Head Rattle

DBIx::Class join, prefetch

2010-08-13T12:06:00.005-05:00

Over the last 15 years I've joined two database tables into a one-to-many relationship about a billion times. But I've never had any software let me loop the left table and right tables separately before. Turns out this magic has been in DBIx::Class for several years.

Runnable demo.

When table 'foo' is in a one-to-many relationship with table 'bar', you can:


my $foo_rs = $schema->resultset('Foo')->search(
   {},
   {
      join     => 'bars',
      prefetch => 'bars',
      order_by => 'me.id',
   }
);

while (my $foo = $foo_rs->next) {
   printf "%s\n", $foo->id;
   if (my $bar_rs = $foo->bars) {
      while (my $bar = $bar_rs->next) {
         printf "   %s\n", $bar->desc;
      }
   }
}

Output:


1
2
   aaa
   bbb
   ccc
3

Still one SQL statement against the database (fast!). Much prettier than ugly manual de-duping of redundant columns.

quibids.com, you're my hero!

2010-08-07T16:11:00.012-05:00

Holy crap! The people running this auction site must be making a fortune!

Quibids.com is an auction site where you pay to bid. Each bid costs $0.60 and raises the bid price on the item by 1 penny. Items start at 1 penny. I'm watching the bids on a $1600 laptop climb from $50 up to $73 and beyond. A $1600 laptop for only $73? What a bargain, right? Yup, if everyone else would stop bidding and let you win. Hint: They won't.

It says right here that this item "recently sold for $422.59." Someone saved $1200! Good for them! In the process, quibids.com raked in $25,355.40 (42,259 * $0.60) in fees on the sale of a single $1,600 laptop! HOLY CRAP!

Capitalism rules! I need to launch one of these sites and only charge $0.50 per bid!

Update: This ad says "Honda Civic Sold for $2,642!" There's another $158,520 in bidding fees for Quibids.com. Also, for the company spin: Does QuiBids make excessive profit on their auctions? (Of course not! We have to pay rent and stuff! -grin-)

OS X "Address Book" sync fail to Google

2010-07-28T20:15:00.010-05:00

I assumed this would all "just work" in 2010, but I guess I was wrong. My toys:


OS X 10.6.4 MacBook, OS X 10.6.4 Mac mini
   Mail, Address Book, iCal
Google
   Mail + Contacts, Calendar
HTC Evo 4G (Android 2.1) mobile phone
   Mail, People, Calendar

My email and calendar sync everywhere. Woot! OS X Address Book, however, completely fails to sync to Google. There's a checkbox in Preferences for "Synchronize with Google" that appears to work, but every time I quit Address Book and restart it, that box is no longer checked.

Apparently lots of people spend years fighting this stuff, or spend $100/year for Apple MobileMe. I prefer just giving up on Address Book, satisfied that almost everything Just Works.

Update: Sheesh. OK, so the sync does work even without MobileMe if you work your butt off every time. e.g.: (1) Change a contact in Address Book. (2) Open Preferences, check the "Sync with Google" checkbox (yes, you have to do this every time you open Address Book. Somehow it remembers your username and password though) (3) Right click the MobileMe sync in the top menu bar. "Sync now". (4) Log out of Google Mail. (5) Log back into Google Mail. Done -- your contact change is in Google.

Adventure in Serenia

2010-06-08T13:57:00.005-05:00

I wonder if my parents or my brother remember me playing this classic in the basement in Livonia, Michigan on our IBM PCjr. I sure do. One of my earliest computery memories.

Motivators: Mapping my brain

2010-06-05T10:21:00.002-05:00

Deadgirl

2010-05-18T13:53:00.006-05:00

From: Jay Hannah
Sent: Tuesday, May 18, 2010 12:36 PM
To: Andria Hannah
Subject: movie

Oops, I forgot. Put 'Deadgirl' somewhere Zach won't find it. Not appropriate.

Thanks,

j

From: Andria Hannah
> Okay. Did mention to him on Sunday to watch the other movies
> we rented and that one was a flat out no from him. So we
> lucked out.

From: Jay Hannah
> I'm very disappointed in your judgment that you let ME watch it.
>
> My mother will be calling you.

From: Andria Hannah
> That bad huh? Was is scary?
>
> So to add to my “Do not let Jay do…..” list, I will include
> looking at the dollar shelf.

From: Jay Hannah
> Um, no it was... um...
>
> Let's just say I don't want Zach thinking about zombie sex
> slaves.
>
> waaaaaaaay off the "how to treat women" planet for any 13
> year old.
>
> Or 34 year old.

From: Andria Hannah
> Got it. Maybe that should be back in Family Videos
> “secret room”.

From: Jay Hannah
> Well, it's definitely not porn.
>
> It's just... um...
>
> Give it watch and you tell me what it is. :)
>
> In it's defense, the only guy that lives to the end is
> the only guy that doesn't use the dead girl as a sex
> slave... So I guess it should be in the romantic comedy
> section. :)

Catalyst and Quality Assurance bliss

2010-05-13T17:59:00.004-05:00

I've fallen in love with website testing. Again. Catalyst and WWW::Mechanize are awesome. The scenario below takes several monotonous and error prone minutes to QA as a human, or several seconds as a series of automated tests. New feature + test coverage == Joy!!

$work[0] test count is back over 3,000 again and Hudson is keeping an eye on everything for us every 30 minutes. Very cool.


$ perl -Ilib t/avail_book_SG-autoenroll_cancel.t 
[debug] Statistics enabled
1..21
ok 1 - GET http://localhost.omnihotels.com/
ok 2 - Content-type:
ok 3 - title>
ok 4 - Select a City
ok 5 - No errors
ok 6 - !- BEGIN: om/rr/RR1_2.tt -->
ok 7 - !- BEGIN: om/rr/RR1_3.tt -->
ok 8 - !- BEGIN: om/rr/RR1_4.tt -->
ok 9 - !- BEGIN: om/rr/RR1_5.tt -->
ok 10 - Res ID(s) are 40002401426
ok 11 - SG number 62379458 created by sg_auto_enroll checkbox
ok 12 - click Activate Account Password & Preferences
ok 13 - !- BEGIN: om/sg/SI4.tt -->
ok 14 - submit SI4 (form fields should have been defaulted for us)
ok 15 - !- BEGIN: om/sg/SI3.tt -->
ok 16 - submit SI3
ok 17 - !- BEGIN: om/sg/SG6.tt -->
ok 18 - GET /?Phoenix_state=clear&pagedst=RR2
ok 19 - !- BEGIN: om/rr/RR1_5.tt --> Retrieved 40002401426 for cancellation
ok 20 - Click 'Cancel Reservation'
ok 21 - Reservation 40002401426 cancelled
------------------------------------------------
$ cat t/avail_book_SG-autoenroll_cancel.t 
use Test::WWW::Mechanize::Catalyst 'Phoenix';

use strict;
use Test::More tests => 21;
use FindBin qw($Bin);
use lib "$Bin/lib";
use phoenix_test;

my %SI3_args = (
   loginName => ('jhannah' . time),
   password  => 't123',
   EMAIL     => 'jhannah@omnihotels.com',
   Question  => 'CITY',
   Answer    => 'Shmomaha',
);

my $mech = Test::WWW::Mechanize::Catalyst->new;
my $pt = phoenix_test->new(mech => $mech);

my $cro_resno = $pt->book(sg_auto_enroll => 'on');
my $msg = qr/Your Select Guest number is (\d+)/;
my ($sgnum) = ($mech->content =~ $msg);
ok($sgnum,                                    
   "SG number $sgnum created by sg_auto_enroll checkbox");

$msg = 'Activate Account Password & Preferences';
$mech->follow_link_ok({text => $msg},
   "click $msg");

my $msg = '!- BEGIN: om/sg/SI4.tt -->';
$mech->content_contains($msg,                 $msg);
$mech->submit_form_ok({},                     
   "submit SI4 (form fields should have been defaulted for us)");

my $msg = '!- BEGIN: om/sg/SI3.tt -->';
$mech->content_contains($msg,                 $msg);
$mech->submit_form_ok({
   with_fields => \%SI3_args,
},                                            "submit SI3");

my $msg = '!- BEGIN: om/sg/SG6.tt -->';
$mech->content_contains($msg,                 $msg);

$pt->cancel($cro_resno);

Science can answer moral questions

2010-05-08T11:40:00.004-05:00

Listened to this on my iPod yesterday. Watched it on YouTube today. Very powerful if you let it sink in.

Science can answer moral questions

I like this piece a lot more than when he spends most of his energy attacking religion. I already agree with him on most of that material, so it's far less interesting to me and too aggressive for my comfort.

Far better to focus on positive changes in science rather than "that over there is patently stupid."

Wind tunnel workplace

2010-04-29T09:34:00.004-05:00

Arrived at work this morning and the front doors were locked (odd) and one of them was propped open with a sign (odder). The lobby was filled with a loud metallic rattling / vibration sound. I stared up towards the noise as other slightly confused people wandered around also wondering what was going on. Both elevator doors were slightly open even though the elevator cars were not on this floor. (Someone could have fallen into the shaft if they decided to try a little?)

An annoyed management type appeared and told us that the power company had done something this morning (this wasn't our fault, she assured us defensively) which knocked out the "air handlers." She didn't seem to know really what that meant and wasn't in the mood to try to explain anything to the likes of me.

Attempting to head to my office the next security door had a green light (unlocked), but still wouldn't open. It took some serious tugging to gain entry. The hallway was like a mild wind tunnel. Not enough pressure to really effect people, but plenty to effect the doors on both ends. One held shut, the other held open by the pressure. In the next hallway, directly connected to my office, was more whistling of air in a hurry to get elsewhere. Many office doors propped open with trash containers. Home remedy attempts to lessen the noises?

Outside there's only a slight breeze today.

I obviously have no idea how modern architecture works. This is not a special air pressure building as far as I know. I had no idea buildings of this size (8 stories) need powered "air handler" units or the whole building goes a little wacky.

Portland's marketplace of ideas... in Omaha

2010-04-13T08:47:00.004-05:00

In Portland tomorrow night:

Robert Buels presents "The Amazing Miracle of DBIx::Class"

Rob will give an introduction to and overview of DBIx::Class. It's an object-relational mapping framework, much better than the old Class::DBI, and it will make your life easier if you are currently writing a lot of SQL in your Perl.

In Omaha tonight:

Randal "merlyn" Schwartz (who lives in Portland) presents "Forget the ORM! Persistent Data with non-traditional databases."

What an Object-Relational Mapper is, why it sucks, and a couple dozen alternatives (most open source, many with Perl bindings).

Gratuitous Moosey ego stroking

2010-04-07T11:51:00.006-05:00

The Godfather of Moose gave me mad shout-outs on his blog for some minor tweaking I did to the Moose website.

Later I expressed some of my recent concern about academia, and he offered this sage advice:

11:37 <@stevan> jhannah: go into their lab, climb up on one of the work benches and yell "ANY OF YOU NANCY BITCHES STEAL MY CODE AND I WILL CUT YOU INTO LITTLE PIECES"
11:37 <@stevan> then kick over a few bunson burners and walk out
11:37 <@stevan> they wont bother you in the lunch room anymore
11:38 <@perigrin> stevan did something like this in Art School
11:38 <@perigrin> 'cept s/bunson burners/cerulean blue/
11:38 <@stevan> I offcentered their pots on the wheel

Gource: Programmers as action heroes

2010-04-03T10:44:00.003-05:00

Check out the history of Perl development 1988-present. As you can see, when you speed it up enough and use lots of colors and movement suddenly programming is exciting to watch! (For a few minutes.) :)

They created that with Gource (watch other, even prettier videos).

At $work[0] we have CVS + SVN history back to 2000. It'd be neat to throw Gource against that and see what I (and my coworkers) have been doing with our lives for the last 10 years.

Catalyst::Plugin::AutoCRUD is a sexy beast

2010-03-31T18:42:00.011-05:00

Wow. It took me about 30 seconds to add AutoCRUD to my existing Catalyst application. And now I've got a very shiny web 2.0'y CRUD (Create, Read, Update, Delete) application for all my databases. Double clicking pulls up the edit window.

Yes, this wheel has been invented scores of times over the last 10 years. But boy is this one shiny.

Firefly shot me 51 days into the future

2010-03-22T11:25:00.005-05:00

I feel pretty good about my project this weekend. I used the University of Nebraska Firefly Cluster for a real project for the first time, completing 51.6 DAYS worth of data crunching while I slept between 3am and 9:30am this morning. The code I ran is my fork + branch of a bunch of Perl from Harvard against the latest human genome from UCSC. Masochists can read all the gory details (username: guest password: guest) and suggest improvements.

Computers are pretty cool sometimes. :)

ack is awesome!

2010-03-04T17:08:00.004-06:00

Wow! People have been telling me this for years, but I was getting along OK with my old school Unix craziness:

$ find ./ | grep -v svn | xargs grep '\-\>Promotion'

But today I couldn't get that working. Something with xargs escaping of -> just refused to fly.

So I installed ack and ran it:

# cpan App::Ack
$ ack '\-\>Promotion'

And it found what I was looking for with zero fuss!

Control/SG.pm
335:      $self->Promotion($promo_hash);

View/Web/Phoenix/lib/Phoenix/Controller/SG.pm
2844:      $c->log->debug("you have these PromotionCode's already: " . (join ", ", keys %{$sg->Promotion}));
2846:      unless ($sg->Promotion->{$preauth}) {

Holy buckets! That is AWESOME! Thanks Andy!

Pipeline evolution - again!

2010-02-19T20:46:00.003-06:00

It evolved again! This too, shall pass. :)

Actor Colin Firth on meditation

2010-02-18T05:38:00.006-06:00

WHYY in Philadelphia, Terry Gross, Fresh Air, Feb 3 2010:

Starting at 28m mark.

Did you practice meditation?

Not seriously. I just tried to learn to be quiet a little bit. I actually went to a monastery. A Buddhist monastery to learn something about meditation. I have never practiced it with any great discipline, but I did find it to be, even in its probably shallowest and least-disciplined form, I did find it to be somewhat helpful because however fortunate my lifestyle is, it is not always the most restful.

What made you go in the first place to the Buddhist monastery? What did you want?

Restfulness. I've always been very attracted to the randomness and the unpredictability of my profession. I enjoy not knowing what's next. I enjoy the passionate commitment to something that is going to be gone soon. It's a strange creative promiscuity if you like. Where I move on to the next thing and commit myself with equal immersion and delight in something as if the one before just never existed. I think it's very exciting, but it can create this kind of upheaval because there's no continuity. And however thrilled I am by what I'm doing. However stimulated I am by it, it can be difficult to get back to a sort of a core. One of the things you're doing is taking on different people's lives. You're changing character. You're changing personalities. I find it's not always easy to shake them off. Before you shake one off you're taking another one on. I think for an actor getting back to a sense of who you are without all of that I think can be quite a challenge.

This was about 15 or so years ago. There was quite a bit of upheaval on a personal level. I was single at the time and it seemed that I was always at my happiest when I was employed -- I think there's something perfectly healthy about that -- but I was always happiest when I was engaged in something that was distracting me. I think it was, I felt it was time to discover how to celebrate life or to take joy in life when I wasn't distracted.

-end quote-

I don't really relate to the upheaval sentiment. And I'm not an actor. But the constantly distracting myself sentiment resonates with me. It's too bad the interview ended there. I would have liked to hear more about what meditation taught him, and how.

I consider it most likely that mine is a brain chemistry problem. Probably most expeditiously corrected with medication, not years of monastic study. But I have yet to solve that riddle, so don't know for sure. Stay tuned. I should get this one figured out sometime in the next 40 years or so.

Pipeline evolution

2010-02-16T09:26:00.006-06:00

Over the last couple of weeks I've been writing and changing a bunch of software trying to answer some research questions. I find the visual evolution of this pipeline interesting. Maybe you will too.

Sneak peak of the first chart:

$76M? Thanks Catalyst!

2010-02-10T11:38:00.002-06:00

Woot! Catalyst, our favorite Perl web development framework, served us well in 2009:

Over $76 million in revenue was booked through omnihotels.com, a 13.5% increase over the previous year; 460,902 room nights were booked during 2009, representing a 28% increase.

...so complex that you need a large IDE to comprehend it

2010-02-06T11:19:00.002-06:00

This is an excerpt from an Omaha.pm thread today.

We're discussing Eliminating Inheritance Via Smalltalk-Style Traits by Curtis "Ovid" Poe.

In his paper, Curtis wrote:
Anyone forced to use "vi" (not even "vim") while trying to create an emergency patch of broken code over a slow telnet connection at 2:30 in the morning is going to get very irritated if your codebase is so complex that you need a large IDE to comprehend it.

Trey wrote:
That is kind of silly. If you're shop is using IDE and developing under that sort of framework, your support people should be familiar with the code and the methods used to program it/maintain it.

Agreed. And have the capacity to perform emergency maintenance remotely via whatever means are necessary to do so.

I don't think he's arguing that slow Internet connections are a good idea. I think he's saying they happen.

Trey wrote:
That's sort of like saying that somebody is going to be irritated because they can't stoke up a hydroelectric plant with bellows...So what??

I love your analogy. :) So what? So your business is losing money in the scenario he describes.

I see this an indictment of relying too heavily on fancy developer tools to gloss over crappy code. If my code sucks in text form, but when I right-click on it a million lines of code in my IDE jumps to my rescue and explains it to me in pretty colors, then I'm helpless without that IDE. That sounds like a bad idea.

In the stack of technology ignorance and dependency I've planted my flag here:

- I don't really know or care about sub-atomic particles.
- I don't really know or care how electrons flow through conductors.
- I don't really know or care about chip design.
- I don't really know or care how hard drives, memory, and monitors actually work.
- I don't really know or care how the Linux kernel works.
- I don't really know or care how perl is written (in C).
- I don't really know or care how most of perl's core packages work (in Perl/XS/C).
- I don't really know deeply or care how most of the CPAN modules I use work (in Perl/XS/C).
- I know EXACTLY how the text of the Perl I wrote works. I do recursive grep's through text files to find out anything I need to know.
- Syntax highlighting is a crutch for the weak.
- Method auto-discovery is a crutch for the weak.
- Per-keystroke debugging is a crutch for the weak.
- Re-runnable images of crashes are a crutch for the weak.
- All that other fancy crap in your IDE is fancy crap I don't need. For the weak. :)

Objectively, my gut-opinions about exactly where that line is are silly. Aren't they?

If you take me and my Apple laptop running Terminal.app to ssh into a server and run vi, and next to me you sit a .NET guy running the latest Visual Studio on a mapped drive; is the total complexity of my dependency stack much smaller than his? (OS X is how many millions of lines of code?)

I don't know. I've now spent an hour arguing with myself about it. :)

In any event, I don't thing it's the use or avoidance of an IDE that makes good or poor code. You can create beautiful or ugly code with the simplest or fanciest of tools.

I do think he has a point. If your "...codebase is so complex that you need a large IDE to comprehend it." Then you're doing something wrong. Use an IDE because you want to, not because it's impossible to survive your mess without it.

/me shakes his fist at XML Spy addicts

Ponder,

j

Omaha's First-Ever Catalyst Workshop: Success!

2009-12-14T22:18:00.002-06:00

And there was much rejoicing!

I thoroughly enjoyed presenting the workshop. Thanks for coming! We'll have to do it again (or an advanced / specific topics version) someday soonish?

See you in January!

I'm suing Facebook

2009-12-13T09:09:00.003-06:00

Great. Now I'm suing Facebook for an application I've never used or even heard of, and it's up to me to opt out via snail mail.

It's disgusting how many leeches on society are getting rich off of me and millions of my fellow citizens who are defaulted and locked into (or at least penalized if we try to extract ourselves from) things unless we take action against them. I'm looking at you Wall Street, 401K, IRA. I'm looking at you, class action lawyers.

If you want to get rich being a slimeball, fine. But leave me out of it.

Incidentally, did I mention that it's annoying that a typo on a store credit card application 2 years ago has destroyed the credit history of MY social security number? That too, I find distasteful.

Bah! Humbug!

Omaha's first-ever Catalyst Wed Dev Workshop

2009-11-12T07:14:00.001-06:00

Trying a new format at next month's meeting:

http://jays.net/wiki/Catalyst_Workshop

Wish me luck! Should be fun. :)

Future Perl snuck up on me

2009-11-04T21:06:00.005-06:00

Apparently I'm out of touch. Look at all this Perl6:: stuff implemented in Perl5. For example, Catalyst uses Perl6::Junction.

And Moose is starting to look like Perl7 to me. Here perigrin explains what this code is doing.

These ain't your momma's Perl. Heck, these ain't even 2005's Perl. :)

Collision: Is Religion Absurd, or Good for the World?

2009-10-23T10:11:00.002-05:00

Last fall, we went on tour debating the topic "Is Religion Good For The World?" Our arguments were captured on film for a new documentary, Collision. Are our morals dictated to us by a supreme entity or do discoveries made by science and reason, make Atheism a natural conclusion? You decide.

Religion Is Absurd
by Christopher Hitchens

Religion will always retain a certain tattered prestige because it was our first attempt as a species to make sense of the cosmos and of our own nature, and because it continues to ask "why". Its incurable disability, however, lies in its insistence that the answer to that question can be determined with certainty on the basis of revelation and faith.

We do not know, though we may assume, that our pre-homo sapiens ancestors (the erectus, the Cro-Magnons and the Neanderthals, with whom we have a traceable kinship as we do with other surviving primates) had deities that they sought to propitiate. Alas, no religion of which we are now aware has ever taken their existence into account, or indeed made any allowance for the tens and probably hundreds of thousands of years of the human story. Instead, we are asked to believe that the essential problem was solved about two-to-three thousand years ago, by various serial appearances of divine intervention and guidance in remote and primitive parts of what is now (at least to Westerners) the Middle East.

This absurd belief would not even deserve to be called quixotic if it had not inspired masterpieces of art and music and architecture as well as the most appalling atrocities and depredations. The great cultural question before us is therefore this: can we manage to preserve what is numinous and transcendent and ecstatic without giving any more room to the superstitious and the supernatural. (For example, can one treasure and appreciate the Parthenon, say, while recognizing that the religious cult that gave rise to it is dead, and was in many ways sinister and cruel?) A related question is: can we be moral and ethical in our thoughts and actions without the servile idea that our morals are dictated to us by a supreme entity?

I believe that the answer to both of these questions is in the affirmative. Tremendous and beautiful things have been achieved by science and reason, from the Hubble telescope to the sequencing of the DNA of obscure viruses. All of these attainments have tended to remind us, however, that we are an animal species inhabiting a rather remote and tiny suburb of an unimaginably large universe. However, this sobering finding -- and it is a finding -- is no reason to assume that we do not have duties to one another, to other species, and to the biosphere. It may even be easier to draw these moral conclusions once we are free of the egotistic notion that we are somehow the centre of the process, or objects of a creation or a "design". Dostoevsky said that without belief in god men would be capable of anything: surely we know by now that the belief in a divine order, and in divine orders, is an even greater license to act as if normal restraints were non-existent?

If Moses and Jesus and Mohammed had never existed -- let alone Joseph Smith or Mary Baker Eddy or Kim Jong Il or any of the other man-made prophets or idols -- we would still be faced with precisely the same questions about how to explain ourselves and our lives, how to think about the just city, and how to comport ourselves with our fellow-creatures. The small progress we have made so far, from the basic realization that diseases are not punishments to the noble idea that as humans we may even have "rights", is due to the exercise of skepticism and doubt, and to the objective scrutiny of hard evidence, and not at all to faith or certainty. The real "transcendence", then, is the one that allows us to shake off the notion of a never-dying tyrannical father-figure, with its unconsoling illusion of redemption by human sacrifice, and assume our proper proportion as people condemned to be free, and able to outgrow the fearful tutelage of a supreme supervisor who does not forgive us the errors he has programmed us to make.

***

Atheists Suck at Being Atheists
by Pastor Douglas Wilson

From the perspective of a Christian, the refusal of an atheist to be a Christian is dismaying, but it is at least intelligible. But what is really disconcerting is the failure of atheists to be atheists. That is the thing that cries out for further exploration.

We can understand a cook who sets out to prepare a reduction sauce, having it simmer on the stove for three days. But what we shouldn't get is the announcement afterwards that he has prepared us a soufflé. The atheistic worldview is nothing if not inherently reductionistic, whether this is admitted or not. Everything that happens is a chance-driven rattle-jattle jumble in the great concourse of atoms that we call time. Time and chance acting on matter have brought about, in equally aimless fashion, the 1927 New York Yankees, yesterday's foam on a New Jersey beach, Princess Di, the arrangement of pebbles on the back side of the moon, the music of John Cage, the Fourth Crusade, and the current gaggle representing us all in Congress.

If the universe actually is what the materialistic atheist claims it is, then certain things follow from that presupposition. The argument is simple to follow, and is frequently accepted by the sophomore presidents of atheist/agnostic clubs at a university near you, but it is rare for a well-published atheistic leader to acknowledge the force of the argument. To acknowledge openly the corrosive relativism that atheism necessarily entails would do nothing but get the chimps jumping in the red states. To swallow the reduction would present serious public relations problems, and drive Fox News ratings up even further. Who needs that?

So if the universe is what the atheist maintains it is, then this determines what sort of account we must give for the nature of everything -- and this includes the atheist's thought processes, ethical convictions, and aesthetic appreciations. If you were to shake up two bottles of pop and place them on a table to fizz over, you could not fill up an auditorium with people who came to watch them debate. This is because they are not debating; they are just fizzing. If you were to shake up one bottle of pop, and show it film footage of some genocidal atrocity, the reaction you would get is not moral outrage, but rather more fizzing. And if you were to shake it really hard by means of art school, and place it in front of Michelangelo's David, or the Rose Window of Chartres Cathedral, the results would not really be aesthetic appreciation, but more fizzing still.

If the atheist is right, then I am not a Christian because I have mistaken beliefs, but am rather a Christian because that is what these chemicals would always do in this arrangement and at this temperature. The problem is that this atheistic assumption does the very same thing to the atheist's case for atheism. The atheist gives us an account of all things which makes it impossible for us to believe that any account of all things could possibly be true. But no account of things can be tenable unless it provides us with the preconditions that make it possible for our "accounting" to represent genuine insight. Atheism fails to do this, and the failure is a spectacular one. Nor does atheism allow us to have any fixed ethical standard, or the possibility of beauty.

It does no good to appeal to the discoveries made by science and reason, for one of the things that reason has apparently brought us is atheism. Right? And not content to let sleeping dogs lie, reason also brings us the inexorable consequences of atheism, which includes the unpalatable but necessary conclusion that random neuron firings do not amount to any "truth" that corresponds to anything outside our heads. This, ironically enough, includes atheism, and so we find ourselves falling out of the tree, saw in one hand and branch in the other.

Contrast this with the Christian gospel -- God the Father is the Maker of heaven and earth. He sent His Son to be born one of us; this Son died on gibbet for our sins, as the ultimate and final human sacrifice, and He rose from the dead on the third day following. Having ascended into Heaven and taken His place at the right hand of His Father, He sent His Holy Spirit into the world in order to transform it, a process that is still ongoing. Now obviously, this is a message that can be believed or disbelieved. But the reason for mentioning it here includes the important point that such a set of convictions makes it possible for us to believe that reason can be trusted, that goodness does not change with the evolutionary times, and that beauty is grounded in the very heart of God. Someone who believes these things doesn't believe that we are just fizzing.

You can deny that this God exists, of course, and you can throw the whole cosmos into that pan of reduction sauce. And you can keep the heat on by publishing one atheist missive after another. But what you should not be allowed to do is cook the whole thing bone dry and call the crust on the bottom an example of the numinous or transcendent. Calling it that provides us with no reason to believe it -- and numerous reasons not to.

Read more at: http://www.huffingtonpost.com/christopher-hitchens/collision-is-religion-abs_b_326673.html

Term::ProgressBar

2009-10-08T09:29:00.003-05:00

Here's a super easy CPAN module I started using last week. Ever have a long running process that a human is watching, and you want to add a progress bar? Here you go!

use Term::ProgressBar;
my $progress = Term::ProgressBar->new({
   name  => 'MySlowThing()',
   count => 100,
   ETA   => 'linear', 
});
$progress->max_update_rate(1);

for (1..100) {
   sleep 1;
   $progress->update($_);
}

Gives you a nifty ASCII timer bar with major and minor movements, updating clock, the whole nine. :)

MySlowThing():  26% [====        *     ]1m16s Left

GraphViz prettyness

2009-09-13T08:39:00.005-05:00

My first mapping of bioinformatics alignment score to how dark a GraphViz line should appear, and switching colors based on other criteria... Perl++ GraphViz++

I don't think it's very informative, but there's no denying it's pretty. :)

Just A Throw Away Line

2009-08-13T08:15:00.005-05:00

It's fascinating to me how serendipitous life often is. We just attended a week long World Religions Encounter, including hour upon hour of lectures and site visits for exposure to beliefs ranging from Wiccan to Zoroastriansim, and of all the things said and experienced there the thought that struck me most forcefully came from a casual comment made by a fellow conference-goer during a bus tour: "The larger our island of knowledge, the longer the shore of uncertainty."

The end of the scientific pier

2009-07-31T11:06:00.001-05:00

"We've entered into this very difficult space. Where we have learned enough to know that we know much less than we thought."
--Robert Krulwich, After Life, Radio Lab, WNYC

Perl, Catalyst: $100M in sales this year

2009-07-30T20:55:00.005-05:00

If I'm reading this spreadsheet correctly, it appears our $work website is on pace to book just shy of $100 million this year. Thanks Linux, GNU, Apache, Perl, CPAN!

Open source: A cast of thousands paying my mortgage, one patch at a time. I'm glad I can pitch in in small ways too! :)

Chiselling chunks off of BioPerl

2009-07-17T15:26:00.005-05:00

There's been renewed conversation about breaking BioPerl up into smaller distributions. I'm trying to help, citing the Catalyst development model as an example of how the world could be better.

For some values of 'better'. -grin-

perl5 introspection (thanks Moose!)

2009-06-17T08:41:00.002-05:00

Many dynamic languages have a way to get a list of all methods for an object built into them.

I don't think perl5 does. But Moose adds it. :)

$ cat j.pl
package X;
use Moose;
sub dosomething1 {}
sub dosomething2 {}
sub dosomething3 {}

package main;
my $x = X->new();
print join ", ", sort $x->meta->get_all_method_names;
print "\n";

$ perl j.pl
BUILDALL, BUILDARGS, DEMOLISHALL, DESTROY, DOES, does, 
dosomething1, dosomething2, dosomething3, dump, meta, new

Neato. :)

More info on Moose: http://moose.perl.org

Perl, Template Toolkit, and GraphViz

2009-05-18T06:50:00.010-05:00

Our largest Catalyst application (ssl.omnihotels.com) is composed of 184 templates. I get lost sometimes while template diving, and forget the parent node(s) of my current node.

Inspired by The Perl Review Issue 4.1, I decided to give GraphViz a stab. To my surprise, I got it working very quickly. I wrote a quick CGI hack that lets me click on any of my templates from a list on the left, and it draws an INCLUDE diagram of all downstream templates for me. Here's a screen shot of the CGI in action:

Pretty slick, huh? Here's what it drew for our wrapper.tt, which is the parent of many of our templates:

You could throw the same crude implementation at any tree, really. I think I'll try all the use statements in our in-house perl code base next. :)

The source code is here: http://github.com/jhannah/sandbox/graphviz. Enjoy!

wget mysqltuner.pl

2009-05-05T13:32:00.002-05:00

Oh, that's cute. The DNS domain mysqltuner.pl is set up to a redirect to the text version of the program mysqltuner.pl. I hadn't seen that trick before. :)

mysqltuner.pl is a pretty slick little program with color ASCII output to give you a quick rundown of the status of, and suggestions of how to improve, the health of your MySQL databases. I like it. :)

Tweak the Perl regex engine: assign to pos()

2009-05-03T16:36:00.004-05:00

OK, Perl is way too cool.

I was minding my own business, searching for every occurrence of 'CCAGC' in E-coli, when I hit a snag. Several hundred of my known locations weren't showing up.

Why? Because the Perl regular expression engine, by default, starts searching for the next occurrence of something after the end of the occurrence it just found. This is what most humans want. But you may notice that in the string 'CCAGCCAGC' the thing I'm searching for ('CCAGC') overlaps itself, so the regex engine doesn't see the second one.

"Crap," I thought.

But this is Perl -- maybe there's a way? 30 seconds in the documentation (perldoc -f pos) and it said I could assign to pos(). Really? Sweet! Problem solved!


#!/usr/bin/perl

use strict;

open (IN, "E_coli.seq");
my $seq = <IN>;
chomp $seq;
close IN;

my $find_this = 'CCAGC';
while ($seq =~ /$find_this/g) { 
   my $start = pos($seq) - length( $find_this ) + 1;
   my $stop  = pos($seq);
   pos($seq) = $start;
   print "   Found $find_this at [$start..$stop]\n";
}

Two of Life's Greatest Joys

2009-05-01T05:11:00.005-05:00

I think in their heart of hearts each parent hopes that their children will be like them. After all, they usually invest a great deal of energy throughout the child-rearing to "raise them up right" (that is, "right" as the parents interpret it). That only makes sense: if you're an idealist, say, you naturally hope your kids will have high ideals.

But what the parenting manuals fail to mention is that the greatest blessing kids bring may not be the ways in which they resemble or emulate you, but in the ways they differ from (and may even challenge) you. Their interests, their life views, their choices, their knowledge--all these, and more, are often "beyond" you, that is, they are often beyond your understanding AND beyond your life experience. As they mature, this becomes increasingly evident. It seems ever more true, as Gibran writes of children:

You may give them your love but not your thoughts,
For they have their own thoughts.
You may house their bodies but not their souls,
For their souls dwell in the house of tomorrow,
which you cannot visit, even in your dreams.
You may strive to be like them, but seek not to make them like you.
For life goes not backward nor tarries with yesterday.

The poet likens this life process to archery, the parents being the bow and the children the arrows. It's an image that gives me great joy as I see my sons see and do things beyond my ken, but not beyond my love for them.

Swirly bacteria

2009-04-27T11:14:00.005-05:00

Spent yesterday drawing pretty pictures of bacterial genomes with Perl, BioPerl, and R. Given the genetic sequence of different bugs (ACCTGTCGATGCTA...) we're looking for fingerprints in the composition of those sequences. Pick out the 200 most frequest 5-letter "words" (oligos), sort and plot those, and maybe we can see the fingerprint of each bug.

It seems to work. The black line is E. coli., which is very different from Staph. aur. (red and green) and Staph. epi. (blue). You'll also notice that the 2 Staph aur. lines are very close to each other, since they're almost identical; they're very similar to yet distinct from Staph. epi; and distant from E. coli.

Cool, huh? The details (username: guest, password: guest)

Einstein for dummies... wait, a little less dummy please

2009-04-02T13:41:00.006-05:00

Strangely, even after 30 minutes on Wikipedia, I still don't understand quantum mechanics.

I'm trying to figure out how/why my shiny new faster-than-light radio can't work given that all my quantums are entangled and I've got the "spooky" knob on my action at a distance cranked all the way up.

The Simple English Wikipedia tries to help but falls short. I need some of Albert's pre-tween publications or something? :)

Dilbert moment

2009-03-27T11:02:00.001-05:00

Can't help laughing at this email from $coworker. Spooky similarity to far too many of my own emails recently. :)

I don't know who needs to coordinate the work or who needs to do what so if whoever needs to lead the charge can coordinate with whoever needs to do whatever else, I would appreciate it.

How Death Lost Its Fear

2009-03-17T08:49:00.001-05:00

How Death Lost Its Fear
By Jack Marinchek Platinum Quality Author

Guess what? I found out the answer to the mystery of death. The problem is I don't have any way of verifying the answer. But so what? The road to wisdom and knowledge often times doesn't lead to all answers. Right?

I may get a lot of people mad at me when I publish this article. "So what", I say. For sure the Grim Reaper is mad at me. Probably some religious people that believe they have all of the answers, also. I can live with that.

Let me explain quickly why I have chosen the subject of death to write about. During the last two years I have had three life threatening major surgeries. Honest. Don't misjudge me. Prior to this, I have never really been sick in my life.

The docs say the effects of smoking don't normally catch up to someone until he hits his 70's. I smoked two packs a day for thirty five years. So, you figure it out.

Well anyway, I had a ruptured appendix, cancer in the appendix and colon, life threatening radiation poisoning, (part of the cancer treatment), and carotid artery blockage (90%). With all of that stuff behind me, I now feel fit as a fiddle.

I work out six days a week. I am a 2nd Degree Black Belt (Tae Kwon Do). You can't hold me down. I will turn 72 years of age this December. Like I got energy to burn.

I have become a very relaxed and easy going person. I love and relish life. Each day is very exciting for me. Why? One reason is because I keep getting answers to all of the questions I have been asking myself for the last seventy years.

You know, simple down to earth questions we all ask ourselves. Things about life and living. "What's it all about Alphie?"

Now that I have a genuine appreciation of my mortality, I can't help but wonder what happens when death arrives? I have always been very comfortable with the concept of dying. Actually, it's no longer a theoretical concept for me. No sir. It's a forthcoming and shadowing reality.

Well, I am an oft and on church goer. I am religious in a spiritual sense. I don't drive myself nuts about "dotting the I's and crossing the T's" of religious doctrine. "Live and let live" is my model.

Maybe you would like to know where I am coming from? I'll give you a hint. I am a student of world religions and I am a big fan of Huston Smith, "The World Religions". With this in mind, you can appreciate the fact that I have a hard time with the concept of One True Religion. From my viewpoint, all of the World Religions are the True Religion.

Where does this leave us regarding the discussion of death. In terms of possibility thinking, I believe the Ultimate Reality can be no reality. In another words, "you get oblivion...nothing."

On the other hand, according to the Myths and Theologies, you may get your "heaven", whatever that may be. Frankly I am not worried about it.

Who knows? Maybe "hell" will work its way into this ultimate reality. You never know for sure, right? Come on Mr. Death.

Here's what I think happens when we meet death. We get exactly what we think we will get or "expect". Why not? This law of expectation seems to be operating quite perfectly on this planet Earth. Just check out the power of Belief, positive thinking, miracles, you know, the whole package of "the Secret".

For that matter, let's keep it simple. Just look at the phenomenon of medical testing. Scientists have given research objects fake and real drugs. Some of these pills have medical healing effects and others have zero healing effects in them.

In most cases, people who take the empty pills feel "healed" or better just like the people who take the real "McCoy". The point being, the power of belief and expectation can knock your socks off.

Two world celebrated religious Leaders, Jesus and Buddah, were known to have exhorted people on how to get what they want out of life. Jesus, "Truly I tell you, if you have faith the size of a mustard seed, you will say to this mountain, 'Move from here to there,' and it will move; and nothing will be impossible for you."

Let's not forget His Reverence, the Buddah, "A monk who is skilled in concentration can cut the Himalayas in two."

Scientists have proven how the power of thoughts can effect human beings and physical matter thousands of miles away from the person who is sending "the positive thought". God help us, it can also be a negative thought. But anyway, I think you get the picture.

We get in life exactly what we believe. Unfortunately many people don't know how to work with the powerhouse dynamite SubConscious Mind that we all possess. I really don't know either, for that matter. At least not in perfect sense. Joseph Murphy, " the Power of Your Subconscious Mind", will give you a good idea for starters.

We can't knock religious people. If it works why not use it? Again, the medical community has proven that religious people have a high tolerance for sickness and frustration. In another words, as group, religious people seem to be less affected by the normal calamities of living. Maybe it's because we get what we expect.

Maybe the key to living life the best we can, is to have honest to goodness dynamic positive expectations. Like the "street reality" language of "money talks and bs walks".

Maybe, the Ultimate Reality is much simpler then we think. Scientists have proven with special photography that things, animate and inanimate, that die don't disappear. Their "energy" force continues to exist. This is measured by different colors this energy emits. Check out Kirlian photography.

Ok. We have had our discussion on death and the power of expectation and belief. Many years ago, I was in the hospital room of my dying father. He was dying from Hodgkin's disease. He was a regular church going guy. And, he took his religion seriously.

Anyway, when my dad was dying, I remember him saying to me, "Those streets are beautifully lined with gold." You see, he saw heaven just like it was told to him in his Bible. God love him, he believed it. He died right after that. There was no fear of death for this guy.

So, in conclusion, I believe we all get what we expect to get, both in this life and very possibly in the Next. Goodbye Mr. Fear. And, so long Mr. Death. We are no longer partners.

p.s. Kiss off Grim Reaper.

Jack Marinchek is the publisher of the site, http://standforyourgreatness.com/, which features- inspirational information on life improvement, getting jobs and income, travel, and real estate relocation

Article Source: http://EzineArticles.com/?expert=Jack_Marinchek

SICI (Search for IntraCellular Intelligence)

2009-03-17T07:01:00.008-05:00

Much like SETI (Search for Extra-Terrestrial Intelligence), I spent all day yesterday searching protein sequences for periodicity using chemical property filters, entropy, Fourier transformations, and R.

None of the ~80 graphs I generated looked like an old dude with a beard...

deafferret on Twitter

2009-03-10T14:24:00.001-05:00

Anyone following this blog might also want to keep up with me as deafferret on Twitter. That's my micro-blog. (Each post 140 characters or less, posts more frequent than this blog.)

Genome center information management

2009-03-04T18:59:00.001-06:00

Awesome.

More awesome: I actually understand what he's talking about and why nowadays. I've come so far. :)

A carbon atom and four hydrogen atoms

2009-03-02T07:17:00.007-06:00

Spent all of Sunday tying DNA methylation data into my JCVI project. Another classic battle inside my brain:

I'm fascinated by everything we (humanity) knows about this process, and the fact that sitting in Omaha, NE on my laptop, my mentor and I can harness that information, creating millions of data points in a database of my design using software I wrote. What a wondrous time we live in, flush with opportunity to explore the universe.

I'm repulsed by the ambiguity of the datasets we work with. How can we not know what's actually happening? What's the point of me gathering a million possibilities? How is drowning in maybes helpful? My brain panics! Call me when we can know something!

Science seems to be about spotting and exploring trends in noisy data. My computer programmer brain likes on and off, black and white. Trends are tough for me to swallow. This recurring theme convinces me that I make a good scientist's side-kick, and a lousy scientist. :)

Awe-stricken, and Inspired

2009-02-28T07:04:00.003-06:00

We went with dear friends Thursday night to Broadway Across America's production of "Cirque Dreams," an event somewhat indescribable but roughly a hybrid of music, drama, and circus. The sets, costumes, and lighting were incredible, depicting jungle life both day and night. But the jaw-dropping centerpiece was the "Oh my God!" artistry and skill of the performers. Seeing the contortionists in a jumble of backwards heads-touching-toes configurations, watching the strong men create a massive pyramid of bulky strength, holding your breath as trapeze artists suspended one another far overhead by grip of ankle and wrist...how truly in-credible! This is the second such performance I've seen, each of which left me with two main after effects: one, gratitude for the gift of artistry, be it motion and choreography, or sight and sound; and second, the challenge of knowing that only those willing to truly discipline and devote themselves at an exceptional degree are "free" to offer such gifts. I am inspired to find the artistry of my own life and honor it by fuller expression. Therein, methinks, lies the joy.

A Poem to Ponder

2009-02-28T07:02:00.000-06:00

What I Believe

by Michael Blumenthal

I believe there is no justice,
but that cottongrass and bunchberry
grow on the mountain.

I believe that a scorpion's sting
will kill a man,
but that his wife will remarry.

I believe that, the older we get,
the weaker the body,
but the stronger the soul.

I believe that if you roll over at night
in an empty bed,
the air consoles you.

I believe that no one is spared
the darkness,
and no one gets all of it.

I believe we all drown eventually
in a sea of our making,
but that the land belongs to someone else.

I believe in destiny.
And I believe in free will.

I believe that, when all
the clocks break,
time goes on without them.

And I believe that whatever
pulls us under,
will do so gently.

so as not to disturb anyone,
so as not to interfere
with what we believe in.

"What I Believe" by Michael Blumenthal, from Days We Would Rather Know. © Pleasure Boat Studio, 2005. Reprinted with permission.

An Ode to Snow

2009-02-28T06:46:00.003-06:00

The snow is falling this morning, with about an inch on the ground since we went to bed last night. How amazing the way it transforms the view from our window! No wonder some call it a "blanket"--the earth, bare and parched most of the winter, now looks like it's snuggled beneath a downy quilt. And the top of each tree limb is pillowed in white. So peaceful. And so quiet in the pre-dawn hour, the only sound the soothing coo of a solitary mourning dove. The scene has brightened some as the sun begins to rise, but millions of snowflakes hold the warming rays at bay as they join their brethren to create out of grey sameness a black-and-white contrast that reveals the world in its essential shapes and forms. "How silently, how silently, the wondrous gift is given!"

Optimism

2009-02-24T07:04:00.000-06:00

I really liked today's entry in The Writer's Almanac:

Optimism

by Jane Hirshfield

More and more I have come to admire resilience.
Not the simple resistance of a pillow, whose foam returns over and
over to the same shape, but the sinuous tenacity of a tree: finding the
light newly blocked on one side,
it turns in another.
A blind intelligence, true.
But out of such persistence arose turtles, rivers, mitochondria, figs—
all this resinous, unretractable earth.

"Optimism" by Jane Hirshfield, from Given Sugar, Given Salt. © Harper Collins, 2002. Reprinted with permission.

Can You Copter This?

2009-02-21T22:06:00.002-06:00

Hey, check out the artistic symmetry of Copter Dude navigating the ups and downs of his private stairwell...

Counting letters is simple, right?

2009-02-17T16:39:00.004-06:00

Fun brain twister. Stumped our entire department!

How many letter F's appear below?

   FINISHED FILES ARE THE RE 
   SULT OF YEARS OF SCIENTI 
   FIC STUDY COMBINED WITH 
   THE EXPERIENCE OF YEARS...

Email your answer to jay(at)jays(dot)net.

Anger and grief

2009-02-16T07:10:00.003-06:00

Note to future self: When both you and your spouse are grieving on the same day with two separate focuses you need to be extremely vigilant about your emotions. Intense anger feels real, but is actually a defense mechanism against your sadness. The anger becomes a needle which will eventually burst the grief balloon and you'll finally realize what was actually going on. If possible, try to recognize the real root emotion sooner rather than later. You'll both be better off.

Reinventing the wheel for fun and profit

2009-02-14T10:55:00.008-06:00

I was all proud of myself last week and impressed the other kids when I wrote an amino acid property converter in about 15 minutes.

$ perl properties.pl TLPDILHASGPPGPPGQPEQPGAGR
               small 1011000111111111010011110
            aromatic 0000001000000000000000000
           non_polar 0100111101001001000001110
                tiny 1000000111001001000001110
             charged 0001001000000000001000001
           aliphatic 0100110000000000000000000
            positive 0000001000000000000000001
               polar 1001001010000000101100001

Little did I know that mine was inferior to Bio::Tools::OddCodes, which I could have downloaded for free in about 1 minute.

But, in my defense, not knowing that tool existed it would have taken me longer to find it (not knowing what I was searching for) than to write my own from scratch.

And as a programmer, it's far more fun and satisfying to spend 15 minutes solving a problem and impressing people than to spend 15 minutes searching the Internet for something you may never find.

So perhaps reinventing the wheel is good for morale sometimes. Trivial wheels, at least. :)

Where were YOU when it happened?

2009-02-13T17:44:00.005-06:00

1234567887jhannah@klab:~$ perl -e 'print time'
1234567887jhannah@klab:~$ perl -e 'print time'
1234567888jhannah@klab:~$ perl -e 'print time'
1234567888jhannah@klab:~$ perl -e 'print time'
1234567889jhannah@klab:~$ perl -e 'print time'
1234567889jhannah@klab:~$ perl -e 'print time'
1234567890jhannah@klab:~$ perl -e 'print time'
1234567894jhannah@klab:~$ perl -e 'print time'
1234568608jhannah@klab:~$

I'll never forget this day... -sniff!-

http://www.1234567890day.com/

Called my nerd friend Josh to see how his 1234567890 party was going (woooo!! wooo!!) and he forgot this was today. He's in Hawaii with his wife and kid totally missing out. As I sat alone in my cubicle surrounded by my nerdly giggling I couldn't help feeling sorry for him. What a loser.

Endnotes for Earnie

2009-02-05T19:56:00.003-06:00

After the memorial celebration, Earnie, we returned home and gathered (where else?) around the island in your family kitchen—the centrifugal center of comfort and warmth. I’d been thinking about your railroading hobby, which was illustrated during the service and was so evident in the living room nearby—train sets, time tables, photos, and the like.

“I’ve been wondering,” I asked, “whether Earnie would have been a railroad engineer, or a conductor?” I explained my idea of the engineer as the driving force—he fires the engines, throttles up, and lets ‘er rip. I think of the conductor, on the other hand, as the overseer—he punches out details, worries that the train runs on time, makes sure folks get where they want to go. I hardly got the question out before your wife and your eldest child both replied, nearly in unison, “Both!” We all laughed, and sensed that you would have laughed right along with us. So much to do, so little time.

I don’t know just what will happen to your To Do notebooks now, Earnie. I imagine they will be cherished mementoes of your vision and passion. After these several days with your dearest friends and family I’d been thinking a lot about the guiding traits of your life and have arrived at two that seemed most evident in the stories told by friends and family. One is “irrepressible enthusiasm”—a child-like zest for life, for living large. The other is “forever possibilitizing”—the visionary quality of Don Quixote as he sallied forth on both adventure and misadventure, always dreaming the impossible dream. I can only think that even now you are “about your Father’s business” in that same spirit.

Whatever happens to your To Do lists, I’m assured of one thing. Having been welcomed into the homes and lives of your beloved wife and children, there’s no doubt that you’ve passed along the Earnie DNA of humor, drive, and compassion that will live on through them. Coupled with the singular Marilyn DNA, your children, grandchildren, and all who follow in your line will surely lead lives both exceptional and contributive. I see each of you in each of them, and I know the circle of life continues.

What I don’t know is why your life ended so soon. Wouldn’t it have been better for all if you’d seen your grandkids grow up, if you’d taken more trips with Marilyn, if you’d been around longer for Susanna, and John, and David? As I said at your memorial, death is an inscrutable Mystery. But I trust you now know more about all this than I do. And I trust, as you did, in Love as the eternal reality undergirding even that which we cannot see.

I regret we didn’t spend more time together in these years since college. I’m going to check out that “Bucket List” movie and watch it again, because there’s something Earnie-like in there about friendship and life and death I need to hear again—something about living life to the full, whether it be a single day or many years. In this and many other ways I’ll remember you, and will be looking to the time spoken of in Genesis, when in Zion we shall again embrace and rejoice together, in that blessed union of souls. (Kind of a “Graceland Forever” sort of thing.)

I look forward to our adventuring once again, in God’s due time. Meanwhile, I am comforted by the thought of Robert Browning, who wrote, “Ah, a man’s reach should exceed his grasp, or what’s a heaven for?”

I’d tell you to “Rest In Peace” but somehow that just doesn’t fit. So instead I’ll just say what you might tell a railroad conductor/engineer: “Ever Onward!”

Using the G Word Again

2009-02-05T19:41:00.005-06:00

Here's a column I wrote for KC Star's "Midwest Voices," which didn't get published there but by golly now it sees the light of day on Head Rattle:

When our economy melted down like an ice cream cone in July, hardly anybody asked why we were holding that triple-scooper in the first place. We just kept licking furiously as it ran down our arm, looking around sheepishly for some way to clean up the mess.

Let’s get real. We have a super-size problem because we’ve developed a super-size appetite. Like that guy who tried living on a fast food diet for thirty days, saying Yes every time he was asked, “Would you like that super-sized?” The unhealthy consequences are a cautionary tale: Super-size U.S.—Coming Soon to Economies Everywhere!

It’s even affected our appetite for housing. The average American home today is twice the size of homes in the ‘50s. Why? Because we have twice as many children? Hardly. Actually we have far fewer children. So why do we have these humongous home mortgage love handles?

In all the blaming after the meltdown a long-forgotten word gained new currency. Well, two words, actually, melded like red-hot lava: “corporate greed.” Yes, yes, cried the angry horde. They are to blame, those greedy corporations! Down with them, the greedy CEOs!

True, grasping corporations and CEOs who think they’re worth 400 times their workers need a day of reckoning, and may it come soon. But once we’ve removed “corporate” from “corporate greed,” we’ll be face-to-face with, well, ourselves.

Dare we mention the Seven Deadly Sins these days? Few could name them, much less recall in our profit-driven world that Greed is key among them. And even those in the so-called Dark Ages who would have known what we have apparently forgotten: Greed is the Mother of all Sins.

Theologian Phyllis Tickle posted a remarkable essay on this topic in Beliefnet’s “Sin Series”. World religions have declared for centuries that avarice is the root of all evils, she notes, but our national motto has become “United in the Sin of Avarice.”

It’s a painful realization. The majority of us are stockholders these days, either individually or through retirement plans, and lots of us work for corporations. So these are our greedy CEOs, our greedy corporations. And those are our maxed-out credit cards, our wastrel politicians, our gas-guzzling SUVs.

Lots of us hopped on this roller coaster for the giddy ride up; now we’re all going to take the downward plunge together. So go ahead: scream all you like.

Bushed No Longer

2009-02-05T18:09:00.003-06:00

I'm ever so slowly adjusting to the change in presidential leadership. For eight years I've felt our nation has been hijacked by an alien ideology that has undone much of the gains of recent decades. When the American public re-elected Bush for a second term I first felt disbelief, followed by a prolonged period of grief. Now I'm beginning to warm to a sense of hope, ever so slowly.

I couldn't quite describe my feelings until I read the account of Garrison Keillor, who attended President Obama's inauguration. He described the crowd's "profound silence" when Bush's presence was announced, and the "low and heartfelt rumble of booing" when Cheney appeared. All this contrasted sharply with the jubilant roar of the crowd when the Obamas appeared. There was, however, a later roar for the Current Occupant:

"When the chopper lifted up above the Capitol and we saw it in the sky heading for the airport, a million jubilant people waved and hollered for all they were worth. It was the most spontaneous, universal moment of the day. It was like watching the ice go out on the river."

That's the perfect metaphor to describe how I'm feeling these days: like the ice going out on the river.

Mother Dear

2009-01-28T09:46:00.002-06:00

It was the sort of thing real Moms just do, so subtle it’s taken me several days to really catch on. While her four sons were home last weekend, in her 85th year, Mom quietly bequeathed to us each a piece of our heritage, a part of her legacy.

I first noticed mine lying on the piano bench: a stack of artwork I created as a child. They were mostly things I would have brought home from school—art projects large and small, some crude in earlier years, some more refined later on. A bit yellowed and brittle, they were long-forgotten, yet strangely familiar, like hearing a snatch of a song from long ago that you can’t quite put a name to but later find yourself humming over and over.

Leafing through the stack, I could easily imagine why Mom might have saved some of them all these years. Several were Mother’s Day cards, like the one with a bouquet of colorful tulips on the cover and a message inside written in my best nine-year-old longhand: “You are the best mother in all the world. Love, Jim.” The card from the previous year showed that as an eight-year-old I was still writing in block letters, but with a beginning sense of rhyme and verse: “Mother’s Day is here. I love you Mother Dear.” Apparently I made not just one, but two, cards that year, the other reading “I love you Mother Dear. I hope you don’t shed a tear.” I read those words with a jolt of recognition. In recent years, intentionally but for no conscious reason, I have begun calling Mom “Mother Dear.” To read that same term of endearment in my own handwriting from more than fifty years ago gave me a keen sense of déjà vu and a renewed connection to the child I once was.

The earliest of Jimmy’s Mother’s Day collection was when I was six years old: a tissue-paper bouquet on the cover, and inside a native American canoe and tipi with an orange moon overhead, and the simple inscription, “Mother.” As I examined the cards more closely I noticed that Mom had inscribed the year of their creation on each one, much as an artist would date a completed work. And then I began to understand why the personalized Mother’s Day greetings were only a small part of a much more extensive preservation project that also included “My Animal Book,” “My Circus Book,” “My Bird Book,” and “My Abraham Lincoln Book.” Why would she have saved all these things, even those not made expressly for her?

Then I realized: these art works weren’t primarily about her, the recipient. They were primarily about us, the creators. She cherished us, and our accomplishments. We were all “keepers,” as an angler might say—and that’s the way it’s always been. Through these many years she’s held us dear, sacrificed for us, valued our gifts, and called forth our best. These yellowed and tattered works of crayon and construction paper are emblematic of a lifetime of encouragement, of devotion, of endearment.

When Mom sat down at the piano on the morning we left and played a medley of familiar songs I realized anew where her sons gained their love of music. As the notes washed over me, and as John, the eldest, recorded it all on video, it seemed that life had come full circle. Now we yearn to preserve her music, her memories, her contributions. We want to keep them safe in a treasured space deep in our heart. And some day, we hope to pass them on to our children, so they in turn can and pass them on to theirs, in the great circle of life.

Here truly is our heritage, and our legacy—to know ourselves beloved, and to love.

Jim Hannah
January 27, 2009

Cloth physics, genetics research

2008-12-31T07:21:00.004-06:00

peterthomas introduced me to this interactive cloth physics demonstration via Twitter. It's awesome. Click it!

This is what I was hoping my bionerdary would reveal. Perhaps the rules of biology are very complex, but as you discover them useful patterns emerge, systems are revealed, and eventually you can actually do useful things.

I'm not quitting, but I think I've lost hope that genetics research will reveal itself in the useful way cloth physics does in my lifetime. Perhaps biology is too complex for my feeble mind. Perhaps it is too complex for the collective efforts of all of humanity to encapsulate effectively. Or perhaps, long after I'm dead, our children will pull up little "curing cancer" simulators on their computers and wonder what took us so long.

In any event, my desire to witness tangible progress arising from my daily/monthly work seems a poor fit for the current state of the art in mankind's attempts to grok biology via computers.

2008-12-29T08:38:00.002-06:00

The daily poem from Writer's Almanac recently delivered what may be my very favorite poem of the Christmas season. As is the case so often, it's being aware of the commonplace and "ordinary" that so often brings epiphany, even in the parking lot of Wal-Mart:

Coming Out of Wal-Mart

by Mark DeFoe

The child, puny, paling toward albino,
hands fused on the handlebars of a new bike.
The man, a cut-out of the boy, gnome-like,
grizzled, knotted like a strange root,
guides him out, hand on the boy's shoulder.
They speak, but in language softer than hearing.

The boy steers the bike as if he steered
a soap bubble, a blown glass swan, a cloud.

On the walk they go still. Muzak covers them.
Sun crushes. The man is a tiny horse,
gentle at a fence. The boy's eyes are huge
as a fawn's.

He grips hard the orange and pink,
and purple and green striped handlebars,
smiling the fixed sweet smile of the sainted.

"Coming Out of Wal-Mart" by Mark DeFoe,
from The Green Chair. © Pringle Tree Press

Hidden Markov Models

2008-12-14T18:59:00.007-06:00

Great quote from Cryptogenomicon:

David Lipman commented that the only thing that made HMMs interesting was their name - there’s something’s hidden, and a Russian is involved.

Read more about HMMs.

Not only is that hilarious, but his 95-page HMMER Users Guide includes such indispensable sections as "How to avoid reading this manual" and "How to avoid using this software (links to similar software)".

As scientists go, you gotta love this guy. :)

Warren in route to Antarctica!

2008-12-14T08:40:00.002-06:00

My wife's father Warren has left our home sweet home in Nebraska, USA corn fields to fly to the other side of the globe and is currently steaming towards Antarctica. I drew a Google Map.

Today he's "at Sea" (that's all the official itinerary says for 9 of the 17 days of the cruise -laugh-). He has left the Auckland Islands, heading towards Macquarie Island.

First Snow

2008-12-09T11:29:00.002-06:00

From my writer's desk at the second story window, I have a bird's eye view of the back yard and the season's first snow. It has come, as it so often does, quietly, blanketing the earth with a hush. The hum of traffic is muffled, the only sound a wind chime stirred by a breeze that also flutters the few remaining leaves that cling to maple and magnolia; the oak and ash are long since bare. The floor of the tree house is covered now in white, and the garden has only a few dark patches where leaves show through. Small drifts have formed on the roof of the garage, and occasional gusts cause it to swirl upward, then fall to the earth below. An occasional squirrel scampers across the yard, and earlier I saw one mourning dove on its usual perch a few feet away, but for the most part the wildlife seems to have taken shelter as if in protest of temperatures that have dipped into the thirties when yesterday they were in the fifties. I mowed the yard then, and had to remove my jacket; today only a few wheel marks show for my labors, and they are fast disappearing.

The blanket of quiet and snow has covered me with serenity. I sense that beneath the often-frantic pace of life there is a season calling me to quiet reflection as a balance to my usual frantic doing. And I'm reminded that the ingredients of peace are very basic: shelter, food, clothing. Today I have all these, plus the warming glow of raspberry tea and the quiet hum of a MacBook Pro. I'm a blessed man.

Feels good, makes no sense

2008-12-04T06:45:00.006-06:00

I keep mulling over this chant from The Great Debaters that I watched last night.

Who is the judge?
The judge is God.
Why is he God?
Because he decides who wins or loses. Not my opponent.
Who is your opponent?
He does not exist.
Why does he not exist?
Because he is a mere dissenting voice of the truth I speak!

It feels powerful. Yet my brain can't help picking it apart, and it doesn't seem to fit in my head.

The judge is God? What is this God thing? How does that response answer or clarify anything?

God decides who wins or loses? Not my opponent? And not me? If God decides and God is all powerful then I'm just a puppet of God's whim, aren't I? So I don't control anything? Why are my actions and decisions important then?

My opponent does not exist, but he's a dissenting voice? But "a dissenting voice" would exist. As a voice. That dissents. Dissenting the truth I speak? On my debate team? Where someone decides on a coin flip which side of an argument I am to take? So the coin flip always lands on truth whenever it decides which side I am to take? What if I argue both sides? My opponents are always lying? Even when they take both sides?

Artsy stuff tends to do this to me. My emotional brain is fascinated by these shiny trinkets so it keeps picking them up, again and again, for reconsideration. But my analytical brain (which is dominant) can't make heads or tails out of those cryptic "answers".

Space junk

2008-11-19T06:42:00.002-06:00

Reading about space junk this morning because an astronaut lost a briefcase-sized tool bag yesterday.

Great reader comment from waldo:

They demoted Pluto from the list of planets because it hadn't
cleaned up it's orbit. If this littering keeps up we'll have to demote earth too.

YAY! CHESS!

2008-11-12T07:13:00.005-06:00

Received this pic in an advert from wholesalechess.com today.

This images totally resonates with me. This is exactly what a typical Omaha Chess Club meeting looks like. And the hot pump-wearing chess groupies are always clamoring to ride in the carts when we all go out chess shopping before and after every meeting. Sneaky chess paparazzi must have been hiding in the bushes since we didn't issue any press cards last month.

Jealous much?

2008-11-11T19:17:00.002-06:00

In case you didn't know, I married a hottie: The Nexus Team

Scroll right to the Andrias. :)

Undead source code

2008-11-08T09:57:00.006-06:00

I wrote a little web tool in 2000 while Justin Hopkins was interning with me. I used it for a couple months, then forgot about it. Then, suddenly:

On Jan 14, 2005, at 2:47 PM, Wayne & Susie Griswold wrote:
> Jay, where's my friend the Optimal Bitmask Thingy?
> I can't live without it and the link doesn't work anymore!

-laugh- Someone uses that? I fixed the link.

Then I forgot about it again.

On Nov 6, 2008, at 5:46 PM, Wayne & Susie Griswold wrote:
> Jay, it's been a few years, but when I went looking for my
> favorite bitmask tool, the Optimal Bitmask Thingy, it was
> gone!!! Can you make the link work again? Please?

-laugh- Raised from the dead again:

Jay's IP Optimum Bitmask Thingy

Justin and Josh might get a kick out of the fact that this tool
refuses to die, 9 years later. :)

Enjoy. :)

Why don't municipalities SAVE, then spend?

2008-11-08T09:51:00.003-06:00

To: planetmoney(at)npr(dot)org

Hi guys. I love the Planet Money podcast. Maybe you can help me understand this.

It seems so simple. Yet I never hear anyone talk about it.

David(?), near the end of the Wisconsin/Ireland/Germany podcast:
"There is a tragedy here too. Over the last 30 years there have been a series of financial innovations that have just been plain good. They have allowed city governments, local governments to get money more cheaply."

Every year a million finance professionals invent new, complex ways to enrich themselves without actually producing anything. Every such web will eventually collapse under the weight of collective greed.

...

So why don't cities and individuals SAVE money, THEN spend it?

Why don't we all do this?

I hope you can help me understand. :)

Thanks,

Jay Hannah
Omaha, NE
http://jays.net

Dream job? Pass.

2008-11-07T11:58:00.004-06:00

I don't understand me.

17 months after starting my part-time adventures in genetics research (showing up at the medical center 3 days a week), I am now trying to find someone else with my skill set to take this job on, full time. I'm not leaving, but apparently I don't really want this gig full time either.

I think it's the money. Plus the current lack of some big, computationally extensive pipeline for me to wrestle every day and be the expert on. I like knowing big balls of code inside and out, and having people need me for high powered data nerd ninja action. Plus the lack of other people like me sitting here. Lack of coworkers is depressing.

Or maybe it's just the money.

YOU are rich

2008-11-07T11:20:00.006-06:00

How do so many Christians take so much of the Bible seriously and ignore this one?

It is easier for a camel to go through the eye of a needle, than for a rich man to enter into the kingdom of God. (Matthew 19:24)

If you're going to believe the Bible it seems to me that perhaps women will be fine, but if you're male and have Internet access (rich!), then you're in trouble.

Right?

Entering the Bloggersphere

2008-10-30T16:59:00.002-05:00

It is said that once you expand your world you cannot return to the self you were before crossing over. So it is for me with "blogging". It reminds me of my pet grandmice as they are placed carefully into their exercise ball. As they move forward, taking what must seem to them normal steps, that colorful little sphere careens forward at incredible speed. In a flash they are propelled across the room. Unless good fortune heads the projectile down the hallway (certainly the vermin have no control of it), the outcome is .....Yikes! Who put that wall in my path?
Ok. I'm in the bloggersphere. Taking the first step now.....
Traveler

The Restless Tide

2008-10-24T17:48:00.001-05:00

Through the years I’ve often read poems and sung songs about the ocean’s “restless tide,” but until we stayed overnight at Maine’s Little River Lighthouse its meaning never really connected. That reality began to soak in as our little boat ferried us to the island at high tide, our guides explaining that the dock would be high and dry during low tide. We were told that the water level here varies as much as 28 feet between the tides, and this twice a day!

From the moment we set foot in the boat until we disembarked a day later we were surrounded by the ocean’s ebb and flow, an incessant surround sound somehow both soothing and unsettling—soothing in its rhythmic regularity, unsettling in its chaotic churning.

For an Iowa farm boy like me the constant spew of foam and spray had no parallel; even the wind was more buffet than breeze. I began to think about how different must be the life outlook of an Iowa farmer and a Maine fisherman. What would it be like to cast your net upon the restless sea rather than plow straight furrows in terra firma? How would it differ to rely on a daily catch rather than a single autumn harvest? And does it take more courage to gamble daily on the vagaries of the ocean, or to risk it all on one big jackpot?

I’m thinking that for hardiness and courage the edge likely goes to the Mainian, although for sweat and grit the Iowa farmer comes right alongside. Either of them, in comparison to a city-dweller, is to be envied for a living connection with land or sea, and the courage to embrace a love that both gives and takes away.

Noah's Ark

2008-10-24T17:44:00.001-05:00

Buzz Carver has been on the ocean since childhood, and has spent the last twenty years as a full-time lobsterman off the coast of central Maine. Last Tuesday night he took four of us Midwesterners out to sea so we could get some sense of the vocation that claims him and his father before him. He only ran a dozen or so lobster traps for our benefit, rather than the 250 he might haul in a routine work day. But it was enough to get a pretty good sense of what he does all day long, year-round.

It’s a pretty basic routine: boat out to any one of his more than 700 lobster traps, marked by a bright pink-over-yellow buoy. Snag the rope with a hooked gaff, lashing it to a hydraulic winch to bring it alongside. Haul the metal trap aboard and remove the lobsters inside (measuring each one carefully, tossing back males that are too small and females designated for breeding). Empty the mesh bag that holds the old bait and replace it with new salted herring. Then throw the trap back overboard and head for the next one.

It used to be they stopped lobstering in the winter, but now the catch goes on year-round. The difference in the colder months is that Buzz travels to more distant sites, up to thirty miles from his bayside home. It’s hard and sometimes dangerous work, but as his boat cuts through the water, throwing plumes of foam from the prow, as he pulls alongside a rocky isle to point out a family of seals, as the seagulls circle overhead and the sun begins to set in crimson colors…Well, this is obviously a man who has found an enviable merger of vocation and avocation.

Never mind that the price paid by Canadian-controlled processing plants plummeted this week from $4 a pound to $2, that acts of trap vandalism and pilfering are on the increase, that it costs $100 to purchase each trap and the accompanying gear, that state and federal fishing regulations are often inconsistent and inept.

Buzz is a Maine lobsterman, and hopes to always be. And his son, Noah? Suffice to say that when Buzz was finally able to buy his first new boat a year ago he didn’t name it for his wife Suzanne, as customary. Instead, painted on the stern is a scripture passage from Genesis, and in larger letters the name of his craft: Noah’s Ark.

A year in the life?

2008-10-24T11:30:00.003-05:00

-ponder- I guess this "Integration Candidates" page I just made is sort of a list of possibly general use tools I've worked on over the last year... : BioCMS (RT username: guest, password: guest)

Shrink, episode 1.5.1

2008-10-15T07:48:00.008-05:00

I've come up with a new theory about the dynamics of my motivation system.

As long as I can remember I've had a bordering-on-maniacal obsession with efficiency in my work. Computer programming is a great way to try to fill this hole: everything is off or on, black or white, efficiency gains can all be measured objectively and quantitatively (this program runs 26.4% faster than this other program). My work (lines of source code) is easily presented to other people, proving that I performed difficult labor. Tangible gains can by proven on a daily basis.

I need a plan. I need a direction. I need structure. I need to attack problems. I need to see myself progressing. I need to prove to myself, and anyone else who cares, that I am succeeding. Every day.

In science most substantive things take months or years. It's hard to prove that you're making substantive progress daily, weekly, even monthly. It often (to me) feels like floundering around hopelessly, grasping with overly educated guesses at various straws while blathering incessantly¹.

My new theory goes something like this: My pattern of mental self abuse² has taught me that if I can't prove that I made tangible progress today, then I haven't, and I'm a slacker. This feedback system declares the vast majority of academia a monumental waste of time. School is massively inefficient because it attempts to broadly prepare you for future challenges, many of which may never happen.

So the feedback loop in my head, every day in chemistry, goes something like this: "Why am I attempting to memorize factoid number 700? I'm never going to use this, and I've already forgotten most of the factoids so far. Why are you sitting here? You suck at this." My mental defenses kick in, saying "but I'm good at programming. I can prove it. Look at my paychecks! Look at my source code!"

Hopefully this spring semester I can break that feedback loop and be OK with investing, in a massively inefficient manner, "in myself." By knowing and forgetting more chemistry. And math. To get the degree. Which may be good to have. Someday.

Because this week I realized some of it does stick. Listening to a JCVI genius present 4 hours of material this week, he threw out some key words I never would have loosely understood without that semester of chemistry. 5 months later I do remember the gist of a few nuggets of what I learned through that book I can't help hating. (I'll just keep telling myself that 5% sticks and that's OK. -laugh-)

So, through constant meditation and daily affirmations maybe I can survive getting this degree. In the year 2014 Zach will be out of high school and maybe I can try out a "dream job" w/ JCVI or NCBI or something...

I guess we'll find out. :)

1. Hyperbole. But you get the gist.
2. My shrink rated me a 10 on a 10 scale. That surprised me. :)

Shady Characters

2008-09-25T20:37:00.003-05:00

Here's one of my very favorite picture of the beloved and I, snapped by brother Lynn as we adjusted an umbrella during the Michigan graduation fete last spring...a candid moment of togetherness.

Pedal On!

2008-09-25T17:36:00.003-05:00

After several years of cycling I finally signed on for an organized ride. I'm hooked! It was great having a new route, all mapped out, with stops for snacks and lunch, plus a whole mob of other enthusiasts to chat up as we stood in line at the porta-potty. By the end of the day we'd pedaled 49.5 miles, and my biking buddies were urging me to consider riding the MS 160 next years. I just may do it...the immediate goal being a 61-mile ride in my 61st year.

Bulbs, Bulbs, and More Bulbs

2008-09-25T17:23:00.003-05:00

Some five years ago my friend Sam Rose gave me 150 or so day lilies; recently I dug them up to give them some growing space. How incredible the increase! I still had my 150 plants, but also mailed a boxful to Sam in Arizona and to Brother John in Nebraska, plus gave a wheelbarrow full to friends Bud and Mark. Mother Nature, thou art one prolific lady!

Monarch Reveries

2008-09-25T16:36:00.004-05:00

For several years I've been on the lookout for a caterpillar of the monarch butterfly, with no success. I've even allowed milkweeds to grow in our fence row--the host plant around which the monarch life cycle revolves. Still no caterpillars (except for the plastic one my jokester neighbor planted). Then a few weeks ago as I was digging up the day lily bed there it was, the zebra-striped green-white-and-yellow crawler remembered from my childhood, when the Hannah boys grew them by the score. Fantastic! I transplanted it to the milkweed, where it began at once eating voraciously, just as I remembered. Then two days later it disappeared. I thought a bird must have eaten it, since usually they form their cocoon right on the milkweed. Bummer. Then a day or so later I happened to glance to the side as I was going up the back steps and there he was, our caterpillar, suspended upside-down, curled up in the beginning of a new life stage. Within two days the familiar gold-rimmed pale-green cocoon formed, and in my daily comings and goings I watched for signs of hatching out, only to come home one evening to find that my friend had taken flight. I didn't get to see him on the wing, but my imagination soared as I thought of his long journey to winter in Mexico. All of which has brought me to a new item on my Bucket List, joining the migration to see the wintering site firsthand. I've seen small monarch clusters in Iowa and in Michigan; how amazing it would be to see entire mountainsides robed in flutters of orange and black!

Guns, or Butter?

2008-09-25T16:30:00.003-05:00

We shared in a United Nations peace vigil last Sunday. A display by the American Friends Service Committee (the Quakers) illustrated the cost in human life exacted by the war in Iraq—142 pairs of combat boots, each one representing a soldier from Missouri or Kansas killed in the war to date. A few pairs of civilian shoes were interspersed with the boots, representative of the hundreds of thousands of Iraqis who have likely died in the war (but whose deaths we don’t tally, being only collateral damage).

And then there’s the financial cost of the war. Pointing out that one day of the Iraqi war costs $720 million, a series of banners fluttered the message that we could have instead done any of the following:
• Provided a $1,700 health insurance policy for 423,529 children
• Granted 4-year scholarships of $20,000 to 34,904 state university students
• Hired 12,478 elementary school teachers at $57,000 each
• Provide renewable electricity for 1,274,336 homes at $565 each
• Offered Head Start to 95,364 kids ay $7,550 per kid
• Built homes for 6,482 families at $111,000 each
• Provided free school lunches for 1,153,846 kids at $624 per year
• Built 84 new elementary schools at $8.5 million each
• Offered healthcare to 163,525 people at $4,400 per year

In just nine days of Iraq war expenditures we could do ALL of the above. Imagine what could be done with five years of war expenditures! Surely a trillion dollars should have bought us more than it has. (Unless you’re Shell Oil, who this week opened the first Western-owned oil company office in Iraq since 1972, when the nation’s oil supplies were nationalized. Now there’s a great investment!)

Decades ago President Eisenhower lamented that each bomb built is at the expense of needed social services, and in his 1961 farewell address to the nation he sounded a prophetic note of caution, saying "In the councils of government, we must guard against the acquisition of unwarranted influence, whether sought or unsought, by the military industrial complex. The potential for the disastrous rise of misplaced power exists and will persist. We must never let the weight of this combination endanger our liberties or democratic processes. We should take nothing for granted. Only an alert and knowledgeable citizenry can compel the proper meshing of the huge industrial and military machinery of defense with our peaceful methods and goals, so that security and liberty may prosper together."

Evidence that this counsel went unheeded is reflected in the words of Martin Luther King, Jr., speaking six years later about the Vietnam War and the spirit of militarism, saying “A nation that continues year after year to spend more money on military defense than on programs of social uplift is approaching spiritual death.”

Ask not for whom the bell tolls…

Improve your vision today! Remove your glasses!

2008-09-24T09:02:00.002-05:00

Hopped on the motorcycle this morning in heavy fog. Odometer: 7777. After about 3 seconds I couldn't see through my visor. Visor up. After 3 more seconds I couldn't see through my glasses. Glasses off.

Shitty vision + heavy fog + your body IS the crumple zone? Bad Idea.

Either I've never pulled that trick before, or I've forgotten. Eyelids are the best windshield wipers ever. Next time I'll bring contacts or Lasik eye surgery with me. :)

Windows Is Shutting Down

2008-09-22T07:30:00.001-05:00

Windows is Shutting Down

by Clive James

Windows is shutting down, and grammar are
On their last leg. So what am we to do?
A letter of complaint go just so far,
Proving the only one in step are you.

Better, perhaps, to simply let it goes.
A sentence have to be screwed pretty bad
Before they gets to where you doesnt knows
The meaning what it must be meant to had.

The meteor have hit. Extinction spread,
But evolution do not stop for that.
A mutant languages rise from the dead
And all them rules is suddenly old hat.

Too bad for we, us what has had so long
The best seat from the only game in town.
But there it am, and whom can say its wrong?
Those are the break. Windows is shutting down.

"Windows Is Shutting Down" by Clive James from Opal Sunset: Selected poems, 1958–2008. © W.W. Norton & Company, 2008.

Shrink, episode 1.3

2008-09-19T08:15:00.005-05:00

New theory: I have a tape recorder in the back of my head playing my personal mix tape of Greatest Hits of Verbal Self Abuse. I think I constructed this system in high school when I started running 3 miles, 3 nights a week to lose weight to date girls. It motivated the hell out of me. I beat myself mercilessly with a wide array of creative self loathing. By any objective measure, my physical transformation was a great success. Unfortunately I never felt good about any gains I made because I was too busy hating the way I looked, and by extension hating myself, no matter what.

Over the last 18 years I don't think I've consciously recognized that the tape recorder is still back there. Still looping. Now I'm practicing recognizing it. And hitting the off button.

Maybe I can make a new tape. It will have some positive things to say about me. :)

Law and the Long War

2008-09-17T06:57:00.005-05:00

A great book I'm reading: Law and the Long War: The Future of Justice in the Age of Terror. His excellent intro lays out the gulf between the two major opposing perspectives on the Bush administration's actions, and argues for middle ground. So far I'm on the human rights side of the argument and not in the middle ground at all, but I just started the book, so maybe he'll convince me.

Maybe Erin and Pete can find some middle ground too? :)

Shrink, episode 1.2.2

2008-09-13T17:48:00.001-05:00

Huh, nope. I found a counter-example, and my example from earlier is working fine now. Maybe the crazy is sleeping. :)

Shrink, episode 1.2.1

2008-09-13T11:00:00.003-05:00

Fascinating. I am unable to attach any positivity with emotional weight to my own actions. The clinician in my head finds this curious and intriguing. My emotional brain finds these attempts at physical therapy very painful. The clinician watches, enthralled by all the baseless, hyperbolic drama. It wonders why we choose to torture the poor creature.

Shrink, episode 1.2

2008-09-12T11:12:00.002-05:00

I offered my self diagnosis: (1) I have pinned my self esteem on my work for so long that now that my "career path" seems to be sending me through Chemistry (really bad) and Calculus (maybe won't be so bad?) my self worth is taking serious body blows. (2) While politicians have no sense of shame, or can ever point out any mistakes they have ever made, I have the opposite problem. I can tell you 3 things I screwed during my morning commute today.

Sue introduced me to cognitive behavioral therapy and Dr. David Burns 10 forms of twisted thinking. I definitely need work on "3. Mental filter", and "4. Discounting the positive". I'm going to keep a log of my crazy and see what I come up with. :)

Grassius debugus

2008-09-05T12:35:00.003-05:00

Helped a guy at Grassius use -link and Bio/Graphics/FeatureFile.pm link_pattern() today. Yay me! :)

Run on the bank. In reverse.

2008-08-31T08:02:00.006-05:00

I got an email from Kiva today saying that they've made a systems change so that I get Kiva credit back not when a loan has been fully repaid, but every time Kiva receives partial payment back from the field partner. So, suddenly I had a bunch of Kiva credit I wasn't expecting until next year.

Cool! So I hopped out to kiva.org to grab me some more loans, to find that only 3 loans were available to fund. Usually there are hundreds. And those 3 were actually funded already (Kiva is a little laggy about updating loan statuses). So apparently this systems change has suddenly freed up hundreds of thousands of dollars in donor's money, causing a flood of new loan purchases, to the point where they've run out of people to loan money to!

As Jane Sladen said: "kind of like trying to buy Elton John tickets on line - click before they're gone!!"

So here I am with Kiva credit and nobody to loan money to. What a terrific problem to have! This bump is a little weird but I'm sure after a few days the newly improved cash flow of donors will enable Kiva to give more loans, faster overall.

(Hopefully nobody decides to pull their money out instead of waiting patiently for loan opportunities. I'm sure Kiva will soon catch up with the total capacity of their donor pool.)

Watch your spelling, nerd boy

2008-08-23T15:31:00.003-05:00

pixilated -adjective
1. slightly eccentric or mentally disordered.
2. amusingly whimsical, prankish, silly, or the like.
[Origin: 1840–50, Americanism; pix(ie) + (tit)illated]

pixelated -adjective
1. pertaining to a printed image which has been digitized; visible as a pattern of pixels; also written pixellated

We aren't in 1850 any more, Toto.

Midwest tour

2008-08-23T08:27:00.004-05:00

My Geocaching travelbug U. S. Navy (2 of 4) has been making the rounds since April 2006.

The Dark Knight

2008-08-10T22:12:00.003-05:00

Sometimes the movie lives up to the hype, and in my view The Dark Knight is one of those. I find Batman's voice a bit unreal, and the two-face dude (DA Harvey Dent) is totally over the top, but that, I suppose, is understandable since it is, after all, based on a comic. What I did find believable was the dual nature of shadow and light found even in our heroes--a conundrum well expressed in the movie's title. Harvey particularly shows how a "good guy" can go over to "the dark side." This seemed completely believable. Actually Batman himself seems so principled that at times I had a hard time relating to him. In the scene where Batman has a clear opportunity to run down The Joker with his Batmobile but instead swerves and wrecks the vehicle...well, as much as I consider myself nonviolent I think in a case of "him or me" I would have chosen him, the maestro of chaos. Wouldn't you owe it to the public, really? But on the other hand, I sure wouldn't want to return to the days of the vigilante and every man wearing the law on his hip. Ah, yes: paradox again.

Blinded by the white

2008-08-08T07:23:00.002-05:00

Wow. What is Lucky wearing? Perhaps all his TVs have drawn him into The Matrix? Or maybe he's been hanging out with Vin Diesel?

Lock-in, or Lock-out?

2008-08-06T15:16:00.002-05:00

Even after 39 years of marriage, and five years of dating preceding it, there remain variances of perception between my beloved and me that crop up unexpectedly, like the stones heaved up by frost each spring in fields that last fall were clear. They're common things, usually, which makes them all the more unexpected when stumbled upon. The latest came to focus as I was locking the back door as I left for a bike ride. "Oh, don't lock me IN," Sharon said. "I'm not," I replied, "I'm locking others OUT."

The incident was amusing on one hand, and disconcerting on the other. My intent was to take what I considered reasonable security precautions as I left, making it less likely that an intruder might enter the home. What I did for Sharon's protection, however, was received as over protection. She chooses in this, and a number of other matters, to live in what she views as trust rather than fear. Well and good. But the rub comes when my natural tendencies toward security conflict with her desires for risk-taking. If I leave the door unlocked, even at her request, I do so with a nagging sense that I'm not being responsible in my care for her. Part of this is probably selfish: I wouldn't want to live with the guilt in the unlikely event that something happened. But part of it is simply an expression of who I am, and the way I convey care or concern.

I'm reminded of a book title that asks, "Do I Have to Give Up Me to Be Loved by You?" The answer, it seems to me, is "Yes, but..." Yes, I choose to change my behavior often in accommodation to the needs and wishes of my companion, as she does for me. Why else be married, if we both just want to live unto ourselves? Our differences are as vital as our likenesses in our marriage covenant, perhaps more so in creating growth. This is just the nature of relationships, which means allowing the other to have effect upon your life. BUT if I give up too much of my self to be in relationship with another, then I'm not really being true to myself, or offering to the other the gift of my uniqueness.

My beloved and I have bumped into this paradox repeatedly throughout the years, so much so that we have posted on our bedroom dresser this passage from Leviticus 19:34-- "The alien who resides with you shall be to you as the citizen among you; you shall love the alien as yourself."

Seeing Through Glass, Darkly

2008-08-06T13:18:00.001-05:00

How are we ever going to really “go green” here in the US without an integrated approach to conservation and the environment? A case in point: last year it was possible in Independence to recycle glass containers, either by paying the trash hauler or by taking it to a recycling center. Today you can do neither. Why? The official explanation is that is no longer “economically viable” to recycle glass, since its major ingredient—sand—is so readily and inexpensively available.

I think of that explanation with distress every time I now throw away glass after several decades of trying faithfully to “reduce, re-use, and recycle.” It seems so obviously short-sighted to consider only the cost of glass manufacture when determining “economic viability.” What about the cost of hauling the stuff to a landfill, maintaining the landfill, and creating new landfills? Oh, that.

Well, if you throw in all THAT expense just maybe it might be a viable option. But industry doesn’t look much beyond the bottom dollar for their investors, and government doesn’t look much beyond re-election by the taxpayers, and neither looks much beyond the press of immediate issues, so who cares all that much about a few tons of glass bottles?

Years from now, when people are mining our landfills to reclaim the treasured resources we’ve squandered, what will they think of us? Surely seeing all our discards, not the least of which will be glass, they’ll view us as fools and wastrels.

Warts and All

2008-08-06T13:12:00.002-05:00

Our bath house at Morris Park has two seemingly permanent occupants. Nearly every time I open the door and turn on the light I’ve learned to look in the corner for Tom and Tess—a pair of toads who seem to find the dark and the damp, crawling with insects, an ideal home.

The names were Sharon’s doing. Although I’ve long respected toads for their role in gobbling up insects harmful to the garden, I’ve never before been on a first-name basis.

Observing them, it’s difficult for me to see the infatuation children’s writers seem to have for these lumpy creatures. They seem to do very little other than sit around waiting for lunch to crawl by, and if you pick them up they pee on you. Hardly adorable traits. Nor do they seem particularly wise as sometimes depicted in children’s books; this particular pair seems barely able to keep from being squished in the door as it opens and closes.

Maybe I just haven’t had a sufficiently long-term association out of which new perceptions might arise. Karen Stark, who came over for campfire foil meal tonight, says she once had a toad that seemed to enjoy being petted—even turning over on its back to be stroked on the stomach! They’re not like frogs at all, she hastened to assure us.

So I guess tomorrow I’ll quit with the tip-toe, hands-off approach and see if I can form a more lasting relationship. Maybe I can at least quash the persistent urban legend that humans give you warts.

Postscript: This morning only Tess remained in the bath house, squatting in the center of the shower drain. Tom apparently was off hunting and gathering, as all good males are wont to do. By afternoon, Tess had also departed, which I take to mean that my twice-daily intrusions may have led them to choose a less-frequented neighborhood. Ah, the challenges of inter-species dialogue!

Fawn Memories

2008-08-06T12:58:00.003-05:00

One more step and I’d have literally stumbled upon it. While dutifully cutting brush in the middle of an Iowa field, eyes scanning for the next nuisance weed, I glanced down just in time to stop mid-stride. Curled into a tan-and-white ball, hidden in the knee-high grass, was a lone fawn, lying completely still. The mother would have fled long ago, seeing my approach, but had obviously left strict instructions (or was it simply instinct?) not to move under any circumstances. I too froze, not wanting to harm or startle the young one, then spent fifteen minutes or so just taking it all in—a spotted marvel I felt privileged to have seen. When Sharon arrived on the scene I called her over, then went to the car to get a camera. Through all this the fawn remained frozen without the slightest twitch, other than the occasional blink of an eye lid. In the end we backed off to leave her in peace, and for ourselves felt a deep sense of peace as well.

Sons of Anarchy, Esq.

2008-07-30T07:59:00.007-05:00

I just saw a promo of a new TV show about bikers/gangs called "Sons of Anarchy." In the ad, a bad-ass lookin' biker dude looks with disdain at the dork in the truck next to his bike at a stop light and says "we're all free men, protected by The Constitution."

Perhaps he doesn't understand the definition of the word "anarchy?" I'm pretty sure citing legal documents is the last thing an anarchist is supposed to do when arguing his political/ethical world views.

Out of Africa?

2008-07-24T16:07:00.002-05:00

One of our tickets* is about cheek swabbing people to find out where their ancestors came from. This Wikipedia page is awesome: Human mitochondrial DNA haplogroup.

* RT#356 username guest, password guest.

Beauty everywhere

2008-07-22T08:58:00.003-05:00

Last night playing Ghost Recon 2 my medic got stuck in a wall (bug) so I shot him in the head so he'd fall backwards, then patched him up. Problem solved.

This morning on my motorcycle I was following a large maple tree on a truck. At a stoplight I got the chance to hide in the foliage and touch the pretty leaves from the comfort of my bike. (Hard to sniff anything in the full face helmet though.)

Arrived at work and some gal is bitching that her stylist did her highlights wrong again.

My Walden Pond. July 22, 2008.