At the end of a Hollywood blockbuster, when the vanquished villain declares that he should have won and that we haven’t seen the last of him, we all know what it means: the sequel is coming.

So, Hollywood’s top lobbyist, former Senator Chris Dodd, followed a familiar script last week after sweeping online protests derailed the Stop Online Piracy Act (Sopa) and Protect IP Act (Pipa), a pair of legislative proposals backed by movie and music distributors. Dodd snarled that his opponents had misled the public and vowed to continue pressing for new laws to combat unauthorized copying of intellectual property. Coming soon to a congressional hearing room near you, it’s Sopa II: Revenge of the Content Industries.

. . . . Even Dodd’s enemies acknowledge that these sites pose a problem, though many question industry estimates about its scope.

Those of us who opposed the excesses of Sopa and Pipa need to prepare for the next round. . . . At a minimum, Congress must address three other problems as well.

First and foremost, Sopa II needs to take due process seriously. . . .

Second, the standards for judging infringement must be clear and must be consistent with existing intellectual property law. . . .

Finally, these bills cannot shift IP owners’ duty to safeguard their own rights onto innocent bystanders like Google, eBay or Facebook. Open online forums enable millions of daily communications from ordinary people. Intermediaries cannot examine every post searching for links to pirates. That’s why federal law exempts them from liability for nearly everything their users post independently – even fraud or defamation. IP already gets special treatment, because intermediaries must remove infringing material if rightsholders complain.

But the struggles inherent in the transition from old and established ways of doing business are ongoing and will continue to be. Today’s example comes from the world of science. As the New York Times reports, “For centuries, [scientific] research [was]cdone in private, then submitted to science and medical journals to be reviewed by peers and published for the benefit of other researchers and the public at large.  . . . Peer review can take months, journal subscriptions can be prohibitively costly, and a handful of gatekeepers limit the flow of information. It is an ideal system for sharing knowledge, said the quantum physicist Michael Nielsen, only ‘if you’re stuck with 17th-century technology.’”

But Dr. Nielsen and others argue that science can happen much more quickly and accurately using the new technologies, and reality is catching up to their ideals (even as established institutional players such as universities and grant-makers still depend on the “traditional published paper” as their exclusive criterion of judgment):

Open-access archives and journals like arXiv and the Public Library of Science (PLoS) have sprung up in recent years. GalaxyZoo, a citizen-science site, has classified millions of objects in space, discovering characteristics that have led to a raft of scientific papers.

On the collaborative blog MathOverflow, mathematicians earn reputation points for contributing to solutions; in another math experiment dubbed the Polymath Project, mathematicians commenting on the Fields medalist Timothy Gower’s blog in 2009 found a new proof for a particularly complicated theorem in just six weeks.

And a social networking site called ResearchGate — where scientists can answer one another’s questions, share papers and find collaborators — is rapidly gaining popularity.

Editors of traditional journals say open science sounds good, in theory. In practice, “the scientific community itself is quite conservative,” said Maxine Clarke, executive editor of the commercial journal Nature, who added that the traditional published paper is still viewed as “a unit to award grants or assess jobs and tenure.”