Back at home things continued to degenerate. Selena often worked late, and talked to him less than ever.
“I love you,” he said. “Selena, I love you.”
“I know.”
He tried to throw himself into his work. They were at the same lab, they could go home late together. Talk like they used to about their work, which though not the same, was still genomics in both cases; how much closer could two sciences be? Surely it would help to bring them back together.
But genomics was a very big field. It was possible to occupy different parts of it, no doubt about that. They were proving it. Smith persevered, however, using a new and more powerful electron microscope, and he began to make some headway in unraveling the patterns in his fossilized DNA.
It looked like what had been preserved in the samples he had been given was almost entirely what used to be called the junk DNA of the creature. In times past this would have been bad luck, but the Kohl labs in Acheron had recently been making great strides in unraveling the various purposes of junk DNA, which proved not to be useless after all, as might have been guessed, evolution being as parsimonious as it was. Their breakthrough consisted in characterizing very short and scrambled repetitive sequences within junk DNA that could be shown to code instructions for higher hierarchical operations than they were used to seeing at the gene level—cell differentiation, information order sequencing, apoptosis and the like.
Using this new understanding to unravel any clues in partially degraded fossil junk DNA would be hard, of course. But the nucleotide sequences were there in his EM images—or, to be more precise, the characteristic mineral replacements for the adenine-thymine and cytosine-guanine couplets, replacements well established in the literature, were there to be clearly identified. Nano-fossils, in effect; but legible to those who could read them. And once read, it was then possible to brew identical sequences of living nucleotides, matching the originals of the fossil creature. In theory one could re-create the creature itself, though in practice nothing like the entire genome was ever there, making it impossible. Not that there weren’t people trying anyway with simpler fossil organisms, either going for the whole thing or using hybrid DNA techniques to graft expressions they could decipher onto living templates, mostly descendants of the earlier creature.
With this particular ancient dolphin, almost certainly a freshwater dolphin (though most of these were fairly salt tolerant, living in river mouths as they did), complete resuscitation would be impossible. It wasn’t what Smith was trying to do anyway. What would be interesting would be to find fragments that did not seem to have a match in the living descendants’ genome, then hopefully synthesize living in vitro fragments, clip them into contemporary strands, and see how these experimental animals did in hybridization tests and in various environments. Look for differences in function.
He was also doing mitochondrial tests when he could, which if successful would permit tighter dating for the species’ divergence from precursor species. He might be able to give it a specific slot on the marine mammal family tree, which during the early Pliocene was very complicated.
Both avenues of investigation were labor-intensive, time-consuming, almost thoughtless work—perfect, in other words. He worked for hours and hours every day, for weeks, then months. Sometimes he managed to go home on the tram with Selena; more often he didn’t. She was writing up her latest results with her collaborators, mostly with Mark. Her hours were irregular. When he was working he didn’t have to think about that; so he worked all the time. It was not a solution, not even a very good strategy—it even seemed to be making things worse—and he had to attempt it against an ever-growing sense of despair and loss; but he did it nevertheless.
“What do you think of this Acheron work?” he asked Frank one day at work, pointing to the latest printout from the Kohl lab, lying heavily annotated on his desk.
“It’s very interesting! It makes it look like we’re finally getting past the genes to the whole instruction manual.”
“If there is such a thing.”
“Has to be, right? Though I’m not sure the Kohl lab’s values for the rate adaptive mutants will be fixed are high enough. Ohta and Kimura suggested ten percent as the upper limit, and that fits with what I’ve seen.”
Smith nodded, pleased. “They’re probably just being conservative.”
“No doubt, but you have to go with the data.”
“So—in that context—you think it makes sense for me to pursue this fossil junk DNA?”
“Well, sure. What do you mean? It’s sure to tell us interesting things.”
“It’s incredibly slow.”
“Why don’t you read off a long sequence, brew it up and venter it, and see what you get?”
Smith shrugged. Whole-genome shotgun sequencing struck him as slipshod, but it was certainly faster. Reading small bits of single-stranded DNA, called expressed sequence tags, had quickly identified most of the genes on the human genome; but it had missed some, and it ignored even the regulatory DNA sequences controlling the protein-coding portion of the genes, not to mention the so-called junk DNA itself, filling long stretches between the more clearly meaningful sequences.
Smith expressed his doubts to Frank, who nodded, but said, “It isn’t the same now that the mapping is so complete. You’ve got so many reference points you can’t get confused where your bits are on the big sequence. Just plug what you’ve got into the LanderWaterman, then do the finishing with the Kohl variations, and even if there are massive repetitions, you’ll still be okay. And with the bits you’ve got, well they’re almost like ests anyway, they’re so degraded. So you might as well give it a try.”
Smith nodded.
That night he and Selena trammed home together. “What do you think of the possibility of shotgun sequencing in vitro copies of what I’ve got?” he asked her shyly.
“Sloppy,” she said. “Double jeopardy.”
A new schedule evolved. He worked, swam, took the tram home. Usually Selena wasn’t there. Often their answering machine held messages for her from Mark, talking about their work. Or messages from her to Smith, telling him that she would be home late. As it was happening so often, he sometimes went out for dinner with Frank and other lane mates, after the evening workouts. One time at a beach restaurant they ordered several pitchers of beer, and then went out for a walk on the beach, and ended up running out into the shallows of the bay and swimming around in the warm dark water, so different from their pool, splashing each other and laughing hard. It was a good time.