There is an ugly situation developing at the Bronx High School of Science, my alma mater, the once flagship school of a public education system that was the envy of the nation. The majority of the Bronx Science faculty is in open revolt, the principal is being publicly ridiculed, and the education of the students and the school’s reputation are being undermined by the imposition of questionable educational theories.

As an alumnus, I have long been distressed that Bronx Science has taken a secondary position among New York City high schools to Stuyvesant. Part of this change in fortune has to do with location. Stuyvesant sits on the Lower Manhattan waterfront in a shiny building of recent vintage. Bronx Science is located in a remote section of the Bronx in a structure that was state-of-the-art back in the 1960s, when I roamed the halls. Today it looks frayed.

After a decade of being eclipsed by Stuyvesant, former Schools Chancellor Harold Levy recognized that bold, innovative leadership might restore the school’s luster. When a popular assistant principal, William Stark, was poised to take charge, Mr. Levy, a Bronx Science alumnus, thought he had a better idea. “Why not a Nobel laureate as principal?” he asked.

This was the germ of what could have been a brilliant concept. Private schools often have a head who works on “big picture” concerns such as development and fund-raising, and a principal attending to the day-to-day minutiae of running the school. But Mr. Levy pictured some prominent scientist leaving the laboratory and moving into the principal’s office.

Mr. Levy found that Nobel laureates have other fish to fry. So he turned the selection process back to the then-Bronx high school superintendent, Norman Wechsler. With no one on the horizon, Mr. Wechsler tapped Mr. Stark, left dangling for months as acting principal. But two hours before Mr. Stark got the nod, he accepted a job as principal of Manhasset High School on Long Island.

Angry parents and alumni demanded action and got it. Mr. Wechsler and his office were removed from oversight of the school, which was placed under the chancellor’s direct supervision. The reviled Mr. Levy needed to find a new principal fast.

Valerie Reidy was the assistant principal of the biology department and on no one’s short list to assume the top job. But she found herself in the right place at the right time, proof of the Peter Principle, which holds that in a hierarchy, employees rise to the level of their incompetence. Mr. Levy appointed her, and no one was prepared to challenge “the first woman principal” of the school.

In the reorganization of the schools by the Bloomberg administration, control over Bronx Science was given to Region 1, filled with troubled high schools. Parent leaders objected to Bronx Science, which draws its students from across the city, being lumped in with ordinary schools. They viewed it as a violation of the agreement for direct control by the chancellor. There was concern that the school would come under the direction of Superintendent Irma Zardoya, whom a former parks commissioner, Henry Stern, a Bronx Science alumnus, calls “no friend of programs for gifted children.”

To the chagrin of the then-Parents Association president, Stefan Mayer, Ms. Reidy lobbied pliable parents to drop their objections. “This is a double step backwards,” Mr. Mayer said.

The Bronx Science faculty has been known as dedicated to the school and its mission. But they found themselves at odds with Ms. Reidy. When a guidance counselor objected to cuts in her department – there is one counselor for every 650 students – Ms. Reidy eliminated her position, forcing her to transfer. The need for counseling was demonstrated last fall, when a 10th-grade student died of a heroin overdose.

Teachers are upset with Ms. Reidy’s instructional mandates, mirroring Region 1 and Tweed policies imposed in the lower grades. Teachers are encouraged to use “progressive” techniques, in this case “pure discovery,” a pedagogy that dissuades teachers from assigning readings in a subject before it is raised in the classroom. Students are supposed to “discover” knowledge “naturally” as they go along. This is counterintuitive in a school where students are known to devour textbooks from cover to cover.

One chemistry teacher, Robert Drake, who holds a Ph.D. in his subject and has taught at the college level, was admonished when a student used the word “equilibrium.” “How did she know this term?” he was asked. It hadn’t been covered in the classroom. The unsatisfactory rating, the first in Mr. Drake’s more than 30-year career, spurred him to go to war with Ms. Reidy.

Making fun of Ms. Reidy’s conceit in demanding that she be addressed as “doctor” – she holds an honorary doctorate from her alma mater, the College of Mount Saint Vincent – he has begun an “anti-quack” campaign to rid the school of Ms. Reidy and what Mr. Drake thinks is her snake-oil pedagogy. His campaign is catching on. Meanwhile, Ms. Reidy has not returned numerous calls for comment.