Monday, April 27, 2009

"Intelligent Designer" comes back in the comments

"Intelligent Designer" (Randy) finally got around to responding (see the comments) to my response to his refute...
Our different perspectives about the nature of DNA do indeed account for some of our disagreement. I don’t consider DNA to be a hodgepodge of genes in no particular order interspersed with vast amounts of gibberish. Instead I think that the majority of DNA appears to gibberish because the current scientific understanding of DNA has barely scratched the surface of what is really there. It only makes sense that scientists would figure out what the protein-coding sequences of DNA do first. It doesn’t make sense to jump to the conclusion that the rest of it is junk.

But let’s say for the sake of argument that you are right about the nature of DNA. Even in that case my argument is still valid. As you recall my calculation regarding the probability of information used a 151 character sequence. The average length of a gene is 1210 base pairs and is hardly equivalent to the three of four letter words used in your example.
Randy has taken the safe approach by claiming that the DNA that is currently considered "junk" by geneticists will eventually be found to be important. It's safe because it's a position that can't be falsified. There's no way I can possibly prove that "junk DNA" will never be found to have an important function. He can lurk in that nebulous "one day we may discover its importance" realm forever, because he has until the end of the universe to be disproven. All I can say is that since he can not show that "junk DNA" has a function, there's no evidence of a function. Generally speaking, the burden of proof is on the person who asserts the existence of a thing, not the person who denies it. To use a cliche, I can assert that there's an invisible, intangible dragon living in the shed behind my house, but do you have any reason to believe my assertion? Without any evidence that junk DNA serves a purpose (beyond adding to the medium in which mutation and subsequent selection can work), there's no reason to assume we will eventually find one. So "Yes", Randy, it does make sense to assume that DNA that has no known function is junk.

As to the rest of his case, no I don't see the validity. The average length of a gene may be 1210 base pairs (I haven't done a fact check on that), but the current average length of a gene is irrelevant. There are certainly many shorter genes, and there's no reason to assume that the current average must apply all the way back to the original molecule that started the process of evolution. I've already linked to a good explanation of abiogenesis, which works with self-replicating molecules that are composed entirely of junk DNA. You can get the ball rolling with pure static, so you don't need to have hundreds of base pairs in some kind of functional code for evolution to begin. From abiogenesis forward, any DNA strand that forms the simplest of productive genes is gravy.

Wednesday, April 22, 2009

The Ticking Time Bomb Challenge

I’m hearing this argument on talk radio a lot lately.

You are a government agent who has discovered a plot to set off a nuclear weapon in the US. You have captured one of the terrorists involved in the plot, and you are convinced that your captive knows where to find the bomb. You are also convinced that the bomb will go off in just a few hours, so time is of the essence. Would you torture the captive to make him tell you the location of the bomb?
This argument is designed to get you to admit that the federal government should not publicly outlaw “aggressive interrogation” techniques like waterboarding. If you say “yes”, you agree that such techniques should not be forbidden; if you say “no”, you put the well-being of one terrorist ahead of the lives of thousands of American citizens.

Let me go on record as saying that the government should unequivocally outlaw torture. Not only is it unethical, it’s an unreliable means of getting information. Victims of torture do not necessarily tell the truth. Generally speaking, they tell the torturer whatever they think will make the torture stop, whether it’s true or not. In the hypothetical situation, the interrogator really doesn’t have a way to tell if the captive is lying; anything the captive says could lead agents on a wild goose chase, making it even less likely that they’ll succeed in stopping the bomb.

But let’s say that I really am convinced that my captive has the information needed to save thousands of American lives and that I’m convinced I can get that information from him in time to do something about it. In that case, yes, I will use “aggressive techniques” to extract the information. I will not, however, complain when I’m sent to prison for torturing the guy. If the information was worth his pain and suffering, then it’s also worth my personal freedom.

Can we give this argument a rest, now?

Wednesday, April 15, 2009


This is a picture I took on my last trip to Pennsic, made into a poster with the BigHugeLabs motivational poster maker.

The Ashleys should get a kick out of it.

Tuesday, April 14, 2009

Reclaiming the Blade

This is apparently due for DVD release soon (if it isn't out already).

Monday, April 06, 2009

SciFi’s Ghost Hunters

I have roommates who find Ghost Hunters amusing. I suppose it is, if you like watching a study of how not to conduct proper scientific research.

If you’re unfamiliar with the premise, The Atlantic Paranormal Society (TAPS), which consists of a couple of plumbers and their friends, go to “haunted” locations and attempt to verify whether paranormal activity is occurring. Needless to say, these people have little idea how to properly conduct such an investigation, and their methods are ripe for confirmation bias.

Normally, the TAPS crew visits a location in response to a request from the owners or residents. Their first action upon arriving is to question the “witnesses” of “paranormal” events, asking what they thought they saw and where they thought the saw it. With these “hot spots” identified, they set up cameras and microphones to record activities in those particular locations. The team then spends the night at the site, wandering through the hot spots, trying to provoke reactions from “spirits”, and recording any “significant” instrument readings or “personal experiences” consistent with the stories they were told. Need I mention that they do this in the dark, making them all the more susceptible to “chills” and other spooky feelings.

Like I said, their method is ripe for confirmation bias. Any unexplained noise or “chill” or draft is easy to attribute to paranormal activity. They do dismiss many events that can easily be traced to something mundane, but they seldom actually dismiss claims of a haunting (if ever - I've never seen it happen), because there are always a few “personal experiences” for which they found no specific mundane explanation.

The most obvious thing that their method lacks is any type of control, and I mean “control” in the scientific sense often associated with drug trials. In a drug trial, some test patients get a placebo instead of the drug being tested, so they have the same experience as the other patients, just no actual chemical. The patients don’t know whether their drug is the real thing or a placebo, so they can’t prejudice the results of the test with their knowledge (it's well known that receiving treatment -- even placebo treatment -- affects the expression of a patient's symptoms).

TAPS could do something similar in their investigations. First, they need some blinding. The investigators who spend the night in the site looking for evidence of paranormal activity can’t be the people who interview the original “witnesses”; knowing where events are supposed to happen taints the evidence. Second, they need to create some “placebo hot spots” – attribute some paranormal activity to locations on the site where the witnesses haven’t actually reported anything. Write out the full list of “hot spots” and “placebo hot spots” – with no distinction between them of course – for the investigators who will spend the night at the site. Finally, have a third team of investigators (more blinding) to analyze the evidence that the on-site team gathered without actually speaking to the on-site team first, again seeking to minimize confirmation bias.

If the experiences of the site's witnesses are connected to actual paranormal events, you would expect the true “hot spots” to generate significantly more instrument readings and “personal experiences” than the placebo “hot spots”. If there’s no significant difference between the two, then you can safely dismiss the activity in the “hot spots” as investigator error.

But Ghost Hunters would never institute such a rigorously scientific method of investigating a “haunted” site. That would inevitably result in an endless string of negative results, and they won’t be able to generate ratings with results like that, so they will undoubtedly continue to use the useless protocols they currently follow.

Thursday, April 02, 2009


Some YouTube whiz crashed Airwolf into Star Wars. I am amused.