Author: gulley

That which must not be mentioned

Okay, having just moved to WordPress, I must almost immediately report a problem. I have, at great expense, uncovered a truly weird bug. Believe it or not, you can’t make a post with the word perl in it. I had to resort to some tag trickery to get this to display. Here’s what I actually had to type:

p<span>erl</span>

Utterly bizarre.

At least I figured out why my post a few days ago didn’t work. I’m running WordPress 2.0.5, freshly downloaded. Can any WordPress users out there confirm if they’re seeing this too?

Welcome to WordPress, reprise

I realize my post about Movable Type and WordPress the other night may have been a little incoherent, particularly if you’re not familiar with blogging software. The engine that drives this blog is now provided by a software package called WordPress. Up until the beginning of this week, it was provided by Movable Type.

I had been thinking about moving to WordPress for some time, but I am a late adopter and generally lazy. It was the comment spam that finally put me over the edge. Movable Type has comment spam blocking tools, but I tried several and I couldn’t get them to work. I only have a certain amount of time each night to spend on this kind of thing, and if I blow through that installing and re-installing something that doesn’t work, I get very irritated. Someone at SixApart (the Movable Type folks) had written what looked to be a very nice spam-blocking plugin. I was excited to try it and be done with my spam scourge. But there was a long involved process to install it that involved unzipping archives, FTP transfers, rebuilding the site, inserting a special string in three different files, rebuilding the site again, then swearing when it didn’t work.

I took my troubles to the support site for the plugin. In an uncivil moment, I mentioned that I had “blown two hours trying to make this work” and was “feeling frustrated.” The plugin author responded quickly, and pointed out quite rightly that he hadn’t charged me a dime for his plugin, and that if I followed the steps carefully I would probably get it working. Upon reading his reply, I quickly concluded that we were both right. He didn’t deserve to be chastised for a gift, but I had good reason to be frustrated. The problem was Movable Type. It was just too damned fiddly and it smelled of overripe perl scripts. It was just never going to be easy to install a spam blocker.

This finally kicked me in the pants and got me to move my bags over to a newer cleaner architecture with WordPress. And it’s working for me very well. Aside from my inauspicious start the other night, flushing my very first post…

Beautiful colors on Flickr

I’ve discovered a really fun Flickr party trick. If you want to turn your brain off and just stare at some amazing eye candy, pick a fun term to search for. Suppose you choose Hawaii. But what you really want are dramatic, luscious pictures of Hawaii, not somebody’s bad holiday snapshots. In that case you just click on the “View: Most interesting” link. Then you get a set of Hawaii pictures sorted by the interestingness quality algorithm, which is something like Google’s PageRank. On beyond that, suppose you’re going to do a conference talk about Hawaii and you want to punch things up a little. You’re probably going to want some freely distributable Creative Commons interesting pictures of Hawaii. A quick visit to the Advanced Search page makes this no problem.

But here’s the grand finale: from tag search results page, you can dial up an automatic slideshow sorted by interestingness. And you can roll it all into one juicy URL like this:

http://www.flickr.com/photos/tags/hawaii/interesting/show/

Now you’re ready to blow some time. Pick one and go… color, burning man, Barcelona, Yellowstone, splash.

Now that’s the internet I used to dream about back in 1995.
[via O’Reilly Radar]

Moved to WordPress

Here’s a sad story. I wrote a long post explaining why I was so happy to be moving from creaky old Movable Type to shiny new WordPress.

And then I saved it.

And then WordPress ate it.

So now I am writing this short, sad post instead of my long happy post.

Nevertheless, I am glad to be moving on from Movable Type.

Wordie and Ninjawords

If you like words (and I know that you do), then you need to pay a visit to Wordie. They have a really good tag line: “Like Flickr, but without the photos.” The premise is so simple that you can’t possibly suspect you’ll get sucked into it until it’s too late.

Here’s how it works. Get a free account, start typing in words. Any words will do, but if you’re a natural fit for Wordie, you’ll start creating lists of personal favorites in no time at all. In addition to my first list of words, I made Fancy-pants words for rhetorical devices and Words that sound naughtier than they are. Like Flickr, there’s a social aspect to the whole thing that links you, through your words, to other people’s lists. Not much to it, really, but good clean fun.

And since I’m on the topic of words, here’s a resource that you may find useful: Ninjawords.com. It’s just a really fast dictionary. Again, it’s a very simple tool, but well made. If you use a dictionary server very much, you’ll find that they have long load times, mostly because of all the ads attached to them. Ninjawords is based on a non-proprietary dictionary, so they don’t feel the need to advertise. Also, they have an appealing URL structure, if you’re linking to definitions from a document: http://www.ninjawords.com/tundish. Couldn’t be simpler.

Ideas, models, and design

starfish-robot.jpg
Discussions of the relative merits of intelligent design and natural selection fill endless web pages, but it strikes me that these discussions consistently overlook the nature of design itself. Intelligent design happens all the time; we may disagree on whether God or pasta-themed deities design, but we can at least agree that humans do it.

But what is design? Or, put another way, if God is doing intelligent design, then what exactly is he doing?

What a designer does is rapidly iterate through a bunch of ideas, testing them against his experience, rejecting some and keeping others for further tuning. The precursor ideas for this process come from variations on pre-existing designs. In other words, design is a process of selection with descent and variation.

If God is a designer, then maybe he’s doing it right now with lions, lemurs, begonias, and bloggers through the subtle but decidedly unmiraculous process of natural selection. You don’t have to damage science to imagine Galapagos finch beaks as God’s thoughts unfolding. Of course, that’s a matter of taste and scarcely debatable. It doesn’t prove anything and it doesn’t “mean” anything, but it is one way to frame the problem so we can just move on.

Design is predicated on an experiential model of reality. The intelligent design that humans do differs from the “design” that happens in natural selection primarily by the rate at which generational culling happens. Humans have the benefit of rapidly simulating how a design will perform without needing to build it first. Increasingly we will give this skill to our synthetic descendants. Here’s a beautiful example of how modeling operates at the boundary of action and thought.

The Cornell Computational Synthesis Lab: Robotics Self Modeling

Be sure and watch the video of the damaged robot struggling to walk. Depending on your outlook, it’s either very disturbing or spine-tinglingly beautiful. Either way, I promise you it’s a bona fide glimpse of the future.

Visualizing biological experiments

Video blogs are getting more and more interesting. This one, My JoVE, isn’t really a blog so much as a repository of valuable information for biologists, but it aspires to become a kind of video journal. JoVE stands for Journal of Visualized Experiments, and they’re trying to attack two big problems in biological research: “low transparency and reproducibility of biological experiments, … and time-consuming learning of experimental techniques.” Here’s their answer to the question: why a video-based scientific journal?

As every practicing biology researcher knows, it takes days, weeks or sometimes months and years to learn and apply new experimental techniques. It is especially difficult to reproduce newly published studies describing the most advanced state-of-the-art techniques. Thus, a major part of the Ph.D. and post-doctoral training in life sciences is devoted to learning laboratory techniques and procedures.

They are addressing two needs specific to the biology community, but they are picking up another one along the way: educating non-biologists and interested amateurs. You can find lots of experimental protocols online (see OpenWetWare), but these suffer from a few shortcomings: they use unfamiliar vocabulary, unavailable equipment, and they are often written in the stilted science-report prose that is beaten into all student scientists.

But like the how-to videos at instructables.com, these videos are delightfully conversational, and anybody can look at the shape of an Erlenmeyer flask without having to know the specific term for it. I am unlikely to buy an electron microscope any time soon, but I like to know what it looks like to drive one. I will certainly admit that watching someone use micro-forceps to invert the cuticle on a fruit fly larva and fish out the central nervous system is very far from knowing how to do it yourself. Still, it’s amazing how much those summer camp arts-and-crafts skills pay off in the lab.
(Spotted on the Sciencebase Science Blog)

For the love of chemical synthesis

Now this is why I read blogs: Paul Docherty is head-over-heels in love with chemical synthesis and wants to tell you all about it. And I want him to tell me about it. His blog, TotallySynthetic.com is crackling with enthusiasm and filled with lovely diagrams and little stories that report on the latest news in the world of organic chemical synthesis. This is exactly what you don’t get in a typical chemistry class. Can you imagine how many chemists we’d have if high school teachers were half as thrilled as this?

Here’s a sampling from today’s post, Modern Aldol Methods for the Total Synthesis of Polyketides.

With all this focus on polyketide/macrolide synthesis, I thought I’d highlight an interesting review in this week’s Angewandte; a genuine masterclass in the aldol reaction.

There’s nothing pretentious about it. It’s all sinewy facts knotted together with excitement, punctuated by little self-effacing asides like “I was quite taken with this transformation, but it obviously shows that I need to brush up on my diazo chemistry…” Somehow I feel as though I’m learning something terribly useful, even though I don’t understand a word of it.

I’ve always loved technical jargon as used by someone joyfully immersed in it, whether it’s 19th century sailing terminology or dental jargon. Bring on your ipsilateral translation of the condyle, your girt lines and masting falls! Money pays the bills, but it’s Kocienski–Julia olefination that makes the world go around.

Pop Sci blogging fun

Popular Science magazine also hosts a blog, and it’s got a bunch of fun stuff on it. I had always thought of the old school Popular Science as a pretty silly magazine, mostly about hyped up quasi-science fluff. But it’s gotten a lot better over the last few years, and their blog is so entertaining that it definitely drives me to purchase the actual paper magazine more often.

They’ve been a real tear with their last few entries. I don’t know if they’re getting any work done on the magazine, because somebody’s doing an awful lot of web surfing. Here are a few choice items from the past week:

Watch a racing motorcycle crash and burst into flame. The rider is okay, and there is an interesting discussion of why this kind of thing never happens with cars, but did with this motorcycle. Goodbye, Moto

Watch a crane trying to lift a truck out of a river and back onto a bridge. As it happens, the truck pulls the crane down into the river. The Breakdown: Crane Overboard!

Every physics teacher who teaches the concept of resonance needs to show this in their class. A Boeing Chinook helicopter has two rotors, and if they start exciting vibration modes of the fuselage when it’s sitting on the ground, bad things can happen. If the word “resonance” doesn’t sound so bad, take a look at this video: Shake, Shake Chinook.

And don’t miss the African watering hole cam. It’s a live video feed with sound, and there’s something very appealing about listening to crickets on another continent.