Revisiting the Vaccine/Autism Myth

Arstechnica, a favorite site of mine, links to a recent publication that looks at the history behind the mercury/vaccine/autism so-called war. The Ars article also provides a few insights of its own.

I’ve written before about my take on the fear people have about vaccines causing autism. I’ve also written about how we must be savvy media consumers, particularly when the media content pertains to our health.  It seems I need to eat some crow, as my original post shows I fell into the trap that many people did – Wakefield’s work was not initially related to mercury concerns in vaccines, and hence autism.

So today I’m just re-iterating my belief that vaccines are still a good idea for our children. The PLoS Biology article is a nice summary of how things went wrong, and hopefully we can begin to dispel myths and get back to scientific facts. it’s hard when our emotions and, more importantly, our children’s safety are involved. But we owe it to ourselves, our children, and our community to get the facts before making decisions that affect us all.

The recent H1N1 scare should certainly make parent’s ears perk up when combined with statements such as

Last year in Minnesota, five children contracted Hib, the most common cause of meningitis in young children before the vaccine was developed in 1993. Three of the children, including a 7-month-old who died, hadn’t received Hib vaccines because their parents either refused or delayed vaccination.

Preventable death and disease.  The H1N1 lesson should be that we are succeptible to disease, and that we should prepare ourselves and our community as much as possible ahead of time.  Vaccines help us do that.

Nice Demo of Benchmarking and Optimizing a WordPress Blog

Optimize WordPress for speed

Here are the results from my current (old) system for comparison:

Benchmarking thebside.ca (be patient).....done

Server Software:        Apache/2.2.9
Server Hostname:        thebside.ca
Server Port:            80

Document Path:          /
Document Length:        26643 bytes

Concurrency Level:      10
Time taken for tests:   126.358 seconds
Complete requests:      100
Failed requests:        0
Write errors:           0
Total transferred:      2716600 bytes
HTML transferred:       2664300 bytes
Requests per second:    0.79 [#/sec] (mean)
Time per request:       12635.836 [ms] (mean)
Time per request:       1263.584 [ms] (mean, across all concurrent requests)
Transfer rate:          21.00 [Kbytes/sec] received

Connection Times (ms)
min  mean[+/-sd] median   max
Connect:        0    5  21.1      1     108
Processing:  3432 12418 1510.4  12669   15194
Waiting:     2785 7833 906.1   7867    9657
Total:       3433 12423 1507.4  12669   15195

Percentage of the requests served within a certain time (ms)
50%  12669
66%  12956
75%  13106
80%  13145
90%  13978
95%  14549
98%  14919
99%  15195
100%  15195 (longest request)

Specs of the old machine:


Athlon XP 2100+, 756 MB RAM

hdparm -tT /dev/sda1

/dev/sda1:
Timing cached reads:   336 MB in  2.00 seconds = 167.97 MB/sec
Timing buffered disk reads:  192 MB in  3.03 seconds =  63.40 MB/sec

Now below are the numbers for my new hardware, though they may deteriorate as I add additional services.

Benchmarking localhost (be patient).....done

Server Software: Apache/2.2.11
Server Hostname: localhost
Server Port: 80

Document Path: /
Document Length: 28407 bytes

Concurrency Level: 10
Time taken for tests: 12.385 seconds
Complete requests: 100
Failed requests: 0
Write errors: 0
Total transferred: 2890200 bytes
HTML transferred: 2840700 bytes
Requests per second: 8.07 [#/sec] (mean)
Time per request: 1238.451 [ms] (mean)
Time per request: 123.845 [ms] (mean, across all concurrent requests)
Transfer rate: 227.90 [Kbytes/sec] received

Connection Times (ms)
min mean[+/-sd] median max
Connect: 0 9 30.1 0 119
Processing: 782 1220 163.2 1205 1781
Waiting: 499 790 145.2 757 1344
Total: 782 1229 182.8 1205 1781

Percentage of the requests served within a certain time (ms)
50% 1205
66% 1243
75% 1286
80% 1308
90% 1516
95% 1666
98% 1734
99% 1781
100% 1781 (longest request)

And the new server’s specs?

AMD Athlon Dual Core 5050e, 4GB RAM

hdparm -tT /dev/sda

/dev/sda:
Timing cached reads: 1292 MB in 2.00 seconds = 646.06 MB/sec
Timing buffered disk reads: 252 MB in 3.00 seconds = 83.94 MB/sec

So things are looking good!

TED Talks Again

A few interesting TED talks:

  1. Are we in control of our own decisions by Dan Ariely.  Another take on Barry Schwartz’s awesome idea centered on the “Paradox of Choice” (here’s a TED talk of his own from 2005 on the topic – HIGHLY recommended).  Dan’s point is that what we set as defaults in forms, webpages,or any means of collecting information can have a dramatic impact on the results collected.
  2. Searing photos of war by James Nachtwey.  This is the kind of presentation that makes me sit up, look around, and ask “Am I really spending my time wisely today?”  It makes me want to go out and really put myself out there, to try to make the world a better place.  It appeals to the idealist in me.  On a realist level though I do believe I’m going to provide as much support as I can to MSF this year.
  3. The LIFE project by Frans Lanting. An interesting use of photography to tell the history of the world in Frans’s eyes.  I’m not sure it is as effective as he hoped it would be.  I know that when I started watching it I wasn’t “wow – zoom!” about the photos themselves.  He certainly paints a vivid story though, with technically interesting pictures.

Maybe I Need A UPS

Well that was fun.

Power outage = blown integrated network card = no network access on server + limited PCI slots = removal of one TV tuner for temporary network access.

Good lord, now we can only record one TV show at a time!  How can we live like this, forcing us to prioritize our TV habits!

Now if I want a long term solution (which I do): new network card = new motherboard = new CPU + new memory.

It’s a rebuild!

So forgive me if things are weird or missing on theBside over the next little while.  I have both the old and new server up and running and am moving data as I can.  The transition should be seamless.  Should be.  Just might be a slow one.

Not sure about a UPS as the surge came through the network cable (I think), and I already have a surge protector on the server.  However I’ve also lost a hard drive due to a power outage before, so maybe I should just pony up the cash.

I think I’ll keep a list of valuable and used resources on here in case this happens again, or if anyone else is interested in what I’m doing.

  • Decided to use Ubuntu Server rather than desktop, as it comes with a few pre-configured applications I wanted to install
  • Decided to not use Mythbuntu this time, as I don’t like the XFCE environment, and can easily add the Mythbuntu repo if I wanted their custom stuff
  • Followed this guide to get the old PVR’s database synchronized/replicated with the new one going forward (don’t give the full bin log path on the slave, just the filename as per SHOW MASTER STATUS)
  • Will use rsync to automatically synchronize the mythtv recordings between the two, since the databases are sync’d (set up rsyncd on new server as per the Ubuntu Community Doc)
  • Will use symlinks to a separate partition (/srv) rather than /var/lib/mythtv for the root of myth – it just feels more accessible and it is easy to put on its own filesystem
  • Used reiserfs rather than xfs, though I’m not really sure why – I may change this before proceeding (Update – changed to xfs, may follow this for tweaking if performance seems to be less than ideal.  MythTV itself says to not use reiser for fear of corrupted videos.  OK then!)
  • Followed this documentation to get LDAP replication setup (don’t forget to change phpldapadmin’s config.php)
  • Followed this guide on setting up mailing lists in my LDAP directory, and this guide to change the reply-to field for the mailing list (don’t forget to run postmap /etc/postfix/generic when you change the generic file!)
  • Gallery2 installed – have to uncomment the alias in the apache config file.  The login.txt file goes in the directory in apache.conf too.  Update /etc/php5/apache2/php.ini to have more memory.  /etc/gallery2/config.php includes the baseURI if it needs modification (remove the internal hostname).
  • Roundcube setup – don’t forget to install roundcube-mysql and edit the debian-db.php.
  • phprecipebook – seems I had two people register themselves on the old system.  I thought I had disabled that – hack maybe?  I’m now on the latest version so we’ll see if that happens again.  I decided to create a special user for the recipedb, rather than use the root account (bad idea Kirk, bad!)  just create the symlink in /var/www and update the database info in the custom file.
  • Migrating Mythtv is going to be more complicated.  Just to make sure I’m not doing an inadvertent upgrade too, I upgraded my old server to 9.04.  Let the package maintainers handle the upgrade steps I says.  I then followed this tutorial on migrating to a new host.  I ran into the duplicate entry problem described in the comments.  I followed this idea of replacing the INSERT commands with REPLACE INTO commands and I was able to import the SQL commands nicely.  I ended up discovering the hostname was in some of the tables, so I decided to just follow the first tuturoal’s advice – pull specific parts of the databse, drop the mythconverg database, reintall the backend, and then apply the specific updates as per the tutorial so I don’t lose my recorded history.
  • Getting MythTV to work: follow the suggestion in this link to stop the incessant spam mail every 10 minutes – how did this bug get passed beta?!?