comission, the NSA, and Pepsico® to silence me, so they had to do it. At least being forced to miss one, I am now free from the “I’ve been posting to these since the beginning, I can’t miss one now!” treadmill.

That means, loyal readers, that you get to see this post a month before everyone else! Hooray! Stick it to The Man™! Comically paranoid rantings aside, it also means I can split this up into more than one post, which may be more readable considering how much ground the article in question actually covers. Today’s Classic Scientific Paper is:

Nathan, L:”Improvements in the fermentation and maturation of beers.”; 1930; J. Inst. Brewing; 36; pp538-550

I ran across this reference recently while working my way through an industrial microbiology text[1] that I checked out of the campus library. According to the author of this text, “The use of cylindro-conical vessels in the brewing of lager was first proposed by Nathan (1930)[…]”, referring to the now-ubiquitous style of metal fermenter seen in small brewpubs and “MegaBladderwashCo” large-scale industrial breweries alike. Based on this I had expected the reference to be a digression on the design, construction, and testing of the fermenter. When inter-library loan managed to get me a copy of the paper, I found something much more involved.

The paper is a presentation made by Dr. Leopold Nathan in 1930 to the Scottish section of the Institute of Brewing. The topic was not simply a fermenter design but the entire “Nathan System” of brewing which appears to be the basis of modern large-scale brewing, especially for Lager-type beers. At this point, Dr. Nathan had apparently already been developing this system for about thirty years (apparently starting with a German patent in 1908, which I’ve yet to find a copy of), so as you might guess it was not just a single invention but a whole collection of them. Compared to the more rustic techniques frequently in use at the time, the “Nathan System” of brewing promised to provide faster production, more consistent results, and a better final product. It does this mainly by improving the removal of “trub” (the cloudy bits of protein and such that settle out of the malt-water – the “wort” – after you boil it), preventing infection of the beer with undesirable organisms during the cooling, hops-infusion, and aeration, and by eliminating the need to “age” the brew to make it palatable. The most important improvement in the “Nathan Process” seems to be how he treats the wort between boiling and “pitching”.

For anyone unfamiliar with the brewing process, here’s a Grossly Oversimplified review of the steps:

  • Boil some malt-sugar dissolved in water to sterilize it and to help coagulate the “trub” proteins so they’ll settle out of the liquid.
  • Cool the malt solution and aerate it so that the yeast will grow in it.
  • “Pitch” your yeast into the now-cooled-and-aerated malt-water, in a container that will keep air out while letting out the carbon dioxide bubbles that the yeast will give of during the fermentation
  • Wait until the yeast get done fermenting, then put the resulting liquid into bottles/kegs/casks/whatever.

Diagram showing the containment vessel, cooling system, and sterile-air generator for the 'Nathan method' of brewing
I’ve added a couple of labels to that image from the paper, which I’m guessing was itself copied from a contemporary patent of Dr. Nathan’s. There are two purposes to this part of the Nathan Process – To cool and aerate the wort quickly without exposing it to risk of contamination, and to move trub and volatile sulfur compounds that would otherwise make the brew taste and smell funny. The hot boiled wort is pumped directly into an insulated vat (labelled “A” in the diagram) from the boiling kettle. At this stage the wort is hot enough to prevent anything from landing in it and growing. Then, the hot wort is pumped from the top of this vat into a clean-room containing a cooling device that the wort is poured on, cooling and aerating it as it flows through. Infection is prevented here by the fact that the room has a continuous stream of “sterilized” (or at least well-filtered) air, which is exhausted through the vent in the ceiling. The cooled, aerated wort is then pumped back out of the room and into the bottom of the insulated container below the still-hot wort.

Because of the large open cooling room with its constant stream of clean air, the cooling and aeration step also allows the volatile sulfurous compounds of “jungbukett” (The “Bouquet of Youth”; the unpleasant smells and tastes of immature beer, described in this paper as ‘onion-like’) to evaporate off and be carried away. Since waiting for these compounds to break down was apparently a primary reason for having to “age” lager before selling it, this not only improves the quality but eliminates the need to store the beer for months after fermentation.

The now-chilled wort then rests back in vat “A” and the trub settles out onto horizontal plates inside the vat, where it stays behind when the clarified wort is pumped out to the fermenters.

I did some poking around, and this appears to be what is described in US Patent# 1,581,194 (application filed in August of 1921), in case you are bored and want to look that up. If not, or if you don’t want to deal with the frustrating hassle of trying to view TIFF files in your browser, I intend to provide a followup post with some more details of the process and some interesting bits I found in it, and I’ll include a pdf of the patents, assuming anyone wants them.

Oh, one last thing – I’ve had no luck getting any biographical information about Dr. Leopold Nathan. Unfortunately when you search for “Leopold Nathan”, the results are clogged with references to a murdering smartass named “Nathan Leopold” instead. Doesn’t Google™ realize that brewmeisters are far more important than obscure murderers? No pictures of him, either, so I can’t even say whether his hairstyle is cooler than Eduard Buchner’s or not.

[1] Stanbury PF, Whitaker A, Hall SJ:”Principles of Fermentation Technology (2nd edition)”; 1995; Elsevier Science, Ltd; Tarrytown NY


They say “When life gives you lemons, make lemonade”. What if life gives you snot instead?

Someone's slime-covered handNow, see, this is what happens when I’m too poor to buy nice distracting new toys for myself. (No, not the hand in the picture – that’s not mine, it’s just there for illustration.)

I found a pot that I’d rinsed well but then left filled with water in the sink to soak, to help remove the last of the rice bits stuck to it. It hadn’t gotten stinky or fuzzy or anything, but it had gone…viscous. Like a light sewing-machine oil. Naturally, I took appropriate action to deal with it.

I fed it.

Glucose (“dextrose”), to be precise. It’s since been dumped into an old glass jar and the original pot thoroughly scrubbed with hot soapy water. At this point (a day later) the slime is closer to the viscosity of vegetable oil now. And I fed it again.

I wonder what it is? I mean, obviously it’s bacteria-snot, but what kind? I suppose if I had some iodine I could check to see if it’s a polysaccharide (evidently this test works on polysaccharides besides starch). If only I had a microscope, I could at least get some basic hints as to what’s producing the slime. Maybe I can maintain a culture and figure it out later, if I can ever afford a real microscope. Perhaps I could even attempt a strain-improvement program to increase the production rate…

Uh…I did mention I was a nerd, right? Okay then.

I wonder if anyone at work has a bacteriological microscope setup that I could use?…

I have a shocking confession to make.

I think I may be a nerd.

No, no, don’t try to deny it. I think it pretty much has to be true for someone who reads a 10-page scientific paper (hover or click here to see the reference) in order to learn that bacteria-snot is slimy. Yes, I am a nerd. And for that I am deeply, deeply….

Oh, who am I kidding? I like being a nerd.

Stainless Steel fermenters at a breweryFor one thing, being a nerd allows me to fully enjoy one of the perks that my job gives me – namely access to a lot of scientific papers that I otherwise wouldn’t be able to afford to obtain access to from the greedy [insert your favority profanity here] who insist on charging $30 for permission to look at a decades-old articles for a day. I should add that this perk includes Inter-Library Loan for articles that I can’t get online, and the service on campus is great so far. Same day delivery of a classic article from 1930 in what I’m guessing most people would probably consider an obscure journal.

It doesn’t have quite the same thing in it that I expected from the source that pointed me to it, but I think it can still be considered “classic”. I need to re-read it more carefully to make a final decision on this, but I think I have my next “The Giant’s Shoulders” article in time for this month’s upcoming issue. And, yes, the picture attached to this post is a hint (and, no, it’s not directly related to the bacteria-snot article mentioned above in any way…)

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

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

I think I may be an Applied Microbiology nerd.

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

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

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