WASHINGTON — Merrill Lynch & Co., which for months has shied away from responding to criticism that the brokerage house’s aggressive move into banking threatens the deposit insurance system, has decided to enter the reform debate.

In a comment letter filed last week with the Federal Deposit Insurance Corp., the company predictably defended itself against charges that its addition of more than $48 billion to insured deposits at banks in New Jersey and Utah during the past nine months could dilute the Bank Insurance Fund to the point that all banks would have to start paying premiums for the first time in five years.

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