Life Happens

This post has been a long time coming... there's really no other way to save it.  But as I sit here, contemplative, on the six-month 'anniversary' of my father's death, it only seems fitting to recap the profound changes the last half year has brought me.

I don't often think about whether December 21 and June 21 fall on the same day of this week, but this year I am.  And they do, for the record.  On a Tuesday just like any other day, I lost one of my best friends.  It's taken a lot of time to notice how profound of an effect my father's departure has had on me.  After all, how do you notice when something is slightly less there than it was?  We would only talk to each other over the phone, but we hadn't seen each other since December 2009... because I'd been off pursuing a degree that was making me miserable, living each day of the darkest portion of my life, just trying to muddle through and make it out the other end.

We didn't just talk occasionally.  It was every day, every spare second; if ever I were in the car driving alone, I'd call him just to chat.  If there were some random detail that reminded me of a conversation we'd once had - inside joke or not - it was his voice on the other line.

So I was buying a new jacket, called my mom to tell her, and instead found out Dad was dead - not immediately, of course, because where's the drama in that?  But my fiance and I hopped a plane to Oregon the next day.

And it was right then that something in me changed.  I'd spent the last two years of my life hideously depressed, feeling trapped and hopeless, like nothing in the world would ever be right.  Suddenly it wasn't, and my skewed perspective reset.  The quibbles and the trials were dwarfed in comparison; I sprang into action, an agent of change now myself.

It was profoundly moving to hear how he had impacted others' lives at the funeral.  Still, I didn't cry - everyone treated me like I was crazy or calloused, insensitive, unfeeling... but he wouldn't have wanted sadness over his departure, not really.  So I wrote his obituary and composed a 'eulogy' of sorts, infused it with the humor he so often incorporated into his life.  I coordinated arrangements to help Mom through it all, hacked e-mail accounts, tried to get all the proverbial ducks in a row - Dad had always taken care of finances and utilities and the like, but that would now need to be shifted into Mom's name.

Less than a month had passed when Mom informed me she'd be in a car accident in which her car was totaled; it was then I realized that ... someday, she too would pass on, that this would not be my only experience with a parental death.  It wasn't that I was morbidly obsessed with it - though genuinely a bit shaken - but rather a calm acceptance or realization of what was to come.  In many ways, I could empathize... yes, I'd lost my father, but she'd lost her soulmate, something I find utterly unthinkable.  She was now living alone in a life they'd built together, surrounded by reminders always taunting her about what she'd lost.  I began to make a more conscious effort to be there for her, to try to fill some of the companionship my father had provided: to listen to her vent when she'd had a bad day or at least to ask how her day had been.

The wedding was August 12 and we had scheduled a trip to meet with vendors toward the end of February.  It was bittersweet; we got much accomplished and were able to hone our ideas of what a wedding was to each of us, but with each new decision, Mom's wound was torn anew.  Then came March: a blitzkrieg tour of European universities for continuing education, me toward my Ph.D. and Andy toward a post-doc position.  The trip did not go nearly as planned, to say the least; there were myriad bumps on the road, and it was here that I first truly started to fear that the wedding shouldn't go through as planned.

I finally came to accept this shortly after we'd sent out invitations to all of our friends and loved ones.  We each had the exquisite pleasure of contacting them all to say, "No, we're really not going to get married so please don't show up."  Along with this decision, I decided not to go to Europe, not to continue toward a Ph.D.  In a matter of days, I had derailed my entire life plan and severed contact with one of my best friends, in the process inflicting great pain upon him.  And yet I was calm and self-assured that - difficult as it was - it was the right decision.

Oh, and one of my cats ran away.  People keep saying cats come back - he's not going to come back.

...so in the last six months, my life has changed more than I ever could have conceived... somewhat unexpectedly, a major part of this change is that I have gained a greater capacity for coping with life's little stresses and as such am no longer in counseling.  In fact, we have been tapering me off my crazy meds so that I am now relying on me for me...

I'm not the same girl I was six months ago when my father passed away, and it's largely because of him that I've been able to regain control of my life, to set it back on a path that is fitting for me.  The world did not end when my father died; it didn't even end on May 21, at least not the world as I perceive it.  In many ways, his death provided me the strength I needed to form a new life - for that I will always be grateful.

But I just wanted to take the time to say:

Daddy, I miss you.

Politically correct rantings of the incensed

At some point during my life, it became apparent that the things that were emphasized while growing up - compassion, teamwork, respectfulness - are not rights, but merely privileges of which others can/will deprive you at a moment's whim.  Now somehow it's the rhetoric - and not the truth - that matters.  Our political battlefield is exemplary in this right: if someone wants to reduce tax cuts on the rich, they're a socialist and decried as highly unpatriotic, an agent of the evil lurking in unknown caverns around the globe.  But what of our civic duty to seek the kernel of wisdom in all things and to nurture this kernel to fruition?

A grim view of the state of political discourse?

Most of my faith in the institutions instilled in me from my early childhood - largely due to a highly religious upbringing - has been eroded during the process of graduate school.  With very few exceptions, graduate students are expected to behave more as caged dogs than human beings, fighting and clawing our way over the backs of others to get the quintessential result to tout in front of the rest of the world as they gape in awe at our accomplishments.  Scarily, this dog-eat-dog nature is not just interlab, but often times intralab.

This is a perfectly natural phenomenon, when considered.  It's like sibling rivalry, except your parents are supposed to love you, whereas your advisor may remain perfectly apathetic, thereby retaining the option of encouraging the back-biting and undermining - all in the name of science.  It isn't hard to understand why science is misunderstood - even mistrusted - given the atmosphere of competition and 'survival of the fittest' so commonplace throughout the genre.  It's no wonder some scientists are driven to fraud, forging results just to alleviate the constant pressure to make something happen (make just one something happen).  According to Wikipedia:

Fabrication is the falsification of data, information, or citations in any formal academic exercise. This includes making up citations to back up arguments or inventing quotations. Fabrication predominates in the natural sciences, where students sometimes falsify data to make experiments "work". It includes data falsification, in which false claims are made about research performed, including selective submitting of results to exclude inconvenient data to generating bogus data.
Bibliographical references are often fabricated, especially when a certain minimum number of references is required or considered sufficient for the particular kind of paper. This type of fabrication can range from referring to works whose titles look relevant but which the student did not read, to making up bogus titles and authors.
There is also the practice of dry-labbing—which can occur in chemistry or other lab courses, in which the teacher clearly expects the experiment to yield certain results (which confirm established laws), so the student starts from the results and works backward, calculating what the experimental data should be, often adding variation to the data. In some cases, the lab report is written before the experiment is conducted—in some cases, the experiment is never carried out. In either case, the results are what the instructor expects.

And that's not even the worst outcome that's been seen.  (For the record, this is a link to a late-90's New York Times article on a graduate student at Harvard who committed suicide in an attempt to affect change in the graduate school system - no gruesome pictures, and a very interesting read if you're curious about the psychology that often plagues graduate students.)

So we try to rise above, try to turn the other cheek, remain aloof from the back alley dealings and machinations of Science, as we were once taught so emphatically to do.  The only problem is that distance often seems enough to fully eject us from the mainstream of science.  We lose our competitive edge, we lack comparative dedication, we seem unconcerned with science herself, rather than with the politics and bureaucracy pervading every niche.

The Grad Student Gap (AKA The Bane of My Existence, The Great Demoralizer, etc.)

And there it is - politics.  Is our method of political discourse what leads us astray, even as it spills into other fields?  In our winner-take-all system, compromise is a four-letter word.  To meet in the middle is to show weakness, abandon the interest of your constituents - someone has to lose or we've not done it correctly.  To demonstrate that 'our side' is more meritorious of getting their way, we keep prolific catalogs of every injustice, every mistake, never forgiving or forgetting as it would be disadvantageous to us getting our way.

I don't know about you, but I don't think my father would be proud if I acted like that in everyday situations.  Call me a hippie, but life - to me - is about the interconnections, between people and places and things and ideas.  That's why I find science so fascinating, seeing how everything fits together so perfectly; even the zombie-inducing fungus I mentioned in the last post is really a staggering caper of nature.

What's the use of being 'right' if in doing so we doom ourselves and our world?

So here's your homework assignment, kiddos: go out there and do what you think is right in the world.  Be the change, make a difference.  Try to see something from someone else's perspective.  Enjoy the experiences, whether victory, defeat, or somewhere in betwixt.  Meanwhile I'll sit here and rage against the machine, trying to lead by doing and words rather than just words.

Sci-fi buffet, episode I: Zombies are REAL

It's about time for me to actually start this series, though I do have a number of scientifically relevant things to discuss with you all, dear followers.  But for tonight, let us start with one that will rock your socks off: zombies are real.

For any fans of the Resident Evil series, this should rock your world.  Those of you that fantasize of the zombie apocalypse - or zombpocalypse, as it is know to the hardcore, at least in a phonetic sense - your moment of vindication has arrived.  And if your favorite book is "World War Z" - like Nathan Fillion, who is absolutely the best anything ever *sigh* - here is your proof.

courtesy of National Geographic

ZOMBIE ANTS!!!!!!!

Okay, perhaps not as frightening as the husk of a former human being lurching toward you with that hungry, vacant look in their now-soulless eyes, but we've all got to start somewhere, and it seems like zombie-ism has its foot in the door.

Now this ant is not a reindeer/elk/ant hybrid.  No, the stalks that you see in the picture above growing out of the ants head are in fact one of four species of fungus recently discovered in Brazil which can exert mind control over the host ant.  What this means is that the fungus, once exposed to its host, can take over the ant's brain and wait until the ant relocalizes to an ideal spot for fungal cultivation.  At this point, it then kills the host so that the fungus is able to proliferate and make a go at world domination.

David Hughes, an entomologist at Penn State was quoted in the National Geographic article from whence the picture was borrowed as:

 This potentially means thousands of zombie fungi in tropical forests across the globe await discovery.

Of the four species yet discovered, each appears to be specifically adapted to a corresponding species of ant, over which it can exert optimal mind control.  If there are truly thousands of zombie fungi out there, what else may fall prey to these maniacal mushrooms?  (N.B.: Fungus is more than just mushrooms, so I'm a bad scientist for that alliteration)   Time is the only one who can tell, but let's all just hope that we don't end up pod people to an indigenous strain of fungus, bent on taking over the world.

Also particularly interesting, beyond simply specializing in what hosts to take over, the fungi apparently have evolved different mechanisms of transmission to further the spread of their particular fungi.  For example, some cause the host organism to develop long spines emanating from the thorax, which - upon contact with another ant of the same species - allows the fungi to move to a shiny new host.  Other fungi take a more grim approach, generating explosive spores in the body of fallen host ants which serve as a proximity mine; when any other ant gets too close, GO BOOM! and the spores take their rightful place as the new owners of the ant brain.

courtesy of National Geographic

The fungi continue to replicate and renew inside the ant carcasses until they eventually emerge.  See above for "before" and below for...

courtesy of National Geographic

AFTER!  Diabolical, no?  But highly effective as all the necessary resources for growth can be scavenged from the deceased host.  Life is a game of survival of the fittest, and this fungus is fit to be tied... but I don't want to have to touch it to tie it, so you do it.

The good news is that given how specialized the species of fungus discovered so far have been, we're relatively safe from swarms of zombie ants (so long as we don't live in Brazil's rain forests).  But evolution has a funny way, so imagine what things may come...

Actually, don't.  It's creepy!

Weddingpalooza 2011

General rule of thumb for future life decisions: if it seems like it will be utter lunacy, the likelihood is it will be.

As my fiancé and myself return from a Blitzkrieg campaign of wedding planning in Middle-of-Nowhere, Oregon, we find ourselves depleted of energy but alight with new ideas about the many wondrous things that can be done with this wondrous celebration of blissful love.  And then overly fatigued once more when we begin to think of how said celebration will tax our limited resources of time, money, etc.

After embarking to Oregon on an utterly ludicrous itinerary brought about by the cashing in of frequent flier miles (Champaign through Chicago through Dallas to Portland), we arrived at in the midst of a snowstorm – epically rare in the Willamette Valley and yet the second into which we’ve traveled in the last two months.  The drive from the airport to the quiet town in which my mother resides – though I should say ‘at the top of which my mother resides’ – was fraught with icy roads, hordes of snowplows, and low visibility, unnerving to say the least.  Eventually, fourteen hours after our initial departure, we arrived at a place where we could catch some shuteye.

Unfortunately, this brief respite was just that – all too brief.  Our plans for the following day were to head to the high desert of Oregon, which as you might imagine is at a higher elevation than that at which we denizens of the Willamette Valley reside.  And the snowstorm raged on.  In an effort to circumvent the snow, rolling in from the north, we headed south, to cross the Cascade Mountains not at the apex of Mount Hood but rather on a smaller state highway that crawls through a lower (less than 5000 feet elevation at the highest point) swath of the mountains.  This effort was in vain; the blizzard hounded us, obfuscating our view of the road, slowing down all the cars to just above a dull crawl, and lessening traction just enough to keep you – and your car – on your toes.

But we persisted to keep our rigorously regimented schedule of vendor interviews, attempting to maximize our efficiency during our sole pre-wedding trip to the destination.  After only one incident of less than optimal traction, we arrived safely at our first appointment.  The deluge of questions and counter-questions began in earnest.  What sort of colors did we envision for the wedding?  Were we more string lights or Chinese lantern type people?  Did we want to have all the traditional trappings of the wedding ceremony, like the tossing of the bouquets and garters?  Had we selected the music for the processional, the recessional, the first dance, the father-daughter dance, etc.?  Our brains began to feel numb and puddle-y, with good reason.

Amazingly, we were able to rally on our quest for plans and answers.  In a testament to our compatibility, we managed to have mostly coinciding answers under fire.  We felt somewhat relieved, but oh so fatigued.  Four appointments and a misplaced state-issued id – crucial to our ability to return home post-madness – later, we exhaustedly fell into our hotel beds, garish but inviting all the same.

Upon realizing that we had not considered libations for the reception, we rallied to go test out a local brewpub to sample their ales.  At the pub, there was standing room only – even that was in sparing quantities.  We unanimously decided against a 60-minute wait to be seated, and wandered around the downtown area to find another establishment to sate our hunger.  A directory conveniently located on the corner assisted us in finding a restaurant boasting fine Italian cuisine; something about the day we’d had so far really resonated with carbo-loading.  We were somewhat disheartened, then, when we entered to find that the place had been repurposed to a mishmash diner of sorts, serving only three Italian items, standard deli fare, and breakfast at all hours of the day or night.

Alas, sweet sleep, giving plenty of time for sufficient rest before our 8 am appointment the next morning.  But we had not set our alarms – mine principally due to the lack of screen visibility of my phone resulting from a recent laundering mishap – and so were awakened by a somewhat harried call from my fiancé at quarter till 8, asking if we were ready to depart as we surely should be.

We hurriedly gathered our supplies, readied the room for checkout and set off on our way.  In the hullabaloo, we conveniently misplaced the address for the meeting, which resulted in a scenic tour of the residential areas of town, eventually leading to the planned meeting place.  Another full day of meetings awaited; from our previous days’ ventures, portions of the journey seemed vaguely familiar.  Finally, all consultations concluded, so we picked up my id and headed off across the mountains again.  This time, the sky was graciously clear so that no snow impeded our view, but we wove in and out of the mountains in the darkness, flickering the high beams on and off as each dearth of traffic would permit.

The next appointment was to sample wedding cake flavors, a sacrifice we begrudgingly made for the sake of our special day.  Then we were off to a fourth grade basketball game, followed by milling about a mall for several hours to meet up with a few more vendors.  A one and a half hour wrap up with the planner helped us debrief after our frantic weekend campaign and we headed home to sleep.

We were so appreciative of our return itinerary – Portland through Dallas to Champaign – for its relative simplicity as compared to the flight out.  Unbeknownst to us, a storm had been brewing over the whole of Illinois.  Fifteen minutes before we were scheduled to land, we encountered some ‘weather’ so jarring that it allowed us to experience the sensation of zero gravity.  Admittedly, this could be cool, but generally in situations in which one gets to elect to have this experience.  After emerging from the heart-quickening turbulence, our captain announced that we would soon be landing – in Madison, WI.

The usual trials and tribulations of a cancelled and/or paused flight led us to queue for an hour or two to secure overnight shelter.  We exited to the shuttle loading station at which no shuttle had yet shown.  Hailing a taxi and inviting a friend or two from the halted plane allowed us to arrive at our hotel slightly earlier, quite fortuitous considering 57 people would soon be vying to get checked in and get some much coveted sleep.  We were also lucky enough to secure for ourselves a place on the 5:30 am shuttle back to the airport so that we would have ample time to pass through security and board our 7:00 am flight back to Champaign.

But five hours of rest seems far too cruel an amount when you are facing the prospect of emerging from a warm bed to stalk out into the wintry night.  Alas, we persevered, taking the last two seats on the shuttle; the ride was unsurprisingly quiet, full of half-zombified voyagers caressing their hot caffeinated beverages.  Much to the chagrin of many an experienced Madison traveler, our cadre of crewmates arrived at the lesser-known security checkpoint, veritably gumming up the works – which by all accounts were normally quite sleekly streamlined.

At 5:55 am at the Madison airport, there is not much in the way of libation and food options.  We procured a bagel with cream cheese and a coffee for my beloved, a giant sugary cinnamon roll for myself (so as to compensate for my aversion to the caffeinated beverage in an energy sense).  At the gate, we were somewhat amused to hear that the flight had been delayed an hour due to the fact that the crew would not be able to get sufficient quantities of sleep had they undergone the same process that all we weary travelers had.

But we made it.  We returned to Champaign, with better and more concrete ideas in our minds, having now a skeleton of something that vaguely resembles a wedding.  An exercise in fatigue, but fortuitously not in futility.  And after a full day of work, we’re really quite exhausted.

Don't you forget about me - a stream of consciousness exercise

As I teeter on the precipice of the mystical convergence currently attempting to sabotage my life, I find myself careening slowly down the slippery slope of sanity.  Okay, so the convergence isn't 'mystical' so much as the whole "when it rains, it pours" phenomenon that we all seem to encounter at one point or another in our lives.  At the moment, I can fully appreciate why the Mayas believed the world was going to end in 2012, and I may well be doing my part to accomplish this feat.

Luckily for all of us, I don't seem to be the only one attempting to bring about the end of the world as we know it.  I'm not usually a political person, but I do have strongly held beliefs about what is right and decent, many of which are currently at odds with the proposed budgets being bandied about in Washington.  Granted we all have our notions and our druthers about what works and what doesn't, but the Congress seems to be taking a fairly large swath of cut and run politics to try to tidy up our mounting national debt.

Don't get me wrong: yeah, I think balancing the budget is a great idea.  But doing it by cutting EPA funding to monitor greenhouse gas emissions seems a tad short-sighted.  I don't follow the news in great detail, but I have seen an OBSCENE amount of publications and reports lately about how climate change is going to affect the world, and I think it would be incredibly foolish of us not to act now to try to get things under control.  As jingoist as America tends to be and as much as we might like to occasionally pretend that while no man is an island, a country very well can be - it's not true.  As one who has long contemplated the indelible mark she is leaving on the world, I can attest to the fact that there are always ripples in the pond, always consequences of the wingbeats.  I also don't hold to a doom and gloom viewpoint, that no matter what we do we'll always make things worse.  But whatever happened to the philosophy that one should leave a place in as good of a condition - if not better - than how they found it?  And why would this be a bad policy to keep in mind as we make decisions that will ultimately affect the future of not only our progeny but mayhaps also our planet?

Among other things being cut to try to tidy up the bottom line: arts funding for things like the Public Broadcasting Company, money for organizations like Planned Parenthood, ... and a few more things from the EPA.  If you'd like to read more about the amendments to this proposed budget, the New York Times has been doing a great job keeping we, the American public, up to date.

The goal of these budget cutbacks is to regain $60 billion, a not insubstantial sum.  But according to the 2010 Census, American currently has on the order of 300 million citizens, which means that $200 more tax revenue from each citizen each year would offset all the cuts currently being made.  It seems logical to me that a two-pronged approach - cutting back on some things and increasing revenue - would make the most fiduciary sense in the long term.  I would rather pay an extra 5% tax than lose the EPA, and I don't think I'm alone.

Of course, thinking about the EPA reminds me of my currently delegated responsibility in my research lab: submitting waste solvent for disposal.  We do this on a weekly schedule so it's really not a hassle, but the amount of planning and effort that goes into this weekly event is staggering.  I don't often think so far outside of my post, but waste management is actually a very intriguing notion.  Imagine if you will working in a job where each week, you come pick up some mystery chemicals of which you have been tasked to dispose.  Some of these chemicals are best treated by reacting with another solution to neutralize them, some are buried, and some are burned.  ...and there it is.

Given the sheer number of explosive compounds in your average chemistry lab - ones that are prone to go boom without the addition of a spark - the idea of setting fire to said mystery chemicals is terrifying!  Therefore it is imperative that we identify the contents of our waste to the best of our abilities so as not to lead to unexpected havoc further down the line.  We sometimes refer to this as "not crossing the streams"... which they also advise not to do in Ghostbusters, unless you happen to be up against an all-too-large marshmallow man bent on the destruction of your town.  Hey, and in Ghostbusters, that ghoulie was only released because of non-compliance with an EPA-like agency!  Everything comes full circle.

Speaking of not crossing the streams, as I sit here in lab with a mixture of two clear liquids, I am finding myself fascinated with the fluid dynamics of miscible solvents.  It's truly beautiful, combining water with acetonitrile (Wiki linked here) and watching the wisps dance about the container walls, spinning and twirling this way and that, slowly becoming one despite initial resistance.

...in the end, I find it highly worth it to invest in the quality of our world, don't you?

Cataloging other digital publications

In addition to going for it via this blog, I have also sought forms of (pro bono) gainful employment.  Here are the links to other such writings that have been published on the web:

04/05/2011:  http://www.dailyillini.com/special/moms-day-guide-2011/2011/04/05/mothers-grandmothers-make-for-the-greatest-role-models
                     http://www.dailyillini.com/special/moms-day-guide-2011/2011/04/05/relationship-with-mom-undergoes-transformation-after-dad-pass


03/30/2011:  http://fwix.com/champaignil/share/7273bbe1ce/take_a_look_theyve_cooked_a_book

03/16/2011:  http://media.www.dailyillini.com/features/2011/03/16/asb-an-alternative-from-the-ordinary

03/08/2011:  http://www.dailyillini.com/features/2011/03/08/studying-abroad-no-obstacle-for-unofficial-celebrations

03/01/2011:  http://www.theurbn.com/2011/03/simulated-mars-mission-reaches-halfway-point-surface-walks/


02/14/2011:  http://www.theurbn.com/2011/02/study-probes-crew-effects-traveling-mars/

COMING SOON - Sci-fi buffet

Color me a geek, but I love me some good sci-fi television and/or video.  As my betrothed and I sit here tonight watching "Die Another Day", it occurs to me that there is an unrivaled amount of material for coverage that would be amazing.

In the coming days, I will highlight different productions and the kernels of science truth underlying them.  After all, the best science fiction is that with a tinge of possibility.

Nature v. nuture

I love kids.  Alright, I said it.  It's out there on the interwebs for all to see and know.  They're such fascinating little specimens, what we would all be like had the world not gotten in the way.  But on occasion, I wonder for how much genetics can really account.

Perhaps this preoccupation begins with my mother, who is a twin.  As might be expected, she and her twin have a heightened sense of sibling rivalry when it comes to each other, which has continued to flourish into their 60's.

Here is one of my favorite pictures of the two from their youth - and also the start of my questions.  You have two children who are born into an identical environment, raised by the same family, arguably loved the same amount - so why does my mother (on the left) lack the apparent happiness of my aunt (on the right)?  What's really fascinating is that they are still differentiable by these smiles, which they continue to produce upon photographic opportunities.

At what point along the way does our environment take over in the creation of our personalities, if it does so at all?  Well, okay, yes it does contribute.  That's the beauty of twins, especially identical ones - all the same genetic material, but a different overall outcome somehow.  While it would seem natural to assume equal treatment, the amount of variables contributing to each experience each day is vastly staggering.

This was truly brought to mind last night while babysitting two darling little boys.  The younger one has the most adorable blue eyes and at some point along the way, he seemed to have figured this out.  I've often conversed with his mother about whether the boys get different treatment because of their mannerisms.  But is it because their genes directly influence their behavior or because the responses to their genes do?  The younger one is cute and knows it, so he uses this to his advantage - is this a cute-linked behavior gene or just because it's a trait to which we are all drawn?  ("Who's a cute little boy?" "Aren't you such a smart little girl?")  Do these comments of encouragement we feed to children ultimately determine the personalities they will develop?

Okay, well, I'm curious about this so I'll research and report back to you all throughout this week.  Stay tuned!  =)

As promised: Antibiotics are awesome!

Forget World War I.  The real great war is modern medicine.

The interesting thing about bacteria is that they're everywhere.  A large amount of human physiology and function depend on the tiny microbes co-inhabiting our bodies.  Now this may seem disgusting, but in truth, bacteria often get a bad rap.  They only become a problem in the classic case of "wrong place, wrong time".

Take for example the bacteria currently colonizing my sinus cavities.  These little guys probably aren't all bad.  Bacteria contribute to the natural functions of our eyes, our digestive tract, our reproductive tract, and even our skin.  The problem occurs when this natural biological ecology gets thrown out of balance.  This can generally happen through either overpopulation or when a rogue bacterium wanders into one of the regions of the body that is generally free of flora (enter my sinuses).

Okay okay... regardless of the bad rap, when we need to get healthy, where do we turn?  Thankfully, on a very basic level, bacteria are quite different from ourselves.  This may seem obvious, but the basic biochemistry decorating the exterior of the bacteria and the manners in which they protect themselves from the outside world are sufficiently divergent as to allow us to target them in a quite clever manner.

Augmentin is a combination of amoxicillin and clavulinic acid, a potent one-two punch that goes after the bacterial cell wall, which serves to protect the bacteria.  The cell wall also allows bacteria to sequester essential ions that provide for production of energy.  Without this energy, the bacteria cease to be.  Therefore, the goal of our drug is to halt the production of the cell wall.  Amoxicillin and clavulanic acid are able to accomplish this goal due to a close resemblance to a key portion of the cell wall, the D-alanine-D-alanine dipeptide:

Amoxicillin, like all members of the family of antibiotics known as beta-lactams, contains a characteristic moiety (shown below in red) that serves as a mimic of the terminal D-alanine-D-alanine.

Due to this resemblance, amoxicillin is able to bind to the active site of the enzymes responsible for synthesizing the bacterial cell wall - and quite well at that.  Through this binding, the enzymes are irreversibly shut off, causing a build-up of molecules that are precursors to the final cell wall.  These molecules then initiate the degradation of the wall, imitating conditions under which a cell wall would be reorganizing.

However, this was not the be all and the end all to this story.  The bacteria fought for their lives and found a manner in which to win.  By producing another enzyme called beta-lactamase, the bacteria are able to degrade the beta-lactam antibiotic before it is able to interfere with cell wall biogenesis.

Now enters clavulinic acid, shown here:

While clavulanic acid does contain the beta-lactam moiety (see red above), unlike amoxicillin it is not bactericidal in and of itself.  However, due to its structural proximity to antibiotic beta-lactams, clavulanic acid is able to inhibit the beta-lactamase enzymes that degrade the beta-lactam antibiotics that inhibit the enzymes responsible for the synthesis of the cell wall.

In essence, this chess match is why antibiotics are awesome.  When it comes to it, the bacteria have two options: to be killed or to adapt and become even more powerful than we could possibly imagine.  Both choices are made, but the antibiotic assures that only the strong survive and that the good (from a treatment standpoint) die young.  This is why there is such outcry against the overuse of antibiotics - while it does not *create* new superbugs, it does assure that the relative proportion of resistant bacteria is ever increasing.

Anyway, the complex layers upon layers of action and reaction are somewhat boggling to consider.  Who would have thought medicine would have so many tactics and tricks up its sleeves?

For the reader who desires to know more, I highly encourage a trip to Wikipedia.  Many of the terms - including the compounds discussed above - can be found there and in a fair amount of detail.  Given the references at the bottom of all Wikipedia entries, your descent further down the rabbit hole is entirely at your discretion.

Redemption a-go-go: A post-script and/or appendage... appendectomy?

The true quandary of perceived failure - not just in graduate school, but rather in life in general - is how much of our identity we tie up in the things we do.  To quote "Batman Begins":

It's not who you are underneath, it's what you do that defines you.

So when we choose a life path at which we excel time after time, we develop a strong sense of identity.  I, chemist.  But once reality kicks in and things begin to fall apart, with what are we left?  To me, it's all a part of the process of growing up, much like that first time we discover our parents are fallible, human... can be wrong.  Yes, it's earthshaking, but in the end, it helps us grow to better understand and appreciate them.  So to should it be with self failure.


Perhaps the hidden moral is to diversify, embrace all of the little things that bring one joy, so that when such a situation arises, our entire self-conception is not bet on the one dark horse.  People are so intrinsically multi-faceted; it's a shame to focus on just one piece.

Redemption a-go-go

After six years of successively failed experiments, a light miraculously appears at the end of the tunnel.  An interview in Germany - of all places - for admission into a seemingly reputable graduate school.  Suddenly, everything seems worth it - granted, I never thought it was not worth it, but sometimes the prospect of graduate school can seem a bit bleak.

The nature of a graduate student is generally that of Sisyphus.  Every day, we toil to push the same boulder up the same craggy slope, only to find on most days that we lose our footing and must start anew.  It ends up being like nothing we've ever experienced before.  If we ballpark the academic history of your average graduate student, it goes something like:

Top of class high school > Top of class college > "Why is nothing working?" graduate student

Now this is by no means a universal experience, but to those who do go through this phenomenon, it can be quite ground-shaking.  It makes you question your core value and whether all the people who said you could do this were in fact out of their minds.

Exacerbating the situation is the dogma that if you work hard, things will fall into place.  I recall so many frustrated conversations with my father trying to spur me onward by saying that maybe I just wasn't applying myself enough.  But in a field so akin to voodoo where we cannot see most of the mitigating factors contributing to the overall outcome, sometimes effort and tenacity just isn't enough.

So here I sit, with an unprecedented opportunity to get a change of scenery, a fresh start toward a goal which I'd ultimately love to achieve.  For the things I want to accomplish, more 'qualifications' are undoubtedly better than less.  And I could not be more thrilled at the possibility.

A befuddled ponderance

In an era of instant gratification, there seem to be a lot of things that remain enshrouded in mystery.  Perhaps I am being morbid, but the interface of death and information is something of incredible interest to me of late.  Now undoubtedly, this is in part - if not almost entirely - drudged up by the recent passing of my father; it is fueled without question by the reception of news that my mother was involved in a car accident this morning.

To me, there exists a quandary regarding the triviality of information so easily disseminated.  I can tweet about the egg white omelet I had for breakfast, instantly allow anyone in the world who so chooses to partake of this fact.  But something that truly matters - a loved one in need being the example that springs to mind - can remain unknown for indiscriminate periods of time.  I found out that my father had had a heart attack because I was calling my mother to tell her about a new winter coat I had just purchased.  Such a life changing piece of news was articulated as it was due to mere chance - it seems a perversion.

In addition to his volunteer activities (he served as a court appointed special advocate and spent time entertaining children being evaluated for signs of abuse), my father had an active presence in the online world.  As was always his custom, he made a distinct effort to stay hip to the times so that he could better connect with those important to him, including his four daughters who were spread out over three states.  He played World of Warcraft - a game to which I introduced him to help whittle away some of his newly acquired time after he retired - and excelled at this.  But this profound online presence now creates a startling dilemma:

What do we do with a virtual entity when the one to whom it belongs is really dead?

In looking into these matters, I have a few things which I will share here for future knowledge, dear readers:

-Facebook does provide the option for family members to "memorialize" the account of a deceased relative.  This ensures that the account is not toyed with post-mortem, but is allowed to remain as a testament to its previous owner.  For the immediate family members, it appears that there is an option to remove the account from the world wide web altogether; I shied away from this as it seemed somewhat contradictory to my father's technological nature.

-World of Warcraft will allow for the account of a deceased player to be transferred over to a member of the immediate family.  The family member will then be able to log on as one of the deceased's characters to spread the news of the player's demise.  This is something toward which I have been working for a while, as in such a game, one is likely to interact with the same group of people daily, even coming to be an integral portion of the game for other players.  It is important to me that his fellow gamers not feel as if he had abandoned them or become unexpectedly undependable.  However, this requires proof of death and so this remains unchecked on the 'to-do' list as I await a copy of the death certificate.

As strange as it may seem, all of our technology is still somewhat in its infancy.  As it reaches adolescence, issues such as these begin to be addressed.  But what is the best policy?  How should we proceed?  In a virtual world where we can feign to be anything, how do we address issues of such gravity?

While I lack answers, I think these are worthwhile questions to begin considering.  Perhaps in the future, wills will detail the division of all assets, in addition to how to handle our online gremlins.  Only time will tell.

How to be a nerd

I've heard that the best way to learn is to make a series of connections in your brain, which would - somewhat ironically - create a spiderweb of sorts in your skull.  The more you learn, the more latent pathways can be subconsciously awakened, allowing you to jump from one topic to something seemingly completely unrelated.

Clearly this does not have to relate to merely science, but as science is my quasi-expertise, for me it often does.  For example, when I am frustrated, I commonly say/type "ARGH!"  However, after a course in which we were 'forced' to memorize all of the amino acids and their structures, "ARGH!" soon took on a whole new life as the frustration peptide:

This peptide is cool for a number of reasons, not the least of which is the resemblance of part of the side chain of arginine (highlighted in red) to the flux capacitor of "Back to the Future" fame:

(borrowed from instructables.com)

These webs of connections create endless possibilities for inside jokes, nerded up pop culture references, and snarky apparel as can be seen by the sheer number of sites marketing t-shirts referring to LeBron James leaving the Cavs, for example.  Hey, I've got a number of ideas for such shirts myself.

Regardless of what you're into, the truth of being a nerd is just to be into it.  Be unabashed and outspoken and enthusiastic.  So what if people think you're crazy because of how excited you get every time you discuss your college D & D campaigns?  Let your freak flag fly and your mind wander through the paths you've slowly been building all your life.

COMING SOON - Antibiotics are awesome!

As I battle a sinus infection, I forge ahead with plenty of weapons in my arsenal.  Perhaps the coolest in the opinion of a geek like me is my antibiotic, sold under the tradename of Augmentin... 

Keep checking back as I reveal what I find so fascinating about the drug and further discuss the unfortunately gooey details of the war being waged within my head!

Things I want for myself

At the urging of my bestie, Bean, I've taken up the notion to blog.  Actually, by all accounts, it's a sound practice for those of us who romanticize about becoming denizens of the world of the published word.  But why do I aspire to fall in to these ranks?

I find science fascinating - it has and always will be my friend.  But I think the true beauty of science lies in the sharing of it.  Actually, I find that to be true for most things in life.  If we were all islands, what would be the point?  No no, we are meant to share and partake of and rejoice in and engage on the things that surround us on a daily basis.  Though we may not initially realize it, science is a lot of it.

For the last six years, I have been a labrat, spending my time hidden away behind closed doors, chilling out with bacteria I've convinced to perform the lion's share of my work.  It's been a blissfully amazing experience - and conversely one of the most frustrating of my life.  If we take the definition of insanity to be the tendency to repeat ones actions over and over, anticipating a different result, then graduate students are crazy, myself included.  There is so much we don't know, can't see... so many layers of complexity all building up to our macroscale world.  And so we toil, each day, repeating the same experiments, attempting to steal sweet victory from the universe in the form of a novel result, one with particularly meaningful implications.  Once these results are obtained, we write them up, publish them in specialized journals, far away from the eyes of most of the public.

But science is cool!  It really is!  The way that the world around us works is almost magical.  It flips my geek switch, makes me want to help others see the world through the periscope of science - I get gabby and chipper and a little bit giddy.

So here is my goal: to secure for myself a place in the world where I can enlighten those souls sitting tentatively on the sidelines of science, awaiting a chance to jump in.  I love science and I love writing and I love teaching... this is gonna be good.