Monday, December 14, 2009

Omaha's First-Ever Catalyst Workshop: Success!

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!

Sunday, December 13, 2009

I'm suing Facebook

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!

Thursday, November 12, 2009

Omaha's first-ever Catalyst Wed Dev Workshop

Trying a new format at next month's meeting:

Wish me luck! Should be fun. :)

Wednesday, November 4, 2009

Future Perl snuck up on me

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. :)

Friday, October 23, 2009

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

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:

Thursday, October 8, 2009


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',

for (1..100) {
sleep 1;

Gives you a nifty ASCII timer bar with major and minor movements, updating clock, the whole nine. :)
MySlowThing():  26% [====        *     ]1m16s Left

Sunday, September 13, 2009

GraphViz prettyness

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. :)

Thursday, August 13, 2009

Just A Throw Away Line

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."

Friday, July 31, 2009

The end of the scientific pier

"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

Thursday, July 30, 2009

Perl, Catalyst: $100M in sales this year

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! :)

Friday, July 17, 2009

Chiselling chunks off of BioPerl

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-

Wednesday, June 17, 2009

perl5 introspection (thanks Moose!)

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
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
dosomething1, dosomething2, dosomething3, dump, meta, new
Neato. :)

More info on Moose:

Monday, May 18, 2009

Perl, Template Toolkit, and GraphViz

Our largest Catalyst application ( 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, 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: Enjoy!

Tuesday, May 5, 2009


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

Sunday, May 3, 2009

Tweak the Perl regex engine: assign to pos()

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!


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";

Friday, May 1, 2009

Two of Life's Greatest Joys

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.

Monday, April 27, 2009

Swirly bacteria

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)

Thursday, April 2, 2009

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

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? :)

Friday, March 27, 2009

Dilbert moment

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.

Tuesday, March 17, 2009

How Death Lost Its Fear

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,, which features- inspirational information on life improvement, getting jobs and income, travel, and real estate relocation

Article Source:

SICI (Search for IntraCellular Intelligence)

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...

Tuesday, March 10, 2009

deafferret on Twitter

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.)

Wednesday, March 4, 2009

Genome center information management


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

Monday, March 2, 2009

A carbon atom and four hydrogen atoms

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. :)

Saturday, February 28, 2009

Awe-stricken, and Inspired

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 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

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

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!"

Tuesday, February 24, 2009


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


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.

Saturday, February 21, 2009

Can You Copter This?

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

Tuesday, February 17, 2009

Counting letters is simple, right?

Fun brain twister. Stumped our entire department!

How many letter F's appear below?
Email your answer to jay(at)jays(dot)net.

Monday, February 16, 2009

Anger and grief

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.

Saturday, February 14, 2009

Reinventing the wheel for fun and profit

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.
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. :)

Friday, February 13, 2009

Where were YOU when it happened?

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

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.

Thursday, February 5, 2009

Endnotes for Earnie

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

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

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.

Wednesday, January 28, 2009

Mother Dear

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