There are a lot of negatives in bicycling,from the negative metabolic effects Sisson pointed out in this article to the very position the human body assumes while riding a bicycle.
As a former bicycle racer(in the 1970's) and an avid bicycle tourist also during that time(I have logged over 4,000 miles touring) I can honestly say YES,the negative impacts of cycling are very real.
First,the body's position on a typical diamond-framed lightweight racing bike is not "optimum" you are perched atop a narrow saddle and no matter how much you spend for it,racing style saddles are NOT "comfortable" nor are they kind to your body. This saddle design has been proven to cause numbness in men in their crotch region that can lead to long term impotency issues. More than 70% of your body weight mass is supported by your saddle. Then there are issues with your elbows and arms wich support the other 30% of your total body mass. As a former bike racer,I experienced a lot of elbow,shoulder and hand pain during the grueling races I participated in,this can lead to osteoporosis in those joints later on in life(after age 50) In racing,one can also blow out their knee's if their foot position and pedaling motion is not absolutally optimum,also the degree of "float" on your clipless pedals is really important to get it RIGHT,or long term pedaling in this motion can lead to chronic knee damage.
As with any excercising,cycling too hard or too long can have it's negative effects on the human body. Today,after 40 years of cycling,I now ride a Recumbent wich eliminates 95% of the issues I had from lower back pain to crotch numbness and arm and hand pain but since *most* of you on this forum have poo poohed me in the past about the use of "Bents" I no longer write about them.
The bottom line is: how much do WE want to ride and how much of a risk of damage to out body are we willing to take?