Monday, October 24, 2011

Physics Project Idea: Mythbusters Statistics

Do you remember that episode of Mythbusters where the build team wanted to test whether or not firing an object backwards with a certain velocity while going forwards with the same velocity would cancel out the momentum?

In it, they went through dozens of tests, trying to get the air cannon to fire with exactly the right velocity and finally they got it so it canceled out just perfectly and the ball dropped straight down?

Very cool demonstration except for one thing: Doing dozens of tests and then picking the one you want to be right doesn't actually tell you anything. What would really be necessary is seeing if the average actually comes out to be zero.

This would require getting all the high speed footage from all the tests, analyzing it, finding the average, and standard deviation (which is related to the experimental uncertainty) to see whether or not the average truly fell where it should. Quite a bit of work, but I bet students would love it.

Topics it would address:
Velocity and/or momentum as vectors
Relative Motion
Coordinate Systems
Experimental Procedure
Experimental Uncertainty

Monday, October 10, 2011

Book Review - Zoo City

Awhile back, I heard an interview on NPR with author Lauren Beukes who had recently won the prestigious Arthur C. Clarke Award for her book Zoo City. It sounded rather interesting, and the Kindle edition was a nice $0.99 so I grabbed a copy.

The premise is about a former drug addict, Zinzi December who has the magical gift of being able to track lost objects. She also has the unusual circumstance of having an animal familiar: A sloth. Many characters have such animals with them (reminiscent of His Dark Materials), and they are gained when a character has an exceptionally remorseful incident in their past.

Zinzi is hired by a music producer to hunt down a missing singer which gets her into all sorts of troubles. While it is an engaging and fast paced read, my final conclusion is that this book was lacking. Mostly in the character motivation and background departments.


Zinzi's animal familiar was picked up because she feels remorse over being involved in her brother's death. Yet this isn't well explained. It's just left free floating.

The final villains also lack any credible reason for much of what they do. One is simply trying to rid himself of his animal because those that are burdened with them are stereotyped and looked down upon. This much is clear, but the fact that it's possible to transfer the animals to other isn't hinted at early on, and as such, it's a very quick "Where did that come from?" when that's what the character does. Very much a deux ex.

There's two other baddies that, in the end, get away, and their motivations are never explored at all. At best, they're just out for some money making them annoyingly one-dimensional.

The singer is found, but ends up being a brat who thinks her manager is out to kill her. She's right, but given that it wasn't made clear how she could have known that, her actions lack conviction.

Another frequent topic is how those that are followed by animals are constantly in fear of a mysterious power known as the Undertow, which will kill them horribly and is only kept at bay by the animals. This power too is never explained. That's not the end of the world to me. Mysterious powers abound in sci-fi and fantasy. Star Wars was better when the Force was just an "energy field" and not a ham-fisted attempt to rationalize it with "midichlorians".


This lack of motivation didn't make me want to stop reading. I continually hoped that it would be resolved, but upon reaching the end, I was just disappointed.

I'm somewhat curious if this book is just the first in a series, or a larger universe since it ends rather abruptly with villains, as well as the protagonist, still on the run and several loose ends. If that's the case, I may be tempted to continue reading, but on its own, this book didn't fare well with me.

Thursday, October 06, 2011

Book Review - Relics of Eden

My birthday was this past Monday and as a present, I requested a Kindle. I got one, so immediately I looked over my reading list and started grabbing books.

The first one I picked up was Relics of Eden: The Powerful Evidence of Evolution in Human DNA by Daniel Fairbanks. I really liked the idea behind this book. After all, it's often been said that even completely ignoring the fossil record, homology, and every other field of biology, genetics would be suitable to establish evolution beyond a reasonable doubt. Yet books like Greatest Show on Earth don't give it much of a nod. The most we're treated to is the evolutionary requirement that chromosome 2 in humans have been the result of fusion from an ancestral species.

Relics of Eden takes this same idea, but provides numerous more examples. The first chapter goes through the chromosome 2 fusion. The second, examines Barbara McClintock's study of corn which led to the discovery of transposons. When these were analyzed, they showed the same sort of divergence in humans and our closely related cousins as evolution would predict.

The third chapter is about "Bogus Genes" which are often duplicated genes that have been disabled by mutations. One of the lessons here is that evolution predicts that, since these pseudogenes aren't being selected for, they should have accumulated more mutations. This evolutionary prediction, as Fairbanks points out, is confirmed. This chapter also discusses the GLUO pseudogene which is disabled in humans and, in other species, serves to produce vitamin C. The function of this gene wouldn't likely be selected for since humans had a wealth of vitamin C in their diet and as such, the presence of this gene is much like a vestigial organ. Another gene, glucocere-brosidase gene (GBA), is repeated but one copy also shows a deletion of 55 base pairs in humans, chips, and gorillas, but not in orangutans have both functioning, and squirrel monkeys only have a single gene. Such patterns make sense in the light of evolution: The duplication happened after the divergence from the line that would lead to squirrel moneys, and the deletion happened after the speciation in which orangutans broke off. Another example of this listed is the cytochrome c pseudogene family which shows a similar pattern and confirms the divergences.

The fourth chapter is trying to figure out exactly when humans, chips, and gorillas split apart, or which one did first, a problem the author calls the "trichotomy problem". The answer can be found in mitochondrial DNA which reveals gorillas split off first. This can be independently checked using nuclear DNA.

Chapter 5 looks at more connections to selection effects in genetics. Like with pseudogenes, mutations tend to accumulate more in exons which aren't selected for. The chapter also explores the NANOG gene which can also be used to look for patterns of divergence.

Chapter 6 is about the inversions in genes between chimps and humans how evolution can explain these.

The last chapter that's really about evidence for evolution is chapter 7 which looks at diversity. Specifically looked at the dispersion of genes in humans alone, tracing specific genes (such as descendants of Gengis Khan) as they spread as well as looking at the origin of humans in sub-Saharan Africa.

Chapter 8 was a look at what evolution is. It's mostly a look at how scientists define it today with some historical nods to Darwin and a few mentions of some of the non-genetic evolutionary evidences (such as the development of whales and dolphins). It also has a bit on how genetics can be used to construct phylogenetic trees.

The 9th chapter is "When faith and reason clash". It is an abbreviated history of Intelligent Design and Creationism which is so brief, it fails to draw some important distinctions, like the direct development of ID from Creationism. The author treats them as independent and that simply ain't so.

The final chapter is on breaking down the divide between science and faith. In my opinion, it should simply be tossed out. It's accommodationist noise. It says nothing more than "Some people can compartmentalize." Yet it fails to address the frequent fallacies committed by those that do (such as Ken Miller).

After this "last chapter", you're still actually only half way through the book. There's 3 appendices. The first two are more evidences that are even more technical. The first looks more in depth at the NANOG gene previously mentioned. The second is more on the inversions in genes discussed earlier as well. The final one is a short history of Genetics.

So what's my overall feeling of the book? It has a ton of great information. However, it was poorly organized. It seemed to toss most of the information first, and then organize it later, after most readers would likely be confused at the significance. I think the writing could have been greatly improved by essentially reversing the book (appendices included), teaching more about the history of evolution and genetics, then looking at how the evidence fit those predictions. I also think that the way the evidence was presented could have been much stronger. It should be made much clearer that every way these evolutionary trees are constructed, no matter which gene, pseudogene, chromosomal reversal, or other genetic bit mentioned, they always come out the same and provide independent evidence. While it's hinted at weakly, it's never directly compared to the parsimony of a designer independently making all these changes in order to fool us. I've seen that argument presented elsewhere, and it's devastating to ID/Creationism. Yet the author sidesteps it.

Another note is that this book is rather technical. While the terms are defined, they are then immediately used heavily and readers are expected to keep up. Having done a great deal of reading on evolution over the past decade, and teaching a bio course, I followed along without too many problems, but an inexperienced reader would likely struggle. The introduction to terms could be improved as well as the usage when terms are required later.

So in closing, not bad, but needs an overhaul in the organization for the average reader.

Monday, October 03, 2011

Why Science?

In my review of Sagan's Demon Haunted World, I mentioned my favorite chapter was on the short-sightedness of asking "What's the benefit?" from scientific investigations. The answer is "We don't know, but they're huge." Sagan discussed Maxwell's tinkering with E&M leading to everything from toasters to TVs.

Most people can at least see that connection, but in Astronomy, connections are often more difficult to point out. Astronomy is a prime tool for testing basic physics, which can then, in turn, be applied to all sorts of things, but that's a logic train most people can't quite follow.

But recently, Discovery News had a cool article about how research looking at spectroscopy in stars, may be turned to medical applications.

Archon 35 Recap

This past weekend was Archon 35. Archon is a sci-fi/fantasy convention, as opposed to my more typical anime convention and although I like sci-fi/fantasy, I'm not generally up to date on much of it, and certainly don't know much of the older portions of the genre that many of the attendees adore.

Despite this, I had a blast this year. Friday I gave my Astronomy in Japan presentation to a small audience, but we suspect this was partially due to us closing the door to keep the hall sounds out and them locking to the outside thus stemming the audience population. Oops.

Regardless, one of the people that came in was Elonka Dunin, who was running a 2012 panel later that evening and asked me to join it. I hesitantly agreed, not knowing whether it was going to be debunking or crazy conspiracy theory hour but it turned out to be the former and was a bunch of fun.

My last panel I was on was Friday night and looking at bad science in movies. While this was fun, since it wasn't something I had much time to prepare (I only found out I was on panels when I looked at the schedule 2 days before and my name was on it), so it tended to be more ranting than prepared deconstructions. But what was more fun was at the end, we tied it back to the role of the media in the larger picture of science literacy and how we do at it as a country. This was the last panel in the room for the day, and as such, we abused it, going over time by an hour with a good 80% of the audience staying to discuss science education in the larger scheme of things.

Whenever I wasn't at panels, I'd grabbed my telescope from my car and, with a solar filter, aimed it at the Sun out front which had several large sunspots. I'd meant to get it back out at night, but the panel went so far over time, not many people were still around.

Saturday I didn't host or attend any panels and sat out again with the telescope. That night, I did get the telescope out again and pointed it at Jupiter with a few hundred people stopping by. After resting for awhile and socializing with one of the people that viewed Jupiter, I got the telescope back out (at 3am) and we ended up in the courtyard of the hotel (where there was a good number of people) for another viewing and astronomy lesson. Ended up staying out till the Sun came up before finally turning in.

Sunday I was pretty sleep deprived and left early so I could sleep the rest of the day.

Overall, this is probably the most fun I've had at Archon and I can't wait for next year.