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…)

Obscure scientific papers, Mad Science, Travel, and other randomness

First – an amazingly astute observation that I’m ashamed to have not previously noticed myself (click image to go to it’s original site and see it full-size…):
Most 'Mad Scientists' are actually just 'mad engineers'...

I’m proud to say that I think testing Mad Hypotheses is great, and will continue to try to be a Mad Scientist. And a “Dirty Old Man” someday, but that’s a whole separate issue.

Second – I am really loving the perks of my new job – namely access to the college library system. I had previously mentioned (see last couple of paragraphs) a certain article that I wanted to get my hands on:

Greenberg LA:”The Definition of an Intoxicating Beverage”;Q J Stud Alcohol. 1955 Jun;16(2):316-25

Not only does the medical library have copies of a Czechoslovakian microbiology journal, the main library had a set of this old journal, too. I have my bedtime reading for tonight…

Thirdly – Another Giant’s Shoulders carnival has come and gone. I now believe that Eduard Buchner had hit upon not only a useful truth of living systems, but also a nifty alternative “mad scientist” hairstyle. Now I need to come up with one for next month. It’s been getting me thinking, though. That blog carnival is intended for “Classic” papers. Implied is that the papers are somehow important to the development of some scientific field or other. I’d like to see a variation on the “old papers” theme focussing on random old papers (where “old” might mean a few years or decades, depending on the subject) that people have found useful or interesting. Stuff that isn’t necessarily ground-breaking and has perhaps been forgotten or lost to obscurity but still has useful things to teach us. Naturally, I’m thinking especially Microbiology (and especially Microbiology other than Medicine) and Food Science. The Carnival could be called something like “Second Chance Science” or something of the sort. Just a thought.

Fourth – speaking of “Microbiology Other Than Medicine” and Food Science, apparently The National Academies of Science want to know what scientific topics people most want to read about. As usual, “microbiology” appears to have been relegated in their breakdown to merely a subset of either medicine/diseases, “biology”, and perhaps a small subset of “energy” and “Feeding the World” (no, seriously). The survey includes space to tell them what they’re missing – I heartily encourage anyone who cares to make sure you take the survey, and mention industrial and environmental microbiology and food science as subjects they shouldn’t continue to neglect.

And, finally – next week I need to make a very-long-overdue run back up to Idaho to grab some things from the old house and make sure it’s still standing, the water’s really turned off, nothing unnecessary is running, etc. 1600 miles of driving each way. Ugh. Anybody got any good recommendations for things to listen to on the trip? Other than having a chance to finally grab some things that I am missing, maybe I’ll at least have a chance to visit New Belgium Brewing Company again, since my route goes right past it. So long as I’m not driving by on Christmas day (when I assume they’ll be closed) I may have a chance.

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

I was going to call it “Oxygen Sucks”…

I mentioned I’ve been “working” (playing) with recording audio during my commute to and from work, in hopes of turning the audio into a regular podcast. I was originally going to call it “Oxygen Sucks”, which is why today’s attached/enclosed audio (only about 7 minutes long) refers to itself as such…

Officially, though, I think “Stir-Fried Random” is a better name, so I’ll go with that henceforth. The first real episode is under way already, so I could put it up as early as the next few days. Today’s episode is in mp3 format, though starting next episode I’d like to offer both mp3 and Ogg Vorbis, at least, the latter format having better audio quality at the same bitrate (and being Legally Free for use). As a bonus, I gather Firefox 3.1 should offer native playback support for it, too…

I’d appreciate commentary on the content (even if you don’t listen but merely want to comment on the show notes) and audio quality. No login needed, anonymous comments allowed.

Show notes may be found below This Direct-Download link for the audio

Continue reading I was going to call it “Oxygen Sucks”…

“A Proposed Structure for the Nucleic Acids”

Hello again, girls and boys and whatever else may be out there reading. It’s time once again for this blog’s contribution to The Giant’s Shoulders (hosted this time over at “Second Order Approximation“). This month I’m looking at something even smaller than usual. Inspired by my new job in the biochemistry department where they seem to do a substantial amount of X-ray crystallography (which I do not – yet – understand as well as I’d like), I thought I’d drop all the way down to the molecular level and talk about a fundamental discovery that helped make modern molecular microbiology possible: the structure of DNA.

Yes, it was over a half-century ago that an accomplished scientist, working with X-ray images produced from crystallized nucleic acids, published the first proposed structure for for them – the famous Triple Helix.

Continue reading “A Proposed Structure for the Nucleic Acids”

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

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 bookI 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.