The Signs of Design, Part 1: ATP synthase and the Arabic language

Bismillahi ar-rahman ar-rahim

In the Quran we are told to reflect and think about various signs: “these are signs for people of understanding” or “these are signs for reflection”. The alternating day and night, the shadow that follows the Sun, the creation of the camel, the lofty sky and the steady mountains are all signs of Allah’s actions which point to his Qualities which ultimately point to His Presence and right to be worshipped and acknowledged.

So, in part 1 of this series I want to focus on ATP synthase and certain remarkable points about the arabic language and to just show their design. The qualities that I’m about to expose are indicative of being designed in and of themselves and are quite self-evident once pointed out.

ATP synthase

I studied this enzyme during my Biochemistry degree and I was really fascinated by it and it’s one of the things that really convinced me that everything fits together at the atomic level, and it is impossible for every single thing to fit together by chance, but that is what we observe right down to the atomic level. I will have more to say about this point philosophically in future articles but for now I just want to focus on ATP synthase.

This is where I get to shine a little as a Biochemistry nerd. Enzymes are named a certain way, and essentially their name tells you its function. Enzymes end with “-ase”, click on the link for a short wikipedia article on why. This particular enzyme synthesises ATP (ATP synthase).

The structure of the ATP synthase is complex yet elegant, and its elegance stems from the “lever-like” preciseness of its function. ATP synthase in its structure is equivalent to a molecular water-mill and I’ll explain the biochemical process with this analogy to make it clear because it is so beautiful how the macroscopic systems that we observe have their parallels in the microscopic world. A world within a world.

ATP short for adenosine triphosphate is the energy molecule of the cell and is manufactured within tiny organelles called mitochondria. It is basically an adenosine molecule with a train of 3 phosphate molecules attached in a chain to it. The connection between the 2nd and 3rd phosphate molecule is highly energetic and the energy released from its cutting causes the shape of enzymes to change which allows them to carry out their function. This is the basic principle of enzymes and ATP within our cells. Mitochondria make ATP by joining ADP (adenosine diphosphate [has just 2 phosphate groups]) to another phosphate group. And when this ATP is broken down, this results in ADP and a phosphate group (PO43−). So in actual fact the cell recycles its ADP and ATP stores in perfect balance to its needs.

Let’s get back to the mitochondria. The mitochondria have two skins as it were (we call them membranes in biology jargon). In between the skins is just a sea of protons or hydrogen ions (H+). The ATP synthase is embedded within the inner membrane with its rotating head in the sea of protons and the ATP synthesis part is on the other side towards the inside of the mitochondria. In between the membranes is full of positive charges and the inside of the mitochondria is negative relative to it. Hence there is a natural flow of protons from the positive sea to the negative space inside the mitochondria, creating a river of proton-motive force. You can imagine it like a river, but of positively charged balls. This river turns the rotating “mill” of the ATP synthase causing it to combine ADP with a phosphate group but I want to delve into the actual details of this mechanism just so that you can open your eyes and become awed.

I hope the pictures alone will be quite stunning and make you think. But of course I’m going to get heavy on the technical details, so I ask that you pay close attention to the names of subunits and components as I reference them.

There are 3 broad parts of this enzyme split between two halves (F0 and F1). The F0 half is imbedded in the second inner membrane of the mitochondria exposing it to the sea of protons, and the F1 is inside the mitochondrial matrix. The 3 parts are the rotating c rings attached to the epsilon (ε) and gamma (γ) stalk. The stalk interacts with another ring of alpha (α) and beta (β) subunits. Attached to this complex is the a subunit that has two half-channels which is then attached to two b subunits which in turn is attached to the delta(δ) subunit which is attached to the alpha-beta hexamer (6 parts).

Now let’s focus on the half-channels and see how the flowing protons makes the c ring rotate.

a and c ring interaction atp synthase

This is a model of how the protons flow across the membrane. A proton can enter from the sea of protons into the first channel but can only proceed about half-way. Then it gets attached to an Aspartic acid residue in the middle of the c subunit (which is a protein double alpha helix). The proton being positive neutralises the aspartic acid (which was negative) thus allowing it to rotate through the hydrophobic membrane (charges cannot pass through “oily” environments but since it is neutral it is free to rotate). When the c unit that grabbed a proton rotates all the way, it reaches the second channel that is “proton-poor” and naturally releases the proton it was carrying.  Now that it is negatively charged the Aspartic acid residue moves to the 1st channel to get another proton. It is this movement from 2nd to the 1st channel which drives the rotation of the c ring.

Just to add the spice to this detail, this is an aspartic acid residue:

aspartic acid residue
The red COO can take a H+ and become neutralised to COOH.

Glory and Praise to God, how he made an amino acid with the perfect atomic arrangement to act as the proton carrier which fuels our energy productions and therefore our biological life!

Are we done yet? Far from it! This is but one half of the story of this amazing enzyme.

The river of protons causes the rotation of the c ring which is attached to the γ stalk also causing it to rotate. In the F1 part there is also a ring of alternating α and β subunits. The β subunits are exactly the same (homologous) except that their conformation (shape) changes depending on which face of the γ stalk they are interacting with at any time.

Depending on which face of the stalk a β subunit is interacting with it can be in 3 different conformations, and in fact a β subunit goes through each conformation in a single 360° rotation of the stalk.

3 conformations of beta units in atp synthase

So the 3 different β subunits are represented with 3 different colours. Focus on the orange one and notice how the shape of its “mouth” (active site) changes as the inner stalk rotates. In one arrangement the orange subunit is in the L (loose) conformation which allows binding of an ADP molecule and a phosphate molecule. In the next conformation when the stalk rotates by 120° the β subunit tightens to the T (tight) conformation thus combining the ADP and phosphate to form ATP. Then in the next 120° rotation of the stalk the β subunit takes the O (open) conformation and releases ATP. Just take a minute to imagine this and what this would look like. Or just watch this video of it happening: atp synthase.

Interestingly the rotation to synthesise ATP in the clockwise direction, but in the opposite direction would lead to ATP hydrolysis to form ADP and a phosphate molecule. The ATP synthase enzyme is nearly 100% efficient, meaning that all the energy from the rotation is converted into the ATP molecule (Berg et al., 2012).

Furthermore the F1 part has the enzymatic activity of synthesising ATP. The problem though is that in the absence of something like the proton-motive force, the concentrations of ATP and ADP in solution stay the same (in equilibrium). So the F0 part provides the energy required to released the synthesised ATP molecule (Berg et al., 2012).

ATP synthase is only the last cog in the whole mitochondrial machinery each part being sophisticated and elegantly fitting together. The illusion of design? If it looks like a duck, walks like a duck and quacks like a duck, then it’s a duck. If you watch the video ATP synthase operates like any well-oiled machine does, or like a water-mill. And a machine does not get produced one aspect at a time. No, the whole function of a machine rises and falls by its structure. And the thing is you will find virtually similar ATP synthases in all eukaryotes (plants, mammals, fungi, fish and birds). And little things like bacteria also have the ATP synthase enzyme which is embedded in their cellular membrane. If you find a similar ATP synthase in all forms of life including the forms that existed the earliest in time, it means that the molecule formed virtually within a few million years (according to the evolution narrative). And something as complex as this one protein complex could not have formed sequentially bit by bit.

atp synthase of mycobacteria
ATP synthase in mycobacteria

If this enzyme was present in all forms of life with a similar construction and arrangement of subunits, then we can’t say there is evidence for the sequential selection and development of ATP sythase. There is no evidence for a more “primitive” version of ATP synthase. It’s kind of just there as part of the energy production of all cells. Moreover it is self-evident that it is all the parts together that make the enzyme function as it does.


  1. Berg, J., Tymoczko, J., Stryer, L. (2012) Biochemistry. pp. 563-568.W. H. Freeman and Company, Basinstoke, England.

The Arabic Language

The points I make here, I got from a lecture by Hamza Yusuf.

In this lecture Hamza Yusuf explains that the arabic language is definitely divinely designed. Arabic words have trilateral (3 letters) roots (some have 4 or 5 or 6 but these are rare).

Take the root (نَفَسَ) nafasa as an example. It means breath. Arabic is written right to left. Now if you replace the sa with various letters you start getting different but related meaninings (to do with movement of wind):

نَفَثَ nafatha = to spit, to exhale

نَفَحَ nafaha = the blowing of wind, to spread a scent. Also notice that the “ha” is in the word for wind as well: رِيح (reeh)

نَفَخَ nafakha = to blow forecfully, breathe into (notice the “kha” which is a strong letter)

Hamza Yusuf also makes a point that in non-religious linguistics the phoneme (unit of sound) is meaningless, but they are wrong as the Quran has verses which are just strings of letters with a mysterious meaning. For example in the first verse of Sura Al-Baqara (2nd chapter) it is: “Alif, Laam, Meem.”

Indeed, the letters are symbolic of greater meaning than is apparent to us. There is a very interesting interplay with the letters used and the meanings of the words. I’ll give two examples, one from Hamza Yusuf and one of my own observations.
The word for greed is طمع (tama’a). Notice how each of the letters are hollow,they have hollow circles, just how the concept of greed is filling a void that can never be filled.

A personal observation I’ve made of this type is in the two words: عسير (‘aseer meaning difficult) and يسير (yaseer meaning easy). Notice how for the word “difficult” it is difficult to prounce the first letter “ayn” compared with the “ya” in the word for easy.

If all of this wasn’t interesting by itself, here comes the really interesting part. Look at the word Allah (الله). It is made of three letters. The start of the name starts at the very beginning of human articulation the “a” sound, from deep within the throat. Then you move to the “la” sound towards the front of the mouth and then you exhale to release the “ha” sound again back from deep within the throat. Enunciating the name starts you from the beginning of articulation, takes you through the mouth and back again to the throat in a circle. From Allah we came and to Him we return.

Furthermore the “la” sound is itself a soothing sound, that mothers used to calm their babies: “la la la”, hence you get lullaby.

Oh I’m not done yet, there’s even more.

In the shahada (testimony of faith) it is just made up of only 3 letters as well: لَا إِلاه إِلَّا الله La ilaha illallah.
The 3 letters are ا, ل, and ه which together spell both إِلاه meaning god and الله meanning Allah (which is God’s Proper Name).

Notice how the first part of the testimony of faith is easy and simple to say, light on the tongue (and I mean light in both senses of the term).

Now the second part of the testimony of faith has its own secrets and interesting points: مُحَمَّدٌ الرَّسُولُ الله (Muhammadu-r-rasoolallah). Because of the particular letters the word “Muhammadun” becomes assimilated into the next word “ar-rasool”. The “un” gets assimilated into the “ar” becoming “ur”. This symbolically shows the Prophet Muhammad being completely tied to his role of “Messenger of Allah” and intimately connected with Him. Furthermore this part of the testimony is harder for the tongue as well as the heart to say and acknowledge. It’s easy for us to express faith in God but harder for us to practice this faith in our lives, the Messenger being the practical role model in worshipping God.


That’s all I had to say and I hope I’ve illustrated the beauty and brilliance of design in both our living cells and the arabic language. It is remarkable.

In future articles I hope to write about other signs and how they are signs. I hope this has really affected you and made you reflect. Otherwise read it again until its significance penetrates your mind.

If you enjoyed please comment below your thoughts and leave a like. I look forward to your comments. 🙂


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