Life with Baby

Time stands still, time rushes forward.

A day is gone and what has happened?

Change her diaper, feed her, make a trip to the doctor, go get food, do the laundry, do some more laundry, make another trip to the doctor.

Did I miss a day? When did I last sleep?

Yet, when she opens her bright wide eyes and sneaks a peak, my heart melts.

When she cracks a wry smile, I just want to hold her close.

What if she could be like this forever, so tiny in my hands, so beautiful?

She waves her arms about and alights one gently on her cheek.

She is my one joy, my being, my life.

She is my baby.

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Why vote?

In last Sunday’s New York Times magazine, the economists that brought us Freakonomics argued that a rational individual should abstain from voting. According to them, virtually no election is decided by a single vote so the cost for voting is never compensated by any payoff. Their conclusion of why we (or some of us) actually do vote is because of the social esteem gained by being seen voting by our peers. They predict that internet voting may actually reduce voter turnout because we would no longer get this social payoff.

It seems to me that using social prestige as the basis for selecting a leader is a shaky way to maintain a democracy. The real intent of an election is to determine which candidate is favoured by the majority of the populace. For the most part, our current method accomplishes this task (insert your favourite Florida 2000 joke here) although it has two main problems.

The first is that making everyone vote to determine who is preferred is wasteful. In statistics, this is known as an overpowered experimental design. We only need to sample a fraction of the population to obtain an estimate of the election result. The error on the estimate scales with the square root of the sample size. In an election, when enough people have voted so that the error in the estimated result is less then the eventual margin, additional polling won’t give you any new information. This is why a single vote doesn’t matter.

In a practical sense, this is already what we do because only a fraction of the population votes. However, the fraction that votes is not guaranteed to be a representative sample of the population. Any bias in how the sample is selected will bias the estimate. This leads to the second problem with elections. In a close election, who shows up to vote could skew the results. One facet of election strategy is to enhance the turnout of your voters and suppress that of your opponent’s. This never seemed very democratic to me.

If we really wanted to elect leaders based on what the true majority wishes then an election is not the optimal method. What we really should be doing is to scientifically select a sample of the population to vote. Of course deciding on how to choose this sample will never be perfect. There will also be some misrepresentation (like underrepresentation of homeless people) but I think we can certainly do better than what we have now. If we wanted to be really efficient we could even use a bootstrap method to estimate the error compared to the estimated margin of victory on the fly. Now, I’d like to see some brave politician suggest this scheme.

Dark Genome

Cosmologists are very troubled by the fact that they can’t account for (depending on whom you ask) 90% to 99% of the mass and energy of the universe. The nature of this “Dark Matter” is the most pressing problem of their field. However, biologists don’t seem nearly as perturbed by the fact that the purpose of a similar fraction of the mammalian genome is completely unknown. They are so unconcerned that only a small fraction of the genome is in the genes that code for proteins that much of the non-coding region is simply called junk DNA.

It has always perplexed me why most of our DNA would be junk. I can’t believe that 90% of the DNA has no use whatsoever. It would seem much more likely that this so-called junk DNA is necessary for genetic regulation. After all, the main reason I am different from another person is not in the differences in the proteins I carry but in how and when they are expressed. Darwin himself recognized that much of the variation in nature must be due to regulation.

A very nice paper by Peter Andolfatto in the October 20 issue of Nature shows that in the fruit fly between 40% to 70% of the DNA nucleotides situated between genes are under selection pressure by evolution. He showed this in a very clever way. He analyzed the DNA of two species of DrosophilaD. melanogaster and D. simulans and looked at the level of polymorphism (differences within a species) and divergence (differences between species) in the genome. As a control he looked at synonymous sites (region in the coding region of DNA where a change in the nucleotide does not change the amino acid it codes for because of redundancies in the nucleotide triplet code).

Andolfatto found that the rate of mutation in non-coding regions is slightly lower than in synonymous sites indicating these sites have undergone negative selection pressure. Additionally, he found that the divergence rate in selected sites was increased relative to the polymorphism indicating that they also experience positive selection pressure. In other words, most mutations in these regions are deleterious and thus are selected against but every once in a while a nucleotide substitution confers some advantage and this is selected for. The bottom line is that these non-coding regions are crucial for the survival of the organism.

What these non-coding regions are for is unknown. The current dogma says that gene expression is controlled by sets of transcription factors that act on various promoter regions. According to Alex Kondrashov in the accompanying News and Views piece, current estimates of the fraction of functionally important segments of mammalian non-coding DNA is less than 15%. Although, an equivalent study still needs to be done in mammals, I’m betting that a significant portion of what is thought of as junk DNA is used for regulation and in a completely novel way.