Saturday, November 13, 2010

Apologies for the long delay - I'm writing papers for publication. In the meantime, check out this comparison of CSI science vs real science at Forensic Science.

Saturday, October 2, 2010

Science article for artificial life

Looks like the Science article for the artificial bacterial cell is publically available, so here's a link to the full text:

For those who prefer PDF, look to the left of the article and you'll find a link.

Those of you who don't feel like going through it - no worries! My next post will be a breakdown of this article.

Thursday, September 30, 2010

Intelligent design is real

This is an 18 minute video of Craig Venter announcing the creation of synthetic life. There so much to talk about with this one, and it's going to take multiple posts. Consider this, then, a bit of preview of some of the stuff I want to get into here in the future.

Wednesday, September 29, 2010

"Lies, damned lies and statistics."

Someone once said to me that it was easier to discuss statistics with someone who is ignorant of statistics rather than someone who knows a little bit about it, as the person who has some knowledge will probably get it wrong. This is largely, I suspect, because it's very easy to overlook assumptions and seemingly minor bits of information which turn out to be extremely important.

This is a 20 minute TEDtalk from 2005 which I quite like which illustrates that point.

PS. If you've never been to TED, you ought to. There are plenty of really interesting talks there.

Thursday, September 23, 2010

Why creationism makes a better scientific theory than intelligent design

The scientific method looks something like this:

1. Make an observation: Things fall down.

2. Think up some explanation for that observation. This is a hypothesis: There is a force between objects which draws them together.

3. Make a prediction based on the hypothesis: The amount of force is based on mass.

4. Devise an experiment to test the the prediction: Build an instrument which would be able to measure the attractive force between objects. See if the attractive force - if it’s there! - correlates with mass.

If the predicted observation doesn’t happen, you reject the hypothesis and go back to the drawing board, using the new observations that you’ve collected to build a better hypothesis. If the predicted observation does happen, you see if the results are reproducible and consistent. When you’re really sure that that what you’ve got isn’t a chance anomaly but a repeatable, consistent observation, then you put a little checkmark next to the hypothesis and say, “We’re pretty sure this is a good explanation.” A scientific theory could be thought of as a group of hypotheses intended to explain related phenomena. A good scientific theory is one which has lots of supporting evidence - that is, it has been used to make lots of testable predictions which have led to repeatable, consistent observations that support the hypotheses. A bad scientific theory does not make accurate predictions.

It turns out that creationism (by which I mean things like Young Earth Creationism) has all the makings of a (bad) scientific theory while intelligent design (ID) does not, even though ID claims to be scientific. It’s all in how science is structured.

Creationism as scientific theory

When you structure creationism* like a scientific theory, it looks like this:

1. Observation: There is holy scripture which describes the origin of the universe, life and everything.

2. Hypothesis: The holy scripture is a literal description of the origin of the universe, life and everything.

3. Prediction: The holy scripture says that the Earth is 5000-10000 years old.

4. Experiment: Estimate the age of the Earth through the use of radiometric age dating or some other acceptable and technically sound method of dating**.

Structurally, everything fits. You can test creationism scientifically, and you can even modify the hypothesis to try again. Admittedly, this modification is usually done by asserting that the holy scripture in question isn’t a literal description of the origin of the universe, life and everything, which in turn is just a fancy way of saying, “The explanation isn’t in the holy scripture.”

ID as scientific theory

1. Observation: There are some really complex stuff in nature. That stuff is so complex that even removing one little bit makes it impossible for the complex part to do what it does (this is called irreducible complexity). A common, non-biological example is a mouse trap. Take away any part, and it ceases to function as a mouse trap.

2. Hypothesis: Some unknown designer created or designed the complex stuff in nature.

3. Prediction: ???

Let’s set aside for a minute the questionable nature of the originating observation (though go see this wikipedia article for a more thorough explanation of irreducible complexity and criticisms), ID proponents will try to tell you that they predict that there will be other irreducibly complex stuff. That’s not a prediction. That’s the originating observation. When you observe that stuff falls down, you can’t drop a ball and go “Hey, it fell down! So my theory of invisible spirits pulling stuff down is true!”

All right, what else? Some might argue that you can come up with some testable predictions of the unknown designer. The problem is that there’s virtually nothing to go on about this unknown designer. ID proponents have claimed that they are not affiliated with a religion, so you can’t rely on holy scripture, like creationists. In this situation, aliens, Sauron, the flying spaghetti monster, invisible pink unicorns and any other entity who could have some form of “designing” power are fair game. So, how do you choose which one to pursue? What other observation do you have which allows you to make any assertions about the unknown designer, especially when ID doesn’t require that the designer design more than once? “I have evidence of aliens!” is all well and good, but you need to connect aliens to the irreducibly complex thing.

What ID proponents want you to believe is that the prediction “The theory of evolution is wrong” is an acceptable prediction for ID. Yes, if ID is a correct explanation then the theory of evolution might be wrong, but this is not an acceptable prediction based on scientific method. Which is a pretty good thing for ID supporters, since if it was then it would be acceptable to say that if the theory of evolution is true, then ID is wrong. And since there is a lovely pile of evidence supported through the use of the scientific method, for the theory of evolution, this would mean that ID would be “proven” wrong.

Which is why ID is gaining momentum while creationism is sliding to the wayside. Creationism leads to testable predictions and can be subjected to the scientific method***. Intelligent Design can’t but that also means that you can’t use the scientific method to refute it.

* While I mean young earth creationism here, you could probably slide in any religion with holy scripture which is meant to be taken literally.
** For more on the methods used to date the Earth, here’s a Wikipedia article. As it turns out, the Earth is about 4.54 billion years old.
*** That the scientific method often shows that literal interpretation of holy scriptures is faulty is another story.

Friday, September 17, 2010

A genetics primer

When I write posts, I try to keep the jargon down to a minimum and explain the terms that I use. I don't want to turn this into a primer about genetics blog, as there are plenty of resources that exist. Of course, the problem is finding a good one when you aren't sure about your knowledge to begin with....

That being said, I recently stumbled across the Learn. GeneticsTM site, maintained by the University of Utah. Instead of the usual wall of text, they have little flash animations which make the info easier to absorb. There are also interactive modules and virtual labs so you can try out techniques that are used in laboratories during molecular studies. I have to admit to a certain amount of geeky glee as I cloned a virtual mouse.

I like this site well enough to put a link to it on the side. If you feel like playing around in a virtual lab and picking up some basic genetics, go check it out!

Thursday, September 16, 2010

Is Race Genetic addendum

In my Is Race Genetic? series, I didn't really touch on the implications of using race as a way of telling if someone is more likely to be susceptible to certain diseases, or if they are going to respond adversely/favourably to a particular medical treatment. In case you're curious, here's a link to a paper called "Genetic variation, classification and 'race'" by Jorde and Wooding published in 2004*.

To quote the abstract:

New genetic data has enabled scientists to re-examine the relationship between human genetic variation and 'race'. We review the results of genetic analyses that show that human genetic variation is geographically structured, in accord with historical patterns of gene flow and genetic drift. Analysis of many loci now yields reasonably accurate estimates of genetic similarity among individuals, rather than populations. Clustering of individuals is correlated with geographic origin or ancestry. These clusters are also correlated with some traditional concepts of race, but the correlations are imperfect because genetic variation tends to be distributed in a continuous, overlapping fashion among populations. Therefore, ancestry, or even race, may in some cases prove useful in the biomedical setting, but direct assessment of disease-related genetic variation will ultimately yield more accurate and beneficial information.

When they get into examples, the jargon gets a little heavy but the main points they're trying to make are pretty good. If you've read my series, you'll probably want to scroll down to the section called "Genetic variation, race and medicine."

*Those of you who pay attention to detail will notice that this was published before Witherspoon et al.'s paper, which I talked about in the series. That's okay - I think their points still stand.