Short answer
The Qur'an says God (﷾) inspired the bee to build its homes and to follow the paths of its Lord. It says a drink of many colours comes out of the bees' bodies, and that there is healing in it. Each point is true. For centuries learned men taught that honey fell from the sky and bees only gathered it. In fact bees take in nectar and change it inside their bodies. Honey comes in many shades, from almost colourless to dark amber. Today it is used in hospitals as a wound dressing. The Prophet Muhammad (ﷺ) could not read, and the Qur'an calls all this a sign for those who think.
Full explanation
The verses
The Qur'an says that Allah (﷾) inspired the bee and gave it its homes and its paths. It says a drink of varying colours comes from within the bee's body, and that this drink holds healing. The Arabic word for inspired is awha. The Qur'an uses it for revelation to prophets, and also for the guidance God (﷾) places in His creatures, as here.
“And thy Lord taught the Bee to build its cells in hills, on trees, and in (men's) habitations; Then to eat of all the produce (of the earth), and find with skill the spacious paths of its Lord: there issues from within their bodies a drink of varying colours, wherein is healing for men: verily in this is a Sign for those who give thought.”
What the learned world believed
Aristotle, a Greek thinker of the fourth century BCE, taught that bees build their comb from flowers. But he taught that honey falls from the air and the bees only gather it. Pliny, a Roman writer of the first century, said honey came down as a dew at the rising of the stars. This was the educated view of the ancient world.
Aristotle writes that bees build their comb from flowers, but that honey is distilled from dew in the air and settles chiefly at the rising of certain stars or when a rainbow is in the sky. The bee, he says, does not make honey; it only gathers what falls from the air.
Pliny writes that honey comes from the air, falling as a dew around the rising of the stars, and that the bees gather it from leaves and flowers. He wonders whether it is the sweat of the sky or a kind of saliva of the stars.
What bees actually do
A worker bee drinks nectar into its honey stomach, in its abdomen, and adds enzymes (natural substances that change it). It passes the nectar to house bees, who store it in the comb. There it thickens into honey. So the drink does come from within the bee, as the verse says. The verse says where the drink is made, not which opening it leaves by. Honey also comes in many shades, from almost colourless to dark amber.
The standard textbook on honeybee biology. It describes how worker bees carry nectar in their honey stomach, add enzymes to it, pass it to other workers, and store it in the comb, where water evaporates from it until it becomes honey. The honey stomach (crop) lies in the bee's abdomen. It also explains that the foragers and honey-makers of the hive are females; the males (drones) do none of this work.
The official U.S. grading standard for honey. It sorts honey by colour into seven classes, from water white, the palest, through extra white, white, extra light amber, light amber and amber, to dark amber.
The paths of its Lord
The verse tells the bee to follow the paths of its Lord. The Arabic calls these paths dhulul (made smooth and easy for it). A forager flies far from the hive, steers by the sun even under cloud, and finds its way home. Then it tells the others where the flowers are by dancing. The ability is built into the bee. The Qur'an calls it inspiration.
Reports decades of experiments showing that forager honeybees find their way by the sun, even when it is hidden by cloud, and that on returning to the hive they tell other bees the direction and distance of food by a dance. Von Frisch shared the 1973 Nobel Prize for this work.
“And thy Lord taught the Bee to build its cells in hills, on trees, and in (men's) habitations; Then to eat of all the produce (of the earth), and find with skill the spacious paths of its Lord: there issues from within their bodies a drink of varying colours, wherein is healing for men: verily in this is a Sign for those who give thought.”
Healing in honey
Honey was folk medicine for centuries. Trials now show it heals partial-thickness burns (burns that go partway through the skin) faster than standard dressings. Lab studies show it stops the growth of wound bacteria, including strains that resist antibiotics.
A systematic review of trials of honey as a wound dressing. It finds that honey heals partial-thickness burns more quickly than conventional dressings, while the evidence for other kinds of wound is weaker.
Laboratory study of bacteria taken from infected wounds. Honey stopped the growth of every strain tested, including antibiotic-resistant strains such as MRSA.
The Prophet (ﷺ) and honey
The Prophet (ﷺ) told a man to give his sick brother honey. When it seemed not to work, he said Allah (﷾) had spoken the truth. Scholars explain that he meant the verse saying honey holds healing. The man persisted, and his brother was cured.
Abu Sa'id al-Khudri reports that a man told the Prophet (ﷺ) his brother had a stomach complaint, and the Prophet told him to give him honey. The man came back more than once saying it had not worked, and each time the Prophet said to give him honey, adding that Allah had spoken the truth and it was the brother's stomach that was wrong. He drank honey again and was cured.
Why this is a sign
Beekeepers had long known that honey comes from the hive. The error was in the learned books. The Prophet (ﷺ) could not read, so the books of Aristotle and Pliny were closed to him. Anyone who took their learning would have taken the honey-dew error with it. The Qur'an instead says the drink comes from within the bee's body. It closes by calling the bee a sign for those who think.
“And thou wast not (able) to recite a Book before this (Book came), nor art thou (able) to transcribe it with thy right hand: In that case, indeed, would the talkers of vanities have doubted.”
“And thy Lord taught the Bee to build its cells in hills, on trees, and in (men's) habitations; Then to eat of all the produce (of the earth), and find with skill the spacious paths of its Lord: there issues from within their bodies a drink of varying colours, wherein is healing for men: verily in this is a Sign for those who give thought.”
Perspectives
The Islamic perspective
The Qur'an, revealed to the Prophet Muhammad (ﷺ), says truly where honey comes from, that its colours vary and that it heals. The learned world held that honey fell from the sky. The Qur'an calls the bee a sign of God's (﷾) guidance.
The Qur'an says a drink of varying colours, with healing in it, comes from within the bees' bodies.
Aristotle and Pliny taught that honey falls from the air and that bees only gather it.
Honey is made inside the bee. Nectar is carried in the honey stomach, worked on with enzymes, and given out again as honey.
Honey heals partial-thickness burns faster than conventional dressings and in the laboratory it stops the growth of antibiotic-resistant wound bacteria.
The Prophet (ﷺ) prescribed honey for a sick man and said Allah (﷾) had spoken the truth about it.
The bee's sure navigation and its dance are what the Qur'an calls God's (﷾) inspiration and the paths of its Lord. The Arabic calls these paths dhulul, made smooth for it.