No, seriously. Well, sort of seriously.

“At last, Acme has conquered topological and engineering frontiers to manufacture genuine glass Klein Bottles. These are the finest closed, non-orientable, boundary-free manifolds sold anywhere in our three spatial dimensions.”

They have hats, too.

In Seed Magazine’s endorsement of Barack Obama, they make this rather startling claim:

“Far more important is this: Science is a way of governing, not just something to be governed. Science offers a methodology and philosophy rooted in evidence, kept in check by persistent inquiry, and bounded by the constraints of a self-critical and rigorous method. Science is a lens through which we can and should visualize and solve complex problems, organize government and multilateral bodies, establish international alliances, inspire national pride, restore positive feelings about America around the globe, embolden democracy, and ultimately, lead the world. More than anything, what this lens offers the next administration is a limitless capacity to handle all that comes its way, no matter how complex or unanticipated.”

I suppose the “methodology and philosophy” of science (whatever that may be) may serve as a productive metaphor for some aspects of governance. In particular, routine and rigorous assessment of the outcomes of policies and subsequent adjustments of those policies seems like a good idea that roughly corresponds with “the scientific method” of doing things. There is also a tradition of adhering to the observable truth, without regard to personal or institutional consequences, which is expressed to a remarkable, albeit incomplete degree in scientific institutions. Politics could hugely benefit from adopting such a valuation of truth.

But governance is about so much more than facts. It’s about values. It’s all mixed up with equity, and justice, and consent, and consensus, and the lack of consensus, and figuring out just what the hell our goals for our society are anyway. I’m not sure exactly what “science” is, but I’m pretty certain it is not a way of governing human communities. I think it’s strange that the Seed editors would even make such a claim. Robert McNamara for president!

I’ve updated my research plan, again. It’s becoming a hobby. Now with improved narrative, and references to attest to its scholarly character.

2 months ago I was wandering around in rented cars, waking up to the dawn in improvised Forest Service campgrounds, cooking up bacon and eggs and coffee on camp stoves, breaking down my tent then rushing out into the piñon-juniper woodlands with a gps antenna magneted to my bandanna, a compass around my neck and a camera in my hand, documenting the landscapes that were going to become my study sites. I would drive and hike around in a rush to look at things until I decided I had to look at something in particular very slowly. Then I would stare at it. Mostly bushes and trees and soil and water courses. Also hills and valleys. I visited Sierra Vista and Tombstone and Arizona and Flagstaff and Cedar Ridge and Tuba City, and mostly places in between, like Cochise County and the San Pedro River and the Coconino forest and Waputki and the Little Colorado canyon and the rangelands of Navajo Nation. I took a train to New Mexico and did similar things there. Then I took a train home. It was a good time. There was a lot I missed because I was in a hurry to look at semi-arid vegetation, but there was a lot I saw because I was looking for semi-arid vegetation. I wrote about it a bit here.

Because I had a camera in my hand and because New Mexico and especially Arizona are so damn visual, I took a lot of photos. I’ve finally posted some of them up here.

Annoyed that I apparently couldn’t attend the Scientific Applications with Google Earth Conference without registering with the “Google Checkout” financial system, I emailed to ask if there were any other payment methods available. Well, I waited for a couple of weeks for their “Contact Us” link to go live, then once I had an email address to email to, I emailed it. No response came, then a form request that I complete the sign-up by joining Google Checkout. I was worried I was going to have to show up thrusting a greasy $20 bill at whoever looked official, but I’ve now received assurance that if I just bring a check with me everything will be fine.

So that’s all good then. Not that the informational aspects of our public and private lives has ceased to be increasingly mediated and recorded by a single for-profit stockholder-beholden corporate entity. But at least you can pay for their scientific conferences by check.

For the curious, I’ve posted a more detailed version of my thesis research plan. Which is currently being executed.

Also, I’m nearly done developing some of my photos from my summer research trip, and that gallery will be up soon.

Chris Darimont is a wolf researcher who used to hang out with some of the people I used to hang out with in Victoria. As a wolf researcher, he claims traditional pride of place amongst the tribe of ecologists. As such, your contemporary future-looking ecologist might be tempted to disparage him as a megafauna fetishist, but I gather he actually does some interesting, post-Mowat research.

So it’s nice to see that the Government of Canada has equipped him with an NSERC grant and posted him off to Southern California. Other NSERC fellows I have known have found great success in these United States before returning to enrich the Dominion. And Chris is drawn towards the human side of the picture, so good luck with that, I’ll follow when I figure the I’m up for it.

Science holds a suspicious bias against publishing negative results. Negative data is still data, if it is unequivocally so. If someone undertakes to demonstrate a relationship which we would expect, based on existing theory, to exist, and that relationship cannot be found, then that person has made a significant contribution to our understanding. If you in your work as a research scientist have ever been startled to discover such a missing relationship, then you probably didn’t publish or couldn’t publish on that result. Perhaps some other scientist is even now repeating your experiment, because you were unable to reach them with this information through the typical approach of academic publishing. When they get their results, they probably won’t publish either.

This is macho nonsense, and looks like a serious hole in the fuselage of the scientific enterprise.

I sometimes complain that I’d like to found a “Journal of Negative Results” to counter this bias. It turns out one already exists (hooray!):

Journal of Negative Results

They’ve been publishing studies which “test novel or established hypotheses/theories that yield negative or dissenting results” since 2004. Albeit sparsely. From the first volume, Temperature and desiccation do not affect aggregation behaviour in high shore littorinids in north-east England, is just the kind of study we need to see.

Even more exciting is that there is also a real, very serious, not-just-to-make-a-point,

Journal of Negative Results in Biomedicine

which has been been publishing peer-reviewed work since 2002. For example, one of the most-accessed articles from the journal is Quantitative competitive reverse transcription polymerase chain reaction is not a useful method for quantification of CD4 and CD8 cell status during HIV infection.

Next step: get the JoNegRes for Ecology and Environmental Biology up to full steam. I need that information.

After getting irritated at humankind’s inability to accept that some things are genuinely uncertain, I open my podcasting device and hey presto:

Resilience: Adaptation and Transformation in Turbulent Times — A World Of Possibilities, May 6th

It opens with Buzz Holling (who NRE 580 alumnus will remember for panarchy theory) on adaptation, uncertainy, adeterminism, non-equilibrium, and such like in the general world. Then it moves onto Brian Walker talking about much of the same in ecosystem management, plus control fetishism. Then it moves on from there. Recorded at a Stockhlom conference on applying biology-based resilience theory to social systems. The idea of which is now creeping me out. Except that maybe, just maybe, this is a group of people that can be trusted to think rationally across disciplines. Maybe. Anyhow, it’s good listening.

Brian Walker’s talk reminded me of a lecture on conservation management from my undergrad, wherein Thom Nudds announced that if you manage to get an ecosystem to not cycle you’ve flatlined it, so congratulations on that.

All Your Tomorrows Today is a Ken Hollings/BBC documentary about the early days of RAND Corporation. Assembled by Curtis LeMay’s post-war Airf Force and highly influential to US cold war political strategy, the RAND people were early systems thinkers, and their systems were comprised largely of nations and nuclear weapons. They desired rationality on topics that don’t lend themselves to rationality. And perhaps shouldn’t, but don’t suggest that to the main characters in this story.

I particularly like one critic’s suggestion that RAND generated a “rumor of war”, which is his term for a set of disjointed facts which give the illusion of representing the whole truth. These people are what Dean Bavington would decry as ‘epistimological’ complexity thinkers. They are willing to see the world as complex, but only as an intermediary step to understanding it deterministically. And just think, they had the ear of the people who had their finger on the button.

And yes, there is coverage of the invention of the internet. I knew the standard story about it being a communication system meant to withstand a nuclear strike, but I didn’t realize just how literally and directly that was true. Although set in the Santa Monica sun, the whole story is frankly spooky.

Here’s a fun bit of Google Earth-utilizing research:

Magnetic alignment in grazing and resting cattle and deer, Begall et al, PNAS

“We demonstrate by means of simple, noninvasive methods (analysis of satellite images, field observations, and measuring “deer beds” in snow) that domestic cattle (n = 8,510 in 308 pastures) across the globe, and grazing and resting red and roe deer (n = 2,974 at 241 localities), align their body axes in roughly a north–south direction.”

Apparently this work follows on from previous research the team has done on the sensing of magnetic fields by naked mole rats. In this case, they used Google Earth to scroll around looking for cows, then once they had documented 8510 of them, decided they tend to lie down facing north-south. And likewise for deer.

Here’s some more from NPR.

“Holland says that other researchers should confirm the finding. One way of doing that would be to “start going out and putting magnets on the heads of cows and horses and deer, to see how that affects them,” he says. “That’s one of the more traditional ways of testing if they have a magnetic sense.”

If they really do have an internal compass, he says, the magnet would mess it up.”

I’m not sure what metric you would use to measure an Apollo Project, but it seems as though the Large Hadron Collider may be an Apollo-scale project. Everything custom-built, the tolerances are minute, and the scale and complexity is unthinkable. And it’s almost done.

A physicist I met at a party explained to me that a fundamental paradigm regarding the way matter is organized will be confirmed or contra-indicated pretty much as soon as they turn the thing on. I don’t remember the details, but I remember being deeply impressed. Then somebody started fighting.

From CERN User’s Pages:

Special Announcements

LHC access
Please consult new access conditions before entering the tunnel

Important information for all regular CERN dosimeter holders: Do not forget to read your dosimeter, even if you have not entered the controlled radiation areas

Information importante pour les utilisateurs de dosimètre régulier : N’oubliez pas de lire votre dosimètre, même si vous n’êtes pas entrés dans les zones contrôlées

Prevention – Diagnosis – Eliminating noise
4 to 8 August 2008, 9 a.m. to 4 p.m., Infirmary, Bld. 57

Prévention - Dépistage - Stop au bruit
du 4 au 8 août 2008, de 9h à 16h, Infirmerie, Bât. 57

The National Aeronautics and Space Administration was signed into existence 50 years ago today. The Economist has a good, reasonably breif, article about the intentions and directions of the agency. Being the Economist, it’s partially speculation about potential private-industry virtues of “space exploration”. But the article is more about the division between the dreams of the manned and unmanned branches of the agency. It also mentions the earth-observing program, which I think is a third NASA branch unto itself. The article suggests the unmanned probe makers may tolerate the manned exploration romantics just as cover and funding-bait. And possibly vice a versa. Maybe the earth-observers can likewise use both the manned and the unmanned missions as an infrastructure to exploit. Either dream is closer to the original mandate of the massive NASA bureaucracy than building satellites to measure the environment, which could be a hard sell on it’s own. Or maybe, nowadays, astronauts and probes both just draw away money and steam it off into space.

Many happy returns? — The Economist

Also see A Rocket to Nowhere, from a few years back.

For several weeks I have been meaning to read up on Lenski et al’s 20-year test tube experiment, in which they observed the rise of novel, beneficial traits in populations of bacteria they stored in a closet. It’s interesting to me because (if I read the summaries right) only some of the test tubes evolved the traits, which suggests an interesting contingency in evolution. I love ragged ass evolution.

The research is interesting to the folks at Conservapedia because they don’t like anything that purports to demonstrate evolution. Because they are intelligent design supporters. Or, as this nuclear magnetic resonance spectroscopy researcher puts it, an “army of homeschooled numbnuts”. Now now. So they sent some letters demanding to see the data. The correspondence is well documented elsewhere, but I wanted to draw attention to this particular reference from Lenski, made after some goading from the conservapedia crowd:

(Read the whole damn thing on conservapedia itself if you want)

“It is my impression that you seem to think we have only paper and electronic records of having seen some unusual E. coli. If we made serious errors or misrepresentations, you would surely like to find them in those records. If we did not, then – as some of your acolytes have suggested – you might assert that our records are themselves untrustworthy because, well, because you said so, I guess. 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.”

From the log of the space station crew:

5 JAN 2001: Finished the 2nd disk of “2010″. Something strange about watching a movie about a space expedition when you’re actually on a space expedition.

Oh they so watched 2010 just so they could breezily make that comment.

Woke up to find this elegant little conceptualization in my inbox. It’s from Jim Lyons, who is one of the alpha boffins on the ridiculously helpful netlogo-users discussion group. While I was preparing my hangover, apparently Jim was preparing something for me to peer at through it.

(I stuck an online version here if you want to see it go. I recommend slowing it down a little.)

Simple Chaos
Posted by: “Jim Lyons”
This simple model exhibits chaotic behavior with very little code.

Each turtle moves towards the centroid of the others, accelerating at a
rate inversely proportional to its distance from that point — except
when the distance is below a certain small threshhold, it just coasts.

As you watch the turtles wander erratically, remember that the code
they are executing is entirely deterministic — randomness is used only
to set their starting positions. Even so, very slight differences at
the beginning produce very different outcomes, the defining
characteristic of chaotic systems.

It is really quite entertaining, and is fun with more than 3 turtles,
too. (It even works with only two turtles.)

Paste this code into the Procedures of a new NetLogo 4 model. In the
Interface, make setup and go buttons and set View Updates to On Ticks.
Enjoy!

Jim Lyons

————-
turtles-own [ vx vy ] ; x and y components of velocity

to setup ;by observer
clear-all
ask patches [ set pcolor sky + 3 ]
create-ordered-turtles 3
[ set shape "circle" jump 1 + random-float .1 ]
end

to go ;by observer, forever
foreach sort turtles [ ask ? ; this keeps order same
[ setxy (xcor + vx) (ycor + vy) ; update position
; find centroid of others
let $x mean [xcor] of other turtles
let $y mean [ycor] of other turtles
let $d distancexy $x $y
if $d > .02 ; apply acceleration if not too close
[ facexy $x $y ; so dx and dy yield components
set vx .9 * vx + .01 * dx / $d
set vy .9 * vy + .01 * dy / $d
]
]]
display
end

From Wikipedia’s article on the Lincoln Bedroom:

“A holograph copy of the Gettysburg Address is displayed on the desk. This copy is the only one of five that is signed, dated, and titled by Lincoln.”

What are the implications?

Steve Steinberg argues that human terrain mapping, and in particular emergent group simulation, may be a damaging technology we are developing without due thought to it’s consequences.

With regard to Paul Torrens‘ work:

“The next example was more disturbing. The scenario this time is a public demonstration, similar to the WTO protests that occurred in Seattle a few years ago. The model includes such details as tear gas which causes civilians to stampede, extremists who are trying to instigate violence, and mounted police. Torrens shows that changing a few small initial conditions controls whether the protest spins out of control or not, and suggests this simulation is a valuable tool for policing. Indeed. Demonstrating either startling ignorance or touching naïveté, Torrens argues that this scenario is really a public health issue, due to the possibility of injury. Well, yes – but, more importantly, it’s a democratic, human rights issue, and improving the state’s ability to squash demonstrations doesn’t strike me as a desirable development.”

I’m currently listening to Brian Wynn in the How to Think About Science series. He tells a story reminiscent of the physicists wagering the apocalypticness of the first atomic bomb explosion. Wikipedia provides a slightly drier, but more complete recounting of the decision to use water to put out the reactor fire at the Windscale Pile 1, Oct 11 1957.

I’m also reminded of this photo I took at the Los Alamos science history museum a few years ago.

Best blog post title of recent memory:

Tony Blair Tastes Like Desiccated Coconut…

And not a bad post either. Apparently Tony Blair really does taste like dessicated coconut, to a certain fellow with something called “lexical-gustatory synesthesia”. Now I want lexical-gustatory synesthesia, although not necessarily for the purposes of Tony Blair.

NYT: Asking a Judge to Save the World, and Maybe a Whole Lot More

“But Walter L. Wagner and Luis Sancho contend that scientists at the European Center for Nuclear Research, or CERN, have played down the chances that the collider could produce, among other horrors, a tiny black hole, which, they say, could eat the Earth. Or it could spit out something called a “strangelet” that would convert our planet to a shrunken dense dead lump of something called “strange matter.” Their suit also says CERN has failed to provide an environmental impact statement as required under the National Environmental Policy Act.

Although it sounds bizarre, the case touches on a serious issue that has bothered scholars and scientists in recent years — namely how to estimate the risk of new groundbreaking experiments and who gets to decide whether or not to go ahead.”

I’m reminded of the (variously reported, often contradictory) stories of Fermi and others at the Trinity site laying bets on whether the atom bomb would ignite an atmospheric chain reaction consuming the state of New Mexico. I guess the stakes are higher this time.

As marvelous as the blissed-out semi-dance sequence which forms the meat of this demonstration may be, my favourite part is how committed the impossibly MITish man who introduces the proceedings is to the merits of depicting protein formation “in the dance idiom”.

This seems a little hard to credit at first blush, but a report from somebody called the Cooperative Research Centre for Spatial Information is claiming that lack of open access to spatial information might have cost the Australian GDP about 7%. Damn. Here’s Open Access New reporting on the subject.

PZ Myers is a biologist-blogger-creationism-debunker. Last week he went with his family and a friend to a screening of Expelled, which is some kind of pro intelligent design documentary. Before he got in, he was pulled out of the line by rent-a-cops and told to leave the premises. Yes, a biologist so dangerous he must be expelled.

But that’s not the funny part. Read his post to find out the funny part.

There’s something compelling about this map of the walking paths of the Apollo 11 astronauts on moon, superimposed on a baseball diamond for scale.

Like, they were really there walking around on the holy crap moon.

A bit. They didn’t go very far. If I was on a brand new world I wouldn’t go far from the car either.

Dean Bavington is a prof at the School of Natural Resources. He co-teaches one of my classes this semester. I’m not sure exactly how to describe what he studies, some kind of science studies/science philosophy thing with an emphasis on cod. Interesting guy with interesting ideas, sure enough.

His episode is available at the CBC. I haven’t heard it yet, but I started listening to earlier episodes in anticipation and they’re good, especially #1, with Simon Schaffer.

What the hell? Why did we just fire our national science adviser?

All politics, no science, for Harper — Toronto Star

And why, when somebody asked about it in parliment, did the response come from Jim Prentice, the industry minister?

Has science recently become less relevant to policy? Did having somebody around to do high-level non-partisan synthesis of policy-relevant science just suddenly seem like an expensive luxury?

Well, here’s what Minister Prentice had to, uh, say:

Industry Minister Jim Prentice rose to respond. “Under the science and technology strategy which this government has put forward, there is an intent to focus the science and technology strategy to harness more resources.”

Sweet jesus, what language is he speaking? I’m terrifed that it might be english.

Here’s Adam Bly of Seed on the topic:

Canada’s Future

This cross-genre rant is great. Evolutionary programming to design physical objects never ceases to entertain me. Add in a Mr. Furious-ANGRY anti-intelligent design rant, plus some truly stupid animation humour, and you have a uncomfortable and (I think) hilarious one-of-a-kinder.

“The clock genome is a matrix containing the information of who binds to who and what their properties are.

Remember, the theory of evolution is NOT abiogenesis.

Arguing that because I wrote this program and I am intelligent somehow proves intelligent design is being incredibly ignorant.

IF the purpose of this simulation was to test abiogensis then you would have a point but it’s not so you don’t.”

You’ve read all the front-page headlines so you know by now that it’s the 50th anniversary of Lego (give or take a few days). Oh man, hurray! Over at Boing Boing Gadgets, Joel has a list of the 9 lego sets he lusted over most. I remember pining over 7 to 9 too, but I totally had numbers 1 and 2! For a while my folks had a Christmas tradition of tagging the biggest gift as being “from Santa” and parking it in plain sight in front of the tree. I remember coming down to find the #375 castle awaiting me. I also remember my parents reflecting on being up all christmas-eve-night putting the 779 pieces together. I don’t think either they or I really took the santa concept very seriously.

I’m also pretty stoked that this year (give or take a year) is the 40th anniversary of Logo. Logo is a programming language–in fact a legitmate derivative of Lisp, the most revered of computer languages–but they didn’t tell us elementary school students that when we used it. They cleverly told us it was an art tool. I used it extensively for my art-ucation on our family’s Franklin Ace 1000, the Icons at school, and one heady summer when my dad brought an Icon back from his shcool and let me keep it in my bedroom. A computer in my bedroom! It sat next to my lego bins. I don’t use lego very much in my daily life, but I’m still using a version of logo for my graduate research today. I like that.

This video from the Logothings website is great:

Hey look, them kids are hacking in lisp!

The Sliding Rocks of Racetrack Playa

It’s like a highschool physics question that was never intended to be more than hypothetically abstract brought to life at grand scale.

One of the most interesting mysteries of Death Valley National Park is the sliding rocks at Racetrack Playa (a playa is a dry lake bed). These rocks can be found on the floor of the playa with long trails behind them. Somehow these rocks slide across the playa, cutting a furrow in the sediment as they move.

Mind boggling. On the one hand, it seems wildly improbably that a combination of utter flatness, utter slipperiness, sufficient wind, and the presence of a few, isolated objects would come together just so to make the phenomenon possible. Especially if you accept that some of these rocks are 100s of pounds. On the other hand, if it does happen at racetrack playa, it seems improbable that the conditions are so exquisitely specific that they’ve never come together anywhere else.

And no one has ever seen it happening?