In your case, if your computer programmer is doing great work and he is brilliant, what does it matter what time he comes to work? 

Here is a real world example from my own past businesses:

I had a young college CS graduate working for me, he was wicked smart and a gamer, and he periodically come in late…. even 11am some mornings.  It bothered my sensibilities that he came in late frequently so one day I pulled him aside to talk about my concerns and inquire what was going on for him? Why was he frequently late?  He said, “I’m sorry, last night I was up gaming until 4am and I was tired.  He said, further, but truly, the reason I come in late most mornings is because it is so distracting to work here, I get most of my work done after everyone goes home and it is quiet… and he truly stayed at the office some nights until 11pm or midnight.  So I said to him, ok, you are such a great valued player for us, let’s make the environment better for you; you now start work every day at 11am and can stay as long as you like to get things done; just get it all done.  He said, great.  And the result, he was solely responsible for software design and coding genuis that allowed us to change our business model from a 9% GM to 68% GM within months.  We were literally printing money through the applied acts of his genius.  Now what would have happened if I had been a time-clock stickler?  Well I will tell you what would happen….. a year later I sold that company for a record multiple on Recurring Monthly Revenue (RMR)  at closing (multiple not to be disclosed), and it was an awesome day. I remember coming back in and stroking him a personal check from proceeds of the sale…. he was that good. 

Then something terrible happened.  The new owners had a time clock mentality handicap, required him to start coming in to work early, and he said, the culture has changed and now sucks, and I am quitting.  Was it at all necessary that he come into work early for him to get his work done? No, so he quit. The new owners just did not understand how to get the most from their great people.  And they paid for a resource that left them shortly after acquisition because they did not understand how to manage people.

I have other stories of similar management understanding and helping get the most from employees… and they produced similar wins.  We are not working with robots, but human beings, and when we understand how to motivate our employees, they can do great things.  It’s a core part of creating a culture that works productively and gets things done right the first time.