Currently a very interesting and rather important debate is happening within the discipline of ecology. Scientific debates are usually not very public, not because anybody has anything to hide, but because they tend to be rather technical and difficult to follow. The debate over novel ecosystems is much more public, however, mainly because some of the players are science journalists, like Emma Marris, and because the idea already has important policy implications.
Based on the idea that humans are modifying their environment (which is undisputed, one should think), many natural ecosystems are now being transformed into what have been called “novel ecosystems” by adding or removing species from them. And likely humans have been altering nature since day one. Once alteration happens, however, different approaches to the phenomenon can be adopted: live with the new ecosystem, study it, use it, or try to restore it, among others.
It is worth noting that many ecosystems that we find appealing have little to do with what scientists would describe as largely undisturbed ecosystems. One example are anthropogenic heaths found in Europe: they exist on typically poor soils and need to be grazed, often by sheep.

Lueneburg Heath, photo by Willow, from Wikipedia (http://en.wikipedia.org/wiki/Heath#mediaviewer/File:L%C3%BCneburger_Heide_109.jpg)
Without human management these ecosystems would disappear quickly. These should count as human-induced novel ecosystems, right? But they are well studied and rather valuable to humans in multiple ways. They are beautiful, and often preferred destinations for tourists.
What is the value of such anthropogenic heaths? How do we compare them to relatively undisturbed habitats in the heart of the Amazonian jungle? Take Yasuni National Park in Ecuador, probably the wildest place I personally have ever visited. (Not that Yasuni is completely untouched by humans, but practically no ecosystem falls into that category anymore.)
To me some of the debate over novel ecosystems we see in the scientific community today has to do with differences in the underlying values: shall we embrace the new as inevitable or try keep as much undisturbed nature as we can? In my opinion both things need to be done. To me (and here the scientist is speaking), a relatively undisturbed area has more value and I think we have the moral obligation to protect those. But still we must accept that many ecosystems have been irreversibly transformed by humans, often via invasive species (as I discussed in a previous post). And we must also acknowledge that there are irreversible changes in ecosystems due to large scale changes in the environment like global climate change. (Though we should not ignore that many ecosystems will not necessarily be devastated by climate change, but may actually be resilient to change.)
As a scientific idea, the concept of novel ecosystems was introduced only a short while ago, and is now under debate and scientific scrutiny. There is a recent scholarly book on the topic (Novel Ecosystems, ed. Hobbs, Higgs, & Hall (2013)); two of the editors published one of the first review papers on the subject (Hobbs et al. (2009)) in the respected journal TREE. While the concept is appealing to many, it was recently critiqued as scientifically not yet ready by a group around the ecologist Daniel Simberloff, a titan in his field (Murcia et al (2014)). One of the most pointed criticisms from that review is that the acceptance of novel ecosystems by governments and managers might open the “door to impunity” giving decision makers get an easy way out of tough conservation problems. Again, it is the value system we are talking about. As our world changes rapidly, the discussion about how best to conserve nature is important and has to happen now.