On Tuesday morning, Valeant Pharmaceuticals Intl Inc. (TSX:VRX)(NYSE:VRX) CEO Michael Pearson hosted a second conference call to address allegations about the company. This came after Bill Ackman, whose fund holds 21.5 million shares, said the first call was too “scripted.”

As would be expected, this call featured only about 15 minutes of prepared remarks, followed by over an hour of questions. We take a look at the three major takeaways below.

1. Blaming bad PR

Mr. Ackman has also been critical of Valeant’s communication strategy in general, claiming the company did not respond quickly enough–nor forcefully enough–to its many critics. On the call, Mr. Pearson acknowledged this problem at the company, saying that it was “a painful learning experience for me, personally.”

Both men may be right, but the shorts argue that a lack of communication isn’t Valeant’s biggest problem.

2. Philidor

When Mr. Pearson opened the line up for questions, he said that he wouldn’t comment on Philidor because Valeant is still investigating what happened. This certainly does not pass the smell test. Valeant’s current troubles are directly tied to Philidor’s practices, and there are many unresolved questions about the specialty pharmacy.

Remember, this investigation is not exactly an independent one. It is being led by a special board committee, and all of the major people involved are Valeant shareholders. So, in a sense, Valeant is investigating itself. No one has any doubt that the investigation will exonerate Valeant.

At the same time, Mr. Pearson said that “it’s impossible to have full knowledge of everything.” He was referring to what really happened at Philidor. Such a statement hardly inspires confidence, and ironically it came after he admitted that communication is a problem.

3. Moving on

Mr. Pearson said he wasn’t ready to update any guidance numbers, saying that he would do so in December, when Valeant hosts its Investor Day. But he did say that Valeant would be replacing Philidor within 90 days, likely with multiple relationships, and will not have an option to buy any of these companies.

He also emphasized how confident he is, in part because Philidor accounted for only 7% of the company’s revenue. Other parts of the business remain unaffected; for example, drugs from the recently acquired Salix are showing fantastic growth.

As for questions about Mr. Pearson himself, there is no question that he is staying on to see the company through this mess. And for those of you who wanted more colour from the CEO (which should be everyone who listened in on the call), you’ll get to hear him speak to the U.S. Congress in December.

Until then, we still have not gotten to the bottom of all these issues, and Valeant’s stock remains far too risky for my taste.

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Fool contributor Benjamin Sinclair has no position in any stocks mentioned. Tom Gardner owns shares of Valeant Pharmaceuticals. The Motley Fool owns shares of Valeant Pharmaceuticals.