Evolving locomotion

This is another “What I love about the web” moment.
I was reading Pharyngula (as I do so often), and his piece “Evolutionists get all the fun” led me to Mark’s ruthless debunking of yet another piece of creationist rubbish by Granville Sewell, who seems to be holding up the left-hand end of the bell curve of IQ in math professors. But that’s not what this all about. At the top of PZ’s post was a picture:
breve image
And I recognized this picture: it looked as if it came from a video clip that Dan Dennett had shown to us in class last spring. Clicking through the link in Mark’s piece took me to the breve home page:

What is breve?
breve is a free, open-source software package which makes it easy to build 3D simulations of decentralized systems and artificial life. Users define the behaviors of agents in a 3D world and observe how they interact. breve includes physical simulation and collision detection so you can simulate realistic creatures, and an OpenGL display engine so you can visualize your simulated worlds.
breve is available for Mac OS X, Linux and Windows in the download section.

Wonderful – but life is hectic right now, I don’t have time to play with this. Not to worry: if you’re running on a Mac, there’s a breveCreatures screensaver which repeatedly runs 20 trials and evolves the most successful “creatures”. In this case the fitness function is “distance travelled from origin”. So now I can go about my day, checking in occasionally to see how evolution is going.
I have to say, though, that PZ falls into a classic trap in his posting. He writes:

One thing I noted right away in the simplest demo (“Walker.tz”) is that there’s no symmetry imposed on the systems, so the poor creatures are afflicted with four limbs that may each have completely different properties, making them particularly thrashworthy. There really ought to be something in the code to require the two upper forelimbs, for instance, to have identical controls, with some kind of central regulatory circuitry that could impose phase differences. Are there no structuralists and developmental biologists among the coders at breve?

No, no, no, PZ! Symmetry is a consequence of evolution, not a constraint. Suppose the most efficient walker turns out to be asymmetrical?! I’m reminded of Dawkins’ “The Extended Phenotype”, where in Chapter One he quotes Fisher: “No practical biologist interested in sexual reproduction would be led to work out the detailed consequences experienced by organisms having three or more sexes; yet what else should he do if he wishes to understand why the sexes are, in fact, always two?”
Anyway, all Mac users are encouraged to grab breve and indulge in a little desktop evolution.

Heads-up: celebratory imbibition

In anticipation of my departure for Seattle on August 8, a few of us will be getting together for drinks on Friday August 4. The rendezvous point is the Naked Fish on the Middlesex Turnpike on Billerica, MA. I’ll be getting there at 5pm; some of us will be staying on for dinner (they do a really good Coconut Encrusted Haddock). Pass the word to any Sun, ex-Sun, ex-Mosaic, ex-PC-NFS, or ex-386i folks that you know….

Unreadable (and unrippable) CDs

Like many others, I followed the Sony rootkit saga with interest, feeling relieved that as a Mac user I was probably immune to such stuff. But I guess DRM is inescapable. Recently I’ve purchased two CDs that play just fine in a CD player but are unreadable on my Mac (or on a PC). The first was Enya’s latest, Amarantine. I inserted it into my PowerBook, the drive made seeking noises for a few seconds, and then the CD was ejected. Hmm. Last weekend I picked up At Blackwater Pond : Mary Oliver Reads Mary Oliver. Same thing. Frustrating.
UPDATE: The folks at Beacon Press (publishers of the Mary Oliver CD) got back to me and said they hadn’t seen this before. So I decided to shut down my Powerbook and reboot it. Normally I just put it to sleep when I’m travelling; I often go for several months without rebooting. After this I was able to read the Mary Oliver CD, although ripping was unusually slow – around 1.2x. Sadly, the Enya CD remains unreadable.

Persistence of addressing

A few days ago I mentioned that “It’s going to be interesting to hunt down all of the places which have my Sun address”. Yesterday I came across one of them: PayPal. And changing it was quite a trip.
It’s easy to add a new email address to PayPal, so I did that. But then I wanted to make this address the primary one, and delete my sun.com address. To accomplish this, PayPal wanted to send a confirming email to the current primary address – but that address had been deactivated on the day of my RIF. The workaround was interesting. First, I had to log in. [“Something you know.”] Then PayPal showed me the last four digits of my credit card, and asked for the full number. [“Something you have, but could be stolen.”] Next, PayPal indicated that it had my phone number on file, and asked if it could call me. When I clicked Yes, a four digit code was displayed, my phone rang [“Something you have that can’t be stolen.”], and I was instructed to enter the code using my phone [“Something ephemeral that you know.”] . This satisfied PayPal that I was who I claimed to be, and the change was effected.
How does this stack up as an identity solution? It certainly exploits existing technology to the full….

"Geek-to-geek" at SeeBeyond

Last September I wrote about the “geek-to-geek” event that I organized at StorageTek: an opportunity for several dozen senior engineers from Sun and StorageTek to meet each other, network, discuss issues of mutual interest, and so forth. That event seemed to work well, so yesterday we held a second one, at the Monrovia, CA facilities of SeeBeyond. SeeBeyond was the premier vendor of EAI (Enterprise Application Integration) software that Sun acquired last year.
The basic integration of the organizations and product lines is going well: we’ve announced the Java Integration Suite which brings together the key integration and composite application capabilities from both companies. However we wanted to broaden the horizontal connections: to bring in people from various parts of Sun to learn from each other. And in particular Greg Papadopoulos joined us for the first half of the day to lead a discussion of the “software as service” ideas that he presented at last week’s Sun Analysts Summit.
We followed the same format that had worked in Louisville: a series of 5-minute self-introduction presentations, open discussion to capture issues of interest, a working lunch, and then afternoon breakout sessions. (And for Sun employees: all of the materials will be posted on my internal blog by the end of the week.)
Herewith a few pictures; full size images are in my gallery:
g2g#1
g2g#2
Jerry Waldorf making a point. (Yes, the classroom layout is sub-optimal; this approach works better if you can arrange people in a circle or horseshoe. But it wasn’t a big problem. And yes, I did PhotoShop one image a bit to remove whiteboard contents.)
g2g#3
Greg attacks a virgin expanse of whiteboard, while Mark Hapner looks on.
g2g#4
The result: I actually prefer this to the version in Greg’s slides. Maybe we need a “scribbled whiteboard” template in StarOffice….
Thanks to all who helped make this happen, especially the intrepid “day-trippers” from northern California, and Judy for pizza and logistics.

A damp squib

Well, it looks as if “the first big one” is going to turn out to be a non-event. It seems that the pressure gradient was so great that it sucked in more (relatively) warm air from the ocean than was expected, keeping the temperatures quite a bit higher than needed for snow. (Right now it’s 39F in Boston.) I drove in to the office without any problems….

The first big one of the new year

It looks as if I’m going to be working from home tomorrow: the first serious snowstorm of the year is headed our way. As usual, the geek in me prefers to get this forecast in metereologist-speak, straight from the NWS Taunton Forecast Discussion (my emphasis):

THIS WILL NOT BE A VERY DEEP LOW WITH SFC PRESSURE JUST BELOW 1000 MB BUT COUPLED WITH HIGH PRES TO THE N WILL RESULT IN VERY STRONG ENE GRADIENT WITH IMPRESSIVE ATLANTIC INFLOW. IT WILL ALSO BE A SLOW MOVER AS IT GETS CAPTURED BY UPPER LOW RESULTING IN LONG DURATION OF PRECIP AND HIGH WINDS ALONG THE COAST TUE/TUE NIGHT.
NAM/GFS AND EVEN REGIONAL GEM ARE SIMILAR WITH QPF TUE/TUE NIGHT OF 1-1.5" SE NEW ENG...0.5"-1" VCNTY I-90...BUT SHARP CUTOFF N OF PIKE DECREASING TO LESS THAN 0.1" ACRS S NH. ...

Note that QPF denotes the precipitation measured as liquid water. The challenge with a storm like this is to translate QPF into snowfall:

SHARP QPF GRADIENT AND PTYPE ISSUES WILL MAKE FOR VERY DIFFICULT SNOW FCST FOR TUE. PARTIAL THICKNESS PROFILES SUGGEST PRECIP CHANGING TO MOSTLY SNOW ON TUE IN THE INTERIOR NW OF I-95 INCLUDING BOS AREA BUT THIS IS NOT A SLAM DUNK NEAR I-95 AS THERE IS A HINT OF WARM AIR ALOFT WHICH COULD AFFECT SNOW ACCUM IN THIS REGION. ... CROSS SECTIONS SHOW BEST SNOW GROWTH NEAR MASS PIKE FROM BAF-ORH-BOS ALONG WITH STRONG BANDING SIGNAL IN DEFORMATION AXIS. ...
GFS SNOW AMT TOOL INDICATING OVER 12" IJD-ORH-BOS AND EVEN 10" PVD BUT DUE TO UNCERTAIN THERMAL PROFILE AND QPF GRADIENT DECIDED TO TONE THIS DOWN AND GO WITH 4-10" IN THE WATCH AREA WITH HIGHEST AMOUNTS NEAR OR JUST S OF MASS PIKE. ...
WINDS WILL BE A CONCERN WITH THIS STORM AS 50-60 KT NE LLJ REACHES S COAST TUE MORNING PERSISTING INTO TUE NIGHT.

So although the official forecast says “New snow accumulation of 6 to 10 inches possible”, we see that this is the result of interpreting the output from a tool that’s predicting over 12 inches! We’ll see…. And the forecast of high winds suggests that power outages are likely; time to check batteries in flashlights. (I also tend to bump up the thermostat program before a storm like this, so as to keep the house a few degrees warmer than usual.)
UPDATE 5:48pm: Well, the forecast seems to be changing rapidly. Latest prediction is for just 2 to 4 inches of snow, with more ice and sleet. The heaviest snowfall is now predicted to hit Smithfield in northern Rhode Island – 8-12 inches. I wonder how it will actually come out…..