This question relates to a curious feature of how genetic information is organized in the DNA of many organisms. The sequence of bases that make up DNA encode a corresponding sequence of amino acids which make up proteins. Molecular biologists had at first assumed that in a gene, all the DNA coding for a protein would be continuous, and that is what they found when they first looked at the genes of prokaryotes (bacteria and other simple cells). When researchers looked at more complex (eukaryotic) cells, however, they found that the encoding DNA is typically discontinuous: stretches of encoding DNA (called exons) are interspersed with long stretches of non-encoding DNA (called introns). After the DNA is transcribed into a string of RNA--but before the RNA is translated into protein--the introns are edited out. Although introns have sometimes been loosely called "junk DNA," the fact that they are so common and have been preserved during evolution leads many researchers to believe that they serve some function.

Ashok Bidwai, an assistant professor in the department of biology at West Virginia University, elaborates:

"It is widely believed that introns are remnants of genetic sequences that once served as spacers between the stretches of DNA that coded for specific, comparatively simple proteins. During the evolution of complex proteins, regions of the genetic code (known as domains) may have been shuffled and brought together to generate new sequences that code for novel protein structures that took on new functions. This hypothesis is based on the observation that the relative positions of introns in genes remain largely the same in organisms as diverse as Drosophila melanogaster (the fruit fly), Caenorhabditis elegans (a widely studied nematode), mice and humans. Walter Gilbert of Harvard University has laid out many of the details of this hypothesis.

"In addition, some researchers have proposed that introns serve as a mechanism that selects for genes that will be expressed early (rather than late) during the development of an organism. This idea is not based on extensive experimentation, however, so its plausibility is uncertain."

Sandro J. de Souza, who works in Walter Gilbert's laboratory at Harvard University, expands on the prevailing intron hypothesis:

"Questions about the function of introns appeared immediately after their discovery in 1977. What is the role of introns? Why are they here in our genes? Almost 20 years later we still do not have definitive answers, even though some DNA databases now contain around 500 megabases of sequences--that is, strings of genetic code that represent 500 million chemical letters of our genome.

"First, let's start with some classifications. There are at least five different types of introns. Some of them are ribozymes, RNA molecules that are catalytically active, meaning that they facilitate certain chemical reactions; some of these ribozymes are able to perform a reaction in which they splice themselves out of the original transcript. The most common type of intron is called a spliceosomal or nuclear intron; the name comes from the cellular machinery, known as the spliceosome, which is responsible for splicing and making sure that the genetic sequences in introns are not translated into junk proteins. This type of intron is the one found in the nuclear genes of humans.

"In general, nuclear introns are widespread in complex eukaryotes, or higher organisms. Simple prokaryotes and eukaryotes (such as fungi and protozoa) lack them. In complex multicellular organisms (such as plants and vertebrates), introns are about 10-fold longer than the exons, the active, coding parts of the genome. The sequence and length of introns vary rapidly over evolutionary time.

"Introns do sometimes have identifiable functions. Scientists have found clear examples of 'functional nuclear introns' that can accommodate sequences important for the expression of the gene on which the intron resides. This function is not a general feature of introns, however, because several genes that lack introns express themselves normally (histones and olfactory receptor genes, for instance). There are also cases in which introns contain genes for small nuclear RNA, which is important for the translation of messenger RNA, an intermediary between DNA and proteins. Nuclear introns can also be important in a process called alternative splicing, which can produce multiple types of messenger RNA from a single gene. Although these examples demonstrate a constructive role for introns, they cannot explain why introns are so ubiquitous in our genes.

"In 1978 Walter Gilbert of Harvard expressed a different view of the nature of introns (in the same report in which he coined the terms 'exon' and 'intron'). He suggested that introns could speed up evolution by promoting genetic recombinations between exons. This process (which he called 'exon shuffling') would be directly associated with formation of new genes. Introns, from this perspective, have a profound purpose. They serve as hot spots for recombination in the formation of new combinations of exons. In other words, they are in our genes because they have been used during evolution as a faster pathway to assemble new genes. Over the past 10 years, the exon shuffling idea has been supported by data from various experimental approaches.

"Several genome projects will be concluded in the next decade. They are expected to yield a huge amount of information about intron sequences. The new data should solve most of our basic questions about the functions of introns.