Friday, February 29, 2008

News, or History?

“The only thing new in the world is the history you don’t know.” Whether or not Harry S Truman actually said it, the actor who portrayed him on President’s Day at the Truman Library offered that pithy one-liner during a “White House press conference.” The whole morning was one of hands-on history, including samples of home-baked cookies from “Presidential Cookies” cook book, and a host of intriguing interactive displays. (It was my best Presidents Day ever, making me think I may add the presidential libraries to our Encouter-All-the-National-Parks-of-the-US-and-Canada itinerary.)

But those few words attributed to Truman (along with a dozen fresh-baked cookies and a cookbook for Mom) were my major “take away,” summarizing what I’ve of late increasingly realized.

(I wonder if Truman knew that the writer of Ecclesiastes said it much earlier: there’s nothing new under the sun. Probably so. From early childhood he was an avid reader, particularly of history and great lives.)

Somehow whenever I find a good historical book or documentary it still astounds me to discover, You know, those folks hundreds or thousands of years ago were pretty much like me. They pondered the same mysteries, exhibited the same emotions, strove for the same goals, suffered the same disappointments.

It’s also pretty amazing to discover that much of the technology we pride ourselves on in our “modern” world actually has root in discoveries hundreds or thousands of years ago—possibly even including flight, surgery, war machines and other marvels we consider inventions of our own day. Who knew? …Only those who read their history. Ever hear of DaVinci?

While this realization is, on one hand, rather comforting (the past is perhaps not all that foreign to the present, and those who lived it weren’t all that foreign to me), it is also rather disconcerting. I’ve witnessed the great truth of the adage, “Those who ignore their history are doomed to repeat it.” For instance, the invasion of Iraq has so many similarities to the invasion of Viet Nam just forty years earlier that you have to marvel how anyone could have been so ill-informed as to think we would be greeted as “liberators.” I guess they only read the history books about France’s warm welcome of the Allied soldiers, not the history of the Middle East, where one occupier after another has had to admit defeat, century upon century.

Truth be told, I doubt that Commander-in-Chief Bush had much knowledge of either event. The expression that from the outset of his presidency seemed to best characterize him was “singularly incurious”—the exact opposite of President Truman. By contrast, Bush seemed to be almost proud of being a non-reader. Little wonder, then, that he missed Martin Luther King’s sermon, “Beyond Vietnam,” which, with a few very minor adjustments, was a prophetic cautionary tale about repeating our error of the past. Truman was right, and bears repeating: “The only thing new in the world is the history you don’t know.”

Thursday, February 28, 2008


         PNAS     PNAS              PNAS

Am I the only one distracted by PNAS being written all over the place? PNAS

PNAS        PNAS               PNAS

Whoah. This is way too cool.

Jim Rogers, Ph.D totally freaked me out yesterday with his presentation. Staggeringly cool. Abstract below. (Reading abstracts is boring, but trust me: this presentation was off da hook for programmer wanna-be bionerds. -grin-)

Is this exactly up my alley? Perhaps this will finally motivate me to learn C? :)

Emergent Information Processing in Biochemical Networks:
New Results and Challenges for Understanding Cells

As our understanding of biochemical pathway structures increases, it is clear that these pathways form networks of astonishing complexity. This creates an immediate challenge in trying to make sense of the enormous amount of data that studies of these systems generate. The field of bioinformatics has arisen in recent years to meet this challenge, and has been very successful in helping laboratory biochemists interpret their vast data, allowing them to understand the complex structures of the chemical networks they study. However, even when these chemical network structures are worked out, it is often times still not clear how these structures actually function or why they are so complex. This has led to the need for another level of quantitative analysis of biochemical systems. In this talk, results of such a study will be presented that show that some of these cellular networks have emergent information processing ability. In addition, there will be a general discussion of the future of biochemical analysis and the important role that computer scientists may have in the process of understanding basic cell biology and disease.

Ooo! You can read online here: Emergent decision-making in biological signal transduction networks

Wednesday, February 27, 2008


Anyone seen my father? His daily blog entry is now 17 days overdue... :)

-poke-, -poke-

Weekly bioinformatics meeting

Here's a whirlwind tour of my 10:45 meeting this morning and the Wikipedia pages I cruised while trying to follow along.

MCBIOS 2008, "a regional iSCB conference," presented by OKBIOS: tandem repeats, variable number tandem repeats, protein structure prediction, and glycobiology.

Thursday, February 21, 2008

Oh, crap! I have to get ready!

My wife works at home. Last week I was sitting in her office on the family Mac reading email when she panicked because she was going to be late for work.

8:51 - "Oh crap! I have to get ready!"
8:52-8:56 - Commute to bathroom, get ready, commute back to the office.
8:57 - Succesfully arrived at work with 3 minutes to spare.

-laugh- What a sweet deal.

Why am I spending an hour in the car every day?

Ah, Chemistry. I love you.

You have rules. Thousands of them. Good for you. You have exceptions to those rules. Thousands of them. Way to go.

Ag is silver. Sure. Why wouldn't it be? And it's electron configuration is [Kr] 5s1 4d10, not [Kr] 5s2 4d9. Of course! Rules are for breaking, right? Absolutely. Hell, you keep good company, silver! Half of Period 5 breaks the rules. What's the point in having rules if you're just going to follow them? You incorrigible little imp, you! :)

Chemistry, you're a cheeky monkey and I love you.

P.S. Fuck off.

Tuesday, February 19, 2008

Data diving for diseases

If you squint you may see breast cancer hiding in this picture. If you spot it please send me an email. In the meantime, we'll keep kicking out these heat maps of gene expression data from microarrays.

Only perl can parse Perl

I got thrown into yet another new-to-me ball of Perl today and thought it would be really cool if I could kick out a GraphViz graph of all the subroutine calls, like Alan Ferrency attempted back in 2000: Looks like nobody has really pulled this off and sent it to CPAN? #perl-help sent me to PPI which cites Randal's famous line: "the only thing that can parse Perl is perl"!

Bummer... If only I had unlimited free time I could probably get close-enough? I'll email Alan and see if it's moved since 2000. :)

Eric Maki inspired me in Issue 4.1 (Winter 2007) of The Perl Review. But his is Perl op codes, not Perl 5 subroutine calls... -ponder-

Wednesday, February 13, 2008


Actually gamed a little tonight while the computer was updating itself. Beat another dungeon in The Legend of Zelda: Phantom Hourglass on Zach's Nintendo DS.

Monday, February 11, 2008

Roadtrip to Lincoln bionerdiary, Crash

( aviary, only with biology and nerds. get it?)

Heading to Lincoln on Friday to meet a professor there and get a feel for his secret high-profile cutting edge research... I hope he's designing four-assed monkies.

My Netflix movie was Crash. Started off pretty disgusting, and I feared I was in for a non-stop racial stereotype fest. After surviving the first few sequences, the interweaving of the character development started to show, and the rest of the movie was terrific. Hopefully these shocking examples of bigotry are rare indeed in 2008. We have evolved, haven't we?

Crash was as intense as Mr. Brooks, a movie stunning it its power and the raw evil of its characters. Mr. Brooks is an excellent movie. And no one should see it.

Both films tap deep into the shock receptors of our reptile brains. Seems a strange way to make a living. Not at all how I earn a buck, staring at a computer screen all day pushing bits and bytes around inside some servers...

Sunday, February 10, 2008

Truly A Good Death

Death is not always the enemy, but sometimes a friend. Sharon and I presided yesterday over one such interment and memorial service. Evelyn Barwise: 90 years old, beloved of her familiy and friends, still living in her home ater 60 years, hoping against hope that she would not have to move into assisted living. Her wish was granted last Tuesday as she died quietly in her home, with no heroics or drama, just as she would have wished. The interment at Oak Ridge with the immediae family was a time to reflect on "ashes to ashes, dust to dust," and the passing of life's seasons during a time of winter, with spring but a few weeks away. At the memorial service grand-daughter Alissa read her essay about the meaning of "Gramms' " life, and surely no finer tribute was more beautifully expressed. Other glimpses of this outstanding lady were caught up in selections she had made of music, verse, and scripture, most memorable the words of Victor Hugo read in closing: "Be like the bird who, halting in his flight on a limb too slight, feels it give way beneath him, yet sings, knowing he hath wings."

Thursday, February 7, 2008

2nd dream job "offer" today

Not quite two years into my bio* adventure, I've had my second bite of possible full time employment in my dream field, where I can Make A Difference.

Oh, but the money... That beautiful, seductive mistress that has treated me so well over the last 8 years...

I just can't seem to break free and accept my dream job -- making less than half of what I made merely one year ago... Step back to my 1998 salary after rubbing elbows with the execs and a billionaire?

Are these my dream jobs? Am I a money addict? Does the smaller paycheck overshadow the careers that had me so lovestuck mere months ago?

My job / life satisfaction algorithms are causing me much guilt, confusion, and frustration.

At least this time it's me torturing me, not The Man and The System... :) This hamster needs to pick a treadmill.

Wednesday, February 6, 2008

Saving Jimmy

I was born "James," moved through early childhood as "Jimmy," and have lived most of my now-sixty years as "Jim."

"James" was one of the good Bible names chosen by my parents, following the pattern of John and Stephen selected for my two older brothers. Mom still calls me James, plus a very few very close friends who realize that it can be a moniker of intimacy, not just formality. "James B." is my secret favorite, expressed by my buddy "John T."--both of us including our middle initial to create a rhyming duo.

"Jimmy," though, in the moniker to which I am most attached. I recall these early childhood years with a kind of rosy glow, especially the memories of long journeys in the woods, encounters with the wonders of nature, and leisurely time with brothers spent playing ball, raising insects, creating hideaways, and just doing what boys do. Taste, smell, sight, touch---everything then was direct and intense, unencumbered with onerous responsibility.

In adult years, "Jim" took over as provider/doer/achiever. There are a number of things I've done in that capacity in which I take considerable pride, but central among them is the way I've kept Jimmy alive. On occasions I've had internal duologues in which I've been able to say to him, "I've never forgotten you, no matter how busy I've been. I've worked hard to provide what was needful, and some toys along the way. I'm sorry that sometimes you may have felt neglected, But now...Hey, it's called second childhood. Can you come out and play?"

Tuesday, February 5, 2008

sodium hypocloRITE ME!

Memorizing all of this is the beginning of how I (hopefully) survived my CHEM test yesterday. Hate, hate, hate. -shudder-

Super Tuesday: Primarily Obama?

I voted today for Barack Obama, with a sense of satisfaction unlike any I can recall for decades. I know, I know. It's politics, and one should never get starry-eyed about that shadowy world where more often than not promises made are promises broken. Remember our current president's promises to eschew nation-building, to be a uniter, to leave no child behind, to offer a compassionate conservatism, etc. ? But I never believed those promises from the outset, and I was not surprised when exactly the opposite was delivered by The Decider and his fascist-inclined ideologues.

These past seven years have cast a pall of cynicism over me. When three years ago the nation elected The Decider for a second term (having not won the popular vote the first election) I was alternately incredulous, in denial, angry--all the traditional stages of grief but one: acceptance. I posted a sign of mourning on my office door that day and have as best I knew how endured the hijacking of our nation, reversing so much of what I consider The American Dream. The dismantling of the middle class, the waging of preemptive war, the civil liberties lost to the Patriot Act, the acceptance of torture, the rollback of environmental gains...and that's just the short list. History, I'm convinced, will have a MUCH longer critique of the Bush-whacked years, including unimaginable corruption in the erstwhile "moral" party.

Today I cast a vote to hope once again. Maybe our system can work once again; maybe we can rise beyond red state/blue state divisiveness; maybe we can regain our sense of decency and direction in a manner worthy of world respect. My thoughts today are with Barack Obama, who describes his emotions while walking on the Washington Mall in the quiet of the evening:

"And in that place I think about America and those who built it. This nation's founders, who somehow rose above petty ambitions and narrow calculations to imagine a nation unfurling across a continent. And those like Lincoln and King, who ultimately laid down their lives in the service of perfecting an imperfect union. And all the faceless, nameless men and women, slaves and soldiers and tailors and butchers, constructing lives for themselves and their children and grandchildren, brick by brick, rail by rail, calloused hand by calloused hand, to fill in the landscape of our collective dreams. It is that process I wish to be part of. My heart is filled with love of this country." (The Audacity of Hope, pp. 361-2)

Goosberry Days Gone By

How do you speak of an epiphany, the Glory of a Gooseberry?

It’s hard to express such keen passion for a berry commonplace even in its day, yet now so increasingly insignificant most people have never even heard of it, much less seen or tasted one. So few seem to even know the word itself that I sometimes fear I will be its last living witness. A goose…berry? they ask quizzically. You mean, like, the droppings of a Canadian goose? And they chuckle at their own wit.

I just smile knowingly. No, no, you poor benighted soul, I think to myself, then repeat aloud, a gooseberry. You know, the berry on that thorn bush you find growing along the edge of the woods, or in corners of the pasture. Those light green berries with yellow stripes, the ones with skin so translucent skin you can see the seeds and the juicy flesh inside. They have this black, bristly tail, and…

But by then I’m usually arrested mid-sentence by totally blank looks, or glances that say, So what’s the big deal? And I most often retreat into, Oh, just wondered. I used to pick ‘em when I was a kid and it was kinda cool… So what’s new with you?

After several such encounters I realized that goose-berrying is no more about than berries than cycling is about bicycles.

It’s about three young brothers wandering the woods day upon day, reveling in glorious freedom. It’s about defying the clutch of thorns to wrest away treasured booty. It’s about lying on the soft earth with berry buckets full, reading shape-shifter clouds. It’s about a warm summer sun stored alive in plump berries and bronzed arms.

And, yes, it’s about the work of “stemming” the berries— using thumb and index finger to one by one laboriously pinch off the “blackheads,” driven to endure by Mom’s promise that “If you pick and stem them, I’ll bake you a pie.”

Finally, it’s about Mom mixing the berries with great scoops of sugar and tumbling them into the dough of a deep-dish pie pan, followed by the oh-so-tantalizing aroma of bubbly anticipation, and then, oh then, the sweet/tart taste of warm pie and flaky crust, ice cream atop, wolfed down to the last sticky morsel in lip-smacking abandon.

If I had but one day to live again it would surely be one such as this. How fortunate I have been, to taste what future generations may well consider only the ramblings of an unhinged old man.

But I have tasted, and I have known.

I lived in the glory days of the wild gooseberry.