Melding $11.3 billion worth of research and development budgets from two different companies won't be easy for Pfizer (NYSE:PFE). But at least it has a plan now for its structure after its acquisition of Wyeth (NYSE:WYE) -- including keeping eight senior executives from its new purchase.

The biggest change will come from a split of the biologics and small-molecule research groups. As long as that doesn't create an unreasonable level of duplication in the support departments, the split seems intelligent to me. Protein-based biologics like those made by Amgen (NASDAQ:AMGN) and Genentech have little in common with traditional small-molecule drugs. Chemists won't be much help to biochemists in trying to purify proteins, so you might as well get them out of the way.

But what does the company do about research areas like oncology, which span both research groups? While their molecules may look nothing alike, researchers developing an antibody-based drug for cancer should surely be discussing their findings with researchers developing a small-molecule drug. In the end, though, this change in structure might not mean a whole heck of a lot, as long as the research groups are still holding the same meetings they always were.

The big problem with this integration -- and, although their impending union is smaller, let's throw Merck (NYSE:MRK) and Schering-Plough (NYSE:SGP) in there, too -- is that the integrations take time, and they suck energy out of researchers. How many scientists are sitting in Pfizer's and Wyeth's laboratories right now, discussing the upcoming changes, instead of running experiments? And post-acquisition, there will surely be plenty of meetings to determine which drug candidates to drop, and which to continue.

Pfizer claims to have learned its lessons after the acquisition of Pharmacia and Warner-Lambert, but I'd rather see proof than simply take management's word for it. Pfizer will be considerably larger after its acquisition; whether it can turn that size into increased productivity remains to be seen.

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Fool contributor Brian Orelli, Ph.D., has no beef with chemists, even though his background is in biochemistry and genetics. He doesn't own shares of any company mentioned in this article. The Fool has an ideally sized disclosure policy.