June 13, 2015

In a bit of a pickle

Q: Isn’t this microbiome stuff cool?

A: <suspiciously> Yes?

Q: In the Herald. “Eating sauerkraut, pickles and yoghurt may be the answer for young adults suffering from social anxiety.” We didn’t know that before scientists starting measuring gut microbes, did we?

A: I’m not sure we know that now.

Q: They even found “the effect was greatest among those at genetic risk for social anxiety disorder as measured by neuroticism”.  This sort of interdisciplinary approach is a real step forward, surely? Genes and microbes and personality changes?

A: Yes, in principle, but there weren’t any genes or microbes or personality changes measured in this research.

Q: Not any?

A: No

Q: Oh.

A: They asked, on one occasion, about what they called ‘fermented foods’ and measured social anxiety, and found a correlation.

Q: How strong?

A: ‘Fermented food’ intake explained nearly 2% of the variation in social anxiety

Q: You mean nearly 20%?

A: I mean nearly 2%. The correlation was -0.13, and you square it to get proportion of variation explained.

Q: Oh. Um. Sometimes the story says ‘fermented’ and sometimes it says ‘pickles’ and then there’s this mention of chocolate? What’s up with that?

A: They asked about ten food classes: fruit and veg, and nine things they lumped together into ‘fermented foods’. From the research paper

2. yogurt, 3. kefir, or food or beverages that contain yogurt; 4. soy milk, or foods or beverages that contain soy milk; 4. miso soup; 5. sauerkraut; 6. dark chocolate; 7. juices that contain microalgae; 8. pickles; 9. tempeh; and 10. kimchi

Q: But soy milk isn’t fermented. Or dark chocolate. And what do they include in ‘pickles’?

A: Whatever a US undergraduate student would include, so probably more vinegar-preserved cucumbers and peperoncini than real lactic-fermented pickles

Q: And they just added these all up?

A: Yes. And then took the inverse hyperbolic sine.

Q: The what now?

A: Some people reported eating much more fermented food than the rest, so they used a mathematical transformation to reduce the impact of these measurements. The effect is that they’re focusing mostly on low levels of consumption (weekly), not high levels (multiple per day).

Q: Is that a problem?

A: No, it’s fine. It’s just that they seemed to have done it because they have a thing about Normal distributions rather than because that’s what they wanted to focus on.

Q: I thought it was statisticians who had a thing about Normal distributions?

A: Not for a few decades now, but yes, our bad originally.

Q: Ok, how about the genes. How did they avoid measuring any genes?

A: Look more carefully at what you quoted. They defined “at genetic risk of social anxiety” by a measure of neuroticism

Q: How genetic is … no, wait, we’ve been there. You’re going to tell me the estimated heritability, then explain it doesn’t answer my question.

A: Glad to see someone’s paying attention.

Q: Could it just be that there are cultural differences in reporting social anxiety and also in eating things like tempeh, miso, and kimchi?

A: It’s not out of the question.

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Thomas Lumley (@tslumley) is Professor of Biostatistics at the University of Auckland. His research interests include semiparametric models, survey sampling, statistical computing, foundations of statistics, and whatever methodological problems his medical collaborators come up with. He also blogs at Biased and Inefficient See all posts by Thomas Lumley »