There's a movement among secular humanists to call themselves "The Brights," a cynical attempt to rebrand themselves as a minority with a positive-sounding name. Richard Dawkins compares this to the appropriation of the word "gays" by the homosexual community. Can a persecuted minority force the opposition to use this term, associating secularists with brightness in all its connotations? So far, the answer seems to be no; how many right-wing groups have you heard use the term?

The movement itself immediately divided the secular humanists: some thought it was a great idea, others considered it arrogant and condescending. I'm with the latter. To see why this is potentially a huge, backfiring PR disaster, I'll examine the analogy to "gays" more closely. Like everything else, these names are not created equal. They exist on a spectrum from good to horrible, like this:

|----------------------------|-------------------------------------------------------|------------------------------|
"The Happys"......."The Gays".................................................."The Brights"..... "The Insufferable Assholes"

It really speaks for itself.  ¶ 10:50 AM

  Writing music and writing prose are reciprocals for me. For music, I have the song in my head, often more than just a little snippet of melody: fully orchestrated scores that go on and on. But I have no skill, either with recognizing notes or playing them out. If I pick up my violin or sit at my keyboard and try to bang out the notes, I can't even find the first one. It's trapped in my head; I can't get it out. I can't sing, can't transcribe directly to notation, nothing. Eventually I lose my train of thought and it gets lost by the wayside.

For writing, I feel like I can pick out the words I need and arrange them in some more than simply functional way. I have just enough organization, clarity, and brevity I think... but I have no narrative. I can't design a plot further than a backdrop and perhaps a one-dimensional character; I can sometimes string together pleasant words, but they have no real context; I get bogged down in style without a plan for where I'm going with it. In short, I have nothing to write about: no great life lesson or enlightenment, no personal journey of discovery or coming-of-age, no real concept of a life lived outside academia and my home and friends. They say you write what you know, and I want to write about more than science. But I have to live something else first, and that's where it falls off.

Music and writing. My dysfunctional yin and yang.  ¶ 1:10 AM

  My Review of Freakonomics

The scientific fidelity of social science is a topic of heated contention in academics. Steven Levitt and Stephen Dubner have successfully brought this debate to the mainstream in the form of their joint book, Freakonomics. But do they make a strong case for validating statistical analyses of an infinitely complex human society?

As any statistician will tell you, one of the major pitfalls of their field is the confusion of correlation and causation. Just because X and Y have similar trends does not necessarily mean that X caused Y or that Y caused X. Numerous times throughout the book, Levitt and Dubner chastise various experts, pundits, and conventional wisdoms for failing to observe this basic tenet. Yet so tempting is this trap that the authors fall right in along with their targets.

Take, for example, the chapter on parenting. A full six paragraphs are devoted to warning about correlation versus causation, the caution of which is thrown immediately to the wind with a set of highly dubious stabs at the causes of various correlations regarding parenting. The data in question comes from Levitt's regression analysis of numerous factors which conventional wisdom believes may play some role in the academic outcome of children. So, for example, correlations were found between a child's test scores and the number of books the parents have in their house, but not how often the parents read to the child. So far, so good. The authors then conclude from similar datapoints that it is the nature of the parents' lives that influence a child's scores, not what the parents do. Granted, it has a certain logical appeal, but it amounts to no more than an educated guess. What's wrong with that? you may ask.

The problems with this example illustrate some of the major difficulties associated with social science. What you may notice about the correlations is that - by necessity - they lack a certain level of detail. What *kind* of books to the parents have? What kind do they read to their child? How often does a child actually pick up one of numerous books? These are questions for which there are few or no practical solutions. The reasons are manifold, including: the number of data points may never be enough (consider how many categories you may have to break predominating book types into: comic books, encyclopedias, TV trivia, etc.); you never know which test subject is lying, exaggerating, or remembering incorrectly; and you can never be sure that test scores are the right thing to measure.

This last difficulty is made more extreme when you consider the following quote from Freakonomics: "Sorry. Culture cramming may be a foundational belief of obsessive parenting, but the ECLS data show no correlation between museum visits and test scores." There should be little surprise at the lack of correlation: there are very few things that a museum offers that would help on the SATs or state exams. But that doesn't mean that museum visits have no positive impact on the intelligence of a child. The authors make the mistake of equating test scores to intelligence. It may very well be true that a child that goes to museums will score no better on entrance exams than a child that doesn't, but it may affect which hobbies they take up, their job performance, and various other important aspects of life that have little or nothing to do with measurable intelligence.

Similar errors in thinking occur throughout the book. In the bagel-seller example, statistics are carelessly and bizarrely used to justify a stance on morality. Because only 13% of people failed to pay for bagels when left out with a payment box, the authors conclude that the majority - in fact, 87% - of people have an innate honesty. I was floored by this kind of uncritical thinking. People may have paid out of fear of getting caught or out of guilt, but not necessarily out of honesty. But more so than that, honesty in one small area of life does not an honest man make. If Dubner and Levitt wanted to conclude simply that statistics is useful for understanding human motivation, that would be fine. But to make sweeping generalizations about whether humans are born innately good or innately bad on a single study is simply irresponsible.

The only positive thing to say about Freakonomics is that it makes you think. But any controversial book can do that. Though there are some fairly solid examples in the book such as regards the real estate agents, the sumo wrestlers, and the cheating teachers, overall the book is uncritical of its own thinking. It would be fine if Levitt and Dubner acknowledged that there may be other interpretations at least as good as their own, but they choose instead to pontificate their own views, in flagrant violation of their professed objectivism. And oddly enough, I happen to agree with most of their views, just not with how they reached them. Levitt is clearly a brilliant man, and I hope he continues to churn out interesting statistical correlations on unusual subjects... but he and Dubner ought to leave the interpretations to others.  ¶ 5:20 PM

  Regarding the EPR paradox: it seems that the violation of locality is based on the semantics of the word "information," as used in "the instantaneous transfer of information across distances." But information is a property of knowledge on the part of an observer. Just because he "knows" something doesn't make it real.

Instead of spin states of separating particles, imagine the sides of a coin. If I flip and observe a coin on a glass table, I will always know what a person looking under the table will see with 100% probability. It would appear that the information from the heads side has transfered instantaneously to the tails side despite nonlocality (the coin has a thickness). But information isn't something that's "sent" through space; it depends on the consciousness of the observer. If we take the obvservation of heads as a collapse of the wave function of my side of the coin, my internal knowledge that the other side is tails does not mean that the tails side has had its wave function collapsed. The incompleteness seen in the EPR paradox may be in the philosophical association between knowledge and reality.


Furthermore, quantum entanglement is sometimes treated as though the theoretical particles are completely separate entities, and so the "spooky action" is occuring between unrelated objects. However, the particles are no more separate from each other than are the sides of a coin. They may be apart in space, but they are conceptually entagled because they may be viewed as parts of the same system.  ¶ 9:47 AM

  The smoking gun of evolution?

Synteny is the concept that gene order is conserved across species. So, for example, the hoxb gene family sits in order from hoxb1 through hoxb9 as you move along human chromosome 17. If you look at these genes in the mouse and zebrafish, they're still ordered 1 through 9, but on mouse chromosome 11 and zebrafish chromosome 19. This conservation of gene order holds true for large segments of genomes across birds, fish, insects, mammals, and probably more.

Now the reason synteny alone isn't a compelling enough argument for evolution is the idea of God's blueprint. The reason, so the argument goes, that gene order (and more detailed sequence) is conserved is because God has a general blueprint for all creatures that represents the optimal conditions for development. So our genomes are similar by design, not because of common ancestors. In fact, the general gene order on human chromosome 17 happens to be almost entirely conserved on mouse chromosome 11.

But the rest of the genome isn't such a perfect fit. The large segments of synteny are broken up between species, approximately 420 segments between mouse and human. Now that we have genomic sequence information, the breakpoints can be defined. For example, where mouse chromosome 11 stops looking like human chromosome 17, it starts looking like human chromosome 1. The immediate implication is that at some point in evolution, the human/mouse ancestor either had mouse chromosome 11 and this split in humans into human chromosomes 1 and 17 (and others), or the ancestor had human chromosome 17 and it fused with human chromosome 1 (and others) in mice.

That's where some recent papers come into play. Researchers noticed that these synteny breakpoints had an overabundance of segmental duplications surrounding them. That means that chunks of chromosome near the breakpoints somehow duplicated (probably through a process called non-homologous end joining and maybe breakage-fusion-bridge cycles). Instead of the computed 18% of breakpoints being associated with these "seg dups" if they were randomly distributed, 25% were associated. [It's important to note that this number excludes repeats at the centromere and telomere (ie, the ends) of chromosomes because those repeats are believed to occur through mechanisms that may not be involved in speciation.]

So, even if God had a blueprint for gene order, the "smoking gun" of evolution is that these segmental duplications mark events in evolutionary history where ancestral chromosomes broke apart and fused together to give the modern array of species and genomes. Furthermore, many of the synteny breakpoints occur at locations where human diseases are known to be caused by chromsome breaks and fusions. This led to the hypothesis that many breakpoints are "fragile regions" of the genome that are more likely to participate in speciation. It's the most parsimonious explanation for the data (not that that ever deterred creationists), and begins to give some insight as to what that ancestral organism was like.

Incidentally, my friend Bryan is working on creating an artificial ancestral genome of a plant pathogen by first comparing all the known variants and deriving the ancestor based on sequence and gene order. It would be exciting in the far future to find the human "missing link" genetically even without fossil evidence.  ¶ 10:55 PM

  I've moved the blog to blogspot.com because it wouldn't publish to the knapphouse website. This should motivate me a little more (or at least remove a major obstacle) to write more often. I've found that trying to record myself talking makes me too self conscious to say anything useful, so I'll have to just try and remember.  ¶ 5:24 PM

  What Dostoyevsky could not forsee in the relation of mathematical reason to capriciousness is that one day science would avail itself of its apparent stolid regimentation. That is what quantum physics revels in: the discovery of randomness as the essence of the physical world; that what we can never measure because of Heisenberg, because of Einstein-Podolsky-Rosen: that is what gives true awe to what we sense. Modern physics is not an attempt to explain that randomness -- that quantum flux -- but only attempts to catalog it; not, as it were, to understand its literal truth, but rather to marvel at its creative fury.

Every new quantum equation serves to add a new brushstroke to the oeuvre, to approach with dazzling color an asymptote of comprehension and predictability; and not out of pure aesthetics, to be sure, or even any secular faith, but rather out of satisfaction at the non-rigidity of it all. So science and art can converge not because they are similar, but because the creativity of mankind spurs them both on similar paths, paths which meet at the heart of the human desire to have a chaotic peace of mind.  ¶ 2:38 AM