Andrew von Eschenbach is a man of many metaphors from metamorphosing caterpillars to diaper-soiling infants. Most of them will make you laugh, unless of course you are working for one of the companies regulated by him.

The FDA commissioner, however, is blunt when it comes to describing what’s happening today in healthcare, which he calls “the most profound transformation in the history of medicine.”

Speaking at a recent conference held by the San Francisco Bay Area’s biotechnology association BayBio, Von Eschenbach said as our understanding of disease moves to a genetic, molecular and cellular level, science and technology are driving changes whether we like it or not. Unlike caterpillars, which always transform into butterflies, he said we have a choice in this metamorphosis. Rather than being just participants, we can be “architects of what it will be.”

The problem von Eschenbach sees is that his agency is not equipped for this molecular metamorphosis. His vision for the future of the FDA involves an agency more closely engaged with the companies it regulates as the agency becomes more “proactive and interactive” on the front end.

That will involve its working with a company even before the company makes an application in order to define the science and ensure the work will clear regulatory hurdles. He also said that the agency would be engaged to a greater extent in postmarketing and postapproval studies of the effects of products on patients.

To do this, the agency has a tough balancing act ahead of it. Von Eschenbach will need to be responsive to public concerns about safety and about the influence drug companies exert over his agency because of the critical funding they provide through user fees. At the same time, he will need to be responsive to industry and patients concerned about the effects that regulatory changes have on the speed at which new therapies and devices are brought to market. He will also have to be mindful of changes that could hurt young companies in the sector as they try to raise capital to develop next-generation products.

“Only a six-month-old with a dirty diaper likes change,” he said.

What will guide the agency through these changes is an understanding of its role. The FDA is “a bridge from discovery and development to the delivery of these new inventions?and not a barrier,” he said. This led von Eschenbach to another metaphor, one that was enough to give any pharma executive butterflies.

He said the FDA has to get rid of speed bumps and potholes, but also to erect more guard rails. “If you are starting to weave a bit, we’ll guide you back. We may take a coat of paint off you, but we’ll keep you from going off the road. But it’s so you go faster,” he said. “A Formula 1 goes 200 miles per hour safely with rigor, precision and discipline. You dot every i and cross every t, and you go faster. That’s the way we’re going to do regulation.”

If you notice a long line of pharmaceutical executives lined up outside your local Earl Scheib waiting for the manager’s special to get a few dents banged out and a fresh coat of paint, you’ll know the commissioner and his road crew have been hard at work.