The concept of the gene is perhaps the most critical thing for students of molecular biology to grasp. Even people with little exposure to science usually know that "genetic" refers to traits that people are born with and can transmit to their offspring, even if they have no knowledge of the underlying mechanism for this. By the same token, a typical adult is aware that children inherit traits from both parents, and that for whatever reason, certain traits "win out" over others.

Anyone who has seen a family with, for example, a blonde mother, a dark-haired father, four dark-haired and one blonde child has an intuitive grasp of the idea that some physical traits, be they physically evident ones like hair color or height or less obvious characteristics such as food allergies or metabolic problems, are more likely to maintain a strong presence in the population than others.

The scientific entity linking all of these concepts together is the allele. An allele is nothing more than a form of a gene, which in turn is a length of DNA, or deoxyribonucleic acid, that codes for a particular protein product in the bodies of living things. Humans have two copies of every chromosome and therefore have two alleles for every gene, located on corresponding parts of matching chromosomes. The discovery of genes, alleles and the overall mechanisms of inheritance and their implications for medicine and research offer a truly fascinating area of study for any science enthusiast.

In the mid-1800s, a European monk named Gregor Mendel was busy devoting his life to developing an understanding of how traits are passed from one generation of organisms to the next. For centuries, farmers had been breeding animals and plants in strategic ways, intending to produce offspring with valued characteristics based on the traits of the parent organisms. Because the exact means by which hereditary information was transmitted from parents to offspring was unknown, these were inexact endeavors at best.

Mendel focused his work on pea plants, which made sense because plant generation times are short, and there were no ethical concerns in play as there might have been with animal subjects. His most important finding initially was that if he bred plants together that had distinctly different characteristics, these were not blended in the offspring but instead showed up whole or not at all. In addition, some traits that were apparent in one generation but were not evident in the next could re-emerge in later generations.

For example, the flowers associated with pea plants are either white or purple, with no intermediate colors (like lavender or mauve) appearing in offspring of these plants; in other words, these plants did not behave like paint or ink. This observation was contrary to the prevailing hypothesis of the biological community at the time, where the consensus favored some sort of blending through generations. All told, Mendel identified seven different traits of pea plants that manifested in binary ways, with no intermediate forms: flower color, seed color, pod color, pod shape, seed shape, flower position and stem length.

Mendel recognized that in order to learn as much as he could about inheritance, he needed to be certain that the parent plants were purebred, even if he did not yet know how this happened at the molecular level. So when he was studying the genetics of flower color, he started by selecting one parent from a batch of flowers that had produced only purple flowers for many generations and the other from a batch derived from many generations of exclusively white flowers. The result was compelling: All of the daughter plants in this first generation (F1) were purple.

Further breeding of these F1 plants produced an F2 generation of flowers that were both purple and white, but in a 3-to-1 ratio. The inevitable conclusions were that the factor producing purple color was somehow dominant over the factor producing white color, and also that these factors could remain latent yet still be passed to subsequent generations and reappear as if nothing had happened.

The 3-to-1 purple-flower-to-white-flower ratio of the F2 plants, which held for the other six pea-plant traits in specimens derived from purebred parents, caught Mendel's attention because of the implications of this relationship. Clearly, a mating of strictly white plants and strictly purple plants must have produced daughter plants that received only the purple "factor" from the purple parent and only the white "factor" from the white parent, and in theory these factors must have been present in equal amounts despite the F1 plants all being purple.

The purple factor was plainly dominant, and can be written with the capital letter P; the white factor was termed recessive, and can be represented by the corresponding small letter p. Each of these factors later came to be knows as alleles; they are simply two varieties of the same gene, and they always appear in the same physical location. For example, the gene for coat color might be on chromosome 11 of a given creature; this means that whether the allele codes for brown or whether it codes for black, it can be reliably found on that spot on both copies of the 11th chromosome carried by the creature.

If, then, the all-purple F1 generation contained the factors P and p (one on each chromosome), all of the "types" of these plants could be written Pp. A mating between these plants, which as stated resulted in three purple plants for every white plant, could yield these combinations:

PP, Pp, pP, pp

in equal proportions, if and only if each allele was transmitted to the next generation independently, a condition Mendel believed to be satisfied by the re-emergence of white flowers in the F2 generation. Looking at these letter combinations, it is clear that only when two recessive alleles appear in combination (pp) are white flowers produced; three out of every four F2 plants held at least one P allele and were purple.

With this, Mendel was well on his way to fame and fortune (not really; his work peaked in 1866, but was not published until 1900, after he had passed on). But as groundbreaking as the idea of dominant and recessive alleles was, there was more vital information to be extracted from Mendel's experiments.

The above discussion centers on flower color, but it could have focused on any of the other six traits Mendel identified as arising from dominant and recessive alleles. When Mendel bled plants that were pure for one trait (e.g., one parent had exclusively wrinkled seeds and the other had exclusively round seeds), the appearance of other traits bore no mathematical relationship to the ratio of round to wrinkled seeds in subsequent generations.

That is, Mendel did not see wrinkled peas being any more or less likely to be short, white, or bear any of the other pea traits he has identified as recessive. This has come to be known as the principle of independent assortment, which simply means that traits are inherited independently of each other. Scientists know today that this results from the way chromosomes line up and otherwise behave during reproduction, and it contributes to the all-important maintenance of genetic diversity.

The principle of segregation is similar, but related to within-trait inheritance dynamics rather than between-trait dynamics. Put simply, the two alleles you have inherited have no loyalty to each other, and the reproductive process does not favor either one. If an animal has dark eyes because of the presence of a pair one dominant allele and one recessive allele for this gene (call this pairing Dd), this says absolutely nothing about where each of these alleles will end up in a subsequent generation.

The D allele might be passed on to a particular baby animal, or it might not, and similarly for the d allele. The term dominant allele sometimes confuses people in this context, because the word seems to imply greater reproductive power, even a form of conscious will. In fact, this aspect of evolution is as blind as any other, and "dominant" refers only to what traits we happen to see in the world, not what is "ordained."

An allele, again, is simply a variant form of a gene. As described above, most alleles come in two forms, one of which is dominant over the other. Keeping this firmly in mind helps avoid wading into muddy waters when it comes to solidifying these concepts in your mind. A non-biological example of the aforementioned principles, however, may add clarity to the concepts introduced here.

Imagine the important details your life being represented by the equivalent of a long strand of DNA. Part of this strand is set aside for "job," another part for "car," another for "pet," and so on. Imagine for the sake of simplicity (and for the purpose of fidelity to the "DNA" analogy) that you can only have one of two jobs: Manager or laborer. You can also only have one of two vehicle types: compact car or SUV.

You can like one of two movie genres: comedy or horror. In the terminology of genetics, this would mean that there are genes for "car," "movie" and "job" in the "DNA" describing the fundamentals of your everyday existence. The alleles would be the specific choices at each "gene" location. You would receive one "allele" from your mother and one from your father, and in each case, if you wound up with one of each "allele" for a given "gene," one of these would completely mask the presence of the other.

For example, assume that driving a compact car was dominant over driving an SUV. If you inherited two copies of the compact-car "allele," you would drive a compact car, and if you inherited two SUV "alleles" instead, you would drive a sport-utility vehicle. But if you inherited one of each type, you would drive a compact car. Note that to extend the analogy properly, it must be emphasized that one of each allele could not result in a preference for a hybrid of a compact car and an SUV, like a mini-SUV; alleles either result complete manifestations of the traits they are associated with or they are completely silent. (This is not always true in nature; in fact, traits determined by a single pair of alleles are actually rare. But the topic of incomplete dominance is beyond the scope of this exploration; consult the Resources for further learning in this area.)

Another important thing to remember is that in general, alleles pertaining to a given gene are inherited independently of the alleles pertaining to other genes. Thus, in this model, the kind of car you prefer to drive owing strictly to genetics has nothing to do with your line of work or your taste in films. This follows from the principle of independent assortment.