Mashaallah very nicely written.i would like to add another point to it which came into my mind while i was reading this conversation Allah's presence in this universe is like a software n universe like a hardware ( as one cannot see a soft ware but it makes the comp go on.)
n v should enquire about the stand of Quran in matter of aquisition of knowledge in general n that of science in particular.there r few verses of Quran which i would like to quote

We created not the heavens,the earth n all b/w them,but for just purpose n the hour is surely coming(when this will be manifest) (15:85)

He it is Who fashions you inthe wombs as He pleases.there is no Allah except He,the Exalted,the Wise(3:6)

proclaim!in the name of ur Lord n Cherisher, Who created
men out of a congealed blood. proclaim!n ur Lord is most bountiful,He Who taught the use of pen ,taught men that which he never knew(96:1-5)


as far as scientific indications in Quran r concerned almost one -eighth of the total number of verses in Quran r devoted to science n technology.if one gets a proper knowledge of Quran than it will be very easy for that person to talk to any one about anything even to the atheists who donot believe in presence of Allah n believe more in science.

kuch teray zehen main aqal e rasa hai keh nahein
aqal sey pooch raha hai key khuda hai key nahein
chusm e beena ho salamut tu ho rooshun tujh per
zarrey zarrey main Khuda jalwa numa hai key nahein

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Allah is He,than Whom there is no God ;the Sovereign,the Holy One,the Source of Peace(n Perfection),the Guardian of Faith,the Preserver of Safety,the Exalted in Might,the Irresistible,the justly Proud glory to Allah!(High is He)above the partners they attribute to Him.(Surah e Hashar,verse #23)