Wanaosadiki kwamba sayansi inaongoza kwenye kutokuamini kuwepo kwa Mungu wanashikilia dhana isiyo ya kisayansi ya naturalism ya kifalsafa. Naturalism ya kifalsafa huunda "miwani" ambayo huwekwa machoni mwa mtu ili kuelewa dunia. Ukivaa miwani yenye rangi ya manjano, utaona rangi gani? Manjano. Vivyo hivyo, ukivaa miwani ya naturalism ya kifalsafa, utaona ulimwengu usio na Mungu. Naturalism ya kifalsafa huunda jinsi mtu anavyoiona dunia. Naturalism ya kifalsafa ni imani tu. Profesa Michael Ruse, mwanafalsafa asiyeamini kuwepo kwa Mungu, anakiri ukweli huu: "Ukitaka kukubali, nimekuwa nikisema kila wakati kwamba naturalism ni kitendo cha imani…." 356
Kwa nini ni imani? Naturalism haina mantiki, kwa sababu inaamini kwa upofu kwamba kila kitu kinaweza kufafanuliwa kupitia michakato ya kimwili, licha ya ukweli kadhaa usiopatana nayo; yaani, ukweli unaopinga nadharia. 357 Kwa mfano, sisi wote tunakutana leo kwenye mgahawa saa kumi na mbili jioni, na siku inayofuata polisi wanakuja nyumbani kwangu kunikamata kwa tuhuma za kumuua mtu kwa wakati ule ule ambao tulikuwa tukila chakula cha jioni. Ukweli usiopatana na tuhuma hizo ni kwamba nilikuwa pamoja nawe nikila wakati wa mauaji. Mahali nilipothibitishwa kuwepo kunapinga tuhuma za polisi kwamba nilitenda mauaji hayo. Huenda ukajiuliza, ni ukweli gani huu unaopinga ambao unaifanya naturalism ya kifalsafa isiwe na mantiki? Sura kadhaa zilizotangulia ni mwanzo mzuri. Naturalism ya kifalsafa haiwezi kueleza kwa kutosha tatizo gumu la fahamu (angalia Sura ya 7), ukomo na utegemezi wa ulimwengu (angalia Sura ya 5 na 6), kupangwa kwa sheria na mpangilio wa ulimwengu (angalia Sura ya 8), kuwepo kwa maadili ya lengo (angalia Sura ya 9) na mengine mengi. Kwa kuzingatia haya, ni kwa nini mtu angekubali kwa upofu falsafa kama hiyo, ambayo inamzuia kuruhusu uhalisia useme wenyewe? Wanaoamini kuwa hakuna Mungu wengi wana dhana kama hizo za kinaturalism. Kwa hivyo, haishangazi kwamba wanazipuuza hitimisho za hoja za kuwepo kwa Mungu. Kwa kawaida wao hukataa hoja nzuri, kwa sababu wamefungwa macho na dhana potofu kwamba kila kitu lazima kielezwe kwa michakato ya kimwili, na kwamba hawawezi kamwe kukubali maelezo ya kimaumbile yaliyo nje ya ulimwengu huu. Hata hivyo, naturalism ya kimbinu si tatizo kwa uthiolojia, hasa uthiolojia wa Kiislamu. Naturalism ya kimbinu si tatizo kwa uthiolojia wa Kiislamu kwa sababu mapokeo ya Kiislamu yanakubali kwamba ulimwengu mzima umeundwa na sababu za kimwili, na sababu hizi ni udhihirisho wa mapenzi ya Mwenyezi Mungu. Baadhi ya wanaatheism, hata hivyo, huchanganya naturalism ya kimbinu na naturalism ya kifalsafa. Kwa sababu hitimisho na nadharia za kisayansi haziwezi kurejelea uwezo na uumbaji wa Mungu (naturalism ya kimbinu), haimaanishi kwamba Mungu hayupo (naturalism ya kifalsafa). Kama mwanabiolojia wa mageuzi Scott C. Todd alivyosema, "mwanasayansi, kama mtu binafsi, yuko huru kukubali uhalisia unaovuka naturalism"358.
Atheists who believe that science leads to atheism hold the non-scientific assumption of philosophical naturalism. Philosophical naturalism forms the ‘lenses’ that are put on one’s eyes to understand the world. If you wore some yellow tinted glasses, what colour are you going to see? Yellow. Similarly, if you put on the lenses of philosophical naturalism, all you will see is a universe without God. Philosophical naturalism shapes the way one sees the world. Philosophical naturalism is simply a faith. The atheist Professor Michael Ruse admits this fact: “If you want a concession, I’ve always said that naturalism is an act of faith….” 356 Why is it a faith? Well, naturalism is incoherent, as it blindly believes that everything can be explained via physical processes, despite a number of recalcitrant facts; in other words, facts that resist a theory.357 For example, we both meet today at a restaurant at six o’clock, and the following day the police come to my house to arrest me on suspicion of murdering someone at the same time we were having dinner. The recalcitrant fact would be that I was with you eating at the time of the murder. My proven whereabouts resist the police’s suspicions that I committed the murder. You may be wondering, what are these recalcitrant facts that render philosophical naturalism as incoherent? Well, many of the previous chapters are a good starting point. Philosophical naturalism cannot adequately explain the hard problem of consciousness (see Chapter 7), the finitude and dependency of the universe (see Chapters 5 and 6), the fine-tuning of the laws and the order in the universe (see Chapter 8), the existence of objective morals (see Chapter 9) and much more. In light of this, why would anyone blindly adopt such a philosophy, which prevents one from allowing reality to speak for itself? Many atheists have such naturalistic presuppositions. Therefore, it is not surprising that they dismiss the conclusions of theistic arguments. Usually they reject good arguments, because they are blinded with the false assumption that everything has to be explained by physical processes and that they can never entertain supernatural explanations. Methodological naturalism however is not a problem for theism, especially Islamic theism. Methodological naturalism is not a problem for Islamic theism because the Islamic tradition accepts that the whole universe is made up of physical causes and these causes are a manifestation of the Divine will. Some atheists, however, conflate methodological naturalism with philosophical naturalism. Just because scientific conclusions and theories cannot refer to God’s power and creativity (methodological naturalism), it doesn’t follow that God doesn’t exist (philosophical naturalism). As evolutionary biologist Scott C. Todd said, “the scientist, as an individual, is free to embrace a reality that transcends naturalism”358.