IRREDUCIBLE COMPLEXITY AND INTERDEPENDENCE - EVIDENCE FOR AN INTELLIGENT CREATOR

ABOUT THE TINY MACHINES AND BIOCHEMICAL PATHWAYS THAT RUN LIVING ORGANISMS

Every pathway and nano-machine requires multiple protein/enzyme components to work. How did lucky accidents create even one of the components, let alone 10 or 20 or 30+ at the same time, often in a necessary programmed sequence? Evolutionary biochemist Franklin Harold wrote, "we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations" - Creation Ministries International

Creationists and proponents of Intelligent Design talk about irreducible complexity.
 
What does that mean?  It means that no matter where we look in biology, at ecosystems, inside plants, people, animals or microorganisms, each tiny component has to co-operate with other tiny components or we cease to exist. Every bit has to be present right from the start in an organism or it will have no life. The evidence is overwhelming for a supernatural designer of all living things.

A watch is a good example. Take essential bits away and you may as well throw the entire watch away. If you were to find a watch anywhere else in space you would immediately recognize that an intelligent being built and designed it. This line of reasoning is called teleology.

A WORD OF CAUTION

Scientists, such as Dr. Michael Behe recognize the amazing apparent design of living systems. Only those who claim this as evidence of a Creator can be called creationists. Supporters of Intelligent Design do not necessarily invoke a Creator. They do not seem to know what they wish to invoke, but they are a step closer to God, being convinced that organisms look as though they have been deliberately designed.

 

 

A FUNDAMENTAL IRREDUCIBLE TRILOGY IN BIOLOGY

 

Every living system depends on DNA either directly or indirectly. An amazing fundamental aspect is that DNA is dependent for its synthesis on proteins while protein synthesis is dependent on messenger RNA (mRNA) which is dependent for its synthesis on the code on DNA. They are interdependent. On top of that, the ribosomes which make protein have a structural RNA component while proteins are required for the synthesis of mRNA from DNA. (DNA helix copyright CBC@arttoday.com 2002).

 

 

 

 

 

 

 

 

 

 

 

 


 
ENERGY SUPPLY IN LIVING SYSTEMS

Without a suitable and adequate energy supply our bodies would soon perish. Apart from food and water oxygen is essential for our survival. It is the slow, efficient and regulated 'burning' of foodstuffs that gives us our energy. Scientists call the process oxidation, which must occur in small stepwise processes for it to be useful in living cells.
 
The amazing thing is that, while a healthy cell requires oxygen, the contents of the cell are in an exact opposite state - in a reducing environment that is starved of oxygen. If the cell were given free access to oxygen its delicate biochemical systems would be destroyed.

Consider our own tissues. Our tissues need lots of oxygen to function. Oxygen is not pumped directly as molecular oxygen into our tissues, is it? It arrives via our red blood cells. When they are a bright red we know that they are saturated with oxygen. But they are not simply carriers of free molecular oxygen that could bubble off and destroy the delicate mechanisms within a cell.


The paradox is that cells need access to oxygen, but free oxygen inside a cell would destroy the cell contents. For example, the interior tissues of apples are oxygen free. That is why apples remain fresh.  Cut an apple and the apple will brown. Exposure to oxygen begins to destroy the cells. That's why a good cook keeps apple slices under water until required. The water prevents free access to oxygen. You could equally well keep them immersed in an antioxidant - but that would be expensive. This is the paradox that living cells have to cope with. To overcome this paradox the cells use oxygen carriers. 


Haemoglobin

The red cells in our blood have a complex pigment called haemoglobin. It is a very special molecule that has an affinity for free, molecular oxygen. It binds molecular oxygen so that the cell contents don't 'know' that it's there. However, it binds the oxygen ever so slightly so that parts of the cell responsible for 'burning' foodstuffs can readily access the oxygen. It’s a wonderfully designed system that all of us take for granted. It really is a miraculous system.
 
The reason that inhaled motor car fumes can be deadly is that the fumes contain carbon monoxide (CO) which too easily displaces molecular oxygen from haemoglobin so that the red cells arrive at their destination without oxygen. We then die through lack of oxygen because haemoglobin binds CO 250 times more readily than oxygen. Cyanide is a poison for the same reason.


Toxins and molecules, such as haemoglobin, work on 'lock and key' principles where the 3-dimensional structure of the molecule and its precise composition determines whether the protein can lock onto a specific substance, but also release them when required. Immuno-globulins, so essential to our immune system, work on similar principles. If something goes wrong with their configuration and precise composition a person cannot resist infection or poisoning.

This illustration shows red blood cells travelling in the liquid plasma of blood through a capillary. Each of the red cells has 280,000,000 molecules of haemoglobin. Haemoglobin is an example of a complex metallo-protein (metallo) because it contains four iron atoms surrounded by 16 nitrogen atoms (haeme groups) that give it the capacity to bind oxygen.

 

The chemical formula of the red pigment that is haemoglobin is:   
   C(2952)H(4664)O(832) N(812) S(8)Fe(4)

 

 

 

 

 

 

 

 

In adults the molecule is made in different parts of immature red cells in the bone marrow. In immature red blood cells, the heme group is synthesized in a series of complex steps in the mitochondria and then in the cytosol, the aqueous component of the cell, within which the various organelles such as mitochondria and particles are suspended. The globin protein parts are synthesized by ribosomes in the cytosol which are assembled together as haemoglobin molecules that remain in the red blood cell as it matures. During maturation the mitochondria and the nucleus are pre-programmed to self-destruct. This allows the cell to contain more haemoglobin and have its distinctive bi-concave shape which aids diffusion - this shape would not be possible if the cell had a nucleus in the way.

'Because of the lack of nuclei and organelles, mature red blood cells do not contain DNA and cannot synthesize any RNA, and, consequently, cannot divide and have limited repair capabilities. The inability to carry out protein synthesis means that no virus can evolve to target mammalian red blood cells'. 

https://en.wikipedia.org/wiki/Red_blood_cell

 

 

 

 

 


 

 

 

 

 

 

 

 

 


The 6 genes for haemoglobin reside in the nucleus of the immature red cells. In adults haemoglobin is a globular protein made of four sub-units where each subunit is a metallo-protein itself. In foetal haemoglobin two extra special genes are required to increase its affinity for oxygen. These also reside in the immature cells. The mother plays no part in foetal blood production. Therefore adults and embryos appear to use a different set of 6 genes from the total of 8 haemoglobin genes.

In the human embryo the first site of blood formation is the yolk sac. Before birth the liver becomes the most important red blood cell-forming organ in the embryo, but it is then succeeded by the bone marrow, which in adult life is the only source of both red and white blood cells. (See also the Article on ‘Why Mary had to be a virgin’ which has a bearing on this).


I wonder whether God did this intentionally to show his involvement in the process that gives life. 'For the life of the flesh is in the blood' (Leviticus 7:11), which is why we take communion - not just to remember Him. As you will read in the prophetic articles on the Age of the Earth 6 is the number of man and 8 is the number for a new beginning or birth. Babies were circumcised on the 8th day even as Jesus was. Six genes are required for haemoglobin in adults while 8 genes are required in total for haemoglobin. Could this just be a coincidence?
 
Six genes, on chromosome 11, code the adult haemoglobin proteins. Chromosome 11 contains many other genes and is comprised of 135,000,000 letters of the DNA code representing 4-4.5 % of the total DNA in cells. Of course, a lot more than 6 genes are involved in making haemoglobin because there have to be mechanisms for assembling each haemoglobin molecule. It really boggles the mind.

The first diagram below shows two subunits interlocking, each subunit with its iron atom (haeme group). The diagram below shows the complete molecule comprised of the four sub-units. The genes code for the specific sequences of the 20 essential amino acids that make up each protein chain. A common mutation of a haemoglobin gene, in some populations, leads to sickle-cell aenemia, which is very deleterious.  The cells look like flat sickles and can become rigid and stick in small capillaries causing severe problems. Thus the amino acid composition is vital for the three-dimensional configuration of this globular protein, which gives it its function and also affects the shape of the red blood cell. Everything is vital. One dies or is detrimentally affected if something goes wrong with haemoglobin synthesis and assembly!!

This means that the  whole idea of reproducing life in a test tube from scratch is bankrupt. Having a viable cell, with a proper membrane and containing some complex proteins, is insufficient for its long term survival and reproduction. Experimental chemists trying to create artificial cells haven’t even reached the stage of artificially synthesizing a cell like this. Moreover, even if they did, where are they going to get the genes and protein synthesis apparatus from to get their first artificial living cell? Chemists trying to re-create a living cell from a primeval soup in a test tube are living an impossible dream. To create a living cell, one needs a living cell to start with. Those who continue to pursue such research are  deluding themselves. The search for the origin of life, employing experimental science is bordering on intellectual  foolishness.

The complete globular metallo-protein with its four haeme groups shown in green

The molecular model for the complete haemoglobin molecule was taken from https://en.wikipedia.org/wiki/Hemoglobin  [By Richard Wheeler (Zephyris) 2007. Created with en:pymol from en:PDB enzyme 1GZX. PDB; PDB ENZYME; Released under the GNU Free Documentation License].

 

The molecules and the mechanisms that assist their assembly and transport to desired locations are pre-programmed on the DNA that we inherited from Adam.

Haemoglobin is only one example, of a myriad of essential molecules. God created Adam as a mature being, with full capacity to speak and hear. This is what I mean by irreducible complexity, where a host of systems have to work together for molecules to be placed where they are needed and to perform their precise functions.

OXYGEN PRODUCTION AND CONSUMPTION DURING METABOLISM
 
Plants and photosynthetic micro-organisms supply the world with oxygen. It’s a process that requires sunlight. Oxygen is a daily renewable resource and is an absolute requirement for us and all animals, and everything else which contain mitochondria that consume oxygen.
 
The colour green is everywhere around us. Plants are green because their chloroplasts contain chlorophyll. Chlorophyll is a pigment that acts as an antenna molecule, in conjunction with other molecules, to transfer the energy in suitable packages from sunlight to the chloroplasts. Chloroplasts are little organs or organelles within certain tissues of plant cells. Chloroplasts utilise the energy obtained from sunlight, in highly controlled fashion, to manufacture sugars and oxygen from water and carbon dioxide. They also make other important molecules, such as fatty acids and amino acids, as well as molecules in their specialized plant immune responses. Surprised? We shall only consider their ability to split water molecules into oxygen and to generate useful energy to make sugars.

Mitochondria consume the oxygen that chloroplasts make. They are essential for supplying cells with energy whether in people, animals, plants or fungi. They convert sugars and fats back to carbon dioxide and water, releasing energy in a chemical form called ATP, but only if supplied with oxygen. Plants have their own mitochondria. Even fungi and moulds have their own mitochondria.
 
Without mitochondria all life would cease and even viruses would cease to exist. Viruses are dependent on pre-existing living cells for survival and reproduction. They can’t just evolve from minerals in a primeval soup. They are dependent on genes that pre-exist in other organisms!
 
Chloroplasts and mitochondria interact within and between organisms. Co-operation of this kind, such as between chloroplasts and mitochondria, requires the co-existence of many functional and highly regulated genes, each performing their task in the right place at the right time. Each gene codes for a particular protein. In the photo below note the many parallel membrane folds within each liver mitochondrion where electrochemical gradients are generated that we shall talk about. These are the cristae. The small black balls attached to a double membrane in the lower right of the photo are ribosomes attached to a rough endoplasmic reticulum. Ribosomes are the machines that make protein. These are not the ‘lollipop’ structures I am about to discuss in relation to electrochemical gradients. The lollipops are smaller and cannot be seen in this photograph.

The essential F-ATPase protein complex (‘the lollipops’ or ATP synthase or ATPase) that is in our cells is what will be discussed next. This complex requires 8 different genes to make the protein subunits it is comprised of not counting all the other proteins and factors required for the assembly and directional orientation of the complex in the membranes (cristae).  I call it a 'lollipop’ structure because at a magnification of round about 30,000, that is exactly what the complex looks like – like ping-pong balls on stalks protruding out of the membrane. I wish I had kept the photos I took with the electron microscope in 1976. I found a similar one on this site:  

http://slideplayer.com/slide/244448/1/images/16/Electron+micrograph+of+mitochondrial+membranes.jpg

The other complexes in the membrane, shown in green in the schematic diagram below, make up the so-called electron transport chains embedded in certain membranes. Their co-operation and orientation in the chloroplast and mitochondrial membranes is as critical as the orientation of the ‘lollipops’. All these components must be present, in their correct orientation, in each tiny organelle, otherwise nothing works. When I saw the ATPases under the electron microscope, in my own preparations, I noted that they existed in multiple rows and that not a single ‘lollipop’ was pointing in the wrong direction. The reader should also note that the orientation of ATPases in mitochondria is in reverse to that in chloroplasts because of the direction of the electric and chemical fields directed by their membrane-embedded electron transport chains (see below).

HOW THE F-ATPase WORKS
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One of the first things that occurs in chloroplasts is that, through a complex chain of events in the membranes involving other proteins, the energy of sunlight is harnessed to make an electrical and chemical gradient of protons (H+, the red balls) across the membrane. Any gradient whatsoever always wants to ‘cool’ down or dissipate, just like your hot cup of coffee, and return to its original state or, in our example, to room temperature. But how can the excess of protons on one side return to the other side of the membrane? These membranes are very special. They don't allow protons to just drift across. They are impermeable to protons.

There are two driving forces that exert immense pressure to return the red balls to the other side of the membrane. 
1. Their high chemical concentration on only one side of the membrane.
2. The high positive charge they have created because they have been forcefully accumulated. The positive charge in the tiny compartment is mutually repelling them, directing them to return to the other side of the membrane, if they can.

As sunlight continues, the electrical and concentration gradient of protons becomes immense and the internal positive electrical charge repelling the protons built up. Where are the protons to go? As it happens, the ATPase complex, embedded in the membrane, is the only possible escape route, because it has a central channel for protons but it does present a resistance. The protons have to be driven through the narrow channel by the fierce electro-chemical gradient. Voltages across these very thin membranes reach about 0.18V and higher, which works out to an enormously steep electrical gradient across the immensely thin membrane.

As the protons are forcefully propelled through the channel the mobile rotor part of the complex turns and, in so doing, catalyses low energy ADP molecules to be converted to high energy ATP molecules. The 'T' in ATP means a trinity of phosphorus molecules. The energy equivalent of ATP is then transported by mechanisms and in sugars to all parts of the plant or, in our case as humans not containing chloroplasts, from the mitochondria to other cell components. Without a continual generation of ATP every cell would die of exhaustion. Brain cells die extremely quickly. High energy ATP is required to drive a host of other chemical reactions in our bodies. Providentially, in ATP we have another 'trinity' essential for life.

In mitochondria the ‘lollipops’ are reversed in direction because the electro-chemical gradient is now being formed in the intermembrane space. In other words, the electrochemical gradient is reversed. Therefore the ‘lollipop’ structures also have to be assembled in a reverse orientation or they will accomplish nothing. The function of the ‘lollipops’ is critical. Because they are responsible for making ATP, the protein complex, (the ‘lollipop’ structure) is called an ATPase. Isn't it fascinating, that to function, they have to have a rotor-like protein that must be able to rotate? That is ingenious micro-engineering.

For the discerning scientist:

 

In F-ATPases there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, which itself is driven by the movement of protons through the Fo complex C subunit’ (quoted from Wikipedia on ATP synthetase subunits).

 

BACTERIAL ROTORS - AMAZING NANO-MOLECULAR ENGINES

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https://uncommondescent.com/irreducible-complexity/incredible-bacterial-rotors-varying-torques-imaged/

https://www.youtube.com/watch?v=fFq_MGf3sbk

 


You will have to see these motors on YouTube to believe it. The flagellae, which propel sperm and bacteria, are driven by these exquisitely designed miniature molecular motors (nano-motors).


I can do no better than to refer you to professional YouTube simulations of how a typical flagellar motor is constructed and driven by the energy derived either from ATP or some other high-energy molecules (the video on my home page). The simulations of nano-machines, demonstrated on YouTube have been derived from extremely high resolution electron microscopy and the results of experimental molecular and biochemical data.

COULD HUMANS  BE GREEN AND RUN ON SOLAR POWER LIKE PLANTS ?

‘Lucky’ for plants, you might say? Wouldn’t it be great if we had chloroplasts and could run mostly on solar power. Imagine how much money we could save on our grocery bills. The only energy benefit we currently get directly from sunlight is to keep ourselves warm. What if genetic engineers could introduce into our cells all the genes necessary to make chloroplasts? That would be useful in summer when we could take most of our clothing off and allow the sun to recharge our batteries, so to speak. Would chloroplasts be helpful? They might also protect us from getting skin cancer. Plants make sunscreen to protect themselves from overexposure to UV radiation. Did you know that? It’s easy to calculate whether green men could exist by drinking mineral water, breathing carbon dioxide and making their own oxygen.

 

It turns out that for sunlight to provide enough energy for us to stay alive, we would either have to walk around holding huge solar panels or our bodies would have to thin out and make large surfaces equivalent to having green ‘leaves’ and stay at rest. In short, we essentially would have to become sedentary plants not wasting energy on brain function.

When my daughter was proof reading this section she commented, ‘I like the picture I get in my mind

here of a man weighed down carrying solar panels and a real flat woman - at least she’s thin here which

is what most women want and I could use some rest’.

To obtain energy all non-green living things need to consume organic material, which is then digested and used to produce ATP as well as the building blocks required in the cell or organism. Certain bacteria have special genes so that they can exist independent of sunlight in extreme environments, but they lack all the other genes they would need to become more complex organisms. The question remains as to where they obtained their genes and genetic apparatus from in the first place. They are not simple things as the public and media may assume!

Herbivores eat plants that can synthetize essential amino acids and sugars that higher organisms depend on. Carnivores, therefore, have to ultimately eat herbivores in the food chain. Herbivores have to eat a lot of plants to make it energetically worthwhile. That’s why we see caterpillars, cattle and deer spending much of their time grazing. They are specialized eating machines. We are at the end of the food chain except in special circumstances when predators feed on us!

CONCLUSION

 

Listen to and watch these special YouTube presentations on nano-motors in bacteria. Afterwards, if you still believe in chance and random evolution of life from a chemical soup in a primeval ocean, then God help you! Harken to your creator’s call.

https://www.youtube.com/watch?v=a_5FToP_mMY&t=7s  

 

In this video, can you pick up the fact that arguments opposing intelligent design by the last two speakers are beside the point and that Dr Behe's claim for irreducible complexity of the motor, based on its clearly designated function, stands? Until there is a flexible flagellum attached to act as a propeller and the motor spins concurrently there is no benefit in natural selection selecting either. The stationary syringe on toxic bacteria is equally and perfectly structured for its task. In case of the mousetrap analogy, why should the tie clip evolve into anything other if it perfectly performs its task?

Even Dr. Richard Dawkins, the famous evolutionist, admits that DNA carries digital information just like a computer. It requires the assembly and co-operation of 50 different and specific types of proteins to enable the bacterial flagellar motor to work - fifty different genes that carry unique digital information.

https://www.youtube.com/watch?v=prFZTMIKOi4

Whichever way you choose to go it will be clearly a choice according to your faith, faith in evolution and random chance or faith that God created. Which is it going to be? God gives us the dignity to make that choice.

'But without faith it is impossible to please Him for he who comes to God

must believe that He is and that He is a rewarder of those who diligently seek Him'. (Hebrews 11:6)

 

 

Email: charles.pallaghy@gmail.com

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