On a foggy April night in 1868, Capt. Beal stands on deck watching for the pilot boat to guide his ship into Boston Harbor. He’s returning to “the world’s smartest city,” a place that has expanded and been reshaped with great industry, a once “quaint village” that’s now a modern metropolis. Beal marvels at these changes as a bright light appears in the water, but it’s not the pilot boat he expected. There’s no time to adjust course; his schooner tears a lifeboat in two, sending its passengers into the water. Before the crew can rescue them, the fog lifts, and Beal sees “at least half a dozen ships” in distress. Some are sinking; others have crashed into the wharf, catching fire. When Beal consults his navigational instruments, the needle of every compass is spinning wildly. All at once, the technology he always relied on has betrayed him.

This is the vivid and frightening opening scene of Matthew Pearl’s latest novel, “The Technologists.”

Pearl is the author of the best-selling historical mysteries “The Dante Club,” “The Poe Shadow” and “The Last Dickens,” which revolve around great writers and their work. With “The Technologists,” Pearl has written another historical mystery, but this time his story depicts the battle between Harvard University and a then-upstart little school called the Massachusetts Institute of Technology. Great writers have been replaced by grand institutions.

The sunken boats are only the first catastrophe to strike Boston. More disasters follow soon, acts of sabotage accomplished with the aid of technology so advanced, so mysterious, that some observers are blaming necromancy and the devil. Who can sort this out?

Only those plucky kids at MIT. Members of the class of 1868, MIT’s first graduates, make up much of the cast: three seniors and the school’s first female student, Ellen Swallow. They face many obstacles as they try to solve this mystery because nobody trusts MIT. In 1868 the school is considered nearly pagan in its view of science. Better are the ways still taught at Harvard, by men like Professor Agassiz, who, when he’s not derailing the MIT students’ investigation, hopes to refute Darwin’s theories using “Christian principles.”

”The Technologists: A Novel” by Matthew Pearl (Random House)

By pitting these two sides against each other — MIT vs. Harvard, hard science vs. Christianity — Pearl clarifies the battle of real interest to him: modernization vs. tradition. One Harvard jock states the case clearly in the opening pages: “Science cannot substitute for culture.” Let the battle begin!

All this makes for a promising build-up. Soon enough, though, one glaring problem appears. Despite an abundance of dramatic potential, there’s fairly little dramatic tension in the first half of the novel. In the second half, lots of people have been hurt, Boston is in a panic, and the sleuths are well on the villain’s trail — all of which is exciting, once you get to it. But for a long time, the most pressing concern in the book is whether or not MIT will survive the suspicion and doubt cast on it as a new scientific institution. In 2012, most of us know the answer to that mystery. It’s difficult to muster much worry for an underdog that now has an endowment worth $9.9 billion.

The trick, early on, would have been to create characters with vigor and the potential to surprise. While the fortunes of MIT are never seriously in doubt, the fate of sympathetic individuals could arouse our concern. Unfortunately, only one character in this novel ever engenders real human feeling, an actress named Christine Lowe, but she turns out to be a bit of window dressing.

Still, by the end, “The Technologists” is a marvel of moving parts. It creates a colorful portrait of Boston in the midst of modernization, provides all the twists and turns a mystery lover could ask for, and offers several thrillingly described scenes of destruction. For better, but sometimes for worse, Matthew Pearl builds ruthlessly efficient machines.

LaValle’s newest novel, “The Devil in Silver,” will be published in August.

The Technologists

By Matthew Pearl

Random House. 496 pp. $26