Thursday, July 26, 2007

The Scoville scale of dangerous questions

Taped to the wall just next to where I am writing this is a cut-out from an old issue of "New Scientist" that describes the Scoville scale. This scale describes the hotness (spicyness) of food on a linear scale. The hotness is determined by diluting a known amount of a food item until you no longer can taste the burning sensation. The rating a food item gets on the scale is represented directly by the amount of dilution necessary. While a typical Jalapeno pepper measures a paltry 2,500-8,000 on this scale, the Guiness Book of record desribes a pepper that measure 580,000(!) and there is even one that measure 855,000!!!. Pretty hot. That's interesting and all, but what has this got to do with ID? Well, William Dembski proposes that we should ask some dangerous questions for materialism and grade them on the Scoville scale. Asks he:

What would happen if the general public not only disbelieved materialism (as it is, they disbelieve it now) but also decided to cease funding it out of their tax dollars?
I'll let the ID crowd worry about that question and ask a similar one on my own:
What would happen if the general public not only embraced non-materialism (even more than now) but also decided to cease funding materialistic science, instead channeling all those tax dollars into non-materialistic "science"?

- What would happen if prayer studies superceded drug trials?

- What would happen if divining became a legitimate scientific tool?

- What would happen if "God-did-it" became a valid scientific explanation?

I'd say that the above would rate fairly highly on the scale, some possibly coming close to the equivalent of pure capsaicin.

Small note: I just noticed that this is my 100th post on this blog. Hurrah for me.

Wednesday, July 25, 2007

I am so smart. S-M-R-T!

With a bit of practice, that is.

Tuesday, July 24, 2007

Oh, the irony

Casey Luskin of the Discovery Institute wonders:
Question: What do you do when a theory logically predicts both (a) and not (a)?
Answer: Apparently you heavily promote it.
Luskin is referring to a couple of evolutionary papers that appear to do just that. It would seem that a theory that can predict both one thing and it's absolute opposite would be absolutely useless as far as science goes. And he would be right - to an extent. There are some problems with Luskins argument, however. (1) Predicting both (a) and not (a) is NOT necessarily bad. To see why, consider this: if (x) then (a); if (y) then not (a). Both (a) and not (a) are predicted but the conclusion depends on the premises of the argument. So, predicting two opposite outcomes is not necessarily a bad thing at all. (2) Evolutionary theory on it's own doesn't make any predictions. It is the auxilliary propositions added to them that do. So in a scenario where hyposesis (x) predicts (a) and hypothesis (y) predicts not (a) and (a) is the outcome, hypothesis (x) makes the successful prediction. Fine, you might say, but if evolution can make contradictory hypothesis it would still be able to predict anything. What is important to note, however, is that there are restrictions as to which auxilliary propositions can be used - they must be independently supported. For a starter, we're not allowed to assume that the theory we are testing is true, for then we would be indulging in circular reasoning. Second, we can't use the observations that we based our auxilliary proposition on to test our theory, for if we did, we could simply have our proposition predict whatever is observed. Lets use this knowledge to explain why Luskin is wrong when he claims that evolution predicts both (a) and not (a). Writes Luskin:
The first article about the evolution of Waterfowl genitalia contends, “Scientists had speculated that male waterfowl evolved longer phalluses to give them a competitive edge over those not as well-endowed when it came to successfully fertilizing females.” That makes sense, I suppose. But the article makes one admission that strikingly contradicts that little just-so hypothesis: “Most birds lack phalluses, organs like human penises. Waterfowl are among the just 3 percent of all living bird species that retain the grooved phallus…” If long phalluses are so advantageous for reproduction, why did so many birds supposedly lose them? Darwinists will look back retroactively and tell us that, in the environmental conditions for most bird species, long phalluses weren’t advantageous. The problem in so doing is that they now have a theory which can explain both (a) long phalluses, and also not (a).
The auxilliary proposition here (male waterfowl evolved longer phalluses to give them a competitive edge) can be tested by performing a "simple" experiment. One can take two male populations of fowl; one has short phalluses, one has long ones. Allowing for mating with female fowl, one would observe which population was the most reproductively successful. If the population with the long phalluses was more successful then the proposition is strengthened since it predictied that this would happen. Notice that the proposition does not require you to assume that evolution is true what-so-ever. Neither are you recycling old "known" observations.

Let us now have a look at one of Luskin's favorite ID predictions, namely that ID predicts that the should be no junk DNA. Luskin has made this claim so many times that my eardrums (or should that be retinas?) are starting are going numb. Let's examine how ID would fare under the above conditions. First of all, can we avoid circular reasoning for reaching this conclusion? As it turns out, no, we can't. ID makes no assumptions what-so-ever about the supposed designer. (The following is taken virtually verbatim from an article I wrote previously) In fact, ID does not and CAN NOT tell us anything about the designer; It cannot tell us anything about the designer’s intentions or purposes any more than it can tell us anything about whether the designer prefers brown over blue. The "junk-DNA claim" seems to stem from the observation (by IDists) that when human designers design things, they don’t tend to put junk into their designs. We should then reasonably expect that the “intelligent designer” would not have put junk into the design of our DNA. So, the claim comes down to is that since we can predict, based on human behaviour that there should be little junk DNA, it also follows that ID would predict the very same thing. An observant reader might notice something iffy here – namely that ID does not say anything about the designer. More precisely, ID says nothing about the designer thinking and acting like a human and even if it did, it says nothing about the designer’s desires about junk DNA. In order for ID to predict something regarding the existence of junk in DNA or anything for that matter, it will have to add some form of assumption about the designer’s intents or purposes. That assumption would include something about the designer's desires to put junk into DNA. I.e. the conclusion would also be found in the assumptions - pure circularity. So, ID is just as happy to predict the non-existence of junk in DNA as it is happy to predict it's ample existence.

Let's now, as opposed to Luskin's circular argument, go full circle and return the reason for this post, namely Luskin's initial assertion:
Question: What do you do when a theory logically predicts both (a) and not (a)?
Answer: Apparently you heavily promote it.
Which theory does that sound like?

Edited to add: EVOLUTIONBLOG has also commented on Luskin's post.

Monday, July 23, 2007

A de novo-'Out of Nowhere'-Gene

At uncommondescent, PaV find it interesting how "Darwinists" explain things. He is referring to a gene - hydra - found in various species of the fruit fly Drosophila that appears to not to be related to other genes in any known genome. What is interesting, according to PaV, is that since gradual accumlation of mutations in a duplicated gene is an unlikely source for this gene, the scientists that described it actually propose an alternative explanation for how this gene might have ended up in the flies genomes. The explanation proposed is that a virus which carried a transposon that inserted itself into an ancestral fly genome. PaV says:
While that’s, hypothetically possible, right now there’s no way of proving that since, per the author, “You cannot find any related genes in the fly genome or any species’ genome, and that is what is unique.” (my emphasis) Is this simply grasping at straws? Or, are they onto something? I guess time will tell.
Being that I have done some research into bacterial horizontal gene transfer, especially regarding integrons and gene cassettes, I don't find the researchers proposed explanation particularly far-fetched. To explain why, I must first give a quick explanation of what integrons/gene cassettes are. They all consist of a gene that codes for a protein known as an integrase. Near this gene is an attachment site where the integrase can either insert of excise something known as gene cassettes. Gene cassettes, in turn, consist of a recombination site (recognised by the integrase) and most often an ORF that is typically some hundreds of bases long. ORFs found in gene cassettes often carry adaptive traits such as antibiotic resistance but more to the point it is fairly common for them to not have any known homologues - just as in the case of hydra. So when the researchers propose that hydra was transferred from another organism, I don't think thay are grasping for straws at all. I'm more surprised that such genes are not found more often. Granted, integrons/gene cassettes are only known to exist in prokaryotes, but it not exactly unheard of that foreign DNA can insert itself into eukaryotes either (think HIV and herpes virus).

What I find interesting is that PaV finds it interesting how "Darwinists"explain things. Proposing a plausible explanation is simply good science and shouldn't be sneered at.

Friday, July 13, 2007

Casey Luskin seems to have a bit of a problem performing probability calculations. His claim is that, for a mouse with a mutation rate of 2*10^-9 per base pair per generation, it would take 125 million years for every single base pair to become subsituted (in the absense of selection).

"Carroll claims that the mutation rate for mice is 2 x 10^-9 per base pair per generation, and other sources indicate that mouse generation time is 3 months. This means that a non-functional mouse 'pseudogene' should be completely rewritten in about 125 million years. According to Neo-Darwinists, humans and mice supposedly shared a common ancestor between 75 and 125 million years ago, which means that any such shared 'pseudogenes' could have been 60%-100% rewritten by neutral mutations. Could we still recognize a 'pseudogene' [were it] 60% rewritten? 75%? 100%?"
The calculation is fairly simple to perform, and I'll break it in 3 steps:
(1): Mutation rate = 2 * 10-9 mutated-base-pair / generation = 0.000000002 mutated-base-pair / generation.
(2): 0.000000002 mutated-base-pair / generation * 4 generations / year = 0.000000008 mutated-base-pair / year.
(3): Take the inverse to make the units "years per mutated-base-pair" (i.e., how long will it take to guarantee that a given base pair is mutated or "rewritten"), and you get 125,000,000 years per any given mutated-base-pair.

One can also frame the calculation slightly differently by recognizing that there are 4 generations per year for mice:
0.000000002 mutated-base-pair / generation * 125,000,000 year * 4 generation / year = 1 mutated-base-pair.

So, 0.000000002 * 125,000,000 *4 = 1 is his probability argument, which is, of course, extremely wrong. Casey Luskin, you can't simply add probabilites together. If you could, then you would be 200% certain that all bases would be substituted after 250 million years. This is obviously nonsensical. Using this "logic", Luskin should also argue that after six rolls with a dice, you are 100% certain to get a "1". A more correct calculation would be to take 1 minus the inverse of the probability of a substitution raised to the power of the number of possibilities for substitutions:

1-(0.999999998^(4*125,000,000))=0.63. I.e. after 125,000,000 years, there is a 63% chance that any given base pair has mutated once. (There is also a roughly 40% chance that any base pair has mutated twice and a 25% chance that it has mutated three times. Several mutations at the same site could potentially restore the original base pair.)

"Evolutionists" sometimes accuse creationists of not understanding probability calculations, something that sometimes is warranted and sometimes is not. In Luskin's case it certainly is.

Monday, July 09, 2007

This blog is rated:

Free Online Dating

Well, not really. It's really rated:

Free Online Dating

The only offensive words that showed up on this blog, according to mingle, was 'dead' - three times. I wonder what would happen if I started writing more about sex, sex, sex and drugs, drugs, drugs. See, I couldn't even muster entering any ruder words than those. Rceommended for "general audiences" it is.

Sunday, July 08, 2007

Seems like the "tagging" that has been doing the rounds at a number of blogs has reached my corner of the blogosphere. In order for me not to be afflicted with eternal misfortune, having to sacrifice my first-born and having to eat only haggis for the rest of my life, these rules must be obeyed:

1. We have to post these rules before we give you the facts.
2. Players start with eight random facts/habits about themselves.
3. People who are tagged need to write their own blog about their eight things and post these rules.
4. At the end of your blog, you need to choose eight people to get tagged and list their names.
5. Don't forget to leave them a comment telling them they're tagged, and to read your blog.

Rather than give a boring account of some boring aspects of my life, .... nah, I'll give a boring account of some boring aspect of my life - a short account of why this blog exists. It all started many years ago in this very galaxy when:

1. I started reading popular science magazines in my early teens.

2. I used to be a well-paid computer programmer.

3. While reading "New Scientist" some eight years ago, I came across a side bar saying something along the lines of "Creationism is alive and kicking in the US". Growing up in a largely secular society, I thought such religious devotion was virtually non-existent. Boy, was I wrong.

4. I got interested in the evolution vs ID/creationism debate and my interest in science switched from "general" to more biology-focused.

5. I left my lucrative job to pursue a career in science.

6. I started debating creationists in various forms in different internet fora such as Skeptic Friends and later Uncommon Descent.

7. I got banned from posting at Uncommon Descent.

8. I set up this blog so that I can moan all I want, without the risk of censorship, about some of the nonsense the ID/creationist crowd put forth.

The unfortunates I will expose to this chain-mail curse are as follows:

Fresh Brainz

Aude Sapere

Vetenskap & Förnuft

Rationally Speaking

Science Avenger

A History of Histrionics


I think that I will probably be the first to tag myself, leading to an infinite tag-loop (yeah, I know I have already been tagged, but that is not against the rules):

The DesignInterference