A final rejection will be upheld on appeal if the Applicant does not provide a substantive response to one of the grounds for rejection included in an Office action. In this case, a pro se applicant failed to respond to a rejection on ground of indefinite. There is currently some debate as to the standard for indefiniteness applicable during patent prosecution. This opinion includes a good review of the prevailing views. But the question of whether these particular claims were indefinite was never reached. The applicant’s failure to follow the USPTO’s procedural rules could not be remedied by an appeal.
This case does not mean that arguments are waived on appeal if not raised during prosecution. It just means that the applicant needs to respond with some argument or some amendment to each independent claim rejection.