Making Friends with Microbes

This, my first sourdough bread, could be the beginning of a beautiful friendship.

Are you afraid of animals?

What about plants?

I would not want to be at the mercy of a great white shark, and I never intend to wipe my face with poison ivy. But I have never met anyone who is categorically afraid of either plants or animals. However I cannot say the same for microorganisms, whether bacteria, fungi, or protozoa; it is not uncommon for an adult to express an unqualified aversion to them.

The prototypical pathological beahvior I am thinking of is the compulsive use of Purell hand sanitizer. I want to know how big of a party they threw at Purell headquarters when the H1N1 virus came out a couple of years ago. All of a sudden the dispensers were ubiquitous in public places, the implication being that using Purel was an extra layer of precaution on top of using soap and water when leaving the bathroom. Enter a room, use Purel. You won't get sick that way.

Of course, pathogenic microbes present a serious danger, significantly greater than that presented by predatory animals or poisonous plants. And basic sanitary practices developed in light of our understanding of microbes go a long way toward keeping us alive and healthy well into our old age. But we should not let a few rotten apples ruin our perception of the whole bushel.

The vast majority of microbes we encounter are benign, and we even depend on many in order to live. Bacterial cells within us actually outnumber our own cells by a good margin (they are much smaller), and they help us by assisting in digestion, by keeping the bad guys from getting a foothold, and by who knows what else. So when I think about microbes I think more of the good guys, or at least the indifferent guys, and I actively cultivate (no pun intended) a positive relationship with them. For example, I know this is controversial but rather than cooking the good with the bad in my milk, I buy milk from trusted farmers who take good care of their cows. Then I drink it raw, thinking fondly of the good work the associated bacteria will do in me.

I even keep microbes as pets. While my housemates have a dog abd others keep potted plants, I have on our kitchen counter a little colony of yeast and bacteria. Every morning I feed them some flour and some water and in return every few days they flavor and leaven my bread. I am still getting the hang of it, but I am new to this and all pet ownership is touch and go at first.

I realize that I may be too credulous, and like an owner of a Burmese python my trust may one day come back to bite me. But I would rather not overstep sensible habits like washing my hands with soap and in so doing put myself in opposition to the whole weight of no less than three taxonomic kingdoms.

People are meant to live as part of an ecosystem of flora and fauna, both micro- and mega-, and not as atoms in a sea of sterility. When we attempt to inabit the latter we come out less healthy because our bodies are simply not designed for such a context. What's more we dilute our weaponry when we use it indiscriminately against all things microscopic and not just against the bad guys.

In short, there is a such thing as too much caution when it comes to our invisible and ever-present companions. We have much to gain by acknowledging and cultivating a right relationship with them, even while maintaining proper vigilance against those who would destroy us.

I hate virsuses though. Get me away from viruses. They freak me out.

Grand Randomness

First cousins, all 25% Puerto Rican in theory.

Given that this vacation in the North Carolina Outer Banks may be the biggest confluence of my family ever, I have been thinking a lot about family and how it forms us individually. It's amazing to see all of the parts of the great machine in motion together over an extended period of time.

One thought I had concerns genetic inheritance from grandparents. We know that half of our DNA comes from each of our parents, and their DNA comes equally from their parents. It might seem reasonable to assume that we therefore get exactly a quarter of our makeup from each of our four grandparents, but I realized that assumption is not quite accurate.

The reason is that our DNA is grouped into chromosomes, 23 each from our mother and our father. This quantization prevents uniform inheritance. Right off the bat since we receive an odd number of chromosomes from each parent, we cannot receive an even number from each of our parents' parents. If I have 12 chromosomes from my mother's father, I have 11 from my mother's mother, and the split cannot be made even.

Moreover, there is nothing guaranteeing an even split. Whether or not each chromosome from our mother comes from her mother or her father is essentially a coin flip, and like coin flips the selection for each chromosome is independent. So, the fact that the chromosome 8 my mom passes on to me might come from her mother has no bearing on whether or not chromosome 9 does. That means it is theoretically possible for her to pass on only her mother's chromosomes or only her father's, though that is only as likely as flipping 23 heads or 23 tails in a row (about one in four million). Such children are genetically equivalent to children of one grandparent, and genetically unrelated to the other!

Therefore consider first cousins. There is good reason to expect they could take after their shared grandparents to differing degrees because they will inherit different proportions of their grandparents' DNA (to say nothing of the fact that they are inheriting from different subsets of that code due to having different parents).

How significant is this variation? Well, if my calculations are correct a full 32% of people inherit the most equitable 11/12 split from a given pair of grandparents, and 91% are no worse than an 8/15 split. So most people are relatively even combinations of their grandparents. But the flip side of that conclusion is that about one in eleven inheritances gets twice as much of one grandparent as the other. Since we inherit from two sets of grandparents, it is almost double that probability that we have at least one lopsided inheritance.

If these assumptions hold (and I don't expect they are changed by higher order effects), 18% of people, almost one in five, has received a lopsided amount of DNA from one grandparent.The effects of that randomness only multiply through subsequent generations, meaning it's even more likely inheritance from great grandparents isn't equitable. After all, we all have 64 great great great great grandparents, but only 46 chromosomes total. Someone (or 18 people) is going to be squeezed out, save for other effects like crossing over.

For me there are two takeaways of this reasoning. The first is that it is indeed possible to take after a particular grandparent more than the others, as far as genetics go anyway. The second is that it would be really fun to get everyone in my family's genomes sequenced so that all of this movement could be charted through the family tree rather than merely speculated on.