Progress is awesome. This week has largely been a reading week for me; I'm trying to get up to speed on a new idea that we're working on. As a result I've been downloading and printing out lots of scientific papers (I think I killed a few trees). I know, reading scientific papers doesn't seem too exciting, but the awesome part is that a whole lot of these papers were printed before I was born. The oldest one I'm reading was published in 1954.
Apparently someone rediscovered the fact that when you drop candy into soda, you can get a geyser effect, and it's been making the rounds on the internet (see this video or this video). It was even featured on NPR.
People are billing it as an "explosion" but it's really not. Wikipedia claims that it's a result of adding gum arabic and lowering surface tension of the soda, but that doesn't wash with me - lots of sodas already have gum arabic, and the amount you're adding is going to be minimal (and in solid form). In fact, if anything, since gum arabic is a mixture of carbohydrates and proteins, I would actually expect that it would increase surface tension slightly. What's probably going on is that by dropping candies (Mentos, in this case - I used Nerds when I was a kid) into a bottle of fresh soda, you suddenly and dramatically increase the number of potential nucleation points for the carbon dioxide in solution to come out of solution as bubbles. Those bubbles of gas take up more space than dissolved gas would (example: when divers get "the bends") causing the liquid to be ejected forcefully from the neck of the bottle.
In a true display of my extreme geekiness, I have written a baseball simulator to run through all 9! (9 factorial = 362,880) permutations of the lineup in order to determine which one is optimal. There was a bit of talk on some of the sabermetric sites about lineup optimization a few weeks ago, and someone suggested that the best way would be to write a simulator, so I did. It's been a pretty good opportunity to brush up on my programming skills.
It's basically a Monte Carlo simulator that generates a random number and compares it against a player's statistics to determine whether the result of that particular at bat should be a walk, single, double, etc. This simulator doesn't take into account sac flys, sac bunts, steals, or double plays, so it consistently underestimates the run totals, but it should provide a reasonable first order approximation. I've written in a hook for a possible routine for double plays, and it ought to be possible to take sacrifices and speed into account as well, but that would probably require a significant rewrite and consequently increase the run time. I've spent the last few days tweaking the code to get it to run as fast as possible, but for any sort of statistical validity it still takes about 2 1/2 days to run through all the permutations (at about 150,000 to 250,000 games per lineup, we're talking about 72 billion simulated games). Currently I'm testing it out against the 2005 Astros, using the aggregated stats for the pitchers in one slot.
The current version of the code is here; I compile it with the following command on Mac OS X running on a G4-based machine:
gcc -o simulator_gsl simulator_gsl_switch.c -lgsl -mdynamic-no-pic -fast -mcpu=7450 -g
It requires the GNU Scientific Library (hence the -lgsl option on the command line) because it uses the GSL random number generator library; the Mersenne Twister random number generator helped shave a few percent off the overall run time. I originally wrote the scoring function using if/else statements, but have rewritten the subroutine using the switch/case conditionals, which is also slightly faster. I'm trying to see if there are any other places I can eke out a little better performance, but I think the real project will be to rewrite the code so that it can run in parallel on multiple CPUs. Parallel processing should provide nearly linear acceleration (this problem is, as they say, "embarrasingly parallel"), and I have a few older computers around that could contribute CPU time...
Anyway, once I'm done running the program against the 2005 Astros lineup, I'll post the results here.
Update: For those who want to download and compile the program to run it themselves, feel free. It will ask you for a tab-delimited text file with the player statistics in it. It should have the extension .txt, and each player should be given their own line in the file with stats in this order: name, plate appearances, walks, hits, doubles, triples, homers, strikeouts, GIDP, hit by pitch.
Those of you who know me know how furious I get when I encounter the ridiculous lies of creationists and proponents of "intelligent design." Well, evolution won a big battle this week - Judge Jones handed down a ruling in the Kitzmiller vs. Dover case. Some of you may not know about this case (or have only heard of it through The Daily Show's special series "Evolution Schmevolution"), but basically what happened is that in Dover, Pennsylvania, the school board tried to change biology standards to mandate a 50/50 split in time teaching both evolution and "intelligent design" in science classes. It was a pretty good sign when the entire school board was voted out during the November elections, but the fight was also taken to the courts, and the ruling plus opinion was just released yesterday.
Basically, Judge Jones saw through every false argument that creationists and IDers have ever proposed, and decided in favor of real science by completely crushing every argument that the IDers put forth in his 139 page ruling. I'm not going hash through everything here, because there are several good roundups all over the web already. But I will point you to my favorite post (by PZ Myers) that shows even how flimsy the argument by defense expert witness Dr. Michael Behe was, and that Judge Jones saw right through it.
This is a big win for science, and rational behaviour in general. While the decision isn't precedent-setting in other jurisdictions, it will certainly be referenced, and because the judge did such a thorough job in crushing ID arguments in his ruling, I think it unlikely that ID will ever win a court challenge unless there is a drastic sea change in culture (possible) and rational thought dies a complete, horrible death (unlikely - I hope).
I saw a quote the other day by a conservative Christian (sorry, I can't find it right now) who believes in evolution and was against creationism and ID. To paraphrase, it went something like this: "Faith is believing in something that can't be proven. To not believe in something that has been proven is just obstinate." And that about sums it up - you can't prove the existence of God, and unless you're a Biblical literalist, you can have faith and still believe evolution is correct.
Apparently stupidity is contagious. The Education Oversight Committee in South Carolina just voted to weaken science standards.
A proponent of teaching various theories of human origin, which include creationism, gained support Monday from the state’s public school reform oversight panel.
At the urging of Sen. Mike Fair, R-Greenville, the Education Oversight Committee voted 8-7 to strike from high school biology standards wording that tied schools to teaching only evolution.
...
“This is unprecedented,” said Dale Stuckey, the state Department of Education chief lawyer. “It’s my interpretation of the law that (EOC members) have no authority to change the standards.”
The state Department of Education writes standards all teachers must follow in designing their daily lessons. The oversight panel signs off on what the agency and the state school board approve.
This is absolutely depressing. The standards were written by the Department of Education in discussion with experts in the field of biology, and now they're being gutted by theoconservative politicians. Notice how they're always Republicans.
Fair said Monday he is merely “trying to get students more engaged” in looking at the origins of life from different perspectives. He said he is not campaigning to put the teaching of “creationism” on par with evolution.
Monday’s vote enraged educators from the college and public school ranks in the audience.
“Science is not democracy,” said Jerry Waldvogel, a Clemson University professor.
“Science is not negotiated,” said Doug Florian, a College of Charleston professor.
“Science is based on evidence,” said Joe Pollard, a Furman University professor.
Fair's statement is misleading. If you want to discuss alternate viewpoints on the origins of life, by all means go ahead, but don't weaken biology standards to do so. Add some standards that require creation myths to be taught in history/mythology/philosophy and be sure to include multiple myths such as the Judeo-Christian, Hopi Indian, Hindu, and Ancient Greek versions. Teach kids to recognize that these viewpoints were created by ancient cultures to explain what could not be known to them at the time, and then teach them that using the scientific method we have been able to learn how the Earth was likely formed, and how diversity of species has arisen.
The truth of the matter is that science isn't a subject where constructing internally consistent arguments is enough to create a valid theory. Your internally consistent argument must also be backed up by external evidence. Not one shred of physical evidence has ever been produced to back up creationism or "intelligent design." There are certainly things in nature we can't explain (yet) but as PZ Myers wrote today:
There will always be things we don't know and science that falls short. Pointing out a weakness in my theory, however, does not provide support for your theory, and this tactic of the creationists of responding to requests for evidence with whines about something they don't like about evolution is getting old and tired.
CREATIONISTS RESPOND: In last weeks Low End Theory debut, yours truly took a (gentle) swipe at the masses of Americans who dont want Darwins teachings anywhere near their childrens ears. Some readers tsk-tsked your humble narrator, pointing out that politics have no place in Gizmodo. So noted.Pathetic. Support of evolution isn't a political stance. It's realism. There _shouldn't be_ a debate. There are no other _scientific_ theories that explain the facts.
Biological marvels like the optical precision of an eye, the little spinning motors that propel bacteria and the cascade of proteins that cause blood to clot, they say, point to the hand of a higher being at work in the world. In one often-cited argument, Michael J. Behe, a professor of biochemistry at Lehigh University and a leading design theorist, compares complex biological phenomena like blood clotting to a mousetrap: Take away any one piece - the spring, the baseboard, the metal piece that snags the mouse - and the mousetrap stops being able to catch mice.This is a ridiculous argument. One, here is an example of a how a mousetrap could be "reducibly complex." Two, evolution provides a method for the development of highly complex biological structures that cannot function with the removal of a single piece. I could go on, but suffice it to say that the NY Times piece gives "intelligent design" an air of credibility that it doesn't deserve. Like I've said before, and will probably end up saying a million times over again, "intelligent design" is *not science*. There are no experiments that you can design that can disprove the existence of an "intelligent designer," which is the very _definition_ of science - can you formulate an experiment that would provide evidence to contradict your hypothesis? If you're going to do what the ID movement does, then you're not doing science. Some of them claim that evolutionary processes like mutation and selection were "designed by a higher power." Well, if you're going to admit that those processes work, why do you need a higher power? I don't, and you can't design an experiment to test it, either. Ridiculous.
Bush compared the current debate to earlier disputes over "creationism," a related view that adheres more closely to biblical explanations. As governor of Texas, Bush said students should be exposed to both creationism and evolution. On Monday the president said he favors the same approach for intelligent design "so people can understand what the debate is about." The Kansas Board of Education is considering changes to encourage the teaching of intelligent design in Kansas schools, and Christian conservatives are pushing for similar changes in other school districts across the country. "I think that part of education is to expose people to different schools of thought," Bush said. "You're asking me whether or not people ought to be exposed to different ideas, the answer is yes." The National Academy of Sciences and the American Association for the Advancement of Science have both concluded that there's no scientific basis for intelligent design and oppose its inclusion in school science classes. "The claim that equity demands balanced treatment of evolutionary theory and special creation in science classrooms reflects a misunderstanding of what science is and how it is conducted," the academy said in a 1999 assessment. "Creationism, intelligent design, and other claims of supernatural intervention in the origin of life or of species are not science because they are not testable by the methods of science."Let's re-read that last line together, shall we? "Creationism, intelligent design, and other claims of supernatural intervention in the origin of life or of species are not science because they are not testable by the methods of science." This is a joint statement by the NAS and the AAAS, perhaps the two premier scientific organizations in the US. If you're going to take anyone's opinion about the subject, it should be their opinion. What the hell does Bush know? He claims that people should be exposed to different ideas. I agree with that, but should they be taught ID as science? No. Faith, religion, philosophy maybe, but not as science.
Isn't it amazing how everything seems to provide evidence for evolution? The brain shrinks in some form of pygmy homo erectus. Thats evolution! Ancient genes survive millions of years unchanged. That's evolution?! Women have orgasms. That's evolution! Although not all women have orgasms and they still manage to reproduce hmm luckily with the right spin...That's evolution! We live in a civil society with people working for cooperative goals. That's evolution! Unfortunately some people murder and rape. Just an unfortunate side-effect, but that's evolution. Not only is everything evidence for evolution but evolution explains everything! No its not circular reasoning its Evolution! Thank goodness we don't need to resort to God to explain the world around. Now we have Evolution! Its the all-encompassing answer to the ultimate question (I always thought it was 42). The evolutionist has reached the omniscient nirvana. maybe we should start meeting at the biology lab on Sunday mornings. We can sing some Evolution Hymns. Do they exist? Don't worry they'll evolve. I'll just start selectively pressing some keys on the organ and type a few letters while blindfolded. Okay I'm getting a little carried away...chalk it up to evolution.Zimmer responds in this post but Doug responds again in the comments. Here's an excerpt that goes to show that he has no idea what he's talking about:
The problem with Evolution is that it is never defined. Rather, it is defined (or its definition assumed) based on the context of the thought. One may make a statement like: We can see evolution in action when bacteria evolves resistence _[sic]_ to antibiotics. In the first instance of "evolution" its definition is assumed to be - common descent with modification, such that all organisms can be traced back to a common anscestor. The second instance, the word "evolves" refers to a population emerging based on "natural selection" favoring an attribute for survival. The assumption that underlies this equivocation is that given enough time the second will add up to the first. This is an erroneous assumption as selection can only choose from already existing choices and therefore has no power to explain the origin of the choices.He makes the erroneous assumption that the existing choices, as it were, only have one function. Even in his own given example, it would be easy to imagine the existence of an enzyme necessary for regular metabolic function of the bacterium but that has very marginal activity for breaking down a toxin (in this case, antibiotics). Maybe it even has no activity at all. But factor in mutation, and all bets are off. If you start with marginal enzymatic activity, but apply selective pressure, in relatively no time at all you'll have an enzyme that is good at eliminating the antibiotic. Even if you have no enzymes at all present in the cell that have functional ability, a mutation might result in something that binds to the antibiotic, thereby retarding its action, and eventually, it may evolve into an enzyme that not only binds, but cleaves the antibiotic. Random mutation has more power than you might think. Hell, whole research groups have been formed to harness the power of directed molecular evolution to develop new and novel catalysts. PZ Myers has a great post up summarizing the path that yeast took in developing the alcohol dehydrogenase family of enzymes, which beautifully illustrates the concept of genes can have more functions that their primary ones.