Friday, December 21, 2007

Learning to write by reading a writer writing to readers

I recently checked this book out from a library. Yes, I confess that I skipped the first two volumes, as this third tome is a compilation of letters written by Clive Staples Lewis in the years of his prominence as a writer (namely, from 1950-1963).

It has an amazingly thorough index, which allows the purveyor to consider particular themes, books, concepts, people, or almost anything that you can imagine, as written about by Lewis to a variety of different people including children, literary peers, friends, and other luminaries of his day.

Several things strike me about Lewis' writing, in its most personal form of expression.

One is that his letters, even when brief, are written with care. How idly do my fingers type on an IM or e-mail, or yes, even a blog. This must change, and change it must.

Second, his love of reading permeates his writing. So many letters are full of spontaneous quotes of Shakespeare, Greek and Latin writers, and even when writing to Tolkien, he uses a quote from The Fellowship of the Ring.

Third, he has the view of the world that I am hoping to consistently apply to my life. From writing about morality in general to the particulars of a decision on divorce made by Anglican bishops to writing a letter completely in Latin to a Roman Catholic Dom, Lewis sought communication with all of God's people. Which makes me wonder, what would he have thought about the latest doings in Canterbury and the rest of the world? But I suppose that is a subject more fittingly addressed on Contrarian Presbyterian.

o.k., this is weird

I received a spam e-mail from myself today.

Has this happened to anyone else out here?

At any rate, this e-mail from me ended up in my Spam Box. My address and the link they put at the end are altered and deleted so as to not give either of us any more unwanted press....

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Merry Christmas, Fellow Nerds

Like its fellows, this picture is worth a thousand words.

I thought it was so funny because December 25th stands out as an island among days where different people in my building have signed up to use the confocal microscope.

The whole idea of Christmas and what it means may be lost to most humans walking about this globe, and maybe C.S. Lewis had it right when he said we need to replace the term "x-mas" with "The Feast of the Nativity", but you can't deny that people see the importance of this day qua this day.

What will your day be full of?

Tuesday, December 18, 2007

the best news i have heard in months

Peter Jackson and New Line Cinema are enemies no more!!!

There will be TWO movies based on The Hobbit, to be released in 2010 and 2011!!

Oh the JOY!!!!

read about it here:

Sunday, December 16, 2007

the tea party is ON!!

In honor of the Boston Tea Party,
is taking donations on this day.

You have under 12 hours to contribute to beat this great patriot's previous record of money raised in one day.

Get there and join the REVOLUTION!

Saturday, December 15, 2007

i believe that i myself am the future?

We live in a cruel, sickeningly cruel era. In the midst of the parasitic protests for more for me, and the maddening mockery of "menos" for thee,
rays of hope shine, emanating albeit softly from those who advocate freedom,
goodness, and all of those other wonderful things more rare than gold on this present horizon.

This may be no more clearer to me when I reflect on my existence as a parent. For some reason this culture of death has not only forgone love for comfort, it is quick to seek out sources of cultivation and praise, and to target them for scrutiny and mockery. These things are funneled, isolated, anything but placed under the spotlight. For after all, a moment's consideration would let the resplendence of life and love outshine the notions of the nuclear family, ten year plans, early retirement, and the other catch phrases disguised to anesthetize the heart's cries of anguish as it thinks of chances squandered, thrown into the mire that will inevitably
mire the heart itself.

To that end, I must earnestly ask those traveling on life's road with me--are we ourselves ends in and of ourselves? Can we look back and call a life well-lived if it was set up to solely ensure the best scenario, a scenario that only placed the camera on the director himself?

Oh no, my friends. This will never satiate the human condition. We are all farmers,
the question is what are we planting into our field, and what will that do to the
earth and its other inhabitants--these other inhabitants whose very existence is
scorned and brushed aside for things like "me" time.

"Unless a grain of wheat falls to the ground and dies"
we build a house upon shimmering worthless lies......
My mathoms may not give the greatest yield if measured by annual returns,
but "wealth" is one fruit of the field, it must not let us spurn,
the truly cherished, valued things in life, that raise the poorest man's head
but tear until they are dead the rich who drown in their own strife.

Friday, December 14, 2007

lessons learned from little lads

I woke up this morning with a sore throat.
Having a sore throat is the sort of illness where one can't help but complain, despite the fact that the
injury is really quite manageable. I was in the mood to complain about my irritation. As my son arose
this morning, his faithful greeting of "Hi, dad" was more gruff than usual.
{I say more gruff than usual because he has a habit of lowering his voice to sound more tough, in case those of you
who haven't had the blessing of talking to him are confused, but I digress.}

Noting this deepening and scratched tone to his voice, I asked, "Hey man, do you have a sore throat?"

"Yes", came the baritone call from my 7 year-old.

"Aw, man, so do I. I guess we both do."

There it was, I had set up my chance to commiserate. What would he say to remind me that misery loves company?

"Too bad", was his blunt but quite accurate assessment of our mutually inflammed throats.

My wife and I started laughing, for quite a bit of time, so much that we had to explain to him the simplicity and
truth in his comment. He thought we were laughing at him for saying something silly, but really I had been the one who was
pensively puerile.

The truth is that it's too bad when little trials come our way, but they come for a reason. For whatever reason, at that moment little Jonathan was years beyond my tired and childish attitude of this morning, and he knew that complaining solves nothing.

Thursday, December 13, 2007

Surely you jest, dearest Jonathan!

No, poorest readers and friends, I am speaking truly when I tell you that I want another blog.

The problem I have had with blogging as of late is that my other two blogs,


are so focused on specific forms of expression that I cannot really share other things that are on my mind. And to that end, I have started

As the headline to this blog states, Tolkien invented this Hobbitish word that greatly captures our desire to cling to things that we can't quite throw away or polish and put in a display case.

So what will you find at this latest iteration of my thoughts expressed in electronic form?


That is-my thoughts that I have as I walk down this road of life. Perhaps this site will be more characteristic of your typical blog.

Who knows? We shall see, we shall see.....

Friday, December 7, 2007

I accuse you all of abhoring all accusatives

I recently discussed ways in which our modern English is neglecting the nominative.

At the same time, we also take the accusative and almost always assign it to some abject address.

After all, when was the last time you heard someone say "To whom are you referring?" I will wager that for every time you heard that you heard at least twenty sentences that went something like this: "Who are you talking about?"

The latter is grammatically grotesque, whereas the former is fine.

I realized this clearly because of my current employment, which has me surrounded by people whose second language is English. At first I wanted to correct some of their usages of the word "whom", when I realized that I had been the one in error.

So be careful, kids, and be sure to use "whom" whenever your interrogatory pronoun is the object of the sentence!

Tuesday, November 27, 2007

Twenty-First Century Festering Wounds-7

Armed with the knowledge of genetics research, I felt ready to cure Sam Vespucci.
The real question that needed to be answered to get to a cure, was what on earth I was supposed to do with the knowledge of the gene that had crippled his ability to clot properly. Coagulation was the key, but really how did knowing what was wrong do us (and more importantly, Sam) any good?

I wanted a few months to mull these thoughts over, maybe present these meetings at a high-impact science conference, so that I could formulate the best way to be there for this dying soul, but such a luxury was not mine to be grasped.

I had to take this basic understanding and convert into some sort of life-saving elixir, and do it fast. But was such a thought impossible, left to the mythical worlds of alchemy and magic?

It was not clear, but there was only one thing that was clear to do, and that was to try to apply this knowledge. The WASP gene is critically important for clotting and other forms of cellular skeleton building, and Mr. Vespucci had lowered his expression of this gene. Could I turn the gene on somehow? Replace it with some other factor? Perhaps something artificial? Nothing sounded like a logical, or at least possible solution.

As my mind raced from option to option, it was clear that my tools in the laboratory would not suffice. Would I only be able to tell Sam why he was dying, without telling him of a way to avoid his demise? I hoped and yes, I even prayed, that he would survive thanks to some insight that I could provide. I hadn't slept in days, pondering literature on WASP as a molecule, but it didn't make sense. It's not as though he was born with a clotting problem. What happened to this guy to make him so unable to clot?

Greg Kim, my M.D. friend, gave me a call. It was the call that I had dreaded since I had started this project.
"It appears that Sam is in full shock. His wound has been infiltrated yet again, and this time it looks like it may go systemic. His whole body will be a crawling bacteria incubator in a few moments. If you have made any progress with how WASP could be important, now is your chance."

I started stuttering, wanted to say something, but nothing would satisfy our question. Nothing intelligible left my lips, except for the clear message that I was unable to give an answer.

"You don't know, do you? Well then, I'm wasting my time on the phone."

The phone hung up on the other end, as Dr. Kim doubtless had to go off to attend todo all that I could, but I was still hopeless. What could I do with my knowledge? If it was merely kept up in this storehouse of facts called my brain, it would make for interesting party conversations, but without any ability help someone it would have been better to have never known what was wrong.

Like the man on death row who knows the date of his doom, had I merely told him the composition of the chemicals in the lethal injection? Would he even come out of the sepsis that poisoned his body and mind? Would I spend the rest of my life knowing that I had come close to a cure but had faltered at the end? I needed to see him at least one more time, perhaps that would help.

Leaving my office, my eyes wavered from side to side through the halls of labs, hoping that some clue would open my eyes to the way to apply my knowledge, but to no avail. I might as well have looked at a blank slate. Nothing came to me.

Pulling into the hospital, I parked in the temporary area. Parking tickets and car towings could come and go, that was unimportant. What mattered most was to not let this chance to see Mr. Vespucci at least one more time slip away.

When I crossed the threshold to his room, I remembered the first day when we met. The odor that first knocked me to the floor had worsened to new heights, or should I say depths. He was unresponsive but still alive as a team of medical technicians used that frighteningly harsh cleansing apparatus to remove the bacteria from his wound. Hopefully that would stop the constant flow of new bacteria into his blood. But would his body be able to clear the bacteria that was there?

His temperature had surged to 103.8 degrees Fahrenheit, and it seemed that nothing would stem the tide that swelled waves of death into this room. I was so powerless, that again, I could not help but cry out to whatever god may have been listening at the time.

The team took a break from swabbing the wound in his thigh, and the once pristine webs of plastic fabric had so much blood and pus that you would never have guessed that the apparatus was once man-made. It looked like some sort of pulsing alien life form.

As I kept the contents of my stomach deep within by trying to take my mind off of the gore that was so repulsive, I asked the resident M.D. a question that may be the most important question I have asked while walking the face of this earth.

"Um, excuse me, but who is the vendor of these surgical swabs?"

He told me the company, which was famous for making various hi-tech swabs out of forms of polystyrene that were touted to be the best in the business, far superior to any soft cotton-based swab. Realizing this, my heart sank precipitously, before it rose into the heavens. For at that moment, I realized what was wrong with Sam. You see, I had called the swab frighteningly harsh, and by that all I had meant was that it must hurt like the worst torments to have one's wound cleansed. Such soul splintering pain would be the worst case scenario for you or me if we had to have the same procedure done on one of our wounds, but we were not dealing with a festering wound on your leg or my leg. We were talking about Sam Vespucci's problem, and after all, his mutation in WASP made things not just painful, but maybe it had made him unable to clot by the mere force of our procedure!

The expression "the cure is worse than the disease" usually speaks of some strategy that is fundamentally flawed. In this case, I wondered if that blood and pus-covered swab had been the perfect cure for your standard 21st century wound-a wound that would be healed by cells that had enough WASP to do the job. And maybe Sam never had a clotting problem before because he had never had a polystyrene based swab rubbing his cells to the point where they could no longer work. It was all so clear!

The resident had opened a fresh swab to finish the job, and as my mind raced a mile a second I jumped up from my science-inspired dream to grab his arm.

"I've got it, I've got it, I've got it. You are killing him by saving him. Put that damned tool down this instant!" I sounded like a raving lunatic, and if I hadn't worn my lab coat (which I almost never do) he probably would have punched me in the face.

"Greg, Greg, get over here!" Greg Kim rushed to the room, looking at me and his exasperated resident. My words were jumbled and I tripped over myself, but in a frenzy I was able to convey the general idea that the technologically advanced swab was just too much for his WASP-mutated cells to handle.

"Calm down Andrew. I don't think that you're right, and even if you were, I think the patient won't survive this episode. But let's give it a shot. Johnston, you heard the man. Get us some soft gauze, the kind that we used to use when I was training, and let's see if you can get that wound cleaned up."

I let out a deep breath and knew that this could work. Even if it didn't I would never have another shot at understanding how this one gene could weaken his cells so.

It wasn't clear that Sam would live long enough to see whether my hypothesis would work. I tried to watch his vital signs near his bed, but I had no energy left after all of this literature searching and pondering. I fell asleep, and as I lost consciousness I sincerely prayed for the third time in my life, and like the other two prayers, they were all uttered on the same day.

Monday, November 26, 2007

21st century festering wounds - sextus

The results were in, the experiments were done. We had found that in Samuel Vespucci's cells, several genes were somehow lowered in their expression. And for whatever reason, all of these genes were lying in a straight row on the X Chromosome.

But which gene was to blame for this strange malady?

I could not figure it out.

I surveyed the list of genes that came up as strange on the gene chip, with no strong clues.

However, as my eyes scanned neighboring genes, the picture became clear to me. The proverbial moment of clarity is sometimes depicted as a light bulb going off, and I had had times in my life when it seemed like I had grasped the experience of a true epiphany. But that was all washed away in comparison to this moment.

For at the moment, the bulbs flashed, the scales fell from my eyes, all of these metaphorical bursts of epiphany were true at the same time.

WASP!!! WASP!!! WASP is not expressed properly in Samuel!!!

I could not stop shouting and screaming the word WASP, as my colleagues looked at me with befuddled jaws gaping.

"Come on, you don't know WASP? It even has a wikipedia entry on it. Look it up as Wiskott-Aldrich Syndrome, not the insect or White Anglo-Saxon Protestant.....This is it!!!!" The gene wasn't on the list that we got from our experiment, but it was wedged right between some of the other genes that we found on the X-chromosome. It was as clear as day to me now, but not to my student.

Who could blame these poor cellular biologists, whose worlds revolved around Dictyostelium discoideum, the slime mold that spends most of its time as a single cell? Studying this molecule in such an organism is not as logical as studying the other molecules that we prefer to work on, but as far as humans go, WASP is definitely worth studying. Humans who lack this gene completely develop serious diseases, and many times this manifests itself by problems with, yes, clotting.

My graduate student and her friends from the lab next door listened to my tirade as they looked up more info on WASP, and I knew what I had to do to bring about a change. I was sure I could save Sam. I just needed to get to him in time.

Saturday, November 24, 2007

21st century festering wounds - cinco

I have been involved with science as boss or worker for 17 years now.

Some days have passed leisurely, because a big paper from my group had come out and I knew that was a guarantee that I'd make the next promotion or get the next grant. At other times I was unable to sleep before I heard whether our latest hypothesis could be backed up with reliable data. Naturally, this was especially true when funding was bad.

But all of that was rubbish compared to this current matter matter of Samuel Vespucci. With every passing hour I was so thankful to the gods or Buddha or the blind forces determined by Newton and friends that I was not an MD.

To be a medical doctor would have caused me to die of a heart attack or some other stress-induced malady. There's something about my mind that makes me able to project my mind into the body of someone in pain. Call it extreme empathy, or whatever you call it, it was so unsettling for me to have seen Sam have another break in the bacterial colony that had spread from his leg back into his bloodstream.

My good friend Dr. Kim was handling that with severe treatments reserved generally for cancer patients--small molecules called "cytokines" were added to Sam's i.v. that provoked his immune system to get to work and kill the bacteria had bought Sam some time, but we all knew that if he lost consciousness, he would be gone. The DNR was signed and none of his family could convince him otherwise.

And so I got to the lab a bit earlier than usual, and hoped we could find something.

As it happened, my graduate student Karen had already been working on analyzing the genes from Sam.

To do this, we used some powerful technology where every gene in the body can be identified in terms of whether it was turned on or turned off. This was done using a small chip, hence the name gene chip.

She was sitting at the computer with a frown. Turning to me, she said, "I'm sorry Andrew, but I think our gene chip has a problem. If you look at all of the genes, they are all pretty consistent between the healthy patient sample, but it seems like a bunch are a bit lower in expression. I think there was some sort of a smudge on the chip that made Sam's cells look like genes were turned off."

"Yeah, but all we have to do is look at the chip and see if that's true. And what do you mean, a bunch? And didn't you run replicates to be sure things like this didn't mess up your experiment?"

"Oh yes, yes, of course", she replied somewhat defensively. I had trained her well enough to do this but things seemed so odd that I had to ask.

"Ok, well, can I see this list of genes, and see what you mean?"
There were over 30,000 genes in the study, and they were listed in terms of how much they were expressed.

This was the list on the screen that she showed me that day:

In every instance, Samuel's cells had for some reason lowered the amount of expression of these genes. It was like those genes were somehow muted compared to cells from you or me.

"So Karen, you think these chips, which run several thousand dollars for each one, were all smudged in the same spot?? Come to think of it, where are those genes on the chip? Are they even in a row????"

"Hm.....let me see." She took the list of genes and organized them based on where they were on the little chip, and suddenly the grouping was lost.

It was then that we realized that those genes weren't in a row on the piece of plastic used to measure them.

"Wait a minute--I'm going about this all backwards....what if you sorted based on location in the human genome?"

With a few clicks and a few more seconds, we realized what was wrong----
The chip wasn't broken, affecting the genes in one row---to our shock, the genes were all in a row, if you looked at where they actually were on one part of one chromosome.

Friday, November 23, 2007

High Koo's --------- j

how soft your embrace
so anxious to meet anew
and stay in your sight

how soft your embrace
the treasure that changed my life
by ending my life

it has been too long
so anxious to meet anew
each second endless

i'll do all i can
to make you smile, never turn
and stay in your sight

High Koo's -------- i

measure resentment
pound by pound it buries you
and spits on your grave

measure resentment
in the way you won't reveal
the hollow inside

the weight has a toll
pound by pound it buries you
suffocates your breath

eulogy of shame
he tells your life as it's not
and spits on your grave

High Koo's ------- h

cold distance between
the span of my fingers and
your lonely gazes

cold distance between
a heart might not see at all
but sense what is lost

i'd call your face close
the span of my fingers and
the fear that lingers

i remember how
we looked away and turned to
your lonely gazes

High Koo's ------ g

pour out a prayer
screaming silent in your arms
yes, your soft reply

pour out a prayer
and wait for what he answers
hope no matter what

trials of my patience
screaming silent in your arms
i can't wait anymore

why do they suffer?
is justice merely unseen?
yes, your soft reply

High Koo's ----- f

a trace of your care
will not sustain this poor child
you left while i cried

a trace of your care
leaves my heart waiting for you
i need your return

the feigned harmony
will not sustain this poor child
he craves a real hope

you won't stay i know
i can't stand to say goodbye
you left while i cried

High Koo's ---- e

vices do not halt
as selfish plots will thicken
and his schemes unfold

vices do not halt
affairs rise as the soul dies
he has sold his self

the mire tastes so good
as selfish plots will thicken
the day grows darker

nightfall hides his hate
the lies are told to gain lust
and his schemes unfold

High Koo's --- d

her smile is enough
to melt me when i'm frozen
awaken this heart

her smile is enough
soothing the deepest anguish
bringing this sweet joy

dawn, come to bring life
to melt me when i'm frozen
crush my last goodbye

stuck in this late eve
with no strength i am drowning
awaken this heart

High Koo's -- c

anchor it fast child
you never can let it slip
then will peril flee

anchor it fast child
before the times grow hard
don't lose hope again

the cycle turns on
you can never let it slip
await the day of strength

growing to full strength
the youth prevails to flourish
then will peril flee

High Koo's-a

soft you swindle me
grasping for the one to come
homesick i leave home

soft you swindle me
the flatters crush my sight
as pride ends this life

broke the iron gates
grasping for the one to come
this fire won't be stopped

the porch light was cold
speaking pages in silence
homesick i leave home

High Koo's - b

my tears have all dried
waiting for the night to come
you could not answer

my tears have all dried
and left the stain to smoulder
i hid them, each one

i bundle my hopes
waiting for the night to come
but dawn seems so far

i will always knock
pleading reason for your heart
you could not answer

Wednesday, November 21, 2007

high koo's -- prefatory address

I wrote these about 10 years ago, but I post them now because someone quizzed me about my poetry, asking me if I knew the author. I realized he had a copy of one of my epic poems that I will refrain from posting here (or elsewhere).

At any rate, these haikus were written at Koo's Cafe, though never performed there or anything approaching such levels of pretension. I had a lot of fun using repetition to provide structure and establish an overall theme in each one. Enjoy or don't, but I'll at least feel nostalgic.

Monday, November 19, 2007

Nominative No-Nos

One grammatical error that really bothers me is the abuse of the nominative.

Oh the accusative--that precious jewel neglected by so many youth in favor of that noxious nominative.

As young children, most of us were taught that we were wrong to say things like,

"Me and Joey want to play Nintendo, mom!"

or even worse

"Why can't me and him play Nintendo, mom?"

[Parenthetically, every time I remember how much time I spent playing Nintendo/Commodore/Apple games, I make a mental note to be more lenient.]

Clearly those sentences are grammatically grotesque, and so we were taught to say,

"Joey and I want to play Nintendo, mom!"


"Why can't he and I play Nintendo, mom?"

This was a great rule to make sure the nominative is used when it is supposed to be used, but of course that raises another question:

What is this elusive nominative; that word that I've been abusing in its own right, as a means to bother you who have forgotten or never learned it?

Put simply, it is the form of a pronoun that is the subject of a sentence. Put even more simply, when you have words like I/me and he/him, we see that both I and me and he and him refer to the same person.

In these two sentences, we see what is intuitive to most of us:

I hate him.
He hates me.

In the top sentence I am doing the hating, while in the bottom he is.

Thus, I and he indicate those that are the subject, indicating them to be nominative pronouns.

Perhaps it is the egocentrism of a child's mind that puts themselves as the subject of every sentence, but as a general rule, saying "he and I" is correct as long as you and this fictitious he are the subject. But if you are the object, our amiable amateur the accusative approaches the arsenal.

For the accusative case means just the opposite--it comprises the object of the sentence.

Returning to our small sentences, "him" and "me" refer to those who are being hated in the two sentences, so "him" and "me" make up the object of the sentence, which we call the accusative case.

So as children, our teachers were right to tell us to not say "me and Joe", as long as this counsel was specific to a situation where "I" was the subject. But if the sentence is about "me", of course we should have used "me"!

Unfortunately, we understood the fear of the accusative as some sort of immutable law, and we ended up neglecting poor Mr. Accusative.

How does this manifest itself? I'll put a quote from a friend's blog, that shows how we can turn our grammar minds off for fear of offending the overly simplistic teacher/parent that taught us to never neglect the nominative.

"earlier this week ****, who is four, was looking at a picture of he and i that was taken when he was a little over a year old."

Now I'm sure this particular friend would not make this error all of the time, and it was probably a mistake which slipped out due to busyness etc., but the point is that this mistake slips out quite frequently among many modern Americans. I would argue that this is due to a primordial fear of using "him" "me" when conjoined to another pronoun. Maybe it also comes from a fear of being branded an uncultured individual, clasping a Coors saying, "Me and him done loved that NASCAR race!", but that is another layer worthy of considerations at some other point in the space-time continuum.

At any rate, here's another way to challenge one's grammar, which I am sure is familiar to some:
If we take the errant sentence and isolate the two pronouns, the error becomes much easier to see.

Keeping the first pronoun we have:
"earlier this week ****, who is four, was looking at a picture of he that was taken when he was a little over a year old."

Keeping the second pronoun we have:
"earlier this week ****, who is four, was looking at a picture of i that was taken when he was a little over a year old."

None of us would ever use the nominative in place of the accusative when it's just one word on its own, and I would argue that this is because we were drilled so thoroughly on the specific matter of how to avoid the accusative.

So let us all shake our primordial fears and embrace "me and him" as we should.

That's what me and him said about I and he, at least.

I kid, I kid (though mostly to myself).

Thursday, November 15, 2007

21st century festering wounds-IV

Samuel Vespucci walked out of my door to use the restroom. I was still puzzled over the apparent disconnect between what I had told him, that I was confident we'd be able to find a cure for his festering wound, and how he had responded to such a claim. What was wrong?

I for one would be happy to hear that there was a new way to possibly cure me. But then again I'd never had more than a broken nose, so what did I know of true illness?

I thought I had done the typical scientist thing of using too much jargon, but then again, I said things as simply as possible.

Suddenly I realized something else was amiss, when I heard another crashing sound in the halls. Samuel had fallen to the ground and was clutching at his wounded thigh.

With words that I dare not repeat for fear that some day an innocent tongue would see these words that I write and be as blemished as a "sailor" like myself felt, he belted out cries of anguish. It was horrible.

My hands fluttered and fumbled as I started dialing on my cellular phone for Dr. Kim. Fortunately, another professor in the department was an M.D./Ph.D., and she came to the rescue while we waited for an ambulance.

I was not permitted to board, so I got into my car and followed.
"So this is what ambulance chasers do."

As I arrived I parked in a visitor lot but had no patience to get my parking permit from the kiosk. I proceeded inside to try to find Sam, and maybe my friend Dr. Greg Kim.

Dr. Kim was there to meet me.

"Hey Greg-how is Sam?"

He looked at me with the sort of a smile that only a doctor could produce at a time like this. Sincerely processed to ensure maximal comfort, he said, "We're doing everything we can, and I hope that means he will stabilize. But I'm not ready to state that that is the prognosis. How are things on your end?"

"Um, about that, I just got the samples today. He dropped them off and then a few minutes later he fell to the ground. So, no, no progress yet."

"Well, Drew, you can go in and see Mr. Vespucci."

I entered the isolation room in the ER, and while conscious, Sam looked even feebler than before, almost childlike.

"Hey Andrew, looks like I got to your office too late. I thought you were like House MD--that guy and his cronies usually start by thinking they cured the patient and then realizing they were wrong. You didn't even get a chance to be wrong."

I tried not to frown, but realized I was cringing. "I know, Sam, I know. Just hang in there. It's not too late for us to make a breakthrough."

I tried to muster words that would frame a convincing argument, but as my countenance greyed with doubt, Sam interjected.

"I've signed it, Andrew. The DNR--do not resuscitate. If I go under one more time, I don't want to come back up. I've come too close to death too many times to have hope that this won't be just another palliative treatment. You know that word, right?"

It was familiar to me, but having focused on cellular biology I could not place its exact definition. As my mind searched, Vespucci began chanting a rote quote, apparently from the dictionary.

"PALLIATIVE: ALLEVIATING PAIN AND SYMPTOMS WITHOUT ELIMINATING THE CAUSE." The words were so bitterly recited that I couldn't help but feel pity in a new way. What I thought pity before at times such as funerals was no longer pity to me. That emotion was merely a bit of smug sentimentality. This new depth of sorrow was something I had never experienced, and would forever more be pity to me.

He went on, "That's all this is, you hear me? And if that's all you can do, I don't need you people."

His face cringed into a look reminiscent of a fearful animal, as he broke into tears, and at that moment, I could not blame him.

All that I could do was hope to save him.

Wednesday, November 14, 2007

The original Sopranos?

I recently finished The Winter of Our Discontent, one of John Steinbeck's last novels.

For all of its alleged (but unproven) literary faults, in terms of rambling soliloquies and other venial scribal sins [which actually put a timeliness and reality to the narrative, but I'm digressing again], the way morality is treated puts a striking parallel between this work and my favorite 21st century program, The Sopranos.

Of course, this is not to say that these are both gangster stories--instead, I am speaking on a deeper level of the moral themes--how morality is perceived and practiced, and how we as the observers are left scratching our heads as to whether we want to root for a given character, or whether we hope they get it.

Even superficially, there is the character of Alfio Marullo, whose Italian background leads people to question whether he is "connected". Even deeper, Marullo's integrity is ambiguous. Is he noble man, or is he not?

There is the East Coast town-nestled on the Atlantic Ocean, I am reminded of the Sopranos again, because the portrayal of the area used to seem so foreign to me as a Californian. Now in my Maryland-soaked life, the pages and screens are more alive than ever.

Then we have the actual protagonist, Ethan Hawley-in some senses he is a nobody, but in other senses he is American royalty. The friction between these two realities leads to a universally American portrayal of what it means to succeed in this country.

And as the Sopranos ends, so too does this novel.

But, since one of my few readers is a Steinbeck fan who has yet to read this, I will say no more.

Saturday, November 3, 2007

21st century festering wounds-tertius

I was sitting in a seminar watching a new researcher present their findings. Clumsily, sloppily, forgetting the background and assuming we all cared about every detail this person was working on, I did what I always dreamed of doing--I blurted out and screamed, "What is your problem?!?!? Do you think we really care about your meaningless experiments that will probably never even be published???"

He looked at me, lips quivering because he knew I would be evaluating his performance at his Ph.D. defense, and started to cry.

Suddenly I was standing on a beach with the head of the lab that competes directly with me, and she softly whispered, "It's ok--we'll get off this island some day. I'm sure our loved ones are doing everything they can to find us."

Twelve minutes after hitting the ground, I awoke to find my senior graduate student standing over me, repeating my name. My hopes of silencing the bothersome chatter of an annoying student, and my fears of being stranded with my scientific archenemy were all that--dreams, nightmares, aspirations, and worries. Where was I? Oh yes, back in the office, dealing with the wound that would not heal itself.

Poor Samuel Vespucci was speechless, but not as unnerved as I had been from hitting the ground. Regaining my equilibrium was difficult but manageable. To think, I hadn't even seen the wound whose smell had knocked me off of my feet! It was then that I realized that another aspect of my personality that had kept me from medical school; that is, that seeing real people in pain was far too much for me to tolerate. It's much better to speculate about death and disease on the molecular level, after all.

Nonetheless, I apologized for such the interruption, and took as deep of a breath as possible as to feel calm, without imbibing the strong stench of the wound.

"Mr. Vespucci. You must forgive my weakness. I see you are carrying a styrofoam box. Presumably this contains the biopsies of your cells and the bacteria that are growing around them?"

He nodded, hands still trembling, and set the box on my desk. I did not fall to the ground this time. No, the excitement of starting a project that would put my knowledge of the cell to use had me as giddy as a schoolboy, or so the saying goes. Personally, I was never giddy as a schoolboy, but that is another story.

"OK, Mr. Vespucci--we have everything we need to get this search started. Our goal here is to identify any cellular or genetic anomalies that may underlie....sorry sorry sorry, I do that all of the time with laypeople. This is what we are going to do, Sam. We can tell when a cell looks strange, and we can tell when a gene looks strange. If anything is the matter, we are the ones to find it. I know exactly what a happy healthy clot should look like, and all of the cells that work on building that clot. We don't know who is not doing their job, but when we get to it, we will. You hang in there, and I'll get back to you as soon as I can. Now, do you have any questions?"

"Yes, um, where is the bathroom?"

With that he left, and for some reason, it was clear that he did not share my enthusiasm about the chance to find out what was wrong.

Friday, November 2, 2007

Using "while" to contrast things

Well, my grammar-minded amigos, I am glad to say that I'm back with some food for thought on the English language.

I've been quite busy trying to employ it in my trade, and have found myself quite lacking in what is needed to succeed.

One vignette worth sharing is the use of the word "while".

I was writing about different things that I discovered in my research, and when I wanted to compare two scenarios, I often would choose to write "while".

To give a mock example:

"While test tube A was blue, test tube B was green."

What I have learned is that this is verboten, as while denotes a chronological perspective.

Thus, one should abstain from "while" when making contrasts. "In contrast" works to replace it, but if the two scenarios are not so opposed to each other, "whereas" will also suffice.

So put the "while" down while you are writing contrasts!!!

21st century festering wounds-part the second

I live the typically atypical life of a scientist. Focused on a few molecules out of the staggering myriads that comprise life as we know it, I delight in connecting minutiae to diseases and the minions that deal them to the innocent and the guilty alike. Because of my delight in unraveling such mysteries, my path crossed Samuel Vespucci's one unusually cold summer day.

As I said before, Samuel was getting tired of the same unsettling procedure of having his leg wound literally scrubbed clean. He wasn't sure if he could take another treatment, but was not quite suicidal enough to let apathy take its course.

Because of this unending anguish and frustration with the status quo, it was then that he came to me.

I was working on my latest grant and faxing yet another form regarding my newest publication, when a human came to the door.

"Who could this be? Too old to be one of my students, too young {and definitely too poor} to be a rich codger with goodwill and a plan to donate our institution money." I thought this and similar thoughts to myself, and then noticed a strange gaping curve going into one of the man's legs.

With the graceless demeanor you would expect from someone in my profession, I continued mulling the possibilities over as he stared at me blankly.

Suddenly, it hit me. My latest attempt to connect my work on the bricks that make up a cell (called cytoskeletal proteins by nerds like me) to human diseases was staring me in the face! I remembered a strange e-mail I had received from a friend from college. Gregory Kim had gone on the road towards success, and saw the light that somehow flew past me by enrolling in medical school. Instead of slogging away for little pay, studying an organism that most people have never heard of--have YOU heard of Dictyostelium discoideum???----Greg was helping people directly, and being paid far more directly than I was as a junior faculty at an albeit prestigious institution.

And this was important to me on that cool summer day because I remembered Greg was part of the team that was baffled and befuddled by our friend Samuel Vespucci.

He had contacted me because I had been the guy to go to when a problem was strange. Call me a real-life House, M.D., without the limp, but when a zany answer was needed to solve an even zanier problem, I had a knack for finding the right answers. Perhaps that is why I opted to take the lower paycheck and stick with science.

"Andrew, you've got to drop everything you've got--we have a case unlike any other. Persistent infection with no signs of healing. Laceration was eaten away into a subinguinal..........."---Greg's frenzied voice called me one morning a few weeks ago, telling me all about Samuel's condition. He described the case in more detail, but it would sound like repetitive drivel to the non-clinician, so I will spare you the gory and droll details.
"Look Andrew, I'll e-mail you a reminder, but you've just GOT to see this Vespucci case for yourself."

All of these experiences of my youth, career choices, and current dedication to try to solve this mystery were playing and replaying in my head, as suddenly the world went back into focus and I remembered where I was---standing in my office on a cold summer day, starting at Samuel. As I began to introduce myself, the smell from Samuel's wound introduced itself to me.

It was then that I instantly vomited and lost consciousness.

Wednesday, October 10, 2007

21st century festering wounds

Samuel Vespucci walked into his doctor's office. Dreading yet another visit but knowing he would die if he missed his appointment, he tapped his feet anxiously in the waiting room.

Despite the fear, there was a methodical feeling to the occasion. He knew the drill by heart now. So rote, but so unbelievably searing, like each time in the past, he filled out the forms. Sure, this time they were 20 minutes late, but the same sights and smells pervaded the room.

And when I bring up smells, I should state here and state it clear: the air was putrid with decay. For you see, Samuel was suffering from a persistent bacterial infection. Only a scientist like myself could call out loudly and say, "Yep, that is E. Coli!", with a twisted trill of triumph in my voice.

Believe, me, that's my usual response when I smell bacteria. However, when I met him some weeks after this hospital visit, there was something more pressing to first note and then subsequently cast as far out of my mind as conceivable, and that was because of the way the air was heavy with the aroma of death.

But, as usual, I am getting ahead of myself. For my role does not enter this story at this point in the space-time continuum.

He walked into the doctor's office, let the nurse measure his blood pressure and take other vitals. Same as it ever was, nothing was wrong, except for the huge pus-filled gash in his body. Of course, that meant that everything was wrong.

Prone to sepsis, Mr. Vespucci clung between the precipice of relative health and fevers full of sweat and delusional dreams that could only be dispelled by extreme doses of antibiotics.

He had had 4 near death experiences, and the fevers kept spiking dangerously close to temperatures that could damage his mind. But things had changed; the situation was even worse.

Uncomfortable in his gown, Mr. Vespucci's attending doctor finally entered the waiting room. Sweat dripping from his brow as he anticipated the inevitable, Samuel felt even more disturbed watching the young resident look back and forth from the charts.

"Um, yeah...Mr. Vespucci, I am Doctor Rothfuchs. It's a pleasure to finally meet you--I see from your file that you are suffering from persistent bacterial infections with significant subinguinal lymph node involvement. As you well know, clonotypic analysis of this particular strain has revealed a fascinating mutation in the large ribosomal subunit of your E. Coli, which renders this specific isolate impervious to any sort of antibiotic-based therapeutic. I hear we may name this subspecies E. Coli Vespucciensis, and it may lead to our hospital being mentioned on the news!"

But that was neither here nor there to one dying man. It was the procedure, and the procedure alone that carried any value to Sam Vespucci.

"Yes, yes, I have heard this all before. Please spare me the details," grumbled Sam. "Let's get on to the treatment."

"Ok, yes, fine, fine--I have never seen your wound before. Can you lift up your gown so that I can begin the procedure?"

The resident's voice wavered in pitch, tone, and rhythm, as Sam's arm reached to open the bottom part of his gown. Removing a makeshift bandage revealed that across the outside part of his right thigh was a seven inch gash in the shape of an oval. It was 2 inches deep, and resembled a stagnant pond covered in a film of moss. Only this film was no green goop---it was a macabre mixture of pus, bacteria, and blood.

Overwhelmed, Dr. Rothfuchs staggered back, and stifled the desire to cough as he looked away and sighed deeply. Of course, sighing deeply was the last thing he needed, as the smell of the wound wafted even more strongly with the wound exposed.

"Sorry, sorry. I had tried to prepare myself, but it was more than I had expected. I am really hopeful that this is the last round of this therapy."

Of course, Sam wasn't--and he had heard other residents say the thing enough times to know that to be dubious.

And with that, Dr. Rothfuchs proceeded to open a large pouchlike bag, which contained a jar of bluish fluid and a large contraption that resembled a q-tip, except for the fact that it was 2 feet long.

"I'm sorry to have to do this, but this is the only way we can kill this strain of bacteria."

While Sam Vespucci and Dr. Rothfuchs knew what was coming, a person who was unlucky enough to have stumbled upon this procedure would have been incredulous that such a treatment was considered humane in the 21st century.

Sam had laid himself down on the examining table, hands feverishly gripping the sides, as Dr. Rothfuchs washed the wound with the blue fluid (which was a combination of soaps and alcohols) and dug deep into the wound with the large swab. He grit his teeth as the procedure went on, and some 15 minutes later, the cleaning apparatus was filth laden, while Mr. Vespucci's leg resembled your garden variety red seen at the butcher's market. Dr. Rothfuchs lay a new set of gauze on the wound, taped it up, and shook Sam's hand. He was pale, had shed some tears, but was still breathing. After all, this was the 12th time he had had this procedure performed.

"I really wish there could be some way for this wound to resolve and heal so that we could stop this regimen, but for whatever reason it looks just as fresh as it did on the day of your accident. Of course, our research department is still looking into all possible mutations that could have arisen. As you may know, Mr. Vespucci, this is a difficult search, as hundreds of genes and many cell types are essential for the coordinated process of wound healing. From fibroblasts to fibrinogen......"----but Dr. Rothfuchs was cut short.

"Listen Doc, you have to understand---if this doesn't get better within a few months, I just, I mean, I don't know if I can take it much longer." Hobbling out of the room, Samuel Vespucci said goodbye to the familiar faces, but could not look his familiar pain in the face.

Monday, September 3, 2007

is there one foundation?

I have thought about this song over the last week, and am convinced that its opening line is characteristic of the antagonism to the apostles seen in Protestants, particularly those of independent mindsets.

Even my own Presbyterian hymnal completely misquoted the verse that should come to mind, which is Ephesians 2:20. It states that the church is "built on the foundation of the apostles and prophets, with Christ Jesus himself as the chief cornerstone."

I found these lyrics on the website cyberhymnal--at least there it has the consistency to quote a passage from 1 Corinthians 3, which says, "For no one can lay any foundation other than the one already laid, which is Jesus Christ." Of course, that context is contrasting Christ with "wood" or "hay" or "stubble".

The question is, when we think it's honoring God to say that only Jesus matters, are we denigrating the means through which He works? Methinks YES.

Of course, this song brings up other thoughts about the unity of the church, the basis of which has been also heavily on my mind as of late. Overall, I read the lyrics and see some good things, and some good intentions that have gone awry in this world, as the ages have gone on......
The Church’s one foundation
Is Jesus Christ her Lord,
She is His new creation
By water and the Word.
From heaven He came and sought her
To be His holy bride;
With His own blood He bought her
And for her life He died.

She is from every nation,
Yet one o’er all the earth;
Her charter of salvation,
One Lord, one faith, one birth;
One holy Name she blesses,
Partakes one holy food,
And to one hope she presses,
With every grace endued.

The Church shall never perish!
Her dear Lord to defend,
To guide, sustain, and cherish,
Is with her to the end:
Though there be those who hate her,
And false sons in her pale,
Against both foe or traitor
She ever shall prevail.

Though with a scornful wonder
Men see her sore oppressed,
By schisms rent asunder,
By heresies distressed:
Yet saints their watch are keeping,
Their cry goes up, “How long?”
And soon the night of weeping
Shall be the morn of song!

’Mid toil and tribulation,
And tumult of her war,
She waits the consummation
Of peace forevermore;
Till, with the vision glorious,
Her longing eyes are blest,
And the great Church victorious
Shall be the Church at rest.

Yet she on earth hath union
With God the Three in One,
And mystic sweet communion
With those whose rest is won,
With all her sons and daughters
Who, by the Master’s hand
Led through the deathly waters,
Repose in Eden land.

O happy ones and holy!
Lord, give us grace that we
Like them, the meek and lowly,
On high may dwell with Thee:
There, past the border mountains,
Where in sweet vales the Bride
With Thee by living fountains
Forever shall abide!

Saturday, July 21, 2007

What suicide really is...

I must admit that there has never been anyone close to me who has actually committed suicide, but the concept has fascinated me. No, I am not talking about gory scenes in abandoned rooms so much as I am thinking of certain individuals who had so much going for them but they ended up squandering their gifts. This more protracted form of suicide is pervasive in our day and age, and is something from which one should always run. Of course, there are also the famous people who have committed suicide and the public is well aware of them, whose deaths generally sadden and frustrate the world.

Last night I came across such a jaw-dropping quote on this matter from G.K. Chesterton's Orthodoxy that I have to cite it in full. Read on, but please be ready for some serious analysis of this world:

....Grave moderns told us that we must not even say "poor fellow", of a man who had blown his brains out, since he was an enviable person, and had only blown them out because of their exceptional excellence. Mr. William Archer even suggested that in the golden age there would be penny-in-the-slot machines, by which a man could kill himself for a penny. In all this I found myself utterly hostile to many who called themselves liberal and humane. Not only is suicide a sin, it is the sin. It is the ultimate and absolute evil, the refusal to take and interest in existence; the refusal to take the oath of loyalty to life. The man who kills a man, kills a man. The man who kills himself, kills all men; as far as he is concerned he wipes out the world. His act is worse (symbolically considered) than any rape or dynamite outrage. For it destroys all buildings: it insults all women. The thief is satisfied with diamonds; but the suicide is not: that is his crime. He cannot by bribed, even by the blazing stones of the Celestial City. The thief compliments the things he steals, if not the owner of them. But the suicide insults everything on earth by not stealing it. He defiles every flower by refusing to live for its sake. There is not a tiny creature in the cosmos at whom is death is not a sneer. When a man hangs himself on a tree, the leaves might fall off in anger and the birds fly away in fury: for each has received a personal affront. Of course there may be pathetic emotional excuses for the act. There often are for rape, and there almost always are for dynamite. But if it comes to clear ideas and the intelligent meaning of things, then there is much more rational and philosophic truth in the burial at the crossroads and the stake driven through the body, than in Mr. Archer's suicidal automatic machines. There is a meaning in burying the suicide apart. The man's crime is different from other crimes-for it makes even crimes impossible.

Saturday, July 14, 2007

How a Kinase Kills

Dead bodies are strewn across hospitals, and why?

Some philosophers attribute this to God's wrath for our first parents' choice of eating forbidden fruit.

Others might call this the harsh reality of a universe without plan or purpose.

Other hybrids of these extremes exist.

But that is neither here nor there to this blog. What we want to know is the how of death, on a molecular level. This may sound like chest-pounding propaganda, but my first exposé will be about the set of molecules that interested me during my Ph.D. studies.

Browsing the most recent contents of Nature, Science, and Cell, I realized that a new discovery has been made in that field. Call it coincidental, but I am back in my old stomping grounds, reading about my former favorite molecule, Phosphoinositide 3-Kinase.

So what is PI3K, and why should you care?

Like all kinases, PI3K's job is to add a phosphate molecule to some other molecule. As the name implies, PI3K puts a phosphate on the number 3 position of phosphoinositides.

What is a phosphoinositide, and why should you care?

It's a lipid--think about grease; no, not that tawdry musical with John Travolta, or McDonald's. We're talking about cells here, and lipids are found predominantly in the membranes of cells.

Ok--so phosphate molecules are being placed on lipids that are on the membranes of cells. Why should you care?

Physically speaking, YOU don't care, but some molecules do. For, you see, phosphate molecules are highly charged, and you know what people say about true love. Just as the air can be charged with romance, a phosphate's charge can attract new "mates" to the membrane of a cell. What does that do, and why should you care?

This photo is out of date, but I drew it for a publication, and I can't resist including it here. In this circumstances, PI3K is composed of two subunits, labeled as p85 and p110. But you should get the picture---many molecules are drawn to the membrane for a molecular conversation. Overall, that conversation has a pretty uniform message--grow, reproduce, and SURVIVE!

In this case, T cells receive messages through their receptors for foreign molecules, and one chief carrier pigeon is our friend, Phosphoinositide 3-Kinase, which makes those little plus signs (that signify the phosphorylated lipids), which starts the conversation between many molecules whose names are immaterial to this discussion. But again, the message is important---cells are told to grow, divide, and survive.

Now, if we think about what is so bad about growing, reproducing and surviving, our thoughts may turn to apocalyptic fears of the world's sustainability, but again, we are talking about cells and organisms.

The real problem behind too much growth and reproduction on an organismal level is, of course, cancer.

That word, which may be more stigma than understanding to some of my readers, is simply uncontrolled growth of cells. As scientists began looking for mutations in genes that were common to cancer patients, it was a beautiful but tragic fact that molecules related to PI3K were often found to be the culprits at hand in many instances of cancer. This image shows a breast cancer cell-dividing rapidly, which in this particular cancer, has over a 50% chance of being mutated in the PI3K pathway.

In my next installment, I will try to explain what the new findings are, and why they are interesting.
Hopefully this introduction will be enough to chew on for now. But the method to the madness is hopefully clear now.

Until then, I remain as always, your obedient servant.

Wednesday, July 11, 2007

ave israel??

How can Revelation 12 not be about Mary? Help me out, here...

Read it for yourself:
The Woman and the Dragon

12:1 And a great sign appeared in heaven: a woman clothed with the sun, with the moon under her feet, and on her head a crown of twelve stars. 2 She was pregnant and was crying out in birth pains and the agony of giving birth. 3 And another sign appeared in heaven: behold, a great red dragon, with seven heads and ten horns, and on his heads seven diadems. 4 His tail swept down a third of the stars of heaven and cast them to the earth. And the dragon stood before the woman who was about to give birth, so that when she bore her child he might devour it. 5 She gave birth to a male child, one who is to rule all the nations with a rod of iron, but her child was caught up to God and to his throne, 6 and the woman fled into the wilderness, where she has a place prepared by God, in which she is to be nourished for 1,260 days.
Satan Thrown Down to Earth

7 Now war arose in heaven, Michael and his angels fighting against the dragon. And the dragon and his angels fought back, 8 but he was defeated, and there was no longer any place for them in heaven. 9 And the great dragon was thrown down, that ancient serpent, who is called the devil and Satan, the deceiver of the whole world—he was thrown down to the earth, and his angels were thrown down with him. 10 And I heard a loud voice in heaven, saying, “Now the salvation and the power and the kingdom of our God and the authority of his Christ have come, for the accuser of our brothers [1] has been thrown down, who accuses them day and night before our God. 11 And they have conquered him by the blood of the Lamb and by the word of their testimony, for they loved not their lives even unto death. 12 Therefore, rejoice, O heavens and you who dwell in them! But woe to you, O earth and sea, for the devil has come down to you in great wrath, because he knows that his time is short!”

13 And when the dragon saw that he had been thrown down to the earth, he pursued the woman who had given birth to the male child. 14 But the woman was given the two wings of the great eagle so that she might fly from the serpent into the wilderness, to the place where she is to be nourished for a time, and times, and half a time. 15 The serpent poured water like a river out of his mouth after the woman, to sweep her away with a flood. 16 But the earth came to the help of the woman, and the earth opened its mouth and swallowed the river that the dragon had poured from his mouth. 17 Then the dragon became furious with the woman and went off to make war on the rest of her offspring, on those who keep the commandments of God and hold to the testimony of Jesus. And he stood [2] on the sand of the sea.

Protestants generally vary between saying this is about either Israel, the Church, or both. But Roman Catholics see this as being Mary, the Mother of our Lord.

If I'm keeping track of score, this is one point for the Papists, in my book. But maybe you umpires would make another call from where you stand?

Tuesday, June 26, 2007

My problem with theonomy - 1?

It is far beyond the bounds my ability to adequately describe or defend theonomy, today at least. If you're not familiar with this term, here is a good start on the matter.

What I would simply like to do is invoke a familiar experience and hope to provide what it is that bothers me about an issue that I often find myself shamefacedly defending. Other times I go the route of the covert operative, and conceal my sympathy with my view.

Ultimately, the bumper sticker/t-shirt/cliche has it right.

What strikes me about this debate about ethics and law is that the precondition for living under a godly civil government, in terms of its explicit foundations and legislation is a plurality or majority of godly people who are dedicated to such a concept. Thus, I would like to argue that almost every problem associated with theonomy is an instance of the "5 year old with the car keys" fallacy. Just as Greg Bahnsen created a fallacy that became infamous (or famous, depending on your view) during his debate with Gordon Stein, in describing the "cookies in the cookie jar" fallacy, I would like to make a new term for the problem with theonomists as they have existed throughout the years. For, just as a small child thinks he or she knows what to do with a car, the boldness of most theonomists is actually based on an overemphasis on abstractions over reality.

For just as a 5 year old has no firm grasp or concept of what life would be like as someone who is old enough to drive, the theonomist who raises eyebrows with his or her outlandish claims has no firm grasp of what life would be like if Christians were living godly lives as the plurality/majority of society. Sure, one can look back to certain epochs, but in many ways that's just as helpful as the 5 year old looking at their siblings who drive. It may help one understand the shadow of the matter, without providing any substantial grasp of the matter.

As a result, we must be wary of any 5 year old who thinks they know exactly what they would do if they had a driver's license today. Similarly, the theonomist who ignores their status as a minority and focuses on Biblical ethics as an abstract principle becomes disconnected from reality to the point where the outlandish ideas and claims that have been made by some (but will not be recounted here) come up.

To be fully punny, what I am "driving" at is this: we should understand our place in the world and focus on that. There is no need to emphasize discussion of what the best Christian society would do, if there is not even consensus over the concept of one truth being good, let alone that of the Christians.

For now, we should nurture the things that we do have, which, as I hope this blog serves to illustrate, is more than a little.

Monday, June 25, 2007

The Heart of the Matter

I recently heard a sermon on Chapter 14 of St John's Gospel. Being interested in learning languages, I regularly carry a Greek New Testament to church. Hoping to learn via immersion, I read the Greek while hearing the English.

At any rate, a grammatical curiosity struck me.

This is the Greek for John 14:1

μη ταρασσεσθω υμων η καρδια πιστευετε εις τον θεον και εις εμε πιστευετε

In English translations, there is a big divergence in translating the word καρδια, which, like cardiologist, deals with the heart.

As I read the Greek and heard the translation, I noticed an inconsistency between what I saw in Greek and what the pastor read. Checking multiple translations through my phone, the divergence was clear. Here are 2 examples that illustrate this, from the NKJV and the ESV.

1 “Let not your heart be troubled; you believe in God, believe also in Me. (NKJV)
1"Let not your hearts be troubled. Believe in God; believe also in me. (ESV)

It seemed like almost every translation preferred "hearts" over "heart".

Now, καρδια for "heart" is indubitably singular, and the υμων of "your" is certainly plural but the question arises, why would a singular word be translated as plural?

Why would there be just one heart for all of the disciples?

Knowing that there is nothing new under the sun, I checked google for any discussion of this matter. Indeed, this has been commented upon by others, with regard to a different part of John here.

It seems like modern translators are unhappy with many individuals having one heart.
But I would respond to any skepticism that "hearts" should be "heart" by pointing out that when Jesus talks about evil in the hearts of those who doubt him in Matthew 9:4, we read και ιδων ο ιησους τας ενθυμησεις αυτων ειπεν ινα τι υμεις ενθυμεισθε πονηρα εν ταις καρδιαις υμων.

Clearly, there are some occasions where a plural form of καρδια such as καρδιαις is acceptable. But again, what is the "heart" of the matter?

I think that meditating on the notion that Jesus spoke to his disciples and referred to them as having one heart is something we deeply need.

It would surely be fascinating if Jesus would use a singular heart to talk about our lives. In our day and age, it is almost impossible to believe that there is only one body of Christ, but this is the case. And I almost wonder if this issue of preferring multiple hearts is not due to our society's preference for individualism. Greek may just be more amenable to thinking more corporately, but I doubt it, given Matthew 9:4.

Perhaps if we thought of passages such as John 14:6 in a more holistic sense, we would have a better grasp of who we are as the Church. And it might point to one reason why images such as these were painted--for they serve to remind us of the one heart that really matters, and that we are joined it to as Christians.

Wednesday, June 20, 2007

the ultimate signal to transduce

I started this blog to collate my thoughts on science. In the upcoming postings, my goal is to summarize the specific findings of a particular paper and make them intelligible to the non-scientist. My Ph.D. was focused on signal transduction, which is the idea of how cells receive, interpret and pass on messages. Similarly, I am here to receive, interpret and pass on messages to you.
We'll see how well this goes......

Friday, June 15, 2007

Still a work in progress--but complete structurally

Is Derrida in the Mosque? Muslim Apologists as Quintessential Deconstructionists


Among systems of thought, ideological evolution is far from uncommon. From the idealistic politician who promises never to change his views upon being elected to the simple farmer who wants to do things “the way things always were done”, the idea of change for the sake of change is opposed almost unanimously. This notion is exceptionally true in the world of classical religion, where eternal and timeless truths should be the tools of the trade. However, this is not true of many modern trends, as emphasized in schools of thought such as those inhabited by deconstructionist philosophers. In a manner akin to Pontius Pilate’s inquiry of Christ, these thinkers aim to ask “Quid est veritas?” by undermining the notion of veritas on a fundamental level. In response to this, Christianity has made many great strides towards defending itself, ultimately through pointing to the one who is truth itself. The idea of a supreme God as the source of truth and morality is appealed to by great thinkers throughout the religious thinkers of multiple faiths, such as Thomas Aquinas, Averroes, and Maimonides. In earlier centuries, this train of thought was echoed by scientific thinkers such as Isaac Newton. However, from the mid-19th century onwards, the role of philosophy and science as the handmaiden of religion was severed, as the intellectual establishment turned to a view of religion as an enemy of scientific progress. Further, the teachings of purportedly inspired religious texts were called into question by many scientific discoveries ranging from the age of the universe to the number of ribs in the different sexes. While treating the nature of the response to these challenges adequately is beyond the scope of this article, this historical vignette is important, for it shows the dialectical tension between religion and science. While Christianity has largely operated on the defensive in attempting to show the consonance between the Bible and modern religious findings, Islamic scholars have often gone on the offensive by attempting to demonstrate the prescience of the Qur’anic utterances. The purpose of this article is to analyze some of these claims, which operate on the premise that Muhammad could not possibly have known the scientific truths contained in the Qur’an apart from divine revelation. On the contrary, this article aims to demonstrate that this whole thesis is based on a deconstructionist assumption that language can be used without regard to historical context. As a consequence, these claims of foreknowledge fail the test of criticism, and call the inspiration of the Qur’an into question.

Religion and science-harmony, neutrality, or conflict?
Mankind’s search for the truth throughout the ages has taken on varied forms, from the austere realm of the monastery to the fast-paced but somewhat sterile view of the world embodied by modern laboratory science. The struggle over who ought to be the arbiter of truth has surely seen more peaceful days, when different fields of learning respected one another. In the modern age, the notion that studies of the natural world can coincide with theological and philosophical reflection is often challenged by both theologians and scientists alike. In prior centuries, the same conflict existed, but religious thinking was preferred over a more materialistic mindset. For example, Galileo challenged the validity of interpreting certain passages in the Bible in a geocentric manner. One such verse is Psalm 104:5, which states, “He set the earth on its foundations, so that it should never be moved.” The Copernican revolution had taken place, but some religious thinkers would not accommodate such an interpretation of the world because the Bible seemed to contradict that view. Because of that, Galileo and his views were condemned.
In more recent centuries, the tables have turned. As the intellectual heavyweights of the world have become increasingly skeptical of classical religion, it is the religious establishment that must answer the heresy trials of the church of the academic world. What can be said in response to this? While this issue is too lengthy to adequately address here, it is important to point out that ultimately when passages such as Psalm 104:5 are criticized, one must understand them within their historical and grammatical context. Thus, the term “foundation” is improperly understood when taken in the staunchly literalistic sense that was done by geocentric thinkers. Considering the Hebrew language and culture, it is clear that one can understand this phrase in a more simple sense, in considering the fact that our physical world is relatively stable, despite being ultimately quite motile. Again, delving into the details of this sort of argumentation is beyond the scope of this discussion. The important thing to grasp is that those who hold the Bible to be inspired by God must have an answer; is the passage in question in conflict with science because science has misinterpreted the data, or has the message of Scripture been misunderstood? The only other option would seem to be that advocated by those skeptical of the sacred book in question, which is that the scientific findings are proof of the man-made nature of the purportedly sacred book. Thus, in defending one’s faith, these matters are of paramount importance. It is to these matters that our attention is turned, in the context of the Islamic faith.

The conflict of the Qur’an and modern scientific understanding
Like Jews and Christians, Muslims hold that their God has revealed truth about the spiritual and physical aspects of the world through their sacred books. In understanding Islam, one critical challenge to the scientific understanding of the world provided from the Qur’an is the problem of embryological development. In discussing the nature of fetal development, several Suras in the Qur’an repeat a description of the nature of the growing baby using a specific word which when transliterated using Roman letters is ‘Alaqa. A typical Sura is 23:12-14, which reads:
"Verily We created man from a product of wet earth, then placed him as a drop of seed in a safe lodging, then We fashioned the drop a clot (‘alaqa), and of the clot (‘alaqa) We fashioned a lump, and of the lump We fashioned bones, and We clothed the bones (with) meat. Then We produced it as another creation."
As Dr. William Campbell documents in his book The Qur’an and the Bible in the Light of History and Science, the notion that the embryo is a clot is heavily dependent upon Greek philosophers such as Hippocrates, Aristotle, and Galen, for these thinkers made similar descriptions of the developing fetus. In this scenario of embryogenesis, the menstrual blood is not released during pregnancy because it comprises one aspect of the fetus’ body, while the more essential characteristics of the baby are derived from the sperm of the father. To cite one of these thinkers to elucidate this point, the following quotes from Hippocrates are collated in Campbell’s work:
“Sperm is a product which comes from the whole body of each parent, weak sperm coming from the weak parts, and strong sperm from the strong parts.” Section 8, p 321
Coagulation of Mother's blood
“The seed (embryo), then, is contained in a membrane ... Moreover, it grows because of its mother's blood, which descends to the womb. For once a woman conceives, she ceases to menstruate...” Section 14, p. 326
“At this stage, with the descent and coagulation of the mother's blood, flesh begins to be formed, with the umbilicus.” Section 14, p. 326
“As the flesh grows it is formed into distinct members by breath ... The bones grow hard ... moreover they send out branches like a tree ...” Section 17, p. 328
Thus, the argument is that this progression from semen to clot to bones as seen in Sura 23 is derived from the common but inaccurate medical understanding of ancient Greek thinkers. Of course, there are many Muslim doctors today who are well acquainted with the Qur’an and embryology. What has their response been?

Muslim apologists strike back-should scientists kneel in submission to the Qur’an?
As stated above, Dr. William Campbell has been one of the main critics of the inspiration of the Qur’an, especially with regard to the scientific claims contained therein. What is important to note is the basis for his writing The Qur’an in the Light of Science and the Bible, was in response to a book with a similar title. As a medical doctor, Campbell was offering a refutation of a book, The Bible, The Quran and Science, which was written by another medical doctor, Dr. Maurice Bucaille. Here, Dr. Bucaille states his reasons for seeing no conflict between the Qur’an and modern scientific understanding.
“ I had to stop and ask myself: If a man was the author of the Qur'an, how could he have written facts in the Seventh century A.D. that today are shown to be in keeping with modern scientific knowledge?....What human explanation can there be to this observation? In my opinion there is no explanation; there is no special reason why an inhabitant of the Arabian Peninsula should....have had scientific knowledge on certain subjects that was ten centuries ahead of our own.”
Instead of merely showing that the verses of the Qur’an do not say something that is enmeshed in the flaws of the medical understanding its time, Bucaille and others take the offensive in the argument and try to demonstrate that the Qur’an is not simply lacking in scientific error. No, their claim is based on the thought that many Suras contain scientific knowledge that was unattainable in the 7th century. So, how do they deal with the problem of embryology? Dr. William Campbell notes these arguments, and points out that the solution lies in refusing to translate ‘Alaqa as clot. Instead, Dr. Bucaille translates the word to be “thing which clings”, while another apologist, Dr. Keith Moore considers an even better translation to be “leech-like” substance. This seems to be especially apropos because the developing embryo does bear a superficial resemblance to a leech at one point.
What is Dr. Campbell’s rebuttal to this? He points out the consistent translation of ‘Alaqa as a clot in older versions of the Qur’an, and shows Islamic scholars treating ‘Alaqa as a clot. First, he collates the following translations of the Qur’an from multiple languages, and shows no precedence of translating ‘Alaqa as a leech-like substance or a thing that clings:

* French, un grumeau de sang (a small lump of blood) - Kasimirski, 1948 (last Ed. during life of author was 1887)[3]
* a leech-like clot - Yusuf Ali, (translation of 1938) 1946[4]
* a clot - Pickthall, (translation of 1940) 1977[5]
* a clot - Maulana Muhammad Ali, 1951[6]
* a clot - Muhammad Zafrulla Khan, 1971[7]
* French, de caillot de sang (clot of blood) - Hamidullah, 1981[8]
* French, un caillot de sang - Masson, 1967
* a clot of blood - N. J. Dawood, 1980[9] Approved by the Supreme Sunni and Shii Councils of the Republic of Lebanon
* Indonesian, segumpal darah (lump of or clot of blood) - Indonesian Department of Religious Affairs, 1984
* Farsi, khoon basteh (a clot of blood) - Mehdi Elahi Ghomshehi
* Chinese, xue kuai (blood clot)
* Malay, darah beku (blood clot)
Furthermore, Campbell documents hadiths and writings of thinkers such as Avicenna, who translate ‘Alaqa in a manner consistent with the classical usage of clot. What is the reply made by Muslim apologists such as Dr. Bucaille?
Campbell quotes Dr. Bucaille’s response:
“What is more likely to mislead the inquiring reader is, once again, the problem of vocabulary ...The majority of translations describe, for example, man's formation from a 'blood clot' or an 'adhesion'. A statement of this kind is totally unacceptable to scientists specializing in this field... This shows how great the importance of an association between linguistic and scientific knowledge is when it comes to grasping the meaning of Quranic statements on reproduction."
Overall, Campbell has stated his objections to inconsistencies, but I would argue that he has not contextualized them appropriately. While holding to inconsistencies is notable, the implications of doing so are unclear if the nature of doing so is not appropriately explained. To clarify the situation, our thoughts will turn to analyze this phenomenon in the context of modern philosophical developments. In doing so, the underlying basis this strategy will be revealed.

The cure is worse than the disease-the flaw of deconstructionist thinking
In calling the standard translation of ‘Alaqa into question, the Muslim apologist produces a rebuttal that seems intriguing. Indeed, how could such difficult aspects of biology be grasped by a simple illiterate Arab living in the 7th century? In a world where Christians tend to fly from defending their holy book from defense largely from fleeing debate, the boldness shown by these Muslim apologists is convicting, but how did they arrive at such boldness? In considering the solution offered by these defenders of the Qur’an, we do not encounter the work of philosophers such as Averroes and Avicenna. Instead, we are meeting the work of a modern day philosopher who was no Muslim-and his name is Jacques Derrida. Often called the founder of the deconstructionist school of thought, Derrida emphasized the importance of subjectivity in understanding literature, which challenged the relevance of studying literature within a particular mindset of the author, as a means to find the meaning of the text. Instead, he challenged the fixity of meaning by arguing that one cannot read a text as though it was a fixed thing. In his work entitled “Plato’s Pharmacy”, Derrida discussed the correct translation of the Greek word pharmakon. The discussion bears a striking similarity to the work of Muslim apologists on interpreting ‘Alaqa as a thing that hangs or a leech-like substance.
“We hope to display in the most striking manner the regular, ordered polysemy that has, through skewing, indetermination, or overdetermination, but without mistranslation, permitted the rendering of the same word by "remedy," "recipe," "poison," "drug," "philter," etc. It will also be seen to what extent the malleable unity of this concept, or rather its rules and the strange logic that links it with its signifier, has been dispersed, masked, obliterated, and rendered almost unreadable not only by the imprudence or empiricism of the translators, but first and foremost by the redoubtable, irreducible difficulty of translation. It is a difficulty inherent in its very principle, situated less in the passage from one language to another, from one philosophical language to another, than already, as we shall see, in the tradition between Greek and Greek; a violent difficulty in the transference of a non-philosopheme into a philosopheme. With this problem of translation we will thus be dealing with nothing less than the problem of the very passage into philosophy. (71-72)”
In Derrida’s work, the intellectual justification of pluralism is fulfilled, because any piece of literature is open to the active interpretation by the reader. In this process, the meaning of every word can be altered and will inevitably be altered by the background that the reader brings to the text. He argued that the word Pharmakon is not mistranslated when any of the multiple possible definitions are provided. Thus, objectivity is lost for the sake of the creative activity of the reader.
As a result, when we consider the argument that if one imposes a new meaning to words like ‘Alaqa one arrives at modern scientific truth, we must realize that the Muslim apologist is borrowing from the worldview of the deconstructionist. But in accepting that perspective to defend one aspect of the truth of Qur’an, the integrity of all truth is lost. As a result, the cure to the challenge against the historical interpretation of the Qur’an, which was based on a scientifically untrue Greek philosophy comes via a view of the Qur’an that is based on a modern philosophy that has no basis for supporting ultimate truth of any kind.

In analyzing the response to a scientific challenge to the inspiration of the Qur’an, we have seen that the argument for understanding the word ‘Alaqa in a manner that is outside of its historical context is a classic move made by deconstructionist thinkers. Of course, discussing embryonic development is only one aspect of Qur’anic teachings on the natural world. It is helpful to note in passing that other critical examples of Suras that are argued to have supernatural knowledge of scientific details include descriptions of water flow in oceans (Sura 55:19-20), the orbits of the planets (Sura 81:15-16), and even genetics (Sura 80:18-20). What is striking is in all of these cases the Muslim apologists arrive at apparently modern conclusions by deconstructing the text of the Qur’an, with no regard to historical interpretation or literary analyses. Because of this, a vast disconnect between Islam as a religion of truth and the deconstructionist thinking that defends it emerges, and calls the whole scheme into question. As our Muslim friends and colleagues try to defend the integrity of the Qur’an, we must humbly endeavor to demonstrate that the philosophical foundations behind such defenses are completely inconsistent with the particular claims of Islam as truth and beauty. Without such an approach, we will be divorced from our religion’s greatest principle of love. With it, we will shine as lights.

Recommended Reading:
A Website Critical of the Qur’an and Science:
A website defending the Qur’an’s view of science:
The Qur’an in the Light of Science and the Bible-Dr. William Campbell
The Bible, The Quran and Science, by Dr. Maurice Bucaille.

The Qur’an in the Light of Science and the Bible-Dr. William Campbell
The Bible, The Quran and Science, by Dr. Maurice Bucaille.
Plato’s Pharmacy – Jacques Derrida

Saturday, June 2, 2007

synergy is bad????

θεου γαρ εσμεν συνεργοι θεου γεωργιον θεου οικοδομη εστε

Tuesday, April 17, 2007

21st Century Emancipation Proclamations, Part Four

This report comes to you via Ronald Reul Neiklot, friend of the reporter Clive Staples, who wrote "21st Century Emancipation Proclamations". He posts the last part of this series here on the internet because, tragically, Clive had fallen in the shower and passed away. It is to the memories of Clive Staples held dearly by his family and friends that this last article is dedicated.

Dear readers,
I had promised to report on my experiences of late after the war to protect the unborn, but have thus far been unable to find the avenue to do so. Rueters has suppressed all attempts to report it. I hope at some point to find some means to transmit this report to you. It has not faced the rigours of editorial amelioration, and for that I must ask your apologies. For now, I must find some means to stay alive before it is too late-but is it already?

I clambered up the steps of the Los Angeles Roman Catholic Church, where I was to meet the Archbishop of that region, Pontius Canterbury. We were to discuss how the research done at the National Institutes of Health had repudiated the legitimacy of abortion while showing that the dogmas of mainline Christianity were vindicated, when I realized that there was much more to this rendezvous than would have been clear from my initial phone call.

For you see, Pontius Canterbury was on a mission. That may sound like stating the obvious, but when I say this I am not talking about saving souls or helping the poor.

Entering his office, I saw what looked more like a battlefield station than a place of monastic study and reflection. Before I had the chance to ask what his large collection of maps, flowcharts, and photographs represented, he instantly began interviewing me, as it were.

"Is it too late? Have they gotten to you already?", wavered his deep voice. "I have read your recent Rueters articles on the war, and by all accounts, you do not seem to be one of those who have been 'infiltrated'."

I hesitated, and questioned his sanity, responding, "Why sir, I don't know the meaning of this. If you're referring to the SMU, or Suppression of the Murderers of the Unborn, as President Greyback calls it, I'm not quite sure I follow. My articles have discussed the, shall we say, less pleasant aspacts of the liberation of the unborn. But you, after all, are a Catholic bishop. Are you not pro-life? Shouldn't this be a moment of celebration?"

"Ah, my dear lad, do you not see that the title given to these late events is in and of itself sufficient to show you that something is awry?"

And it was from this point that he began to talk about people as people, and not political pawns. Those who had clung to now outdated notions of choice vs. oppression, as opposed to death vs. life, as we all now freely admit, were sincere in their understanding of jurisprudence. They just happened to have missed the boat intellectually on the matter of biology.

What was worse was to hear more about the Hiram Smith massacre--that Smith's view of injustice could be justified solely because he was right about abortion made no sense to this pro-life bishop.

And as the catalogue of atrocities grew larger and larger, it became clear that to Archbishop Canterbury, and myself, this was not a thing of the past.

He documented how people driving hybrid cars were being taxed out of suspicion that they were once pro-choice. Further, those who did not attend church were harassed by the police, minorities were subjected to government mandated ultrasounds to see if they were pregnant (as abortions were performed on this group more than others), and if so, special monitoring would ensure that these pregnant women would not take steps to perform an illegal abortion. In the meantime, Greyback-sponsored companies that made those ultrasound machines and police cars were growing richer.

It was too much to take in. Vertigo and nausea swept over my soul and I fell to the ground, thinking of the immensity of this program.

"My dearest lad, if by now you cannot see by now that there is a movement to alter the structure of this government where anyone who does not support Greyback's agenda will continue to be oppressed in new avenues--not just abortion--I'm afraid I will never convince you."

"But Mr. Canterbury, what can I do?"

And here, dear readers, I must interrupt and tell you that the answer to this question never came in. A knock at the door broke the flow of our conversation, and a flood of some sort of tear gas entered in the room, masked officers came and handcuffed us.

Neither Archbishop Canterbury nor myself were able to move. What is worse was the fact that some property in this chemical was able to produce a blindness and deafness. All I knew then was that large hands grasped me and I was placed in some lorry of sorts. I was taken back to my flat and awoke some time later--time was a blur, but as I turned on the boob tube I realized that it was now 4 days after my interview with the Archbishop. Checking for the news, horror found new limits in my mind as I read that the Archbishop had been reported to be dead. In this account, he had committed suicide for having been one who was supporting back-alley abortions.

It seemed impossible, and any doubts that this was a cover for something larger were assuaged by a note on my desk.

It read:

"If you stop talking,

you will start living."

I came to the point where I realized that if I were to continue living as though what I had heard from Archbishop Canterbury was accurate, that I would be living life on the run forever. There would be no parley with this enemy that would keep him pacified. And so I set to write this last report. Will it find you, dear readers? I can only hope and pray that it does. It sounds odd of me to refer to praying, as I never had before I began this series. But stranger things have happened in the world.

Note from RR Neiklot: The text ended here, and I imagine Clive had more to say, but we will never know how he wanted this story to end.

----Clive Staples, Ronald Reul Neiklot et al., are fictitious people, as is all of this tommyrot.