Refutation of those who deny the Hadeeth of flies
29-9-2010 | IslamWeb
Question:
Do you know of scientific research that substantiates the Hadeeth in which the Prophet, sallallaahu ‘alayhi wa sallam, says that if a fly falls in a cup, one should dip it and then remove it, which consequently returns the beverage to its original state?
Answer:
All perfect praise be to Allaah, the Lord of the worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His Slave and Messenger.
Abu Hurayrah 
narrated on the authority of the Prophet, sallallaahu ‘alayhi wa sallam, that once a fly falls in one's cup, one should dip it and then remove it because one of the fly's wings carries disease and the other carries a cure. [Al-Bukhari]
This authentic Prophetic Hadeeth appears confusing to some people due to their ignorance.
In the past Al-Khattaabi 
mentioned that some people wondered how could disease and cure be combined in the fly's wings? How could a fly recognize that one of its wings carries disease so that it would dip it first? Such inquisitive words are signs of ignorance or feigned ignorance. A lot of creatures have inherent contradictory characteristics and Allaah The Almighty inspires His creation, so that each functions in harmony. The One who inspired the bee to al hivesadip one wing first and hold the other up.
In this age, some people argue that this Hadeeth contradicts scientific, empirical principles, as flies are a main cause of disease transmission, so how can they bring about a cure?
They forget that most scientific bases on which they found their arguments are nothing but theories. Many are the theories that describe something as right at some time, then later describe it as false after a short or long period of time. How can revealed texts be put on equal footing with changeable theories? How can a person, who is more likely to be ignorant than to be knowledgeable, judge the revelation that has been conveyed by the Prophet, sallallaahu ‘alayhi wa sallam?
As a matter of fact, modern science has discovered the miracle of this Hadeeth. The Egyptian magazine At-Tawheed (issue 5, 1297 AH -1977 AD) published an article by Dr. ’Ameen Ridha, professor of osteology at Alexandria University. In his article Dr. Ridha mentions that science has discovered that the fly carries at the same time both the germs which cause disease and the bacteria which attacks it.
Therefore, a Muslim must believe in whatever was said by the Prophet, sallallaahu ‘alayhi wa sallam, either established by empirical modern science or not, because no theory overrules the sayings of Allaah The Almighty and His Messenger.
And Allaah Knows best.