We then spent most of the day hanging around Portland together, including a visit to the mighty and wonderful Powell’s City of Books (one of the last, great independent book stores) and checking in at GECCO to get my registration stuff. Tom totally loved Powell’s (“I could get lost in here!”), and has in fact spent large amounts of my money and his time there this week while I was at the conference. We also went out and saw Toy Story 3 that night, which turned out to be every bit as good as everyone’s said it is – lots of fun and very well written.

Day 8 was our last college visit in this part of the world, as we headed up to Olympia, Washington (2 hours north of Portland) to visit Evergreen State College. This was a real eye opener for both of us. I knew Evergreen was cool (and another of the small number of public liberal arts colleges in the U.S.), but didn’t know a lot of the details, and I think we both found the unusual curriculum and environment really interesting and thought provoking.

I had arranged beforehand to meet some of the computing faculty at Evergreen so we could learn a little more about their program as part of a program review we’re doing at Morris, so after the information session and tour we met up with Sherri Shulman and then headed over to meet her husband and fellow CS faculty, Neal Nelson. When Neal walked in, there was this very weird moment where we both those we knew each other but weren’t sure why. Duh, duh, and double duh – Neal was my undergraduate thesis advisor at Reed! I’d lost track of him when he left Reed in 1988, and I somehow thought he’d gone into industry so I wasn’t even looking to find him anywhere in our travels. Given all that and the the fact that his name doesn’t particularly stand out (and that I’m really crap with names), I totally didn’t consider the possibility that I knew this Neal guy we were going to see. After recovering from that somewhat awkward start, Sherri, Neal, and I had a really excellent conversation that ran a couple of hours easy. Lots of catching up on old times, as well as discussing undergraduate computing curriculum with limited resources in a public school – many thanks to both of them for all their time!

After returning to Portland, we went to Papa Haydn’s, possibly the best source of wonderfully scrumptious and rich desserts that I know of in the U.S. I had a wonderful Autumn Meringue and it was just like being a college student again (without the metabolism of a 20 year old). We used to walk out to Papa Haydn’s from Reed (maybe a 30 minute walk) several times a year and indulge, and was so cool to go back and find that it really hadn’t changed much in all those years.

That night was the opening reception at GECCO, so Tom and I hung around for a few hours eating little snacky things and chatting with various folks. Tom had never met most of my EC friends and colleagues, and he was very cool at meeting a bunch of strangers that are, even worse, all science nerds to a very high degree. Luckily it’s a really cool group of people, and I think he actually enjoyed himself.

By Day 9 I’d actually skipped out on the bulk of the first two days at GECCO, so at this point I essentially abandoned my son to the wilds of downtown Portland and started pretending to be a scientist for a bit. He spent most of his time hanging at Powell’s and reading books, while I listened to people talk about their cool evolutionary computation research.

That night I did actually skip out on the last session, though, and went back to Reed to join a bunch of faculty that have a regular Friday beer and food gathering at Woodstock Wine and Deli up the hill from campus. Jim had invited me to join them, and it was a great chance to meet some people I knew that I’d missed before (like Ray Mayer) and a bunch of other faculty that are new to the college since I was a student there in the dim past.

I wasn’t the only one meeting up with old friends, as Tom met up with Perry Webster from Morris (currently attending the University of Portland) and hung with her and a family friend pretty much the whole evening, which was a neat chance for him to spend a little time with people more his age :-).

Day 10 was much the same, although I stayed at the conference pretty late because the poster session and associated reception was that evening.

Day 11 (today) was the end of the conference, including eating lunch in the hotel sports bar with a bunch of very enthusiastic Europeans watching the World Cup final! Eli Mayfield (UMM ’09, now a grad student at Carnegie Mellon studying natural language processing) gave a talk today, and did a really excellent job. Tom and I went out to Jake’s Famous Crawfish with Eli and Bill Tozier. Jake’s was a great seafood house back in the day, and they didn’t disappoint, providing us with excellent food to go with the fine conversation. That was a great way to end our time in Portland!

Now we’re off to bed, and tomorrow we drive south to Tule Lake and Lava Beds National Monument. With a little luck we may hook up with Wayne Manselle in Eugen on the way!

Via TechDirt I found this very cool video on how our “standard” notions of incentives don’t always work very well, especially when it comes to cognitive work. There’s a ton of cool ideas in the video (and more in the TechDirt piece, including some cool links).

The incentives in the talk are typically money, but I suspect that there are interesting things to be said about grades as an incentive in the academy. Does anyone know of work along those lines?

One really interesting story is about Atlassian, an Australian software company. (Their stuff is cool, and we’ve used some of it here at UMM in the past, but it’s gotten pricey and we’ve moved to other tools.) Apparently Atlassian gives their employees a 24 period every quarter to work on whatever they want, and then they have a party where people share what they’ve done. This apparently leads to a ton of cool ideas, bug fixes, and development. So, so cool.

How could we apply that here in the academy? What if we gave everyone in our Computer Science discipline a 24 hour period to work on whatever they wanted to and then had a big party where people shared what they did? Could we do it? Would it make sense if we did? What would it mean? We’d probably have to cancel at least our CSci classes that day, and probably make sure that no one was giving an exam the next day, etc., etc.

Because we would only control our discipline’s behavior, though, we wouldn’t give many of the students the freedom they’d need to really take advantage of the opportunity. It would presumably work a lot better if we did this across the entire campus – no classes, no exams, no papers due, and then some sort of event (or set of events distributed across campus) at the end for people to share their results.

Hmmm…

Since President Obama’s announcement of the Educate to Innovate program in November 2009, an encouraging number of technology and media companies, non-profit organizations and government agencies have been working in concert to strengthen the nation’s approach to science education. But the reality is that the lion’s share of transformation must come from within: from school systems, in the case of K-12 education, and from the academy, in the case of higher education.

A position paper recently issued by the Nature Publishing Group illustrates this point in the context of higher education. A significant majority, 77 percent, of the 450 faculty surveyed for the paper consider their educational responsibilities to be equally as important as research responsibilities. Only 6 percent consider research more important than education. Yet when asked to appoint a hypothetical candidate to an open tenure position in their department, the majority chose a star researcher with poor teaching skills over both a star teacher with little research background and a candidate equally skilled, though not notable, in both teaching and research.

The ripple effects of this mindset in the academy are damaging to the goals of universities.

CACM page spread featuring UMM CSci alum Tyler Hutchison at MICS

The May, 2010, issue of the Communications of the ACM (CACM – the flagship magazine of the ACM) features a photograph of UMM CSci alum Tyler Hutchison presenting research work done with Andy Korth and Nic McPhee at MICS 2007. The article is “Student and Faculty Attitudes and Beliefs About Computer Science”. Andy and Tyler won the best student paper award at that year’s MICS for their paper “On the impact of geography and local mating in evolutionary computation”. The photo (taken by me during Tyler and Andy’s joint MICS presentation) features some of Tyler’s artwork illustrating the material.

The graphics folks at CACM found my photo on Flickr, and contacted me via Flickr offering to pay me a small fee if I’d be willing to let them use it. I happily said "Yes", and the rest is history.

As well as being a cool computer-science-type, Tyler is also a cool comic-art-type, and did the nifty drawings for the cover of our book "A field guide to genetic programming".

Happy, happy, happy.

But I’m easily amused :-).

In fairness, this could well be the one and only time I ever get published in CACM. I’m not all that likely to submit an article to them (in part because I don’t tend to write things they might want), so this could easily be the pinnacle of my career in terms of the number of people in my field seeing my work.

Weird.

But cool.

Never forget who the true enemy is, from Abstruse Goose

Ray Comfort’s inanity over on U.S. News & World Report comes to mind:

We don’t find a half-evolved cow or bee. None of the 1.4 million species on the Earth has half an eye.

Such deliberate cluelessness and misrepresentation – it’s unfortunate the U.S. News & World Report will publish nonsense generated by someone who’s clearly only using half a brain.

Teaching kindergarteners is like herding kittens

Timna Wyckoff (one of our biologists and mother of a kindergartener) arranged to have all the local kindergarten kids comes to the science building for 90 minutes to learn a little bit about science. They were divided up into groups of about twelve, and each group spent about 30 minutes at three of the six stations we’d set up.

I talked with them about their experience using computers at school (mostly “playing games”) and how the computer did things like draw pictures on the screen. (We determined that it wasn’t elves or fairies or tiny mice with little glasses and hats that took coffee breaks when you turned the computer off.) We then talked about how computers are machines, like their fridge or a car, and let them look inside a couple of old boxes destined for the scrap heap. This led to a bit on how computers are general purpose machines instead of single purpose machines (“Can you drive your fridge to the store?”), and how what the do is determined by the program they run. It turns out that computers are in fact machines specifically designed to follow lists of instructions, and programs are lists of instructions created by computer scientists that tell the computer how to do certain things (like draw dinosaurs on the screen). We then headed into a semi-tangential (but concrete for 5 and 6 year olds) discussion of recipes as a instructions, and people as machines for following those instructions. Finally, if and as time allowed (and it varied quite a bit across my three groups), they all got numbers, stood in a line, and pretended they were a computer running through the bubble sort algorithm. (Yeah, bubble sort. Don’t shoot me – it’s easy to run through with little kids.)

I spent a total of 90 minutes doing this three times, plus some setup at the beginning and tear down at the end, and I’m exhausted. If nothing else, this reinforced my belief that a good teacher of young kids is a real treasure. These are bright, enthusiastic kids, but they don’t always focus real well, and my short morning is enough to send me scurrying back to teaching adults. (To be honest, my students don’t always focus well, but they’re much less likely to distract everyone around them in the process.)

This was my first time doing this, and my little script was an amalgam of lots of ideas from KK, Timna, and WeatherGrrrl, and various students and alum responding to my request for ideas on Twitter. Many thanks to all of them for their ideas and feedback!

Rosalind Franklin on hiking trip in the Alps. Image from the National Library of Medicine's Profiles in Science project.

Today, 24 March, is Ada Lovelace Day, honoring the remarkable woman that is arguably the first computer programmer, working a full century before the construction of the first electronic machines that we would typically recognize as modern computers. In honor of her work and the crucial but typically underreported contributions of women in technology, over 1,700 are writing today “about a woman in technology whom I admire”. This is my contribution.

When Charles Darwin published his landmark Origin of species 150 years ago, he played a critical role in transforming biology from an exercise in bug collecting and guesswork to a science, with testable hypotheses that could give meaning to all the data people were collecting in the field, and tie down some of the more wild-eyed speculations. One of the huge holes (a gap Darwin freely acknowledged) was the how of inheritance. That inheritance existed was empirically obvious, but the mechanism by which it occurred was a complete mystery. In subsequent years, the work of Mendel and others shed crucial light on the properties of that mechanism, but still left open the key question of how exactly it happened.

This puzzle was solved in the 1950′s, with a central breakthrough being the discovery of the double helix structure of DNA. The fact that DNA is composed of two strands bound together, each carrying essentially the same information, meant that it can be split and copied, allowed the genetic code to be copied and transmitted from one cell to another in cell division, and ultimately from one individual to another in reproduction.

It is hard to overstate the impact of this achievement, which totally revolutionized the methods and approach of biology, ultimately leading to modern molecular biology, gene sequencing (including the Human Genome Project), reconstruction of phylogenetic trees, gene therapies, genetically modified organisms, and new medical diagnostic tools. All of this depends crucially on the discovery of the role and structure of DNA, firmly placing those discoveries among the most important of modern science.

But who then do we credit for this remarkable achievement? The names that readily come to mind are Watson and Crick, that dynamic duo at Cambridge immortalized in Watson’s The double helix (I recommend the Norton Critical Edition). If one looks to the Nobel Committee for guidance, a less well known name is added to those of Watson and Crick: Maurice Wilkins. Wilkins worked at King’s College London, where empirical data was collected that was vital to Watson and Crick’s ability to build the celebrated double helix model. The three were jointly awarded the 1962 Nobel Prize for Physiology or Medicine, “for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material”.

Missing from this pantheon, however, is Rosalind Franklin: the person who painstakingly collected and analyzed that empirical data, including X-ray crystallography described by J. D. Bernal as “among the most beautiful X-ray photographs of any substance every taken”. It was her methodical study of DNA (which was already widely believed to be crucial in the transmission of genetic information due to the Avery-MacLeod-McCarty experiment) that led to the key insights into DNA’s structure. She herself understood well in advance of Watson and Crick’s breakthrough that what she called the B Form of DNA almost certainly had a double helix structure, but chose to complete her analysis of the A Form (where there was still uncertainty regarding the structure) before engaging in what she considered the speculative business of building models before all the data was in.

Yet while she methodically collected and studied, the impatient boys up the road gained indirect access to her images and measurements, data that was crucial to their model building, apparently without Franklin every knowing how much they’d obtained, and how important it had been. Franklin worked under Wilkins at King’s but was barely on speaking terms with him, and there is no evidence that she knew that Wilkins had shared some of her key data with Watson, or that a UK Medical Research Council review process gave Watson indirect access to detailed summaries of her work. Her untimely death five years later due to cancer was almost a decade before Watson’s book first publicly discussed the back channels he’d used to access her data. It seems likely, then, that she never fully understood how important her own work was to their achievements, and Watson’s deprecating portrayal of Franklin both as a person and as a scientist in his book did little to improve her reputation.

In fact, however, Franklin was clearly a gifted and dedicated scientist who made numerous valuable contributions in her short life in areas such the structure of coals, the structure of viruses, and the structure of DNA. Her work on DNA, for example, included the design and application of new imaging equipment, the collection of numerous of images from different angles, and the laborious hand calculations needed to extract quantitative measurements from those images. At the time of Watson and Crick’s famous model building, Franklin was trying to finish up her work at King’s so she could start a new position at Birkbeck, a move already delayed several months. Would she have developed the double helix model on her own if she’d been better supported at King’s, less distracted by the move? We’ll never know. It is clear, however, that her data was vital to Watson and Crick’s success, providing the empirical foundation for their theoretical leap.

Why, then, was she not recognized by the Nobel committee in 1962, alongside Watson, Crick, and Wilkins? The short, simple answer is that she was dead by then, and there are no posthumous Nobel Prizes. Less clear, though, is whether she would have gotten the award if she’d still been alive. As well as prohibiting posthumous awards, the Nobel rules also limit the number of co-recipients to three, and Watson, Crick, and Wilkins formed a full set. It would be pretty hard to justify bumping either Watson or Crick from the podium, since their paper contained the key theoretical breakthrough and would likely have the most significant long-term impact. Wilkins, on the other hand, was a different matter. He’d done little to contribute to Franklin’s work, and his own work had been far less significant to Watson and Crick’s insight. He was, however, her boss and a senior scientist, while she was effectively just a scientific hired hand at King’s, serving a two year position and moving on. And, of course, she was a woman, and the Nobels have not been kind to women, especially in the sciences. We can obviously never know what would have happened had she still been alive in 1962, but it seems naive to feel any certainty that she would have been recognized in Stockholm if she had lived.

For people looking to learn more there’s lots on-line, with all the associated pros and cons. Brenda Maddox’s Rosalind Franklin: The dark lady of DNA is a very nice biography and certainly helped a great deal in writing this. The epilogue to that work makes a nice antidote to the not entirely convincing epilogue to Watson’s The double helix.

Rosalind Franklin at the microscope. Image from the National Library of Medicine's Profiles in Science project.

The first is a really fine piece of election season film making (thank to Pharyngula for the tip):

Favorite quotes: Cheney reminding us that “Some people lie” (speaking from experience there?) and Pat Buchanan saying that McCain will “make Cheney look like Gandhi”. Wow – that’s something I really don’t want to see.

Then, after you’ve found the tissue box or finished smashing the crap out of the couch cushion in anger and frustration, you can lighten up with this bit of silliness courtesy of Joe R.:

I think it’s arguably a bit long (they felt like they had to get the whole lecture into one song), and watching the “dancers” gets a bit painful in places. Still, it’s well written and fun, and I like the chorus. It’s cool to see people trying different ways of getting the word out and, for better or worse, I suspect that more people will learn a little physics from this sort of thing than from “normal” sources. There are 34,925 people following the Mars Phoenix lander on Twitter, and over 4,000 (as of today) following CERN. Hopefully all this is a cool sign for the future of a populace engaged in science!

And this sort of stuff really makes certain academics nervous — they worry that somehow the only way they’ll keep their job is to do this kind of thing in class — and that’s gotta be worth something.

photo credit: Unhindered by Talent

• Democracies are very unlikely to attack other democracies. So more democracies for the win?
• Countries that educate girls and women tend to greatly reduce the risk of conflict.

On a vaguely related point, a SciAm 60 Second Science podcast from way back in late May looks (briefly) at some of the significant problems that researchers are having getting women, especially older women, involved in medical trials.

Women were also more likely than men to say that they’re too old or not healthy enough [to participate in a trial] … But women over 65 are one of the fasted growing segments of the population. … our ability to improve care, develop new treatments and find cures depends on research and educating aging women about their role in medical breakthroughs.

Damn – women are apparently important! Treating half the population like dirt is not only ethically dodgy – it has negative practical consequences as well!

Who’d'a’thunk?

Hmmm… Applying vaunted American know-how to find new solutions to the problem of energy independence? What an odd, odd thought, especially when McCain supports a tiny, slow band-aid that … well … won’t really help at all.

We were in Fargo a few days ago buying a car. We sold our one and only car when we went abroad, and are currently on borrowed wheels. There was serious discussion of not even getting a car, or perhaps leasing a car for the winter months while going without a petrol powered vehicle in the summer when we can bike around town. In the end, though, we decided to go ahead and buy a shiny blue Honda Fit. (This is the second time we’ve bought the exact same car as my sister a year or two after she bought hers. We’re not very original, I’m afraid. That, and my sister rocks!)

The Honda dealer said that the demand for Civics, hybrids, and Fits has been really high, and they’ve had periods where they haven’t had any Civics to show people, including used ones! (And this is North Dakota, where I suspect trucks have long out-numbered compacts.) Given that most people won’t keep a car for all of the 7 years it will be before we see any of the off-shore oil from McCain’s proposal, Obama’s plan seems to be much more in touch with the mood of the populace.

What I’d really like is for the U.S. people (and government) to realize that there’s real value in basic scientific research, and understand that kind of research is going to have to be an important part of any solution to the current energy and climate problems.

While in Fargo we also bought Sub-Evil a new bike, and will probably buy a new bike for WeatherGirl in the next week or two. This, combined with the fact that mine is getting a substantial tune-up at the moment, means we’ll all be on two spiffy wheels as much as possible, at least when the weather allows.