Saturday, October 25, 2008

The DNA Network

The DNA Network

My favourite games. [Genomicron]

Posted: 25 Oct 2008 06:56 PM CDT

One of the reasons I was interested in giving some comments on the science in Spore is that I am a big fan of video games but rarely have a chance to play anymore. The discussion about Spore (which I wasn't asked to evaluate as a game per se) got me thinking back on the games I have really enjoyed playing. So, just for fun, I have come up with this list of some of my favourite games. Now, these go back to my elementary school days in the 1980s, so bear with me. It's a mix of console and computer games and is a little behind the times as I don't have much time for games anymore. Here they are largely in chronological order.

1. Gorf, Advanced Dungeons & Dragons, Baseball, and Tron: Deadly Discs

Included for nostalgic reasons, these are some of my favourite games from the first consoles we owned when I was very young. Gorf on the Commodore VIC-20, and then Advanced Dungeons & Dragons and Baseball (Yer out!) on Intellivision. My father and I played baseball until our hands hurt (not hard on the awkward controllers). I once (and only once) got 1,000,000 points on Tron: Deadly Discs and got to see the Guardians. (Just outside this list: Astrosmash).

2. Super Mario Bros. (I and III), Metroid, and Legend of Zelda

My cousins are part Japanese and had Nintendo at home two years before it came out in North America -- when it finally arrived, I had to get one specifically to play Super Mario Bros. Later, I went to see the crappy movie The Wizard just for the advance footage of Super Mario 3 (worth it) and I spent $80 of my tips from working as a busboy to get it as soon as it was released (worth it). And no, I don't need warp zones to finish either of them. Absent from this list: Super Mario 2. Metroid and Zelda also consumed many hours of my youth.


I pretty much got a Game Boy just for this game, having become hooked on it in the arcade. Easily one of the greatest games made.

4. Wing Commander (I, III, and Prophecy)

I don't usually like flight sims, but space ones I do. We played this game a lot in high school. So much, in fact, that we once left Wing Commander running on a computer in one of the classrooms, but managed to convince the teacher that it was a screen saver. It only got better with WCIII. Mark Hamill as Blair? Awesome.

5. Mortal Kombat

My buddy and I could finish this on one quarter when we were undergrads (yep, games used to cost 25c). Of course, we spent a lot more getting to that point. FINISH HIM! (Over, down, over, high punch).

6. Doom (I and II)

Not so scary now, but back then playing with the lights out and the sound up was a challenge.

7. StarCraft

This game is still popular and there is even a professional league dedicated to it.

8. Perfect Dark

This game was great for playing with my brother on his Nintendo 64. For starters, you could be on the same team and fight simulated agents. Is anything cooler than a laptop gun?

9. Warcraft III

This realtime strategy had amazing cut scenes and extraordinary gameplay along with an exceptional story line.

10. Halo

One of the best selling games ever, and for good reason.

Ok, your lists?

More on the importance of model organisms [adaptivecomplexity's blog]

Posted: 25 Oct 2008 03:56 PM CDT

Since Palin's comments on fruit fly research are getting some commentary, it's a good time to review the value of model organisms in basic research.

One of the things budding geneticists, biochemists and cell biologists learn very quickly when they enter grad school is that studying humans is usually not the best way to successfully tackle the most interesting research questions. You can ask questions about human biology, but to answer them you generally turn to an elite club sometimes called the Security Council of biology: the bedrock group of five model organisms.

read more

The Science of Spore [Genomicron]

Posted: 25 Oct 2008 01:11 PM CDT

Is Spore meant to be just a game, with no suggestion that it has scientific content?

Help high school kids do genetic engineering and make glowing bacteria [Discovering Biology in a Digital World]

Posted: 25 Oct 2008 12:35 PM CDT

Why should professional scientists have all the fun?

Researchers have been engineering glowing cats, and selling glowing fish at pet stores. High school kids can do genetic engineering too, if they have the right equipment. And you can help them get the equipment by contributing to our DonorsChoose fund drive.

If you're willing to help students, they'll be able to do biotechnology in the class room and learn about DNA. They'll put genes for green fluorescent protein into bacteria and see how that bit of invisible liquid in a test tube gets used to make a glowing protein.

Even better, SEED magazine will be contributing money as well, making the impact of your donation grow. And did I mention prizes? There could be prizes, too. Either contribute to my challenge (below) or any of the others listed here. If you do donate $10 or more, forward your receipt to You can win some nifty stuff like a subscription to SEED, flash drives, exclusive Sb mugs, and other stuff.

Read the comments on this post...

McCain Palin going after fruit flies [The Tree of Life]

Posted: 25 Oct 2008 12:26 PM CDT

As if scientists did not have enough reasons to vote against McCain-Palin who seem to have decided that Bush was overly supportive of science. Now Palin is attacking of all things "fruit-fly research." Lovely. Proof that they are both clueless (not knowing what a fruit fly is probably) and anti-science at the same time. For more on this see:

Fruit flies. I kid you not. [Genomicron]

Posted: 25 Oct 2008 11:24 AM CDT

I have complained recently about the state of basic research support in Canada, as the current government is pushing for more short-sighted, applied, industry-oriented work. This is as nothing compared to the attitude of some politicians south of the 49th.

Here is how a recent paper of mine began*:
Through all the major transitions in genetics over the past 100 years – from early mutation and mapping studies involving countless crosses and phenotypic analyses, to karyotyping and polytene chromosome banding, to the application of allozymes in population-level surveys, to the advent of complete genome sequencing and the rise of "evo-devo" – the fly Drosophila melanogaster has maintained its uncontested status as a preeminent model organism (Brookes, 2001; Beller & Oliver, 2006). Several entire volumes have been devoted to its use in experimental genetics (e.g., Demerec & Kaufmann, 1996; Powell, 1997; Sulivan et al.,2000; Henderson 2003; Ashburner et al., 2005), and it is estimated that there are well over 1,000 research groups worldwide who use Drosophila as a key model (Clark et al., 2003). As Demerec & Kaufmann (1996, p.1) put it, "it would not be an exaggeration to say that we have learned more about the basic laws of heredity from the study of this fly than from work on all other organisms combined."
Here is what Palin has to say about wasting money on fruit fly work. I kid you not.


* Yes, I know Drosophila technically is not a fruit fly, but it is often referred to this way.


It is even worse... apparently this actually referred to applied studies on the olive fruit fly (Bactrocera oleae) which is a major agricultural pest (one can only imagine what she says about basic research).

Here is what the Congressman who earmarked it stated:
"The Olive Fruit Fly has infested thousands of California olive groves and is the single largest threat to the U.S. olive and olive oil industries," he said. "I secured $748,000 for olive fruit fly research and irradiation in the (fiscal year 2008) appropriations bill for the U.S. Department of Agriculture. The USDA will use some of that funding for their research facility in France. This USDA research facility is located in France because Mediterranean countries like France have dealt with the Olive Fruit Fly for decades, while California has only been exposed since the late 1990s. This is not uncommon; the USDA has several international research facilities throughout the world, including Australia, China and Argentina."

Hat tips: Pharyngula, Chance and Necessity, Mike the Mad Biologist

Sarah Palin: Why Are We Wasting Money on Fruit Fly Research? [adaptivecomplexity's blog]

Posted: 25 Oct 2008 09:19 AM CDT

Sarah Palin is opposed to the basic model organism research that forms the bedrock of biomedical research.

Over at Pharyngula, go listen to her mock the fact that we spend money on

projects that have little or nothing to do with the public good. Things like fruit fly research in Paris, France. I kid you not.

Don't just read the quote - you've got to hear the mocking inflection of her voice as she says "fruit fly research".

read more

Evolution: Education and Outreach special issue -- evolution of eyes. [Genomicron]

Posted: 25 Oct 2008 07:30 AM CDT

I was planning to wait until the issue was actually in print, or at least until all the articles were available in preprint, but there is already some buzz starting so here it is. The upcoming issue of Evolution: Education and Outreach, of which I was editor, is a special issue dedicated to eye evolution. The table of contents:

Evolution: Education and Outreach
Volume 1 Issue 4
The evolution of eyes
Edited by T. Ryan Gregory


1. Introduction by T. Ryan Gregory

2. Casting an Eye on Complexity by Niles Eldredge

Original science / evolution reviews

3. The Evolution of Complex Organs by T. Ryan Gregory

4. Opening the "Black Box": The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey

5. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky

6. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin

7. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young

8. Charting Evolution's Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse

9. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich

10. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter

11. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris

12. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer

13. Suboptimal optics: vision problems as scars of evolutionary history by Steven Novella (coming soon)

Curriculum articles

14. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa

15. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead

16. Bringing Homologies Into Focus by Anastasia Thanukos

Book reviews

17. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley

PZ Myers is coming to town. [Genomicron]

Posted: 25 Oct 2008 07:19 AM CDT

In support of my hypothesis that PZ Myers had several clones of himself produced so that he could travel all around while still teaching courses, I noted a poster on my way to the lab yesterday that indicates that he will be in Guelph on Saturday Nov. 1, speaking in Thornbrough 1200 at 2 pm. Cost will be $2 (that's a bargain -- only $1.60 US!). This time I will actually try to attend, having skipped the Evolution 2008 conference in his part of the world.

You can go in a Crunk-Car if you wish [A Free Man » Science]

Posted: 25 Oct 2008 12:25 AM CDT

“Where does a lot of that earmark money end up anyway? […] You've heard about some of these pet projects they really don't make a whole lot of sense and sometimes these dollars go to projects that have little or nothing to do with the public good. Things like fruit fly research in Paris, France. I kid you not

-Sarah Palin, October 24

Damn it. I had placed a voluntary moratorium  on political posts here at A Free Man. My vote is in. My guy is well ahead. I was happy to get on with my life here on the other side of the world and ignore the nonsense of the last few weeks of this campaign. But this is just ridiculous. Sarah Palin is probably not going to be the Vice President. But she is a dangerous idiot. And in the Republican party, dangerous idiots are a little like bad pennies.

Here’s the background on what’s inspired this particular rant. Basically, Palin was talking about funding for autism research and in her inimitable sarcastic/moronic style dismissed both basic and collaborative research in a single breath of hot air.

Governor Palin, basic research drives innovation in the life sciences. Most of the advances in medicine over the last century have been initiated in labs that were working on what seems, to an outsider (or a dangerous idiot), as pointless research. Because of the ethics that scientists live by, most genetic research has to be undertaken in model organisms. These are critters like yeast, roundworms, mice and fruit flies. These are organisms that are amenable to genetic manipulation. Because we understand their evolutionary relationship (I know, evolution, scary and evil) to man we can make assumptions, for example, about what’s happening in your brain based on things that happen in a mouse’s brain. Probably not much of a leap there.

As for the France bit, scientists - unlike politicians - work best in a collaborative manner. Most major advances are done by groups of scientists from different universities who work toward the common goal of gaining knowledge about a particular topic. Sometimes, those collaborations cross national borders. Now, I know you were trying to drum up the hatred of France that worked so well for the Republicans back in the ‘02 midterms, but come on. If I can speak personally, it would have taken me another couple of years to finish my Ph.D. without a collaboration with a group that was working on a similar problem in Germany. I’m not particularly fond of Germans, but I put that personal prejudice aside and just got on with it - for mutual benefit.  This is how science works. Maybe, Governor Palin, you could try a similar approach to governing.

Governor Palin, just because you don’t understand it doesn’t mean it is not for the “public good”. Don’t you have some Russians to look out for up in Alaska?

With apologies to Dr. Seuss and Art Buchwald:

Sarah L. Palin will you please go now!
The time has come.
The time has come.
The time is now.
Just go.
I don’t care how.
You can go by foot.
You can go by cow.
Sarah L. Palin will you please go now!
You can go on skates.
You can go on skis.
You can go in a hat.
Please go. Now.


Check out NATUI’s “My fruit flies are smarter than Palin” shirts. The t-shirt every Drosophila geneticist needs.

I’m all about the Treepeople covers this week, but this Carly Simon cover just seemed perfect. Treepeople were an Idaho band that used to tear up the Seattle clubs back during my time there. They were led by Doug Martsch, who subsequently went on to form the outstanding Built To Spill. If you like what you hear you can buy Treepeople's records from C/Z Records.

This posting includes an audio/video/photo media file: Download Now

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