Put aside the old chestnut of people copying the latest Lady Gaga album or The Hunger Games (whether movie or book) without permission. There's plenty of fighting over that, replete with collateral damage from proposals such as the US's Sopa bill, but the lines for détente on straight-out copying are drawn: there's been uptake of all-you-can-eat subscriptions through services such as Spotify or Netflix, and pay-per-item stores such as the iTunes store.

No, the deepest and most pressing problem of intellectual property online is derivative use. What we build is made possible by the work of others who precede us. "If I have seen further it is by standing on ye sholders of Giants," wrote Isaac Newton, in a modest moment. Indeed, Newton's very quote can be traced back to others at least as far as the 12th century. When we create, we in fact rest upon a succession of shoulders of varying sizes.

In today's digital environment, the linkages between past and present work are more readily laid bare. Quotes morph as they are retweeted, while often leaving a trail of bread crumbs back to Tweet Zero. YouTube videos include soundtracks and images from other videos – enough that copyright-minded robots can detect the fingerprints of those earlier works and throw up a red flag against a new use.

Derivative uses are often regulated by intellectual property system. If these rules of ownership are construed too broadly – with too much control permitted to someone upstream – then anyone with the misfortune of coming along later risks trouble from those who came before. If the rules of ownership are construed too narrowly, then the present arguably pays too little respect – in the form of money – to the future. If someone made The Hunger Games movie without clearing it with Suzanne Collins, she'd be understandably put out, and the law allows her to exact a price for bringing her book to life on the screen.

It's broad ownership that poses the biggest danger to the internet and the activities upon or even near it. For example, fears of derivative use of older works may run so deep that commercials, movies, and television shows in need of a newspaper as a prop all use the same copy of a fake newspaper from the 1960s. Otherwise, the theory goes, the publisher of an actual newspaper used could allege copyright infringement for working its newsprint into a film scene. As the ability to create new work is democratised, creators won't have legal departments to sort out permissions nor, as Lawrence Lessig argued in his book Remix, should they have to find them. The ability to make new work from old work – especially if that new work is different enough that it doesn't dent the market for the old work – is something that benefits all creators, since so few can claim not to have a giant or 10 supporting them underneath.

This issue isn't just limited to books, movies, and music. Content zips around the internet thanks to code – programming code. And code is subject to intellectual property laws. For a while it looked like copyright would raise the largest questions here, as programmers would include others' code in their own later and possibly better works. The free software movement provided an answer to copyright questions by replicating foundational code without actually copying it: GNU is an operating system designed to replace copyrighted Unix with a free version. So long as GNU (which stands for "GNU's Not Unix") didn't actually include any Unix code, the reasoning went, it was safe from an infringement claim, while programs written for Unix could still easily be made to run on it – meaning that a bunch of Unix applications wouldn't have to be rewritten wholesale for there to be a library of titles available to run on GNU.

But then patents got into the picture. With patents, there need not even be copying for infringement to happen. If someone has patented the use of a laser pointed to play with a cat (unfortunately not a hypothetical), then anyone with an independent inspiration to exercise a feline is potentially infringing. With the rise of software patents, engineers coding new stuff – whether within a large software company or as kids writing smartphone apps – are exposed to a claim that somewhere a prior patent is being infringed.

The software patent mess has become acute enough that even incumbents are looking for ways out. There's the prospect of legal reform – possible if enough parties, including powerful ones, are fed up with standing only on the shoulders of lawyers. And there are steps towards disarmament. This week Twitter announced that it would no longer require its engineers to assign all patent rights for their work-related inventions to the company. Instead, engineers allow Twitter to use the patents defensively but not offensively – at least not without both the engineers and the company agreeing to such a use. With luck other companies will see the wisdom of this approach and follow suit.

The most enduring front in the battle over code may end up over something even more foundational than an operating system. Up next are software languages and APIs, the raw material from which our digital edifices are built. Arguments continued this week in the case of Oracle v Google, in which Oracle claims that the Java programming language is itself copyrighted, as are the ways in which software can be written to expect to run in some version of it. If Oracle wins, projects like GNU will be in danger: simply rewriting Unix from scratch as GNU wouldn't free the Platonic programming language behind Unix of copyright limitations. If a language itself can be copyrighted – and Oracle and Google, in otherwise solemn briefing, engage on whether Game of Thrones's Dothraki or Avatar's Na'vi can be so protected – then anyone speaking or writing in Dothraki or Na'vi would have to answer to those works' creators.

That's why the key to today's battles over intellectual property lies with derivative works: once Lego claims ownership to anything built with its blocs, or Oracle to anything written in Java, whole swaths of creativity and innovation are blocked to no good end.

Let us see far, and appreciate the help we've had achieving our vantage point – without permitting anyone along the long chain that came before us to claim undue credit for the view.

Copyright 2012 Jonathan Zittrain; Creative Commons Attribution Noderivatives 3.0 licence

• This article was amended on 20 April 2012. The version originally published referred to Java as "the Sun programming language" before introducing the name "Java" itself. Sun, the company that developed Java, was later taken over by Oracle, which is now suing Google over Java copyright. This has now been reworded for clarity