The science still doesn't seem clear - for example, a recent study in the UK (presumably the largest ever) showed no evidence of increased infertility: http://online.liebertpub.com/doi/pdf/10.1089/jomh.2014.0012

That's if he uses a saddle.

What's the alternative? Standing on the pedals? Or are there other styles of seat, not covered by the word "saddle"?

There are "noseless" saddles and saddles with a channel down the middle that may help protect the sensitive bits. http://www.thebirdwheel.com/noseless-saddles-tested-updated

But my biased opinion is buy a recumbent! Fewer back, neck, and nether region issues, plus, they have comfy seats! http://www.bacchettabikes.com/recumbent-bikes/

VERY comfy seats! http://www.hpvelotechnik.com/produkte/scorpion_plus20/index_...

A long wheelbase (crank behind the front wheel) and a more upright riding position is perfect in city traffic. On my commuter, my eye level is about even with drivers in crossover vehicles.

OK, that's closer to what I thought. I was kind of thrown off by the previous comment, which I read as implying "there are things besides 'saddles' that you can use".