Carl Zimmer says that our current gene theory

needs a total makeover:

One of the biggest of these projects is an effort called the Encyclopedia of DNA Elements, or Encode for short. Hundreds of scientists are carrying out a coordinated set of experiments to determine the function of every piece of DNA in the human genome. Last summer they published their results on 1 percent of the genome — some 30 million “letters” of DNA. The genetic code is written in letters, like the title of the movie “Gattaca,” with each letter standing for a molecule called a base: guanine (G), adenine (A), thymine (T), cytosine (C). The Encode team expects to have initial results on the other 99 percent by next year.

Encode’s results reveal the genome to be full of genes that are deeply weird, at least by the traditional standard of what a gene is supposed to be. “These are not oddities — these are the rule,” said Thomas R. Gingeras of Cold Spring Harbor Laboratory and one of the leaders of Encode.

A single so-called gene, for example, can make more than one protein. In a process known as alternative splicing, a cell can select different combinations of exons to make different transcripts. Scientists identified the first cases of alternative splicing almost 30 years ago, but they were not sure how common it was. Several studies now show that almost all genes are being spliced. The Encode team estimates that the average protein-coding region produces 5.7 different transcripts. Different kinds of cells appear to produce different transcripts from the same gene.

Even weirder, cells often toss exons into transcripts from other genes. Those exons may come from distant locations, even from different chromosomes.

So, Dr. Gingeras argues, we can no longer think of genes as being single stretches of DNA at one physical location.

But wait, there's more:

But it turns out that the genome is also organized in another way, one that brings into question how important genes are in heredity. Our DNA is studded with millions of proteins and other molecules, which determine which genes can produce transcripts and which cannot. New cells inherit those molecules along with DNA. In other words, heredity can flow through a second channel.