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Modern scientific theory today finds itself quite close to the Qur'an. There are at least two reasons behind this observation. The first is the lack of inconsistencies between the Qur'an and observable natural phenomena. Science has not been able to produce theories or experiments that fundamentally contradict the Qur'an. Had our science done so, either our understanding of the Qur'an or of the world would have been to blame: the Qur'an itself is true for all times. The second reason for the remarkable harmony between the Qur'an and science is the presence in the Qur'an itself of very clear and positive encouragement to contemplate and investigate the world around us. As the verses quoted above indicate, Allah has not forbidden man to question, and in fact, it seems He wants us to do so.
However, the Qur'an goes beyond simply encouraging all human beings to be aware of the natural world. It also contains widely dispersed references on a variety of subjects which are not only scientifically accurate, but in some cases, quite advanced relative to the time of the Prophet Muhammad . For the Muslim who reads and understands these references, they serve to strengthen his or her faith of course. For the non-Muslim who questions the authenticity or authorship of the Qur'an, these references provide some interesting answers. One possible reason for these Qur'anic verses which describe the natural world can be found in the following verse:
[41:53] Soon will We show them Our Signs in the (farthest) horizons, and within themselves, until it becomes manifest to them that it is the Truth...
The historical event which this verse alludes to is the conquest of Makkah. However, almost every verse in the Qur'an carries a historical and a universal meaning, and therefore one possible interpretation of this verse is that it refers to the gradual discovery of greater and greater natural "evidence" of the Creator's involvement in our world. Two of the most important and most fascinating goals of modern science are to peer farther and farther out to the edge of the universe, and to look deeper and deeper into the structure of the human body. It is in these two areas that we find the "signature" of Allah's creative power at its strongest.
[16:8] ...and He creates other things beyond your knowledge...
[24:45] ...Allah creates what He wills...
These two verses, among others, indicate that Allah has not 'finished' creation; rather, it is an ongoing process. This is very significant from a scientific point of view because we are gradually beginning to observe and understand certain natural phenomena which are still in a process of formation. One prime example is our observation of still- emerging galaxies from huge clouds of nebulae. Another is the evolution of species, with its associated evidence of strange and exotic "intermediate" life forms turned into fossils. These two examples are just the tip of the iceberg; the following excerpt from the physicist Paul Davies' book The Cosmic Blueprint underscores the growing awareness of continuous creation:
"An increasing number of scientists and writers have come to realize that the ability of the physical world to organize itself constitutes a fundamental, and deeply mysterious, property of the universe. The fact that nature has creative power, and is able to produce a progressively richer variety of complex forms and structures, challenges the very foundation of contemporary science. 'The greatest riddle of cosmology,' writes Karl Popper, the well-known philosopher, 'may well be...that the universe is, in a sense, creative.'" 
[30:41] Rottenness (decay/corruption) has appeared on land and sea because of what the hands of men have earned, that (Allah) may give them a taste of some of their deeds, in order that they may turn back (from evil).
[7:31] O Children of Adam! Wear your beautiful apparel at every time and place of prayer; eat and drink, but waste not by excess, for Allah does not love those who waste.
The importance of understanding the ecological consequences of our actions as individuals or as a society was not fully appreciated until this century. We now understand that we cannot alter the face of the earth indiscriminately without paying some penalty, which may be disastrous. We also understand that caution ought to be applied globally, not just locally but truly "on land and sea". Ecological awareness does not imply asceticism however. According to the Qur'an, we are not forbidden to take pleasure in this life, however we are forbidden from wasting resources needlessly.
[57:25] ...And We sent down iron in which is mighty harm, as well as many benefits for mankind...
Iron is one of two metals found abundantly on the earth (aluminum being the other). It was known to many ancient civilizations, and is the most important metal we use today. The general description of it in the Qur'an was accurate in the time of the ancients, and it is even more so today: iron is the basis for most weapons of war and most of the everyday tools which we work with.
[21:30] ...And We made every living thing from water...
[24:45] And Allah has created every animal from water...
Modern scientific theory on the origin of life was not firmly established up until the last two or three centuries. Prior to that, the predominant theory on the origin of life was based on a concept called "spontaneous generation" where living creatures literally popped out of inanimate matter spontaneously and continuously. This view was discredited with the work of many Renaissance scientists including Harvey and Redi, and in the 1850's, Louis Pasteur's research on bacteriology sealed the coffin on this theory. Starting with the work of Huxley up to the present day, an alternative theory has been proposed where life is understood to have emerged from a long, increasingly complex chain of chemical reactions. These reactions are believed to have begun in the depths of the oceans because the atmosphere was not sufficiently developed to protect living organisms from ultraviolet radiation:
"...it is believed that early forms of life developed in oceans or pools...It has been suggested that the colonization of land, about 425,000,000 years ago, was possible only because enough ozone was then produced to shield the surface from ultraviolet light for the first time." 
This idea of life originating in the oceans is strongly supported by the two Qur'anic verses quoted above.
It is important to note however that the Qur'an does NOT contain an exclusive endorsement for evolution. While the verses quoted above indicate beyond any doubt that Allah created all living things from water, there are many other verses that emphasize His Absolute power over everything.
[41:39] "...For He (Allah) has power over all things."
[3:47] "...when He has decreed a matter, He only says to it, 'Be', and it is."
[30:22] And among His Signs is the creation of the heavens and the earth, and the variations in your languages and your colors; verily in that are Signs for those who know.
[49:13] O mankind! We created you from a male and female, and made you into nations and tribes, that you may know each other. Verily the most honored of you in the sight of Allah is the one who is most deeply conscious of Him...
The racial and linguistic differences between humans are not meant as reasons to discriminate. Allah simply describes this diversity as a part of His creative power, and He does not single out any race as being inherently superior to the others. The emphasis in [49:13], in fact, is to learn to communicate with one another.
Most of us are familiar with the water cycle from our classes in middle school, where we learned how a drop of seawater evaporates, then becomes a drop of rainwater, and then finally returns to the sea via rivers or underground channels. The first person in modern times to understand this process was Bernard Palissy who described it correctly in 1580 . Prior to him, most of the ancient Greek and Roman scholars had various incomplete or incorrect theories on the water cycle (Plato, for example, believed that precipitation eventually descended into the abyss called Tartarus and from there it fed into the oceans ).
The Qur'an does not give a complete description of the water cycle from start to end, however there are a few precise references to specific stages. Perhaps the most fascinating of these references are the following two verses on rain clouds:
[30:48] It is Allah Who sends the winds, and then they raise clouds: then He spreads them in the sky as He wills and makes them dark, then you see the drops issue from the midst of them...
[24:43] Don't you see how Allah drives clouds with force, then joins them together, then makes them into a heap? - then you see the drops issue from the midst of them. And He sends down from the sky mountains (of clouds) wherein is hail: He strikes therewith whom He pleases and He turns it away from whom He pleases. The flash of His lightning well-nigh snatches away the sight.
The two verses are describing the stages in the formation of rain clouds, which is in turn a stage in the water cycle. A close examination of these two verses suggests that they make reference to two different phenomena, one of "spreading" the clouds and the other of "joining" them together, two different processes by which rain clouds might be formed.
Modern meteorology has come to this very conclusion within the last two centuries. [17,18,19]
There are two types of clouds which can yield precipitation, and they are classified by their shape: stratus (layer-type) and cumulus (heap- type). The precipitative layer clouds are further subdivided into stratus and nimbostratus (nimbo meaning rain). The first verse above on rain clouds ([30:48]) precisely sums up the formation of layer rain clouds. It is known today that these types of clouds are started under conditions of gradual, rising winds:
"...and then they [winds] raise clouds..." [30:48]
Next, the cloud takes on its distinctive shape, that of a layer:
"...then He spreads them..." [30:48]
If the conditions are right (i.e. low enough temperature, high enough humidity, etc.), the cloud droplets further condense into (larger) rain droplets, and we observe this effect from the ground as a darkening of the cloud layer:
"...and makes them dark..." [30:48]
Finally, drops of rain fall from the cloud.
"...then you see the drops issue from the midst of them..." [30:48]
The second type of precipitative cloud is the heap type, and it is subdivided into cumulus, cumulonimbus, and stratocumulus. These clouds are characterized by being puffy-shaped and piled upon each other. Cumulus and cumulonimbus are the true heap clouds - stratocumulus is a form of degenerated, spread-out cumulus . The second verse above on rain clouds ([24:43]) describes the formation of heap rain clouds. These clouds are formed under conditions of strong updrafts (thermals) and downdrafts of air:
"...drives clouds with force..." [24:43]
As the puffs of clouds form, they may unite into a single giant cloud, all piled up on top of one another:
"...then joins them together, then makes them into a heap..." [24:43]
At this point, either a cumulus or a cumulonimbus cloud has formed - either of which can yield rain. The rest of the verse is applicable to the case of a cumulonimbus (which is familiar to all of us as the towering thunderstorm cloud). If the heap cloud assumes large vertical proportions, then it can appear to the observer on the ground as a huge mountain or hill, but more importantly, by extending high into the atmosphere, the upper cloud droplets can freeze and thereby yield hail [17, 18]:
"...And He sends down from the sky mountains (of clouds) wherein is hail..." [24:43]
Finally, cumulonimbus clouds (i.e. thunderstorms) can have one last vivid property: lightning [17, 18]:
"...The flash of His lightning well-nigh snatches away the sight..." [24:43]
Other Qur'anic verses deal with more stages in the water cycle.
[23:18] And We send down water from the sky according to (due) measure, then We cause it soak into the soil. And We are most certainly able to withdraw it.
This is a single verse stating that rainfall is absorbed into the ground and that it can eventually be removed (drained).
[13:17] He sends down water from the sky, and the rivers flow, each according to its measure...
[39:21] Don't you see that Allah sends down rain from the sky, and leads it through the springs in the earth?...
Two methods by which absorbed rainfall is moved are described here: surface and underground rivers.
There are other references in the Qur'an to the water cycle (e.g. [40:13], [23:18], [25:48], [29:63], and others) , and all of them have the same property as the verses quoted above: modern scientific findings are fully compatible with them .
A few other verses also deal with water but in a slightly different context. They are not nearly as numerous as the verses on the water cycle.
[56:68-69] Do you see the water which you drink? Do you bring it down from the cloud or do We?
This rhetorical question emphasizes our inability to fulfill one of our oldest dreams: to control the rain. The fact is we cannot make it rain unless a pre-existing cloud is in the vicinity - and then only under the proper conditions, and even then we are not assured of success. The cloud should have different sized cloud particles, a high rate of condensation from the rising air, and good vertical development. If all of these characteristics are present, then we MAY coax some more rain out through cloud seeding and various other techniques. However, modern meteorologists are unsure of its effectiveness. Regardless, it is the presence of the necessary preconditions which we have no control over, and this ultimately stops us from arbitrarily bringing down the water of any cloud in the form of rain .
The following verse describes a property of large rivers.
[25:53] It is He who has caused to mix freely the two great bodies of water, this one pleasant-tasting and sweet and this one salty and bitter, and He made between them a barrier and a forbidding ban.
A description of the estuaries of large rivers is supplied by the verse above. These estuaries are relatively unusual because the outgoing fresh water of the river does not immediately mix with the salt water of the sea into which the river empties. Instead, the fresh water penetrates deep into the salt water body before any mixing occurs, far from the mouth of the river. Small rivers do not have this property. 
Finally, one more reference to clouds.
[52:44] And were they to see a piece of the sky falling down, they would (only) say "Heaps of clouds!"
Another reference to clouds but this time in the context of responding to a challenge by an earlier peoples who ridiculed a prophet by asking him to cause a piece of the sky to fall on them, apparently thinking it to be a solid cap around the earth. Allah refutes their challenge here, declaring that they would only find a pile of clouds, something all of us would understand today. 
The Qur'an has an extensive amount of information on the growth of the human embryo and fetus, especially the former. Before presenting this information, it may be helpful to provide a brief outline of human development in the womb as modern science understands it. 
We will examine some of these stages in greater detail as the verses in the Qur'an require. First, however, two verses which give a general overview of human development:
[71:14] ...seeing that it is He (Allah) Who has created you in stages...
[35:11] And Allah created you from dust, then from a drop...
The first verse is a very general, yet accurate description of our creation as coming in stages (see the six-step outline above). The second verse puts some perspective on the whole affair: how man originally came from dust (Adam), and then from a drop.
There are at least four specific details regarding human development in the Qur'an which modern science has revealed only within the last few centuries, and in some cases only in this present century. The first concerns the emission of semen:
[75:37] Was he (man) not a drop of semen emitted?
In spite of the large amount of liquid which can be produced by a man during human intercourse, this verse emphasizes that only a small drop of it is important.
The second important detail in the Qur'an on human development is the description of the fertilizing liquid (i.e. semen):
[86:6] He (man) is created from a gushing liquid.
[76:2] We created the human from a drop which is a mixture...
[32:8] Then He (Allah) made his (Adam's) progeny from a quintessence of a despised liquid.
The second and third verses relate to the contents of semen. Modern science has established that semen is in fact a composition of different secretions which come from four different glands during ejaculation: the testicles, the seminal vesicles, the prostate gland, and the urinary tract glands. The actual sperm cells come from the testicles; the other three glands produce no fertilizing agents. The Qur'an goes farther than just informing us that semen is a mixture of liquids. It tells us in [32:8] that only the "quintessence" of the liquid is used (the "despised" comes from the fact that semen is emitted from the same place as urine, and thus may be despicable in some people's sight). The Arabic word for "quintessence" in this verse signifies extracting the absolute best out of something. The numbers tell the story: a normal ejaculation involves about 3 ml of fluid containing between 120,000,000 and 150,000,000 sperm cells. Of these cells, only one fertilizes the egg in the female, and this is the point which [32:8] alludes to .
A third detail of human development mentioned in the Qur'an concerns the newly fertilized egg:
[75:37-38] Was he (man) not a drop of semen emitted? Then he did become something leech-like which clings...
Recent observations of the fertilized egg in the womb have revealed that the egg literally implants itself into the uterine wall. It "clings" in the strongest sense, and it remains like so in the early stage of development. On top of that, the developing organism acts as a leech on the female host in the sense that it draws its sustenance directly from its mother's body .
Finally, the Qur'an gives a fascinating account of embryological development (the first three months) in the following verses (certain words have been transliterated directly from the Arabic):
[23:14] ...We made the drop into an ALAQAH (leech-like structure), and then We changed the ALAQAH into a MUDGHAH (chewed-like substance), then We changed the MUDGHAH into IDHAAM (bones, skeleton), then We clothed the IDHAAM with LAHM (flesh, muscles), then We caused him to grow and come into being as another creation.
[22:5] ...We created you out of dust, then out of a drop, then out of a MUDGHAH, partly formed and partly unformed...
Verse [23:14] divides embryological development into four stages. The first stage picks up right after fertilization ("drop"), and is characterized by an ALAQAH or "leech-like structure" which describes how the egg implants itself into the uterus (see above). The second stage describes the embryo as evolving into a MUDGHAH which means something which has been chewed (especially a piece of meat), or which has the appearance of having been chewed. This seemingly crude description is in fact quite accurate: after the fertilized egg lodges itself in the uterus, it begins to receive its first nutrients and energy from its mother. Consequently, it begins to grow especially rapidly, and after a week or two it looks like a ragged piece of meat to the naked eye. This effect is enhanced by the development of small buds and protrusions which will eventually grow into complete organs and limbs.
The next two stages described in verse [23:14] tell of bones being made from the MUDGHAH, followed by the "clothing" of the bones with flesh or muscles. If we follow the progress of the embryo with our own eyes, we find that after approximately four weeks, a process called 'differentiation' begins, where groups of cells within the embryo transform themselves to form certain large organs. One of the earliest structures to develop in this stage is the cartilaginous basis of the human skeleton (in subsequent months, the cartilage hardens or ossifies). It is followed soon after by the appearance of a host of other organs including muscles, ears, eyes, kidneys, heart, and more. This maintains the order described in the Qur'an. Verse [23:14] concludes with the growth of the organism in the womb (and simple growth is the primary characteristic of the fetal stage) followed by its birth.
Verse [22:5] adds one more interesting note on the embryo. In this verse, the MUDGHAH is qualified with the phrase
"partly formed and partly unformed."
As alluded to above, our modern observations of embryological development have revealed how different structures and organs develop one after another through differentiation. This gives rise to unusual situations where the embryo is unevenly formed (i.e. lungs but no ears for example). [11,16]
Of all the references in the Qur'an to scientific matters, the most numerous are on the creation and structure of the universe and the earth. This area is singled out in several verses like the one below as an example of Allah's creative power:
[45:3] Verily, in the heavens and the earth are signs for those who believe.
For a much more detailed exposition of the Qur'an and cosmology (and science in general), interested readers should consider reading M. Bucaille's book 'The Bible, The Qur'an, and Science' . Below, a brief summary of some of the more powerful verses.
First, a verse which makes a small note regarding the age of mankind with respect to the universe:
[76:1] Has there not been over Man a long period of Time when he was not yet a thing thought of?
The Arabic word for "Time" in this verse is "Dahr" and it can mean either all of eternity or simply a tremendously long time. Modern science can help us understand this verse better. The first appearance of humans on this earth is estimated to have occurred on the order of one million years ago. The age of the universe, on the other hand, is estimated at roughly fifteen billion years. If we normalize the age of the universe to one day, then man would be less than six seconds old.
The following verse deals with the creation of the heavens and the earth.
[50:38] And We created the heavens and the earth and all between them in six days, and nothing touched us of weariness.
Notice the sharp counterpoint to the Bible at the end of this verse regarding whether Allah "rested" after the sixth day from tiredness. However, a more subtle yet perhaps vastly more important difference is brought out when we look at the first verse in the Bible, Genesis [1:1]:
Bible [1:1] In the beginning, God created the heavens and the earth.
There is no mention of "and all between them", as opposed to the Qur'an (which refers to this in several verses, no less). Modern science has just within this last century discovered that much of the mass of the universe is contained in the vast spaces between galaxies and stars (ignoring for the moment the possibility of 'dark matter' which would only make a stronger point). In spite of having only a single hydrogen atom every few cubic meters on average (interstellar material), the universe is so huge that the "empty" space may account for more of the total universe's mass than all the stars combined - at the very least, it is a significant amount. Thus, it is an important omission to leave out "all between" the earth and the other stars and galaxies ("heavens").
As to the debate which has wracked Christianity and Judaism for centuries regarding the meaning of "six days", the word "days" in classical Arabic has a secondary meaning of a "very long time" or an "era" . The Qur'an, however, presents a conclusive answer to this question via the following three verses scattered throughout the text:
[22:47] And yet they ask you to hasten on the Punishment! But Allah will not fail in His promise. Verily a Day in the sight of your Lord is like a thousand years of your reckoning.
[32:5] He (Allah) directs (all) affairs from the heavens to the earth: in the end will (all affairs) go up to Him on a Day the space whereof will be (as) a thousand years of your reckoning.
[70:4] The angels and the Spirit ascend to Him in a Day the space whereof is (as) fifty thousand years.
It is clear from these verses that a "day" in the Qur'an can easily have different meanings in different contexts, and is thus not constrained to mean a strict 24-hour period.
The next two verses address certain details of creation.
[21:30] Don't those who reject faith see that the heavens and the earth were a single entity then We ripped them apart?...
[41:11] Moreover, He applied His design to the heavens, while it was (yet) vapor,and He said to it and to the earth, "Come (into being), willingly or unwillingly." They said, "We do come in obedience."
Verse [21:30] foreshadows the modern cosmological theory known as the Big Bang theory wherein all matter is presumed to have originated from a violent explosion. Verse [41:11] refers to a later stage in creation, one in which a cosmologist would describe the universe as filled with a nebulous gas undergoing a slow coalescence into gross structures such as clusters, galaxies, stars, and so on. The words of these two verses may seem coarse and simplistic to the modern eye, but this does not detract from their general accuracy.
Then there are verses that speak of the sun and the moon.
[25:61] Blessed is He Who put in the heavens constellations, and put in it a lamp and a light-giving moon.
This verse emphasizes the sun as a direct source of light ("lamp"), whereas the moon is not given this title. Man has long since established that the moon's light is simply reflected sunlight.
[55:5] The sun and the moon follow precise courses.
The meaning of this verse is obvious, and we have known the mathematical description of these "courses" since Kepler and Newton formulated them several centuries ago.
[21:33] It is He Who created the night and the day, and the sun and the moon: all swim along, each in its rounded course.
This verse supplements the previous one: here, we learn that the sun and moon follow "rounded courses." It is significant that the Arabic word used here - "falak" - does not mean circular course, just rounded. Kepler was the first European astronomer to realize that the paths of the planets and the moon are elliptical. It was not until later, though, that astronomers also realized that the sun has an orbit as well - around the center of the Milky Way.
The Qur'an contains a number of verses on the structure and contents of the universe. There are too many to list here, but the following three form an interesting sample:
[51:47] And the heavens We did create with Our Hands, and We do cause it to expand.
Flatly stating what Einstein refused to believe at first, this verse anticipates Hubble's discovery of the expanding universe by approximately thirteen centuries. This verse makes a very clear point that the expansion is continuous (until the Day of Judgement, which is guaranteed by Allah to come upon us unexpectedly).
[42:29] And among His signs is the creation of the heavens and the earth, and the living creatures that He has scattered through both of them...
[45:13] And He has subjected to you (man), from Him, all that is in the heavens and on earth: behold, in that are signs indeed for those who reflect.
These two verses are extremely interesting. Not only does the first one very strongly imply the existence of living creatures on other planets throughout the universe, but the second tells us that the heavens are "subject" to us. With a little imagination, we (or perhaps our children) can begin dreaming of the possibility of interstellar travel - and not just confined to our own solar system!
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