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2022 Microbiome Course and Symposium by ISB

ISB Microbiome Webinar

The best bargain in scientific education last week was the 2022 Virtual Microbiome Series, a free online course sponsored by the Institute for Systems Biology.

Day One: How to go from a raw microbiome sequence to a human-readable summary report showing the percentage abundance of each microbe. (Two-hour video here)

Day Two: Predict your microbiome’s response to food. Given one of the microbiome results generated on Day One plus some information about the metabolites in a specific diet, use the software package MICOM to estimate how the overall microbiome will change. The presenter, Christian Diener, is one the authors of that package and demonstrated it with microbiome data taken from various groups around the world, showing what happens if you feed a hunter-gatherer diet to a person with the typical western diet and vice versa. These tools have been validated experimentally, and though they are still in a crude state, we can imagine in a few years an app that can tell, based on your current microbiome test results, how your body will respond to a particular type of food. (Three hour video here)

One of many plots you’ll learn to generate in these YouTube videos. Each dot represents one person’s sample. The y-axis is various microbes. Microbes that grow more quickly in this diet show up higher on the y-axis.

I can’t emphasize enough how well-done and easy-to-follow this was. Any motivated Personal Scientist with a weekend to spare ought to be able to do the same analysis using their own microbiome test results.

Personal Scientist of the Week

Maybe somebody like Brian Naughton. For about $150 in supplies, he shows how to sequence a human genome at home. You’ll need some equipment, obviously, but only a few thousand dollars’ worth.

The rest of his blog, Boolean Biotech, is well worth perusing: How to set up your own biotech, his CGM analysis, and much more.

On the Calendar

Please don’t miss the Keating Memorial Self-Research Talks and Wiki Launch, to be held on Thursday October 27th at 9:00 AM PDT / 6:00 PM CEST. (It’s a worldwide event, so they’re making it easier to attend for people not on the US west coast).

We’ll be presenting our latest results from oral microbiome testing, both from Bristle (which we discussed in Personal Science Week - 29 Sep 2022 ) and a brand new one from Viome.

More on COVID susceptibility

In Personal Science Week 6 Oct 2022 , we published some techniques to measure COVID susceptibility. Now there’s one more. In a new paper Mentzer et al., 2022, scientists from Oxford looked at the genetics of a thousand people enrolled in a COVID vaccination trial. According to their preliminary data, people with HLA-DQB1*06 alleles were less likely to experience PCR-confirmed breakthrough infection. 23andme reports HLA-DQB1 status here. For me, it’s all Ts and Gs (no As). If I’m reading the paper correctly, that means I’m less likely to get a breakthrough infection. Although the difference in infection rates is statistically significant, don’t get too excited: the overall difference is small, meaning you’ll likely be infected either way.

Religion in Science

One trend I note with amusement is the recent popularity of religious ceremonies at science conferences. The ISB event began with a word of prayer1, followed by a reading of sacred scripture, then a blessing from two clergy to ensure the proceedings align with Holy Faith. Religion has always been a force behind Western science – a few generations ago, such prayers were expected. Then as now, fear of excommunication means nobody dares express reservations about such mixing of science and religion. As a Personal Scientist, I have no particular reason to support or oppose these Sacred Rituals, but I wonder if the professional scientists apply the same level of critical thinking to their religion as they do to their science.

About Personal Science

Listen to experts, but be skeptical. That’s the idea behind Personal Science, where we use the techniques of science to understand and solve personal questions. Often, but not always, Personal Science involves quantitative or statistical reasoning based on self-collected raw data, but the overall thought processes can apply to every aspect of daily life.

In general, Personal Science requires a skeptical, yet open-minded curiosity about the world, humility in the face of incomprehensible complexity, and a constant desire to be proven wrong. Personal Scientists, above all, rely on their own direct experience, never taking somebody else’s word for it. Nullius in verba — take no one’s word for it.

1

I’m referring of course to the somber “land acknowledgement”, the reading of the Code of Conduct, and the blessings of the DEI officers. I don’t know anybody who disagrees with the principle of being nice to others, just like I don’t know anybody who thinks religion should be banned. But what does any of that have to do with science?

Personal Science

Personal Science Week - 20 Oct 2022