Sunday, July 28, 2013

Good Morning Jack...

Letter to my Son
Sunday, 28 July

gordoMars

Good Morning Jack…

When we last talked you were very enthused with your writing.  The story you related expressed a personal conviction and an insight into human nature I would not have had the maturity to know at your age.  You have always given me good reason to hope your future will be one of promise fulfilled.  From a very early age your mother has always spoken with great faith in your character and your capacity to achieve your goals.  There are no certainties, though.  Life offers the fortunate few the opportunities to make a real difference for the better in the lives they affect.  I know your strengths and I believe fortune looks kindly on you.

The other day I felt there was purpose to my life and there was a renewed clarity in my thinking.  I had such energy making plans and carrying out tasks.  The following day I crashed.  It was just as clear to me I was a lifelong fool.  I had no prospects.  I was doomed to find comfort only with delusions.  Today I felt neutral about most everything life offered me.  I did what I needed to do but without joy. 

The facts of my life had not changed from one day to the next.  I assessed the essential nature of my life through the filter of emotions whose origins are a mystery to me.  They seem as uncontrolled by me as are the weather systems that sweep through the area.  Some feelings linger.  Some are briefly felt.  They can be mild.  They can be intense.  They all come and go. 

I don’t imagine myself unusual in experiencing such regular swings in mood.  It’s undoubtedly a part of everyone’s life.  How do we handle these ups and downs?  How do we manage with any consistency the work we set about each day to do?  I suppose we could medicate ourselves and use drugs to induce highs when our sense of self is low.  The initial results will undoubtedly seem encouraging.  How much more rewarding life has become once we use chemicals to manage our mind.  The problem is we come to avidly believe this course of action as being a real solution, despite the mounting evidence you can’t cheat Mother Nature.   Once you’ve drank from the mythological fountain of everlasting happiness your mind will be unwilling to let go of your own personally groomed fairy tale.  The dry laws of physic apply to all things real and alive.  There is a mathematical precision in the manner in which life sustains its balance.  Our actions are values assigned to variables that reside in the grammar of equations and the results don’t require our consent.  Nature settles its accounts without concern for human consequences – yours, mine or anyone’s. 

At some point the chemically altered mind comes to cherish a life that was once simply a matter of normally shifting daily moods.  There was a time when you experienced contentment because you accomplished something truly worthwhile.  Happiness did not require a monetary transaction.  There are moments of annoyance and discomfort each day but it is a relief compared to feeling resentment, rage and paranoia as a permanent condition.  Being dependent in the company of likewise dependent people is to exist within a collapsed realm, where all thoughts are blind to any possibility outside one’s own overwhelming, persistent need. 

Would it be wrong to feel happiness in the simple act of just being alive?  If happiness doesn’t seem a justifiable reward for merely living day to day then can we settle for a sense of satisfaction with our life?  If being satisfied with ourselves still seems an unjustifiable reward for our small accomplishments then doesn’t it seem to be a healthy practice to hold within us a pleasant but humble feeling of acceptance?   I think somewhere here lays the personal attraction of Harvey’s friend, Elwood P. Dowd.  If that name doesn’t ring a bell then I suggest you look into the story of a six foot three inch invisible pooka and his amiable friend.  He’ll happily give you his card and invite you to dinner.  It’s the least he’s willing to do.

Love,
           Dad



Thursday, July 25, 2013

Opportunistic Bacteria


Bacterial Spores

Cells are of microscopic size because of their inefficient means to distribute resources internally.  The processes providing for life require a continuous supply of molecules, such as oxygen, that are absorbed by the cell’s outer membrane.  Relying largely on diffusing critical resources across a cell’s interior to reach metabolizing sites, makes it nearly impossible for a cell to become the size required to be seen with the unaided eye.

Most bacteria are many times smaller than are the cells found in the tissues of plants and animals.  Bacterial, or prokaryotic cells, do not have the complex interior structures found in the eukaryoticcells that make up multicellular organisms.  Bacteria’s reliance on their more elemental structure does not, by itself, explain their minuscule size.  A look at the advantages gained by drastically reducing the cell’s volume from its theoretical limit provides clues into the harsh nature of the bacterial environment. 

Diminishing the cell’s size aids in its relative capacity to absorb nutrients from its surroundings.  The absorption area of the cell increases proportionally as its volume is reduced.  A resource becomes more plentiful, while there is a corresponding decreased need for it, due to the cell’s smaller size.   This provides the basis for increased metabolism and a higher rate for synthesizing proteins and nucleic acids that are critical to the cell’s growth.  Bacterial cells often divide into two sister cells once they reach twice their original size.  Bacteria are notorious for their potential for exponential growth.  Some species, under optimal conditions, have been known to produce an entirely new generation within the space of twenty minutes.  A time span of several hours is more likely but the rate of reproduction is still dynamic when compared with the population growth demonstrated by Eukaryota cells, such as the amoeba.

Rapid population growth is usually the strategy of a species that also suffers a very high mortality rate.  Bacteria behave in an opportunistic manner, indicating conditions needed for their survival may have a very short time-frame   An instance of rotting plant or animal tissue in an otherwise dry environment makes available a rich organic soup to a community of bacteria.  The bacterial population quickly explodes in number.  They thrive only briefly, though, before the intense sun exhausts their world of moisture and other unfavorable environmental factors take hold.  Individual bacteria react to their increasingly hostile surroundings by synthesizing a shell that encloses and protects their molecule of DNA.  This is a spore, but unlike the spores used by fungus for reproduction, this structure is a lifeboat with the singular purpose of survival.  Its hard outer casing resists the fatal effects of high temperatures, dryness, harsh chemicals or being frozen in liquid, any of which would lead to the destruction of the delicate DNA molecule.  The spore is at rest, void of the many ingredients needed for metabolism, so it exists in a state of suspended animation. 

Only when a life sustaining environment is once again detected, will the encapsulated DNA instigate chemical reactions that lead to the full restoration of life processes.  It may be a very long wait before wind makes the spore airborne or a stream from rainfall carry it to a new opportunity to prosper – fallen fruit rotting beneath a tree or an open wound in a dying animal.  The microbial life form resumes its organizational efforts that keep it one important step above the level of death… breaking chemical bonds to generate the energy needed to power its synthesis of magnificently complicated molecules, that are used to build structures to enable life, and structures to insure its perpetual preservation, in copy after succeeding copy, throughout the long history of life on this planet, Earth.

Biology Topics:

Eukaryotic Cell

Protein Creation

Molecular Basis of Life

Living - Why?



Sunday, July 21, 2013

Good Morning Jessicca...

Letter to my Daughter
Sunday, 21 July


Doorway

Good Morning Jessicca…

Pull back the curtain and you will find a time when it was thought all serious people decided, for perpetuity, what they would be in life once they grew up.  This was a miraculous period that followed completion of basic schooling.  By now girls knew something of boys and boys knew something of girls and everyone had done their homework enough to know a little bit about everything.  All things true would come to a glorious completion as we tied a bow with the love of our life, and assessed our aptitudes in order to choose a career that would help make love, family and security, all possible.  Wendy and Peter Pan, shedding their childhood notions, meet at the wedding alter in their first step of commitment for two adults sharing all the twists, surprises and rewards offered in life.

A few people my age might actually describe their life in this manner but, for many of us, this was the mythology of a simpler time.  There no longer is the sense of inevitable opportunity and domestic certainty young people once naively felt about their life before them.  Today there are still enormous opportunities for smart people with the skills to keep pace with the rapidly evolving demands of this society.  For those of us not exhibiting the capabilities profitable to the various enterprises of our time we are left to feel fortunate we remain standing on a treadmill whose pace seems ever increasing.

Actually, what is described here probably holds true for at least the past hundred years.  There never really was an optimal time for people whose expectations exceeded their marketability, in an environment where the price of personal labor is as much governed by supply and demand as is any product offered on a retail shelf.  Prior to the twentieth century you could opt out of the demands of civilization and choose to take your chances on a sprawling frontier west of the Mississippi.  Pioneers lived a life of beauty and brutality, opportunity and uncertainty of matching expanse.  The laws governing your actions were merciless in judgment, but you were free to call all the decisions you made to be entirely your own.  Success in your venture could provide magnificent reward.  Losing out to the elements would leave you only with the pride of having died free.  Your story might be one passed down through the generations if only they first stumble upon your bones.

The degree of our desire determines the intensity of our ambition.  The more we want from our life, the greater the mountain and steeper the slope that first must be scaled.  Hard work and devotion to one’s calling is no guarantee for ultimate success but personal effort and sacrifice is as fundamental to achievement as purchasing a ticket is to winning the lottery.  This seems an obvious truth if your wish is to own a grand home on a hill.  It may be no less true, though, if what you seek is spiritual in intensity.  The difference may lie only in the path of applied effort.

Life is a wellspring in seeming defiance of nature’s laws, an expression of high improbability.  You and I are free to pursue whatever fancies may enter our mind.  It is well for us, though, to retain always the healthiest of perspectives and celebrate each day the extraordinary nature of our own conscious existence.  The fact that you presently are is all that you have to safely take for granted.   Anything more has the ethereal substance of personal wish.

Love,
           Dad



Thursday, July 18, 2013

Protein Creation


RNAs role in making Protein

Building essential proteins from raw organic materials is a complicated process that is of no small cost to the individual cell.  As with most everything involving cell life the initial instruction must originate in the nucleus, home for the governing molecule – DNA.  Much as a computer program is coded entirely using a sequence of zeros and ones, the instructions regulating life in the cell are also sequences, but ones coded in chemical bonds

The large double helix molecule of DNA that resides in the nucleus does not directly involve itself with the mechanics needed to sustain life.  Instead it relies upon its complement, a single strand of RNA, to deliver its instructions to the appropriate component of the cell.  In order to understand how a message is coded it is important to know that both DNA and RNA are long strings of four different types of nucleotides linked together.  DNA and RNA both include the nitrogenous bases, known as adenine, guanine and cytosine.  Thymine is the fourth nitrogen base in DNA while uracil is the equivalent base in RNA. 

Transmitting coded instructions from DNA to the messenger RNA, mRNA, requires a bonding attraction between the various nucleotides.  Thus, adenine on DNA attracts the uracil of RNA and cytosine attracts guanine.  Of course, the reverse is also true – guanine bonds with cytosine and thymine with adenine.  RNA will deliver its message in a fashion complementary to the original DNA code.  It might be thought of as a mirror image but it nonetheless remains a faithful transcription of the genetic instruction.

The completed mRNA nucleic strand finds its way outside the nucleus and proceeds to a point of protein construction.  Most often this involves one of many tiny sites associated with a long, membrane that extends out from the nucleus and into the cell’s metabolizing interior.  This membrane area is called rough endoplasmic reticulum because of the ribosomes, spherical structures that generously populate its outer surface.  It is the role of the ribosome to translate nucleic information into the sequence of amino acids necessary to make a specific form of protein.

A single protein can include hundreds of amino acids of which there are only twenty basic types.  It is the order of these amino acids, when linked together, which give the protein polymer its particular molecular characteristics – what molecule is attracted to it, what type of bond is created, what function is provided the cell.  How does the ribosome radically transform nucleotides such as uracil and guanine, found on mRNA, into a protein amino acid such as tryptophan?

We should first know that there is a triplet of nucleotides that uniquely identify each amino acid type.  For instance, a sequence of uracil – guanine – guanine provides the code for the amino acid tryptophan.   Unfortunately, tryptophan needs help if it is to bond with this triplet of nitrogenous bases.  There needs to be an intermediary provided by the ribosome, and there is.   Again we call on the services of RNA.  This time it is a relatively short strand, transfer RNA (tRNA), which links to a specific amino acid on its one end, and provides a complement of nitrogenous bases on the other. 

The triplet code, or codon, for tryptophan was uracil – guanine – guanine.  Its complement for base-pairing would be the anticodon adenine – cytosine – cytosine.  When the messenger RNA gives the codon for tryptophan, the ribosome site provides the corresponding tRNA.  Tryptophan is attached to it at one end, and the appropriate anticodon at the other end provides the complementary bond.  Once the amino acid establishes its link to the previous amino acid on this developing protein sequence, the tRNA is released in order to establish another bond with an amino acid of identical type.  It is in this stitching manner that the ribosome makes available a new protein polymer for the cell to use.

The molecules associated with living forms are far larger and more complex than any molecule exclusive to inanimate matter.  The reaction cycles necessary to construct these macromolecules are also extraordinary in both their complexity and the choreography of their timing.  The cell is the center of all life.  It extracts energy from its environment, discriminately chooses necessary resources from its surroundings, manages chemical reactions to power the synthesis of new parts, and organizes and regulates all its diverse activities using only a finely tuned molecular intelligence.

Biology Topics:

Opportunistic Bacteria

Molecular Basis of Life

Limited Male

Living - Why?




Monday, July 15, 2013

Eukaryotic Cell


Eukaryotic animal cell

There are three basic components to the cell.  There is a nucleus, or nucleus-like area, that contains the information that governs the cell.  There is a protective barrier encapsulating the cell, made of a membrane and maybe a cell wall.  The interior of the cell contains a gelatinous substance called the cytoplasm in which various components exist, performing the cell’s metabolism – providing for the cell’s energy needs and synthesizing its structures.  This is the basic make-up of a generic cell most familiar to people’s conception.  It is called a Eukaryotic cell and it makes up all the cells of the plants and animals surrounding us, including ourselves.  There are other forms of life, such as bacteria, whose cells have fewer components and they are called prokaryotic cells.  There exists also an even simpler living form that is categorized as the virus.  Its minimal nature challenges the cell model for all living things.

Possibly the most important fact to consider is that all life’s functions fit within a single, microscopic cell.

The nucleus has a double membrane separating it from the metabolizing portion of the cell.  Contained within this area are nucleic acids.  The most important of these is DNA – the repository of the entire cell’s genetic information.  This long molecular structure is best known for its role in inheritance during reproduction but it also provides all the necessary instructions to maintain the life of the cell.  This macromolecule is made up of a long sequence of units composed of nitrogenous bases.  There are four different bases represented in varying order.  A triplet of these bases provides the code for a specific amino acid.  There are twenty amino acids used in various combinations to make the many proteins important to life.  The sequence of the many amino acids contained within each protein determines the molecule’s characteristics.  Enzymes that catalyze the cell’s many chemical reactions are made of proteins as are much of the cell’s structure.

Suspended within the cytoplasm that surrounds the nucleus are various structures with specific functions.  A tubular structure arises from the nuclear membrane and creates a maze within the cell.  This endoplasmic reticulum is the site for the synthesis of proteins and of fats, called lipids, which are important to membrane construction.  The structure most important for making chemical energy available to the cell is the mitochondria.  This is the sight for the creation of the energy transfer molecule, ATP, and for respiration – utilizing the conversion of oxygen to carbon dioxide in order to provide the cell’s energy.  Mitochondria are self-replicating.  They have their own DNA, leading to the speculation that at some point in biological history they were a separate living entity that joined in a mutually beneficial relationship with the ancestor to the Eukaryotic cell, much as fungus and algae have joined in a symbiotic relationship to form lichen.  Another of these self-contained cell structures, call organelles, is the Golgi apparatus – a complex of stacked vesicles that provides for digestion and storage.  A fundamental organelle in plant cells is the chloroplast, the location for photosynthesis, making the cell an autotroph – capable of sustaining itself on nonliving, inorganic matter.

The cell depends on lipids to give its membrane flexibility.  Cholesterol is a water insoluble molecule embedded in the membrane to toughen the protective barrier.  Proteins are used in a similar manner as well as enabling the selective transport of material into the cell and in expelling waste from the cell’s interior.  The cell also utilizes reactions of various proteins to specific stimulus as a means of detecting the nature of the external environment. 

The depiction of the cell in a generalized diagram is a simple abstraction giving no appreciation for the cell’s extraordinary complex role in providing the basis for life.  This word depiction is likewise only a vague overview that, at best, should stimulate questions as the starting point for further inquiry.  Each statement of fact poses new questions that, when answered, in turn provide more questions.  At this point we are located at the very top of a rapidly widening pyramid that can never find its ultimate base.  When following the path of any science the final conclusion remains always over the horizon.

Biology Topics:

Archaeopteryx

Opportunistic Bacteria

Molecular Basis of Life 

Limited Male




Sunday, July 14, 2013

Good Morning Justin...

Letter to my Son
Sunday, 14 July

Eastern Box Turtle

Good Morning Justin…

Early Thursday morning, around seven, I ran across a turtle.  It would have escaped my attention as it moved quietly in the bushes near the house but the yellow markings on its shell caught my eye.  It’s an Eastern Box Turtle.  The shell of this one appears to be about five inches long.  I think I've found Elvira because the turtle’s eyes are brown.  Elroy would likely have orange or red eyes.  There are other characteristics you can use to determine whether the turtle qualifies for the Ladies Room or not but they seemed indeterminate to me.  For instance, the plastron, or underside of the male turtle is supposed to be somewhat concave while the female’s is flat.  I thought Elvira’s plastron a bit indented but it’s not obvious.  Also the female’s shell is more domed than the male.  This turtle’s shell just didn't look as domed as the female pictured on line.  Only the eye color appeared clear cut to me.  It’s not a one hundred percent indicator but, since I have no experience sexing turtles, I went with it and gave Elvira the key to the Powder Room.  One more thing – I think her tail should have been broader and flatter if she were a boy. 

Elvira now lives in a wilder habitat, away from homes and roads.  There are just too many cars and lawnmowers around here to give her much chance of surviving long.  In the wild she can live a hundred years.  Did you get a look at her legs?  They’re stumpy and they stick out her sides.  If you want nimble cornering and speed this just isn't the way to go.   Try placing a long stick between your knees.  Now time yourself running the fifty yard dash.  Send me a post card when you get there.  Of course, if you’re a turtle eating plants and crawling insects you’re not in any rush.  Things can get pretty exciting, though, if a fox with a taste for turtle takes an interest in you.  Your shell is your suit of armor.  Make as small as you can and tuck yourself inside.  Make sure nothing soft sticks out.  The fox will probably paw at you and sniff about.  Pray he can’t roll you over on your back.  This could go on quite a while if the fox has nothing better to do.  He may not even be all that hungry.  You’re just an interesting diversion on an otherwise sleepy afternoon.  Oh, great.  He’s trying to gnaw on you.  So long as this continues you won’t be able to properly digest your breakfast.  All this stress is giving you indigestion.  Now would be the perfect time to give off a powerful stench of heroic scale.  You’d think you’d have been issued such a weapon for defense in situations like this.  What an oversight. 

If I’m the turtle I feel blessed because I’m too dull-witted to fully appreciate the predicament I’m in.  I’m not imagining all the terrible things that might happen to me.  I’m not crying out, “Why me, Lord?”  I’m just alone with myself, cooped up tight inside my own shell, pondering very slowly the efforts of the big bad wolf futilely blowing on my house of bricks.  I’m trying to sort things out.  Am I afraid or am I just annoyed?  It’s hard to say.  I can’t seem to hold onto any single train of thought long enough to decide how I feel.  It’s like trying to focus on the music in a supermarket.  It so easily slips out of consciousness. 

The commotion outside has stopped.  When did this happen?  I must have been thinking about crickets.  I like the ones missing a leg best.  A plump leaf moist with dew sounds tasty right now.  Is it berry season, yet?  It feels stuffy.  Isn’t there something I’m supposed to be thinking about?  I’m all sealed up tight inside because… because… oh.  Yeah.  I should slowly take a peek around. 

After living one hundred years one half inch off the ground what conclusions are there for a turtle to make?  It feels good lying in shallow puddles following breakfast.  Plants are easier to catch than insects.  Elroy bumping into Elvira is a truly rare chance meeting.

Love,
           Dad


Wednesday, July 10, 2013

Happy Birthday, Jacob!

Letter to my Son
Wednesday, 10 July


Jacob's Desert Solitaire

Happy Birthday Jacob!

As of today you now have had fourteen years to assess the situation on this planet.  How’s it going?  It can seem a bit overwhelming at times, right?  When you think about it you realize your life is an epic in the making.  Think of the time needed, the miles traveled and the hundreds of people involved – teachers, students, friends, villains, relatives, brothers and sister, Mom and Dad; not to mention all those extras needed for crowded events you attend.  Of course, they each have their own epic in the making.  The scope of all these interwoven lives is just mind-boggling. 

Let’s back up and start with a cake.  Somewhere in human history, probably around the time people developed the idea of the calendar, someone had the notion of birthdays.  For instance, you were born in the summer, on the tenth day of the month named in honor of Julius Caesar – July.  Someone else thought it would be a good idea to celebrate each date of birth of one’s life with baking a cake.  I’m sure that quickly caught on.  We all gather around the cake, exchange greetings of happiness and have a little party.  Of course, people always wanted to know how old you have just become.  How many times now have you traveled all the way around the sun?  By the way, let’s celebrate not only your birth but how many years you have been with us. 

Well, years before, some life of the party had stuck a burning candle smack in the center of the cake to add spectacle and cheer to the proceedings.  It was a big hit.  Now another clever person has just come up with the idea to have a candle burning for each year of one’s life.  Oh, that won’t do, adds another.  The candles are too big!  We’d need a really huge cake or itsy bitsy candles.  It is a great idea, though.  In fact, it is so great we will just have to make skinny little candles special for the cake.  And so they did.  Somewhere in all this merry making people also felt the desire to give gifts of appreciation to the one whose birth was being celebrated.  This gesture also grew grander with time.  Let’s conceal the gift in wrapping so that it becomes a surprise when opened.  The wrapping would become vivid with color and elaborated with ribbon.  It soon got to the point where you felt you were undressing the prize.  Oh, look!  It’s just what I wanted. 

All was well and good when it came time for the birthday.  People eagerly gathered for these family events.  Still, there was something fundamental missing.  People lacked the means to express this shared moment of joy.  “Hip Hip Hurrah!” simply didn't cut it.  It made for a moment of awkward frustration with everyone gathered around the lighted cake with nothing in particular to say.  Thankfully, a couple of sisters with a piano in a parlor somewhere came up with a simple song everyone could sing in tune and feel great doing it.  It was a master stroke.  It quickly became the crescendo to birthday parties celebrated everywhere.  All seemed in harmony and of good feeling, almost.  No, we still have the problem of the burning candles.  We can’t very well eat the cake like this.  What to do.  You know what I think?  I think the solution came as a spontaneous burst of expression.  The scene is set.  Everyone is gathered together as the cake is brought in.  People begin to sing.

   Happy Birthday to you,
   Happy Birthday to you,
   Happy Birthday dear Jacob,
   Happy Birthday to you.

Then someone exclaims, “Blow out the candles.”
“No, wait,” someone else chimes in.  “First make a wish.  If you blow out all the candles in one breathe your wish will come true.”
Yes, yes, everyone agreed.  This was a fine idea.  But they also secretly felt you got your wish anyway, even if you couldn't put out all the candles in a single blow.  After all, it was your birthday.

Life is good.  Enjoy your birthday.  My picture for you this year is what I call “Jacob’s Desert Solitaire.”  If it seems to you undone maybe it was left for you to finish.  Your art has always been a delight for me.  Happy Birthday, Jacob!

Love,
          Dad


Monday, July 8, 2013

Molecular Basis of Life


Single Cell Algae

The mostly lifeless realm we know as our universe has no appearance of a recognizable plan beyond the physical laws that govern its actions.  The laws familiar to most of us are explained in mechanical terms and deal with, in a general way, the conservation of mass and energy.  Some aspects of our experience still elude real understanding.  People come up with analogies to explain gravity, for instance, but we don’t really know much about it.  It’s like the monk Mendel tending his peas and describing the effects of genetics without knowing anything about the nature of atoms, molecules or DNA.  We've discovered the existence of Black Holes but we don’t know their meaning other than that they provide a clue to a greater mystery.  Time is believed an aspect of physical dimension but what is the nature of this relationship?  We experience time as a sequence of events proceeding always in one predictable direction.  Is what registers in our biological minds all that there is to know about this phenomenon?  Not likely.  Atoms are no longer thought of as the fundamental building blocks of matter.  They appear now as discrete organizations of substances existing in a realm that doesn't defined them as clearly being of mass or energy.  We are dabbling on a fringe that threatens to break open our current notion of reality.

Our cumulative knowledge of the physical realm does not yet provide the basis for understanding the quality of ‘being alive.’  We are surrounded by entities of various sizes and shape that exhibit life.  We intuitively sense all manner of living creation as the result of a mystical vitality.  Life may form from dust and ash but it contains the breath of God.  The essence of life has been far too complex to entertain other explanations that rely solely upon an argument of reason.  This has mainly to do with our inadequate fact-based information describing the processes responsible for life.  The evidence obtained thus far, though, through the method of science, provides a compelling new narrative of life’s workings, but it still lacks a final chapter.  

Life continuously draws from its surroundings to maintain life.  Life reacts to, and sometimes learns from, its own life experiences.  Life creates new instances of itself.  Life goes to extraordinary lengths to sustain its quality of being alive, but life for the individual, must inevitably end.  When an entity can no longer sustain the processes it needs to live, it becomes disorganized.  Its activities are reduced to the quiet state of inanimate matter.  Its organic material is available for animals to consume and plants to, eventually, absorb.  Molecular resources that aren't salvaged by other living beings eventually break down into simpler, less exotic forms - structures not currently employed in the dazzling production of life.  

Microscopic cells are the simplest, most basic forms that exhibit independent life.  They are credited with providing for every complex plant and animal that inhabits our surroundings.  There is not an insect that crawls, a bird that flies, a tree that grows or a flower that blooms that doesn't result exclusively from cells.  While too small for our eyes to detect cells have size enough to display elaborate complexity.  Each cell is a carefully regulated environment encapsulated within a barrier that selects what resources may enter its domain and what is necessary to expel from it.  Its centralized information center oversees its many factories that synthesis a diverse variety of complex protein molecules needed for maintaining its structure and metabolizing energy.  Numerous reaction cycles must be constantly sustained if the delicate balance required for life is to be maintained. 

Life results from an elaborate choreography of processes that are entirely guided by the physical properties that dictate the interaction of molecules.  How this works and what it all inevitably means makes for a story still in the writing.

Biology Topics:

Protein Creation

Eukaryotic Cell

Archaeopteryx

Living - Why?



Sunday, July 7, 2013

Good Morning Jack...

Letter to my Son
Sunday, 7 July


Neighborhood

Good Morning Jack…

I hope only for the best in health and happiness for you, your mother, brothers and sister.  Hope is never a casual expression.  The world sometimes presents us with sinister turns.  The people I care for most can sometimes seem to have a frail hold on life.  Still, nothing is gained dwelling in darkness and I think it best to enjoy the light of day.  We live to stay involved.

Each of us is furnished a familiar outlook on life that also displays characteristics unique to ourselves.  We all desire much of the same things but we set about procuring these goals in a manner that reveals our own shades of personal meaning.  In so doing we fill the niches of humanity.  At some point in life our time spent planning for the future is encroached upon by our estimations on how we’ve already done.  Our life, seen in retrospect, makes for an interesting narrative.  Certainly there are some who have turned their early intentions into accomplishments and they now walk the path they always envisioned for themselves.  Yet, the decisions they made along the way and the events that led to this point in their life were beyond their ability to foresee.  We fulfilled our predictions to a splendid degree but the manner of our achievement is a story spiced with intrigue. 

There are those of us not quite so resolute in our goals.  Our youthful intentions often seemed murky, even to ourselves.  The journey began without a plotted course.  The destination was never adequately settled.  Critical decisions were improvised.  What does one make of this manner of voyage?  Was there a notable result beyond that of personal discovery?  This captain’s log may hold a tale of misadventure, shameful lapse of character and brilliant survival skills.  The ship finally makes port safely, having to show for its extended effort a cargo hold that is empty save for two rare albino coconuts. 

Popeye’s goal in life was to win the heart of Olive Oyl.  He worked very hard at it.  Olive always appreciated his effort and devotion to her but she never could quite overcome her attraction to Bluto’s animal magnetism.  Bluto was a narcissist and I doubt Olive Oyl meant anything more to him than a prize of conquest.  Bluto was no good.  When he swept Olive up with his powerful arms, holding her pressed to his barrel chest while he carried her off, she would scream for Popeye and vainly struggle to be free.  Deep inside, though, she was enthralled with the feeling of being a helpless captive to desire and she would sigh, “Oh, my!”  Meanwhile, ever faithful Popeye would come running, crying out, “I’ll save you, Olive.”

Ain’t life a bitch?  If only Bluto could be trusted.  If only Olive would settle down.  If only Popeye wasn’t such a mumbling nitwit.  If only what was good for you wasn’t a can of spinach – leaves soggy with vinegar. 

One of the goals in most everyone’s life is to win someone’s heart.  We have our reasons to develop our personal capabilities as far as we can take them but it all seems to be in the context of being a part of another person’s life.  The desire to accomplish great things can lose much of its luster once the person you most care for is suddenly gone.  It doesn’t mean we quit.  We find new motivations to continue on but it hasn’t the same sense of sharing as before.  If you’re a Neanderthal there’s enormous gratification in dragging the impressive carcass of a freshly killed animal to the cave entrance of the woman you love.  If it turns out she has left then all you can see is decaying flesh and an issue with flies.  You leave it for the hyenas.  You head in the direction of the setting sun.  Who knows what waits for you over the horizon?

Love,
          Dad



Monday, July 1, 2013

Living, Why?


Amoeba cell

Physical matter, the material that exhibits universal properties such as mass and dimension, also reveals the potential for displaying the characteristic we describe as life, and by extension, the means to render awareness, consciousness and self-identity.  Everything that is attributed to the nature of life adheres to the laws of chemistry and physics, the laws that govern the physical realm.  There is nothing having to do with life that doesn't also have to do with the nature of the physical universe.  Much as the phenomenon of gravity defies contemporary explanation, so too does the means leading to animal consciousness and human awareness and other complex human attributes described by Freud and others in terms such as ego and id.  One may feel disturbed by this apparent all-encompassing mechanistic explanation that governs even our most treasured spiritual beliefs and desires.  Yet, how profound it is to ponder that our most captivating thoughts and warmest emotions are all derived from the makings of this world’s cold and seemingly heartless atoms.   Over time science will fill in the answers as to how these phenomenon come about, but it will still be left to the human imagination to provide the answer as to why.  Take heart.  The story of Genesis need never be extinguished by the discoveries of physicists.  The more we learn the more intriguing becomes the underpinnings of existence.

The fundamental physical process of life is captured by the cell.  Everything beyond the single cell is an elaboration of this fact much as everything you see in the world about you is an elaboration on the material building blocks we categorize as atoms.  Existence is unknowable to us without atoms and life has no basis without cells. 

The cell is alien to most of us.  It is outside our experience. It is too small to notice yet it is extraordinarily complex.  Its processes and behaviors obey only the chemical dictates of its various, organized molecules.  In place of tissue are lipids and proteins.  In place of a digestive tract are specialized molecules, such as enzymes, that break specific chemical bonds to release the energy needed to power the cell’s activities.  Nucleic acids serve as the cell’s nervous system, governing its events through the use of molecular messengers to carefully regulate and sustain this very basic, but elaborate balancing act that appears to us as life.  What makes it live?  All the elements that determine its existence are readily found in its lifeless, inanimate surroundings.  Molecules are everywhere.  Yet the molecular structures found in soil, liquid or air show none of the complexity required of molecules to organize and animate the independent existence of the cell.  How did these choice, atomic structures first come about?  That question is currently being grappled within labs that attempt to recreate the circumstances of pre-life earth.  There is much argument over the conclusions being drawn.  Yet, initial experiments indicate a predisposition of various molecular structures to form fundamental organic compounds deemed necessary for the earliest life forms to come about.  Scientists are nowhere near creating life in the lab but clues to the basis of life’s origins have emerged.  There are plausible explanations based on scientific methods of discovery being discussed. 

Science is a tool.  It is limited to what can be found out through experience and observation.  It has no ability for determining the ultimate question about existence as to, “Why?”  Why should physical matter result in life?  Why should life generate our human degree of consciousness?  Why should there be existence, at all?  Why should we always be asking, “Why?”  Why?

Biology Topics:

Molecular Basis of Life

Limited Male

Opportunistic Bacteria 

Dragonfly