Archives for: June 2008
Although I’m probably only one of five people on the planet who have not read it, the blockbuster success The DaVinci Code is just another indication that we humans have an innate curiosity about codes and their relationships and meanings. This blog will take us into the ultimate code of them all: The Code of Life.
By general agreement, a code is a rule for converting a piece of information into another form or representation, not necessarily of the same type. For example, I often write computer programs, most often to do some particular job or another on my website. Most programmers refer to this a “writing code.” Computer programming code appears to the non-programmer as a series of arcane jottings and numbers, but to both the programmer and computer, this code is in reality a series of highly specific instructions, executed step by step, that result in the computer performing some real world action; perhaps posting a message to an internet bulletin board or sending along an email.
Since computer programs are often rather large affairs with many loops and computations, writing good computer code is a daunting -if at other times stimulating- pursuit. It can be reassuring to remember that at any moment in time only very simple, rather dumb things are happening. What makes the computer program so powerful is that all these simple dumb things are happening extremely fast with a tremendous degree of accuracy.
Very few computer programmers can ever claim to have written a perfect program straight off. There are too many places that things can go wrong, computers being the terribly literal creatures that they are. For example, a command that tells a computer to print Hello World! to the screen might look like this:
23. PRINT “Hello World!”;
Simple enough, eh? Like the way we humans typically read books (from front to back and top to bottom) computers execute code from the top down. Thus, our line of computer code is numbered 23, so we can assume that there are twenty odd lines of computer code in front that will be executed before our screen lights up with the words “Hello World!” Perhaps line 22 tells the computer to make the screen font red, in which case our “Hello World!” would be rendered in red colored type. If we remove that line and run the program again, our font color goes back to black.
Look at our line 23 again and you will notice that the phrase you see -- Hello World! -- is in quotes, because in our simple computer language putting a phrase in quotes tells the computer where is the beginning and end of what you want sent to the screen is located. Without this type of instruction, computers are actually quite dumb, and have to rely on us to tell them where the beginning and end of various human things lie. Also notice that at the end of the line is a semi-colon, which in our little computer language tells the computer that this is the end of that particular line of code, so move down one line and execute that command next.
Computers are so literal that a mistake of even one character can cause a program to malfunction. For example, if you saw this line:
23. PRIINT “Hello World!”;
You’d probably guess that something is supposed to be printed. However the computer does not see PRIINT as the equivalent of PRINT. On the other hand if your code looked like this:
23. PRINT “Hello Wurld!”;
The program would probably still execute, since as far as the computer is concerned the command is correct and it’s in quotes, so it assumes that this is probably what you wanted. Once the command is correct, the computer doesn’t care if you tell it to write “Hello Wurld” or “Kick Me”. As long as its own language is correct, the computer will chug happily along, performing its assigned tasks.
Like computers, first impressions, and that light switch on the bathroom wall, genetics is remarkably digit business: On-Off; Yes-No; Love-Hate. So even if it looks complicated at times, don’t be fooled: It’s not. Just remember, like computers, genetics is simply a lot of small things happening in a clear-cut manner and if you get perplexed or lost, just take a step or two backwards and start again.
The mechanism of the genome is surprisingly similar to our simple line of computer code; so simple in fact that I will provide you with an “executive summary” of the whole affair in just two paragraphs.
A molecule called DNA periodically assembles copies of various parts of itself that are called RNA. RNA then travels to other parts of the cell where it is read as an instruction template, assembling chains of amino acids into something very useful: protein molecules of delightfully complex three dimensional shapes that are most often a class of proteins called enzymes.
Enzymes are special speed-up molecules that greatly foster the production and metabolism of the body’s tissues and secretions. Without them many biochemical reactions would occur so slowly as effectively negate their value. Just think about the difference between soaking a dirt stain in plain water for four days, versus soaking it for four minutes in a solution of water and laundry detergent and you’ll get an appreciation for the action of enzymes.
Enzymes catalyze many of the reactions involving proteins, fats, carbohydrates and minerals. Hormones, mucus, neurotransmitters, you name it; they are all made from enzymes.
It sobering and a bit humbling, to ponder the fact that when we eat any kind of protein, we’re actually consuming the results of something’s DNA and some of their DNA as well. However we usually break down dietary proteins to their amino acid building blocks and start all over again.
Occasionally, wild molecular gyrations occur as the incredibly DNA long molecule prepares to replicate by winding itself up tighter and tighter on a tubular scaffold of its own creation. Splitting from the ends much like an old Manila hemp rope would, each of the two unraveling single strands then begins to assemble a copy of its missing partner, producing two unique strands of DNA and creating two daughter replicas from one original.
What happens is surprisingly simple. Good things are like that; a strong underpinning of fact and analysis, and a veneer of simplicity and common sense. Now why, on the other hand, is quite a different story.
Eye color is far more complex than is generally appreciated, ranging from blue, gray, green, green/blue, brown, and others, varying with different populations. As with skin pigmentation, eye and hair color results from the degree of melanin pigment deposited in the tissue. Humans have several eye color genes. Two best understood are named BEY2 (brown eye) located on chromosome 15 and GEY (green/blue eye) located on chromosome 19. Interestingly, the human “secretor” blood type gene is linked to the GEY gene, since they are both found on chromosome 19. This may explain why the percentage of secretors in the population rises as one heads further north, since the percentage of green and blue eyes increases as well.
There is one peculiarity of eye structure which has been used in making racial distinctions called the epicanthic eye-fold, a fold of flesh that covers the upper eyelid, and sometimes even the upper eyelashes, when the eyes are wide open. It gives the eyes a narrower appearance. It may be an evolutionary defense against both the extreme cold as well as the extreme light that occurs in the Eurasian arctic and north. It has also been suggested that the fold provides some protection against dust in areas of desert such as that found in the deserts of northern China and Mongolia as well as parts of Africa.
Although almost universal amongst Central and Northern Asians, there is a wide distribution of the epicanthic fold across the world. It is also found in significant numbers amongst Amerindians, the Khoisan of Southern Africa and some people of Sami (Lapp) origin. The presence of epicanthic folds is common in many, though not all, groups of East Asian and Southeast Asian descent. Due to classic genetics children of a parent with a pronounced epicanthic fold and one without an epicanthic fold will have varying degrees of epicanthic folds as a result. On the other hand, high orbits, with no folds, are characteristic of certain Balkan populations and of most Near Eastern peoples.
Hair texture is measured by the degree of fineness or coarseness, which varies according to the diameter of each individual hair. There are four major types of hair texture, which are fine, medium, coarse and wiry (sometimes referred to as wooly). Head hair grows at the rate of approximately 1.25 centimeters, or about 0.5 inches, per month, and it has been speculated that the significance of long head hair may be adornment leading to what evolutionary biologists call “Fisherian Runaway Sexual Selection”, in which an prospective mate’s health is gauged by lustrous hair, leading to a greater rate of selection for those individuals with the gene –the same mechanism that probably led to those beautiful peacock feathers.
Scalp hair varies tremendously between races; the scalp hair of most Asians has the greatest thickness and the roundest cross-section, which produces a thick, straight hair. In Europeans the hair is more oval and finer; in Negroes it is flattened, resulting in small wiry, or “kinky” curls. There are at least three kinds of kinky hair. There is short kinky hair that covers the whole scalp evenly, as with most African peoples. There is short kinky hair that grows in tufts with seemingly bare spaces between, as in some East African groups. Then there is the longer kinky hair of the peoples of the Southwest Pacific islands. The hair of the Australian Aborigines is curly or wavy, except for one small group in Queensland who have what is called "frizzy" hair, or hair that is slightly kinky. It has been speculated that wiry hair texture has an advantage in being difficult to penetrate by stinging insects and tends to wick sweat effectively, keeping it away from the face, two distinct benefits in hot, humid environments. Only persons of African descent usually have this type of hair, although some Europeans can have extremely curly or frizzy hair.
Blonde hair is produced by an absence of melanin and may be attempt to optimize UV penetration of the scalp (maximizing vitamin D levels in the northern climes)
Having red hair is associated with the recessive version of the MC1R gene on chromosome 16, which also codes for fair skin and freckles. Four out of five redheads have this gene variant, which is found at its greatest frequency in Scotland and Ireland. Some authorities suggest that red-haired people may be descendents of a blending of Neanderthal and Cro-Magnon peoples while others suggest that the gene is more recent, well after the human migration from Africa, so that the geographical distribution of red hair would be due to post-glacial expansions from Europe.
The tendency of the two eyebrows to blend over the nose, called “concurrency” is found in its highest frequency in the Middle East, but is also common among Southern Europeans.
The summer of 1968 beckoned and looked very promising. Balmy days for us kids often spent butterfly collecting, trading comic books, listening to baseball on the radio, and playing afternoon stickball, a uniquely New York City street game involving a stick --usually appropriated from an unwatched broom-- and a hard pink rubber ball manufactured by the AJ Spaulding Company universally referred to as a “Spalldeen.”
However my dreams for such a bucolic near future came to a screeching halt one afternoon when I was greeted by my little brother at the door with news that we would all soon be flying in an airplane! That sounded exciting enough, but further elaboration disclosed a darker truth: We would be flying to the village of my mother’s birth in North East Spain. My knowledge of the place was minimal at best: I had only seen rather quaint photographs with scallop-cut edges of what appeared to be a ramshackle, sleepy and sun baked town populated by sunburned farmers with dazzling white teeth clustering around a new tractor, scooter or calf. It looked foreign, smelly and somewhat ominous.
Soon enough we headed for the airport to begin our journey. Modern, security-frazzled, airline customers may not realize or remember just how much of an event traveling by airplane was in the mid 1960’s. Washed and scrubbed, wearing rayon shirts and thin ties, mother in Sunday best complete with pill box hat, we journeyed the Atlantic in the marvelous Boeing 707.
Fully jet-lagged we landed many hours later at Barcelona airport and were greeting by a deputation from the village, 150 screaming, waving and wildly gesticulating Catalans, for this was, as I would soon be told “Catalonia, not Spain.” From Barcelona we soon began our travels westward, into the Llobregat river valley and the mountains of the Montserrat, strangely carved peaks that are the results of eons of erosion by now-extinct giant rivers. This is an enchanted land; not for nothing are Catalan artists overrepresented in the Surrealist art movement.
Winding down roads of choking dust, we made our way to the town, or pueblo. Until then having grown up in the restrained, plasticized and sanitized habits that characterized the USA in the 1960’s, I was in now way prepared for the coarse, almost brusque mannerisms of these folks. The gesticulated wildly, seemed to argue about everything, screamed at each other from their windows and talked at an amazingly rapid-fire rate of delivery. It’s phenomenally fertile land, and the local people are rumored to be the only people in Spain who can “make bread out of stones.” The closest town, which is at the border between Catalonia and Aragon, was described as being “renowned for its figs, and the thick-headedness of the inhabitants.”
Culture shock soon set in. A shy kid to start off, I was soon just happy to find a quiet place and read my bon voyage present, a huge book on the Battle of Gettysburg. Unlike my little brother, who was muy sympatico, eating in the café and yelling at the soccer games on the one TV like everyone else, I just felt alienated. One had to be careful with their choice of friends. The headless automaton jumping around my aunt’s kitchen spurting blood all over the place was just shortly before the chicken with two different colored eyes that I had so carefully observed that morning. Cute, friendly rabbits were soon rendered into grotesque hanging parodies of the “visible body” model that I had built that Christmas.
Being the wonderful people that they are, my family soon began to try to get me to come out of my shell. One of my uncles took notice of my liking of history, and soon we were off in his tiny car, visiting Visigoth and Roman ruins. Another uncle, a simple but lovable farmer, would take me out to his fields, hold a finger up to his lips so as to say “let’s keep this secret to ourselves” and begin pushing aside sagebrush, rubble and other weeds, revealing a lovely Roman husband and wife gravestone. Gradually, I began to open up to this wonderfully simple and pure world.
Around midday we would break for lunch and siesta, which never varied all that much; a medium sized fish, called a “sardine”, stuck on a branch and placed around perimeter of a small fire, some olives and almonds from the field, followed by a peach or pear. Since it was still too hot to go back to work we’d look at clouds or the distant hills and at one point I asked him what lay beyond those hills.
“Saragossa.” He said.
“And beyond that?”
“And beyond that?”
“The Basques. But they are different than us, and a little crazy.”
It would take a lot for a Catalan to call someone else “different”, and to a Catalan, the Basques may well be the only qualifying group. Like the Catalans, the Basques are very independent minded, with great cultural sensitivity and were consequently heavily repressed during the Franco dictatorship. Similarly, they have experienced a phenomenal cultural renaissance in the years following his death.
An ancient people, or more correctly a “people island,” they have resisted virtually all attempts at assimilation, forced or otherwise. In the Basque language there is no name for “Basque”. There is a name for the language that Basques speak, Euskera and a Basque is simply defined as a Euskaldun, someone who speaks Euskera.
But we would have to go back farther still to get a grip on the Basques. You have to go back to a very cold, dry time without agriculture. The Basques, you see, are sort of living fossils, probably the most direct link we genetically possess to a distinct people that can be traced back to the Pleistocene Age.
The upper right-hand corner of Spain has some of the most interesting dialects to be found in the world over such a small piece of geography. Catalan, the language of my family, is an ancient Latin derived tongue, probably closer to the Latin of the Romans than either modern day French or Spanish.
For a romance language, Catalan has a surprising number of consonants, with the free use of the letter x as an example. But for all its unique qualities, Catalan is a relative newcomer, the Romans having inhabited the area roughly two-thousand years ago. Prior to that the population was a hybridization of two earlier groups, rather short, dark haired and eyed indigenous people, called Iberians and taller, lighter transplanted Celts who arrived a few hundred years prior to the Romans in search (like their modern-day counterparts) of a warmer climate. These two groups intermingled freely, fused and produced what historians called the “Celt-Iberians.”
Yet these modern languages are distinct from Basque Euskera or any of the Semitic or African languages as well. English with it clipped and nasally sounds; German with its guttural mega words; French, with its mellifluous hints of romance and Hindi, with its beautiful Sanskrit writing all share Indo-European as a common ancestor.