Biology
59 posts · all topics
Biohacking and Shifting Science
Exploring the historical and contemporary shifts in scientific paradigms, and the phenomenon of biohacking.
Gideon's Wisdom of Crowds Experiment
R analysis of a wisdom of crowds experiment where Google+ followers guessed cheerios in a jar, with outlier detection and plots.
I'm a secretor
The Gut Guardians podcast interview with Alanna Collen included an interesting reference to the FUT2 gene, which the podcast hosts says has been linked to response to high…
Measuring my uBiome diversity
While there are few agreed-upon standards for what constitutes a good or bad microbiome, nearly everyone agrees that a diverse microbiome is better than one that is less…
For potato starch, maybe less is more?
A friend who is enthusiastic about the affect potato starch had on his sleep, suggested that maybe my less-than-stellar results were caused by the amount I had been…
A gut bacteria for caffeine metabolism?
23andme says I’m a slow caffeine metabolizer because I have the AC genotype at SNP rs762551 . You’d think that means I’m extra sensitive to caffeine before bedtime,…
Overselling the microbiome
Here’s the cover of a magazine I saw yesterday in the grocery store checkout lane: I thought about submitting it to Jonathan Eisen's list of Overselling the Microbiome…
Which species do I track?
At the Microbiome breakout during last week’s Quantified Self Conference , several people were interested in the list of organisms I track. Here’s the list, along with my…
[book] Epidemic of Absence
View on Amazon Ecosystems go all the way up and all the way down. Just as humans affect -- and are affected -- by the bigger world of…
What I learned at Quantified Self 2015
I’m back from two jam-packed days at the QS15 (the Quantified Self Conference ) held at Fort Mason, in San Francisco, and I have a few impressions. There…
Zocdoc vs OpenTable
The idea behind ZocDoc is brilliant: a modern, super-easy web site that lets you book a doctor appointment as easily as OpenTable lets you book restaurant reservations. ZocDoc…
Bacteroides plebeius and me
Japanese people are able to digest sushi better than other people thanks to enzymes in Bacteroides plebeius , a bacterium that was first discovered in 2005 and later…
My gut diversity through time
Clark Ellis posts a nice summary of his uBiome results over at the uBiome Blog and now, with more detail at The Self-Taught Author blog . A long…
A year without Seth Roberts
Hard to believe it’s been a full year . http://www.seth-roberts-memorial.com/
Potato starch doesn't help my sleep
I've been experimenting with the relationship between sleep and resistant starch, taking a few tablespoons of Bob's Red Mill potato starch, which some people think improves sleep by…
Upcoming talk: Your Microbiome, Your Health
If you’re in the Seattle area on April 29th, I hope you’ll come to a talk I’ll be giving for The STEAM Vent , a local science event…
Yup, statins make me smarter
After a fifteen day test , I’ve concluded that 20mg of simvastatin daily has a major effect on my results on Seth Robert’s Brain Reaction Time (BRT) test.…
I’m rich!
The uBiome blog posts the results of a large (n>500) study of their users that shows a fascinating relationship between household income and a large change in a…
Will statins make me smarter too?
For the next two weeks, I’ll conduct a new test to measure the effect of simvastatin on my Brain Reaction Time. Two or three Kirkland fish oil pills…
What potato starch really did to my gut
As suspected, there was a glitch in my latest uBiome results . Apparently a server hiccupped, so the scientists there recomputed my sample and sure enough, the new…
A mistake in my fourth uBiome sample?
[ Update : uBiome recomputed my results, which are now much closer to what I expected. I'll update with a more detailed post soon.] After all that analysis…
Did raw potato starch wreck my gut?
What if you were in New York City and somebody gave you a list of the GPS coordinates for every coffee shop in the area. If you knew…
Looking into my mouth microbiome
The gut biome is interesting enough, but bacteria colonize just about every part of the body, so recently I’ve been studying my uBiome mouth test results . The…
Fish oil, even when it's not a pill
An interesting result when I measured my BRT today: Note how today’s result was noticeably higher than for the past few days. I've been traveling, and I didn't…
Using tools to analyze my uBiome results
To study my uBiome samples more carefully, I’ve written a few tools that you may find helpful too. You’ll need to know a little about the statistical programming…
How to analyze a uBiome sample in Excel
Although I’ve done three samples at this point, I’m by no means a uBiome expert, but hopefully the following guide will be useful to others who are trying…
My uBiome third sample
Eventually it will be possible, perhaps routine, to get regular real-time updates to what’s happening among the bacteria crawling all over our insides, but for now the best…
[book] The Rise of Superman
The Rise of Superman: Decoding the Science of Ultimate Human Performance by Steven Kotler is mostly about extreme sports — the people behind really crazy activities like kayaking…
[book] Missing Microbes
Another fantastic book, by Martin Blaser , professor of microbiology at NYU: Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues . Microbes, a word…
What's in my microbiome?
Although I was an early customer of 23andme, I found the results unsatisfying because there is so little that is actionable . I mean, you don't need a…
Notes on Seth Roberts Memorial Symposium
I had a long-planned family reunion in Maine the week of the Ancestral Health Symposium in Berkeley this month, so it was just not possible for me to…
My sleep genes
I’ve tracked and analyzed my sleep for years, and of course I also have a long-time interest in understanding my genome , but I’ve been unable to combine…
Where are the starfish?
We’re on vacation this week in Coastal Maine, and yesterday at low tide we saw this on a beach south of Belfast: Sadly, west coast starfish are victims…
Personalized genetic analysis
The biggest problem with all the great new self-measuring tools is the torrent of data they produce. You could devote your life to analyzing your results and not…
What's the appendix for?
My appendix was removed when I was five years old, at the hands of a well-meaning country doctor who thought it would cure my chronic childhood tummy aches.…
Y-Combinator Sam Altman's Future Predictions
From this week's Econtalk podcast Sam Altman, president of startup accelerator Y Combinator, mentions three interesting startup investment trends: wearables (it's inevitable that we'll all have computing devices…
Microbes over time
Lawrence David, at Duke University, tracked two people’s microbes for a year , offering a rare peek into how the makeup of the gut changes over time. Similar…
The FDA needs to be more Bayesian
John Wilbanks is one of my favorite open science geeks (I even met him once in person, when he did a presentation for Microsoft Research). In a blog…
Is there such a thing as a "generic" apple?
When you eat any food, shouldn't you care more about the particular piece you are eating, rather than the generic values listed in an app or book about…
The Post-Pasteurian world
As a long-time fan of food writer Michael Pollan (read more here and here ), it was inevitable that I’d read his latest, Cooked- A Natural History of…
The argument for regulating information
When Nobel Peace prizewinner Liu Xiaobo was imprisoned by Chinese authorities, his captors were unafraid that he alone, a single individual without guns, an army, or even military…
Is the FDA the only source of experts?
An SFGate blog, supports the FDA’s decision to prevent informed consumers from having our genes sequenced halt the marketing of 23andme: Silicon Valley whines any time regulators bog…
Sun exposure and health
People born in the Fall tend to live longer than those born in the Spring. That’s the statistically significant conclusion based on a dataset of over one million…
Don’t brush after mealtimes
Advice from the WSJ health column : "When you eat or drink something acidic, the pH in your mouth goes down and can take some time to go…
[Book] Epidemic of Absence
View on Amazon Ecosystems go all the way up and all the way down. Just as humans affect -- and are affected by -- the bigger world of…
Easy homemade yogurt
Among the many important aspects of health that science can’t yet explain is the role of microbes , zillions of them in every part of your body, with…
The inevitability of human enhancement
I watched a TED talk by Juan Enriquez ( Will our kids be a different species?) that wasn’t particularly informative if you’re up to date on biology, but…
I’m a builder
I was devastated to read, in the latest Atlantic , that one of my favorite female writers, Sandra Tsing Loh, is divorcing. In an excellent summary of several…
Better stay away from cocaine
A new study reported on the 23andme blog shows a link between cocaine-induced paranoia and the SNP rs9387522. Turns out that I have the TT variation of this…
No more Vitamin D shortage
Late last Summer at my annual physical, my doctor tested my Vitamin D levels and found that, like most residents of the Northwest, I was well below optimal…
Do It Yourself Biology in Seattle
I finally was able to attend one of the DIYBio meetings this weekend, and now my mind is reeling from all the interesting possibilities I heard. DIYBio is…
Steven Pinker on Personal Genomics
The Jan 11th edition of the New York Times Magazine has a cover story by my favorite thinker describing his experiences with genome testing, and he finds the…
Obama’s slave ancestors
The country is justifiably excited at the thought of a first lady in the White House who is the descendent of a slave . Michelle Obama’s great-great grandfather,…
What’s in my genes? Results from 23andme
My DNA test results arrived much sooner than I expected. They tell you six to eight weeks, but it was more like two or three. The company that…
Time to analyze my DNA
Our local public radio station, KUOW, aired a program on Personal DNA Testing that convinced me to finally get off my duff and order my own DNA testing…
Family reunion at the Mayflower
We brought the kids yesterday to Plymouth, Massachusetts to see the Plimouth Plantation , and the full-size replica of the Mayflower. My wife's family can trace itself back…
Count me in
The new August 2008 issue of Wired describes the Personal Genome Project, an upcoming ambitious attempt to collect DNA and more from 100,000 individuals. Of course I immediately…
Craig Venter
Best known as the guy whose private company, Celera, single-handedly beat tied the international government-funded Human Genome Project in the race to sequence human DNA, Craig Venter stopped…
I'm an Indian!
A few months ago I asked my 90-year-old grandmother to rub the inside of her cheek with a soft cotton swab, and then I sent it to the…