"Science Spore?"

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I came across this interesting forum on Spore. I hope SpongB6F1 won’t mind if I quote this posting at length, as I think it is very insightful.

“Science Spore” would be ideal.

…

I think many people will claim that although some kind of abstract commitment to science would have been nice in Spore, what they really want is just some decent, engaging and clever gameplay, instead of a rigid pattern of repetitive, simplistic grinding tasks.

But I think these are two very interrelated issues. The gameplay elements that attracted many of us to the game were precisely the “sciencey” parts. Because by science we’re not talking about the propounding of abstract theorems or doing calculus problems here–the science parts most of us want are basically just the interesting game mechanics everyone is talking about (e.g. functional consequence to parts placement in Creature, or a more realistic Creature ecosystem and behavior system, or any number of sci-fi features we wanted in Space, etc.).

These are science-related not because of any didactic teaching of facts, but in their basic nature and the mental approach you’d have to take to them. Such as trial and error, experimentation, exploration of the world, problem solving, inducing general principles of how the world works, etc. E.g. figuring out what kinds of creature design would be effective. Figuring out what kinds of creature behaviors and strategies are appropriate for which niche, etc.

So in asking for a “Science Spore,” most of us are really asking for a game that actually engages our minds on some level. That’s why we play games in the first place.

I am, of course, pleased to see that many others are interested in a game like Spore that incorporates some actual evolution, and that there is even hope that this will arrive in the form of an expansion or sequel someday. But would there be a market?

My favourite games.

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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.

3.Tetris

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?

Fruit flies. I kid you not.

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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.

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

Update:

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

PZ Myers is coming to town.

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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.

A bizarre comment from John Hawks

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If you don’t read John Hawks‘s blog, you probably should. He regularly has interesting posts about human evolution, and he appears to be someone who is sincerely interested in research and education. You can imagine, therefore, that it would be puzzling to me that he so badly missed the point about a recent review of the video game Spore in Science magazine.

John’s basic points in the post appear to be:

1) The scientists who critiqued the scientific basis of the game are “whiners”.

2) Dude, it’s only a game.

3) He hasn’t played the game, but there is no reason to criticize it from a scientific viewpoint.

4) Science shmience, the review should have told us how fun it is instead.

Some context is perhaps necessary here. The game has been promoted as being about science, in particular evolutionary processes. You can check out part of the documentary that was produced by National Geographic here. SETI has endorsed it on their webpage. A representative from the developer was quoted in the article as noting “Since the game’s release we’ve received a lot of interest from various schools and universities around the world, so that’s a good sign that there’s a lot of interest in [the] academic/education community.” Dude, it’s not just a game.

Within this context, a scientific journal contacted several researchers to provide comments on the game from the perspective of the science. It would seem reasonable, therefore, that the comments we gave were about science. If you want to see a review of how entertaining or interesting from a gaming perspective it may be, Science is not the right publication.

John also dislikes some of our ideas about how the game could be made more realistic, if indeed the goal was to simulate biology. We suggested some things like having consequences for design choices, a cost for major physical updates (e.g., less than 100% refund for exchanging parts), and some limitation on how much you can change in any single upgrade. All of these features can be found in other games.

Science and Spore.

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Tomorrow’s issue of Science features a new installment of “The Gonzo Scientist” by writer John Bohannon. This edition is all about Spore, the game that is based on “evolution” from primordial ooze to interstellar society [Flunking Spore]. I had heard about the game on blogs, but I had not really planned to play it until John asked a few of us to give our perspective on the science behind it.

I can’t say I didn’t have fun with this, although it is a shame that the game bears little relation to actual evolution (see here for apparent claims otherwise).

Here’s the creature Niles Eldredge and I came up with, dubbed Punky Quillibra:

You can read our review at the wiki that John made.

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Updates:

Small genome sizes in pterosaurs, too.

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My colleagues Chris Organ and Andrew Shedlock, who provided evidence that theropod dinosaurs already had (somewhat) reduced genome sizes prior to the evolution of birds (Organ et al. 2007) have followed up their study by estimating the genome sizes of several species of pterosaurs.

Pterosaurs were the first vertebrates to evolve powered flight, having taken to the air 70 million years before birds and 150 million years prior to bats. Interestingly (though perhaps not surprisingly at this point), they seem to have possessed reduced genome sizes, and these downsizings of DNA amount began before flight arose.

On the other hand, it is clear that the estimates for non-avian dinosaurs are not as small as modern birds and that the estimated ancestral genome size for birds was larger than the genome seen in various groups. Patterns can be observed in terms of flight ability across living avian species. Notably, my student Chandler Andrews showed that genome size is correlated with wing loading (and indication of flight capacity) within perching birds, and we are currently writing up major projects on bird groups with different flight ability as well as a study of hummingbirds; Jill Smith, another student, also has a large bat study to write up.

The story thus seems to be that genome reduction occurred in the dinosaur lineage of which birds are descendants before flight (so did feathers, bipedalism, and other characteristics), but were later further adjusted when flight arose (as were feathers, etc.). The same reductions before flight probably occurred in the pterosaur and bat ancestors. So it’s not flight per se that matters, but a feature linked with flight.

As Organ and Shedlock put it, “we hypothesize that a metabolic intensity required for flight, not flight itself, explains the correlated evolution between genome size and flight in amniotes.” — this seems very plausible given the growing amount of data on this topic.

References

Andrews, C.B., S.A. Mackenzie, and T.R. Gregory. Genome size and wing parameters in passerine birds. Proceedings of the Royal Society of London B, in press.

Organ, C.L., A.M. Shedlock, A. Meade, M. Pagel, and S.V. Edwards. 2007. Origin of avian genome size and structure in non-avian dinosaurs. Nature 446: 180-184.

Organ, C.L. and A.M. Shedlock. 2008. Palaeogenomics of pterosaurs and the evolution of small genome size in flying vertebrates. Biology Letters, in press.

Zimmer, C. 2007. Jurassic genome. Science 315: 1358-1359.