The apparent controversy, though, is too good not to glom onto, and many authors have used it as a construct to present results. This is fine except that it clouds the emerging picture of climate change in the tropical Pacific.
A new paper by Nurhati et al (2009) includes this El Nino/La Nina kind of argument to highlight new isotopic measurements of coral reefs in the central Pacific. The geochemical techniques are applied to coral at three central Pacific islands, and show monthly-resolved temperature and salinity records over the 20th Century. The bottom line seems to be that there are statistically significant linear trends toward fresher, warmer water around these islands. The authors say that these trends are more consistent with more El Nino-like conditions in the central Pacific, are similar to other estimates of temperature changes, and is in line with modeling studies showing decreased upwelling of deep water in a warming world. Only in the final paragraph do the authors finally reveal that this El Nino stuff shouldn't be taken too seriously,
... this analogy likely over-simplifies the complexity of tropical Pacific anthropogenic climate change. Indeed, any of a number of large-scale climate changes that are likely to occur in a greenhouse world might overwhelm or at the very least fundamentally reshape the expected impacts of an “El Niño-like” trend. ... In this regard, the prominent warming and freshening trends uncovered in the coral reconstructions undoubtedly represent a combination of dynamics that are fundamentally different than those associated with the ENSO phenomenon.