apt-get update


Refreshes the repositories and fetches information about packages that are available online.

apt-get upgrade


Downloads and installs updates for all installed packages - as long as it doesn't bother dependencies (install new packages, remove old ones or crosses a repo source (switch a package from one repo to another)).

apt-get dist-upgrade


Does the same as "upgrade" but upgrades a package also when dependencies or sources are changed (something you want to avoid on servers without further testing).

To conclude - an update can break things but it is necessary!
So if you are on a desktop you should normally do a: 

sudo apt-get update &amp;&amp; sudo apt-get dist-upgrade


Without destroying something.

On a server most of the times a: 

sudo apt-get update &amp;&amp; sudo apt-get upgrade


should be enough AND security updates should be installed automatically (on servers and desktops)

TL;DR!

Yes you should update php in this example - cause it is a security fix (what can be seen through the numbering scheme of php and else it would not have been pushed into the "upgrade" branch of ubuntu...

Is apt-get upgrade a dangerous command?
I am currently reviewing a paper and feel suspicious about their numerical results. I feel their results have been slightly modified to exhibit their superiority compare to other comparative methods.  

I cannot give an exact mathematical reason why I think their numerical results have been manipulated, but it is so odd that in all 15 scenarios they have been better. Actually, I am pretty sure that their method is better than his benchmarks but not always. Maybe they modified some scenarios.   

As I don't have a mathematical reason why I think some of their numbers are altered, should I ask for their computer code and run them myself?  
