The Synthetic Yeast Project: What it is, and why you should care

What it is: The world’s first project to build a whole genome of a eukaryotic organism, based on Saccharomyces cerivisiae, entirely out of bits of DNA stuck together by geneticists in labs. Now, to break that down:

Eukaryotic: Organisms with cells with nuclei. (Prokaryotic) cells without nuclei are limited to bacteria and archaea (which look a lot like bacteria to folk who aren’t microbiologists). Cells with nuclei comprise everything else, from yeast all the way up to us.

Genome: Cell software. A genome alone doesn’t do much for you; it’s like having Microsoft Office without a computer. But plug the genome into the right machine (i.e. a cell with mitochondria and ribosomes and other such equipment) and that machine will follow the genome’s instructions.

Build: Most genomes are duplicates of existing genomes, made when cells reproduce themselves. They evolved on their own. Scientists can alter those existing genomes by applying chemicals that induce mutations in DNA, or by using any one of a variety of techniques* to replace a section of existing DNA with new DNA, or to add a whole new DNA sequence. Geneticists can create those DNA sequences in labs, outside of cells, and stick them together. Assembling small bits of DNA in this fashion is genetics bread and butter. This project, however, involves creating and sticking together a whole yeast genome’s worth of DNA, and then putting it inside a cell and letting it run.

Entirely: Scientists build bits of genetic code out of lab-created DNA all the time. Heck, I’ve done it myself, and (don’t be a prude, now) I even started when I was a teenager**. Building an entire genome is a project multiple orders of magnitude larger than putting together a little chunk of DNA. If routine genetic engineering is writing one really well-crafted sentence, then this is composing the complete works of Shakespeare several times over.

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How to answer the question: is this good wine?

How do you decide whether something is good? Wine is a loaded subject, so let’s take a steak. If you’re looking for calories, steak is good: it has lots of them. If you’re looking for nutrients and specifically for protein, or for vitamin B12, it’s also good. If you’re looking for nutrients and trying to avoid fat, it’s bad. If you’re making a decision based on function, and you’re a nursing mother, maybe it’s good because you need the iron and those B vitamins. If you’re looking to support an environmental ideology, it’s good or bad depending on where the steak came from. If you’re making a meal for guests, it’s good or bad depending on whether the steak is the right degree of special for the occasion and whether it will communicate the right message to people you’re trying to impress. It may be bad to eat because you can’t afford it. If you’re a vegetarian or vegan, or observe a Hindu diet, it’s not good to eat because it isn’t food; end of story.

You can’t just call the steak “good” or “bad.” In general, this is a thing we recognize. I really like the – now regrettably old-fashioned – idea of “household management.” Good household managers adeptly maneuver amongst these value registers* to make “good” choices for their household constituency, balancing a budget and good care for people and personal or family values and time and a dozen other things. Household management shouldn’t be put down. It’s a complex bunch of skills, as might be observed by the number of start-ups Silicon Valley-types create to help the average person with disposable income not have to learn them.

People increasingly outsource those decisions. A lot of us really want someone else to tell us whether something is good to eat! Making all of those decisions is hard work, and it’s far simpler to have someone else tell you what to do. So, combined with a lot of insecurity about weight and health and the health of the planet, we have Atkins and Weil and nutritiondata.com and Michael Pollan and Slow Food and myplate.gov (the new, hip, engaging and interactive and multicultural replacement for the old stodgy American food pyramid). In the Netherlands, “healthier” packaged foods can carry little stickers with a phrase that means “I choose consciously” because the government wants to tell you what to eat without actually telling you what to eat.

Why could the household manager balance all of those many different values? First, if we’re talking about the old-fashioned house or farm wife, it was a big part of her full-time job. Second, she had fewer options. “What should I make for dinner?” For her, cultural constraints would define what “dinner” could be; for me,I might be German and Irish and Polish but I’m far more likely to think about Vietnamese or Greek for dinner or, more likely, combining a bunch of food traditions. I have way more options. She had ingredients limited by season and location; I can get most things most of the time. She had a limited number of dishes she learned from relatives and friends; I can access an infinite number of recipes on the internet. She may have felt some social pressure to make familiar things; I feel social pressure to make unfamiliar things and to keep experimenting and learning.

And she had fewer options in the store. “Let’s have ham for dinner.” “Which ham?” I can buy the cheap ham or the expensive ham, or I can buy Mr. MacDougal’s ham or Mr. Clyde’s ham (and we’re Irish, so I buy MacDougal’s ham because we know the MacDougals). Or we raise hogs so I’m going to pull a ham out of storage.

“Let’s have wine with dinner.” “Which wine?” The store (or stores, the six or seven different stores, at least, that you could visit on your way home) offers infinite options. Spending more money doesn’t get me better wine. I don’t buy German wine because I’m German. I can’t choose from “everyday,” “nice,” and “company’s coming” wine. (I do in fact choose MacDougal’s wine because I know MacDougal, but I’m in a bit of a privileged position on that one. And, yes, I realize that contemporary wine marketing is in part about making sure that the consumer has “met” MacDougal.)

I have a whole lot fewer cultural constraints, and I have a whole lot more options, so I have to become a wine expert. I have to become a household manager who specializes in wine. Fine, if I’m employed by some very rich person for exactly that purpose. Awkward if I have a full-time job and a few other hobbies and a kid or a dog or no dishwasher. Or, I have to outsource my value-making decisions to someone else. I have to get someone else to tell me: is this a good wine?

Here’s where I mix my own value registers. Thinking about how we value food in many different ways comes from a talk Annemarie Mol** gave at the University of Otago yesterday. Dr. Mol is a very, very well-known scholar from the Netherlands. Her PhD is in philosophy, and she’s a professor of anthropology, and her work is used a lot in science studies and sociology, and what all of that means is that she’s the kind of creative thinker who asks new questions and doesn’t fit well into the usual academic boxes.

But what she said about how we value food dovetails with the conversation the Wine Curmudgeon has provoked about how wine quality and wine price and wine value have become separated in ways that make his beat of finding and reviewing good, cheap wines increasingly hard. I, and some of the other folks who replied to the WC’s rant, think that good cheap wines are still plentiful but that finding them requires an increasing investment in time and education. We’re compelled to learn more and new ways of valuing things because “is this a good wine?” isn’t a question we can answer easily by looking at a price tag or a label or even a wine review, thanks to the incestuous relationship between wine writing and wine marketing.

Dr. Mol and the Wine Curmudgeon are both good writers, for different reasons. Knowing that requires a lot of education. So how to answer the question? How to decide “is this good wine?” We have some options:

  1. Take the time and effort to educate yourself. Become a good household manager. (This is what the wine world in general tells us.)
  2. Limit your choices. Decide that you want to learn only about Oregon pinot noir, or that you’re German and therefore you’re going to drink German wine, or that you only drink cheap wine and that’s just fine. (Another thing the wine world in general recommends.)
  3. Be okay with moving amongst different value registers. Let yourself say, “this is a good wine for today” without feeling like it needs to be a rule or the One Right Thing. (Kudos to the numerous wine writers championing this way of drinking.)

I actually don’t have an answer. On the one hand, it’s just wine. It’s just a steak. On the other hand, yes, our choices have consequences. Maybe making “the right” decision shouldn’t fall entirely on our heads – maybe someone else should be making all of this easier for us, and plenty of people are trying. But I think the bigger question, whether you’re memorizing the complete work of Jancis Robinson or looking for organic labels or picking up something with a critter on the label, might be: “is this a good way to live?”

 

 

 

*To use the technical term. Switching or moving amongst registers is how someone like Dr. Mol would talk about what the household manager does to think about whether the steak is good to eat.

**Mol may be a highfalutin academic, but she’s one of those rare few amongst that breed whose writing is fun to read. If you’re interested in how we make values happen in healthcare, or in patient choice, or how we make decisions about food or taking care of people, and you like reading non-fiction, look her up.

Research on reassembling: Root systems, soil structure, and wine quality


25 seconds of your time could help a PhD student in need. There’s a 3-question survey at the bottom of this post. Do me the favor of answering it when you’ve finished reading? Thanks!


 

If your usual reaction to scientific research involves muttering about taking things out of context, take heart. Historians will look back on our time and call it the era of systems. After a century or so of studying factors in isolation, wine research is now full of studies trying to put them back together again. You’d expect research on terroir to be at the front of that move, and it is. New research out of Friuli in northern Italy is a good example, tying soil type and root structures together with wine quality. Their findings – that wines have the most character when vines can develop large roots through the full soil depth – aren’t shocking, but it’s one more tally mark on the “soil structure matters” side of things.

The researchers found 14 vineyards on different soil types, all Friulano* (same clone, same rootstock), a white variety common in the region, all between 15 and 20 years old, and all pruned and cultivated in the same way with herbicided undervine strips and ground cover between the rows. And then they got busy. They used some pretty elaborate apparatus to measure soil water content. They dug a lot of holes to investigate soil structure. They measured transpirable soil water, reflecting not just how much water is in the soil but how tightly the soil is holding on to that water and how available it is to vines. It’s been shown that that measure corresponds to leaf water potential, which shows how well-hydrated the vine is and, indirectly, how well it’s able to take up water from the soil. They dug three meter-deep trenches in every vineyard to document the full root structure. They did this for three years, and each year they made 200 kg batches of wine, then had a trained panel taste them yearly for three years after bottling (the wines were made in 2006-2008). 

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