Honey Bees Miracle in the Quran
Some Islamic apologists claim that the Quran contains miracles regarding bees.
In the Quran there is something strange about number 16 and the bees. Chapter 16 is called "The Bees". The only verse that mentions the bees is made up of 16 words. And those words are made up of 16 different letters.
It turned out that bees have something odd in their chromosomes. Female bees have 16 pairs of chromosomes while males have 16 chromosomes (Males have no father. Males are unfertilized eggs of the mother, just like Jesus).
Muhammad never said that the number of the chapter is 16. The numbering was made later by Islamic scholars. It's not a part of the revelation, therefore it's not relevant.
The words of 16:68 are:
وَأَوْحَىٰ رَبُّكَ إِلَى النَّحْلِ أَنِ اتَّخِذِي مِنَ الْجِبَالِ بُيُوتًا وَمِنَ الشَّجَرِ وَمِمَّا يَعْرِشُونَ
Waawha (1) rabbuka (2) ila (3) alnnahli (4) ani (5) ittakhithee (6) mina (7) aljibali (8) buyootan (9) wamina (10) alshshajari (11) wamimma (12) yaAArishoona (13)
19 letters: و أ ح ى ر ب ك إ ل ن ت خ ذ ي م ا ج ش ع
So the word count is 13, not 16. And there are 19 different letters. And the verse number is not 16, but 68.
And "Female bees have 16 pairs of chromosomes" means they have 32 chromosomes.
Feminine Form "Miracle"
Apologists think that grammatical gender is the same thing as physical gender:
Worker bees, those who gather pollen and make the honey, are actually all females. Male bees do not make honey. This was only known recently. However 1400 years ago the Quran refers to bees that generate the honey as females (the Arabic grammar is in the female mode):
[Quran 16.68-69] And your Lord (Allah) revealed to the bees: Build your hives in mountains, trees and in what they build. Then eat (for females) from every fruit and follow (for females) your Lord's enslaved paths, from its bellies (بُطُونِهَا) exits drink of different colors, in it healing for man. These are signs for those who contemplate.
For the word "eat": "Kuli" is for females; "Kul" is for males. The Quran used "Kuli" (females). For the word "follow a path": "Usluki" is for females; "Usluk" is for males. The Quran used "Usluki" (females). For the word "its bellies": "butuniha" is for females; "butunihim" is for males. The Quran used "butuniha" (females). How could an illiterate man who lived 1400 years ago have known that those honey making bees are females?
It doesn't bother them that the word "bees" in the verse is masculine .
Then they completely ignored that the word "build" is also feminine and that the Arabic original اتخذى doesn't literally mean "build", but "take". So Allah commanded the bees to "take (feminine) as a house". Now if grammatical gender means physical gender, then it's a scientific error, because Allah told it to female bees, while in reality male bees also take the hives as their houses.
Apologists also lack basic knowledge of Arabic. All Arabic nouns are divided on rational (includes humans, jinns..) and irrational (includes non-living objects, animals, trees..) and plurals of irrational nouns are treated grammatically as feminine singular.  So when the Quran uses grammatically feminine forms of verbs, then in this context it's just a grammatical form that is used for plurals of irrational nouns. It doesn't mean physically feminine gender.
The apologist claim "butunihim is for males" would work only for rational nouns. For example if "their bellies" referred to "men". But if "their bellies" refers to irrational nouns like "animals", then it's butunihaa.
Certain nouns in Arabic, especially those referring to plants, animals and other inanimate objects that often appear in groups, have a special collective declension. For those nouns, the formally singular noun has plural semantics, or refers to the objects as an undistinguished mass. In these nouns, the singular is formed by adding the feminine suffix ـَة (-ah), which forms the so-called singulative (اِسْمُ ٱلْوَحْدَةِ ʼismu l-waḥdah lit. "noun of unity").
"Bee" is one of those words. It's not that نحل (nahl) is "a male bee" and نحلة (nahla) is "a female bee". نمل is collective and نحلة is singulative . If the Quran talked about a single bee, then it would have no other option than to use the grammatically feminine form (with ة). Because the "masculine form" (without ة) actually has the meaning of plural.
Butuniha بُطُونِهَا in Arabic means multiple stomachs of a single female. Today we know that a honey bee has an extra stomach dedicated for honey.
For the word "its bellies": "butuniha" is for a single female. "butunihin" is for multiple females. The Quran used "butuniha" single female.
How could an illiterate man who lived 1400 years ago have known that a honey bee has an extra stomach for honey?
Butuni (بطون) is plural, but -ha (ها) can mean either feminine singular or plural of irrational nouns. And since "bees" (نمل) in Arabic is an irrational noun, then in this context بطونها means "their bellies". It doesn't mean female.
When the Quran says:
And He taught Adam the names - all of them (كلها, kulla-haa).
The word transalted as "them" is ها, which according to apologists refers to female singular. Does it mean Allah taught him only one female name? And the translation should be "all of her"?
Drilling into rock
Bees build their hives from their own wax however scientists just discovered bees that build hives in wood and even in solid rock.
Some bees can even drill in solid rock.
"And your Lord (Allah) revealed to the bees: Build your hives in mountains, trees and in what they build..." God ordered the bees to drill in mountains (solid rock), trees (wood) in addition to the known wax hives.
How could an illiterate man who lived 1400 years ago have known that bees can drill in solid rock?
It literally says "take your houses" not "build". And the verse doesn't say "drill". "Take mountain as a house" can mean live there. And they can live in holes that are already there in the mountains.
The same trick of presenting the singulative form as "for females" was used in other miracles as well: