The long, slow end (or, I finished my PhD today!)

I submitted my PhD today! Two and a half years and three days after I began, I carried four copies of my dissertation – all 96,866 words of it – to the University of Otago graduate school and walked away with a chocolate-covered marshmallow fish and a smile. I owe my very sincerest thanks to everyone who’s so generously helped me along the way, including folks in the Washington State and New Zealand wine industries and readers here who’ve poked and prodded and asked good questions. 

My thesis is titled “Through the grapevine: In search of a rhetoric of industry-oriented science communication.” It’s gist is, briefly, that people study scholarly science writing amongst scientists, and popular science writing for general audiences, but pay a lot less attention to science writing for professional audiences (like winemakers and growers) who might use scientific information in some way and who also know a lot about the subjects of scientific research. Industry-oriented science communication should make industry knowledge a real part of the conversation and communicate science as local knowledge in context – one kind of knowledge, alongside industry knowledge as another kind. By writing about science in context, acknowledging industry knowledge as real and valid knowledge, and making connections between science and industry locations, I’m arguing that the way we write about scientific research can invite better research-industry collaborations and help make research more relevant to practice.

You can find more detailed explanations of parts of the project under the publications tab on this website. If you’d like to know more, send me an email. I’ll be happy to have a conversation, send you all or part of the thesis, or try to point you in the direction of other resources.

Don’t call me Dr. Szymanski yet. In the United States, PhD studies finish with an oral defense with your committee. Assuming that you pass, that defense ends with your advisor shaking your hand and congratulating Dr. Szymanski, and there you go, plus a regalia-clad graduation sometime thereafter. The New Zealand process is different, so today was only the beginning of the end. The graduate school will send soft-bound copies of my thesis off to three anonymous examiners chosen by my advisor. Those scholars will read my work, make comments about things they want me to change, and recommend a grade: pass with minor revisions, pass with major revisions, revise and resubmit (i.e. we fail you, but we think you can pass on a second try), or fail (i.e. we don’t think you can save this ship). Those comments get sent back to me and I have a month or three to make whatever changes those examiners have requested. I send it back. At least one of the examiners takes a look at my changes and, if everyone’s satisfied, the graduate school confers my degree, and I’m finally – after about six months – Dr. Szymanski. I can then do the regalia-clad graduation thing some months thereafter, but I won’t, because I’ll be in Scotland by then.

I’ll be in Scotland by then! As of the beginning of May, I take up a post-doctoral research position at the University of Edinburgh. I’ll be joining the Engineering Life team to study sociopolitical/cultural sides of the Synthetic Yeast project, a massive effort to create the first working, laboratory-created eurkaryotic genome — of Saccharomyces cerevisiae, naturally. (I wrote about the project in some detail a few months ago). The project has obvious implications for the wine industry, is fascinating in terms of the trajectory of human-yeast coevolution, and plays into changes in how we see the relationships between life and engineering. The team I’ll be joining at the University of Edinburgh is outstanding. I’m looking forward to being in the center of the science and technology studies world, on an island with some of the best wine availability in the world, and within weekend skipping distance of many of Europe’s great wine regions.

Again, I owe my very sincerest thanks to everyone who has contributed their time, knowledge, and good will to my doctoral studies. And I look forward to getting to know the UK wine scene. If you’re in or near Edinburgh, send me a note! 

Social microbes and Schizosaccharomyces pombe

 

If there’s been a theme to the wine microbiology research of the past few years, it’s been microbial communities. Don’t just study one yeast or bacteria at once; look at an environment’s microbial population. And if there’s been a supporting theme, it’s been non-Saccharomyces yeast. Don’t just look at Saccharomyces cerevisiae; pay attention to at least some of the other, marginalized members of the microbial community, and ask what they can do for you.

Those two themes are obviously related. Studying microbial communities means noticing all of the auxiliary players in the environment. Noticing those players usually leads to asking what they’re doing and then to asking how you can exploit them. In another way, though, those two themes don’t overlap half often enough. Plenty of studies of non-Saccharomyces organisms keep on plodding on in the old microbiology tradition of poking and prodding at one or a few species as though they’ll work alone outside the lab.

Very forgivable in one sense. When we don’t know much about an organism in the first place, sussing out its individual characteristics before querying how it behaves in mixed company doesn’t seem unreasonable. It’s also fair to say that plenty of winemaking involves making an effort to kill all existing microbes before inoculating one selected S. cerevisiae strain that’s supposed to work alone. Then again, single-microbe studies remind me of studies of individual primates held in solitary captivity, which are not only deeply unethical but not very useful. What primate, humans included, is going to behave normally when held in solitary confinement? I’m not claiming that solitary microbe studies are unethical, or that they do harm to the microbes involved, but we have plenty of evidence that microbes are social.* Data from solitary confinement studies is limited.

So a new study on Schizosaccharomyces pombe is heading in an interesting direction, but yields data with some limitations for winemaking.

Is S. pombe a spoilage organism? That’s like asking whether dandelions are weeds: yes, in the lawns of a golf course; no, when you’re growing them for salad greens. S. pombe produces unpleasant quantities of acetic acid. It also efficiently (and even completely) metabolizes malic acid. Scott Labs sells S. pombe “teabags” that can be dropped into overly acidic tanks or barrels and then fished back out again, after malic acid has been degraded but before volatile acidity gets out of hand. New research (open-access article) has considered whether some S. pombe strains, carefully selected for low acetic acid production, might be suitable as primary fermentation organisms to be used instead of S. cerevisiae rather than afterwards. The team was able to find several low acetic-producers, able to ferment a must to dryness (albeit they tested final alcohol concentrations in the 12-12.5% range), and still able to simultaneously metabolize malic acid. Their perfunctory sensory testing, however, pretty much only judged for major faults: acidity, reduction, acceptable aroma. So when the researchers conclude that these strains might be a good option for high-acidity musts instead of malolactic fermentation, they’ve yet to account for whether that solution produces a delicious product or merely an acceptable one. Still, these strains might be incredibly useful in combination, or when a vat of something undrinkably acidic needs to be made inoffensive enough to be blended away into something else. But how do these microbes behave in company, when asked to cooperate on the job of making a drinkable wine?

I hope that this project steps forward in two directions. One: better sensory analysis. Two: what happens when S. pombe and S. cerevisiae (and perhaps some other bugs) are asked to play together.


*The Foster Lab at Oxford is up to interesting research on cooperation between microbes and other species. Here’s another (albeit dated; 2007) excellent resource on microbial sociability, from Annual Reviews in Ecology, Evolution, and Systematics. Unfortunately, it’s also behind an academic publisher’s paywall.

Legal closure follows scientific closure on arsenic in wine

Reporting from California-based people who’ve been keeping eyes on this thing (W. Blake Gray at Wine-Searcher, Ben O’donnell at Wine Spectator) says that a California judge has dismissed the much-discussed lawsuit charging that a large pile of California wines contain dangerous amounts of arsenic and mislead consumers into thinking that they’re safe. The lawsuit has smacked of an ill-advised attempt to promote a fundamentally flawed business from the outset. Mr. Hicks and company started a company called Beverage Grades trying to sell consumers ratings for individual wines’ healthfulness, then set out to prove that consumers needed this kind of protection from fraudulently toxic wine. I’m speculating, and the plaintiffs may have had additional ulterior motives – a clinical phobia of poisoning by heavy metals, perhaps? — but it’s hard to ignore the business connection. 

I haven’t followed the legal side of the case, but I’ve written about the baselessness of the scientific side when Mr. Hicks first began pandering his wine rating business, when the lawsuit was first raised, and when a peer-reviewed scientific evaluation on the arsenic-in-wine question was published in the venerable American Journal of Enology and Viticulture in February this year. Throughout, BeverageGrades and the lawsuit’s plaintiffs have kept their own data under wraps while the independent scientific studies not only made theirs public, but passed them through scientific review. Even apart from everything else, that one fact tells you everything you need to know.

I’d love to claim scientific “closure” on the issue. I can’t, quite, but only because medical juries are still out on precisely where safe thresholds for arsenic consumption sits. But we can definitely say this: from a scientific, data-driven perspective, arsenic in wine isn’t a problem. Unless you’re literally drinking wine like water, in which case you have bigger issues. And while we’re at it, since arsenic is found naturally in water and soil, many of your other ordinary foods and beverages contain small amounts of it, and that’s both normal and okay.

We can’t quite claim legal closure on this story – given the plaintiffs’ track record, appealing today’s decision wouldn’t be out of character. But let’s say that, like the scientific story, the odds are looking very good indeed.