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?

If I don’t have words for a flavor, do I still taste it?

Language shapes reality. The words that we use to describe physical things and abstract ideas help shape how we see them. The way we express our thoughts clarify what we are thinking. The words that we use to describe flavors change what and how we taste.

Case in point: how many times have I been to a wine tasting or shared a bottle with company, listened to someone else say that they taste mushroom flavors, and suddenly find myself recognizing mushrooms in the wine, too? Partly power of suggestion, perhaps, but not entirely so; if myself come up with a descriptor to which I can put a name, I find myself coming back to that flavor over and over again. Even if other, unspecified flavors are equally (or more) prominent, my brain has a handle — a specific word — to draw it back to the flavor I recognize. 

What if I had  (gasp!) never eaten mushrooms? I would never come up with the notion that a wine tasted like mushrooms, and I wouldn’t be able to recognize what someone else meant if they called a wine “mushroomy.” Drawing on different sensory experiences, I might call the same mushroom-like flavor “earthy” or “meaty.” But if I define a given sensation as “earthy” instead of “mushroomy,” does that change the way I sense that flavor? Will my brain use its repertoire of stored sensory experiences to make its perception of the flavor in my mouth more like the sensory memory with which I have associated it?

So, a teenaged girl from the Languedoc, a civil engineer from Kansas City, a physical education teacher from Brussels, a Nepalese farmer, and an Egyptian nurse walk into a bottle of Australian Shiraz. Do they all taste the same thing?

Other musings from Freakonomics at the NY Times.

Of Barbera and Basil

I may right now be eating the best meal I’ve enjoyed on my own since arriving in Pullman (the qualifier “on my own” serves to exclude the several lovely dinners I’ve made for and/or shared with friends here.) A great big bowl of brothy Swiss chard, soup-steamed (my term for steaming greens until the liquid evaporates and they begin to brown, then adding extra liquid, turning the heat down, and cooking briefly until the greens are very tender and a small amount of richly-flavored broth has formed), seasoned with crushed white peppercorns and crushed nutmeg, with a big double-handful of chopped fresh large-leaf basil added just before turning the heat off. After removing the skillet from the hot burner, I broke a very farm-fresh egg on top, disturbed the yolk with my cooking chopsticks, and covered the pan while lighting my candles, putting on the dinner music, and laying out my tea tray. The egg was just barely set, cooked by the heat of the greens, by the time I was ready to carefully slide the whole thing into an oversized soup plate (carefully, so that the egg remains on top.) With a bowl of tiny farmers’ market apricots (Goldstrike and Rivals and something with a “Prince” in the name, if I recollect aright) and a glass of Barbera, The whole thing is made especially special by virtue of its origin: the chard, basil, and egg all came from a nearby homestead/farm where I spent all Saturday afternoon chopping veggies and harvesting basil and whatnot. I feel perfectly decadent.

What makes this worth mentioning is the Barbera. This glass is the end of a bottle of Columbia Winery’s 2008 Small Lot Series that a winemaker friend opened up with me this past week. Neither of us was tremendously impressed with the wine that evening. It showed solid Barbera varietal character – black pepper and white cardamom on the nose, bright red cherry fruit overlaid with more pepper and piney spice notes – but suffered from announcing its alcohol content to the nose and pharynx. The overall impression was young, hot, and simple. Nothing wrong with it, but nothing spectacularly right, either.

We tasted the wine without food and perhaps at a slightly higher temperature than would have ideally flattered it. Now next to my basil-laden egg in a green nest, my impressions have changed. The basil, in its herbaceous spicy glory, has worked surprising magic to draw black pepper spiciness out of the wine. The cherry fruit has simultaneously become just a bit richer and darker such that the pepper doesn’t dominate so much as accentuate. Even though it hasn’t suddenly developed great complexity, this Barbera has become much, much more pleasant to drink. Hmmm…Barbera and basil? Or even just Barbera and food? I may be showing my unfamiliarity with Italian cuisine by not having thought of this before accidentally discovering it.

No; not just Barbera and food. Next to the sweet-tart apricots, the Barbera becomes bitingly thin and acidic, with metallic graphite minerals emerging that were before barely apparent. I wonder if apricots baked in basil cream, or apricots stuffed with an herbed ricotta would be a better combination?

This, then, is the great joy of tasting wine with food. Every combination won’t be wonderful, but the whole experience will be enjoyably interesting.