Yummy mold!

Fuzzy mold growing in a petri dishYes, I mean “mold” as in “fuzzy fungus”, not as in “something you put JellO® in to harden into a funny shape”. I’m not even talking about “Blue Cheese”, though blue cheese is pretty good too. I’m actually referring to Fusarium venenatum.

Okay, the picture linked here is actually F. oxysporum, one of several Fusarium species that are crop diseases (mmmmm, rotted moldy potatoes…), but I haven’t found a picture of a F. venenatum culture yet. Anyway, before going to bed I just wanted to mention that I’ve run into the first genuinely good “meat substitute” that I’ve tasted so far, and it’s made of mold.

They evidently grow it in vats, dry it into mats, mix it with some egg white to hold it together, and then make meat-like food product out of it. “They” being Astra-Zeneca, who appear to be the owners of the “Quorn®” trademark.

The chicken-like food product (“Chik’n”) patties they make are actually passable imitations of chicken, and actually taste good. They make a breaded Gruyere-“Chik’n” patty thing that I will probably go out and buy more of, of my own free will – which will be a first for “vegetarian” food for me.

Makes me wonder what I’d get if I subjected another known edible mold like Penicillium roquefortii (Mmmmmm…Blue Cheese) to the same process. Would I get blue “meat”?…

And, no, I’m not actually a paid shill for Astra-Zeneca or Marlowe Foods (who distribute the “Quorn®” products), though as I mentioned a while back to the dairy industry in my “Margarine makes you stupid” post, if anyone wants to HIRE me as a paid shill independent advocate, I could sure (yes, still) use a good microscope. Come on, Astra-Zeneca! A fancy biotech company such as yourselves must surely have dozens of surplus microscopes laying around!…

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.

This Week = No Fun, but here’s an update anyway…

Busy week with unpleasant surprises, but I ain’t dead yet. You’re probably wondering what a hot dog that’s apparently eagerly anticipating eating itself has to do with that. The answer is: nothing, but it does relate to something I have been intending to post about for a long time, but haven’t since I didn’t have access to the paper…

So, in lieu of blasting out Twitter®-style updates on my Laconica feed that nobody reads anyway (a few people no doubt see the echo of them on Twitter® itself, but I don’t know if anyone cares…), here are a couple of what-I’m-doing-now updates before I go to bed:

  • I just shot off an email to the webmaster (the only contact I could find who might have the relevant information) of the Institute of Brewing and Distilling, trying to get access to a classic paper published in the Journal of the Institute of Brewing and Distilling for the upcoming “On the Shoulders of Giants” carnival.
  • There’s no way I can afford the ~$300US that it would cost to join the group, nor even at the moment to pay the typical $30 or so that greedy paywall-imprisoned publishers charge for individual articles. However, they appear to be opening up their archives to the public, for which I think they deserve substantial praise. Still, they haven’t worked their way back to the first few decades of the 20th century yet, so I had to email and ask if there was a way to get the article in question. If not, I’ll see if there’s any way to get it through inter-library loan in time.

  • “Small Things Considered” asks “What Microbiological Discovery in 2008 Did You Find Especially Interesting?” Which brings us to the “self-eating” thing.
  • The paper on caffeine’s induction of macroautophagy (“self-eating”) in yeast (and what happens when benzoic acid is also present) finally escaped from the paywall prison in January, and I now have a copy. I at least thought it was full of interesting implications (along with some useful knowledge), so I’ll hopefully be posting about it soon.

  • I’m also a computer nerd
  • Particularly when it comes to things like Linux. I’ve been thinking of trying to do some recordings on a couple of practical subjects that interest me for “Hacker Public Radio”

  • And of course, I still need to do some Xanthomonas snot Xanthan Gum experiments.

I am an attention-whorewilling to listen to my readers’ interests, so if anyone has suggestions or comments feel free to post them…

“Untersuchungen über Bacterien”

Cultures of Blastomyces dermitiditis, showing how it grows like a mold at one temperature and like a yeast at another.Once again I’m down to the last minute, trying to juggle too many things and almost missing this month’s “Giant’s Shoulders” blog carnival. Almost.

Today we go once again all the way back to the Victorian era, to see that if you thought bacterial taxonomy was difficult now, imagine what it was like over 130 years ago:
Cohn F:”Untersuchungen über Bacterien”; Beiträge zur Biologie der Pflanzen; 1875, vol 1; pp 127-222
(Or “Researches regarding Bacteria”, in “Contributions towards the Biology of Plants”)

This paper is an overview of the problem of categorizing bacteria among the types of living things, and makes some early suggestions. I don’t think it’ll spoil too much of the punchline to point out that not only is the journal about the biology of plants, but the paper also starts out with Cohn describing how he came to work at the “plant physiological institute”. Cohn’s assertion that bacteria are definitely a form of plant actually stuck for at least another three-quarters of a century or so – I have a copy of a 1945 book on bacteriology that actually has a short discussion on why bacteria are categorized as plants rather than animals (or “animalcules”, even). That’s only part of what’s interesting about this paper, though.

Cohn discusses a number of problems with the nature of bacteria in his time. For one thing, he says there had been little real effort to even come up with a coherent scheme for classifying bacteria at that point. He does mention one previous attempt to come up with a system, but on the whole it seems everyone is just coming up with terminology on the fly – even taking Pasteur himself to task for throwing around a variety of terms related to microbes without distinguishing what the terms actually refer to. The reason for this, really, is just that figuring out pretty much anything in detail about bacteria was a seriously difficult problem at the time. Cohn explains why; how it is really impossible to make out more than general shape and size from microscopic examination, and how the lack of any detectable sexual reproduction makes it impossible to do positively identify members of the same species. In fact, even very obvious differences in appearance might not be definitive. It was suspected (and later demonstrated) that some of what appeared to be completely different fungi were actually just different life-stages of the same fungus. (Hopefully you can see the picture at upper right, with the bacteria/yeast-like growth on one tube and the obvious and very different fuzzy mold-type growth on the other. Both are actually the fungus Blastomyces dermitiditis.) Just as some of Cohn’s contemporaries considered that perhaps all molds and yeasts were really just different stages of life of the same organism, perhaps the same might also be true of bacteria?

Cohn does, after all, promote the notion of bacteria as a type of fungus. You may even remember an old word for bacteria: Schizomycetes, that is “fission-fungi” (that is, fungi that reproduce by splitting in half rather than producing spores). This makes sense if you consider that bacteria are more like plants and algae than animals, and fungi were considered to be plants that lacked chlorophyll. Although lamenting that it was not feasible to really separate out individual bacteria to determine whether they ever changed form – this was still three years before Joseph Lister actually did so – Cohn unwaveringly felt that bacteria were in fact made up of several different genera and species, and set out an early attempt at classification.

Once again, Our Friend the American Society for Microbiology hosts a translation of this paper, complete with a couple of paragraphs of more modern editorial commentary at the end. It’s well worth a look.

A photographic portrait of Ferdinand Julius CohnUnfortunately, I don’t think Ferdinand Cohn’s hairstyle is nearly as spiffy as Eduard Buchner’s cool “Colonel Sanders Guest Stars on Miami Vice” look. I think he looks kind of like a slightly-better-fed Sigmund Freud with a bad comb-over. But that’s just me.