Poring over the raw genetic data, Mark Daly noticed a startling pattern. An expert in statistical genetics and a fellow at MIT's Whitehead Institute for Biomedical Research, Daly was scouring a region of human chromosome 5, a place that colleagues strongly suspected contained a gene that puts people at risk for a devastating digestive condition called Crohn's disease.

The sequence spelled out in the DNA letters A, T, G, and C was almost identical in all the samples Daly examined-each from a different person. As Daly expected, sprinkled every thousand letters or so were spots where a single letter tended to vary from one person to another. Then came the surprise. Many of these single-letter variations seemed to occur together, as if they were tightly linked across long stretches of the DNA. In other words, whenever Daly looked at an individual copy of one of the sections of DNA and found an A at one of these positions, he would find a G at the next one, about a thousand letters away, a C in a third position still further down the line, and so on. After roughly tens of thousands of letters, another pattern began; the long stretches of linked variants, it seemed, divided the chromosome into neatly defined blocks. What's more, for any given stretch of the chromosome, there were only four or five versions of these blocks that kept showing up in the different individuals Daly studied. Daly realized he was staring at evidence of an underlying structure to the human genome. He was also looking at the beginnings of biology's next big project-and its next big controversy.