Gut Flora and Cognition

Posted on October 26, 2012 by Scott Jackisch

You may already know this, but I was surprised to hear that the microbes living in an on our bodies outnumber our own cells 10 to 1 and collectively contain orders of magnitude more genetic information. I guess that’s not necessarily saying much since the common potato has almost twice as many genes as a human. There is actually a huge effort in the EU to sequence the DNA of the human microbiome called MetaHIT.

MetaHIT discovered that there are 3, err 2 distinct microbiome population types callled enterotypes. One enterotype is dominated by the Bacteroides genus of microbes and is related to high fat or protein diets. This the one a lot of fat people have. The Prevotella enterotype is characterized by high carb diets and I assume is related to better metabolic health.

Gut flora have been implicated in everything from mood regulation to diabetes. The fecal transplant stories are pretty freaky too. This is a treatment for bacterial infections (primarily Clostridium difficile?) that involves transferring fecal matter from a healthy relative into the colon of a person desperately ill with a bacterial infection. Once the gut flora is fixed, it takes care of the other bad bugs hanging around. Some people also think there might be a connection between autism and gut flora problems.

I don’t want to get all Larry Smarr about it, but I am interested in getting my gut flora sequenced. So I joined this study on the Genomera citizen science platform organized by the smart and cool Melanie Swan: Microbiome Profiling Response to Probiotic in a Healthy Cohort. Here is the description:

Critical to digestive health, the microbiome is a newly available personal health data stream. Join this first-ever participant-organized citizen science microbiome project! Second Genome will provide microbiome sequencing to analyze potential shifts in the gut microbiome before and after 4 weeks of a daily dose of an OTC probiotic such asCulterelle® (Lactobacillus GG). A personalized report will be provided to each participant with the global shift in microbiome bacterial abundance by individual and study group, and a personalized profile of ratios pre and post intervention of Firmicutes, Bacteroidetes, Helicobacter pylori, and the most abundant 10-15 bacterial taxa at the phylogenetic family level (DRAFT of sample report). Human genetic SNPs related to Ulcerative Colitis andCrohn’s Disease are optionally requested to see if they may have a connection with microbiome profiles.

It’s $800 for the sequencing from Second Genome (which I hear is a good price) and I encourage anyone interested to join up. We need more people to join before we can begin the study, so spread the word. Check out Melanie’s blog when you get a chance, she covers a lot of QS, Futurist, and other modern topics.

Sorry, I know the title is Gut Flora and Cognition, but I don’t have much to say on that since the data isn’t in yet. I suspect he work on mood or autism might pan out. Those are cognitive things. Also, I intend to recommend people track their cognitive performance with Quantified Mind during the probiotic study to see if this gut intervention makes you smarter or stupider. Though I think that this article makes a good point when the author questions “the ability of a single strain of bacteria to impact on the vast inner ecosystem of the human gut.” So a tiny dose of just a few strains of bacteria taken orally seems unlikely to have much impact. Still, we shall see, we shall see.

Intrinsic Motivation is Authentic

Posted on October 25, 2012 by Scott Jackisch

Intrinsic and extrinsic motivation have been coming up in my conversations lately. The Habit Design folks will say that only intrinsic motivation works. If that is true, it throws a wrench into the plans of sites like Beeminder that provide people extrinsic motivation to meet their goals by charging them for defection. I am not sure which side to take there. Extrinsic motivation can certainly work, but it may not be preferrable.

I have had projects that languished because I didn’t find them interesting and the clients didn’t pester me for status updates. Left to my own devices, I will only work on projects that are fun or novel. But when clients do demand project updates, I do get motivated to work on the less fun stuff. One friend likened this to outsourcing your boss. Why be your own boss when you can delegate that task to someone else? But ideally I would be able to find something intrinsically motivating about every project. If I can’t, I should just pass it along to my associates to handle. When we say everyone should do work that they enjoy, we are really saying that they should be intrinsically motivated to do their work. Kurzweil said that he feels that he retired at age 5 since he loves his work.

I heard an interview on the radio with psychologist Madeline Levine a few weeks ago. She was talking about child development and she made some interesting points about letting kids fail so that they can learn and be independent. She also talked about teaching kids intrinsic motivation. One example she gave was asking kids how much they learned from a test at school as opposed to focusing on what the grade was. She calls this intrinsic motivation authentic. That’s an unusual way to define authentic, but it makes sense. Authentic people are more intrinsically than extrinsically motivated. Of course the line between internal and external can get a bit fuzzy. Much of what we value is learned from others after all. We don’t llive in a vacuum. But I do think that we take ownership of values and goals at some point.

One fellow I was talking with tonight brought up the Buddhist idea that desire is suffering. Just eliminate desire and they suffering goes away. That’s sort of like James’ equation:

Self-esteem = Success / Pretensions

As you can see, simply reducing pretensions to a low enough value can give even the biggest loser an enormous sense of self-esteem. Which is sort of how I feel about that Buddhist idea. Why bother with life at all if you desire nothing? But I guess they are trying to escape from some horrid endless cycle of reincarnation or something. That’s why I like my mindfullness stripped of all that superstitious bullshit. But introspection might perversely be a way to discover what truly motivates us. Now I just need to write up some more specific instructions on that and I will have a self-help best seller on my hands.

Scientific leaps of faith, how much can we trust science?

Posted on October 23, 2012 by Scott Jackisch

I’ve been thinking a lot lately about problems with science. These epistemological questions come to mind:

What is knowledge?
How is knowledge acquired?
To what extent is it possible for a given subject or entity to be known?

So it’s a huge elephant of a field, but I will nibble at it one bite at a time.

I should point out that I make my living as a systems engineer, so I like to distinguish between theory and practice. I tend to think of science as being more theoretical and engineering as being practical. Also, I am sympathetic to the constructivists, so I tend to agree with Feynman’s “If I Can’t Build it, I Don’t Understand it.”

This question of how much faith we can put in science initially came to mind when we were asking how much we can trust medicine. A family member had cancer and we started researching the best treatment options. The first problem we encountered was that medicine can’t keep up with science. i.e. doctors can’t keep up with the deluge of journal articles. But the next problem is more germane to this discussion, namely conflict of interest.

Corporate funding of research in agriculture for example has surpassed government funding since the 1990’s. One can certainly see why corporations would want to control the research in their respective fields given the importance of science in determining public policy. Manipulation of research can be very subtle. It spans the range of selectively funding research that supports industry interests to setting the actual scientific standard to favor industry. (i.e. determining methodology and setting thresholds, etc.) I would love to hear how my libertarian friends would respond to this. Fire away, I am moving on.

Another point worth mentioning is related to Quantified Self and self-knowledge. I had a conversation last year with a big QS guy who was pondering the relationship between self-tracking and science. In one sense, findings from this n=1 self tracking cannot be generalized to larger populations. But in another sense you can learn things that matter to yourself which might never be extracted from the n=many findings which average out all individual differences. (That said, huge amounts of this n=1 data is being aggregated by sites like MedHelp and used in research.)

But my main point from the previous paragraph is that there is a lot to be learned about ourselves that is currently innaccessible to science. Meditation might be a good example. Science can tell you the health outcomes of meditators or measure the brain wave frequencies of meditators. But, it can’t reveal your own individual thought patterns to yourself the way mindfulness training might. So the knowledge provided by science is in many ways incomplete.

An anti-atheist rant I saw on a friend’s Facebook page went on about how science constrains your world view to a box and included some nice Max Planck quotes:

“Anybody who has been seriously engaged in scientific work of any kind realizes that over the entrance to the gates of the temple of science are written the words: ‘Ye must have faith.'”
– Max Planck

It’s just nice to be reminded of that, but I don’t want to get into it too much. I’d rather place faith in a bunch of bickering scientists than a shaman on peyote or a pedophilic priest. But one other point that was brought up was that scientific consensus does change over time. And this is a good point. We should temper the confidence we have in current findings. Entire scientific paradigms have been routinely discarded throughout history. (Some are more stable to be sure, check out Egyptian medical procedures circa 1600 BC: examination, diagnosis, treatment and prognosis. Pretty decent.)

But then we get into some of the current problems with how research is generated today. Publication bias is partly (wholly?) a problem where positive results are more likely to be published than negative results. This paper even asserts:

Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias.

That’s nice. I feel so much better about science now.

Next we come to the issue of reproducibility. Apparantly a lot of studies are never reproduced and can’t be replicated outside the author’s lab. It might be up to the private sector to separate the wheat from the chaff. And according to a Bayer study from last year, they are finding plenty of chaff. It’s easy to see that no one gets ahead in academia by replicating someone else’s work, so there are some incentive problems around that. And who would even publish replicated results apart from PLoS? (Serious, I am asking. Post links in the comment section.)

Now, I do want to point out that scientists are sort of aware of this problem and there is plenty of work going on to identify bad research. However, from arguments on Prop 87 to drawing distinctions between holism and reductionism the way Monica Anderson likes to do, I’m tending to downgrade my confidence in science lately. But then again, my initial value was probably pretty high. It’s not like I am going to go on a vision quest the next time I need to get new knowledge about the universe.