The phrase "to challenge the consensus" means to question or oppose the commonly accepted beliefs or opinions held by a group of people. Full definition
Based on the correspondent's last paragraph, it seems likely there is an ideological basis involved for challenging the consensus on population numbers. (dotearth.blogs.nytimes.com)
For the progress of science, it is essential that new ideas and concepts that challenge the consensus get heard and can compete for research funding. (judithcurry.com)
There were at least a couple of posters that challenged the consensus view. (skepticalscience.com)