Monday, November 30, 2009

Vitamin Water is a Stupid Product

Alas. It’s been a long time since work has kept me up till 3am. But I have something to share - I loved this Saturday Morning Breakfast Cereal comic:


Tuesday, November 24, 2009

Spotted any strangelets yet?

A press release yesterday from CERN has announced that the LHC has completed its first particle collisions successfully. Hooray for particle physics!


Now for the hard part – not breaking the machine again.

But CERN, if you have to get repairs done again, for Higgs’ sake get an up front quote. You know how bad those particle accelerator mechanics are an untrustworthy bunch.

CERN: Two circulating beams bring first collisions in the LHC

Thursday, November 19, 2009

A thousand taxonomists cried out into the night…

Whoever said cladistics were useless?

Certainly I haven’t.*

An example has just surfaced that shows the importance of taxonomy to this day. Sadly, taxonomists’ vindication may come at the cost of a species of fish, the flapper skate, now recognized as critically-endangered. Classification of this fish as the same species as the related blue skate has allowed the flapper to be fished almost to extinction, and all because of a classification error.

skatePictured: The Flapper Skate. So cute!

So while the fact remains that taxonomy is mostly an outdated field, there might still be some role for the science of natural classification yet. Just not in any of the important sciences.

Wired Science: ID Error Leaves Fish at Edge of Extinction

*This may be a lie.

Friday, November 13, 2009

Knock on wood – LHC might be operational in one week

After more than a year down after various technical problems have kept it from starting, the Large Hadron Collider at CERN in Geneva is planned to be operational next week. The world’s largest experiment may soon be under way.

A week is not much time for anyone to get their tin foil hats on again, but I’m sure we can count on some crazies coming out of the woodwork once they get hold of this news. Bring on the fireworks.


Wired Science: LHC To Finally Start Next Week, Again

Thursday, November 12, 2009

Evolution in the Test Tube – Cool 20-year experiment demonstrates natural selection


Richard Lenski is the Awesomest Scientist of All Time. Yes, even more awesome than Doc Brown.

In the ongoing “debate” over evolution going on in the educational system, one claim that the creationists have made is that evolution has not been demonstrated to occur as we watch it. Enter a particularly elegant 20-year study conducted by Dr. Richard Lenski at Michigan State University.

First published a year ago, Lenski’s group has now followed up with a second genomic study on populations of initially citrate-metabolism-deficient bacteria that were cultured in the presence of excess citrate. In these conditions, it was an obvious benefit to any bacterium that would develop the ability to use citrate as an energy and carbon source, as it would then be able to grow faster than the other cells in the culture.

E_coliSeen above: E. coli, not growing

Over tens of thousands of generations, the bacteria did just that, and accumulated beneficial mutations, allowing them to utilize the extra carbon source, and thus gain selective advantage over the bacteria that did not gain these beneficial mutations. This takes incredible foresight, planning, and a little bit of fortuity, but it worked, and 21 years later the research has been published in PNAS and Nature.

While the research is exciting, the enjoyment I truly got associated with this work was not with the scientific publication itself, but Lenski’s response to inquiries of an insidious nature from Conservapedia founder Andrew Schlafly. Click that link to Conservapedia. I dare you. I was sucked into an hour of frustration reading their “balanced alternative to the liberal-slanted Wikipedia” articles, and you should have to endure it as well.

The entirety of Lenski and Schlafly exchange is presented on both the Bad Science blog and RationalWiki. I’ll just place my favourite excerpts here, but I encourage you to read the exchange in its entirety.

Excerpts from Lenski’s response:

I offer this lengthy reply because I am an educator as well as a scientist. It is my sincere hope that some readers might learn something from this exchange, even if you do not.

But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants. In other words, it’s not that we claim to have glimpsed “a unicorn in the garden” – we have a whole population of them living in my lab! [] And lest you accuse me further of fraud, I do not literally mean that we have unicorns in the lab. Rather, I am making a literary allusion. []

So, will we share the bacteria? Of course we will, with competent scientists. Now, if I was really mean, I might only share the ancestral strain, and let the scientists undertake the 20 years of our experiment. Or if I was only a little bit mean, maybe I’d also send the potentiated bacteria, and let the recipients then repeat the several years of incredibly pain-staking work that my superb doctoral student, Zachary Blount, performed to test some 40 trillion (40,000,000,000,000) cells, which generated 19 additional citrate-using mutants. But I’m a nice guy, at least when treated with some common courtesy, so if a competent scientist asks for them, I would even send a sample of the evolved E. coli that now grows vigorously on citrate.

However, if an incompetent or fraudulent hack (note that I make no reference to any person, as this is strictly a hypothetical scenario, one that I doubt would occur) were to make false or misleading claims about our strains, then I’m confident that some highly qualified scientists would join the fray, examine the strains, and sort out who was right and who was wrong. That’s the way science works.

You may be unable to understand, or unwilling to accept, that evolution occurs. And yet, life evolves! [] From the content on your website, it is clear that you, like many others, view God as the Creator of the Universe. I respect that view. I find it baffling, however, that someone can worship God as the all-mighty Creator while, at the same time, denying even the possibility (not to mention the overwhelming evidence) that God’s Creation involved evolution. It is as though a person thinks that God must have the same limitations when it comes to creation as a person who is unable to understand, or even attempt to understand, the world in which we live. Isn’t that view insulting to God?

Anyway, Richard Lenski is pretty much my hero.

RichardLenskiWith that incredible beard, how could he not be?

See also:

ScienceDaily: Time In A Bottle: Scientists Watch Evolution Unfold
Lenski Group Page:
The New Paper (Nature, Oct 2009): Genome evolution and adaptation in a long-term experiment with Escherichia coli
The Original Paper (PNAS, June 2008): Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
Full Documentation of Lenski’s creationist badgering and response (Bad Science): All time classic creationist pwnage