The friar is describing dawn; the sun is just peaking out sending rays unto the clouds. The sunlight is not full yet, but there is enough light to create just shadows of darkness instead of pure night. He is picking flowers and weeds that can be either healing or poisonous.
Friar goes on to explain how earth is like a mother and a grave (you bury loved ones in the earth, but the earth also gives life to plants that grow from the dirt). Plants use the nutrients from the soil to grow. There are poisonous plants, but they are not all bad because every plant has it's use, and there are good plants, but if over or misused can become poisonous.
If you misuse good things, the can become evil. At the same time, if you take action to correct something evil, you can make it good. Like plants, men have both good and evil. If they have too much evil, they will not survive.
THe meaning is that man is very much like nature, containing both good and evil. However, we all have the power to control how that good and evil is used - both in nature and in ourselves.