Can Occam’s razor slice through a Scorpion?

Occam’s Razor: use the simplest means possible to accomplish your goal.

Scorpion: 1) An arachnid; 2) a genetic method, patented by ETS Labs, for detecting bacteria and yeasts in wine (or grape juice, or beer) samples based on real-time fluorescence PCR (poymerase chain reaction.)

Can Occam’s Razor slice through a Scorpion?

“Plurality should not be posited without necessity” or, in the words of William of Ockham, “Pluralitas non est ponenda sine neccesitate.” According to The Skeptic’s Dictionary, the eponym was awarded to the monk from Ockham because he used the argument so often, even though it was already a common tenent of Medieval logic. Philosophers refer to the Razor in arguing over the existence of God, but most of us translate the phrase as “Don’t make it more complicated than necessary (stupid.)”

If Ockham’s monastery pew became a time machine one day and he was transported to 2010, the philosopher might be curious about the many incredible scientific advances we’ve made in the past 800 years.

In addition to being a cousin of the tarantula, Scorpion is ETS Labs’ patented name for a genetic method to detect common spoilage yeast and bacteria in wine samples. Send ETS Labs 60 mL of your wine and they will send back a report listing which, if any organisms are swimming around in your tank or barrel or bottle. Scorpion analysis relies on differences between the genomes of different organisms. Probes designed to bind to DNA sequences that uniquely identify a species are labeled (“tagged”) with fluorescent markers. Toss probes specific to many different organisms into a wine sample, and the tags show which probes are bound and, therefore, which organisms are in the sample. (This is a gross oversimplification, but I’m trying to avoid a detailed discussion of RT-PCR here. For a little more detail, see ETS Labs’ website.)

The first assignment for my wine microbiology lab this semester is to identify the bacteria and/or yeast contaminating an unidentified wine sample. The professor will give each group two wines — one spiked with nasties — and ask us to give him a report on what we found in the wine and how we found it. The first part of the assignment is to propose a method for attacking the problem: when we have the wine, how will we analyze it?

Oooohhh…There are lots of ways to analyze wine, and I could show my prof that I know about them by including all sorts of nifty things in my report. Scorpion analysis is outside my budget, but I could always run my own genetic tests if I can find out where to buy the right genetic probes.

Or I could smell it. “The nose knows” may be cheesy (why cheesy? Why not yogurty, or cucumbery? There’s a whole ‘nother kettle of fish…) but such aphorisms arise because they are true. Looking at my lab manual and the list of microorganisms that could be the unknown contaminant, each has a peculiar smell. Brettanomyces bruxellensis is probably the most famous — many wine lovers can identify “Brett” — but Pediococcus parvulus, Acetobacter, and Lactobacillus species have distinctive aromas, too, as I know from culturing them in the lab.

Oenococcus oeni, a bacteria very often responsible for malolactic fermentation, is a little trickier to identify based on smell alone, so I might need to move up to the next level of complexity (by the way, we aren’t allowed to use taste as part of our analysis; some of my classmates are underage.) If my nose isn’t quite sure, I can drip a few milliliters of wine onto a Petri dish and see what grows. We make Petri dishes full of growth media for yeast and bacteria by combining sugar, some protein and a few other basic nutrients, and adding agar — a gelatin-like substance from seaweed — to make it solidify. Culture media in a dish is essentially Jello (mmmm….yeast extract-flavored Jello!) Any bacteria and yeast in my wine will grown and reproduce on this media and, after a few days in a nice warm incubator, each little microbe will have grown into a colony of identical offspring microbes that I can see with my naked eye. Different bacteria and different yeasts have different colony morphologies; they look different; even within the same species, different strains can have different morphologies. One of my favorite strains of Brettanomyces bruxellensis looks like this.

Between smell and colony morphology, I expect excellent odds of correctly identifying the bugs my professor has hidden in my wine. My nose, and Jello in a Petri dish. In terms of levels of complexity, I think that I’m ranking far below genetic testing even if I do need to use the Jello. I could spend several hundred dollars to use the fancier technology, but why bother when the good, old-fashioned, simple method will do? Now, I’m not at all knocking ETS Labs; Scorpion is a potent analysis when you need to know “how much” as well as “what,” for complex microbial problems, and for busy wineries amongst other things. Scorpion analysis definitely has its place, but this isn’t it.

Occam’s razor: 1

Scorpion: 0

What are phenols?

Phenols are aromatic alcohols, which means that they are molecules that consist of a six-carbon aromatic ring with a hydroxyl (OH) group attached to one of the ring carbons. To an organic chemist, “aromatic” means that the ring includes an unpaired electron that is shared among all of the carbon atoms of the ring and. Electrons are like people: they like to be paired, are a little unstable when single, and tend to react with other molecules in search of a partner.

The most basic phenol is represented as

 More complex members of the phenol family are distinguished by having other things attached to one or more of the other ring carbons.

Because phenols have a free-floating (“delocalized”) electron, they form very strong hydrogen bonds with each other and other compounds with an unpaired electron. Non-covalent bonds – the bonds that form in-between molecules, including hydrogen bonds – help govern melting and boiling points: the stronger and more numerous the non-covalent bonds, the more energy input it takes to break them. When non-covalent bonds break, molecules move around more and move further from each other, resulting first in the melting of a solid and then, when the input of even more energy causes even more movement, in the boiling of a liquid.

ERGO: phenols have very high melting and boiling points. ERGO: phenols are solids at room temperature. ERGO: phenols, including the colorful ones that make red wine red and the flavorful ones that add depth and character to wine exist in wine as suspended particles. ERGO: they can be removed by filtering. ERGO: enough filtration can cause a wine to lose color, flavor, and mouth-feel (in part) because phenols are lost in the filtration process.

There are three major categories of wine-related phenols: p-hydroxybenzoic acids, cinnamic acids, and flavanoids. What do they do for wine? Phenols are responsible for a major part of the color and flavor of wine. They are, In fact, so important in so many ways that I’ll save more details for another post devoted solely to the topic.

For now, back to Fenema’s Food Chemistry!

Violet wine

“Although there are almost innumerable shade of differences in the colour of wine, they are all variety of two, the reddish and the yellowish color. I say reddish, for we know no kind of wine that is actually red or yellow. What we call red in wine is violet, mixture of red and blue. We do not in chemistry speak of the reddish wine as red, but designate its hue by the term wine-colour.”

– from G.J. Mulder’s Chemistry of Wine, 1857, London. p198

Sometimes, generalization for the sake of simplicity is worthwhile. Inaccuracies on the scale of generalizations can make communication so much easier. Can you imagine how Mulder might have asked one of his chemist friends what sort of wine he would like with his roast chicken?