As if I didn’t have enough to worry about already…

Apparently, the Itty Bitty Kitty Committee thinks I don’t have enough to do.

A very small, young orphaned kitten.
Why me? Don’t misunderstand, he’s an adorable little wretch, and there’s no way I’d have suggested the Minister of Rocktology abandon an orphaned kitten, but I still think we are well beyond Maximum Safe Cat Density already.

Here’s some trivia I read somewhere: supposedly, most felines have pretty much the same general behavioral responses and temperament. This means a housecat (Felis catus) is about as amenable to being a pet as, say, a tiger (Panthera tigris).

A very small, young kitten sitting on a faux-fur blanket with a printed picture of a tiger on it
As I remember it being described, the only real difference is that when a specimen of Panthera tigris decides to dart out from behind the couch to attack your ankle for no apparent reason, the effect on your ankle is somewhat more severe, hence the relative popularity of less-bodily-harm-capable Felis catus as pets.

I rate “Kodama” (as we’ve named him) here at around one picotiger worth of ferocity, though that seems to be increasing rapidly as he gets proper feeding and play.

Still…why couldn’t it have at LEAST been a puppy, if it had to be anything at all?…

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.

Don’t forget to feed and walk your mitochondria

Yes, I’m still here – though I don’t know if any of YOU are.

The pay at my job is somewhat low for the skillset it requires, but makes up for that by having a very reasonable workload, a pleasant work environment, and certain perks – like access to the electronic journals that my employer subscribes to. I added an RSS feed from pubmed intended to cover my main interests – basically edible and industrial microbiology and biotechnology. Every day, a list of 300-600 or so new scientific articles pops up in my feedreader and I scan through the titles looking for anything interesting to me. Unintentionally, my selection appears to also result in quite a bit of diabetes, obesity, and sports medicine research. Lately I’ve taken a moderate interest in our own most blatantly bacterial components, the mitochondria.

Mitochondria are kind of like a nearly 2-billion-year-long case of typhus (or Rocky Mountain Spotted Fever, if you prefer). After infecting our ancestors (and now us) for so long, they’ve been reduced to dependency on living in our cells. Perhaps a bit like the progression from wolves to Chinese Crested dogs. On the other hand, having thoroughly domesticated them, we get a lot of use out of them, and couldn’t live without them. Their ability to harness the electron-sucking power of oxygen means we get almost 20 times more energy out of our food than we otherwise would, which is a good thing since biologically speaking, keeping the hideously complicated mess of biochemistry that makes up a human body takes a ridiculous amount of biochemical energy compared to that of normal organisms (i.e. prokaryotes).

Lately in the stream of new publications I’ve been seeing a number of papers suggesting that a lack of proper mitochondrial activity might be related to obesity and related problems (e.g. “metabolic syndrome”, type 2 diabetes and insulin resistance, obesity-related “inflammation”, and so on) and even some age-related problems, both physical and mental. There is some seriously interesting research going on into treatments to potentially stimulate mitochondrial activity and whether this might help solve a number of health problems.

So…take good care of your mitochondria. For the past couple of weeks I’ve been trying to pay special attention to properly feeding my mitochondria and making sure I take them for regular walks (and paddling trips and so on). It could, of course, be purely psychosomatic, but right now I feel better than James Brown

There’s a fair amount of rational skepticism over using drugs or nutritional supplements to stimulate mitochondria, but here’s a tip that I suspect everyone’s doctor would accept: make sure you take your mitochondria for regular walks. Frequent exercise (particularly endurance exercise) seems to be a scientifically well-accepted way to induce production of more mitochondria.

But now I have to go to bed. My main complaint with work these days is that it eats up essentially my entire day, leaving me with just enough time for some household chores between getting up in the morning and going to bed in the evening. Not their fault I live almost and hour and a half from work, though (and at least the commute is through relatively low-traffic and scenic terrain.). Still, it makes it hard to get blog posts and podcasts done (episode 4, on the subject of “heat-fixing” of bacteria for microscopy – particularly Mycobacterium tuberculosis – will be out as soon as I can manage. Still pondering the subject of Episode 5. I’m saving the “Two Mass Spectrometers, High Performance Liquid Chromatography, and a Female Donkey” episode for later when I manage to surpass the “nearly 3” listeners that I seem to be stuck at…)

“Stir-Fried Stochasticity” podcast: pilot episode

Cornelia the Happy Mutt with a tennis ballI’m still not sure I know why I have a desire to push recordings of my voice onto a more or less innocent worldwide population, but I do. And now I have a real theme to wrap an attempt at a podcast (or as I prefer – “oggcast”) around: scientific papers.

I finally got annoyed at press-release-based science stories one too many times, and thought to myself “why does almost nobody who does these stories at least cite the dang thing so I can go look it up and see what’s really in it, if they can’t be bothered to actually read and report on it themselves rather than just the press-release?” The story in question was the recent one about how babies understand dog-language (or something like that). Since I consider the dog to be a philosophical role-model, I wanted to read the actual paper and see if it was as silly as the headlines made it sound or (as I suspected) less flashy but more solid…but even “Science Daily” didn’t cite it.

Finally talking myself out of putting off doing audio recording, I tracked down the original paper, read it, and whipped out a rough show discussing what I found in the paper. I had fun doing it, so I’d like to turn it into a series.

I’ve put up a utilitarian page at with both a built-in <audio> tag interface and direct-download links for both Ogg Vorbis and MP3 versions.

I’m still deciding exactly how I’m going to decide on the papers to cover – should I pick obscure, forgotten ones that almost nobody else would ever read again without me stumbling on them and talking about them? Classic papers? Papers related to recent news stories like this one? All of the above? Depending on how long I end up trying to make the episodes, perhaps starting with some kind of scientific question and then reporting on a selection of papers I dig up to address the question, or just a selection of papers on the same subject? I’ve already gotten a request for an episode on the theme of prokaryotic extracellular polysaccharides…

The rate at which I can convince myself to try to crank these out (and improve their quality) is directly proportional to how much interest there might be out there in them, so please don’t hesitate to let me know if you think this might be interesting. Please don’t let me slack off! Also, feel free to correct me if I’m wrong about anything I mention in the show or the attached show notes.

If you don’t want to comment here, you can also email me at epicanis at

Thank you, and good night…

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!…

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.

Über alkoholische Gärung 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 Über alkoholische Gärung ohne Hefezellen

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’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 Anybody out there have any other suggestions?

Continue reading Nerd Reading Spasm!