Musings on "good" bacteria, antibiotics, and brain function

The growing trend recognising that gut bacteria affect all other body systems, the brain, of course, included, is often accompanied by what I think is a faulty assumption. That assumption is that there are healthy strains of bacteria that are difficult to cultivate that we should specifically insert into the gut (through pills, yogurt, or transplants, for example) and then keep alive by feeding with high fiber plants in order to maintain health.

The main reason I find this implausible is that it's not evolutionarily supported. There is just no strong evidence that evolving humans ate fibrous plants with any regularity. Moreover, any gut bacteria that we can't easily keep living inside us seem unlikely to have evolved there. It makes no sense that regularly eating something we didn't evolve to eat regularly, to keep alive something that doesn't appear to have evolved a strong penchant to stay alive in us, would be the only, let alone best way to maintain an inner environment conducive to health.

There do seem to be positive effects from taking probiotics, but I question the interpretation of that. One hypothesis I have is that the main benefit of probiotics is that they in turn displace worse strains of bacteria. If this is correct, then another, possibly better solution may be to minimise the worse bacteria by not feeding them. One way to not feed them would be to avoid fibrous plants.

(Please see my related post on germ-free mice, where I show that mice with no gut bacteria, contrary to common interpretation, are healthier than those with bacteria.)

Another possible explanation, is that these bacteria we are pushing mainly help people digest fibrous plants. So in people who eat fibrous plants, it is better to work to maintain these bacteria, than not to. However, this, too has the obvious alternative solution.

Antibiotics and the brain

I just learned about the potential benefits of antibiotics in autism. The author of the linked article has found evidence that negative symptoms of autism may be mitigated by taking antibiotics. His own son, for example, had improved eye contact, speech, energy, and motor control. This prompted him to look for clinical evidence, and he did find some preliminary such.

Some antibiotics appear to improve brain function. Animal studies have shown cognitive improvements in, for example, mouse models of schizophrenia, and Alzheimer's. The mechanisms are unclear.

Often researchers suppose that such properties of antibiotics are coincidental, and unrelated to the antibiotic effects. For example, minocycline, the antibiotic used in the latter study, has been shown to have antioxidant properties that are neuroprotective. The mechanism is unknown, and I am not aware of people testing the hypothesis that the antioxidant property is a downstream effect of bacterial modulation.

I did find one nice exception to this. Antibiotics are known to improve cognition in hepatic encephalopathy. In this study, the researchers tried to discover a plausible mechanism for that. What they found was that there was a shift in the activity of different gut bacteria, resulting in an increase of many types of fatty acids in the blood. They speculated that these fatty acids, which brains like to use, were reponsible for the cognitive improvements.

Antibiotics often get a bad rap, because some conditions appear to get worse after you take them. People explain this with the story that after you've taken them, your gut is now prey to the "bad" bacteria, which for some reason never explained, naturally takes over in place of the "good" bacteria that "should" be there. This all appears rather backwards to me. I would think that if we were feeding our guts naturally, we wouldn't have to go out of our way to ensure this didn't happen.

What is salient to me is that supressing our gut bacteria, or changing the way they function from the default, is often having a positive effect that goes away when we go back to our normal way of treating those bacteria -- feeding them our Western diets. The common wisdom for dealing with that is to force in bacteria optimised for an onslaught of plant fiber. One wonders what would happen if instead, we just stopped the onslaught.

On Happiness

This post is not my usual fare. It's personal and it's not even about meat.

In the spring of 2014, many things were coming together for me. Areas that had been stuck were moving forward, particularly in my intellectual / career life. My love life was improving, too, though there were still important difficulties. The most exciting thing of all was that I had found, applied to, and been admitted to the Recurse Center, a computer science program in New York City.

I arrived there in the beginning of June for the happiest three months of my life before or since. I was living independently in a tiny dorm room in Manhattan just north of Houston. It had few amenities, and only shared bathrooms. Yet I loved it. It was a 15 minute walk to the Recurse Center. I loved to start and end my days with a refreshing walk through the city, and despite its reputation, I found the people I passed to be radiating good cheer.

I always arrived at the Center early to gather my thoughts about what I learned the previous day, and set my focus for the day ahead. I programmed, read tutorials, went to presentations, and wrote about what I was doing every day as an exercise in transparency. I stayed until bedtime. I felt independent, free, creative, and competent, and I attributed it all to New York and the Recurse Center.

A miraculous thing happened. Halfway though the program I met an extraordinary person with whom I fell madly, helplessly in love. I hadn't been looking for love. Love was the furthest thing from my mind, because I was focused on my creativity, and was too happy to want for anything. But finding it took me to new heights of joy.

When I returned to Boulder, I returned to unhappiness, and I believed it was situational. You see, I'd been practising resentment and blame for my life circumstances for years, for everything from the geographical location I was unhappy with, to my professional stagnation, to the mundane responsibilities of life. This was so unlike me. I have long believed that if something was worth doing, it was worth doing well, and more than that—it was worth actually enjoying it! I believed that having made a choice of action, one should take it on as fully as possible, putting in all of one's heart. But I wasn't doing that, and I hadn't been for some time.

I was making a big mistake. I was letting circumstances dictate my happiness. Now don't get me wrong. I am a material being. There is nothing more spiritual than taking delight in the present reality of the material world. It was good to allow New York City and the Recurse Center to fill me with happiness. It was right to take pleasure in my friend and lover, Sean Baker, who touched me more deeply than I've ever been touched, physically, emotionally, and intellectually, and with whom I have shared the most intimate of moments over fine things and crass things alike.

The mistake was to depend on these things for my happiness. If I can be happy in a dorm not much larger than my current bathroom, then I can find joy in Boulder, Colorado. In fact, it has surely been a continuous effort not to enjoy such a beautiful city, an effort that was worse than a waste. Today I talked to a man who moved here but two weeks ago from L.A., and instead of launching into my caveats and complaints, I simply told him what I liked about it, and I meant it.

The biggest mistake of all was to depend on my lover for happiness, for in him I saw my only salvation from the rest of it. So I forwent nearly everthing else I loved, in order to spend every possible moment with him, so as to bask in my delight of him, to get my happiness from him. This was not only unfair, but just plain backwards. The whole reason we were able to connect in the first place, was because I was radiating joy. I had something to give. I was fun and easy and emotionally self-sufficient, and the point of being together was to mutually amplify our joy into more joy. If I want to be happy, all I need to do is embrace my creative desires, surround myself with things that give me pleasure, and be the amazing person I know I am in my heart. And then, like during my stay at the Recurse Center, I will be happy, independent, free, and a magnet for miracles.