Tortured analogy

Embattled Conservatives Look To Star Wars For Guidance [io9.com].

Items of note

I've been busy starting up a new research project that I intend to present results from at the end of May, so I haven't had time to blog much, but here are a variety of small things that attracted my attention.

I was pleasantly surprised to find that the awesome doxygen source code documentation tool is now even more awesome: starting from version 1.5.5 it can now be used with Fortran! WRITE(6,'(A)') 'Praise the Parser!'

Speaking of programming: Intelligent Design Sort - it never gets old - praise the Sorter!

Pascal Boyer admits he has a problem: he is really interested in crackpots. Admittedly crackpots are a fascinating, if understudied, from a sociological point, but Boyer attempts to remedy this with his analysis of the group. He reproduces the well-known finding that a large fraction of crackpots have engineering backgrounds, but he does make some valid points (that appear obvious in hindsight, as all good analyses should), in particular: "the crackpot alternative is, almost universally, less mathematically challenging than the standard account" and "The crackpot theory is based on textbooks" with no exposure or understanding of actual research literature.

While we're on the subject of cranks, I must admit that I view most flavors of libertarianism with scorn, so I have a soft spot for those uncivil bloggers who ridicule it: Gavin M. over at Sadly, No! dissects Glenn Reynolds's libertarian conservatism and finds feudalism.

Still on the subject of cranks, PFAW dissect Orson Scott Card's absurdist bigotry using the scalpel of sarcasm.
http://www.rightwingwatch.org/content/does-national-organization-marriage-want-overthrow-government
I still do not understand why people think "Ender's Game" was great.

Finally dispensing with the crank theme, and moving onto more serious stuff (although with a Speculative Fiction flavor), I could not agree more with the following argument (hat tip io9):

"But the one—the most absolutely key, the rock star green technology—that I champion over all others is birth control: vasectomies, IUDs, the pill, condoms. I don't care which kind you or your family prefers or finds most appropriate, I love them all. Any technology that reduces the absolute number of consumers (and particularly Americans and Europeans who consume the most) now that's a TECHNOLOGY!" — Pump Six And Other Stories author Paolo Bacigalupi, interviewed at EcoGeek.org.

If you, like me, had not previously heard of this Stanley Fish guy the NYT has added to their Opinion section, this (rather old) Slate article "The Indefensible Stanley Fish" by Judith Shulevitz will provide you with some useful background information. (Note clever segue from Speculative Fiction to tedious postmodernist analysis of Fiction.)

Finally some science! Evidence of forethought in Chimpanzees: Ed Yong at Not Exactly Rocket Science nicely summarizes the story of Santino the Chimp's premeditated ammunition collection for later attacks on Zoo visitors.

NPR

This article at Daily Kos sums up many of the reasons why I haven't bothered listening to NPR since 2004 - their excessive reliance on talking heads from (mainly right wing) Think Tanks, and their credulous acceptance of whatever the pundits say.

Game AI

The guys at Penny Arcade were referring to Wanted: Weapons of Fate when they created this comic, but it sadly applies to most game AIs.

My favourite example of this (and I don't mean that in a sarcastic way) are the mercenaries in Far Cry 2 who camp out by the gas (petrol) stations. One shot at a pump, and Oh the humanity!

Fedora upgrade problems solved?

Just to follow up from last week's post on my problems upgrading my x86_64 workstation to Fedora 10, I think I now have everything fully functional once again.

The booting/grub problems were definitely related to grub's attempted probing for a floppy drive (/var/log/messages will show kernel I/O errors associated with fd0), even though I've never had a floppy drive in the system and it had never caused a problem before. It appears this is not an uncommon problem, see e.g. here and here, but its not obvious why I'd only experience this now with Fedora 9 an 10.

The command line workaround (install grub to the MBR using the grub shell with "grub --no-floppy," setup (hd0,0), etc, instead of using grub-install) is not ideal as it appears that any kernel update (e.g. when updating the system after a DVD upgrade) will run grub-install itself and fall foul of the problem.

In the end I had to switch off floppy support completely in the BIOS (even though no floppy drive or any associated cabels were present in my system) to solve this problem.

Upgrading from Fedora 8 -> Fedora 9, and then Fedora 9 -> Fedora 10 using the x86_64 DVD install/upgrade disks ultimately worked, in a fashion, but displayed some annoying features that reminded me why I switched to the yum upgrade method before.

The problem is that after "upgrading" and rebooting I found many packages (indeed, the majority) had not been updated to Fedora 9. I presume the reason is that a fully up-to-date Federa 8 system has packages that are more recent, with higher version numbers, than the original Fedora 9 DVD distribution, and that the DVD upgrade process then does not replace the fc8 packages with the fc9 packages.

I had to run "yum update" at least twice (why twice? I don't know why it didn't pick up all the packages that needed updating the first time) before the older Fedora 8 packages were replaced with normal fc9 packages. Even with a fast internet connection updating > 1000 packages takes a full day or so. I then had the same problem with Fedora 9 -> Fedora 10, where the situation was so bad that after the basic DVD upgrade firefox and konqueror simply didn't work at all. Then yet another day waiting for "yum update" to complete.

I did discover some useful yum tips here, in particular how to force yum-fastestmirror to retest the mirror speeds without doing "yum clean all." (Important if you've just spent several hours downloading hundreds of packages, but they haven't yet been installed before the transaction check found a problem, and you need to download more but the once-fast mirror you were downloading from is now incredibly slow.)

The update process was exacerbated by some odd changes the DVD upgrade made to my networking setup that basically messed up /etc/resolv.conf and my DNS configuration. It took me a while to work out that the "Error: Cannot find a valid baseurl for repo: fedora" was basically a DNS/dhclient problem. I don't remember DVD upgrades messing with network settings before, so I'm not sure how or why this happened.

To add insult to injury my rsync backup scripts then no longer worked because the newly installed Gvfs (specificaly ~/.gvfs) breaks rsync. The work-around is to add .gvfs to the rsync excludefile, but what a pain!

All in all a very tiring upgrade process, and all the more annoying because the exact same upgrades for i386/i686 work fine on my other machines. I presume part of the problem, in particular with the DVD upgrade, was leaving the upgrade so late after Fedora 9 and Fedora 10 had come out, so I may upgrade the x86_64 workstation to Fedora 11 relatively soon after it comes out. But on the other hand I don't like to upgrade to a new Fedora version before some of the kinks in the new version are worked out...

Fedora upgrade problems

I've been having a lot of trouble with my main workstation this week, brought on by an attempted yum upgrade from Fedora 8 x86_64 to Fedora 10 x86_64, but probably complicated by hardware problems associated with the floppy drive (or lack of it, to be more precise) that then messed up (and continue to mess up) the grub bootloader.

I had to do a full system restore yesterday from my incremental rsync backups (which worked wonderfully), but I'm still struggling with the system and was forced to do a rpm database rebuild this morning. The DVD-based Fedora 9 upgrade I set running last night, although supposedly successful, in truth failed thanks to grub-install's (which seems to be run whenever you install a new kernel) insistence on probing for a floppy drive even when there isn't one present and even when the device.map correctly excludes fd0 (note that recent versions of grub-install do not have or honor a --no-floppy command line option, despite what people on the Internet seem to think). Attempts to run grub-install from the command line simply hang, and /var/log/messages starts showing kernel I/O errors associated with fd0 (which I'm pretty sure I dont have!).

The messed up Fedora 9 install also seem to have messed up rpm, as on booting I found that even simple rpm queries would hang and /var/lib/rpm/ had the classic __db* files.

Still, looking on the bright side it has been a good test of my linux sysadmin knowledge.

My rsync backup method (based on Mike Rubel's incremental rsync backup with hard links method described here, see also Kevin Korb's page on rsync backups) works well and restore's easily. Note that the method's Rubel and Korb describe don't quite work on my system as rsync can't handle the number of files of my system in one go - I basically run the method by script separately on each of /boot /bin /etc /home /var etc etc).

I still remember how to use the grub command line to find files and boot, even if grub.conf is totally messed up, and I've learnt (the hard way) that grub-install can't quite be trusted and that its better to use the grub shell to install grub to the MBR (Remember to use "grub --no-floppy" to prevent probing for a floppy, even if you dont have on).

The annoying rpm stale locks and corrupted rpm database thing can be fixed ... "rpm -vv -rebuilddb" worked, thankfully.

I'm still surprised that the basic yum upgrade failed, as I've done yum upgrades from Fedora 8 directly to Fedora 10 successfully before, although only with i686 systems and not an x86_64 system. Based on the error messages I experienced it seems that /usr/lib64/libc.so.6 is the problem child in the jump from Fedora 8 to Fedora 10. I really should have done Fedora 8 -> Fedora 9 -> Fedora 10, or burnt myself an upgrade DVD and done a DVD-based upgrade.

That the DVD upgrade from my recovered Fedora 8 system to Fedora 9 also failed (because of the grub/fd0 problem) does suggest that a classic DVD upgrade, and not doing a yum upgrade would not have prevented me from experiencing problems (although it might have saved me a full days work). However I do find it hard to believe two separate problems, one software and one hardware related, would appear simultaneously.

I'm still waiting for the Fedora 9 yum update to finish before I shutdown and go poking inside the machine to see if I can find out what is causing my floppy drive problems. Without solving that issue there is no point attempting to upgrade to Fedora 10...

Anyway, time will tell whether I can get the system safely upgraded to Fedora 10.

Dyson

The NYT magazine covers Freeman Dyson in a multi-page article by Nicholas Dawidoff: "The Civil Heretic." Sadly the elderly Dyson is now more famous for his current climate change contrarianism than his more interesting earlier work, or even the fun but speculative stuff like Dyson Spheres or Project Orion.

This prompted Andrew Revkin to produce a somewhat more nuanced discussion of Dyson on his Dot Earth blog: "Some Inconvenient Thinkers", although it annoyingly stops short of actually discussing why Dyson is wrong, and instead pretty falls into modern journalism's classic statement of false objectivity: "He might be right, he might be wrong. What do you think?"

Climate Progress (who really seem to dislike Revkin despite the fact he's generally does a decent job of covering science and climate change - he's certainly infinitely better than Tierney) then produced a rather uncivil blog article pointing out how Dyson has been far from civil when discussing actual qualified climate scientists. Although uncivil, it at least has some discussion of why Dyson's beliefs are simply absurd, and links to Only In It For The Gold's calmer explanation of Dyson's mistakes.

Ultimately I think Dyson's contrarianism is not as harmful as many of the other climate change contrarians, largely because Dyson's rejection of climate change are not driven by political or economic biases, but rather a mistaken belief in his scientific ability. Its somewhat sad to see once great scientists go off the deep end when they get old. Some, like Fred Hoyle, go off the deep end even before they get old.