Does leaving the lid on make a difference to whether the meat in a soup softens/cook properly? I've been coooking soup with a pot lid off and notice the meat is still tough when cooking.  It could be the due to the lid or some other factor.

I put a thermometer in the soup water and it seems to be at a good temp for simmering meat(90-95c) and I can see the bubbles appearing every seconds or so.  However the meat is still tough.

I put the lid back on and cook then it seems to soften ok.  Considering I can see the simmering bubbles and the thermometer shows a simmer can you explain why and if putting the lid on is making a difference?

Thanks
The only thing that gets the connective tissue in tough cuts to loosen is heat. With the lid on, you've got more insulation. I'd bet you a shiny nickle that the meat towards the bottom of the pot was a touch more cooked than the meat at the top of the pot— you're losing a lot of heat where all of that liquid is hitting room-temperature air. With my immersion circulators, for example, I can't keep the water bath much above 70c without covering them, but the second I cover it, the temperature shoots right up. So sure, the lid likely made it cook a little more quickly and evenly. That said, allowing your cooking liquid to evaporate and intensify as you stew your meat can be a good thing too.