Monthly Archives: July 2007

Weekly Raptor

Harris’s hawks are the only raptors known to hunt cooperatively. Falconers have only started taking advantage of this in the past few decades. The fact that early reports of groups of these hawks shared kills was originally taken as meaning that they were behaviorally like vultures. The actual situation turned out to be much more interesting. Here’s a picture of our three birds at the end of 2002, Rusty with the two males we had trapped about five weeks earlier.

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Fuji S2 Pro, Nikkor G 70-300mm.

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Harry Potter and the Satisfying Ending

I can’t claim to have re-read the whole Harry Potter series before reading the final volume, Harry Potter and the Deathly Hallows, but I enjoyed the final book anyway.

One thing that I’ve appreciated in Rowling’s work is the premise that Harry’s specialness is primarily due to contingent external factors, and these are combined with intrinsic traits that could be part of anyone’s personality. Essentially, Rowling dispensed with almost all the usual mythological framework of inherited position, the sort of thing that was painfully essential to C.S. Lewis’s Narnia stories. It is part of what makes Harry accessible to all sorts of readers: it is non-exclusionary in a way that much of the fantasy literature cannot claim. In this regard, Rowling’s description in Harry Potter and the Order of the Phoenix of the choice by Voldemort in pursuing Harry rather than Neville Longbottom is a repudiation of the usual way in which prophecies get handled in fantasy.

So if you are one of the few people left who read the rest but haven’t yet picked up a copy of the new book, I think that you are going to like it. I think that the scriptwriters will have an excellent base for the movie adaptation, too, so I’m now looking forward to the final movie in the series, which I think is slated to open sometime in 2010.

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AiG and Cheerleaders

AiG recently bragged about the 100,000th visitor to their “Creation Museum”:

Less than two months after opening its doors to the public, the Creation Museum hosted its 100,000th guest this past weekend—a milestone not expected for months to come and a sign, museum officials say, of the continuing popularity of the critically acclaimed high-tech facility.

Mike Burleson adds this bit of commentary:

Apparently, all the negative publicity from Evolutionists has had the opposite effect, and is helping to drum up business!

As of June 24th, AiG was talking about how they might top their target of 250,000 visitors annually, extrapolating from the attendance data to that point to say they might get 549,000 visitors in the first year. 100,000 is slightly more people than one gets by dividing out AiG’s prediction for the year by the time the museum has been opened.

There is, of course, no data to support the causal conjecture made by Burleson, continuing a long tradition of unfounded antievolution speculation.

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Rudy Raff Reviews

Rudy Raff has a pair of book reviews, for Edward Humes’ “Monkey Girl” and the Laurie Godfrey and Andrew J. Petto anthology, “Scientists Confront Intelligent Design and Creationism”.

Rudolf A. Raff (2007)
Intelligent design judged and found wanting: A review of Monkey Girl, by Edward Humes, and Scientists Confront Intelligent Design and Creationism, edited by Andrew J. Petto and Laurie R. Godfrey

Evolution & Development 9 (4), 402^V404. doi:10.1111/j.1525-142X.2007.00177.x

I get a mention…

Wesley Elsberry analyzes the highly publicized but highly bogus “explanatory filter,” which is claimed to allow design to be discovered in nature. This filter is, along with irreducible complexity, one of the two supposed intellectual foundations of a new science of ID.

And, of the two, the one that is claimed to be most basic. Dembski has asserted that Behe’s irreducible complexity is a subset of Dembski’s specified complexity.

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What’s That Part?

I’m working on some circuit designs and going through some of the components I have on hand. Part of the Great Winnowing in moving earlier this year was tossing all sorts of paper, including various electronics databooks. So when I hit the net looking for a datasheet for a part “CA3030″, I was coming up with nothing until I ran across the DataSheet Archive. These folks are apparently doing for electronics databooks what the Internet Archive does for, well, the Internet, or the WWW part thereof. They have scanned a lot of old databooks, and have information archived about all sorts of parts, including obsolete parts. Since I’ve been collecting chips since the late 1970s, this is very handy for searches.

So I was able to retrieve a datasheet for my CA3030 chips (they are an op-amp with all sorts of compensation options), my CA3048 (quad op-amps), LM567 (tone decoder), and even a AY-3-8500-1 (video games chip). The only part so far that the archive hasn’t come up with the goods on is my SN76488N sound effects chip that I got from Radio Shack back around 1979, but I do happen to still have its paper datasheet.

One of the circuits I want to make would combine analog signal processing with digital logic. I’m looking to have three analog inputs that will be massaged to get a peak voltage with appropriate decay rate, then use voltage comparators to get digital signals out, so I can tune the sensitivity of the circuit. Here’s the stuff I haven’t completely worked out yet… Let’s say I have inputs Left, Right, and Center. I want to be able to have three digital outputs (1, 2, and 3), where if the Left input goes high first, 1 goes high; if Right goes high first, 2 goes high; and if Center goes high first, 3 goes high. A latch and a little control circuitry for Latch Enable can get me this far. If I get fancier later, I could expand the options for outputs, perhaps using an encoding so that how close in time the inputs go high would determine the pattern of outputs and latch them. The time course I’m looking at would be that there would be a pattern in which the three inputs would go high within about one millisecond of each other, depending upon the exact distances separating the sensors and the location of the stimulus. I could reset the digital part after about 1.5 ms or so to get a new reading. Now that I’ve written this down, I’m seeing that two latches, one 3-input NOR, and two or three quad 2-input NANDs can get me pretty close to setting up the unencoded outputs. Some more will be needed to have this be resettable on demand.

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Life in East Lansing

Diane and I went out on the town last Friday night. There was an outdoor free concert in a plaza in East Lansing featuring “The Lost Marbles”, not to be confused with that other band of the same name in Minnesota. After all, that other band can’t claim that its keyboardist chairs the zoology department at MSU. Diane took Ritka; I took my camera.

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Also saw Betty Cheng there, who remarked that we could pretty easily get a Devolab meeting going based on the number of folks from the lab in attendance. We also know the wife of one of the band’s guitar players through the agility club here in town. We had a fine time, and finished up with an after-concert dinner with Donna and Rick from agility down at the Chipotle restaurant.

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Wildlife… Inside

I got up this morning and headed out to my desk in the living room. Somewhere in there I realized that I had company. A very green mantis was perched on my printer. Fortunately, he was perched on a piece of paper, so I was able to move him outside without a whole lot of fuss.

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Nikon D2Xs, Tamron 17-50mm f/2.8 lens, ISO 800.

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The Drupal CMS

Something I’ve been dealing with recently is configuration of Drupal CMS-based websites. The, TalkDesign, and Online Zoologists websites all were based upon CivicSpace, which itself was a package of modules running Drupal underneath. What with changes in the server software, I was noticing some accumulated problems with the sites, and recently switched them over to use a somewhat newer release of Drupal in the 4.7 series.

The upgrade process was an adventure in itself. When they say to turn off all but the core modules and to set the default theme to “bluemarine”, they really, really mean it. Oh, and make sure that you are logged in as “admin” (user 0) when you do make a backup of your current database. With one of my sites, I had to step back and try again.

A big issue in the upgrades was that I wanted an additional user role, and when I tried making one under the old system, half of my permissions table got cleared, and I couldn’t restore the system to its previous state. So the new installations all permit the additional role. Something that perplexed me for a while was that in a group of about 6 nodes, some allowed the new user role edit permission, and some did not, while all of them, I thought, ought to. I eventually found a comment on the Drupal site about a set of permissions I had forgotten about, which is that each input format can be permitted or excluded from use by the user role. So beyond the node permissions, there was an additional set of permissions to be set.

One thing that changed was that I was using the “interlaced” theme under Drupal 4.6. Under 4.7, though, the version does not seem to show sidebars, which makes navigation pretty difficult. So at the moment I am using the “pushbutton” theme for 4.7 on all the sites. The AE site has a modified header background image. At my level of knowledge, Drupal theming is a time-consuming activity, and so I don’t know when I might get a change to do any more theme tweaking. I’d like to develop a PHP-based theme. I did one of those as a demonstration for NCSE, and there is a lot of potential for customization there. In the meantime, though, the “pushbutton” theme is working just fine.

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Fraptorday: Weekly Raptor

Back in 2002, Diane’s apprentice Andrea was getting her passage tiercel red-tailed hawk, Lavan, trained. Part of that involved free-flying Lavan to bagged game. These are two pictures from one of those outings.

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Fuji S2 Pro, Nikkor G 70-300mm lens.

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Work and Not Work

Let’s see, following my talk last week I was treated to one of those nasty summer colds. While I’m still hacking (the lovely phrase “productive cough” is all too familiar at the moment), I am on the mend.

Between the new laptop from the lab (a MacBook Pro with 4 GB of RAM) and the newly refurbished workstation (AMD Athlon X2 2.4 GHz with 2 GB of RAM), I’ve suddenly got some spiffy computational capability on the desktop here. Last week, I was able to get some changes committed to the Avida development code branch (and a bug found by one of my colleagues in about 15 minutes). I basically added two new instructions and some configuration values to control when/if they apply, plus the ability to set a “carrying capacity” that is smaller than the world grid size. I’m now working on runs to see what difference these changes make.

Diane entered an idea in the iRobot Create Challenge for a scholarship robot, and was selected as a recipient. I didn’t get one of my own, but we can likely use the same base and put in two submissions to the contest. Diane’s idea concerns using the robot as a prototype for a sound recorder that could approach animals in the wild and get good recordings. Mine concerned transferring programs evolved using Avida to the robot to demonstrate some basic orientation behaviors.

For things that aren’t work related, Diane and I are working toward having a pen for quail and/or chukar partridge. This is back about 150′ beyond the backyard fence, which hopefully will be far enough away from the hawks that they don’t get over-excited by the prey birds. I have a number of writing projects that need attention desperately.

Tomorrow I have some meetings and some work to do in the lab.

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More Backyard Wildlife

Yesterday, Diane, Ritka, Farli, and I went out in the back area beyond the fenced yard here. I wasn’t paying particular attention to Ritka, but Ritka had found some interesting scent. Our attention was caught, though, when a half-dozen birds broke cover and flew off, the smallest of them as large as a full-grown pheasant. We have wild turkey in the area. The smaller birds we are assuming are young of the year.

Down at the pond, there is a mallard hen with a half-dozen half-grown ducklings. We had a load of sand dropped off next to the pier at the pond, giving us a few feet of sandy beach rather than mud. It makes it a bit more pleasant to check out what’s up. We can hear frogs toward evening. And we have had a fair number of lightning bugs, too.

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The NRA Finally Notices

Will the ACLU and the NRA finally find common cause? The issue is that in the general free-for-all shredding of constitutional rights by our government, the NRA has picked up in particular the threat posed by Sen. Frank Lautenberg’s (NJ) proposed legislation, the “Denying Firearms and Explosives to Dangerous Terrorists Act of 2007″ (S.1237). The NRA, in a Wayne LaPierre opinion piece in the July 2007 “American Hunter”, says that Attorney General Alberto Gonzalez and the Department of Justice are supporting this bill, which would give the AG’s office the power, via suspicion alone, to permanently deprive a citizen of firearms and ammunition, and on top of that, the AG’s office could refuse to divulge any and all reasons for doing so under the blanket justification of “national security”.

The Bush administration is on record affirming the Second Amendment as an individual right, yet this bill trashes the Constitution, mocking the protections guaranteed by the Bill of Rights. It would arbitrarily take away your rights — without charges, without an arrest, without a trial and without a conviction — just because the attorney general says so. It denies citizens all due process of law at the sole discretion of government — something that must never happen in America.

Bad news, Wayne. You are behind the times. This has already happened in America, and you didn’t even notice. AG Gonzalez hasn’t “thought about” habeus corpus, citizens are already denied due process rights in their person, and by any measure you care to make, I think it is inevitable to concede that the terrorists won the war on terror. The NRA was irrelevant to the process of wholesale erosion of our freedoms precisely because it didn’t notice what was going on beyond the particular personal property protection of the 2nd amendment for firearms.

Good luck stopping S.1237, though; dumping a sandbag or two where the levee used to be may not materially help things, but at least it would be doing something.

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More Workstation Tweaking

This exercise is reminding me of things I used to know. One that I ran into was that you can only have four primary partitions on a single physical disk. This meant that the way I had originally installed Xubuntu, using manually sized root and swap partitions, took up two primary partitions and kept me from using the big chunk of disk I had left free for formatting with FAT32.

So my approach on fixing this was direct, not elegant. Given that I hadn’t been able to resize the FreeBSD partition in the original Ghost session, I booted from a FreeBSD 6.2 install CD, deleted all the partitions except the Windows one, then setup a 50GB partition for FreeBSD, a 50GB partition for Linux, and the remaining 334GB with a Linux identifier. I installed the X-Developer distribution package for FreeBSD, then rebooted with the Xubuntu live CD. I installed QTPartEd and used that to nuke the 50GB Linux partition. Then I could run the Xubuntu install and get the convenient option of using the largest block of free space on my drive. Trying to install with the partition identified already as Linux only gave me a manual partition option, which didn’t seem to allow for setting up the swap partition as a logical partition. With Xubuntu installed, I also had a working Grub boot loader again, and could now boot back into Windows again.

That still left me with the problem of getting my newly accessible hard disk space formatted in FAT32. The folks at Microsoft did not give Windows XP the tools to format any partition larger than 32GB in FAT32; they want you to use NTFS. There are certain advantages to the NTFS system, or at least I’ve been told that over and over. Unfortunately, the support for NTFS in other operating systems is still short of the “rock-solid” you would like for something that gets near data you might cherish. Therefore, FAT32 as the shared data storage format of choice. I found a utility online called fat32format. This is a small command-line utility, and the web page linked has a very good discussion of its use. Following the directions there, I set the partition up in the Windows Disk Management utility, but with “leave it unformatted” as my option. Following that with “fat32format e:” gave me the formatted disk I was after in just a couple of seconds.

Right now, I’m copying off a batch of photos from a USB hard disk to the local disk, figuring that my ultimate in speed of processing will be with them there.

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Fraptorday: Weekly Raptor

Here’s a picture from the end of the year in 2002. We had Rusty out in the field with the two new hawks, Beater and Biter, who we had trapped in mid-November.

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Fuji S2 Pro, Nikkor G 70-300mm lens, probably ISO 800.

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Workstation Update

I had had a bit of a sore throat starting on Monday. I kept myself in zinc lozenges and Chloraseptic, and made it through my talk Wednesday night. However, on the trip back from Grand Rapids, I could feel myself getting sicker. Thursday brought with it a pretty good set of symptoms for upper respiratory infection, including the sore throat, congestion, fever.

Thursday also saw the arrival of the new parts for the workstation. So in between timeouts to lay down and sleep, I worked on getting my machine back in business.

Continue reading

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LA Times Science Files for 2007/07/10

These are items compiled by staff of the LA Times.

    Restoring mildewed memories

    Diamondhead, Miss. – As after any natural disaster, the belongings most mourned by Hurricane Katrina survivors were family photos – irreplaceable moments of celebration, youth and loved ones frozen in time. So two photojournalists launched Operation Photo Rescue. By Ann Simons, Times Staff Writer.

    West Nile already in 26 counties in state

    SAN FRANCISCO – West Nile virus is off to an early start this year with reports of the disease in 26 California counties, prompting health officials to call on the public to take aggressive preventive measures. By Richard C. Paddock, Times Staff Writer.

    The fur flies over spaying proposal

    SACRAMENTO – A retired game show host is vying with a famous canine film star this week over a proposal to require Californians to spay or neuter their pets, a bill that has sparked emotional debate and created the largest volume of public response of any measure in the state Legislature this year. By Patrick McGreevy, Times Staff Writer.

    Marina seen as a threat to Baja estuary

    SAN JOSE DEL CABO, MEXICO – In a rocky, dun landscape dominated by saguaro and prickly pear, the estuary of the San Jose River is an oasis-like explosion of green. But population growth in the Los Cabos region is placing the rich marsh under assault, environmentalists say. To build the newest big tourist project, a marina called Puerto Los Cabos, developers carved out a huge chunk of the estuary. By Hictor Tobar, Times Staff Writer.

    Hurricane center chief is forced out

    MIAMI – In what people here are calling “the ‘cane mutiny,” forecasters at the National Hurricane Center succeeded Monday in getting their commander ousted. Just six months into the job and in the midst of an active storm season, Director Bill Proenza was put on leave and replaced by his deputy, said Anson Franklin, spokesman for the National Oceanic and Atmospheric Administration. By Carol J. Williams, Times Staff Writer.

    Cleaner locomotive starts its port duty

    Jeff Robinson settled into the driver’s seat of his new, low-emission locomotive Monday, released the air brakes and moved a throttle lever, making the engine roar and his train rumble forward with 9,000 tons of imported goods in tow. The locomotive could easily have been mistaken for a 1950s model, But under the hood was an example of cutting-edge diesel-electric technology: a V-12, 2,000-horsepower machine that dramatically cuts unhealthful emissions. By Louis Sahagun, Times Staff Writer.

    Live Earth: Dead on arrival

    “If you want to save the planet, I want you to start jumping up and down. Come on, mother-[bleepers]!” Madonna railed from the stage at London’s Live Earth concert Saturday. “If you want to save the planet, let me see you jump!” What else could capture the canned juvenilia of a 48-year-old centimillionaire – who owns nine homes and has a “carbon footprint” nearly 100 times larger than the norm – hectoring a bunch of well-off, aging hipsters to show their Earth-love by jumping up and down like children? By Jonah Goldberg.

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Laughter is the Best… Well, It’s Something

Steve Story at the “After the Bar Closes” forum riffed off of some posted questions comprising a final exam in rhetoric offered by William Dembski, to create a new question. I think the new question should be more widely heard:

14. You are the head of a PR company in Seattle. You have $4 million a year to try to promote Science X. In 20 years Science X has solved no problems, performed no experiments, and generated neither hypotheses nor interest from serious researchers. You don’t even bother to publish your fake journal anymore. Virtually all scientists say Science X is an enormous pantload and obviously fraudulent. Despite all this, a small percentage of zealous nitwits believe in Science X and buy your books and attend your fake conferences. Explain, in 300 words, whether you should get leather or fabric interior for your new Jaguar.

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New Workstation Parts Ordered

My general philosophy on the workstations I build is to try to find the best current bang for the buck. So in upgrading my recently-deceased workstation, I turned to the assistance of my friends online to help make it possible (thanks again), and then to to actually put the order together.

On Newegg, they provide a pretty good search facility that allows you to specify desired properties of what you are buying. Keying off a CNet review of dual-core processors, I decided that my upgrade to my old Athlon should be an Athlon X2. That in turn meant that I would be looking at AMD motherboards sporting the AM2 socket. Given that I’ve learned that Avida is not a disk-intensive program, and I’d like to run Avida on my home workstation, I decided to go with a motherboard capable of handing DDR2 800 (PC2 6400) memory. So pretty much what this was shaping up as was to identify a motherboard and then proceed to sort through the options for CPU, memory, video, and hard disk.

My first thought was perhaps to go with the ASUS M2V-MX Socket AM2 VIA K8M890 Micro ATX AMD Motherboard, bargain-priced at $56.99. It’s a Micro-ATX format board, does well on the user reviews, and has two PCI slots for expansion. The reviews make it clear, though, that this board is essentially an entry-level board.

But then I thought that if I’ll be perhaps sitting down to work at this workstation for several years, as I did my last one, that maybe I should keep on with the search. So I came across the ASUS M2N-SLI Deluxe Socket AM2 NVIDIA nForce 570 SLI MCP ATX AMD Motherboard, a motherboard with over 600 user reviews and 63% of those giving it 5 stars. It is an ATX format board, has 3 PCI slots, 2 PCI Express x1 slots, and 2 PCI Express x2 slots. There’s 4 USB ports, 2 Ethernet ports, and even a Firewire port built-in. It’s a chunk more expensive at $139.99. This is the one I’ve ordered.

Newegg often offers “combo” deals, where if you buy a second product you get a pretty good discount. Checking the “combo” deals for my selected motherboard showed that I could get the 2.4 GHz Athlon X2 CPU with it for a combined price of $228. OK, that’s not bad.

Off to look at memory. Some of the user reviews had noted good things about the G.Skill memory. So I found it as G.SKILL 2GB (2 x 1GB) 240-Pin DDR2 SDRAM DDR2 800 (PC2 6400) Dual Channel Kit Desktop Memory, two 1GB sticks, for $89.99. Not bad. I remember paying about $100 each for 1MB SIMMs for a computer back in the 1980s. But, wait, there are combo deals here, too. And mostly they combine memory and CPU purchases. So the combination of the 2.4 GHz Athlon X2 and this memory comes to $168. Hmmm. I can save ten bucks by buying the motherboard on its own and going for the combo package of memory and CPU, so I do.

Since the motherboard doesn’t have on-board graphics, I need a video card. Apparently, the new hotness is found in the PCI Express x16-based cards. I don’t have any of those hanging around, so I need one. In going through the Newegg listings, I’m looking for PCI Express x16 interface, high user review score, high numbers of reviews, and low price. Hey, I’m not into video games. I shudder to think of getting hooked on video games now. I have enough stuff on my plate as it is. So I found the FREETECH PX6200TD-128M GeForce 6200 128MB DDR PCI Express x16 Video Card at $39.99. There’s lots of good user reviews and notes about how this is an excellent deal for the money. Seems good to me.

That leaves the issue of a boot disk. I have loads of IDE drives hanging around, but not many that are of reasonable capacity and that I know are clear of useful data. Plus, the motherboard only supports one IDE interface with two devices, and one of those is going to be an optical drive of some sort. Plus, it seems a shame to get an SATA capable board and not put that to use. So I’m going for the Western Digital Caviar SE16 WD5000AAKS 500GB 7200 RPM SATA 3.0Gb/s Hard Drive at $109.99, or slightly under $0.22/GB of space. I’m thinking that I can set that up in a three-way boot configuration, just as I had briefly working on my old workstation, with a Windows , FreeBSD, and a Xubuntu install. The GRUB boot loader installed by Xubuntu can be set to provide a menu to select the other systems. I’m thinking 60 to 80GB each for the bootable partitions, then set up the remainder as shared working space. There are some issues with using FAT32 as a filesystem, but cross-operating system operability is not one of them. The limiting factor, as usual, seems to be Windows.

So, the great workstation update is underway, and comes in a bit under $500. I should have the parts from Newegg next week.

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Anybody Interested in Sponsoring this Blog?

Given that I’m out my main workstation (my 2001 ECS K7S5A Athlon-powered machine having gone kerput last week), am not rolling in dough, but do have a moderately well-trafficked weblog here, I’d be willing to consider a sponsorship arrangement. On the one side, I’m looking for a computer that’s pretty current in technology terms (dual-core CPU of some variety), and I’d be willing to host a banner ad here for a reasonable term to get it. Of course, the banner ad has to be G-rated and not pushing stuff that I otherwise would be taking objection to. Interested? Leave a comment and we can talk.

Update: An unnamed donor has sprung for enough to get my workstation upgraded. Thanks!

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